protein folding protocols - universitas...

Edited by

Yawen BaiRuth Nussinov

Protein FoldingProtocols

METHODS IN MOLECULAR BIOLOGY™ 350

Edited by



Protein Folding Protocols

M E T H O D S I N M O L E C U L A R B I O L O G Y™

John M. Walker, SERIES EDITOR

380. Immunological Tolerance: Methods and Protocols,edited by Paul J. Fairchild, 2007

379. Glycovirology Protocols, edited by Richard J.Sugrue, 2007

378. Monoclonal Antibodies: Methods and Protocols,edited by Maher Albitar, 2007

377. Microarray Data Analysis: Methods andApplications, edited by Michael J. Korenberg, 2007

376. Linkage Disequilibrium and AssociationMapping: Analysis and Application, edited byAndrew R. Collins, 2007

375. In Vitro Transcription and Translation Protocols:Second Edition, edited by Guido Grandi, 2007

374. Quantum Dots: Methods and Protocols, editedby Charles Z. Hotz and Marcel Bruchez, 2007

373. Pyrosequencing® Protocols, edited by SharonMarsh, 2007

372. Mitochondrial Genomics and ProteomicsProtocols, edited by Dario Leister and JohannesHerrmann, 2007

371. Biological Aging: Methods and Protocols, edited byTrygve O. Tollefsbol, 2007

370. Adhesion Protein Protocols, Second Edition, editedby Amanda S. Coutts, 2007

369. Electron Microscopy: Methods and Protocols,Second Edition, edited by John Kuo, 2007

368. Cryopreservation and Freeze-Drying Protocols,Second Edition, edited by John G. Day and GlynStacey, 2007

367. Mass Spectrometry Data Analysis in Proteomics,edited by Rune Matthiesen, 2007

366. Cardiac Gene Expression: Methods and Protocols,edited by Jun Zhang and Gregg Rokosh, 2007

365. Protein Phosphatase Protocols: edited by GregMoorhead, 2007

364. Macromolecular Crystallography Protocols:Volume 2, Structure Determination, edited by SylvieDoublié, 2007

363. Macromolecular Crystallography Protocols:Volume 1, Preparation and Crystallizationof Macromolecules, edited by Sylvie Doublié, 2007

362. Circadian Rhythms: Methods and Protocols,edited by Ezio Rosato, 2007

361. Target Discovery and Validation Reviewsand Protocols: Emerging Molecular Targetsand Treatment Options, Volume 2, edited byMouldy Sioud, 2007

360. Target Discovery and Validation Reviewsand Protocols: Emerging Strategies for Targetsand Biomarker Discovery, Volume 1, edited byMouldy Sioud, 2007

359. Quantitative Proteomics, edited by SalvatoreSechi, 2007

358. Metabolomics: Methods and Protocols, edited byWolfram Weckwerth, 2007

357. Cardiovascular Proteomics: Methods and Protocols,edited by Fernando Vivanco, 2006

356. High-Content Screening: A Powerful Approachto Systems Cell Biology and Drug Discovery,edited by Ken Guiliano, D. Lansing Taylor,and Jeffrey Haskins, 2007

355. Plant Proteomics: Methods and Protocols, editedby Hervé Thiellement, Michel Zivy, CatherineDamerval, and Valerie Mechin, 2006

354. Plant–Pathogen Interactions: Methods andProtocols, edited by Pamela C. Ronald, 2006

353. DNA Analysis by Nonradioactive Probes: Methodsand Protocols, edited by Elena Hilario and John. F.MacKay, 2006

352. Protein Engineering Protocols, edited by KristianMüller and Katja Arndt, 2006

351. C. elegans: Methods and Applications, edited byKevin Strange, 2006

350. Protein Folding Protocols, edited by Yawen Baiand Ruth Nussinov, 2007

349. YAC Protocols, Second Edition, edited by AlasdairMacKenzie, 2006

348. Nuclear Transfer Protocols: Cell Reprogrammingand Transgenesis, edited by Paul J. Verma and AlanTrounson, 2006

347. Glycobiology Protocols, edited by InkaBrockhausen-Schutzbach, 2006

346. Dictyostelium discoideum Protocols, edited byLudwig Eichinger and Francisco Rivero, 2006

345. Diagnostic Bacteriology Protocols, Second Edition,edited by Louise O'Connor, 2006

344. Agrobacterium Protocols, Second Edition:Volume 2, edited by Kan Wang, 2006

343. Agrobacterium Protocols, Second Edition:Volume 1, edited by Kan Wang, 2006

342. MicroRNA Protocols, edited by Shao-Yao Ying, 2006341. Cell–Cell Interactions: Methods and Protocols,

edited by Sean P. Colgan, 2006340. Protein Design: Methods and Applications,

edited by Raphael Guerois and Manuela López de laPaz, 2006

339. Microchip Capillary Electrophoresis: Methodsand Protocols, edited by Charles S. Henry, 2006

338. Gene Mapping, Discovery, and Expression:Methods and Protocols, edited by M. Bina, 2006

337. Ion Channels: Methods and Protocols, edited byJames D. Stockand and Mark S. Shapiro, 2006

336. Clinical Applications of PCR, Second Edition,edited by Y. M. Dennis Lo, Rossa W. K. Chiu, and K. C.Allen Chan, 2006

335. Fluorescent Energy Transfer Nucleic AcidProbes: Designs and Protocols, edited by VladimirV. Didenko, 2006

334. PRINS and In Situ PCR Protocols, SecondEdition, edited by Franck Pellestor, 2006

http://www.humanapress.com/Product.pasp?txtCatalog=HumanaBooks&txtCategory=&txtProductID=1%2D59745%2D068%2D5&isVariant=0http://www.humanapress.com/Product.pasp?txtCatalog=HumanaBooks&txtCategory=&txtProductID=1%2D59745%2D069%2D3&isVariant=0

M E T H O D S I N M O L E C U L A R B I O L O G Y™


Edited by

Yawen BaiLaboratory of Biochemistry, National Cancer Institute,

National Institutes of Health, Bethesda, MD

and

Ruth NussinovCenter for Cancer Research Nanobiology Program SAIC,

National Cancer Institute-Frederick, Frederick, MDand Department of Human Genetics, Sackler School of Medicine,

Tel Aviv University, Tel Aviv, Israel

© 2007 Humana Press Inc.999 Riverview Drive, Suite 208Totowa, New Jersey 07512

www.humanapress.com

All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted inany form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwisewithout written permission from the Publisher. Methods in Molecular BiologyTM is a trademark of TheHumana Press Inc.

All papers, comments, opinions, conclusions, or recommendations are those of the author(s), and do notnecessarily reflect the views of the publisher.

This publication is printed on acid-free paper. ∞ANSI Z39.48-1984 (American Standards Institute)

Permanence of Paper for Printed Library Materials.Cover illustration: Figure 3 from Chapter 15, "Intermediates and Transition States in Protein Folding," byD. Thirumalai and Dmitri K. Klimov.

Production Editor: Erika J. Wasenda

Cover design by Patricia F. Cleary

For additional copies, pricing for bulk purchases, and/or information about other Humana titles, contactHumana at the above address or at any of the following numbers: Tel.: 973-256-1699; Fax: 973-256-834;E-mail: [email protected]; or visit our Website: www.humanapress.com

Photocopy Authorization Policy:Authorization to photocopy items for internal or personal use, or the internal or personal use of specificclients, is granted by Humana Press Inc., provided that the base fee of US $30.00 per copy is paid directlyto the Copyright Clearance Center at 222 Rosewood Drive, Danvers, MA 01923. For those organizationsthat have been granted a photocopy license from the CCC, a separate system of payment has been arrangedand is acceptable to Humana Press Inc. The fee code for users of the Transactional Reporting Service is:[1-58829-622-9/07 $30.00].

Printed in the United States of America. 10 9 8 7 6 5 4 3 2 1

eISBN:1-59745-189-4

ISSN:1064-3745

Library of Congress Cataloging in Publication Data

Protein folding protocols / edited by Yawen Bai and Ruth Nussinov.

p. ; cm. -- (Methods in molecular biology ; 350)

Includes bibliographical references and index.

ISBN 1-58829-622-9 (alk. paper)

1. Protein folding. 2. Proteins--Conformation. 3. Proteins--Analysis.

[DNLM: 1. Protein Folding. 2. Protein Conformation. 3. Proteins--analysis. QU 55 P96635 2006] I. Bai,Yawen. II. Nussinov, Ruth. III. Series: Methods in molecular biology (Clifton, N.J.) ; 350.

QP551.P695822 2006

572'.633--dc22

2006002791

www.humanapress.comwww.humanapress.com

v

Preface

Protein Folding Protocols presents protocols for studying and characterizingsteps and conformational ensembles populating pathways in protein foldingfrom the unfolded to the folded state. It further presents a sample of approachestoward the prediction of protein structure starting from the amino acid sequence,in the absence of overall homologous sequences. Protein folding is a crucialstep in the transfer of genetic information from the DNA to the protein. TheGenome Project has led to a huge number of available DNA sequences and,therefore, protein sequences. The Structural Genomics initiative largely aimsto obtain “new” folds not currently present in the Protein Data Bank. Yet, thenumber of available structures inevitably lags behind the number of sequences.At the same time, an equally important problem is to find out the types andscope of dissimilar (nonhomologous) protein sequences that adopt a similarfold. Assembling data and comprehension of the sequence space of proteinfolds should be very useful in computational protein structure prediction. Thiswould enhance the scope of homology modeling, which currently is the methodof choice. Thus, experimental and theoretical studies on the relationship betweensequence and structure are critical. Figuring out the relationship between sequenceand structure would further assist in the prediction of fibril structures observed inprotein misfolding diseases, and in figuring out the conformational changesand dynamics resulting from mutations. Protein folding is one of the mostimportant and challenging problems in current molecular and chemical biology.This book reviews some of the recently developed methods for studying proteinfolding.

The starting point of a folding process is the unfolded state. Eliezer describeshow some of the local structural properties of the unfolded state may be charac-terized using multidimensional nuclear magnetic resonance (NMR). Gebel andShortle review how the global structures of the unfolded state may be charac-terized by measuring the residual dipolar couplings, again with NMR. Anotherstate that generally occurs in the process of protein folding is the rate-limitingtransition state. Pandit and coworkers describe how it can be characterized byusing the psi value analysis. Rao and coworkers employ molecular dynamicssimulation to characterize the transition state of small proteins. They propose atechnique to estimate the folding probability of those structures that aresampled along near-equilibrium, constant temperature molecular dynamicssimulations. Bai and coworkers describe how the native-state hydrogen exchangemethod could be combined with protein engineering to populate the intermediate

vi Preface

state for high-resolution structure determination by multidimensional NMR.Lassalle and Akasaka describe how the high-pressure NMR technique can beused to denature proteins and populate partially unfolded intermediates.Thirumalai and Klimov describe the use of computer simulations and simplemodels to investigate the formation of the intermediates. They show that theequilibrium intermediates occur “on pathway” and that there is a substantialprobability that they be revisited after the native state is reached, in contrast tokinetic intermediates. Haspel and coworkers described how a building block-based protein folding model may be used toward a reduction of the computa-tional complexity of protein folding. The model is based on the cutting of thetarget protein sequences into building block fragments that are relatively stableand whose conformations in solution are similar to those observed when thefragments are chain connected in the protein molecule from which they werederived.

One of the cutting-edge methods for studying protein folding is the singlemolecule technique. Ng and coworkers show that atomic force microscopy maybe used to study the process of protein folding and unfolding. Schuler describeshow the single molecule technique coupled with fluorescence resonance transfermay be used to study the population of proteins under equilibrium conditionsand the process of kinetic folding. The study of very fast folding process, in thetime-scale of microseconds or less, constitutes another important area in currentprotein folding studies. Gai and coworkers describe the use of T-jump coupledwith infrared spectroscopy to characterize such a fast folding process. Fierzand coworkers outline a new method that uses triplet–triplet energy transfer tomeasure conformational dynamics in polypeptide chains in the unfoldedensembles, which can set the uplimit of folding times. Streicher and Makhatadzedescribe recent advances in the analysis of conformational transition in peptidesusing differential scanning calorimetry. Zhou describes the replica exchangemolecular dynamics (REMD) method for enhanced sampling of the conforma-tional space. REMD couples molecular dynamics trajectories with a temperatureexchange Monte Carlo process. Replicas are run in parallel at different tempera-tures. This procedure allows surmounting local barriers encountered in thesimulation. REMD has proven to be a very powerful tool, and it is increasinglyused in MD simulations for small proteins/peptides. Jernigan and Kloczowskidescribe a computational result that relates the packing regularities of biologicalstructures to their dynamics. Prediction of protein structures is the central issue ofprotein folding studies. Casadio and coworkers describe how protein structuresmight be predicted with and without the existence of homologs. This feat hasbeen achieved with the aid of machine learning-based methods specificallysuited for predicting structural features. For protein–protein interaction, a

knowledge-based strategy may provide predictions of putative interactionpatches on the protein surface.

It behooves us to note that not all proteins fold into stable conformations.Recently, there has been an increasing amount of data that a large percentageof the proteins exist in what is commonly called the natively disordered state.This state describes a spectrum of conformations with variable stabilities. Althoughon its own the stability of the native state is low (hence the term disordered),binding to its partner enhances its stability. Thus, here too, the native state isthe functional state. Folding, misfolding, and protein disorder are all related toeach other. Progress in the understanding of one assists in comprehension ofthe other. Above all, all relate to protein function and misfunction.

Altogether, Protein Folding Protocols is a comprehensive collection ofchapters describing a broad range of techniques to study, predict, and analyzethe protein folding process. It covers experiment and theory, bioinformaticsapproaches, and state-of-the-art simulation protocols for better sampling of theconformational space. Protein folding remains one of the most challengingproblems in the biological/natural sciences. Making progress in this area willhave tremendous implications, ranging from drug design, functional assignment,comprehension of the nature of regulation, figuring out molecular machines, viralentry into cells, and putting together cellular pathways and their dynamics. Thechallenge still remains; however, experiment and theory have been makingsteps toward an eventual practical solution.


Preface vii

ix

Contents

Preface ..............................................................................................................vContributors .....................................................................................................xi

1. Infrared Temperature-Jump Study of the Folding Dynamicsof α-Helices and β-Hairpins

Feng Gai, Deguo Du, and Yao Xu ......................................................... 12. The Use of High-Pressure Nuclear Magnetic Resonance

to Study Protein FoldingMichael W. Lassalle and Kazuyuki Akasaka ....................................... 21

3. Characterization of Denatured Proteins Using ResidualDipolar Couplings

Erika B. Gebel and David Shortle ....................................................... 394. Characterizing Residual Structure in Disordered Protein States

Using Nuclear Magnetic ResonanceDavid Eliezer ....................................................................................... 49

5. Population and Structure Determination of Hidden FoldingIntermediates by Native-State Hydrogen Exchange-DirectedProtein Engineering and Nuclear Magnetic Resonance

Yawen Bai, Hanqiao Feng, and Zheng Zhou ...................................... 696. Characterizing Protein Folding Transition States Using Ψ-Analysis

Adarsh D. Pandit, Bryan A. Krantz, Robin S. Dothager,and Tobin R. Sosnick ...................................................................... 83

7. Advances in the Analysis of Conformational Transitionsin Peptides Using Differential Scanning Calorimetry

Werner W. Streicher and George I. Makhatadze ............................. 1058. Application of Single Molecule Förster Resonance Energy

Transfer to Protein FoldingBenjamin Schuler .............................................................................. 115

9. Single Molecule Studies of Protein FoldingUsing Atomic Force Microscopy

Sean P. Ng, Lucy G. Randles, and Jane Clarke ................................. 13910. Using Triplet–Triplet Energy Transfer to Measure Conformational

Dynamics in Polypeptide ChainsBeat Fierz, Karin Joder, Florian Krieger,

and Thomas Kiefhaber .................................................................. 169

11. A Hierarchical Protein Folding Scheme Based on the BuildingBlock Folding Model

Nurit Haspel, Gilad Wainreb, Yuval Inbar, Hui-Hsu (Gavin) Tsai,Chung-Jung Tsai, Haim J. Wolfson,and Ruth Nussinov ........................................................................ 189

12. Replica Exchange Molecular Dynamics Method for ProteinFolding Simulation

Ruhong Zhou ..................................................................................... 20513. Estimation of Folding Probabilities and Φ Values From Molecular

Dynamics Simulations of Reversible Peptide FoldingFrancesco Rao, Giovanni Settanni,

and Amedeo Caflisch .................................................................... 22514. Packing Regularities in Biological Structures Relate

to Their DynamicsRobert L. Jernigan and Andrzej Kloczkowski ................................... 249

15. Intermediates and Transition States in Protein FoldingD. Thirumalai and Dmitri K. Klimov................................................. 277

16. Thinking the Impossible: How to Solve the Protein FoldingProblem With and Without Homologous Structures and More

Rita Casadio, Piero Fariselli, Pier Luigi Martelli,and Gianluca Tasco ...................................................................... 305

Index ............................................................................................................ 321

x Contents

Contributors

KAZUYUKI AKASAKA • Department of Biotechnological Science, Schoolof Biology-Oriented Science and Technology, Kinki University, KinokawaCity, Wakayama Prefecture, Japan

YAWEN BAI • Laboratory of Biochemistry, National Cancer Institute, NationalInstitutes of Health, Bethesda, MD

AMEDEO CAFLISCH • Department of Biochemistry, University of Zürich,Zürich, Switzerland

RITA CASADIO • Biocomputing Group, CIRB/Department of Biology,University of Bologna, Bologna, Italy

JANE CLARKE • Department of Chemistry, University of Cambridge, MedicalResearch Council Center for Protein Engineering, Cambridge, UK

ROBIN S. DOTHAGER • Department of Biochemistry, University of IllinoisChampaign-Urbana, Urbana, IL

DEGUO DU • Department of Chemistry, University of Pennsylvania,Philadelphia, PA

DAVID ELIEZER • Department of Biochemistry and Program in StructuralBiology, Weill Medical College of Cornell University, New York, NY

PIERO FARISELLI • Biocomputing Group, CIRB/Department of Biology,University of Bologna, Bologna, Italy

HANQIAO FENG • Laboratory of Biochemistry, National Cancer Institute,National Institutes of Health, Bethesda, MD

BEAT FIERZ • Department of Biophysical Chemistry, Biozentrum, Universityof Basel, Basel, Switzerland

FENG GAI • Department of Chemistry, University of Pennsylvania,Philadelphia, PA

ERIKA B. GEBEL • Department of Biological Chemistry, Johns HopkinsUniversity School of Medicine, Baltimore, MD

NURIT HASPEL • Department of Exact Sciences, School of Computer Science,Tel Aviv University, Tel Aviv, Israel

YUVAL INBAR • Department of Exact Sciences, School of Computer Science,Tel Aviv University, Tel Aviv, Israel

ROBERT L. JERNIGAN • Department of Biochemistry, Biophysics, and MolecularBiology, Laurence H. Baker Center for Bioinformatics and BiologicalStatistics, Iowa State University, Ames, IA

KARIN JODER • Department of Biophysical Chemistry, Biozentrum, Universityof Basel, Basel, Switzerland

xi

THOMAS KIEFHABER • Department of Biophysical Chemistry, Biozentrum,University of Basel, Basel, Switzerland

DMITRI K. KLIMOV • Bioinformatics and Computational Biology Program,School of Computational Sciences, George Mason University, Manassas, VA

ANDRZEJ KLOCZKOWSKI • Department of Biochemistry, Biophysics,and Molecular Biology, Iowa State University, Ames, IA

BRYAN A. KRANTZ • Department of Microbiology and Molecular Genetics,Harvard Medical School, Boston, MA

FLORIAN KRIEGER • Department of Biophysical Chemistry, Biozentrum,University of Basel, Basel, Switzerland

MICHAEL W. LASSALLE • Exploratory Research for Advanced Technology“Actin Filament Dynamics” Project, Japan Science and TechnologyCorporation, Hyogo, Japan

GEORGE I. MAKHATADZE • Department of Biochemistry and MolecularBiology, Penn State College of Medicine, Hershey, PA

PIER LUIGI MARTELLI • Biocomputing Group, CIRB/Department of Biology,University of Bologna, Bologna, Italy

SEAN P. NG • Department of Chemistry, University of Cambridge, MedicalResearch Council Center for Protein Engineering, Cambridge, UK

RUTH NUSSINOV • Center for Cancer Research Nanobiology Program SAIC,National Cancer Institute-Frederick, Frederick, MD and Departmentof Human Genetics, Sackler School of Medicine, Tel Aviv University,Tel Aviv, Israel

ADARSH D. PANDIT • Department of Biochemistry and Molecular Biology,University of Chicago, Chicago, IL

LUCY G. RANDLES • Department of Chemistry, University of Cambridge,Medical Research Council Center for Protein Engineering, Cambridge, UK

FRANCESCO RAO • Department of Biochemistry, University of Zürich, Zürich,Switzerland

BENJAMIN SCHULER • Department of Biochemistry, University of Zürich,Zürich, Switzerland

GIOVANNI SETTANNI • Department of Biochemistry, University of Zürich,Zürich, Switzerland

DAVID SHORTLE • Department of Biological Chemistry, Johns HopkinsUniversity School of Medicine, Baltimore, MD

TOBIN R. SOSNICK • Department of Biochemistry and Molecular Biology,University of Chicago, Chicago, IL

WERNER W. STREICHER • Department of Biochemistry and Molecular Biology,Penn State College of Medicine, Hershey, PA

xii Contributors

GIANLUCA TASCO • Biocomputing Group, CIRB/Department of Biology,University of Bologna, Bologna, Italy

D. THIRUMALAI • Institute for Physical Science and Technologyand Department of Chemistry and Biochemistry, University of Maryland,College Park, MD

CHUNG-JUNG TSAI • Center for Cancer Research Nanobiology ProgramSAIC, National Cancer Institute-Frederick, Frederick, MD

HUI-HSU (GAVIN) TSAI • Center for Cancer Research Nanobiology ProgramSAIC, National Cancer Institute-Frederick, Frederick, MD

GILAD WAINREB • Department of Human Genetics, Sackler Schoolof Medicine, Tel Aviv University, Tel Aviv, Israel

HAIM J. WOLFSON • School of Computer Science, Tel Aviv University, Tel Aviv,Israel

YAO XU • Department of Chemistry, University of Pennsylvania,Philadelphia, PA

RUHONG ZHOU • Department of Chemistry, Columbia University, New York,NY and Computational Biology Center, IBM Thomas J. Watson ResearchCenter, Yorktown Heights, NY

ZHENG ZHOU • Laboratory of Biochemistry, National Cancer Institute,National Institutes of Health, Bethesda, MD

Contributors xiii

1

From: Methods in Molecular Biology, vol. 350: Protein Folding ProtocolsEdited by: Y. Bai and R. Nussinov © Humana Press Inc., Totowa, NJ

1

Infrared Temperature-Jump Study of the FoldingDynamics of α-Helices and β-Hairpins

Feng Gai, Deguo Du, and Yao Xu

SummaryThe laser-induced temperature-jump (T-jump) technique in conjunction with infrared spec-

troscopy provides a versatile means to study the early events in protein folding. Compared withthe commonly used stopped-flow kinetic methods, the T-jump initiation technique offers a fastertime resolution. It allows the study of protein folding processes occurring on the nanosecond-to-microsecond time-scales. In addition, infrared spectroscopy is a powerful tool for character-izing backbone conformation and dynamics. In this chapter, we mainly discuss the applicationof this technique to the study of the helix–coil transition dynamics and the mechanism of β-hairpinformation.

Key Words: α-Helix; β-hairpin; dynamics; infrared; protein folding; temperature-jump.

1. IntroductionThe folding rates of proteins and peptides span many orders of magnitude.

Using the technique of stopped-flow kinetics in conjunction with site-directedmutagenesis and hydrogen-deuterium exchange, it has been possible to studythe sequence of folding events of many single-domain proteins on the millisec-ond time-scale in great detail (1–3). However, the folding of monomeric α-helicesand β-hairpins occurs on the nanosecond-to-microsecond time-scale (4–7) andhas only recently been studied experimentally. Although many computationaland theoretical studies have also contributed significantly to our understandingof how these short peptides fold, a comprehensive review of relevant studies isbeyond the scope of this chapter.

The α-helix and β-sheet are common secondary structure elements in proteins.Therefore, understanding their folding mechanisms will shed light on the ques-tion of how proteins fold. However, because of their fast folding rate, studying thefolding dynamics of monomeric helices and β-hairpins requires a fast initiation

method. Although many photo or photochemical initiation methods are capableof triggering a folding/unfolding event on the nanosecond or even picosecondtime-scale (8–15), the laser-induced temperature-jump (T-jump) technique(4,16–21) has been the most widely used in the study of the dynamics of thehelix–coil transition (16,22) and β-hairpin formation (23,24), as well as other fastevents in protein folding (25–30). The primary reason for this is that it does notrequire the additional chemical modification of the polypeptide of interest, eventhough it is limited to conditions where the peptide undergoes a net folding orunfolding transition. This contrasts with other photochemical triggering methods,which generally involve the removal of a designed conformational constraint byemploying a laser pulse. For example, an aryl disulfide bond has been used toconstrain an alanine-based peptide to be distorted from its equilibrium form, andafter photolysis the dissociation of the disulfide bond generates two thiol radicals,and the peptide then commences to fold into an α-helical conformation (9,31).Similarly, the reversible photoisomerization of azobenzene, linking two cysteineresidues in a designed peptide, has also been demonstrated to have the capabilityto control the helix content in steady state (12) and has recently been used to studythe early folding kinetics of α-helices and β-hairpins (32–34).

Because several reviews on the T-jump method, as well as its application onthe study of fast events in protein folding, have already existed in the literature(4,19–21,35), here we only briefly discuss the laser-induced T-jump method.This method utilizes very short laser pulses centered around 1.5 or 1.9 µm toheat up a H2O or D2O sample solution within a very short period of time, e.g.,a few nanoseconds (36). The resulting T-jump amplitude depends on the pumpvolume and the pulse energy, whereas the useful observation time window, inwhich the temperature remains approximately constant, is governed by the timeit takes for the heat to diffuse out of the laser interaction volume, which rangesfrom a few to tens of milliseconds, depending on the setup (19). Because thestability of a protein, or its free energy, depends on temperature, a rapid increasein temperature thus allows, with the use of an appropriate conformationalprobe, the measurement of the T-jump-induced relaxation kinetics and, there-fore, the folding and unfolding rates of the system of interest. For example, fora simple two-state scenario, e.g., U ⇔ N (U and N represent the unfolded andthe folded states, respectively), the observed relaxation rate constant is exactlythe sum of the folding (kf) and unfolding (ku) rate constants. Thus, the foldingand unfolding rate constants can be obtained individually if the equilibrium con-stant (Keq = kf/ku) of this two-state reaction at the final temperature is known.

2. T-Jump Infrared TechniqueThe fast T-jump initiation technique can be combined with a variety of time-

resolved spectroscopic methods, such as fluorescence (37), circular dichroism

2 Gai, Du, and Xu

(38–40), and vibrational spectroscopy (41–45), to study protein folding andconformational dynamics. In particular, infrared (IR) spectroscopy has beenproven to be versatile in such studies. For example, the IR amide bands arevaluable markers of protein secondary structures, whereas some of the aminoacid side chain vibrations are suitable reporters of local environment (45,46).Among the eight amide vibrational modes, the amide I band, which arisesmostly from the amide C = O stretching vibration, is the most intense and isbest characterized (41,47). The amide I band of proteins or peptides has longbeen used as a global conformational reporter. The exact shape and position ofthe amide I band of a protein, however, are determined by many factors, includ-ing various couplings among individual vibrators, hydrogen bonding, solvation,and backbone conformations (44,45). As a result, it is often difficult to quanti-tatively interpret amide I bands of proteins because they are almost invariablycongested with components arising from different structural ensembles. Toobtain site-specific structural information, a commonly used technique is isotopeediting, wherein one or several amide 12C = Os are substituted with 13C = Os.Because of the isotopic effect, the amide I absorbance of the 13C-labeled car-bonyls shifts toward the lower frequency, therefore, (sometimes) permittingsite-specific studies (48,49).

Infrared studies of proteins in aqueous solution are complicated by the factthat H2O absorbs very strongly in the spectral region that overlaps with theamide I band. D2O, on the other hand, has a relatively low absorbance between1400 and 1800 cm-1 and is therefore commonly employed in IR studies (in D2Othe amide I band is referred to as amide I′). In a T-jump IR experiment, how-ever, the T-jump pulses will induce a change in the D2O absorbance. To recoverthe protein signal, therefore, the solvent signal should be appropriately meas-ured and subtracted from the total absorbance change measured with the pro-tein sample.

The 3-ns and 1.9-µm T-jump pulse of our T-jump infrared apparatus (17,35)is generated via Raman shifting the 1.06-µm output of an injection-seededNd:YAG laser in a Raman cell containing a mixture of H2 and Ar. The latterhelps to stabilize the 1.9-µm output and also improve the beam quality. A stablepump source is rather important for T-jump experiments because the kineticevents in protein folding are temperature dependent. A continuous wave leadsalts infrared diode laser, which is tunable from 1550–1800 cm-1, is used as theprobe. Transient absorbance changes of the sample induced by the T-jumppulses are detected by a 50 MHz MCT detector, and digitization of the signal isaccomplished by a digital oscilloscope. To ensure a uniform T-jump distributionwithin the laser interaction volume, a thin optical path length, typically 52 µm,is used. Furthermore, to provide information for both background subtractionand T-jump amplitude determination, a sample cell with dual compartments

Folding Dynamics of α-Helices and β-Hairpins 3

is used to measure the T-jump-induced signals of both the peptide sample andreference (i.e., buffer) under the same conditions. Characterizing the T-jumpamplitude is done by using the T-jump-induced absorbance change of the bufferat the probing frequency ν, ∆A(∆T, ν) and the following equation: ∆A(∆T, ν) =a(ν)*∆T + b(ν)*∆T2, where ∆A is the absorbance change, ∆T = Tf – Ti is the T-jumpamplitude; where Tf and Ti correspond to the final and initial temperatures, respec-tively; and a(ν) and b(ν) are constants that are determined by measuring the tem-perature dependence of the Fourier transform infrared (FTIR) spectra of the buffersolution.

3. Helix–Coil Transition DynamicsSeminal works of Schellman et al., Lifson et al., and Poland et al. formed the

basis of our understanding of the thermodynamics of monomeric helices(50–53). The classical helix–coil transition theory is characterized by a nucle-ation event, wherein the first helical hydrogen bond formed between the amidecarbonyl of residue i and the amide hydrogen of residue i + 4 is generated. Aseries of propagation steps then follow the nucleation step, in which the pre-formed helical structures become elongated. Because the nucleation step isentropically unfavorable, it has been suggested that it encounters the largest freeenergy barrier during the course of helix formation. Because the helix–coil tran-sition takes place on the nanosecond time-scale, however, it was only recentlythat its kinetics were studied and the mechanism of this seemingly simple fold-ing process was being understood (9,13,16,22,33,34,54–56). Of course, manycomputational studies (57–65) have also significantly enhanced our understand-ing of the mechanism of the helix–coil transition, but an extensive review onthis subject is beyond the scope of this chapter.

The laser-induced T-jump method, in conjunction with various spectroscopictechniques (16,17,22,54–56), has been playing a major role in investigating thekinetic properties of the helix–coil transition. For example, Williams et al. (16)studied the folding kinetics of the Fs peptide (sequence: [A]5-[AAARA]3-A-NH2)using a T-jump infrared technique and found that the relaxation process inducedby a T-jump from 9.3 to 27.4°C could be described by a single exponential func-tion with a time constant of approx 160 ns, indicating that the helix–coil transitionis a submicrosecond event. However, by using a fluorescent probe (MABA)attached at the N-terminus of the Fs peptide, Thompson et al. (17) observed amuch faster relaxation process (~20 ns at 303 K). They attributed this relaxation torapid fraying of the helix ends in response to the T-jump. Using a “kinetic zipper”model, they have also calculated the decay of the average helix content and theirresults indicate that a slower rate should account for the transition between thehelix-containing and nonhelix-containing structural ensembles, owing to theenergy barrier associated with the nucleation process. Subsequently, these authors

4 Gai, Du, and Xu

(54) reported the observation of a slower relaxation process (220 ns at 300 K) in a21-residue helical peptide, Ac-WAAAH+(AAAR+A)3A-NH2, with a tryptophanresidue in position 1 to serve as the fluorescent probe. This relaxation is tempera-ture dependent and has an apparent activation energy of approx 8 kcal/mol. Usingultraviolet resonance Raman as a probe, Lednev et al. (55,56) also observed a sin-gle exponential relaxation process that is weakly temperature dependent for the Fspeptide, following a 3-ns T-jump pulse (66). Using hexafluoroisopropanol as acosolvent, Andersen et al. have also been able to study the folding kinetics of a hel-ical peptide from its cold denatured states (67). Using a photoswitchable peptide,Hamm et al. (33) recently demonstrated that the helix–coil transition dynamicscould be studied from the picosecond-to-microsecond time-scale, and their resultshighlighted the complexity of the kinetics of helix formation.

Using the T-jump IR method, we have studied the temperature dependenceof the helix–coil transition rate of an alanine-based, 21-residue helical peptideand observed a relatively large activation energy for the T-jump-induced relax-ation process, approx 15.5 kcal/mol (18). Presumably, part of the observedenergetic barrier is originated from the temperature dependence of the solventviscosity, as suggested by the study of Hofrichter et al. (68). However, thisresult also suggests that the free energy barrier encountered in the helix forma-tion may not be dominated by the entropic cost associated with the nucleationevents, as suggested by the classical helix–coil transition theory. Instead, anenthalpic penalty, probably associated with the process of desolvation or thebreaking of nonnative interactions existed in the denatured state (69), may alsocontribute significantly to the folding free energy barrier.

To further study the helix–coil transition kinetics in a site-specific manner,we have employed the isotope-editing strategy previously discussed (49).Specifically, we studied the T-jump-induced relaxation kinetics of three alanine-based helical peptides that contain a block of 13C-labeled alanines indicated byunderlines:

NL peptide: Ac-YGSPEAAAKA4KA4r-CONH2ML peptide: Ac-YGSPEA3KAAAAKA4r-CONH2CL peptide: Ac-YGSPEA3KA4KAAAAr-CONH2

where r represents D-arginine, serving as an efficient C-cap (70). As shown(Fig. 1), the red-shifted amide I′ band of the 13C-labeled carbonyls indeed pro-vides site-specific structural information. For example, the 13C = O signal of theCL peptide is much weaker than that of the ML and NL peptides, indicative ofa frayed C-terminus (71). In addition, we found that the T-jump-induced relax-ation kinetics of these peptides show nonexponential behaviors and are sensi-tive to both initial and final temperatures (Fig. 2). Taken together, these resultssuggest that the nucleation process is fast and probably inseparable from the


6

Fig. 1. Temperature-dependent equilibrium (top traces) and difference (bottom traces) FTIR spectra of the labeled and nonlabeled pep-tides, as indicated in the plot. Difference spectra were generated by subtracting the spectrum collected at the lowest temperature fromthe spectra collected at higher temperatures. The bands at approx 1600 and 1636 cm–1 are assigned to the amide I′ absorbance of the 13C-labeled and nonlabeled residues, respectively. (Reproduced with permission from ref. 71.)

propagation event, and the helix formation may be described as a diffusionsearch process. Consistent with our observation (71), several computer simula-tion studies (62,65,72–74) have also revealed the complex nature of the dynamicsof helix formation.

To understand how peptide sequence affects the kinetics of the helix–coil transi-tion, we further studied (30) a series of alanine-based peptides of different lengths,with either excellent or poor end-capping groups, as shown in the following:

AKAn peptides: YGAKAAAA(KAAAA)nG, n = 2 – 6SPEn peptides: YGSPEAAA(KAAAA)nr, n = 2 – 5

Here, r also represents D-arginine and is one of the best C-caps (70), and theSer-Pro-Glu tripeptide (SPE) serves as a helix-stabilizing N-cap (71).

Athough it has long been recognized that helix-capping sequences providevery significant thermodynamic stability to the α-helix (75–80), their role in thekinetics of helix formation has not been previously studied. One possibility isthat the role of end-caps is to lock in pre-existing helices, and the other is thatthey can effectively serve as helix initiators. These two opposing views lead todifferent experimental results. If the capping is not involved in initiation, therate of helix initiation should not be much affected for peptides with different


Fig. 2. T-jump induced relaxation kinetics of the ML peptide probed at 1600 cm-1.The T-jump is from different initial temperatures to the same final temperature, as indi-cated. The smooth lines are fits to a stretched exponential function. The data obtainedin response to a T-jump of 10.1–14.3°C have been scaled for comparison.

end-caps. On the other hand, if capping interactions are able to initiate helixformation then the rate of helix formation should be very profoundly affected.Our results show definitively that efficient end-capping sequences can not onlystabilize pre-existing helices, but also promote helix formation through increas-ing the rate of helix folding (Fig. 3).

The peptide length is another factor that may also profoundly affect thedynamics of the helix–coil transition, as indicated by a number of theoreticalstudies (58,81). If the kinetically and thermodynamically difficult step in theprocess of the coil-to-helix transition is initiation of a single turn of the helix, asone proceeds in peptide length from short to long the rate of helix formationshould not be drastically affected. Only a small increase would be observedowing to a linear, length-dependent increase in the probability of initiation as thepeptide is lengthened. However, our results show that the peptide length has arather complicated effect on the kinetics of the helix–coil transition. For example,we found that the relaxation rates of these peptides following a T-jump of 1–11°Cshow rather complex behaviors as a function of the peptide length (Fig. 3), indisagreement with early theoretical predictions. These results are not readilyexplicable by theories in which alanine is taken to have a single helical propensity.However, if one were to assume that the propagation constant, s, depends on chainlength (82,83), the mean first-passage times of the coil-to-helix transition obtained,

8 Gai, Du, and Xu

Fig. 3. Logarithm of the relaxation rates of AKAn (∆) and SPEn (O) peptides follow-ing a T-jump from 1 to 11°C.

based on the model developed by Straub et al. (81), show similar dependence onthe peptide length as those observed experimentally (30).

4. β-Hairpin Folding DynamicsA β-hairpin structure is characterized by two antiparallel strands linked by a

short turn or loop. Owing to its small size and simplicity, as well as the possiblerole of functioning as a folding nucleus (84–88), the β-hairpin motif has beenincreasingly used to probe factors that govern the conformational stability aswell as the folding mechanism of β-sheets (89–91). The first experimental studyof β-hairpin folding kinetics on the microsecond time-scale was carried out byMuñoz et al. (23), who measured the folding time of a 16-residue β-hairpinderived from the C-terminal fragment (41–56) of protein G (92). Subsequently,a large number of theoretical and computational studies have been performed(93–104), aiming to understand the mechanism of β-hairpin folding. Manystudies suggested that several factors, including the rigidity of the turn and therelative position of the hydrophobic cluster, may have rather complex effects onthe folding free energy landscape and, therefore, the rate of β-hairpin formation.

The results of Muñoz et al. (23) indicated that the GB1 β-hairpin folds in atwo-state manner with a folding time constant of 6 µs at 297 K. Subsequently,these authors developed a statistical zipper model (93) to explain the apparenttwo-state folding behavior of this β-hairpin and suggested that folding begins withthe formation of the turn. Recently, Xu et al. (24) studied the folding kinetics ofa 15-residue β-hairpin designed by Jiménez et al. (105,106). This β-hairpin con-tains a type I + G1 β-bulge turn and shows a fairly broad thermal unfolding tran-sition (24). However, its folding rate, measured by the T-jump IR technique, issurprisingly fast. At 300 K, the folding time of this β-hairpin is approx 0.8 µs,only two to three times slower than that of α-helix formation. Therefore, theresults of Muñoz et al. and Xu et al. suggest that the folding times of β-hairpinsmay vary greatly depending on the peptide sequence. Consistent with this pic-ture, the recent work of Dyer and coworkers showed that the folding rate of aseries of cyclic β-hairpins (107) is significantly faster than that of linear β-hairpins.Although for linear β-hairpins, the folding rate could be substantially acceleratedby a shorter connecting loop (108). In addition, it was found that the nature ofthe thermally denatured states can also have dramatic effects on the rate ofβ-hairpin folding (109,110).

Although those studies previously described firmly demonstrated that β-hairpinsfold on the submillisecond time-scale, the marked differences in the peptidesequence of those systems studied makes it difficult to explicitly determine thekey factors that control the rate of β-hairpin folding. Thermodynamically, it iswell known that a stable β-hairpin results from an intricate interplay among sev-eral factors, such as hydrogen bonding, electrostatic interaction, turn preference,


and hydrophobic packing of side chains (111–115). For example, a stable β-hairpinconformation is often the result of a strong turn-promoting sequence and a sta-bilizing hydrophobic cluster. To provide a better understanding of the kineticrole of the turn and hydrophobic cluster in β-hairpin folding, we have recentlyexamined the folding kinetics of a series of sequence-related β-hairpins (116),i.e., tryptophan zippers (117). As shown in Table 1, the 12-residue tryptophanzippers (trpzips) studied here differ only in the turn composition, whereastrpzip4 is a triple mutant of the GB1 β-hairpin in the hydrophobic cluster region.As expected, the thermal melting temperatures of these trpzips span a widerange, demonstrating the effect of sequence on stability (see Table 1) (116,118).

Although trpzip4 and the GB1 β-hairpin differ from each other only in thecomposition of the hydrophobic cluster, comparing their folding kinetics willpermit us to determine the kinetic role of the hydrophobic clusters found in theseβ-hairpins. Using the method of T-jump fluorescence, Eaton et al. (23) haveshown that the GB1 β-hairpin folds in approx 6 µs at 297 K. Although trpzip4 ismore stable, it folds with a similar rate. At 297 K, its folding time constant isextrapolated to be approx 15 µs (Table 2). On the contrary, their unfolding ratesdiffer significantly. At 297 K, the GB1 β-hairpin unfolds in approx 6 µs (23),whereas the unfolding time constant of trpzip4 is approx 234 µs. The similarfolding rates exhibited by the GB1 β-hairpin and trpzip4 suggest that their fold-ing free energy barriers are also quite similar. However, the slower unfolding rateof trpzip4 indicates that it has a larger unfolding free energy barrier, comparedwith the GB1 β-hairpin. Moreover, these results suggest that mutations to thehydrophobic side chains in the GB1 peptide do not significantly alter the freeenergy of the folding transition state. In other words, the native hydrophobic sidechain–side chain contacts have not been formed in the transition state structuralensemble. Therefore, the role of a strong cross-strand hydrophobic cluster, such

10 Gai, Du, and Xu

Table 1Sequences of Trpzips and the GB1 Peptidea

Peptide Sequence Tm (°C) Ref.

Trpzip1 SWTWEGNKWTWK 49.9 (117)Trpzip2 SWTWENGKWTWK 71.9 (117)Trpzip3 SWTWEDPNKWTWKb 80.1 (116)Trpzip3-I SWTWDATKWTWK 16.8 (116)Trpzip4 GEWTWDDATKTWTWTE 70.4 (116)GB1 GEWTYDDATKTFTVTE 24.3 (23)

aAlso shown are the thermal melting temperatures (Tm) of these β-hairpins (Adapted from ref. 116).

bDP stands for D-Pro.

as the one found in trpzips, is to primarily prevent the unfolding of the folded β-hairpin conformation. Extensive φ-value analysis (119) on the folding kineticsof trpzip4 further confirmed this conclusion (120).

The folding kinetics of the four 12-residue trpzips have been studied byeither T-jump IR, or T-jump fluorescence, or both (104,116). It has been shownthat for trpzip2 and trpzip3 both methods yielded nearly identical results(104,116). As shown in Table 2, the unfolding rate constants of these 12-residuetrpzips are only different by a factor of three or less. However, their folding rateconstants differ by as much as 30 times (e.g., comparing trpzip3 with trpzip3-I).Taken together, these results suggest that the turn sequence is a strong determi-nant of the β-hairpin folding rate but has a rather small effect on the unfoldingrate, consistent with a β-hairpin folding model wherein the rate-limiting eventin folding is the formation of the turn (or loop).

It is well established that the turn sequence is an important determinant ofthe turn conformation and thereby, other features of β-hairpin conformation,such as the pattern of interstrand hydrogen bonding and residue pairing (121).Moreover, strong turn-promoting sequences, such as those containing a DPresidue (91,122), often correspond to a relatively low entropic cost upon turnformation. For example, Gellman et al. (91) have recently shown that the highturn-forming propensity of the DPG segment decreases the equilibrium entropiccost of β-hairpin formation relative to the more flexible NG segment.Interestingly, trpzip3, which contains a strong turn-promoting sequence, DPN,exhibits the fastest folding rate among the 12-residue trpzips studied. Accordingto Gellman et al. (91), the excellent turn preference of DPN may be attributedto the conformational rigidity of the DP residue, which effectively reduces theentropic penalty, ∆Sturn, upon turn formation. As indicated by results from thisand other studies (23,24,107), the free energy barrier of β-hairpin folding isdominated by the unfavorable entropic cost for the formation of the transitionstate. Therefore, within the framework of the folding transition state theory, it


Table 2Folding/Unfolding Rate Constants and Equilibrium Entropic Changesof the 12-Residue Trpzips

Trpzip1a Trpzip2a Trpzip3 Trpzip3-I Trpzip4 GB1b

kf–1 (µs) 6.3 ± 0.3 2.5 ± 0.05 1.7 ± 0.2 52.2 ± 4.5 14.9 ± 0.6 6.0

ku–1 (µs) 18.3 ± 3.1 24.7 ± 3.0 12.2 ± 2.1 37.5 ± 3.4 234.0 ± 10.7 6.0

∆Sf (cal K–1 mol-1) –13.4 –5.7 –2.6 –31.9 –13.4 –39.0

At 23°C and those of trpzip4 and the GB1 peptide at 24°C. ∆Sf at temperature T was calcu-lated using the following equation: ∆Sf = –[∆Sm + ∆Cp·ln(T/Tm)]. (Adapted from ref. 116.)

aData from ref. 104.bData from ref. 23.

is reasonable to assume that kf is proportional to exp(α·∆Sturn/R), where α is aconstant. Although it is difficult to explicitly determine ∆Sturn for a given β-hairpin, the following relationship is valid, ∆Sf = ∆Sturn + ∆Sstrand; where∆Sf is the total folding entropic change obtained from thermal melting experi-ments, and ∆Sstrand is the entropic change associated with the folding of thestrands. Thus, kf is proportional to exp[α·(∆Sf – ∆Sstrand)/R]. It is easy to showthat the latter equation leads to the following relationship, ln(kf) = ρ + α·(∆Sf –∆Sstrand)/R. , where ρ is a constant. For the four 12-residue trpzips previously dis-cussed, an approximate but quite reasonable assumption is that they have thesame ∆Sstrand. Such an assumption would lead directly to a relationship whereinln(kf) is linearly proportional to ∆Sf. Indeed, such a linear correlation isobserved for the four 12-residue trpzips (Fig. 4), where faster folding correlateswith smaller entropic change. These results further strengthen our argumentthat the turn (or the turn region) is a key determinant of the folding rate of β-hairpins and clearly demonstrate that stronger turn-promoting sequences,such as those that contain a DP residue, increase the stability of β-hairpins byincreasing the folding rate. Finally, it is worth pointing out that one should notsimply interpret the term ∆Sturn invoked here as the differences in disorderedloop entropy because it only corresponds to a fraction of the entropic changedetermined from the thermal unfolding studies. In addition, one should bear in

12 Gai, Du, and Xu

Fig. 4. ln(kf) vs ∆Sf at 296 K for the 12-residue trpzips (Table 2). (Reproduced withpermission from ref. 116.)

mind that the thermally denatured states of β-hairpins may be quite compactand temperature dependent (123,124). Therefore, the ∆Sf listed in Table 2 maynot totally measure the entropy difference between the native state and anextended (or random) conformational ensemble.

In summary, these results suggest a folding mechanism in which the turn(or loop) plays an important role in determining the rate of β-hairpin folding.Moreover, a good turn-promoting sequence or a strong interstrand hydrophobiccluster can help to stabilize the folded conformation of β-hairpins. However, theformer increases the stability of a β-hairpin primarily by increasing its folding rate,whereas the latter affects the stability primarily by decreasing its unfolding rate.

5. ConclusionThe T-jump IR method provides a versatile means to study the conformational

dynamics of peptides and proteins. Compared with the commonly used stopped-flow kinetic methods, the T-jump technique can initiate a conformational processon the nanosecond time-scale and, thus, offers a faster time resolution. The exam-ples presented in this chapter illustrated how this technique can be applied to thestudy of the dynamics of some primary events in protein folding. In conjunctionwith the techniques of isotope-editing and site-directed mutagenesis, the T-jumpIR method will allow the study of the early folding events in even greater detail.

AcknowledgmentsWe wish to thank our colleagues in the Gai research group for their contri-

butions to this work, particularly Cheng-Yen Huang, Ting Wang, Yongjin Zhu,and Rolando Oyola. We also wish to thank our collaborators for their contribu-tions, particularly Drs. W. F. DeGrado and Z. Getahun. Support for this workwas provided by the National Institutes of Health (GM-065978, RR-001348)and the NSF (CHE-0094077).

References1. Dyson, H. J. and Wright, P. E. (1996) Insights into protein folding from NMR.

Annu. Rev. Phys. Chem. 47, 369–395. 2. Eftink, M. R. and Shastry, M. C. R. (1997) Fluorescence methods for studying

kinetics of protein-folding reactions. Methods Enzymol. 278, 258–286. 3. Englander, S. W. (2000) Protein folding intermediates and pathways studied by

hydrogen exchange. Annu. Rev. Biophys. Biomol. Struct. 29, 213–238.4. Eaton, W. A., Muñoz, V., Thompson, P. A., Henry, E. R., and Hofrichter, J. (1998)

Kinetics and dynamics of loops, α-helixes, β-hairpins, and fast-folding proteins.Acc. Chem. Res. 31, 745–753.

5. Dyer, R. B., Gai, F., Woodruff, W. H., Gilmanshin, R., and Callender, R. H. (1998)Infrared studies of fast events in protein folding. Acc. Chem. Res. 31, 709–716.


6. Bieri, O. and Kiefhaber, T. (1999) Elementary steps in protein folding. Biol. Chem.380, 923–929.

7. Eaton, W. A., Muñoz, V., Hagen, S. J., Jas, G. S., Lapidus, L. J., and Henry, E. R.(2000) Fast kinetics and mechanisms in protein folding. Annu. Rev. Biophys. Biomol.Struct. 29, 327–359.

8. Jones, C. M., Henry, E. R., Hu, Y., et al. (1993) Fast events in protein folding initi-ated by nanosecond laser photolysis. Proc. Natl. Acad. Sci. USA 90, 11,860–11,864.

9. Volk, M., Kholodenko, Y., Lu, H. S. M., Gooding, E. A., DeGrado, W. F., andHochstrasser, R. M. (1997) Peptide conformational dynamics and vibrationalStark effects following photoinitiated disulfide cleavage. J. Phys. Chem. B. 101,8607–8616.

10. Wittung-Stafshede, P., Lee, J. C., Winkler, J. R., and Gray, H. B. (1999)Submillisecond folding of monomeric λRepressor. Proc. Natl. Acad. Sci. USA 96,6587–6590.

11. Hansen, K. C., Rock, R. S., Larsen, R. W., and Chan, S. I. (2000) A method forphotoinitating protein folding in a nondenaturing environment. J. Am. Chem. Soc.122, 11,567, 11,568.

12. Kumita, J. R., Smart, O. S., and Woolley, G. A. (2000) Photo-control of helix con-tent in a short peptide. Proc. Natl. Acad. Sci. USA 97, 3803–3808.

13. Huang, C.-Y., He, S., DeGrado, W. F., McCafferty, D. G., and Gai, F. (2002)Light-induced helix formation. J. Am. Chem. Soc. 124, 12,674, 12,675.

14. Abbruzzetti, S., Crema, E., Masino, L., et al. (2000) Fast events in protein fold-ing: structural volume changes accompanying the early events in the N→I transi-tion of Apomyoglobin induced by ultrafast pH jump. Biophys. J. 78, 405–415.

15. Barth, A. and Corrie, J. E. T. (2002) Characterization of a new caged proton capa-ble of inducing large pH jumps. Biophys. J. 83, 2864–2871.

16. Williams, S., Causgrove, T. P., Gilmanshin, R., et al. (1996) Fast events in pro-tein folding: helix melting and formation in a small peptide. Biochemistry 35,691–697.

17. Thompson, P. A., Eaton, W. A., and Hofrichter, J. (1997) Laser temperature jumpstudy of the helix ↼⇁ coil kinetics of an alanine peptide interpreted with a ‘kineticzipper’ model. Biochemistry 36, 9200–9210.

18. Huang, C.-Y., Klemke, J. W., Getahun, Z., DeGrado, W. F., and Gai, F. (2001)Temperature-dependent helix-coil transition of an alanine based peptide. J. Am.Chem. Soc. 123, 9235–9238.

19. Hofrichter, J. (2001) Laser temperature-jump methods for studying foldingdynamics. Methods Mol. Biol. 168, 159–191.

20. Callender, R. and Dyer, R. B. (2002) Probing protein dynamics using temperaturejump relaxation spectroscopy. Curr. Opin. Struct. Biol. 12, 628–633.

21. Gruebele, M., Sabelko, J., Ballew, R., and Ervin, J. (1998) Laser temperaturejump induced protein refolding. Acc. Chem. Res. 31, 699–707.

22. Herberhold, H. and Winter, R. (2002) Temperature- and pressure-induced unfold-ing and refolding of Ubiquitin: a static and kinetic Fourier transform infraredspectroscopy study. Biochemistry 41, 2396–2401.

14 Gai, Du, and Xu

23. Muñoz, V., Thompson, P. A., Hofrichter, J., and Eaton, W. A. (1997) Foldingdynamics and mechanism of β-hairpin formation. Nature 390, 196–199.

24. Xu, Y., Oyola, R., and Gai, F. (2003) Infrared study of the stability and foldingkinetics of a 15-residue β-hairpin. J. Am. Chem. Soc. 125, 15,388–15,394.

25. Sabelko, J., Ervin, J., and Gruebele, M. (1999) Observation of strange kinetics inprotein folding. Proc. Natl. Acad. Sci. USA 96, 6031–6036.

26. Hagen, S. J. and Eaton, W. A. (2000) Two-state expansion and collapse of apolypeptide. J. Mol. Biol. 301, 1019–1027.

27. Sadqi, M., Lapidus, L. J., and Muñoz, V. (2003) How fast is protein hydrophobiccollapse? Proc. Natl. Acad. Sci. USA 100, 12,117–12,122.

28. Zhu, Y., Alonso, D. O. V., Maki, K., et al. (2003) Ultrafast folding of α-3D: a denovo designed three-helix bundle protein. Proc. Natl. Acad. Sci. USA 100,15,486–15,491.

29. Zhu, Y., Fu, X., Wang, T., et al. (2004) Guiding the search for a protein’s maxi-mum rate of folding. Chem. Phys. 307, 99–109.

30. Wang, T., Zhu, Y., Getahun, Z., et al. (2004) Length dependent helix-coil transitionkinetics of nine alanine-based peptides. J. Phys. Chem. B. 108, 15,301–15,310.

31. Lu, H. S. M., Volk, M., Kholodenko, Y., Gooding, E., Hochstrasser, R. M., andDeGrado, W. F. (1997) Aminothiotyrosine disulfide, an optical trigger for initia-tion of protein folding. J. Am. Chem. Soc. 119, 7173–7180.

32. Chen, R. P., Huang, J. J., Chen, H.-L., Jan, H., et al. (2004) Measuring the refold-ing of β-sheets with different turn sequences on a nanosecond time scale. Proc.Natl. Acad. Sci. USA 101, 7305–7310.

33. Bredenbeck, J., Helbing, J., Kumita, J. R., Woolley, G. A., and Hamm, P. (2005)α-Helix formation in a photoswitchable peptide tracked from picoseconds tomicroseconds by time-resolved IR spectroscopy. Proc. Natl. Acad. Sci. USA 102,2379–2384.

34. Bredenbeck, J., Helbing, J., Sieg, A., et al. (2003) Picosecond conformationaltransition and equilibration of a cyclic peptide. Proc. Natl. Acad. Sci. USA 100,6452–6457.

35. Zhu, Y., Wang, T., and Gai, F. (2005) Laser-induced T-jump method, a noncon-ventional photo-releasing approach to study protein folding. In: Dynamic Studiesin Biology: Phototriggers, Photoswitches and Caged Biomolecules, (Goeldner, G.and Givens R. eds.), Wiley-VCH Verlag GmbH, Weinheim, pp. 461–478.

36. Palmer, K. F. and Williams, D. (1974) Optical properties of water in the nearinfrared. J. Opt. Soc. Am. 64, 1107–1110.

37. Beechem, J. M. and Brand, L. (1985) Time-resolved fluorescence of proteins.Annu. Rev. Biochem. 54, 43–71.

38. Adler, A. J., Greenfield, N. J., and Fasman, G. D. (1973) Circular dichroism andoptical rotatory dispersion of proteins and polypeptides. Methods Enzymol. 27,675–735.

39. Zhang, C. F., Lewis, J. W., Cerpa, R., Kuntz, I. D., and Kliger, D. S. (1993)Nanosecond circular dichroism spectral measurements: extension to the far-ultraviolet region. J. Phys. Chem. 97, 5499–5505.


40. Wen, Y. X., Chen, E., Lewis, J. W., and Kliger, D. S. (1996) Nanosecond time-resolved circular dichroism measurements using an upconverted Ti:sapphirelaser. Rev. Sci. Instrum. 67, 3010–3016.

41. Krimm, S. and Bandekar, J. (1986) Vibrational spectroscopy and conformation ofpeptides, polypeptides, and proteins. Adv. Protein Chem. 38, 181–364.

42. Kitagawa, T. and Hirota, S. (2002) Raman spectroscopy of proteins. In: Handbookof Vibrational Spectroscopy, (Chalmers, J. M. and Griffiths, P. R., eds.), John Wileyand Sons, New York, pp. 3426–3446.

43. Spiro, T. G. and Czernuszewicz, R. S. (1995) Resonance Raman spectroscopy ofmetalloproteins. Methods Enzymol. 246, 416–460.

44. Fabian, H. and Mantele, W. (2002) Infrared spectra of proteins. In: Handbook ofVibrational Spectroscopy, (Chalmers, J. M. and Griffiths, P. R., eds.), John Wileyand Sons, New York, pp. 3399–3425.

45. Barth, A. and Zscherp, C. (2002) What vibrations tell about proteins. Q. Rev.Biophys. 35, 369–430.

46. Getahun, Z., Huang, C.-Y., Wang, T., De Leon, B., DeGrado, W. F., and Gai, F.(2003) Using nitrile-derivatized amino acids as infrared probes of local environ-ment. J. Am. Chem. Soc. 125, 405–411.

47. Susi, H. (1972) Infrared spectroscopy. Conformation. Methods Enzymol. 26,455–472.

48. Decatur, S. M. and Antonic, J. (1999) Isotope-edited infrared spectroscopy of hel-ical peptides. J. Am. Chem. Soc. 121, 11,914, 11,915.

49. Huang, C.-Y., Getahun, Z., Wang, T., DeGrado, W. F., and Gai, F. (2001) Time-resolved infrared study of the helix-coil transition using 13C-labeled helical pep-tides. J. Am. Chem. Soc. 123, 12,111–12,112.

50. Schellman, J. A. (1958) The factors affecting the stability of hydrogen-bondedpolypeptide structures in solution. J. Phys. Chem. 62, 1485–1494.

51. Zimm, B. H. and Bragg, J. K. (1959) Theory of the phase transition between helixand random coil in polypeptide chains. J. Chem. Phys. 31, 526–535.

52. Lifson, S. and Roig, A. (1961) On the theory of helix-coil transition in polypep-tides. J. Chem. Phys. 34, 1963–1974.

53. Poland, D. and Scheraga, H. A. (1970) Theory of Helix-Coil Transition inBiopolymers, Academic Press, New York and London.

54. Thompson, P. A., Muñoz, V., Jas, G. S., Henry, E. R., Eaton, W. A., and Hofrichter, J.(2000) The helix-coil kinetics of a heteropeptide. J. Phys. Chem. B. 104, 378–389.

55. Lednev, I. K., Karnoup, A. S., Sparrow, M. C., and Asher, S. A. (1999)Nanosecond UV resonance Raman examination of initial steps in α-helix second-ary structure evolution. J. Am. Chem. Soc. 121, 4076–4077.

56. Lednev, I. K., Karnoup, A. S., Sparrow, M. C., and Asher, S. A. (1999) α-Helixpeptide folding and unfolding activation barriers: a nanosecond UV resonanceRaman study. J. Am. Chem. Soc. 121, 8074–8086.

57. Daggett, V. and Levitt, M. (1992) Molecular dynamics simulations of helix denat-uration. J. Mol. Biol. 223, 1121–1138.

58. Brooks, C. L. (1996) Helix-coil kinetics: folding time scales for helical peptidesfrom a sequential kinetic model. J. Phys. Chem. 100, 2546–2549.

16 Gai, Du, and Xu

59. Schaefer, M., Bartels, C., and Karplus, M. (1998) Solution conformations andthermodynamics of structured peptides: molecular dynamics simulation with animplicit solvation model. J. Mol. Biol. 284, 835–848.

60. Duan, Y. and Kollman, P. A. (1998) Pathways to a protein folding intermediateobserved in a 1-microsecond simulation in aqueous solution. Science 282,740–744.

61. Takada, S., Luthey-Schulten, Z., and Wolynes, P. G. (1999) Folding dynamicswith nonadditive forces: a simulation study of a designed helical protein and arandom heteropolymer. J. Chem. Phys. 110, 11,616–11,629.

62. Hummer, G., Garcia, A. E., and Grade, S. (2001) Helix nucleation kinetics frommolecular simulations in explicit solvent. Proteins 42, 77–84.

63. Shimada, J., Kussell, E. L., and Shakhnovich, E. I. (2001) The folding thermody-namics and kinetics of crambin using an all-atom Monte Carlo simulation. J. Mol.Biol. 308, 79–95.

64. Doshi, U. and Muñoz, V. (2004) Kinetics of α-helix formation as diffusion on aone-dimensional free energy surface. Chem. Phys. 307, 129–136.

65. Sorin, E. J. and Pande, V. S. (2005) Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophys. J. 88, 2472–2493.

66. Nishii, I., Kataoka, M., Tokunaga, F., and Goto, Y. (1994) Cold denaturation ofthe molten globule states of Apomyoglobin and a profile for protein folding.Biochemistry 33, 4903–4909.

67. Werner, J. H., Dyer, R. B., Fesinmeyer, R. M., and Andersen, N. H. (2002)Dynamics of the primary processes of protein folding: helix nucleation. J. Phys.Chem. B. 106, 487–494.

68. Jas, G. S., Eaton, W. A., and Hofrichter, J. (2001) Effect of viscosity on the kinet-ics of α-helix and β-hairpin formation. J. Phys. Chem. B. 105, 261–272.

69. Chowdhury, S., Lei, H. X., and Duan, Y. (2005) Denatured-state ensemble and theearly-stage folding of the G29A mutant of the B-domain of protein A. J. Phys.Chem. B. 109, 9073–9081.

70. Schneider, J. P. and DeGrado, W. F. (1998) The design of efficient α-helicalC-capping auxiliaries. J. Am. Chem. Soc. 120, 2764–2767.

71. Huang, C.-Y., Getahun, Z., Zhu, Y., Klemke, J. W., DeGrado, W. F., and Gai, F.(2002) Helix formation via conformation diffusion search. Proc. Natl. Acad. Sci.USA 99, 2788–2793.

72. Hummer, G., Garcia, A. E., and Grade, S. (2000) Conformational diffusion andhelix formation kinetics. Phys. Rev. Lett. 85, 2637–2640.

73. Elmer, S. and Pande, V. S. (2001) A new twist on the helix-coil transition: a non-biological helix with protein-like intermediates and traps. J. Phys. Chem. B. 105,482–485.

74. Bryngelson, J. D., Onuchic, J. N., and Wolynes, P. G. (1995) Funnels, pathways,and the energy landscape of protein folding: a synthesis. Proteins 21, 167–195.

75. Presta, L. G. and Rose, G. D. (1988) Helix signals in proteins. Science 240,1632–1641.

76. Richardson, J. S. and Richardson, D. C. (1988) Amino acid preferences for specificlocations at the ends of alpha helices. Science 240, 1648–1652.


77. Regan, L. (1993) What determines where α-helices begin and end? Proc. Natl.Acad. Sci. USA 90, 10,907–10,908.

78. Aurora, R., Creamer, T. P., Srinivasan, R., and Rose, G. D. (1997) Local interac-tions in protein folding: lessons from the α-helix. J. Biol. Chem. 272, 1413–1416.

79. Aurora, R. and Rose, G. D. (1998) Helix capping. Protein Sci. 7, 21–38.80. Dasgupta, S. and Bell, J. A. (1993) Design of helix ends. Amino acid prefer-

ences, hydrogen bonding and electrostatic interactions. Int. J. Pept. Prot. Res.41, 499–511.

81. Buchete, N. -V. and Straub, J. E. (2001) Mean first-passage time calculations forthe coil-to-helix transition: the active helix Ising model. J. Phys. Chem. B. 105,6684–6697.

82. Kennedy, R. J., Tsang, K.-T., and Kemp, D. S. (2002) Consistent helicities fromCD and template t/c data for N-templated polyalanines: progress toward resolu-tion of the alanine helicity problem. J. Am. Chem. Soc. 124, 934–944.

83. Ohkubo, Y. Z. and Brooks, C. L. (2003) Exploring Flory’s isolated-pair hypothesis:statistical mechanics of helix–coil transitions in polyalanine and the C-peptide fromRNase A. Proc. Natl. Acad. Sci. USA 100, 13,916–13,921.

84. Guo, Z. Y. and Thirumalai, D. (1995) Kinetics of protein folding: nucleationmechanism, time scales, and pathways. Biopolymers 36, 83–102.

85. Gruebele, M. and Wolynes, P. G. (1998) Satisfying turns in folding transitions.Nat. Struct. Biol. 5, 662–665.

86. Grantcharova, V. P., Riddle, D. S., Santiago, J. V., and Baker, D. (1998) Importantrole of hydrogen bonds in the structurally polarized transition state for folding ofthe src SH3 domain. Nat. Struct. Biol. 5, 714–720.

87. Martinez, J. C., Pisabarro, M. T., and Serrano, L. (1998) Obligatory steps in pro-tein folding and the conformational diversity of the transition state. Nat. Struct.Biol. 5, 721–729.

88. Walkenhorst, W. F., Edwards, J. A., Markley, J. L., and Roder, H. (2002) Earlyformation of a beta hairpin during folding of staphylococcal nuclease H124L asdetected by pulsed hydrogen exchange. Protein Sci. 11, 82–91.

89. Serrano, L. (2000) The relationship between sequence and structure in elemen-tary folding units. Adv. Protein Chem. 53, 49–85.

90. Searle, M. S. (2001) Peptide models of protein β-sheets: design, folding and insightsinto stabilising weak interactions. J. Chem. Soc., Perkin Trans. 2, 1011–1020.

91. Espinosa, J. F., Syud, F. A., and Gellman, S. H. (2002) Analysis of the factors thatstabilize a designed two-stranded antiparallel β-sheet. Protein Sci. 11, 1492–1505.

92. Blanco, F. J., Rivas, G., and Serrano, L. (1994) A short linear peptide that foldsinto a native stable β-hairpin in aqueous solution. Nat. Struct. Biol. 1, 584–590.

93. Muñoz, V., Henry, E. R., Hofrichter, J., and Eaton, W. A. (1998) A statistical mechan-ical model for β-hairpin kinetics. Proc. Natl. Acad. Sci. USA 95, 5872–5879.

94. Dinner, A. R., Lazaridis, T., and Karplus, M. (1999) Understanding β-hairpin for-mation. Proc. Natl. Acad. Sci. USA 96, 9068–9073.

95. Pande, V. S. and Rokhsar, D. S. (1999) Molecular dynamics simulations ofunfolding and refolding of a β-hairpin fragment of protein G. Proc. Natl. Acad.Sci. USA 96, 9062–9067.

18 Gai, Du, and Xu

96. Klimov, D. K. and Thirumalai, D. (2000) Mechanisms and kinetics of β-hairpinformation. Proc. Natl. Acad. Sci. USA 97, 2544–2549.

97. Bonvin, A. M. J. J. and van Gunsteren, W. F. (2000) β-Hairpin stability and fold-ing: molecular dynamics studies of the first β-hairpin of tendamistat. J. Mol. Biol.296, 255–268.

98. Garcia, A. E. and Sanbonmatsu, K. Y. (2001) Exploring the energy landscape ofa β-hairpin in explicit solvent. Proteins 42, 345–354.

99. Zhou, R., Berne, B. J., and Germain, R. (2001) The free energy landscape for β-hairpin folding in explicit water. Proc. Natl. Acad. Sci. USA 98, 14,931–14,936.

100. Klimov, D. K. and Thirumalai, D. (2002) Stiffness of the distal loop restricts thestructural heterogeneity of the transition state ensemble in SH3 domains. J. Mol.Biol. 317, 721–737.

101. Zhou, Y. and Linhananta, A. (2002) Role of hydrophilic and hydrophobic contactsin folding of the second β-hairpin fragment of protein G: molecular dynamicssimulation studies of an all-atom model. Proteins 47, 154–162.

102. Ma, B. and Nussinov, R. (2003) Energy landscape and dynamics of the β-hair-pin G peptide and its isomers: topology and sequences. Protein Sci. 12,1882–1893.

103. Bolhuis, P. G. (2003) Transition-path sampling of β-hairpin folding. Proc. Natl.Acad. Sci. USA 100, 12,129–12,134.

104. Snow, C. D., Qiu, L., Du, D., Gai, F., Hagen, S. J., and Pande, V. S. (2004) Trpzipper folding kinetics by molecular dynamics and temperature-jump spec-troscopy. Proc. Natl. Acad. Sci. USA 101, 4077–4082.

105. Santiveri, C. M., Santoro, J., Rico, M., and Jiménez, M. A. (2002) Thermodynamicanalysis of β-hairpin-forming peptides from the thermal dependence of 1H NMRchemical shifts. J. Am. Chem. Soc. 124, 14,903–14,909.

106. de Alba, E., Jiménez, M. A., Rico, M., and Nieto, J. L. (1996) Conformationalinvestigation of designed short linear peptides able to fold into β-hairpin struc-tures in aqueous solution. Fold. Des. 1, 133–144.

107. Maness, S. J., Franzen, S., Gibbs, A. C., Causgrove, T. P., and Dyer, R. B. (2003)Nanosecond temperature jump relaxation dynamics of cyclic β-hairpin peptides.Biophys. J. 84, 3874–3882.

108. Dyer, R. B., Maness, S. J., Peterson, E. S., Franzen, S., Fesinmeyer, R. M., andAndersen, N. H. (2004) The mechanism of β-hairpin formation. Biochemistry 43,11,560–11,566.

109. Dyer, R. B., Maness, S. J., Franzen, S., Fesinmeyer, R. M., Olsen, K. A., andAndersen, N. H. (2005) Hairpin folding dynamics: the cold-denatured state ispredisposed for rapid refolding. Biochemistry 44, 10,406–10,415.

110. Xu, Y., Wang, T., and Gai, F. (2006) Strange temperature dependence of the foldingrate of a 16-residue β-hairpin. Chem. Phys., in press.

111. Blanco, F. J., Ramirez-Alvarado, M., and Serrano, L. (1998) Formation andstability of β-hairpin structures in polypeptides. Curr. Opin. Struct. Biol. 8,107–111.

112. Gellman, S. H. (1998) Minimal model systems for β-sheet secondary structure inproteins. Curr. Opin. Chem. Biol. 2, 717–725.


113. Kobayashi, N., Honda, S., Yoshii, H., and Munekata, E. (2000) Role of side-chains in the cooperative β-hairpin folding of the short C-terminal fragmentderived from streptococcal Protein G. Biochemistry 39, 6564–6571.

114. Tsai, J. and Levitt, M. (2002) Evidence of turn and salt bridge contributions toβ-hairpin stability: MD simulations of C-terminal fragment from the B1 domainof protein G. Biophys. Chem. 101-102, 187–201.

115. Fesinmeyer, R. M., Hudson, F. M., and Andersen, N. H. (2004) Enhanced hairpinstability through loop design: the case of the protein GB1 domain hairpin. J. Am.Chem. Soc. 126, 7238–7243.

116. Du, D., Zhu, Y., Huang, C.-Y., and Gai, F. (2004) Understanding the key factors thatcontrol the rate of β-hairpin folding. Proc. Natl. Acad. Sci. USA 101, 15,915–15,920.

117. Cochran, A. G., Skelton, N. J., and Starovasnik, M. A. (2001) Tryptophan zippers:stable, monomeric β-hairpins. Proc. Natl. Acad. Sci. USA 98, 5578–5583.

118. Owrutsky, J. C., Raftery, D., and Hochstrasser, R. M. (1994) Vibrational relax-ation dynamics in solutions. Ann. Rev. Phys. Chem. 45, 519–555.

119. Matouschek, A., Kellis, J. T., Serrano, L., and Fersht, A. R. (1989) Mapping thetransition state and pathway of protein folding by protein engineering. Nature340, 122–126.

120. Du, D., Tucker, M. J., and Gai, F. (2006) Understanding the mechanism of β-hairpinfolding via φ-value analysis. Biochemistry 45, 2668–2678.

121. de Alba, E., Jiménez, M. A., and Rico, M. (1997) Turn residue sequence determinesβ-hairpin conformation in designed peptides. J. Am. Chem. Soc. 119, 175–183.

122. Rose, G. D., Gierasch, L. M., and Smith, J. A. (1985) Turns in peptides and pro-teins. Adv. Protein Chem. 37, 1–109.

123. Yang, W. Y., Pitera, J. W., Swope, W. C., and Gruebele, M. (2004) Heterogeneousfolding of the trpzip hairpin: full atom simulation and experiment. J. Mol. Biol.336, 241–251.

124. Yang, W. Y. and Gruebele, M. (2004) Detection-dependent kinetics as a probe offolding landscape microstructure. J. Am. Chem. Soc. 126, 7758–7759.

20 Gai, Du, and Xu

21

From: Methods in Molecular Biology, vol. 350: Protein Folding ProtocolsEdited by: Y. Bai and R. Nussinov © Humana Press Inc., Totowa, NJ

2

The Use of High-Pressure Nuclear Magnetic Resonanceto Study Protein Folding

Michael W. Lassalle and Kazuyuki Akasaka

SummaryRecent development of high-pressure cells for a variety of spectroscopic methods has enabled

the use of pressure as one of the commonly used perturbations along with temperature and chemicalperturbations to study folding/unfolding reactions of proteins. Although various high-pressure spec-troscopy techniques have their own significance, high-pressure nuclear magnetic resonance (NMR)is unique in that it allows one to gain residue-specific and atom-detailed information from proteinsunder pressure. Furthermore, because of a peculiar volume property of a protein, high-pressureNMR allows one to obtain structural information of a protein in a wide conformational space fromthe bottom to the upper region of the folding funnel, giving structural reality for the “open” state ofa protein proposed from hydrogen exchange. The method allows a link between equilibrium foldingintermediates and the kinetic intermediates, and manifests a new view of proteins as dynamicentities amply fluctuating among the folded, intermediate, and unfolded sub ensembles. This chapterbriefly summarizes the technique, the principle, and the ways to use high-pressure NMR for studyingprotein folding.

Key Words: Pressure; protein folding; thermodynamic stability; volume change; structures offolding intermediates; high-pressure NMR; pressure-jump.

1. IntroductionPressure perturbation is increasingly important in studies of protein folding,

stability, conformational flexibility, and aggregation. A keyword search on HighWireand Medline with keywords: high pressure-protein-nuclear magnetic resonance(NMR) shows that there has been a dramatic increase in the number of pressure-related studies of proteins (Fig. 1). The dramatic increase is assisted by technicaldevelopments for high-pressure studies in a variety of spectroscopic measurementsat high pressure including X-ray scattering (1,2), fluorescence (3–6), Fourier-transform infrared spectroscopy (6–10) and ultraviolet-visible derivative spectroscopy

(11), kinetic processes under pressure (12,13), and pressure-jump techniques(14–16). In particular, the recent advancement in high-pressure NMR techniqueshas renewed interest in high-pressure studies of proteins, it allows to gain residue-specific or atom-detailed information from proteins under pressure.

2. MaterialsBuffers to be used for pressure studies are preferred to have little variation of

pKa with pressure. There is no complete buffer in this sense, but the followingbuffers are relatively inert to pressure variation. One must be aware, however,that those buffers inert to pressure variation tend to be more susceptible to tem-perature variation. Useful buffers are maleic acid (∆Vo = –5.1 cm3mol-1), MES(∆Vo = 3.9 cm3mol-1), Tris (∆Vo = 4.3 cm3mol-1), or imidazole buffers (∆Vo =1.8 cm3mol-1) (17). As chemical shift standard, the singlet signal of DSS is tobe set at origin (δ = 0). However, this often overlaps with some methyl protonsignals in the 1H NMR spectrum. The authors found that dioxane can be usedas a convenient secondary standard, as it gives a sharp singlet at δ = 3.75 ppmdownfield from DSS nearly independently of pressure.

3. Methods3.1. High-Pressure NMR Techniques

Recent contributions to high-pressure NMR study of proteins are mainlyattributable to the groups of Jonas (18) and Akasaka (19), in addition to those

22 Lassalle and Akasaka

Fig. 1. Keyword search in HighWire and Medline as function of publication year.Circles: key words utilized: high pressure-protein. Triangle: key words utilized: highpressure-protein-nuclear magnetic resonance.

of Kalbitzer (20), Wand (21), and Markley (22). The heart in designing high-pressure NMR techniques is how to design a pressure-resistant cell in a smallsignal detection space by maintaining the highest possible homogeneity in bothstatic and radiofrequency magnetic fields without losing sensitivity of detec-tion. Typically two cell designs have been utilized. The former group (18) pre-ferred an autoclave design, which has the advantage of larger sample volumeand high attainable pressure (~900 MPa). Here, receiver coils must be self-designed within the autoclave. The cell contains sufficient volume and appliesvery well to recording one-dimensional (1D)1H NMR spectra of proteins. Amajor problem lies in the difficulty to obtain well-resolved two- or multidimen-sional spectra where multiple nuclei must be simultaneously excited within ahighly homogeneous static and radiofrequency magnetic fields spanning theentire sample space. The latter group (19) developed pressure-resisting cells(Fig. 2) made up initially of glass, then of quartz (both hand-made) (23), andused them on a commercial NMR probe. This is the on-line cell high-pressureNMR system described in some detail in the following section. Although theinner space of the pressure-resistive cell is so small (typically ~20 µL; Fig. 2)that the signal intensity is inherently low, the field homogeneity can be extremelygood and allows all two- or multidimensional spectral measurements, giving

High-Pressure NMR for Protein Folding 23

Fig. 2. A pressure-resisting quartz cell and the protecting Teflon capsule used for theon-line cell high-pressure nuclear magnetic resonance system.

excellent high resolution multidimensional spectra as those obtained with nor-mal 5-mm tubes at 1 bar. Therefore, the on-line cell high-pressure method hasa higher versatility than the autoclave method for protein studies. Some effortshave been made to increase the sample volume by utilizing sapphire cells withlimited success (20,21).

The maximum pressure range of the quartz cell method is normally limitedfrom 200 to approx 400 MPa (because cells break at higher pressure), this rela-tively mild pressure range has been sufficient in many proteins to a variety of stud-ies including folding intermediates (24), conformational dynamics (25), localdisordering (26), kinetic intermediates (27), stability (28), energy-landscapes (29),and dissociation/association of proteins (30). Although many proteins may notfully unfold below approx 400 MPa, 100% unfolding is actually not required inhigh-pressure NMR measurements because the onset of full unfolding is recog-nized if all the cross peaks begin to lose their intensities, say up to approx 20%, ina concerted matter in a typical well-resolved two-dimensional (2D) NMR spectra.The applicability of variable-pressure NMR to studies of folding intermediates isalso assured by recognizing the general tendency for the decreasing order of terti-ary structure as pressure is increased (31). In this chapter, we will concentrate oureffort solely to highlight the advantages of high-pressure NMR in the study of ther-modynamic stability and folding, but the concept and the method of analysis areapplicable to results of any high-pressure spectroscopic measurements.

3.1.1. The On-Line Cell High-Pressure NMR System

The heart of the success of the on-line cell high-pressure NMR method relieson the preparation of pressure-resistive sample cells (23) (Fig. 2). As mentioned,the starting material generally used is transparent quartz capsules or quartz cap-sules made by synthetic silica. First a perfect clean surface must be obtained; weachieved this goal by etching the glass inside and outside with a dilute hydroflu-oric acid solution and by removing micro cracks with fire polishing. Then thequartz capsules are opened at scratched points, and the ends are heated to makea long tail (o.d. = 0.3–1 mm; length = 400–700 mm), a short sealed tail (o.d. =0.1–0.5 mm; length = 1–2 mm), and a cell body. The short sealed tail enables abottom design with a small tensile force in a small area. Finally, pyroxylin coatingof the short tail, cell body, and long tail is performed. Our final cell has an insidediameter about 0.8–1.0 mm and an outside diameter of 3.0–3.7 mm.

The high-pressure cell assembly consists of a hand oil-pump, a pressureintensifier, and a Heise-Bourdon gage. A 6 m-long SUS-316 high-pressuretube (o.d./ i.d. = 3.0/0.6 mm) transmits the pressure to the top of the high-pressure cell-separator assembly. This assembly consists of a polytetrafluo-roethylene (PTFE) safety jacket and the NMR tube described above with along flexible tail that was bonded to an SUS-316 nozzle with a thermo hard-

24 Lassalle and Akasaka

ening epoxy adhesive (Araldite AT1). The nozzle is connected through a PTFEconnector tube to a PTFE inner tube, which is embedded in a BeCu separatorcylinder. Within the PTFE inner tube, two PTFE pistons with a length of 3–4mm and with diameter about 0.05 mm smaller than the i.d. of the PTFE innertube are seated. The space between upper and lower pistons is filled with per-fluoro-polyether, as it is insoluble in both organic solvent and water and actsas separator between the pressure transmitting system and the NMR sample.An 80:20 mixture of motor oil and kerosene is used as pressure transmittingfluid. Both the NMR tube with flexible long tail and the PTFE inner tube upto the lower PTFE piston are filled with the sample solution, whereas the high-pressure tube up to the upper piston contains the pressure transmitting fluid.

3.2. Methods for Determining Thermodynamic Parameters From High-Pressure Experiment

3.2.1. Basic Equations for Two-State Transition

The thermodynamic stability of proteins has been much less explored in thepressure axis than in the temperature or chemical axis. However, if the solutionconditions (chemical compositions) are fixed, the conformational stability of aprotein ∆G = Gunfolded – Gfolded is a simultaneous function of both temperatureand pressure; thus defining a three-dimensional Gibbs free energy surface onthe pressure–temperature plane. Several excellent papers (29,32–34) on multi-dimensional energy landscapes have been published.

The basic equations governing the stability of proteins on the p and/or T axesare given in the following:

1. By taking the pressure dependence of ∆G to the first order at constant temperature,

(1)

and to the second order,

(1′)2. By taking the “exact” expression for temperature dependence of ∆G and the pressure

dependence of ∆G to the second order,

(2)

Performing a Taylor expansion and neglecting higher order terms with respect to temperature, this equation equals the following:

+ − +( – ) ( – ) ( – )( – )∆ ∆ ∆V p p p p p p T To o o o oβ α2

2

∆ ∆ ∆ ∆G G S T T C T TT

T

protein folding protocols - universitas...

Documents