experimental structure determination pp1 exp3d · assignment coverage: define geometry (fitting...

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title: Experimental structure determinationshort title: pp1_exp3D

lecture: Computational Biology 1 - Protein structure (for Informatics) - TUM summer semester

/45© Burkhard Rost

Videos: YouTube / www.rostlab.org THANKS :. EXERCISES: Special lectures:

• 05/24 Predrag Radivojac - Indiana University • TBD - Thomas Hopf • TBD - Jonas Reeb No lecture:

• 05/05 Ascension day • 05/10 Student assembly (SVV) • 05/17 Whitsun holiday • 06/26 Corpus Christi LAST lecture: June 28 (followed by 2 wrap-up sessions) Examen: June 30, 2016: lecture time room TBD

• Makeup: TBC: Oct 18 & 20, 2016 - lecture time

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CONTACT: Lothar Richter richter@rostlab.orgAnnouncements

Dmitrij Nechaev

Lothar Richter

© Burkhard Rost

Recap: 3D prediction by

comparative modeling

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Zones

Day

light

Zon

e

Twili

ght Z

one

Mid

nigh

t Zon

eprofile - profile

sequence - profilesequence - sequence

sequ

ence

sim

ilar

->

stru

ctur

e sim

ilar

B Rost (1997) Fold Des 2:S19-24B Rost (1999) Protein Eng 12:85-94

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human - fly - bacteria

3gft: Y Tong et al. & H Park (unpublished) / 4IW3: JS Scotti (unpublished)3lbn: G Buhrman et al. & C Mattos (2010) PNAS 107:4931-6.2y8e: M Walden, HT Jenkins, TA Edwards (2011) Acta Crystallogr F 67:744

green: 3gft K-Ras - human lime: 3lbn Rash - human orange: 2y8e Rab6 - fly purple: 2y8e hydroxylase P putida

Andrea Schaffer-

hans

Slide from:

PIDE: pairwise identical residues

19%

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MODELLERlots of whistles and bells, downloadable, very accurate

SWISS-MODELautomated, increasingly comprehensive and flexible

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Comparative modeling methods

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Comparative modeling/homology modeling most accurate way to predict structure as good and as complete as the templateè depends on quality and similarity of template mostly driven by accuracy of alignmentè driven by alignment quality loop modeling: still not fully there, yet side chain modeling: unclear how well we do

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Conclusion: Comparative modeling

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Comparative modeling applicable to about 50% of all proteins

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3D prediction from first principles?

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Goal of structure prediction

Epstein & Anfinsen, 1961:sequence uniquely determines structure

• INPUT: sequence

3D structureand function

• OUTPUT:

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protein folding from first principles should then be

possible

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60s - Washington Post 70s - New York Times 90s - Washington Post

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Protein structure prediction problem* solved!

*Problem: “predict the 3D structure of a protein from sequence alone”

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How would you assess prediction

performance?

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Critical Assessment of Structure Prediction April-May (Organizers): collect experimental structures (since 2004 from structural genomics) June-August: Prediction seasondeadline: predictions in before experimental structures are published September-November: Assessors divine December: Meeting to discuss results

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CASP: how it works

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CASPOnly homology modeling good

No general prediction of 3D from sequence, yet Important improvements in many fields!

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Protein Structure Prediction

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Servers, META-servers, META-META, …

© Burkhard Rost

3D from experimental co-ordinates

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3D details - 3D cartoon

© Burkhard Rost

Structure by experiment

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Experiments determine protein structure

Number Percentage

PDB 84,413 1Xray 75,068 89NMR 8,723 10

EM ElectronMicroscopy 428 1

PDB (Protein Data Bank) Helen Berman (Rutgers Univ, New Brunswick) &

Phil Bourne (UCSD San Diego)

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Protein structure by X-ray crystallography

© Wikipedia

Myoglobin structure * JC Kendrew, G Bodo, HM Dintzis, RG Parrish, H Wyckoff & DC Phillips (1958) Nature 181:662-6* THIS 1mbo: SE Philips JMB 142:531-54(image Wikipedia Aza Toth)(Hemoglobin: Max Perutz 1959)

Number Percentage

PDB 84,413 1

Xray 75,068 89

NMR 8,723 10

EM ElectronMicroscopy

428 1

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Protein structure by NMR* spectroscopy

© Wikipedia

Number PercentagePDB 84,413 1

Xray 75,068 89

NMR 8,723 10

EM ElectronMic

428 1

* NMR: Nuclear Magnetic Resonance

NMR tube

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Protein structure by NMR* spectroscopy

© Wikipedia

900 MHz NMR machine

1ssu: Y Kamikubo et al. & HJ Dyson (2004) Biochemistry 43:6519-34

Number PercentagePDB 84,413 1

Xray 75,068 89

NMR 8,723 10

EM ElectronMic

428 1

* NMR: Nuclear Magnetic Resonance

NYSBC - City College New

York City

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Protein structure by cryo-EM

© Wikipedia

Number PercentagePDB 84,413 1

Xray 75,068 89

NMR 8,723 10

EM ElectronMic

428 1

* EM: Cryo-Electron Microscopy

4 Ångstrøm 8Å 16Å 32Å GroEL - J Wang & DC Bosvert (2004) 1j4z Images: Vossman 2007 - Wikipedia

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Protein structure by cryo-EMNumber Percentage

PDB 84,413 1

Xray 75,068 89

NMR 8,723 10

EM ElectronMic

428 1

* EM: Cryo-Electron Microscopy

T Ju, M Baker, W Chiu (2006) Computer-Aided Design 39:352-60

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Structure resolution

© PDB

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Notation: protein structure 1D, 2D, 3DPQITLWQRPLVTIKIGGQLKEALLDTGADDTVL

PP PQQQYFFQVISSIVRLLSTLWWQEDRKQAKRRRPQPPPPPVVTKFVVLIITTKEKAALIVHYKKFIILVIEENGGGGGTGQQKRRPPLWWVVFKVEESKKVVGLGLLILLLLLVVDDDDDTTTTTGGGGGAAAAADDDDDDDAKESSTTVIIVIVVVIVL

1281757077

120238169200247114740

904

466268

11831

1241

292449726217

102691

140

1109760691481976248590

690

730

415371597395000

5851300

79586900

EEEEE

EEEEEE

EEEEEEE

EE

EEEEE

EEEEEE

EE

kcal/mol0 -1 -2 -3 -4 -5

1 10 20 30 40 50 60 70 80 90

1

10

20

30

40

50

60

70

80

90

1D1D 2D2D 3D3D

© Burkhard Rost

Secondary structure stabilized by

hydrogen bonds

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1951 e.g. :L Pauling and RB Corey (1951) Configurations of Polypeptide Chains with Favored Orientations Around Single Bonds: Two New Pleated Sheets PNAS 37: 729-40 1953 e.g.: L Pauling and RB Corey (1953) Two Rippled-sheet Configurations of Polypeptide Chains, and a Note About the Pleated Sheets PNAS 39: 253-6

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Linus Pauling: introduce concept

Linus Pauling

Nobel Foundation: The Nobel Prize in Chemistry 1954 was awarded to Linus Pauling "for his research into the nature of the chemical bond and its application to the elucidation of the structure of complex substances”. http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1954/

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Hydrogen-bond formation

© Wikipediahttp://www.ausetute.com.au/proteins.html

strandhelix

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3D details - 3D cartoon

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3D details - 3D cartoon

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Pauling Nobel Prize 1954 -

first protein structure when?

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First protein structures

John Kendrew Max Perutz

myoglobin

JC Kendrew et al. & DC Phillips (Mar 1958) Nature 181: 662–6.

hemoglobin

MF Perutz et al. & AC North (1960) Nature 185: 416-22.

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Different evaluation criteria applied:

Assignment coverage: DEFINEGeometry (fitting ideal sec str segments)FM Richards & CE Kundrot (1988) Proteins 3:71-84

Enthalpic energy: DSSPW Kabsch & C Sander (1983) Biopolymers 22:2577-637

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Secondary structure assignment

© Burkhard Rost

Secondary structure from 3D structure

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3D details - 3D cartoon

HHHHHHHLLL

EEEEE

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How to “annotate” 1D-secondary

structure from 3D co-ordinates?

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Answer the question in groups

??

???

© Wikipedia

How to assign secondary structure from 3D structure?

/45© Burkhard Rost

Different evaluation criteria applied:

Assignment coverage: DEFINEGeometry (fitting ideal sec str segments)FM Richards & CE Kundrot (1988) Proteins 3:71-84

Enthalpic energy: DSSPW Kabsch & C Sander (1983) Biopolymers 22:2577-637

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Secondary structure assignment

45© Burkhard Rost DSSP: W Kabsch & C Sander (1983) Biopolymers 22: 2577-2637

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DSSP: Coulomb

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L Pauling & RB Corey (1953) PNAS 39:247-252L Pauling, RB Corey & HR Branson (1951) PNAS 37:205-234W Kabsch & C Sander (1983) Biopolymers 22:2577-2637

DSSP

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Pauling’s H-bond pattern used in DSSP

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Assignment coverage: DEFINEGeometry (fitting ideal sec str segments)FM Richards & CE Kundrot (1988) Proteins 3:71-84

Enthalpic energy: DSSPW Kabsch & C Sander (1983) Biopolymers 22:2577-637

Expert assignment: STRIDED Frishman & P Argos (1995) Proteins 23:566-79

Predictability: NNass

Continuous: DSSPcontC Andersen, AG Palmer, S Brunak & B Rost (2002) Structure 10:175-84

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Other ideas to assign secondary structure

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3 methods (DSSP, DEFINE, P-Curve)

agree in 30% of HEL

assignments completely

44N Colloc’h et al & JP Mornon (1993) Prot Engng 6:377-82

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01: 04/11 Tue: no lecture 02: 04/13 Thu: no lecture 03: 04/19 Tue: Organization of lecture: intro into cells & biology 04: 04/21 Thu: Intro I - acids/structure - domains 05: 04/26 Tue: Alignment 1 06: 04/28 Thu: Alignment 2 07: 05/03 Tue: Alignment 3 08: 05/05 Thu: SKIP: Ascension Day 09: 05/10 Tue: SKIP: student assembly (SVV) 10: 05/12 Thu: & experimental structure determination & secondary structure assignment 11: 05/17 Tue: SKIP: Whitsun holiday (05/15-17) 12: 05/19 Thu: 1D: Secondary structure prediction 1 13: 05/24 Tue: Predrag Radivojac: Protein disorder 14: 05/26 Thu: SKIP: Corpus Christi 15: 06/31 Tue: 1D: Secondary structure prediction 2 16: 06/02 Thu: 1D: Transmembrane structure prediction 1 17: 06/07 Tue: 1D: Transmembrane structure prediction 2 / Solvent accessibility prediction 18: 06/09 Thu: 2D prediction 1 19: 06/14 Tue: 2D prediction 2 - Thomas Hopf 20: 06/16 Thu: 3D prediction / Nobel prize symposium 21: 06/21 Tue: 1D: Disorder prediction 22: 06/23 Thu: recap 1 23: 06/28 Tue: recap 2 24: 06/30 Thu: examen, no lecture 25: 07/05 Tue: examen alternative, no lecture 26: 07/07 Thu: examen, no lecture 27: 07/12 Tue: wrap up exercises - no lecture 28: 07/14 Thu: wrap up exercises - no lecture

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Lecture plan (CB1 structure)