Peptide Aggregation and Pore Formation in a Lipid Bilayer; a Combined CG and AA MD StudyLea Thøgersen, University of Aarhus

Pushing the Boundaries of Biomolecular Simulation

June 11, 2008

Outline Introduction

Results

Conclusions

Coarse-Grained Molecular Dynamics

Alamethicin

Modelling Setup

NAMD CG vs MARTINI CG

Microsecond Action

Structure

Reverse Coarse-Graining

Water Pore Formation

Structural Changes

Coarse Grained MD – Why?

• Reduction in degrees of freedom

• Fast frequenzy movements removed

• Smoother potential surface

• Longer time steps can be taken

• Microsecond simulations possible

All-atom MD: time step of 1-2 fs, time frame sampled ~ 100 ns

Coarse-grained MD: time step of 20-50 fs, time frame sampled ~ 1 μs

Co

ars

e-g

rain

ing

Coarse Grained Molecular DynamicsShelley, Shelley, Reeder, Bandyopadhyay, Klein;

A Coarse Grain Model for Phospholipid Simulations J. Phys. Chem. B (2001) 105 4464

Shih, Arkhipov, Freddolino, Schulten;Coarse Grained Protein-Lipid Model with Application to Lipoprotein Particles J. Phys. Chem. B (2006) 110 3674

NAMD CG

Marrink, de Vries, Mark;Coarse Grained Model for Semiquantitative Lipid Simulations J. Phys. Chem. B (2004) 108 750

MARTINI CG

Marrink, Risselada, Yefimov, Tieleman, de Vries;The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations J. Phys. Chem. B (2007) 111 7812

Monticelli, Kandasamy, Periole, Larson, Tieleman, Marrink;The MARTINI Coarse-Grained Force Field: Extension to Proteins J. Chem. Theory and Comput. (2008) 4 819

20 amino acid antimicrobiel peptide.

Part of the immune system (for fungi).

Forms channels in membranes which allow water and ions to go through.

Destroys membrane potential.

Alamethicin

Motivation:

Potentially a good and simple membrane channel model

Insight into this family of proteins could be valuable in the development of antibiotics

Gln7

Glu18

Gln19

Widely Accepted Channel Model

Tieleman, Hess, Sansom; Analysis and Evaluation of Channel Models: Simulations of Alamethicin. Biophys. J. (2002) 83 2392

Spaar, Münster, Salditt; Conformation of Peptides in Lipid Membranes Studied by X-Ray Grazing Incidence Scattering.Biophys. J. (2004) 87 396

Modelling Setup

25 peptides330 DMPC lipids26452 water~117000 atoms~ 11700 beadsPBC 120 Å × 124 Å × 90 Å

To study alamethicin interactionwith membrane and each other

Apolar

Polar

Nonpolar

Charged

hydrogenbonddonor acceptor both none

hydrogenbonddonor acceptor both none

NAMD CG versus MARTINI CG

NAMD CG MARTINI CG

1

4

4

1

21

24

2

degree of polarity 1-5

degree of polarity 1-5

(MARTINI)

(NAMD)

AA

GLY ALA AIB

NAMD

MARTINI

Nda

N0 C5 C4

C CCNda Nda

32 ns7 ns

Alamethicin BehaviorAlamethicin

Hydrophilicsidechains

LipidPolar headgroup

Non-polartails

C-term

N-term

120 ns

Peptide Aggregation I0-1 μs

Peptide Aggregation II0 μs 1 μs 4 μs

MA

RT

INI

NA

MD

Structure of the Clusters

0 0.5 1

Gln7Gln7

Helix Tilt

0

0.01

0.02

0.03

0.04

0 30 60 90 120Helix tilt / deg.

Alamethicin, DMPC lipidpeptid:lipid - 1:15 15N-Aib8 alamethicin

Exp

θ = 10˚

MD

Vosegaard, Bertelsen, Pedersen, Thøgersen, Schiøtt, Tajkhorshid, Skrydstrup, Nielsen;Resolution Enhancement in Solid-State NMR of Oriented Membrane Proteins by Anisotropic Differential Linebroadening JACS (2008) 130 5028

θ

Aib8

Reverse Coarse-Graining

CG t = 0μs CG

t = 1μsAA - rev CG

t = 1μsAA

after SA

AA t = 0μs

CG water vs AA water

900-1000 ns

δ-δ+δ+

Class: Polar

5.0Å 2.8Å

TIP3P model

35-40 ns

Structural Changes

18 of 25 peptides remain α-helical

Conclusions

Alamethicin monomers readily aggregate and

form clusters that grow in size over time.

Large diversity in form of clusters and structure

of peptides.

Reverse CG required to

obtain detailed water interaction

validate results obtained on the long time scale

Acknowledgements

Emad Tajkhorshid & the NAMD peopleTheoretical and Computational Biophysics GroupUniversity of Illinois at Urbana-Champaign, USA

Birgit Schiøtt& the Biomodelling GroupDepartment of ChemistryUniversity of Aarhus, Denmark

Niels Christian Nielsen & Thomas VosegaardLaboratory for Biomolecular NMR spectroscopyDepartment of ChemistryUniversity of Aarhus, Denmark

Funding: &