Simulations of the folding and aggregation of peptides, proteins and lipids.

BRISBANE School of Molecular and Microbial Sciences (SMMS)Chemistry Building (#68)University of QueenslandBrisbane, QLD 4072,Australia

Email a.mark@uq.edu.auPhone: +61-7-33469922 FAX: +61-7-33654623Centre Secr: +61-7-33653975

GRONINGEN Lab. of Biophysical Chemistry University of Groningen Nijenborgh 4 email 9747 AG GRONINGEN The Netherlands

tel +31.50.3634457fax: +31.50.3634800tel secr: +31.50.3634323email:a.e.mark@rug.nl secr: mdsecr@fmns.rug.nl

http://md.chem.rug.nl

Alan E. Mark Herman BerendsenSiewert-Jan Marrink

Peptide folding and assembly:

Our best example of peptide folding to date is a the beta-hexapeptide shown on the following slides (solvent Methanol).

1. This system is fully reversible. 2. We have simulations of this and other systems to > 200ns at temperatures from 180 -> to 450K.3. We have replica exchange simulations of a slightly modified system

showing 1000’s of individual folding events. 4. As far as we can determine our modified system approaches full

convergence in 200-400 ns. 5. Trajectories are available.

-Peptides

i) -amino-acids (additional backbone carbon)ii) Stable 2nd structure.iii) Non-degradable peptide mimetics

(e.g. highly selective somatastatin analogue)

D. Seebach, B. Jaun + coworkersorganic chem ETH-Zurich

-Heptapeptide (M) 31-helix in MeOH at 298 K

(left-handed)

Daura, X., Bernhard, J., Seebach, D., van Gunsteren, W. F. and Mark, A. E. (1998)

J. Mol. Biol. 280, 925-932.

unfold fold unfold fold fold unfoldunfold

-Heptapeptide, 340 K

Starting structure

-Heptapeptide, 360 K

Gfolding = -RT ln (folded/unfolded)

Predict Probability of Individual Microstates in Solution

G=~6 kJ/mol G=~8 kJ/molG=0 kJ/mol G=~9 kJ/mol G=~9 kJ/mol

Daura, X., van Gunsteren, W. F. and Mark, A. E. (1999) Proteins: Struct. Funct. Genet. 34, 269-280.

Folding Pathways

Simulations of peptide folding

As part of our program we are looking a range of larger peptides. So far gettingreversible folding from random starting structures has proved difficult for systems > 20 a.a.

In particular we are investigating a series of related helical peptides (~20 a.a.) with fast folding kinetics

AP A5(A3RA)3A

YGA Ac-YG(AKA3)2AG-NH2

YGG Ac-YGG(KA4)3K-NH2

So far results are limited but we have seen reversible transitions. An example is given below.

AP A5(A3RA)3A

Ref: Lednev I. K. et al. J. Am. Chem. Soc. 1999, 121, 8074-8086.

A 21 amino acid, mainly alanine, α-helical peptide (AP). The folding/unfolding activating barriers based on an nanosecond UV resonance Raman study. ~8 kcal/mol activation barrier; reciprocal rate constant ~240±60 ns at 37 °C (310 K).

MD simulation start from the α-helix structureThe GROMOS 45A3 force field was adopted

Coil β-Sheet β-Bridge Bend Turn α-helix 5-Helix 3-HelixTime (ps)

Res

idu

e

Secondary structure

The secondary structure as a function of time shows one refolding transition in 100ns.

N-ter

C-ter

0 ns (starting structure)

N-ter

C-ter

10 ns

N-ter

C-ter

30 ns

C-ter

N-ter

50 ns

N-ter

C-ter

75 ns

N-ter

C-ter

70 ns

N-terC-ter

80 ns

N-ter C-ter

85 ns

N-ter

C-ter

100 ns

Other peptide systems on which we have simulations showing partial folding or assemble include:

1. Various amyloid forming peptides on surfaces.2. Betanova (a designed triple stranded peptide)3. A series of coiled-coils.4. WW domain peptide (~20 a.a. peptide studied by replica exchange)5. Several proteins showing recovery from mild denaturing conditions.

Spontaneous Aggregation of Lipids and

Surfactants

I believe this is one area where complexity analysis should be able to perform well as the systems show spontaneous generation of order.

We have multiple simulations of: 1. Bilayer formation (course grained and in atomic detail)2. Vesicle formation (course grained and in atomic detail)3. Phase transitions (course grained and in atomic detail)4. Membrane and vesicle fusion.

Note: these are highly reproducible collective processes involving 100’s to 1000’s of lipids.A few examples are given below.

S.J. Marrink

A

Ceq

CB

DeqC*

Spontaneous assembly of phospholipds into a bilayer

0 ns 0.2 ns 3 ns

10 ns 20 ns 25 ns

Density Evolution Showing the Generation of Orderde

nsit

y

water head groups lipid tails

S.J. Marrink