Molecular simulations of polypeptides under

confinement

CHEN633: Final ProjectRafael Callejas-Tovar

Artie McFerrin Department of Chemical EngineeringTexas A&M University

Instructor: Prof. Perla B. Balbuena

Outline

1. The protein folding problem2. Protein-folding dynamics and

molecular simulations3. Paper: “Molecular dynamics

simulations of poly(alanine) peptides”

Some definitions

• Amine group +

• Carboxylic acid group +

• Side-chain Amino acid

• Chain of amino acids

• Peptide bonds

Polypeptide • One or more

polypeptides

Protein

http://en.wikipedia.org/wiki/Protein

What is protein folding?

• Process by which a polypeptide folds into its characteristic and functional 3-D structure from a random coil

http://en.wikipedia.org/wiki/Protein_folding

Unfolded polypeptide: No

3-D structure

Native state (thermodynamically

stable)

Amino acid

interactions

What is protein folding?

• Correct 3-D structure is essential to function

• Failure to fold into native structure produces inactive proteins that are usually toxic – Several neurodegenerative and other

diseases caused by unfolded proteins –Many allergies are caused by the folding

of the proteins

http://en.wikipedia.org/wiki/Protein_folding

The protein folding problem

• Anfinsen’s Thermodynamic Hypothesis– Nobel Prize in Chemistry (1972)

Christian B. Anfinsen– Native structure:• Depends only on amino acid sequence and

conditions of solution• DO NOT depend on the kinetic folding route

Dill, K.A., Ozkan, S.B., Shell, M.S., and Weikl, T.R., The Protein Folding Problem. Annual Review of Biophysics, 2008. 37(1): p. 289-316.http://en.wikipedia.org/wiki/Anfinsen%27s_dogmahttp://en.wikipedia.org/wiki/Christian_B._Anfinsen

The protein folding problem

• What is the folding code?• What is the folding mechanism?• Can we predict the native structure

of a protein from its amino acid sequence?

Dill, K.A., Ozkan, S.B., Shell, M.S., and Weikl, T.R., The Protein Folding Problem. Annual Review of Biophysics, 2008. 37(1): p. 289-316.http://techglimpse.com/index.php/ibms-blue-gene-exploring-protein-folding-mystery.php

Protein structure prediction: Levinthal's paradox

• Number of possible conformations available to a given protein is astronomically large– Even a small protein of 100 residues would

require more time than the universe has existed to explore all possible conformations (1026 seconds) and choose the appropriate one

• The “paradox”: Most small proteins fold spontaneously on a millisecond or even microsecond time scale

Dill, K.A., Ozkan, S.B., Shell, M.S., and Weikl, T.R., The Protein Folding Problem. Annual Review of Biophysics, 2008. 37(1): p. 289-316.http://en.wikipedia.org/wiki/Levinthal%27s_paradox

Protein-folding dynamics and molecular simulations

• Computer-based molecular minimization methods applied since 1960

• Molecular dynamics with high parallelized codes–More global and less detailed

information– Physics-based reduced models– All-atom models Scheraga, H.A., Khalili, M., and Liwo, A., Protein-Folding Dynamics: Overview of Molecular Simulation Techniques.

Annual Review of Physical Chemistry, 2007. 58(1): p. 57-83. http://bits.blogs.nytimes.com/2007/11/12/ibm-blue-gene-still-the-fastest-computer/

“Molecular dynamics simulations of poly(alanine) peptides”

Palenčár, P. and Bleha, T., Journal of Molecular Modeling, 17(9): p. 2367-2374 (2011)

What is the objective?

• Exploring the folding of poly(alanine) (PA) peptides

Secondary structures

• (Ala)n of intermediate lengths

Structure and confinement

• How the helical structure of a PA molecule is affected due to confinement?

Why is this important?

• Poly(alanine): best-known representative of the polypeptide group– Its folding is of considerable interest, as

alanine (Ala) is generally viewed as the most helix-stabilizing amino acid residue

How did they do it?

• All-atoms molecular dynamics simulations– NVT without solvent and AMBER-99φ

force-field

Palenčár, P. and Bleha, T., Folding of Polyalanine into Helical Hairpins. Macromolecular Theory and Simulations, 2010. 19(8-9): p. 488-495.

Free &confine

d

Acetyl & methyl amide for charge

neutralityGetting initial

configurations

(…about the α-helix)

• Right-handed coiled or spiral conformation– Every backbone N-H group donates a H

bond to the backbone C=O group of the amino acid four residues earlier

http://en.wikipedia.org/wiki/Alpha_helix

What did they get?

ConversionStraight α-helix

α-hairpins

Melting/cooling curve

Incr

eas

e

3 10 PPIIH H H H

Chain length and confinement effects

Abundance of structures with NH segments at 303K

• (Ala)40: – Straight helices

• (Ala)45:– Two-leg (2L) α-hairpins

prevails

• (Ala)60:– No straight helices– two-leg (2L) α-hairpins

prevails

• Confined (Ala)60: – three-leg (3L) α-hairpins

prevails

Chain length and confinement effects

Abundance of structures with NH segments at 303K

• (Ala)40: – Straight helices

• (Ala)45:– Two-leg (2L) α-hairpins

prevails

• (Ala)60:– No straight helices– two-leg (2L) α-hairpins

prevails

• Confined (Ala)60: – three-leg (3L) α-hairpins

prevails

Stabilization energies at 303K

• Stability of folded structures decreases with the number of folds

Shape of the PA chains

2

2

12 rod-like objects

~ 6 random coils

1 compact objectsg

R

R

• Unconfined: Random at high T

• Shape is modified greatly by chain length

• Shape transition caused by confinement

Effect of the confinement on the energy contributions

Unconfined Confinement

PA peptide on a cubic cavity(Ala)60 chains confined to a cube

Hairpin-like structures (cube 0.39)

Moderateconfineme

nt

Degree of confinement

What are their conclusions?

• Conformational structures– Highly sensitive to chain length

• Under confinement–Multi-legs hairpins observed– Considerable reduction on overall helicity

of PA molecules– Helical chains transform into compact

structures resembling the organization of integral membrane proteins (stacked α helices)

References

• Dill, K.A., Ozkan, S.B., Shell, M.S., and Weikl, T.R., The Protein Folding Problem. Annual Review of Biophysics, 2008. 37(1): p. 289-316. http://dx.doi.org/10.1146/annurev.biophys.37.092707.153558

• Scheraga, H.A., Khalili, M., and Liwo, A., Protein-Folding Dynamics: Overview of Molecular Simulation Techniques. Annual Review of Physical Chemistry, 2007. 58(1): p. 57-83. http://dx.doi.org/10.1146/annurev.physchem.58.032806.104614

References

• Palenčár, P. and Bleha, T., Molecular dynamics simulations of the folding of poly(alanine) peptides. Journal of Molecular Modeling, 2011. 17(9): p. 2367-2374. http://dx.doi.org/10.1007/s00894-011-0997-4

• Palenčár, P. and Bleha, T., Folding of Polyalanine into Helical Hairpins. Macromolecular Theory and Simulations, 2010. 19(8-9): p. 488-495. http://dx.doi.org/10.1002/mats.201000034

References

• Sikorski, A. and Romiszowski, P., Computer simulation of polypeptides in a confinement. Journal of Molecular Modeling, 2007. 13(2): p. 327-333. http://dx.doi.org/10.1007/s00894-006-0147-6