1. Molecular simulations of polypeptides under confinement CHEN633: Final Project Rafael Callejas-Tovar Artie McFerrin Department of Chemical Engineering Texas A&M University Instructor: Prof. Perla B. Balbuena

2. Outline 1.The protein folding problem 2.Protein-folding dynamics and molecular simulations 3.Paper: “Molecular dynamics simulations of poly(alanine) peptides”

3. 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

4. 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

5. 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

6. 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_dogma http://en.wikipedia.org/wiki/Christian_B._Anfinsen

7. 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

8. 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 (10 26 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

9. 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/

10. “Molecular dynamics simulations of poly(alanine) peptides” Palenčár, P. and Bleha, T., Journal of Molecular Modeling, 17(9): p. 2367-2374 (2011)

11. 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?

12. 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

13. How did they do it? All-atoms molecular dynamics simulations – NVT without solvent and AMBER-99 φ 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 & confined Free & confined Acetyl & methyl amide for charge neutrality Getting initial configurations

14. (…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

15. What did they get? Conversion Straight α- helix α-hairpins Melting/cooling curve Increase

16. Chain length and confinement effects Abundance of structures with N H 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

17. Chain length and confinement effects Abundance of structures with N H 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

18. Stabilization energies at 303K Stability of folded structures decreases with the number of folds

19. Shape of the PA chains Unconfined: Random at high T Shape is modified greatly by chain length Shape transition caused by confinement

20. Effect of the confinement on the energy contributions UnconfinedConfinement

21. PA peptide on a cubic cavity (Ala) 60 chains confined to a cube Hairpin-like structures (cube 0.39) Moderate confinement Moderate confinement Degree of confinement

22. 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)

23. 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 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 http://dx.doi.org/10.1146/annurev.physchem. 58.032806.104614

24. 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 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 http://dx.doi.org/10.1002/mats.201000034

25. 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 http://dx.doi.org/10.1007/s00894-006- 0147-6