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

Outline 1.The protein folding problem 2.Protein-folding dynamics and molecular simulations 3.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

What is protein folding? Process by which a polypeptide folds into its characteristic and functional 3-D structure from a random coil 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

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, (1): p

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, (1): p

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, (1): p

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, (1): p

“Molecular dynamics simulations of poly(alanine) peptides” Palenčár, P. and Bleha, T., Journal of Molecular Modeling, 17(9): p (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-99 φ force-field Palenčár, P. and Bleha, T., Folding of Polyalanine into Helical Hairpins. Macromolecular Theory and Simulations, (8-9): p Free & confined Free & confined Acetyl & methyl amide for charge neutrality Getting 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

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

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

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

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

Shape of the PA chains 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 UnconfinedConfinement

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

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, (1): p Scheraga, H.A., Khalili, M., and Liwo, A., Protein- Folding Dynamics: Overview of Molecular Simulation Techniques. Annual Review of Physical Chemistry, (1): p

References Palenčár, P. and Bleha, T., Molecular dynamics simulations of the folding of poly(alanine) peptides. Journal of Molecular Modeling, (9): p Palenčár, P. and Bleha, T., Folding of Polyalanine into Helical Hairpins. Macromolecular Theory and Simulations, (8-9): p

References Sikorski, A. and Romiszowski, P., Computer simulation of polypeptides in a confinement. Journal of Molecular Modeling, (2): p