Molecular dynamics simulations of a highly charged peptide from an SH3 domain: Possible sequence-function relationship

• Published in: Proteins, structure, function, and bioinformatics Vol. 45; no. 1; pp. 4 - 15
• Main Authors: Krueger, Brent P., Kollman, Peter A.
• Format: Journal Article
• Language: English
• Published: New York John Wiley & Sons, Inc 01.10.2001
• Subjects: Computer Simulation; CORMA; helical propensity; MM-PBSA; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; particle mesh Ewald; Peptides - chemistry; Pfam; Protein Folding; src Homology Domains; Structure-Activity Relationship; Thermodynamics
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.1118

A seven‐residue peptide that is highly conserved in SH3 domains despite being far from the active site has been shown by NMR to be stable in solution. This peptide, biologically important because it is a likely folding nucleus for SH3 domains, provides a challenging subject for molecular dynamics because it is highly charged. We present stable, 10‐ns simulations of both the native‐like diverging turn structure and a helical model. Free energies of these two conformations, estimated through MM‐PBSA analysis using several force fields, suggest a comparable free energy (ΔΔG ≤6 kcal/mol) for native and helix conformations. NOE intensities calculated from the native trajectory reproduce experimental data quite well, suggesting that the conformations sampled by the trajectory reasonably represent those observed in the NMR experiment. The molecular dynamics results, as well as sequence analysis of a diverse 690‐member family of SH3 domain proteins, suggest that the presence of two elements is essential for formation of the diverging turn structure: a pair of residues with low helical propensity in the turn region and, as previously recognized, two hydrophobic residues to close the end of the diverging turn. Thus, these two sequence features may form the structural basis for the function of this peptide as a folding nucleus in this family of proteins. Proteins 2001;45:4–15. © 2001 Wiley‐Liss, Inc.