Monte Carlo simulations of the peptide recognition at the consensus binding site of the constant fragment of human immunoglobulin G: the energy landscape analysis of a hot spot at the intermolecular interface.
Monte Carlo simulations of molecular recognition at the consensus binding site of the constant fragment (Fc) of human immunoglobulin G (Ig) protein have been performed to analyze structural and thermodynamic aspects of binding for the 13-residue cyclic peptide DCAWHLGELVWCT. The energy landscape analysis of a hot spot at the intermolecular interface using alanine scanning and equilibrium-simulated tempering dynamics with the simplified, knowledge-based energy function has enabled the role of the protein hot spot residues in providing the thermodynamic stability of the native structure to be determined. We have found that hydrophobic interactions between the peptide and the Met-252, Ile-253, His-433, and His-435 protein residues are critical to guarantee the thermodynamic stability of the crystallographic binding mode of the complex. Binding free energy calculations, using a molecular mechanics force field and a solvation energy model, combined with alanine scanning have been conducted to determine the energetic contribution of the protein hot spot residues in binding affinity. The conserved Asn-434, Ser-254, and Tyr-436 protein residues contribute significantly to the binding affinity of the peptide-protein complex, serving as an energetic hot spot at the intermolecular interface. The results suggest that evolutionary conserved hot spot protein residues at the intermolecular interface may be partitioned in fulfilling thermodynamic stability of the native binding mode and contributing to the binding affinity of the complex.
Verkhivker
Gennady M
GM
Agouron Pharmaceuticals, Inc., Department of Computational Chemistry, Pfizer Company, San Diego, California 92121-1111, USA. gennady.verkhivker@pfizer.com
Bouzida
Djamal
D
Gehlhaar
Daniel K
DK
Rejto
Paul A
PA
Freer
Stephan T
ST
Rose
Peter W
PW
D000409:Alanine / Q000737:chemistry; D001665:Binding Sites; D003198:Computer Simulation; D016384:Consensus Sequence; D006801:Humans; D007127:Immunoglobulin Constant Regions / Q000737:chemistry / Q000378:metabolism; D007141:Immunoglobulin Fc Fragments / Q000737:chemistry* / Q000378:metabolism*; D007074:Immunoglobulin G / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry / Q000378:metabolism*; D010456:Peptides, Cyclic / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation; D013816:Thermodynamics
D007127:Immunoglobulin Constant Regions; D007141:Immunoglobulin Fc Fragments; D007074:Immunoglobulin G; D010455:Peptides; D010456:Peptides, Cyclic; C465445:cyclic(aspartyl-cysteinyl-alanyl-tryptophyl-histidyl-leucyl-glycyl-glutamyl-leucyl-valvyl-tryptophyl-cysteinyl-threonyl); D000409:Alanine