Gennady M. Verkhivker

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. Proteins 2002;48:539–557.

Computational detection of the binding‐site hot spot at the remodeled human growth hormone–receptor interface

A hierarchical computational approach is used to identify the engineered binding‐site cavity at the remodeled intermolecular interface between the mutants of human growth hormone (hGH) and the extracellular domain of its receptor (hGHbp). Multiple docking simulations are conducted with the remodeled hGH–hGHbp complex for a panel of potent benzimidazole‐containing inhibitors that can restore the binding affinity of the wild‐type complex, and for a set of known nonactive small molecules that contain different heterocyclic motifs. Structural clustering of ligand‐bound conformations and binding free‐energy calculations, using the AMBER force field and a continuum solvation model, can rapidly locate and screen numerous ligand‐binding modes on the protein surface and detect the binding‐site hot spot at the intermolecular interface. Structural orientation of the benzimidazole motif in the binding‐site cavity closely mimics the position of the hot spot residue W104 in the crystal structure of the wild‐type complex, which is recognized as an important structural requirement for restoring binding affinity. Despite numerous pockets on the protein surface of the mutant hGH–hGHbp complex, the binding‐site cavity presents the energetically favorable hot spot for the benzimidazole‐containing inhibitors, whereas for a set of nonactive molecules, the lowest energy ligand conformations do not necessarily bind in the engineered cavity. The results reveal a dominant role of the intermolecular van der Waals interactions in providing favorable ligand–protein energetics in the redesigned interface, in agreement with the experimental and computational alanine scanning of the hGH–hGHbp complex. Proteins 2003.

Parallel simulated tempering dynamics of ligand-protein binding with ensembles of protein conformations

Abstract Simulated tempering dynamics with the simplified energy model and the ensemble of protein conformations have been performed for the SB203386 inhibitor binding with HIV-1 protease. Equilibrium simulations with multiple protein conformations implicitly incorporate protein flexibility and rank HIV-1 protease conformations according to the average ligand–protein interaction energies. Subsequent energy refinement with a molecular mechanics force field accurately quantifies the energetics of the low-energy ligand binding modes. The results suggest that the mobility of the SB203386 inhibitor is effectively restricted to two symmetry-related binding modes and this may prevent the inhibitor from adapting to distorted binding sites in mutant conformations.

Protein conformational transitions coupled to binding in molecular recognition of unstructured proteins: Deciphering the effect of intermolecular interactions on computational structure prediction of the p27Kip1 protein bound to the cyclin A–cyclin-dependent kinase 2 complex

The relationship between folding mechanism coupled to binding and structure prediction of the tertiary complexes is studied for the p27Kip1 protein which has an intrinsically disordered unbound form and undergoes a functional folding transition during complex formation with the phosphorylated cyclin A–cyclin‐dependent kinase 2 (Cdk2) binary complex. Hierarchy of p27Kip1 structural loss determined in our earlier studies from temperature–induced Monte Carlo simulations and subsequent characterization of the transition state ensemble (TSE) for the folding reaction have shown that simultaneous ordering of the p27Kip1 native intermolecular interface for the β‐hairpin and β‐strand secondary structure elements is critical for nucleating a rapid kinetic transition to the native tertiary complex. In the present study, we investigate the effect of forming specific intermolecular interactions on structure prediction of the p27Kip1 tertiary complex. By constraining different secondary structure elements of p27Kip1 in their native bound conformations and conducting multiple simulated annealing simulations, we analyze differences in the success rate of predicting the native structure of p27Kip1 in the tertiary complex. In accordance with the nucleation–condensation mechanism, we have found that further stabilization of the native intermolecular interface for the β‐hairpin and β‐strand elements of p27Kip1, that become ordered in the TSE, but are hardly populated in the unbound state, results in a consistent acquisition of the native bound structure. Conversely, the excessive stablization of the local secondary structure elements, which are rarely detected in the TSE, has a detrimental effect on convergence to the native bound structure. Proteins 2005.

Hierarchy of simulation models in predicting molecular recognition mechanisms from the binding energy landscapes: Structural analysis of the peptide complexes with SH2 domains

Computer simulations using the simplified energy function and simulated tempering dynamics have accurately determined the native structure of the pYVPML, SVLpYTAVQPNE, and SPGEpYVNIEF peptides in the complexes with SH2 domains. Structural and equilibrium aspects of the peptide binding with SH2 domains have been studied by generating temperature‐dependent binding free energy landscapes. Once some native peptide–SH2 domain contacts are constrained, the underlying binding free energy profile has the funnel‐like shape that leads to a rapid and consistent acquisition of the native structure. The dominant native topology of the peptide–SH2 domain complexes represents an extended peptide conformation with strong specific interactions in the phosphotyrosine pocket and hydrophobic interactions of the peptide residues C‐terminal to the pTyr group. The topological features of the peptide–protein interface are primarily determined by the thermodynamically stable phosphotyrosyl group. A diversity of structurally different binding orientations has been observed for the amino‐terminal residues to the phosphotyrosine. The dominant native topology for the peptide residues carboxy‐terminal to the phosphotyrosine is tolerant to flexibility in this region of the peptide–SH2 domain interface observed in equilibrium simulations. The energy landscape analysis has revealed a broad, entropically favorable topology of the native binding mode for the bound peptides, which is robust to structural perturbations. This could provide an additional positive mechanism underlying tolerance of the SH2 domains to hydrophobic conservative substitutions in the peptide specificity region. Proteins 2001;45:456–470.

Navigating ligand–protein binding free energy landscapes: universality and diversity of protein folding and molecular recognition mechanisms

Abstract Thermodynamic and kinetic aspects of ligand–protein binding are studied for the methotrexate–dihydrofolate reductase system from the binding free energy profile constructed as a function of the order parameter. Thermodynamic stability of the native complex and a cooperative transition to the unique native structure suggest the nucleation kinetic mechanism at the equilibrium transition temperature. Structural properties of the transition state ensemble and the ensemble of nucleation conformations are determined by kinetic simulations of the transmission coefficient and ligand–protein association pathways. Structural analysis of the transition states and the nucleation conformations reconciles different views on the nucleation mechanism in protein folding.