Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction.

Protein-peptide interactions are often associated with large-scale conformational changes that are difficult to study either by classical molecular modeling or by experiment. Recently, we have developed the CABS-dock method for flexible protein-peptide docking that enables large-scale rearrangements of the protein chain. In this study, we use CABS-dock to investigate the binding of the p53-MDM2 complex, an element of the cell cycle regulation system crucial for anti-cancer drug design.

Competition between self-inclusion and drug binding explains the pH dependence of the cyclodextrin drug carrier - molecular modelling and electrochemistry studies.

A non-toxic lipoic acid derivative of β cyclodextrin (βCDLip) with an electron-rich aromatic linker was studied as a carrier for the drug doxorubicin with the aim of decreasing the toxic side effects of this drug. The modified cyclodextrin strengthened the drug binding and differentiated the complex-forming ability with dependence on pH. The stability constants of the complexes were evaluated by voltammetry and spectrofluorometry.

Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking.

Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of protein-peptide interactions is usually divided into two stages: prediction of the binding site at a protein receptor surface, and then docking (and modeling) the peptide structure into the known binding site. This paper presents a comprehensive CABS-dock method for the simultaneous search of binding sites and flexible protein-peptide docking, available as a user's friendly web server.

Low-temperature molecular dynamics simulations of horse heart cytochrome c and comparison with inelastic neutron scattering data.

Molecular dynamics (MD) simulation combined with inelastic neutron scattering can provide information about the thermal dynamics of proteins, especially the low-frequency vibrational modes responsible for large movement of some parts of protein molecules. We performed several 30-ns MD simulations of cytochrome c (Cyt c) in a water box for temperatures ranging from 110 to 300 K and compared the results with those from experimental inelastic neutron scattering. The low-frequency vibrational modes were obtained via dynamic structure factors, S(Q, ω), obtained both from inelastic neutron scattering experiments and calculated from MD simulations for Cyt c in the same range of temperatures.

The role of water in activation mechanism of human N-formyl peptide receptor 1 (FPR1) based on molecular dynamics simulations.

The Formyl Peptide Receptor 1 (FPR1) is an important chemotaxis receptor involved in various aspects of host defense and inflammatory processes. We constructed a model of FPR1 using as a novel template the chemokine receptor CXCR4 from the same branch of the phylogenetic tree of G-protein-coupled receptors. The previously employed template of rhodopsin contained a bulge at the extracellular part of TM2 which directly influenced binding of ligands.