For many targets of pharmaceutical importance conformational changes of the receptor protein are relevant during the ligand binding process. A new docking approach, ReFlexIn (Receptor Flexibility by Interpolation), that combines receptor flexibility with the computationally efficient potential grid representation of receptor molecules has been evaluated on the retroviral HIV-1 (Human Immunodeficiency Virus 1) protease system. An approximate inclusion of receptor flexibility is achieved by using interpolation between grid representations of individual receptor conformations. For the retroviral protease the method was tested on an ensemble of protease structures crystallized in the presence of different ligands and on a set of structures obtained from morphing between the unbound and a ligand-bound protease structure. Docking was performed on ligands known to bind to the protease and several non-binders. For the binders the ReFlexIn method yielded in almost all cases ligand placements in similar or closer agreement with experiment than docking to any of the ensemble members without degrading the discrimination with respect to non-binders. The improved docking performance compared to docking to rigid receptors allows for systematic virtual screening applications at very small additional computational cost.

Accounting for receptor flexibility is an essential component of successful protein–ligand docking but still marks a major computational challenge. For many target molecules of pharmaceutical relevance, global backbone conformational changes are relevant during the ligand binding process. However, popular methods that represent the protein receptor molecule as a potential grid typically assume a rigid receptor structure during ligand–receptor docking. A new approach has been developed that combines inclusion of global receptor flexibility with the efficient potential grid representation of the receptor molecule. This is achieved using interpolation between grid representations of the receptor protein deformed in selected collective degrees of freedom. The method was tested on the docking of three ligands to apo protein kinase A (PKA), an enzyme that undergoes global structural changes upon inhibitor binding. Structural variants of PKA were generated along the softest normal mode of an elastic network representation of apo PKA. Inclusion of receptor deformability during docking resulted in a significantly improved docking performance compared with rigid PKA docking, thus allowing for systematic virtual screening applications at small additional computational cost. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011

The majority of biological processes involve the association of proteins or binding of other ligands to proteins. The accurate prediction of putative binding sites on the protein surface can be very helpful for rational drug design on target proteins of medical relevance, for predicting the geometry of protein-protein as well as protein-ligand complexes and for evaluating the tendency of proteins to aggregate or oligomerize. A variety of computational methods to rapidly predict protein-protein binding interfaces or binding sites for small drug-like molecules have been developed in recent years. The principles of methods available for protein interface and pocket detection are summarized, including approaches based on sequence conservation, as well as geometric and physicochemical surface properties. The performance of several Webaccessible methods for ligand binding site prediction has been compared using protein structures in bound and unbound conformation and homology modeled proteins. All methods tested gave very promising predictions even on unbound and homology modeled protein structures, thus indicating that current methods are robust in relation to modest conformational changes associated with the ligand binding process.

Membrane electroporation is the method to directly transfer bioactive substances such as drugs and genes into living cells, as well as preceding electrofusion. Although much information on the microscopic mechanism has been obtained both from experiment and simulation, the exis- tence and nature of possible intermediates is still unclear. Here, we investigated the equilibrium effect of external electric fields on the membrane structure, the effect of membrane-embedded proteins on the stability of membranes, and the kinetics of the electropore formation process, applying molecular dynamics simulations. The results show a quadratic change of the membrane capacitance with the applied voltage, and a significant stabilization of membranes by proteins. For electropores, an average pore radius of 0.47±0.15nm was obtained, in favourable agreement with conductance measurements and electrooptical experiments of lipid vesicles. A linear dependency of the activation energy for prepore formation on the applied field is seen, with quantitative agreement between experi- ment and simulation. The distribution of preporation times suggests a four state pore formation model.