Biomedical subjects

I A Vakser

Publications and source records attributed to I A Vakser.

9 recordsLinked to original sources

PubMed1997

Construction of a 3D model of cytochrome P450 2B4.

A three-dimensional structural model of rabbit phenobarbital-inducible cytochrome P450 2B4 (LM2) was constructed by homology modeling techniques previously developed for building and evaluating a 3D model of the cytochrome P450choP isozyme. Four templates with known crystal structures including cytochrome P450cam, terp, BM-3 and eryF were used in multiple sequence alignments and construction of the cytochrome P450 2B4 coordinates. The model was evaluated for its overall quality using available protein analysis programs and found to be satisfactory. The model structure was stable at room temperature during a 140 ps unconstrained full protein molecular dynamics simulation. A putative substrate access channel and binding site were identified. Two different substrates, benzphetamine and androstenedione, that are metabolized by cytochrome P450 2B4 with pronounced product specificity were docked into the putative binding site. Two orientations were found for each substrate that could lead to the observed preferred products. Using a geometric fit method three regions on the surface of the model cytochrome P450 structure were identified as possible sites for interaction with cytochrome b5, a redox partner of P450 2B4. Residues that may interact with the substrates and with cytochrome b5 have been identified and mutagenesis studies are currently in progress.

Amino Acid Sequence↗

PubMed1997

Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex.

A single protein-protein pair, the complex of the influenza virus hemagglutinin with an antibody (Fab BH151), was suggested for prediction at the second experiment on the Critical Assessment of Techniques for Protein Structure Prediction. To predict the structure of the complex, we applied our docking program GRAMM at a decreased resolution (to accommodate the conformational inaccuracies). The lowest-energy match showed a remarkable "low-resolution" surface complementarity between the molecular structures. After receiving the experimental structure of the complex we had a chance to verify our assumptions and results. The analysis of the hemagglutinin-antibody interface revealed several significant conformational changes in the side chains, which resulted in deep interpenetrations of the hemagglutinin and the antibody structures. This confirmed our initial assumption that the structural changes will be beyond the tolerance of high-resolution rigid-body docking. The comparison of the predicted low-resolution match, submitted as the solution, and the experimentally determined complex showed significant structural discrepancies in the orientation of the antibody, due to the low-resolution character of the docking. Because of the severe structural errors, no residue-residue contacts were predicted correctly. However, a significant part of the antigenic site was determined. This illustrates the practical value of the present methodology for the initial prediction of the binding site, as well as points out the problem of transition from the low-resolution predictions of protein-protein complexes to the accurate structure.

Antibodies, Viral↗

PubMed1996

Low-resolution docking: prediction of complexes for underdetermined structures.

One of the most fundamental questions concerning ligand-receptor interaction is whether such a process of intermolecular association is generally determined by local structural elements of the participating molecules, or whether there are also large-scale motifs in molecule structures that facilitate complex formation. From the point of view of practical docking computations, the elaborate character of local structural details in ligand-receptor interaction creates a large number of false-positive matches, which interfere with determination of the best fit. Another significant obstacle in protein docking is the problem of structural data inaccuracy (poor structure resolution, conformational changes upon complex formation, etc.). Our study [Vakser (1995) Protein Eng., 8, 371-377], based on ultralow (approximately 7 A resolution) representation of molecular structures, allowes to average all high-resolution structural details, and still predict most of the structural features of the ligand-receptor complex. The approach dramatically improves the signal-to-noise ratio in determination of the best fit, and moves the structure inaccuracy tolerance to the range of the macrostructure. In the present paper, we describe a further validation of the main principles of this approach and a detailed analysis of the low-resolution docking results. This includes clustering of ligand positions around the receptor molecule and cross-validation of ligands and receptors from different complexes. We also discuss the important implications of the approach to the multiple-minima problem and a possible role of different structural elements in the recognition mechanism.

Animals↗

PubMed1996

Long-distance potentials: an approach to the multiple-minima problem in ligand-receptor interaction.

The multiple-minima problem is a classical problem in molecular structure prediction. For ligand-receptor systems, a possible direction to alleviate this major obstacle is to simplify the objective function (intermolecular energy) and smooth its profile. We introduce long-distance atom-atom potentials for ligand-receptor interactions. The longer ranges result in averaging of the energy potential at a given point. Our simplified force field is based on a trivial empirical representation of interatomic interactions as a step function. We demonstrate that the intermolecular energy calculation by a systematic search with such a simplified long-distance force field delivers the global minimum (crystallographically determined position of the ligand) by radically suppressing local minima (or false-positive fits). The effectiveness of the approach is demonstrated on different molecular complexes of known structure.

Algorithms↗

PubMed1996

Main-chain complementarity in protein-protein recognition.

The existing theoretical approaches to protein-protein recognition concentrate on the details of the molecular surface at atomic resolution, while a possible role of the main chain in complex formation has been largely unexplored. To address this problem, we represented the molecules by C alpha atoms and applied the step-function potentials for intermolecular energy calculations. Since our goal was not to predict, as accurately as possible, the structure of a protein-ligand complex, but to reveal the role of the backbone in the formation of such a complex, all the potentials were identical and C alpha centered. Thus, for the specific purposes of our study, we do not simulate the difference in the side chains at the molecular surface. The structures were taken from known co-crystallized complexes. The intermolecular energy calculation was performed by a systematic 6-D search on a grid. The results revealed that in all cases tested (except antigen-antibody) the positions of the ligand at the binding site on the receptor corresponded to the lowest-energy configurations of the complex. The complementarity between the backbones, in general, may facilitate the initial placement of the ligand at the binding site of the receptor. At the same time, the identity and the specific conformation of the surface side chains play a crucial role in the next stage of the complex formation.

Binding Sites↗

PubMed1995

Protein docking for low-resolution structures.

A typical problem for a docking procedure is how to match two molecules with known 3-D structure so as to predict the configuration of their complex. A very serious obstacle to docking is an inherent inaccuracy in the 3-D structures of the molecules. In general, existing molecular recognition techniques are not designed for cases where (i) conformational changes upon macromolecular complex formation are substantial or (ii) the X-ray data on one or both (macro) molecules are not available, and the structures, based on alternative sources (NMR, modeling), are not well defined. We designed a direct computer experiment using molecules totally deprived of any structural features smaller than 7 A. This was performed on the basis of a previously developed docking algorithm. The modified procedure was applied to a number of known protein complexes taken from the Brookhaven Protein Data Bank. In most cases, a pronounced trend towards the correct structure of the molecular complex was clearly indicated and the real binding sites were predicted. The distinction between the prediction of the antigen-antibody complex and other molecular pairs may reflect important differences in the principles of complex formation. The results strongly suggest the use of our recognition procedure for docking studies where the detailed structures of the molecules are lacking.

Algorithms↗

PubMed1994

Hydrophobic docking: a proposed enhancement to molecular recognition techniques.

In the classical procedures for predicting the structure of protein complexes two molecules are brought in contact at multiple relative positions, the extent of complementarity (geometric and/or energy) at the surface of contact is assessed at each position, and the best fits are retrieved. In view of the higher occurrence of hydrophobic groups at contact sites, their contribution results in more intermolecular atom-atom contacts per unit area for correct matches than for false positive fits. The hydrophobic groups are also potentially less flexible at the surface. Thus, from a practical point of view, a partial representation of the molecules based on hydrophobic groups should improve the quality of the results in finding molecular recognition sites, as compared to full representation. We tested this proposal by applying the idea to an existing geometric fit procedure and compared the results obtained with full vs. hydrophobic representations of molecules in known molecular complexes. The hydrophobic docking yielded distinctly higher signal-to-noise ratio so that the correct match is discriminated better from false positive fits. It appears that nonhydrophobic groups contribute more to false matches. The results are discussed in terms of their relevance to molecular recognition techniques as compared to energy calculations.

Algorithms↗

PubMed1992

Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.

A geometric recognition algorithm was developed to identify molecular surface complementarity. It is based on a purely geometric approach and takes advantage of techniques applied in the field of pattern recognition. The algorithm involves an automated procedure including (i) a digital representation of the molecules (derived from atomic coordinates) by three-dimensional discrete functions that distinguishes between the surface and the interior; (ii) the calculation, using Fourier transformation, of a correlation function that assesses the degree of molecular surface overlap and penetration upon relative shifts of the molecules in three dimensions; and (iii) a scan of the relative orientations of the molecules in three dimensions. The algorithm provides a list of correlation values indicating the extent of geometric match between the surfaces of the molecules; each of these values is associated with six numbers describing the relative position (translation and rotation) of the molecules. The procedure is thus equivalent to a six-dimensional search but much faster by design, and the computation time is only moderately dependent on molecular size. The procedure was tested and validated by using five known complexes for which the correct relative position of the molecules in the respective adducts was successfully predicted. The molecular pairs were deoxyhemoglobin and methemoglobin, tRNA synthetase-tyrosinyl adenylate, aspartic proteinase-peptide inhibitor, and trypsin-trypsin inhibitor. A more realistic test was performed with the last two pairs by using the structures of uncomplexed aspartic proteinase and trypsin inhibitor, respectively. The results are indicative of the extent of conformational changes in the molecules tolerated by the algorithm.

Algorithms↗

PubMedDate not supplied

[Amphiphilic properties of angiotensin and its fragments].

Many biologically active peptides are supposed to interact with specific receptors mainly due to hydrophobic forces. In order to obtain a more detailed information about the peptide molecule behavior at the "water-non-polar-phase" boundary an approach to the calculation of stable conformations on such a boundary has been developed. This approach is used for investigation of the amphiphilic properties of angiotensin and its six fragments. The results of calculations of transfer energies of these peptides from the water environment to the phase boundary are in agreement with the experimental data.

Angiotensin II↗