Using molecular dynamics simulations in conjunction with home-developed Split Integration Symplectic Method we effectively decouple individual degrees of freedom of water molecules and connect them to corresponding thermostats. In this way, we facilitate elucidation of structural, dynamical, spectral, and hydration properties of bulk water at any given combination of rotational, translational, and vibrational temperatures. Elevated rotational temperature of the water medium is found to severely hinder hydration of polar molecules, to affect hydration of ionic species in a nonmonotonous way and to somewhat improve hydration of nonpolar species. As proteins consist of charged, polar, and nonpolar amino-acid residues, the developed methodology is also applied tocritically evaluate the hypothesis that the overall decrease in protein hydration and the change in the subtle balance between hydration of various types of amino-acid residues provide a plausible physical mechanism through which microwaves enhance aberrant protein folding and aggregation.
COBISS.SI-ID: 5014554
The combination of theoretical models of macromolecules that exist at different spatial and temporal scales has become increasingly important for addressing complex biochemical problems. This work describes the extension of concurrent multiscale approaches, introduces a general framework for carrying out calculations, and describes its implementation into the CHARMM macromolecular modeling package. This functionality, termed MSCALE, generalizes both the additive and subtractive multiscale scheme [e.g., quantummechanical/molecular mechanical (QM/MM) ONIOM-type] and extends its support to classical force fields, coarse grained modeling [e.g., elastic network model (ENM), Gaussian network model (GNM), etc.], and a mixture of them all. The MSCALE scheme is completely parallelized with each subsystem running as an independent but connected calculation. One of the most attractive features of MSCALE is the relative ease of implementation using thestandard message passing interface communication protocol. This allows external access to the framework and facilitates the combination of functionality previously isolated in separate programs. This new facility is fully integrated with free energy perturbation methods, Hessian-based methods,and the use of periodicity and symmetry, which allows the calculation of accurate pressures. We demonstrate the utility of this new technique with four examples: (1) subtractive QM/MM and QM/QM calculations; (2) multiple force field alchemical free energy perturbation; (3) integration with the SANDER module of AMBER and the TINKER package to gain access to potentials notavailable in CHARMM; and (4) mixed resolution (i.e., coarse grain/all-atom)normal mode analysis. The potential of this new tool is clearlyestablished, and in conclusion, an interesting mathematical problem is highlighted, and future improvements are proposed.
COBISS.SI-ID: 4653594
Exploitation of locally similar 3D patterns of physicochemical properties on the surface of a protein for detection of binding sites that may lack sequenceand global structural conservation. An algorithm, ProBiS is described that detects structurally similar sites on protein surfaces by local surface structure alignment. It compares the query protein to members of a database ofprotein 3D structures and detects with sub-residue precision, structurally similar sites as patterns of physicochemical properties on the protein surface. Using an efficient maximum clique algorithm, the program identifies proteins that share local structural similarities with the query protein and generates structure-based alignments of these proteins with the query. Structural similarity scores are calculated for the query protein's surface residues, and are expressed as different colors on the query protein surface. The algorithm has been used successfully for the detection of protein-protein,protein-small ligand and protein-DNA binding sites.
COBISS.SI-ID: 4395802
Generalization of an earlier algorithm has led to the development of new localstructural alignment algorithms for prediction of protein-protein bindingsites. The algorithms use maximum cliques on protein graphs to define structurally similar protein regions. The search for structural neighbors in the new algorithms has been extended to all the proteins in the PDB and the query protein is compared to more than 60000 proteins or over 300000 single-chain structures. The resulting structural similarities are combined and used to predict the protein binding sites. This study shows that the location of protein binding sites can be predicted by comparing only local structural similarities irrespective of general protein folds.
COBISS.SI-ID: 4491290
A semiregular element of a permutation group is a non-identity element having all cycles of equal length in its cycle decomposition. The existence of semiregular automorphisms in fullerenes is discussed. In particular, the family of fullerene graphs is described via the existence of semiregular automorphisms in their automorphism groups.
COBISS.SI-ID: 4178202