Is there an advantageous arrangement of aromatic residues in proteins? Statistical analysis of aromatic interactions in globular proteins.

The aim of this study was to evaluate the favorability of different conformations of aromatic residues in proteins by analysing the occurrence of particular conformations. The clustering of protein structures from the Protein Data Bank (PDB) was performed. Conformations of interacting aromatic residues were analyzed for 511 282 pairs in 35 493 protein structures sharing less than 50% identity.

FoldNucleus: web server for the prediction of RNA and protein folding nuclei from their 3D structures.

Motivation: To gain insight into how biopolymers fold as quickly as they do, it is useful to determine which structural elements limit the rate of RNA/protein folding.

Summary: We have created a new web server, FoldNucleus. Using this server, it is possible to calculate the folding nucleus for RNA molecules with known 3D structures-including pseudoknots, tRNAs, hairpins and ribozymes-and for protein molecules with known 3D structures, as long as they are smaller than 200 amino acid residues.

What handedness and angles between helices has the studied three-helical protein domain?

We have created a new server FoldHandedness. Using this server it is possible: (i) to define the regions of helices from two issues (from the PDB file and using the last version of the DSSP program), (ii) to determine the handedness for any chosen three helices and (iii) to calculate the angle and sign between the chosen pairs of the helices for large proteins and complexes of proteins with DNA or RNA.

Right- and left-handed three-helix proteins. I. Experimental and simulation analysis of differences in folding and structure.

Despite the large number of publications on three-helix protein folding, there is no study devoted to the influence of handedness on the rate of three-helix protein folding. From the experimental studies, we make a conclusion that the left-handed three-helix proteins fold faster than the right-handed ones. What may explain this difference? An important question arising in this paper is whether the modeling of protein folding can catch the difference between the protein folding rates of proteins with similar structures but with different folding mechanisms.

Development and testing of PFFSol1.1, a new polarizable atomic force field for calculation of molecular interactions in implicit water environment.

A detailed calculation of protein interactions with explicitly considered water molecules takes enormous time. If water is considered implicitly (as media rather than as molecules), calculations become faster. These calculations are less precise, unless one uses voluminous computations of solvent-accessible areas.

Assessment of performance of the general purpose polarizable force field QMPFF3 in condensed phase.

The recently introduced force field (FF) QMPFF3 is thoroughly validated in gas, liquid, and solid phases. For the first time, it is demonstrated that a physically well-grounded general purpose FF fitted exclusively to a comprehensive set of high level vacuum quantum mechanical data applied as it is to simulation of condensed phase provides high transferability for a wide range of chemical compounds. QMPFF3 demonstrates accuracy comparable with that of the FFs explicitly fitted to condensed phase data, but due to high transferability it is expected to be successful in simulating large molecular complexes.