We have compiled the first and largest database of disordered patterns from the PDB (version from 28 June 2010).
New database ComSin including structures in bound and unbound states has been created.
A new method (IsUnstruct) based on the Ising model for prediction of disordered residues from protein sequence alone has been developed. According to this model, each residue can be in one of two states: ordered or disordered.
The kinetic scheme describing the amyloid formation process has been constructed taking into account the last experimental data. Computer simulation has shown that the model adequately describes the corresponding stages of amyloid formation.
Several additional scales obtained from the statistics of protein structures have been calculated for prediction of amyloidogenic regions using the amino acid sequence. One of them has been used both for the prediction of amyloidogenic regions and for the residues protected from hydrogen-deuterium exchange. Our analysis demonstrates that the involvement of the amino acid residues which are situated in amyloidogenic regions into the folding nucleus formation is more intensive than that of the residues which are in non-amyloidogenic regions.
Mechanical properties of two immunoglobulin-binding domains of proteins L and G which have similar spatial structures but different amino acid sequences have been investigated by using the method of molecular dynamics. The investigation of mechanical properties of proteins has shown that intermediate states appear on the unfolding pathways of proteins L and G. It turned out that protein G is more stable mechanically than protein L.
We are the first who have constructed a unique database of protein pairs from thermophililic and mesophilic organisms. Comparison of proteins from thermophilic and mesophilic organisms has shown that the first has more close packing of the exterior part of protein (external residues accessible for water molecules) than the second one. Packing of the interior part of proteins (residues not accessible for water molecules) is the same in both cases.
Estimation of the folding rates of globular proteins with known three dimensional structures has been obtained using the method of Monte Carlo. The obtained refolding time values correlate reasonably well with the experimental data. The search for the optimal relationship between the average conformational entropy and the average energy of interactions between contacts for fast folding has been done. We have demonstrated that, among proteins of the same size, alpha/beta proteins are the most compact and have the slowest folding rates. We have shown here that dimensionless structural parameters describing the protein shape have low correlation with protein folding rates. At the same time structural determinants taking into account both the protein shape and its size show good agreement with experimentally observed rates of protein folding.
Reliable differences in the details of internal construction of the same protein globules determined by X-ray analysis, on the one hand, and NMR on the other have been reveale