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We discuss the effect of isothermal and adiabatic evaporation of water on the state of a water-protein droplet. The discussed problem is of current importance due to development of techniques to perform single molecule experiments using free electron lasers. In such structure-dynamic experiments the delivery of a sample into the X-ray beam is performed using the microdroplet injector. The time between the injection and delivery is in the order of microseconds. In this paper we developed a specialized variant of all-atom molecular dynamics simulations for the study of irreversible isothermal evaporation of the droplet. Using in silico experiments we determined the parameters of isothermal evaporation of the water-protein droplet with the sodium and chloride ions in the concentration range of 0.3 M at different temperatures. The energy of irreversible evaporation determined from in silico experiments at the initial stages of evaporation virtually coincides with the specific heat of evaporation for water. For the kinetics of irreversible adiabatic evaporation an exact analytical solution was obtained in the limit of high thermal conductivity of the droplet (or up to the droplet size of -100 Å). This analytical solution incorporates parameters that are determined using in silico. experiments on isothermal droplet evaporation. We show that the kinetics of adiabatic evaporation and cooling of the droplet scales with the droplet size. Our estimates of the water-protemi droplet. freezing rate in the adiabatic regime in a vacuum chamber show that additional techniques for stabilizing the temperature inside the droplet should be used in order to study the conformational transitions of the protein in single molecules. Isothermal and quasi-isothermal conditions are most suitable for studying the conformational transitions upon object functioning. However, in this case it is necessary to take into account the effects of dehydration and rapid increase of ionic strength in an aqueous microenvironment surrounding the protein.

Frediction of the three-dimensional structure of a protein from its amino acid sequence can be considered as a global optimization problem. In this paper, the Chaotic Artificial Bee Colony (CABC) algorithm was introduced and applied to 3D protein structure prediction. Based on the 3D off-lattice AB model, the CABC algorithm combines global search and local search of the Artificial Bee Colony (ABC) algorithm with the Chaotic search algorithm to avoid the problem of premature convergence and easily trapping the local optimum solution. The experiments carried out with the popular Fibonacci sequences demonstrate that the proposed algorithm provides an effective and high-performance method for protein structure prediction.

The paper describes results of testing of "recognition ability" of different substitution matrices and various pseudo-potentials (taken from literature or designed by us) to recognize protein structures and produce the sequence-to-structure alignments. Numerical estimates of "identifying power" of various matrices and pseudo-potentials are obtained for different levels of similarity between amino acid sequences of spatially-similar proteins. It is shown that substitution matrices work much better than pseudo-potentials at a high level of similarity of sequences of spatially-similar proteins, but some pseudo-potentials overcome substitution matrices at a low level of sequence similarity.

The paper describes creation and analysis of a database 3Dfold_test. This database consists of a large set of pairs of spatially-similar structures of protein domains and of an accompanying, much larger control set of "decoys", i.e., spatially-dissimilar protein structures, having approximately the same size and compactness as each member of a pair of spatially-similar proteins. The database 3Dfold_test can be found at the site http://phys.protres.ru/resources/prediction analogy/3Dfold/.

The approach described in this paper on the prediction of folding nuclei in globular proteins with known three dimensional structures is based on a search of the lowest saddle points through the barrier separating the unfolded state from the native structure on the free-energy landscape of protein chain. This search is performed by a dynamic programming method. Comparison of theoretical results with experimental data on the folding nuclei of two dozen of proteins shows that our model provides good phi value predictions for proteins whose structures have been determined by X-ray analysis, with a less limited success for proteins whose structures have been determined by NMR techniques only. Consideration of a full ensemble of transition states results in more successful prediction than consideration of only the transition states with the minimal free energy. In conclusion we have predicted the localization of folding nuclei for three dimensional protein structures for which kinetics of folding is studied now but the localization of folding nuclei is still unknown.

The possibility to derive the analogs of native proteins by the chemical synthesis is considered to be a serious argument for the concept of posttranslational protein folding. The present paper analyzes for the first time chemically synthesized proteins to reveal whether they are relevant to the problem of protein folding. The results enable the following conclusions to be drawn. The acquisition of the peculiar conformations by the chemically synthesized proteins to exhibit the specific functions is conditioned by the highly marked features of the secondary and tertiary structures of the corresponding native proteins. These features will make themselves evident only if favorable conditions are carefully chosen during the experiments for each individual protein. Thus, in our opinion, the possibility to derive a synthetic protein is hardly evidence for the posttranslational folding of proteins.

An amino acid sequence pattern conserved among a family of proteins is called motif. It is usually related to the specific function of the family. On the other hand, functions of proteins are achieved by their 3D structures. Specific local structures, called structural motifs, are considered related to their functions. However, searching for common structural motifs in different proteins is much more difficult than for common sequence motifs. We are attempting in this study to convert the information about the structural motifs into a set of one-dimensional digital strings, i.e., a set of codes, to compare them more easily by computer and to investigate their relationship to functions more quantitatively. By applying the Delaunay tessellation to a 3D structure of a protein, we can assign each local structure to a unique code that is defined so as to reflect its structural feature. Since a structural motif is defined as a set of the local structures in this paper, the structural motif is represented by a set of the codes. In order to examine the ability of the set of the codes to distinguish differences among the sets of local structures with a given PROSITE pattern that contain both true and false positives, we clustered them by introducing a similarity measure among the set of the codes. The obtained clustering shows a good agreement with other results by direct structural comparison methods such as a superposition method. The structural motifs in homologous proteins are also properly clustered according to their sources. These results suggest that the structural motifs can be well characterized by these sets of the codes, and that the method can be utilized in comparing structural motifs and relating them with function.

The present paper deals with the damages that are induced by numerous agents, such as gamma-radiation, UV-radiation, visible fluorescent light radiation, and a wide range of chemical agents, and lead to the formation of DNA-protein cross-links. This is the most unknown and obscure type of damage to cells. It is, however, well known that these damages are reparable.

This paper is devoted to a computer system designed for formal description and knowledge about protein structural-functional determinants. Structural-functional determinant is a region of amino acid sequence with certain structural, functional or evolutionary properties specific for each class of macromolecules. Here the problem is solved by a special method which allows to design programs able to distinguish these structural-functional determinants. The method is based on the expert system technology and integrated data bases.

The structure of long loop regions in proteins is considered. It is shown that long loops can be represented as combinations of small standard structures described in our previous papers. Relationship between the structures and the amino acid sequences of the loop regions is discussed.

The paper summarizes data on the nature of signals (mainly amino acid sequences) determining the intracellular movement of newly formed polypeptide chains: their secretion, incorporation into the cytoplasmic or endoplasmic reticular membranes, into different compartments of mitochondria and chloroplasts. Some information is given about the polypeptide transport into the nucleus and microbodies (glyoxysomes, peroxysomes, glucosomes). The intracellular movement of polypeptides is supposed to be proteolytically controlled.

On the basis of the suggested in previous paper [1] model of high-frequency motions of indol group forming a part of tryptophan residue side group parameters of indol groups torsional vibrations in tryptophan-containing synthetic polypeptides and proteins were analysed. Results of conformational analysis and experimental data on polarized luminescence obtained in [2-5] were used.

A differential method is described for measuring dielectric constants and losses in aqueous protein solutions at millimetrerange wavelengths. Employment of the method allows to improve the accuracy of determining the degree of hydratation. A method has also been suggested for taking into account the contribution of ions to the dielectric constant of solutions. The differential method was used to study hydratation of nine globular proteins. The data obtained are compared with the corresponding values provided by other experimental techniques and with theoretical predictions based on some models of hydratation. Good agreement is obtained with results provided by the isopiestic and NMR techniques. The discrepancy shown for hemoglobin is discussed in the paper. As has been shown, the dielectric method registers a monomolecular surface layer of water only. With pH varying between 4.0 and 3.2, a significant increase is observed in the hydratation of serum albumin. Presumably, this effect is connected with a N--F conformational transition.

The paper summarizes results of calorimetric studies of protein denaturation and of dissolution of non-polar substances in water. The analysis of the available experimental data shows that the positive contribution of the hydrophobic interactions in stabilization of the protein compact state is due to van der Waals interactions between the protein non-polar groups, while the contribution of water solvation by these groups, in spite of the widely spread opinion, appears to be always negative. This destabilizing action of water solvation on the protein increases as the temperature decreases, and at a significantly low temperature causes unfolding of the compact structure of protein, i. e. cold denaturation.

A structural unit common for all the known beta-proteins as well as for some others is considered in the paper. The simplest variant of this unit consists of four consecutive beta-strands denoted as a, b, c and d. Three of the strands, a, b and d, form an antiparallel beta-sheet, and the fourth, c, lies in the other layer of a layered protein sandwich structure. The strands, b and d, are parallel in the beta-sheet and together with the c-strand fold into a right-handed bcd-superhelix which is analogous to the superhelix formed by beta alpha beta regions. An a-strand is found between the strands b and d and antiparallel to them. Such locally ordered regions of proteins are described here as abcd-units. In all the known proteins the abcd-unit was found to be always at the edge of a protein bilayer. The remaining strands of a molecule or a domain are always located on the same side of the abcd-unit where the d-strand lies. It is shown that the packing of beta-strands in the beta-proteins depends on the packing of the other strands. The structural approach suggested here allows the packing of beta-strands in three-dimensions to be obtained if the abcd-unit is taken as the embryo of folding.

It is widely believed that the unique primary structure of a given protein is quite necessary for its folding into a certain three-dimensional structure as well as for its functioning and is a result of a directed selection in the course of biological evolution. The present paper provides arguments in favour of an alternative point of view according to which typical three-dimensional structures of globular proteins are characteristic even for random sequences of amino acid residues. Therefore it may be possible that primary structures of proteins are mainly examples of random amino acid sequences slightly edited in the course of biological evolution to impart them some additional (functional) meaning.

The purpose of this paper is to present a new approach to the study of mechanical properties of globular proteins and to summarize some of our results. The approach is based on the analysis of mechanical, viscoelastic properties of a protein monocrystal which is used as a probe of mechanical properties of a protein molecule. As a first rough approximation a protein molecule can be considered as a material resembling molecular crystals and glass-like polymers with the Young's modulus E = 2 - 10 GN . m-2. More detailed information concerning the anisotropy of elasticity and that of inhibitor effect strongly suggests that the lysozyme molecule is a construction having a special hinge-bending degree of freedom. The force constant estimated from our data for this degree of freedom is (0,4-1) . 10(13) erg . rad-2 . mol-1.

The paper gives a review of the literature publications on protein methylation and probable donors of methyl groups. It presents experimental data demonstrating the capability of 14CH3-B12 to methylate in vitro proteins of tRNA methylases from Zajdela ascite hepatoma and rat liver as well as commercial RNase and albumin preparations.