The temperature dependence of the partial heat capacity of the native protein structure in an aqueous solution has been analyzed. It is shown that the strictly linear temperature dependence is due to the contributions of the vibrational and conformational components, which indicates volume consistensy and the absence of conformational transitions up to the main two-state transition. The two-level structural and functional organization of the protein three-dimensional structure are considered in relation to the energy and conformational entropy properties in accordance with the principles of the organization of the protein macromolecule.Communicated by Ramaswamy H. Sarma.

The PM3/PM7 semi-empirical quantum-chemical methods were for the first time used to calculate and analyze the geometric configuration parameters of silicon analogs of the 20 proteinogenic L-amino acids. Enthalpies of formation and dipole moments were calculated along with conformational parameters. Bond lengths of the silicon analogs were shown to significantly exceed the bond lengths in the carbon amino acids. Intramolecular hydrogen bonding was found to be possible in the silicon analog of aspartate, like in carbon aspartate. The lowest thermodynamic stability was observed for aromatic and heterocyclic amino acid analogs. The role that an aromatic analog may play in silicon compounds differs from the respective role in carbon compounds as a result of longer interatomic distances and weaker π conjugation. A polyalanine chain model was used to demonstrate that the α-helical conformation corresponds to the global minimum of the heat of formation in both carbon and silicon peptides.

При помощи полуэмпирической квантово-химической методики PM3/РМ7 впервые рассчитаны и проанализированы геометрические особенности молекул кремниевых аналогов 20 протеиногенных L-аминокислот и проводится их сравнение с углеродными аминокислотами. Помимо конформационных параметров определены значения энтальпий образования и дипольных моментов изученных соединений. Показано, что длины связей в кремниевых аналогах аминокислот значительно превосходят длины связей в углеродных аминокислотах. В кремниевом аналоге аспартата (как и в углеродном аспартате) возможно образование внутримолекулярной водородной связи. Наименьшей термодинамической стабильностью характеризуются ароматические и гетероциклические аналоги аминокислот, причем вопрос ароматичности в кремниевых соединениях носит иной характер, нежели в соединениях углерода, из-за более длинных межатомных расстояний и более слабого пи-сопряжения. На модели полиаланиновой цепи показано, что как в углеродном, так и в кремниевом пептиде глобальный минимум теплоты образования такой молекулы соответствует конформации альфа-спирали.

The advanced high performance computing methods are used to study the stability and conformational dynamics of the bacterial enzyme lipase LipA, its mutants, and the close homologous enzyme CLE whose substrate is polylactic acid-based plastics. From the analysis of the GPU molecular dynamics of native lipases and their mutants the amino acid residues whose point substitutions can markedly improve the thermostability of the enzymes under study without deteriorating their activity are determined.

The analysis of temperature-induced unfolding of proteins in aqueous solutions was performed. Based on the data of thermodynamic parameters of protein unfolding and using the method of semi-empirical calculations of hydration parameters at reference temperature 298 K, we obtained numerical values of enthalpy, free energy, and entropy which characterize the unfolding of proteins in the ‘gas phase’. It was shown that specific values of the energy of weak intramolecular bonds (∆Hint), conformational free energy (∆Gconf) and entropy (∆Sconf) are the same for proteins with molecular weight 7–25 kDa. Using the energy value (∆Hint) and the proposed approach for estimation of the conformational entropy of native protein (SNC), numerical values of the absolute free energy (GNC) were obtained.

In this study an algorithm for increasing the thermostability of the globular human peroxyredoxin 6 antioxidant enzyme is described. A recombinant form of this protein was produced based on the analysis of the amino-acid composition of this enzyme in rats (Rattus rattus). The original concept of increasing the thermostability of small globular proteins using alternative hydrogen bonding of the peripheral acidic and basic amino-acid residues was substantially improved by GPU-accelerated molecular-dynamics simulations.

We performed thermodynamic analysis of temperature-induced unfolding of mesophilic and thermophilic proteins. It was shown that the variability in protein thermostability associated with pH-dependent unfolding or linked to the substitution of amino acid residues on the protein surface is evidence of the governing role of the entropy factor. Numerical values of conformational components in enthalpy, entropy and free energy which characterize protein unfolding in the “gas phase” were obtained. Based on the calculated absolute values of entropy and free energy, a model of protein unfolding is proposed in which the driving force is the conformational entropy of native protein, as an energy of the heat motion (T·SNC) increasing with temperature and acting as an factor devaluating the energy of intramolecular weak bonds in the transition state.

The uniqueness of life on our planet has been an important topic of discussion in scientific literature for many decades. The most particular findings are in the fields of the structure of biomolecules and the mechanisms of their conformational and chemical transfers since they underlie all the biospheric processes of our planet. The compounds based on carbon are the subject of study of organic chemistry, which has an appropriate thoroughly developed classification of such substances; a number of approaches have been proposed for the analysis of composition and structure of the organic compounds, and a theoretical basis has been created, which describes the character of various chemical bonds involving carbon atoms. At the same time, since quite a while, there is a widely discussed hypothesis (Alison, 1968) concerning the possibility of existence of compounds, which are similar to organic, but are based on silicon atoms. Even in interstellar medium, among all the diversity of molecules detected, 84 are based on carbon, and 8 on silicon (Lazio, 2000), including four hybrid types, i.e. containing both silicon and carbon. According to approximate evaluations, the contents ratio of carbon to silicon in the space equals to 10:1, though the Earth’s crust consists of 87% of silicon in the form of oxides. In the Periodic Table, silicon is situated in the same group IV, like carbon. These two elements are largely similar in the structure of their valent electronic shells, and their noteworthy that previously it was stated (Lazio, 2000) that silicon-containing compounds are not as diverse in structure as carbon compounds. Despite having higher mass and radius, the atoms of silicon form double and triple covalent bonds (Wang et al., 2008). Therefore, the issue concerning the existence of silicon structures similar to carbon biomolecules, as well as the question of hypothetical “biochemical” processes involving non-carbonic analogs of aminoacids, carbohydrates, proteins, lipids, and other biomolecules, is still a matter of discussion in scientific and popular science literature. It is particularly notable that the modern methods of computational chemistry allow carrying out the estimating calculations of the structure and dynamics of such compounds, which is quite similar to the known approaches of substance modeling de novo in drug design. For instance, first by calculations (Nagase, Kudo, & Aoki, 1985), and later on experimentally (Abersfelder, White, Rzepa, & Scheschkewitz, 2010), aromaticity of cyclic carbohydrate-like derivatives of silicon was studied. In the present study, we used quantum-chemical semiempirical PM3 and ab initio B3LYP/6-311G(d,p) level of theory to investigate the peculiarities of several structural and thermodynamic parameters of molecules, which can be assumed as complete silicon analogs of carbonic L-amino acids and other biomolecules, so-called bricks of life: carbohydrates, nitrogenous bases, fatty acids, as well as vitamins and caffeine. The quantum-mechanical calculations that we made displayed that the molecules of silicon amino acids possess higher thermodynamic stability compared to carbon analogs. Thereby, silicon amino acids have a similar conformation freedom, increased values of dipole moment, as well as more pronounced electron-donor characteristics. Silicon analogs of carbohydrates, fatty acids, and nitrogenous bases are as well considered as heavier thermodynamically stable compounds, having special features in 3D-organization and worth further experimental study. The present work also deals with the question of the existence and stability of “alpha-helices” composed of silicon amino acids, because in the molecules of Si-analogs of aspartate and glutamate, we have discovered effective formation of intramolecular hydrogen bond (due to the side chain), which is highly important for Pauling–Corey alpha helix formation in natural L-amino acids (Kondratyev, Kabanov, & Komarov, 2010). Our estimations show that an “alpha helix” composed of 10 silicon alanine analogs is more stable in isolated state than a linear form of such macromolecule, which was not observed for a molecule of the same composition having a carbon backbone.

The results of theoretical studies of the structural and dynamic features of peptides and small proteins have been presented that were carried out by quantum chemical and molecular dynamics methods in high-performance graphic stations, “table supercomputers,” using distributed calculations by the CUDA technology.

Small monomeric proteins from mesophilic and thermophilic organisms were studied. They have close structural and physical and chemical properties but vary in thermal stability. A thermodynamic analysis of heat unfolding was made and integral enthalpy of unfolding (DeltaH(unf)), heat capacity of hydration (DeltaC(p)(hyd)) and enthalpy of hydration (DeltaH(hyd)) and of the buried surface area (DeltaASA) of nonpolar and polar groups as well as the enthalpy of disruption of intramolecular interaction (DeltaH(int) in gas phase) at 298 K were determined. The absence of correlation between protein thermostability and energetic components suggests that regulatory mechanism of protein thermal stabilization has entropic nature.

To elucidate the mechanism of protein thermostabilization, the thermodynamic properties of small monomeric proteins from mesophilic and thermophilic organisms have been analyzed. Molecular dynamics simulations were employed in the study of dynamic features of charged and polar side chains of amino acid residues. The basic conclusion has been made: surface charged and polar side chains with high conformational mobility can form alternative hydrogen bonded (H-bonded) donor-acceptor pairs. The correlation between the quantitative content of alternative H-bonds per residue and the temperature of maximal thermostability of proteins has been found. The proposed mechanism of protein thermostabilization suggests continuous disruption of the primary H-bonds and formation of alternative ones, which maintain constant the enthalpy value in the native state and prevent a rapid increase of the conformational entropy with the rising temperature. The analysis of the results show that the more residues located in the N- and C-terminal regions and in the extended loops that are capable of forming alternative longer-range H-bonded pairs, the higher the protein thermostability.

A theoretical framework is presented to analyze how solvent water contributes to the X-ray scattering profile of protein solution. Molecular dynamics simulations were carried out on pure water and an aqueous solution of myoglobin to determine the spatial distribution of water molecules in each of them. Their solution X-ray scattering (SXS) profiles were numerically evaluated with obtained atomic-coordinate data. It is shown that two kinds of contributions from solvent water must be considered to predict the SXS profile of a solution accurately. One is the excluded solvent scattering originating in exclusion of water molecules from the space occupied by solutes. The other is the hydration effect resulting from formation of a specific distribution of water around solutes. Explicit consideration of only two molecular layers of water is practically enough to incorporate the hydration effect. Care should be given to using an approximation in which an averaged electron density distribution is assumed for the structure factor because it may predict profiles considerably deviating from the correct profile at large K.

The temperature adaptation of pyrrolidone carboxyl peptidase (PCP) from a hyperthermophile, Pyrococcus furiosus (PfPCP), was characterized in the context of an assembly form of the protein which is a homotetramer at neutral pH. The PfPCP exhibited maximal catalytic activity at 90-95 degreesC and its activity was higher in the temperature range 30-100 degreesC than its counterpart from the mesophilic Bacillus amyloliquefaciens (BaPCP). Thermal stability was monitored by differential scanning calorimetry (DSC). Two clearly separated peaks appeared on the DSC curves for PfPCP at alkaline and acidic pH. Using the oxidized PfPCP and two mutant proteins (PfC188S and PfC142/188S), it was found that the peaks on the high and low temperature sides of the DSC curve of PfPCP were produced by the forms with an intersubunit disulfide bridge between the two subunits and without the bridge, respectively, indicating the stabilization effect of intersubunit disulfide bridges. The denaturation temperature (T-d) Of PfPCP with intersubunit disulfide bridges was higher by 53 degreesC at pH 9.0 than that of BaPCP An analysis of the equilibrium ultracentrifugation patterns showed that the tetrameric PfC142/188S dissociated into dimers with decreasing pH in the acidic region and became monomer subunits at pH 2.5. The heat denaturation of PfPCP and its two Cys mutants was highly reversible in the dimeric forms, but completely irreversible in the tetrameric form. The Td Of PfC142/188S decreased as the enzyme became dissociated, but the monomeric form of the protein was still folded at pH 2.5, although BaPCP was completely denatured at acidic pH. These results indicate that subunit interaction plays an important role in stabilizing PCP from P. furiosus in addition to the intrinsic enhanced stability of its monomer.

The effect of glycerol on the heat stability of porcine muscle lactate dehydrogenase (isoenzyme M(4)) was studied by differential microcalorimetry, circular dichroism, and analytical ultracentrifugation. In the presence of glycerol the melting curves exhibited two peaks, at 45-50 and 60-65 degrees C. The higher-temperature peak corresponded to heat denaturation with irreversible breakdown of tertiary structure and unwinding of alpha-helical regions, could be described as an irreversible one-step transition with a rate constant of first order in protein concentration, and did not depend on glycerol concentration. The lower-temperature microcalorimetric peak was asymmetrical, could be interpreted in terms of predenaturation, glycerol-induced transitions, was not associated with protein aggregation, and had no correlates in spectral or kinetic measurements.

A semi-empirical method has been used to estimate the thermodynamic parameters of hydration of buried surface areas of ribonuclease S, lysozyme and myoglobin from the model of complete unfolding according to Ooi et al. ((1987) Proc. Natl. Acad. Sci. USA 84, 3086–3090). The buried surface area of proteins is considered as the difference between the accessible surface area of native protein and the completely extended polypeptide chain according to Lee and Richards ((1971) J. Mol. Biol. 55, 379–400). The contributions of nonpolar and polar protein groups to the general value of Gibbs energy, enthalpy, entropy and heat capacity of hydration have been determined. The obtained results on the thermodynamic behavior of proteins in the process of complete unfolding are in good agreement with the results of microcalorimetric studies of thermal denaturation.