[Structure of crambin in solution, crystal and in the trajectories of molecular dynamics simulations].

The mechanisms of the three-dimensional crambin structure alterations in the crystalline environments and in the trajectories of the molecular dynamics simulations in the vacuum and crystal surroundings have been analyzed. In the crystalline state and in the solution the partial regrouping of remote intramolecular packing contacts, involved in the formation and stabilization of the tertiary structure of the crambin molecule, occurs in NMR structures. In the crystalline state it is initiated by the formation of the intermolecular contacts, the conformational influence of its appearance is distributed over the structure. The changes of the conformations and positions of the residues of the loop segments, where the intermolecular contacts of the crystal surroundings are preferably concentrated, are most observable. Under the influence of these contacts the principal change of the regular secondary structure of crambin is taking place: extension of the two-strand beta structure to the three-strand structure with the participation of the single last residue N46 of the C-terminal loop. In comparison with the C-terminal loop the more profound changes are observed in the conformation and the atomic positions of the backbone atoms and in the solvent accessibility of the residues of the interhelical loop. In the solution of the ensemble of the 8 NMR structures relative accessibility to the solvent differs more noticeably also in the region of the loop segments and rather markedly in the interhelical loop. In the crambin cryogenic crystal structures the positions of the atoms of the backbone and/or side chain of 14-18 of 46 residues are discretely disordered. The disorganizations of at least 8 of 14 residues occur directly in the regions of the intermolecular contacts and another 5 residues are disordered indirectly through the intramolecular contacts with the residues of the intermolecular contacts. Upon the molecular dynamics simulation in the vacuum surrounding as in the solution of the crystalline structure of crambin the essential changes of the backbone conformation are caused by the intermolecular contacts absence, but partly masked by the structure changes owing to the nonpolar H atoms absence on the simulated structure. The intermolecular contact absence is partly manifested upon the molecular dynamics simulation of the crambin crystal with one protein molecule. Compared to the crystal structure the lengths of the interpeptide hydrogen bonds and other interresidue contacts in an average solution NMR structure are somewhat shorter and accordingly the energy of the interpeptide hydrogen bonds is better. This length shortening can occur at the stage of the refinement of the NMR structures of the crambin and other proteins by its energy minimizations in the vacuum surroundings and not exist in the solution protein structures.

[Protein conformational dynamics of crambin in crystal, solution and in the trajectories of molecular dynamics simulations].

Atomic displacement parameters--B factors of the eight crambin crystal structures obtained at 0.54-1.5 angstroms resolution and temperatures of 100-293K have been analyzed. The comparable contributions to the B factor values are the intramolecular motions which are modeled by the harmonic vibration calculations and derived from the molecular dynamics simulation (MD) as well as rigid body changes in the position of a protein molecule as a whole. In solution for the average NMR structure of crambin the amplitudes of the backbone atomic fluctuations of the most residues of the segments with the regular backbone conformations are close to the amplitudes of the small scale harmonic vibrations. For the same residues the probability of the medium scale fluctuations fixed by the hydrogen exchange method is very low. The restricted conformational mobility of those segments is coupled with the depressed amplitudes of the fluctuation changes of the tertiary structure registered by the residue accessibility changes in an ensemble of NMR structures that forms the average NMR structure of crambin. The amplitudes of temperature fluctuations of backbone atoms and the tertiary structure raise in the segment with the irregular conformations, turn and loops. In the same segments the amplitudes of the calculated harmonic vibrations also increase, but to a lesser extent and especially in the interhelical loop with the most strong and complicated fluctuation changes of the backbone conformation. In solution for the NMR structure in this loop the conformational transitions occur between the conformational substates separated by the energy barriers, but they are not observed even in the long 100 ns trajectories from the MD simulation of crambin. These strong local fluctuation changes of the structure may play a key role in the protein functioning and modern performance improvements in the MD simulation techniques are oriented to increase the probability of protein appearance in the trajectories from the MD simulations.

[Crystallographic and NMR spectroscopic protein structures: the inter-residue contacts].

Inter-residue pair contacts have been analyzed in detail for the four pairs of protein structures determined both by X-ray analysis (X-ray) and nuclear magnetic resonance (NMR). At contact distances < or = 4.0 angstroms in the four NMR structures the overall number of pair contacts are less by 4-9% and pair contacts are in average shorter by 0.02-0.16 angstroms than those in corresponding X-ray structures. In each of four structure pairs 83-94% of common pair contacts are formed by the same residues in both structures and rest 6-17% ones are longer own pair contacts formed by the different residues in the NMR and X-ray structures. The amount of the longer own contacts is higher in the X-ray structure of the pair. In the each NMR structure there are three types of common pair contacts, which are shorter, longer or equal length in comparison with identical pair contacts in the X-ray structure of the same protein. The methodological different shortened common pair contacts predominate in the known distant dependence of the inter-residue contact densities of the 60-61 pair of the NMR/X-ray structure. Among four pairs analyzed the contact shortening proceeds upon the energy minimization of the crambin NMR structure and upon the resolving by the program X-PLOR with decreased atom van der Waals radius of the NMR structures of ubiquitin, hen lysozyme and monomeric hemoglobin. An extent of the NMR contact shortening decreased as the amount of NMR information upon the calculation of the NMR structures increased. Among 60-61 pairs of NMR/X-ray structures the main difference between alpha-helical and beta-structural proteins on the inter-residue distant dependence of the average contact densities arises from the strong alpha/beta difference in the local backbone geometry.

[Hydrogen exchange and proteolytic degradation of ribonuclease A. The local splitting of the native structure and the conformation of loop segmentes].

The limited proteolytic sites or nicksites are present only in one of the five loops of the RNase A molecule. The splitted loop 15-23 connects two structural domains in the hinge region of the interdomain contacts of the V-shaped molecule. The other four loops are inside two domains, 64-71 and 112-115 in the domain I (1-19, 47-81, 102-106) and 36-42 and 88-95 in the domain II (20-46, 82-101). Because of enhanced chain flexibility of the splitted loop in the pH-dependent conformational isomerization, deformation of its structure is slighter under the influence of the intermolecular contacts in the crystal lattice and more significant changes occur in loop conformation at the formation of the 3D swapped dimer of the RNase A molecule. The proteolytic splitting of the 15-23 loop proceeds due to the local fluctuation of the native protein structure.

[The mechanisms of the proteolytic degradation of native globular proteins. The role of local and global fluctuations of the native structure].

Analysis of the proteolytic degradation of the native protein structure carried out by the comparison of the temperature dependence of the hydrogen exchange and proteolytic splitting rates of the hen egg-white lysozyme and human Hb and apoHb. Acceleration of the burst-like (all or none) proteolytic degradation in the high temperature range is provided by the intensification of the global fluctuations with overall unfolding revealed by hydrogen exchange. For Hb and apoHb the rate of burst-like proteolytic degradation and hydrogen exchange weakly depends on temperature in the range, where hydrogen exchange reveals only local fluctuations of the native protein structure. The splitting of the two proteins proceeds by the selfaccelerated burst-like mechanism with the initial rate-limiting single cleavage owing to the local fluctuation of the native structure. The local fluctuations play important role also upon the intracellular burst-like degradation of native proteins.

[Hydrogen exchange and proteolytic degradation of ribonuclease A. Similarities and distinctions of the kinetic mechanisms].

The studies by IR spectroscopy of the temperature dependence of the H-D exchange rate of the RNase A peptide NH atoms permit one to characterize two types of conformation fluctuations, local and global. A comparison with the temperature dependence of the proteolytic degradation rate of RNase A shows that similar in nature fluctuations allow for the H-D exchange of NH atoms and the splitting of peptide bonds of the native protein. In the low temperature region, both processes occur through local fluctuations, by way of the EX2 mechanism, and in the high temperature region, they occur through global fluctuations with the overall denaturation desorganization of the native structure, by way of the EX1 mechanism. The biphasic dependence of the rate of H-D exchange and proteolytic degradation of RNase A on urea concentration is also explained by the combination of local and global fluctuations.

[Hydrogen exchange and the proteolytic degradation of ribonuclease A. The position of the centers of the high-temperature splitting by proteases and the structure of denatured molecules].

The information on the high-temperature proteolytic degradation of RNase A has been analyzed. It has been shown that a few peptide bonds primarily splitted by trypsin, chymotrypsin and thermolysin are localized only in the N-terminal part of structural domain II of the native molecule. The same peptide bonds are splitted by proteases with the highest rate upon the denaturation in the presense of trifluoroethanol or the renaturation from concentrated urea solutions and after the desorganization of the native structure by the reduction of all four S-S bonds of RNase A. According to the data on hydrogen exchange in the native RNase A molecule, the dynamic stability of the tertiary structure of domain II is lower than that of domain I because of the lesser amount of the internal bulky nonpolar residues Val, Ile, and Phe. For the same reason, this part of the molecule in different nonnative forms of RNase A is less compact and more flexible and is splitted with the highest rate in the segment 31-39 enriched by long cationic residues Lys and Arg. A common feature of the conformation of the flexible disordered backbone of all RNase A nonnative structures considered is the predominance of short PPII helices, which provides a high rate of the restoration of the native secondary and tertiary structures upon renaturation or self-organization and global fluctuations of the native structure revealed by the hydrogen exchange and proteolytic degradation.

[The conformational dynamics of the tetramer hemoglobin molecule as revealed by hydrogen exchange. III. Influence of the heme removal].

Two main types of conformational fluctuations--local and global are characteristic of the native protein structure and revealed by hydrogen exchange. The probability of those fluctuations changes to a different extent upon hemoglobin oxygenation, changing of pH, splitting of the intersubunit contacts. To compare with the influence of the heme removal the rate of the H-D exchange of the peptide NH atoms of the human apoHb was studied at the pH range 5.5-9.0 and temperature 10-38 degrees C by the IR spectroscopy. The removal of the heme increases the rate of the H-D exchange of the 80% peptide NH atoms with the factor retardation of the exchange rate (P) in the range approximately 10(2)-10(8). For the most of the peptide NH atoms the probability of the local fluctuations weakly depends on the temperature, the enthalpy changes upon all such local conformational transitions deltaH(op) degrees are 0-15 kcal/M. Characterized by the stronger temperature dependence the global fluctuations are not arised upon the temperature increases up to 38 degrees C at pH 7.0 inspite of in these conditions the slow denaturation and aggregation of apoHb begin to occur. Upon the destabilization of the apoHb structure by the simultaneous decreasing of pH to 5.5 and temperature to 10 degrees C the global fluctuations of the apoHb native structure described by deltaH(op)o < 0 begin to intensify. The mechanism of the overall intensification of the local fluctuations upon the heme removal, the peculiarity of the heat denaturation of apoHb in conditions, close to that existing upon the selfassembly of Hb in vivo, and analogy between low temperature global fluctuations and cold denaturation of globular proteins are discussed.

[The conformational dynamic of the tetramer hemoglobin molecule as revealed by hydrogen exchange. II. Influence of the intersubunit contact splitting].

The rate of the H-D exchange of the peptide NH atoms of the isolated alpha and beta subunits of human Hb were studied at the pH range 5.5-9.0 and 20 degrees C by the IR spectroscopy. The factor retardation of the exchange rate of subunits -P in the range -10(2)-10(7). In comparison with tetramer Hb the probability of local fluctuations (1/P) is increased to a slightly greater extent for the monomeric alpha subunits then for the tetramer beta subunits. Unlike Hb oxygenation of subunits does not influence on the probability of the local fluctuations and subunits have no the pH-dependent change of the value 1/P observable for the ligand Hb. The possible mechanisms of the overall intensification of the local fluctuations upon the splitting of the Hb tetrameric contacts between subunits are discussed with the inviting of the structural crystallographic data.

[The conformational dynamic of the tetramer hemoglobin molecule as revealed by hydrogen exchange. I. Influence pH, temperature and ligand binding].

The rate of the H-D exchange of the peptide NH atoms of the different forms of human Hb was studied at the range of pH 5-10 and temperature 10-63 degrees C by the IR spectroscopy. The pH-dependence of the H-D exchange rate is accordance with the EX2 mechanism. Two pH-dependent conformers of ligand forms of Hb existes at 10-30 degrees C with lower probability of local fluctuations of the alkaline conformer. The difference between two conformers vanishes at 40 degrees C with the appearance of the third conformer with higher probability of local fluctuations. The deoxyHb at 20 degrees C and pH range 6-9 has no pH-dependent conformers and the probability of local fluctuations is considerably reduced in comparison to the acid conformer of ligand Hb. Upon the destabilization of the ligand Hb structure by the pH decreasing to 5.0 at 20 degrees C or the temperature increasing up to 50-60 degrees C at pH 7.1 the global fluctuations of the native structure are intensified providing the H-D exchange of the slowest exchanging NH atoms. The nature of the local and global fluctuations and possible similarity between the two pH-dependent conformers of ligand Hb and its functional R and R2 states revealed by the X-ray analysis and NMR spectroscopy were discussed.

[Dynamic structure of globular proteins: conformational rigidity and fluctuational motility]. / Dinamicheskaia struktura globuliarnykh belkov: konformatsionnaia zhestkost' i fluktuatsionnaia podvizhnost'.

The data on medium-scale fluctuation of globular proteins revealed by hydrogen exchange, proteolytic degradation and 1H NMR are considered. It is shown that the main features of those conformational transitions including their cooperativity can be described within the model that is based on mobile equilibrium defects of a solid characterized by the integrity of properties of the polymeric monocrystal and the molecular organic crystal. The extent of the fluctuational motility of the protein structure is regulated by strain energy. The functional isomerization of the protein is realized as generalized collective fluctuation induced by destabilization of the structure. The hydration of the backbone may play an important role providing the conformational rigidity of the protein, the extent of hydration being varied upon temperature changes and in the presence of organic co-solvents. Unlike the solid, the liquid-like state of the protein globula is characterized by high fluctuational motility and very narrow distribution of probabilities of medium-scale fluctuations.