Effect of heavy water on the viability of bacteria

Influence of heavy water (D2O) on the membrane energization, the efflux of hydrogen ions and the respiration of bacteria E. coli M-17 was studied. As has been shown, heavy water of a low concentration (0.05-0.20% v/v) activates and of a high concentration (above 10%) inhibits the absorption of lipophilic cation tetraphenylphosphonium (TPP+) and of oxygen by cells. The return of these characteristics to the initial levels after the removal of D2O points to a reversible action of D2O. A protective effect of D2O towards membrane energization and rate of respiration on dried cells was observed. This fact is in agreement with the data on viability of bacteria. The indicated protective action increases at the stage of rehydration in the presence of D2O.     

Effect of heavy water on metabolism of a symbiotic organism

The metabolism of the symbiotic organism medusomycete (tea fungus) and the influence of D2O on its development was studied by high-resolution NMR methods using isotopically enriched (by 13C and 2H) metabolites. The results demonstrate that D2O influences the selective utilization of certain protonated substrates during the formation of triose phosphates. It was found that protonated isotopomers derived from the first glucose fragment C1-C2-C3 are predominantly utilized. This explains why the metabolism slows down by a factor of 2 to 3 if D2O concentration in the medium increases. It was also shown that approximately 10% of the organisms are in the state of dynamic extracellular endosymbiosis. This state is characterized by the ability to exchange the metabolic products through close intercellular contacts. As a result of the metabolic exchange, a multicellular organism is formed, with metabolic elements localized in different partners. A distinguishing feature of this organism is the ability to accumulate the internal resources of carbon, thus making it better adapted to the unfavorable environment.     

Reaction pattern of Photosystem II: oxidative water cleavage and protein flexibility

This short communication addresses three topics of photosynthetic water cleavage in Photosystem II (PS II): (a) effect of protonation in the acidic range on the extent of the ‘fast’ ns kinetics of P680^+· reduction by Y_Z, (b) mechanism of O–O bond formation and (c) role of protein flexibility in the functional integrity of PS II. Based on measurements of light-induced absorption changes and quasielastic neutron scattering in combination with mechanistic considerations, evidence is presented for the protein acting as a functionally active constituent of the water cleavage machinery, in particular, for directed local proton transfer. A specific flexibility emerging above a threshold of about 230 K is an indispensable prerequisite for oxygen evolution and plastoquinol formation.     

Effect of heavy metals on tissue protein of an edible fish Cirrhinus mrigala as dependent on pH and water hardness

The goal of the study was to investigate the influence of nickel and chromium at different pH and water hardness on the protein content of muscle tissues of Cirrhinus mrigala fingerlings by Fourier transform infrared spectroscopy. FTIR spectra revealed significant differences in absorbance intensities between control and metal-exposed muscle tissues, reflecting a change in protein content and state caused by heavy metal toxicity; metal accumulation in tissue was markedly increased at alkaline pH and to a lesser extent in hard water.     

Evolutionary flexibility of protein complexes

Background  

Proteins play a key role in cellular life. They do not act alone but are organised in complexes. Throughout the life of a cell, complexes are dynamic in their composition due to attachments and shared components. Experimental and computational evidence indicate that consecutive addition and secondary losses of components played a major role in the evolution of some complexes, mostly without affecting the core function. Here, we analysed in a large scale approach whether this flexibility in evolution is only limited to a distinct number of complexes or represents a more general trend.     

Accuracy of protein flexibility predictions

Protein structural flexibility is important for catalysis, binding, and allostery. Flexibility has been predicted from amino acid sequence with a sliding window averaging technique and applied primarily to epitope search. New prediction parameters were derived from 92 refined protein structures in an unbiased selection of the Protein Data Bank by developing further the method of Karplus and Schulz (Naturwissenschaften 72:212–213, 1985). The accuracy of four flexibility prediction techniques was studied by comparing atomic temperature factors of known three-dimensional protein structures to predictions by using correlation coefficients. The size of the prediction window was optimized for each method. Predictions made with our new parameters, using an optimized window size of 9 residues in the prediction window, were giving the best results. The difference from another previously used technique was small, whereas two other methods were much poorer. Applicability of the predictions was also tested by searching for known epitopes from amino acid sequences. The best techniques predicted correctly 20 of 31 continuous epitopes in seven proteins. Flexibility parameters have previously been used for calculating protein average flexibility indices which are inversely correlated to protein stability. Indices with the new parameters showed better correlation to protein stability than those used previously; furthermore they had relationship even when the old parameters failed. © 1994 Wiley-Liss, Inc.     

The impact of protein flexibility on protein-protein docking

Accounting for protein flexibility in protein-protein docking algorithms is challenging, and most algorithms therefore treat proteins as rigid bodies or permit side-chain motion only. While the consequences are obvious when there are large conformational changes upon binding, the situation is less clear for the modest conformational changes that occur upon formation of most protein-protein complexes. We have therefore studied the impact of local protein flexibility on protein-protein association by means of rigid body and torsion angle dynamics simulation. The binding of barnase and barstar was chosen as a model system for this study, because the complexation of these 2 proteins is well-characterized experimentally, and the conformational changes accompanying binding are modest. On the side-chain level, we show that the orientation of particular residues at the interface (so-called hotspot residues) have a crucial influence on the way contacts are established during docking from short protein separations of approximately 5 A. However, side-chain torsion angle dynamics simulations did not result in satisfactory docking of the proteins when using the unbound protein structures. This can be explained by our observations that, on the backbone level, even small (2 A) local loop deformations affect the dynamics of contact formation upon docking. Complementary shape-based docking calculations confirm this result, which indicates that both side-chain and backbone levels of flexibility influence short-range protein-protein association and should be treated simultaneously for atomic-detail computational docking of proteins.     

NMR: prediction of protein flexibility

We present a protocol for predicting protein flexibility from NMR chemical shifts. The protocol consists of (i) ensuring that the chemical shift assignments are correctly referenced or, if not, performing a reference correction using information derived from the chemical shift index, (ii) calculating the random coil index (RCI), and (iii) predicting the expected root mean square fluctuations (RMSFs) and order parameters (S2) of the protein from the RCI. The key advantages of this protocol over existing methods for studying protein dynamics are that (i) it does not require prior knowledge of a protein's tertiary structure, (ii) it is not sensitive to the protein's overall tumbling and (iii) it does not require additional NMR measurements beyond the standard experiments for backbone assignments. When chemical shift assignments are available, protein flexibility parameters, such as S2 and RMSF, can be calculated within 1-2 h using a spreadsheet program.     

Effect of heavy metals on nitrate and protein metabolism in sugar beet

Nitrate content, activities of nitrate reductase and glutamine synthetase, soluble protein content, and proportion of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPCO) protein in total proteins were measured in leaves of Beta vulgaris L. plants affected by nickel, cadmium, and molybdenum in concentrations of 10^-4, 10^-2, and 1 mM. The most harmful effect on the above mentioned parameters had Cd, less harmful Ni, whereas Mo stimulated the investigated parameters. The proportion of RuBPCO protein showed a high tolerance to heavy metals. This revised version was published online in July 2006 with corrections to the Cover Date.     

Relationship of protein flexibility to thermostability

Thermostability of proteins arises from the simultaneous effect of several forces, which in fact lead to decreased flexibility of the polypeptide chain. This is verified by flexibility indices, which are derived from normalized B-values of individual amino acids in several refined three-dimensional structures. Flexibility indices show that overall flexibility is reduced when thermostability is increased. Protein molecules require both flexibility and rigidity to function, but the higher the temperature optimum and stability the more rigid is the structure needed to compensate for increased thermal fluctuations. Flexibilities of proteins performing the same catalytic activity seem to be about the same at their temperature optima, but the more rigid thermostable proteins reach the flexibility of thermolabile proteins at higher temperatures. In several proteins such as allosteric enzymes, some local sites of flexibility are highly conserved. The relevance of reduced flexibility to overall stability of proteins is also discussed. Flexibility indices and profiles can be used in the design of more stable proteins by site-directed mutagenesis.     

Effect of heavy water on the germination of a number of species of seeds

Summary The effect of deuteriation on the germination rate of seeds is studied as a possible screening technique prior to the cultivation of a plant in high concentrations of D₂O. There appears to be a simple relationship between size of the seed and germination capacity in high deuterium concentrations. Larger seeds may be more successful in germinating because of greater hydrogen-containg food reserves.     

Continuum secondary structure captures protein flexibility

The DSSP program assigns protein secondary structure to one of eight states. This discrete assignment cannot describe the continuum of thermal fluctuations. Hence, a continuous assignment is proposed. Technically, the continuum results from averaging over ten discrete DSSP assignments with different hydrogen bond thresholds. The final continuous assignment for a single NMR model successfully reflected the structural variations observed between all NMR models in the ensemble. The structural variations between NMR models were verified to correlate with thermal motion; these variations were captured by the continuous assignments. Because the continuous assignment reproduces the structural variation between many NMR models from one single model, functionally important variation can be extracted from a single X-ray structure. Thus, continuous assignments of secondary structure may affect future protein structure analysis, comparison, and prediction.     

模拟海拔3600m低氧环境对人的认知灵活性的影响

目的：探讨模拟高原低氧环境对人认知灵活性的影响。方法：低氧舱模拟海拔3600m低氧环境,采用任务转换范式观察低氧模拟各阶段的认知灵活性,同时监测焦虑状态及基本生理指标的变化。23名无高原生活经验、平均年龄25．1岁的男性受试者参加了实验。结果：与低氧暴露1个月后的基础对照相比,低氧阶段的反应时转换损失显著增加;低氧阶段焦虑水平显著高于适应阶段;在适应阶段,焦虑水平与反应时转换损失显著负相关;而在降舱阶段,焦虑水平与反应时转换损失显著正相关。结论：中度低氧暴露影响人的认知灵活性和焦虑状态;低氧暴露前,焦虑可促进个体的认知灵活性;低氧暴露后,焦虑会阻碍个体的认知灵活性。     

Increased flexibility decreases antifreeze protein activity

Antifreeze proteins protect several cold-blooded organisms from subzero environments by preventing death from freezing. The Type I antifreeze protein (AFP) isoform from Pseudopleuronectes americanus, named HPLC6, is a 37-residue protein that is a single α-helix. Mutational analysis of the protein showed that its alanine-rich face is important for binding to and inhibiting the growth of macromolecular ice. Almost all structural studies of HPLC6 involve the use of chemically synthesized protein as it requires a native N-terminal aspartate and an amidated C-terminus for full activity. Here, we examine the role of C-terminal amide and C-terminal arginine side chain in the activity, structure, and dynamics of nonamidated Arg37 HPLC6, nonamidated HPLC6 Ala37, amidated HPLC6 Ala37, and fully native HPLC6 using a recombinant bacterial system. The thermal hysteresis (TH) activities of the nonamidated mutants are 35% lower compared with amidated proteins, but analysis of the NMR data and circular dichroism spectra shows that they are all still α-helical. Relaxation data from the two nonamidated mutants indicate that the C-terminal residues are considerably more flexible than the rest of the protein because of the loss of the amide group, whereas the amidated Ala37 mutant has a C-terminus that is as rigid as the wild-type protein and has high TH activity. We propose that an increase in flexibility of the AFP causes it to lose activity because its dynamic nature prevents it from binding strongly to the ice surface.     

Hierarchical and multi-resolution representation of protein flexibility

MOTIVATION: Conformational rearrangements during molecular interactions are observed in a wide range of biological systems. However, computational methods that aim at simulating and predicting molecular interactions are still largely ignoring the flexible nature of biological macromolecules as the number of degrees of freedom is computationally intractable when using brute force representations. RESULTS: In this article, we present a computational data structure called the Flexibility Tree (FT) that enables a multi-resolution and hierarchical encoding of molecular flexibility. This tree-like data structure allows the encoding of relatively small, yet complex sub-spaces of a protein's conformational space. These conformational sub-spaces are parameterized by a small number of variables and can be searched efficiently using standard global search techniques. The FT structure makes it straightforward to combine and nest a wide variety of motion types such as hinge, shear, twist, screw, rotameric side chains, normal modes and essential dynamics. Moreover, the ability to assign shapes to the nodes in a FT allows the interactive manipulation of flexible protein shapes and the interactive visualization of the impact of conformational changes on the protein's overall shape. We describe the design of the FT and illustrate the construction of such trees to hierarchically combine motion information obtained from a variety of sources ranging from experiment to user intuition, and describing conformational changes at different biological scales. We show that the combination of various types of motion helps refine the encoded conformational sub-spaces to include experimentally determined structures, and we demonstrate searching these sub-spaces for specific conformations.