Extreme temperature tolerance of a hyperthermophilic protein coupled to residual structure in the unfolded state

Understanding the mechanisms that dictate protein stability is of large relevance, for instance, to enable design of temperature-tolerant enzymes with high enzymatic activity over a broad temperature interval. In an effort to identify such mechanisms, we have performed a detailed comparative study of the folding thermodynamics and kinetics of the ribosomal protein S16 isolated from a mesophilic (S16_meso) and hyperthermophilic (S16_thermo) bacterium by using a variety of biophysical methods. As basis for the study, the 2.0 Å X-ray structure of S16_thermo was solved using single wavelength anomalous dispersion phasing. Thermal unfolding experiments yielded midpoints of 59 and 111 °C with associated changes in heat capacity upon unfolding (ΔC_p⁰) of 6.4 and 3.3 kJ mol^− 1 K^− 1, respectively. A strong linear correlation between ΔC_p⁰ and melting temperature (T_m) was observed for the wild-type proteins and mutated variants, suggesting that these variables are intimately connected. Stopped-flow fluorescence spectroscopy shows that S16_meso folds through an apparent two-state model, whereas S16_thermo folds through a more complex mechanism with a marked curvature in the refolding limb indicating the presence of a folding intermediate. Time-resolved energy transfer between Trp and N-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-yl)methyl iodoacetamide of proteins mutated at selected positions shows that the denatured state ensemble of S16_thermo is more compact relative to S16_meso. Taken together, our results suggest the presence of residual structure in the denatured state ensemble of S16_thermo that appears to account for the large difference in quantified ΔC_p⁰ values and, in turn, parts of the observed extreme thermal stability of S16_thermo. These observations may be of general importance in the design of robust enzymes that are highly active over a wide temperature span.     

Stability and folding kinetics of a ubiquitin mutant with a strong propensity for nonnative beta-hairpin conformation in the unfolded state

A F45W mutant of yeast ubiquitin has been used as a model system to examine the effects of nonnative local interactions on protein folding and stability. Mutating the native TLTGK G-bulged type I turn in the N-terminal beta-hairpin to NPDG stabilizes a nonnative beta-strand alignment in the isolated peptide fragment. However, NMR structural analysis of the native and mutant proteins shows that the NPDG mutant is forced to adopt the native beta-strand alignment and an unfavorable type I NPDG turn. The mutant is significantly less stable (approximately 9 kJ mol(-1)) and folds 30 times slower than the native sequence, demonstrating that local interactions can modulate protein stability and that attainment of a nativelike beta-hairpin conformation in the transition state ensemble is frustrated by the turn mutations. Surprising, alcoholic cosolvents [5-10% (v/v) TFE] are shown to accelerate the folding rate of the NPDG mutant. We conclude, backed-up by NMR data on the peptide fragments, that even though nonnative states in the denatured ensemble are highly populated and their stability further enhanced in the presence of cosolvents, the simultaneous increase in the proportion of nativelike secondary structure (hairpin or helix), in rapid equilibrium with nonnative states, is sufficient to accelerate the folding process. It is evident that modulating local interactions and increasing nonnative secondary structure propensities can change protein stability and folding kinetics. However, nonlocal contacts formed in the global cooperative folding event appear to determine structural specificity.     

Stability and activity of Dictyoglomus thermophilum GH11 xylanase and its disulphide mutant at high pressure and temperature

The functional properties of extremophilic Dictyoglomus thermophilum xylanase (XYNB) and the N-terminal disulphide-bridge mutant (XYNB-DS) were studied at high pressure and temperature. The enzymes were quite stable even at the pressure of 500 MPa at 80 °C. The half-life of inactivation in these conditions was over 30 h. The inactivation at 80 °C in atmospheric pressure was only 3-times slower. The increase of pressure up to 500 MPa at 80 °C decreased only slightly the enzyme's stability, whereas in 500 MPa the increase of temperature from 22 to 80 °C decreased significantly more the enzyme's stability. While the high temperature (80–100 °C) decreased the enzyme reaction with short xylooligosaccharides (xylotetraose and xylotriose), the high pressure (100–300 MPa) had an opposite effect. The temperature of 100 °C strongly increased the K_m but did not affect the k_cat to the same extent, thus indicating that the interaction of the substrate with the active site suffers before the catalytic reaction begins to decrease as the temperature rises. Circular dichroism spectroscopy showed the high structural stability of XYNB and XYNB-DS at 93 °C.     

Stability of proteins: temperature, pressure and the role of the solvent

We focus on the various aspects of the physics related to the stability of proteins. We review the pure thermodynamic aspects of the response of a protein to pressure and temperature variations and discuss the respective stability phase diagram. We relate the experimentally observed shape of this diagram to the low degree of correlation between the fluctuations of enthalpy and volume changes associated with the folding-denaturing transition and draw attention to the fact that one order parameter is not enough to characterize the transition. We discuss in detail microscopic aspects of the various contributions to the free energy gap of proteins and put emphasis on how a cosolvent may either enlarge or diminish this gap. We review briefly the various experimental approaches to measure changes in protein stability induced by cosolvents, denaturants, but also by pressure and temperature. Finally, we discuss in detail our own molecular dynamics simulations on cytochrome c and show what happens under high pressure, how glycerol influences structure and volume fluctuations, and how all this compares with experiments.     

Fatty-acid composition of cells and lipopolysaccharides in different Yersinia species under the conditions of growth at low temperature

Y. pestis, Y. pseudotuberculosis, Y. enterocolitica, Y. frederiksenii, Y. intermedia, Y. kristensenii and Y. ruckeri grown at 4 degrees C were characterized by fatty acid composition with a high content of C16:1 and C18:1, as well as the proportion of saturated to nonsaturated fatty acids equal to, on the average, 2.0. In Yersinia lipopolysaccharides a relatively high level of C16:1 and C12:0 was observed with the prevalence of 3-OH-C14:0. In the fatty-acid spectra of both cells and lipopolysaccharides no essential difference was noted. Thus, during growth at low temperature differences, earlier detected in the studied Yersinia species grown at 37 degrees C and making it possible to divide 7 Yersinia species into 2 groupes, were completely leveled. These results confirmed the close phylogenetic relationship between the Yersinia species under study and were indicative of more pronounced biological community of Yersinia under the conditions of growth at low temperature.     

Characterization of the residual structure in the unfolded state of the Delta131Delta fragment of staphylococcal nuclease

The determination of the conformational preferences in unfolded states of proteins constitutes an important challenge in structural biology. We use inter-residue distances estimated from site-directed spin-labeling NMR experimental measurements as ensemble-averaged restraints in all-atom molecular dynamics simulations to characterise the residual structure of the Delta131Delta fragment of staphylococcal nuclease under physiological conditions. Our findings indicate that Delta131Delta under these conditions shows a tendency to form transiently hydrophobic clusters similar to those present in the native state of wild-type staphylococcal nuclease. Only rarely, however, all these interactions are simultaneously realized to generate conformations with an overall native topology.     

Comparison of measured and predicted residual lung volume in determining body composition of collegiate wrestlers

This investigation compared percent fat obtained via underwater weighing using measured and predicted residual lung volume (RLV) in euhydrated and hypohydrated collegiate wrestlers (N = 67). RLV was measured using O(2) rebreathing or O(2) dilution and predicted using 3 equations-Equation 1: (0.019 x height [cm]) + (0.0115 x age [years]) - 2.24; Equation 2: (0.017 x age [years]) + (0.06858 x height [in.]) - 3.477; and Equation 3: (0.0275 age [years]) + (0.0189 height [cm]) - 2.6139. Percent fat determined using RLV Equation 2 did not differ from the value obtained using measured RLV in the euhydrated (10.9 +/- 5.1 vs. 11.5 +/- 5.6% fat) or hypohydrated (10.8 +/- 5.1 vs. 12.3 +/- 5.6% fat) trials. All other percent fat values differed (p < 0.05) from the value obtained using measured RLV in euhydrated subjects. The use of RLV Equation 2 may be a practical alternative to measured RLV in determining percent fat in euhydrated and hypohydrated collegiate wrestlers.     

不同pH条件下除臭生物滤池微生物种群结构的分子生态分析

采用分子生物学方法研究生物滤池中不同pH环境下的微生物种群的基因多样性,通过扩增细菌16SrRNA基因的V3可变区,结合应用变性梯度凝胶电泳(DGGE)技术分析除臭生物滤池的生物种群的结构变化,并回收主要的DNA片段,采用PCR测序及T载体克隆测序,明确优势菌群的系统发育地位。结果表明,除臭生物滤池在不同的pH条件下,微生物的多样性及其丰度存在较大差别,强酸性对微生物具有较高的选择作用,与中性条件相比,微生物种群多样性相对较低。同时在滤池的不同层次上也表现出明显的空间分布多样性差异,序列比对显示硫氧化细菌在除臭过程中占有优势地位。为更好的处理恶臭气体提供可靠的科学依据,同时也为生物除臭的应用提供一定的理论基础     

Stabilizing roles of residual structure in the empty heme binding pockets and unfolded states of microsomal and mitochondrial apocytochrome b5

The microsomal (Mc) and mitochondrial (OM) isoforms of mammalian cytochrome b5 are the products of different genes, which likely arose via duplication of a primordial gene and subsequent functional divergence. Despite sharing essentially identical folds, heme-polypeptide interactions are stronger in OM b5s than in Mc b5s due to the presence of two conserved patches of hydrophobic amino acid side chains in the OM heme binding pockets. This is of fundamental interest in terms of understanding heme protein structure-function relationships, because stronger heme-polypeptide interactions in OM b5s in comparison to Mc b5s may represent a key source of their more negative reduction potentials. Herein we provide evidence that interactions amongst the amino acid side chains contributing to the hydrophobic patches in rat OM (rOM) b5 persist when heme is removed, rendering the empty heme binding pocket of rOM apo-b5 more compact and less conformationally dynamic than that in bovine Mc (bMc) apo-b5. This may contribute to the stronger heme binding by OM apo-b5 by reducing the entropic penalty associated with polypeptide folding. We also show that when bMc apo-b5 unfolds it adopts a structure that is more compact and contains greater nonrandom secondary structure content than unfolded rOM apo-b5. We propose that a more robust beta-sheet in Mc apo-b5s compensates for the absence of the hydrophobic packing interactions that stabilize the heme binding pocket in OM apo-b5s.     

Modeling the effects of assimilable nitrogen and temperature on fermentation kinetics in enological conditions

We propose a dynamic model of alcoholic fermentation in wine-making conditions. In this model, the speed at which CO(2) is released is related to the effects of the main factors involved in fermentation in wine-making conditions: temperature (which can vary within a predefined range) and nitrogen additions (which must not exceed the maximal authorized level). The resulting model consists of ordinary differential equations including numerous parameters that need to be identified and important interactions between explicative variables. These parameters were identified by uncoupling the effects of variables during specific experiments. The results were validated on another series of experiments in different conditions.     

Influence of the menstrual cycle on the sweating response measured by direct calorimetry in women exposed to warm environmental conditions

The whole body sweating response was measured at rest in eight women during the follicular (F) and the luteal (L) phases of the menstrual cycle. Subjects were exposed for 30-min to neutral (N) environmental conditions [ambient temperature (Ta) 28 degrees C] and then for 90-min to warm (W) environmental conditions (Ta, 35 degrees C) in a direct calorimeter. At the end of the N exposure, tympanic temperature (Tty) was 0.18 (SEM 0.06) degrees C higher in the L than in the F phase (P less than 0.05), whereas mean skin temperature (Tsk) was unchanged. During W exposure, the time to the onset of sweating as well as the concomitant increase in body heat content were similar in both phases. At the onset of sweating, the tympanic threshold temperature (Tty,thresh) was higher in the L phase [37.18 (SEM 0.08) degrees C] than in the F phase [36.95 (SEM 0.07) degrees C; P less than 0.01]. The magnitude of the shift in Tty,thresh [0.23 (SEM 0.07) degrees C] was similar to the L-F difference in Tty observed at the end of the N exposure. The mean skin threshold temperature was not statistically different between the two phases. The slope of the relationship between sweating rate and Tty was similar in F and L. It was concluded that the internal set point temperature of resting women exposed to warm environmental conditions shifted to a higher value during the L phase compared to the F phase of the menstrual cycle; and that the magnitude of the shift corresponded to the difference in internal temperature observed in neutral environmental conditions between the two phases.     

Studies of the unfolding of an unstable mutant of staphylococcal nuclease: Evidence for low temperature unfolding and compactness of the high temperature unfolded state

Fluorescence and circular dichroism data as a function of temperature were obtained to characterize the unfolding of nuclease A and two of its less stable mutants. These spectroscopic data were obtained with a modified instrument that enables the nearly simultaneous detection of both fluorescence and CD data on the same sample. A global analysis of these multiple datasets yielded an excellent fit of a model that includes a change in the heat capacity change, ΔC_p, between the unfolded and native states. This analysis gives a ΔC_p of 2.2 kcal/mol/·K for thermal unfolding of the WT protein and 1.3 and 1.8 kcal/mol/K for the two mutants. These ΔC_p values are consistent with significant population of the cold unfolded state at ∼0°C. Independent evidence for the existence of a cold unfolded state is the observation of a separately migrating peak in size exclusion chromatography. The new chromatographic peak is seen near 0°C, has a partition coefficient corresponding to a larger hydrodynamic radius, and shows a red-shifted fluorescence spectrum, as compared to the native protein. Data also indicate that the high-temperature unfolded form of mutant nuclease is relatively compact. Size exclusion chromatography shows the high temperature unfolded form to have a hydrodynamic radius that is larger than that for the native form, but smaller than that for the urea or pH-induced unfolded forms. Addition of chemical denaturants to the high-temperature unfolded form causes a further unfolding of the protein, as indicated by an increase in the apparent hydrodynamic radius and a decrease in the rotational correlation time for Trp140 (as determined by fluorescence anisotropy decay measurements). Proteins 28:227–240, 1997 © 1997 Wiley-Liss Inc.     

Estimating the energetic contribution of hydrogen bonding to the stability of Candida methylica formate dehydrogenase by using double mutant cycle

An homology model of Candida methylica formate dehydrogenase (cm FDH) was constructed based on the Pseudomonas sp. 101 formate dehydrogenase (ps FDH) structure. In wild type cm FDH, Thr169 and Thr226 can form hydrogen bonds with each other. We measured the interaction energy between the two threonines independent of other interactions in the proteins by using a so-called double mutant cycle and assessing the protein stability from the concentration of guanidine hydrochloride needed to denature 50% of the molecules. We conclude that the hydrogen bonds stabilize the wild type protein by -4 kcal mol(-1).     

Manipulation of temperature and illumination conditions for enhanced beta-carotene production by mutant 32 of Rhodotorula glutinis

AIMS: Enhancement in the production of beta-carotene by the hyper producer mutant 32 of Rhodotorula glutinis by manipulation of temperature and illumination. METHODS AND RESULTS: Growth and beta-carotene production was investigated in a 1 litre fermenter at different temperature and illumination conditions. The optimum temperature for growth and beta-carotene production was 30 and 20 degrees C, respectively. At 30 degrees C, beta-carotene production was 125 +/- 2 mg l-1 and accounted for 66% of the total carotenoids in 72 h; at 20 degrees C, it was 250 +/- 7 mg l-1 and accounted for 92% of total carotenoid content. Continuous illumination of the fermenter by 1000 lx white light hampered growth as well as carotenoid synthesis. At 30 degrees C, illuminating the fermenter in late logarithmic phase resulted in a 58% increase in beta-carotene production with a concurrent decrease in torulene; at 20 degrees C, however, it showed no appreciable increase. SIGNIFICANCE AND IMPACT OF THE STUDY: Proper manipulation of culture conditions enhanced beta-carotene production by R. glutinis which makes it a significant source of beta-carotene.     

Structural analysis and prediction of protein mutant stability using distance and torsion potentials: role of secondary structure and solvent accessibility

Platelet-activating factor receptor (PAFR) is a member of G-protein coupled receptor (GPCR) superfamily. Understanding the regulation mechanisms of PAFR by its agonists and antagonists at the atomic level is essential for designing PAFR antagonists as drug candidates for treating PAF-mediated diseases. In this study, a 3D model of PAFR was constructed by a hierarchical approach integrating homology modeling, molecular docking and molecular dynamics (MD) simulations. Based on the 3D model, regulation mechanisms of PAFR by agonists and antagonists were investigated via three 8-ns MD simulations on the systems of apo-PAFR, PAFR-PAF and PAFR-GB. The simulations revealed that binding of PAF to PAFR triggers the straightening process of the kinked helix VI, leading to its activated state. In contrast, binding of GB to PAFR locks PAFR in its inactive state.     

Effects of solvent viscosity and different guanidine salts on the kinetics of ribonuclease A chain folding

The kinetics of folding of the two forms of unfolded ribonuclease A have been measured as a function of solvent viscosity by adding either glycerol or sucrose. The aim is to find out if either reaction is rate limited by segmental motion whose rate depends on external friction. The fast folding reaction (U₂ ? N) is known to be the direct folding process, and the slow folding reaction (U₁ ? N) is known to be rate limited by an interconversion between two forms (U₁ ? U₂) which are present after unfolding in strongly denaturing conditions. No dependence on solvent viscosity is found, either for the direct folding reaction or for the interconversion reaction. Each folding reaction has also been tested to see if its rate depends on the concentration of one or more partly folded intermediates, by adding denaturants destabilize any partly folded structures. Different guanidine salts are used as denaturants to vary the denaturing effectiveness of the salt while holding the guanidinium ion concentration constant. The rates both of the direct folding reaction and of the interconversion reaction decrease in relation to the denaturing effectiveness of the salt. However, there is a basic difference between the responses of the fast and slow folding reactions to low concentrations of denaturants. Although each folding reaction produces native protein, there is an 800-fold decrease in the rate of the fast folding reaction in 1M guanidine thiocyanate and only a 13-fold decrease in the rate of the slow folding reaction. This is consistent with the fast reaction being the direct folding process and the slow reaction being rate limited by the initial conversion of the slowrefolding to the fast-refolding form. Both the lack of viscosity dependence and the effects of denaturants indicate that the formation of structure is rate limiting in the direct folding reaction, U₂ ? N. The failure to find a viscosity dependence for the interconversion reaction, U₁ ? U₂, indicates that in this reaction also friction-limited segmental motion is not the rate-limiting process. Since the U₁ ? U₂ interconversion still occurs when the polypeptide chain is completely unfolded, the surprising result is that its rate in refolding conditions depends significantly on a reaction intermediate which is “denatured” by guanidine salts.     

Lipid composition in leaves of cucumber genotypes as affected by different temperature regimes and grafting

The lipid composition of leaves has been investigated in different genotypes of cucumber ( Cucumis sativus L.), which differ in temperature requirement for cultivation. In addition the effects of hardening by low but non-chilling temperature, soil heating and grafting (on the chilling-resistant C. ficifolia L.) on lipid composition have been studied. Content and composition of phospholipids and sterols were determined as well as phospholipid/sterol ratio, and fatty acid composition of total lipids and the different phospholipids.
The effects of genetic differentiation and of the various culture treatments on lipid composition of the leaves were very different. Genetic differentiation was evident as higher levels of Iinolenic acid in several phospholipids in the more cold-tolerant cultivars. Hardening the plants by low temperature resulted in a higher phospholipid level (especially phosphatidyl choline), more unsaturated phospholipid, and lowering of the sterol/phiospholipid ratio, all properties which may contribute to a higher membrane fluidity and lower growth temperature limit. Soil healing reduced the phospholipid level of the leaves slightly, and a higher content of 3- trans -hexadece-noic acid in phosphatidyl glycerol was observed. Grafting cucumber on the cold-resistant rootstock of C. ficifolia also raised the level of trans -hexadecenoic acid in phosphatidyl glycerol. The role of this fatty acid in the functioning of the chloroplast is discussed.     

A residual structure in unfolded intestinal fatty acid binding protein consists of amino acids that are neighbors in the native state

Much of the recent effort in protein folding has focused on the possibility that residual structures in the unfolded state may provide an initiating site for protein folding. This hypothesis is difficult to test because of the weak stability and dynamic behavior of these structures. This problem has been simplified for intestinal fatty acid binding protein (IFABP) by incorporating fluorinated aromatic amino acids during synthesis in Escherichia coli. Only the labeled residues give signals by (19)F NMR, and the 1D spectra can be assigned in both the native and unfolded states by site-directed mutagenesis. One of the two tryptophans (W82), one of the four tyrosines (Y70), and at least four of the eight phenylalanines (including F68 and F93) of IFABP are involved in a structure that is significantly populated at concentrations of urea that unfold the native structure by fluorescence and CD criteria. These residues are nonlocal in sequence and also contact each other in the native structure. Thus, a template of nativelike hydrophobic contacts in the unfolded state may serve as an initiating site for folding this beta-sheet protein.