Structural adaptation of the subunit interface of oligomeric thermophilic and hyperthermophilic enzymes

Enzymes from thermophilic and, particularly, from hyperthermophilic organisms are surprisingly stable. Understanding of the molecular origin of protein thermostability and thermoactivity attracted the interest of many scientist both for the perspective comprehension of the principles of protein structure and for the possible biotechnological applications through application of protein engineering. Comparative studies at sequence and structure levels were aimed at detecting significant differences of structural parameters related to protein stability between thermophilic and hyperhermophilic structures and their mesophilic homologs. Comparative studies were useful in the identification of a few recurrent themes which the evolution utilized in different combinations in different protein families. These studies were mostly carried out at the monomer level. However, maintenance of a proper quaternary structure is an essential prerequisite for a functional macromolecule. At the environmental temperatures experienced typically by hyper- and thermophiles, the subunit interactions mediated by the interface must be sufficiently stable. Our analysis was therefore aimed at the identification of the molecular strategies adopted by evolution to enhance interface thermostability of oligomeric enzymes. The variation of several structural properties related to protein stability were tested at the subunit interfaces of thermophilic and hyperthermophilic oligomers. The differences of the interface structural features observed between the hyperthermophilic and thermophilic enzymes were compared with the differences of the same properties calculated from pairwise comparisons of oligomeric mesophilic proteins contained in a reference dataset. The significance of the observed differences of structural properties was measured by a t-test. Ion pairs and hydrogen bonds do not vary significantly while hydrophobic contact area increases specially in hyperthermophilic interfaces. Interface compactness also appears to increase in the hyperthermophilic proteins. Variations of amino acid composition at the interfaces reflects the variation of the interface properties.     

Thermostability of salt bridges versus hydrophobic interactions in proteins probed by statistical potentials

The temperature dependence of the interactions that stabilize protein structures is a long-standing issue, the elucidation of which would enable the prediction and the rational modification of the thermostability of a target protein. It is tackled here by deriving distance-dependent amino acid pair potentials from four datasets of proteins with increasing melting temperatures (Tm). The temperature dependence of the interactions is determined from the differences in the shape of the potentials derived from the four datasets. Note that, here, we use an unusual dataset definition, which is based on the Tm values, rather than on the living temperature of the host organisms. Our results show that the stabilizing weight of hydrophobic interactions (between Ile, Leu, and Val) remains constant as the temperature increases, compared to the other interactions. In contrast, the two minima of the Arg--Glu and Arg--Asp salt bridge potentials show a significant Tm dependence. These two minima correspond to two geometries: the fork--fork geometry, where the side chains point toward each other, and the fork--stick geometry, which involves the N(epsilon) side chain atom of Arg. These two types of salt bridges were determined to be significantly more stabilizing at high temperature. Moreover, a preference for more-compact salt bridges is noticeable in heat-resistant proteins, especially for the fork--fork geometry. The Tm-dependent potentials that have been defined here should be useful for predicting thermal stability changes upon mutation.     

The archaeal Sac10b protein family: conserved proteins with divergent functions

Here we review the present state of structural and functional studies of the Sac10b protein family, a class of highly conserved 10 kDa nucleic acid-binding proteins in archaea. Based on biochemical and structural studies, these proteins were originally assigned a role in the structural organization of chromatin; Sac10b proteins of hyperthermophilic archaea, for example, showed tight, unspecific DNA binding. More recently, however, Sac10b proteins of mesophilic archaea were found to interact preferentially with specific DNA sequences thereby affecting the expression of distinct genes. Furthermore, Sac10b proteins of hyperthermophilic, thermophilic and mesophilic archaea were also shown to bind to RNA with distinct affinities and specificities but functional consequences of RNA binding of these proteins, besides perhaps RNA stabilization, have not yet been observed. To better understand the physiological meaning of the various interactions of Sac10b proteins with nucleic acids, future work should concentrate on elucidating the molecular structures of complexes of Sac10b proteins of hyperthermophilic and mesophilic archaea with DNA and RNA. In addition, existing and new X-ray and NMR structures of individual hyperthermophilic Sac10b proteins may represent very good models for introducing thermostability especially in enzymes for industrial use.     

Is there a unique melting temperature for two-state proteins?

Thermal unfolding (or folding) in many proteins occurs in an apparent two-state manner, suggesting that only two states, unfolded and folded, are populated. At the melting temperature, Tm, the two states coexist. Using lattice models with side chains we show that individual residues become structured at temperatures that deviate from Tm, which implies that partially folded conformations make substantial contribution to thermodynamic properties of two-state proteins. We also find that the folding cooperativity for a given residue is linked to its accessible surface area. These results are consistent with the experiments on GCN4-like zipper peptide, which showed that local melting temperatures differ from Tm. Analysis of thermal unfolding of six proteins shows that deltaT/Tm approximately N(-1), where deltaT is the transition width and N is the number of residues. This scaling allows us to conclude that, when corrected for finite size effects, folding cooperativity can be captured using coarse grained models.     

The chaperonin of the archaeonSulfolobus solfataricus

The chaperonin of the hyperthermophilic archaeonSulfolobus solfataricus, briefly Ssocpn, was purified by a fast and high-yield procedure. Ssocpn, a 920 kDa-complex of two different subunits, displays a potassium-dependent ATPase activity with a temperature optimum at 80°C. The ability of Ssocpn to function in vitro was investigated using different protein substrates. Ssocpn promotes correct refolding of thermophilic and mesophilic enzymes from their chemically unfolded state; moreover, Ssocpn prevents the irreversible inactivation of native proteins by suppressing their precipitation upon heating. Both the activity in assisting refolding of unfolded proteins and that in preventing heat denaturation of native proteins require the hydrolysis of ATP. The chaperone-based strategies in different technological fields are discussed, and the advantages in using archaeal chaperonins are underlined.     

Is there a relationship between protein thermal stability and the denaturation heat capacity change?

It is shown the non-occurrence of a correlation between the values of the denaturation temperature and those of the denaturation heat capacity change for a set of 13 proteins possessing the ‘SH3-type’ fold from both mesophilic and thermophilic microorganisms. This seems to be a rather general result, because, fixed the size and the folding pattern, the denaturation heat capacity change is a nearly constant quantity, within the uncertainty limits of experimental determinations, regardless of the thermal stability of the protein. A precise definition of the thermodynamics of the hydrophobic effect is presented to clarify that the above finding does not imply that the hydrophobic effect does not play a role in the extra-thermal stability of thermophilic and hyperthermophilic proteins.     

Enantiomeric resolution of 2-aryl propionic esters with hyperthermophilic and mesophilic esterases: contrasting thermodynamic mechanisms

The enantiomeric resolution of 2-aryl propionic esters by hyperthermophilic and mesophilic esterases was found to be governed by contrasting thermodynamic mechanisms. Entropic contributions predominated for mesophilic esterases from Candida rugosa and Rhizomucor miehei, while enthalpic forces controlled this resolution by the esterase from the extremely thermoacidophilic archaeon, Sulfolobus solfataricus P1. This disparity in thermodynamic mechanism can be attributed to the differences in conformational flexibility of mesophilic and thermophilic enzymes as they relate to the temperature range (4-70 degrees C) examined.     

Thermophile-specific proteins: the gene product of <Emphasis Type="Italic">aq_1292</Emphasis> from <Emphasis Type="Italic">Aquifex aeolicus</Emphasis> is an NTPase

Background  

To identify thermophile-specific proteins, we performed phylogenetic patterns searches of 66 completely sequenced microbial genomes. This analysis revealed a cluster of orthologous groups (COG1618) which contains a protein from every thermophile and no sequence from 52 out of 53 mesophilic genomes. Thus, COG1618 proteins belong to the group of thermophile-specific proteins (THEPs) and therefore we here designate COG1618 proteins as THEP1s. Since no THEP1 had been analyzed biochemically thus far, we characterized the gene product of aq_1292 which is THEP1 from the hyperthermophilic bacterium Aquifex aeolicus (aaTHEP1).     

Isolation,Purification, and Properties of a Novel Small Heat Shock Protein from the Hyperthermophile <Emphasis Type="Italic">Sulfolobus solfataricus</Emphasis>

The isolation, purification, and properties of a putative small heat shock protein (sHsp), named SsHSP14.1, from the hyperthermophilic archaeon Sulfolobus solfataricus have been investigated. The sHsp was successfully expressed and purified from Escherichia coli. In vivo chaperone function of SsHSP14.1 for preventing aggregation of proteins during heating was investigated. It was found that recombinant SsHSP14.1 with a molecular mass of 17.8 kDa prevented E. coli proteins from aggregating in vivo at 50 °C. This result suggested that SsHSP14.1 confers a survival advantage on mesophilic bacteria by preventing protein aggregation at supraoptimal temperatures. In vitro, the purified SsHSP14.1 protein was able to prevent Candida antarctica lipase B from aggregation for up to 60 min at 80 °C. Moreover, the SsHSP14.1 enhanced thermostability of bromelain extending its half-life at 55 °C by 67%.     

Melting and Annealing Peak Temperatures of Poly(butylene succinate) on the Same Hoffman-Weeks Plot Parallel to Tm=Tc Line

The crystallization and melting behavior of polymers is of theoretical importance. In this work, poly(butylene succinate)(PBS) was selected as an example to study such behavior at low supercooling via introduction of the extended-chain crystal(ECC) of the same polymer as nucleating agent. The crystallization of PBS with its ECC as nucleating agent in a wide temperature range(90–127 °C) and the following melting behavior were studied. It is revealed that the melting point(T_m, for T_c≥113 °C) and the annealing peak temperature(T_a, for T_c=90–100 °C) show similar asymptotic behavior. Both T_m and T_a approach to a value of ca. 3.3 °C higher than the corresponding T_c when the crystallization time tc approaches the starting point. That is to say, the Hoffman-Weeks plot is parallel to T_m=T_c line. The crystallization line became parallel to the melting line when PBS was crystallized at T_c higher than 102 °C. Based on these results, we propose that the parallel relationship and the intrinsic similarity between the T_a and the T_m observed at the two ends of the T_c range could be attributed to the metastable crystals formed at the beginning of crystallization.     

Melting Temperature of Individual Electrospun Poly(vinylidene fluoride) Fibers Studied by AFM-based Local Thermal Analysis

Thermal properties such as melting temperature can well reflect the microstructure of the polymer material, and have practical implications in the application of nanofibers. In this work, we investigated the melting temperature of individual electrospun poly(vinylidene fluoride)(PVDF) nanofibers with diameters ranging from smaller than 200 nm to greater than 2 μm by the local thermal analysis technique. The PVDF fibers obtained under four different conditions were found to crystallize into α and β phases, and the fiber mats showed typical values in the crystallinity and T_m with no significant difference among the four. However, analyses at single fiber level revealed broad distribution in diameter and T_m for the fibers produced under identical electrospinning condition. The T_m of individual nanofibers was found to remain constant at large diameters and increase quickly when reducing the fiber diameter toward the nanoscale, and T_m values of 220-230 ℃ were observed for the thinnest nanofibers, much higher than the typical values reported for bulk PVDF. The T_m and molecular orientation at different positions along a beaded fiber were analyzed, showing a similar distribution pattern with a minimum at the bead center and higher values when moving toward both directions. The results indicate that molecular orientation is the driving mechanism for the observed correlation between the T_m and the diameter of the nanofibers.     

聚醚醚酮酮（PEEKK）－含联苯聚醚醚酮酮（PEBEKK）共聚物的T_g和T_m转变

不同联苯含量的ＰＥＥＫＫ－ＰＥＢＥＫＫ共聚物的ＤＳＣ结果表明，随着联苯含量的增加，共聚物的玻璃化转变温度几逐渐升高；共聚物的熔点Ｔｍ明显地依赖于联苯含量，当联苯含量ｎＢ＝０．３５时，Ｔｍ值最４小。热处理可以显著地改善共聚物的结晶性，并出现熔融重结晶双峰。     

含间苯基聚芳醚酮的合成与性能研究

含间苯基聚芳醚酮的合成与性能研究林权，张万金，吴忠文，尹玖梅（吉林大学化学系，长春，１３００２１）（中国科学院长春应用化学研究所）关键词聚芳醚酮，间苯基，熔点，结晶度聚芳醚酮作为一类耐高温特种工程塑料，由于具有优异的热、电、机械性能，已被广泛应用于电...     

O2 penetration and proton burial depth in proteins: applicability to fold family recognition

Paramagnetically induced relaxation effects of O2 and the nitroxide 4-hydroxy TEMPO were measured for the amide protons of perdeuterated rubredoxin from the hyperthermophilic archaeon Pyrococcus furiosus and the mesophilic bacterium Clostridium pasteurianum. For both O2 and the impermeant nitroxide, the induced relaxation at the static solvent inaccessible amide sites is dominated by long-range interactions with the paramagnetic species in the bulk aqueous phase. The upper bound of O2 solubility in the internal matrix of the rubredoxins is one-tenth that of the bulk aqueous phase. Furthermore, the difference between the oxygen solubilities inside the two rubredoxins is at most 1% that of bulk water O2 solubility, suggesting that there are only modest differences in this measure of fluidity for the mesophile vs hyperthermophile protein interiors. Calculations based on the assumption of a paramagnet uniformly distributed on the protein exterior yield accurate predictions at nearly all amide sites for the minimum relaxation value observed from either the O2 or nitroxide data. Model calculations indicate that the readily obtained paramagnetically induced relaxation effects should prove effective in recognition of structural homology for proteins that are too widely diverged for sequence-based recognition.     

Optimized measurement temperature gives access to the solution structure of a 49 kDa homohexameric β-propeller

Ph1500 is a homohexameric, two-domain protein of unknown function from the hyperthermophilic archaeon Pyrococcus horikoshii. The C-terminal hexamerization domain (Ph1500C) is of particular interest, as it lacks sequence homology to proteins of known structure. However, it resisted crystallization for X-ray analysis, and proteins of this size (49 kDa) present a considerable challenge to NMR structure determination in solution. We solved the high-resolution structure of Ph1500C, exploiting the hyperthermophilic nature of the protein to minimize unfavorable relaxation properties by high-temperature measurement. Thus, the side chain assignment (97%) and structure determination became possible at full proton density. To our knowledge, Ph1500C is the largest protein for which this has been achieved. To minimize detrimental fast water exchange of amide protons at increased temperature, we employed a strategy where the temperature was optimized separately for backbone and side chain experiments.     

Metastability release of the form alpha of trehalose by isothermal solid state vitrification

Kinetic investigations of the polymorphic form alpha of anhydrous trehalose have been performed below its apparent melting temperature (Tm) by differential scanning calorimetry (DSC) and X-ray diffraction. The results reveal a spontaneous isothermal vitrification process which indicates that the phase alpha is in a very unusual superheating situation. This behavior has been attributed to the fact that the effective melting temperature (Tm(eff)) of the phase alpha is likely to be located far below the glass transition temperature (Tg) of this compound. The high viscosity of the liquid trehalose between Tm(eff) and Tg is thus invoked to explain the long lifetime of the phase alpha in this temperature range.     

Enzymatic synthesis of 2-deoxy-β-glucosides and stereochemistry of β-glycosidase from Sulfolobus solfataricus on glucal

The hyperthermophilic member of family 1 of the glycosyl hydrolases, the β-glycosidase from the archaeon Sulfolobus solfataricus (Ssβ-gly), has been used for an efficient synthesis of β-2-deoxyglucosides and for stereochemical studies of the reactions of glucal in the presence of alkyl and pyranosidic acceptors. Protonation of the double bond of glucal resulting in the equatorially disposed proton was observed and an indication of the protonating amino acid in the active site was obtained by the use of a mutant enzyme. The regioselectivity in the formation of β-2-deoxyglucosides of pyranosidic acceptors is different from that reported for mesophilic biocatalysts.     

Thermal and optical properties of Tm3+ doped tellurite glasses

Ultraviolet, visible (UV/VIS) and differential thermal analysis (DTA) measurements were carried out in order to investigate the optical and thermal properties of various 0.5 mol.% Tm2O3 containing (1 - x)TeO2 + xLiCl glasses in molar ratio. The samples were prepared by fusing the mixture of their respective reagent grade powders in a platinum cricuble at 750 degrees C for 30 min. DTA curves taken in the 23-600 degrees C temperature range with a heating rate of 10 degrees C/min reveal a change in the value of the glass transition temperature, Tg, while melting was not observed for the glasses containing LiCl content less than 50 mol.%. These glasses were found to be moisture-resistant. However, the glasses with LiCl content higher than 50 mol.%, in which a melting peak was observed at Tc = 401 degrees C, were moisture-sensitive. Absorption measurements in the UV/VIS region of the glasses without Tm2O3 content show that the Urbach cutoff occurs at about 320 nm and, is relatively independent of the LiCl content. Six absorption bands were observed in the Tm2O3 doped glasses corresponding to the absorption of the 1G4, 3F2, 3F3 and 3F4, 3H5 and 3H4 levels from the 3H6 ground level of Tm3+ ions. The spectra also show that the integrated absorption cross-section of each band depends on the glass composition. Judd-Ofelt theory was used to determine the Judd-Ofelt parameters as well as the radiative transition probabilities for the metastable levels of Tm3+ ions in (0.3)LiCl + (0.7) TeO2: 0.01 Tm2O3 glass which is moisture-resistant.     

Molecular dynamics simulations of a hyperthermophilic and a mesophilic protein L30e

Molecular dynamics (MD) simulations were used to study the hyperthermophilic ribosomal protein L30e from archaeon Thermococcus celer at 300 and 350 K, and its mesophilic homologue, yeast L30e, at 300 K in explicit solvent for a period of 5.0 ns. Three trajectories obtained from the MD simulations were stable throughout the simulation period, such as total potential energy, radius of gyration, root-mean-square deviation, and secondary structures assignment. At 300 K, T. celer L30e is less flexible than its mesophilic homologue, and this difference becomes more pronounced at 350 K. Salt bridge networks, one triad and one hexad, are present at the surface of T. celer L30e. The ion pairs forming these salt bridges maintain close contact at a higher temperature, suggesting that these networks contribute to the protein’s hyperthermal stability. By contrast, we found no such networks to be present in yeast L30e. For charged residue I in T. celer L30e, the ΔΔGsolvI value and its corresponding ΔECoulI value possess opposite signs. This indicates that for T. celer L30e, a change in the solvation free energy of a charged residue due to increasing temperature is compensated by a change in the residude’s Coulombic interaction energy with the rest of the protein.     

结晶／结晶共混体系PPS／PEEK中PPS组分的结晶熔融行为（Ⅱ）──熔融条件对退火样品的影响

结晶／结晶共混体系ＰＰＳ／ＰＥＥＫ中ＰＰＳ组分的结晶熔融行为（Ⅱ）──熔融条件对退火样品的影响麦堪成，许家瑞，梅震，曾汉民（广州中山大学材料科学研究所，广州，５１０２７５）关键词聚苯硫醚，聚醚醚酮，结晶熔融行为，熔融双峰聚苯硫醚（ＰＰＳ）的结晶熔融行...