Refined crystal structure of a superoxide dismutase from the hyperthermophilic archaeon Sulfolobus acidocaldarius at 2.2 A resolution

Functional characterization of a manganese superoxide dismutase from Avicennia marina: insights into its role in salt, hydrogen peroxide, and heavy metal tolerance

Avicennia marina is a salt-tolerance plant with high antioxidant and antibacterial potential. In the present work, a gene encoding MnSOD from Avicennia marina (AmSOD2) was cloned in the expression vectors pET28a. The resulting constructs were transformed into Escherichia coli strains Rosetta (DE3). Following the induction with Isopropyl β-D-1-thiogalactopyranoside, the protein His-AmSOD2 was expressed but dominantly found in the insoluble fraction of strain R-AmSOD2. Due to detection of mitochondrial transit peptide in the amino acid sequence of AmSOD2, the transit peptide was removed and AmSOD2 without transit peptide (tAmSOD2) was expressed in E. coli and dominantly found in the soluble fraction. The enzyme His-tAmSOD2 exhibited a molecular mass of 116 kDa in native condition. Nevertheless, in reducing conditions the molecular mass is 28 kDa indicating the enzyme His-tAmSOD2 is a tetramer protein. As shown by ICP analysis there is one mole Mn2+ in each monomer. The Pure His-tAmSOD2 was highly active in vitro, however the activity was almost three-fold lower than His-AmSOD1. Whereas the high stability of the recombinant His-AmSOD1was previously shown after incubation in a broad range pH and high temperature, His-tAmSOD2 was stable up to 50 °C and pH 6 for 1 h. The gene expression analysis showed that the gene encoding AmSOD2 is expressed in root, shoot and leaves of A. marina. In addition, the results show that the expression in the leaves was enhanced after treatment of plant with NaCl, H2O2, Cd2+ and Ni2+ indicating the important role of MnSOD in the resistant mechanism of mangroves.

Environmentally Friendly Quinolones Design for a Two-Way Choice between Biotoxicity and Genotoxicity through Double-Activity 3D-QSAR Model Coupled with the Variation Weighting Method

Quinolone (QN) antibiotics are widely used, which lead to their accumulation in soil and toxic effects on ryegrass in pasture. In this study, we employed ryegrass as the research object and selected the total scores of 29 QN molecules docked with two resistant enzyme structures, superoxide dismutase (SOD, PDB ID: 1B06) and proline (Pro, PPEP-2, PDB ID: 6FPC), as dependent variables. The structural parameters of QNs were used as independent variables to construct a QN double-activity 3D-QSAR model for determining the biotoxicity on ryegrass by employing the variation weighting method. This model was constructed to determine modification sites and groups for designing QNs molecules. According to the 3D contour map of the model, by considering enrofloxacin (ENR) and sparfloxacin (SPA) as examples, 23 QN derivatives with low biotoxicity were designed, respectively. The functional properties and environmental friendliness of the QN derivatives were predicted through a two-way selection between biotoxicity and genotoxicity before and after modification; four environmentally friendly derivatives with low biotoxicity and high genotoxicity were screened out. Mixed toxicity index and molecular dynamics methods were used to verify the combined toxicity mechanism of QNs on ryegrass before and after modification. By simulating the combined pollution of ENR and its derivatives in different soils (farmland, garden, and woodland), the types of combined toxicity were determined as partial additive and synergistic. Binding energies were calculated using molecular dynamics. The designed QN derivatives with low biotoxicity, high genotoxicity, and environmental friendliness can highly reduce the combined toxicity on ryegrass and can be used as theoretic reserves to replace QN antibiotics.

The Crystal Structure of the Manganese Superoxide Dismutase from Geobacillus stearothermophilus: Parker and Blake (1988) Revisited

Superoxide dismutase (SOD) is an almost ubiquitous metalloenzyme in aerobic organisms that catalyses the disproportionation of superoxide. Geobacillus stearothermophilus MnSOD is the only published MnSOD structure that does not have its coordinates publicly available, yet it is one of the more cited structures in the SOD literature. The structure has now been refined with modern programs, yielding a significantly improved structure which has been deposited in the Protein Data Bank. Importantly, the further refined structure reveals the presence of a catalytically important fifth ligand, water, to the metal centre, as observed in other SOD structures.

Semiholoenzyme optimizes activity and stability of a hyperthermostable iron-superoxide dismutase

Metal ion coordination is an essential step for the maturation of metalloenzymes. Generally, the metal coordination sites are thought to be fully occupied to achieve the maximum activity and stability. In this research, we compared the structural features, activity and stability of the apo-, semiholo- and holo-forms of a hyperthermostable tetrameric Fe-superoxide dismutase (SOD). Strikingly, the three forms of enzymes had similar compact tetrameric structures. Removal of iron ions destabilized subunit-subunit interactions during guanidine hydrochloride-induced unfolding. The partially metalized semiholoenzyme possessed most of the activity and identical hyperthermostability of the holoenzyme, but weaker propensity to aggregate. Furthermore, both of the iron content and activity of the semiholoenzyme were unaffected by a 200-fold excess iron ions in solutions, suggesting that conformation of the apo-subunits were forced to the close state by the iron-containing subunits. These observations suggest that fully metalized enzyme is probably nonessential for multimeric metalloenzymes and the semiholoenzyme may be a better choice. The unique properties of semiholoenzyme also provide the organisms a compromised solution to survival under metal deficiency conditions.

Principles for enhancing virus capsid capacity and stability from a thermophilic virus capsid structure

The capsids of double-stranded DNA viruses protect the viral genome from the harsh extracellular environment, while maintaining stability against the high internal pressure of packaged DNA. To elucidate how capsids maintain stability in an extreme environment, we use cryoelectron microscopy to determine the capsid structure of thermostable phage P74-26 to 2.8-Å resolution. We find P74-26 capsids exhibit an overall architecture very similar to those of other tailed bacteriophages, allowing us to directly compare structures to derive the structural basis for enhanced stability. Our structure reveals lasso-like interactions that appear to function like catch bonds. This architecture allows the capsid to expand during genome packaging, yet maintain structural stability. The P74-26 capsid has T = 7 geometry despite being twice as large as mesophilic homologs. Capsid capacity is increased with a larger, flatter major capsid protein. Given these results, we predict decreased icosahedral complexity (i.e. T ≤ 7) leads to a more stable capsid assembly.

Viral capsids need to protect the genome against harsh environmental conditions and cope with high internal pressure from the packaged genome. Here, the authors determine the structure of the thermostable phage P74-26 capsid at 2.8-Å resolution and identify features underlying enhanced capsid capacity and structural stability.

Debaryomyces hansenii up regulates superoxide dismutase gene expression and enhances the immune response and survival in Pacific red snapper (Lutjanus peru) leukocytes after Vibrio parahaemolyticus infection

Application of yeast is increasing to improve welfare and promotes growth in aquaculture. The halotolerant yeast Debaryomyces hansenii is normally a non-pathogenic yeast with probiotic properties and potential source of antioxidant enzymes as superoxide dismutase. Here, first, we characterized the sequence features of MnSOD and icCu/ZnSOD from Pacific red snapper, and second, we evaluated the potential antioxidant immune responses of the marine yeast Debaryomyces hansenii strain CBS004 in leukocytes which were then subjected to Vibrio parahaemolyticus infection. In silico analysis revealed that LpMnSOD consisted of 1186 bp, with an ORF of 678 bp encoding a 225 amino acid protein and LpicCu/ZnSOD consisted of 1090 bp in length with an ORF of 465 bp encoding a 154 amino acid protein. Multiple alignment analyzes revealed many conserved regions and active sites among its orthologs. In vitro assays using head-kidney and spleen leukocytes immunostimulated with D. hansenii and zymosan in response to V. parahaemolyticus infection reveled that D. hansenii strain CBS004 significantly increased transcriptions of MnSOD and icCu/ZnSOD genes. Flow cytometry assay showed that D. hansenii was able to inhibit apoptosis caused by V. parahaemolyticus in the Pacific red snapper leukocytes and enhanced the phagocytic capacity in head-kidney leukocytes. Immunological assays reveled an increased in superoxide dismutase and peroxidase activities, as well as, in nitric oxide production and reactive oxygen species production (respiratory burst) in fish stimulated with D. hansenii. Finally, our results. These results strongly support the idea that marine yeast Debaryomyces hansenii strain CBS004 can stimulate the antioxidant immune mechanism in head-kidney and spleen leukocytes.

Engineering Proteins for Thermostability with iRDP Web Server

Engineering protein molecules with desired structure and biological functions has been an elusive goal. Development of industrially viable proteins with improved properties such as stability, catalytic activity and altered specificity by modifying the structure of an existing protein has widely been targeted through rational protein engineering. Although a range of factors contributing to thermal stability have been identified and widely researched, the in silico implementation of these as strategies directed towards enhancement of protein stability has not yet been explored extensively. A wide range of structural analysis tools is currently available for in silico protein engineering. However these tools concentrate on only a limited number of factors or individual protein structures, resulting in cumbersome and time-consuming analysis. The iRDP web server presented here provides a unified platform comprising of iCAPS, iStability and iMutants modules. Each module addresses different facets of effective rational engineering of proteins aiming towards enhanced stability. While iCAPS aids in selection of target protein based on factors contributing to structural stability, iStability uniquely offers in silico implementation of known thermostabilization strategies in proteins for identification and stability prediction of potential stabilizing mutation sites. iMutants aims to assess mutants based on changes in local interaction network and degree of residue conservation at the mutation sites. Each module was validated using an extensively diverse dataset. The server is freely accessible at http://irdp.ncl.res.in and has no login requirements.

Communities in the iron superoxide dismutase amino acid network

Amino acid networks (AANs) analysis is a new way to reveal the relationship between protein structure and function. We constructed six different types of AANs based on iron superoxide dismutase (Fe-SOD) three-dimensional structure information. These Fe-SOD AANs have clear community structures when they were modularized by different methods. Especially, detected communities are related to Fe-SOD secondary structures. Regular structures show better correlations with detected communities than irregular structures, and loops weaken these correlations, which suggest that secondary structure is the unit element in Fe-SOD folding process. In addition, a comparative analysis of mesophilic and thermophilic Fe-SOD AANs' communities revealed that thermostable Fe-SOD AANs had more highly associated community structures than mesophilic one. Thermophilic Fe-SOD AANs also had more high similarity between communities and secondary structures than mesophilic Fe-SOD AANs. The communities in Fe-SOD AANs show that dense interactions in modules can help to stabilize thermophilic Fe-SOD.

A novel mechanism of protein thermostability: a unique N-terminal domain confers heat resistance to Fe/Mn-SODs

Superoxide dismutases (SODs), especially thermostable SODs, are widely applied in medical treatments, cosmetics, food, agriculture, and other industries given their excellent antioxidant properties. A novel thermostable cambialistic SOD from Geobacillus thermodenitrificans NG80-2 exhibits maximum activity at 70°C and high thermostability over a broad range of temperatures (20–80°C). Unlike other reported SODs, this enzyme contains an extra repeat-containing N-terminal domain (NTD) of 244 residues adjacent to the conserved functional SODA domain. Deletion of the NTD dramatically decreased its optimum active temperature (OAT) to 30°C and also impaired its thermostability. Conversely, appending the NTD to a mesophilic counterpart from Bacillus subtilis led to a moderately thermophilic enzyme (OAT changed from 30 to 55°C) with improved heat resistance. Temperature-dependant circular dichroism analysis revealed the enhanced conformational stability of SODs fused with this NTD. Furthermore, the NTD also contributes to the stress resistance of host proteins without altering their metal ion specificity or oligomerisation form except for a slight effect on their pH profile. We therefore demonstrate that the NTD confers outstanding thermostability to the host protein. To our knowledge, this is the first discovery of a peptide capable of remarkably improving protein thermostability and provides a novel strategy for bioengineering thermostable SODs.

Formation of high-order oligomers by a hyperthemostable Fe-superoxide dismutase (tcSOD)

Hyperthermostable proteins are highly resistant to various extreme conditions. Many factors have been proposed to contribute to their ultrahigh structural stability. Some thermostable proteins have larger oligomeric size when compared to their mesophilic homologues. The formation of compact oligomers can minimize the solvent accessible surface area and increase the changes of Gibbs free energy for unfolding. Similar to mesophilic proteins, hyperthermostable proteins also face the problem of unproductive aggregation. In this research, we investigated the role of high-order oligomerization in the fight against aggregation by a hyperthermostable superoxide dismutase identified from Tengchong, China (tcSOD). Besides the predominant tetramers, tcSOD could also form active high-order oligomers containing at least eight subunits. The dynamic equilibrium between tetramers and high-order oligomers was not significantly affected by pH, salt concentration or moderate temperature. The secondary and tertiary structures of tcSOD remained unchanged during heating, while cross-linking experiments showed that there were conformational changes or structural fluctuations at high temperatures. Mutational analysis indicated that the last helix at the C-terminus was involved in the formation of high-order oligomers, probably via domain swapping. Based on these results, we proposed that the reversible conversion between the active tetramers and high-order oligomers might provide a buffering system for tcSOD to fight against the irreversible protein aggregation pathway. The formation of active high-order oligomers not only increases the energy barrier between the native state and unfolded/aggregated state, but also provides the enzyme the ability to reproduce the predominant oligomers from the active high-order oligomers.

Improving the thermostability of a mesophilic family 10 xylanase, AuXyn10A, from Aspergillus usamii by in silico design

To improve the thermostability of a mesophilic GH family 10 xylanase, AuXyn10A, from Aspergillus usamii E001, its modification was performed by in silico design. Based on the comparison of B-factor values, a mutant xylanase ATXyn10 was predicted by substituting a segment YP from Tyr(25) to Pro(34) of AuXyn10A with the corresponding one from Asn(24) to Ala(32) of TaXyn10, a thermophilic GH family 10 xylanase from Thermoascus aurantiacus. Analysis of a TaXyn10 crystal structure indicated that there is a close interaction between segments YP and FP. For that reason, another mutant xylanase ATXyn10(M) was designed by mutating Ser(286) and His(288) of ATXyn10 into the corresponding Gly(285) and Phe(287) in the FP of TaXyn10. Then, two ATXyn10- and ATXyn10(M)-encoding genes, ATxyn10 and ATxyn10 (M), were expressed in Pichia pas toris GS115. The temperature optimum of recombinant (re) ATXyn10(M) was 60 °C, 10 °C higher than that of reAuXyn10A. Its thermal inactivation half-life (t(1/2)) at 55 °C was 10.4-fold longer than that of reAuXyn10A. As compared with reAuXyn10A, reATXyn10(M) displayed a slight decrease in K(m) value and a significant increase in V(max) value from 6,267 to 8,870 U/mg.

Purification, Characterization, and Molecular Cloning of a Thermostable Superoxide Dismutase fromThermoascus aurantiacus

A thermostable superoxide dismutase [(SOD) EC 1.15.1.1] from a Thermoascus aurantiacus var. levisporus was purified to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) homogeneity by a series of column chromatographies. The molecular mass of a single band of the enzyme was estimated to be 16.8 kDa by SDS-PAGE. The molecular mass was estimated to be 33.2 kDa by gel filtration on Sephacryl S-100, indicating that the enzyme was composed of two identical subunits of 16.8 kDa each. N-terminal amino acid sequencing (seven residues) yielded VKAVAVL. Using RACE-PCR, a Cu, Zn-SOD gene was cloned from T. aurantiacus var. levisporus. The sequence was 705 bp and contained a 468 bp ORF encoding a Cu, Zn-SOD of 155 amino acid residues.

Structure of the Aeropyrum pernix L7Ae multifunctional protein and insight into its extreme thermostability

Archaeal ribosomal protein L7Ae is a multifunctional RNA-binding protein that directs post-transcriptional modification of archaeal RNAs. The L7Ae protein from Aeropyrum pernix (Ap L7Ae), a member of the Crenarchaea, was found to have an extremely high melting temperature (>383 K). The crystal structure of Ap L7Ae has been determined to a resolution of 1.56 Å. The structure of Ap L7Ae was compared with the structures of two homologs: hyperthermophilic Methanocaldococcus jannaschii L7Ae and the mesophilic counterpart mammalian 15.5 kD protein. The primary stabilizing feature in the Ap L7Ae protein appears to be the large number of ion pairs and extensive ion-pair network that connects secondary-structural elements. To our knowledge, Ap L7Ae is among the most thermostable single-domain monomeric proteins presently observed.

Application of principal component analysis to determine the key structural features contributing to iron superoxide dismutase thermostability

Iron superoxide dismutase (Fe-SOD) is predominantly found in bacteria and mitochondria. The thermal stability of Fe-SOD from different sources can vary dramatically. We have studied the influence of structural parameters on Fe-SOD thermostability by principal component analysis (PCA). The results show that an increased α-helical and turn content, an increased α-helix and loop length, an increase in the number of main-main chains and charged-uncharged hydrogen bonds, a decrease in the 3(10) -helix content, and a decreased β-strand and loop length are all important factors for Fe-SOD thermostability. Interestingly, the use of charged residues to form salt bridges is tendentious in thermophilic Fe-SOD. Negatively charged Arg and positively charged Glu are efficiently used to form salt bridges. The cooperative action of the exposed area, the hydrogen bonds, and the secondary structure plays a crucial role in resisting high temperatures, which demonstrates that the increased stability of thermophilic Fe-SOD is provided by several structural factors acting together.

Structural analysis and molecular modelling of the Cu/Zn-SOD from fungal strain Humicola lutea 103

The native form of Cu/Zn-superoxide dismutase, isolated from fungal strain Humicola lutea 103 is a homodimer that coordinates one Cu(2+) and one Zn(2+) per monomer. Cu(2+) and Zn(2+) ions play crucial roles in enzyme activity and structural stability, respectively. It was established that HLSOD shows high pH and temperature stability. Thermostability of the glycosylated enzyme Cu/Zn-SOD, isolated from fungal strain H. lutea 103, was determined by CD spectroscopy. Determination of reversibility toward thermal denaturation for HLSOD allowed several thermodynamic parameters to be calculated. In this communication we report the conditions under which reversible denaturation of HLSOD exists. The narrow range over which the system is reversible has been determined using the strongest test of two important thermodynamic independent variables (T and pH). Combining both these variables, the "phase diagram" was determined, as a result of which the real thermodynamic parameters (ΔC(p), ΔH(exp)°, and ΔG(exp)°) was established. Because very narrow pH-interval of transitions we assume they are as result of overlapping of two simple transitions. It was found that ΔH(o) is independent from pH with a value of 1.3 kcal/mol and 2.8 kcal/mol for the first and the second transition, respectively. ΔG(o) was pH-dependent in all studied pH-interval. This means that the transitions are entropically driven, these. Based on this, these processes can be described as hydrophobic rearrangement of the quaternary structure. It was also found that glycosylation does not influence the stability of the enzyme because the carbohydrate chain is exposed on the surface of the molecule.

A tandem duplication of manganese superoxide dismutase in Nosema bombycis and its evolutionary origins

Microsporidia are a group of obligate intracellular eukaryotic parasites with small genomes. They infect animals from a wide variety of phyla, including humans. Two manganese superoxide dismutase (MnSOD) genes, designated NbMnSOD1 and NbMnSOD2, were found to be organized in a tandem array within the Nosema bombycis genome. The genes, both 678 bp in length, were found to be more similar to each other than they are to homologous genes of other Microsporidia, suggesting that the tandem duplication occurred subsequent to the development of this lineage. Reverse transcript PCR shows that mRNA for both genes is present in the spores. Analysis of the primary structure, hydrophobic cluster analysis, target signal analysis, and phylogenetic analysis all indicate that NbMnSOD1 is dimeric and targeted to the cytosol. NbMnSOD2 seems to have changed more rapidly and is under less evolutionary constraint than NbMnSOD1 suggesting that NbMnSOD2 may function under different conditions or in different tissues of its host rather than simply resulting in an increase in expression. A phylogenetic analysis of MnSOD sequences from eukaryotes, Archaea, and bacteria shows the microsporidial MnSODs to be grouped with the bacteria suggesting a possible horizontal gene transfer.

Iron-sulfur world in aerobic and hyperthermoacidophilic archaea Sulfolobus

The general importance of the Fe-S cluster prosthetic groups in biology is primarily attributable to specific features of iron and sulfur chemistry, and the assembly and interplay of the Fe-S cluster core with the surrounding protein is the key to in-depth understanding of the underlying mechanisms. In the aerobic and thermoacidophilic archaea, zinc-containing ferredoxin is abundant in the cytoplasm, functioning as a key electron carrier, and many Fe-S enzymes are produced to participate in the central metabolic and energetic pathways. De novo formation of intracellular Fe-S clusters does not occur spontaneously but most likely requires the operation of a SufBCD complex of the SUF machinery, which is the only Fe-S cluster biosynthesis system conserved in these archaea. In this paper, a brief introduction to the buildup and maintenance of the intracellular Fe-S world in aerobic and hyperthermoacidophilic crenarchaeotes, mainly Sulfolobus, is given in the biochemical, genetic, and evolutionary context.

Identification of residual structure in the unfolded state of ribonuclease H1 from the moderately thermophilic Chlorobium tepidum: comparison with thermophilic and mesophilic homologues

Ribonucleases H from organisms that grow at different temperatures demonstrate a variable change in heat capacity upon unfolding (DeltaC degrees (P)) [Ratcliff, K., et al. (2009) Biochemistry 48, 5890-5898]. This DeltaC degrees (P) has been shown to correlate with a tolerance to higher temperatures and residual structure in the unfolded state of the thermophilic proteins. In the RNase H from Thermus thermophilus, the low DeltaC degrees (P) has been shown to arise from the same region as the folding core of the protein, and mutagenic studies have shown that loss of a hydrophobic residue in this region can disrupt this residual unfolded state structure and result in a return to a more mesophile-like DeltaC degrees (P) [Robic, S., et al. (2002) Protein Sci. 11, 381-389; Robic, S., et al. (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 11345-11349]. To understand further how residual structure in the unfolded state is encoded in the sequences of these thermophilic proteins, we subjected the RNase H from Chlorobium tepidum to similar studies. Analysis of new chimeric proteins reveals that like T. thermophilus RNase H, the folding core of C. tepidum RNase H plays an important role in the unfolded state of this protein. Mutagenesis studies, based on both a computational investigation of the hydrophobic networks in the core region and comparisons with similar studies on T. thermophilus RNase H, identify new residues involved in this residual structure and suggest that the residual structure in the unfolded state of C. tepidum RNase H is more restricted than that of T. thermophilus. We conclude that while the folding core region determines the thermophilic-like behavior of this family of proteins, the residue-specific details vary.

Contributions of the C-terminal helix to the structural stability of a hyperthermophilic Fe-superoxide dismutase (TcSOD)

Hyperthermophilic superoxide dismutases (SODs) are of particular interest due to their potential industrial importance and scientific merit in studying the molecular mechanisms of protein folding and stability. Compared to the mesophilic SODs, the hyperthermostable Fe-SODs (TcSOD and ApSOD) have an extended C-terminal helix, which forms an additional ion-pairing network. In this research, the role of the extended C-terminus in the structural stability of TcSOD was studied by investigating the properties of two deletion mutants. The results indicated that the ion-pairing network at the C-terminus had limited contributions to the stability of TcSOD against heat- and GdnHCl-induced inactivation. The intactness of the C-terminal helix had dissimilar impact on the two stages of TcSOD unfolding induced by guanidinium chloride. The mutations slightly decreased the Gibbs free energy of the dissociation of the tetrameric enzymes, while greatly affected the stability of the molten globule-like intermediate. These results suggested that the additional ion-pairing network mainly enhanced the structural stability of TcSOD by stabilizing the monomers.

Structure, stability, and folding of ribonuclease H1 from the moderately thermophilic Chlorobium tepidum: comparison with thermophilic and mesophilic homologues

Proteins from thermophilic organisms are able to function under conditions that render a typical mesophilic protein inactive. Pairwise comparisons of homologous mesophilic and thermophilic proteins can help to identify the energetic features of a protein's energy landscape that lead to such thermostability. Previous studies of bacterial ribonucleases H (RNases H) from the thermophile Thermus thermophilus and the mesophile Escherichia coli revealed that the thermostability arises in part from an unusually low change in heat capacity upon unfolding (DeltaC(p)) for the thermophilic protein [Hollien, J., and Marqusee, S. (1999) Biochemistry 38, 3831-3836]. Here, we have further examined how nearly identical proteins can adapt to different thermal constraints by adding a moderately thermophilic homologue to the previously characterized mesophilic and thermophilic pair. We identified a putative RNase H from Chlorobium. tepidum and demonstrated that it is an active RNase H and adopts the RNase H fold. The moderately thermophilic protein has a melting temperature (T(m)) similar to that of the mesophilic homologue yet also has a surprisingly low DeltaC(p), like the thermophilic homologue. This new RNase H folds through a pathway similar to that of the previously studied RNases H. These results suggest that lowering the DeltaC(p) may be a general strategy for achieving thermophilicity for some protein families and implicate the folding core as the major contributor to this effect. It should now be possible to design RNases H that display the desired thermophilic or mesophilic properties, as defined by their DeltaC(p) values, and therefore fine-tune the energy landscape in a predictable fashion.

Structural basis for thermostability revealed through the identification and characterization of a highly thermostable phosphotriesterase-like lactonase from Geobacillus stearothermophilus

A new enzyme homologous to phosphotriesterase was identified from the bacterium Geobacillus stearothermophilus (GsP). This enzyme belongs to the amidohydrolase family and possesses the ability to hydrolyze both lactone and organophosphate (OP) compounds, making it a phosphotriesterase-like lactonase (PLL). GsP possesses higher OP-degrading activity than recently characterized PLLs, and it is extremely thermostable. GsP is active up to 100 degrees C with an energy of activation of 8.0 kcal/mol towards ethyl paraoxon, and it can withstand an incubation temperature of 60 degrees C for two days. In an attempt to understand the thermostability of PLLs, the X-ray structure of GsP was determined and compared to those of existing PLLs. Based upon a comparative analysis, a new thermal advantage score and plot was developed and reveals that a number of different factors contribute to the thermostability of PLLs.

The first structure of a cold-adapted superoxide dismutase (SOD): biochemical and structural characterization of iron SOD from Aliivibrio salmonicida

Superoxide dismutases (SODs) are metalloenzymes that catalyse the dismutation of the superoxide radical anion into O(2) and H(2)O(2) in a two-step reaction. The crystal structure of the iron superoxide dismutase from the cold-adapted and fish-pathogenic bacterium Aliivibrio salmonicida (asFeSOD) has been determined and refined to 1.7 A resolution. The protein has been characterized and compared with the closely related homologous iron superoxide dismutase from the mesophilic Escherichia coli (ecFeSOD) in an attempt to rationalize its environmental adaptation. ecFeSOD shares 75% identity with asFeSOD. Compared with the mesophilic FeSOD, the psychrophilic FeSOD has distinct temperature differences in residual activity and thermostability that do not seem to be related to structural differences such as intramolecular or intermolecular ion bonds, hydrogen bonds or cavity sizes. However, an increased net negative charge on the surface of asFeSOD may explain its lower thermostability compared with ecFeSOD. Activity measurements and differential scanning calorimetry measurements revealed that the psychrophilic asFeSOD had a thermostability that was significantly higher than the optimal growth temperature of the host organism.

Crystal structure of a family 16 endoglucanase from the hyperthermophile Pyrococcus furiosus--structural basis of substrate recognition

Bacterial and archaeal endo-beta-1,3-glucanases that belong to glycoside hydrolase family 16 share a beta-jelly-roll fold, but differ significantly in sequence and in substrate specificity. The crystal structure of the laminarinase (EC 3.2.1.39) from the hyperthermophilic archaeon Pyrococcus furiosus (pfLamA) has been determined at 2.1 A resolution by molecular replacement. The pfLamA structure reveals a kink of six residues (72-77) at the entrance of the catalytic cleft. This peptide is absent in the endoglucanases from alkaliphilic Nocardiopsis sp. strain F96 and Bacillus macerans, two proteins displaying an overall fold similar to that of pfLamA, but with different substrate specificity. A deletion mutant of pfLamA, lacking residues 72-75, hydrolyses the mixed-linkage beta-1,3-1,4-glucan lichenan 10 times more efficiently than the wild-type protein, indicating the importance of the kink in substrate preference.

Proteomics Analysis of Thermoplasma acidophilum with a Focus on Protein Complexes

Two-dimensional gel electrophoresis (2DE) and MALDI-TOF MS were used to obtain a global view of the cytoplasmic proteins expressed by Thermoplasma acidophilum. In addition, glycerol gradient ultracentrifugation coupled to 2DE-MALDI-TOF MS analysis was used to identify subunits of macromolecular complexes. With the 2DE proteomics approach, over 900 spots were resolved of which 271 proteins were identified. A significant number of these form macromolecular complexes, among them the ribosome, proteasome, and thermosome, which are expressed at high levels. In the glycerol gradient heavy fractions, 10 as yet uncharacterized proteins (besides the well known ribosomal subunits, translation initiation factor eIF-6-related protein, elongation factor 1, and DNA-dependent RNA polymerase) were identified that are putative building blocks of protein complexes. These proteins belong to the categories of hypothetical or conserved hypothetical proteins, and they are present in the cytosol at low concentrations. Although these proteins exhibit homology to known sequences, their structures, subunit compositions, and biological functions are not yet known.

Characterization of a hyperthermostable Fe-superoxide dismutase from hot spring

A new gene encoding a thermostable Fe-superoxide dismutase (tcSOD) was identified from a metagenomic library prepared from a hot spring sample. The open reading frame of tcSOD encoded a 211 amino acid protein. The recombinant protein was overexpressed in Escherichia coli and confirmed to be a Fe-SOD with a specific activity of 1,890 U/mg using the pyrogallol method. The enzyme was highly stable at 80 degrees C and retained 50% activity after heat treatment at 95 degrees C for 2 h. It showed striking stability across a wide pH span from 4 to 11. The native form of the enzyme was determined as a homotetramer by analytical ultracentrifugation and gradient native polyacrylamide gel electrophoresis. Fe(2+) was found to be important to SOD activity and to the stability of tcSOD dimer. Comparative modeling analyses of tcSOD tetramer indicate that its high thermostability is mainly due to the presence of a large number of intersubunit ion pairs and hydrogen bonds and to a decrease in solvent accessible hydrophobic surfaces.

The crystal structure of a hyperthermostable subfamily II isocitrate dehydrogenase from Thermotoga maritima

Isocitrate dehydrogenase (IDH) from the hyperthermophile Thermotoga maritima (TmIDH) catalyses NADP+- and metal-dependent oxidative decarboxylation of isocitrate to alpha-ketoglutarate. It belongs to the beta-decarboxylating dehydrogenase family and is the only hyperthermostable IDH identified within subfamily II. Furthermore, it is the only IDH that has been characterized as both dimeric and tetrameric in solution. We solved the crystal structure of the dimeric apo form of TmIDH at 2.2 A. The R-factor of the refined model was 18.5% (R(free) 22.4%). The conformation of the TmIDH structure was open and showed a domain rotation of 25-30 degrees compared with closed IDHs. The separate domains were found to be homologous to those of the mesophilic mammalian IDHs of subfamily II and were subjected to a comparative analysis in order to find differences that could explain the large difference in thermostability. Mutational studies revealed that stabilization of the N- and C-termini via long-range electrostatic interactions were important for the higher thermostability of TmIDH. Moreover, the number of intra- and intersubunit ion pairs was higher and the ionic networks were larger compared with the mesophilic IDHs. Other factors likely to confer higher stability in TmIDH were a less hydrophobic and more charged accessible surface, a more hydrophobic subunit interface, more hydrogen bonds per residue and a few loop deletions. The residues responsible for the binding of isocitrate and NADP+ were found to be highly conserved between TmIDH and the mammalian IDHs and it is likely that the reaction mechanism is the same.

Characterisation of manganese superoxide dismutase from Phytophthora nicotianae

Three polypeptides with manganese superoxide dismutase (MnSOD) activity were found in mycelium, zoospores and germinated cysts of Phytophthora nicotianae. Their relative molecular weights in non-denaturing gels were approximately 34.5, 36 and 50 kDa. No evidence for the presence of either iron or copper/zinc SODs was detected at any of the developmental stages examined. The level of activity of the MnSOD polypeptides was similar in mycelia and spores. Degenerate PCR was used to amplify partial genes of two different MnSODs, designated PnMnSODI and PnMnSOD2, from P. nicotianae. Southern blot analysis indicated that there are two PnMnSOD1 genes in the P. nicotianae genome. Full length sequence was obtained for one of these genes, PnMnSOD1a, from a P. nicotianae bacterial artificial chromosome (BAC) library. RNA blots probed with PnMnSOD1 showed similar levels of expression in vegetative and sporulating hyphae, lower levels in germinated cysts and no detectable expression in zoospores. PnMnSOD1a had 96%, 97 % and 99 % amino acid identity with homologous genes from P. ramorum, P. infestans and P. sojae, respectively. The second gene cloned from P. nicotianae, PnMnSOD2, had only 38 % amino acid identity with PnMnSOD1a and was homologous to MnSODs that possessed an N-terminal mitochondrial targeting sequence in Phytophthora species and other eukaryotes. Southern blots indicated that there is one copy of PnMnSOD2 in the P. nicotianae genome. PnMnSOD2 was expressed at similar levels in mycelia and germinated cysts but PnMnSOD2 transcripts were not detectable in zoospores.

Crystal structure and structural stability of acylphosphatase from hyperthermophilic archaeon Pyrococcus horikoshii OT3

To elucidate the structural basis for the high stability of acylphosphatase (AcP) from Pyrococcus horikoshii OT3, we determined its crystal structure at 1.72 A resolution. P. horikoshii AcP possesses high stability despite its approximately 30% sequence identity with eukaryotic enzymes that have moderate thermostability. The overall fold of P. horikoshii AcP was very similar to the structures of eukaryotic counterparts. The crystal structure of P. horikoshii AcP shows the same fold betaalphabetabetaalphabeta topology and the conserved putative catalytic residues as observed in eukaryotic enzymes. Comparison with the crystal structure of bovine common-type AcP and that of D. melanogaster AcP (AcPDro2) as representative of eukaryotic AcP revealed some significant characteristics in P. horikoshii AcP that likely play important roles in structural stability: (1) shortening of the flexible N-terminal region and long loop; (2) an increased number of ion pairs on the protein surface; (3) stabilization of the loop structure by hydrogen bonds. In P. horikoshii AcP, two ion pair networks were observed one located in the loop structure positioned near the C-terminus, and other on the beta-sheet. The importance of ion pairs for structural stability was confirmed by site-directed mutation and denaturation induced by guanidium chloride.

Packing-based difference of structural features between thermophilic and mesophilic proteins

Twenty pairs of thermophilic and mesophilic proteins were compared in terms of residue packing distribution to obtain structural features related to protein thermostability. Based on residue packing concept, structural features of residues such as residue packing distribution, inner/outer position, secondary structure and water solvation were investigated. The statistical tests revealed that higher frequency in well-packed state of residues, lower frequency in exposed state and higher frequency in well-packed state of inner positioned residues, and higher frequency in well-packed state of 3/10 helix residues could be general structural features thermophilic proteins have.

A thermostable manganese-containing superoxide dismutase from the thermophilic fungus Thermomyces lanuginosus

A thermostable superoxide dismutase (SOD) from a Thermomyces lanuginosus strain (P134) was purified to homogeneity by fractional ammonium sulfate precipitation, ion-exchange chromatography on DEAE-Sepharose, Phenyl-Sepharose hydrophobic interaction chromatography, and gel filtration on Sephacryl S-100. The molecular mass of a single band of the enzyme was estimated to be 22.4 kDa, using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Using gel filtration on Sephacryl S-100, the molecular mass was estimated to be 89.1 kDa, indicating that this enzyme was composed of four identical subunits of 22.4 kDa each. The SOD was found to be inhibited by NaN3, but not by KCN or H2O2, suggesting that the SOD in T. lanuginosus was of the manganese superoxide dismutase type. The SOD exhibited maximal activity at pH 7.5. The optimum temperature for the activity was 55 degrees C. It was thermostable at 50 and 60 degrees C and retained 55% activity after 60 min at 70 degrees C. The half-life of the SOD at 80 degrees C was approximately 28 min and even retained 20% activity after 20 min at 90 degrees C.

Thermodynamics of core hydrophobicity and packing in the hyperthermophile proteins Sac7d and Sso7d

The influence of core hydrophobicity and packing on the structure and stability of the hyperthermophile proteins Sac7d and Sso7d have been studied by calorimetry, circular dichroism, and NMR. Valine 30 is positioned in Sac7d to allow a cavity-filling Val --> Ile substitution which occurs naturally in the homologous more thermostable Sso7d. The cavity-filling mutation in Sac7d has been characterized and compared to the reciprocal Ile --> Val mutation in Sso7d. A detailed analysis of the stability of the proteins was obtained by globally fitting the variation of DSC parameters and circular dichroism intensities as a function of temperature (0-100 degrees C), salt (0-0.3 M), and pH (0-8). A global analysis over such a range of conditions permitted an unusually precise measure of the thermodynamic parameters, as well as the separation of the thermodynamics of the intrinsic unfolding reaction from the linked effects of protonation and chloride binding associated with acid-induced folding. The results indicate differences in the energetics of unfolding Sac7d and Sso7d that would not be apparent from an analysis of DSC data alone using conventional methods. The sign and magnitude of the changes in DeltaG, DeltaH, TDeltaS, and DeltaC(P) of unfolding resulting from core Ile/Val substitutions in the two proteins were consistent with differences in hydrophobicity of Val and Ile and negligible changes in packing (van der Waals) interactions. The benefit of increased hydrophobicity of the core increased with temperature, with maximal effect around 116 degrees C. Increased hydrophobicity of the core achieved not only an increase in the free energy of unfolding, but also a lateral shift of the temperature of maximal stability to higher temperature.

Biochemical properties and regulated gene expression of the superoxide dismutase from the facultatively aerobic hyperthermophile Pyrobaculum calidifontis

Superoxide dismutase (SOD) was purified from a facultatively aerobic hyperthermophilic archaeon, Pyrobaculum calidifontis VA1. The purified native protein from aerobically grown cells exhibited 1,960 U of SOD activity/mg and contained 0.86 +/- 0.04 manganese and <0.01 iron atoms per subunit. The gene encoding SOD was cloned and expressed in Escherichia coli. Although the recombinant protein was soluble, little activity was observed due to the lack of metal incorporation. Reconstitution of the enzyme by heat treatment with either Mn or Fe yielded a highly active protein with specific activities of 1,970 and 434 U/mg, respectively. This indicated that the SOD from P. calidifontis was a cambialistic SOD with a preference toward Mn in terms of activity. Interestingly, reconstitution experiments in vitro indicated a higher tendency of the enzyme to incorporate Fe than Mn. When P. calidifontis was grown under anaerobic conditions, a majority of the native SOD was incorporated with Fe, indicating the cambialistic property of this enzyme in vivo. We further examined the expression levels of SOD and a previously characterized Mn catalase from this strain in the presence or absence of oxygen. Northern blot, Western blot, and activity measurement analyses revealed that both genes are expressed at much higher levels under aerobic conditions. We also detected a rapid response in the biosynthesis of these enzymes once the cells were exposed to oxygen.

Structures of thermophilic and mesophilic adenylate kinases from the genus Methanococcus

The crystal structures of adenylate kinases from the thermophile Methanococcus thermolithotrophicus and the mesophile Methanococcus voltae have been solved to resolutions of 2.8A and 2.5A, respectively. The structures of the enzymes are similar to that of the adenylate kinase from archaeal Sulfolobus acidocaldarius in many respects such as the extended central beta-sheets, the short LID domain, and the trimeric state. The analysis of unligated and AMP-bound subunits of M.voltae suggests that movements of two mobile domains are not independent of each other. The methanococcal structures are examined with respect to their lack of the "invariant" Lys residue within the phosphate-binding loop, and two Arg residues in the LID domain are proposed as substituting residues based on their conservation among archaeal adenylate kinases and mobility within the structures. Since S.acidocaldarius adenylate kinase has the invariant Lys residue as well as the two Arg residues, its phosphate-binding loop is examined and compared with those of other adenylate kinases. On the basis of the comparison and other available biochemical data, the unusual conformation of the Lys residue in S.acidocaldarius adenylate kinase is explained. Despite possessing 78% sequence identity, the methanococcal enzymes exhibit significantly different thermal stabilities. To study the determinants of thermostability, several structural features including salt-links, hydrogen bonds, packing density, surface to volume ratio and buried surface area are compared between the enzymes. From their difference in apolar buried surface area, hydrophobic interaction is proposed to be a basis for the disparate thermostabilities, and the corresponding free energy difference is also estimated. Results of previous mutational studies are interpreted in terms of the crystal structures, and support the importance of hydrophobic interactions in thermostability.

Structural basis for thermostability of beta-glycosidase from the thermophilic eubacterium Thermus nonproteolyticus HG102

The three-dimensional structure of a thermostable beta-glycosidase (Gly(Tn)) from the thermophilic eubacterium Thermus nonproteolyticus HG102 was determined at a resolution of 2.4 A. The core of the structure adopts the (betaalpha)(8) barrel fold. The sequence alignments and the positions of the two Glu residues in the active center indicate that Gly(Tn) belongs to the glycosyl hydrolases of retaining family 1. We have analyzed the structural features of Gly(Tn) related to the thermostability and compared its structure with those of other mesophilic glycosidases from plants, eubacteria, and hyperthermophilic enzymes from archaea. Several possible features contributing to the thermostability of Gly(Tn) were elucidated.

Comparative analysis of thermoadaptation within the archaeal glyceraldehyde-3-phosphate dehydrogenases from mesophilic Methanobacterium bryantii and thermophilic Methanothermus fervidus

To gain insight into the molecular determinants of thermoadaptation within the family of archaeal glyceraldehyde-3-phosphate dehydrogenases (GAPDH), a homology-based 3-D model of the mesophilic GAPDH from Methanobacterium bryantii was built and compared with the crystal structure of the thermophilic GAPDH from Methanothermus fervidus. The homotetrameric model of the holoenzyme was initially assembled from identical subunits completed with NADP molecules. The structure was then refined by energy minimization and simulated-annealing procedures. PROCHECK and the 3-D profile method were used to appraise the model reliability. Striking molecular features underlying the difference in stability between the enzymes were deduced from their structural comparison. First, both the increase in hydrophobic contacts and the decrease in accessibility to the protein core were shown to discriminate in favor of the thermophilic enzyme. Besides, but to a lesser degree, the number of ion pairs involved in cooperative clusters appeared to correlate with thermostability. Finally, the decreased stability of the mesophilic enzyme was also predicted to proceed from both the lack of charge-dipole interactions within alpha-helices and the enhanced entropy of unfolding due to an increase in chain flexibility. Thus, archaeal GAPDHs appear to be governed by thermoadaptation rules that differ in some aspects from those previously observed within their eubacterial counterparts.