Thermostable Factor Research Articles

Traversing DNA-Protein Interactions Between Mesophilic and Thermophilic Bacteria: Implications from Their Cold Shock Response.

Cold shock proteins (CSPs) are small, acidic proteins which contain a conserved nucleic acid-binding domain. These perform mRNA translation acting as "RNA chaperones" when triggered by low temperatures initiating their cold shock response. CSP- RNA interactions have been predominantly studied. Our focus will be CSP-DNA interaction examination, to analyse the diverse interaction patterns such as electrostatic, hydrogen and hydrophobic bonding in both thermophilic and mesophilic bacteria. The differences in the molecular mechanism of these contrasting bacterial proteins are studied. Computational techniques such as modelling, energy refinement, simulation and docking were operated to obtain data for comparative analysis. The thermostability factors which stabilise a thermophilic bacterium and their effect on their molecular regulation is investigated. Conformational deviation, atomic residual fluctuations, binding affinity, Electrostatic energy and Solvent Accessibility energy were determined during stimulation along with their conformational study. The study revealed that mesophilic bacteria E. coli CSP have higher binding affinity to DNA than thermophilic G. stearothermophilus. This was further evident by low conformation deviation and atomic fluctuations during simulation.

Recombinant coagulation factors and their use in clinical practice

As is known, fresh frozen donor plasma is a blood component, which includes thermolabile and thermostable coagulation factors. Indications for transfusion of fresh frozen plasma are conditions in which there is a deficiency of plasma coagulation factors — bleeding, overdose of indirect anticoagulants, disseminated intravascular coagulation syndrome in the hypocoagulation phase. However, there are conditions not caused by the deficiency of all clotting factors, but associated with a lack of any link. These conditions include the most common congenital hemophilia A (factor VIII deficiency) and hemophilia B associated with factor IX deficiency, von Willebrand disease, as well as rare coagulopathy caused by a deficiency of other coagulation factors (proaccelerin, proconvertin, factor XI, fibrinogen). In such situations, it is more appropriate to replace the missing blood factors with drugs obtained from donor plasma (plasma coagulation factors) or obtained by genetic engineering (recombinant coagulation factors). Recombinant coagulation factors (RCFs) are lyophilized preparations of glycoproteins that have the biological activity of a blood coagulation factor isolated from plasma and are intended for replacement therapy in diseases associated with disorders of the blood coagulation system. The use of recombinant coagulation factors, unlike plasma ones, completely eliminates the risk of transmission of bloodborne infections, and also makes it possible to establish production regardless of the presence or absence of donor plasma reserves. The development, production and use of recombinant coagulation factors is a completely new step in the development of hematology and the treatment of hereditary diseases, which include congenital coagulopathy.

Understanding Thermostability Factors of Barley Limit Dextrinase by Molecular Dynamics Simulations.

Limit dextrinase (LD) is the only endogenous starch-debranching enzyme in barley (Hordeum vulgare, Hv), which is the key factor affecting the production of a high degree of fermentation. Free LD will lose its activity in the mashing process at high temperature in beer production. However, there remains a lack of understanding on the factor affecting the themostability of HvLD at the atomic level. In this work, the molecular dynamics simulations were carried out for HvLD to explore the key factors affecting the thermal stability of LD. The higher value of root mean square deviation (RMSD), radius of gyration (Rg), and surface accessibility (SASA) suggests the instability of HvLD at high temperatures. Intra-protein hydrogen bonds and hydrogen bonds between protein and water decrease at high temperature. Long-lived hydrogen bonds, salt bridges, and hydrophobic contacts are lost at high temperature. The salt bridge interaction analysis suggests that these salt bridges are important for the thermostability of HvLD, including E568–R875, D317–R378, D803–R884, D457–R214, D468–R395, D456–R452, D399–R471, and D541–R542. Root mean square fluctuation (RMSF) analysis identified the thermal-sensitive regions of HvLD, which will facilitate enzyme engineering of HvLD for enhanced themostability.

Improving the thermostability and stress tolerance of an archaeon hyperthermophilic superoxide dismutase by fusion with a unique N-terminal domain.

The superoxide dismutase from the archaeon Sulfolobus solfataricus (SODSs) is a well-studied hyperthermophilic SOD with crystal structure and possible thermostability factors characterized. Previously, we discovered an N-terminal domain (NTD) in a thermophilic SOD from Geobacillus thermodenitrificans NG80-2 which confers heat resistance on homologous mesophilic SODs. The present study therefore aimed to further improve the thermostability and stress tolerance of SODSs via fusion with this NTD. The recombinant protein, rSODSs, exhibited improved thermophilicity, higher working temperature, improved thermostability, broader pH stability, and enhanced tolerance to inhibitors and organic media than SODSs without any alterations in its oligomerization state. These results suggest that the NTD is an excellent candidate for improving stability of both mesophilic and thermophilic SOD from either bacteria or archaea via simple genetic manipulation. Therefore, this study provides a general, feasible and highly useful strategy for generating extremely thermostable SODs for industrial applications. Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-016-1854-9) contains supplementary material, which is available to authorized users.

<i>In-silico</i> Rational Protein Engineering and Design Approach to Improve Thermostability of a Haloalkane Dehalogenase Enzyme

Thermostability of enzymes is a major prerequisite for use in industrial enzymology. There are as such no simple general principles for achieving thermostability in case of enzymes as many factors are required to fulfil for different enzymes. The present study describes computational methods to design thermostable haloalkane dehalogenase enzyme using the crystal structure available Protein Data Bank (PDB ID: 1EDE). In in silico design strategy rule-based approaches such as disulfide bond geometry, new hydrophobic pocket design, new salt bridge construction and multiple mutations (combination of the above approaches) were introduced to the original enzyme. After each design strategy the functional effect was confirmed in terms of enzyme substrate binding by molecular docking using Autodock vina tool. Best design strategy was evaluated by comparative molecular dynamics simulation applying simulated annealing method at 8 ns using GROMACS tool. The surface hydrophobicity which is the key factor for thermostability in haloalkane dehalogenase was obtained from the simulation result. Upon optimizing the parameters, thermostability of mutant enzyme under consideration was also confirmed by the 5 ns molecular dynamics simulation at 400, 500 and 600 K.

Quality Matters: Extension of Clusters of Residues with Good Hydrophobic Contacts Stabilize (Hyper)Thermophilic Proteins

Identifying determinant(s) of protein thermostability is key for rational and data-driven protein engineering. By analyzing more than 130 pairs of mesophilic/(hyper)thermophilic proteins, we identified the quality (residue-wise energy) of hydrophobic interactions as a key factor for protein thermostability. This distinguishes our study from previous ones that investigated predominantly structural determinants. Considering this key factor, we successfully discriminated between pairs of mesophilic/(hyper)thermophilic proteins (discrimination accuracy: ∼80%) and searched for structural weak spots in E. coli dihydrofolate reductase (classification accuracy: 70%).

Understanding Thermostability Factors of Aspergillus niger PhyA Phytase: A Molecular Dynamics Study

Molecular dynamics simulation was used to study the dynamic differences between native Aspergillus niger PhyA phytase and a mutant with 20% greater thermostability. Atomic root mean square deviation, radius of gyration, and number of hydrogen bonds and salt bridges are examined to determine thermostability factors. The results suggest that, among secondary structure elements, loops have the most impact on the thermal stability of A. niger phytase. In addition, the location rather than the number of hydrogen bonds is found to have an important contribution to thermostability. The results also show that salt bridges may have stabilizing or destabilizing effect on the enzyme and influence its thermostability accordingly.

A simple statistical method for discrimination of thermophilic and mesophilic proteins based on amino acid composition

In this study, the amino acid composition of thermophilic and mesophilic protein sequences was systematically analysed to obtain the thermostable factors. We found that the residues, Ala, Val, Leu, Ile, Thr, Gln, Glu, Lys and Arg showed a significant difference between these two kinds of proteins. On the basis of this information, a simple statistical method for discriminating Thermophilic and Mesophilic Proteins was developed, and the result was good. The accuracy of our method for back-check validation was 82.0%, and for another two independent testing data sets were 88.2% and 89.8%, respectively. The influence of protein size and specific residues on discrimination was also discussed.

Increased number of Arginine-based salt bridges contributes to the thermotolerance of thermotolerant acetic acid bacteria, Acetobacter tropicalis SKU1100

Thermotolerant acetic acid bacteria (AAB), Acetobacter tropicalis SKU1100, can grow above 40°C. To investigate the basis of its thermotolerance, we compared the genome of A. tropicalis SKU1100 with that of mesophilic AAB strain Acetobacter pasteurianus IFO3283-01. The comparative genomic study showed that amino acid substitutions from large to small residue and Lys to Arg occur in many orthologous genes. Furthermore, comparative modeling study was carried out with the orthologous proteins between SKU1100 and IFO3283-01 strains, indicating that the number of Arg-based salt bridges increased in protein models. Since it has been reported that Arg-based salt bridges are important factor for thermo-stability of protein structure, our results strongly suggest that the increased number of Arg-based salt bridges may contributes to the thermotolerance of A. tropicalis SKU1100 (the thermo-stability of proteins in A. tropicalis SKU1100).

Human embryonic stem cells secrete soluble factors that inhibit cancer cell growth.

The aim of this study was to determine whether normal human embryonic stem cells (hESC) would secrete factors that arrest growth of human epithelial cancer cell lines. Cell proliferation was examined using the MTT assay then haemocytometer cell counts. Staining with propidium iodide followed by flow cytometry was used to detect cell cycle stages. Heat denaturation and molecular fractionation experiments were also performed. We found that hESC conditioned medium (hESC CM) inhibited SKOV-3 and HEY cell proliferation. Similar results were also obtained when we used breast and prostate cancer cell lines, whereas little or no inhibitory effect was observed when human fibroblasts were tested. Moreover, a co-culture model confirmed that inhibition of cancer cell proliferation is mediated by soluble factors produced by hESCs. We also determined that the proportion of cancer cells in G(1) phase was increased by hESC CM treatment, accompanied by decrease in cells in S and G(2)/M phases, suggesting that the factors slow progression of cancer cells by cell cycle inhibition. Heat denaturation and molecular fractionation experiments indicated a low molecular weight thermostable factor was responsible for these properties. Our findings provide evidence that the human embryonic microenvironment contains soluble factor(s) that are capable of inhibiting growth of cancer cells, and that exposure to such factors may represent a new cancer treatment strategy.

Preparation and Characterization of Carbon Nanotubes-Coated Cordierite for Catalyst Supports

The carbon nanotubes-coated cordierite (CNTs-cordierite) was fabricated by pyrolysis of ethine on cordierite with iron catalyst, which was penetrated into the cordierite substrate by vacuum impregnation. The cordierite substrate, carbon naontubes, and CNTs-cordierite were characterized by SEM, TEM/HREM, BET, and TGA. The results show that the carbon nanotubes were distributed uniformly on the surface of cordierite. A significant increase in BET surface area and pore volume was observed, and a suitable pore-size distribution was obtained. On the CNTs-cordierite, carbon nanotubes penetrated into the cordierite substrate, which led to a remarkable stability of the CNTs against ultrasound maltreatment. Growth time is an important factor for thermostability and texture of the sample. The mass increased but the purity decreased with the growth time, which caused the exothermic peak shift to low temperature, and the corresponding full width half maximum (FWHM) of the peak in DTG increased.

The crystal structure of Aq_328 from the hyperthermophilic bacteria Aquifex aeolicus shows an ancestral histone fold.

The structure of Aq_328, an uncharacterized protein from hyperthermophilic bacteria Aquifex aeolicus, has been determined to 1.9 A by using multi-wavelength anomalous diffraction (MAD) phasing. Although the amino acid sequence analysis shows that Aq_328 has no significant similarity to proteins with a known structure and function, the structure comparison by using the Dali server reveals that it: (1) assumes a histone-like fold, and (2) is similar to an ancestral nuclear histone protein (PDB code 1F1E) with z-score 8.1 and RMSD 3.6 A over 124 residues. A sedimentation equilibrium experiment indicates that Aq_328 is a monomer in solution, with an average sedimentation coefficient of 2.4 and an apparent molecular weight of about 20 kDa. The overall architecture of Aq_328 consists of two noncanonical histone domains in tandem repeat within a single chain, and is similar to eukaryotic heterodimer (H2A/H2B and H3/H4) and an archaeal histone heterodimer (HMfA/HMfB). The sequence comparisons between the two histone domains of Aq_328 and six eukaryotic/archaeal histones demonstrate that most of the conserved residues that underlie the Aq_328 architecture are used to build and stabilize the two cross-shaped antiparallel histone domains. The high percentage of salt bridges in the structure could be a factor in the protein's thermostability. The structural similarities to other histone-like proteins, molecular properties, and potential function of Aq_328 are discussed in this paper.

In vitro decondensation of the sperm chromatin in Holothuria tubulosa (sea cucumber) not affecting proteolysis of basic nuclear proteins

Sea urchin and sea star oocyte extracts contain proteolytic activities that are active against sperm basic nuclear proteins (SNBP). This SNBP degradation has been related to the decondensation of sperm chromatin as a possible model to male pronuclei formation. We have studied the presence of this proteolytic activity in Holothuria tubulosa (sea cucumber) and its possible relationship with sperm nuclei decondensation. The mature oocyte extracts from H. tubulosa contain a proteolytic activity to SNBP located in the macromolecular fraction of the egg-jelly layer. SNBP degradation occurred both on sperm nuclei and on purified SNBP, histones being more easily degraded than protein Ø(o) (sperm-specific protein). SNBP degradation was found to be dependent on concentration, incubation time, presence of Ca(2+), pH, and this activity could be a serine-proteinase. Thermal denaturalization of the oocyte extracts (80 degrees C, 10-15 min) inactivates its proteolytic activity on SNBP but does not affect sperm nuclei decondensation. These results would suggest that sperm nuclei decondensation occurs by a mechanism different from SNBP degradation. Thus, the sperm nuclei decondensation occurs by a thermostable factor(s) and the removal of linker SNBP (H1 and protein Ø(o)) will be a first condition in the process of sperm chromatin remodeling.

Protein thermostability: structure-based difference of amino acid between thermophilic and mesophilic proteins

Structural distributions of each amino acid were compared between 20 pairs of thermophilic and mesophilic proteins to obtain thermostable factors. Five kinds of residual structure states such as fully-exposed, exposed, partially exposed (or partially buried), buried, well-buried states were considered for analyzing the structural patterns of amino acids. The statistical tests revealed that lower frequency in partially exposed state of SER, lower frequency in exposed state and higher frequency in well-buried state of ALA, higher frequency in buried state of GLU, higher frequency in exposed state of ARG, etc. could be critical factors related with protein thermostability.

Lonomia genus caterpillar toxins: Biochemical aspects

In 1967 we reported for the first time five cases of an acquired bleeding disorder in humans which developed after contact with saturnidae caterpillars. Since that time, other cases have been reported in Brazil, French Guyana, Peru, Paraguay and Argentina. The caterpillars have been identified as Lonomia achelous (LA) in Venezuela and northern Brazil and as Lonomia obliqua (LO) in southern Brazil. All patients present pain and a burning sensation at the site of contact. Within a few hours hematomas and hematuria are seen in combination with intracerebral and intraperitoneal hemorrhage (in some cases also renal failure). Hematological tests show: mild anemia with leucocytosis; prolonged PT, PTT and ThT; decreased fibrinogen, factor V, factor XIII, plasminogen and α2-antiplasmin levels; increased factor VIII:c, von Willebrand factor, and FDPs/D-dimers levels with normal ATIII and platelets. Factor VII, factor II and PC levels varied. Several activities similar to or directed against blood clotting factors have been identified in LA: fibrinolytic enzymes, which degrade fibrinogen producing abnormal FDPs; prothrombin activators: one direct and one factor Xa-like; a thermostable factor V activator; a thermolabile factor V inhibitor; a factor XIII proteolytic/urokinase-like activity; and a kallikrein-like activitiy. In LO three activities have been described: a prothrombin activator called ‘ Lonomia obliqua prothrombin activator protease’ (LOPAP); a factor X activator; and a phospholipase A 2-like activity called Lonomiatoxin. No fibrinolytic activity has been described in LO. Subcutaneous injection of crude hemolymph and some chromatographic fractions of LA induce a decrease in fibrinogen, plasminogen and factor XIII. Intravenous injection of factor XIII proteolytic/urokinase-like activity induce a dose-dependent thrombolysis with a decrease in plasmatic factor XIII without hemorrhagic manifestations. Intradermal injection of LO bristle extracts in rats and rabbits produce incoagulability whereas intravenous injection of LOPAP induced DIC in mice.

Extremely thermostable elongation factor G from Aquifex aeolicus: cloning, expression, purification, and characterization in a heterologous translation system.

The fus gene of the translation factor G (EF-G) from the hyperthermophilic bacterium Aquifex aeolicus was cloned under control of a phage promoter and overexpressed in Escherichia coli with the T7 RNA polymerase system. A heat denaturation step at 95 degrees C was used to purify the protein from the cell extract. This approach simplified the chromatographic procedures and decreased the protein loss since most of Escherichia coli proteins were denatured and precipitated. Ten milligrams of the highly purified protein was isolated from 4 liters of induced culture. The overproduced EF-G was active in ribosome-dependent GTP hydrolysis and a poly(U)-directed polyphenylalanine translation system with E. coli 70S ribosomes. The method presented here might facilitate functional and structural studies of important components of the protein biosynthesis system.

Mirror image mutations reveal the significance of an intersubunit ion cluster in the stability of 3-isopropylmalate dehydrogenase

The comparison of the three-dimensional structures of thermophilic ( Thermus thermophilus) and mesophilic ( Escherichia coli) 3-isopropylmalate dehydrogenases (IPMDH, EC 1.1.1.85) suggested that the existence of extra ion pairs in the thermophilic enzyme found in the intersubunit region may be an important factor for thermostability. As a test of our assumption, glutamine 200 in the E. coli enzyme was turned into glutamate (Q200E mutant) to mimic the thermophilic enzyme at this site by creating an intersubunit ion pair which can join existing ion clusters. At the same site in the thermophilic enzyme we changed glutamate 190 into glutamine (E190Q), hereby removing the corresponding ion pair. These single amino acid replacements resulted in increased thermostability of the mesophilic and decreased thermostability of the thermophilic enzyme, as measured by spectropolarimetry and differential scanning microcalorimetry.

Thermostable hepatocyte growth factor and energy metabolism in rats after partial hepatectomy

The relationship between energy metabolism in the remaining liver tissue after 60% hepatectomy and the activity of low-molecular-weight thermostable hepatocyte growth factor was studied in rats. The energy status of the liver was markedly reduced 6 h and to a greater degree 12 h after the operation, judging from the levels of ATP, ADP, AMP, and energy potential. The energy status improved (energy potential increased to 95% of the initial level) 24–72 h after the operation. This coincided with a decrease in hexokinase and phosphofructokinase activities and an increase in glucose-6-phosphate dehydrogenase and isocitrate dehydrogenase activities, indicating suppressed glycolysis and activation of the Krebs' cycle. High activity of low-molecular-weight thermostable hepatocyte growth factor was detected 24–72 h after resection of the liver (with maximum activity after 48 h). The activity of the hepatocyte growth factor increased if the range of energy potential surpassed the level sufficient for maintaining protein production, which is an energy-consuming process, but lower than the normal level.

Crystal structure of the β-glycosidase from the hyperthermophilic archeon Sulfolobus solfataricus: resilience as a key factor in thermostability

Enzymes from hyperthermophilic organisms must operate at temperatures which rapidly denature proteins from mesophiles. The structural basis of this thermostability is still poorly understood. Towards a further understanding of hyperthermostability, we have determined the crystal structure of the β-glycosidase (clan GH-1A, family 1) from the hyperthermophilic archaeon Sulfolobus solfataricus at 2.6 Å resolution. The enzyme is a tetramer with subunit molecular mass at 60 kDa, and crystallises with half of the tetramer in the asymmetric unit. The structure is a (βα) 8 barrel, but with substantial elaborations between the β-strands and α-helices in each repeat. The active site occurs at the centre of the top face of the barrel and is connected to the surface by a radial channel which becomes a blind-ended tunnel in the tetramer, and probably acts as the binding site for extended oligosaccharide substrates. Analysis of the structure reveals two features which differ significantly from mesophile proteins; (1) an unusually large proportion of surface ion-pairs involved in networks that cross-link sequentially separate structures on the protein surface, and (2) an unusually large number of solvent molecules buried in hydrophilic cavities between sequentially separate structures in the protein core. These factors suggest a model for hyperthermostability via resilience rather than rigidity.

Segmental demyelination induced by cerebrospinal fluid of progressive spastic paraparesis: correlation with altered proteolytic parameters

Progressive spastic paraparesis (PSP) is a demyelinating disease of the central nervous system. We studied the ability of the cerebrospinal fluid (CSF) of patients to induce alterations in rat peroneal nerves, and to modify the proteolytic activity of trypsin in vitro. Subperineurial injection of native or heated CSF of patients induced segmental demyelination and other cytological alterations 5–7 days later, in the infiltrated zone, while proximal and distal regions were normal. The CSF of normal subjects did not induce demyelination, but upon heating, it did so. Trypsin was strongly inhibited by the normal CSF but upon heating, its inhibitory activity was replaced by a strong potentiation. In contrast, native and heated CSF of patients potentiated trypsin. Our findings indicate that (1) the normal CSF contains a thermostable factor that potentiates trypsin whose function is overruled by thermolabile protease inhibitors; (2) the CSF of PSP patients has a reduced inhibitory activity and a conserved ability to potentiate trypsin; and (3) the CSF is endowed with a pathogenic power that correlates with an unchecked potentiating activity. We propose that the imbalance of a protease system may play a role in the pathogenesis of PSP lesions.