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Effects of hydrated water on protein unfolding 总被引:5,自引:0,他引:5
The conformational stability of a protein in aqueous solution is described in terms of the thermodynamic properties such as unfolding Gibbs free energy, which is the difference in the free energy (Gibbs function) between the native and random conformations in solution. The properties are composed of two contributions, one from enthalpy due to intramolecular interactions among constituent atoms and chain entropy of the backbone and side chains, and the other from the hydrated water around a protein molecule. The hydration free energy and enthalpy at a given temperature for a protein of known three-dimensional structure can be calculated from the accessible surface areas of constituent atoms according to a method developed recently. Since the hydration free energy and enthalpy for random conformations are computed from those for an extended conformation, the thermodynamic properties of unfolding are evaluated quantitatively. The evaluated hydration properties for proteins of known transition temperature (Tm) and unfolding enthalpy (delta Hm) show an approximately linear dependence on the number of constituent heavy atoms. Since the unfolding free energy is zero at Tm, the enthalpy originating from interatomic interactions of a polypeptide chain and the chain entropy are evaluated from an experimental value of delta Hm and computed properties due to the hydrated water around the molecule at Tm. The chain enthalpy and entropy thus estimated are largely compensated by the hydration enthalpy and entropy, respectively, making the unfolding free energy and enthalpy relatively small. The computed temperature dependences of the unfolding free energy and enthalpy for RNase A, T4 lysozyme, and myoglobin showed a good agreement with the experimental ones.(ABSTRACT TRUNCATED AT 250 WORDS) 相似文献
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N-hydroxy-2-naphthylamine (NOH-2NA). an active metabolite of human occupational bladder carcinogens, induced, in V79 Chinese hamster cells. chromosomal aberrations which were suppressed in the presence of catalase and/or superoxide dismutase. The induction of the aberrations was more efficient in a more basic pH in parallel with the generation of hydrogen peroxide from NOH-2NA. The possible role of the oxidation product of NOH-2NA in the induction of the aberrations is discussed. 相似文献
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The thermal transition of RNase T1 was studied by two different methods; tryptophan residue fluorescence and circular dichroism. The fluorescence measurements provide information about the environment of the indole group and CD measurements on the gross conformation of the polypeptide chain. Both measurements at pH 5 gave the same transition temperature of 56 degrees C and the same thermodynamic quantities, delta Htr (= 120 kcal/mol) and delta Str (= 360 eu/mol), for the transition from the native state to the thermally denatured state, indicating simultaneous melting of the whole molecule including the hydrophobic region where the tryptophan residue is buried. Stabilization by salts was observed in the pH range from 2 to 10, since the presence of 0.5 m NaCL caused an increase of about 5 degrees C to 10 degrees C in the transition temperature, depending on the pH. The fluorescence measurements on the RNase T1 complexed with 2'-GMP showed a transition with delta Htr =167 kcal/mol and delta Str =497 eu/mol at a transition temperature about 6 degrees C higher than that for the free enzyme. The large value of delta Htr for RNase T1 indicates the highly cooperative nature of the thermal transition; this value is much higher than those of other globular proteins. Analysis of the CD spectrum of thermally denatured RNase T1 suggests that the denatured state is not completely random but retains some ordered structures. 相似文献
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The native conformation of a protein may be expressed in terms of the dihedral angles, phi's and psi's for the backbone, and kappa's for the side chains, for a given geometry (bond lengths and bond angles). We have developed a method to obtain the dihedral angles for a low-energy structure of a protein, starting with the X-ray structure; it is applied here to examine the degree of flexibility of bovine pancreatic trypsin inhibitor. Minimization of the total energy of the inhibitor (including nonbonded, electrostatic, torsional, hydrogen bonding, and disulfide loop energies) yields a conformation having a total energy of -221 kcal/mol and a root mean square deviation between all atoms of the computed and experimental structures of 0.63 A. The optimal conformation is not unique, however, there being at least two other conformations of low-energy (-222 and -220 kcal/mol), which resemble the experimental one (root mean square deviations of 0.66 and 0.64 A, respectively). These three conformations are located in different positions in phi, psi space, i.e., with a total deviation of 81 degrees, 100 degrees and 55 degrees from each other (with a root mean square deviation of several degrees per dihedral angle from each other). The nonbonded energies of the backbones, calculated along lines in phi, psi space connecting these three conformations, are all negative, without any intervening energy barriers (on an energy contour map in the phi, psi plane). Side chains were attached at several representative positions in this plane, and the total energy was minimized by varying the kappa's. The energies were of approximately the same magnitude as the previous ones, indicating that the conformation of low energy is flexible to some extent in a restricted region of phi, psi space. Interestingly, the difference delta phi i+1 in phi i+1 for the (i + 1)th residue from one conformation to another is approximately the same as -delta psi i for the ith residue; i.e., the plane of the peptide group between the ith and (i + 1)th residues re-orient without significant changes in the positions of the other atoms. The flexibility of the orientations of the planes of the peptide groups is probably coupled in a cooperative manner to the flexibility of the positions of the backbone and side-chain atoms. 相似文献
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Tsutomu Nakayama Motohisa Kaneko Masahiko Kodama 《Bioscience, biotechnology, and biochemistry》2013,77(12):3219-3220
Thermostable purine nucleoside phosphorylases, PUN PI and PUNPII, have been purified from Bacillus stearothermophilus JTS 859. The characterization of PUNPI was reported previously. [Hori et al.9 Agric. Biol. Chem. 53, 2205 (1989)] PUNPII had a molecular weight of 113,000, consisting of 4 identical subunits (Mw 28,000). The isoelectric point was 5.3. The Michaelis constants for inosine, guanosine, and adenosine were 0.22, 0.34, and 0.075 mm, respectively. The optimal temperature of the reaction was 70°C. The enzyme was stable at 70°C. Although other reported purine nucleoside phosphorylases were SH-enzymes, PUNPII was not a SH-enzyme because the enzyme reaction was not inhibited by PCMB and iodoacetic acid, the optimal pH of the enzyme reaction was from 7.0 to 11.0, and the enzyme did not contain cysteine.PUNPII and PUNPI were different in several points. Not PUNPI but PUNPII could catalyze the phosphorolysis of adenosine. Specific activity of PUNPI and II for inosine were 405 and 50.6 μmol/min/mg protein at 60°C, respectively. PUNPI was stable at 80°C. PUNPII was stable at 70°C, but was denatured at 80°C. 相似文献
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M. Michael Gromiha Motohisa Oobatake Hidetoshi Kono Hatsuho Uedaira Akinori Sarai 《Journal of Protein Chemistry》1999,18(5):565-578
In order to understand the mechanism of protein stability and to develop a simple method for predicting mutation-induced stability changes, we analyzed the relationship between stability changes caused by buried mutations and changes in 48 amino acid properties. As expected from the importance of hydrophobicity, properties reflecting hydrophobicity are strongly correlated with the stability of proteins. We found that subgroup classification based on secondary structure increased correlations significantly, and mutations within -strand segments correlated better than did those in -helical segments, which may result from stronger hydrophobicity of the -strands. Multiple regression analyses incorporating combinations of three properties from among all possible combinations of the 48 properties increased the correlation coefficient to 0.88 and by an average of 13% for all data sets. Analyzing the stability of tryptophan synthase mutants with Glu49 replaced by all other residues except Arg revealed that combining buriedness, solvent-accessible surface area for denatured protein, and unfolding Gibbs free energy change increased the correlation to 0.95. Consideration of sequence and structural information (neighboring residues in sequence and in space) did not significantly strengthen the correlations in buried mutations, suggesting that nonspecific interactions dominate in the interior of proteins. 相似文献
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Yamada M Tohno Y Takakura Y Tohno S Moriwake Y Minami T 《Biological trace element research》2003,91(1):57-66
To elucidate compositional changes of the tendons with aging, the authors investigated age-related changes of element contents
in the tendon of the iliopsoas muscle by inductively coupled plasma-atomic emission spectrometry. The subjects consisted of
14 men and 14 women, ranging in age from 4 to 102 yr. The insertion tendons of the iliopsoas were removed from the cadavers
after ordinary dissection and also surgically from patients with congenital dislocation of the hip. It was found that both
Mg and P in the tendon of the iliopsoas muscle increased significantly with aging, but the other elements, such as S, Ca,
Na, Zn, Fe, and Si, hardly changed with aging.
With regard to the relationship among element contents, extremely significant correlations were found between P and S contents,
between Mg and Na contents, and between S and Zn contents. In addition, very significant correlations were found between Si
and either S or Zn contents. However, there was no significant correlation between Ca and P contents. These results revealed
that with regard to age-related changes of element contents and the relationships among element contents, the tendon of the
iliopsoas muscle was different from the Achilles tendon, in which both Mg and P decreased significantly with aging and there
were significant correlations each other among the contents of S, Mg, and P. 相似文献
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Gromiha MM An J Kono H Oobatake M Uedaira H Prabakaran P Sarai A 《Nucleic acids research》2000,28(1):283-285
ProTherm 2.0 is the second release of the Thermo-dynamic Database for Proteins and Mutants that includes numerical data for several thermodynamic parameters, structural information, experimental methods and conditions, functional and literature information. The present release contains >5500 entries, an approximately 67% increase over the previous version. In addition, we have included information about reversibility of data, details about buffer and ion concentrations and the surrounding residues in space for all mutants. A WWW interface enables users to search data based on various conditions with different sorting options for outputs. Further, ProTherm has links with other structural and literature databases, and the mutation sites and surrounding residues are automatically mapped on the structures and can be directly viewed through 3DinSight developed in our laboratory. The ProTherm database is freely available through the WWW at http://www.rtc.riken.go.jp/protherm.html 相似文献
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