Abstract:
:In globular proteins, there are intermolecular hydrogen bonds between protein and water molecules, and between water molecules, which are bound with the proteins, in addition to intramolecular hydrogen bonds. To estimate the contribution of these hydrogen bonds to the conformational stability of a protein, the thermodynamic parameters for denaturation and the crystal structures of five Thr to Val and five Thr to Ala mutant human lysozymes were determined. The denaturation Gibbs energy (DeltaG) of Thr to Val and Thr to Ala mutant proteins was changed from 4.0 to -5.6 kJ/mol and from 1.6 to -6.3 kJ/mol, respectively, compared with that of the wild-type protein. The contribution of hydrogen bonds to the stability (DeltaDeltaG(HB)) of the Thr and other mutant human lysozymes previously reported was extracted from the observed stability changes (DeltaDeltaG) with correction for changes in hydrophobicity and side chain conformational entropy between the wild-type and mutant structures. The estimation of the DeltaDeltaG(HB) values of all mutant proteins after removal of hydrogen bonds, including protein-water hydrogen bonds, indicates a favorable contribution of the intra- and intermolecular hydrogen bonds to the protein stability. The net contribution of an intramolecular hydrogen bond (DeltaG(HB[pp])), an intermolecular one between protein and ordered water molecules (DeltaG(HB[pw])), and an intermolecular one between ordered water molecules (DeltaG(HB[ww])) could be estimated to be 8. 5, 5.2, and 5.0 kJ/mol, respectively, for a 3 A long hydrogen bond. This result shows the different contributions to protein stability of intra- and intermolecular hydrogen bonds. The entropic cost due to the introduction of a water molecule (DeltaG(H)()2(O)) could be also estimated to be about 8 kJ/mol.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Takano K,Yamagata Y,Funahashi J,Hioki Y,Kuramitsu S,Yutani Kdoi
10.1021/bi9910169subject
Has Abstractpub_date
1999-09-28 00:00:00pages
12698-708issue
39eissn
0006-2960issn
1520-4995pii
bi9910169journal_volume
38pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::Calcium is required for the substrate binding and for the chemical step of the interfacial catalytic turnover cycle of pancreatic phospholipase A2 (PLA2), but not for the binding of the enzyme to the interface. The role of calcium and other divalent cations (C) is analyzed for the effect on the substrate binding and k...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9728607
更新日期:1998-09-08 00:00:00
abstract::Human S100B(beta beta) is a small intracellular EF-hand calcium-binding protein that consists of two noncovalently associated 91-residue beta monomers. The three-dimensional structures of S100B reveal the dimer interface consists of four alpha-helices (I, I' and IV, IV') packed in an X-type bundle. In this study, guan...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0118052
更新日期:2002-03-19 00:00:00
abstract::Biogenesis of the Gram-negative outer membrane involves the chaperone seventeen kilodalton protein (Skp). A Skp trimer is currently thought to bind its unfolded outer membrane protein (uOMP) substrates. Using sedimentation equilibrium, we discovered that Skp is not an obligate trimer under physiological conditions and...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.5b00806
更新日期:2015-12-08 00:00:00
abstract::Deuterium-labeled dihydroorotates bearing one, two, or three deuteriums at the pair of C4 and C5 positions have been synthesized in high isotopic and chiral purity and characterized by NMR and mass spectroscopy. These substrates have been used with the FMN-containing biosynthetic dihydroorotate oxidase from Crithidia ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00307a033
更新日期:1984-06-05 00:00:00
abstract::Anatoxin-a and homoanatoxin-a are two potent cyanobacterial neurotoxins. We recently reported the identification of the gene cluster responsible for the biosynthesis of these toxins as well as the in-vitro reconstitution of the first steps of this biosynthesis. We now report experimental evidence supporting the propos...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi200892a
更新日期:2011-08-23 00:00:00
abstract::To understand the stabilization, folding, and functional mechanisms of proteins, it is very important to understand the structural and thermodynamic properties of the molten globule state. In this study, the global structure of the acid molten globule state, which we call MG1, of horse cytochrome c at low pH and high ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi101806b
更新日期:2011-04-19 00:00:00
abstract::The folding of the enzyme indole-3-glycerol-phosphate synthase (IGPS), a member of the (alpha/beta)8 fold family, has been studied. At least two folding intermediates have been detected using spectroscopic and activity measurements in combination with gel filtration chromatography. These two intermediates are produced...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi963133z
更新日期:1997-05-06 00:00:00
abstract::Lactone-hydrolyzing enzymes derived from some Bacillus species are capable of disrupting quorum sensing in bacteria that use N-acyl-l-homoserine lactones (AHLs) as intercellular signaling molecules. Despite the promise of these quorum-quenching enzymes as therapeutic and anti-biofouling agents, the ring opening mechan...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi061238o
更新日期:2006-11-07 00:00:00
abstract::Inheritance of apoE4 is a strong risk factor for the development of late-onset sporadic Alzheimer's disease (AD). Several lines of evidence suggest that apoE4 binds to the Alzheimer Abeta protein and, under certain experimental conditions, promotes formation of beta-sheet structures and amyloid fibrils. Deposition of ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0114269
更新日期:2001-12-11 00:00:00
abstract::In two recent papers, we reported the effects of several point mutations on the thermodynamics of the thermal unfolding of the lysozyme of phage T4 as determined by differential scanning calorimetry. The mutants studied were R96H [Kitamura, S., & Sturtevant, J.M. (1989) Biochemistry 28, 3788-3792] and T157 replaced by...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00121a009
更新日期:1992-02-18 00:00:00
abstract::The interaction of poly[(G-C)] and poly[d(G-m5C)] with the antitumor antibiotic elsamicin A, which binds to alternating guanine + cytosine tracts in DNA, has been studied under the B and Z conformations. Both the rate and the extent of the B-to-Z transition are diminished by the antibiotic, as inferred by spectroscopi...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00161a051
更新日期:1992-11-24 00:00:00
abstract::The interaction of the 20-kDa pore-forming domain of colicin A with phospholipid vesicles was investigated by gel permeation chromatography, analytical centrifugation, and electron microscopy. Under the experimental conditions of this study, this peptide was found to interact only with vesicles containing negatively c...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00445a029
更新日期:1989-09-19 00:00:00
abstract::We have used time-resolved phosphorescence anisotropy to investigate the effects of essential light chain (ELC) isoforms (A1 and A2) on the interaction of skeletal muscle myosin with actin, to relate structural dynamics to previously reported functional effects. Actin was labeled with a phosphorescent probe at C374, a...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi3014467
更新日期:2013-03-05 00:00:00
abstract::31P NMR spectra of equilibrium mixtures of enzyme-bound reactants and products of the adenylate kinase reaction (formula; see text) were analyzed by using computer simulations based on density matrix theory of chemical exchange. Since adenylate kinase has the unique feature that the reactants in the reverse direction ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00300a025
更新日期:1984-02-28 00:00:00
abstract::The multimeric cytochromes described to date in sulfate- and sulfur-reducing bacteria are associated with diverse respiratory modes involving the use of elemental sulfur or oxidized sulfur compounds as terminal acceptors. They exhibit no structural similarity with the other cytochrome c classes and are characterized b...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9707741
更新日期:1997-09-02 00:00:00
abstract::Metal homeostasis and resistance in bacteria is maintained by a panel of metal-sensing transcriptional regulators that collectively control transition metal availability and mediate resistance to heavy metal xenobiotics, including As(III), Cd(II), Pb(II), and Hg(II). The ArsR family constitutes a superfamily of metal ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi100490u
更新日期:2010-08-10 00:00:00
abstract::While the iron-molybdenum cofactor (FeMoco) of nitrogenase, a constituent of the active site for nitrogen reduction, can be extracted into N-methylformamide (NMF) and pyrrollidinone, the inability to solubilize it in any other organic solvents has hampered further understanding of its structure and chemical properties...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00450a024
更新日期:1989-11-28 00:00:00
abstract::Dendritic cell-specific intracellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN) is a C-type lectin highly expressed on the surface of antigen-presenting dendritic cells. DC-SIGN mediates interactions among dendritic cells, pathogens, and a variety of epithelia, myeloid cells, and endothelia by binding to high...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi5005014
更新日期:2014-09-09 00:00:00
abstract::We have studied a group of fusion peptides of influenza hemagglutinin in which the N-terminal amino acid, Gly (found in the wild-type peptide), has been systematically substituted with Ala, Ser, Val, or Glu. The activity of the intact hemagglutinin protein with these same substitutions has already been reported. As a ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0107187
更新日期:2001-07-31 00:00:00
abstract::The DNA binding domain (DBD) of p53 folds by a complex mechanism that involves parallel pathways and multiple intermediates, both on- and off-pathway. This heterogeneity renders DBD particularly susceptible to misfolding and aggregation. The origins of parallel folding mechanisms are not well understood. DBD folding h...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi062106y
更新日期:2007-03-13 00:00:00
abstract::Nitrobenzamido ligands linked to the DNA intercalator 9-aminoacridine via poly(methylene) chains induce single-strand nicks in DNA upon irradiation with long-wavelength ultraviolet light (lambda greater than or equal to 300 nm). Optimal photocleavage activity was found for the reagent 9-[[6-(4-nitrobenzamido)hexyl]ami...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00417a021
更新日期:1988-08-23 00:00:00
abstract::The alpha-helix [Pauling, L., Corey, R. B., & Branson, H. R. (1951) Proc. Natl. Acad. Sci. U.S.A. 37, 205-211] is a common motif in both proteins and peptides. Despite intense investigation, predictive understanding of helices is still lacking. A recent hypothesis [Presta, L. G., & Rose, G. D. (1988) Science 240, 1632...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00081a001
更新日期:1993-08-03 00:00:00
abstract::The hairpin ribozyme is an RNA enzyme that performs site-specific phosphodiester bond cleavage between nucleotides A-1 and G+1 within its cognate substrate. Previous functional studies revealed that the minimal hairpin ribozyme exhibited "gain-of-function" cleavage properties resulting from U39C or U39 to propyl linke...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi051550i
更新日期:2005-11-08 00:00:00
abstract::Recognition for proteolysis by trypsin depends almost exclusively on tight binding of arginine or lysine side chains by the primary substrate specificity pocket. Although extended subsite interactions are important for catalysis, the majority of binding energy is localized in the P1 pocket. Analysis of the interaction...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9530191
更新日期:1996-05-14 00:00:00
abstract::SH2 domains are protein modules which interact with specific tyrosine phosphorylated sequences in target proteins. The SH2 domain of the Src kinase binds with high affinity to a tyrosine phosphorylated peptide containing the amino acids Glu, Glu, and Ile (EEI) at the positions +1, +2, and +3 C-terminal to the phosphot...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi982974y
更新日期:1999-04-20 00:00:00
abstract::The synthesis of gangliosides GM3, GM2, GM1, and GD1a solely lacking the fatty acid moiety, and thus called lysogangliosides in analogy to lysophospholipids, is described. Since a selective elimination of the fatty acid residue has not been achieved as yet, the gangliosides were first subjected to alkaline hydrolysis....
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00323a042
更新日期:1985-01-15 00:00:00
abstract::Bacillus subtilis CsoR (Bsu CsoR) is a copper-sensing transcriptional repressor that regulates the expression of the copZA operon encoding a copper chaperone and a Cu efflux P-type ATPase, respectively. Bsu CsoR is a homologue of Mycobacterium tuberculosis CsoR (Mtb CsoR), representative of a large Cu(I)-sensing regul...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi900115w
更新日期:2009-04-21 00:00:00
abstract::We have measured the concentration of mRNAs coding for immunoglobulins, k and lambda type light chains and gamma 1 type heavy chain, in mouse spleen cells activated by bacterial lipopolysaccharide or sheep red blood cells. These mRNAs were quantitated by hybridization to radioactive DNA complementary to highly purifie...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00645a018
更新日期:1977-12-27 00:00:00
abstract::Identical first-order rate constants for phosphorylation of the calcium ATPase of sarcoplasmic reticulum by bound inorganic phosphate (Pi) of 25 +/- 2 s-1 with empty vesicles and 25 +/- 1 s-1 with vesicles that were passively loaded with 40 mM Ca2+ were obtained by treating the reaction as an approach to equilibrium (...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00009a039
更新日期:1995-03-07 00:00:00
abstract::The composition of the molybdate-stabilized glucocorticoid receptor (GR) complex has been investigated with a monoclonal antibody against the steroid-binding Mr 94 000 (94K) GR protein. It was concluded that one antibody molecule binds one 94K GR molecule. This finding constituted the basis for calculating the number ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00344a041
更新日期:1985-11-05 00:00:00