Solvent interaction of a Hsp70 chaperone substrate-binding domain investigated with water-NOE NMR experiments.


:The interaction of solvent of the substrate binding domain of the bacterial heat shock 70 chaperone protein DnaK was studied in its apo form and with bound hydrophobic substrate peptide, using refined nuclear magnetic resonance experiments. Distinct differences between the two states of the protein were observed. According to our data, the apo form interacts more extensively with solvent than the peptide-bound form. Significantly, the open hydrophobic substrate binding cleft of DnaK in the apo form is found to contain several molecules of water which are displaced by the binding of the hydrophobic substrate, the peptide NRLLLTG. The solvent in the hydrophobic cleft has a residence time longer than 400 ps. It is predicted that the displacement of this trapped water must contribute to the binding free energy of the natural hydrophobic substrates of this class of protein-folding chaperone proteins.






Cai S,Stevens SY,Budor AP,Zuiderweg ER




Has Abstract


2003-09-30 00:00:00












  • Splicing Site Recognition by Synergy of Three Domains in Splicing Factor RBM10.

    abstract::Splicing factor RBM10 and its close homologues RBM5 and RBM6 govern the splicing of oncogenes such as Fas, NUMB, and Bcl-X. The molecular architecture of these proteins includes zinc fingers (ZnFs) and RNA recognition motifs (RRMs). Three of these domains in RBM10 that constitute the RNA binding part of this splicing ...


    pub_type: 杂志文章


    authors: Serrano P,Hammond JA,Geralt M,Wüthrich K

    更新日期:2018-03-13 00:00:00

  • Engineering a Protein Binder Specific for p38α with Interface Expansion.

    abstract::Protein binding specificities can be manipulated by redesigning contacts that already exist at an interface or by expanding the interface to allow interactions with residues adjacent to the original binding site. Previously, we developed a strategy, called AnchorDesign, for expanding interfaces around linear binding e...


    pub_type: 杂志文章


    authors: Hussain M,Angus SP,Kuhlman B

    更新日期:2018-07-31 00:00:00

  • Relationship between Amphipathic β Structures in the β1 Domain of Apolipoprotein B and the Properties of the Secreted Lipoprotein Particles in McA-RH7777 Cells.

    abstract::Our previous studies demonstrated that the first 1000 amino acid residues (the βα1 domain) of human apolipoprotein (apo) B-100, termed apoB:1000, are required for the initiation of lipoprotein assembly and the formation of a monodisperse stable phospholipid (PL)-rich particle. The objectives of this study were (a) to ...


    pub_type: 杂志文章


    authors: Manchekar M,Kapil R,Sun Z,Segrest JP,Dashti N

    更新日期:2017-08-08 00:00:00

  • Characteristics of the isolated apical plasmalemma and intracellular tubulovesicles of the gastric acid secreting cells: demonstration of secretagogue-induced membrane mobilization.

    abstract::Separation of the gradient-purified gastric microsome into two membrane subfractions of distinct enzymatic and phospholipid composition has been achieved by mild SDS (0.033% w/v) treatment followed by sucrose gradient centrifugation of the pig and rabbit gastric microsomes. While the high-density membranes had all of ...


    pub_type: 杂志文章


    authors: Ray TK,Das PK,Nandi J,Banerjee A,Bandopadhyay S

    更新日期:1988-12-13 00:00:00

  • Conservation of electrostatic properties within enzyme families and superfamilies.

    abstract::Electrostatic interactions play a key role in enzyme catalytic function. At long range, electrostatics steer the incoming ligand/substrate to the active site, and at short distances, electrostatics provide the specific local interactions for catalysis. In cases in which electrostatics determine enzyme function, orthol...


    pub_type: 杂志文章


    authors: Livesay DR,Jambeck P,Rojnuckarin A,Subramaniam S

    更新日期:2003-04-01 00:00:00

  • Cytochrome P450 from Photobacterium profundum SS9, a piezophilic bacterium, exhibits a tightened control of water access to the active site.

    abstract::We report cloning, expression in Escherichia coli, and purification of cytochrome P450 from a deep-sea bacterium Photobacterium profundum strain SS9 (P450-SS9). The enzyme, which is predominately high spin (86%) in the absence of any added ligand, binds fatty acids and their derivatives and exhibits the highest affini...


    pub_type: 杂志文章


    authors: Sineva EV,Davydov DR

    更新日期:2010-12-21 00:00:00

  • Accumulation of immunoglobulin messenger ribonucleic acid in immunized mouse spleen.

    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...


    pub_type: 杂志文章


    authors: Honjo T,Shimizu A,Tsuda M,Natori S,Katatoka T,Dohmoto C,Mano Y

    更新日期:1977-12-27 00:00:00

  • Ion concentration and temperature dependence of DNA binding: comparison of PurR and LacI repressor proteins.

    abstract::Purine repressor (PurR) binding to specific DNA is enhanced by complexing with purines, whereas lactose repressor (LacI) binding is diminished by interaction with inducer sugars despite 30% identity in their protein sequences and highly homologous tertiary structures. Nonetheless, in switching from low- to high-affini...


    pub_type: 杂志文章


    authors: Moraitis MI,Xu H,Matthews KS

    更新日期:2001-07-10 00:00:00

  • 20-Iodo-14,15-epoxyeicosa-8(Z)-enoyl-3-azidophenylsulfonamide: photoaffinity labeling of a 14,15-epoxyeicosatrienoic acid receptor.

    abstract::Endothelium-derived epoxyeicosatrienoic acids (EETs) relax vascular smooth muscle by activating potassium channels and causing membrane hyperpolarization. Recent evidence suggests that EETs act via a membrane binding site or receptor. To further characterize this binding site or receptor, we synthesized 20-iodo-14,15-...


    pub_type: 杂志文章


    authors: Chen Y,Falck JR,Manthati VL,Jat JL,Campbell WB

    更新日期:2011-05-10 00:00:00

  • Uracil DNA-glycosylase/glyceraldehyde-3-phosphate dehydrogenase is an Ap4A binding protein.

    abstract::A 37 kDa protein that binds to diadenosine tetraphosphate (Ap4A) was purified from human HeLa cells and identified as uracil DNA glycosylase/glyceraldehyde-3-phosphate dehydrogenase (UDG/GAPDH). Utilizing photoaffinity labeling with [alpha-32P]8N3-Ap4A, an Ap4A binding protein of 37 kDa was identified from HeLa cell n...


    pub_type: 杂志文章


    authors: Baxi MD,Vishwanatha JK

    更新日期:1995-08-01 00:00:00

  • A mutational analysis of binding interactions in an antigen-antibody protein-protein complex.

    abstract::Alanine scanning mutagenesis, double mutant cycles, and X-ray crystallography were used to characterize the interface between the anti-hen egg white lysozyme (HEL) antibody D1.3 and HEL. Twelve out of the 13 nonglycine contact residues on HEL, as determined by the high-resolution crystal structure of the D1.3-HEL comp...


    pub_type: 杂志文章


    authors: Dall'Acqua W,Goldman ER,Lin W,Teng C,Tsuchiya D,Li H,Ysern X,Braden BC,Li Y,Smith-Gill SJ,Mariuzza RA

    更新日期:1998-06-02 00:00:00

  • Structure of the ternary complex formed by a chemotaxis receptor signaling domain, the CheA histidine kinase, and the coupling protein CheW as determined by pulsed dipolar ESR spectroscopy.

    abstract::The signaling apparatus that controls bacterial chemotaxis is composed of a core complex containing chemoreceptors, the histidine autokinase CheA, and the coupling protein CheW. Site-specific spin labeling and pulsed dipolar ESR spectroscopy (PDS) have been applied to investigate the structure of a soluble ternary com...


    pub_type: 杂志文章


    authors: Bhatnagar J,Borbat PP,Pollard AM,Bilwes AM,Freed JH,Crane BR

    更新日期:2010-05-11 00:00:00

  • Circular dichroism and fluorescence studies of homogeneous antibodies to type III pneumococcal polysaccharide.

    abstract::The near-ultraviolet circular dichroism (CD) of three homogeneous anti-type III pneumococcal antibodies in the absence and the presence of the specific hexasaccharide ligand was studied. In addition recombinations and hybridizations of H and L chains derived from two of these antibodies were carried out and the CD spe...


    pub_type: 杂志文章


    authors: Jaton JC,Huser H,Blatt Y,Pecht I

    更新日期:1975-12-02 00:00:00

  • Structural, dynamic, and chemical characterization of a novel S-glycosylated bacteriocin.

    abstract::Bacteriocins are bacterial peptides with specific activity against competing species. They hold great potential as natural preservatives and for their probiotic effects. We show here nuclear magnetic resonance-based evidence that glycocin F, a 43-amino acid bacteriocin from Lactobacillus plantarum, contains two β-link...


    pub_type: 杂志文章


    authors: Venugopal H,Edwards PJ,Schwalbe M,Claridge JK,Libich DS,Stepper J,Loo T,Patchett ML,Norris GE,Pascal SM

    更新日期:2011-04-12 00:00:00

  • Physical dissection of the structural elements responsible for regulatory properties and intersubunit interactions of protein kinase CK2 beta-subunit.

    abstract::The noncatalytic beta-subunit of protein kinase CK2 has been shown to display various and in some respects antagonistic effects on the catalytic alpha-subunit [Boldyreff et al. (1993) Biochemistry 32, 12672-12677; Meggio et al. (1994) Biochemistry 33, 4336-4342]. We have now examined the ability of peptides encompassi...


    pub_type: 杂志文章


    authors: Marin O,Meggio F,Sarno S,Pinna LA

    更新日期:1997-06-10 00:00:00

  • Identification of the serine residue phosphorylated by protein kinase C in vertebrate nonmuscle myosin heavy chains.

    abstract::Two-dimensional mapping of the tryptic phosphopeptides generated following in vitro protein kinase C phosphorylation of the myosin heavy chain isolated from human platelets and chicken intestinal epithelial cells shows a single radioactive peptide. These peptides were found to comigrate, suggesting that they were iden...


    pub_type: 杂志文章


    authors: Conti MA,Sellers JR,Adelstein RS,Elzinga M

    更新日期:1991-01-29 00:00:00

  • Purification and immunogenicity of fusion VP1 protein of foot and mouth disease virus.

    abstract::A procedure has been developed to purify foot and mouth disease virus (FMDV) VP1 surface antigens from recombinant Escherichia coli. The VP1 antigens are expressed as fusion proteins derived from the E. coli Trp operon and VP1 surface protein of FMDV. The procedure is capable of recovering greater than 96% of the desi...


    pub_type: 杂志文章


    authors: Shire SJ,Bock L,Ogez J,Builder S,Kleid D,Moore DM

    更新日期:1984-12-18 00:00:00

  • Mechanistic studies on full length and the catalytic domain of the tandem SH2 domain-containing protein tyrosine phosphatase: analysis of phosphoenzyme levels and Vmax stimulatory effects of glycerol and of a phosphotyrosyl peptide ligand.

    abstract::SHP-1, a protein tyrosine phosphatase containing two tandem SH2 domains, is autoinhibited at rest by its N-terminal SH2 (N-SH2) domain. Relief from autoinhibition and a subsequent 10-60-fold increase in V(max) have been observed upon N-SH2 domain engagement by a specific phosphotyrosyl ligand or upon deletion of the S...


    pub_type: 杂志文章


    authors: Wang J,Walsh CT

    更新日期:1997-03-11 00:00:00

  • Role of proximal His93 in nitric oxide binding to metmyoglobin. Application of continuum solvation in Monte Carlo protein simulations.

    abstract::Monte Carlo protein simulations with continuum solvation were used to explore the conformational mobility of NO within the active site of metmyoglobin. To the best of our knowledge this is the first application of a continuum solvation model for exploring protein binding sites. The usefulness of the Monte Carlo confor...


    pub_type: 杂志文章


    authors: Keserü GM,Menyhárd DK

    更新日期:1999-05-18 00:00:00

  • Specific RNA binding by Q beta coat protein.

    abstract::The interaction between the bacteriophage Q beta coat protein and its specific binding site on Q beta genomic RNA was characterized by using a nitrocellulose filter binding assay. Q beta coat protein bound to a synthetic 29-nucleotide RNA hairpin with an association constant of 400 microM-1 at 4 degrees C, 0.2 M ionic...


    pub_type: 杂志文章


    authors: Witherell GW,Uhlenbeck OC

    更新日期:1989-01-10 00:00:00

  • GTP-stimulated phosphorylation of P-glycoprotein in transporting vesicles from KB-V1 multidrug resistant cells.

    abstract::We have previously shown that GTP can replace ATP as an energy source to support vinblastine transport by the multidrug transporter P-glycoprotein (Pgp) in plasma membrane vesicles isolated from the multidrug resistant cell line KB-V1 [Lelong et al. (1992) FEBS Lett. 304, 256-260]. Like [gamma-32P]ATP, [gamma-32P]GTP ...


    pub_type: 杂志文章


    authors: Lelong IH,Cardarelli CO,Gottesman MM,Pastan I

    更新日期:1994-08-02 00:00:00

  • Functional roles of metal binding domains of the Archaeoglobus fulgidus Cu(+)-ATPase CopA.

    abstract::CopA, a thermophilic membrane ATPase from Archaeoglobus fulgidus, drives the outward movement of Cu(+) or Ag(+) [Mandal et al. (2002) J. Biol. Chem. 277, 7201-7208]. This, as other P(IB)-ATPases, is characterized by a putative metal binding sequence (C(380)PC(382)) in its sixth transmembrane fragment and cytoplasmic m...


    pub_type: 杂志文章


    authors: Mandal AK,Argüello JM

    更新日期:2003-09-23 00:00:00

  • A heuristic approach to the analysis of enzymic catalysis: reaction of delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-alpha-aminobutyrate and delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-allylglycine catalyzed by isopenicillin N synthase isozymes.

    abstract::Isopenicillin N synthase (IPNS) catalyzes the oxidative cyclization of delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine to isopenicillin N. It is proposed that the multiple products produced from certain substrate analogues result from pathway branching after formation of a ferryl oxene intermediate. We have been int...


    pub_type: 杂志文章


    authors: Blackburn JM,Sutherland JD,Baldwin JE

    更新日期:1995-06-06 00:00:00

  • Human CD4 Metastability Is a Function of the Allosteric Disulfide Bond in Domain 2.

    abstract::CD4 is expressed on the surface of specific leukocytes where it plays a key role in the activation of immunostimulatory T-cells and acts as a primary receptor for HIV-1 entry. CD4 has four ecto-domains (D1-D4) of which D1, D2, and D4 contain disulfide bonds. Although disulfide bonds commonly serve structural or cataly...


    pub_type: 杂志文章


    authors: Owen GR,Channell JA,Forsyth VT,Haertlein M,Mitchell EP,Capovilla A,Papathanasopoulos M,Cerutti NM

    更新日期:2016-04-19 00:00:00

  • Identification of human CYP2C19 residues that confer S-mephenytoin 4'-hydroxylation activity to CYP2C9.

    abstract::CYP2C19 is selective for the 4'-hydroxylation of S-mephenytoin while the highly similar CYP2C9 has little activity toward this substrate. To identify critical amino acids determining the specificity of human CYP2C19 for S-mephenytoin 4'-hydroxylation, we constructed chimeras by replacing portions of CYP2C9 containing ...


    pub_type: 杂志文章


    authors: Tsao CC,Wester MR,Ghanayem B,Coulter SJ,Chanas B,Johnson EF,Goldstein JA

    更新日期:2001-02-20 00:00:00

  • Human 3'-phosphoadenosine 5'-phosphosulfate synthetase (isoform 1, brain): kinetic properties of the adenosine triphosphate sulfurylase and adenosine 5'-phosphosulfate kinase domains.

    abstract::Recombinant human 3'-phosphoadenosine 5'-phosphosulfate (PAPS) synthetase, isoform 1 (brain), was purified to near-homogeneity from an Escherichia coli expression system and kinetically characterized. The native enzyme, a dimer with each 71 kDa subunit containing an adenosine triphosphate (ATP) sulfurylase and an aden...


    pub_type: 杂志文章


    authors: Lansdon EB,Fisher AJ,Segel IH

    更新日期:2004-04-13 00:00:00

  • O(2)-evolving chlorite dismutase as a tool for studying O(2)-utilizing enzymes.

    abstract::The direct interrogation of fleeting intermediates by rapid-mixing kinetic methods has significantly advanced our understanding of enzymes that utilize dioxygen. The gas's modest aqueous solubility (<2 mM at 1 atm) presents a technical challenge to this approach, because it limits the rate of formation and extent of a...


    pub_type: 杂志文章


    authors: Dassama LM,Yosca TH,Conner DA,Lee MH,Blanc B,Streit BR,Green MT,DuBois JL,Krebs C,Bollinger JM Jr

    更新日期:2012-02-28 00:00:00

  • Amino acid 305 determines catalytic center accessibility in CYP3A4.

    abstract::Site-directed mutagenesis has been used to replace alanine 305 with phenylalanine (A305F) and serine (A305S) in the active site of cytochrome P450 3A4 (CYP3A4). Enzyme kinetics for diazepam, erythromycin, nifedipine, and testosterone metabolism have been determined for both mutants and wild-type CYP3A4. The A305F muta...


    pub_type: 杂志文章


    authors: Fowler SM,Riley RJ,Pritchard MP,Sutcliffe MJ,Friedberg T,Wolf CR

    更新日期:2000-04-18 00:00:00

  • Purification and characterization of selenomethionyl thymidylate synthase from Escherichia coli: comparison with the wild-type enzyme.

    abstract::Replacement of methionine (Met) residues by selenomethionine (SeMet) was recently shown to facilitate the crystallographic analysis of protein structure through the application of multi-wavelength anomalous diffraction techniques [Yang et al. (1990) Science (Washington, D.C.) 249, 1398-1405]. The availability of SeMet...


    pub_type: 杂志文章


    authors: Boles JO,Cisneros RJ,Weir MS,Odom JD,Villafranca JE,Dunlap RB

    更新日期:1991-11-19 00:00:00

  • Crystal structure of the petal death protein from carnation flower.

    abstract::Expression of the PSR132 protein from Dianthus caryophyllus (carnation, clover pink) is induced in response to ethylene production associated with petal senescence, and thus the protein is named petal death protein (PDP). Recent work has established that despite the annotation of PDP in sequence databases as carboxyph...


    pub_type: 杂志文章


    authors: Teplyakov A,Liu S,Lu Z,Howard A,Dunaway-Mariano D,Herzberg O

    更新日期:2005-12-20 00:00:00