当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Electrostatic interactions in the denatured state and in the transition state for protein folding: effects of denatured state interactions on the analysis of transition state structure.

Electrostatic interactions in the denatured state and in the transition state for protein folding: effects of denatured state interactions on the analysis of transition state structure.

Abstract：

:The development of electrostatic interactions during the folding of the N-terminal domain of the ribosomal protein L9 (NTL9) is investigated by pH-dependent rate equilibrium free energy relationships. We show that Asp8, among six acidic residues, is involved in non-native, electrostatic interactions with K12 in the transition state for folding as well as in the denatured state. The perturbed native state pK(a) of D8 (pK(a) = 3.0) appears to be maintained through non-native interactions in both the transition state and the denatured state. Mutational effects on the stability of the transition state for protein (un)folding are often analyzed in respect to change in ground states. Thus, the interpretation of transition state analysis critically depends on an understanding of mutational effects on both the native and denatured state. Increasing evidence for structurally biased denatured states under physiological conditions raises concerns about possible denatured state effects on folding studies. We show that the structural interpretation of transition state analysis can be altered dramatically by denatured state effects.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Cho JH,Raleigh DP

doi

10.1016/j.jmb.2006.04.038

subject

Has Abstract

pub_date

2006-06-23 00:00:00

pages

1437-46

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(06)00512-2

journal_volume

359

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Conformation of the coat protein of filamentous bacteriophage Pf1 determined by neutron diffraction from magnetically oriented gels of specifically deuterated virions.

    abstract：:The structure of filamentous bacteriophage Pf1 has been studied using neutron diffraction from magnetically oriented gels of native and valine-deuterated phage. Neutron diffraction intensities were measured to approximately 8 A resolution along the equator and first six layer-lines, and differences due to the deuterat...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(88)90387-7

    authors： Stark W,Glucksman MJ,Makowski L

    更新日期：1988-01-05 00:00:00

  • Isolation and characterization of ribosomal DNA variants from Sciara coprophila.

    abstract：:The ribosomal RNA multigene family in the fungus fly Sciara coprophila contains a total of only 65 to 70 repeat units. We explored the types and frequencies of variant repeats in this small multigene family by characterizing different cloned rDNA variants from Sciara. Although we did not observe any intergenic spacer ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(89)90286-6

    authors： Kerrebrock AW,Srivastava R,Gerbi SA

    更新日期：1989-11-05 00:00:00

  • Bile acid interactions with rabbit ileal lipid binding protein and an engineered helixless variant reveal novel ligand binding properties of a versatile beta-clam shell protein scaffold.

    abstract：:The intracellular ileal lipid binding proteins (ILBPs) are involved in the transport and enterohepatic circulation of bile acids. ILBPs from different species show high sequence and structural homology and have been shown to bind multiple bile acid ligands with differing degrees of selectivity and positive co-operativ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.06.024

    authors： Kouvatsos N,Thurston V,Ball K,Oldham NJ,Thomas NR,Searle MS

    更新日期：2007-08-31 00:00:00

  • Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: molecular dynamics calculations.

    abstract：:Starting from the glycophorin A dimer structure determined by NMR, we performed simulations of both dimer and monomer forms in explicit lipid bilayers with constant normal pressure, lateral area, and temperature using the CHARMM potential. Analysis of the trajectories in four different lipids reveals how lipid chain l...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.4072

    authors： Petrache HI,Grossfield A,MacKenzie KR,Engelman DM,Woolf TB

    更新日期：2000-09-22 00:00:00

  • Translational activation in coliphage Qbeta: on a polycistronic messenger RNA, repression of one gene can activate translation of another.

    abstract：:We present evidence for translational activation of the Qbeta coliphage maturation cistron, mediated by the presence of Qbeta replicase. This activation does not require RNA replication, translation of a second gene, or any direct protein-RNA binding at the maturation gene initiation site. Our data support a model in ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.1194

    authors： Priano C,Arora R,Jayant L,Mills DR

    更新日期：1997-08-22 00:00:00

  • The C-Box Region of MAF1 Regulates Transcriptional Activity and Protein Stability.

    abstract：:MAF1 is a conserved negative regulator of RNA polymerase (pol) III and intracellular lipid homeostasis across species. Here, we show that the MAF1 C-box region negatively regulates its activity. Mutations in Caenorhabditis elegans mafr-1 that truncate the C-box retain the ability to inhibit the transcription of RNA po...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2016.12.012

    authors： Pradhan A,Hammerquist AM,Khanna A,Curran SP

    更新日期：2017-01-20 00:00:00

  • Preparation and X-ray characterization of four new crystal forms of jacalin, a lectin from Artocarpus integrifolia.

    abstract：:Four new crystal forms of the anti-T lectin from jackfruit (Artocarpus integrifolia) have been prepared and characterized. Three of them, two monoclinic (P21, a = 59.4 A, b = 83.3 A, c = 63.5 A, beta = 107.7 degrees; C2, a = 106.1 A, b = 53.9 A, c = 128.0 A, beta = 95.0 A) and one orthorhombic (C222(1), a = 98.1 A, b ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)80174-s

    authors： Banerjee R,Dhanaraj V,Mahanta SK,Surolia A,Vijayan M

    更新日期：1991-10-05 00:00:00

  • Expressed gene clusters associated with cellular sensitivity and resistance towards anti-viral and anti-proliferative actions of interferon.

    abstract：:Interferons (IFN) are multi-functional proteins that induce a large number of genes which mediate many biological processes including host defense, cell growth control, signaling, and metabolism. Bioinformatics analysis of the 3'-untranslated regions of IFN-stimulated genes (ISGs) showed that the AU-rich elements (ARE...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.07.065

    authors： Khabar KS,Al-Haj L,Al-Zoghaibi F,Marie M,Dhalla M,Polyak SJ,Williams BR

    更新日期：2004-09-17 00:00:00

  • SAXS and X-ray crystallography suggest an unfolding model for the GDP/GTP conformational switch of the small GTPase Arf6.

    abstract：:The small GTPases Arf1 and Arf6 have nonoverlapping functions in cellular traffic despite their very high sequence and structural resemblance. Notably, the exquisite isoform specificity of their guanine nucleotide exchange factors and their distinctive sensitivity to the drug brefeldin A cannot be explained by any str...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.08.002

    authors： Biou V,Aizel K,Roblin P,Thureau A,Jacquet E,Hansson S,Guibert B,Guittet E,van Heijenoort C,Zeghouf M,Perez J,Cherfils J

    更新日期：2010-10-01 00:00:00

  • Amplification of distinct subfamilies of short interspersed elements during evolution of the Salmonidae.

    abstract：:There are at least three different kinds of short interspersed repetitive elements in salmonid genomes. Of these, members of the HpaI family are found to be most widely distributed in salmonid species. The HpaI family is present with high copy numbers in all members of the subfamily Salmoninae, such as salmon, trout a...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1540

    authors： Kido Y,Himberg M,Takasaki N,Okada N

    更新日期：1994-09-02 00:00:00

  • Purification and crystallization of fumarase C from Escherichia coli.

    abstract：:Fumarase C purified from Escherichia coli has been crystallized in the presence of polyethylene glycol in both a citrate buffer at pH 5.3 and a 3-(4-morpholino)-propanesulfonic acid buffer at pH 7.5 yielding two crystal forms. An orthorhombic C222(1) form was obtained in citrate at pH 5.3 and an orthorhombic I222 form...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1264

    authors： Weaver TM,Levitt DG,Banaszak LJ

    更新日期：1993-05-05 00:00:00

  • A model for the mechanism of polymerase translocation.

    abstract：:A general mechanism for polymerase translocation is elaborated. The central feature of this mechanism is that a rapid translocational equilibrium is established after each cycle of nucleoside monophosphate incorporation such that the polymerase distributes itself by diffusional sliding between all accessible positions...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0707

    authors： Guajardo R,Sousa R

    更新日期：1997-01-10 00:00:00

  • Analysis of replicative intermediates produced during bacteriophage phi 29 DNA replication in vitro.

    abstract：:Replication of bacteriophage phi 29 DNA initiates at either end of its linear double-stranded DNA molecule and proceeds by a strand-displacement mechanism. In the present paper we have used an in vitro phi 29 DNA replication system to analyse by electron microscopy the replicative intermediates produced at different r...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90589-x

    authors： Gutiérrez C,Sogo JM,Salas M

    更新日期：1991-12-20 00:00:00

  • Distribution of surface-exposed and non-accessible amino acid sequences among the two major structural domains of the S-layer protein of Aeromonas salmonicida.

    abstract：:The tetragonally arranged crystalline surface protein array (A-layer) of the fish pathogenic bacterium Aeromonas salmonicida is a virulence factor. Circular dichroism studies in the presence or absence of 0.1% sodium dodecyl sulfate showed that the secondary structure of A-protein, and its 39,439 molecular weight amin...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1550

    authors： Doig P,McCubbin WD,Kay CM,Trust TJ

    更新日期：1993-10-20 00:00:00

  • Directed evolution of an anti-prion protein scFv fragment to an affinity of 1 pM and its structural interpretation.

    abstract：:Bovine spongiform encephalopathy (BSE) is a fatal neurodegenerative prion disease affecting cattle that is transmissible to humans, manifesting as a variant of Creutzfeldt-Jakob disease (vCJD) likely following the consumption of meat contaminated with BSE prions. High-affinity antibodies are a prerequisite for the dev...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.07.027

    authors： Luginbühl B,Kanyo Z,Jones RM,Fletterick RJ,Prusiner SB,Cohen FE,Williamson RA,Burton DR,Plückthun A

    更新日期：2006-10-13 00:00:00

  • Deletion analysis of the lambda tR1 termination region. Effect of sequences near the transcript release sites, and the minimum length of rho-dependent transcripts.

    abstract：:In order to determine how much of the natural sequence is required for function of the lambda tR1 rho-dependent terminator, and to determine the minimum length required, we made two deletion series of a tR1 derivative that contains mostly foreign DNA, encoding C-rich RNA, substituted for the natural upstream sequences...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1229

    authors： Hart CM,Roberts JW

    更新日期：1994-04-01 00:00:00

  • Negative regulation of AAA + ATPase assembly by two component receiver domains: a transcription activation mechanism that is conserved in mesophilic and extremely hyperthermophilic bacteria.

    abstract：:Only a few transcriptional regulatory proteins have been characterized in extremely hyperthermophilic organisms, and most function as repressors. Structural features of the NtrC1 protein from the hyperthermophilic bacterium Aquifex aeolicus suggested that this protein functions similarly to the sigma(54)-polymerase ac...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.08.003

    authors： Doucleff M,Chen B,Maris AE,Wemmer DE,Kondrashkina E,Nixon BT

    更新日期：2005-10-21 00:00:00

  • A cross-talk between hypoxia and TGF-beta orchestrates erythropoietin gene regulation through SP1 and Smads.

    abstract：:Erythropoietin (Epo) is the humoral regulator of red blood-cell production. Low oxygen tension increases the Epo levels by enhancing transcription, through the hypoxia-inducible factor (HIF)-1, a transcriptional modulator in oxygen-regulated gene expression. In the present work, a cooperative interaction between hypox...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2003.12.023

    authors： Sánchez-Elsner T,Ramírez JR,Sanz-Rodriguez F,Varela E,Bernabéu C,Botella LM

    更新日期：2004-02-06 00:00:00

  • Potential conformational heterogeneity of p53 bound to S100B(ββ).

    abstract：:The negative regulatory domain (NRD) of the p53 tumor suppressor is intrinsically disordered. It contains several posttranslational modification (PTM) sites that are important for regulation of p53 activity. Calcium-dependent binding of dimeric S100B(ββ) to p53-NRD blocks access to these PTM sites and disrupts the p53...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2013.01.001

    authors： McDowell C,Chen J,Chen J

    更新日期：2013-03-25 00:00:00

  • Cytochrome c and SDS: a molten globule protein with altered axial ligation.

    abstract：:Saccharomices cerevisiae (yeast iso-1) cytochrome c has been investigated in the presence of 100 mM SDS in order to simulate the interaction of cytochrome c with membrane. Under these circumstances, a high spin species with detached methionine axial ligand is observed through NMR, in analogy to findings on the horse h...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2003.12.045

    authors： Bertini I,Turano P,Vasos PR,Bondon A,Chevance S,Simonneaux G

    更新日期：2004-02-13 00:00:00

  • Flexibility and variability of TIMP binding: X-ray structure of the complex between collagenase-3/MMP-13 and TIMP-2.

    abstract：:The excessive activity of matrix metalloproteinases (MMPs) contributes to pathological processes such as arthritis, tumor growth and metastasis if not balanced by the tissue inhibitors of metalloproteinases (TIMPs). In arthritis, the destruction of fibrillar (type II) collagen is one of the hallmarks, with MMP-1 (coll...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.11.072

    authors： Maskos K,Lang R,Tschesche H,Bode W

    更新日期：2007-03-02 00:00:00

  • Impact of mutations on the allosteric conformational equilibrium.

    abstract：:Allostery in a protein involves effector binding at an allosteric site that changes the structure and/or dynamics at a distant, functional site. In addition to the chemical equilibrium of ligand binding, allostery involves a conformational equilibrium between one protein substate that binds the effector and a second s...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2012.11.041

    authors： Weinkam P,Chen YC,Pons J,Sali A

    更新日期：2013-02-08 00:00:00

  • Transforming growth factor-beta (TGF-beta) binding to the extracellular domain of the type II TGF-beta receptor: receptor capture on a biosensor surface using a new coiled-coil capture system demonstrates that avidity contributes significantly to high aff

    abstract：:Mature TGF-beta isoforms, which are covalent dimers, signal by binding to three types of cell surface receptors, the type I, II and III TGF-beta receptors. A complex composed of the TGF-beta ligand and the type I and II receptors is required for signaling. The type II receptor is responsible for recruiting TGF-beta in...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00360-7

    authors： De Crescenzo G,Pham PL,Durocher Y,O'Connor-McCourt MD

    更新日期：2003-05-16 00:00:00

  • A generic mechanism of beta2-microglobulin amyloid assembly at neutral pH involving a specific proline switch.

    abstract：:Although numerous measurements of amyloid assembly of different proteins under distinct conditions in vitro have been performed, the molecular mechanisms underlying the specific self-association of proteins into amyloid fibrils remain obscure. Elucidating the nature of the events that initiate amyloid formation remain...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.01.013

    authors： Eichner T,Radford SE

    更新日期：2009-03-13 00:00:00

  • Energetics of MazG unfolding in correlation with its structural features.

    abstract：:MazG is a homodimeric alpha-helical protein that belongs to the superfamily of all-alpha NTP pyrophosphatases. Its function has been connected to the regulation of the toxin-antitoxin module mazEF, implicated in programmed growth arrest/cell death of Escherichia coli cells under conditions of amino acid starvation. Th...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.05.086

    authors： Drobnak I,Korencic A,Loris R,Marianovsky I,Glaser G,Jamnik A,Vesnaver G,Lah J

    更新日期：2009-09-11 00:00:00

  • Isolation and characterization of conditional alleles of the yeast SIR2 gene.

    abstract：:Sir2 is a protein deacetylase that mediates transcriptional silencing at the HM loci, telomeres, and rDNA repeats in yeast. To identify functionally significant regions of the Sir2 protein, we have characterized two types of mutations. First, we used random mutagenesis to create temperature-sensitive alleles of the SI...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.01.044

    authors： Hickman M,McCullough K,Woike A,Raducha-Grace L,Rozario T,Dula ML,Anderson E,Margalit D,Holmes SG

    更新日期：2007-04-13 00:00:00

  • Molecular evolution of the HBII-52 snoRNA cluster.

    abstract：:HBII-52 is a human brain-specific C/D box snoRNA that potentially regulates the editing and/or alternative splicing of the serotonin receptor. Forty-two nearly identical copies of the HBII-52 gene are located immediately downstream of the SNRPN protein-coding gene in an imprinted locus associated with Prader-Willi syn...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.06.057

    authors： Nahkuri S,Taft RJ,Korbie DJ,Mattick JS

    更新日期：2008-09-12 00:00:00

  • Characterization of long-range structure in the denatured state of staphylococcal nuclease. II. Distance restraints from paramagnetic relaxation and calculation of an ensemble of structures.

    abstract：:Structural analysis of delta131delta, a fragment model of the denatured state of staphylococcal nuclease, has been extended by obtaining long-range distance restraints between chain segments by paramagnetic relaxation enhancement. Fourteen unique PROXYL spin labels were introduced at sites that are solvent-exposed in ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.0953

    authors： Gillespie JR,Shortle D

    更新日期：1997-04-25 00:00:00

  • Sequence analysis of the complete Caenorhabditis elegans myosin heavy chain gene family.

    abstract：:The sequences of three myosin heavy chain (MHC) genes from Caenorhabditis elegans, myo-1, 2 and 3, are presented. These genes, together with unc-54, comprise the entire nematode sacromeric MHC family. Comparison of nematode MHC sequences and sarcomeric, smooth and non-muscle MHCs from other organisms highlights conser...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(89)90229-5

    authors： Dibb NJ,Maruyama IN,Krause M,Karn J

    更新日期：1989-02-05 00:00:00

  • Refined crystal structure of beta-lactamase from Staphylococcus aureus PC1 at 2.0 A resolution.

    abstract：:The crystal structure of a class A beta-lactamase from Staphylococcus aureus PC1 has been refined at 2.0 A resolution. The resulting crystallographic R-factor (R = sigma h parallel Fo[-]Fc parallel/sigma h[Fo], where [Fo] and [Fc] are the observed and calculated structure factor amplitudes, respectively), is 0.163 for...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90527-d

    authors： Herzberg O

    更新日期：1991-02-20 00:00:00