当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Multiple roles of prolyl residues in structure and folding.

Multiple roles of prolyl residues in structure and folding.

Abstract：

:To explore the ways that proline residues may influence the conformational options of a polypeptide backbone, we have characterized Pro-->Ala mutants of cellular retinoic acid-binding protein I (CRABP I). While all three Xaa-Pro bonds are in the trans conformation in the native protein and the equilibrium stability of each mutant is similar to that of the parent protein, each has distinct effects on folding and unfolding kinetics. The mutation of Pro105 does not alter the kinetics of folding of CRABP I, which indicates that the flexible loop containing this residue is passive in the folding process. By contrast, replacement of Pro85 by Ala abolishes the observable slow phase of folding, revealing that correct configuration of the 84-85 peptide bond is prerequisite to productive folding. Substitution of Pro39 by Ala yields a protein that folds and unfolds more slowly. Removal of the conformational constraint imposed by the proline ring likely raises the transition state barrier by increasing the entropic cost of narrowing the conformational ensemble. Additionally, the Pro-->Ala mutation removes a helix-termination signal that is important for efficient folding to the native state.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Eyles SJ,Gierasch LM

doi

10.1006/jmbi.2000.4002

keywords:

subject

Has Abstract

pub_date

2000-08-18 00:00:00

pages

737-47

issue

3

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(00)94002-6

journal_volume

301

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Direct visualization of dynamics and co-operative conformational changes within RecA filaments that appear to be associated with the hydrolysis of adenosine 5'-O-(3-thiotriphosphate).

    abstract：:Highly co-operative structural transitions and conformational changes can be directly observed in bundles of filaments formed by the RecA protein of Escherichia coli. These filaments have been formed with RecA protein, DNA and the ATP analog adenosine 5'-O-(3-thiotriphosphate) (ATP-gamma-S). We show that while ATP-gam...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)91036-o

    authors： Yu X,Egelman EH

    更新日期：1992-05-05 00:00:00

  • The RecB nuclease domain binds to RecA-DNA filaments: implications for filament loading.

    abstract：:The E. coli RecBCD enzyme facilitates the loading of RecA onto single-stranded DNA produced by the combined helicase/nuclease activity of RecBCD. The nuclease domain of RecB protein, RecB(nuc), has been previously shown to bind RecA. Surprisingly, RecB(nuc) also binds to phage and eukaryotic homologs of RecA, leading ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.06.042

    authors： Lucarelli D,Wang YA,Galkin VE,Yu X,Wigley DB,Egelman EH

    更新日期：2009-08-14 00:00:00

  • Cooperative and non-cooperative DNA binding modes of catabolite control protein CcpA from Bacillus megaterium result from sensing two different signals.

    abstract：:Carbon catabolite repression (CCR) of several operons in Bacillus subtilis and Bacillus megaterium is mediated by the cis-acting cre sequence and trans-acting catabolite control protein (CcpA). We describe purification of CcpA from B. megaterium and its interaction with regulatory sequences from the xyl operon. Specif...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0820

    authors： Gösseringer R,Küster E,Galinier A,Deutscher J,Hillen W

    更新日期：1997-03-07 00:00:00

  • Detecting patterns in protein sequences.

    abstract：:The detection of conserved sequence patterns (motifs) in related proteins often yields valuable structural and functional insights. We describe a method that utilizes rigorous statistics and a depth-first search procedure to efficiently and exhaustively search a set of proteins for significant patterns up to a specifi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1407

    authors： Neuwald AF,Green P

    更新日期：1994-06-24 00:00:00

  • Use of a 3D structure data base for understanding sequence-dependent conformational aspects of DNA.

    abstract：:The roll-twist-slide correlation in the DNA crystal structures that are collected in the Nucleic Acid Data Base is analyzed in order to obtain a general understanding of the effects of the nucleotide sequence on the 3D structure of a dinucleotide step. It is concluded that the differences between the pyrimidine bases ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.1406

    authors： Suzuki M,Amano N,Kakinuma J,Tateno M

    更新日期：1997-12-05 00:00:00

  • Self-interaction of pneumolysin, the pore-forming protein toxin of Streptococcus pneumoniae.

    abstract：:The pathogenically important cholesterol-binding pore-forming bacterial "thiol-activated" toxins (TATs) are commonly believed to be monomeric in solution and to undergo a transition on membrane binding mediated by cholesterol to an oligomeric pore. We present evidence, gained through the application of a number of bio...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2258

    authors： Gilbert RJ,Rossjohn J,Parker MW,Tweten RK,Morgan PJ,Mitchell TJ,Errington N,Rowe AJ,Andrew PW,Byron O

    更新日期：1998-12-11 00:00:00

  • Methylation of the promoter region may be involved in tissue-specific expression of the mouse terminal deoxynucleotidyl transferase gene.

    abstract：:The terminal deoxynucleotidyl transferase gene (TdT) is expressed in mice only in early B and T lymphoid precursors a few days after birth. Transactivating factors have been shown to contribute to the lymphoid specific expression of TdT, but they do not account entirely for the restriction of its expression to early p...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.3079

    authors： Nourrit F,Coquilleau I,D'Andon MF,Rougeon F,Doyen N

    更新日期：1999-09-17 00:00:00

  • Isolation and characterization of visible light-sensitive mutants of Escherichia coli K12.

    abstract：:Six mutants of Escherichia coli K12 that are sensitive to visible light have been isolated. Five of them, including an amber mutant, are defective in a gene that maps near 11 minutes on the linkage map of the chromosome, and this gene has been designated visA. The sixth mutant, which was isolated from bacteria that ca...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90180-e

    authors： Miyamoto K,Nakahigashi K,Nishimura K,Inokuchi H

    更新日期：1991-06-05 00:00:00

  • Crystals of seryl-tRNA synthetase from Escherichia coli. Preliminary crystallographic data.

    abstract：:Crystals of seryl-tRNA synthetase from Escherichia coli can be grown from ammonium sulphate/octyl glucoside solutions in two days. The crystals appear to be very suitable for X-ray analysis, diffracting to at least 2.8 A resolution and being resistant to radiation damage. The crystals are monoclinic (space group C2) w...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90232-4

    authors： Leberman R,Berthet-Colominas C,Cusack S,Härtlein M

    更新日期：1987-01-20 00:00:00

  • Recruitment, Duplex Unwinding and Protein-Mediated Inhibition of the Dead-Box RNA Helicase Dbp2 at Actively Transcribed Chromatin.

    abstract：:RNA helicases play fundamental roles in modulating RNA structures and facilitating RNA-protein (RNP) complex assembly in vivo. Previously, our laboratory demonstrated that the DEAD-box RNA helicase Dbp2 in Saccharomyces cerevisiae is required to promote efficient assembly of the co-transcriptionally associated mRNA-bi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2016.02.005

    authors： Ma WK,Paudel BP,Xing Z,Sabath IG,Rueda D,Tran EJ

    更新日期：2016-03-27 00:00:00

  • The pH-dependent structural variation of complementarity-determining region H3 in the crystal structures of the Fv fragment from an anti-dansyl monoclonal antibody.

    abstract：:The Fv fragment from an anti-dansyl antibody was optimally crystallized into two crystal forms having slightly different lattice dimensions at pH 5.25 and 6.75. The two crystal structures were determined and refined at high resolution at 112 K (at 1.45 A for the crystal at pH 5.25 and at 1.55 A for that at pH 6.75). I...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2931

    authors： Nakasako M,Takahashi H,Shimba N,Shimada I,Arata Y

    更新日期：1999-08-06 00:00:00

  • Ion-coupling determinants of Na+-driven and H+-driven flagellar motors.

    abstract：:The bacterial flagellar motor is a tiny molecular machine that uses a transmembrane flux of H(+) or Na(+) ions to drive flagellar rotation. In proton-driven motors, the membrane proteins MotA and MotB interact via their transmembrane regions to form a proton channel. The sodium-driven motors that power the polar flage...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00096-2

    authors： Asai Y,Yakushi T,Kawagishi I,Homma M

    更新日期：2003-03-21 00:00:00

  • Molecular requirements for duplex recognition and cleavage by eukaryotic RNase III: discovery of an RNA-dependent DNA cleavage activity of yeast Rnt1p.

    abstract：:Members of the double-stranded RNA (dsRNA) specific RNase III family are known to use a conserved dsRNA-binding domain (dsRBD) to distinguish RNA A-form helices from DNA B-form ones, however, the basis of this selectivity and its effect on cleavage specificity remain unknown. Here, we directly examine the molecular re...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.02.059

    authors： Lamontagne B,Hannoush RN,Damha MJ,Abou Elela S

    更新日期：2004-04-23 00:00:00

  • Characterization of in vitro and in vivo mutations in non-conserved nucleotides in the ribosomal RNA recognition domain for the ribotoxins ricin and sarcin and the translation elongation factors.

    abstract：:The sarcin/ricin domain in 23 S/28 S rRNA is crucial for ribosome function, since it constitutes at least part of the binding site for the elongation factors and hence is essential for binding aminoacyl-tRNA and for translocation. The domain is also the site of action of ricin and sarcin and analysis of the effect of ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2337

    authors： Macbeth MR,Wool IG

    更新日期：1999-01-15 00:00:00

  • Genome-wide survey of prokaryotic O-protein phosphatases.

    abstract：:Complex and diverse signal transduction circuits are responsible for the efficient functioning of cellular network. Protein kinases and O-protein phosphatases are primarily responsible for propagating such stimuli within a eukaryotic cell. However, there is limited understanding of O-protein phosphatases in the prokar...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.07.004

    authors： Bhaduri A,Sowdhamini R

    更新日期：2005-09-23 00:00:00

  • The nucleolar PICT-1/GLTSCR2 protein forms homo-oligomers.

    abstract：:The human "protein interacting with carboxyl terminus 1" (PICT-1), also designated as the "glioma tumor suppressor candidate region 2 gene product", GLTSCR2, is a nucleolar protein whose activity is, as yet, unknown. Contradictory results regarding the role of PICT-1 in cancer have been reported, and PICT-1 has been s...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2014.04.006

    authors： Borodianskiy-Shteinberg T,Kalt I,Kipper S,Nachum N,Katz S,Pauker MH,Barda-Saad M,Gerber D,Sarid R

    更新日期：2014-06-12 00:00:00

  • Erythromycin-induced stabilization of ermA messenger RNA in Staphylococcus aureus and Bacillus subtilis.

    abstract：:Erythromycin-induced stabilization of ermA mRNA was studied in Staphylococcus aureus, its original host background, and in Bacillus subtilis, subcloned on plasmid vectors. By RNA blot analysis it was shown that 40 nM-erythromycin specifically increased the chemical half-life of ermA mRNA from 2.5 to 17.5 minutes where...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(88)90116-7

    authors： Sandler P,Weisblum B

    更新日期：1988-10-20 00:00:00

  • Statistical test for the comparison of samples from mutational spectra.

    abstract：:The Monte Carlo estimate of the p value of the hypergeometric test is described and advocated for the testing of the hypothesis that different treatments induce the same mutational spectrum. The hypergeometric test is a generalization of Fisher's "exact" test for tables with more than two rows and two columns. Use of ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90669-3

    authors： Adams WT,Skopek TR

    更新日期：1987-04-05 00:00:00

  • Crystal structure of ferric Aplysia limacina myoglobin at 2 X 0 A resolution.

    abstract：:The three-dimensional structure of ferric myoglobin from the mollusc Aplysia limacina has been refined at 2 X 0 A resolution. The crystallographic R factor, calculated at this stage, is 0 X 194. Despite its high content of apolar residues (both aromatic and aliphatic), Aplysia limacina myoglobin, which contains only o...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(85)90285-2

    authors： Bolognesi M,Coda A,Gatti G,Ascenzi P,Brunori M

    更新日期：1985-05-05 00:00:00

  • Sequence-structure signals of 3D domain swapping in proteins.

    abstract：:Three-dimensional domain swapping occurs when two or more identical proteins exchange identical parts of their structure to generate an oligomeric unit. It affects proteins with diverse sequences and structures, and is expected to play important roles in evolution, functional regulation and even conformational disease...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00614-4

    authors： Dehouck Y,Biot C,Gilis D,Kwasigroch JM,Rooman M

    更新日期：2003-07-25 00:00:00

  • Crystal structure of cyanovirin-N, a potent HIV-inactivating protein, shows unexpected domain swapping.

    abstract：:The crystal structure of cyanovirin-N (CV-N), a protein with potent antiviral activity, was solved at 1.5 A resolution by molecular replacement using as the search model the solution structure previously determined by NMR. The crystals belong to the space group P3221 with one monomer of CV-N in each asymmetric unit. T...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2693

    authors： Yang F,Bewley CA,Louis JM,Gustafson KR,Boyd MR,Gronenborn AM,Clore GM,Wlodawer A

    更新日期：1999-05-07 00:00:00

  • Calorimetric analysis of binding of two consecutive DNA strands to RecA protein illuminates mechanism for recognition of homology.

    abstract：:RecA protein recognises two complementary DNA strands for homologous recombination. To gain insight into the molecular mechanism, the thermodynamic parameters of the DNA binding have been characterised by isothermal calorimetry. Specifically, conformational changes of protein and DNA were searched for by measuring var...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.10.042

    authors： Takahashi M,Maraboeuf F,Morimatsu K,Selmane T,Fleury F,Norden B

    更新日期：2007-01-19 00:00:00

  • Transition of chromatin from the "10 nm" lower order structure, to the "30 nm" higher order structure as followed by small angle X-ray scattering.

    abstract：:Chromatin oligomers undergo a conformational change from a "10 nm" lower order structure at low concentration of salt to a "30 nm" higher order structure, with increasing NaCl or MgCl2 concentration. We have extended our previously reported hydrodynamic and light-scattering measurements of the folding of well-defined ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90353-6

    authors： Greulich KO,Wachtel E,Ausio J,Seger D,Eisenberg H

    更新日期：1987-02-20 00:00:00

  • Structure of a foreign peptide displayed on the surface of bacteriophage M13.

    abstract：:The use of filamentous bacteriophage M13 as a vehicle for display of foreign peptides and proteins provides a means for the construction of therapeutic, diagnostic and technological tools of broad utility. The usefulness of this technology is dependent on the ability of an inserted peptide to act as a ligand when fuse...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1489

    authors： Kishchenko G,Batliwala H,Makowski L

    更新日期：1994-08-12 00:00:00

  • Relative binding affinities of OmpR and OmpR-phosphate at the ompF and ompC regulatory sites.

    abstract：:In Escherichia coli, porin gene expression is regulated, in part, by the two-component regulatory system consisting of the two proteins EnvZ and OmpR. EnvZ is an integral inner membrane protein that is phosphorylated by cytoplasmic ATP on a histidine residue. EnvZ modulates the activity of OmpR by phosphorylation and ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.1985

    authors： Head CG,Tardy A,Kenney LJ

    更新日期：1998-09-04 00:00:00

  • 2.5 A structure of aspartate carbamoyltransferase complexed with the bisubstrate analog N-(phosphonacetyl)-L-aspartate.

    abstract：:In an X-ray diffraction study using the method of multiple isomorphous replacement, the structure of aspartate carbamoyltransferase (EC 2.1.3.2) complexed with the bisubstrate analog N-(phosphonacetyl)-L-aspartate (PALA) has been solved to 2.5 A. Ten rounds of model building and 123 cycles of restrained reciprocal spa...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90265-8

    authors： Krause KL,Volz KW,Lipscomb WN

    更新日期：1987-02-05 00:00:00

  • RNase E and polyadenyl polymerase I are involved in maturation of CI RNA, the P4 phage immunity factor.

    abstract：:Bacteriophage P4 immunity is controlled by a small stable RNA (CI RNA) that derives from the processing of primary transcripts. In previous works, we observed that the endonuclease RNase P is required for the maturation of CI RNA 5'-end; moreover, we found that polynucleotide phosphorylase (PNPase), a 3' to 5' RNA-deg...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/S0022-2836(02)00085-2

    authors： Briani F,Del Vecchio E,Migliorini D,Hajnsdorf E,Régnier P,Ghisotti D,Dehò G

    更新日期：2002-04-26 00:00:00

  • Structure of the minimal interface between ApoE and LRP.

    abstract：:Clusters of complement-type ligand-binding repeats (CRs) in the low-density lipoprotein receptor (LDLR) family are thought to mediate the interactions with their various ligands. Apolipoprotein E (ApoE), a key ligand for cholesterol homeostasis, has been shown to interact with LDLR-related protein 1 (LRP) through thes...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.03.022

    authors： Guttman M,Prieto JH,Handel TM,Domaille PJ,Komives EA

    更新日期：2010-04-30 00:00:00

  • Guided evolution of enzymes with new substrate specificities.

    abstract：:A gene library was constructed coding for all possible variants of two amino acids (101, 102) in a solvent-exposed surface return loop (alpha E-beta D) of Bacillus stearothermophilus L-lactate dehydrogenase (bsLDH). All but one of 38 enzyme variants examined were thermally stable and had native-like hydrodynamic prope...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0626

    authors： el Hawrani AS,Sessions RB,Moreton KM,Holbrook JJ

    更新日期：1996-11-22 00:00:00

  • Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain.

    abstract：:ThiI is an enzyme responsible for the formation of the modified base S(4)U (4-thiouridine) found at position 8 in some prokaryotic tRNAs. This base acts as a sensitive trigger for the response mechanism to UV exposure, providing protection against its damaging effects. We present the crystal structure of Bacillus anth...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.11.013

    authors： Waterman DG,Ortiz-Lombardía M,Fogg MJ,Koonin EV,Antson AA

    更新日期：2006-02-10 00:00:00