Native-like partially folded conformations and folding process revealed in the N-terminal large fragments of staphylococcal nuclease: a study by NMR spectroscopy.

Abstract:

:The N-terminal large fragments of staphylococcal nuclease (SNase), SNase110 (1-110 residues), SNase121 (1-121 residues), and SNase135 (1-135 residues), and the fragment mutants G88W110, G88W121, V66W110 and V66W121 were studied by heteronuclear multidimensional NMR spectroscopy. Ensembles of co-existent native-like partially folded and unfolded states were observed for fragments. The persistent native-like tertiary interaction drives fragments to be in partially folded states, which reveal native-like beta-barrel conformations. G88W and V66W mutations modulate the extent of inherent native-like tertiary interaction in fragment molecules, and in consequence, fragment mutants fold into native-like beta-subdomain conformations. In cooperation with the inherent tertiary interaction, 2 M TMAO (trimethylamine N-oxide) can promote the folding reaction of fragments through the changes of unfolding free energy, and a native-like beta-subdomain conformation is observed when the chain length contains 135 residues. Heterogeneous partially folded conformations of 1-121 and 1-135 fragments due to cis and trans X-prolyl bond of Lys116-Pro117 make a non-unique folding pathway of fragments. The folding reaction of fragments can be characterized as a hierarchical process.

journal_name

J Mol Biol

authors

Feng Y,Liu D,Wang J

doi

10.1016/s0022-2836(03)00660-0

keywords:

subject

Has Abstract

pub_date

2003-07-18 00:00:00

pages

821-37

issue

4

eissn

0022-2836

issn

1089-8638

pii

S0022283603006600

journal_volume

330

pub_type

杂志文章
  • Proteolytic and conformational control of virus capsid maturation: the bacteriophage HK97 system.

    abstract::Bacteriophage capsid assembly pathways provide excellent model systems to study large-scale conformational changes and other mechanisms that regulate the formation of macromolecular complexes. These capsids are formed from proheads: relatively fragile precursor particles which mature by undergoing extensive remodeling...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0538

    authors: Conway JF,Duda RL,Cheng N,Hendrix RW,Steven AC

    更新日期:1995-10-13 00:00:00

  • Structural insight into the dioxygenation of nitroarene compounds: the crystal structure of nitrobenzene dioxygenase.

    abstract::Nitroaromatic compounds are used extensively in many industrial processes and have been released into the environment where they are considered environmental pollutants. Nitroaromatic compounds, in general, are resistant to oxidative attack due to the electron-withdrawing nature of the nitro groups and the stability o...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.03.052

    authors: Friemann R,Ivkovic-Jensen MM,Lessner DJ,Yu CL,Gibson DT,Parales RE,Eklund H,Ramaswamy S

    更新日期:2005-05-20 00:00:00

  • Ligand-induced conformational rearrangements promote interaction between the Escherichia coli enterobactin biosynthetic proteins EntE and EntB.

    abstract::Siderophores are small-molecule iron chelators that many bacteria synthesize and secrete in order to survive in iron-depleted environments. Biosynthesis of enterobactin, the Escherichia coli catecholate siderophore, requires adenylation of 2,3-dihydroxybenzoic acid (2,3-DHB) by the cytoplasmic enzyme EntE. The DHB-AMP...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.08.036

    authors: Khalil S,Pawelek PD

    更新日期:2009-10-30 00:00:00

  • Modular structure of the trigger factor required for high activity in protein folding.

    abstract::The Escherichia coli trigger factor is a peptidyl-prolyl cis/trans isomerase (PPIase) which catalyzes proline-limited protein folding extremely well. It has been found associated with nascent protein chains as well as with the chaperone GroEL. The trigger factor utilizes protein regions outside the central catalytic d...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1206

    authors: Zarnt T,Tradler T,Stoller G,Scholz C,Schmid FX,Fischer G

    更新日期:1997-09-05 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

  • Determinants of BH3 binding specificity for Mcl-1 versus Bcl-xL.

    abstract::Interactions among Bcl-2 family proteins are important for regulating apoptosis. Prosurvival members of the family interact with proapoptotic BH3 (Bcl-2-homology-3)-only members, inhibiting execution of cell death through the mitochondrial pathway. Structurally, this interaction is mediated by binding of the alpha-hel...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.03.058

    authors: Dutta S,Gullá S,Chen TS,Fire E,Grant RA,Keating AE

    更新日期:2010-05-21 00:00:00

  • The foldon universe: a survey of structural similarity and self-recognition of independently folding units.

    abstract::We have identified independently folding units, so called "foldons", from non-homologous proteins representing different folds. We applied simple statistical arguments in order to estimate the size of the foldon universe required to construct all foldable proteins. Various alignment procedures yield about 2600 foldons...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1205

    authors: Panchenko AR,Luthey-Schulten Z,Cole R,Wolynes PG

    更新日期:1997-09-12 00:00:00

  • Ribosomal proteins L11 and L10.(L12)4 and the antibiotic thiostrepton interact with overlapping regions of the 23 S rRNA backbone in the ribosomal GTPase centre.

    abstract::The Escherichia coli ribosomal protein (r-protein) L11 and its binding site on 23 S ribosomal RNA (rRNA) are associated with ribosomal hydrolysis of guanosine 5'-triphosphate (GTP). We have used hydroxyl radical footprinting to map the contacts between L11 and the backbone riboses in 23 S rRNA, and to investigate how ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1655

    authors: Rosendahl G,Douthwaite S

    更新日期:1993-12-20 00:00:00

  • Peptide mimic of the HIV envelope gp120-gp41 interface.

    abstract::The human immunodeficiency virus envelope glycoprotein (Env) is composed of surface (gp120) and transmembrane (gp41) subunits, which are noncovalently associated on the viral surface. Human immunodeficiency virus Env mediates viral entry after undergoing a complex series of conformational changes induced by interactio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.12.001

    authors: Kim S,Pang HB,Kay MS

    更新日期:2008-02-22 00:00:00

  • Homologous DNA targeting with RecA protein-coated short DNA probes and electron microscope mapping on linear duplex molecules.

    abstract::We demonstrate that RecA protein-coated, short single-stranded DNA probes paired with a specific homologous DNA sequence in a linear duplex target molecule and accurately targeted the selected DNA sequence. RecA protein-coated complementary ssDNA probes were reacted with linear duplexes, and the homologously paired mo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1431

    authors: Révet BM,Sena EP,Zarling DA

    更新日期:1993-08-05 00:00:00

  • A fibrin-specific monoclonal antibody from a designed phage display library inhibits clot formation and localizes to tumors in vivo.

    abstract::Fibrin formation from fibrinogen is a rare process in the healthy organism but is a pathological feature of thrombotic events, cancer and a wide range of inflammatory conditions. We have designed and constructed an antibody phage display library (containing 13 billion clones) for the selective recognition of the N-ter...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2014.07.023

    authors: Putelli A,Kiefer JD,Zadory M,Matasci M,Neri D

    更新日期:2014-10-23 00:00:00

  • RNA-dependent folding and stabilization of C5 protein during assembly of the E. coli RNase P holoenzyme.

    abstract::The pre-tRNA processing enzyme ribonuclease P is a ribonucleoprotein. In Escherichia coli assembly of the holoenzyme involves binding of the small (119 amino acid residue) C5 protein to the much larger (377 nucleotide) P RNA subunit. The RNA subunit makes the majority of contacts to the pre-tRNA substrate and contains...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.05.001

    authors: Guo X,Campbell FE,Sun L,Christian EL,Anderson VE,Harris ME

    更新日期:2006-06-30 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

  • NMR Investigation of the Interaction between the RecQ C-Terminal Domain of Human Bloom Syndrome Protein and G-Quadruplex DNA from the Human c-Myc Promoter.

    abstract::Bloom syndrome protein (BLM) is one of five human RecQ helicases that participate in DNA metabolism. RecQ C-terminal (RQC) domain is the main DNA binding module of BLM and specifically recognizes G-quadruplex (G4) DNA structures. Because G4 processing by BLM is essential for regulating replication and transcription, b...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2019.01.010

    authors: Lee S,Lee AR,Ryu KS,Lee JH,Park CJ

    更新日期:2019-02-15 00:00:00

  • Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis.

    abstract::Catalytic antibodies 6D9 and 9C10, which were induced by immunization with a haptenic transition-state analog (TSA), catalyze the hydrolysis of a nonbioactive chloramphenicol monoester derivative to generate a bioactive chloramphenicol. These antibodies stabilize the transition state to catalyze the hydrolysis reactio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.03.023

    authors: Oda M,Ito N,Tsumuraya T,Suzuki K,Sakakura M,Fujii I

    更新日期:2007-05-25 00:00:00

  • Biochemical and structural characterization of a novel family of cystathionine beta-synthase domain proteins fused to a Zn ribbon-like domain.

    abstract::We have identified a novel family of proteins, in which the N-terminal cystathionine beta-synthase (CBS) domain is fused to the C-terminal Zn ribbon domain. Four proteins were overexpressed in Escherichia coli and purified: TA0289 from Thermoplasma acidophilum, TV1335 from Thermoplasma volcanium, PF1953 from Pyrococcu...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.10.060

    authors: Proudfoot M,Sanders SA,Singer A,Zhang R,Brown G,Binkowski A,Xu L,Lukin JA,Murzin AG,Joachimiak A,Arrowsmith CH,Edwards AM,Savchenko AV,Yakunin AF

    更新日期:2008-01-04 00:00:00

  • Binding of fibulin-1 to nidogen depends on its C-terminal globular domain and a specific array of calcium-binding epidermal growth factor-like (EG) modules.

    abstract::The calcium-binding basement membrane protein fibulin-1C was shown to bind nidogen in a calcium-dependent fashion. Fibulin-1C consists of small N (domain 1) and C-terminal (domain III) globular structures connected by a central rod (domain II) composed of nine epidermal growth factor (EG) modules, eight of which posse...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1244

    authors: Adam S,Göhring W,Wiedemann H,Chu ML,Timpl R,Kostka G

    更新日期:1997-09-19 00:00:00

  • The code for directing proteins for translocation across ER membrane: SRP cotranslationally recognizes specific features of a signal sequence.

    abstract::The signal recognition particle (SRP) cotranslationally recognizes signal sequences of secretory proteins and targets ribosome-nascent chain complexes to the SRP receptor in the endoplasmic reticulum membrane, initiating translocation of the nascent chain through the Sec61 translocon. Although signal sequences do not ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2014.06.014

    authors: Nilsson I,Lara P,Hessa T,Johnson AE,von Heijne G,Karamyshev AL

    更新日期:2015-03-27 00:00:00

  • Sampling bottlenecks in de novo protein structure prediction.

    abstract::The primary obstacle to de novo protein structure prediction is conformational sampling: the native state generally has lower free energy than nonnative structures but is exceedingly difficult to locate. Structure predictions with atomic level accuracy have been made for small proteins using the Rosetta structure pred...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.07.063

    authors: Kim DE,Blum B,Bradley P,Baker D

    更新日期:2009-10-16 00:00:00

  • An objective assessment of conformational variability in complexes of hepatitis C virus polymerase with non-nucleoside inhibitors.

    abstract::A major target for antiviral therapy against hepatitis C virus (HCV) is the HCV polymerase nonstructural protein 5B (NS5B). Huge efforts have been devoted to the development of nucleoside and non-nucleoside inhibitors (NNIs) of NS5B. An offshoot of these efforts has been the structural characterization of the interact...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.10.001

    authors: Caillet-Saguy C,Simister PC,Bressanelli S

    更新日期:2011-12-02 00:00:00

  • A second higher vertebrate B-type lamin. cDNA sequence determination and in vitro processing of chicken lamin B2.

    abstract::The chicken nuclear lamina is composed of at least three proteins called lamins A, B1 and B2. In addition, putative precursors are transiently expressed during in vivo synthesis of lamins A and B2. Here we report the complete sequence of lamin B2 as it is deduced from a cloned cDNA. Comparison of lamin B2 with lamins ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90505-6

    authors: Vorburger K,Lehner CF,Kitten GT,Eppenberger HM,Nigg EA

    更新日期:1989-08-05 00:00:00

  • The replisome organizer (G38P) of Bacillus subtilis bacteriophage SPP1 forms specialized nucleoprotein complexes with two discrete distant regions of the SPP1 genome.

    abstract::Initiation of Bacillus subtilis bacteriophage SPP1 DNA replication requires the products of genes 38, 39 and 40 (G38P, G39P and G40P). G38P specifically binds two discrete regions, which are 32.1 kb apart in a linear map of the SPP1 genome. One of these target sites, which maps at the left end of the phage genome, wit...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1060

    authors: Missich R,Weise F,Chai S,Lurz R,Pedré X,Alonso JC

    更新日期:1997-07-04 00:00:00

  • The ever changing moods of calmodulin: how structural plasticity entails transductional adaptability.

    abstract::The exceptional versatility of calmodulin (CaM) three-dimensional arrangement is reflected in the growing number of structural models of CaM/protein complexes currently available in the Protein Data Bank (PDB) database, revealing a great diversity of conformations, domain organization, and structural responses to Ca(2...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2014.05.016

    authors: Villarroel A,Taglialatela M,Bernardo-Seisdedos G,Alaimo A,Agirre J,Alberdi A,Gomis-Perez C,Soldovieri MV,Ambrosino P,Malo C,Areso P

    更新日期:2014-07-29 00:00:00

  • Cryo-negative staining reveals conformational flexibility within yeast RNA polymerase I.

    abstract::The structure of the yeast DNA-dependent RNA polymerase I (RNA Pol I), prepared by cryo-negative staining, was studied by electron microscopy. A structural model of the enzyme at a resolution of 1.8 nm was determined from the analysis of isolated molecules and showed an excellent fit with the atomic structure of the R...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00510-2

    authors: De Carlo S,Carles C,Riva M,Schultz P

    更新日期:2003-06-20 00:00:00

  • Structure of the actin molecule determined from electron micrographs of crystalline actin sheets with a tentative alignment of the molecule in the actin filament.

    abstract::Electron microscopy and image processing of negatively stained crystalline sheets induced from Acanthamoeba actin have been used to yield a three-dimensional reconstruction of the actin molecule, including data to a maximum resolution of 15 A. This model shows actin to be an asymmetric, wedge-shaped molecule. A three-...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(83)80103-x

    authors: Smith PR,Fowler WE,Pollard TD,Aebi U

    更新日期:1983-07-05 00:00:00

  • Structure of cryptic lambda prophages.

    abstract::When Escherichia coli cells lysogenic for bacteriophage lambda are induced with ultraviolet light, cells carrying cryptic lambda prophages are occasionally found among the apparently cured survivors. The lambda variant crypticogen (lambda crg) carries an insertion of the transposable element IS2, which increases the f...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90289-0

    authors: Redfield RJ,Campbell AM

    更新日期:1987-12-05 00:00:00

  • 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

  • Differential surface accessibility of alpha(187-199) in the Torpedo acetylcholine receptor alpha subunits.

    abstract::We have probed the surface accessibility of residues alpha187 to alpha199 of the Torpedo acetylcholine receptor with monoclonal antibody 383C, which binds uniquely to these residues. However, 383C binds to only one of the two alpha subunits in the membrane-bound receptor, neither of the two subunits in carbamylcholine...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2001

    authors: Fairclough RH,Twaddle GM,Gudipati E,Lin MY,Richman DP

    更新日期:1998-09-18 00:00:00

  • Nuclear magnetic resonance studies of the internal dynamics in Apo, (Cd2+)1 and (Ca2+)2 calbindin D9k. The rates of amide proton exchange with solvent.

    abstract::The backbone dynamics of the EF-hand Ca(2+)-binding protein, calbindin D9k, has been investigated in the apo, (Cd2+)1 and (Ca2+)2 states by measuring the rate constants for amide proton exchange with solvent. 15N-1H correlation spectroscopy was utilized to follow direct 1H-->2H exchange of the slowly exchanging amide ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90524-n

    authors: Skelton NJ,Kördel J,Akke M,Chazin WJ

    更新日期:1992-10-20 00:00:00

  • Functional expression of a chimeric myosin-containing motor domain of Chara myosin and neck and tail domains of Dictyostelium myosin II.

    abstract::We succeeded in expressing a chimeric myosin that comprises the motor domain of characean algal myosin, (the fastest known motor protein), and the neck and tail domains of Dictyostelium myosin II. Although the chimeric myosin showed an ATPase activity comparable to that of muscle myosin (15 times higher than that of t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4883

    authors: Kashiyama T,Ito K,Yamamoto K

    更新日期:2001-08-17 00:00:00