Order of steps in the cytochrome C folding pathway: evidence for a sequential stabilization mechanism.

Abstract:

:Previous work used hydrogen exchange (HX) experiments in kinetic and equilibrium modes to study the reversible unfolding and refolding of cytochrome c (Cyt c) under native conditions. Accumulated results now show that Cyt c is composed of five individually cooperative folding units, called foldons, which unfold and refold as concerted units in a stepwise pathway sequence. The first three steps of the folding pathway are linear and sequential. The ordering of the last two steps has been unclear because the fast HX of the amino acid residues in these foldons has made measurement difficult. New HX experiments done under slower exchange conditions show that the final two foldons do not unfold and refold in an obligatory sequence. They unfold separately and neither unfolding obligately contains the other, as indicated by their similar unfolding surface exposure and the specific effects of destabilizing and stabilizing mutations, pH change, and oxidation state. These results taken together support a sequential stabilization mechanism in which folding occurs in the native context with prior native-like structure serving to template the stepwise formation of subsequent native-like foldon units. Where the native structure of Cyt c requires sequential folding, in the first three steps, this is found. Where structural determination is ambiguous, in the final two steps, alternative parallel folding is found.

journal_name

J Mol Biol

authors

Krishna MM,Maity H,Rumbley JN,Lin Y,Englander SW

doi

10.1016/j.jmb.2006.04.035

subject

Has Abstract

pub_date

2006-06-23 00:00:00

pages

1410-9

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(06)00499-2

journal_volume

359

pub_type

杂志文章
  • Crystallization and preliminary diffraction studies of recombinant human granulocyte-stimulating factor (KW2228).

    abstract::Human granulocyte colony-stimulating factor (hG-CSF) specifically stimulates proliferation of neutrophils. Two crystal forms of a mutant of hG-CSF expressed in Escherichia coli have been obtained using the hanging drop vapour diffusion method. One form is triclinic, space group P1, with cell dimensions a = 37.3 A, b =...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(90)90143-A

    authors: Nagahara Y,Konishi N,Yokoo Y,Hirayama N

    更新日期:1990-07-05 00:00:00

  • The capsid size-determining protein Sid forms an external scaffold on phage P4 procapsids.

    abstract::Although the phages P2 and P4 build their capsids from the same precursor, the product of the P2 N gene, the two capsids differ in size: P2 builds a 60 nm, T = 7 capsid from 420 subunits, whereas P4 makes a 45 nm, T = 4 capsid from 240 subunits. This difference leads to substantial changes in shell geometry and subuni...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0416

    authors: Marvik OJ,Dokland T,Nøkling RH,Jacobsen E,Larsen T,Lindqvist BH

    更新日期:1995-08-04 00:00:00

  • Diffusing and colliding: the atomic level folding/unfolding pathway of a small helical protein.

    abstract::Proteins with ultra-fast folding/unfolding kinetics are excellent candidates for study by molecular dynamics. Here, we describe such simulations of a three helix bundle protein, the engrailed homeodomain (En-HD), which folds via the diffusion-collision model. The unfolding pathway of En-HD was characterized by seven s...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.06.074

    authors: DeMarco ML,Alonso DO,Daggett V

    更新日期:2004-08-20 00:00:00

  • A genetic analysis of crystal growth.

    abstract::The regulation of crystal morphology by proteins is often observed in biology. It is a central feature in the formation of hard tissues such as bones, teeth and mollusc shells. We have developed a genetic system in the bacterium Escherichia coli to study the protein-mediated control of crystal growth. We have used the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3682

    authors: Brown S,Sarikaya M,Johnson E

    更新日期:2000-06-09 00:00:00

  • Nucleation and polymerization of sickle hemoglobin with Leu beta 88 substituted by Ala.

    abstract::We have measured the solubility, and the rates of homogeneous and heterogeneous nucleation on sickle hemoglobin (HbS beta 6 Glu-->Val) additionally modified by site-directed mutagenesis to possess Ala rather than Leu at beta 88, which forms part of the receptor site for beta 6 Val in the sickle polymer. The solubility...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0749

    authors: Cao Z,Liao D,Mirchev R,Martin de Llano JJ,Himanen JP,Manning JM,Ferrone FA

    更新日期:1997-02-07 00:00:00

  • Exploring conformational space with a simple lattice model for protein structure.

    abstract::We present a low resolution lattice model for which we can exhaustively generate all possible compact backbone conformations for small proteins. Using simple structural and energetic criteria, for a variety of proteins, we can select for lattice structures that have significant similarities with their known native str...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(94)90040-x

    authors: Hinds DA,Levitt M

    更新日期:1994-11-04 00:00:00

  • Specific RNA-binding antibodies with a four-amino-acid code.

    abstract::Numerous large non-coding RNAs are rapidly being discovered, and many of them have been shown to play vital roles in gene expression, gene regulation, and human diseases. Given their often structured nature, specific recognition with an antibody fragment becomes feasible and may help define the structure and function ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2014.03.003

    authors: Sherman EM,Holmes S,Ye JD

    更新日期:2014-05-15 00:00:00

  • Coordinated transcriptional regulation of Hspa1a gene by multiple transcription factors: crucial roles for HSF-1, NF-Y, NF-κB, and CREB.

    abstract::Although the transcript level of inducible heat shock protein 70.3 (Hsp70.3, also known as Hspa1a) is altered in various disease states, its transcriptional regulation remains incompletely understood. Here, we systematically analyzed the Hspa1a promoter to identify major cis elements and transcription factors that may...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2013.09.008

    authors: Sasi BK,Sonawane PJ,Gupta V,Sahu BS,Mahapatra NR

    更新日期:2014-01-09 00:00:00

  • The conserved asparagine in the HNH motif serves an important structural role in metal finger endonucleases.

    abstract::The HNH motif is a small nucleic acid binding and cleavage module, widespread in metal finger endonucleases in all life kingdoms. Here we studied a non-specific endonuclease, the nuclease domain of ColE7 (N-ColE7), to decipher the role of the conserved asparagine and histidine residues in the HNH motif. We found, usin...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.02.044

    authors: Huang H,Yuan HS

    更新日期:2007-05-04 00:00:00

  • Proteasome Structure and Assembly.

    abstract::The eukaryotic 26S proteasome is a large multisubunit complex that degrades the majority of proteins in the cell under normal conditions. The 26S proteasome can be divided into two subcomplexes: the 19S regulatory particle and the 20S core particle. Most substrates are first covalently modified by ubiquitin, which the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2017.05.027

    authors: Budenholzer L,Cheng CL,Li Y,Hochstrasser M

    更新日期:2017-11-10 00:00:00

  • Kinetics of expression of inducible beta-galactosidase in murine fibroblasts: high initial rate compared to steady-state expression.

    abstract::We have constructed a murine fibroblast cell line in which synthesis of beta-galactosidase can be induced by incubation with isopropyl-beta-D-thiogalactopyranoside (IPTG). This was obtained by transfection by both a plasmid expressing lacI and a second plasmid expressing lacZ from a modified simian virus 40 (SV40) pro...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0496

    authors: Jacobsen KD,Willumsen BM

    更新日期:1995-09-22 00:00:00

  • The RecG branch migration protein of Escherichia coli dissociates R-loops.

    abstract::The RuvAB and RecG proteins of Escherichia coli promote branch migration of Holliday junction intermediates in genetic recombination. Both are structure-specific helicases that unwind and rewind DNA at the junction point. The helicase activities of these proteins were investigated using RNA:DNA hybrid molecules. RuvAB...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0671

    authors: Vincent SD,Mahdi AA,Lloyd RG

    更新日期:1996-12-13 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

  • Wild-type alpha 1-antitrypsin is in the canonical inhibitory conformation.

    abstract::alpha 1-Antitrypsin is the archetypal member of the serine proteinase inhibitor or serpin superfamily. Members of the family show structural homology based on a dominant A beta-sheet and a mobile reactive centre loop. Our recent crystal structure of alpha 1-antitrypsin stabilized with a point mutation showed the loop ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1006/jmbi.1997.1458

    authors: Elliott PR,Abrahams JP,Lomas DA

    更新日期:1998-01-23 00:00:00

  • Role of a single amino acid in the evolution of glycans of invertebrates and vertebrates.

    abstract::Structures of glycoconjugate N-glycans and glycolipids of invertebrates show significant differences from those of vertebrates. These differences are due largely to the vertebrate beta1,4-galactosyltransferase-1 (beta4Gal-T1), which is found as a beta1,4-N-acetylgalactosaminyltransferase (beta4GalNAc-T1) in invertebra...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.10.034

    authors: Ramakrishnan B,Qasba PK

    更新日期:2007-01-19 00:00:00

  • Context-dependent remodeling of structure in two large protein fragments.

    abstract::Protein folding involves the formation of secondary structural elements from the primary sequence and their association with tertiary assemblies. The relation of this primary sequence to a specific folded protein structure remains a central question in structural biology. An increasing body of evidence suggests that v...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.08.020

    authors: Schellenberg MJ,Ritchie DB,Wu T,Markin CJ,Spyracopoulos L,MacMillan AM

    更新日期:2010-10-01 00:00:00

  • Conformational properties of the aggregation precursor state of HypF-N.

    abstract::The conversion of specific proteins or protein fragments into insoluble, ordered fibrillar aggregates is a fundamental process in protein chemistry, biology, medicine and biotechnology. As this structural conversion seems to be a property shared by many proteins, understanding the mechanism of this process will be of ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.04.002

    authors: Campioni S,Mossuto MF,Torrassa S,Calloni G,de Laureto PP,Relini A,Fontana A,Chiti F

    更新日期:2008-06-06 00:00:00

  • Nucleotide-Free sB-Raf is Preferentially Bound by Hsp90 and Cdc37 In Vitro.

    abstract::The molecular chaperone Hsp90 and its cofactor Cdc37 are required for the stability of protein kinases in the cellular environment. Upon pharmacological inhibition of Hsp90, the Hsp90-dependent kinases are degraded quickly by the proteasome. Clear physiological evidence for the formation of heterooligomeric complexes ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.09.002

    authors: Eckl JM,Daake M,Schwartz S,Richter K

    更新日期:2016-10-09 00:00:00

  • A structural-informatics approach for mining beta-sheets: locating sheets in intermediate-resolution density maps.

    abstract::Here, we report a new computational method, called sheetminer, for mining beta-sheets in the density maps at intermediate resolutions of 6 to 10A. The method employs a multi-step ad hoc morphological analysis of density maps to identify the unique characteristics of beta-sheets. It was tested on density maps from 12 p...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00859-3

    authors: Kong Y,Ma J

    更新日期:2003-09-12 00:00:00

  • Mutations improving the folding of phage P22 tailspike protein affect its receptor binding activity.

    abstract::Four previously isolated mutations in Salmonella phage P22 tailspike protein were used to study the relationship between protein stability, folding, and function. Tailspike protein binds and hydrolyzes the repetitive O-antigen structure in Salmonella lipopolysaccharide. Four mutations (V331G, V331A, A334V, A334I) are ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3165

    authors: Baxa U,Steinbacher S,Weintraub A,Huber R,Seckler R

    更新日期:1999-10-29 00:00:00

  • Preliminary crystallographic analysis of the breakage-reunion domain of the Escherichia coli DNA gyrase A protein.

    abstract::The 64 x 10(3) Mr N-terminal breakage-reunion domain of the Escherichia coli DNA gyrase A protein was purified from an over-expressing strain. When complexed with the gyrase B protein, this truncated A protein has all of the enzymic properties of the full-length counterpart, although with reduced efficiency in some ca...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/S0022-2836(05)80162-7

    authors: Reece RJ,Dauter Z,Wilson KS,Maxwell A,Wigley DB

    更新日期:1990-10-20 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

  • Determining the Limitations and Benefits of Noise in Gene Regulation and Signal Transduction through Single Cell, Microscopy-Based Analysis.

    abstract::Stochastic fluctuations, termed "noise," in the level of biological molecules can greatly impact cellular functions. While biological noise can sometimes be detrimental, recent studies have provided an increasing number of examples in which biological noise can be functionally beneficial. Rather than provide an exhaus...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2017.03.007

    authors: Harton MD,Batchelor E

    更新日期:2017-04-21 00:00:00

  • Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation.

    abstract::The catalytic or functionally important residues of a protein are known to exist in evolutionarily constrained regions. However, the patterns of residue conservation alone are sometimes not very informative, depending on the homologous sequences available for a given query protein. Here, we present an integrated metho...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00207-9

    authors: Ota M,Kinoshita K,Nishikawa K

    更新日期:2003-04-11 00:00:00

  • Crystal structure of a ternary complex between human prostate-specific antigen, its substrate acyl intermediate and an activating antibody.

    abstract::Human prostate-specific antigen (PSA or KLK3) is an important marker for the diagnosis and management of prostate cancer. This is an androgen-regulated glycoprotein of the kallikrein-related protease family secreted by prostatic epithelial cells. Its physiological function is to cleave semenogelins in the seminal coag...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.11.052

    authors: Ménez R,Michel S,Muller BH,Bossus M,Ducancel F,Jolivet-Reynaud C,Stura EA

    更新日期:2008-02-29 00:00:00

  • Organization and evolution of repeated DNA sequences in closely related plant genomes.

    abstract::In common with many other eukaryotic species, the genomes of species in the genus Allium contain a high proportion of repeated DNA sequences, which may be implicated in the considerable differences in genome size that are seen between even very closely related species. The gross organization of repetitive sequences wi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(83)80189-2

    authors: Evans IJ,James AM,Barnes SR

    更新日期:1983-11-15 00:00:00

  • Shape-specific nucleotide binding of single-stranded RNA by the GLD-1 STAR domain.

    abstract::Proteins containing the STAR RNA-binding domain fulfill vital roles in RNA biogenesis, yet a detailed understanding of STAR domain RNA binding specificity is lacking. In Caenorhabditis elegans, the STAR protein GLD-1 directly binds the 28 nucleotide recognition element TGE within the 3' untranslated region of tra-2 mR...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.11.049

    authors: Lehmann-Blount KA,Williamson JR

    更新日期:2005-02-11 00:00:00

  • Desmin and vimentin intermediate filament networks: their viscoelastic properties investigated by mechanical rheometry.

    abstract::We have investigated the viscoelastic properties of the cytoplasmic intermediate filament (IF) proteins desmin and vimentin. Mechanical measurements were supported by time-dependent electron microscopy studies of the assembly process under similar conditions. Network formation starts within 2 min, but it takes more th...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.03.005

    authors: Schopferer M,Bär H,Hochstein B,Sharma S,Mücke N,Herrmann H,Willenbacher N

    更新日期:2009-04-24 00:00:00

  • Pentameric and decameric structures in solution of serum amyloid P component by X-ray and neutron scattering and molecular modelling analyses.

    abstract::Human serum amyloid P component (SAP) is a normal plasma glycoprotein and the precursor of amyloid P component which is a universal constituent of the abnormal tissue deposits in amyloidosis. X-ray and neutron scattering data showed that pentameric or decameric ring structures for SAP in solution are readily distingui...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1271

    authors: Ashton AW,Boehm MK,Gallimore JR,Pepys MB,Perkins SJ

    更新日期:1997-09-26 00:00:00

  • Pulse-chase analysis of the in vivo assembly of the bacteriophage T4 tail.

    abstract::The in vivo assembly pathway of the complex tail of bacteriophage T4 virus was determined using pulse-chase analysis as a non-invasive alternative to the in vitro experiments previously used to map assembly. Bacteriophage T4 mutants defective in head assembly were used to infect cultures of Escherichia coli in order t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3551

    authors: Ferguson PL,Coombs DH

    更新日期:2000-03-17 00:00:00