Cooperative unfolding of a metastable serpin to a molten globule suggests a link between functional and folding energy landscapes.

Abstract:

:Alpha-1 antitrypsin (alpha(1)-AT) is a member of the serpin class of protease inhibitors, and folds to a metastable state rather than its thermodynamically most stable native state. Upon cleavage by a target protease, alpha(1)-AT undergoes a dramatic conformational change to a stable form, translocating the bound protease more than 70 A to form an inhibitory protease-serpin complex. Numerous mutagenesis studies on serpins have demonstrated the trade-off between the stability of the metastable state on the one hand and the inhibitory efficiency on the other. Studies of the equilibrium unfolding of serpins provide insight into this connection between structural plasticity and metastability. We studied equilibrium unfolding of wild-type alpha(1)-AT using hydrogen-deuterium/exchange mass spectrometry to characterize the structure and the stability of an equilibrium intermediate that was observed in low concentrations of denaturant in earlier studies. Our results show that the intermediate observed at low concentrations of denaturant has no protection from hydrogen-deuterium exchange, indicating a lack of stable structure. Further, differential scanning calorimetry of alpha(1)-AT at low concentrations of denaturant shows no heat capacity peak during thermal denaturation, indicating that the transition from the intermediate to the unfolded state is not a cooperative first-order-like phase transition.. Our results show that the unfolding of alpha(1)-AT involves a cooperative transition to a molten globule form, followed by a non-cooperative transition to a random-coil form as more guanidine is added. Thus, the entire alpha(1)-AT molecule consists of one cooperative structural unit rather than multiple structural domains with different stabilities. Furthermore, our results together with previous mutagenesis studies suggest a possible link between an equilibrium molten globule and a functional intermediate that may be populated during the protease inhibition.

journal_name

J Mol Biol

authors

Tsutsui Y,Wintrode PL

doi

10.1016/j.jmb.2007.05.039

subject

Has Abstract

pub_date

2007-08-03 00:00:00

pages

245-55

issue

1

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(07)00675-4

journal_volume

371

pub_type

杂志文章
  • Three-dimensional structure of FEZ-1, a monomeric subclass B3 metallo-beta-lactamase from Fluoribacter gormanii, in native form and in complex with D-captopril.

    abstract::The beta-lactamases are involved in bacterial resistance to penicillin and related compounds. Members of the metallo-enzyme class are now found in many pathogenic bacteria and are thus becoming of major clinical importance. The structures of the Zn-beta-lactamase from Fluoribacter gormanii (FEZ-1) in the native and in...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)01271-8

    authors: García-Sáez I,Mercuri PS,Papamicael C,Kahn R,Frère JM,Galleni M,Rossolini GM,Dideberg O

    更新日期:2003-01-24 00:00:00

  • The effect of a hydrophobic N-terminal probe on translational pausing of chloramphenicol acetyl transferase and rhodanese.

    abstract::The effect on translational pausing of a hydrophobic probe, coumarin, at the N terminus of nascent peptides was investigated. Two different proteins, bacterial chloramphenicol acetyltransferase and bovine rhodanese, were synthesized by coupled transcription/translation in a cell-free system derived from Escherichia co...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2481

    authors: Tsalkova T,Kramer G,Hardesty B

    更新日期:1999-02-12 00:00:00

  • Structural analysis of T4 DNA helix destabilizing protein (gp32 I) crystal by electron microscopy.

    abstract::Low dose electron diffraction and imaging techniques have been applied to the study of the crystalline structure of gp32*I, a DNA helix destabilizing protein derived from bacteriophage T4 gene 32 protein. A quantitative analysis of intensities from electron diffraction patterns from tilted, multilayered gp32*I crystal...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(83)80182-x

    authors: Cohen HA,Chiu W,Hosoda J

    更新日期:1983-09-05 00:00:00

  • The geometry of interactions between catalytic residues and their substrates.

    abstract::The process of deducing the catalytic mechanism of an enzyme from its structure is highly complex and requires extensive experimental work to validate a proposed mechanism. As one step towards improving the reliability of this process, we have gathered statistics describing the typical geometry of catalytic residues w...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.03.055

    authors: Torrance JW,Holliday GL,Mitchell JB,Thornton JM

    更新日期:2007-06-15 00:00:00

  • Mechanism of codon recognition by transfer RNA and codon-induced tRNA association.

    abstract::The steps of UUC recognition by tRNAPhe were analysed by temperature-jump measurements. At ion concentrations close to physiological conditions we found three relaxation processes, which we assigned to (1) formation of codon-anticodon complexes, (2) a conformational change of the anticodon loop coupled with Mg2+ bindi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(84)90085-8

    authors: Labuda D,Striker G,Porschke D

    更新日期:1984-04-25 00:00:00

  • Human T cell cyclophilin18 binds to thiol-specific antioxidant protein Aop1 and stimulates its activity.

    abstract::Cyclophilins (CyPs) define a family of proteins binding to the immunosuppressive drug cyclosporin A (CsA). They are evolutionary highly conserved proteins being present in both pro- and eukaryotes and in different subcellular locations. CyPs possess enzymatic activity, namely peptidyl-prolyl cis-trans isomerase (PPIas...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.1644

    authors: Jäschke A,Mi H,Tropschug M

    更新日期:1998-04-10 00:00:00

  • Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli.

    abstract::Mechanisms of folding and misfolding of membrane proteins are of interest in cell biology. Recently, we have established single-molecule force spectroscopy to observe directly the stepwise folding of the Na+/H+ antiporter NhaA from Escherichia coli in vitro. Here, we improved this approach significantly to track the f...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.10.028

    authors: Kedrov A,Janovjak H,Ziegler C,Kuhlbrandt W,Muller DJ

    更新日期:2006-01-06 00:00:00

  • Biophysical characterization of structural properties and folding of interleukin-1 receptor antagonist.

    abstract::Structural properties and folding of interleukin-1 receptor antagonist (IL-1ra), a therapeutically important cytokine with a symmetric beta-trefoil topology, are characterized using optical spectroscopy, high-resolution NMR, and size-exclusion chromatography. Spectral contributions of two tryptophan residues, Trp17 an...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.02.031

    authors: Latypov RF,Harvey TS,Liu D,Bondarenko PV,Kohno T,Fachini RA 2nd,Rosenfeld RD,Ketchem RR,Brems DN,Raibekas AA

    更新日期:2007-05-11 00:00:00

  • Ro ribonucleoprotein assembly in vitro. Identification of RNA-protein and protein-protein interactions.

    abstract::The human Y RNAs, small RNAs with an unknown function, are complexed with at least three proteins: the 60,000 M(r) Ro protein (Ro60), the 52,000 M(r) Ro protein (Ro52) and the La protein (La). In this study we examined the intermolecular interactions between the components of these so-called Ro ribonucleoprotein (Ro R...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90890-v

    authors: Slobbe RL,Pluk W,van Venrooij WJ,Pruijn GJ

    更新日期:1992-09-20 00:00:00

  • Modelling transcriptional interference and DNA looping in gene regulation.

    abstract::We describe a hybrid statistical mechanical and dynamical approach for modelling the formation of closed, open and elongating complexes of RNA polymerase, the interactions of these polymerases to produce transcriptional interference, and the regulation of these processes by a DNA-binding and DNA-looping regulatory pro...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.04.041

    authors: Dodd IB,Shearwin KE,Sneppen K

    更新日期:2007-06-22 00:00:00

  • Characterisation of epitopes on human p53 using phage-displayed peptide libraries: insights into antibody-peptide interactions.

    abstract::We previously described the use of a phage-displayed library of random hexapeptides to define and localise the epitope on the human tumor suppressor protein p53 recognised by the monoclonal antibody PAb240. Here we have extended these results to a further eight anti-p53 monoclonal antibodies and to two further librari...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0202

    authors: Stephen CW,Helminen P,Lane DP

    更新日期:1995-04-21 00:00:00

  • Monomers of the Escherichia coli SSB-1 mutant protein bind single-stranded DNA.

    abstract::The Escherichia coli wild-type single strand binding (SSB) protein is a stable tetramer that binds to single-stranded (ss) DNA in its role in DNA replication, recombination and repair. The ssb-1 mutation, a substitution of tyrosine for histidine-55 within the SSB-1 protein, destabilizes the tetramer with respect to mo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90611-9

    authors: Bujalowski W,Lohman TM

    更新日期:1991-01-05 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

  • Canonical antigen-binding loop structures in immunoglobulins: more structures, more canonical classes?

    abstract::Grafting the antigen-binding loops onto a human antibody scaffold is a widely used technique to humanise murine antibodies. The success of this approach depends largely on the observation that the antigen-binding loops adopt only a limited number of canonical structures. Identification of the correct canonical structu...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3839

    authors: Decanniere K,Muyldermans S,Wyns L

    更新日期:2000-06-30 00:00:00

  • Protein unfolding, and the "tuning in" of reversible intermediate states, in protic ionic liquid media.

    abstract::Protic ionic liquids (PILs) are currently being shown to be as interesting and valuable to chemical manipulations as the well-known aprotic ionic liquids (APIL). PILs have the additional advantage that the proton activity (PA) can be adjusted by the choice of Bronsted base and Bronsted acid used in their formation. In...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.02.050

    authors: Byrne N,Angell CA

    更新日期:2008-05-02 00:00:00

  • Dielectric constant of sickle cell hemoglobin. Dielectric properties of sickle cell hemoglobin in solution and gel.

    abstract::The dielectric constants of sickle cell hemoglobin were determined before and after gelation. The dielectric properties of oxy and deoxy sickle cell hemoglobin in solution are nearly identical to those of oxy and deoxy hemoglobin A. Only in the gel state did deoxy sickle cell hemoglobin display dielectric behavior dif...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(83)80307-6

    authors: Delalic Z,Takashima S,Adachi K,Asakura T

    更新日期:1983-08-15 00:00:00

  • Recognition of 5'-YpG-3' sequences by coupled stacking/hydrogen bonding interactions with amino acid residues.

    abstract::The combined biochemical and structural study of hundreds of protein-DNA complexes has indicated that sequence-specific interactions are mediated by two mechanisms termed direct and indirect readout. Direct readout involves direct interactions between the protein and base-specific atoms exposed in the major and minor ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.10.071

    authors: Lamoureux JS,Maynes JT,Glover JN

    更新日期:2004-01-09 00:00:00

  • Intermicrobial Interactions as a Driver for Community Composition and Stratification of Oral Biofilms.

    abstract::The oral cavity is accessible to microorganisms, and biofilms are present throughout on hard and soft tissues. The shedding of epithelial cell layers is usually effective for controlling biofilm development on soft tissues. Innate immune mechanisms are not so effective against biofilms on tooth surfaces, and oral hygi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2015.09.022

    authors: Jakubovics NS

    更新日期:2015-11-20 00:00:00

  • Molecular basis for the specificity of p27 toward cyclin-dependent kinases that regulate cell division.

    abstract::The cyclin-dependent kinase inhibitors (CKIs) bind to and directly regulate the catalytic activity of cyclin-dependent kinase (Cdk)/cyclin complexes involved in cell cycle control and do not regulate other, closely related Cdks. We showed previously that the CKI, p27, binds to Cdk2/cyclin A though a sequential mechani...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.04.019

    authors: Lacy ER,Wang Y,Post J,Nourse A,Webb W,Mapelli M,Musacchio A,Siuzdak G,Kriwacki RW

    更新日期:2005-06-17 00:00:00

  • Site-specific structural variations accompanying tubular assembly of the HIV-1 capsid protein.

    abstract::The 231-residue capsid (CA) protein of human immunodeficiency virus type 1 (HIV-1) spontaneously self-assembles into tubes with a hexagonal lattice that is believed to mimic the surface lattice of conical capsid cores within intact virions. We report the results of solid-state nuclear magnetic resonance (NMR) measurem...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2013.12.021

    authors: Bayro MJ,Chen B,Yau WM,Tycko R

    更新日期:2014-03-06 00:00:00

  • Single-stranded DNA binding properties of the UvsX recombinase of bacteriophage T4: binding parameters and effects of nucleotides.

    abstract::Bacteriophage T4 provides an important model for the biochemistry and genetics of DNA metabolism. Phage-encoded proteins conduct all essential steps of T4 DNA replication, repair, and recombination. Central to these three processes is the T4 UvsX protein, a member of the filamentous, ATP-dependent class of general rec...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2124

    authors: Ando RA,Morrical SW

    更新日期:1998-11-06 00:00:00

  • Mapping the Resistance Potential of Influenza's H+ Channel against an Antiviral Blocker.

    abstract::The development of drug resistance has long plagued our efforts to curtail viral infections in general and influenza in particular. The problem is particularly challenging since the exact mode of resistance may be difficult to predict, without waiting for untreatable strains to evolve. Herein, a different approach is ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.08.007

    authors: Assa D,Alhadeff R,Krugliak M,Arkin IT

    更新日期:2016-10-09 00:00:00

  • Probing a tRNA core that contributes to aminoacylation.

    abstract::The contribution of the tRNA "core" to aminoacylation is beginning to be recognized. One example is the core region of Escherichia coli tRNA(Cys), which has been shown by biochemical studies to be important for aminoacylation. This core has several layers of unusual base-pairs, which are revealed by the recent crystal...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3353

    authors: Hamann CS,Hou YM

    更新日期:2000-01-28 00:00:00

  • 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

  • Isolation and characterization of a previously unrecognized myosin heavy chain gene present in the Syrian hamster.

    abstract::A full length (25,000 base-pair) myosin heavy chain gene completely contained within a single cosmid clone was isolated from a Syrian hamster cosmid genomic library. Sequence comparison of the 3' untranslated region indicated the presence of a 75% homology with the rat embryonic myosin heavy chain gene. Extensive 5' f...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/0022-2836(91)90251-z

    authors: McCully JD,Wang RX,Kellam B,Sole MJ,Liew CC

    更新日期:1991-04-20 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

  • Structural, biochemical, and in vivo characterization of the first virally encoded cyclophilin from the Mimivirus.

    abstract::Although multiple viruses utilize host cell cyclophilins, including severe acute respiratory syndrome (SARS) and human immunodeficiency virus type-1(HIV-1), their role in infection is poorly understood. To help elucidate these roles, we have characterized the first virally encoded cyclophilin (mimicyp) derived from th...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.08.051

    authors: Thai V,Renesto P,Fowler CA,Brown DJ,Davis T,Gu W,Pollock DD,Kern D,Raoult D,Eisenmesser EZ

    更新日期:2008-04-18 00:00:00

  • Brujita Integrase: A Simple, Arm-Less, Directionless, and Promiscuous Tyrosine Integrase System.

    abstract::Mycobacteriophage Brujita is an unusual temperate phage in which establishment of superinfection immunity is dependent on chromosomal integration. Integration is mediated by a non-canonical tyrosine integrase (Int) lacking an N-terminal domain typically associated with binding to arm-type sites within the phage attach...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.04.023

    authors: Lunt BL,Hatfull GF

    更新日期:2016-06-05 00:00:00

  • Structure-based identification of a ricin inhibitor.

    abstract::Ricin is a potent cytotoxin which has been used widely in the construction of therapeutic agents such as immunotoxins. Recently it has been used by governments and underground groups as a poison. There is interest in identifying and designing effective inhibitors of the ricin A chain (RTA). In this study computer-assi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0865

    authors: Yan X,Hollis T,Svinth M,Day P,Monzingo AF,Milne GW,Robertus JD

    更新日期:1997-03-14 00:00:00

  • Apoprotein structure in the LH2 complex from Rhodopseudomonas acidophila strain 10050: modular assembly and protein pigment interactions.

    abstract::The refined structure of the peripheral light-harvesting complex from Rhodopseudomonas acidophila strain 10050 reveals a membrane protein with protein-protein interactions in the trans-membrane region exclusively of a van der Waals nature. The dominant factors in the formation of the complex appear to be extramembrano...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.0966

    authors: Prince SM,Papiz MZ,Freer AA,McDermott G,Hawthornthwaite-Lawless AM,Cogdell RJ,Isaacs NW

    更新日期:1997-05-02 00:00:00