Protein-protein interaction regulates proteins' mechanical stability.

Abstract:

:Elastomeric proteins are molecular springs found not only in a variety of biological machines and tissues, but also in biomaterials of superb mechanical properties. Regulating the mechanical stability of elastomeric proteins is not only important for a range of biological processes, but also critical for the use of engineered elastomeric proteins as building blocks to construct nanomechanical devices and novel materials of well-defined mechanical properties. Here we demonstrate that protein-protein interactions can potentially serve as an effective means to regulate the mechanical properties of elastomeric proteins. We show that the binding of fragments of IgG antibody to a small protein, GB1, can significantly enhance the mechanical stability of GB1. The regulation of the mechanical stability of GB1 by IgG fragments is not through direct modification of the interactions in the mechanically key region of GB1; instead, it is accomplished via the long-range coupling between the IgG binding site and the mechanically key region of GB1. Although Fc and Fab bind GB1 at different regions of GB1, their binding to GB1 can increase the mechanical stability of GB1 significantly. Using alanine point mutants of GB1, we show that the amplitude of mechanical stability enhancement of GB1 by Fc does not correlate with the binding affinity, suggesting that binding affinity only affects the population of GB1/human Fc (hFc) complex at a given concentration of hFc, but does not affect the intrinsic mechanical stability of the GB1/hFc complex. Furthermore, our results indicate that the mechanical stability enhancement by IgG fragments is robust and can tolerate sequence/structural perturbation to GB1. Our results demonstrate that the protein-protein interaction is an efficient approach to regulate the mechanical stability of GB1-like proteins and we anticipate that this new methodology will help to develop novel elastomeric proteins with tunable mechanical stability and compliance.

journal_name

J Mol Biol

authors

Cao Y,Yoo T,Zhuang S,Li H

doi

10.1016/j.jmb.2008.03.046

subject

Has Abstract

pub_date

2008-05-16 00:00:00

pages

1132-41

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(08)00366-5

journal_volume

378

pub_type

杂志文章
  • Identification of the receptor-recognition surface of bombyxin-II, an insulin-like peptide of the silkmoth Bombyx mori: critical importance of the B-chain central part.

    abstract::Bombyxin-II, a brain-secretory peptide of the silkmoth Bombyx mori, shares 40% sequence identify and the characteristics core structure with human insulin. In spite of the structural similarity, no cross-activity is observed between them. To localize the active region of bombyxin-II, we have synthesized chimeric molec...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0589

    authors: Nagata K,Hatanaka H,Kohda D,Kataoka H,Nagasawa H,Isogai A,Ishizaki H,Suzuki A,Inagaki F

    更新日期:1995-11-10 00:00:00

  • Integrated Use of Biochemical, Native Mass Spectrometry, Computational, and Genome-Editing Methods to Elucidate the Mechanism of a Salmonella deglycase.

    abstract::Salmonellais a foodborne pathogen that causes annually millions of cases of salmonellosis globally, yet Salmonella-specific antibacterials are not available. During inflammation, Salmonella utilizes the Amadori compound fructose-asparagine (F-Asn) as a nutrient through the successive action of three enzymes, including...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2019.08.017

    authors: Sengupta A,Wu J,Seffernick JT,Sabag-Daigle A,Thomsen N,Chen TH,Capua AD,Bell CE,Ahmer BMM,Lindert S,Wysocki VH,Gopalan V

    更新日期:2019-11-08 00:00:00

  • FlgB, FlgC, FlgF and FlgG. A family of structurally related proteins in the flagellar basal body of Salmonella typhimurium.

    abstract::The flagellar basal body of Salmonella typhimurium consists of four rings surrounding a rod. The rod, which is believed to transmit motor rotation to the filament, is not well characterized in terms of its structure and composition. FlgG is known to lie within the distal portion of the rod, in the region where it is s...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(90)90365-S

    authors: Homma M,Kutsukake K,Hasebe M,Iino T,Macnab RM

    更新日期:1990-01-20 00:00:00

  • Discerning the structure and energy of multiple transition states in protein folding using psi-analysis.

    abstract::We quantify the degree to which folding occurs along a complex landscape with structurally distinct pathways using psi-analysis in combination with a protein engineering method that identifies native, non-covalent polypeptide interactions and their relative populations at the rate-limiting step. By probing the proximi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.01.018

    authors: Krantz BA,Dothager RS,Sosnick TR

    更新日期:2004-03-19 00:00:00

  • In vitro selection of RNAs aminoacylated by Escherichia coli leucyl-tRNA synthetase.

    abstract::To investigate systematically the RNA sequences necessary for aminoacylation by Escherichia coli leucyl-tRNA synthetase, RNAs with leucylation activity were isolated by in vitro selection from a library of tRNALeu variants possessing randomized sequences in the D-loop, the variable arm, and the T-loop. After two round...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2111

    authors: Asahara H,Nameki N,Hasegawa T

    更新日期:1998-10-30 00:00:00

  • Weighting aligned protein or nucleic acid sequences to correct for unequal representation.

    abstract::Aligned sequences from the same family (e.g. the haemoglobins) are seldom representative of the entire family. This is because (1) the sequence databases are heavily skewed toward a small number of organisms and (2) only a minute fraction of all the different family members have been sequenced. For many applications, ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/S0022-2836(99)80003-5

    authors: Sibbald PR,Argos P

    更新日期:1990-12-20 00:00:00

  • The crystal structure of the actin binding domain from alpha-actinin in its closed conformation: structural insight into phospholipid regulation of alpha-actinin.

    abstract::Alpha-actinin is the major F-actin crosslinking protein in both muscle and non-muscle cells. We report the crystal structure of the actin binding domain of human muscle alpha-actinin-3, which is formed by two consecutive calponin homology domains arranged in a "closed" conformation. Structural studies and available bi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.01.002

    authors: Franzot G,Sjöblom B,Gautel M,Djinović Carugo K

    更新日期:2005-04-22 00:00:00

  • Molecular basis for mutation in a surface protein expressed by malaria parasites.

    abstract::Plasmodium knowlesi parasites isolated from a rhesus monkey vaccinated with a 143,000/140,000 Mr merozoite surface protein no longer expressed this protein. To study the molecular basis for the mutations, a lambda gt11 cDNA expression library constructed from the original parasite clone was screened with rabbit antise...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(88)90204-5

    authors: Hudson DE,Wellems TE,Miller LH

    更新日期:1988-10-05 00:00:00

  • AMP sensing by DEAD-box RNA helicases.

    abstract::In eukaryotes, cellular levels of adenosine monophosphate (AMP) signal the metabolic state of the cell. AMP concentrations increase significantly upon metabolic stress, such as glucose deprivation in yeast. Here, we show that several DEAD-box RNA helicases are sensitive to AMP, which is not produced during ATP hydroly...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2013.05.006

    authors: Putnam AA,Jankowsky E

    更新日期:2013-10-23 00:00:00

  • Stabilization of native protein fold by intein-mediated covalent cyclization.

    abstract::A mutant version of the N-terminal domain of Escherichia coli DnaB helicase was used as a model system to assess the stabilization against unfolding gained by covalent cyclization. Cyclization was achieved in vivo by formation of an amide bond between the N and C termini with the help of a split mini-intein. Linear an...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.12.037

    authors: Williams NK,Liepinsh E,Watt SJ,Prosselkov P,Matthews JM,Attard P,Beck JL,Dixon NE,Otting G

    更新日期:2005-03-04 00:00:00

  • Epitopes fused to F-pilin are incorporated into functional recombinant pili.

    abstract::In order to develop a system which allows infection by an epitope-specific phage-antibody via an F-pilus expressing that epitope, a study on the expression of foreign sequences on F-pilin was undertaken. Initially, a plasmid library was constructed with random sequences encoding one to five amino acid residues fused t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.1773

    authors: Rondot S,Anthony KG,Dübel S,Ida N,Wiemann S,Beyreuther K,Frost LS,Little M,Breitling F

    更新日期:1998-06-12 00:00:00

  • The entericidin locus of Escherichia coli and its implications for programmed bacterial cell death.

    abstract::Antidote/toxin gene pairs known as "addiction modules" can maintain plasmids in bacterial populations by means of post-segregational killing. However, several chromosome-encoded addiction modules may provide an entirely distinct function in the programmed cell death of moribund subpopulations under starvation conditio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.1894

    authors: Bishop RE,Leskiw BK,Hodges RS,Kay CM,Weiner JH

    更新日期:1998-07-24 00:00:00

  • Spectroscopic studies on histone-DNA interactions. I. The interaction of histone (H2A, H2B) dimer with DNA: DNA sequence dependence.

    abstract::Binding of the histone (H2A, H2B) dimer with chicken erythrocyte DNA has been studied by salt-titration spectroscopy in equilibrium conditions. The circular dichroism of DNA near 275 nm is depressed by the interaction with (H2A, H2B) at low concentrations of salt. The depression increases with increasing amounts of (H...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90699-1

    authors: Oohara I,Wada A

    更新日期:1987-07-20 00:00:00

  • Two conformations of RNA polymerase II revealed by electron crystallography.

    abstract::A new two-dimensional crystal form of yeast RNA polymerase II was obtained in which the conformation of the enzyme appears "open", allowing entry of DNA, as required for the initiation of transcription. By contrast, a previous crystal form contained the enzyme in a "closed" conformation, appropriate for retention of D...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1273

    authors: Asturias FJ,Meredith GD,Poglitsch CL,Kornberg RD

    更新日期:1997-10-03 00:00:00

  • Ligand-induced stabilization of PPARgamma monitored by NMR spectroscopy: implications for nuclear receptor activation.

    abstract::Nuclear receptors are ligand-dependent transcription factors that are mediators of the action of lipophilic hormones and other endogenous ligands and are the targets of drugs useful in a variety of therapeutic areas. Peroxisome proliferator-activated receptor (PPAR)gamma is a nuclear receptor that, acting as a heterod...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3636

    authors: Johnson BA,Wilson EM,Li Y,Moller DE,Smith RG,Zhou G

    更新日期:2000-04-28 00:00:00

  • Intracellular antibody capture technology: application to selection of intracellular antibodies recognising the BCR-ABL oncogenic protein.

    abstract::The expression of antibodies inside cells to ablate protein function has the potential for disease therapy and for target validation in functional genomics. However, due to inefficient expression or folding, only a few antibodies or antibody fragments, usually as single-chain Fv antibody fragments (scFv), bind their a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2002.5403

    authors: Tse E,Lobato MN,Forster A,Tanaka T,Chung GT,Rabbitts TH

    更新日期:2002-03-15 00:00:00

  • The Role of RNA in Biological Phase Separations.

    abstract::Phase transitions that alter the physical state of ribonucleoprotein particles contribute to the spacial and temporal organization of the densely packed intracellular environment. This allows cells to organize biologically coupled processes as well as respond to environmental stimuli. RNA plays a key role in phase sep...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2018.05.003

    authors: Fay MM,Anderson PJ

    更新日期:2018-11-02 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

  • Single-cell analysis of lambda immunity regulation.

    abstract::We have examined expression of the lambdacI operon in single cells via a rex Colon, two colons gfp substitution. Although average fluorescence agreed with expectations for expression of lambda-repressor, fluorescence fluctuated greatly from cell-to-cell. Fluctuations in repressor concentration are not predicted by pre...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.09.037

    authors: Baek K,Svenningsen S,Eisen H,Sneppen K,Brown S

    更新日期:2003-11-28 00:00:00

  • A mechanistic insight into SMAC peptide interference with XIAP-Bir2 inhibition of executioner caspases.

    abstract::X-linked inhibitor of apoptosis protein (XIAP) inhibits apoptosis mainly through inhibition of caspase-9 and executioner caspases of -3 and -7. The inhibition of the former protease is implemented through the bacculoviral inhibitory repeat-3 (Bir3) domain, while the inhibition of the latter is accomplished by the inte...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.05.082

    authors: Abhari BA,Davoodi J

    更新日期:2008-09-05 00:00:00

  • DNA deletion of mitochondrial introns is correlated with the process of senescence in Podospora anserina.

    abstract::In the filamentous fungus Podospora anserina, the unavoidable phenomenon of senescence is associated with specific mitochondrial rearrangements and particularly with the amplification of some regions of the mitochondrial chromosome. Mechanisms responsible for these rearrangements are still unknown. The implication in ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1558

    authors: Sainsard-Chanet A,Begel O,Belcour L

    更新日期:1993-11-05 00:00:00

  • Molecular dynamics simulation of dark-adapted rhodopsin in an explicit membrane bilayer: coupling between local retinal and larger scale conformational change.

    abstract::The light-driven photocycle of rhodopsin begins the photoreceptor cascade that underlies visual response. In a sequence of events, the retinal covalently attached to the rhodopsin protein undergoes a conformational change that communicates local changes to a global conformational change throughout the whole protein. I...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.08.045

    authors: Crozier PS,Stevens MJ,Forrest LR,Woolf TB

    更新日期:2003-10-24 00:00:00

  • Efficient recovery of high-affinity antibodies from a single-chain Fab yeast display library.

    abstract::Yeast display is a powerful technology for the isolation of monoclonal antibodies (mAbs) against a target antigen. Antibody libraries have been displayed on the surface of yeast as both single-chain variable fragment (scFv) and antigen binding fragment (Fab). Here, we combine these two formats to display well-characte...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.04.019

    authors: Walker LM,Bowley DR,Burton DR

    更新日期:2009-06-05 00:00:00

  • Cooperation of TOM and TIM23 complexes during translocation of proteins into mitochondria.

    abstract::Translocation of the majority of mitochondrial proteins from the cytosol into mitochondria requires the cooperation of TOM and TIM23 complexes in the outer and inner mitochondrial membranes. The molecular mechanisms underlying this cooperation remain largely unknown. Here, we present biochemical and genetic evidence t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2014.07.015

    authors: Waegemann K,Popov-Čeleketić D,Neupert W,Azem A,Mokranjac D

    更新日期:2015-03-13 00:00:00

  • cAMP-dependent protein kinase A selects the excited state of the membrane substrate phospholamban.

    abstract::Phosphorylation of membrane proteins is a central regulatory and signaling mechanism across cell compartments. However, the recognition process and phosphorylation mechanism of membrane-bound substrates by kinases are virtually unknown. cAMP-dependent protein kinase A (PKA) is a ubiquitous enzyme that phosphorylates s...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.06.041

    authors: Masterson LR,Yu T,Shi L,Wang Y,Gustavsson M,Mueller MM,Veglia G

    更新日期:2011-09-16 00:00:00

  • Structure-function analysis of a bacterial deoxyadenosine kinase reveals the basis for substrate specificity.

    abstract::Deoxyribonucleoside kinases (dNKs) catalyze the transfer of a phosphoryl group from ATP to a deoxyribonucleoside (dN), a key step in DNA precursor synthesis. Recently structural information concerning dNKs has been obtained, but no structure of a bacterial dCK/dGK enzyme is known. Here we report the structure of such ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.12.010

    authors: Welin M,Wang L,Eriksson S,Eklund H

    更新日期:2007-03-09 00:00:00

  • Crystal structure of BstYI at 1.85A resolution: a thermophilic restriction endonuclease with overlapping specificities to BamHI and BglII.

    abstract::We report here the structure of BstYI, an "intermediate" type II restriction endonuclease with overlapping sequence specificities to BamHI and BglII. BstYI, a thermophilic endonuclease, recognizes and cleaves the degenerate hexanucleotide sequence 5'-RGATCY-3' (where R=A or G and Y=C or T), cleaving DNA after the 5'-R...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.02.074

    authors: Townson SA,Samuelson JC,Vanamee ES,Edwards TA,Escalante CR,Xu SY,Aggarwal AK

    更新日期:2004-05-07 00:00:00

  • Location of filamentous phage minor coat proteins in phage and in infected cells.

    abstract::We show that all minor coat proteins of phage f1 are integral inner membrane proteins prior to assembly. Hence all phage structural and morphogenetic proteins are localized in the membrane of the infected cell, consistent with models of phage assembly in which morphogenesis is coincident with phage extrusion. Our data...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0393

    authors: Endemann H,Model P

    更新日期:1995-07-21 00:00:00

  • Intriguing conformation changes associated with the trans/cis isomerization of a prolyl residue in the active site of the DsbA C33A mutant.

    abstract::Escherichia coli DsbA belongs to the thioredoxin family and catalyzes the formation of disulfide bonds during the folding of proteins in the bacterial periplasm. It active site (C30-P31-H32-C33) consists of a disulfide bridge that is transferred to newly translocated proteins. The work reported here refers to the DsbA...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.01.049

    authors: Ondo-Mbele E,Vivès C,Koné A,Serre L

    更新日期:2005-04-01 00:00:00

  • Enhancing the contrast of ApoB to locate the surface components in the 3D density map of human LDL.

    abstract::A 26 Å resolution map of the structure of human low-density lipoprotein (LDL) was obtained from electron cryomicroscopy and single-particle image reconstruction. The structure showed a discoidal-shaped LDL particle with high-density regions mainly distributed at the edge of the particle and low-density regions at the ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.10.034

    authors: Liu Y,Atkinson D

    更新日期:2011-01-07 00:00:00