当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Computational design of calmodulin mutants with up to 900-fold increase in binding specificity.

Computational design of calmodulin mutants with up to 900-fold increase in binding specificity.

Abstract：

:Calmodulin (CaM) is a ubiquitous second messenger protein that regulates a variety of structurally and functionally diverse targets in response to changes in Ca(2+) concentration. CaM-dependent protein kinase II (CaMKII) and calcineurin (CaN) are the prominent CaM targets that play an opposing role in many cellular functions including synaptic regulation. Since CaMKII and CaN compete for the available Ca(2+)/CaM, the differential affinity of these enzymes for CaM is crucial for achieving a balance in Ca(2+) signaling. We used the computational protein design approach to modify CaM binding specificity for these two targets. Starting from the X-ray structure of CaM in complex with the CaM-binding domain of CaMKII, we optimized CaM interactions with CaMKII by introducing mutations into the CaM sequence. CaM optimization was performed with a protein design program, ORBIT, using a modified energy function that emphasized intermolecular interactions in the sequence selection procedure. Several CaM variants were experimentally constructed and tested for binding to the CaMKII and CaN peptides using the surface plasmon resonance technique. Most of our CaM mutants demonstrated small increase in affinity for the CaMKII peptide and substantial decrease in affinity for the CaN peptide compared to that of wild-type CaM. Our best CaM design exhibited an about 900-fold increase in binding specificity towards the CaMKII peptide, becoming the highest specificity switch achieved in any protein-protein interface through the computational protein design approach. Our results show that computational redesign of protein-protein interfaces becomes a reliable method for altering protein binding affinity and specificity.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Yosef E,Politi R,Choi MH,Shifman JM

doi

10.1016/j.jmb.2008.09.053

subject

Has Abstract

pub_date

2009-02-06 00:00:00

pages

1470-80

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(08)01193-5

journal_volume

385

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Contextual constraints on synonymous codon choice.

    abstract：:We have studied the statistical constraints on synonymous codon choice to evaluate various proposals regarding the origin of the bias in synonymous codon usage observed by Fiers et al. (1975), Air et al. (1976), Grantham et al. (1980) and others. We have determined the statistical dependence of the degenerate third ba...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(83)90063-3

    authors： Lipman DJ,Wilbur WJ

    更新日期：1983-01-25 00:00:00

  • ADP-binding to origin recognition complex of Saccharomyces cerevisiae.

    abstract：:The origin recognition complex (ORC), a possible initiator of chromosomal DNA replication in eukaryotes, binds to ATP through its subunits Orc1p and Orc5p. Orc1p possesses ATPase activity. As for DnaA, the Escherichia coli initiator, the ATP-DnaA complex is active but the ADP-DnaA complex is inactive for DNA replicati...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.04.045

    authors： Takenaka H,Makise M,Kuwae W,Takahashi N,Tsuchiya T,Mizushima T

    更新日期：2004-06-25 00:00:00

  • Modulator of drug activity B from Escherichia coli: crystal structure of a prokaryotic homologue of DT-diaphorase.

    abstract：:Modulator of drug activity B (MdaB) is a putative member of the DT-diaphorase family of NAD(P)H:oxidoreductases that afford cellular protection against quinonoid compounds. While there have been extensive investigations of mammalian homologues, putative prokaryotic members of this enzyme family have received little at...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.03.053

    authors： Adams MA,Jia Z

    更新日期：2006-06-02 00:00:00

  • Substrate specificity of the DNA unwinding activity of the RecBC enzyme of Escherichia coli.

    abstract：:The RecBC enzyme of Escherichia coli promotes genetic recombination of phage or bacterial chromosomes. The purified enzyme travels through duplex DNA, unwinding and rewinding the DNA with the transient production of potentially recombinogenic single-stranded DNA. The studies reported here are aimed at understanding wh...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(85)90414-0

    authors： Taylor AF,Smith GR

    更新日期：1985-09-20 00:00:00

  • Analysis of the CYT-18 protein binding site at the junction of stacked helices in a group I intron RNA by quantitative binding assays and in vitro selection.

    abstract：:The Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (CYT-18 protein) functions in splicing group I introns by promoting the formation of the catalytically active structure of the intron RNA. Previous studies showed that CYT-18 binds with high affinity to the P4-P6 domain of the catalytic core and that there is...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0439

    authors： Saldanha R,Ellington A,Lambowitz AM

    更新日期：1996-08-09 00:00:00

  • Folding mechanism of FIS, the intertwined, dimeric factor for inversion stimulation.

    abstract：:FIS, the factor for inversion stimulation, from Escherichia coli and other enteric bacteria, is an interwined alpha-helical homodimer. Size exclusion chromatography and static light scattering measurements demonstrated that FIS is predominately a stable dimer at the concentrations (1-10 microM monomer) and buffer cond...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2003.11.013

    authors： Topping TB,Hoch DA,Gloss LM

    更新日期：2004-01-23 00:00:00

  • An EM view of the FokI synaptic complex by single particle analysis.

    abstract：:FokI is a type IIS restriction endonuclease that recognizes the 5'-GGATG-3' sequence and cleaves non-specifically at 9 and 13 base-pairs away on the top and bottom strands, respectively, to produce a 5' overhang. FokI is a bipartite endonuclease with separate recognition and cleavage domains. Because of its bipartite ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.04.066

    authors： Vanamee ES,Berriman J,Aggarwal AK

    更新日期：2007-07-06 00:00:00

  • Isolation and nucleotide sequence analysis of the beta-type globin pseudogene from human, gorilla and chimpanzee.

    abstract：:The beta-globin gene cluster of human, gorilla and chimpanzee contain the same number and organization of beta-type globin genes: 5'-epsilon (embryonic)-G gamma and A gamma (fetal)-psi beta (inactive)-delta and beta (adult)-3'. We have isolated the psi beta-globin gene regions from the three species and determined the...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(84)90256-0

    authors： Chang LY,Slightom JL

    更新日期：1984-12-25 00:00:00

  • Fluorine-19 nuclear magnetic resonance as a probe of the solution structure of mutants of 5-fluorouracil-substituted Escherichia coli valine tRNA.

    abstract：:In order to utilize 19F nuclear magnetic resonance (NMR) to probe the solution structure of Escherichia coli tRNAVal labeled by incorporation of 5-fluorouracil, we have assigned its 19F spectrum. We describe here assignments made by examining the spectra of a series of tRNAVal mutants with nucleotide substitutions for...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)90528-r

    authors： Chu WC,Feiz V,Derrick WB,Horowitz J

    更新日期：1992-10-20 00:00:00

  • Extensive methylation of a part of the CpG island located 3.0-4.5 kbp upstream to the chicken alpha-globin gene cluster may contribute to silencing the globin genes in non-erythroid cells.

    abstract：:Here, we show that in the chicken genome, the domain of alpha-globin genes is preceded by a CpG island of which the downstream part ( approximately 0.65 kbp) is heavily methylated in lymphoid cells; it is either non-methylated or undermethylated in erythroid cells. Recombinant plasmids were constructed with the corres...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.3775

    authors： Razin SV,Ioudinkova ES,Scherrer K

    更新日期：2000-06-16 00:00:00

  • Amino acid periodicities and their structural implications for the evolutionarily conservative central domain of some silkmoth chorion proteins.

    abstract：:The central domain is an evolutionarily conservative region that is invariant in length in the A and Hc-A families of silkmoth chorion proteins. This domain shows strong sixfold periodicities for various amino acid residues, such as glycine and large non-polar residues. The periodicities and their phase relationships,...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(85)90132-9

    authors： Hamodrakas SJ,Etmektzoglou T,Kafatos FC

    更新日期：1985-12-05 00:00:00

  • Generation, affinity maturation, and characterization of a human anti-human NKG2D monoclonal antibody with dual antagonistic and agonistic activity.

    abstract：:In humans, NKG2D is an activating receptor on natural killer (NK) cells and a costimulatory receptor on certain T cells and plays a central role in mediating immune responses in autoimmune diseases, infectious diseases, and cancer. Monoclonal antibodies that antagonize or agonize immune responses mediated by human NKG...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.09.008

    authors： Kwong KY,Baskar S,Zhang H,Mackall CL,Rader C

    更新日期：2008-12-31 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

  • 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

  • Interaction Analyses of the Integrin β2 Cytoplasmic Tail with the F3 FERM Domain of Talin and 14-3-3ζ Reveal a Ternary Complex with Phosphorylated Tail.

    abstract：:Integrins, which are heterodimeric (α and β subunits) signal-transducer proteins, are essential for cell adhesion and migration. β cytosolic tails (β-CTs) of integrins interact with a number of cytosolic proteins including talin, Dok1, and 14-3-3ζ. The formation of multiprotein complexes with β-CTs is involved in the ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2016.08.014

    authors： Chatterjee D,Zhiping LL,Tan SM,Bhattacharjya S

    更新日期：2016-10-09 00:00:00

  • Unmasking ligand binding motifs: identification of a chemokine receptor motif by NMR studies of antagonist peptides.

    abstract：:Determining the critical structural features a ligand must possess in order to bind to its receptor is of key importance to the understanding of vital biological processes and to the rational design of small molecule therapeutics to modulate receptor function. We have developed a general strategy for determining such ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00094-9

    authors： Booth V,Slupsky CM,Clark-Lewis I,Sykes BD

    更新日期：2003-03-21 00:00:00

  • NMR solution structure of an oxaliplatin 1,2-d(GG) intrastrand cross-link in a DNA dodecamer duplex.

    abstract：:We have determined, at high resolution, the NMR solution structure of an oxaliplatin-GG DNA dodecamer in the AGGC sequence context by 2D NMR studies. Homonuclear assignment strategies resulted in unambiguous assignment of 203 out of 249 protons, which corresponds to assignment of approximately 81% of the protons. Assi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.06.066

    authors： Wu Y,Pradhan P,Havener J,Boysen G,Swenberg JA,Campbell SL,Chaney SG

    更新日期：2004-08-27 00:00:00

  • The folding energy landscape of the dimerization domain of Escherichia coli Trp repressor: a joint experimental and theoretical investigation.

    abstract：:Enhanced structural insights into the folding energy landscape of the N-terminal dimerization domain of Escherichia coli tryptophan repressor, [2-66]2 TR, were obtained from a combined experimental and theoretical analysis of its equilibrium folding reaction. Previous studies have shown that the three intertwined heli...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.07.080

    authors： Simler BR,Levy Y,Onuchic JN,Matthews CR

    更新日期：2006-10-13 00:00:00

  • Secondary structure and thermostability of the phage P22 tailspike. XX. Analysis by Raman spectroscopy of the wild-type protein and a temperature-sensitive folding mutant.

    abstract：:The thermostable tailspike endorhamnosidase of bacteriophage P22 has been investigated by laser Raman spectroscopy to determine the protein's secondary structure and the basis of its thermostability. The conformation of the native tailspike, determined by Raman amide I and amide III band analyses, is 52 to 61% beta-sh...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(88)90620-1

    authors： Sargent D,Benevides JM,Yu MH,King J,Thomas GJ Jr

    更新日期：1988-02-05 00:00:00

  • The archaeal XPB protein is a ssDNA-dependent ATPase with a novel partner.

    abstract：:XPB is a superfamily 2 helicase with a 3'-5' polarity. In eukaryotes, XPB is an integral subunit of the transcription factor TFIIH, which plays a dual role in DNA opening at RNA polymerase II promoters and in establishing the repair bubble around a DNA lesion in nucleotide excision repair. Eukaryotic XPB has only very...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.12.019

    authors： Richards JD,Cubeddu L,Roberts J,Liu H,White MF

    更新日期：2008-02-22 00:00:00

  • Dystrophin Dp71f associates with the beta1-integrin adhesion complex to modulate PC12 cell adhesion.

    abstract：:Dystrophin Dp71 is the main product of the Duchenne muscular dystrophy gene in the brain; however, its function is unknown. To study the role of Dp71 in neuronal cells, we previously generated by antisense treatment PC12 neuronal cell clones with decreased Dp71 expression (antisense-Dp71 cells). PC12 cells express two...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.07.075

    authors： Cerna J,Cerecedo D,Ortega A,García-Sierra F,Centeno F,Garrido E,Mornet D,Cisneros B

    更新日期：2006-10-06 00:00:00

  • Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility.

    abstract：:The worm-like chain model has often been employed to describe the average conformation of long, intrinsically straight polymer molecules, including DNA. The present study extends the applicability of the worm-like chain model to polymers containing bends or sections of different flexibility. Several cases have been ex...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.1830

    authors： Rivetti C,Walker C,Bustamante C

    更新日期：1998-07-03 00:00:00

  • Aminoglycoside resistance by ArmA-mediated ribosomal 16S methylation in human bacterial pathogens.

    abstract：:Aminoglycosides are a medically important class of antibiotics used to treat serious infections. Methylation of the ribosomal target is an emerging mechanism that produces a high level of resistance to all clinically available aminoglycosides for systemic therapy except streptomycin. ArmA was the first methyltransfera...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.03.038

    authors： Liou GF,Yoshizawa S,Courvalin P,Galimand M

    更新日期：2006-06-02 00:00:00

  • Specification of DNA replication origins and genomic base composition in fission yeasts.

    abstract：:In the "Replicon Theory", Jacob, Brenner and Cuzin proposed the existence of replicators and initiators as the two major actors in DNA replication. Over the years, many protein components of initiators have been shown to be conserved in different organisms during evolution. By contrast, replicator DNA sequences (often...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2013.09.023

    authors： Mojardín L,Vázquez E,Antequera F

    更新日期：2013-11-29 00:00:00

  • Involvement of a stem-loop structure in the location of junction sites in viral RNA recombination.

    abstract：:Recombination between RNAs associated with turnip crinkle virus is thought to occur during plus-strand synthesis at motifs resembling the 5'-ends of genomic, subgenomic and satellite RNAs. Common structural regions encompassing the motifs have been found for major crossover sites on two different minus-strand template...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.0050

    authors： Carpenter CD,Oh JW,Zhang C,Simon AE

    更新日期：1995-02-03 00:00:00

  • pH-dependent stability and folding kinetics of a protein with an unusual alpha-beta topology: the C-terminal domain of the ribosomal protein L9.

    abstract：:The folding kinetics and thermodynamics of the isolated C-terminal domain of the ribosomal protein L9 (CTL9) have been studied as a function of pH. CTL9 is an alpha-beta protein that contains a single beta-sheet with an unusual mixed parallel, anti-parallel topology. The folding is fully reversible and two-state over ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/S0022-2836(02)00015-3

    authors： Sato S,Raleigh DP

    更新日期：2002-04-26 00:00:00

  • Characterization of the Borrelia burgdorferi RNase P RNA gene reveals a novel tertiary interaction.

    abstract：:Characterization of the RNase P RNA gene derived from Borrelia burgdorferi reveals covariation of the conserved nucleotides at positions corresponding to nucleotides 128 and 230 in Escherichia coli RNase P RNA (M1 RNA). Single base substitutions at either of these positions in M1 RNA resulted in a lack of complementat...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1467

    authors： Mattsson JG,Svärd SG,Kirsebom LA

    更新日期：1994-08-05 00:00:00

  • The 1.5 A crystal structure of a bleomycin resistance determinant from bleomycin-producing Streptomyces verticillus.

    abstract：:Bleomycin (Bm)-binding protein, designated BLMA, which is a Bm resistance determinant from Bm-producing Streptomyces verticillus, was crystallized in a form suitable for X-ray diffraction analysis. The diffraction intensity data were collected up to a resolution of 1.5 A with a merging R-value of 0.054 at a completene...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.3404

    authors： Kawano Y,Kumagai T,Muta K,Matoba Y,Davies J,Sugiyama M

    更新日期：2000-01-28 00:00:00

  • Crystal structure of Escherichia coli thioesterase I/protease I/lysophospholipase L1: consensus sequence blocks constitute the catalytic center of SGNH-hydrolases through a conserved hydrogen bond network.

    abstract：:Escherichia coli thioesterase I (TAP) is a multifunctional enzyme possessing activities of thioesterase, esterase, arylesterase, protease, and lysophospholipase. In particular, TAP has stereoselectivity for amino acid derivative substrates, hence it is useful for the kinetic resolution of racemic mixtures of industria...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00637-5

    authors： Lo YC,Lin SC,Shaw JF,Liaw YC

    更新日期：2003-07-11 00:00:00

  • Crystal and molecular structure of barley alpha-amylase.

    abstract：:The three-dimensional structure of barley malt alpha-amylase (isoform AMY2-2) was determined by multiple isomorphous replacement using three heavy-atom derivatives and solvent flattening. The model was refined using a combination of simulated annealing and conventional restrained least-squares crystallographic refinem...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1354

    authors： Kadziola A,Abe J,Svensson B,Haser R

    更新日期：1994-05-27 00:00:00