当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Phosphorylation driven motions in the COOH-terminal Src kinase, CSK, revealed through enhanced hydrogen-deuterium exchange and mass spectrometry (DXMS).

Phosphorylation driven motions in the COOH-terminal Src kinase, CSK, revealed through enhanced hydrogen-deuterium exchange and mass spectrometry (DXMS).

Abstract：

:Previous kinetic studies demonstrated that nucleotide-derived conformational changes regulate function in the COOH-terminal Src kinase. We have employed enhanced methods of hydrogen-deuterium exchange-mass spectrometry (DXMS) to probe conformational changes on CSK in the absence and presence of nucleotides and thereby provide a structural framework for understanding phosphorylation-driven conformational changes. High quality peptic fragments covering approximately 63% of the entire CSK polypeptide were isolated using DXMS. Time-dependent deuterium incorporation into these probes was monitored to identify short peptide segments that exchange differentially with solvent. Regions expected to lie in loops exchange rapidly, whereas other regions expected to lie in stable secondary structure exchange slowly with solvent implying that CSK adopts a modular structure. The ATP analog, AMPPNP, protects probes in the active site and distal regions in the large and small lobes of the kinase domain, the SH2 domain, and the linker connecting the SH2 and kinase domains. The product ADP protects similar regions of the protein but the extent of protection varies markedly in several crucial areas. These areas correspond to the activation loop and helix G in the kinase domain and several inter-domain regions. These results imply that delivery of the gamma phosphate group of ATP induces unique local and long-range conformational changes in CSK that may influence regulatory motions in the catalytic pathway.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Hamuro Y,Wong L,Shaffer J,Kim JS,Stranz DD,Jennings PA,Woods VL Jr,Adams JA

doi

10.1016/s0022-2836(02)01003-3

keywords:

subject

Has Abstract

pub_date

2002-11-08 00:00:00

pages

871-81

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022283602010033

journal_volume

323

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Atomic resolution (1.0 A) crystal structure of Fusarium solani cutinase: stereochemical analysis.

    abstract：:X-ray data have been recorded to 1.0 A resolution from a crystal of Fusarium solani cutinase using synchrotron radiation and an imaging-plate scanner. The anisotropic treatment of thermal motion led to a fivefold increase in accuracy and to a considerable quality improvement in the electron density maps with respect t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.1000

    authors： Longhi S,Czjzek M,Lamzin V,Nicolas A,Cambillau C

    更新日期：1997-05-16 00:00:00

  • Taxonomy and conformational analysis of loops in proteins.

    abstract：:We propose a general classification scheme for loops, aperiodic segments of protein structure. In an effort to avoid the geometric complexity created by non-repeating phi psi angles, a morphologic definition that focuses upon the linearity and planarity of loops is utilized. Out of 432 loops (4 to 20 residues in lengt...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)90553-v

    authors： Ring CS,Kneller DG,Langridge R,Cohen FE

    更新日期：1992-04-05 00:00:00

  • Double strand packing in hemoglobin S fibers.

    abstract：:The sickling variant of human hemoglobin, Hb S (beta 6 Glu-->Val), assembles into 14-strand helical fibers composed of seven pairs of double strands. The organization of the helical double strands closely resembles the parallel, half-staggered, linear strand pairs of the crystals of Hb S characterized by Wishner et al...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1195

    authors： Cretegny I,Edelstein SJ

    更新日期：1993-04-05 00:00:00

  • Prolonged Ca2+ and force transients in myosin RLC transgenic mouse fibers expressing malignant and benign FHC mutations.

    abstract：:Clinical studies have revealed that mutations in the ventricular myosin regulatory light chain (RLC) lead to the development of familial hypertrophic cardiomyopathy (FHC), an autosomal dominant disease characterized by left ventricular hypertrophy, myofibrillar disarray and sudden cardiac death. While mutations in oth...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.06.018

    authors： Wang Y,Xu Y,Kerrick WG,Wang Y,Guzman G,Diaz-Perez Z,Szczesna-Cordary D

    更新日期：2006-08-11 00:00:00

  • On the interaction between gp41 and membranes: the immunodominant loop stabilizes gp41 helical hairpin conformation.

    abstract：:gp41 is the protein responsible for the process of membrane fusion that allows primate lentiviruses (HIV and SIV) to enter into their host cells. gp41 ectodomain contains an N-terminal and a C-terminal heptad repeat region (NHR and CHR) connected by an immunodominant loop. In the absence of membranes, the NHR and CHR ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00040-8

    authors： Peisajovich SG,Blank L,Epand RF,Epand RM,Shai Y

    更新日期：2003-03-07 00:00:00

  • Mechanism of action and in vivo efficacy of a human-derived antibody against Staphylococcus aureus α-hemolysin.

    abstract：:The emergence and spread of multi-drug-resistant strains of Staphylococcus aureus in hospitals and in the community emphasize the urgency for the development of novel therapeutic interventions. Our approach was to evaluate the potential of harnessing the human immune system to guide the development of novel therapeuti...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2013.02.008

    authors： Foletti D,Strop P,Shaughnessy L,Hasa-Moreno A,Casas MG,Russell M,Bee C,Wu S,Pham A,Zeng Z,Pons J,Rajpal A,Shelton D

    更新日期：2013-05-27 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

  • Towards elucidation of the mechanism of UV1C, a deoxyribozyme with photolyase activity.

    abstract：:Among the unexpected chemistries that can be catalyzed by nucleic acid enzymes is photochemistry. We have reported the in vitro selection of a small, cofactor-independent deoxyribozyme, UV1C, capable of repairing thymine dimers in a DNA substrate, most optimally with light at a wavelength of >300 nm. We hypothesized t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.10.062

    authors： Chinnapen DJ,Sen D

    更新日期：2007-02-02 00:00:00

  • A thymine-like base analogue forms wobble pairs with adenine in a Z-DNA duplex.

    abstract：:The DNA hexamer d(CACGPG), in which dP is the ambivalent pyrimidine nucleoside analogue 2'-deoxy-beta-d-ribofuranosyl-(6H,8H-3, 4-dihydropyrimido[4,5-c][1,2]oxazin-7-one), crystallises as a left-handed Z-DNA duplex. X-ray analysis at 1.5 A shows that both P. A base-pairs are of the wobble type. This result appears inc...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2080

    authors： Schuerman GS,Van Meervelt L,Loakes D,Brown DM,Kong Thoo Lin P,Moore MH,Salisbury SA

    更新日期：1998-10-09 00:00:00

  • Nucleotide binding to DNA gyrase causes loss of DNA wrap.

    abstract：:DNA gyrase negatively supercoils DNA in a reaction coupled to the binding and hydrolysis of ATP. Limited supercoiling can be achieved in the presence of the non-hydrolysable ATP analogue, 5'-adenylyl beta,gamma-imidodiphosphate (ADPNP). In order to negatively supercoil DNA, gyrase must wrap a length of DNA around itse...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.01.049

    authors： Heddle JG,Mitelheiser S,Maxwell A,Thomson NH

    更新日期：2004-03-26 00:00:00

  • Probing the assembly of the 3' major domain of 16 S rRNA. Interactions involving ribosomal proteins S2, S3, S10, S13 and S14.

    abstract：:We have used rapid probing methods to follow the changes in reactivity of residues in 16 S rRNA to chemical and enzymatic probes as ribosomal proteins S2, S3, S10, S13 and S14 are assembled into 30 S subunits. Effects observed are confined to the 3' major domain of the RNA and comprise three general classes. (1) Monos...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(88)90468-8

    authors： Powers T,Stern S,Changchien LM,Noller HF

    更新日期：1988-06-20 00:00:00

  • The three-dimensional solution structure of NaD1, a new floral defensin from Nicotiana alata and its application to a homology model of the crop defense protein alfAFP.

    abstract：:NMR spectroscopy and simulated annealing calculations have been used to determine the three-dimensional structure of NaD1, a novel antifungal and insecticidal protein isolated from the flowers of Nicotiana alata. NaD1 is a basic, cysteine-rich protein of 47 residues and is the first example of a plant defensin from fl...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(02)01103-8

    authors： Lay FT,Schirra HJ,Scanlon MJ,Anderson MA,Craik DJ

    更新日期：2003-01-03 00:00:00

  • The role of the L-chain in ferritin iron incorporation. Studies of homo and heteropolymers.

    abstract：:Mammalian ferritins are 24-meric proteins composed of variable proportions of H and L-subunits. The L-chain, in contrast to the H-chain, lacks detectable ferroxidase activity, and its role in ferritin iron incorporation is unclear. In this study, apoferritins were subjected to iron loading with large iron increments t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1325

    authors： Levi S,Santambrogio P,Cozzi A,Rovida E,Corsi B,Tamborini E,Spada S,Albertini A,Arosio P

    更新日期：1994-05-20 00:00:00

  • Conformational isomers of a class II MHC-peptide complex in solution.

    abstract：:A number of kinetic measurements of peptide dissociation from class II MHC-peptide complexes provide compelling evidence for the existence of conformational isomers in solution. There is evidence that T-lymphocytes can distinguish such isomers. However, virtually nothing is known about the structure of these isomers. ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2463

    authors： Schmitt L,Boniface JJ,Davis MM,McConnell HM

    更新日期：1999-02-12 00:00:00

  • Conformational properties of aggregated polypeptides determine ClpB-dependence in the disaggregation process.

    abstract：:Severe thermal stress induces massive intracellular protein aggregation. The concerted action of Hsp70 (DnaK, DnaJ, GrpE) and Hsp100 (ClpB) chaperones results in solubilization of aggregates followed by reactivation of proteins. It was shown that the Hsp70 chaperone system works at the initial step of the disaggregati...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.05.057

    authors： Lewandowska A,Matuszewska M,Liberek K

    更新日期：2007-08-17 00:00:00

  • Correlation between calculated local stability and hydrogen exchange rates in proteins.

    abstract：:The attempt is made to find new correlations between local structural characteristics of proteins and the hydrogen exchange rates of their individual main-chain amides, and to relate such correlations to possible mechanisms of hydrogen exchange. It is found that in bovine pancreatic trypsin inhibitor (BPTI) the surfac...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90317-2

    authors： Rashin AA

    更新日期：1987-11-20 00:00:00

  • Activity, stability and flexibility in glycosidases adapted to extreme thermal environments.

    abstract：:To elucidate the strategy of low temperature adaptation for a cold-adapted family 8 xylanase, the thermal and chemical stabilities, thermal inactivation, thermodependence of activity and conformational flexibility, as well as the thermodynamic basis of these processes, were compared with those of a thermophilic homolo...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00287-0

    authors： Collins T,Meuwis MA,Gerday C,Feller G

    更新日期：2003-04-25 00:00:00

  • Zooming in on the hydrophobic ridge of H-2D(b): implications for the conformational variability of bound peptides.

    abstract：:Class I major histocompatibility complex (MHC) molecules, which display intracellularly processed peptides on the cell surface for scanning by T-cell receptors (TCRs), are extraordinarily polymorphic. MHC polymorphism is believed to result from natural selection, since individuals heterozygous at the corresponding loc...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.5016

    authors： Ciatto C,Tissot AC,Tschopp M,Capitani G,Pecorari F,Plückthun A,Grütter MG

    更新日期：2001-10-05 00:00:00

  • Plasminogen activator inhibitor-2 is highly tolerant to P8 residue substitution--implications for serpin mechanistic model and prediction of nsSNP activities.

    abstract：:The serine protease inhibitor (serpin) superfamily is involved in a wide range of cellular processes including fibrinolysis, angiogenesis, apoptosis, inflammation, metastasis and viral pathogenesis. Here, we investigate the unique mousetrap inhibition mechanism of serpins through saturation mutagenesis of the P8 resid...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.09.008

    authors： Di Giusto DA,Sutherland AP,Jankova L,Harrop SJ,Curmi PM,King GC

    更新日期：2005-11-11 00:00:00

  • Crystal structure at 1.95 A resolution of the breast tumour-specific antibody SM3 complexed with its peptide epitope reveals novel hypervariable loop recognition.

    abstract：:The anti-breast tumour antibody SM3 has a high selectivity in reacting specifically with carcinoma-associated mucin. SM3 recognises the core repeating motif (Pro-Asp-Thr-Arg-Pro) of aberrantly glycosylated epithelial mucin MUC1, and has potential as a therapeutic and diagnostic tool. Here we report the crystal structu...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2209

    authors： Dokurno P,Bates PA,Band HA,Stewart LM,Lally JM,Burchell JM,Taylor-Papadimitriou J,Snary D,Sternberg MJ,Freemont PS

    更新日期：1998-12-04 00:00:00

  • A single tyrosine prevents insertion of ribonucleotides in the eukaryotic-type phi29 DNA polymerase.

    abstract：:Three conserved motifs (named A, B and C) have been proposed to form the polymerization active site in all classes of DNA-dependent polymerases. In eukaryotic-type (alpha-like) DNA polymerases, motif A is characterized by the consensus "Dx2SLYP". Mutants in phi29 DNA polymerase residue Tyr254 of this conserved motif h...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2900

    authors： Bonnin A,Lázaro JM,Blanco L,Salas M

    更新日期：1999-07-02 00:00:00

  • Long-range identification of hepatocyte nuclear factor-3 (FoxA) high and low-affinity binding sites with a chimeric nuclease.

    abstract：:Identifying the complete set of transcription factors that bind the promoter and other regulatory regions of a gene of interest is an essential step in functional genomics. We have developed an original assay for the systematic detection of hepatocyte nuclear factor-3 (HNF-3) binding sites within cloned promoters. Thi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.4788

    authors： Ruminy P,Derambure C,Chandrasegaran S,Salier JP

    更新日期：2001-07-13 00:00:00

  • Effect of the Asn52----Ile mutation on the redox potential of yeast cytochrome c. Theory and experiment.

    abstract：:Theoretical methods for correlation of sequence changes and redox potential of electron transport proteins are examined using the Asn52----Ile mutation in cytochrome c as a test case. The first approach uses the protein dipoles Langevin dipoles (PDLD) method and the high resolution X-ray structures of the native and t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)90546-v

    authors： Langen R,Brayer GD,Berghuis AM,McLendon G,Sherman F,Warshel A

    更新日期：1992-04-05 00:00:00

  • Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVAII) hydrolyzing cyclodextrins and pullulan at 2.6 A resolution.

    abstract：:The crystal structure of Thermoactinomyces vulgaris R-47 alpha-Amylase II (TVAII) has been determined by multiple isomorphous replacement at 2.6 A resolution. TVAII was crystallized in an orthorhombic system with the space group P212121 and the cell dimensions a=118.5 A, b=119.5 A, c=114.5 A. There are two molecules i...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2647

    authors： Kamitori S,Kondo S,Okuyama K,Yokota T,Shimura Y,Tonozuka T,Sakano Y

    更新日期：1999-04-16 00:00:00

  • Analysis of high-resolution electron diffraction patterns from purple membrane labelled with heavy-atoms.

    abstract：:Progress in the structure determination of bacteriorhodopsin, the protein component of purple membrane from Halobacterium halobium has been limited by the lack of three-dimensional phase information between 6 and 3 A resolution. By analogy with X-ray methods, it is possible that heavy-atom labelling of the membrane cr...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/S0022-2836(05)80214-1

    authors： Ceska TA,Henderson R

    更新日期：1990-06-05 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

  • Structure of the myosin projections on native thick filaments from vertebrate skeletal muscle.

    abstract：:Rabbit psoas muscle filaments, isolated in relaxing buffer from non-glycerinated muscle, have been applied to hydrophilic carbon films and stained with uranyl acetate. Electron micrographs were obtained under low-dose conditions to minimize specimen damage. Surrounding the filament backbone, except in the bare zone, i...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(84)90295-x

    authors： Knight P,Trinick J

    更新日期：1984-08-15 00:00:00

  • Potential conformational heterogeneity of p53 bound to S100B(ββ).

    abstract：:The negative regulatory domain (NRD) of the p53 tumor suppressor is intrinsically disordered. It contains several posttranslational modification (PTM) sites that are important for regulation of p53 activity. Calcium-dependent binding of dimeric S100B(ββ) to p53-NRD blocks access to these PTM sites and disrupts the p53...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2013.01.001

    authors： McDowell C,Chen J,Chen J

    更新日期：2013-03-25 00:00:00

  • Galaxy InteractoMIX: An Integrated Computational Platform for the Study of Protein-Protein Interaction Data.

    abstract：:Protein interactions play a crucial role among the different functions of a cell and are central to our understanding of cellular processes both in health and disease. Here we present Galaxy InteractoMIX (http://galaxy.interactomix.com), a platform composed of 13 different computational tools each addressing specific ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2020.09.015

    authors： Mirela-Bota P,Aguirre-Plans J,Meseguer A,Galletti C,Segura J,Planas-Iglesias J,Garcia-Garcia J,Guney E,Oliva B,Fernandez-Fuentes N

    更新日期：2020-09-23 00:00:00

  • The three-dimensional structure of N-succinyldiaminopimelate aminotransferase from Mycobacterium tuberculosis.

    abstract：:Inhibitors of the enzymes of the lysine biosynthetic pathway are considered promising lead compounds for the design of new antibacterial drugs, because the pathway appears to be indispensable for bacteria and because it is absent in humans. As part of our efforts to structurally characterize all enzymes of this pathwa...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.01.023

    authors： Weyand S,Kefala G,Weiss MS

    更新日期：2007-03-30 00:00:00