Internal promoter elements of transfer RNA genes are preferentially exposed in chromatin.

abstract：:Activation of family A G-protein-coupled receptors involves a rearrangement of a conserved interhelical cytoplasmic hydrogen bond network between the E(D)RY motif on transmembrane helix 3 (H3) and residues on H6, which is commonly termed the cytoplasmic "ionic lock." Glu134(3.49) of the E(D)RY motif also forms an intr...

journal_title：Journal of molecular biology

authors： Vogel R,Mahalingam M,Lüdeke S,Huber T,Siebert F,Sakmar TP

更新日期：2008-07-18 00:00:00

abstract：:AP205 is a single-stranded RNA bacteriophage that has a coat protein sequence not similar to any other known single-stranded RNA phage. Here, we report an atomic-resolution model of the AP205 virus-like particle based on a crystal structure of an unassembled coat protein dimer and a cryo-electron microscopy reconstruc...

journal_title：Journal of molecular biology

authors： Shishovs M,Rumnieks J,Diebolder C,Jaudzems K,Andreas LB,Stanek J,Kazaks A,Kotelovica S,Akopjana I,Pintacuda G,Koning RI,Tars K

更新日期：2016-10-23 00:00:00

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

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

abstract：:Structure determination of complex molecular machines requires a combination of an increasing number of experimental methods with highly specialized software geared toward each data source to properly handle the gathered data. Recently, we introduced the two software packages PowerFit and DisVis. These combine high-re...

journal_title：Journal of molecular biology

authors： van Zundert GC,Trellet M,Schaarschmidt J,Kurkcuoglu Z,David M,Verlato M,Rosato A,Bonvin AM

更新日期：2017-02-03 00:00:00

abstract：:The initiator of coliphage lambda DNA replication, lambda O protein, may be detected among other 35S-labeled phage and bacterial proteins by a method based on immunoprecipitation. This method makes it possible to study lambda O proteolytic degradation in lambda plasmid-harboring or lambda phage-infected cells; it avoi...

journal_title：Journal of molecular biology

authors： Wegrzyn G,Pawlowicz A,Taylor K

更新日期：1992-08-05 00:00:00

abstract：:The DnaB protein is the primary replicative helicase in Escherichia coli, and the active form of the protein is a hexamer. It has been reported that the protein forms a ring with strong 3-fold symmetry, which was suggested to be a trimer of dimers. We show that under different conditions, using either ATP, ATP gamma S...

journal_title：Journal of molecular biology

authors： Yu X,Jezewska MJ,Bujalowski W,Egelman EH

更新日期：1996-05-31 00:00:00

abstract：:Protein denatured states are the origin of both healthy and toxic conformational species. Denatured states of ultrafast folding proteins are of interest in mechanistic studies because they are energetically close to the kinetic bottleneck of folding. However, their transient nature makes them elusive to experiment. He...

journal_title：Journal of molecular biology

authors： Thukral L,Schwarze S,Daidone I,Neuweiler H

更新日期：2015-09-25 00:00:00

abstract：:Protein allostery plays a pivotal role in many regulatory processes. Prominent examples are cell-surface receptors, which allosterically transmit ligand-generated signals to their cytoplasmic domains, or bacterial transcription factors, which alternate between a free conformation and a DNA-bound conformation in respon...

journal_title：Journal of molecular biology

authors： Goeke D,Kaspar D,Stoeckle C,Grubmüller S,Berens C,Klotzsche M,Hillen W

更新日期：2012-02-10 00:00:00

abstract：:The X-ray crystal structure of the Escherichia coli stress response protein HDEA has been determined at 2.0 A resolution. The single domain alpha-helical protein is found in the periplasmic space, where it supports an acid resistance phenotype essential for infectivity of enteric bacterial pathogens, such as Shigella ...

journal_title：Journal of molecular biology

authors： Gajiwala KS,Burley SK

更新日期：2000-01-21 00:00:00

abstract：:The bacterial protein Rho triggers transcription termination at the ends of many operons and when transcription and translation become uncoupled. In addition to these genome wide activities, Rho implements regulation of specific genes by dictating whether RNA polymerase terminates transcription within the 5' leader re...

journal_title：Journal of molecular biology

authors： Kriner MA,Groisman EA

更新日期：2015-12-04 00:00:00

abstract：:The pathological and physiological hallmarks of the protein alpha-synuclein (aS) are its misfolding into cytotoxic aggregates and its binding to synaptic vesicles, respectively. Both events are mediated by seven 11-residue amphiphilic pseudorepeats and, most generally, involve a transition from intrinsically unstructu...

journal_title：Journal of molecular biology

authors： Rao JN,Kim YE,Park LS,Ulmer TS

更新日期：2009-07-17 00:00:00

abstract：:The structure of active site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor was determined in the presence of coenzyme NAD+ at 1.88 A resolution with a final R-factor of 0.175. The structure refinement was carried out on the basis of the structure of holo-GAPDH at 2.0 A resoluti...

journal_title：Journal of molecular biology

authors： Song SY,Xu YB,Lin ZJ,Tsou CL

更新日期：1999-04-09 00:00:00

abstract：:Pre-steady-state chemical quenched-flow techniques were used to study DNA unwinding catalyzed by Escherichia coli UvrD helicase (helicase II), a member of the SF1 helicase superfamily. Single turnover experiments, with respect to unwinding of a DNA oligonucleotide, were used to examine the DNA substrate and UvrD conce...

journal_title：Journal of molecular biology

authors： Ali JA,Maluf NK,Lohman TM

更新日期：1999-11-05 00:00:00

abstract：:The SgrAI endonuclease displays its maximal activity on DNA with two copies of its recognition sequence, cleaving both sites concertedly. While most restriction enzymes that act concurrently at two sites are tetramers, SgrAI is a dimer in solution. Its reaction at two cognate sites involves the association of two DNA-...

journal_title：Journal of molecular biology

authors： Wood KM,Daniels LE,Halford SE

更新日期：2005-07-08 00:00:00

abstract：:The visible absorption spectra of carbonmonoxymyoglobin in the temperature range 300 to 20 K are reported and compared with the analogous spectra of carbonomonoxyhaemoglobin. The temperature dependence of the zeroth, first and second moment of the observed bands is analysed to obtain information on the local dynamics ...

journal_title：Journal of molecular biology

authors： Cordone L,Cupane A,Leone M,Vitrano E,Bulone D

更新日期：1988-01-05 00:00:00

abstract：:Mature TGF-beta isoforms, which are covalent dimers, signal by binding to three types of cell surface receptors, the type I, II and III TGF-beta receptors. A complex composed of the TGF-beta ligand and the type I and II receptors is required for signaling. The type II receptor is responsible for recruiting TGF-beta in...

journal_title：Journal of molecular biology

authors： De Crescenzo G,Pham PL,Durocher Y,O'Connor-McCourt MD

更新日期：2003-05-16 00:00:00

abstract：:The SH2 domain of the C-terminal Src kinase [Csk] contains a unique disulfide bond that is not present in other known SH2 domains. To investigate whether this unusual disulfide bond serves a novel function, the effects of disulfide bond formation on catalytic activity of the full-length protein and on the structure of...

journal_title：Journal of molecular biology

authors： Mills JE,Whitford PC,Shaffer J,Onuchic JN,Adams JA,Jennings PA

更新日期：2007-02-02 00:00:00

abstract：:α-Synuclein (αSyn) is an intrinsically disordered protein that can form amyloid fibrils. Fibrils of αSyn are implicated with the pathogenesis of Parkinson's disease and other synucleinopathies. Elucidating the mechanism of fibril formation of αSyn is therefore important for understanding the mechanism of the pathogene...

journal_title：Journal of molecular biology

authors： Fujiwara S,Kono F,Matsuo T,Sugimoto Y,Matsumoto T,Narita A,Shibata K

更新日期：2019-08-09 00:00:00

abstract：:The crystal structure of malate dehydrogenase from Escherichia coli has been determined with a resulting R-factor of 0.187 for X-ray data from 8.0 to 1.87 A. Molecular replacement, using the partially refined structure of porcine mitochondrial malate dehydrogenase as a probe, provided initial phases. The structure of ...

journal_title：Journal of molecular biology

authors： Hall MD,Levitt DG,Banaszak LJ

更新日期：1992-08-05 00:00:00

abstract：:Tumor suppressor p53 plays a central role in tumor suppression. p53 is the most frequently mutated gene in human cancer, and over half of human cancers contain p53 mutations. Majority of p53 mutations in cancer are missense mutations, leading to the expression of full-length mutant p53 (mutp53) protein. While the crit...

journal_title：Journal of molecular biology

authors： Yue X,Zhao Y,Xu Y,Zheng M,Feng Z,Hu W

更新日期：2017-06-02 00:00:00

abstract：:Protein folding is directed by the sequence of sidechains along the polypeptide backbone, but despite this the developement of sidechain interactions during folding is not well understood. Here, the thiol-active reagent, dithio-nitrobenzoic acid (DTNB), is used to probe the exposure of the cysteine sidechain thiols in...

journal_title：Journal of molecular biology

authors： Cliff MJ,Alizadeh T,Jelinska C,Craven CJ,Staniforth RA,Waltho JP

更新日期：2006-12-08 00:00:00

abstract：:Iron uptake by transferrin from triacetohydroxamatoFe(III) (Fe(AHA)3) in the presence of bicarbonate has been investigated between pH 7 and 8.2. The protein transits from the opened apo- to the closed holoform by several steps with the accumulation of at least three kinetic intermediates. All these steps are accompani...

journal_title：Journal of molecular biology

authors： Pakdaman R,Abdallah FB,El Hage Chahine JM

更新日期：1999-11-12 00:00:00

abstract：:The terminal regions of monomeric hook protein from Salmonella typhimurium are known to be highly mobile and exposed to the solvent. Although hook protein exhibits an unusual far-UV circular dichroism spectrum, resembling that of random coil structures, our calorimetric experiments clearly demonstrate that the molecul...

journal_title：Journal of molecular biology

authors： Vonderviszt F,Závodszky P,Ishimura M,Uedaira H,Namba K

更新日期：1995-08-25 00:00:00

abstract：:We have examined the equilibrium and kinetic folding properties of two structurally homologous dihydrofolate reductases, Escherichia coli DHFR (EcDHFR) and murine DHFR (MuDHFR), as a function of temperature and ligand concentration. Conformational heterogeneity in native DHFR is well documented, and the results demons...

journal_title：Journal of molecular biology

authors： Clark AC,Frieden C

更新日期：1999-01-29 00:00:00

abstract：:The sigma 70 (sigma(70)) subunit of Escherichia coli RNA polymerase specifies transcription from promoters that are responsible for basal gene expression during vegetative growth. When sigma(70) is present within polymerase holoenzyme, two of its domains, 2.4 and 4.2, interact with sequences within the -10 and -35 reg...

journal_title：Journal of molecular biology

authors： Vuthoori S,Bowers CW,McCracken A,Dombroski AJ,Hinton DM

更新日期：2001-06-08 00:00:00

abstract：:The detection of conserved sequence patterns (motifs) in related proteins often yields valuable structural and functional insights. We describe a method that utilizes rigorous statistics and a depth-first search procedure to efficiently and exhaustively search a set of proteins for significant patterns up to a specifi...

journal_title：Journal of molecular biology

authors： Neuwald AF,Green P

更新日期：1994-06-24 00:00:00

abstract：:The formation of membraneless organelles (MLOs) by phase separation has emerged as a new way of organizing the cytoplasm and nucleoplasm of cells. Examples of MLOs forming via phase separation are nucleoli in the nucleus and stress granules in the cytoplasm. The main components of these MLOs are macromolecules such as...

journal_title：Journal of molecular biology

authors： Alberti S,Carra S

更新日期：2018-11-02 00:00:00

abstract：:The enthalpy of hydration of polar and non-polar groups upon protein unfolding has been estimated for four globular proteins in the temperature range 5 to 125 degrees C, using structural information on the groups in these proteins exposed to water in the native and unfolded states and volume-corrected calorimetric inf...

journal_title：Journal of molecular biology

authors： Makhatadze GI,Privalov PL

更新日期：1993-07-20 00:00:00

abstract：:The folding pathway of Rd-apocytochrome b562, a four-helix bundle protein, was characterized using Trp and Ala/Gly pair mutations. We found that the Trp mutants (F65W) of both the fully folded Rd-apocytochrome b562 and a partially unfolded intermediate with the N-terminal helix (helix I) unfolded, fold with identical ...

journal_title：Journal of molecular biology

authors： Zhou Z,Huang Y,Bai Y

更新日期：2005-09-30 00:00:00

abstract：:Clostridium botulinum C3 exoenzyme inactivates the small GTP-binding protein family Rho by ADP-ribosylating asparagine 41, which depolymerizes the actin cytoskeleton. C3 thus represents a major family of the bacterial toxins that transfer the ADP-ribose moiety of NAD to specific amino acids in acceptor proteins to mod...

journal_title：Journal of molecular biology

authors： Han S,Arvai AS,Clancy SB,Tainer JA

更新日期：2001-01-05 00:00:00