The salt-dependence of a protein-ligand interaction: ion-protein binding energetics.

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

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

abstract：:The heterogeneous nuclear ribonucleoprotein K protein is an RNA-binding protein found in several subcellular compartments where it is thought to be involved in signaling multiple processes that compose gene expression. K protein contains three K homology (KH) domains that mediate RNA-binding. We used a serial analysis...

journal_title：Journal of molecular biology

authors： Klimek-Tomczak K,Wyrwicz LS,Jain S,Bomsztyk K,Ostrowski J

更新日期：2004-09-24 00:00:00

abstract：:The enzyme encoded by the bgIA gene of Bacillus polymyxa, a type I beta-glucosidase belonging to family I of glycosyl hydrolases, has been purified to homogeneity from an Escherichia coli culture which overexpressed the gene, and crystallized. The crystals, which diffract to 3.0 A resolution, belong to the orthorhombi...

journal_title：Journal of molecular biology

authors： Sanz-Aparicio J,Romero A,Martinez-Ripoll M,Madarro A,Flors A,Polaina J

更新日期：1994-07-15 00:00:00

abstract：:Twenty-four structures of pyridoxal-5'-phosphate (PLP)-dependent enzymes that represent five different folds are shown to share a common recognition pattern for the phosphate group of their PLP-ligands. All atoms that interact with the phosphate group of PLP in these proteins are organized within a two-layer structure...

journal_title：Journal of molecular biology

authors： Denesyuk AI,Denessiouk KA,Korpela T,Johnson MS

更新日期：2002-02-08 00:00:00

abstract：:The molecular mechanisms underlying transcription elongation and their role in gene regulation are poorly characterized in eukaryotes. A number of genes, however, have been proposed to be regulated at the level of transcription elongation, including c-myc, c-fos and c-myb. Here, we analyze the control of transcription...

journal_title：Journal of molecular biology

authors： Pinaud S,Mirkovitch J

更新日期：1998-07-31 00:00:00

abstract：:Sparsomycin, a broad-spectrum antibiotic, acts at the peptidyl transferase centre of the ribosome, stabilizing peptidyl-tRNA binding at the P-site and weakening ternary complex binding. A sparsomycin-resistant mutant was isolated for the archaeon Halobacterium salinarium and shown to lack a post-transcriptional modifi...

journal_title：Journal of molecular biology

authors： Lázaro E,Rodriguez-Fonseca C,Porse B,Ureña D,Garrett RA,Ballesta JP

更新日期：1996-08-16 00:00:00

abstract：:The relationship between the preferred side-chain dihedral angles and the secondary structure of a residue was examined. The structures of 61 proteins solved to a resolution of 2.0 A (1 A = 0.1 nm) or better were analysed using a relational database to store the information. The strongest feature observed was that the...

journal_title：Journal of molecular biology

authors： McGregor MJ,Islam SA,Sternberg MJ

更新日期：1987-11-20 00:00:00

abstract：:The roll-twist-slide correlation in the DNA crystal structures that are collected in the Nucleic Acid Data Base is analyzed in order to obtain a general understanding of the effects of the nucleotide sequence on the 3D structure of a dinucleotide step. It is concluded that the differences between the pyrimidine bases ...

journal_title：Journal of molecular biology

authors： Suzuki M,Amano N,Kakinuma J,Tateno M

更新日期：1997-12-05 00:00:00

abstract：:Many viruses utilize molecular motors to package their genomes into preformed capsids. A striking feature of these motors is their ability to generate large forces to drive DNA translocation against entropic, electrostatic, and bending forces resisting DNA confinement. A model based on recently resolved structures of ...

journal_title：Journal of molecular biology

authors： Migliori AD,Smith DE,Arya G

更新日期：2014-12-12 00:00:00

abstract：:Designed retroaldolases have utilized a nucleophilic lysine to promote carbon-carbon bond cleavage of β-hydroxy-ketones via a covalent Schiff base intermediate. Previous computational designs have incorporated a water molecule to facilitate formation and breakdown of the carbinolamine intermediate to give the Schiff b...

journal_title：Journal of molecular biology

authors： Bjelic S,Kipnis Y,Wang L,Pianowski Z,Vorobiev S,Su M,Seetharaman J,Xiao R,Kornhaber G,Hunt JF,Tong L,Hilvert D,Baker D

更新日期：2014-01-09 00:00:00

abstract：:Set8 is the only mammalian monomethyltransferase responsible for H4K20me1, a methyl mark critical for genomic integrity of eukaryotic cells. We present here a structural model for how Set8 uses multivalent interactions to bind and methylate the nucleosome based on crystallographic and solution studies of the Set8/nucl...

journal_title：Journal of molecular biology

authors： Girish TS,McGinty RK,Tan S

更新日期：2016-04-24 00:00:00

abstract：:The monoclonal anti-tumor antibody BR96 binds a tetrasaccharide, Lewis y (Le(y)), in vitro and recognizes a Le(y)-bearing or Le(y)-related tumor-associated antigen in vivo. The Fab of the murine monoclonal antibody, mBR96 (IgG3, kappa), and the Fab' of its human chimera, cBR96 (IgG1, kappa), and their complexes with L...

journal_title：Journal of molecular biology

authors： Chang CY,Jeffrey PD,Bajorath J,Hellström I,Hellström KE,Sheriff S

更新日期：1994-01-07 00:00:00

abstract：:Bacteriophage with double-stranded, linear DNA genomes package DNA into pre-assembled icosahedral procapsids through a unique vertex. The packaging vertex contains an oligomeric ring of a portal protein that serves as a recognition site for the packaging enzymes, a conduit for DNA translocation, and the site of tail a...

journal_title：Journal of molecular biology

authors： Moore SD,Prevelige PE Jr

更新日期：2002-02-01 00:00:00

abstract：:The multidomain Mac-2 binding protein (M2BP) is present in serum and in the extracellular matrix in the form of linear and ring-shaped oligomers, which interact with galectin-3, fibronectin, collagens, integrins and other large glycoproteins. Domain 1 of M2BP (M2BP-1) shows homology with the cysteine-rich SRCR domain ...

journal_title：Journal of molecular biology

authors： Müller SA,Sasaki T,Bork P,Wolpensinger B,Schulthess T,Timpl R,Engel A,Engel J

更新日期：1999-08-27 00:00:00

abstract：:The three-dimensional structure of a site-directed mutant of the bacterially expressed Fv fragment from monoclonal antibody D1.3, complexed to the specific antigen lysozyme has been determined to a nominal resolution of 1.8 A using X-ray diffraction data. The replacement of VL Trp92 by Asp allows two water molecules t...

journal_title：Journal of molecular biology

authors： Ysern X,Fields BA,Bhat TN,Goldbaum FA,Dall'Acqua W,Schwarz FP,Poljak RJ,Mariuzza RA

更新日期：1994-05-13 00:00:00

abstract：:Many bacteria secrete cellulose, which forms the structural basis for bacterial multicellular aggregates, termed biofilms. The cellulose synthase complex of Salmonella typhimurium consists of the catalytic subunits BcsA and BcsB and several auxiliary subunits that are encoded by two divergently transcribed operons, bc...

journal_title：Journal of molecular biology

authors： Sun L,Vella P,Schnell R,Polyakova A,Bourenkov G,Li F,Cimdins A,Schneider TR,Lindqvist Y,Galperin MY,Schneider G,Römling U

更新日期：2018-09-14 00:00:00

abstract：:Human prostate-specific antigen (PSA or KLK3) is an important marker for the diagnosis and management of prostate cancer. This is an androgen-regulated glycoprotein of the kallikrein-related protease family secreted by prostatic epithelial cells. Its physiological function is to cleave semenogelins in the seminal coag...

journal_title：Journal of molecular biology

authors： Ménez R,Michel S,Muller BH,Bossus M,Ducancel F,Jolivet-Reynaud C,Stura EA

更新日期：2008-02-29 00:00:00

abstract：:A long-standing goal in biology is the complete annotation of function and structure on all protein-protein interactions, a large fraction of which is mediated by intrinsically disordered protein regions (IDRs). However, knowledge derived from experimental structures of such protein complexes is disproportionately sma...

journal_title：Journal of molecular biology

authors： Wong ETC,Gsponer J

更新日期：2019-08-09 00:00:00

abstract：:Due to regulatory feedback, biological networks can exist stably in multiple states, leading to heterogeneous phenotypes among genetically identical cells. Random fluctuations in protein numbers, tuned by specific molecular mechanisms, have been hypothesized to drive transitions between these different states. We deve...

journal_title：Journal of molecular biology

authors： Choi PJ,Xie XS,Shakhnovich EI

更新日期：2010-02-12 00:00:00

abstract：:The accessory gene regulatory (agr) operon of the opportunistic human pathogen Staphylococcus aureus is a prime pathogenesis factor in this bacterium. The agr operon consists of two transcription units, RNAII and RNAIII, which are transcribed from divergent promoters, P2 and P3, respectively. RNAII encodes a quorum-se...

journal_title：Journal of molecular biology

authors： Reynolds J,Wigneshweraraj S

更新日期：2011-10-07 00:00:00

abstract：:A recently developed approach to calculate the pH dependence of protein stability from three-dimensional structure information is applied to the analysis of acid denaturation of sperm whale apomyoglobin. The finite difference Poisson-Boltzmann method is used to calculate pKa values and these are used to obtain titrati...

journal_title：Journal of molecular biology

authors： Yang AS,Honig B

更新日期：1994-04-15 00:00:00

abstract：:The discoidin I genes of Dictyostelium form a small, co-ordinately regulated multigene family. We have sequenced and compared the upstream regions of the DiscI-alpha, -beta and -gamma genes. For the most part the upstream regions of the three genes are non-homologous. The upstream sequences of the beta and gamma genes...

journal_title：Journal of molecular biology

authors： Poole SJ,Firtel RA

更新日期：1984-01-15 00:00:00

abstract：:Proteasomes, major proteolytic sites in eukaryotic cells, play an important part in major histocompatibility class I (MHC I) ligand generation and thus in the regulation of specific immune responses. Their cleavage specificity is of outstanding interest for this process. In order to generalize previously determined cl...

journal_title：Journal of molecular biology

authors： Kuttler C,Nussbaum AK,Dick TP,Rammensee HG,Schild H,Hadeler KP

更新日期：2000-05-05 00:00:00

abstract：:alpha 1-Antitrypsin is the archetypal member of the serine proteinase inhibitor or serpin superfamily. Members of the family show structural homology based on a dominant A beta-sheet and a mobile reactive centre loop. Our recent crystal structure of alpha 1-antitrypsin stabilized with a point mutation showed the loop ...

journal_title：Journal of molecular biology

authors： Elliott PR,Abrahams JP,Lomas DA

更新日期：1998-01-23 00:00:00

abstract：:Transcriptional pausing by RNA polymerase has been the subject of extensive investigations in vitro, yet little is known about its occurrence and significance in vivo. The transient nature of the pausing events makes them difficult to observe inside the cell, whereas their studies in vitro by classical biochemical met...

journal_title：Journal of molecular biology

authors： Toulmé F,Mosrin-Huaman C,Artsimovitch I,Rahmouni AR

更新日期：2005-08-05 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：:Complex gene regulation systems ensure the maintenance of cellular identity during early development in mammals. Eukaryotic small RNAs have emerged as critical players in RNA interference (RNAi) by mediating gene silencing during embryonic stem cell self-renewal. Most of the proteins involved in the biogenesis of smal...

journal_title：Journal of molecular biology

authors： Bodak M,Cirera-Salinas D,Luitz J,Ciaudo C

更新日期：2017-05-19 00:00:00

abstract：:Although it has been known for many years that antibodies display properties characteristic of allosteric effectors, the molecular mechanisms responsible for these effects remain poorly understood. Here, we describe a single-domain antibody fragment (nanobody) that modulates protein function by constraining conformati...

journal_title：Journal of molecular biology

authors： Oyen D,Srinivasan V,Steyaert J,Barlow JN

更新日期：2011-03-18 00:00:00

abstract：:According to a trans -translation model, tmRNA facilitates the resumption of translation that has been stalled on the ribosome with the 3' end of a terminator-less mRNA, to produce a chimera polypeptide of the nascent peptide and the tmRNA-encoding 11 amino acid-tag. The first alanine residue of the tag-sequence is en...

journal_title：Journal of molecular biology

authors： Nameki N,Tadaki T,Muto A,Himeno H

更新日期：1999-05-28 00:00:00

abstract：:The maturation of proteases is governed by prosequences. During the biogenesis of the highly oligomeric eukaryotic 20 S proteasome five different prosequence-containing subunits have to be integrated and processed either by autocatalysis or by neighbouring subunits. To analyse the functional impact of proteasomal pros...

journal_title：Journal of molecular biology

authors： Schmidt M,Zantopf D,Kraft R,Kostka S,Preissner R,Kloetzel PM

更新日期：1999-04-23 00:00:00