Sequence and structure-based prediction of eukaryotic protein phosphorylation sites.

abstract：:Toxin-antitoxin systems consist of a stable toxin, frequently with endonuclease activity, and a small, labile antitoxin, which sequesters the toxin into an inactive complex. Under unfavorable conditions, the antitoxin is degraded, leading to activation of the toxin and resulting in growth arrest, possibly also in bact...

journal_title：Journal of molecular biology

authors： Schmidt O,Schuenemann VJ,Hand NJ,Silhavy TJ,Martin J,Lupas AN,Djuranovic S

更新日期：2007-09-28 00:00:00

abstract：:The ligation of a decadeoxynucleotide containing the EcoRI recognition site forms a series of multimers which appear to be curved based on observed anomalous gel migration in polyacrylamide gels. The degree of DNA curvature present in the recognition sequence, based upon the observed migration anomaly, can be altered ...

journal_title：Journal of molecular biology

authors： Diekmann S,McLaughlin LW

更新日期：1988-08-20 00:00:00

abstract：:Post-translational modifications (PTMs) of histone proteins play a crucial role in the regulation of chromatin structure and functions. Studies in the last few decades have revealed the significance of histone PTMs in key cellular processes including DNA replication, repair, transcription, apoptosis and cell cycle reg...

journal_title：Journal of molecular biology

authors： Azad GK,Swagatika S,Kumawat M,Kumawat R,Tomar RS

更新日期：2018-09-14 00:00:00

abstract：:Eukaryotic cells contain three cytoskeletal filament systems that exhibit very distinct assembly properties, supramolecular architectures, dynamic behaviour and mechanical properties. Microtubules and microfilaments are relatively stiff polar structures whose assembly is modulated by the state of hydrolysis of the bou...

journal_title：Journal of molecular biology

authors： Mücke N,Kreplak L,Kirmse R,Wedig T,Herrmann H,Aebi U,Langowski J

更新日期：2004-01-30 00:00:00

abstract：:Single crystals of the Fab fragment of a murine A/J anti-azophenylarsonate monoclonal antibody have been prepared by the vapor diffusion method. Antibody 3A7 uses the same combination of variable region gene segments (VK, JK, VH, JH) as do anti-azophenylarsonate antibodies bearing a predominant cross-reactive idiotype...

journal_title：Journal of molecular biology

authors： Lin SF,Coll M,Gefter ML,Margolies MN,Wang AH

更新日期：1989-04-20 00:00:00

abstract：:Three viral proteins participate directly in transcription of bacteriophage T4 late genes: the sigma-family protein gp55 provides promoter recognition, gp33 is the co-activator, and gp45 is the activator of transcription; gp33 also represses transcription in the absence of gp45. Transcriptional activation by gp45, the...

journal_title：Journal of molecular biology

authors： Kolesky SE,Ouhammouch M,Geiduschek EP

更新日期：2002-08-30 00:00:00

abstract：:The properties have been determined of a recently identified form of bovine pancreatic trypsin inhibitor, with only two of the three disulphide bonds of the native protein, but possessing a native-like conformation. The kinetics of refolding of the reduced inhibitor were re-measured to elucidate the kinetic role in fo...

journal_title：Journal of molecular biology

authors： Creighton TE,Goldenberg DP

更新日期：1984-11-05 00:00:00

abstract：:Addition of the antimitotic drug vinblastine to solutions of purified tubulin induces the formation of helical polymers whose structure and type of aggregation is determined by the concentration of magnesium. While paracrystalline arrangements of single coils are observed at low concentrations of the ion, for concentr...

journal_title：Journal of molecular biology

authors： Nogales E,Medrano FJ,Diakun GP,Mant GR,Towns-Andrews E,Bordas J

更新日期：1995-12-01 00:00:00

abstract：:The low-angle X-ray diffraction pattern from Lethocerus flight muscle fibres was recorded in rigor or under two conditions that modify crossbridge structure and behaviour, aqueous adenylylimidodiphosphate (AMPPNP) and AMPPNP + calcium in an ethylene glycol-water mixture. The effects on the 38.7 nm layer-line peaks (hk...

journal_title：Journal of molecular biology

authors： Tregear RT,Wakabayashi K,Tanaka H,Iwamoto H,Reedy MC,Reedy MK,Sugi H,Amemiya Y

更新日期：1990-07-05 00:00:00

abstract：:Many medically relevant Gram-negative bacteria use the type III secretion system (T3SS) to translocate effector proteins into the host for their invasion and intracellular survival. A multi-protein complex located at the cytosolic interface of the T3SS is proposed to act as a sorting platform by selecting and targetin...

journal_title：Journal of molecular biology

authors： Bernal I,Börnicke J,Heidemann J,Svergun D,Horstmann JA,Erhardt M,Tuukkanen A,Uetrecht C,Kolbe M

更新日期：2019-09-06 00:00:00

abstract：:Conformational fluctuation plays a key role in protein function, but we know little about the associated structural changes. Here we present a general method for elucidating, at the atomic level, a large-scale shape change of a protein molecule in solution undergoing conformational fluctuation. The method utilizes the...

journal_title：Journal of molecular biology

authors： Kitahara R,Yokoyama S,Akasaka K

更新日期：2005-03-25 00:00:00

abstract：:A combination of Monte Carlo simulated annealing and energy minimization was utilized to determine the conformation of the antifreeze protein from the fish winter flounder. It was found from the energy-optimized structure that the hydroxyl groups of its four threonine residues, i.e. Thr2, Thr13, Thr24, Thr35, are alig...

journal_title：Journal of molecular biology

authors： Chou KC

更新日期：1992-01-20 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：:Quantitatively describing RNA structure and conformational elements remains a formidable problem. Seven standard torsion angles and the sugar pucker are necessary to characterize the conformation of an RNA nucleotide completely. Progress has been made toward understanding the discrete nature of RNA structure, but clas...

journal_title：Journal of molecular biology

authors： Wadley LM,Keating KS,Duarte CM,Pyle AM

更新日期：2007-09-28 00:00:00

abstract：:Recently, the absence of a thermally induced transition has been offered as proof that the unfolded and the molten globule states of apo-alpha-lactalbumin are enthalpically equivalent. In this paper we demonstrate that that argument is thermodynamically incorrect. In addition, it is shown that the absence of a thermal...

journal_title：Journal of molecular biology

authors： Xie D,Bhakuni V,Freire E

更新日期：1993-07-05 00:00:00

abstract：:The homodimeric enzyme form of quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa ATCC 17933 crystallizes readily with the space group R3. The X-ray structure was solved at 2.6 A resolution by molecular replacement. Aside from differences in some loops, the folding of the enzyme is very similar to the larg...

journal_title：Journal of molecular biology

authors： Keitel T,Diehl A,Knaute T,Stezowski JJ,Höhne W,Görisch H

更新日期：2000-04-07 00:00:00

abstract：:Nuclear transport factor 2 (NTF2) mediates nuclear import of RanGDP, a central component of many nuclear trafficking pathways. NTF2 is a homodimer and each chain has independent binding sites for RanGDP and nuclear pore proteins (nucleoporins) that contain FxFG sequence repeats. We show here that the monomer-dimer dis...

journal_title：Journal of molecular biology

authors： Chaillan-Huntington C,Butler PJ,Huntington JA,Akin D,Feldherr C,Stewart M

更新日期：2001-11-30 00:00:00

abstract：:Bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is an important intracellular signaling molecule that affects diverse physiological processes in bacteria. The intracellular levels of c-di-GMP are controlled by proteins acting as diguanylate cyclase (DGC) and phosphodiesterase (PDE) enzymes that synthesiz...

journal_title：Journal of molecular biology

authors： Pallegar P,Canuti M,Langille E,Peña-Castillo L,Lang AS

更新日期：2020-08-07 00:00:00

abstract：:The HNH motif is a small nucleic acid binding and cleavage module, widespread in metal finger endonucleases in all life kingdoms. Here we studied a non-specific endonuclease, the nuclease domain of ColE7 (N-ColE7), to decipher the role of the conserved asparagine and histidine residues in the HNH motif. We found, usin...

journal_title：Journal of molecular biology

authors： Huang H,Yuan HS

更新日期：2007-05-04 00:00:00

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

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

更新日期：2008-12-31 00:00:00

abstract：:A protein is defined as an indexed string of elements at each level in the hierarchy of protein structure: sequence, secondary structure, super-secondary structure, etc. The elements, for example, residues or secondary structure segments such as helices or beta-strands, are associated with a series of properties and c...

journal_title：Journal of molecular biology

authors： Sali A,Blundell TL

更新日期：1990-03-20 00:00:00

abstract：:Based on structural analyses and on the behavior of mutants, we suggest that the polymerase domain of HIV-1 reverse transcriptase (RT) plays a critical role in holding and appropriately positioning the template-primer both at the polymerase active site and at the RNase H active site. For RT to successfully copy the vi...

journal_title：Journal of molecular biology

authors： Gao HQ,Boyer PL,Arnold E,Hughes SH

更新日期：1998-04-03 00:00:00

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

authors： Rashin AA

更新日期：1987-11-20 00:00:00

abstract：:The structure of basic Winged Bean Agglutinin (WBAI) with two dimeric molecules complexed with methyl-alpha-D-galactopyranoside in the asymmetric unit, has been determined by the molecular replacement method and refined with 2.5 A X-ray intensity data. The polypeptide chain of each monomer has the characteristic legum...

journal_title：Journal of molecular biology

authors： Prabu MM,Sankaranarayanan R,Puri KD,Sharma V,Surolia A,Vijayan M,Suguna K

更新日期：1998-03-06 00:00:00

abstract：:Protein engineering experiments and Phi(F)-value analysis of SH3 domains reveal that their transition state ensemble (TSE) is conformationally restricted, i.e. the fluctuations in the transition state (TS) structures are small. In the TS of src SH3 and alpha-spectrin SH3 the distal loop and the associated hairpin are ...

journal_title：Journal of molecular biology

authors： Klimov DK,Thirumalai D

更新日期：2002-04-12 00:00:00

abstract：:The cleavage site of the T4 prohead protease in gene product 68 of bacteriophage T4 has been determined by direct protein sequencing. It is located close to the carboxy-terminal end of a predicted alpha-helix in the sequence Asn-Val-Glu-Ala between the Glu and Ala residues. Secondary structure seems to be more importa...

journal_title：Journal of molecular biology

authors： Keller B,Kellenberger E,Bickle TA,Tsugita A

更新日期：1985-12-05 00:00:00

abstract：:The production of complex multidomain (membrane) proteins is a major hurdle in structural genomics and a generic approach for optimizing membrane protein expression is still lacking. We have devised a selection method to isolate mutant strains with improved functional expression of recombinant membrane proteins. By fu...

journal_title：Journal of molecular biology

authors： Linares DM,Geertsma ER,Poolman B

更新日期：2010-08-06 00:00:00

abstract：:The decrease in conformational stability, delta(delta G), has been measured for 72 aliphatic side-chain mutants from four proteins in which a larger side-chain is replaced by a smaller side-chain so that steric effects are minimal. When these delta(delta G) values are corrected to the same accessibility, namely 100% b...

journal_title：Journal of molecular biology

authors： Pace CN

更新日期：1992-07-05 00:00:00

abstract：:The IS1 element contains two adjacent genes called insA and insB, both required for IS1 transposition and IS1-mediated plasmid cointegration. These two genes are transcribed polycistronically from the promoter in the left terminal inverted repeat of IS1 (insL). We constructed overexpression systems of these genes with...

journal_title：Journal of molecular biology

authors： Machida C,Machida Y

更新日期：1989-08-20 00:00:00

abstract：:The metazoan cell membrane is highly organized. Maintaining such organization and preserving membrane integrity under different conditions are accomplished through intracellular tethering to an extensive, flexible protein network. Spectrin, the principal component of this network, is attached to the membrane through t...

journal_title：Journal of molecular biology

authors： Yasunaga M,Ipsaro JJ,Mondragón A

更新日期：2012-04-06 00:00:00