Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering.

abstract：:Cdc25B is a dual specificity phosphatase involved in the control of cyclin-dependent kinases and the progression of cells through the cell cycle. A series of minimal domain Cdc25B constructs maintaining catalytic activity have been expressed. The structure of a minimum domain construct binding sulfate was determined a...

journal_title：Journal of molecular biology

authors： Reynolds RA,Yem AW,Wolfe CL,Deibel MR Jr,Chidester CG,Watenpaugh KD

更新日期：1999-10-29 00:00:00

abstract：:In common with many other eukaryotic species, the genomes of species in the genus Allium contain a high proportion of repeated DNA sequences, which may be implicated in the considerable differences in genome size that are seen between even very closely related species. The gross organization of repetitive sequences wi...

journal_title：Journal of molecular biology

authors： Evans IJ,James AM,Barnes SR

更新日期：1983-11-15 00:00:00

abstract：:We present the first evidence, in Bacillus subtilis, for gene regulation through the classical mechanism of repressor-operator interaction. The EcoRI-F immunity region (immF) of lysogenic phage phi 105 contains two promoters, PM and PR, in divergent orientations. PM initiates transcription of the phi 105 repressor (c ...

journal_title：Journal of molecular biology

authors： Van Kaer L,Van Montagu M,Dhaese P

更新日期：1987-09-05 00:00:00

abstract：:Protein catalyzed DNA rearrangements typically require assembly of complex nucleoprotein structures. In transposition and integration reactions, these structures, termed synaptic complexes, are mandatory for catalysis. We characterize the Tn5 pre-cleavage synaptic complex, the simplest transposition complex described ...

journal_title：Journal of molecular biology

authors： Bhasin A,Goryshin IY,Steiniger-White M,York D,Reznikoff WS

更新日期：2000-09-08 00:00:00

abstract：:The lectin from the mushroom Psathyrella velutina recognises specifically N-acetylglucosamine and N-acetylneuraminic acid containing glycans. The crystal structure of the 401 amino acid residue lectin shows that it adopts a very regular seven-bladed beta-propeller fold with the N-terminal region tucked into the centra...

journal_title：Journal of molecular biology

authors： Cioci G,Mitchell EP,Chazalet V,Debray H,Oscarson S,Lahmann M,Gautier C,Breton C,Perez S,Imberty A

更新日期：2006-04-14 00:00:00

abstract：:The histone-like nucleoid structuring (H-NS) protein is a global modulator of gene expression in Gram-negative bacteria. VicH, the H-NS protein of Vibrio cholerae, regulates the expression of certain major virulence determinants implicated in the pathogenesis of cholera. We present here the 2.5A crystal structure of t...

journal_title：Journal of molecular biology

authors： Cerdan R,Bloch V,Yang Y,Bertin P,Dumas C,Rimsky S,Kochoyan M,Arold ST

更新日期：2003-11-21 00:00:00

abstract：:Production of seven single surface histidine variants of yeast iso-1-cytochrome c allowed measurement of the apparent pK(a), pK(a)(obs), for histidine-heme loop formation for loops of nine to 83 amino acid residues under varying denaturing conditions (2 M to 6 M guanidine hydrochloride, gdnHCl). A linear correlation b...

journal_title：Journal of molecular biology

authors： Wandschneider E,Bowler BE

更新日期：2004-05-21 00:00:00

abstract：:Post-translational modification of cellular proteins by ubiquitin regulates numerous cellular processes, including innate and adaptive immune responses. Ubiquitin-mediated control over these processes can be reversed by cellular deubiquitinating enzymes (DUBs), which remove ubiquitin from cellular targets and depolyme...

journal_title：Journal of molecular biology

authors： Bailey-Elkin BA,Knaap RCM,Kikkert M,Mark BL

更新日期：2017-11-10 00:00:00

abstract：:l-Gulonate 3-dehydrogenase (GDH) is a bifunctional dimeric protein that functions not only as an NAD(+)-dependent enzyme in the uronate cycle but also as a taxon-specific lambda-crystallin in rabbit lens. Here we report the first crystal structure of GDH in both apo form and NADH-bound holo form. The GDH protomer cons...

journal_title：Journal of molecular biology

authors： Asada Y,Kuroishi C,Ukita Y,Sumii R,Endo S,Matsunaga T,Hara A,Kunishima N

更新日期：2010-09-03 00:00:00

abstract：:The effect of temperature on the velocity of rhodamine phalloidin-labelled F-actin moving in vitro on rabbit skeletal myosin has been studied. Translating actin filaments were visualized by epi-fluorescence in an inverted microscope, equipped with temperature control (+/- 0.2 K) of the stage and objective. Images were...

journal_title：Journal of molecular biology

authors： Anson M

更新日期：1992-04-20 00:00:00

abstract：:The structure of bovine deoxyhaemoglobin has been determined at 2.2 A resolution and refined to an R-factor of 0.193 for all 32,583 reflections, and a free R-factor of 0.249 for 1527 reflections excluded from the refinement. The structure shows no significant differences between the alpha-carbon positions of bovine an...

journal_title：Journal of molecular biology

authors： Perutz MF,Fermi G,Poyart C,Pagnier J,Kister J

更新日期：1993-10-05 00:00:00

abstract：:Differential oxygen binding measurements obtained over the pH range 6.95 to 9.10 at 25 degrees C have allowed a detailed description of the alkaline Bohr effect of human hemoglobin Ao. Phenomenological analysis of the data in terms of the Adair equation shows that: (1) the oxygen binding curves are asymmetrical with t...

journal_title：Journal of molecular biology

authors： Di Cera E,Doyle ML,Gill SJ

更新日期：1988-04-05 00:00:00

abstract：:Only a few transcriptional regulatory proteins have been characterized in extremely hyperthermophilic organisms, and most function as repressors. Structural features of the NtrC1 protein from the hyperthermophilic bacterium Aquifex aeolicus suggested that this protein functions similarly to the sigma(54)-polymerase ac...

journal_title：Journal of molecular biology

authors： Doucleff M,Chen B,Maris AE,Wemmer DE,Kondrashkina E,Nixon BT

更新日期：2005-10-21 00:00:00

abstract：:A library of variant enzymes was created by combined shuffling of the DNA encoding the human Mu class glutathione transferases GST M1-1 and GST M2-2. The parental GSTs are 84 % sequence identical at the protein level, but their specific activities with the substrates aminochrome and 2-cyano-1,3-dimethyl-1-nitrosoguani...

journal_title：Journal of molecular biology

authors： Hansson LO,Bolton-Grob R,Massoud T,Mannervik B

更新日期：1999-03-26 00:00:00

abstract：:Kinetic analysis of a mutant version of Escherichia coli aspartate transcarbamoylase in which Thr82 in the regulatory chain (Thr82r) was replaced by Ala results in a shift in the T <==> R equilibrium towards the T-state. In order to understand the structural determinants of this T-state stabilization, the X-ray struct...

journal_title：Journal of molecular biology

authors： Williams MK,Stec B,Kantrowitz ER

更新日期：1998-08-07 00:00:00

abstract：:Human alpha-galactosidase A (alpha-D-galactoside galactohydrolase; EC 3.2.1.22), the glycosylated lysosomal enzyme deficient in Fabry disease, has been crystallized as a complex with the inhibitor N-6-aminohexanoyl-alpha-D-galactopyranosylamine. The "hanging drop" method of vapor diffusion was used to grow crystals fr...

journal_title：Journal of molecular biology

authors： Murali R,Ioannou YA,Desnick RJ,Burnett RM

更新日期：1994-06-17 00:00:00

abstract：:Three fundamentally different chloroplast ATP synthase samples of increasing complexity were visualized by atomic force microscopy. The samples are distinguishable in respect to the isolation technique, the detergent employed, and the final subunit composition. The homo-oligomer III was isolated following SDS treatmen...

journal_title：Journal of molecular biology

authors： Seelert H,Dencher NA,Müller DJ

更新日期：2003-10-17 00:00:00

abstract：:Siderophores are small-molecule iron chelators that many bacteria synthesize and secrete in order to survive in iron-depleted environments. Biosynthesis of enterobactin, the Escherichia coli catecholate siderophore, requires adenylation of 2,3-dihydroxybenzoic acid (2,3-DHB) by the cytoplasmic enzyme EntE. The DHB-AMP...

journal_title：Journal of molecular biology

authors： Khalil S,Pawelek PD

更新日期：2009-10-30 00:00:00

abstract：:To address the mechanism of thermosensing and its implications for molecular engineering, we previously deconstructed the functional components of the bacterial thermosensor DesK, a histidine kinase with a five-span transmembrane domain that detects temperature changes. The system was first simplified by building a se...

journal_title：Journal of molecular biology

authors： Inda ME,Vazquez DB,Fernández A,Cybulski LE

更新日期：2019-03-01 00:00:00

abstract：:Enzymes exhibit a strong long-range evolutionary constraint that extends from their catalytic site and affects even distant sites, where site-specific evolutionary rate increases monotonically with distance. While protein-protein sites in enzymes were previously shown to induce only a weak conservation gradient, a com...

journal_title：Journal of molecular biology

authors： Sharir-Ivry A,Xia Y

更新日期：2019-09-06 00:00:00

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

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

更新日期：1994-05-27 00:00:00

abstract：:Escherichia coli lac promoter variants are shown to be subject to large synergistic transcriptional activation by catabolite activator protein (CRP) and DNA supercoiling in vitro. Activation was studied for the lac wild-type promoter, a promoter with a variant spacing (lac delta l) and two promoters with variant -10 r...

journal_title：Journal of molecular biology

authors： Meiklejohn AL,Gralla JD

更新日期：1989-06-20 00:00:00

abstract：:The aggregation of alpha-synuclein is believed to be a critical step in the etiology of Parkinson's disease. A variety of biophysical techniques were used to investigate the aggregation and fibrillation of alpha-synuclein in which one of the four intrinsic Tyr residues was replaced by Trp, and two others by Phe, in or...

journal_title：Journal of molecular biology

authors： Kaylor J,Bodner N,Edridge S,Yamin G,Hong DP,Fink AL

更新日期：2005-10-21 00:00:00

abstract：:Switching between the active (ATP and DNA bound) and inactive conformations of the homologous recombination RecA protein is regulated by ATP hydrolysis. First, we use the homologous pairing domain of RecA derived from its mobile loop L2 to show that the interaction of this random coil peptide with the gamma-phosphate ...

journal_title：Journal of molecular biology

authors： Voloshin ON,Wang L,Camerini-Otero RD

更新日期：2000-11-10 00:00:00

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

authors： Taylor AF,Smith GR

更新日期：1985-09-20 00:00:00

abstract：:Helicases are ubiquitous molecular motor proteins that have an important role in the metabolism of nucleic acids. The gene encoding a helicase was cloned from the human malaria parasite Plasmodium falciparum. The polypeptide of 398 amino acid residues has a molecular mass of 45 kDa, contains striking homology to eukar...

journal_title：Journal of molecular biology

authors： Pradhan A,Tuteja R

更新日期：2007-10-19 00:00:00

abstract：:We describe improvements of the currently most popular method for prediction of classically secreted proteins, SignalP. SignalP consists of two different predictors based on neural network and hidden Markov model algorithms, where both components have been updated. Motivated by the idea that the cleavage site position...

journal_title：Journal of molecular biology

authors： Bendtsen JD,Nielsen H,von Heijne G,Brunak S

更新日期：2004-07-16 00:00:00

abstract：:The primary goal of this study was to gain a better understanding of the effect of environment and ionic strength on the pK values of histidine residues in proteins. The salt-dependence of pK values for two histidine residues in ribonuclease Sa (RNase Sa) (pI=3.5) and a variant in which five acidic amino acids have be...

journal_title：Journal of molecular biology

authors： Huyghues-Despointes BM,Thurlkill RL,Daily MD,Schell D,Briggs JM,Antosiewicz JM,Pace CN,Scholtz JM

更新日期：2003-01-31 00:00:00

abstract：:A phage-neutralizing rabbit antiserum collected after immunization with tail-fiberless bacteriophage T4 particles was adsorbed with complete T4 phage. The resulting adsorbed serum inhibited tail fiber attachment in vitro. To identify the antigens against which this inhibitory activity was directed, blocking experiment...

journal_title：Journal of molecular biology

authors： Urig MA,Brown SM,Tedesco P,Wood WB

更新日期：1983-09-15 00:00:00

abstract：:We have determined the sites that are preferentially cleaved by Mn(T4MPyP) (where T4MPyP is the dianion of 5, 10, 15, 20, tetrakis (4-N-methylpyridine)porphyrin) on synthetic DNAs and on both intrinsically curved and average-shaped natural DNA sequences. On the basis of cleavage selectivity and of DNase I footprinting...

journal_title：Journal of molecular biology

authors： Di Mauro E,Saladino R,Tagliatesta P,De Sanctis V,Negri R

更新日期：1998-09-11 00:00:00