Crystallization of complexes of EcoRV endonuclease with cognate and non-cognate DNA fragments.

abstract：:The type III secretion system (T3SS) is essential in the pathogenesis of Yersinia pestis, the causative agent of plague. A small protein, LcrG, functions as a chaperone to the tip protein LcrV, and the LcrG-LcrV interaction is important in regulating protein secretion through the T3SS. The atomic structure of the LcrG...

journal_title：Journal of molecular biology

authors： Chaudhury S,de Azevedo Souza C,Plano GV,De Guzman RN

更新日期：2015-09-25 00:00:00

abstract：:The dependence of the electrophoretic mobility of small DNA rings on topological constraint was investigated in acrylamide or agarose gels as a function of DNA size (from approximately 350 to 1400 base-pairs), gel concentration and nucleotide sequence. Under appropriate adjustment between the size of the DNA and the g...

journal_title：Journal of molecular biology

authors： Zivanovic Y,Goulet I,Prunell A

更新日期：1986-12-05 00:00:00

abstract：:The structure of Mn(III) superoxide dismutase (Mn(III)SOD) from Thermus thermophilus, a tetramer of chains 203 residues in length, has been refined by restrained least-squares methods. The R-factor [formula: see text] for the 54,056 unique reflections measured between 10.0 and 1.8 A (96% of all possible reflections) i...

journal_title：Journal of molecular biology

authors： Ludwig ML,Metzger AL,Pattridge KA,Stallings WC

更新日期：1991-05-20 00:00:00

abstract：:Mutations at solvent-inaccessible core positions in proteins can impact function through many biophysical mechanisms including alterations to thermodynamic stability and protein dynamics. As these properties of proteins are difficult to investigate, the impacts of core mutations on protein function are poorly understo...

journal_title：Journal of molecular biology

authors： Lee SY,Pullen L,Virgil DJ,Castañeda CA,Abeykoon D,Bolon DN,Fushman D

更新日期：2014-04-03 00:00:00

abstract：:Crystals of an inhibitor of trypsin and tissue plasminogen activator from seeds of the legume Erythrina caffra have been obtained by vapour diffusion. The crystals belong to the hexagonal space group P6(1)22 (or its enantiomorph P6(5)22) with cell parameters 73.4 A and 143.0 A. There is one molecule in the asymmetric ...

journal_title：Journal of molecular biology

authors： Onesti S,Lloyd LF,Maeder D,Mistry A,Brick P

更新日期：1989-11-05 00:00:00

abstract：:The effects of regulatory amounts of Ca2+ on the in situ structures of troponin C (TnC) and troponin I (TnI) in whole troponin have been investigated by neutron scattering. In separate difference experiments, 97% deuterated TnC and TnI within whole troponin were studied +/-Ca2+ in 41.6% 2H2O buffers in which protonate...

journal_title：Journal of molecular biology

authors： Stone DB,Timmins PA,Schneider DK,Krylova I,Ramos CH,Reinach FC,Mendelson RA

更新日期：1998-08-28 00:00:00

abstract：:U-insertion/deletion RNA editing in the single mitochondrion of kinetoplastids, an ancient lineage of eukaryotes, is a unique mRNA maturation process needed for translation. Multisubunit editing complexes recognize many pre-edited mRNA sites and modify them via cycles of three catalytic steps: guide RNA (gRNA)-directe...

journal_title：Journal of molecular biology

authors： Hernandez A,Panigrahi A,Cifuentes-Rojas C,Sacharidou A,Stuart K,Cruz-Reyes J

更新日期：2008-08-01 00:00:00

abstract：:Protein-protein interactions within the membrane, partially or fully mediated by transmembrane (TM) domains, are involved in many vital cellular processes. Since the unique feature of the membrane environment enables protein-protein assembly that otherwise is not energetically favored in solution, the structural restr...

journal_title：Journal of molecular biology

authors： Sal-Man N,Gerber D,Shai Y

更新日期：2004-11-26 00:00:00

abstract：:The importance of including different energy contributions in calculations of electrostatic energies in proteins is examined by calculating the intrinsic pKa values of the acidic groups of bovine pancreatic trypsin inhibitor. It appears that such calculations provide a powerful and revealing test; the relevant solvati...

journal_title：Journal of molecular biology

authors： Russell ST,Warshel A

更新日期：1985-09-20 00:00:00

abstract：:The expression of intracellular antibodies (intrabodies) in eukaryotic cells has provided a powerful tool to manipulate microbial and cellular signaling pathways in a highly precise manner. However, there have been several technical issues that have restricted their more widespread use. In particular, single-chain ant...

journal_title：Journal of molecular biology

authors： Gennari F,Mehta S,Wang Y,St Clair Tallarico A,Palu G,Marasco WA

更新日期：2004-01-02 00:00:00

abstract：:We used site-specific recombination catalyzed by the bacteriophage lambda Int system to probe DNA structure and metabolism in vivo. In vitro, the complexity of catenated products was linearly proportional to substrate supercoil density. A system was developed that gave efficient, controlled Int recombination in Escher...

journal_title：Journal of molecular biology

authors： Bliska JB,Cozzarelli NR

更新日期：1987-03-20 00:00:00

abstract：:The precise geometry of the flagellar basal structure anchored in the cytoplasmic membrane was determined by digital stereo-photogrammetry of the images captured by quick-freeze deep-etch replica electron microscopy. In order to examine the structure on the periplasmic side of the membrane, we analyzed the MS ring com...

journal_title：Journal of molecular biology

authors： Katayama E,Shiraishi T,Oosawa K,Baba N,Aizawa S

更新日期：1996-01-26 00:00:00

abstract：:tRNA isodecoders share the same anticodon but have differences in their body sequence. An unexpected result from genome sequencing projects is the identification of a large number of tRNA isodecoder genes in mammalian genomes. In the reference human genome, more than 270 isodecoder genes are present among the approxim...

journal_title：Journal of molecular biology

authors： Geslain R,Pan T

更新日期：2010-02-26 00:00:00

abstract：:A proliferation-inducing ligand (APRIL) is a TNF-like cytokine that stimulates tumor cell growth. Within the TNF ligand superfamily, APRIL is most similar to B-cell activation factor (BAFF) with which it shares 30% sequence identity. APRIL binds the receptors B-cell maturation antigen (BCMA) and TACI with high affinit...

journal_title：Journal of molecular biology

authors： Wallweber HJ,Compaan DM,Starovasnik MA,Hymowitz SG

更新日期：2004-10-15 00:00:00

abstract：:By using a set of 476 ordered DNA clones (in lambda phage vector) that covers the entire chromosome of Escherichia coli K12, we have made an exhaustive survey of tRNA genes in the E. coli genome. Ultraviolet-irradiated bacteria were separately infected with each of the 476 clones and the RNA molecules produced upon in...

journal_title：Journal of molecular biology

authors： Komine Y,Adachi T,Inokuchi H,Ozeki H

更新日期：1990-04-20 00:00:00

abstract：:The contribution of the tRNA "core" to aminoacylation is beginning to be recognized. One example is the core region of Escherichia coli tRNA(Cys), which has been shown by biochemical studies to be important for aminoacylation. This core has several layers of unusual base-pairs, which are revealed by the recent crystal...

journal_title：Journal of molecular biology

authors： Hamann CS,Hou YM

更新日期：2000-01-28 00:00:00

abstract：:The crystal structures of glycosylated native proteinase A, an aspartic proteinase found in the vacuole of Saccharomyces cerevisiae, and its complex with a difluorostatone-containing tripeptide have been determined by molecular replacement to 3.5 A and 2.4 A resolutions, respectively. Superposition of the bound and na...

journal_title：Journal of molecular biology

authors： Aguilar CF,Cronin NB,Badasso M,Dreyer T,Newman MP,Cooper JB,Hoover DJ,Wood SP,Johnson MS,Blundell TL

更新日期：1997-04-11 00:00:00

abstract：:Large rigid-body domain movements are critical to GroEL-mediated protein folding, especially apical domain elevation and twist associated with the formation of a folding chamber upon binding ATP and co-chaperonin GroES. Here, we have modeled the anisotropic displacements of GroEL domains from various crystallized stat...

journal_title：Journal of molecular biology

authors： Chaudhry C,Horwich AL,Brunger AT,Adams PD

更新日期：2004-09-03 00:00:00

abstract：:A central challenge in structure-based ligand design is the accurate prediction of binding free energies. Here we apply alchemical free energy calculations in explicit solvent to predict ligand binding in a model cavity in T4 lysozyme. Even in this simple site, there are challenges. We made systematic improvements, be...

journal_title：Journal of molecular biology

authors： Mobley DL,Graves AP,Chodera JD,McReynolds AC,Shoichet BK,Dill KA

更新日期：2007-08-24 00:00:00

abstract：:Molecular aspects of thermal adaptation of proteins were studied by following the co-evolution of temperature dependence, conformational stability, and substrate specificity in a cold-active lipase modified via directed evolution. We found that the evolution of kinetic stability was accompanied by a relaxation in subs...

journal_title：Journal of molecular biology

authors： Gatti-Lafranconi P,Natalello A,Rehm S,Doglia SM,Pleiss J,Lotti M

更新日期：2010-01-08 00:00:00

abstract：:The solvent-accessible surface area (As) of 46 monomeric proteins is calculated using atomic co-ordinates from high-resolution and well-refined crystal structures. The As of these proteins can be determined to within 1 to 2% and that of their individual residues to within 10 to 20%. The As values of proteins are corre...

journal_title：Journal of molecular biology

authors： Miller S,Janin J,Lesk AM,Chothia C

更新日期：1987-08-05 00:00:00

abstract：:Detachment of flagella in Chlamydomonas reinhardii stimulates a rapid accumulation of tubulin mRNAs. The induced tubulin mRNAs are normally rapidly degraded following flagellar regeneration, but inhibition of protein synthesis with cycloheximide prevents their degradation. alpha-Tubulin poly(A) tail lengths were measu...

journal_title：Journal of molecular biology

authors： Baker EJ,Diener DR,Rosenbaum JL

更新日期：1989-06-20 00:00:00

abstract：:Assembly of normally soluble proteins into ordered aggregates, known as amyloid fibrils, is a cause or associated symptom of numerous human disorders, including Alzheimer's and the prion diseases. Here, we test the ability of discontinuous molecular dynamics (DMD) simulations based on PRIME20, a new intermediate-resol...

journal_title：Journal of molecular biology

authors： Wagoner VA,Cheon M,Chang I,Hall CK

更新日期：2012-03-02 00:00:00

abstract：:The Monte Carlo estimate of the p value of the hypergeometric test is described and advocated for the testing of the hypothesis that different treatments induce the same mutational spectrum. The hypergeometric test is a generalization of Fisher's "exact" test for tables with more than two rows and two columns. Use of ...

journal_title：Journal of molecular biology

authors： Adams WT,Skopek TR

更新日期：1987-04-05 00:00:00

abstract：:Ricin A-chain is an N-glycosidase that hydrolyzes the adenine ring from a specific adenosine of rRNA. Formycin monophosphate (FMP) and adenyl(3'-->5')guanosine (ApG) were bound to ricin A-chain and their structures elucidated by X-ray crystallography. The formycin ring stacks between tyrosines 80 and 123 and at least ...

journal_title：Journal of molecular biology

authors： Monzingo AF,Robertus JD

更新日期：1992-10-20 00:00:00

abstract：:A hallmark of the catalytically essential Walker B motif of P-loop NTPases is the presence of an acidic residue (aspartate/glutamate) for efficient Mg2+ coordination. Although the Walker B motif has been identified in well-studied examples of P-loop NTPases, its identity is ambiguous in many families, for example, in ...

journal_title：Journal of molecular biology

authors： Kanade M,Chakraborty S,Shelke SS,Gayathri P

更新日期：2020-09-18 00:00:00

abstract：:Protein kinase A (PKA) anchoring proteins (AKAPs) tether PKA to various subcellular locations. AKAP121, which tethers PKAII to the outer mitochondrial membrane, includes a K homology (KH) RNA-binding motif. Purified AKAP121 KH domain binds the 3' untranslated regions (3'UTRs) of transcripts encoding the Fo-f subunit o...

journal_title：Journal of molecular biology

authors： Ginsberg MD,Feliciello A,Jones JK,Avvedimento EV,Gottesman ME

更新日期：2003-04-04 00:00:00

abstract：:One aim of computational protein design is to introduce novel enzyme activity into proteins of known structure by predicting mutations that stabilize transition states. Previously, we showed that it is possible to introduce triose phosphate isomerase activity into the ribose-binding protein of Escherichia coli by cons...

journal_title：Journal of molecular biology

authors： Allert M,Dwyer MA,Hellinga HW

更新日期：2007-02-23 00:00:00

abstract：:We have used lacZ reporter genes to assess leftward ribosome frameshifting on sequences containing the quadruplet U UUC followed by several different triplets coding for lysine, isoleucine, or leucine. Limitation for lysine-tRNA provokes leftward frameshifting when the slippery quadruplet is followed by either lysine ...

journal_title：Journal of molecular biology

authors： Barak Z,Lindsley D,Gallant J

更新日期：1996-03-08 00:00:00

abstract：:The structure of empty canine parvovirus capsids shows that residues 37 to the carboxy-terminal residue 584 (VP2 numbering) are ordered in each of the 60 subunits. The central structural motif of each subunit is the eight-stranded antiparallel beta-barrel that has been found in many other virus structures. Five beta-h...

journal_title：Journal of molecular biology

authors： Wu H,Rossmann MG

更新日期：1993-09-20 00:00:00