Exploring conformational space with a simple lattice model for protein structure.

abstract：:Here, we report the first characterization and partial purification of an archaeal tRNA 3' processing activity, the RNase Z from Haloferax volcanii. The activity identified here is an endonuclease, which cleaves tRNA precursors 3' to the discriminator. Thus tRNA 3' processing in archaea resembles the eukaryotic 3' pro...

journal_title：Journal of molecular biology

authors： Schierling K,Rösch S,Rupprecht R,Schiffer S,Marchfelder A

更新日期：2002-03-01 00:00:00

abstract：:The genome of the yeast Saccharomyces cerevisiae contains three complete copies of the genetic information governing cell mating type. Normally, only the information in one of the copies (the MAT locus) is expressed; the other two copies (HML and HMR) are repressed and serve as donors of mating-type sequences that can...

journal_title：Journal of molecular biology

authors： Abraham J,Nasmyth KA,Strathern JN,Klar AJ,Hicks JB

更新日期：1984-07-05 00:00:00

abstract：:Two-component systems are a class of sensors that enable bacteria to respond to environmental and cell-state signals. The canonical system consists of a membrane-bound sensor histidine kinase that autophosphorylates in response to a signal and transfers the phosphate to an intracellular response regulator. Bacteria ty...

journal_title：Journal of molecular biology

authors： Groban ES,Clarke EJ,Salis HM,Miller SM,Voigt CA

更新日期：2009-07-17 00:00:00

abstract：:An alphoid-like human repetitive DNA of the Sau3A family is present extrachromosomally and in the chromosomes. In the chromosomes, the DNA is located on chromosome 11 but related sequences are present in chromosome 17. We characterized the nature of the recombination involved in the excision of the extrachromosomal DN...

journal_title：Journal of molecular biology

authors： Kiyama R,Okumura K,Matsui H,Bruns GA,Kanda N,Oishi M

更新日期：1987-12-20 00:00:00

abstract：:DNA opening is an essential step in the initiation of replication via the Cairns mode of replication. The opening reaction was investigated in a gamma ori system by using hyperactive variants of plasmid R6K-encoded initiator protein, pi. Reactivity to KMnO4 (indicative of opening) within gamma ori DNA occurred in both...

journal_title：Journal of molecular biology

authors： Krüger R,Konieczny I,Filutowicz M

更新日期：2001-03-09 00:00:00

abstract：:The Psi-RNA packaging signal of the human immunodeficiency virus type-1 (HIV-1) genome contains a 35 nucleotide stem-loop, termed SL1, which is important for efficient genome packaging during virus assembly and for reverse transcription during infectivity. The predicted secondary structure of SL1 consists of an upper ...

journal_title：Journal of molecular biology

authors： Lawrence DC,Stover CC,Noznitsky J,Wu Z,Summers MF

更新日期：2003-02-14 00:00:00

abstract：:The structure of a class II fructose-1,6-bisphosphate aldolase in complex with the substrate analogue and inhibitor phosphoglycolohydroxamate (PGH) has been determined using X-ray diffraction terms to a resolution of 2.0 A (1 A=0.1 nm). The crystals are trigonal, space group P3121 with a=b=78.24 A, c=289.69 A. The asy...

journal_title：Journal of molecular biology

authors： Hall DR,Leonard GA,Reed CD,Watt CI,Berry A,Hunter WN

更新日期：1999-03-26 00:00:00

abstract：:Human serum amyloid P component crystallizes from sodium acetate buffer (pH 5.5) in the presence of calcium and polyethylene glycol 6000, at 4 degrees C. The space group is P2(1) and the cell parameters are a = 69.0 A (1 A = 0.1 nm), b = 99.3 A, c = 96.8 A, beta = 96.1. Density considerations supported by neutron scat...

journal_title：Journal of molecular biology

authors： Wood SP,Oliva G,O'Hara BP,White HE,Blundell TL,Perkins SJ,Sardharwalla I,Pepys MB

更新日期：1988-07-05 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：:HBII-52 is a human brain-specific C/D box snoRNA that potentially regulates the editing and/or alternative splicing of the serotonin receptor. Forty-two nearly identical copies of the HBII-52 gene are located immediately downstream of the SNRPN protein-coding gene in an imprinted locus associated with Prader-Willi syn...

journal_title：Journal of molecular biology

authors： Nahkuri S,Taft RJ,Korbie DJ,Mattick JS

更新日期：2008-09-12 00:00:00

abstract：:Foot-and-mouth disease virus (FMDV), a non-enveloped picornavirus, is sensitive to acidic conditions. At pH values below 7 the icosahedral virus capsid, formed from 60 copies of a protomer containing four polypeptides (VP1 to 4), dissociates into 12 pentamers, releasing the viral RNA. Evidence suggests that this acid ...

journal_title：Journal of molecular biology

authors： van Vlijmen HW,Curry S,Schaefer M,Karplus M

更新日期：1998-01-16 00:00:00

abstract：:The production of recombinant proteins in Escherichia coli frequently results in the formation of insoluble protein aggregates called inclusion bodies (IBs). The determinants of IB formation remain poorly understood and are of much interest for biotechnological and research applications, as well as offering insight in...

journal_title：Journal of molecular biology

authors： Trainor K,Gingras Z,Shillingford C,Malakian H,Gosselin M,Lipovšek D,Meiering EM

更新日期：2016-03-27 00:00:00

abstract：:Three ribosomal RNA mutations conferring resistance to the antibiotic kasugamycin were isolated using a strain of Escherichia coli in which all of the rRNA is transcribed from a plasmid-encoded rrn operon. The mutations, A794G, G926A, and A1519C, mapped to universally conserved sites in the 16 S RNA gene. Site-directe...

journal_title：Journal of molecular biology

authors： Vila-Sanjurjo A,Squires CL,Dahlberg AE

更新日期：1999-10-15 00:00:00

abstract：:This is the first structural evidence of alpha-tocopherol (alpha-TP) as a possible candidate against inflammation, as it inhibits phospholipase A2 specifically and effectively. The crystal structure of the complex formed between Vipera russelli phospholipase A2 and alpha-tocopherol has been determined and refined to a...

journal_title：Journal of molecular biology

authors： Chandra V,Jasti J,Kaur P,Betzel Ch,Srinivasan A,Singh TP

更新日期：2002-07-05 00:00:00

abstract：:During pathophysiological muscle wasting, a family of ubiquitin ligases, including muscle RING-finger protein-1 (MuRF1), has been proposed to trigger muscle protein degradation via ubiquitination. Here, we characterized skeletal muscles from wild-type (WT) and MuRF1 knockout (KO) mice under amino acid (AA) deprivation...

journal_title：Journal of molecular biology

authors： Koyama S,Hata S,Witt CC,Ono Y,Lerche S,Ojima K,Chiba T,Doi N,Kitamura F,Tanaka K,Abe K,Witt SH,Rybin V,Gasch A,Franz T,Labeit S,Sorimachi H

更新日期：2008-03-07 00:00:00

abstract：:The nucleic acid content of enriched preparations of mitochondria/tubulofilamentous particles from normal and scrapie-infected hamster brains were examined by electron microscopy. After spreading on collodion-coated grids circular molecules of approximately 15.7 kb corresponding in size to mitochondrial DNA (mtDNA) we...

journal_title：Journal of molecular biology

authors： Narang HK

更新日期：1990-12-05 00:00:00

abstract：:Much data support the concept that the MHC class I-related receptor FcRn serves to regulate immunoglobulin G (IgG) concentrations in serum and other diverse body sites in both rodents and humans. Previous studies have indicated that the human ortholog of FcRn is endowed with unexpectedly high stringency in binding spe...

journal_title：Journal of molecular biology

authors： Zhou J,Johnson JE,Ghetie V,Ober RJ,Ward ES

更新日期：2003-09-26 00:00:00

abstract：:Fish hatching enzymes are zinc metalloproteases that digest the egg envelope (chorion) at the time of hatching. The crystal structure of zebrafish hatching enzyme 1 (ZHE1) has been solved at 1.10 Å resolution. ZHE1 is monomeric, is mitten shaped, and has a cleft at the center of the molecule. ZHE1 consists of three 3(...

journal_title：Journal of molecular biology

authors： Okada A,Sano K,Nagata K,Yasumasu S,Ohtsuka J,Yamamura A,Kubota K,Iuchi I,Tanokura M

更新日期：2010-10-08 00:00:00

abstract：:The steps of UUC recognition by tRNAPhe were analysed by temperature-jump measurements. At ion concentrations close to physiological conditions we found three relaxation processes, which we assigned to (1) formation of codon-anticodon complexes, (2) a conformational change of the anticodon loop coupled with Mg2+ bindi...

journal_title：Journal of molecular biology

authors： Labuda D,Striker G,Porschke D

更新日期：1984-04-25 00:00:00

abstract：:Tissue deposition of normally soluble proteins as insoluble amyloid fibrils is associated with serious diseases including the systemic amyloidoses, maturity onset diabetes, Alzheimer's disease and transmissible spongiform encephalopathy. Although the precursor proteins in different diseases do not share sequence homol...

journal_title：Journal of molecular biology

authors： Sunde M,Serpell LC,Bartlam M,Fraser PE,Pepys MB,Blake CC

更新日期：1997-10-31 00:00:00

abstract：:The SH3 domain is a protein-protein interaction module commonly found in intracellular signaling and adaptor proteins. The SH3 domains of multiple endocytic proteins have been recently implicated in binding ubiquitin, which serves as a signal for diverse cellular processes including gene regulation, endosomal sorting,...

journal_title：Journal of molecular biology

authors： He Y,Hicke L,Radhakrishnan I

更新日期：2007-10-12 00:00:00

abstract：:The function of GroE requires a complex system of allosteric communication driven by protein-nucleotide interactions. These rearrangements couple the binding and hydrolysis of ATP to an overall reaction cycle in which substrate proteins are bound, encapsulated and released. Positive cooperativity with respect to ATP b...

journal_title：Journal of molecular biology

authors： Poso D,Clarke AR,Burston SG

更新日期：2004-05-14 00:00:00

abstract：:The three-dimensional crystal structures of the single mutant M17G and the triple mutant F14G-S15G-M17G of the response regulator protein CheY have been determined to 2.3 and 1.9 angstrom, respectively. Both mutants bind the essential Mg2+ cation as determined by the changes in stability, but binding does not cause th...

journal_title：Journal of molecular biology

authors： Bellsolell L,Cronet P,Majolero M,Serrano L,Coll M

更新日期：1996-03-22 00:00:00

abstract：:Gap junction channels are intercellular channels that form by docking the extracellular loops of connexin protein subunits. While the structure and function of gap junctions as intercellular channels have been characterized using different techniques, the physics of the inter-connexin interaction remain unknown. Moreo...

journal_title：Journal of molecular biology

authors： Rico F,Oshima A,Hinterdorfer P,Fujiyoshi Y,Scheuring S

更新日期：2011-09-09 00:00:00

abstract：:The Rev-erb family is an orphan nuclear receptor acting as a negative regulator of transcription. Rev-erbalpha and Rev-erbbeta are crucial components of the circadian clock and involved in various lipid homeostasis. They are unique nuclear receptors that lack the activation function 2 helix (AF2-helix) required for li...

journal_title：Journal of molecular biology

authors： Woo EJ,Jeong DG,Lim MY,Jun Kim S,Kim KJ,Yoon SM,Park BC,Ryu SE

更新日期：2007-10-26 00:00:00

abstract：:We have mapped the origin of DNA replication (oriB) downstream of the 23 S rRNA gene in each copy of the inverted repeat (IR) of tobacco chloroplast DNA between positions 130,502 and 131,924 (IR(A)) by a combination of approaches. In vivo chloroplast DNA replication intermediates were examined by two-dimensional agaro...

journal_title：Journal of molecular biology

authors： Kunnimalaiyaan M,Shi F,Nielsen BL

更新日期：1997-05-02 00:00:00

abstract：:Upstream interactions of Escherichia coli RNA polymerase (RNAP) in an open promoter complex (RPo) formed at the P(R) and P(RM) promoters of bacteriophage lambda have been studied by atomic force microscopy. We demonstrate that the previously described 30-nm DNA compaction observed upon RPo formation at P(R) [Rivetti, ...

journal_title：Journal of molecular biology

authors： Mangiarotti L,Cellai S,Ross W,Bustamante C,Rivetti C

更新日期：2009-01-23 00:00:00

abstract：:Nuclear protein-coding genes of euglenids (Discoba, Euglenozoa, Euglenida) contain conventional (spliceosomal) and nonconventional introns. The latter have been found only in euglenozoans. A unique feature of nonconventional introns is the ability to form a stable and slightly conserved RNA secondary structure bringin...

journal_title：Journal of molecular biology

authors： Gumińska N,Zakryś B,Milanowski R

更新日期：2021-02-05 00:00:00

abstract：:Ferredoxin-NAD(P)(+) oxidoreductase (FNR) catalyzes the reduction of NAD(P)(+) to NAD(P)H with the reduced ferredoxin (Fd) during the final step of the photosynthetic electron transport chain. FNR from the green sulfur bacterium Chlorobaculum tepidum is functionally analogous to plant-type FNR but shares a structural ...

journal_title：Journal of molecular biology

authors： Muraki N,Seo D,Shiba T,Sakurai T,Kurisu G

更新日期：2010-08-20 00:00:00

abstract：:Using simple design and selective pressure, we have evolved an artificial M13 bacteriophage coat protein. M13 coat proteins first reside in the bacterial inner membrane and subsequently surround the DNA core of the assembled virus. The artificial coat protein (ACP) was designed and evolved to mimic both functions of t...

journal_title：Journal of molecular biology

authors： Weiss GA,Sidhu SS

更新日期：2000-06-30 00:00:00