HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins.

abstract：:The p127 tumor suppressor protein encoded by the lethal(2)giant larvae, l(2)gl, gene of Drosophila melanogaster forms high molecular mass complexes consisting predominantly of p127 molecules. To determine whether p127 can self-assemble in the absence of other binding factors, we analyzed the size of in vitro synthesiz...

journal_title：Journal of molecular biology

authors： Jakobs R,de Lorenzo C,Spiess E,Strand D,Mechler BM

更新日期：1996-12-06 00:00:00

abstract：:The hydrogen exchange behaviour of two stabilised disulfide mutants of barnase has been examined using NMR H/2H exchange measurements. The choice of experimental conditions is crucial in experiments to study the effects of mutations on local and global stability and dynamic behaviour of proteins. If exchange condition...

journal_title：Journal of molecular biology

authors： Clarke J,Hounslow AM,Fersht AR

更新日期：1995-10-27 00:00:00

abstract：:We have produced and characterized two new copper-transporting ATPases, CtrA2 and CtrA3 from Aquifex aeolicus, that belong to the family of heavy metal ion-transporting P(IB)-type ATPases. CtrA2 has a CPC metal-binding sequence in TM6 and a CxxC metal-binding N-terminal domain, while CtrA3 has a CPH metal-binding moti...

journal_title：Journal of molecular biology

authors： Chintalapati S,Al Kurdi R,van Scheltinga AC,Kühlbrandt W

更新日期：2008-05-02 00:00:00

abstract：:Using purified sigma 55 RNA polymerase from Bacillus subtilis in an in vitro transcription system, we have shown that both promoters and terminators of Gram negative origin are recognized by this enzyme. Furthermore, when B. subtilis is transformed with a shuttle vector containing certain of these promoters, synthesis...

journal_title：Journal of molecular biology

authors： Peschke U,Beuck V,Bujard H,Gentz R,Le Grice S

更新日期：1985-12-05 00:00:00

abstract：:The Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (CYT-18 protein) functions in splicing group I introns by promoting the formation of the catalytically active structure of the intron's catalytic core. Previous studies suggested a model in which the protein binds first to the intron's P4-P6 domain, and then ...

journal_title：Journal of molecular biology

authors： Caprara MG,Myers CA,Lambowitz AM

更新日期：2001-04-27 00:00:00

abstract：:Solid-state 2H nuclear magnetic resonance line shapes have been obtained from folded films of oriented Li-DNA molecules with the purine bases selectively labeled with deuterium at the 8-position. From line shape simulations, the static base tilts as well as the anisotropic motional amplitudes were determined as a func...

journal_title：Journal of molecular biology

authors： Brandes R,Vold RR,Kearns DR,Rupprecht A

更新日期：1988-07-20 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：:Nucleocapsid assembly is an essential process in the replication of the non-segmented, negative-sense RNA viruses (NNVs). Unassembled nucleoprotein (N(0)) is maintained in an RNA-free and monomeric form by its viral chaperone, the phosphoprotein (P), forming the N(0)-P complex. Our earlier work solved the structure of...

journal_title：Journal of molecular biology

authors： Yabukarski F,Leyrat C,Martinez N,Communie G,Ivanov I,Ribeiro EA Jr,Buisson M,Gerard FC,Bourhis JM,Jensen MR,Bernadó P,Blackledge M,Jamin M

更新日期：2016-07-03 00:00:00

abstract：:Cathepsin D was purified from bovine liver by a method using two pepstatin A affinity columns. The eluted protein was combined with pepstatin A and the complex crystallized from 15% polyethylene glycol 8000 at pH 5.9. The crystals diffract to a resolution of 3.0 A and have space group P2(1)2(1)2(1) with unit cell dime...

journal_title：Journal of molecular biology

authors： Bieber F,Brachvogel V,Arni R,Fusek M,Metcalf P

更新日期：1992-10-20 00:00:00

abstract：:Peptide deformylases (PDFs) are essential enzymes of the N-terminal protein processing pathway of eubacteria. The recent discovery of two types of PDFs in higher plants, PDF1A and PDF1B, and the detection of PDF1A in humans, have raised questions concerning the importance of deformylation in eukaryotes. Here, we have ...

journal_title：Journal of molecular biology

authors： Serero A,Giglione C,Meinnel T

更新日期：2001-12-07 00:00:00

abstract：:Collagen fibrils are the principle source of mechanical strength in the mutable dermis of the sea cucumber Cucumaria frondosa. To obtain information about the mechanism by which collagen molecules self-assemble into fibrils, we have isolated single intact fibrils with lengths in the range 14-444 microm. These fibrils ...

journal_title：Journal of molecular biology

authors： Trotter JA,Chapman JA,Kadler KE,Holmes DF

更新日期：1998-12-18 00:00:00

abstract：:The 231-residue capsid (CA) protein of human immunodeficiency virus type 1 (HIV-1) spontaneously self-assembles into tubes with a hexagonal lattice that is believed to mimic the surface lattice of conical capsid cores within intact virions. We report the results of solid-state nuclear magnetic resonance (NMR) measurem...

journal_title：Journal of molecular biology

authors： Bayro MJ,Chen B,Yau WM,Tycko R

更新日期：2014-03-06 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：:We previously reported that in Micrococcus luteus, a Gram-positive eubacterium with high genomic G + C content, certain codons ending with A did not appear in coding frames, including termination sites, and tRNAs that translate these codons were not detected. These facts suggest that at least some of them are unassign...

journal_title：Journal of molecular biology

authors： Kano A,Ohama T,Abe R,Osawa S

更新日期：1993-03-05 00:00:00

abstract：:The entire DNA of Rhizobium meliloti MVII /1 cells was isolated preparatively by gentle lysis and sucrose gradient centrifugation. Fractions of the sucrose gradient were investigated by electron microscopy. We found intact megaplasmids in supercoiled and relaxed form and total chromosomes. The length of the megaplasmi...

journal_title：Journal of molecular biology

authors： Burkardt B,Burkardt HJ

更新日期：1984-05-15 00:00:00

abstract：:Three-dimensional domain swapping has emerged as a ubiquitous process for homo-oligomer formation in many unrelated proteins, but the molecular mechanism of this process is still poorly understood. Here we present a mechanism for the swapping reaction in the B1 domain of the immunoglobulin G binding protein from group...

journal_title：Journal of molecular biology

authors： Malevanets A,Sirota FL,Wodak SJ

更新日期：2008-09-26 00:00:00

abstract：:The ribosomal RNA multigene family in the fungus fly Sciara coprophila contains a total of only 65 to 70 repeat units. We explored the types and frequencies of variant repeats in this small multigene family by characterizing different cloned rDNA variants from Sciara. Although we did not observe any intergenic spacer ...

journal_title：Journal of molecular biology

authors： Kerrebrock AW,Srivastava R,Gerbi SA

更新日期：1989-11-05 00:00:00

abstract：:The evolution of new or improved enzyme specificities in prokaryotes has been proposed to involve gene duplication, followed by silencing of one of the duplicates at the transcriptional or translational level. Such "silent gene intermediates" are distinct from "cryptic" genes, which are proposed to have a different ro...

journal_title：Journal of molecular biology

authors： Burns DM,Beacham IR

更新日期：1986-11-20 00:00:00

abstract：:Plasmids were constructed in which a HindIII fragment of rDNA (6.4 x 10(3) base-pairs) was inserted into vectors pGEM-1 and 2 in both orientations. The DNA insert encoded the yeast 35 S precursor rRNA beginning 180 bases upstream from the 5' end of the mature 18 S rRNA and ending 289 bases beyond the 3' end of the mat...

journal_title：Journal of molecular biology

authors： Thweatt R,Lee JC

更新日期：1990-01-20 00:00:00

abstract：:A dynamic structure refinement method for X-ray crystallography, referred to as the normal mode refinement, is proposed. The Debye-Waller factor is expanded in terms of the low-frequency normal modes whose amplitudes and eigenvectors are experimentally optimized in the process of the crystallographic refinement. In th...

journal_title：Journal of molecular biology

authors： Kidera A,Go N

更新日期：1992-05-20 00:00:00

abstract：:Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a glycolytic enzyme that displays several non-glycolytic activities, including the maintenance and/or protection of telomeres. In this study, we determined the molecular mechanism and biological role of the interaction between GAPDH and human telomeric DNA. Using gel...

journal_title：Journal of molecular biology

authors： Demarse NA,Ponnusamy S,Spicer EK,Apohan E,Baatz JE,Ogretmen B,Davies C

更新日期：2009-12-11 00:00:00

abstract：:The X-ray structures of two hemoglobins (Hb) from the sea cucumber Caudina arenicola (an echinoderm) have been determined: a low spin, hemichrome, monomeric Hb-C chain, and a cyanomet-liganded dimeric Hb-D chain. Attempts to obtain crystal structures of the deoxy-liganded and hemichrome forms from the same chain type ...

journal_title：Journal of molecular biology

authors： Mitchell DT,Kitto GB,Hackert ML

更新日期：1995-08-18 00:00:00

abstract：:The folding pathways of four mutants in which bulky hydrophobic residues in the B helix of apomyoglobin (ApoMb) are replaced by alanine (I28A, L29A, I30A, and L32A) have been analyzed using equilibrium and kinetic methods employing NMR, CD, fluorescence and mass spectrometry. Hydrogen exchange pulse-labeling followed ...

journal_title：Journal of molecular biology

authors： Nishimura C,Wright PE,Dyson HJ

更新日期：2003-11-21 00:00:00

abstract：:Syk is an essential non-receptor tyrosine kinase in intracellular immunological signaling, and the control of Syk kinase function is considered as a valuable target for pharmacological intervention in autoimmune or inflammation diseases. Upon immune receptor stimulation, the kinase activity of Syk is regulated by bind...

journal_title：Journal of molecular biology

authors： Grädler U,Schwarz D,Dresing V,Musil D,Bomke J,Frech M,Greiner H,Jäkel S,Rysiok T,Müller-Pompalla D,Wegener A

更新日期：2013-01-23 00:00:00

abstract：:A Rhizobium meliloti DNA region (nodD1) involved in the regulation of other early nodulation genes has been delimited by directed Tn5 mutagenesis and its nucleotide sequence has been determined. The sequence data indicate a large open reading frame with opposite polarity to nodA, -B and -C, coding for a protein of 308...

journal_title：Journal of molecular biology

authors： Göttfert M,Horvath B,Kondorosi E,Putnoky P,Rodriguez-Quiñones F,Kondorosi A

更新日期：1986-10-05 00:00:00

abstract：:Mature TGF-beta isoforms, which are covalent dimers, signal by binding to three types of cell surface receptors, the type I, II and III TGF-beta receptors. A complex composed of the TGF-beta ligand and the type I and II receptors is required for signaling. The type II receptor is responsible for recruiting TGF-beta in...

journal_title：Journal of molecular biology

authors： De Crescenzo G,Pham PL,Durocher Y,O'Connor-McCourt MD

更新日期：2003-05-16 00:00:00

abstract：:Hsp110 proteins act as nucleotide exchange factors of the molecular chaperone Hsp70 in eukaryotes. In addition, they have been reported to stabilize unfolded proteins for subsequent refolding. Hsp110 proteins belong to the Hsp70 superfamily and, in analogy to Hsp70, the substrate-binding site was proposed to be locate...

journal_title：Journal of molecular biology

authors： Polier S,Hartl FU,Bracher A

更新日期：2010-09-03 00:00:00

abstract：:In the absence of nucleotides or cofactors, the Escherichia coli chaperonin GroEL binds select proteins in non-native conformations, such as denatured glutamine synthetase (GS) monomers, preventing their aggregation and spontaneous renaturation. The nature of the GroEL-GS complexes thus formed, specifically the effect...

journal_title：Journal of molecular biology

authors： Falke S,Fisher MT,Gogol EP

更新日期：2001-05-11 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：:Although the transcript level of inducible heat shock protein 70.3 (Hsp70.3, also known as Hspa1a) is altered in various disease states, its transcriptional regulation remains incompletely understood. Here, we systematically analyzed the Hspa1a promoter to identify major cis elements and transcription factors that may...

journal_title：Journal of molecular biology

authors： Sasi BK,Sonawane PJ,Gupta V,Sahu BS,Mahapatra NR

更新日期：2014-01-09 00:00:00