Crystallization and preliminary X-ray diffraction study of the ligand-binding domain of the bacterial chemotaxis-mediating aspartate receptor of Salmonella typhimurium.

abstract：:DNA structures bound to transcription factors are studied by using the crystal coordinates of complexes. Structural characteristics which are found at the sites where a protein secondary structure, an alpha-helix or a beta-sheet binds, can be understood in terms of fitting of the concave surface of the DNA major groov...

journal_title：Journal of molecular biology

authors： Suzuki M,Yagi N

更新日期：1996-02-09 00:00:00

abstract：:The hydrolytic endoribonuclease RNase E, which is widely distributed in bacteria and plants, plays key roles in mRNA degradation and RNA processing in Escherichia coli. The enzymatic activity of RNase E is contained within the conserved amino-terminal half of the 118 kDa protein, and the carboxy-terminal half organize...

journal_title：Journal of molecular biology

authors： Callaghan AJ,Aurikko JP,Ilag LL,Günter Grossmann J,Chandran V,Kühnel K,Poljak L,Carpousis AJ,Robinson CV,Symmons MF,Luisi BF

更新日期：2004-07-23 00:00:00

abstract：:Monovalent cation binding sites on nucleic acids in solution can be localized using the isotopically labeled ammonium ion (15NH4+) as a probe in high resolution NMR spectroscopy experiments. The application of this technique to a series of DNA duplexes reveals a preference for the binding of ammonium cations in the mi...

journal_title：Journal of molecular biology

authors： Hud NV,Sklenár V,Feigon J

更新日期：1999-02-26 00:00:00

abstract：:p50 protein is a member of the Y-box binding transcription factor family and is a counterpart of YB-1 protein. The generic microchip was used to analyze the sequence specificity of p50 binding to single (ss) and double-stranded (ds) oligodeoxyribonucleotides. The generic microchip contained 4,096 single-stranded octad...

journal_title：Journal of molecular biology

authors： Zasedateleva OA,Krylov AS,Prokopenko DV,Skabkin MA,Ovchinnikov LP,Kolchinsky A,Mirzabekov AD

更新日期：2002-11-15 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：:Herpesvirus proteases are essential for the production of progeny virus. They cleave the assembly protein that fills the immature capsid in order to make place for the viral DNA. The recombinant protease of the human gamma-herpesvirus Epstein-Barr virus (EBV) was expressed in Escherichia coli and purified. Circular di...

journal_title：Journal of molecular biology

authors： Buisson M,Valette E,Hernandez JF,Baudin F,Ebel C,Morand P,Seigneurin JM,Arlaud GJ,Ruigrok RW

更新日期：2001-08-03 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：:Hsp16.3, a small heat shock protein from Mycobacterium tuberculosis proposed to form specific trimer-of-trimers structures, acts as a molecular chaperone in vitro. The assembly and re-assembly mechanisms of this oligomeric protein were studied and compared using in vitro transcription/translation and denaturization/re...

journal_title：Journal of molecular biology

authors： Abulimiti A,Fu X,Gu L,Feng X,Chang Z

更新日期：2003-02-28 00:00:00

abstract：:The antibiotic thiostrepton, a thiazole-containing peptide, inhibits translation and ribosomal GTPase activity by binding directly to a limited and highly conserved region of the large subunit ribosomal RNA termed the GTPase center. We have previously used a filter binding assay to examine the binding of ribosomal pro...

journal_title：Journal of molecular biology

authors： Ryan PC,Lu M,Draper DE

更新日期：1991-10-20 00:00:00

abstract：:Actin and myosin are the two main proteins required for cell motility and muscle contraction. The structure of their strongly bound complex-rigor state-is a key for delineating the functional mechanism of actomyosin motor. Current knowledge of that complex is based on models obtained from the docking of known atomic s...

journal_title：Journal of molecular biology

authors： Oztug Durer ZA,Kamal JK,Benchaar S,Chance MR,Reisler E

更新日期：2011-11-25 00:00:00

abstract：:The majority of mitochondrial proteins can be imported into mitochondria following termination of their translation in the cytosol. Import of fumarase and several other proteins into mitochondria does not appear to occur post-translationally according to standard in vivo and in vitro assays. However, the nature of int...

journal_title：Journal of molecular biology

authors： Karniely S,Regev-Rudzki N,Pines O

更新日期：2006-04-28 00:00:00

abstract：:Theoretical methods for correlation of sequence changes and redox potential of electron transport proteins are examined using the Asn52----Ile mutation in cytochrome c as a test case. The first approach uses the protein dipoles Langevin dipoles (PDLD) method and the high resolution X-ray structures of the native and t...

journal_title：Journal of molecular biology

authors： Langen R,Brayer GD,Berghuis AM,McLendon G,Sherman F,Warshel A

更新日期：1992-04-05 00:00:00

abstract：:The papillomavirus E1 protein is essential for viral DNA replication, and phosphorylation of E1 appears to regulate protein function and DNA replication. Serine 584 of bovine papillomavirus E1 is in a conserved motif resembling a CK2 consensus site, and is phosphorylated by CK2 in vitro. Mutation of serine 584 to alan...

journal_title：Journal of molecular biology

authors： Lentz M,Zanardi T,Filzen R,Carter J,Hella M

更新日期：2002-02-22 00:00:00

abstract：:Heterodimeric transcription regulatory proteins that bind palindromic DNA sequences can potentially bind their recognition sites in two opposite orientations. The orientation of transcription factor binding can control transcriptional activity by altering interactions with proteins that bind to adjacent regulatory ele...

journal_title：Journal of molecular biology

authors： Ramirez-Carrozzi VR,Kerppola TK

更新日期：2001-01-19 00:00:00

abstract：:Subtilisin E is synthesized in Bacillus subtilis as a preprosubtilisin. The prepeptide is removed by a signal peptidase, and the propeptide is cleaved from the mature protein by the catalytic domain of subtilisin itself in an autocatalytic fashion. A six residue histidine-tag was attached to the C terminus of prosubti...

journal_title：Journal of molecular biology

authors： Volkov A,Jordan F

更新日期：1996-10-11 00:00:00

abstract：:We showed earlier that the mutation of Leu99 to alanine in bacteriophage T4 lysozyme creates an internal cavity of volume approximately 150 A(3) that binds benzene and a variety of other ligands. As such, this cavity provides an excellent target to study protein-ligand interaction. Here, we use low-temperature crystal...

journal_title：Journal of molecular biology

authors： Liu L,Baase WA,Matthews BW

更新日期：2009-01-16 00:00:00

abstract：:Site-directed mutagenesis has been used to change individual amino acids of the larvicidal 27,000 Mr delta-endotoxin of Bacillus thuringiensis var. israelensis. Basic and acidic residues have been systematically replaced by alanine, and the resulting mutant polypeptides analysed for cytolytic and larvicidal activity, ...

journal_title：Journal of molecular biology

authors： Ward ES,Ellar DJ,Chilcott CN

更新日期：1988-08-05 00:00:00

abstract：:UL9 protein and ICP8 encoded by the herpes simplex virus type 1 (HSV-1) were shown to catalyze a highly active, non-origin-dependent unwinding of DNA. UL9 protein, the HSV-1 origin binding protein, as a modest helicase activity that is greatly stimulated by the HSV-1 single strand (ss) binding protein, ICP8. Here, ele...

journal_title：Journal of molecular biology

authors： Makhov AM,Boehmer PE,Lehman IR,Griffith JD

更新日期：1996-05-24 00:00:00

abstract：:A large conformational change is observed between HIV-1 proteinase in the ligand-free state and in complexes with transition-state inhibitors. Crystal structures of this enzyme have either the flaps open for the native or ligand-free enzyme or the flaps closed for peptidomimetic ligand-bound enzyme. We describe the st...

journal_title：Journal of molecular biology

authors： Wilderspin AF,Sugrue RJ

更新日期：1994-05-27 00:00:00

abstract：:Diffraction data for alpha-chymotrypsin crystals at -10 degrees C were measured at 1.68 A resolution and refined by restrained structure-factor least-squares refinement. The two independent chymotrypsin molecules in the crystallographic asymmetric unit were refined independently. The overall structure of alpha-chymotr...

journal_title：Journal of molecular biology

authors： Tsukada H,Blow DM

更新日期：1985-08-20 00:00:00

abstract：:A cytochrome c kinetic folding intermediate was studied by hydrogen exchange (HX) pulse labeling. Advances in the technique and analysis made it possible to define the structured and unstructured regions, equilibrium stability, and kinetic opening and closing rates, all at an amino acid-resolved level. The entire N-te...

journal_title：Journal of molecular biology

authors： Krishna MM,Lin Y,Mayne L,Englander SW

更新日期：2003-11-28 00:00:00

abstract：:Lysine methylation is a key regulator of protein-protein binding. The amine group of lysine can accept up to three methyl groups, and experiments show that protein-protein binding free energies are sensitive to the extent of methylation. These sensitivities have been rationalized in terms of chemical and structural fe...

journal_title：Journal of molecular biology

authors： Rahman S,Wineman-Fisher V,Al-Hamdani Y,Tkatchenko A,Varma S

更新日期：2021-02-05 00:00:00

abstract：:MEF2 and NKX2-5 transcription factors interact with each other in cardiogenesis and are necessary for normal heart formation. Despite evidence suggesting that these two transcription factors function synergistically and possibly through direct physical interactions, molecular mechanisms by which they interact are not ...

journal_title：Journal of molecular biology

authors： Lei X,Zhao J,Sagendorf JM,Rajashekar N,Xu J,Dantas Machado AC,Sen C,Rohs R,Feng P,Chen L

更新日期：2020-09-04 00:00:00

abstract：:The product of gene C of the temperate bacteriophage P2, the immunity repressor, can be detected as a unique band eluting from phosphocellulose columns at 0.12 M-potassium phosphate when differentially labelled with a radioactive amino acid: the band is absent when phages that either have lost gene C through deletion ...

journal_title：Journal of molecular biology

authors： Lundqvist B,Bertani G

更新日期：1984-09-25 00:00:00

abstract：:Crystals of Proteus vulgaris holotryptophanase have been grown by the hanging-drop technique using polyethylene glycol 4000 as precipitant in the presence of monovalent cations K+ or Cs+. Orthorhombic crystals (P2(1)2(1)2(1)) grown with Cs+ have unit cell parameters a = 115.0 A, b = 118.2 A and c = 153.7 A and diffrac...

journal_title：Journal of molecular biology

authors： Dementieva IS,Zakomirdina LN,Sinitzina NI,Antson AA,Wilson KS,Isupov MN,Lebedev AA,Harutyunyan EH

更新日期：1994-01-14 00:00:00

abstract：:The tyrosyl-tRNA synthetases from Bacillus stearothermophilus (Bst-TyrTS) and Escherichia coli (Eco-TyrTS) are 56% identical in amino acid sequence. To map and characterize the set of interactions that makes Bst-TyrTS more stable than Eco-TyrTS, a family of nine hybrid proteins was constructed between the two enzymes....

journal_title：Journal of molecular biology

authors： Guez-Ivanier V,Hermann M,Baldwin D,Bedouelle H

更新日期：1993-11-05 00:00:00

abstract：:Bifunctional human PAPS synthetase (PAPSS) catalyzes, in a two-step process, the formation of the activated sulfate carrier 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The first reaction involves the formation of the 5'-adenosine phosphosulfate (APS) intermediate from ATP and inorganic sulfate. APS is then further p...

journal_title：Journal of molecular biology

authors： Sekulic N,Dietrich K,Paarmann I,Ort S,Konrad M,Lavie A

更新日期：2007-03-23 00:00:00

abstract：:Drosophila alcohol dehydrogenase (DADH) is an NAD+-dependent enzyme that catalyzes the oxidation of alcohols to aldehydes/ketones and that is also able to further oxidize aldehydes to their corresponding carboxylic acids. The structure of the ternary enzyme-NADH-acetate complex of the slow alleloform of Drosophila mel...

journal_title：Journal of molecular biology

authors： Benach J,Winberg JO,Svendsen JS,Atrian S,Gonzàlez-Duarte R,Ladenstein R

更新日期：2005-01-21 00:00:00

abstract：:Archaeal dual-guide box C/D small nucleolar RNA-like RNAs (sRNAs) bind three core proteins in sequential order at both terminal box C/D and internal C'/D' motifs to assemble two ribonuclear protein (RNP) complexes active in guiding nucleotide methylation. Experiments have investigated the process of box C/D sRNP assem...

journal_title：Journal of molecular biology

authors： Gagnon KT,Zhang X,Agris PF,Maxwell ES

更新日期：2006-10-06 00:00:00

abstract：:In Saccharomyces cerevisiae, the SIF2 gene product is an integral component of the Set3 complex (SET3C), an assembly of proteins with some homology to the human SMRT and N-CoR corepressor complexes. SET3C has histone deacetylase activity that is responsible for repressing a set of meiotic genes. We have determined the...

journal_title：Journal of molecular biology

authors： Cerna D,Wilson DK

更新日期：2005-08-26 00:00:00