Crystal structure of a bZIP/DNA complex at 2.2 A: determinants of DNA specific recognition.

abstract：:Elongation factor G (EF-G) is a large, five domain GTPase that catalyses the translocation of the tRNAs on the bacterial ribosome at the expense of GTP. In the crystal structure of GDP-bound EF-G, domain 1 (G domain) makes direct contacts with domains 2 and 5, whereas domain 4 protrudes from the body of the molecule. ...

journal_title：Journal of molecular biology

authors： Savelsbergh A,Matassova NB,Rodnina MV,Wintermeyer W

更新日期：2000-07-21 00:00:00

abstract：:Nudaurelia capensis omega virus is a T=4, icosahedral virus with a bipartite, positive-sense RNA genome. Expression of the coat protein gene in a baculovirus system was previously shown to result in the formation of procapsids when purified at pH 7.6. Procapsids are round, porous particles (480 A diameter) and have T=...

journal_title：Journal of molecular biology

authors： Tang J,Lee KK,Bothner B,Baker TS,Yeager M,Johnson JE

更新日期：2009-09-25 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：:DBC2 is a tumor suppressor gene linked to breast and lung cancers. Although DBC2 belongs to the RHO GTPase family, it has a unique structure that contains a Broad-Complex/Tramtrack/Bric a Brac (BTB) domain at the C terminus instead of a typical CAAX motif. A limited number of functional studies on DBC2 have indicated ...

journal_title：Journal of molecular biology

authors： Chang FK,Sato N,Kobayashi-Simorowski N,Yoshihara T,Meth JL,Hamaguchi M

更新日期：2006-12-01 00:00:00

abstract：:Mannan-binding lectin (MBL) is the archetypical pathogen recognition molecule of the innate immune defense. Upon binding to microorganisms, reactions leading to the destruction of the offender ensue. MBL is an oligomer of structural subunits each composed of three identical polypeptides. We used atomic force microscop...

journal_title：Journal of molecular biology

authors： Jensenius H,Klein DC,van Hecke M,Oosterkamp TH,Schmidt T,Jensenius JC

更新日期：2009-08-07 00:00:00

abstract：:Guanine-uracil (G.U) wobble base-pairs are a detrimental lesion in DNA. Previous investigations have shown that such wobble base-pairs are more prone to base-opening than the normal G.C base-pairs. To investigate the sequence-dependence of base-pair opening we have performed 5ns molecular dynamics simulations on G.U w...

journal_title：Journal of molecular biology

authors： Seibert E,Ross JB,Osman R

更新日期：2003-07-18 00:00:00

abstract：:We present evidence that the transcription termination factor Rho is autogenously regulated in Escherichia coli. The steady-state level of Rho is increased approximately tenfold in rho mutant cells. In the rho+ revertants, the content of Rho is similar to the wild-type level. A rho-/rho+ merodiploid produces equimolar...

journal_title：Journal of molecular biology

authors： Barik S,Bhattacharya P,Das A

更新日期：1985-04-20 00:00:00

abstract：:Assembly of infectious retroviral particles involves recognition of specific sequences on the viral RNA by the nucleocapsid (NC) domain of the Gag polyprotein, and subsequent stoichiometric binding of the processed NC protein along the entire length of the RNA. NC proteins also act as nucleic acid chaperones. They acc...

journal_title：Journal of molecular biology

authors： Urbaneja MA,Wu M,Casas-Finet JR,Karpel RL

更新日期：2002-05-03 00:00:00

abstract：:The immI region of bacteriophage P1 includes the ant/reb gene, which encodes the antirepressor protein, and the c4 gene, which encodes a repressor molecule that negatively regulates antirepressor synthesis. The antirepressor interferes with the activity of the P1 repressor of lytic function, the product of the c1 gene...

journal_title：Journal of molecular biology

authors： Heisig A,Riedel HD,Dobrinski B,Lurz R,Schuster H

更新日期：1989-10-20 00:00:00

abstract：:We have analysed the hydration of main-chain carbonyl and amide groups in 24 high-resolution well-refined protein structures as a function of the secondary structure in which these polar groups occur. We find that main-chain atoms in beta-sheets are as hydrated as those in alpha-helices, with most interactions involvi...

journal_title：Journal of molecular biology

authors： Thanki N,Umrania Y,Thornton JM,Goodfellow JM

更新日期：1991-09-20 00:00:00

abstract：:Heat shock protein 90 (Hsp90) is an ATP-dependent molecular chaperone responsible for the activation, maturation, and trafficking of several hundred client proteins in the cell. It is well known that (but not understood how) residues far away from Hsp90's nucleotide binding pocket can regulate its ATPase activity, a p...

journal_title：Journal of molecular biology

authors： Rehn A,Moroni E,Zierer BK,Tippel F,Morra G,John C,Richter K,Colombo G,Buchner J

更新日期：2016-11-06 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：:Efficient gene control by antisense RNA requires rapid bi-molecular interaction with a cognate target RNA. A comparative analysis revealed that a YUNR motif (Y=pyrimidine, R=purine) is ubiquitous in RNA recognition loops in antisense RNA-regulated gene systems. The (Y)UNR sequence motif specifies two intraloop hydroge...

journal_title：Journal of molecular biology

authors： Franch T,Petersen M,Wagner EG,Jacobsen JP,Gerdes K

更新日期：1999-12-17 00:00:00

abstract：:STRA13 is a pVHL-dependent bHLH transcription factor up-regulated on the mRNA level in multiple cancer cell lines and implicated recently in the regulation of immune cell homeostasis and autoimmunity. In searching for STRA13-interacting proteins with oncogenic potential by the yeast two-hybrid screening, we identified...

journal_title：Journal of molecular biology

authors： Ivanova AV,Ivanov SV,Zhang X,Ivanov VN,Timofeeva OA,Lerman MI

更新日期：2004-07-16 00:00:00

abstract：:We show here that the specific use of fast or slowly translated codons in the early coding region of a gene may influence both the mRNA stability and premature transcription termination. We first inserted a pair of nearly identical 42-base-pair (bp)-long sequences into codon 3 of the Escherichia coli lacZ gene. The on...

journal_title：Journal of molecular biology

authors： Pedersen S,Terkelsen TB,Eriksen M,Hauge MK,Lund CC,Sneppen K,Mitarai N

更新日期：2019-03-15 00:00:00

abstract：:To search for submolecular foldon units, the spontaneous reversible unfolding and refolding of staphylococcal nuclease under native conditions was studied by a kinetic native-state hydrogen exchange (HX) method. As for other proteins, it appears that staphylococcal nuclease is designed as an assembly of well-integrate...

journal_title：Journal of molecular biology

authors： Bédard S,Mayne LC,Peterson RW,Wand AJ,Englander SW

更新日期：2008-02-29 00:00:00

abstract：:The FNR (fumarate nitrate reduction) protein plays a central role in the global oxygen response of a variety of bacteria. In Escherichia coli, FNR is the master transcriptional regulator of the transition between aerobic and anaerobic growth. Regulation of FNR is achieved by cycling the molecule between three states i...

journal_title：Journal of molecular biology

authors： Tolla DA,Savageau MA

更新日期：2010-04-09 00:00:00

abstract：:Microglia, the resident macrophages of the central nervous system, critically influence neural function during development and in adulthood. Microglia are also profoundly sensitive to insults to the brain to which they respond with process of activation that includes spectrum of changes in morphology, function, and ge...

journal_title：Journal of molecular biology

authors： Ferro A,Sheeler C,Rosa JG,Cvetanovic M

更新日期：2019-04-19 00:00:00

abstract：:We use flexible backbone protein design to explore the sequence and structure neighborhoods of naturally occurring proteins. The method samples sequence and structure space in the vicinity of a known sequence and structure by alternately optimizing the sequence for a fixed protein backbone using rotamer based sequence...

journal_title：Journal of molecular biology

authors： Saunders CT,Baker D

更新日期：2005-02-18 00:00:00

abstract：:The G.U wobble base-pair in the acceptor helix of Escherichia coli tRNAAlais critical for aminoacylation by the alanine synthetase. Previous work by several groups probed the mechanism of enzyme recognition of G.U by a structure-function analysis of mutant tRNAs using either a cell assay (amber suppressor tRNA) or a t...

journal_title：Journal of molecular biology

authors： McClain WH,Jou YY,Bhattacharya S,Gabriel K,Schneider J

更新日期：1999-07-09 00:00:00

abstract：:Polyamines are abundant metabolites that directly influence gene expression. Although the role of polyamines in DNA condensation is well known, their role in RNA folding is less understood. Non-denaturing gel electrophoresis was used to monitor the equilibrium folding transitions of the Tetrahymena ribozyme in the pre...

journal_title：Journal of molecular biology

authors： Koculi E,Lee NK,Thirumalai D,Woodson SA

更新日期：2004-07-30 00:00:00

abstract：:Analysis of the conformational differences between the oxy and deoxy forms of hemoglobin is complicated by shifting coordinate systems and correlated motions between different parts of the molecule. Methods independent of any frame of reference were used to study the differences in structure between the oxy and deoxy ...

journal_title：Journal of molecular biology

authors： Nichols WL,Zimm BH,Ten Eyck LF

更新日期：1997-07-25 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：:To expand the repertoire of chemogenetic tools tailored for molecular and cellular engineering, we describe herein the design of cpRAPID as a circularly permuted rapamycin-inducible dimerization system composed of the canonical FK506-binding protein (FKBP) and circular permutants of FKBP12-rapamycin binding domain (cp...

journal_title：Journal of molecular biology

authors： Lee YT,He L,Zhou Y

更新日期：2020-05-01 00:00:00

abstract：:The movement of the bacterial insertion sequence IS1 often generates cointegrate structures in which donor and target replicons are connected by direct repeats of IS1. The experiments reported here were designed to understand how IS1 transposition is controlled. Our physical characterization of the structures of coint...

journal_title：Journal of molecular biology

authors： Biel SW,Adelt G,Berg DE

更新日期：1984-04-05 00:00:00

abstract：:As high-resolution cryogenic electron microscopy (cryo-EM) structures of ribosomes proliferate, at resolutions that allow atomic interactions to be visualized, this article attempts to give a perspective on the way research on ribosome structure and dynamics may be headed, and particularly the new opportunities we hav...

journal_title：Journal of molecular biology

authors： Frank J

更新日期：2016-09-11 00:00:00

abstract：:The solution structure of a DNA three-way junction (3H) containing two unpaired thymidine bases at the branch site (3HT2), was determined by NMR. Arms A and B of the 3HT2 form a quasi-continuous stacked helix, which is underwound at the junction and has an increased helical rise. The unstacked arm C forms an acute ang...

journal_title：Journal of molecular biology

authors： van Buuren BN,Overmars FJ,Ippel JH,Altona C,Wijmenga SS

更新日期：2000-12-01 00:00:00

abstract：:We have isolated cytoplasmic ribosomes from Euglena gracilis and characterized the RNA components of these particles. We show here that instead of the four rRNAs (17-19 S, 25-28 S, 5.8 S and 5 S) found in typical eukaryotic ribosomes, Euglena cytoplasmic ribosomes contain 16 RNA components. Three of these Euglena rRNA...

journal_title：Journal of molecular biology

authors： Schnare MN,Gray MW

更新日期：1990-09-05 00:00:00

abstract：:A series of DNA heptadecamers containing the DNA analogues of RNA E-like 5'-d(GXA)/(AYG)-5' motifs (X/Y is complementary T/A, A/T, C/G, or G/C pair) were studied using nuclear magnetic resonance (NMR) methodology and distance geometry (DG)/molecular dynamics (MD) approaches. Such oligomers reveal excellent resolution ...

journal_title：Journal of molecular biology

authors： Chou SH,Chin KH

更新日期：2001-09-28 00:00:00

abstract：:Electrostatic interactions appear to be important in the conformation and dynamics of DNA four-way junctions. Particularly, the Coulomb repulsion between two approaching phosphate groups at the site of strand exchange is commonly supposed to have a negative influence on the thermodynamic stability of the fully stacked...

journal_title：Journal of molecular biology

authors： Pikkemaat JA,Overmars FJ,Dreef-Tromp CM,van den Elst H,van Boom JH,Altona C

更新日期：1996-09-27 00:00:00