Force-induced conformational change of bacteriorhodopsin.

abstract：:The mechanism of inhibition of the transcriptional activator nuclear factor kappaB (NF-kappaB) by the inhibitor IkappaB* is central to the understanding of the control of transcriptional activity via this widely employed pathway. Previous studies suggested that IkappaB* , a modular protein with an NF-kappaB binding do...

journal_title：Journal of molecular biology

authors： Sue SC,Cervantes C,Komives EA,Dyson HJ

更新日期：2008-07-25 00:00:00

abstract：:Membrane protein biogenesis in bacteria occurs via dedicated molecular systems SecYEG and YidC that function independently and in cooperation. YidC belongs to the universally conserved Oxa1/Alb3/YidC family of membrane insertases and is believed to associate with translating ribosomes at the membrane surface. Here, we...

journal_title：Journal of molecular biology

authors： Kedrov A,Sustarsic M,de Keyzer J,Caumanns JJ,Wu ZC,Driessen AJ

更新日期：2013-11-15 00:00:00

abstract：:The ATPase activity of acto-myosin subfragment 1 (S1) at low ratios of S1 to actin in the presence of tropomyosin is dependent on the tropomyosin source and ionic conditions. Whereas skeletal muscle tropomyosin causes a 60% inhibitory effect at all ionic strengths, the effect of smooth muscle tropomyosin was found to ...

journal_title：Journal of molecular biology

authors： Popp D,Holmes KC

更新日期：1992-03-05 00:00:00

abstract：:The coat protein of positive-stranded RNA viruses often contains a positively charged tail that extends toward the center of the capsid and interacts with the viral genome. Electrostatic interaction between the tail and the RNA has been postulated as a major force in virus assembly and stabilization. The goal of this ...

journal_title：Journal of molecular biology

authors： Ni P,Wang Z,Ma X,Das NC,Sokol P,Chiu W,Dragnea B,Hagan M,Kao CC

更新日期：2012-06-22 00:00:00

abstract：:One mechanism for the repair of UV-induced DNA damage is the base excision repair pathway. The initial step in this pathway and the specificity for the type of damage that is to be repaired reside in DNA glycosylase/abasic (AP) lyases. Cleavage of the glycosyl bond of the 5' pyrimidine of a cyclobutane pyrimidine dime...

journal_title：Journal of molecular biology

authors： Garvish JF,Lloyd RS

更新日期：2000-01-21 00:00:00

abstract：:The structure of recombinant tick anticoagulant peptide (rTAP) complexed to bovine factor Xa at 3.0 A resolution reveals the structural basis for the specificity and the high affinity of rTAP. Three N-terminal residues, Tyr501, Asn502 and Arg503, play a critical role in the complex formation as suggested by earlier mu...

journal_title：Journal of molecular biology

authors： Wei A,Alexander RS,Duke J,Ross H,Rosenfeld SA,Chang CH

更新日期：1998-01-01 00:00:00

abstract：:An effective strategy for a plasmid to be maintained in a growing population of bacteria is to prevent the proliferation of newly formed daughter cells that lack the plasmid. In this study, we determined that the promiscuous, incompatibility group P plasmid RK2 encodes such a system. To induce large numbers of RK2-fre...

journal_title：Journal of molecular biology

authors： Jovanovic OS,Ayres EK,Figurski DH

更新日期：1994-03-18 00:00:00

abstract：:An essential step in the replication cycle of all retroviruses is the dimerization of genomic RNA prior to or during encapsidation and budding. In HIV-1, a stem-loop structure in the genomic RNA called the dimerization initiation site, or DIS, has been well characterized. However, the identification of the structure(s...

journal_title：Journal of molecular biology

authors： Lanchy JM,Lodmell JS

更新日期：2002-06-07 00:00:00

abstract：:The GTPase Center (GAC) RNA domain in bacterial 23S rRNA is directly bound by ribosomal protein L11, and this complex is essential to ribosome function. Previous cocrystal structures of the 58-nucleotide GAC RNA bound to L11 revealed the intricate tertiary fold of the RNA domain, with one monovalent and several divale...

journal_title：Journal of molecular biology

authors： Welty R,Rau M,Pabit S,Dunstan MS,Conn GL,Pollack L,Hall KB

更新日期：2020-02-14 00:00:00

abstract：:The serendipitous observation of a C-H cdots, three dots, centered O hydrogen bond mediated polypeptide chain reversal in synthetic peptide helices has led to a search for the occurrence of a similar motif in protein structures. From a dataset of 634 proteins, 1304 helices terminating in a Schellman motif have been ex...

journal_title：Journal of molecular biology

authors： Madan Babu M,Kumar Singh S,Balaram P

更新日期：2002-09-27 00:00:00

abstract：:Riboswitches are complex folded RNA domains found in noncoding regions of mRNA that regulate gene expression upon small molecule binding. Recently, Breaker and coworkers reported a tandem aptamer riboswitch (VCI-II) that binds glycine cooperatively. Here, we use hydroxyl radical footprinting and small-angle X-ray scat...

journal_title：Journal of molecular biology

authors： Lipfert J,Das R,Chu VB,Kudaravalli M,Boyd N,Herschlag D,Doniach S

更新日期：2007-02-02 00:00:00

abstract：:Switching between the active (ATP and DNA bound) and inactive conformations of the homologous recombination RecA protein is regulated by ATP hydrolysis. First, we use the homologous pairing domain of RecA derived from its mobile loop L2 to show that the interaction of this random coil peptide with the gamma-phosphate ...

journal_title：Journal of molecular biology

authors： Voloshin ON,Wang L,Camerini-Otero RD

更新日期：2000-11-10 00:00:00

abstract：:A new crystal form of the bovine oligomeric lens protein beta B2 has been grown in the presence of calcium acetate. The crystals are orthorhombic, I222 or I2(1)2(1)2(1), with cell dimensions a = 77.8 A, b = 83.6 A, c = 109.2 A. This new crystal form, which diffracts to at least 2.5 A, has a and b cell dimensions that ...

journal_title：Journal of molecular biology

authors： Bax B,Slingsby C

更新日期：1989-08-20 00:00:00

abstract：:The mRNA-capping process starts with the conversion of a 5'-triphosphate end into a 5'-diphosphate by an RNA triphosphatase, followed by the addition of a guanosine monophosphate unit in a 5'-5' phosphodiester bond by a guanylyltransferase. Methyltransferases are involved in the third step of the process, transferring...

journal_title：Journal of molecular biology

authors： Bollati M,Milani M,Mastrangelo E,Ricagno S,Tedeschi G,Nonnis S,Decroly E,Selisko B,de Lamballerie X,Coutard B,Canard B,Bolognesi M

更新日期：2009-01-09 00:00:00

abstract：:SHP, the capsid-stabilizing protein of lambdoid phage 21, is highly resistant against denaturant-induced unfolding. We demonstrate that this high functional stability of SHP is due to a high kinetic stability with a half-life for unfolding of 25 days at zero denaturant, while the thermodynamic stability is not unusual...

journal_title：Journal of molecular biology

authors： Forrer P,Chang C,Ott D,Wlodawer A,Plückthun A

更新日期：2004-11-12 00:00:00

abstract：:The x-ray structure of LeuT, a bacterial homologue of Na(+)/Cl(-)-dependent neurotransmitter transporters, provides a great opportunity to better understand the molecular basis of monovalent cation selectivity in ion-coupled transporters. LeuT possesses two ion binding sites, NA1 and NA2, which are highly selective fo...

journal_title：Journal of molecular biology

authors： Noskov SY,Roux B

更新日期：2008-03-28 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：:Exocyclic DNA adducts are formed from metabolites of chemical carcinogens and have also been detected as endogenous lesions in human DNA. The exocyclic adduct 3,N(4)-etheno-2'-deoxycytidine (epsilon dC), positioned opposite deoxyguanosine in the B-form duplex of the dodecanucleotide d(CGCGAATTepsilonCGCG), has been cr...

journal_title：Journal of molecular biology

authors： Freisinger E,Fernandes A,Grollman AP,Kisker C

更新日期：2003-06-13 00:00:00

abstract：:The junction-resolving enzymes are a class of nucleases that introduce paired cleavages into four-way DNA junctions. They are important in DNA recombination and repair, and are found throughout nature, from eubacteria and their bacteriophages through to higher eukaryotes and their viruses. These enzymes exhibit struct...

journal_title：Journal of molecular biology

authors： White MF,Giraud-Panis MJ,Pöhler JR,Lilley DM

更新日期：1997-06-27 00:00:00

abstract：:The sigma N class of sigma factors confer upon RNA polymerase the requirement for enhancer-binding activator proteins. The sigma-N (sigma N) protein of Klebsiella pneumoniae was analysed by the assay of purified peptides comprising domains or regions of sigma N defined by proteolysis or by homology alignment, respecti...

journal_title：Journal of molecular biology

authors： Cannon W,Missailidis S,Smith C,Cottier A,Austin S,Moore M,Buck M

更新日期：1995-05-12 00:00:00

abstract：:Urtica dioica agglutinin is a small plant lectin that binds chitin. We purified the isolectin VI (UDA-VI) and crystal structures of the isolectin and its complex with tri-N-acetylchitotriose (NAG3) were determined by X-ray analysis. The UDA-VI consists of two domains analogous to hevein and the backbone folding of eac...

journal_title：Journal of molecular biology

authors： Harata K,Muraki M

更新日期：2000-03-31 00:00:00

abstract：:Simocyclinone D8 (SD8), a potent DNA gyrase inhibitor made by Streptomyces antibioticus, is exported from the producing organism by the SimX efflux pump. The expression of simX is under the control of SimR, a member of the TetR family of transcriptional regulators. SimR represses simX transcription by binding to opera...

journal_title：Journal of molecular biology

authors： Le TB,Stevenson CE,Fiedler HP,Maxwell A,Lawson DM,Buttner MJ

更新日期：2011-04-22 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：:RNAs with interesting secondary and tertiary structures tend to melt in several broad and overlapping transitions over a wide temperature range, and it has been consequently difficult to resolve the thermodynamics of individual unfolding steps. In the case that a ligand selectively binds a single folded state of the R...

journal_title：Journal of molecular biology

authors： Draper DE,Xing Y,Laing LG

更新日期：1995-06-02 00:00:00

abstract：:The amino acid sequence of glycolate oxidase from spinach has been fitted to an electron density map of 2.0 A nominal resolution and the structure has been refined using the restrained parameter least-squares refinement of Hendrickson and Konnert. A final crystallographic R-factor of 18.9% was obtained for 32,888 inde...

journal_title：Journal of molecular biology

authors： Lindqvist Y

更新日期：1989-09-05 00:00:00

abstract：:Contact-dependent growth inhibition (CDI) is a widespread mechanism of inter-bacterial competition mediated by the CdiB/CdiA family of two-partner secretion proteins. CdiA effectors carry diverse C-terminal toxin domains (CdiA-CT), which are delivered into neighboring target cells to inhibit growth. CDI(+) bacteria al...

journal_title：Journal of molecular biology

authors： Morse RP,Willett JL,Johnson PM,Zheng J,Credali A,Iniguez A,Nowick JS,Hayes CS,Goulding CW

更新日期：2015-11-20 00:00:00

abstract：:Biogenesis of β-barrel membrane proteins is a complex, multistep, and as yet incompletely characterized process. The bacterial porin family is perhaps the best-studied protein family among β-barrel membrane proteins that allows diffusion of small solutes across the bacterial outer membrane. In this study, we have iden...

journal_title：Journal of molecular biology

authors： Naveed H,Jimenez-Morales D,Tian J,Pasupuleti V,Kenney LJ,Liang J

更新日期：2012-05-25 00:00:00

abstract：:Murine beta-nerve growth factor (beta NGF) is a 118 amino acid residue polypeptide which, as a functional dimer, plays an important role in the survival and development of certain neuronal populations. The structure of the bis-desocta1-8 form of murine beta NGF has been determined in two different crystal modification...

journal_title：Journal of molecular biology

authors： Holland DR,Cousens LS,Meng W,Matthews BW

更新日期：1994-06-10 00:00:00

abstract：:E. coli single strand (ss) DNA binding protein (SSB) is an essential protein that binds to ssDNA intermediates formed during genome maintenance. SSB homotetramers bind ssDNA in several modes that differ in occluded site size and cooperativity. High "unlimited" cooperativity is associated with the 35 site size ((SSB)35...

journal_title：Journal of molecular biology

authors： Kozlov AG,Shinn MK,Weiland EA,Lohman TM

更新日期：2017-09-01 00:00:00

abstract：:The attempt is made to find new correlations between local structural characteristics of proteins and the hydrogen exchange rates of their individual main-chain amides, and to relate such correlations to possible mechanisms of hydrogen exchange. It is found that in bovine pancreatic trypsin inhibitor (BPTI) the surfac...

journal_title：Journal of molecular biology

authors： Rashin AA

更新日期：1987-11-20 00:00:00