CTL recognition of a protective immunodominant influenza A virus nucleoprotein epitope utilizes a highly restricted Vbeta but diverse Valpha repertoire: functional and structural implications.

abstract：:This study describes an algorithm that finds rho-independent transcription terminators in bacterial genomes and evaluates the accuracy of its predictions. The algorithm identifies terminators by searching for a common mRNA motif: a hairpin structure followed by a short uracil-rich region. For each terminator, an energ...

journal_title：Journal of molecular biology

authors： Ermolaeva MD,Khalak HG,White O,Smith HO,Salzberg SL

更新日期：2000-08-04 00:00:00

abstract：:Ligand-induced cross-linking of the type I interferon (IFN) receptor subunits ifnar1 and ifnar2 induces a pleiotrophic cellular response. Several studies have suggested differential signal activation by flexible recruitment of the accessory receptor subunit ifnar1. We have characterized the roles of the four Ig-like s...

journal_title：Journal of molecular biology

authors： Lamken P,Gavutis M,Peters I,Van der Heyden J,Uzé G,Piehler J

更新日期：2005-07-15 00:00:00

abstract：:Bacteriophage P1 initiates the processive packaging of its DNA at a unique site called pac. We show that a functional pac site is contained within a 161 base-pair segment of P1 EcoRI fragment 20. It extends from a position 71 base-pairs to a position 232 base-pairs from the EcoRI-22 proximal side of that fragment. The...

journal_title：Journal of molecular biology

authors： Sternberg N,Coulby J

更新日期：1987-04-05 00:00:00

abstract：:The electrostatic interactions in the channels of OmpF and PhoE porins from Escherichia coli were analysed on the basis of a macroscopic multi-dielectric model of the protein-membrane complex derived from the respective porin X-ray structures. The membrane was represented as layers of distinct dielectric constants cor...

journal_title：Journal of molecular biology

authors： Karshikoff A,Spassov V,Cowan SW,Ladenstein R,Schirmer T

更新日期：1994-07-22 00:00:00

abstract：:Drosophila projectin is an extremely large protein found within the muscle sarcomeric unit, parallel with the actin and myosin filaments. Projectin has been suggested as the elastic component of C-filaments in insect indirect flight muscles, which is consistent with its localization from the Z band to the tip of the A...

journal_title：Journal of molecular biology

authors： Southgate R,Ayme-Southgate A

更新日期：2001-11-09 00:00:00

abstract：:Protein-primed DNA polymerases form a subgroup of the eukaryotic-type DNA polymerases family, also called family B or alpha-like. A multiple amino acid sequence alignment of this subgroup of DNA polymerases led to the identification of two insertions, TPR-1 and TPR-2, in the polymerisation domain. We showed previously...

journal_title：Journal of molecular biology

authors： Dufour E,Rodríguez I,Lázaro JM,de Vega M,Salas M

更新日期：2003-08-22 00:00:00

abstract：:Non-coding RNAs play pivotal roles in bacterial signaling. However, RNAs from certain phyla (specially high-GC actinobacteria) still remain elusive. Here, by re-engineering the existing genome-wide search approach, we discover a family of structurally conserved RNAs that are present ubiquitously across actinobacteria,...

journal_title：Journal of molecular biology

authors： Mehta D,Koottathazhath A,Ramesh A

更新日期：2020-06-26 00:00:00

abstract：:Motifs N2 and N3, also referred to as switch-1 and switch-2, form part of the active site of molecular motors such as myosins and kinesins. In the case of myosin, N3 is thought to act as a gamma-phosphate sensor and moves almost 6 A relative to N2 during the catalysed turnover of ATP, opening and closing the active si...

journal_title：Journal of molecular biology

authors： Furch M,Fujita-Becker S,Geeves MA,Holmes KC,Manstein DJ

更新日期：1999-07-16 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：:Export of protein into the periplasm of Escherichia coli via the general secretory system is achieved by action of a ternary complex comprising the polypeptide ligand, the chaperone SecB and SecA, a peripheral component of the membrane translocon, which is itself an ATPase. The unfolded ligand is captured initially by...

journal_title：Journal of molecular biology

authors： Crane JM,Mao C,Lilly AA,Smith VF,Suo Y,Hubbell WL,Randall LL

更新日期：2005-10-21 00:00:00

abstract：:Factor B is a key component of the alternative pathway of complement and is cleaved by factor D into the Ba and Bb fragments in the presence of activated C3 (C3b or C3(H(2)O)). The Ba fragment contains three short consensus/complement repeat domains, while the Bb fragment contains a von Willebrand factor type A (vWF-A...

journal_title：Journal of molecular biology

authors： Hinshelwood J,Perkins SJ

更新日期：2000-09-01 00:00:00

abstract：:The group I intron from Tetrahymena thermophila is able to catalyze its own excision from a precursor RNA. The intron recognizes the splice sites through an intron-encoded sequence called the internal guide sequence, or IGS. The 5' and 3' exons are thought to align on the IGS and form a pseudoknot structure consisting...

journal_title：Journal of molecular biology

authors： Sargueil B,Tanner NK

更新日期：1993-10-20 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：:To determine the specific interaction sites of topoisomerase II within the DNA region defined by the footprint of the enzyme, we have investigated the cleavage reaction on double-stranded DNA substrates containing nicks and deletions. Topoisomerase II-mediated cleavage of the DNA substrates is suicidal as the enzyme i...

journal_title：Journal of molecular biology

authors： Alsner J,Sorensen HV,Schmidt VK,Sorensen BS,Westergaard O

更新日期：1996-06-14 00:00:00

abstract：:In actin from many species H73 is methylated, but the function of this rare post-translational modification is unknown. Although not within bonding distance, it is located close to the gamma-phosphate of the actin-bound ATP. In most crystal structures of actin, the delta1-nitrogen of the methylated H73 forms a hydroge...

journal_title：Journal of molecular biology

authors： Nyman T,Schüler H,Korenbaum E,Schutt CE,Karlsson R,Lindberg U

更新日期：2002-04-05 00:00:00

abstract：:Phosphorylation of the translation initiation factor eIF2 on Ser51 of its alpha subunit is a key event for regulation of protein synthesis in all eukaryotes. M156R, the product of the myxoma virus M156R open reading frame, has sequence similarity to eIF2alpha as well as to a family of viral proteins that bind to the i...

journal_title：Journal of molecular biology

authors： Ramelot TA,Cort JR,Yee AA,Liu F,Goshe MB,Edwards AM,Smith RD,Arrowsmith CH,Dever TE,Kennedy MA

更新日期：2002-10-04 00:00:00

abstract：:Binding of the histone (H2A, H2B) dimer with chicken erythrocyte DNA has been studied by salt-titration spectroscopy in equilibrium conditions. The circular dichroism of DNA near 275 nm is depressed by the interaction with (H2A, H2B) at low concentrations of salt. The depression increases with increasing amounts of (H...

journal_title：Journal of molecular biology

authors： Oohara I,Wada A

更新日期：1987-07-20 00:00:00

abstract：:In vitro packaging of bacteriophage SPP1 DNA into procapsids is described and the requirements of this process were determined. Combination of proheads with an extract supplying terminase, DNA and phage tails yielded up to 10(7 )viable phages per milliliter of in vitro reaction under optimized conditions. The presence...

journal_title：Journal of molecular biology

authors： Dröge A,Tavares P

更新日期：2000-02-11 00:00:00

abstract：:Formaldehyde cross-linking was used in a kinetic analysis of RNA polymerase-lacUV5 promoter interactions in open complexes (RP(o)). RP(o) quenched from 37 degrees C to 14 degrees C isomerised to a closed, competitor resistant, complex (RP(LT)). We observed that contacts of the beta' and sigma subunits with the positio...

journal_title：Journal of molecular biology

authors： Brodolin K,Buckle M

更新日期：2001-03-16 00:00:00

abstract：:Understanding the interaction of Arf and Hdm2 has recently become a central issue in cancer biology. In response to hyperproliferative signals, p14(Arf) stabilizes p53 by binding to Hdm2 and inhibits the ubiquitination and subsequent proteosome-dependent degradation of p53. The medical importance of the Arf-Hdm2-p53 r...

journal_title：Journal of molecular biology

authors： Bothner B,Lewis WS,DiGiammarino EL,Weber JD,Bothner SJ,Kriwacki RW

更新日期：2001-11-23 00:00:00

abstract：:Eukaryotic cells contain three cytoskeletal filament systems that exhibit very distinct assembly properties, supramolecular architectures, dynamic behaviour and mechanical properties. Microtubules and microfilaments are relatively stiff polar structures whose assembly is modulated by the state of hydrolysis of the bou...

journal_title：Journal of molecular biology

authors： Mücke N,Kreplak L,Kirmse R,Wedig T,Herrmann H,Aebi U,Langowski J

更新日期：2004-01-30 00:00:00

abstract：:The crystal structure of cyanovirin-N (CV-N), a protein with potent antiviral activity, was solved at 1.5 A resolution by molecular replacement using as the search model the solution structure previously determined by NMR. The crystals belong to the space group P3221 with one monomer of CV-N in each asymmetric unit. T...

journal_title：Journal of molecular biology

authors： Yang F,Bewley CA,Louis JM,Gustafson KR,Boyd MR,Gronenborn AM,Clore GM,Wlodawer A

更新日期：1999-05-07 00:00:00

abstract：:The restriction enzyme R.BbvCI cleaves duplex DNA within a seven base-pair asymmetric recognition sequence, thus: CCTCAGC/GCTGAGG-->CC--TCAGC/GC--TGAGG. We show that R.BbvCI comprises two different subunits, R(1) and R(2); that each subunit contains a catalytic site for DNA strand hydrolysis; and that these sites act ...

journal_title：Journal of molecular biology

authors： Heiter DF,Lunnen KD,Wilson GG

更新日期：2005-05-06 00:00:00

abstract：:Elastomeric proteins are molecular springs found not only in a variety of biological machines and tissues, but also in biomaterials of superb mechanical properties. Regulating the mechanical stability of elastomeric proteins is not only important for a range of biological processes, but also critical for the use of en...

journal_title：Journal of molecular biology

authors： Cao Y,Yoo T,Zhuang S,Li H

更新日期：2008-05-16 00:00:00

abstract：:The pyrogenic toxin toxic shock syndrome toxin-1 from Staphylococcus aureus is a causative agent of the toxic shock syndrome disease. It belongs to a family of proteins known as superantigens that cross-link major histocompatibility class II molecules and T-cell receptors leading to the activation of a substantial num...

journal_title：Journal of molecular biology

authors： Papageorgiou AC,Brehm RD,Leonidas DD,Tranter HS,Acharya KR

更新日期：1996-07-26 00:00:00

abstract：:Yeast display is a powerful technology for the isolation of monoclonal antibodies (mAbs) against a target antigen. Antibody libraries have been displayed on the surface of yeast as both single-chain variable fragment (scFv) and antigen binding fragment (Fab). Here, we combine these two formats to display well-characte...

journal_title：Journal of molecular biology

authors： Walker LM,Bowley DR,Burton DR

更新日期：2009-06-05 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 stochastic boundary molecular dynamics methodology is applied to the active site of the enzyme lysozyme. A comparison is made of in vacuo dynamics results from the stochastic boundary method and a full conventional molecular dynamics simulation of lysozyme. Excellent agreement between the two approaches is obtaine...

journal_title：Journal of molecular biology

authors： Brooks CL 3rd,Karplus M

更新日期：1989-07-05 00:00:00

abstract：:Four-helix bundles are identified and characterized in the subunit interfaces of protein multimers. We find that this motif occurs as often in the interfaces as in the protein monomers. Common and different characteristics demonstrated by the bundles in the two environments suggest the possible stabilization mechanism...

journal_title：Journal of molecular biology

authors： Lin SL,Tsai CJ,Nussinov R

更新日期：1995-04-21 00:00:00

abstract：:The oxazolidinone family is a new class of synthetic antibiotics that bind to the bacterial 50S ribosomal subunit. Two members of the family, linezolid and XA043, were examined for their effects on translational fidelity using a lacZ reporter gene in vivo. Both promoted highly significant frameshifting and nonsense su...

journal_title：Journal of molecular biology

authors： Thompson J,O'Connor M,Mills JA,Dahlberg AE

更新日期：2002-09-13 00:00:00