Recent advances in the molecular biology of hepatitis C virus.

Abstract:

:The Hepatitis C virus is a positive-stranded RNA virus which is the causal agent for a chronic liver infection afflicting more than 170,000,000 people world-wide. The HCV genome is approximately 9.6 kb in length and the proteome encoded is a polyprotein of a little more than 3000 amino acid residues. This polyprotein is processed by a combination of host and viral proteases into structural and non-structural proteins. The functions of most of these proteins have been established by analogy to other viruses and by sequence homology to known proteins, as well as subsequent biochemical analysis. Two of the non-structural proteins, NS4b and NS5a, are still of unknown function. The development of antivirals for this infectious agent has been hampered by the lack of robust and economical cell culture and animal infection systems. Recent progress in the molecular virology of HCV has come about due to the definition of molecular clones, which are infectious in the chimpanzee, the development of a subgenomic replicon system in Huh7 cells, and the description of a transgenic mouse model for HCV infection. Recent progress in the structural biology of the virus has led to the determination of high resolution three-dimensional structures of a number of the key virally encoded enzymes, including the NS3 protease, NS3 helicase, and NS5b RNA-dependent RNA polymerase. In some cases these structures have been determined in complex with substrates, co-factors (NS4a), and inhibitors. Finally, a variety of techniques have been used to define host factors, which may be required for HCV replication, although this work is just beginning.

journal_name

J Mol Biol

authors

Rosenberg S

doi

10.1006/jmbi.2001.5055

keywords:

subject

Has Abstract

pub_date

2001-10-26 00:00:00

pages

451-64

issue

3

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(01)95055-7

journal_volume

313

pub_type

杂志文章,评审
  • Programming microbes using pulse width modulation of optical signals.

    abstract::Cells transmit and receive information via signalling pathways. A number of studies have revealed that information is encoded in the temporal dynamics of these pathways and has highlighted how pathway architecture can influence the propagation of signals in time and space. The functional properties of pathway architec...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2013.07.036

    authors: Davidson EA,Basu AS,Bayer TS

    更新日期:2013-11-15 00:00:00

  • Crystallization and preliminary X-ray analysis of a mutant duck delta II crystallin.

    abstract::A duck delta II crystallin mutant, where histidine 178 has been replaced by an aspartic acid residue, has been purified from a bacterial expression system and subsequently crystallized. The crystals grow as flat plates, with unit cell dimensions a = 94.1 A, b = 99.9 A, c = 108.7 A and beta = 102 degrees. The crystals ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1694

    authors: Abu-Abed M,Turner MA,Atkinson J,Dole K,Howell PL

    更新日期:1994-11-11 00:00:00

  • E. coli transports aggregated proteins to the poles by a specific and energy-dependent process.

    abstract::Aggregation of proteins due to failure of quality control mechanisms is deleterious to both eukaryotes and prokaryotes. We found that in Escherichia coli, protein aggregates are delivered to the pole and form a large polar aggregate (LPA). The formation of LPAs involves two steps: the formation of multiple small aggre...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.07.009

    authors: Rokney A,Shagan M,Kessel M,Smith Y,Rosenshine I,Oppenheim AB

    更新日期:2009-09-25 00:00:00

  • Effect of N2-guanyl modifications on early steps in catalysis of polymerization by Sulfolobus solfataricus P2 DNA polymerase Dpo4 T239W.

    abstract::Translesion DNA polymerases are more efficient at bypass of many DNA adducts than replicative polymerases. Previous work with the translesion polymerase Sulfolobus solfataricus Dpo4 showed a decrease in catalytic efficiency during bypass of bulky N(2)-alkyl guanine (G) adducts with N(2)-isobutylG showing the largest e...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.11.071

    authors: Zhang H,Guengerich FP

    更新日期:2010-02-05 00:00:00

  • Structure of a Novel Dimeric SET Domain Methyltransferase that Regulates Cell Motility.

    abstract::Lysine methyltransferases (KMTs) were initially associated with transcriptional control through their methylation of histones and other nuclear proteins, but have since been found to regulate many other cellular activities. The apical complex lysine (K) methyltransferase (AKMT) of the human parasite Toxoplasma gondii ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2018.08.017

    authors: Pivovarova Y,Liu J,Lesigang J,Koldyka O,Rauschmeier R,Hu K,Dong G

    更新日期:2018-10-19 00:00:00

  • Crystal structure of the Vibrio cholerae cytolysin (VCC) pro-toxin and its assembly into a heptameric transmembrane pore.

    abstract::Pathogenic Vibrio cholerae secrete V. cholerae cytolysin (VCC), an 80 kDa pro-toxin that assembles into an oligomeric pore on target cell membranes following proteolytic cleavage and interaction with cell surface receptors. To gain insight into the activation and targeting activities of VCC, we solved the crystal stru...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.05.045

    authors: Olson R,Gouaux E

    更新日期:2005-07-29 00:00:00

  • A hybrid structural model of the complete Brugia malayi cytoplasmic asparaginyl-tRNA synthetase.

    abstract::Aminoacyl-tRNA synthetases are validated molecular targets for anti-infective drug discovery because of their essentiality in protein synthesis. Thanks to genome sequencing, it is now possible to systematically study aminoacyl-tRNA synthetases from human eukaryotic parasites as putative targets for novel drug discover...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.11.049

    authors: Crepin T,Peterson F,Haertlein M,Jensen D,Wang C,Cusack S,Kron M

    更新日期:2011-01-28 00:00:00

  • The RecG branch migration protein of Escherichia coli dissociates R-loops.

    abstract::The RuvAB and RecG proteins of Escherichia coli promote branch migration of Holliday junction intermediates in genetic recombination. Both are structure-specific helicases that unwind and rewind DNA at the junction point. The helicase activities of these proteins were investigated using RNA:DNA hybrid molecules. RuvAB...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0671

    authors: Vincent SD,Mahdi AA,Lloyd RG

    更新日期:1996-12-13 00:00:00

  • Dissecting the Conformational Dynamics of the Bile Acid Transporter Homologue ASBTNM.

    abstract::Apical sodium-dependent bile acid transporter (ASBT) catalyses uphill transport of bile acids using the electrochemical gradient of Na+ as the driving force. The crystal structures of two bacterial homologues ASBTNM and ASBTYf have previously been determined, with the former showing an inward-facing conformation, and ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2020.166764

    authors: Lu PH,Li CC,Chiang YW,Liu JH,Chiang WT,Chao YH,Li GS,Weng SE,Lin SY,Hu NJ

    更新日期:2021-01-13 00:00:00

  • Linkage of protonation and anion binding to the folding of Sac7d.

    abstract::The temperature, pH, and salt dependence of the folding of recombinant Sac7d from the hyperthermophile Sulfolobus acidocaldarius is mapped using multi-dimensional differential scanning calorimetry (DSC) and folding progress surfaces followed by circular dichroism. Linkage relations are derived to explain the observed ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.1500

    authors: McCrary BS,Bedell J,Edmondson SP,Shriver JW

    更新日期:1998-02-13 00:00:00

  • Dimer form of phosphorylated Spo0A, a transcriptional regulator, stimulates the spo0F transcription at the initiation of sporulation in Bacillus subtilis.

    abstract::The Spo0A protein of Bacillus subtilis is a transcriptional regulator that shows extensive homology to the regulator proteins in bacterial two-component regulatory systems. Phosphorylation of Spo0A is absolutely necessary for the initiation of sporulation. We now show that phospho-Spo0A is a dimer, binds specifically ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0354

    authors: Asayama M,Yamamoto A,Kobayashi Y

    更新日期:1995-06-30 00:00:00

  • High resolution crystal structures of T4 phage beta-glucosyltransferase: induced fit and effect of substrate and metal binding.

    abstract::beta-Glucosyltransferase (BGT) is a DNA-modifying enzyme encoded by bacteriophage T4 that transfers glucose from uridine diphosphoglucose to 5-hydroxymethyl cytosine bases of phage T4 DNA. We report six X-ray structures of the substrate-free and the UDP-bound enzyme. Four also contain metal ions which activate the enz...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4905

    authors: Moréra S,Larivière L,Kurzeck J,Aschke-Sonnenborn U,Freemont PS,Janin J,Rüger W

    更新日期:2001-08-17 00:00:00

  • Direct binding of glyceraldehyde 3-phosphate dehydrogenase to telomeric DNA protects telomeres against chemotherapy-induced rapid degradation.

    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

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.09.062

    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

  • A mechanistic insight into SMAC peptide interference with XIAP-Bir2 inhibition of executioner caspases.

    abstract::X-linked inhibitor of apoptosis protein (XIAP) inhibits apoptosis mainly through inhibition of caspase-9 and executioner caspases of -3 and -7. The inhibition of the former protease is implemented through the bacculoviral inhibitory repeat-3 (Bir3) domain, while the inhibition of the latter is accomplished by the inte...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.05.082

    authors: Abhari BA,Davoodi J

    更新日期:2008-09-05 00:00:00

  • RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box.

    abstract::We have used a hidden Markov model (HMM) to identify the consensus sequence of the RpoD promoters in the genome of Campylobacter jejuni. The identified promoter consensus sequence is unusual compared to other bacteria, in that the region upstream of the TATA-box does not contain a conserved -35 region, but shows a ver...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00034-2

    authors: Petersen L,Larsen TS,Ussery DW,On SL,Krogh A

    更新日期:2003-03-07 00:00:00

  • A novel disulfide bond in the SH2 Domain of the C-terminal Src kinase controls catalytic activity.

    abstract::The SH2 domain of the C-terminal Src kinase [Csk] contains a unique disulfide bond that is not present in other known SH2 domains. To investigate whether this unusual disulfide bond serves a novel function, the effects of disulfide bond formation on catalytic activity of the full-length protein and on the structure of...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.10.076

    authors: Mills JE,Whitford PC,Shaffer J,Onuchic JN,Adams JA,Jennings PA

    更新日期:2007-02-02 00:00:00

  • Use of binding site neighbor-effect parameters to evaluate the interactions between adjacent ligands on a linear lattice. Effects on ligand-lattice association.

    abstract::A method using binding site "neighbor-effect" parameters (NEPs) is introduced to evaluate the effects of interaction between adjacent ligands on their binding to an infinite linear lattice. Binding site overlap is also taken into account. This enables the conditional probability approach of McGhee & von Hippel to be e...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90262-i

    authors: Wolfe AR,Meehan T

    更新日期:1992-02-20 00:00:00

  • Folding of the Tetrahymena ribozyme by polyamines: importance of counterion valence and size.

    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

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.06.008

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

    更新日期:2004-07-30 00:00:00

  • Structure of the PilZ-FimXEAL-c-di-GMP Complex Responsible for the Regulation of Bacterial Type IV Pilus Biogenesis.

    abstract::Signal transduction pathways mediated by cyclic-bis(3'→5')-dimeric GMP (c-di-GMP) control many important and complex behaviors in bacteria. C-di-GMP is synthesized through the action of GGDEF domains that possess diguanylate cyclase activity and is degraded by EAL or HD-GYP domains with phosphodiesterase activity. The...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2013.03.021

    authors: Guzzo CR,Dunger G,Salinas RK,Farah CS

    更新日期:2013-06-26 00:00:00

  • Crystal structure of a T cell receptor Valpha11 (AV11S5) domain: new canonical forms for the first and second complementarity determining regions.

    abstract::We describe the X-ray crystallographic structure of a murine T cell receptor (TCR) Valpha domain ("Valpha85.33"; AV11S5-AJ17) to 1.85 A resolution. The Valpha85.33 domain is derived from a TCR that recognizes a type II collagen peptide associated with the murine major histocompatibility complex (MHC) class II molecule...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4794

    authors: Machius M,Cianga P,Deisenhofer J,Ward ES

    更新日期:2001-07-20 00:00:00

  • Facioscapulohumeral muscular dystrophy region gene 1 is a dynamic RNA-associated and actin-bundling protein.

    abstract::FSHD region gene 1 (FRG1) is a dynamic nuclear and cytoplasmic protein that, in skeletal muscle, shows additional localization to the sarcomere. Maintaining appropriate levels of FRG1 protein is critical for muscular and vascular development in vertebrates; however, its precise molecular function is unknown. This stud...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.06.014

    authors: Sun CY,van Koningsbruggen S,Long SW,Straasheijm K,Klooster R,Jones TI,Bellini M,Levesque L,Brieher WM,van der Maarel SM,Jones PL

    更新日期:2011-08-12 00:00:00

  • Models for the structure of outer-membrane proteins of Escherichia coli derived from raman spectroscopy and prediction methods.

    abstract::The secondary structure of porin, maltoporin and OmpA protein reconstituted in lipid membranes is determined by Raman spectroscopy. The three proteins have similar structures consisting of 50 to 60% beta-strand, about 20% beta-turn, and less than 15% alpha-helix. Employing a method for structural prediction that accou...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(86)90292-5

    authors: Vogel H,Jähnig F

    更新日期:1986-07-20 00:00:00

  • RNase E and polyadenyl polymerase I are involved in maturation of CI RNA, the P4 phage immunity factor.

    abstract::Bacteriophage P4 immunity is controlled by a small stable RNA (CI RNA) that derives from the processing of primary transcripts. In previous works, we observed that the endonuclease RNase P is required for the maturation of CI RNA 5'-end; moreover, we found that polynucleotide phosphorylase (PNPase), a 3' to 5' RNA-deg...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/S0022-2836(02)00085-2

    authors: Briani F,Del Vecchio E,Migliorini D,Hajnsdorf E,Régnier P,Ghisotti D,Dehò G

    更新日期:2002-04-26 00:00:00

  • Insights into strand exchange in BTB domain dimers from the crystal structures of FAZF and Miz1.

    abstract::The BTB domain is a widely distributed protein-protein interaction motif that is often found at the N-terminus of zinc finger transcription factors. Previous crystal structures of BTB domains have revealed tightly interwound homodimers, with the N-terminus from one chain forming a two-stranded anti-parallel beta-sheet...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.05.028

    authors: Stogios PJ,Cuesta-Seijo JA,Chen L,Pomroy NC,Privé GG

    更新日期:2010-07-30 00:00:00

  • Capsid targeting sequence targets foreign proteins into bacteriophage T4 and permits proteolytic processing.

    abstract::A membrane-independent morphogenetic viral signal peptide is identified within bacteriophage T4 internal protein III (IPIII). Utilizing a phagederived expression-packaging-processing system, which packages foreign proteins fused with IPIII into the phage capsid, a synthetic cleavage site introduced at the C terminus o...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0470

    authors: Mullaney JM,Black LW

    更新日期:1996-08-23 00:00:00

  • The structure of Mycobacterium tuberculosis MPT51 (FbpC1) defines a new family of non-catalytic alpha/beta hydrolases.

    abstract::Mycobacterium tuberculosis, the causative agent of tuberculosis, is known to secrete a number of highly immunogenic proteins that are thought to confer pathogenicity, in part, by mediating binding to host tissues. Among these secreted proteins are the trimeric antigen 85 (Ag85) complex and the related MPT51 protein, a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.11.001

    authors: Wilson RA,Maughan WN,Kremer L,Besra GS,Fütterer K

    更新日期:2004-01-09 00:00:00

  • The N-terminal domains of myosin binding protein C can bind polymorphically to F-actin.

    abstract::The regulation of vertebrate striated muscle contraction involves a number of different molecules, including the thin-filament accessory proteins tropomyosin and troponin that provide Ca(2+)-dependent regulation by controlling access to myosin binding sites on actin. Cardiac myosin binding protein C (cMyBP-C) appears ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.07.056

    authors: Orlova A,Galkin VE,Jeffries CM,Egelman EH,Trewhella J

    更新日期:2011-09-23 00:00:00

  • ADP-binding to origin recognition complex of Saccharomyces cerevisiae.

    abstract::The origin recognition complex (ORC), a possible initiator of chromosomal DNA replication in eukaryotes, binds to ATP through its subunits Orc1p and Orc5p. Orc1p possesses ATPase activity. As for DnaA, the Escherichia coli initiator, the ATP-DnaA complex is active but the ADP-DnaA complex is inactive for DNA replicati...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.04.045

    authors: Takenaka H,Makise M,Kuwae W,Takahashi N,Tsuchiya T,Mizushima T

    更新日期:2004-06-25 00:00:00

  • Both N-Terminal and C-Terminal Histidine Residues of the Prion Protein Are Essential for Copper Coordination and Neuroprotective Self-Regulation.

    abstract::The cellular prion protein (PrPC) comprises two domains: a globular C-terminal domain and an unstructured N-terminal domain. Recently, copper has been observed to drive tertiary contact in PrPC, inducing a neuroprotective cis interaction that structurally links the protein's two domains. The location of this interacti...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2020.05.020

    authors: Schilling KM,Tao L,Wu B,Kiblen JTM,Ubilla-Rodriguez NC,Pushie MJ,Britt RD,Roseman GP,Harris DA,Millhauser GL

    更新日期:2020-07-24 00:00:00

  • Inverting enantioselectivity of Burkholderia cepacia KWI-56 lipase by combinatorial mutation and high-throughput screening using single-molecule PCR and in vitro expression.

    abstract::The enantioselectivity of lipase from Burkhorderia cepacia KWI-56 has been inverted using a novel in vitro technique for construction and screening of a protein library by single-molecule DNA amplification by PCR followed by in vitro coupled transcription/translation system termed single-molecule-PCR-linked in vitro e...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00782-4

    authors: Koga Y,Kato K,Nakano H,Yamane T

    更新日期:2003-08-15 00:00:00