abstract：:RIG-I-like receptors (RLRs) are nucleic acid sensors that activate antiviral innate immune response. These molecules recognize diverse non-self RNA substrates and are antagonized by several viral inhibitors. We performed an evolutionary analysis of RLR genes (RIG-I, MDA5, and LGP2) in mammals. Results indicated that p...

journal_title：Journal of molecular biology

authors： Cagliani R,Forni D,Tresoldi C,Pozzoli U,Filippi G,Rainone V,De Gioia L,Clerici M,Sironi M

更新日期：2014-03-20 00:00:00

abstract：:The intracellular innate antiviral response in human cells is an essential component of immunity against virus infection. As obligate intracellular parasites, all viruses must evade the actions of the host cell's innate immune response in order to replicate and persist. Innate immunity is induced when pathogen recogni...

journal_title：Journal of molecular biology

authors： Rustagi A,Gale M Jr

更新日期：2014-03-20 00:00:00

abstract：:Herpes simplex viruses (HSVs) are human pathogens that establish lytic and latent infections. Reactivation from latency occurs intermittently, which represents a lifelong source of recurrent infection. In this complex process, HSV triggers and neutralizes innate immunity. Therefore, a dynamic equilibrium between HSV a...

journal_title：Journal of molecular biology

authors： Ma Y,He B

更新日期：2014-03-20 00:00:00

abstract：:The HIV gp41 protein catalyzes fusion between viral and target cell membranes. Although the ~20-residue N-terminal fusion peptide (FP) region is critical for fusion, the structure of this region is not well characterized in large gp41 constructs that model the gp41 state at different times during fusion. This paper de...

journal_title：Journal of molecular biology

authors： Sackett K,Nethercott MJ,Zheng Z,Weliky DP

更新日期：2014-03-06 00:00:00

abstract：:The 231-residue capsid (CA) protein of human immunodeficiency virus type 1 (HIV-1) spontaneously self-assembles into tubes with a hexagonal lattice that is believed to mimic the surface lattice of conical capsid cores within intact virions. We report the results of solid-state nuclear magnetic resonance (NMR) measurem...

journal_title：Journal of molecular biology

authors： Bayro MJ,Chen B,Yau WM,Tycko R

更新日期：2014-03-06 00:00:00

abstract：:Polyglutamine (polyQ) amyloid fibrils are observed in disease tissue and have been implicated as toxic agents responsible for neurodegeneration in expanded CAG repeat diseases such as Huntington's disease. Despite intensive efforts, the mechanism of amyloid toxicity remains unknown. As a novel approach to probing poly...

journal_title：Journal of molecular biology

authors： Kar K,Arduini I,Drombosky KW,van der Wel PC,Wetzel R

更新日期：2014-02-20 00:00:00

abstract：:Ras GTPase mediates several cellular signal transduction pathways and is found mutated in a large number of cancers. It is active in the GTP-bound state, where it interacts with effector proteins, and at rest in the GDP-bound state. The catalytic domain is tethered to the membrane, with which it interacts in a nucleot...

journal_title：Journal of molecular biology

authors： Kearney BM,Johnson CW,Roberts DM,Swartz P,Mattos C

更新日期：2014-02-06 00:00:00

abstract：:MgtR, a highly hydrophobic peptide expressed in Salmonella enterica serovar Typhimurium, inhibits growth in macrophages through binding to the membrane protein MgtC that has been identified as essential for replication in macrophages. While the Mycobacterium tuberculosis MgtC is highly homologous to its S. Typhi analo...

journal_title：Journal of molecular biology

authors： Jean-Francois FL,Dai J,Yu L,Myrick A,Rubin E,Fajer PG,Song L,Zhou HX,Cross TA

更新日期：2014-01-23 00:00:00

abstract：:Light chain amyloidosis is a devastating disease where immunoglobulin light chains form amyloid fibrils, resulting in organ dysfunction and death. Previous studies have shown a direct correlation between the protein thermodynamic stability and the propensity for amyloid formation for some proteins involved in light ch...

journal_title：Journal of molecular biology

authors： Blancas-Mejía LM,Tischer A,Thompson JR,Tai J,Wang L,Auton M,Ramirez-Alvarado M

更新日期：2014-01-23 00:00:00

abstract：:The recombination directionality factor, Xis, is a DNA bending protein that determines the outcome of integrase-mediated site-specific recombination by redesign of higher-order protein-DNA architectures. Although the attachment site DNA of mycobacteriophage Pukovnik is likely to contain four sites for Xis binding, Xis...

journal_title：Journal of molecular biology

authors： Singh S,Plaks JG,Homa NJ,Amrich CG,Héroux A,Hatfull GF,VanDemark AP

更新日期：2014-01-23 00:00:00

abstract：:Although the transcript level of inducible heat shock protein 70.3 (Hsp70.3, also known as Hspa1a) is altered in various disease states, its transcriptional regulation remains incompletely understood. Here, we systematically analyzed the Hspa1a promoter to identify major cis elements and transcription factors that may...

journal_title：Journal of molecular biology

authors： Sasi BK,Sonawane PJ,Gupta V,Sahu BS,Mahapatra NR

更新日期：2014-01-09 00:00:00

abstract：:Designed retroaldolases have utilized a nucleophilic lysine to promote carbon-carbon bond cleavage of β-hydroxy-ketones via a covalent Schiff base intermediate. Previous computational designs have incorporated a water molecule to facilitate formation and breakdown of the carbinolamine intermediate to give the Schiff b...

journal_title：Journal of molecular biology

authors： Bjelic S,Kipnis Y,Wang L,Pianowski Z,Vorobiev S,Su M,Seetharaman J,Xiao R,Kornhaber G,Hunt JF,Tong L,Hilvert D,Baker D

更新日期：2014-01-09 00:00:00

abstract：:Only a few reports have been published on the interactions between Coxsackievirus B4 (CVB4) and human peripheral blood mononuclear cells (PBMC) but have not been extensively documented. Human serum containing non-neutralizing anti-CVB4 antibodies increased CVB4-induced synthesis of IFNα by PBMC. In this study, we dete...

journal_title：Journal of molecular biology

authors： Alidjinou EK,Sané F,Engelmann I,Hober D

更新日期：2013-12-13 00:00:00

abstract：:Arenaviruses are enveloped, negative-stranded RNA viruses that belong to the family Arenaviridae. This diverse family can be further classified into OW (Old World) and NW (New World) arenaviruses based on their antigenicity, phylogeny, and geographical distribution. Many of the NW arenaviruses are highly pathogenic vi...

journal_title：Journal of molecular biology

authors： Koma T,Huang C,Kolokoltsova OA,Brasier AR,Paessler S

更新日期：2013-12-13 00:00:00

abstract：:Homologous recombination (HR) is an evolutionary-conserved mechanism involved in a subtle balance between genome stability and diversity. HR is a faithful DNA repair pathway and has been largely characterized in the context of double-strand break (DSB) repair. Recently, multiple functions for the HR machinery have bee...

journal_title：Journal of molecular biology

authors： Carr AM,Lambert S

更新日期：2013-11-29 00:00:00

abstract：:Eukaryotic replication origins are activated at different times during the S phase of the cell cycle, following a temporal program that is stably transmitted to daughter cells. Although the mechanisms that control initiation at the level of individual origins are now well understood, much less is known on how cells co...

journal_title：Journal of molecular biology

authors： Yoshida K,Poveda A,Pasero P

更新日期：2013-11-29 00:00:00

abstract：:In the "Replicon Theory", Jacob, Brenner and Cuzin proposed the existence of replicators and initiators as the two major actors in DNA replication. Over the years, many protein components of initiators have been shown to be conserved in different organisms during evolution. By contrast, replicator DNA sequences (often...

journal_title：Journal of molecular biology

authors： Mojardín L,Vázquez E,Antequera F

更新日期：2013-11-29 00:00:00

abstract：:DNA polymerase III, a decameric 420-kDa assembly, simultaneously replicates both strands of the chromosome in Escherichia coli. A subassembly of this holoenzyme, the seven-subunit clamp loader complex, is responsible for loading the sliding clamp (β2) onto DNA. Here, we use structural information derived from ion mobi...

journal_title：Journal of molecular biology

authors： Politis A,Park AY,Hall Z,Ruotolo BT,Robinson CV

更新日期：2013-11-29 00:00:00

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

authors： Davidson EA,Basu AS,Bayer TS

更新日期：2013-11-15 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：:Cytochrome P450cam catalyzes the hydroxylation of camphor in a complex process involving two electron transfers (ETs) from the iron-sulfur protein putidaredoxin. The enzymatic control of the successive steps of catalysis is critical for a highly efficient reaction. The injection of the successive electrons is part of ...

journal_title：Journal of molecular biology

authors： Hiruma Y,Hass MA,Kikui Y,Liu WM,Ölmez B,Skinner SP,Blok A,Kloosterman A,Koteishi H,Löhr F,Schwalbe H,Nojiri M,Ubbink M

更新日期：2013-11-15 00:00:00

abstract：:In eukaryotes, cellular levels of adenosine monophosphate (AMP) signal the metabolic state of the cell. AMP concentrations increase significantly upon metabolic stress, such as glucose deprivation in yeast. Here, we show that several DEAD-box RNA helicases are sensitive to AMP, which is not produced during ATP hydroly...

journal_title：Journal of molecular biology

authors： Putnam AA,Jankowsky E

更新日期：2013-10-23 00:00:00

abstract：:Human pseudouridine (Ψ) synthase Pus1 (hPus1) modifies specific uridine residues in several non-coding RNAs: tRNA, U2 spliceosomal RNA, and steroid receptor activator RNA. We report three structures of the catalytic core domain of hPus1 from two crystal forms, at 1.8Å resolution. The structures are the first of a mamm...

journal_title：Journal of molecular biology

authors： Czudnochowski N,Wang AL,Finer-Moore J,Stroud RM

更新日期：2013-10-23 00:00:00

abstract：:Gene transcription is regulated in response to environmental changes and developmental cues. In mammalian cells subjected to stress conditions such as heat shock, transcription of most protein-coding genes decreases, while the transcription of heat shock protein genes increases. Repression involves direct binding to R...

journal_title：Journal of molecular biology

authors： Kassube SA,Fang J,Grob P,Yakovchuk P,Goodrich JA,Nogales E

更新日期：2013-10-09 00:00:00

abstract：:AMP phosphorylase (AMPpase) catalyzes the initial reaction in a novel AMP metabolic pathway recently found in archaea, converting AMP and phosphate into adenine and ribose 1,5-bisphosphate. Gel-filtration chromatography revealed that AMPpase from Thermococcus kodakarensis (Tk-AMPpase) forms an exceptionally large macr...

journal_title：Journal of molecular biology

authors： Nishitani Y,Aono R,Nakamura A,Sato T,Atomi H,Imanaka T,Miki K

更新日期：2013-08-09 00:00:00

abstract：:Tannins are water-soluble polyphenolic compounds in plants. Hydrolyzable tannins are derivatives of gallic acid (3,4,5-trihydroxybenzoic acid) or its meta-depsidic forms that are esterified to polyol, catechin, or triterpenoid units. Tannases are a family of esterases that catalyze the hydrolysis of the galloyl ester ...

journal_title：Journal of molecular biology

authors： Ren B,Wu M,Wang Q,Peng X,Wen H,McKinstry WJ,Chen Q

更新日期：2013-08-09 00:00:00

abstract：:Selenoproteins are present in all three domains of life and are responsible for a major part of a cell's antioxidant defense against reactive oxygen species. Synthesis of selenoproteins requires the decoding of a UGA codon as selenocysteine (Sec) instead of translation termination. Sec is incorporated into the growing...

journal_title：Journal of molecular biology

authors： Gupta N,DeMong LW,Banda S,Copeland PR

更新日期：2013-07-24 00:00:00

abstract：:Viral suppressors of RNA interference (VSRs) target host gene silencing pathways, thereby operating important roles in the viral cycle and in host cells, in which they counteract host innate immune responses. However, the molecular mechanisms of VSRs are poorly understood. We provide here biochemical and biophysical f...

journal_title：Journal of molecular biology

authors： Gillet FX,Cattoni DI,Petiot-Bécard S,Delalande F,Poignavent V,Brizard JP,Bessin Y,Dorsselaer AV,Declerck N,Sanglier-Cianférani S,Brugidou C,Vignols F

更新日期：2013-07-24 00:00:00

abstract：:Microtubule (MT) stability is related to the hydrolysis of the guanosine triphosphate nucleotide (NT) bound to β-tubulin. However, the molecular mechanism by which the NT state influences the stability of the contacts in the MT lattice remains elusive. Here, we present large-scale atomistic simulations of different tu...

journal_title：Journal of molecular biology

authors： Grafmüller A,Noya EG,Voth GA

更新日期：2013-06-26 00:00:00

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

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

更新日期：2013-06-26 00:00:00

abstract：:The mechanism by which antibodies elicited against protein-derived peptides achieve cross-reactivity with their cognate proteins remains unknown. To address this question, we have carried out the complete thermodynamic characterization of the association of a monoclonal antibody (260.33.12) raised against a peptide (S...

journal_title：Journal of molecular biology

authors： Armstrong A,Hildreth JEK,Amzel LM

更新日期：2013-06-12 00:00:00

abstract：:Cytoplasmic polyadenylation element binding protein (CPEB) provides temporal and spatial control of protein synthesis required for early development and neuronal synaptic plasticity. CPEB regulates protein expression by inhibiting polyadenylation of selected mRNA transcripts, which prevents binding of the ribosome for...

journal_title：Journal of molecular biology

authors： Merkel DJ,Wells SB,Hilburn BC,Elazzouzi F,Pérez-Alvarado GC,Lee BM

更新日期：2013-06-12 00:00:00

abstract：:The emergence and spread of multi-drug-resistant strains of Staphylococcus aureus in hospitals and in the community emphasize the urgency for the development of novel therapeutic interventions. Our approach was to evaluate the potential of harnessing the human immune system to guide the development of novel therapeuti...

journal_title：Journal of molecular biology

authors： Foletti D,Strop P,Shaughnessy L,Hasa-Moreno A,Casas MG,Russell M,Bee C,Wu S,Pham A,Zeng Z,Pons J,Rajpal A,Shelton D

更新日期：2013-05-27 00:00:00

abstract：:A manuscript on allostery signed by Francis Crick and Jeffries Wyman was sent by Crick to Jacques Monod in 1965. Monod transmitted a copy of the manuscript, upon which he had written several comments, to Jean-Pierre Changeux, then a post-doctoral fellow at the University of California Berkeley in the laboratory of How...

journal_title：Journal of molecular biology

authors： Crick FH,Wyman J

更新日期：2013-05-13 00:00:00

abstract：:Proteins are dynamic molecular machines whose structure and function are modulated by environmental perturbations and natural selection. Allosteric regulation, discovered in 1963 as a novel molecular mechanism of enzymatic adaptation [Monod, Changeux & Jacob (1963). J. Mol. Biol.6, 306-329], seems to be the leit motiv...

journal_title：Journal of molecular biology

authors： Miele AE,Bellelli A,Brunori M

更新日期：2013-05-13 00:00:00

abstract：:The nuclear pore complex is the sole mediator of bidirectional transport between the nucleus and cytoplasm. Nup358 is a metazoan-specific nucleoporin that localizes to the cytoplasmic filaments and provides several binding sites for the mobile nucleocytoplasmic transport machinery. Here we present the crystal structur...

journal_title：Journal of molecular biology

authors： Lin DH,Zimmermann S,Stuwe T,Stuwe E,Hoelz A

更新日期：2013-04-26 00:00:00

abstract：:WNK1 [with no lysine (K)-1] is a 250-kDa serine/threonine protein kinase involved in the maintenance of cellular salt levels and is directly linked to a hereditary form of hypertension. Here, we report the solution NMR structure of the autoinhibitory domain of WNK1 (WNK1-AI), a small regulatory subunit that lies immed...

journal_title：Journal of molecular biology

authors： Moon TM,Correa F,Kinch LN,Piala AT,Gardner KH,Goldsmith EJ

更新日期：2013-04-26 00:00:00

abstract：:The cytokine interleukin 13 (IL-13) is a major effector molecule for T-helper type 2 inflammation and is pathogenic in allergic diseases such as asthma. The effects of IL-13 are mediated via a pathway that is initiated by binding to a heterodimeric receptor consisting of IL-13Rα1 and IL-4Rα. Antibodies raised against ...

journal_title：Journal of molecular biology

authors： Ultsch M,Bevers J,Nakamura G,Vandlen R,Kelley RF,Wu LC,Eigenbrot C

更新日期：2013-04-26 00:00:00

abstract：:Although largely deemed as structurally conserved, catalytic metal ion sites can rearrange, thereby contributing to enzyme evolvability. Here, we show that in paraoxonase-1, a lipo-lactonase, catalytic promiscuity and divergence into an organophosphate hydrolase are correlated with an alternative mode of the catalytic...

journal_title：Journal of molecular biology

authors： Ben-David M,Wieczorek G,Elias M,Silman I,Sussman JL,Tawfik DS

更新日期：2013-03-25 00:00:00

abstract：:Imidazole-3-glycerol phosphate synthase is a heterodimeric allosteric enzyme that catalyzes consecutive reactions in imidazole biosynthesis through its HisF and HisH subunits. The unusually slow unfolding reaction of the isolated HisF TIM barrel domain from the thermophilic bacteria, Thermotoga maritima, enabled an NM...

journal_title：Journal of molecular biology

authors： Gangadhara BN,Laine JM,Kathuria SV,Massi F,Matthews CR

更新日期：2013-03-25 00:00:00