Automatic definition of recurrent local structure motifs in proteins.

abstract：:Peptidoglycan recognition proteins (PGRPs) form a recently discovered protein family, which is conserved from insect to mammals and is implicated in the innate immune system by interacting with/or degrading microbial peptidoglycans (PGNs). Drosophila PGRP-SA is a member of this family of pattern recognition receptors ...

journal_title：Journal of molecular biology

authors： Reiser JB,Teyton L,Wilson IA

更新日期：2004-07-16 00:00:00

abstract：:A detailed phylogenetic analysis for mammalian members of the family Herpesviridae, based on molecular sequences is reported. Sets of encoded amino acid sequences were collected for eight well conserved genes that are common to mammalian herpesviruses. Phylogenetic trees were inferred from alignments of these sequence...

journal_title：Journal of molecular biology

authors： McGeoch DJ,Cook S,Dolan A,Jamieson FE,Telford EA

更新日期：1995-03-31 00:00:00

abstract：:The X-ray diffraction pattern of tendon collagen can contain a number of sharp Bragg peaks indicating three-dimensional crystallinity of the sample. Optimal diffraction images have been obtained with a high flux synchrotron X-ray source and a carefully maintained sample environment and staining techniques. The Bragg p...

journal_title：Journal of molecular biology

authors： Wess TJ,Hammersley A,Wess L,Miller A

更新日期：1995-04-28 00:00:00

abstract：:Binary complexes between messenger RNA and E. coli ribosomes were examined. A ribosome-mRNA binary complex on T4 gene 32 mRNA withstood inhibition by antibodies against ribosomal protein S1. Anti-S1 blocks ternary complex formation, as measured by "extension inhibition" or "toeprinting" analysis, only when preincubate...

journal_title：Journal of molecular biology

authors： Hartz D,McPheeters DS,Green L,Gold L

更新日期：1991-03-05 00:00:00

abstract：:The rat Clara cell 17 kDa protein (previously referred to as the rat Clara cell 10 kDa protein) has been reported to inhibit phospholipase A2 and papain, and to also bind progesterone. It has been isolated from rat lung lavage fluid and crystallized in the space group P6(5)22. The structure has been determined to 3.0 ...

journal_title：Journal of molecular biology

authors： Umland TC,Swaminathan S,Furey W,Singh G,Pletcher J,Sax M

更新日期：1992-03-20 00:00:00

abstract：:The cytokine, interleukin-1beta (IL-1beta), adopts a beta-trefoil fold. It is known to be much slower folding than similarly sized proteins, despite having a low contact order. Proteins are sufficiently well designed that their folding is not dominated by local energetic traps. Therefore, protein models that encode on...

journal_title：Journal of molecular biology

authors： Gosavi S,Chavez LL,Jennings PA,Onuchic JN

更新日期：2006-03-31 00:00:00

abstract：:The sigma 70 (sigma(70)) subunit of Escherichia coli RNA polymerase specifies transcription from promoters that are responsible for basal gene expression during vegetative growth. When sigma(70) is present within polymerase holoenzyme, two of its domains, 2.4 and 4.2, interact with sequences within the -10 and -35 reg...

journal_title：Journal of molecular biology

authors： Vuthoori S,Bowers CW,McCracken A,Dombroski AJ,Hinton DM

更新日期：2001-06-08 00:00:00

abstract：:Peptidyl-tRNA hydrolase cleaves the ester bond between tRNA and the attached peptide in peptidyl-tRNA in order to avoid the toxicity resulting from its accumulation and to free the tRNA available for further rounds in protein synthesis. The structure of the enzyme from Mycobacterium tuberculosis has been determined in...

journal_title：Journal of molecular biology

authors： Selvaraj M,Roy S,Singh NS,Sangeetha R,Varshney U,Vijayan M

更新日期：2007-09-07 00:00:00

abstract：:The 3.0-3.1A X-ray structures of the cytochrome b(6)f complex from Mastigocladus laminosus and Chlamydomonas reinhardtii obtained in the presence of the p-side quinone-analogue inhibitor tridecyl-stigmatellin (TDS) are very similar. A difference occurs in the p-side binding position of TDS. In C.reinhardtii, TDS binds...

journal_title：Journal of molecular biology

authors： Yan J,Cramer WA

更新日期：2004-11-19 00:00:00

abstract：:We have determined the three-dimensional organization of ribosomal RNAs and proteins essential for minimal ribosome function. Comparative sequence analysis identifies regions of the ribosome that have been evolutionarily conserved, and the spatial organization of conserved domains is determined by mapping these onto s...

journal_title：Journal of molecular biology

authors： Mears JA,Cannone JJ,Stagg SM,Gutell RR,Agrawal RK,Harvey SC

更新日期：2002-08-09 00:00:00

abstract：:Bile acid molecules are transferred vectorially between basolateral and apical membranes of hepatocytes and enterocytes in the context of the enterohepatic circulation, a process regulating whole body lipid homeostasis. This work addresses the role of the cytosolic lipid binding proteins in the intracellular transfer ...

journal_title：Journal of molecular biology

authors： Pedò M,Löhr F,D'Onofrio M,Assfalg M,Dötsch V,Molinari H

更新日期：2009-12-18 00:00:00

abstract：:PHF1 associates with the Polycomb repressive complex 2 and it was demonstrated to stimulate its H3K27-trimethylation activity. We studied the interaction of the PHF1 Tudor domain with modified histone peptides and found that it recognizes H3K36me3 and H3tK27me3 (on the histone variant H3t) and that it uses the same tr...

journal_title：Journal of molecular biology

authors： Kycia I,Kudithipudi S,Tamas R,Kungulovski G,Dhayalan A,Jeltsch A

更新日期：2014-04-17 00:00:00

abstract：:Ciliary neurotrophic factor (CNTF) is a cytokine sharing structural and functional similarities with interleukin-6 (IL-6) and other helical cytokines that utilize the common signalling chain gp130. While IL-6 induces gp130 dimerization, CNTF, after the initial interaction with the specific, non-signalling receptor sub...

journal_title：Journal of molecular biology

authors： De Serio A,Graziani R,Laufer R,Ciliberto G,Paonessa G

更新日期：1995-12-15 00:00:00

abstract：:Evidence is presented for the participation of the P loop (nucleotides G2250-C2254) of 23 S rRNA in establishing the tertiary structure of the peptidyl transferase center. Single base substitutions were introduced into the P loop, which participates in peptide bond formation through direct interaction with the CCA end...

journal_title：Journal of molecular biology

authors： Gregory ST,Dahlberg AE

更新日期：1999-01-29 00:00:00

abstract：:The lateral diffusion coefficient of fluorescent lipid analogues incorporated in four cubic phases of lipid-water systems was determined by the modulated fringe pattern photobleaching technique. In two of the phases, Q230 and Q224, whose structure is bicontinuous, the diffusion is almost as fast as in the fluid lipid ...

journal_title：Journal of molecular biology

authors： Cribier S,Gulik A,Fellmann P,Vargas R,Devaux PF,Luzzati V

更新日期：1993-01-20 00:00:00

abstract：:The 90-kDa heat shock protein (Hsp90) is a widely conserved and ubiquitous molecular chaperone that participates in ATP-dependent protein remodeling in both eukaryotes and prokaryotes. It functions in conjunction with Hsp70 and the Hsp70 cochaperones, an Hsp40 (J-protein) and a nucleotide exchange factor. In Escherich...

journal_title：Journal of molecular biology

authors： Kravats AN,Doyle SM,Hoskins JR,Genest O,Doody E,Wickner S

更新日期：2017-03-24 00:00:00

abstract：:We have previously shown that transcription of the Xenopus U6 snRNA gene by RNA polymerase III is stimulated in injected Xenopus oocytes by an activator element termed the DSE, which contains an octamer sequence. Data presented here reveal that the DSE contains, in addition, a GC-rich sequence capable of binding Sp1. ...

journal_title：Journal of molecular biology

authors： Lescure A,Tebb G,Mattaj IW,Krol A,Carbon P

更新日期：1992-11-20 00:00:00

abstract：:We have studied the statistical constraints on synonymous codon choice to evaluate various proposals regarding the origin of the bias in synonymous codon usage observed by Fiers et al. (1975), Air et al. (1976), Grantham et al. (1980) and others. We have determined the statistical dependence of the degenerate third ba...

journal_title：Journal of molecular biology

authors： Lipman DJ,Wilbur WJ

更新日期：1983-01-25 00:00:00

abstract：:Expression of the plant protein centroradialis (CEN) leads to a morphological switch between shoot growth and the development of flower structures (inflorescence). We have determined the crystal structure of Antirrhinum CEN to 1.9 A resolution. This structure confirms the CEN proteins as a subset of the family of phos...

journal_title：Journal of molecular biology

authors： Banfield MJ,Brady RL

更新日期：2000-04-14 00:00:00

abstract：:We have studied the use of nearest-neighbor classifiers to predict the secondary structure of proteins. The nearest-neighbor rule states that a test instance is classified according to the classifications of "nearby" training examples from a database of known structures. In the context of secondary structure predictio...

journal_title：Journal of molecular biology

authors： Yi TM,Lander ES

更新日期：1993-08-20 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：:Suppressor of cytokine signalling 3 (SOCS3) is responsible for regulating the cellular response to a variety of cytokines, including interleukin 6 and leukaemia inhibitory factor. Identification of the SOCS box domain led to the hypothesis that SOCS3 can associate with functional E3 ubiquitin ligases and thereby induc...

journal_title：Journal of molecular biology

authors： Babon JJ,Sabo JK,Soetopo A,Yao S,Bailey MF,Zhang JG,Nicola NA,Norton RS

更新日期：2008-09-12 00:00:00

abstract：:Diffraction data for alpha-chymotrypsin crystals at -10 degrees C were measured at 1.68 A resolution and refined by restrained structure-factor least-squares refinement. The two independent chymotrypsin molecules in the crystallographic asymmetric unit were refined independently. The overall structure of alpha-chymotr...

journal_title：Journal of molecular biology

authors： Tsukada H,Blow DM

更新日期：1985-08-20 00:00:00

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

authors： Mullaney JM,Black LW

更新日期：1996-08-23 00:00:00

abstract：:The formation of membraneless organelles (MLOs) by phase separation has emerged as a new way of organizing the cytoplasm and nucleoplasm of cells. Examples of MLOs forming via phase separation are nucleoli in the nucleus and stress granules in the cytoplasm. The main components of these MLOs are macromolecules such as...

journal_title：Journal of molecular biology

authors： Alberti S,Carra S

更新日期：2018-11-02 00:00:00

abstract：:A new inhibitor, H-Ala-Ile-pyrrolidin-2-yl boronic acid, was developed as an inhibitor against prolyl tripeptidyl aminopeptidase with a K(i) value of 88.1 nM. The structure of the prolyl tripeptidyl aminopeptidase complexed with the inhibitor (enzyme-inhibitor complex) was determined at 2.2 A resolution. The inhibitor...

journal_title：Journal of molecular biology

authors： Xu Y,Nakajima Y,Ito K,Zheng H,Oyama H,Heiser U,Hoffmann T,Gärtner UT,Demuth HU,Yoshimoto T

更新日期：2008-01-18 00:00:00

abstract：:It is now appreciated that in addition to their role in humoral immunity, B cells also exert regulatory mechanisms that lead to attenuation of inflammatory responses. The concept of B-cell regulation became well recognized when mice deficient in B cells due to genetic disruption were shown to be refractory to recovery...

journal_title：Journal of molecular biology

authors： Khalil MI,Gurski CJ,Dittel LJ,Neu SD,Dittel BN

更新日期：2021-01-08 00:00:00

abstract：:Horizontally transferred DNA is largely responsible for the dissemination of virulence traits amongst bacteria. Rapid identification of acquired DNA remains difficult as whole-genome sequencing of outbreak strains is impractical, and microarray-based approaches, while powerful, are limited to genes present only in the...

journal_title：Journal of molecular biology

authors： Malloff CA,Fernandez RC,Lam WL

更新日期：2001-09-07 00:00:00

abstract：:We describe here the error specificity of mammalian DNA polymerase eta (pol eta), an enzyme that performs translesion DNA synthesis and may participate in somatic hypermutation of immunoglobulin genes. Both mouse and human pol eta lack intrinsic proofreading exonuclease activity and both copy undamaged DNA inaccuratel...

journal_title：Journal of molecular biology

authors： Matsuda T,Bebenek K,Masutani C,Rogozin IB,Hanaoka F,Kunkel TA

更新日期：2001-09-14 00:00:00

abstract：:We have solved the crystal structure of the acyl carrier protein synthase (AcpS) from Mycobacterium tuberculosis (Mtb) at 1.95 A resolution. AcpS, a 4-phosphopantetheinyl transferase, activates two distinct acyl carrier proteins (ACPs) that are present in fatty acid synthase (FAS) systems FAS-I and FAS-II, the ACP-I d...

journal_title：Journal of molecular biology

authors： Dym O,Albeck S,Peleg Y,Schwarz A,Shakked Z,Burstein Y,Zimhony O

更新日期：2009-11-06 00:00:00