Reversible peptide folding in solution by molecular dynamics simulation.

abstract：:Deoxy- and dideoxynucleotides differ only in whether they have a hydroxyl substituent at C-3' of the ribose moiety, and yet the Klenow fragment DNA polymerase prefers the natural (dNTP) substrate by several thousandfold. We have used this preference in order to investigate how Klenow fragment interacts with the sugar ...

journal_title：Journal of molecular biology

authors： Astatke M,Grindley ND,Joyce CM

更新日期：1998-04-24 00:00:00

abstract：:Filamentous bacteriophage M13 is a single-stranded DNA phage about 65 A in diameter and 9300 A long. X-ray diffraction studies of magnetically oriented fibers of native, mercury and iodine-labeled phage particles have been used to determine the arrangement of the major coat protein, the gene 8 product, in the virion. ...

journal_title：Journal of molecular biology

authors： Glucksman MJ,Bhattacharjee S,Makowski L

更新日期：1992-07-20 00:00:00

abstract：:Protein-protein interactions within the membrane, partially or fully mediated by transmembrane (TM) domains, are involved in many vital cellular processes. Since the unique feature of the membrane environment enables protein-protein assembly that otherwise is not energetically favored in solution, the structural restr...

journal_title：Journal of molecular biology

authors： Sal-Man N,Gerber D,Shai Y

更新日期：2004-11-26 00:00:00

abstract：:A novel virus, ATV, of the hyperthermophilic archaeal genus Acidianus has the unique property of undergoing a major morphological development outside of, and independently of, the host cell. Virions are extruded from host cells as lemon-shaped tail-less particles, after which they develop long tails at each pointed en...

journal_title：Journal of molecular biology

authors： Prangishvili D,Vestergaard G,Häring M,Aramayo R,Basta T,Rachel R,Garrett RA

更新日期：2006-06-23 00:00:00

abstract：:Cutinase belongs to a group of enzymes that catalyze the hydrolysis of esters and triglycerides. Structural studies on the enzyme from Fusarium solani have revealed the presence of a classic catalytic triad that has been implicated in the enzyme's mechanism. We have solved the crystal structure of Glomerella cingulata...

journal_title：Journal of molecular biology

authors： Nyon MP,Rice DW,Berrisford JM,Hounslow AM,Moir AJ,Huang H,Nathan S,Mahadi NM,Bakar FD,Craven CJ

更新日期：2009-01-09 00:00:00

abstract：:We describe multi-conformation simulated annealing-pseudo-crystallographic refinement (MCSA-PCR), a technique developed for predicting the binding mode of a flexible ligand in a flexible binding pocket. To circumvent the local-minimum problem efficiently, this method performs multiple independent cycles of simulated a...

journal_title：Journal of molecular biology

authors： Ota N,Agard DA

更新日期：2001-11-30 00:00:00

abstract：:The molecular structure of the high-potential iron-sulfur protein (HiPIP) isolated from the phototrophic bacterium, Rhodocyclus tenuis, has been solved and refined to a nominal resolution of 1.5 A with a crystallographic R-factor of 17.3% for all measured X-ray data from 30 A to 1.5 A. It is the smallest of the HiPIP ...

journal_title：Journal of molecular biology

authors： Rayment I,Wesenberg G,Meyer TE,Cusanovich MA,Holden HM

更新日期：1992-11-20 00:00:00

abstract：:Fibrin formation from fibrinogen is a rare process in the healthy organism but is a pathological feature of thrombotic events, cancer and a wide range of inflammatory conditions. We have designed and constructed an antibody phage display library (containing 13 billion clones) for the selective recognition of the N-ter...

journal_title：Journal of molecular biology

authors： Putelli A,Kiefer JD,Zadory M,Matasci M,Neri D

更新日期：2014-10-23 00:00:00

abstract：:The region of the Escherichia coli 16 S ribosomal RNA recognized by the ribosomal protein S4 has been defined by assaying a set of 13 16 S rRNA fragments for S4 binding. The fragments were prepared by transcription in vitro, and binding constants were measured in three ways: retention of labeled RNA fragments on nitro...

journal_title：Journal of molecular biology

authors： Vartikar JV,Draper DE

更新日期：1989-09-20 00:00:00

abstract：:6,7-Dimethyl-8-ribityllumazine synthase (lumazine synthase) catalyses the penultimate step in the biosynthesis of riboflavin. In Bacillus subtilis, 60 lumazine synthase subunits form an icosahedral capsid enclosing a homotrimeric riboflavin synthase unit. The ribH gene specifying the lumazine synthase subunit can be e...

journal_title：Journal of molecular biology

authors： Fischer M,Haase I,Kis K,Meining W,Ladenstein R,Cushman M,Schramek N,Huber R,Bacher A

更新日期：2003-02-21 00:00:00

abstract：:To examine the previously proposed retroregulation model of spc mRNA degradation, two strains of Escherichia coli B/r were used; one has wild-type spc and lac operons and the other has a lac operon deletion, a wild-type spc operon, and a Pspc-rplN-lacZ fusion operon lacking the normal control sites of the spc operon (...

journal_title：Journal of molecular biology

authors： Liang ST,Ehrenberg M,Dennis P,Bremer H

更新日期：1999-05-14 00:00:00

abstract：:Infection of Escherichia coli by filamentous bacteriophages is mediated by the minor phage coat protein g3p and involves two distinct cellular receptors, the F' pilus and the periplasmic protein TolA. Recently we have shown that the two receptors are contacted in a sequential manner, such that binding of TolA by the N...

journal_title：Journal of molecular biology

authors： Holliger P,Riechmann L,Williams RL

更新日期：1999-05-14 00:00:00

abstract：:The lumazine synthase/riboflavin synthase complex of Bacillus subtilis consists of an icosahedral capsid of 60 beta subunits enclosing a core of 3 alpha subunits. The preparation of reconstituted hollow capsids consisting of 60 beta subunits and their crystallization in a hexagonal (space group P6(3)22) and in a monoc...

journal_title：Journal of molecular biology

authors： Bacher A,Weinkauf S,Bachmann L,Ritsert K,Baumeister W,Huber R,Ladenstein R

更新日期：1992-06-20 00:00:00

abstract：:Like most cellular RNA enzymes, the bI5 group I intron requires binding by a protein cofactor to fold correctly. Here, we use single-molecule approaches to monitor the structural dynamics of the bI5 RNA in real time as it assembles with its CBP2 protein cofactor. These experiments show that CBP2 binds to the target RN...

journal_title：Journal of molecular biology

authors： Bokinsky G,Nivón LG,Liu S,Chai G,Hong M,Weeks KM,Zhuang X

更新日期：2006-08-25 00:00:00

abstract：:The nuclear pore complex (NPC) is strategically located at continuous junctions of the inner and outer nuclear membranes to catalyze macromolecular transport, without impending the diffusion of small molecules. In this paper, the structural plasticity of 4412 NPCs in isolated nuclear envelopes has been evaluated, util...

journal_title：Journal of molecular biology

authors： Akey CW

更新日期：1995-04-28 00:00:00

abstract：:A 1.9 A resolution X-ray structure of the apo-form of Corynebacterium 2,5-diketo-d-gluconic acid reductase A (2,5-DKGR A), a member of the aldo-keto reductase superfamily, has been determined by molecular replacement using the NADPH-bound form of the same enzyme as the search model. 2,5-DKGR A catalyzes the NADPH-depe...

journal_title：Journal of molecular biology

authors： Sanli G,Blaber M

更新日期：2001-06-22 00:00:00

abstract：:ThiI is an enzyme responsible for the formation of the modified base S(4)U (4-thiouridine) found at position 8 in some prokaryotic tRNAs. This base acts as a sensitive trigger for the response mechanism to UV exposure, providing protection against its damaging effects. We present the crystal structure of Bacillus anth...

journal_title：Journal of molecular biology

authors： Waterman DG,Ortiz-Lombardía M,Fogg MJ,Koonin EV,Antson AA

更新日期：2006-02-10 00:00:00

abstract：:Spiders that spin orb webs secrete seven types of silk. Although the spinning process of the dragline thread is beginning to be understood, the molecular events that occur in spiders' opisthosomal glands, which produce the other fibers, are unknown due to a lack of data regarding their initial and final structures. Ta...

journal_title：Journal of molecular biology

authors： Lefèvre T,Boudreault S,Cloutier C,Pézolet M

更新日期：2011-01-07 00:00:00

abstract：:Autonomously replicating sequences (ARSs) in the yeast Yarrowia lipolytica require two components: an origin of replication (ORI) and centromere (CEN) DNA, both of which are necessary for extrachromosomal maintenance. To investigate this cooperation in more detail, we performed a screen for genomic sequences able to c...

journal_title：Journal of molecular biology

authors： Vernis L,Poljak L,Chasles M,Uchida K,Casarégola S,Käs E,Matsuoka M,Gaillardin C,Fournier P

更新日期：2001-01-12 00:00:00

abstract：:The average structural and dynamic properties of tetragonal hen egg-white lysozyme have been compared, in structures refined at 1.9 A resolution, using data collected at 100 K and 298 K. The molecule expands by 1.8% over this temperature range with the expansion occurring primarily in its small sub-atomic-sized spaces...

journal_title：Journal of molecular biology

authors： Young AC,Tilton RF,Dewan JC

更新日期：1994-01-07 00:00:00

abstract：:YibK is a 160 residue homodimeric protein belonging to the SPOUT class of methyltransferases. Proteins in this group all display a unique topological feature; the backbone polypeptide chain folds to form a deep trefoil knot. Such knotted structures were completely unpredicted, it being thought impossible for a protein...

journal_title：Journal of molecular biology

authors： Mallam AL,Jackson SE

更新日期：2005-03-11 00:00:00

abstract：:This work describes the isolation of mutations in infC, the structural gene for IF3, using different genetic screens. Among 21 mutants characterised, seven were shown to produce stable variant IF3 proteins unable to fully complement a strain carrying a chromosomal deletion of the infC gene. The mutants were also shown...

journal_title：Journal of molecular biology

authors： Sacerdot C,de Cock E,Engst K,Graffe M,Dardel F,Springer M

更新日期：1999-05-21 00:00:00

abstract：:The 8-17 deoxyribozyme is an in vitro selected enzyme capable of sequence-specific cleavage of RNA. While selected to be a magnesium and zinc-utilizing enzyme, the 8-17 DNAzyme has been shown to utilize lead for its catalysis. Fluorescence-based experiments have indicated that the magnesium- and zinc-utilizing version...

journal_title：Journal of molecular biology

authors： Liu Y,Sen D

更新日期：2010-01-15 00:00:00

abstract：:We have applied a search strategy for determining the optimal packing of protein secondary structure elements to the rotational positioning of the seven transmembrane helices of bacteriorhodopsin. The search is based on the assumption that the relative orientations of the helices within the bundle are conditioned prin...

journal_title：Journal of molecular biology

authors： Tuffery P,Etchebest C,Popot JL,Lavery R

更新日期：1994-03-04 00:00:00

abstract：:The visible absorption spectra of carbonmonoxymyoglobin in the temperature range 300 to 20 K are reported and compared with the analogous spectra of carbonomonoxyhaemoglobin. The temperature dependence of the zeroth, first and second moment of the observed bands is analysed to obtain information on the local dynamics ...

journal_title：Journal of molecular biology

authors： Cordone L,Cupane A,Leone M,Vitrano E,Bulone D

更新日期：1988-01-05 00:00:00

abstract：:The multidomain Mac-2 binding protein (M2BP) is present in serum and in the extracellular matrix in the form of linear and ring-shaped oligomers, which interact with galectin-3, fibronectin, collagens, integrins and other large glycoproteins. Domain 1 of M2BP (M2BP-1) shows homology with the cysteine-rich SRCR domain ...

journal_title：Journal of molecular biology

authors： Müller SA,Sasaki T,Bork P,Wolpensinger B,Schulthess T,Timpl R,Engel A,Engel J

更新日期：1999-08-27 00:00:00

abstract：:Quantitative measurements of local chromatin accessibility to DNase I in 15-day chicken embryo erythrocyte nuclei have been performed using a range of nuclease concentrations and real-time TaqMan PCR to monitor the loss of short ( approximately 80 bp) amplicons. At the beta-globin locus, well-established DNase I hyper...

journal_title：Journal of molecular biology

authors： Sapojnikova N,Thorne A,Myers F,Staynov D,Crane-Robinson C

更新日期：2009-02-20 00:00:00

abstract：:In order to develop a system which allows infection by an epitope-specific phage-antibody via an F-pilus expressing that epitope, a study on the expression of foreign sequences on F-pilin was undertaken. Initially, a plasmid library was constructed with random sequences encoding one to five amino acid residues fused t...

journal_title：Journal of molecular biology

authors： Rondot S,Anthony KG,Dübel S,Ida N,Wiemann S,Beyreuther K,Frost LS,Little M,Breitling F

更新日期：1998-06-12 00:00:00

abstract：:Peptide deformylase (PDF) has received considerable attention during the last few years as a potential target for a new type of antibiotics. It is an essential enzyme in eubacteria for the removal of the formyl group from the N terminus of the nascent polypeptide chain. We have solved the X-ray structures of four memb...

journal_title：Journal of molecular biology

authors： Kreusch A,Spraggon G,Lee CC,Klock H,McMullan D,Ng K,Shin T,Vincent J,Warner I,Ericson C,Lesley SA

更新日期：2003-07-04 00:00:00

abstract：:Kinetics of refolding of bovine carbonic anhydrase B have been studied by the "double-jump" technique (i.e. the dependence of protein refolding on delay time in the unfolded state after fast unfolding). It is shown that two stages (the slow with a relaxation time of t1/2 approximately equal to 120 s and the superslow ...

journal_title：Journal of molecular biology

authors： Semisotnov GV,Uversky VN,Sokolovsky IV,Gutin AM,Razgulyaev OI,Rodionova NA

更新日期：1990-06-05 00:00:00