DNA looping alters local DNA conformation during transcription.

abstract：:The exceptional versatility of calmodulin (CaM) three-dimensional arrangement is reflected in the growing number of structural models of CaM/protein complexes currently available in the Protein Data Bank (PDB) database, revealing a great diversity of conformations, domain organization, and structural responses to Ca(2...

journal_title：Journal of molecular biology

authors： Villarroel A,Taglialatela M,Bernardo-Seisdedos G,Alaimo A,Agirre J,Alberdi A,Gomis-Perez C,Soldovieri MV,Ambrosino P,Malo C,Areso P

更新日期：2014-07-29 00:00:00

abstract：:Polar residues are capable of mediating the association of membrane-embedded helices through the formation of side-chain/side-chain inter-helical hydrogen bonds. However, the extent to which native van der Waals packing of the residues surrounding the polar locus can enhance, or interfere with, the interaction of pola...

journal_title：Journal of molecular biology

authors： Dawson JP,Melnyk RA,Deber CM,Engelman DM

更新日期：2003-08-01 00:00:00

abstract：:The yeast a1 and alpha 2 proteins are examples of homeodomain proteins that display cell-type-specific expression. They are co-expressed in only one type of cell, the a/alpha cell, where they repress the expression of a group of target genes. Using purified proteins, we demonstrate that a1 and alpha 2 form a highly sp...

journal_title：Journal of molecular biology

authors： Goutte C,Johnson AD

更新日期：1993-10-05 00:00:00

abstract：:The Rad1-Rad9-Hus1 (9-1-1) complex serves a dual role as a DNA-damage sensor in checkpoint signaling and as a mediator in the DNA repair pathway. However, the intercellular mechanisms that regulate the 9-1-1 complex are poorly understood. Jab1, the fifth component of the COP9 signalosome complex, has a central role in...

journal_title：Journal of molecular biology

authors： Huang J,Yuan H,Lu C,Liu X,Cao X,Wan M

更新日期：2007-08-10 00:00:00

abstract：:The papillomavirus E1 protein is essential for viral DNA replication, and phosphorylation of E1 appears to regulate protein function and DNA replication. Serine 584 of bovine papillomavirus E1 is in a conserved motif resembling a CK2 consensus site, and is phosphorylated by CK2 in vitro. Mutation of serine 584 to alan...

journal_title：Journal of molecular biology

authors： Lentz M,Zanardi T,Filzen R,Carter J,Hella M

更新日期：2002-02-22 00:00:00

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

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

更新日期：2001-07-20 00:00:00

abstract：:Although it has been known for many years that antibodies display properties characteristic of allosteric effectors, the molecular mechanisms responsible for these effects remain poorly understood. Here, we describe a single-domain antibody fragment (nanobody) that modulates protein function by constraining conformati...

journal_title：Journal of molecular biology

authors： Oyen D,Srinivasan V,Steyaert J,Barlow JN

更新日期：2011-03-18 00:00:00

abstract：:Automated protein redesign, as implemented in the program ORBIT, was used to redesign the core of phage T4 lysozyme. A total of 26 buried or partially buried sites in the C-terminal domain were allowed to vary both their sequence and side-chain conformation while the backbone and non-selected side-chains remained fixe...

journal_title：Journal of molecular biology

authors： Mooers BH,Datta D,Baase WA,Zollars ES,Mayo SL,Matthews BW

更新日期：2003-09-19 00:00:00

abstract：:The intracellular ileal lipid binding proteins (ILBPs) are involved in the transport and enterohepatic circulation of bile acids. ILBPs from different species show high sequence and structural homology and have been shown to bind multiple bile acid ligands with differing degrees of selectivity and positive co-operativ...

journal_title：Journal of molecular biology

authors： Kouvatsos N,Thurston V,Ball K,Oldham NJ,Thomas NR,Searle MS

更新日期：2007-08-31 00:00:00

abstract：:Intercellular contacts in multicellular organisms are maintained by membrane receptors called cell adhesion molecules (CAMs), which are expressed on cell surfaces. One interesting feature of CAMs is that almost all of their extracellular regions contain repeating copies of structural domains. It is not clear why so ma...

journal_title：Journal of molecular biology

authors： Chen J,Wu Y

更新日期：2017-04-07 00:00:00

abstract：:To elucidate the interplay between different parts of dimeric single-stranded DNA-binding proteins we have studied the correlated motions in the protein encoded by filamentous phage Pf3 via the combined use of 15N-NMR relaxation experiments, molecular dynamics simulations and essential dynamics calculations. These stu...

journal_title：Journal of molecular biology

authors： Horstink LM,Abseher R,Nilges M,Hilbers CW

更新日期：1999-04-02 00:00:00

abstract：:Translation initiation of human Bip mRNA is directed by an internal ribosomal entry site (IRES) located in the 5' non-translated region. No trans-acting factor possibly involved in this process has as of yet been identified. For the encephalomyocarditis virus and other picornaviruses, polypyrimidine tract-binding prot...

journal_title：Journal of molecular biology

authors： Kim YK,Hahm B,Jang SK

更新日期：2000-11-24 00:00:00

abstract：:The structure and dynamics of rat apo-cellular retinol binding protein II (apo-CRBP II) in solution has been determined by multidimensional NMR analysis of uniformly enriched recombinant rat 13C, 15N-apo-CRBP II and 15N-apo-CRBP II. The final ensemble of 24 NMR structures has been calculated from 3274 conformational r...

journal_title：Journal of molecular biology

authors： Lu J,Lin CL,Tang C,Ponder JW,Kao JL,Cistola DP,Li E

更新日期：1999-03-05 00:00:00

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

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

abstract：:A Rhizobium meliloti DNA region (nodD1) involved in the regulation of other early nodulation genes has been delimited by directed Tn5 mutagenesis and its nucleotide sequence has been determined. The sequence data indicate a large open reading frame with opposite polarity to nodA, -B and -C, coding for a protein of 308...

journal_title：Journal of molecular biology

authors： Göttfert M,Horvath B,Kondorosi E,Putnoky P,Rodriguez-Quiñones F,Kondorosi A

更新日期：1986-10-05 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：:The conformation of NAD+ in the sheep liver sorbitol dehydrogenase-NAD+ binary complex has been investigated using time-dependent proton-proton transferred nuclear Overhauser enhancement measurements to determine interproton distance ratios and distances between bound NAD+ protons. The conformation about both the aden...

journal_title：Journal of molecular biology

authors： Gronenborn AM,Clore GM,Jeffery J

更新日期：1984-02-05 00:00:00

abstract：:NADH:ubiquinone oxidoreductase (complex I) is the first and largest complex in the electron transport chain of mitochondria. The bovine complex purified from cardiac muscle consists of at least 42 different subunits with a combined molecular mass of about 890 kDa. The three-dimensional structure of the complex was det...

journal_title：Journal of molecular biology

authors： Grigorieff N

更新日期：1998-04-17 00:00:00

abstract：:We report here the structure of BstYI, an "intermediate" type II restriction endonuclease with overlapping sequence specificities to BamHI and BglII. BstYI, a thermophilic endonuclease, recognizes and cleaves the degenerate hexanucleotide sequence 5'-RGATCY-3' (where R=A or G and Y=C or T), cleaving DNA after the 5'-R...

journal_title：Journal of molecular biology

authors： Townson SA,Samuelson JC,Vanamee ES,Edwards TA,Escalante CR,Xu SY,Aggarwal AK

更新日期：2004-05-07 00:00:00

abstract：:The ribonucleoprotein (RNP) domain is one of the most common eukaryotic protein domains, and is found in many proteins involved in recognition of a wide variety of RNAs. Two structures of RNA complexes of human U1A protein have revealed important aspects of RNP-RNA recognition, but have also raised intriguing question...

journal_title：Journal of molecular biology

authors： Mittermaier A,Varani L,Muhandiram DR,Kay LE,Varani G

更新日期：1999-12-10 00:00:00

abstract：:We have identified an additional dimerization linkage structure in the genome of Moloney murine leukemia virus (MoMLV). Retroviral genomes have long been known to be linked at their 5' ends to form dimers. In MoMLV, a hairpin loop functioning as a dimer linkage structure (DLS) has previously been identified at nucleot...

journal_title：Journal of molecular biology

authors： Oroudjev EM,Kang PC,Kohlstaedt LA

更新日期：1999-08-20 00:00:00

abstract：:We demonstrate, using transmission electron microscopy and immunopurification with an antibody specific for RNA/DNA hybrid, that intact mitochondrial DNA replication intermediates are essentially duplex throughout their length but contain extensive RNA tracts on one strand. However, the extent of preservation of RNA i...

journal_title：Journal of molecular biology

authors： Pohjoismäki JL,Holmes JB,Wood SR,Yang MY,Yasukawa T,Reyes A,Bailey LJ,Cluett TJ,Goffart S,Willcox S,Rigby RE,Jackson AP,Spelbrink JN,Griffith JD,Crouch RJ,Jacobs HT,Holt IJ

更新日期：2010-04-16 00:00:00

abstract：:The dog lipocalin allergen Can f 2 is an important cause of allergic sensitization in humans worldwide. Here, the first crystal structure of recombinant rCan f 2 at 1.45 A resolution displays a classical lipocalin fold with a conserved Gly-Xaa-Trp motif, in which Trp19 stabilizes the overall topology of the monomeric ...

journal_title：Journal of molecular biology

authors： Madhurantakam C,Nilsson OB,Uchtenhagen H,Konradsen J,Saarne T,Högbom E,Sandalova T,Grönlund H,Achour A

更新日期：2010-08-06 00:00:00

abstract：:Hsp40-like co-chaperones are ubiquitous enzymes that stimulate the protein refolding activity of Hsp70 family chaperones. They are widespread in prokaryotic and eukaryotic systems. In bacteria, the best characterized co-chaperone is the Escherichia coli DnaJ protein. Many γ-proteobacteria encode a functional homologue...

journal_title：Journal of molecular biology

authors： Chintakayala K,Grainger DC

更新日期：2011-08-12 00:00:00

abstract：:Most bacteria possess two type IIA topoisomerases, DNA gyrase and topo IV, that together help manage chromosome integrity and topology. Gyrase primarily introduces negative supercoils into DNA, an activity mediated by the C-terminal domain of its DNA binding subunit (GyrA). Although closely related to gyrase, topo IV ...

journal_title：Journal of molecular biology

authors： Corbett KD,Schoeffler AJ,Thomsen ND,Berger JM

更新日期：2005-08-19 00:00:00

abstract：:HscA, a specialized bacterial Hsp70-class molecular chaperone, interacts with the iron-sulfur cluster assembly protein IscU by recognizing a conserved LPPVK sequence motif. We report the crystal structure of the substrate-binding domain of HscA (SBD, residues 389-616) from Escherichia coli bound to an IscU-derived pep...

journal_title：Journal of molecular biology

authors： Cupp-Vickery JR,Peterson JC,Ta DT,Vickery LE

更新日期：2004-09-24 00:00:00

abstract：:The cylindrical chaperonin GroEL and its cofactor GroES mediate ATP-dependent protein folding in Escherichia coli by transiently encapsulating non-native substrate in a nano-cage formed by the GroEL ring cavity and the lid-shaped GroES. Mechanistic studies of GroEL/ES with heterologous protein substrates suggested tha...

journal_title：Journal of molecular biology

authors： Singh AK,Balchin D,Imamoglu R,Hayer-Hartl M,Hartl FU

更新日期：2020-03-27 00:00:00

abstract：:We have derived a secondary structure model for the c-myc internal ribosome entry segment (IRES) by using information from chemical probing of the c-myc IRES RNA to constrain structure prediction programs. Our data suggest that the IRES is modular in nature, and can be divided into two structural domains linked by a l...

journal_title：Journal of molecular biology

authors： Le Quesne JP,Stoneley M,Fraser GA,Willis AE

更新日期：2001-06-29 00:00:00

abstract：:The terminal deoxynucleotidyl transferase gene (TdT) is expressed in mice only in early B and T lymphoid precursors a few days after birth. Transactivating factors have been shown to contribute to the lymphoid specific expression of TdT, but they do not account entirely for the restriction of its expression to early p...

journal_title：Journal of molecular biology

authors： Nourrit F,Coquilleau I,D'Andon MF,Rougeon F,Doyen N

更新日期：1999-09-17 00:00:00

abstract：:Using computational and sequence analysis of bacterial cold shock proteins, we designed a protein (CspB-TB) that has the core residues of mesophilic protein from Bacillus subtilis(CspB-Bs) and altered distribution of surface charged residues. This designed protein was characterized by circular dichroism spectroscopy, ...

journal_title：Journal of molecular biology

authors： Makhatadze GI,Loladze VV,Gribenko AV,Lopez MM

更新日期：2004-02-27 00:00:00