Mediator Architecture and RNA Polymerase II Interaction.

abstract：:Transcription activator-like effectors (TALEs) recognize DNA through repeat-variable diresidues (RVDs), and TALE-DNA interactions are sensitive to DNA modifications. Our previous study deciphered the recognition of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) by TALEs. Here, we report seven crystal struct...

journal_title：Journal of molecular biology

authors： Liu L,Zhang Y,Liu M,Wei W,Yi C,Peng J

更新日期：2020-02-14 00:00:00

abstract：:Prion diseases are neurodegenerative disorders caused by the misfolding of the cellular prion protein (PrPC). Gerstmann-Sträussler-Scheinker syndrome is an inherited prion disease with one early-onset allele (HRdup) containing an eight-amino-acid insertion; this LGGLGGYV insert is positioned after valine 129 (human Pr...

journal_title：Journal of molecular biology

authors： Fu ZL,Holmes PC,Westaway D,Sykes BD

更新日期：2019-06-28 00:00:00

abstract：:Herpesvirus proteases are essential for the production of progeny virus. They cleave the assembly protein that fills the immature capsid in order to make place for the viral DNA. The recombinant protease of the human gamma-herpesvirus Epstein-Barr virus (EBV) was expressed in Escherichia coli and purified. Circular di...

journal_title：Journal of molecular biology

authors： Buisson M,Valette E,Hernandez JF,Baudin F,Ebel C,Morand P,Seigneurin JM,Arlaud GJ,Ruigrok RW

更新日期：2001-08-03 00:00:00

abstract：:At low ionic strength, the SfiI restriction enzyme cleaved at similar rates both supercoiled and linear DNA with two SfiI sites and linear DNA with one SfiI site. For the substrates with two sites, the majority of the DNA was converted directly to products cut at both sites; the enzyme appears to bind to two sites bef...

journal_title：Journal of molecular biology

authors： Nobbs TJ,Halford SE

更新日期：1995-09-29 00:00:00

abstract：:The repair of double-strand breaks in DNA is an essential process in all organisms, and requires the coordinated activities of evolutionarily conserved protein assemblies. One of the most critical of these is the Mre11/Rad50 (M/R) complex, which is present in all three biological kingdoms, but is not well-understood a...

journal_title：Journal of molecular biology

authors： Moncalian G,Lengsfeld B,Bhaskara V,Hopfner KP,Karcher A,Alden E,Tainer JA,Paull TT

更新日期：2004-01-23 00:00:00

abstract：:The structure of goose egg-white lysozyme (GEWL) has been refined to an R-value of 15.9% at 1.6 A resolution. Details of the structure determination, the refinement and the structure itself are presented. The structure of a complex of the enzyme with the trisaccharide of N-acetyl glucosamine has also been determined a...

journal_title：Journal of molecular biology

authors： Weaver LH,Grütter MG,Matthews BW

更新日期：1995-01-06 00:00:00

abstract：:A combination of Monte Carlo simulated annealing and energy minimization was utilized to determine the conformation of the antifreeze protein from the fish winter flounder. It was found from the energy-optimized structure that the hydroxyl groups of its four threonine residues, i.e. Thr2, Thr13, Thr24, Thr35, are alig...

journal_title：Journal of molecular biology

authors： Chou KC

更新日期：1992-01-20 00:00:00

abstract：:The crystal structure of Thermoactinomyces vulgaris R-47 alpha-Amylase II (TVAII) has been determined by multiple isomorphous replacement at 2.6 A resolution. TVAII was crystallized in an orthorhombic system with the space group P212121 and the cell dimensions a=118.5 A, b=119.5 A, c=114.5 A. There are two molecules i...

journal_title：Journal of molecular biology

authors： Kamitori S,Kondo S,Okuyama K,Yokota T,Shimura Y,Tonozuka T,Sakano Y

更新日期：1999-04-16 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：:Harold Erickson has recently provided a useful analysis of helical structures having one class versus two classes of intersubunit bonds. His analysis is based upon an assumption that the subunits themselves are essentially unchanged upon bond formation (polymerization). He shows that such a structure having two classe...

journal_title：Journal of molecular biology

authors： Egelman EH,DeRosier DJ

更新日期：1991-02-05 00:00:00

abstract：:LIM-kinase activated by GST-Pak1 phosphorylates Acanthamoeba actophorin stoichiometrically and specifically on serine 1. The atomic structure of phosphorylated actophorin determined by X-ray crystallography is essentially identical with the structure of unphosphorylated actophorin. We compared biochemical properties o...

journal_title：Journal of molecular biology

authors： Blanchoin L,Robinson RC,Choe S,Pollard TD

更新日期：2000-01-14 00:00:00

abstract：:Nucleoside diphosphate kinase A (NDPK-A) regulates the alpha1 isoform of the AMP-activated protein kinase (AMPK alpha1) selectively, independent of [AMP] and surrounding [ATP], by a process termed substrate channelling. Here, we show, using a range of empirically validated biochemical techniques, that the muscle form ...

journal_title：Journal of molecular biology

authors： Jovanović S,Jovanović A,Crawford RM

更新日期：2007-08-10 00:00:00

abstract：:The mutants P235A and F236A have been generated and their crystal structure was determined to resolutions of 2.38 and 2.35 A, respectively, in order to understand the residues involved in the formation of the novel arched P-loop of subunit A of the A-ATP synthase from Pyrococcus horikoshii OT3. Both the structures sho...

journal_title：Journal of molecular biology

authors： Kumar A,Manimekalai MS,Balakrishna AM,Priya R,Biuković G,Jeyakanthan J,Grüber G

更新日期：2010-09-03 00:00:00

abstract：:We report the first protein phase-diagram characterized by a combination of volumetric, calorimetric, and spectroscopic techniques. More specifically, we use ultrasonic velocimetry, densimetry, and differential scanning calorimetry, in conjunction with UV absorbance and CD spectroscopy to detect and to characterize th...

journal_title：Journal of molecular biology

authors： Chalikian TV,Völker J,Anafi D,Breslauer KJ

更新日期：1997-11-28 00:00:00

abstract：:The reverse transcriptase (RT) of HIV-1 and feline immunodeficiency virus (FIV) consist of two subunits of 51 kDa (p51) and 66 kDa (p66). In order to elucidate the role of p51 in the heterodimer, chimeric HIV-1/FIV RT heterodimers were constructed and characterized. The FIV RT p51/HIV-1 RT p66 chimera showed a 2.5-fol...

journal_title：Journal of molecular biology

authors： Amacker M,Hübscher U

更新日期：1998-05-15 00:00:00

abstract：:Sirtuins are NAD+-dependent protein deacetylase enzymes that are broadly conserved from bacteria to human, and have been implicated to play important roles in gene regulation, metabolism and longevity. cobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase (Acs) at an active site lysine to stimulate its e...

journal_title：Journal of molecular biology

authors： Zhao K,Chai X,Marmorstein R

更新日期：2004-03-26 00:00:00

abstract：:Riboswitches are complex folded RNA domains found in noncoding regions of mRNA that regulate gene expression upon small molecule binding. Recently, Breaker and coworkers reported a tandem aptamer riboswitch (VCI-II) that binds glycine cooperatively. Here, we use hydroxyl radical footprinting and small-angle X-ray scat...

journal_title：Journal of molecular biology

authors： Lipfert J,Das R,Chu VB,Kudaravalli M,Boyd N,Herschlag D,Doniach S

更新日期：2007-02-02 00:00:00

abstract：:Anterior gradient-2 (AGR2) functions in a range of biological systems, including goblet cell formation, limb regeneration, inhibition of p53, and metastasis. There are no well-validated binding proteins for AGR2 protein despite the wealth of data implicating an important cellular function in vertebrates. The yeast two...

journal_title：Journal of molecular biology

authors： Maslon MM,Hrstka R,Vojtesek B,Hupp TR

更新日期：2010-12-03 00:00:00

abstract：:We carry out a theoretical study of the vibrational and relaxation properties of naturally occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model, we provide a full characterization of the spectrum and eigenmodes of vibration at various tempe...

journal_title：Journal of molecular biology

authors： Micheletti C,Lattanzi G,Maritan A

更新日期：2002-08-30 00:00:00

abstract：:The excessive activity of matrix metalloproteinases (MMPs) contributes to pathological processes such as arthritis, tumor growth and metastasis if not balanced by the tissue inhibitors of metalloproteinases (TIMPs). In arthritis, the destruction of fibrillar (type II) collagen is one of the hallmarks, with MMP-1 (coll...

journal_title：Journal of molecular biology

authors： Maskos K,Lang R,Tschesche H,Bode W

更新日期：2007-03-02 00:00:00

abstract：:Cytokinesis of animal cells requires the assembly of a contractile ring, which promotes daughter cell splitting. Anillin is a conserved scaffold protein involved in organizing the structural components of the contractile ring including filamentous actin (F-actin), myosin, and septins and in forming the subsequent midb...

journal_title：Journal of molecular biology

authors： Jananji S,Risi C,Lindamulage IKS,Picard LP,Van Sciver R,Laflamme G,Albaghjati A,Hickson GRX,Kwok BH,Galkin VE

更新日期：2017-03-10 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：:Cholera toxin B-oligomer was imaged by atomic force microscopy (AFM) on biologically relevant model membranes, such as 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine and egg yolk phosphatidylcholine at room temperature in solution at a resolution in the range of 1 to 2 nm. In addition, two-dimensional arrays we...

journal_title：Journal of molecular biology

authors： Mou J,Yang J,Shao Z

更新日期：1995-05-05 00:00:00

abstract：:With a view to obtaining a more complete view of the composition and structure of the thick filaments of vertebrate skeletal muscle, we have isolated and characterized two new myofibrillar components, H-protein and X-protein. These were purified by hydroxyapatite column chromatography of an impure C-protein preparatio...

journal_title：Journal of molecular biology

authors： Starr R,Offer G

更新日期：1983-11-05 00:00:00

abstract：:Genetic circuits, composed of complex networks of interacting molecular machines, enable living systems to sense their dynamic environments, perform computation on the inputs, and formulate appropriate outputs. By rewiring and expanding these circuits with novel parts and modules, synthetic biologists have adapted liv...

journal_title：Journal of molecular biology

authors： Ma KC,Perli SD,Lu TK

更新日期：2016-02-27 00:00:00

abstract：:Mitochondrial DNA (mtDNA) sequence variation can influence the penetrance of complex diseases and climatic adaptation. While studies in geographically defined human populations suggest that mtDNA mutations become fixed when they have conferred metabolic capabilities optimally suited for a specific environment, it has ...

journal_title：Journal of molecular biology

authors： Dingley SD,Polyak E,Ostrovsky J,Srinivasan S,Lee I,Rosenfeld AB,Tsukikawa M,Xiao R,Selak MA,Coon JJ,Hebert AS,Grimsrud PA,Kwon YJ,Pagliarini DJ,Gai X,Schurr TG,Hüttemann M,Nakamaru-Ogiso E,Falk MJ

更新日期：2014-05-29 00:00:00

abstract：:Previous work has shown that the α-tocopherol transfer protein (α-TTP) can bind to vesicular or immobilized phospholipid membranes. Revealing the molecular mechanisms by which α-TTP associates with membranes is thought to be critical to understanding its function and role in the secretion of tocopherol from hepatocyte...

journal_title：Journal of molecular biology

authors： Zhang WX,Thakur V,Lomize A,Pogozheva I,Panagabko C,Cecchini M,Baptist M,Morley S,Manor D,Atkinson J

更新日期：2011-01-28 00:00:00

abstract：:Crystalline complexes of tyrosyl-tRNA synthetase from Bacillus stearothermophilus were prepared with adenosine, AMP, ATP and PPi, all in the presence of tyrosinol, which binds strongly to the tyrosine binding site but cannot be adenylated by ATP. The hydrolysis of ATP in the presence of crystalline tyrosyl-tRNA synthe...

journal_title：Journal of molecular biology

authors： Monteilhet C,Blow DM,Brick P

更新日期：1984-03-15 00:00:00

abstract：:The loop between the F and G beta strands (FG loop) of the bacteriophage MS2 coat protein subunit forms inter-subunit contacts around the 5-fold and 3-fold (quasi 6-fold) axes of the T=3 protein shell. In capsids, the loop is found in two very different conformations, one in B subunits, which form the 5-fold contact, ...

journal_title：Journal of molecular biology

authors： Stonehouse NJ,Valegård K,Golmohammadi R,van den Worm S,Walton C,Stockley PG,Liljas L

更新日期：1996-02-23 00:00:00

abstract：:Drugs can affect function in proteins by modulating their flexibility. Despite this possibility, there are very few studies on how drug binding affects the dynamics of target macromolecules. FKBP12 (FK506 binding protein 12) is a prolyl cis-trans isomerase and a drug target. The immunosuppressant drug rapamycin exerts...

journal_title：Journal of molecular biology

authors： Sapienza PJ,Mauldin RV,Lee AL

更新日期：2011-01-14 00:00:00