Browsing by Subject "Models, Molecular"
Now showing items 1-20 of 36
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A kinesin motor in a force-producing conformation.
(BMC Struct Biol, 2010-07-05)BACKGROUND: Kinesin motors hydrolyze ATP to produce force and move along microtubules, converting chemical energy into work by a mechanism that is only poorly understood. Key transitions and intermediate states in the process ... -
Cloning and expression of a human kidney cDNA for an alpha 2-adrenergic receptor subtype.
(Proc Natl Acad Sci U S A, 1988-09)An alpha 2-adrenergic receptor subtype has been cloned from a human kidney cDNA library using the gene for the human platelet alpha 2-adrenergic receptor as a probe. The deduced amino acid sequence resembles the human platelet ... -
Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus.
(Nature, 2013-04-25)Current human immunodeficiency virus-1 (HIV-1) vaccines elicit strain-specific neutralizing antibodies. However, cross-reactive neutralizing antibodies arise in approximately 20% of HIV-1-infected individuals, and details ... -
Computational crystallization.
(Arch Biochem Biophys, 2016-07-15)Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process ... -
Computational Methods for RNA Structure Validation and Improvement.
(Methods Enzymol, 2015)With increasing recognition of the roles RNA molecules and RNA/protein complexes play in an unexpected variety of biological processes, understanding of RNA structure-function relationships is of high current importance. ... -
Conductive junctions with parallel graphene sheets.
(J Chem Phys, 2010-03-21)The establishment of conductive graphene-molecule-graphene junction is investigated through first-principles electronic structure calculations and quantum transport calculations. The junction consists of a conjugated molecule ... -
Conformational changes of FtsZ reported by tryptophan mutants.
(Biochemistry, 2011-05-03)E. coli FtsZ has no native tryptophan. We showed previously that the mutant FtsZ L68W gave a 2.5-fold increase in trp fluorescence when assembly was induced by GTP. L68 is probably buried in the protofilament interface upon ... -
Conformational kinetics reveals affinities of protein conformational states.
(Proc Natl Acad Sci U S A, 2015-07-28)Most biological reactions rely on interplay between binding and changes in both macromolecular structure and dynamics. Practical understanding of this interplay requires detection of critical intermediates and determination ... -
Consensus nomenclature for the human ArfGAP domain-containing proteins.
(J Cell Biol, 2008-09-22)At the FASEB summer research conference on "Arf Family GTPases", held in Il Ciocco, Italy in June, 2007, it became evident to researchers that our understanding of the family of Arf GTPase activating proteins (ArfGAPs) has ... -
Control of the orientational order and nonlinear optical response of the "push-pull" chromophore RuPZn via specific incorporation into densely packed monolayer ensembles of an amphiphilic four-helix bundle peptide: characterization of the peptide-chromophore complexes.
(J Am Chem Soc, 2010-08-18)"Push-pull" chromophores based on extended pi-electron systems have been designed to exhibit exceptionally large molecular hyperpolarizabilities. We have engineered an amphiphilic four-helix bundle peptide to vectorially ... -
Crystallization of asymmetric patchy models for globular proteins in solution.
(Phys Rev E Stat Nonlin Soft Matter Phys, 2013-07)Asymmetric patchy particle models have recently been shown to describe the crystallization of small globular proteins with near-quantitative accuracy. Here, we investigate how asymmetry in patch geometry and bond energy ... -
De novo design and molecular assembly of a transmembrane diporphyrin-binding protein complex.
(J Am Chem Soc, 2010-11-10)The de novo design of membrane proteins remains difficult despite recent advances in understanding the factors that drive membrane protein folding and association. We have designed a membrane protein PRIME (PoRphyrins In ... -
Drug design from the cryptic inhibitor envelope.
(Nat Commun, 2016-02-25)Conformational dynamics plays an important role in enzyme catalysis, allosteric regulation of protein functions and assembly of macromolecular complexes. Despite these well-established roles, such information has yet to ... -
Electron tomography of cryofixed, isometrically contracting insect flight muscle reveals novel actin-myosin interactions.
(PLoS One, 2010-09-09)BACKGROUND: Isometric muscle contraction, where force is generated without muscle shortening, is a molecular traffic jam in which the number of actin-attached motors is maximized and all states of motor action are trapped ... -
Emergence of limit-periodic order in tiling models.
(Phys Rev E Stat Nonlin Soft Matter Phys, 2014-07)A two-dimensional (2D) lattice model defined on a triangular lattice with nearest- and next-nearest-neighbor interactions based on the Taylor-Socolar monotile is known to have a limit-periodic ground state. The system reaches ... -
Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor.
(Nat Commun, 2014-06-17)How viral packaging motors generate enormous forces to translocate DNA into viral capsids remains unknown. Recent structural studies of the bacteriophage T4 packaging motor have led to a proposed mechanism wherein the gp17 ... -
Evolutionary genomics and adaptive evolution of the Hedgehog gene family (Shh, Ihh and Dhh) in vertebrates.
(PLoS One, 2014)The Hedgehog (Hh) gene family codes for a class of secreted proteins composed of two active domains that act as signalling molecules during embryo development, namely for the development of the nervous and skeletal systems ... -
FtsZ Protofilament Curvature Is the Opposite of Tubulin Rings.
(Biochemistry, 2016-07)FtsZ protofilaments (pfs) form the bacterial cytokinetic Z ring. Previous work suggested that a conformational change from straight to curved pfs generated the constriction force. In the simplest model, the C-terminal membrane ... -
Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies.
(PLoS Comput Biol, 2010-10-07)A steady increase in knowledge of the molecular and antigenic structure of the gp120 and gp41 HIV-1 envelope glycoproteins (Env) is yielding important new insights for vaccine design, but it has been difficult to translate ...
