368 research outputs found
A hierarchical approach to the prediction of the quaternary structure of GCN4 and its mutants
First published in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 23 (1996) published by the American Mathematical Society.Presented at DIMACS Workshop on Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, March 20-21, 1995.A hierarchical approach to protein folding is employed to examine the folding pathway and predict the quaternary structure of the GCN4 leucine zipper. Structures comparable in quality to experiment have been predicted. In addition, the equilibrium between dimers, trimers and tetramers of a number of GCN4 mutants has been examined. In five out of eight cases, the simulation results are in accordance with the experimental studies of Harbury, et al
Topography Experiment (TOPEX) Software Document Series Volume 7: TOPEX Mission Radar Altimeter Engineering Assessment Report, February 1994
This document describes the GSFC/WFF analysis of the on-orbit engineering data from the TOPEX radar altimeter, to establish altimeter performance. In accordance with Project guidelines, neither surface truth nor precision orbital data are used for the engineering assessment of the altimeter. The use of such data would imply not only a more intensive and complete performance evaluation, but also a calibration. Such evaluations and.calibrations are outside the scope of this document and will be presented in a separate Verification Report
Modal expansions and non-perturbative quantum field theory in Minkowski space
We introduce a spectral approach to non-perturbative field theory within the
periodic field formalism. As an example we calculate the real and imaginary
parts of the propagator in 1+1 dimensional phi^4 theory, identifying both
one-particle and multi-particle contributions. We discuss the computational
limits of existing diagonalization algorithms and suggest new quasi-sparse
eigenvector methods to handle very large Fock spaces and higher dimensional
field theories.Comment: new material added, 12 pages, 6 figure
Warm and Cold Denaturation in the Phase Diagram of a Protein Lattice Model
Studying the properties of the solvent around proteins, we propose a much
more sophisticated model of solvation than temperature-independent pairwise
interactions between monomers, as is used commonly in lattice representations.
We applied our model of solvation to a 16-monomer chain constrained on a
two-dimensional lattice. We compute a phase diagram function of the temperature
and a solvent parameter which is related to the pH of the solution. It exhibits
a native state in which the chain coalesces into a unique compact conformation
as well as a denatured state. Under certain solvation conditions, both warm and
cold denaturations occur between the native and the denatured states. A good
agreement is found with the data obtained from calorimetric experiments,
thereby validating the proposed model.Comment: 7 pages, 2 figure
Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch
Single-stranded RNAs (ssRNAs) are ubiquitous RNA elements that serve diverse functional roles. Much of our understanding of ssRNA conformational behavior is limited to structures in which ssRNA directly engages in tertiary interactions or is recognized by proteins. Little is known about the structural and dynamic behavior of free ssRNAs at atomic resolution. Here, we report the collaborative application of nuclear magnetic resonance (NMR) and replica exchange molecular dynamics (REMD) simulations to characterize the 12 nt ssRNA tail derived from the prequeuosine riboswitch. NMR carbon spin relaxation data and residual dipolar coupling measurements reveal a flexible yet stacked core adopting an A-form-like conformation, with the level of order decreasing toward the terminal ends. An A-to-C mutation within the polyadenine tract alters the observed dynamics consistent with the introduction of a dynamic kink. Pre-ordering of the tail may increase the efficacy of ligand binding above that achieved by a random-coil ssRNA. The REMD simulations recapitulate important trends in the NMR data, but suggest more internal motions than inferred from the NMR analysis. Our study unmasks a previously unappreciated level of complexity in ssRNA, which we believe will also serve as an excellent model system for testing and developing computational force fields
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Integrated product definition representation for agile numerical control applications
Realization of agile manufacturing capabilities for a virtual enterprise requires the integration of technology, management, and work force into a coordinated, interdependent system. This paper is focused on technology enabling tools for agile manufacturing within a virtual enterprise specifically relating to Numerical Control (N/C) manufacturing activities and product definition requirements for these activities
Molecular dynamics simulation of polymer helix formation using rigid-link methods
Molecular dynamics simulations are used to study structure formation in
simple model polymer chains that are subject to excluded volume and torsional
interactions. The changing conformations exhibited by chains of different
lengths under gradual cooling are followed until each reaches a state from
which no further change is possible. The interactions are chosen so that the
true ground state is a helix, and a high proportion of simulation runs succeed
in reaching this state; the fraction that manage to form defect-free helices is
a function of both chain length and cooling rate. In order to demonstrate
behavior analogous to the formation of protein tertiary structure, additional
attractive interactions are introduced into the model, leading to the
appearance of aligned, antiparallel helix pairs. The simulations employ a
computational approach that deals directly with the internal coordinates in a
recursive manner; this representation is able to maintain constant bond lengths
and angles without the necessity of treating them as an algebraic constraint
problem supplementary to the equations of motion.Comment: 15 pages, 14 figure
Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure
Riboswitches are structural elements in the 50 untranslated regions of many bacterial messenger RNAs that regulate gene expression in response to changing metabolite concentrations by inhibition of either transcription or translation initiation. The preQ1 (7-aminomethyl-7-deazaguanine) riboswitch family comprises some of the smallest metabolite sensing RNAs found in nature. Once ligand-bound, the transcriptional Bacillus subtilis and translational Thermoanaerobacter tengcongensis preQ1 riboswitch aptamers are structurally similar RNA pseudoknots; yet, prior structural studies have characterized their ligand-free conformations as largely unfolded and folded, respectively. In contrast, through single molecule observation, we now show that, at nearphysiological Mg2+ concentration and pH, both ligand-free aptamers adopt similar pre-folded state ensembles that differ in their ligand-mediated folding. Structure-based Go¯ -model simulations of the two aptamers suggest that the ligand binds late (Bacillus subtilis) and early (Thermoanaerobacter tengcongensis) relative to pseudoknot folding, leading to the proposal that the principal distinction between the two riboswitches lies in their relative tendencies to fold via mechanisms of conformational selection and induced fit, respectively. These mechanistic insights are put to the test by rationally designing a single nucleotide swap distal from the ligand binding pocket that we find to predictably control the aptamers0 pre-folded states and their ligand binding affinities
The network topology of a potential energy landscape: A static scale-free network
Here we analyze the topology of the network formed by the minima and
transition states on the potential energy landscape of small clusters. We find
that this network has both a small-world and scale-free character. In contrast
to other scale-free networks, where the topology results from the dynamics of
the network growth, the potential energy landscape is a static entity.
Therefore, a fundamentally different organizing principle underlies this
behaviour: The potential energy landscape is highly heterogeneous with the
low-energy minima having large basins of attraction and acting as the
highly-connected hubs in the network.Comment: 4 pages, 4 figures, revtex
The NCAS mobile dual-polarisation Doppler X-band weather radar (NXPol)
In recent years, dual-polarisation Doppler X-band radars have become a widely used part of the atmospheric scientist's toolkit for examining cloud dynamics and microphysics and making quantitative precipitation estimates. This is especially true for research questions that require mobile radars. Here we describe the National Centre for Atmospheric Science (NCAS) mobile X-band dual-polarisation Doppler weather radar (NXPol) and the infrastructure used to deploy the radar and provide an overview of the technical specifications. It is the first radar of its kind in the UK. The NXPol is a Meteor 50DX manufactured by Selex- Gematronik (Selex ES GmbH), modified to operate with a larger 2.4m diameter antenna that produces a 0.98 halfpower beam width and without a radome. We provide an overview of the technical specifications of the NXPol with emphasis given to the description of the aspects of the infrastructure developed to deploy the radar as an autonomous observing facility in remote locations. To demonstrate the radar's capabilities, we also present examples of its use in three recent field campaigns and its ongoing observations at the NERC Facility for Atmospheric Radio Research (NFARR)
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