173 research outputs found
Helix vs. Sheet Formation in a Small Peptide
Segments with the amino acid sequence EKAYLRT appear in natural occurring
proteins both in -helices and -sheets. For this reason, we have
use this peptide to study how secondary structure formation in proteins depends
on the local environment. Our data rely on multicanonical Monte Carlo
simulations where the interactions among all atoms are taken into account.
Results in gas phase are compared with that in an implicit solvent. We find
that both in gas phase and solvated EKAYLRT forms an -helix when not
interacting with other molecules. However, in the vicinity of a -strand,
the peptide forms a -strand. Because of this change in secondary
structure our peptide may provide a simple model for the
transition that is supposedly related to the outbreak of Prion diseases and
similar illnesses.Comment: to appear in Physical Review
Secondary-Structure Design of Proteins by a Backbone Torsion Energy
We propose a new backbone-torsion-energy term in the force field for protein
systems. This torsion-energy term is represented by a double Fourier series in
two variables, the backbone dihedral angles phi and psi. It gives a natural
representation of the torsion energy in the Ramachandran space in the sense
that any two-dimensional energy surface periodic in both phi and psi can be
expanded by the double Fourier series. We can then easily control
secondary-structure-forming tendencies by modifying the torsion-energy surface.
For instance, we can increase/decrease the alpha-helix-forming-tendencies by
lowering/raising the torsion-energy surface in the alpha-helix region and
likewise increase/decrease the beta-sheet-forming tendencies by
lowering/raising the surface in the beta-sheet region in the Ramachandran
space. We applied our approach to AMBER parm94 and AMBER parm96 force fields
and demonstrated that our modifications of the torsion-energy terms resulted in
the expected changes of secondary-structure-forming-tendencies by performing
folding simulations of alpha-helical and beta-hairpin peptides.Comment: 13 pages, (Revtex4), 5 figure
Metadata for ATLAS
This document provides an overview of the metadata, which are needed to characterize ATLAS event data at different levels (a complete run, data streams within a run, luminosity blocks within a run, individual events)
Three-dimensional studies of pathogenic peptides from the c-terminal of Trypanosoma cruzi ribosomal P proteins and their interaction with a monoclonal antibody structural model
The acidic C-terminal peptides from Trypanosoma cruzi ribosomal P proteins are the major target of the antibody response in patients suffering Chagas chronic heart disease. It has been proposed that the disease is triggered by the cross-reaction of these antibodies with the second extra cellular loop of the β1-adrenoreceptor, brought about by the molecular mimicry between the acidic C-terminal peptides and the receptor's loop. To improve the understanding of the structural basis of the autoimmune response against heart receptors, the 3-dimensional structure of the C-terminal peptides of Trypanosoma cruzi ribosomal proteins P0 (EDDDDDFGMGALF) and P2β (EEEDDDMGFGLFD) were solved using the Electrostaticaly Driven MonteCarlo method. Their structures were compared with the second extra-cellular loop of our homology model of human rhodopsin and the existing experimental NMR structures of the C-terminal peptides from human P0 (EESDDDMGFGLFD) and from Leishmania braziliensis P0 (EEADDDMGFGLFD). Docking of Trypanosoma cruzi peptides P0, P2β and human rhodopsin loop into our anti-P2β monoclonal antibody homology model allowed to explore their interactions
Temperature Dependence of Backbone Dynamics in Human Ileal Bile Acid-Binding Protein: Implications for the Mechanism of Ligand Binding
Human ileal bile acid-binding protein (I-BABP), a member of the family of intracellular lipid binding proteins plays a key role in the cellular trafficking and metabolic regulation of bile salts. The protein has two internal and, according to a recent study, an additional superficial binding site and binds di- and trihydroxy bile salts with positive cooperativity and a high degree of site-selectivity. Previously, in the apo form, we have identified an extensive network of conformational fluctuations on the millisecond time scale, which cease upon ligation. Additionally, ligand binding at room temperature was found to be accompanied by a slight rigidification of picosecond-nanosecond (ps-ns) backbone flexibility. In the current study, temperature-dependent N-15 NMR spin relaxation measurements were used to gain more insight into the role of dynamics in human I-BABP-bile salt recognition. According to our analysis, residues sensing a conformational exchange in the apo state can be grouped into two clusters with slightly different exchange rates. The entropy-enthalpy compensation observed for both clusters suggests a disorder-order transition between a ground and a sparsely populated higher energy state in the absence of ligands. Analysis of the faster, ps-ns motion of N-15-H-1 bond vectors indicates an unusual nonlinear temperature-dependence for both ligation states. Intriguingly, while bile salt binding results in a more uniform response to temperature change throughout the protein, the temperature derivative of the generalized order parameter shows different responses to temperature increase for the two forms of the protein in the investigated temperature range. Analysis of both slow and fast motions in human I-BABP indicates largely different energy landscapes for the apo and halo states suggesting that optimization of binding interactions might be achieved by altering the dynamic behavior of specific segments in the protein
The ATLAS trigger - high-level trigger commissioning and operation during early data taking
The ATLAS experiment is one of the two general-purpose experiments due to start operation soon at the Large Hadron Collider (LHC). The LHC will collide protons at a centre of mass energy of 14~TeV, with a bunch-crossing rate of 40~MHz. The ATLAS three-level trigger will reduce this input rate to match the foreseen offline storage capability of 100-200~Hz. This paper gives an overview of the ATLAS High Level Trigger focusing on the system design and its innovative features. We then present the ATLAS trigger strategy for the initial phase of LHC exploitation. Finally, we report on the valuable experience acquired through in-situ commissioning of the system where simulated events were used to exercise the trigger chain. In particular we show critical quantities such as event processing times, measured in a large-scale HLT farm using a complex trigger menu
The ATLAS Trigger/DAQ Authorlist, version 1.0
This is a reference document giving the ATLAS Trigger/DAQ author list, version 1.0 of 20 Nov 2008
The ATLAS Trigger/DAQ Authorlist, version 3.0
This is the ATLAS Trigger/DAQ Authorlist, version 3.0, 11 September 200
The ATLAS Trigger/DAQ Authorlist, version 2.0
This is the ATLAS Trigger/DAQ Authorlist, version 2.0, 31 July 200
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