32,226 research outputs found
Predicted Structures and Dynamics for Agonists and Antagonists Bound to Serotonin 5-HT2B and 5-HT2C Receptors
Subtype 2 serotonin (5-hydroxytryptamine, 5-HT) receptors are major drug targets for schizophrenia, feeding disorders, perception,
depression, migraines, hypertension, anxiety, hallucinogens, and
gastrointestinal dysfunctions.' We report here the predicted structure
of 5-HT2B and 5-HT2C receptors bound to highly potent and selective
5-HT2B antagonist PRX-08066 3, (pKi: 30 nM), including the key binding
residues [V103 (2.53), L132 (3.29), V190 (4.60), and L347 (6.58)]
determining the selectivity of binding to 5-HT2B over 5-HT2A. We also
report structures of the endogenous agonist (5 HT) and a HT2B selective
antagonist 2 (1-methyl-1-1,6,7,8-tetrahydro-pyrrolo
[2,3-g]quinoline-5-carboxylic acid pyridine-3-ylamide). We examine
the dynamics for the agonist-and antagonist-bound HT2B receptors in
explicit membrane and water finding dramatically different patterns of
water migration into the NPxxY motif and the binding site that
correlates with the stability of ionic locks in the D(E)RY region
Study of the Differential Activity of Thrombin Inhibitors Using Docking, QSAR, Molecular Dynamics, and MM-GBSA
Indexación: Web of Science; Scopus.Non-peptidic thrombin inhibitors (TIs; 177 compounds) with diverse groups at motifs P1 (such as oxyguanidine, amidinohydrazone, amidine, amidinopiperidine), P2 (such as cyano-fluorophenylacetamide, 2-(2-chloro-6-fluorophenyl)acetamide), and P3 (such as phenylethyl, arylsulfonate groups) were studied using molecular modeling to analyze their interactions with S1, S2, and S3 subsites of the thrombin binding site. Firstly, a protocol combining docking and three dimensional quantitative structure-activity relationship was performed. We described the orientations and preferred active conformations of the studied inhibitors, and derived a predictive CoMSIA model including steric, donor hydrogen bond, and acceptor hydrogen bond fields. Secondly, the dynamic behaviors of some selected TIs (compounds 26, 133, 147, 149, 162, and 177 in this manuscript) that contain different molecular features and different activities were analyzed by creating the solvated models and using molecular dynamics (MD) simulations.We used the conformational structures derived from MD to accomplish binding free energetic calculations using MM-GBSA. With this analysis, we theorized about the effect of van der Waals contacts, electrostatic interactions and solvation in the potency of TIs. In general, the contents reported in this article help to understand the physical and chemical characteristics of thrombin-inhibitor complexes. © 2015 Mena-Ulecia et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.http://journals.plos.org/plosone/article?id=10.1371/journal.pone.014277
Critical assessment of methods of protein structure prediction: Progress and new directions in round XI
Modeling of protein structure from amino acid sequence now plays a major role in structural biology. Here we report new
developments and progress from the CASP11 community experiment, assessing the state of the art in structure modeling.
Notable points include the following: (1) New methods for predicting three dimensional contacts resulted in a few spectacular
template free models in this CASP, whereas models based on sequence homology to proteins with experimental structure
continue to be the most accurate. (2) Refinement of initial protein models, primarily using molecular dynamics related
approaches, has now advanced to the point where the best methods can consistently (though slightly) improve nearly all
models. (3) The use of relatively sparse NMR constraints dramatically improves the accuracy of models, and another type of
sparse data, chemical crosslinking, introduced in this CASP, also shows promise for producing better models. (4) A new
emphasis on modeling protein complexes, in collaboration with CAPRI, has produced interesting results, but also shows the
need for more focus on this area. (5) Methods for estimating the accuracy of models have advanced to the point where they
are of considerable practical use. (6) A first assessment demonstrates that models can sometimes successfully address biological
questions that motivate experimental structure determination. (7) There is continuing progress in accuracy of modeling
regions of structure not directly available by comparative modeling, while there is marginal or no progress in some other
areas
A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family.
Conformational ensembles are increasingly recognized as a useful representation to describe fundamental relationships between protein structure, dynamics and function. Here we present an ensemble of ubiquitin in solution that is created by sampling conformational space without experimental information using "Backrub" motions inspired by alternative conformations observed in sub-Angstrom resolution crystal structures. Backrub-generated structures are then selected to produce an ensemble that optimizes agreement with nuclear magnetic resonance (NMR) Residual Dipolar Couplings (RDCs). Using this ensemble, we probe two proposed relationships between properties of protein ensembles: (i) a link between native-state dynamics and the conformational heterogeneity observed in crystal structures, and (ii) a relation between dynamics of an individual protein and the conformational variability explored by its natural family. We show that the Backrub motional mechanism can simultaneously explore protein native-state dynamics measured by RDCs, encompass the conformational variability present in ubiquitin complex structures and facilitate sampling of conformational and sequence variability matching those occurring in the ubiquitin protein family. Our results thus support an overall relation between protein dynamics and conformational changes enabling sequence changes in evolution. More practically, the presented method can be applied to improve protein design predictions by accounting for intrinsic native-state dynamics
The cyanobacterial ribosomal-associated protein LrtA from Synechocystis sp. PCC 6803 is an oligomeric protein in solution with chameleonic sequence properties
The LrtA protein of Synechocystis sp. PCC 6803 intervenes in cyanobacterial post-stress
survival and in stabilizing 70S ribosomal particles. It belongs to the hibernating promoting factor
(HPF) family of proteins, involved in protein synthesis. In this work, we studied the conformational
preferences and stability of isolated LrtA in solution. At physiological conditions, as shown by
hydrodynamic techniques, LrtA was involved in a self-association equilibrium. As indicated by
Nuclear Magnetic Resonance (NMR), circular dichroism (CD) and fluorescence, the protein acquired
a folded, native-like conformation between pH 6.0 and 9.0. However, that conformation was not
very stable, as suggested by thermal and chemical denaturations followed by CD and fluorescence.
Theoretical studies of its highly-charged sequence suggest that LrtA had a Janus sequence, with a
context-dependent fold. Our modelling and molecular dynamics (MD) simulations indicate that the
protein adopted the same fold observed in other members of the HPF family ( - - - - - ) at its
N-terminal region (residues 1–100), whereas the C terminus (residues 100–197) appeared disordered
and collapsed, supporting the overall percentage of overall secondary structure obtained by CD
deconvolution. Then, LrtA has a chameleonic sequence and it is the first member of the HPF family
involved in a self-association equilibrium, when isolated in solution.Ministerio de Economía y Competitividad CTQ2015-64445-RMinisterio de Economía y Competitividad BIO2016-78020-RMinisterio de Economía y Competitividad FIS2014-52212-RMinisterio de Economía y Competitividad BIO2016-75634-PFundación Séneca 19353/PI/1
Structural basis for sequence specific DNA binding and protein dimerization of HOXA13.
The homeobox gene (HOXA13) codes for a transcription factor protein that binds to AT-rich DNA sequences and controls expression of genes during embryonic morphogenesis. Here we present the NMR structure of HOXA13 homeodomain (A13DBD) bound to an 11-mer DNA duplex. A13DBD forms a dimer that binds to DNA with a dissociation constant of 7.5 nM. The A13DBD/DNA complex has a molar mass of 35 kDa consistent with two molecules of DNA bound at both ends of the A13DBD dimer. A13DBD contains an N-terminal arm (residues 324 - 329) that binds in the DNA minor groove, and a C-terminal helix (residues 362 - 382) that contacts the ATAA nucleotide sequence in the major groove. The N370 side-chain forms hydrogen bonds with the purine base of A5* (base paired with T5). Side-chain methyl groups of V373 form hydrophobic contacts with the pyrimidine methyl groups of T5, T6* and T7*, responsible for recognition of TAA in the DNA core. I366 makes similar methyl contacts with T3* and T4*. Mutants (I366A, N370A and V373G) all have decreased DNA binding and transcriptional activity. Exposed protein residues (R337, K343, and F344) make intermolecular contacts at the protein dimer interface. The mutation F344A weakens protein dimerization and lowers transcriptional activity by 76%. We conclude that the non-conserved residue, V373 is critical for structurally recognizing TAA in the major groove, and that HOXA13 dimerization is required to activate transcription of target genes
Comment on "Deficiencies in molecular dynamics simulation-based prediction of protein-DNA binding free energy landscapes"
Sequence-specific DNA binding transcription factors play an essential role in the transcriptional regulation of all organisms. The development of reliable in silico methods to predict the binding affinity landscapes of transcription factors thus promises to provide rapid screening of transcription factor specificities and, at the same time, yield valuable insight into the atomistic details of the interactions driving those specificities. Recent literature has reported highly discrepant results on the current ability of state-of-the-art atomistic molecular dynamics simulations to reproduce experimental binding free energy landscapes for transcription factors. Here, we resolve one important discrepancy by noting that in the case of alchemical free energy calculations involving base pair mutations, a common convention used in improving end point convergence of mixed potentials in fact can lead to erroneous results. The underlying cause for inaccurate double free energy difference estimates is specific to the particular implementation of the alchemical transformation protocol. Using the Gromacs simulation package, which is not affected by this issue, we obtain free energy landscapes in agreement with the experimental measurements; equivalent results are obtained for a small set of test cases with a modified version of the AMBER package. Our findings provide a consistent and optimistic outlook on the current state of prediction of protein-DNA binding free energy interactions using molecular dynamics simulations and an important precaution for appropriate end point handling in a broad range of free energy calculations
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