4,081 research outputs found
Computational structureâbased drug design: Predicting target flexibility
The role of molecular modeling in drug design has experienced a significant revamp in the last decade. The increase in computational resources and molecular models, along with software developments, is finally introducing a competitive advantage in early phases of drug discovery. Medium and small companies with strong focus on computational chemistry are being created, some of them having introduced important leads in drug design pipelines. An important source for this success is the extraordinary development of faster and more efficient techniques for describing flexibility in threeâdimensional structural molecular modeling. At different levels, from docking techniques to atomistic molecular dynamics, conformational sampling between receptor and drug results in improved predictions, such as screening enrichment, discovery of transient cavities, etc. In this review article we perform an extensive analysis of these modeling techniques, dividing them into high and low throughput, and emphasizing in their application to drug design studies. We finalize the review with a section describing our Monte Carlo method, PELE, recently highlighted as an outstanding advance in an international blind competition and industrial benchmarks.We acknowledge the BSC-CRG-IRB Joint Research Program in Computational Biology. This work was supported by a grant
from the Spanish Government CTQ2016-79138-R.J.I. acknowledges support from SVP-2014-068797, awarded by the Spanish Government.Peer ReviewedPostprint (author's final draft
Computational protein design with backbone plasticity
The computational algorithms used in the design of artificial proteins have become increasingly sophisticated in recent years, producing a series of remarkable successes. The most dramatic of these is the de novo design of artificial enzymes. The majority of these designs have reused naturally occurring protein structures as âscaffoldsâ onto which novel functionality can be grafted without having to redesign the backbone structure. The incorporation of backbone flexibility into protein design is a much more computationally challenging problem due to the greatly increase search space but promises to remove the limitations of reusing natural protein scaffolds. In this review, we outline the principles of computational protein design methods and discuss recent efforts to consider backbone plasticity in the design process
Inclusion of Enclosed Hydration Effects in the Binding Free Energy Estimation of Dopamine D3 Receptor Complexes
Confined hydration and conformational flexibility are some of the challenges
encountered for the rational design of selective antagonists of G-protein
coupled receptors. We present a set of C3-substituted (-)-stepholidine
derivatives as potent binders of the dopamine D3 receptor. The compounds are
characterized biochemically, as well as by computer modeling using a novel
molecular dynamics-based alchemical binding free energy approach which
incorporates the effect of the displacement of enclosed water molecules from
the binding site. The free energy of displacement of specific hydration sites
is obtained using the Hydration Site Analysis method with explicit solvation.
This work underscores the critical role of confined hydration and
conformational reorganization in the molecular recognition mechanism of
dopamine receptors and illustrates the potential of binding free energy models
to represent these key phenomena.Comment: This is the first report of using enclosed hydration in estimating
binding free energies of protein-ligand complexes using implicit solvatio
Propensity to form amyloid fibrils is encoded as excitations in the free energy landscape of monomeric proteins
Protein aggregation, linked to many of diseases, is initiated when monomers
access rogue conformations that are poised to form amyloid fibrils. We show,
using simulations of src SH3 domain, that mechanical force enhances the
population of the aggregation prone () states, which are rarely populated
under force free native conditions, but are encoded in the spectrum of native
fluctuations. The folding phase diagrams of SH3 as a function of denaturant
concentration (), mechanical force (), and temperature exhibit an
apparent two-state behavior, without revealing the presence of the elusive
states. Interestingly, the phase boundaries separating the folded and
unfolded states at all [C] and fall on a master curve, which can can be
quantitatively described using an analogy to superconductors in a magnetic
field. The free energy profiles as a function of the molecular extension (),
which are accessible in pulling experiments, (), reveal the presence of a
native-like with a disordered solvent-exposed amino terminal
-strand. The structure of the state is identical to that found in
Fyn SH3 by NMR dispersion experiments. We show that the time scale for fibril
formation can be estimated from the population of the state, determined
by the free energy gap separating the native structure and the state, a
finding that can be used to assess fibril forming tendencies of proteins. The
structures of the state are used to show that oligomer formation and
likely route to fibrils occur by a domain-swap mechanism in SH3 domain.Comment: 12 pages, 8 figures, 9 supplementary figures (on 5 more pages), 2
supplementary movies (on youtube
Structural alphabets derived from attractors in conformational space
Background: The hierarchical and partially redundant nature of protein structures justifies the definition of frequently occurring conformations of short fragments as 'states'. Collections of selected representatives for these states define Structural Alphabets, describing the most typical local conformations within protein structures. These alphabets form a bridge between the string-oriented methods of sequence analysis and the coordinate-oriented methods of protein structure analysis.Results: A Structural Alphabet has been derived by clustering all four-residue fragments of a high-resolution subset of the protein data bank and extracting the high-density states as representative conformational states. Each fragment is uniquely defined by a set of three independent angles corresponding to its degrees of freedom, capturing in simple and intuitive terms the properties of the conformational space. The fragments of the Structural Alphabet are equivalent to the conformational attractors and therefore yield a most informative encoding of proteins. Proteins can be reconstructed within the experimental uncertainty in structure determination and ensembles of structures can be encoded with accuracy and robustness.Conclusions: The density-based Structural Alphabet provides a novel tool to describe local conformations and it is specifically suitable for application in studies of protein dynamics. © 2010 Pandini et al; licensee BioMed Central Ltd
Ab initio RNA folding
RNA molecules are essential cellular machines performing a wide variety of
functions for which a specific three-dimensional structure is required. Over
the last several years, experimental determination of RNA structures through
X-ray crystallography and NMR seems to have reached a plateau in the number of
structures resolved each year, but as more and more RNA sequences are being
discovered, need for structure prediction tools to complement experimental data
is strong. Theoretical approaches to RNA folding have been developed since the
late nineties when the first algorithms for secondary structure prediction
appeared. Over the last 10 years a number of prediction methods for 3D
structures have been developed, first based on bioinformatics and data-mining,
and more recently based on a coarse-grained physical representation of the
systems. In this review we are going to present the challenges of RNA structure
prediction and the main ideas behind bioinformatic approaches and physics-based
approaches. We will focus on the description of the more recent physics-based
phenomenological models and on how they are built to include the specificity of
the interactions of RNA bases, whose role is critical in folding. Through
examples from different models, we will point out the strengths of
physics-based approaches, which are able not only to predict equilibrium
structures, but also to investigate dynamical and thermodynamical behavior, and
the open challenges to include more key interactions ruling RNA folding.Comment: 28 pages, 18 figure
CRANKITE: a fast polypeptide backbone conformation sampler
Background: CRANKITE is a suite of programs for simulating backbone conformations of polypeptides and proteins. The core of the suite is an efficient Metropolis Monte Carlo sampler of backbone conformations in continuous three-dimensional space in atomic details.
Methods: In contrast to other programs relying on local Metropolis moves in the space of dihedral angles, our sampler utilizes local crankshaft rotations of rigid peptide bonds in Cartesian space.
Results: The sampler allows fast simulation and analysis of secondary structure formation and conformational changes for proteins of average length
In silico assessment of potential druggable pockets on the surface of α1-Antitrypsin conformers
The search for druggable pockets on the surface of a protein is often performed on a single conformer, treated as a rigid body. Transient druggable pockets may be missed in this approach. Here, we describe a methodology for systematic in silico analysis of surface clefts across multiple conformers of the metastable protein α1-antitrypsin (A1AT). Pathological mutations disturb the conformational landscape of A1AT, triggering polymerisation that leads to emphysema and hepatic cirrhosis. Computational screens for small molecule inhibitors of polymerisation have generally focused on one major druggable site visible in all crystal structures of native A1AT. In an alternative approach, we scan all surface clefts observed in crystal structures of A1AT and in 100 computationally produced conformers, mimicking the native solution ensemble. We assess the persistence, variability and druggability of these pockets. Finally, we employ molecular docking using publicly available libraries of small molecules to explore scaffold preferences for each site. Our approach identifies a number of novel target sites for drug design. In particular one transient site shows favourable characteristics for druggability due to high enclosure and hydrophobicity. Hits against this and other druggable sites achieve docking scores corresponding to a Kd in the ”MânM range, comparing favourably with a recently identified promising lead. Preliminary ThermoFluor studies support the docking predictions. In conclusion, our strategy shows considerable promise compared with the conventional single pocket/single conformer approach to in silico screening. Our best-scoring ligands warrant further experimental investigation
Conformational mechanism for the stability of microtubule-kinetochore attachments
Regulating the stability of microtubule(MT)-kinetochore attachments is
fundamental to avoiding mitotic errors and ensure proper chromosome segregation
during cell division. While biochemical factors involved in this process have
been identified, its mechanics still needs to be better understood. Here we
introduce and simulate a mechanical model of MT-kinetochore interactions in
which the stability of the attachment is ruled by the geometrical conformations
of curling MT-protofilaments entangled in kinetochore fibrils. The model allows
us to reproduce with good accuracy in vitro experimental measurements of the
detachment times of yeast kinetochores from MTs under external pulling forces.
Numerical simulations suggest that geometrical features of MT-protofilaments
may play an important role in the switch between stable and unstable
attachments
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