1,720,996 research outputs found
Relationship between energy distribution and fold stability: Insights from molecular dynamics simulations of native and mutant proteins
No full textMost proteins must fold to a well-defined structure with a minimal
stability to perform their function. Here we use a simple, molecular
dynamics-based, energy decomposition approach to map the principal
energetic interactions in a set of proteins representative of different
folds. This work involves the all-atom simulation and analysis of the
native structures and mutants of five different proteins representative
of an all-alpha (yACPB, Protein A), all-beta (SH3), and a mixed
alpha/beta fold (Proteins G and L). Given a certain structure, a native
sequence and a set Of mutants, we show that our model discriminates the
ability of a mutation to yield a more or less stable protein, in
agreement with experimental data, catching the principal energetic
determinants of protein stabilization. Our approach identifies the
interaction determinants responsible to define a fold and shows that
mutations can either modulate the strength of pair-wise coupling between
residues important for folding or modify the profile of the principal
interactions. Furthermore, we address the question of how to evaluate
the fitness of a sequence to a given structure by comparing the
information contained in the energy map, which recapitulates the
chemistry of the sequence, to that contained in the contact map, which
recapitulates the fold topology. The results show that the better fit
between the energetic properties of the sequence and the fold topology
corresponds to a higher stabilization of the protein. We discuss the
relevance of these observations to the analysis of protein designability
and to the rational evolution of new sequences
Selecting sequences that fold into a defined 3D structure: A new approach for protein design based on molecular dynamics and energetics
No full textThe problem of finding amino acid sequences able to fold into a defined
three-dimensional (3D) structure is at the basis of successful protein
design efforts.
Herein, we present the results of the application of a novel, all-atom
molecular dynamics based, energy decomposition approach to the selection
of sequences able to fold into a given 3D conformation. First, the
energy decomposition approach is applied to natural sequences associated
to a well-defined structure to identify the principal energetic coupling
interactions necessary to stabilize it, defining the specific energetic
signature for the fold. Then, several different sequences are threaded
on the defined 3D structure and only those sequences whose energetic
signature (pattern) is close to that of the natural sequence, according
to a similarity criterion, are selected as able to populate the specific
fold. Furthermore, it is possible to evaluate the fitness of a certain
sequence for a fold by combining the information provided by the
energetic signature to that contained in the contact map. which
recapitulates the fold topology. The results show that the better fit
between the energetic properties of a sequence and the topology
corresponds to a better stabilization of the protein fold by that
sequence. We applied this approach to a library of natural and
artificial WW domain sequences, previously developed by the Ranganathan
group. containing sequences that are experimentally known to be able and
unable to fold into native structures. The results show that our
approach can correctly identify 70\% of the sequences known to populate
the typical WW domain fold. (C) 2009 Elsevier B.V. All rights reserved
Investigating the Mechanism of Peptide Aggregation: Insights from Mixed Monte Carlo-Molecular Dynamics Simulations
No full textAbstractThe early stages of peptide aggregation are currently not accessible by experimental techniques at atomic resolution. In this article, we address this problem through the application of a mixed simulation scheme in which a preliminary coarse-grained Monte Carlo analysis of the free-energy landscape is used to identify representative conformations of the aggregates and subsequent all-atom molecular dynamics simulations are used to analyze in detail possible pathways for the stabilization of oligomers. This protocol was applied to systems consisting of multiple copies of the model peptide GNNQQNY, whose detailed structures in the aggregated state have been recently solved in another study. The analysis of the various trajectories provides dynamical and structural insight into the details of aggregation. In particular, the simulations suggest a hierarchical mechanism characterized by the initial formation of stable parallel β-sheet dimers and identify the formation of the polar zipper motif as a fundamental feature for the stabilization of initial oligomers. Simulation results are consistent with experimentally derived observations and provide an atomically detailed view of the putative initial stages of fibril formation
Predicting Interaction Sites from the Energetics of Isolated Proteins: A New Approach to Epitope Mapping
No full textAbstractAn increasing number of functional studies of proteins have shown that sequence and structural similarities alone may not be sufficient for reliable prediction of their interaction properties. This is particularly true for proteins recognizing specific antibodies, where the prediction of antibody-binding sites, called epitopes, has proven challenging. The antibody-binding properties of an antigen depend on its structure and related dynamics. Aiming to predict the antibody-binding regions of a protein, we investigate a new approach based on the integrated analysis of the dynamical and energetic properties of antigens, to identify nonoptimized, low-intensity energetic interaction networks in the protein structure isolated in solution. The method is based on the idea that recognition sites may correspond to localized regions with low-intensity energetic couplings with the rest of the protein, which allows them to undergo conformational changes, to be recognized by a binding partner, and to tolerate mutations with minimal energetic expense. Upon analyzing the results on isolated proteins and benchmarking against antibody complexes, it is found that the method successfully identifies binding sites located on the protein surface that are accessible to putative binding partners. The combination of dynamics and energetics can thus discriminate between epitopes and other substructures based only on physical properties. We discuss implications for vaccine design
Surface energetics and protein-protein interactions: analysis and mechanistic implications
No full textUnderstanding protein-protein interactions (PPI) at the molecular level
is a fundamental task in the design of new drugs, the prediction of
protein function and the clarification of the mechanisms of
(dis)regulation of biochemical pathways. In this study, we use a novel
computational approach to investigate the energetics of aminoacid
networks located on the surface of proteins, isolated and in complex
with their respective partners. Interestingly, the analysis of
individual proteins identifies patches of surface residues that, when
mapped on the structure of their respective complexes, reveal regions of
residue-pair couplings that extend across the binding interfaces,
forming continuous motifs. An enhanced effect is visible across the
proteins of the dataset forming larger quaternary assemblies. The method
indicates the presence of energetic signatures in the isolated proteins
that are retained in the bound form, which we hypothesize to determine
binding orientation upon complex formation. We propose our method,
BLUEPRINT, as a complement to different approaches ranging from the
ab-initio characterization of PPIs, to protein-protein docking
algorithms, for the physico-chemical and functional investigation of
protein-protein interactions
Exploring Mutation-Driven Changes in the ATP-ADP Conformational Cycle of Human Hsp70 by All-Atom MD Adaptive Sampling
No full textInvestigating Allostery in Molecular Recognition: Insights from a Computational Study of Multiple Antibody-Antigen Complexes
No full textAntibody-antigen recognition plays a key role in the immune response
against pathogens. Here, we have investigated various aspects of this
problem by analyzing a large and diverse set of antibodies and their
respective complexes with protein antigens through atomistic
simulations. Common features of antibody response to the presence of
antigens are elucidated by the analysis of the proteins' internal
dynamics and coordination in different ligand states, combined with the
analysis of the interaction networks implicated in the stabilization of
functional structures. The use of a common structural reference reveals
preferential changes in the dynamic coordination and intramolecular
interaction networks induced by antigen binding and shared by all
antibodies. Such changes propagate from the binding region through the
whole immunoglobulin domains. Overall, complexed antibodies show more
diffuse networks of nonbonded interactions and a general higher internal
dynamic coordination, which preferentially involve the immunoglobulin
(Ig) domains of the heavy chain. The combined results provide atomistic
insights into the correlations between the modulation of conformational
dynamics, structural stability, and allosteric signal transduction. In
particular, the results suggest that specific networks of residues,
shared among all the analyzed proteins, define the molecular pathways by
which antibody structures respond to antigen binding. Our studies may
have implications in practical use, such as the rational design of
antibodies with specifically modulated antigen-binding affinities
Molecular dynamics simulations of proteins and peptides: From folding to drug design
No full textComputer simulations of proteins, lipids and nucleic acids at
equilibrium have become essentially routine. However, the fact remains
that complete sampling of conformational space continues to be a
bottle-neck in the field. The challenge for the future is to overcome
such problems and use computational approaches to understand recognition
and spontaneous self-organization in biomolecular systems (folding,
aggregation and assembly of complexes), processes that cannot be
directly observed experimentally. In this review, examples illustrating
the extent to which simulations can be used to understand these
phenomena in biomolecular systems will be presented along with examples
of methodological developments to increase our physical understanding of
the processes. The study cases will cover the problems of
peptide-receptor recognition and the use of the information obtained for
the design of new non-peptidic ligands; the study of the folding
mechanism of small proteins and finally the study of the initial stages
of peptide self-aggregation
Understanding ligand-based modulation of the Hsp90 molecular chaperone dynamics at atomic resolution
No full textMolecular switching and ligand-based modulation of the 90-kDa heat-shock
protein (Hsp90) chaperone activity may ultimately facilitate
conformational coupling to the ATPase cycle along with activation and
recruitment of the broad range of client proteins. We present an atomic
resolution analysis of the Hsp90 N-terminal domain (NTD) binding energy
landscape by simulating protein dynamics with a range of binding
partners. We show that the activity of the molecular chaperone may be
linked to (i) local folding-unfolding transitions and conformational
switching of the ``active site lid'' upon binding and (it) differences
in the underlying protein dynamics as a function of the binding partner.
This study suggests that structural plasticity of the Hsp90 NTD can be
exploited by the molecular chaperone machinery to modulate enhanced
structural rigidity during ATP binding and increased protein flexibility
as a consequence of the inhibitor binding. The present study agrees with
the experimental structural data and provides a plausible molecular
model for understanding mechanisms of modulation of molecular chaperone
activities by binding partners
An atomistic view of Hsp70 allosteric crosstalk: from the nucleotide to the substrate binding domain and back
No full textThe Hsp70 is an allosterically regulated family of molecular chaperones.
They consist of two structural domains, NBD and SBD, connected by a
flexible linker. ATP hydrolysis at the NBD modulates substrate
recognition at the SBD, while peptide binding at the SBD enhances ATP
hydrolysis. In this study we apply Molecular Dynamics (MD) to elucidate
the molecular determinants underlying the allosteric communication from
the NBD to the SBD and back. We observe that local structural and
dynamical modulation can be coupled to large-scale rearrangements, and
that different combinations of ligands at NBD and SBD differently affect
the SBD domain mobility. Substituting ADP with ATP in the NBD induces
specific structural changes involving the linker and the two NBD lobes.
Also, a SBD-bound peptide drives the linker docking by increasing the
local dynamical coordination of its C-terminal end: a partially docked
DnaK structure is achieved by combining ATP in the NBD and peptide in
the SBD. We propose that the MD-based analysis of the inter domain
dynamics and structure modulation could be used as a tool to
computationally predict the allosteric behaviour and functional response
of Hsp70 upon introducing mutations or binding small molecules, with
potential applications for drug discovery
- …
