109 research outputs found
Lymphotactin: how a protein can adopt two folds
Metamorphic proteins like Lymphotactin are a notable exception of the
empirical principle that structured natural proteins possess a unique three
dimensional structure. In particular, the human chemokine lymphotactin protein
(Ltn) exists in two distinct conformations (one monomeric and one dimeric)
under physiological conditions. In this work we use a Ca Go-model to show how
this very peculiar behavior can be reproduced. From the study of the
thermodynamics and of the kinetics we characterize the interconversion
mechanism. In particular, this takes place through the docking of the two
chains living in a third monomeric, partially unfolded, state which shows a
residual structure involving a set of local contacts common to the two native
conformations. The main feature of two-fold proteins appears to be the sharing
of a common set of local contacts between the two distinct folds as confirmed
by the study of two designed two-fold proteins. Metamorphic proteins may be
more common than expected.Comment: 14 pages, 4 figure
Ratcheted molecular-dynamics simulations identify efficiently the transition state of protein folding
The atomistic characterization of the transition state is a fundamental step
to improve the understanding of the folding mechanism and the function of
proteins. From a computational point of view, the identification of the
conformations that build out the transition state is particularly cumbersome,
mainly because of the large computational cost of generating a
statistically-sound set of folding trajectories. Here we show that a biasing
algorithm, based on the physics of the ratchet-and-pawl, can be used to
identify efficiently the transition state. The basic idea is that the
algorithmic ratchet exerts a force on the protein when it is climbing the
free-energy barrier, while it is inactive when it is descending. The transition
state can be identified as the point of the trajectory where the ratchet
changes regime. Besides discussing this strategy in general terms, we test it
within a protein model whose transition state can be studied independently by
plain molecular dynamics simulations. Finally, we show its power in
explicit-solvent simulations, obtaining and characterizing a set of
transition--state conformations for ACBP and CI2
An implementation of the maximum-caliber principle by replica-averaged time-resolved restrained simulations
Inferential methods can be used to integrate experimental informations and
molecular simulations. The maximum entropy principle provides a framework for
using equilibrium experimental data and it has been shown that replica-averaged
simulations, restrained using a static potential, are a practical and powerful
implementation of such principle. Here we show that replica-averaged
simulations restrained using a time-dependent potential are equivalent to the
principle of maximum caliber, the dynamic version of the principle of maximum
entropy, and thus may allow to integrate time-resolved data in molecular
dynamics simulations. We provide an analytical proof of the equivalence as well
as a computational validation making use of simple models and synthetic data.
Some limitations and possible solutions are also discussed
Metainference: A Bayesian Inference Method for Heterogeneous Systems
Modelling a complex system is almost invariably a challenging task. The
incorporation of experimental observations can be used to improve the quality
of a model, and thus to obtain better predictions about the behavior of the
corresponding system. This approach, however, is affected by a variety of
different errors, especially when a system populates simultaneously an ensemble
of different states and experimental data are measured as averages over such
states. To address this problem we present a Bayesian inference method, called
metainference, that is able to deal with errors in experimental measurements as
well as with experimental measurements averaged over multiple states. To
achieve this goal, metainference models a finite sample of the distribution of
models using a replica approach, in the spirit of the replica-averaging
modelling based on the maximum entropy principle. To illustrate the method we
present its application to a heterogeneous model system and to the
determination of an ensemble of structures corresponding to the thermal
fluctuations of a protein molecule. Metainference thus provides an approach to
model complex systems with heterogeneous components and interconverting between
different states by taking into account all possible sources of errors.Comment: 29 pages, 10 figure
Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle
In order to characterise the dynamics of proteins, a well-established method is to incorporate experimental parameters as replica-averaged structural restraints into molecular dynamics simulations. Here, we justify this approach in the case of interproton distance information provided by nuclear Overhauser effects by showing that it generates ensembles of conformations according to the maximum entropy principle. These results indicate that the use of replica-averaged structural restraints in molecular dynamics simulations, given a force field and a set of experimental data, can provide an accurate approximation of the unknown Boltzmann distribution of a system
Metainference: a Bayesian inference method for heterogeneous systems
Modeling a complex system is almost invariably a challenging task. The incorporation of experimental observations can be used to improve the quality of a model and thus to obtain better predictions about the behavior of the corresponding system. This approach, however, is affected by a variety of different errors, especially when a system simultaneously populates an ensemble of different states and experimental data are measured as averages over such states. To address this problem, we present a Bayesian inference method, called “metainference,” that is able to deal with errors in experimental measurements and with experimental measurements averaged over multiple states. To achieve this goal, metainference models a finite sample of the distribution of models using a replica approach, in the spirit of the replica-averaging modeling based on the maximum entropy principle. To illustrate the method, we present its application to a heterogeneous model system and to the determination of an ensemble of structures corresponding to the thermal fluctuations of a protein molecule. Metainference thus provides an approach to modeling complex systems with heterogeneous components and interconverting between different states by taking into account all possible sources of errors
Structure and dynamics of the integrin LFA-1 I-domain in the inactive state underlie its inside-out/outside-in signaling and allosteric mechanisms.
Lymphocyte function-associated antigen 1 (LFA-1) is an integrin that transmits information in two directions across the plasma membrane of leukocytes, in so-called outside-in and inside-out signaling mechanisms. To investigate the structural basis of these mechanisms, we studied the conformational space of the apo I-domain using replica-averaged metadynamics simulations in combination with nuclear magnetic resonance chemical shifts. We thus obtained a free energy landscape that reveals the existence of three conformational substates of this domain. The three substates include conformations similar to existing crystallographic structures of the low-affinity I-domain, the inactive I-domain with an allosteric antagonist inhibitor bound underneath α helix 7, and an intermediate affinity state of the I-domain. The multiple substates were validated with residual dipolar coupling measurements. These results suggest that the presence of three substates in the apo I-domain enables the precise regulation of the binding process that is essential for the physiological function of LFA-1.This study was supported by the Wellcome Trust and the BBSRC.This is the final version of the article. It first appeared from Cell Press via http://dx.doi.org/10.1016/j.str.2014.12.02
Structural characterization of the interaction of α-synuclein nascent chains with the ribosomal surface and trigger factor
The ribosome is increasingly becoming recognized as a key hub for integrating quality control processes associated with protein biosynthesis and cotranslational folding (CTF). The molecular mechanisms by which these processes take place, however, remain largely unknown, in particular in the case of intrinsically disordered proteins (IDPs). To address this question, we studied at a residue-specific level the structure and dynamics of ribosome-nascent chain complexes (RNCs) of α-synuclein (αSyn), an IDP associated with Parkinson’s disease (PD). Using solution-state nuclear magnetic resonance (NMR) spectroscopy and coarse-grained molecular dynamics (MD) simulations, we find that, although the nascent chain (NC) has a highly disordered conformation, its N-terminal region shows resonance broadening consistent with interactions involving specific regions of the ribosome surface. We also investigated the effects of the ribosome-associated molecular chaperone trigger factor (TF) on αSyn structure and dynamics using resonance broadening to define a footprint of the TF–RNC interactions. We have used these data to construct structural models that suggest specific ways by which emerging NCs can interact with the biosynthesis and quality control machinery
The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments OPEN
The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer's disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements. The free energy landscape of a protein provides a direct representation of the probability of measuring particular values of specific parameters that describe its conformational properties. The knowledge of the free energy landscape of a protein offers therefore the possibility of rationalising important aspects of its behaviour, including its stability, mechanisms of folding and molecular recognition, and the possibility of misfolding and aggregatio
- …