39 research outputs found
Automated Force Field Parameterization for Nonpolarizable and Polarizable Atomic Models Based on Ab Initio Target Data
Classical
molecular dynamics (MD) simulations based on atomistic
models are increasingly used to study a wide range of biological systems.
A prerequisite for meaningful results from such simulations is an
accurate molecular mechanical force field. Most biomolecular simulations
are currently based on the widely used AMBER and CHARMM force fields,
which were parametrized and optimized to cover a small set of basic
compounds corresponding to the natural amino acids and nucleic acid
bases. Atomic models of additional compounds are commonly generated
by analogy to the parameter set of a given force field. While this
procedure yields models that are internally consistent, the accuracy
of the resulting models can be limited. In this work, we propose a
method, general automated atomic model parameterization (GAAMP), for
generating automatically the parameters of atomic models of small
molecules using the results from ab initio quantum mechanical (QM)
calculations as target data. Force fields that were previously developed
for a wide range of model compounds serve as initial guesses, although
any of the final parameter can be optimized. The electrostatic parameters
(partial charges, polarizabilities, and shielding) are optimized on
the basis of QM electrostatic potential (ESP) and, if applicable,
the interaction energies between the compound and water molecules.
The soft dihedrals are automatically identified and parametrized by
targeting QM dihedral scans as well as the energies of stable conformers.
To validate the approach, the solvation free energy is calculated
for more than 200 small molecules and MD simulations of three different
proteins are carried out
Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression
The
weighted histogram analysis method (WHAM) is a standard protocol
for postprocessing the information from biased umbrella sampling simulations
to construct the potential of mean force with respect to a set of
order parameters. By virtue of the WHAM equations, the unbiased density
of state is determined by satisfying a self-consistent condition through
an iterative procedure. While the method works very effectively when
the number of order parameters is small, its computational cost grows
rapidly in higher dimension. Here, we present a simple and efficient
alternative strategy, which avoids solving the self-consistent WHAM
equations iteratively. An efficient multivariate linear regression
framework is utilized to link the biased probability densities of
individual umbrella windows and yield an unbiased global free energy
landscape in the space of order parameters. It is demonstrated with
practical examples that free energy landscapes that are comparable
in accuracy to WHAM can be generated at a small fraction of the cost
Simulating the Distance Distribution between Spin-Labels Attached to Proteins
EPR/DEER spectroscopy is playing
an increasingly important role
in the characterization of the conformational states of proteins.
In this study, force field parameters for the bifunctional spin-label
(RX) used in EPR/DEER are parametrized and tested with molecular dynamics
(MD) simulations. The dihedral angles connecting the C<sub>α</sub> atom of the backbone to the nitroxide ring moiety of the RX spin-label
attached to <i>i</i> and <i>i</i> + 4 positions
in a polyalanine α-helix agree very well with those observed
in the X-ray crystallography. Both RX<sub><i>i</i>,<i>i</i>+4</sub> and RX<sub><i>i</i>,<i>i</i>+3</sub> are more rigid than the monofunctional spin-label (R1) commonly
used in EPR/DEER, while RX<sub><i>i</i>,<i>i</i>+4</sub> is more rigid and causes less distortion in a protein backbone
than RX<sub><i>i</i>,<i>i</i>+3</sub>. Simplified
dummy spin-label models with a single effective particle representing
the RX<sub><i>i</i>,<i>i</i>+3</sub> and RX<sub><i>i</i>,<i>i</i>+4</sub> are also developed
and parametrized from the all-atom simulations. MD simulations with
dummy spin-labels (MDDS) provide distance distributions that can be
directly compared to distance distributions obtained from EPR/DEER
to rapidly assess if a hypothetical three-dimensional (3D) structural
model is consistent with experiment. The dummy spin-labels can also
be used in the restrained-ensemble MD (re-MD) simulations to carry
out structural refinement of 3D models. Applications of this methodology
to T4 lysozyme, KCNE1, and LeuT are shown to provide important insights
about their conformational dynamics
Computational Analysis of the Binding Specificity of Gleevec to Abl, câKit, Lck, and câSrc Tyrosine Kinases
Gleevec,
a well-known cancer therapeutic agent, is an effective
inhibitor of several tyrosine kinases, including Abl and c-Kit, but
displays less potency to inhibit closely homologous tyrosine kinases,
such as Lck and c-Src. Because many structural features of the binding
site are highly conserved in these homologous kinases, the molecular
determinants responsible for the binding specificity of Gleevec remain
poorly understood. To address this issue, free energy perturbation
molecular dynamics (FEP/MD) simulations with explicit solvent was
used to compute the binding affinity of Gleevec to Abl, c-Kit, Lck,
and c-Src. The results of the FEP/MD calculations are in good agreement
with experiments, enabling a detailed and quantitative dissection
of the absolute binding free energy in terms of various thermodynamic
contributions affecting the binding specificity of Gleevec to the
kinases. Dominant binding free energy contributions arises from the
van der Waals dispersive interaction, compensating about two-thirds
of the unfavorable free energy penalty associated with the loss of
translational, rotational, and conformational freedom of the ligand
upon binding. In contrast, the contributions from electrostatic and
repulsive interactions nearly cancel out due to solvent effects. Furthermore,
the calculations show the importance of the conformation of the kinase
activation loop. Among the kinases examined, Abl provides the most
favorable binding environment for Gleevec via optimal proteinâligand
interactions and a small free energy cost for loss of the translational,
rotational, and conformational freedom upon ligand binding. The FEP/MD
calculations additionally reveal that Lck and c-Src provide similar
nonbinding interactions with the bound-Gleevec, but the former pays
less entropic penalty for the ligand losing its translational, rotational,
and conformational motions to bind, examining the empirically observed
differential binding affinities of Gleevec between the two Src-family
kinases
Committor-Consistent Variational String Method
The
treatment of slow and rare transitions in the simulation of
complex systems poses a great computational challenge. A powerful
approach to tackle this challenge is the string method, which represents
the transition path as a one-dimensional curve in a multidimensional
space of collective variables. Commonly used strategies for pathway
optimization include aligning the tangent of the string to the local
mean force or to the mean drift determined from swarms of short trajectories.
Here, a novel strategy is proposed, allowing the string to be optimized
based on a variational principle involving the unidirectional reactive
flux expressed in terms of the time-correlation function of the committor.
The method is illustrated with model systems and then probed with
the alanine dipeptide and a coarse-grained model of the barstar-barnase
protein complex. Successive iterations variationally refine the string
toward an optimal transition pathway following the gradient of the
committor between two metastable states
Computational Study of the âDFG-Flipâ Conformational Transition in câAbl and câSrc Tyrosine Kinases
Protein
tyrosine kinases are crucial to cellular signaling pathways
regulating cell growth, proliferation, metabolism, differentiation,
and migration. To maintain normal regulation of cellular signal transductions,
the activities of tyrosine kinases are also highly regulated. The
conformation of a three-residue motif Asp-Phe-Gly (DFG) near the N-terminus
of the long âactivationâ loop covering the catalytic
site is known to have a critical impact on the activity of c-Abl and
c-Src tyrosine kinases. A conformational transition of the DFG motif
can switch the enzyme from an active (DFG-in) to an inactive (DFG-out)
state. In the present study, the string method with swarms-of-trajectories
was used to computationally determine the reaction pathway connecting
the two end-states, and umbrella sampling calculations were carried
out to characterize the thermodynamic factors affecting the conformations
of the DFG motif in c-Abl and c-Src kinases. According to the calculated
free energy landscapes, the DFG-out conformation is clearly more favorable
in the case of c-Abl than that of c-Src. The calculations also show
that the protonation state of the aspartate residue in the DFG motif
strongly affects the in/out conformational transition in c-Abl, although
it has a much smaller impact in the case of c-Src due to local structural
differences
The Activation of câSrc Tyrosine Kinase: Conformational Transition Pathway and Free Energy Landscape
Tyrosine
kinases are important cellular signaling allosteric enzymes
that regulate cell growth, proliferation, metabolism, differentiation,
and migration. Their activity must be tightly controlled, and malfunction
can lead to a variety of diseases, particularly cancer. The nonreceptor
tyrosine kinase c-Src, a prototypical model system and a representative
member of the Src-family, functions as complex multidomain allosteric
molecular switches comprising SH2 and SH3 domains modulating the activity
of the catalytic domain. The broad picture of self-inhibition of c-Src
via the SH2 and SH3 regulatory domains is well characterized from
a structural point of view, but a detailed molecular mechanism understanding
is nonetheless still lacking. Here, we use advanced computational
methods based on all-atom molecular dynamics simulations with explicit
solvent to advance our understanding of kinase activation. To elucidate
the mechanism of regulation and self-inhibition, we have computed
the pathway and the free energy landscapes for the âinactive-to-activeâ
conformational transition of c-Src for different configurations of
the SH2 and SH3 domains. Using the isolated c-Src catalytic domain
as a baseline for comparison, it is observed that the SH2 and SH3
domains, depending upon their bound orientation, promote either the
inactive or active state of the catalytic domain. The regulatory structural
information from the SH2âSH3 tandem is allosterically transmitted
via the N-terminal linker of the catalytic domain. Analysis of the
conformational transition pathways also illustrates the importance
of the conserved tryptophan 260 in activating c-Src, and reveals a
series of concerted events during the activation process
Comparison between Mean Forces and Swarms-of-Trajectories String Methods
The original formulation
of the string method in collective variable
space is compared with a recent variant called string method with
swarms-of-trajectories. The assumptions made in the original method
are revisited and the significance of the minimum free energy path
(MFEP) is discussed in the context of reactive events. These assumptions
are compared to those made in the string method with swarms-of-trajectories,
and shown to be equivalent in a certain regime: in particular an expression
for the path identified by the swarms-of-trajectories method is given
and shown to be closely related to the MFEP. Finally, the algorithmic
aspects of both methods are compared
Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?
Accurate prediction of standard binding free energies
describing
proteinâligand association remains a daunting computational
endeavor. This challenge is rooted to a large extent in the considerable
changes in conformational, translational, and rotational entropies
underlying the binding process that atomistic simulations cannot easily
sample. In spite of significant methodological advances, reflected
in a continuously improving agreement with experiment, a characterization
of alternate strategies aimed at measuring binding affinities, notably
their respective advantages and drawbacks, is somewhat lacking. Here,
two distinct avenues to determine the standard binding free energy
are compared in the case of a short, proline-rich peptide associating
to the Src homology domain 3 of tyrosine kinase Abl. These avenues,
one relying upon alchemical transformations and the other on potentials
of mean force (PMFs), invoke a series of geometrical restraints acting
on collective variables designed to alleviate sampling limitations
inherent to classical molecular dynamics simulations. The experimental
binding free energy of Î<i>G</i><sub>bind</sub> =
â7.99 kcal/mol is well reproduced by the two strategies developed
herein, with Î<i>G</i><sub>bind</sub> = â7.7
for the alchemical route and Î<i>G</i><sub>bind</sub> = â7.8 kcal/mol for the alternate PMF-based route. In detailing
the underpinnings of these numerical strategies devised for the accurate
determination of standard binding free energies, many practical elements
of the proposed rigorous, conceptual framework are clarified, thereby
paving way to tackle virtually any recognition and association phenomenon
The Activation of câSrc Tyrosine Kinase: Conformational Transition Pathway and Free Energy Landscape
Tyrosine
kinases are important cellular signaling allosteric enzymes
that regulate cell growth, proliferation, metabolism, differentiation,
and migration. Their activity must be tightly controlled, and malfunction
can lead to a variety of diseases, particularly cancer. The nonreceptor
tyrosine kinase c-Src, a prototypical model system and a representative
member of the Src-family, functions as complex multidomain allosteric
molecular switches comprising SH2 and SH3 domains modulating the activity
of the catalytic domain. The broad picture of self-inhibition of c-Src
via the SH2 and SH3 regulatory domains is well characterized from
a structural point of view, but a detailed molecular mechanism understanding
is nonetheless still lacking. Here, we use advanced computational
methods based on all-atom molecular dynamics simulations with explicit
solvent to advance our understanding of kinase activation. To elucidate
the mechanism of regulation and self-inhibition, we have computed
the pathway and the free energy landscapes for the âinactive-to-activeâ
conformational transition of c-Src for different configurations of
the SH2 and SH3 domains. Using the isolated c-Src catalytic domain
as a baseline for comparison, it is observed that the SH2 and SH3
domains, depending upon their bound orientation, promote either the
inactive or active state of the catalytic domain. The regulatory structural
information from the SH2âSH3 tandem is allosterically transmitted
via the N-terminal linker of the catalytic domain. Analysis of the
conformational transition pathways also illustrates the importance
of the conserved tryptophan 260 in activating c-Src, and reveals a
series of concerted events during the activation process