816 research outputs found
Absolute FKBP binding affinities obtained via non-equilibrium unbinding simulations
We compute absolute binding affinities for two ligands bound to the FKBP
protein using non-equilibrium unbinding simulations. The methodology is
straight-forward, requiring little or no modification to many modern molecular
simulation packages. The approach makes use of a physical pathway, eliminating
the need for complicated alchemical decoupling schemes. Results of this study
are promising. For the ligands studied here the binding affinities are
typically estimated within less than 4.0 kJ/mol of the target values; and the
target values are within less than 1.0 kJ/mol of experiment. These results
suggest that non-equilibrium simulation could provide a simple and robust means
to estimate protein-ligand binding affinities.Comment: 9 pages, 3 figures (no necessary color). Changes made to methodology
and results between revision
Are polar liquids less simple?
Strong correlation between equilibrium fluctuations of the potential energy,
U, and the virial, W, is a characteristic of a liquid that implies the presence
of certain dynamic properties, such as density scaling of the relaxation times
and isochronal superpositioning of the relaxation function. In this work we
employ molecular dynamics simulations (mds) on methanol and two variations,
lacking hydrogen bonds and a dipole moment, to assess the connection between
the correlation of U and W and these dynamic properties. We show, in accord
with prior results of others [T.S. Ingebrigtsen, T.B. Schroder, J.C. Dyre,
Phys. Rev. X 2, 011011 (2012).], that simple van der Waals liquids exhibit both
strong correlations and the expected dynamic behavior. However, for polar
liquids this correspondence breaks down - weaker correlation between U and W is
not associated with worse conformance to density scaling or isochronal
superpositioning. The reason for this is that strong correlation between U and
W only requires their proportionality, whereas the expected dynamic behavior
depends primarily on constancy of the proportionality constant for all state
points. For hydrogen-bonded liquids, neither strong correlation nor adherence
to the dynamic properties is observed; however, this nonconformance is not
directly related to the concentration of hydrogen bonds, but rather to the
greater deviation of the intermolecular potential from an inverse power law
(IPL). Only (hypothetical) liquids having interactions governed strictly by an
IPL are perfectly correlating and exhibit the consequent dynamic properties
over all thermodynamic conditions.Comment: 14 pages, 8 figure
What stabilizes the 3_14-helix in beta^3-peptides? A conformational analysis using molecular simulation.
Beta-peptides are analogs of natural alpha-peptides and form a variety of remarkably stable structures. Having an additional carbon atom in the backbone of each residue, their folded conformation is not only influenced by the side-chain sequence but also and foremost by their substitution pattern. The precise mechanism by which the side chains interact with the backbone is, however, hitherto not completely known. In order to unravel the various effects by which the side chains influence the backbone conformation, we quantify to which extent the dihedral angles of a beta^3-substited peptide with an additional methyl group on the central C_alpha-atom can be regarded as independent degrees of freedom and analyze the distributions of these dihedral angles. We also selectively capture the steric effect of substituents on the C_alpha- and C_beta-atoms of the central residue
by alchemically changing them into dummy atoms, which have no non-bonded interactions. We find that the folded state of the beta^3-peptide is primarily stabilized by a steric exclusion of large parts of the unfolded state (entropic effect) and only subsequently by mutual dependence of the psi-dihedral angles (enthalpic effect). The folded state of beta-peptides is stabilized by a different mechanism than that of alpha-peptides
Molecular dynamics simulation of the transport of small molecules across a polymer membrane
The transport of small molecules through a polymer membrane is modeled using the computer simulation technique of molecular dynamics (MD). The transport coefficient is derived from a combination of the excess free energy and the diffusion constant. Both properties are derived from MD simulations, applied to helium and methane in polydimethylsiloxane (PDMS). The diffusional process appears to have the character of a jump diffusion for methane and less so for helium. Jumps are allowed by fluctuations of the size and shape of holes. Experimental diffusion constants are well reproduced. The excess free energies, determined by a particle insertion method, are lower by 5-7 kJ/mol than experimental values. It is shown that, as a result of a higher solubility, methane has a higher permeability constant than helium, despite its lower diffusion constant
Statistical Mechanics of Quantum-Classical Systems with Holonomic Constraints
The statistical mechanics of quantum-classical systems with holonomic
constraints is formulated rigorously by unifying the classical Dirac bracket
and the quantum-classical bracket in matrix form.
The resulting Dirac quantum-classical theory, which conserves the holonomic
constraints exactly, is then used to formulate time evolution and statistical
mechanics. The correct momentum-jump approximation for constrained system
arises naturally from this formalism. Finally, in analogy with what was found
in the classical case, it is shown that the rigorous linear response function
of constrained quantum-classical systems contains non-trivial additional terms
which are absent in the response of unconstrained systems.Comment: Submitted to Journal of Chemical Physic
Polarizable molecular interactions in condensed phase and their equivalent nonpolarizable models
Earlier, using phenomenological approach, we showed that in some cases
polarizable models of condensed phase systems can be reduced to nonpolarizable
equivalent models with scaled charges. Examples of such systems include ionic
liquids, TIPnP-type models of water, protein force fields, and others, where
interactions and dynamics of inherently polarizable species can be accurately
described by nonpolarizable models. To describe electrostatic interactions, the
effective charges of simple ionic liquids are obtained by scaling the actual
charges of ions by a factor of 1/sqrt(eps_el), which is due to electronic
polarization screening effect; the scaling factor of neutral species is more
complicated. Here, using several theoretical models, we examine how exactly the
scaling factors appear in theory, and how, and under what conditions,
polarizable Hamiltonians are reduced to nonpolarizable ones. These models allow
one to trace the origin of the scaling factors, determine their values, and
obtain important insights on the nature of polarizable interactions in
condensed matter systems.Comment: 43 pages, 3 figure
The effect of force-field parameters on properties of liquids:Parametrization of a simple three-site model for methanol
A simple rigid three-site model for methanol compatible with the simple point charge (SPC) water and the GROMOS96 force field is parametrized and tested. The influence of different force-field parameters, such as the methanol geometry and the charge distribution on several properties calculated by molecular dynamics is investigated. In particular an attempt was made to obtain good agreement with experimental data for the static dielectric constant and the mixing enthalpy with water. The model is compared to other methanol models from the literature in terms of the ability to reproduce a range of experimental properties.<br/
Molecular dynamics with coupling to an external bath
In molecular dynamics (MD) simulations the need often arises to maintain such parameters as temperature or pressure rather than energy and volume, or to impose gradients for studying transport properties in nonequilibrium MD. A method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling. The method is easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints. The influence of coupling time constants on dynamical variables is evaluated. A leapâfrog algorithm is presented for the general case involving constraints with coupling to both a constant temperature and a constant pressure bath
Structure, dynamics, and function of the monooxygenase P450 BM-3: insights from computer simulations studies
The monooxygenase P450 BM-3 is a NADPH-dependent fatty acid hydroxylase enzyme isolated from soil bacterium Bacillus megaterium. As a pivotal member of cytochrome P450 superfamily, it has been intensely studied for the comprehension of structure-dynamics-function relationships in this class of enzymes. In addition, due to its peculiar properties, it is also a promising enzyme for biochemical and biomedical applications. However, despite the efforts, the full understanding of the enzyme structure and dynamics is not yet achieved. Computational studies, particularly molecular dynamics (MD) simulations, have importantly contributed to this endeavor by providing new insights at an atomic level regarding the correlations between structure, dynamics, and function of the protein. This topical review summarizes computational studies based on MD simulations of the cytochrome P450 BM-3 and gives an outlook on future directions
Unraveling Binding Effects of Cobalt(II) Sepulchrate with the Monooxygenase P450 BM-3 Heme Domain Using Molecular Dynamics Simulations
One of the major limitations to exploit enzymes in industrial processes is their dependence on expensive reduction equivalents like NADPH to drive their catalytic cycle. Soluble electron transfer (ET) mediators like Cobalt(II)Sepulchrate have been proposed as a cost-effective alternative to shuttle electrons between an inexpensive electron source and enzyme redox center. The interactions of these molecules with enzymes are not elucidated at molecular level yet. Herein, molecular dynamics simulations are performed to understand the binding and ET mechanism of the Cobalt(II)Sepulchrate with the heme domain of cytochrome P450BM-3. The study provides a detailed map of ET mediator binding sites on protein surface that resulted prevalently composed by Asp and Glu amino acids. The Cobalt(II)Sepulchrate do not show a preferential binding to these sites. However, among the observed binding sites, only few of them provide efficient ET pathways to heme iron. The results of this study can be used to improve the ET mediator efficiency of the enzyme for possible biotechnological applications
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