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      Water-Membrane Partition Thermodynamics of an Amphiphilic Lipopeptide: An Enthalpy-Driven Hydrophobic Effect

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          Abstract

          To shed light on the driving force for the hydrophobic effect that partitions amphiphilic lipoproteins between water and membrane, we carried out an atomically detailed thermodynamic analysis of a triply lipid modified H-ras heptapeptide anchor (ANCH) in water and in a DMPC (1,2-dimyristoyl- sn-glycero-3-phosphocholine) bilayer. Combining molecular mechanical and continuum solvent approaches with an improved technique for solute entropy calculation, we obtained an overall transfer free energy of ∼−13 kcal mol −1. This value is in qualitative agreement with free energy changes derived from a potential of mean force calculation and indirect experimental observations. Changes in free energies of solvation and ANCH conformational reorganization are unfavorable, whereas ANCH-DMPC interactions—especially van der Waals—favor insertion. These results are consistent with an enthalpy-driven hydrophobic effect, in accord with earlier calorimetric data on the membrane partition of other amphiphiles. Furthermore, structural and entropic analysis of molecular dynamics-generated ensembles suggests that conformational selection may play a hitherto unappreciated role in membrane insertion of lipid-modified peptides and proteins.

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          The many roles of computation in drug discovery.

          An overview is given on the diverse uses of computational chemistry in drug discovery. Particular emphasis is placed on virtual screening, de novo design, evaluation of drug-likeness, and advanced methods for determining protein-ligand binding.
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            The statistical-thermodynamic basis for computation of binding affinities: a critical review.

            Although the statistical thermodynamics of noncovalent binding has been considered in a number of theoretical papers, few methods of computing binding affinities are derived explicitly from this underlying theory. This has contributed to uncertainty and controversy in certain areas. This article therefore reviews and extends the connections of some important computational methods with the underlying statistical thermodynamics. A derivation of the standard free energy of binding forms the basis of this review. This derivation should be useful in formulating novel computational methods for predicting binding affinities. It also permits several important points to be established. For example, it is found that the double-annihilation method of computing binding energy does not yield the standard free energy of binding, but can be modified to yield this quantity. The derivation also makes it possible to define clearly the changes in translational, rotational, configurational, and solvent entropy upon binding. It is argued that molecular mass has a negligible effect upon the standard free energy of binding for biomolecular systems, and that the cratic entropy defined by Gurney is not a useful concept. In addition, the use of continuum models of the solvent in binding calculations is reviewed, and a formalism is presented for incorporating a limited number of solvent molecules explicitly.
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              Density functional self-consistent quantum mechanics/molecular mechanics theory for linear and nonlinear molecular properties: Applications to solvated water and formaldehyde.

              A combined quantum mechanics/molecular mechanics (QM/MM) method is described, where the polarization between the solvent and solute is accounted for using a self-consistent scheme linear in the solvent polarization. The QM/MM method is implemented for calculation of energies and molecular response properties including the calculation of linear and quadratic response functions using the density-functional theory (DFT) and the Hartree-Fock (HF) theory. Sample calculations presented for ground-state energies, first-order ground-state properties, excitation energies, first-order excited state properties, polarizabilities, first-hyperpolarizabilities, and two-photon absorptions strengths of formaldehyde suggests that DFT may in some cases be a sufficiently reliable alternative to high-level theory, such as coupled-cluster (CC) theory, in modeling solvent shifts, whereas results obtained with the HF wave function deviate significantly from the CC results. Calculations carried out on water gives results that also are comparable with CC calculations in accuracy for ground-state and first-order properties. However, to obtain such accuracy an exchange-correlation functional capable of describing the diffuse Rydberg states must be chosen.
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                Author and article information

                Journal
                Biophys J
                biophysj
                Biophysical Journal
                The Biophysical Society
                0006-3495
                1542-0086
                1 October 2008
                11 July 2008
                1 October 2008
                : 95
                : 7
                : 3269-3277
                Affiliations
                [* ]Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, []Howard Hughes Medical Institute, and []Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0365
                Author notes

                Address reprint requests to Alemayehu A. Gorfe, Tel.: 858-822-0255; Fax: 858-534-4974; E-mail: abebe@ 123456mccammon.ucsd.edu .

                Article
                136481
                10.1529/biophysj.108.136481
                2547422
                18621822
                27cbcf1c-c6a2-4591-bec8-f66c751d0786
                Copyright © 2008, Biophysical Society

                This is an Open Access article distributed under the terms of the Creative Commons-Attribution Noncommercial License ( http://creativecommons.org/licenses/by-nc/2.0/), which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 1 May 2008
                : 11 June 2008
                Categories
                Membranes

                Biophysics
                Biophysics

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