Correlating solvation free energies and surface tensions of hydrocarbon solutes

Sitkoff, Doree; Sharp, Kim A.; Honig, Barry

doi:10.1016/0301-4622(94)00062-x

Cited by 105 publications

(119 citation statements)

References 18 publications

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“…However, most models are tested by using only global quantities such as solvation energies (13,(28)(29)(30)(31)(32)(33)41) or simulation rms deviation and stability (33,44). Although these global metrics provide a ''low resolution'' assessment of the model quality, they fail to directly test the quantities most relevant to the dynamics simulation: forces.…”

mentioning

confidence: 99%

Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms

Wagoner¹,

Baker

2006

Proc. Natl. Acad. Sci. U.S.A.

280

397

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Continuum solvation models provide appealing alternatives to explicit solvent methods because of their ability to reproduce solvation effects while alleviating the need for expensive sampling. Our previous work has demonstrated that Poisson-Boltzmann methods are capable of faithfully reproducing polar explicit solvent forces for dilute protein systems; however, the popular solvent-accessible surface area model was shown to be incapable of accurately describing nonpolar solvation forces at atomic-length scales. Therefore, alternate continuum methods are needed to reproduce nonpolar interactions at the atomic scale. In the present work, we address this issue by supplementing the solvent-accessible surface area model with additional volume and dispersion integral terms suggested by scaled particle models and Weeks–Chandler–Andersen theory, respectively. This more complete nonpolar implicit solvent model shows very good agreement with explicit solvent results and suggests that, although often overlooked, the inclusion of appropriate dispersion and volume terms are essential for an accurate implicit solvent description of atomic-scale nonpolar forces.

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mentioning

confidence: 99%

Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms

Wagoner¹,

Baker

2006

Proc. Natl. Acad. Sci. U.S.A.

280

397

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“…The surface tension parameter may assume a single global value used for all atom types or different values may be assigned for each different type of atom. Although SASA methods have enjoyed surprising success, they are also subject to several caveats, including widely varying choices of surface tension parameter (Chothia, 1974;Eisenberg and McLachlan, 1986;Sharp et al, 1991;Sitkoff et al, 1994a;Elcock et al, 2001) as well as inaccurate descriptions of the detailed aspects of nonpolar solvation energy (Gallicchio and Levy, 2004), peptide conformations (Su and Gallicchio, 2004), and protein nonpolar solvation forces (Wagoner and Baker, 2004). Some of these problems have been fixed by new models which include the small but important attractive van der Waals interactions between solvent and solute (Gallicchio et al, 2000;Gallicchio et al, 2002;Gallicchio and Levy, 2004;Wagoner and Baker, 2006) as well as repulsive solvent-accessible volume terms (Wagoner and Baker, 2006).…”

Section: Iiib1 Nonpolar Solvation-one Popular Approximation For Thmentioning

confidence: 99%

Computational Methods for Biomolecular Electrostatics

Dong

Olsen

Baker

2008

Methods in Cell Biology

116

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An understanding of intermolecular interactions is essential for insight into how cells develop, operate, communicate and control their activities. Such interactions include several components: contributions from linear, angular, and torsional forces in covalent bonds, van der Waals forces, as well as electrostatics. Among the various components of molecular interactions, electrostatics are of special importance because of their long range and their influence on polar or charged molecules, including water, aqueous ions, and amino or nucleic acids, which are some of the primary components of living systems. Electrostatics, therefore, play important roles in determining the structure, motion and function of a wide range of biological molecules. This chapter presents a brief overview of electrostatic interactions in cellular systems with a particular focus on how computational tools can be used to investigate these types of interactions.

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“…It was verified by calculating the three-dimensional/one-dimensional self-compatibility score (26), which was 103.1 (the expected score for a protein of this length is 118.6). The electrostatic potential of the kinase domain was calculated using the program Delphi (27) with parameter for solvation energy charges and atomic radii (28). The binding of the peptide to the kinase domain of DAPK was modeled in analogy to the binding of the peptide substrate to phosphorylase kinase.…”

Section: Methodsmentioning

confidence: 99%

The Pro-apoptotic Function of Death-associated Protein Kinase Is Controlled by a Unique Inhibitory Autophosphorylation-based Mechanism

Shohat¹,

Spivak-Kroizman²,

Cohen³

et al. 2001

Journal of Biological Chemistry

146

147

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Death-associated protein kinase is a calcium/calmodulin serine/threonine kinase, which positively mediates programmed cell death in a variety of systems. Here we addressed its mode of regulation and identified a mechanism that restrains its apoptotic function in growing cells and enables its activation during cell death. It involves autophosphorylation of Ser 308 within the calmodulin (CaM)-regulatory domain, which occurs at basal state, in the absence of Ca 2؉ /CaM, and is inversely correlated with substrate phosphorylation. This type of phosphorylation takes place in growing cells and is strongly reduced upon their exposure to the apoptotic stimulus of C 6 -ceramide. The substitution of Ser 308 to alanine, which mimics the ceramide-induced dephosphorylation at this site, increases Ca 2؉ /CaM-independent substrate phosphorylation as well as binding and overall sensitivity of the kinase to CaM. At the cellular level, it strongly enhances the death-promoting activity of the kinase. Conversely, mutation to aspartic acid reduces the binding of the protein to CaM and abrogates almost completely the death-promoting function of the protein. These results are consistent with a molecular model in which phosphorylation on Ser 308 stabilizes a locked conformation of the CaM-regulatory domain within the catalytic cleft and simultaneously also interferes with CaM binding. We propose that this unique mechanism of auto-inhibition evolved to impose a locking device, which keeps death-associated protein kinase silent in healthy cells and ensures its activation only in response to apoptotic signals.

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Correlating solvation free energies and surface tensions of hydrocarbon solutes

Cited by 105 publications

References 18 publications

Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms

Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms

Computational Methods for Biomolecular Electrostatics

The Pro-apoptotic Function of Death-associated Protein Kinase Is Controlled by a Unique Inhibitory Autophosphorylation-based Mechanism

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