The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii

Qiu, Di; Shenkin, Peter S.; Hollinger, and Frank P.; Still, W. Clark

doi:10.1021/jp961992r

Cited by 985 publications

(1,092 citation statements)

References 27 publications

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“…10,13,24,26,27 However, its performance on larger molecules has generally not been as good, with the trend being more pronounced for molecules having large interior regions. 24,26 Since the GB model shares the same underlying physical approximation-continuum electrostatics-with the PB approach, it is natural, in optimizing the GB performance, to use the PB model as a reference. Agreement with PB calculations is not the only criterion of optimal GB performance; other tests include comparisons to explicit solvent simulations results, and to experiment.…”

Section: Improving the Generalized Born Approximationmentioning

confidence: 99%

Exploring protein native states and large‐scale conformational changes with a modified generalized born model

2004

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Implicit solvation models provide, for many applications, a reasonably accurate and computationally effective way to describe the electrostatics of aqueous solvation. Here, a popular analytical Generalized Born (GB) solvation model is modified to improve its accuracy in calculating the solvent polarization part of free energy changes in large-scale conformational transitions, such as protein folding. In contrast to an earlier GB model (implemented in the AMBER-6 program), the improved version does not overstabilize the native structures relative to the finite-difference PoissonBoltzmann continuum treatment. In addition to improving the energy balance between folded and unfolded conformers, the algorithm (available in the AMBER-7 and NAB molecular modeling packages) is shown to perform well in more than 50 ns of native-state molecular dynamics (MD) simulations of thioredoxin, protein-A, and ubiquitin, as well as in a simulation of Barnase/Barstar complex formation. For thioredoxin, various combinations of input parameters have been explored, such as the underlying gas-phase force fields and the atomic radii. The best performance is achieved with a previously proposed modification to the torsional potential in the Amber ff99 force field, which yields stable native trajectories for all of the tested proteins, with backbone root-mean-square deviations from the native structures being ϳ1.5 Å after 6 ns of simulation time. The structure of Barnase/Barstar complex is regenerated, starting from an unbound state, to within 1.9 Å relative to the crystal structure of the complex.

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Section: Improving the Generalized Born Approximationmentioning

confidence: 99%

Exploring protein native states and large‐scale conformational changes with a modified generalized born model

2004

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“…[44][45][46][47][48][49][50][51][52] In fact, comparative methods generally do not even attempt to model solvation effects. There are only a…”

Section: Combining Physics and Evolution To Improve Protein Structurementioning

confidence: 99%

Evolution and Physics in Comparative Protein Structure Modeling

et al. 2002

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From a physical perspective, the native structure of a protein is a consequence of physical forces acting on the protein and solvent atoms during the folding process. From a biological perspective, the native structure of proteins is a result of evolution over millions of years. Correspondingly, there are two types of protein structure prediction methods, de novo prediction and comparative modeling. We review comparative protein structure modeling and discuss the incorporation of physical considerations into the modeling process. A good starting point for achieving this aim is provided by comparative modeling by satisfaction of spatial restraints. Incorporation of physical considerations is illustrated by an inclusion of solvation effects into the modeling of loops.

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“…We use GB/SA model 37,38 as implicit solvent model to simulate the aqueous environment. GB/SA is a reduced model from the continuum model, which treats the water as continuous medium and there are usually three terms included in the free energy of solvation:…”

Section: Methodsmentioning

confidence: 99%

“…(1) is to use generalized Born (GB) model proposed by Still et al 37 and developed by others. 38 This model calculates DG pol as follows:…”

Section: Methodsmentioning

confidence: 99%

All‐atom contact potential approach to protein thermostability analysis

Chen

Xiao

2006

Biopolymers

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In this paper we use all‐atom potential energy to define and analyze the inter‐residue contacts in mesophilic and thermophilic proteins. Fifteen families of proteins are selected and each family has two representative proteins with greatly different preferred environmental temperatures. We find that both the number and energy of the contacts defined in this way show stronger correlations with the preferred temperatures of proteins than other factors used before. We also find that the charged‐polar and charged‐nonpolar residue contacts not only have larger contact numbers but also have lower single contact energies. Furthermore, the most important is that most of the thermophilic proteins have more charged‐polar and charged‐nonpolar residue contacts than their mesophilic counterparts. This suggests that they may play an important role in the thermostability of proteins, except usual charged–charged and nonpolar–nonpolar residue contacts. Charged residues may exert their profound influence by forming contacts not only with other charged residues but also with polar or nonpolar residues, thus further increasing the strength of contact network and then the thermostability of proteins. © 2006 Wiley Periodicals, Inc. Biopolymers 85: 28–37, 2007.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

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The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii

Cited by 985 publications

References 27 publications

Exploring protein native states and large‐scale conformational changes with a modified generalized born model

Exploring protein native states and large‐scale conformational changes with a modified generalized born model

Evolution and Physics in Comparative Protein Structure Modeling

All‐atom contact potential approach to protein thermostability analysis

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