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

Wagoner, Jason A.; Baker, Nathan A.

doi:10.1073/pnas.0600118103

Cited by 280 publications

(414 citation statements)

References 69 publications

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“…However we should add that some consistent coupling of non polar and polar solvation free energies in the context of computation of the binding free energies is desired and such work is in progress [50]. It is also useful to point to recent important improvements in modelling non polar contributions to free energy of binding, particularly a recognition of non polar attractive and repulsive contributions to free energy of binding which must be modelled separately [51,52,53].…”

Section: Discussionmentioning

confidence: 99%

Poisson–Boltzmann model analysis of binding mRNA cap analogues to the translation initiation factor eIF4E

Szklarczyk

Zuberek

Antosiewicz

2009

Biophysical Chemistry

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This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT AbstractThe electrostatic free energy of binding of two analogues of the 5'-mRNA cap, differing in size and electric charge, to the wild type and mutated eukaryotic initiation factor eIF4E was computed using the finite difference solutions to the Poisson-Boltzmann equation. Two definitions of the solute-solvent dielectric boundary were used: van der Waals model, solvent exclusion (SE) model. The computed electrostatic energies were supplemented by estimations of the non polar and entropic contributions. A comparison with experimental data for the investigated systems was done. It appears that the SE model with additional contribution fits experimental findings better than the van der Waals model does.

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Section: Discussionmentioning

confidence: 99%

Poisson–Boltzmann model analysis of binding mRNA cap analogues to the translation initiation factor eIF4E

Szklarczyk

Zuberek

Antosiewicz

2009

Biophysical Chemistry

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“…In direct contrast, for sequences that fold into well-defined three-dimensional structures a single family of self-similar globular conformations is preferred over all other globular conformations. Furthermore, the surface tension is nearly zero in folded globules [51] because the surface exposed residues are typically charged or polar.…”

Section: Characteristics Of the Dilute Solvent-rich And Concentratementioning

confidence: 99%

A polymer physics perspective on driving forces and mechanisms for protein aggregation

Pappu

Wang

Vitalis

et al. 2008

Archives of Biochemistry and Biophysics

156

172

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Protein aggregation is a commonly occurring problem in biology. Cells have evolved stress-response mechanisms to cope with problems posed by protein aggregation. Yet, these quality control mechanisms are overwhelmed by chronic aggregation-related stress and the resultant consequences of aggregation become toxic to cells. As a result, a variety of systemic and neurodegenerative diseases are associated with various aspects of protein aggregation and rational approaches to either inhibit aggregation or manipulate the pathways to aggregation might lead to an alleviation of disease phenotypes. To develop such approaches, one needs a rigorous and quantitative understanding of protein aggregation. Much work has been done in this area. However, several unanswered questions linger, and these pertain primarily to the actual mechanism of aggregation as well as to the types of intermolecular associations and intramolecular fluctuations realized at low protein concentrations. It has been suggested that the concepts underlying protein aggregation are similar to those used to describe the aggregation of synthetic polymers. Following this suggestion, the relevant concepts of polymer aggregation are introduced. The focus is on explaining the driving forces for polymer aggregation and how these driving forces vary with chain length and solution conditions. It is widely accepted that protein aggregation is a nucleation-dependent process. This view is based mainly on the presence of long times for the accumulation of aggregates and the elimination of these lag times with "seeds". In this sense, protein aggregation is viewed as being analogous to the aggregation of colloidal particles. The theories for polymer aggregation reviewed in this work suggest an alternative mechanism for the origin of long lag times in protein aggregation. The proposed mechanism derives from the recognition that polymers have unique dynamics that distinguish them from other aggregation-prone systems such as colloidal particles.

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“…49,59 The nonpolar free energy is written as 44 (7) where the first term is the cavity term, γ i is the surface tension proportionality constant for atom i, and A i is the solvent exposed surface area of atom i. The second term is the dispersion interaction term which is given by 44 (8) where α i is an adjustable solute-solvent van der Waals dispersion parameter for atom i.…”

Section: Agbnp Implicit Solventmentioning

confidence: 99%

Prediction of Protein Loop Conformations Using the AGBNP Implicit Solvent Model and Torsion Angle Sampling

Felts

Gallicchio

Chekmarev

et al. 2008

J. Chem. Theory Comput.

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The OPLS-AA all-atom force field and the Analytical Generalized Born plus Non-Polar (AGBNP) implicit solvent model, in conjunction with torsion angle conformational search protocols based on the Protein Local Optimization Program (PLOP), are shown to be effective in predicting the native conformations of 57 9-residue and 35 13-residue loops of a diverse series of proteins with low sequence identity. The novel nonpolar solvation free energy estimator implemented in AGBNP augmented by correction terms aimed at reducing the occurrence of ion pairing are important to achieve the best prediction accuracy. Extended versions of the previously developed PLOP-based conformational search schemes based on calculations in the crystal environment are reported that are suitable for application to loop homology modeling without the crystal environment. Our results suggest that in general the loop backbone conformation is not strongly influenced by crystal packing. The application of the temperature Replica Exchange Molecular Dynamics (T-REMD) sampling method for a few examples where PLOP sampling is insufficient are also reported. The results reported indicate that the OPLS-AA/AGBNP effective potential is suitable for high-resolution modeling of proteins in the final stages of homology modeling and/or protein crystallographic refinement.

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

Cited by 280 publications

References 69 publications

Poisson–Boltzmann model analysis of binding mRNA cap analogues to the translation initiation factor eIF4E

Poisson–Boltzmann model analysis of binding mRNA cap analogues to the translation initiation factor eIF4E

A polymer physics perspective on driving forces and mechanisms for protein aggregation

Prediction of Protein Loop Conformations Using the AGBNP Implicit Solvent Model and Torsion Angle Sampling

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