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          : A generalized Born method for accurately reproducing solvation energy of the nonlinear Poisson-Boltzmann equation

Tjong, Harianto; Zhou, Huan‐Xiang

doi:10.1063/1.2735322

Cited by 44 publications

(47 citation statements)

References 44 publications

(43 reference statements)

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“…However, the solvation part calculated by solving the nonlinear PB equation is not decomposable into contributions of individual atoms. However, we showed that the solvation free energy of the nonlinear PB equation can be reproduced well by a generalized Born (GB) method (38,39). The GB solvation free energy consists of one-body and pair contributions (40).…”

Section: Generation Of Transient-complex Ensemble and Calculation Of mentioning

confidence: 99%

Dissection of the high rate constant for the binding of a ribotoxin to the ribosome

Qin

Zhou

2009

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

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Restrictocin belongs to a family of site-specific ribonucleases that kill cells by inactivating the ribosome. The restrictocin–ribosome binding rate constant was observed to exceed 1010 M−1 s−1. We have developed a transient-complex theory to model the binding rates of protein–protein and protein–RNA complexes. The theory predicts the rate constant as ka = ka0 exp(−ΔGel*/kBT), where ka0 is the basal rate constant for reaching the transient complex, located at the outer boundary of the bound state, by random diffusion, and ΔGel* is the average electrostatic interaction free energy of the transient complex. Here, we applied the transient-complex theory to dissect the high restrictocin–ribosome binding rate constant. We found that the binding rate of restrictocin to the isolated sarcin/ricin loop is electrostatically enhanced by ≈300-fold, similar to results found in other protein–protein and protein–RNA complexes. The ribosome provides an additional 10,000-fold rate enhancement because of two synergistic mechanisms afforded by the distal regions of the ribosome. First, they provide additional electrostatic attraction with restrictocin. Second, they reposition the transient complex into a region where local electrostatic interactions of restrictocin with the sarcin/ricin loop are particularly favorable. Our calculations rationalize a host of experimental observations and identify a strategy for designing proteins that bind their targets with high speed.

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Section: Generation Of Transient-complex Ensemble and Calculation Of mentioning

confidence: 99%

Dissection of the high rate constant for the binding of a ribotoxin to the ribosome

Qin

Zhou

2009

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

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“…The speed with which a model can be calculated then offers a major constraint, and it is desirable to have approximations. The Generalized-Born (GB) model [214,217,218] approximates the local-response Poisson or Poisson–Boltzmann models quickly, and is widely used in MD simulations. However, semi-empirical approximation schemes do not necessarily illustrate how more advanced underlying theories can be approximated.…”

Section: Opportunitiesmentioning

confidence: 99%

Gradient models in molecular biophysics: progress, challenges, opportunities

Bardhan

2013

Journal of the Mechanical Behavior of Materials

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In the interest of developing a bridge between researchers modeling materials and those modeling biological molecules, we survey recent progress in developing nonlocal-dielectric continuum models for studying the behavior of proteins and nucleic acids. As in other areas of science, continuum models are essential tools when atomistic simulations (e.g. molecular dynamics) are too expensive. Because biological molecules are essentially all nanoscale systems, the standard continuum model, involving local dielectric response, has basically always been dubious at best. The advanced continuum theories discussed here aim to remedy these shortcomings by adding features such as nonlocal dielectric response, and nonlinearities resulting from dielectric saturation. We begin by describing the central role of electrostatic interactions in biology at the molecular scale, and motivate the development of computationally tractable continuum models using applications in science and engineering. For context, we highlight some of the most important challenges that remain and survey the diverse theoretical formalisms for their treatment, highlighting the rigorous statistical mechanics that support the use and improvement of continuum models. We then address the development and implementation of nonlocal dielectric models, an approach pioneered by Dogonadze, Kornyshev, and their collaborators almost forty years ago. The simplest of these models is just a scalar form of gradient elasticity, and here we use ideas from gradient-based modeling to extend the electrostatic model to include additional length scales. The paper concludes with a discussion of open questions for model development, highlighting the many opportunities for the materials community to leverage its physical, mathematical, and computational expertise to help solve one of the most challenging questions in molecular biology and biophysics.

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“…41–44 However, the accuracy of MD simulations is limited by the accuracy of the ion-dependent force field as well as the completeness of the sampling for the ions and water molecules, 34 As a result, accurate calculations require significant computer resources and exceedingly long computer time even for small RNAs. The classical Counterion Condensation (CC) theory 45 and the (nonlinear) Poisson-Boltzmann (NLPB) theory 46–51 are simple yet useful theories for the prediction of the ion effects. However, both theories ignore ion correlation and ion fluctuations, two potentially important effects for ions around nucleic acids.…”

Section: Introductionmentioning

confidence: 99%

Predicting Ion Effects in an RNA Conformational Equilibrium

et al. 2017

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We develop a partial charge-based Tightly Bound Ion (PCTBI) model for the ion effects in RNA folding. Based on the Monte Carlo Tightly Bound Ion (MCTBI) approach, the model can account for ion fluctuation and correlation effects, and can predict the ion distribution around the RNA. Furthermore, unlike the previous coarse-grained RNA charge models, where negative charges are placed on the phosphates only, the current new model considers the detailed all-atom partial charge distribution on the RNA. Thus, the model not only keeps the advantage of the MCTBI model but also has the potential to provide important detailed information unattainable by the previous MCTBI models. For example, the model predicts the reduction in ion binding upon protein binding and ion-induced conformational switches. For Hepatitis C virus (HCV) genomic RNA, the model predicts a Mg2+-induced stabilization of a kissing motif for a cis-acting regulatory element in the genomic RNA. Extensive theory-experiment comparisons support the reliability of the theoretical predictions. Therefore, the model may serve as a robust starting point for further development of an accurate method for ion effects in RNA conformational equilibrium and RNA-cofactor interactions.

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G Br 6 NL : A generalized Born method for accurately reproducing solvation energy of the nonlinear Poisson-Boltzmann equation

Cited by 44 publications

References 44 publications

Dissection of the high rate constant for the binding of a ribotoxin to the ribosome

Dissection of the high rate constant for the binding of a ribotoxin to the ribosome

Gradient models in molecular biophysics: progress, challenges, opportunities

Predicting Ion Effects in an RNA Conformational Equilibrium

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