<scp>B</scp>
            rownian Dynamics

Madura, Jeffry D.; Briggs, James M.; Wade, Rebecca C.; Gabdoulline, Razif R.

doi:10.1002/0470845015.cba003

Cited by 6 publications

(7 citation statements)

References 86 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Alternatively, many BD programs can impose a Lennard-Jones force at close molecular proximity to prevent a steric clash (Elcock, 2004 ; Huber and McCammon, 2010 ). BD simulation and the theory behind it compose a rich and expansive field, and many sources exist to allow the interested reader to improve his or her knowledge and technique (Ermak and Mccammon, 1978 ; Allen and Tildesley, 1987 ; Gabdoulline and Wade, 1996 ; Elcock et al, 2001 ; Gabdoulline and Wade, 2002 ; Madura et al, 2002 ; Elcock, 2004 ).…”

Section: Investigating Intermolecular Interactionsmentioning

confidence: 99%

Bridging scales through multiscale modeling: a case study on protein kinase A

et al. 2015

View full text Add to dashboard Cite

The goal of multiscale modeling in biology is to use structurally based physico-chemical models to integrate across temporal and spatial scales of biology and thereby improve mechanistic understanding of, for example, how a single mutation can alter organism-scale phenotypes. This approach may also inform therapeutic strategies or identify candidate drug targets that might otherwise have been overlooked. However, in many cases, it remains unclear how best to synthesize information obtained from various scales and analysis approaches, such as atomistic molecular models, Markov state models (MSM), subcellular network models, and whole cell models. In this paper, we use protein kinase A (PKA) activation as a case study to explore how computational methods that model different physical scales can complement each other and integrate into an improved multiscale representation of the biological mechanisms. Using measured crystal structures, we show how molecular dynamics (MD) simulations coupled with atomic-scale MSMs can provide conformations for Brownian dynamics (BD) simulations to feed transitional states and kinetic parameters into protein-scale MSMs. We discuss how milestoning can give reaction probabilities and forward-rate constants of cAMP association events by seamlessly integrating MD and BD simulation scales. These rate constants coupled with MSMs provide a robust representation of the free energy landscape, enabling access to kinetic, and thermodynamic parameters unavailable from current experimental data. These approaches have helped to illuminate the cooperative nature of PKA activation in response to distinct cAMP binding events. Collectively, this approach exemplifies a general strategy for multiscale model development that is applicable to a wide range of biological problems.

show abstract

Section: Investigating Intermolecular Interactionsmentioning

confidence: 99%

Bridging scales through multiscale modeling: a case study on protein kinase A

et al. 2015

View full text Add to dashboard Cite

show abstract

“…24 The NLPB equation is solved by the UHBD program. 4 All UHBD calculations use a coarse grid with a 1.5 Å spacing followed by a fine grid with a 0.5 Å spacing. The dimensions of the coarse and fine grids are 160ϫ 160ϫ 160 and 200 ϫ 200ϫ 200, respectively, for the 55 PDB structures, and are both 140ϫ 140ϫ 140 for the two protein:RNA complexes.…”

Section: Test Systemsmentioning

confidence: 99%

“…[1][2][3][4][5][6][7][8][9][10][11] For most applications on proteins, the linearized PB ͑LPB͒ equation is used; the solvation energy calculated from LPB can closely approach that calculated from the nonlinear PB ͑NLPB͒ equation. 12 However, for nucleic acids, accurate modeling of electrostatic effects requires NLPB.…”

Section: Introductionmentioning

confidence: 99%

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

Tjong

Zhou

2007

The Journal of Chemical Physics

View full text Add to dashboard Cite

The nonlinear Poisson-Boltzmann (NLPB) equation can provide accurate modeling of electrostatic effects for nucleic acids and highly charged proteins. Generalized Born methods have been developed to mimic the linearized Poisson-Boltzmann (LPB) equation at substantially reduced cost. The computer time for solving the NLPB equation is approximately fivefold longer than for the LPB equation, thus presenting an even greater obstacle. Here we present the first generalized Born method, GBr(6)NL, for mimicking the NLPB equation. GBr(6)NL is adapted from GBr(6), a generalized Born method recently developed to reproduce the solvation energy of the LPB equation [Tjong and Zhou, J. Phys. Chem. B 111, 3055 (2007)]. Salt effects predicted by GBr(6)NL on 55 proteins overall deviate from NLPB counterparts by 0.5 kcal/mol from ionic strengths from 10 to 1000 mM, which is approximately 10% of the average magnitudes of the salt effects. GBr(6)NL predictions for the salts effects on the electrostatic interaction energies of two protein:RNA complexes are very promising.

show abstract

“…Harianto Tjong and Huang-Xiang Zhou a͒ The Poisson-Boltzmann ͑PB͒ equation is widely used for modeling electrostatic effects and solvation of biomolecules. [1][2][3][4] There are separate reasons for varying the solvent and solute dielectric constants ͑ s and i ͒ in PB calculations. The former case arises when the solvation energy of a solute in different solvents is of interest.…”

Section: The Dependence Of Electrostatic Solvation Energy On Dielectrmentioning

confidence: 99%

The dependence of electrostatic solvation energy on dielectric constants in Poisson-Boltzmann calculations

Tjong

Zhou

2006

The Journal of Chemical Physics

View full text Add to dashboard Cite

The Poisson-Boltzmann equation gives the electrostatic free energy of a solute molecule (with dielectric constant epsilon(l)) solvated in a continuum solvent (with dielectric constant epsilon(s)). Here a simple formula is presented that accurately predicts the electrostatic free energy for all combinations of epsilon(l) and epsilon(s) from the calculation on a single set of epsilon(l) and epsilon(s) values.

show abstract

B rownian Dynamics

Cited by 6 publications

References 86 publications

Bridging scales through multiscale modeling: a case study on protein kinase A

Bridging scales through multiscale modeling: a case study on protein kinase A

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

The dependence of electrostatic solvation energy on dielectric constants in Poisson-Boltzmann calculations

Contact Info

Product

Resources

About