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Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols

Arghya Chakavorty, Lin Li, Emil Alexov
2016 Journal of Computational Chemistry  
Important component of the binding free energy is the electrostatics, which is frequently modeled via the solutions of the Poisson-Boltzmann Equations (PBE).  ...  However, numerous works have shown that the electrostatic component (ΔΔG elec ) of binding free energy is very sensitive to the parameters used and modeling protocol.  ...  Acknowledgments The work was supported by a grant from NIH, grant number R01GM093937.  ... 
doi:10.1002/jcc.24475 pmid:27546093 pmcid:PMC5030180 fatcat:mestks36bzahhdsykdllhlzmci

On the electrostatic component of protein-protein binding free energy

Kemper Talley, Carmen Ng, Michael Shoppell, Petras Kundrotas, Emil Alexov
2008 PMC Biophysics  
For the hetero-complexes, however, the percentage of the cases for which electrostatics opposed binding varied from 43% to 85%, depending on the protocol and parameters employed.  ...  In this paper we present a comprehensive statistical analysis of the sensitivity of the electrostatic component of binding free energy (Gel) with respect with different force fields (Charmm, Amber, and  ...  Acknowledgements The minimization of the structures used in this work was made possible by a Condor pool deployed and maintained by Clemson Computing and Information Technology.  ... 
doi:10.1186/1757-5036-1-2 pmid:19351424 pmcid:PMC2666630 fatcat:itxmrvsvv5gifdnqceiphocovu

Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase11Edited by A. R. Fersht

Georgios Archontis, Thomas Simonson, Martin Karplus
2001 Journal of Molecular Biology  
A component analysis of the Poisson-Boltzmann free energies is employed to identify speci®c interactions that determine the binding af®nities.  ...  The combined use of molecular dynamics free energy simulations to study one binding process thoroughly, followed by molecular dynamics and Poisson-Boltzmann free energy calculations to study a series of  ...  Schaefer, who has developed a similar decomposition of the electrostatic free energy for interpreting pH effects on ligand binding, were particularly helpful.  ... 
doi:10.1006/jmbi.2000.4285 pmid:11237602 fatcat:3widqanhvfg3lnkjsbukawo5ta

Blockade of Neuronal α7-nAChR by α-Conotoxin ImI Explained by Computational Scanning and Energy Calculations

Rilei Yu, David J. Craik, Quentin Kaas, James Briggs
2011 PLoS Computational Biology  
The protocol using explicit water energy minimization and MM-GB/SA gave the best correlations with experimental binding affinities, with an R 2 value of 0.74.  ...  The electrostatic component was responsible for the selectivity of the various ImI mutants.  ...  Roitberg and Dr. Jason M. Swails for their latest version of script and excellent technical assistance. Author Contributions  ... 
doi:10.1371/journal.pcbi.1002011 pmid:21390272 pmcid:PMC3048385 fatcat:3oq2pvx3kjh2boqq3zpe4ukkje

The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology

F. Fogolari, A. Brigo, H. Molinari
2002 Journal of Molecular Recognition  
The Poisson-Boltzmann equation constitutes one of the most fundamental approaches to treat electrostatic effects in solution.  ...  The theoretical basis of the Poisson-Boltzmann equation is reviewed and a wide range of applications is presented, including the computation of the electrostatic potential at the solvent-accessible molecular  ...  Acknowledgements We wish to thank Professor McCammon for providing us with the UHBD software, and Professor Nicholls and Professor Honig for making GRASP available.  ... 
doi:10.1002/jmr.577 pmid:12501158 fatcat:ilubjsjthzbfhlpgi6fq5ku6me

Poisson-Boltzmann Calculations: van der Waals or Molecular Surface?

Xiaodong Pang, Huan-Xiang Zhou
2012 Communications in Computational Physics  
The Poisson-Boltzmann equation is widely used for modeling the electrostatics of biomolecules, but the calculation results are sensitive to the choice of the boundary between the low solute dielectric  ...  and the high solvent dielectric.  ...  The Poisson-Boltzmann (PB) equation has emerged as one of the most widely used method for modeling biomolecular electrostatics.  ... 
pmid:23293674 pmcid:PMC3535440 fatcat:hkie2cs7rveyjdfaenkvweuoaa

Proton Binding to Proteins: A Free-Energy Component Analysis Using a Dielectric Continuum Model

Georgios Archontis, Thomas Simonson
2005 Biophysical Journal  
It reproduces qualitatively the electrostatic potentials, proton-binding free energies, Marcus reorganization free energies, and pK a shifts from explicit solvent molecular dynamics simulations, and the  ...  Averaging over conformations from the two endpoints of the proton-binding reaction, the protein's atomic degrees of freedom are explicitly modeled.  ...  repair by DNA photolyase: insights from molecular dynamics simulations and electron transfer calculations'' (UC) and ''Study of compstatin, important inhibitor of autoimmune system with high accuracy  ... 
doi:10.1529/biophysj.104.055996 pmid:15821163 pmcid:PMC1305621 fatcat:3og3bwasqvfrxdzln5bddltbzu

Effective energy function for proteins in lipid membranes

Themis Lazaridis
2003 Proteins: Structure, Function, and Bioinformatics  
The electrostatic model is adjusted to match experimental observations for polyalanine, polyleucine, and the glycophorin A dimer.  ...  for reduced screening of electrostatic interactions in the membrane, and (d) an adjustment of the EEF1 aqueous model in light of recent calculations of the potential of mean force between amino acid side-chains  ...  Smith for providing the coordinates of GpA before deposition to the PDB.  ... 
doi:10.1002/prot.10410 pmid:12833542 fatcat:3a4nlhwapfg67kekvetea2pkyi

Insights into affinity and specificity in the complexes of α-lytic protease and its inhibitor proteins: binding free energy from molecular dynamics simulation

Nan-Jie Deng, Piotr Cieplak
2009 Physical Chemistry, Chemical Physics - PCCP  
Analysis of the binding free energy components provides insights into the molecular mechanism of binding specificity.  ...  We report the binding free energy calculation and its decomposition for the complexes of α-lytic protease and its protein inhibitors using molecular dynamics simulation.  ...  Qasim for providing the schematic structures of eglin C and OMTKY3 shown in Fig. 1 ; and Mr Jian Zhan for his technical assistance in maintaining the Linux clusters.  ... 
doi:10.1039/b820961h pmid:19562127 pmcid:PMC4127433 fatcat:2pqxl6wjqnakfbdtbhifu2bgoa

MM-GB(PB)SA Calculations of Protein-Ligand Binding Free Energies [chapter]

Joseph M., Georgios Archontis
2012 Molecular Dynamics - Studies of Synthetic and Biological Macromolecules  
The quantity g ij PB(GB) is determined using the PB model by numerical solution of the Poisson or Poisson-Boltzmann equation (depending on the existence of salt), or using the GB model by an analytical  ...  The polar contributions are accounted for by the generalized Born, Poisson, or Poisson-Boltzmann model, and the non-polar are assumed proportional to the solvent-accessible surface area (SASA), c.f.  ...  Hayes and Georgios Archontis (2012) . MM-GB(PB)SA Calculations of Protein-Ligand Binding Free Energies, Molecular Dynamics -Studies of Synthetic and Biological Macromolecules, Prof.  ... 
doi:10.5772/37107 fatcat:mrhoh6nygnhpzlqdpehy6hewy4

Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf

Holger Gohlke, David A. Case
2003 Journal of Computational Chemistry  
When the polar contribution to the solvation free energy is determined by solving the Poisson-Boltzmann equation (PB) instead, the calculated binding affinity strongly depends on the atomic radii set chosen  ...  Finally, binding free energies estimated from snapshots of the unbound proteins extracted from the complex trajectory result in an underestimate of binding affinity.  ...  The polar contribution was calculated either by solving the Poisson equation (PE) in case of zero salt conditions or the linearized and nonlinearized Poisson-Boltzmann (PB) equations for nonzero salt concentrations  ... 
doi:10.1002/jcc.10379 pmid:14648622 fatcat:cpmv7kwwyraqjfayufvg34ui5y

Comparative Binding Energy (COMBINE) Analysis of Human Neutrophil Elastase Inhibition by Pyridone-containing Trifluoromethylketones

Carmen Cuevas, Manuel Pastor, Carlos Perez, Federico Gago
2001 Combinatorial chemistry & high throughput screening  
of the distance-dependent electrostatic contributions with solventscreened electrostatic interactions calculated by numerically solving the Poisson-Boltzmann equation.  ...  Incorporation of two additional descriptors representing the electrostatic energy contributions to the partial desolvation of both the receptor and the ligands improved the QSAR model, as did the replacement  ...  A finite difference method [46] , as implemented in program DelPhi [39] , was used to solve the linear form of the Poisson-Boltzmann equation and to describe the electrostatic effects of ligand binding  ... 
doi:10.2174/1386207013330742 pmid:11812259 fatcat:7yb5jbnmc5g4xhtzhlvkbpcyly

Calculations of Free-Energy Contributions to Protein–RNA Complex Stabilization

Mark A. Olson
2001 Biophysical Journal  
The problem of calculating binding affinities of protein-RNA complexes is addressed by analyzing a computational strategy of modeling electrostatic free energies based on a nonlinear Poisson-Boltzmann  ...  Solutions to the NLPB equation calculate free energies arising from electronic polarizability and the LRA is constructed from molecular dynamics simulations to model reorganization free energies due to  ...  Electrostatic contributions to binding affinities are calculated from numerical solutions to the Poisson-Boltzmann (PB) equation, and nonpolar interactions are modeled by using solute-solvent cavitation  ... 
doi:10.1016/s0006-3495(01)75836-5 pmid:11566759 pmcid:PMC1301660 fatcat:gfys6uigyfb7vhstam7kroufya

Free Energy Analysis of Protein–DNA Binding: The EcoRI Endonuclease–DNA Complex

B Jayaram, K.J McConnell, Surjit B Dixit, D.L Beveridge
1999 Journal of Computational Physics  
Contributions to binding compounded from subsets of the 24 components provide a basis for advancing a molecular perspective of binding in terms of structural adaptation, electrostatics, van der Waals interactions  ...  the protein and the DNA; and the electrostatic polarization and screening effects, van der Waals components, and cavitation effects of solvation.  ...  The estimated net counterion and added salt effect on binding free energy is +36.2 kcal (0.18 M), which on the scale of numbers involved is close to the finite difference Poisson-Boltzmann estimate of  ... 
doi:10.1006/jcph.1998.6173 fatcat:7sokuyhegnecvmwrdvdho4hsam

Free Energy Calculations and Ligand Binding [chapter]

BjØrn O. Brandsdal, Fredrik Österberg, Martin Almlöf, Isabella Feierberg, Victor B. Luzhkov, Johan Åqvist
2003 Advances in Protein Chemistry  
Acknowledgements Support from the Swedish Research Council (VR) and the Swedish Foundation for Strategic Research (SSF) to J.Å. and from the Norwegian Research Council to B.O.B. is gratefully acknowledged  ...  Solvation free energies are calculated using a numerical solution of the Poisson-Boltzmann equation (Warwicker and Watson, 1982; Gilson and Honig, 1988; Honig and Nicholls, 1995) , and together with a  ...  /Poisson-Boltzmann/Surface Area) (Srinivasan et al., 1998; Kollman et al., 2000) .  ... 
doi:10.1016/s0065-3233(03)66004-3 pmid:14631818 fatcat:ju42axbiffbslmrtj75gehlw7a
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