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Electrostatic potentials of proteins in water: a structured continuum approach

A. Hildebrandt, R. Blossey, S. Rjasanow, O. Kohlbacher, H.-P. Lenhof
2007 Bioinformatics  
Here, we present a novel approach to the computation of electrostatic potentials which allows the inclusion of water structure into the classical theory of continuum electrostatics.  ...  This allows, for the first time, the computation of electrostatic potentials and interactions of large biomolecular systems immersed in water including effects of the solvent's structure in a continuum  ...  We have developed a novel approach to protein electrostatics based on an extension of classical continuum electrostatics accounting for the structure of the water surrounding a biomolecule (Hildebrandt  ... 
doi:10.1093/bioinformatics/btl312 pmid:17237112 fatcat:4x4tlzjvjfdgfcnceaxob5rrom

Structural origins of redox potentials in Fe-S proteins: electrostatic potentials of crystal structures

P.D. Swartz, B.W. Beck, T. Ichiye
1996 Biophysical Journal  
Finally, molecular dynamics simulations of solvent around static rubredoxin crystal structures indicate that water alone is a major factor in dampening the contribution of charged side chains, in accord  ...  For instance, in the rubredoxins, the presence of Val 44 versus Ala 44 causes a backbone shift that explains a -50 mV lower redox potential in one of the four rubredoxins.  ...  , of Phillips Laboratory or the U.S.  ... 
doi:10.1016/s0006-3495(96)79533-4 pmid:8968568 pmcid:PMC1233786 fatcat:bbauyyx3cbclppfnu5yy2rhly4

Electrostatic Potential of Human Immunodeficiency Virus Type 2 and Rhesus Macaque Simian Immunodeficiency Virus Capsid Proteins

Katarzyna Bozek, Emi E. Nakayama, Ken Kono, Tatsuo Shioda
2012 Frontiers in Microbiology  
This work was supported by grants from the Ministry of Education, Culture, Sports, Science, and Technology, and the Ministry of Health, Labour and Welfare, Japan.  ...  The nonlocal electrostatic method allows inclusion of the structure of water molecules in the calculation and describes the system as a continuum.  ...  We used the approximate radius of a water molecule of 1.4 Å and an additional 3 Å to determine how the electrostatic potential changes with distance from the molecule.  ... 
doi:10.3389/fmicb.2012.00206 pmid:22679444 pmcid:PMC3367459 fatcat:mtih6mh2vvfqjcv7qo35iyqsdy

Cavity-water interface is polar [article]

Allan D. Friesen, Dmitry V. Matyushov
2010 arXiv   pre-print
The statistics of the electrostatic field produced by water inside the cavity follow linear response and approach the prediction of continuum electrostatics with increasing cavity size.  ...  We present the results of numerical simulations of the electrostatics and dynamics of water hydration shells surrounding Kihara cavities given by a Lennard-Jones (LJ) layer at the surface of a hard-sphere  ...  of continuum electrostatics in application to nanoscale interfaces of molecular liquids.  ... 
arXiv:1004.1728v2 fatcat:75shqesa7rh2plf34hnkkagpcu

Water Under the BAR

Edward R. Lyman, Haosheng Cui, Gregory A. Voth
2010 Biophysical Journal  
Lipids can modulate membrane protein activity in many different ways.  ...  Among those are the families of WALP and KALP peptides, which consist of a poly-(leucine-alanine) stretch flanked by tryptophans and lysines, respec-  ...  Generally, interactions between ionizable SCs are more attractive and the PMFs are more structured in a lipid bilayer than in water. 2521-Pos Water Under the BAR Edward R.  ... 
doi:10.1016/j.bpj.2009.12.2648 fatcat:kaezmziqybaqjgh5a4kkygtjyy

Dynamic water networks in cytochrome cbb3 oxidase

Vivek Sharma, Mårten Wikström, Ville R.I. Kaila
2012 Biochimica et Biophysica Acta - Bioenergetics  
Here we have used molecular dynamics (MD) simulations, continuum electrostatic approaches, and quantum chemical cluster calculations to identify proton transfer pathways in cytochrome cbb 3 .  ...  Protonation of Glu323 provides a mechanism to tune the redox potential of heme b 3 with possible implications for proton pumping.  ...  Here we study cytochrome cbb 3 oxidase from P. stutzeri using a combination of computational techniques of classical molecular dynamics, continuum electrostatic approaches, and quantum chemical calculations  ... 
doi:10.1016/j.bbabio.2011.09.010 pmid:21963365 fatcat:xermpgcevja7rjch2rkthn33wa

Thermodynamics of Water Entry in Aquaporins

Amir Barati Farimani, Emad Tajkhorshid, Narayana Aluru
2014 Biophysical Journal  
Deficiency of the PNPbased approach is rejection of 60% of proteins with low RMSD and good electrostatic properties.  ...  In both cases the size of ions is involved in the diffusion coefficient calculation. The tool uses the electrostatic potential distribution obtained from the 3D PNP simulations.  ... 
doi:10.1016/j.bpj.2013.11.3108 fatcat:r2lf73xzibf2jo4rbpnk55ocaq

Coarse Grained Ion-Ion and Ion-Water Interactions

See-Wing Chiu, Eric Jakobsson
2012 Biophysical Journal  
However, such continuum solvent approaches can struggle when the discrete nature of water is needed, often at the solute/solvent interface.  ...  large local electrostatic potential.  ... 
doi:10.1016/j.bpj.2011.11.919 fatcat:gvgkxaljqbhfngylt4je43mani

Water under the BAR

Edward Lyman, Haosheng Cui, Gregory A. Voth
2010 Biophysical Journal  
A number of such proteins are now known, and several mechanisms of curvature generation have been suggested, but so far a quantitative understanding of the importance of the various potential mechanisms  ...  In the coarse-grained simulations, we find a strong dependence of the induced curvature on the dielectric screening.  ...  While the electrostatic potential due to the membrane experienced by a protein in bulk salt solution is of course renormalized by the mobile ions, in this case we are concerned with the protein-membrane  ... 
doi:10.1016/j.bpj.2010.06.074 pmid:20858422 pmcid:PMC2941004 fatcat:pfhvu5wk2fg2bly6sx63jxq4dq

Accurate Solutions with the Semi-Explicit Assembly Water Model

Christopher J. Fennell, Charles W. Kehoe, Ken A. Dill
2012 Biophysical Journal  
However, such continuum solvent approaches can struggle when the discrete nature of water is needed, often at the solute/solvent interface.  ...  large local electrostatic potential.  ... 
doi:10.1016/j.bpj.2011.11.917 fatcat:vyd45hoznngtdb42vkcovljmvi

Voltage-Dependent Insertion of Alamethicin at Phospholipid/Water and Octane/Water Interfaces

D.P. Tieleman, H.J.C. Berendsen, M.S.P. Sansom
2001 Biophysical Journal  
Understanding the binding and insertion of peptides in lipid bilayers is a prerequisite for understanding phenomena such as antimicrobial activity and membrane-protein folding.  ...  At cis-positive potentials, alamethicin does not insert into a phospholipid bilayer in 10 ns of simulation, due to the slow dynamics of the peptide and lipids.  ...  In many processes the membrane potential plays a crucial role in the function of membrane proteins.  ... 
doi:10.1016/s0006-3495(01)76018-3 pmid:11159406 pmcid:PMC1301237 fatcat:zsmwtymefjaqhg5pg4p7chmupm

The contribution of electrostatic interactions to the collapse of oligoglycine in water

Karandur, Pettitt
2016 Condensed Matter Physics  
We also describe the approximate thermodynamic changes that occur during the scaling both in terms of intrapeptide potentials and peptide-water potentials, and estimate the electrostatic solvation free  ...  Protein solubility and conformational stability are a result of a balance of interactions both within a protein and between protein and solvent.  ...  This research was performed in part using the Keenland and Stampede systems, part of the National Science Foundation XSEDE resources.  ... 
doi:10.5488/cmp.19.23802 pmid:28943833 pmcid:PMC5607018 fatcat:54tg3momo5b4jlv2cxn5n3fs2i

Dielectric saturation of water in a membrane protein channel

Marcel Aguilella-Arzo, Andreu Andrio, Vicente M. Aguilella, Antonio Alcaraz
2009 Physical Chemistry, Chemical Physics - PCCP  
Protein channels that open aqueous pores through biological membranes provide a complex spatial and electrostatic environment that decreases the translational and rotational mobility of water molecules  ...  Water molecules in confined geometries like nanopores and biological ion channels exhibit structural and dynamical properties very different from those found in free solution.  ...  Acknowledgements The authors acknowledge support from the Spanish Ministry of Education (project FIS2007-60205).  ... 
doi:10.1039/b812775a pmid:19088992 fatcat:7jndonscevcenidfstareg6vym

The electrostatic response of water to neutral polar solutes: Implications for continuum solvent modeling

Hari S. Muddana, Neil V. Sapra, Andrew T. Fenley, Michael K. Gilson
2013 Journal of Chemical Physics  
Thus, accounting for solute electrostriction may be a productive approach to improving the accuracy of continuum solvation models. © 2013 AIP Publishing LLC.  ...  Continuum solvation models are widely used to estimate the hydration free energies of small molecules and proteins, in applications ranging from drug design to protein engineering, and most such models  ...  Thus, the nonlinear electrostatic response of water could play an important role in the hydration of proteins.  ... 
doi:10.1063/1.4808376 pmid:23781802 pmcid:PMC3695974 fatcat:pfmmj2vypbaf7ps6pvrgpi2jae

On the ability of molecular dynamics simulation and continuum electrostatics to treat interfacial water molecules in protein-protein complexes

Guillaume Copie, Fabrizio Cleri, Ralf Blossey, Marc F. Lensink
2016 Scientific Reports  
Interfacial waters are increasingly appreciated as playing a key role in protein-protein interactions.  ...  which contains a large number of waters in its interior.  ...  Support from the Research Federation FRABio (University Lille, CNRS, FR 3688, "Structural and Functional Biochemistry of Biomolecular Assemblies") is gratefully acknowledged.  ... 
doi:10.1038/srep38259 pmid:27905545 pmcid:PMC5131287 fatcat:rqincfknpvgefi772axmtkiksy
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