Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solution
We propose an analytical approach to calculate the effective dielectric function of proteins in aqueous solution. The screening effect if quantified by a measure of enclosure which is based on the distribution of solute atomic volumes around a pair of charges in a macromolecule. For protein conforma...
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| Veröffentlicht in: | Journal of computational chemistry 2003-11, Vol.24 (15), p.1936-1949 |
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| container_end_page | 1949 |
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| container_issue | 15 |
| container_start_page | 1936 |
| container_title | Journal of computational chemistry |
| container_volume | 24 |
| creator | Haberthür, Urs Majeux, Nicolas Werner, Philipp Caflisch, Amedeo |
| description | We propose an analytical approach to calculate the effective dielectric function of proteins in aqueous solution. The screening effect if quantified by a measure of enclosure which is based on the distribution of solute atomic volumes around a pair of charges in a macromolecule. For protein conformations that vary significantly in size and shape, a comparison with finite difference Poisson calculations shows that pair interaction energies, their sums and solvation energies are well reproduced. The approach rivals the speed of simple distance dependent dielectric functions and the accuracy of the generalized Born model. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1936–1949, 2003 |
| doi_str_mv | 10.1002/jcc.10317 |
| format | Article |
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Comput. Chem</addtitle><description>We propose an analytical approach to calculate the effective dielectric function of proteins in aqueous solution. The screening effect if quantified by a measure of enclosure which is based on the distribution of solute atomic volumes around a pair of charges in a macromolecule. For protein conformations that vary significantly in size and shape, a comparison with finite difference Poisson calculations shows that pair interaction energies, their sums and solvation energies are well reproduced. The approach rivals the speed of simple distance dependent dielectric functions and the accuracy of the generalized Born model. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1936–1949, 2003</description><subject>analytical electrostatic interaction (AEI)</subject><subject>continuum dielectric</subject><subject>effective dielectric constant</subject><subject>Electric Conductivity</subject><subject>generalized Born approach</subject><subject>implicit solvent</subject><subject>Macromolecular Substances</subject><subject>Mathematics</subject><subject>Models, Biological</subject><subject>Models, Theoretical</subject><subject>Protein Conformation</subject><subject>Proteins - chemistry</subject><subject>solvation energy</subject><subject>Water - chemistry</subject><issn>0192-8651</issn><issn>1096-987X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2003</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kEtLxDAUhYMoOo4u_AOSleCimrRNMllq0VEZFMHXLqbpDUb70KYd9d-bsaOuXN0D9zuHw0Foh5IDSkh8-GxMEAkVK2hEieSRnIiHVTQiVMbRhDO6gTa9fyaEJIyn62iDpoyyRPARejyx1hkHdYdhrsted66pcWNx9wQYrAXTuTngwkEZZOsMtn1tfiCNK23apmrCsy8Buxrrtx6a3mPflP0C20JrVpcetpd3jG5PT26ys2h2NT3PjmaRSZgUkZBWW53naUy4iXMrteWTggtJcws5k4XQsRFgU5ZTMUkDwnJJJbEkhgQsT8Zob8h9bZtQwXeqct5AWep60UcJJqjkLA3g_gCG4t63YNVr6yrdfipK1GJOFeZU33MGdncZ2ucVFH_kcr8AHA7Auyvh8_8kdZFlP5HR4HC-g49fh25fFBeJYOr-chrKHl8_ZPJY3SVfCHSP-g</recordid><startdate>20031130</startdate><enddate>20031130</enddate><creator>Haberthür, Urs</creator><creator>Majeux, Nicolas</creator><creator>Werner, Philipp</creator><creator>Caflisch, Amedeo</creator><general>Wiley Subscription Services, Inc., A Wiley Company</general><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>20031130</creationdate><title>Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solution</title><author>Haberthür, Urs ; Majeux, Nicolas ; Werner, Philipp ; Caflisch, Amedeo</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3597-79fafabb4206c2bf9af68d6791bfeb59d7a2c7ef45b1784c2b5b9190f02e3ef63</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2003</creationdate><topic>analytical electrostatic interaction (AEI)</topic><topic>continuum dielectric</topic><topic>effective dielectric constant</topic><topic>Electric Conductivity</topic><topic>generalized Born approach</topic><topic>implicit solvent</topic><topic>Macromolecular Substances</topic><topic>Mathematics</topic><topic>Models, Biological</topic><topic>Models, Theoretical</topic><topic>Protein Conformation</topic><topic>Proteins - chemistry</topic><topic>solvation energy</topic><topic>Water - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Haberthür, Urs</creatorcontrib><creatorcontrib>Majeux, Nicolas</creatorcontrib><creatorcontrib>Werner, Philipp</creatorcontrib><creatorcontrib>Caflisch, Amedeo</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of computational chemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Haberthür, Urs</au><au>Majeux, Nicolas</au><au>Werner, Philipp</au><au>Caflisch, Amedeo</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solution</atitle><jtitle>Journal of computational chemistry</jtitle><addtitle>J. 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| ispartof | Journal of computational chemistry, 2003-11, Vol.24 (15), p.1936-1949 |
| issn | 0192-8651 1096-987X |
| language | eng |
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| source | MEDLINE; Wiley Online Library Journals Frontfile Complete |
| subjects | analytical electrostatic interaction (AEI) continuum dielectric effective dielectric constant Electric Conductivity generalized Born approach implicit solvent Macromolecular Substances Mathematics Models, Biological Models, Theoretical Protein Conformation Proteins - chemistry solvation energy Water - chemistry |
| title | Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solution |
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