A New DelPhi Feature for Modeling Electrostatic Potential around Proteins: Role of Bound Ions and Implications for Zeta-Potential.

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  • Author(s): Chakravorty A;Chakravorty A; Jia Z; Jia Z; Li L; Li L; Alexov E; Alexov E
  • Source:
    Langmuir : the ACS journal of surfaces and colloids [Langmuir] 2017 Mar 07; Vol. 33 (9), pp. 2283-2295. Date of Electronic Publication: 2017 Feb 20.
  • Publication Type:
    Journal Article; Research Support, N.I.H., Extramural
  • Language:
    English
  • Additional Information
    • Source:
      Publisher: American Chemical Society Country of Publication: United States NLM ID: 9882736 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1520-5827 (Electronic) Linking ISSN: 07437463 NLM ISO Abbreviation: Langmuir Subsets: MEDLINE
    • Publication Information:
      Original Publication: Washington, DC : American Chemical Society, c1985-
    • Subject Terms:
      Proteins/*chemistry; Hydrogen-Ion Concentration ; Models, Molecular ; Particle Size ; Salts/chemistry ; Static Electricity ; Surface Properties
    • Abstract:
      A new feature of the popular software DelPhi is developed and reported, allowing for computing the surface averaged electrostatic potential (SAEP) of macromolecules. The user is given the option to specify the distance from the van der Waals surface where the electrostatic potential will be outputted. In conjunction with DelPhiPKa and the BION server, the user can adjust the charges of titratable groups according to specific pH values, and add explicit ions bound to the macromolecular surface. This approach is applied to a set of four proteins with "experimentally" delivered zeta (ζ)-potentials at different pH values and salt concentrations. It has been demonstrated that the protocol is capable of predicting ζ-potentials in the case of proteins with relatively large net charges. This protocol has been less successful for proteins with low net charges. The work demonstrates that in the case of proteins with large net charges, the electrostatic potential should be collected at distances about 4 Å away from the vdW surface and explicit ions should be added at a binding energy cutoff larger than 1-2kT, in order to accurately predict ζ-potentials. The low salt conditions substantiate this effect of ions on SAEP.
    • References:
      Phys Rev Lett. 1996 May 13;76(20):3858-3861. (PMID: 10061127)
      J Comput Chem. 2004 Jul 15;25(9):1157-74. (PMID: 15116359)
      Annu Rev Phys Chem. 2010;61:171-89. (PMID: 20055668)
      J Mol Biol. 2013 May 27;425(10):1655-69. (PMID: 23416556)
      Langmuir. 2011 Sep 20;27(18):11597-604. (PMID: 21834579)
      Nucleic Acids Res. 2000 Jan 1;28(1):235-42. (PMID: 10592235)
      Proteins. 2015 Dec;83(12):2186-97. (PMID: 26408449)
      J Comput Chem. 2015 Dec 15;36(32):2381-93. (PMID: 26484964)
      J Biol Chem. 2001 Jan 5;276(1):62-7. (PMID: 11024041)
      J Mol Biol. 1997 Sep 12;272(1):106-20. (PMID: 9299341)
      PLoS Comput Biol. 2013;9(2):e1002924. (PMID: 23468611)
      J Theor Comput Chem. 2014;13(3):. (PMID: 25419028)
      J Phys Condens Matter. 2012 Apr 25;24(16):164205. (PMID: 22466073)
      Nucleic Acids Res. 2010 Jan;38(Database issue):D750-3. (PMID: 19854939)
      Science. 1995 May 26;268(5214):1144-9. (PMID: 7761829)
      Biomolecules. 2016 Apr 28;6(2):. (PMID: 27136595)
      J Phys Chem B. 2016 Aug 25;120(33):8707-21. (PMID: 27146097)
      PLoS Comput Biol. 2012;8(10):e1002696. (PMID: 23055910)
      Biophys J. 2009 Jul 22;97(2):554-62. (PMID: 19619470)
      Protein Sci. 2011 Dec;20(12):2060-73. (PMID: 21953551)
      Mov Disord. 2017 Feb;32(2):241-245. (PMID: 27862270)
      Phys Rev Lett. 2013 Sep 6;111(10):108105. (PMID: 25166715)
      BMC Biophys. 2012 May 14;5:9. (PMID: 22583952)
      Biochim Biophys Acta. 2006 Nov;1764(11):1647-76. (PMID: 17049320)
      Biophys J. 2007 Nov 15;93(10):3340-52. (PMID: 17693468)
      Proc Natl Acad Sci U S A. 2001 Mar 13;98(6):3109-14. (PMID: 11248040)
      Sci Rep. 2016 Mar 18;6:23249. (PMID: 26988596)
      Eur J Biochem. 2004 Jan;271(1):173-85. (PMID: 14686930)
      Methods Mol Biol. 2013;924:243-70. (PMID: 23034752)
      Colloids Surf B Biointerfaces. 2008 Oct 1;66(1):39-44. (PMID: 18583108)
      Langmuir. 2011 Jan 4;27(1):250-63. (PMID: 21128607)
      Biophys J. 1995 Mar;68(3):1120-7. (PMID: 7756531)
      J Comput Chem. 2013 Aug 15;34(22):1949-60. (PMID: 23733490)
      Phys Biol. 2011 Jun;8(3):035001. (PMID: 21572182)
      Biophys J. 2012 Jun 20;102(12):2885-93. (PMID: 22735539)
      Sci Rep. 2016 Aug 17;6:31523. (PMID: 27531742)
      Front Mol Biosci. 2015 Mar 06;2:5. (PMID: 25988173)
    • Grant Information:
      R01 GM093937 United States GM NIGMS NIH HHS
    • Accession Number:
      0 (Proteins)
      0 (Salts)
    • Publication Date:
      Date Created: 20170210 Date Completed: 20180924 Latest Revision: 20230111
    • Publication Date:
      20240829
    • Accession Number:
      PMC9831612
    • Accession Number:
      10.1021/acs.langmuir.6b04430
    • Accession Number:
      28181811