Crossref journal-article
Elsevier BV
Biophysical Journal (78)
Bibliography

Mehler, E. L., & Guarnieri, F. (1999). A Self-Consistent, Microenvironment Modulated Screened Coulomb Potential Approximation to Calculate pH-Dependent Electrostatic Effects in Proteins. Biophysical Journal, 77(1), 3–22.

Authors 2
  1. Ernest L. Mehler (first)
  2. Frank Guarnieri (additional)
References 86 Referenced 151
  1. 10.1016/S0006-3495(97)78851-9 / Biophys. J. / Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties by Alexov (1997)
  2. 10.1006/jmbi.1994.1301 / J. Mol. Biol. / Prediction of pH-dependent properties of proteins by Antosiewicz (1994)
  3. 10.1021/bi9601565 / Biochemistry / The determinants of pKas in proteins by Antosiewicz (1996)
  4. 10.1016/S0006-3495(94)80900-2 / Biophys. J. / Measurement of the individual pKa values of acidic residues of hen and turkey lysozymes by two-dimensional NMR by Bartik (1994)
  5. 10.1021/bi00496a010 / Biochem. / pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model by Bashford (1990)
  6. 10.1021/j100176a093 / J. Phys. Chem. / Multiple-site titration curves of proteins: an analysis of exact and approximate methods for their calculation by Bashford (1991)
  7. 10.1016/S0022-2836(77)80200-3 / J. Mol. Biol. / The protein data bank: a computer-based archival file for macromolecular structure by Bernstein (1977)
  8. 10.1021/jp9623709 / J. Phys. Chem. / Including side chain flexibility in continuum electrostatic calculations of protein titration by Beroza (1996)
  9. 10.1073/pnas.88.13.5804 / Proc. Natl. Acad. Sci. USA / Protonation of interacting residues in a protein by a Monte Carlo method: application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides by Beroza (1991)
  10. 10.1063/1.1733540 / J. Chem. Phys. / Self-consistent-field theory. I. General treatment by Birss (1963)
  11. 10.1002/j.1460-2075.1986.tb04521.x / EMBO J. / X-ray crystal structure of the complex of human leukocyte elastase (PMN elastase) and the third domain of the turkey ovomucoid inhibitor by Bode (1986)
  12. 10.1007/BF01881023 / Z. Phys. / Volumen und Hydrationswärme der Ionen by Born (1920)
  13. 10.1016/S0031-8914(38)80012-4 / Physica / The dielectric constant of dipole liquids by Böttcher (1938)
  14. 10.1002/jcc.540040211 / J. Comp. Chem. / CHARMM: a program for macromolecular energy, minimization, and dynamics calculations by Brooks (1983)
  15. 10.1021/j100406a020 / J. Phys. Chem. / Analysis of the Born model for hydration of ions by Bucher (1986)
  16. 10.1093/protein/7.2.221 / Prot. Eng. / A method for rapidly assessing and refining simple solvent treatments in molecular modelling. Example studies on the antigen-combining loop H2 from FAB fragment McP603 by Collura (1994)
  17. 10.1039/tf9514700756 / Trans. Faraday Soc. / The dielectric constant of the solution in the diffuse and Helmholtz double layers at a charged interface in aqueous solution by Conway (1951)
  18. 10.1016/0022-2836(87)90189-6 / J. Mol. Biol. / Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins by Cornette (1987)
  19. {'key': '10.1016/S0006-3495(99)76868-2_bib19', 'series-title': 'Polar Molecules', 'author': 'Debye', 'year': '1929'} / Polar Molecules by Debye (1929)
  20. 10.1021/ja01685a008 / J. Am. Chem. Soc. / The inter-ionic attraction theory of ionized solutes. IV. The influence of variation of dielectric constant on the limiting law for small concentrations by Debye (1925)
  21. 10.1021/jp960111d / J. Phys. Chem. / Improving the continuum dielectric approach to calculating pKa's of ionizable groups in proteins by Demchuk (1996)
  22. 10.1002/jcc.540100108 / J. Comp. Chem. / Continuum radial dielectric functions for ion and dipole solution systems by Ehrenson (1989)
  23. 10.1093/oxfordjournals.jbchem.a134319 / J. Biochem. (Tokyo) / Enzymatic activity of avian egg-white lysozymes by Fukamizo (1983)
  24. 10.1021/bi00181a032 / Biochemistry / Two crystal structures of the BI immunoglobulin-binding domain of streptococcal protein G and comparison with NMR by Gallagher (1994)
  25. 10.1002/jcc.540070419 / J. Comp. Chem. / Atomic physicochemical parameters for three-dimensional structure-directed quantitative structure-activity relationships I. Partition coefficients as a measure of hydrophobicity by Ghose (1986)
  26. 10.1002/prot.340150305 / Proteins Struct. Func. Genet. / Multiple-site titration and molecular modeling: two rapid methods for computing energies and forces for ionizable groups in proteins by Gilson (1993)
  27. 10.1002/(SICI)1097-461X(1998)69:1<57::AID-QUA8>3.0.CO;2-W / Int. J. Quantum Chem. / A screened Coulomb potential based implicit solvent model: formulation and parameter development by Guarnieri (1998)
  28. 10.1021/j100665a011 / J. Phys. Chem. / Dielectric relaxation spectra of water adsorbed on lysozyme by Harvey (1972)
  29. {'key': '10.1016/S0006-3495(99)76868-2_bib29', 'first-page': 'A198', 'article-title': 'A screened Coulomb potential based implicit solvent model: parametrization and prediction of structures of small peptides', 'volume': '76', 'author': 'Hassan', 'year': '1999', 'journal-title': 'Biophys. J.'} / Biophys. J. / A screened Coulomb potential based implicit solvent model: parametrization and prediction of structures of small peptides by Hassan (1999)
  30. 10.1107/S0108767389009177 / Acta Crys. A. / Segmented anisotropic refinement of bovine ribonuclease A by the application of the rigid-body/TLS model by Howlin (1989)
  31. 10.1021/bi00098a024 / Biochemistry / Human immunodeficiency virus-1 protease. 2. Use of pH rate studies and solvent kinetic isotope effects to elucidate details of chemical mechanism by Hyland (1991)
  32. 10.1016/S0021-9258(18)54237-X / J. Biol. Chem. / Kinetic studies of human immunodeficiency virus type 1 protease and its active-site hydrogen bond mutant A28S by Ido (1991)
  33. {'key': '10.1016/S0006-3495(99)76868-2_bib33', 'first-page': '1185', 'article-title': 'Nuclear magnetic resonance study of the microenvironments of histidine residues of ribonuclease T1 and carboxymethylated ribonuclease T1', 'volume': '89', 'author': 'Inagaki', 'year': '1981', 'journal-title': 'J. Biochem.'} / J. Biochem. / Nuclear magnetic resonance study of the microenvironments of histidine residues of ribonuclease T1 and carboxymethylated ribonuclease T1 by Inagaki (1981)
  34. 10.1021/jp9715944 / J. Phys. Chem. / Calculating acid-dossociation constants of proteins using the boundary element method by Juffer (1997)
  35. 10.1016/0022-2836(92)90260-Q / J. Mol. Biol. / Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution by Katayanagi (1992)
  36. 10.1006/jmbi.1996.0361 / J. Mol. Biol. / Measurement and modelling of sequence-specific pKa values of lysine residues in calbindin D9k by Kesvatera (1996)
  37. 10.1021/bi9630927 / Biochemistry / Pka measurements from nuclear magnetic resonance for the B1 and B2 immunoglobulin G-binding domains of protein G: comparison with calculated values for nuclear magnetic resonance and x-ray structures by Khare (1997)
  38. 10.1063/1.456845 / J. Chem. Phys. / Microscopic simulations of macroscopic dielectric constants of solvated proteins by King (1991)
  39. 10.1002/prot.340010109 / Proteins Struct. Func. Genet. / Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification by Klapper (1986)
  40. 10.1021/bi00445a014 / Biochemistry / Crystal structure of guanosine-free ribonuclease T1, complexed with vanadate, suggests conformational change upon substrate binding by Kostrewa (1989)
  41. {'key': '10.1016/S0006-3495(99)76868-2_bib41', 'first-page': '1215', 'article-title': 'Analysis of the acid-base titration curve of hen lysozyme', 'volume': '87', 'author': 'Kuramitsu', 'year': '1980', 'journal-title': 'J. Biochem.'} / J. Biochem. / Analysis of the acid-base titration curve of hen lysozyme by Kuramitsu (1980)
  42. 10.1021/jm00243a001 / J. Med. Chem. / Calculation of hydrophobic constant (log P) from π and f-constants by Leo (1975)
  43. {'key': '10.1016/S0006-3495(99)76868-2_bib43', 'series-title': 'Theory of Electrons', 'author': 'Lorentz', 'year': '1952'} / Theory of Electrons by Lorentz (1952)
  44. Luo, N., E. Mehler, and R. Osman. 1999. Specificity and catalysis of uracil DNA glycosylase. A molecular dynamics study of reactant and product complexes with DNA. Biochemistry. In press. (10.1021/bi990262h)
  45. 10.1021/ja974307i / J. Amer. Chem. Soc. / pKa shifts in small molecules and HIV protease: electrostatics and conformation by Luo (1998)
  46. {'key': '10.1016/S0006-3495(99)76868-2_bib46', 'first-page': 'A143', 'article-title': 'Self-consistent parametrization of bio molecules for molecular modeling and condensed phase simulations', 'volume': '6', 'author': 'MacKerell', 'year': '1992', 'journal-title': 'Biophys. J.'} / Biophys. J. / Self-consistent parametrization of bio molecules for molecular modeling and condensed phase simulations by MacKerell (1992)
  47. 10.1021/ja00153a017 / J. Amer. Chem. Soc. / An all-atom empirical Emergy function for the simulation of nucleic acids by MacKerell (1995)
  48. 10.1002/jps.2600841206 / J. Pharm. Sci. / Comparative evaluation of the predictive power of calculation procedures for molecular lipophilicity by Mannhold (1995)
  49. 10.1021/bi00264a020 / Biochem. / Analysis of electrostatic interactions and their relationship to conformation and stability of bovine pancreatic trypsin inhibitor by March (1982)
  50. 10.1107/S010876818300275X / Acta Crys. Sect. B. / The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors by Marquart (1983)
  51. 10.1063/1.435187 / J. Chem. Phys. / Self-consistent nonorthogonal group function approximation for polyatomic systems. I. Closed shells by Mehler (1977)
  52. {'key': '10.1016/S0006-3495(99)76868-2_bib52', 'series-title': 'Molecular Electrostatic Potential: Concepts and Applications', 'first-page': '371', 'article-title': 'The Lorentz–Debye–Sack theory and dielectric screening of electrostatic effects in proteins and nucleic acids', 'author': 'Mehler', 'year': '1996'} / Molecular Electrostatic Potential: Concepts and Applications / The Lorentz–Debye–Sack theory and dielectric screening of electrostatic effects in proteins and nucleic acids by Mehler (1996)
  53. 10.1021/jp9537926 / J. Phys. Chem. / A self-consistent, free energy based approximation to calculate pH dependent electrostatic effects in proteins by Mehler (1996)
  54. 10.1021/bi00312a015 / Biochemistry / Electrostatic effects in water-accessible regions of proteins by Mehler (1984)
  55. 10.1093/protein/4.8.903 / Prot. Eng. / Electrostatic effects in proteins: comparison of dielectric and charge models by Mehler (1991)
  56. 10.1021/bi00183a034 / Biochemistry / Individual ionization constants of all the carboxyl groups in ribonuclease HI from Escherichia coli determined by NMR by Oda (1994)
  57. 10.1016/S0021-9258(18)54118-1 / J. Biol. Chem. / Role of Histidine-124 in the catalytic function of ribonuclease HI from Escherichia coli by Oda (1993)
  58. 10.1021/ja01299a050 / J. Amer. Chem. Soc. / Electric moments of molecules in liquids by Onsager (1936)
  59. 10.1021/j100842a024 / J. Phys. Chem. / Further observations on the electrical properties of hemoglobin-bound water by Pennock (1969)
  60. 10.1016/0005-2795(80)90258-5 / Biochim. Biophys. Acta / Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins by Ponnuswamy (1980)
  61. 10.1107/S0108767381098619 / Acta Crys. A. / Structure of triclinic lysozyme and it Cu(2+) complex at 2 angstroms resolution by Ramanadham (1981)
  62. {'key': '10.1016/S0006-3495(99)76868-2_bib62', 'series-title': 'The Hydrophobic Fragmental Constant', 'author': 'Rekker', 'year': '1977'} / The Hydrophobic Fragmental Constant by Rekker (1977)
  63. {'key': '10.1016/S0006-3495(99)76868-2_bib63', 'first-page': '479', 'article-title': 'The hydrophobic fragmental constant: an extension to a 1000 data point set', 'volume': '14', 'author': 'Rekker', 'year': '1979', 'journal-title': 'Eur. J. Med. Chem.'} / Eur. J. Med. Chem. / The hydrophobic fragmental constant: an extension to a 1000 data point set by Rekker (1979)
  64. {'key': '10.1016/S0006-3495(99)76868-2_bib64', 'first-page': '206', 'article-title': 'The dielectric constant of electrolytes', 'volume': '27', 'author': 'Sack', 'year': '1926', 'journal-title': 'Phys. Z.'} / Phys. Z. / The dielectric constant of electrolytes by Sack (1926)
  65. {'key': '10.1016/S0006-3495(99)76868-2_bib65', 'first-page': '199', 'article-title': 'The dielectric constants of solutions of electrolytes at small concentrations', 'volume': '28', 'author': 'Sack', 'year': '1927', 'journal-title': 'Phys. Z.'} / Phys. Z. / The dielectric constants of solutions of electrolytes at small concentrations by Sack (1927)
  66. 10.1021/bi00014a028 / Biochemistry / pH, ionic strength, and temperature dependence of ionization equilibria for the carboxyl groups in turkey ovomucoid third domain by Schaller (1995)
  67. 10.1515/zpch-1936-17611 / Z. Physik. Chem. A. / Der Einfluss einer Ionenladung auf die Acidität einer Säure by Schwarzenbach (1936)
  68. 10.1021/jp963412w / J. Phys. Chem. / Consistent calculations of pKa's of ionizable residues in proteins: semi-microscopic and microscopic approaches by Sham (1997)
  69. 10.1016/S0006-3495(98)77885-3 / Biophys. J. / The effect of protein relaxation on charge–charge interactions and dielectric constants of proteins by Sham (1998)
  70. 10.1016/S0021-9258(18)80108-9 / J. Biol. Chem. / Conformational stability and activity of ribonuclease T1 and mutants by Shirley (1989)
  71. 10.1007/BF00125317 / J. Comp.-Aided Mol. Design. / Automatic log P estimation based on combined additive modeling methods by Suzuki (1990)
  72. 10.1016/0301-4622(90)80053-A / Biophys. Chem. / Electrostatic contributions to the binding of Ca2+ in calbindin mutants: a Monte Carlo study by Svensson (1990)
  73. 10.1021/bi00235a014 / Biochem. / Ion-binding properties of calbindin D9k: a Monte Carlo simulation study by Svensson (1991)
  74. 10.1021/bi00014a029 / Biochemistry / Hydrogen bonds and the pH dependence of ovomucoid third domain stability by Swint-Kruse (1995)
  75. 10.1016/S0021-9258(19)84447-2 / J. Biol. Chem. / The refined structure of vitamin D-dependent calcium-binding protein from bovine intestine by Szebenyi (1986)
  76. 10.1021/j100782a019 / J. Phys. Chem. / Dielectric dispersion of crystalline powders of amino acids, peptides and proteins by Takashima (1965)
  77. 10.1021/ja00881a009 / J. Am. Chem. Soc. / Contribution of hydrophobic interactions to the stability of the globular conformation of proteins by Tanford (1962)
  78. 10.1021/bi00761a029 / Biochemistry / Interpretation of protein titration curves. Application to lysozyme by Tanford (1972)
  79. 10.1002/pro.5560010811 / Protein Sci. / Crystal structure of a complex of HIV-1 protease with a dihydroxyethylene-containing inhibitor: comparisons with molecular modeling by Thanki (1992)
  80. 10.1021/bi00514a028 / Biochemistry / Calculations of enzymatic reactions: calculations of Pka, proton transfer reactions, and general acid catalysis reactions in enzymes by Warshel (1981)
  81. 10.1016/0022-2836(82)90505-8 / J. Mol. Biol. / Calculation of the electric potential in the active site cleft due to α-helix dipoles by Warwicker (1982)
  82. 10.1021/ja01421a013 / J. Am. Chem. Soc. / The free energy of hydration of ions and the electrostriction of the solvent by Webb (1926)
  83. 10.1016/S0021-9258(19)50095-3 / J. Biol. Chem. / Structural and thermodynamic analysis of compensating mutations within the core of chicken egg white lysozyme by Wilson (1992)
  84. 10.1002/prot.340150304 / Proteins Struct. Func. Genet. / On the calculation of pKas in proteins by Yang (1993)
  85. 10.1126/science.2169648 / Science / Structure of ribonuclease H phased at 2Å resolution by MAD analysis of the selenomethionyl protein by Yang (1990)
  86. 10.1016/S0006-3495(95)80042-1 / Biophys. J. / Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility by You (1995)
Dates
Type When
Created 16 years, 7 months ago (Jan. 6, 2009, 7:21 a.m.)
Deposited 3 years, 8 months ago (Dec. 4, 2021, 11:47 a.m.)
Indexed 4 months, 1 week ago (April 9, 2025, 3:30 a.m.)
Issued 26 years, 1 month ago (July 1, 1999)
Published 26 years, 1 month ago (July 1, 1999)
Published Print 26 years, 1 month ago (July 1, 1999)
Funders 0

None

@article{Mehler_1999, title={A Self-Consistent, Microenvironment Modulated Screened Coulomb Potential Approximation to Calculate pH-Dependent Electrostatic Effects in Proteins}, volume={77}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/s0006-3495(99)76868-2}, DOI={10.1016/s0006-3495(99)76868-2}, number={1}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Mehler, Ernest L. and Guarnieri, Frank}, year={1999}, month=jul, pages={3–22} }