Protein electrostatics and pK a blind predictions; contribution from empirical predictions of internal ionizable residues

Proteins: Structure, Function and Bioinformatics

Volumn 79, Issue 12, 2011, Pages 3333-3345

  Olsson, Mats H M ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Homology modeling; Null model; PROPKA; Relative rmsd; Reorganization; Staphylococcal nuclease; Validation

Indexed keywords

ARGININE; ASPARAGINE; BACTERIAL ENZYME; HISTIDINE; LYSINE; MICROCOCCAL NUCLEASE; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; DIELECTRIC CONSTANT; ELECTRIC POTENTIAL; HYDROPHOBICITY; NONHUMAN; PH; PKA; PRIORITY JOURNAL; PROPKA PROTEIN PREDICTOR; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; STATIC ELECTRICITY; CHEMICAL MODEL; CHEMICAL PHENOMENA; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; METABOLISM; METHODOLOGY; MUTATION; PROTEIN CONFORMATION; STATISTICS; THERMODYNAMICS;

HYDROGEN-ION CONCENTRATION; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MICROCOCCAL NUCLEASE; MODELS, CHEMICAL; MODELS, MOLECULAR; MUTATION; PROTEIN CONFORMATION; PROTEINS; STATIC ELECTRICITY; STATISTICS AS TOPIC; THERMODYNAMICS;

EID: 81055157863     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23113     Document Type: Article

References (30)

1. Isom DG, Castaneda CA, Velu PD, Garcia-Moreno B. Charges in the hydrophobic interior of proteins. Proc Natl Acad Sci USA 2010; 107: 16096-16100.
2. Karp DA, Gittis AG, Stahley MR, Fitch CA, Stites WE, Garcia-Moreno B. High apparent dielectric constant inside a protein reflects structural reorganization coupled to the ionization of an internal Asp. Biophys J 2007; 92: 2041-2053.
3. a values of lysine residues buried inside a protein. Proc Natl Acad Sci USA 2011; 108: 5260-5265.
4. Dwyer JJ, Gittis AG, Karp DA, Lattman EE, Spencer DS, Stites WE, Garcia-Moreno B. High apparent dielectric constants in the interior of a protein reflect water penetration. Biophys J 2000; 79: 1610-1620.
5. a values in proteins. Proteins 2002; 48: 388-403.
6. a prediction methods for residues in proteins. J Chem Theory Comput 2008; 4: 951-966.
7. a calculations with extensive side chain rotamer sampling. J Comp Chem 2009; 30: 2231-2247.
8. a calculations. Proteins 2011; 79: 685-702.
9. a-cooperative initiative. Proteins, in press.
10. a values. Proteins 2005; 61: 704-721.
11. Olsson MHM. Improving the desolvation penalty in empirical protein pKa modeling, J Mol Model. (2011) doi: 10.1007/s00894-011-1141-1.
12. a. Proton-transfer reactions, and general acid catalysis reactions in enzymes. Biochemistry 1981; 20: 3167-3177.
13. a values for protein-ligand complexes. Proteins 2008; 73: 765-783.
14. a predictions. J Chem Theory Comput 2011; 2: 525-537.
15. Schutz CN, Warshel A. What are the dielectric "constants" of proteins and how to validate electrostatic models? Proteins 2001; 44: 400-417.
16. Xiang ZX, Honig B. Extending the accuracy limits of prediction for side-chain conformations. J Mol Biol 2001; 311: 421-430.
17. Vriend G. What if-a molecular modeling and drug design program. J Mol Graph 1990; 8: 52.
18. a values of Asp and Glu residues in staphylococcal nuclease. Proteins 2009; 77: 570-588.
19. Gunner MR, Zhu X and Klein MC, MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease, doi: 10.1002/prot.23124.
20. Meyer T, Kieseritzky G and Knapp EW, Electrostatic pKa computations in proteins: Role of internal cavities, doi: 10.1002/prot.23092.
21. Personal communication (2011).
22. Williams LS, Blachly PG, McCammon AT. Measuring the successes and deficiencies of constant pH molecular dynamics: a blind prediction study. doi: 10.1002/prot.23136.
23. Wallace JA, Wang Y, Shi C, Pastoor KJ, Nguyen BL, Xia K and Shen JK, Toward accurate prediction of pKa values for internal protein residues: The importance of conformational relaxation and desolvation energy, 10.1002/prot.23080.
24. Lee FS, Chu ZT, Bolger MB, Warshel A. Calculations of antibody antigen interactions - microscopic and semimicroscopic evaluation of the free-energies of binding of phosphorylcholine analogs to Mcpc603. Protein Eng 1992; 5: 215-228.
25. Sali A, Blundell TL. Comparative protein modeling by satisfaction of spatial restraints. J Mol Biol 1993; 234: 779-815.
26. a in proteins with the microenvironment modulated screened coulomp potential (MM-SCP). doi: 10.1002/prot.23098.
27. Song YF. Exploring conformation sampling with pKa calculations using a hybrid Rosetta-MCCE protocol.
28. Warwicker J. pKa predictions with a coupled finite difference Poisson-Boltzmann and Debye-Hückel method, doi: 10.1002/prot.23078.
29. Kato M, Warshel A. Using a charging coordinate in studies of ionization induced partial unfolding. J Phys Chem B 2006; 110: 11566-11570.
30. Warshel A, Narayszabo G, Sussman F, Hwang JK. How do serine proteases really work. Biochemistry 1989; 28: 3629-3637.