Estimating affinities of calcium ions to proteins

Advances and Applications in Bioinformatics and Chemistry

Volumn 3, Issue 1, 2010, Pages 1-6

  Franke, Stefan ^a   Herfurth, Julia ^a   Hoffmann, Daniel ^a  

^a UNIVERSITY OF DUISBURG ESSEN   (Germany)

Author keywords

Binding; Crystal structure; Free energy; Metal ions; Solvent accessible surface

Indexed keywords

EID: 80051569890     PISSN: None     EISSN: 11786949     Source Type: Journal    
DOI: None     Document Type: Article

References (17)

1. Berridge MJ, Bootman MD, Roderick HL. Calcium signalling: dynamics, homeosta-sis and remodelling. Nat Rev Mol Cell Biol. 2003;4:517-529.
2. 2+-binding helix-loop-helix ef-hand motifs. Biochem J. 2007;405:199-221.
3. Linse S, Forsén S. Determinants that govern high-affinity calcium binding. Adv Second Messenger Phosphoprotein Res. 1995;30:89-151.
4. Berman HM, Westbrook J, Feng Z, et al. The Protein Data Bank. Nucleic Acids Res. 2000;28:235-242.
5. 2+ binding to calmodulin loop. Biophys J. 2006;90:3043-3051.
6. 2+ coordination position 5 of parvalbumin on the calcium-binding affinity: a computational study. J Inorg Biochem. 2006;100:1879-1887.
7. Boguta G, Stepkowski D, Bierzyński A. Theoretical estimation of the calcium-binding constants for proteins from the troponin c superfamily based on a secondary structure prediction method. i. estimation procedure. J Theor Biol. 1988;135:41-61.
8. Boguta G, Stepkowski D, Bierzyński A. Theoretical estimation of the calcium-binding constants for proteins from the troponin c superfamily based on a secondary structure prediction method. ii. applications. J Theor Biol. 1988;135:63-73.
9. Schymkowitz JW, Rousseau F, Martins IC, Ferkinghoff-Borg J, Stricher F, Serrano L. Prediction of water and metal binding sites and their affinities by using the fold-x force field. Proc Natl Acad Sci U S A. 2005;102:10147-10152.
10. Trott O, Olson AJ. Autodock vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2009;31:455-461.
11. Morris GM, Huey R, Lindstrom W, et al. Autodock4 and autodocktools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009;30:2785-2791.
12. Gasteiger J, Marsili M. Iterative partial equalization of orbital electronegativity - rapid access to atomic charges. Tetrahedron. 1980;36: 3219-3228.
13. Word JM, Lovell SC, Richardson JS, Richardson DC. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol. 1999;285:1735-1747.
14. Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. Pdb2pqr: an automated pipeline for the setup of poisson-boltzmann electrostatics calculations. Nucleic Acids Res. 2004;32:W665-W667.
15. Sanner MF, Olson AJ, Spehner JC. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers. 1996;38:305-320.
16. R Development Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria, 2006. ISBN 3-900051-07-0, http://www.R-project.org.
17. Wilson MA, Brunger AT. The 1.0 a crystal structure of ca(2+)-bound calmodulin: an analysis of disorder and implications for functionally relevant plasticity. J Mol Biol. 2000;301:1237-1256.