CO2-formatics: How do proteins bind carbon dioxide?

Journal of Chemical Information and Modeling

Volumn 49, Issue 9, 2009, Pages 2111-2115

  Cundari, Thomas R ^a   Wilson, Angela K ^a   Drummond, Michael L ^a   Gonzalez, Hector Emanuel ^a   Jorgensen, Kameron R ^a   Payne, Stacy ^a   Braunfeld, Jordan ^a   De Jesus, Margarita ^a   Johnson, Vanessa M ^a  

^a UNIVERSITY OF NORTH TEXAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GREENHOUSE GASES; PROTEINS; QUANTUM THEORY; THERMODYNAMICS;

APPROXIMATE MODEL; ATMOSPHERIC CONCENTRATION; BETA-SHEET; BINDING THERMODYNAMICS; CHEMICAL FORCES; FIRST PRINCIPLES; SECONDARY STRUCTURAL ELEMENTS;

CARBON DIOXIDE;

CARBON DIOXIDE; PROTEIN;

ARTICLE; BIOLOGY; BIOMIMETICS; CALIBRATION; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; PROTEIN BINDING; PROTEIN SECONDARY STRUCTURE; QUANTUM THEORY; THERMODYNAMICS;

BIOMIMETICS; CALIBRATION; CARBON DIOXIDE; COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; QUANTUM THEORY; THERMODYNAMICS;

EID: 70349929996     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci9002377     Document Type: Article

References (31)

1. Feely, R. A.; Sabine, C. L.; Hernandez-Ayon, J. M.; Ianson, D.; Hales, B. Evidence for upwelling of corrosive "acidified" water onto the Continental Shelf. Science 2008, 320, 1490-1492.
2. Boden, T. A.; Marland, G.; Andres, R. J. In CO2 Emission Calculations and Trends (EPA/600/R-96/072); U. S. Environmental Protection Agency: Washington, DC, 1996.
3. McCoy, M.; Reisch, M. S.; Tullo, A. H.; Short, P. L.; Tremblay, J. - F.; Storck, W. J.; Voith, M. Facts & Figures of the Chemical Industry. Chem. Eng. News 2008, 86, 35.
4. Kheshgi, H. S. Sequestering atmospheric carbon dioxide by increasing ocean alkalinity. Energy 1995, 20, 915-922.
5. Oelkers, E. H.; Schott, J. Geochemical aspects of CO2 sequestration. Chem. Geol. 2005, 217, 183-186.
6. Orr, F. M., Jr.; Taber, J. J. Use of Carbon Dioxide in Enhanced Oil Recovery. Science 1984, 224, 563-579.
7. Pacala, S.; Socolow, R. Stabilization wedges: Solving the climate problem for the next 50 years with current technologies. Science 2004, 305, 968-972.
8. Howard, J. B.; Rees, D. C. How many metals does it take to fix N2? A mechanistic overview of biological nitrogen fixation. Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 17088-17093.
9. Münck, E.; Bominaar, E. L. Bringing stability to highly reduced Iron- Sulfur clusters. Science 2008, 321, 1452-1453.
10. Mas-Ballesté, R.; Que, L., Jr. Targeting specific C-H bonds for oxidation. Science 2006, 312, 1885-1886.
11. Das, S.; Incarvito, C. D.; Crabtree, R. H.; Brudvig, G. W. Molecular recognition in the selective oxygenation of saturated C-H bonds by a Dimanganese catalyst. Science 2006, 312, 1941-1943.
12. Cotelesage, J. J. H.; Puttick, J.; Goldie, H.; Rajabi, B.; Novakovski, B.; Delbaere, L. T. J. How does an enzyme recognize CO2? Int. J. Biochem. Cell Biol. 2007, 39, 1204-1210.
13. Chemical Computing Group, Montreal, Canada.
14. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiórkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All- atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 1998, 102, 3586-3615.
15. Elstner, M.; Porezag, D.; Jungnickel, G.; Elsner, J.; Haugk, M.; Frauenheim, T.; Suhai, S.; Seifert, G. Self-consistent-charge density- functional tight-binding method for simulations of complex materials properties. Phys. Rev. B 1998, 58, 7260-7268.
16. Density Functional based Tight Binding and more (DFTB+). http://www.dftb-plus.info (accessed June 18, 2009).
17. Density Functional based Tight Binding. http://www.dftb.org/parameters/ download/ (accessed June 18, 2009).
18. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; ong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, Revision C. 02; Gaussian, Inc. : Pittsburgh, PA, 2003.
19. DeYonker, N. J.; Cundari, T. R.; Wilson, A. K. The correlation consistent composite approach (ccCA): An alternative to the Gauss- ian-n methods. J. Chem. Phys. 2006, 124, 114104.
20. Sobolev, V.; Sorokine, A.; Prilusky, J.; Abola, E. E.; Edelman, M. Automated analysis of interatomic contacts in proteins. Bioinformatics 1999, 15, 327-332.
21. Zhang, C. http://www.kukool.com/ligand (accessed June 18, 2009).
22. Golovin, A.; Henrick, K. MSDmotif: Exploring protein sites and motifs. BMC Bioinf. 2008, 9, 312.
23. Kozlowski, L. http://isoelectric.ovh.org (accessed June 18, 2009).
24. Rice, P.; Longden, I.; Bleasby, A. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 2000, 16, 276-277.
25. White, S. H.; Wimley, W. C. Membrane protein folding and stability: Physical principles. Annu. Rev. Biophys. Biomol. Struct. 1999, 28, 319-365.
26. Jaysinghe, S.; Hristova, K.; Wimley, W.; Snider, C.; White, S. H. http://blanco.biomol.uci.edu/mpex (accessed June 18, 2009).
27. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235-242.
28. Lu, Y.; Wang, R.; Yang, C. -Y.; Wang, S. Analysis of ligand-bound water molecules in high-resolution crystal structures of protein-ligand complexes. J. Chem. Inf. Model. 2007, 47, 668-675.
29. Leung, K.; Nielsen, I. M. B.; Kurtz, I. Ab initio molecular dynamics study of carbon dioxide and bicarbonate hydration and the nucleophilic attack of hydroxide on CO2. J. Phys. Chem. B 2007, 111, 4453-4459.
30. Costantini, S.; Colonna, G.; Facchiano, A. M. Amino acid propensities for secondary structures are influenced by the protein structural class. Biochem. Biophys. Res. Commun. 2006, 342, 441-451.
31. Bartlett, G. J.; Porter, C. T.; Borkakoti, N.; Thornton, J. M. Analysis of catalytic residues in enzyme active sites. J. Mol. Biol. 2002, 324, 105.