Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital method

Biophysical Chemistry

Volumn 130, Issue 1-2, 2007, Pages 1-9

  Kurisaki, Ikuo ^a   Fukuzawa, Kaori ^b,c   Komeiji, Yuto ^c,d   Mochizuki, Yuji ^c,e   Nakano, Tatsuya ^c,f   Imada, Janine ^g   Chmielewski, Aneta ^g   Rothstein, Stuart M ^g   Watanabe, Hirofumi ^a,c   Tanaka, Shigenori ^a,c  

^a KOBE UNIVERSITY   (Japan)

^b MIZUHO INFORMATION AND RESEARCH INSTITUTE   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^d NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^e RIKKYO UNIVERSITY   (Japan)

^f NATIONAL INSTITUTE OF HEALTH SCIENCES   (Japan)

^g BROCK UNIVERSITY   (Canada)

Author keywords

Ab initio quantum chemical calculation; Cyclic AMP receptor protein (CRP); DNA binding protein; Fragment molecular orbital (FMO) method; Sequence specific recognition; Transcription factor

Indexed keywords

C REACTIVE PROTEIN; CYCLIC AMP; DNA FRAGMENT;

ANALYTIC METHOD; ARTICLE; CHEMICAL STRUCTURE; MOLECULAR INTERACTION; MOLECULAR STABILITY; POLYMER PRODUCTION; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN STABILITY; QUANTUM CHEMISTRY;

AMINO ACID SEQUENCE; CHEMISTRY, PHYSICAL; CYCLIC AMP; CYCLIC AMP RECEPTOR PROTEIN; DNA; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; QUANTUM THEORY;

EID: 34548779129     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2007.06.011     Document Type: Article

References (20)

1. Kitaura K., Sawai T., Asada T., Nakano T., and Uebayasi M. Pair interaction molecular orbital method: an approximate computational method for molecular interactions. Chem. Phys. Lett. 312 (1999) 319-324
2. Kitaura K., Ikeo E., Asada T., Nakano T., and Uebayasi M. Fragment molecular orbital method: an approximate computational method for large molecules. Chem. Phys. Lett. 313 (1999) 701-706
3. Nakano T., Kaminuma T., Sato T., Akiyama Y., Uebayasi M., and Kitaura K. Fragment molecular orbital method: application to polypeptides. Chem. Phys. Lett. 318 (2000) 614-618
4. Nakano T., Kaminuma T., Sato T., Fukuzawa K., Akiyama Y., Uebayasi M., and Kitaura K. Fragment molecular orbital method: use of approximate electrostatic potential. Chem. Phys. Lett. 351 (2002) 475-480
5. Fedorov D.G., and Kitaura K. Theoretical development of the fragment molecular orbital (FMO) method. In: Starikov E.B., Lewis J.P., and Tanaka S. (Eds). Modern Methods for Theoretical Physical Chemistry of Biopolymers (2006), Elsevier 3-38
6. Fukuzawa K., Komeiji Y., Mochizuki Y., Kato A., Nakano T., and Tanaka S. Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: ab initio fragment molecular orbital study. J. Comput. Chem. 27 (2006) 948-960 ibid. 28 (2007) 2237-2239
7. Fukuzawa K., Kitaura K., Uebayasi M., Nakata K., Kaminuma T., and Nakano T. Ab initio quantum mechanical study of the binding energies of human estrogen receptor-α with its ligands: an application of fragment molecular orbital method. J. Comput. Chem. 26 (2005) 1-10
8. Fukuzawa K., Mochizuki Y., Tanaka S., Kitaura K., and Nakano T. Molecular interactions between estrogen receptor and its ligand studied by the ab Initio fragment molecular orbital method. J. Phys. Chem., B. 110 (2006) 16102-16110 ibid. 110 (2006) 24276
9. Amari S., Aizawa A., Junwei Z., Fukuzawa K., Mochizuki Y., Iwasawa Y., Nakata K., Chuman H., and Nakano T. VISCANA: visualized cluster analysis of protein-ligand interaction based on the ab initio fragment molecular orbital method for virtual ligand screening. J. Chem. Inf. Model. 46 (2006) 221-230
10. Mochizuki Y., Nakano T., Koikegami S., Tanimori S., Abe Y., Nagashima U., and Kitaura K. A parallelized integral-direct second-order Mφ{symbol}ller-Plesset perturbation theory method with a fragment molecular orbital scheme. Theo. Chem. Acc. 112 (2004) 442-452
11. Mochizuki Y., Koikegami S., Nakano T., Amari S., and Kitaura K. Large scale MP2 calculations with fragment molecular orbital scheme. Chem. Phys. Lett. 396 (2004) 473-479
12. ACD/ChemSketch Freeware, Version 10.00 (Advanced Chemistry Development, Inc.: Toronto, ON, Canada, www.acdlabs.com, 2006).
13. Gunasekera A., Ebright Y.W., and Ebright R.H. DNA sequence determinants for binding of the Escherichia coli catabolite gene activator protein. J. Biol. Chem. 267 (1992) 14713-14720
14. Chen S., Vojtechovsky J., Parkinson G.N., Ebright R.H., and Berman H.M. Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking. J. Mol. Biol. 314 (2001) 63-74
15. Humphrey W., Dalke A., and Schulten K. VMD - visual molecular dynamics. J. Mol. Graph. 14.1 (1996) 33-38
16. Kabsch W., and Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (1983) 2577-2637
17. Hamaguchi K. The Protein Molecule (1992), Japan scientific societies press, Japan
18. Ishikawa T., Mochizuki Y., Nakano T., Amari S., Mori H., Honda H., Fujita T., Tokiwa H., Tanaka S., Komeiji Y., Fukuzawa K., Tanaka K., and Miyoshi E. Fragment molecular orbital calculations on large scale systems containing heavy metal atom. Chem. Phys. Lett. 427 (2006) 159-165
19. Raha K., van der Vaart A.J., Riley K.E., Peters M.B., Westerhoff L.M., Kim H., and Merz Jr. K.M. Pairwise decomposition of residue interaction energies using semiempirical quantum mechanical methods in studies of protein-ligand interaction. J. Am. Chem. Soc. 127 (2005) 6583-6594
20. Tiana G., Simona F., De Mori G.M., Broglia R.A., and Colombo G. Understanding the determinants of stability and folding of small globular proteins from their energetics. Protein Sci. 13 (2004) 113-124