DNA repair mechanism by photolyase: Electron transfer path from the photolyase catalytic cofactor FADH- to DNA thymine dimer

Journal of Theoretical Biology

Volumn 210, Issue 2, 2001, Pages 237-248

  Medvedev, Dmitry ^a   Stuchebrukhov, Alexei A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBODIPYRIMIDINE PHOTOLYASE; DNA; FLAVINE ADENINE NUCLEOTIDE; THYMINE DERIVATIVE;

ARTICLE; CALCULATION; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DNA DAMAGE; DNA REPAIR; ELECTRON TRANSPORT; ESCHERICHIA COLI; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING;

EID: 0035926489     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1006/jtbi.2001.2291     Document Type: Article

References (51)

1. - and DNA thymine dimer
2. A well-behaved electrostatic potential based method using charge restraints for determining atom-centered charges: The RESP model
3. Evidence for dinucleotide flipping by DNA photolyase
4. Pathways of electron transfer in Escherichia coil DNA photolyase: Trp306 to FADH
5. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
6. Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free, energies of solvation
7. Calculation of electronic tunneling matrix element in proteins: Comparison of exact and approximate one-electron methods for Ru-modified azurin
8. Conformation of the flavin adenine dinucleotide cofactor FAD in DNA photolyase: A molecular dynamics study
9. Photosensitized pyrimidine dimer splitting by a methoxyindole bound to a dimer-recognizing macrocycle
10. Photoenzymic repair of UV-damaged DNA: A chemist's perspective
11. Binding of E. coli DNA photolyase to a defined substrate containing a single T-T dimer
12. Mechanism of damage recognition by Escherichia coli DNA photolyase
13. New expression for the effective transfer matrix element in long-range electron transfer reactions
14. Determination of rates and yields of interchromophore (Folate → Flavin) energy transfer and intermolecular (Flavin → DNA) electron transfer in Escherichia coli photolyase by time-resolved fluorescence and absorption spectroscopy
15. 2 → T-T) in Anacystis nidulas photolyase
16. The third chromophore of DNA photolyase: Trp-277 of Escherichia coli DNA photolyase repairs thymine dimers by direct electron transfer
17. Photochemistry, photophysics, and mechanism of pyrimidine dimer repair by DNA photolyase
18. Effect of base, pentose, an phosphodiester backbone structures on binding and repair of pyrimidine dimers by Escherichia coli DNA photolyase
19. Evidence from photoinduced EPR for a radical intermediate during photolysis of cyclobutane thymine dimer by DNA photolyase
20. -, the catalytically active form of the cofactor
21. Laser flash photolysis on an intermediate in the repair of pyrimidine dimers by DNA photolyase
22. Ab initio study of long-distance electron tunneling in a model peptide system
23. Structure-based strategies for drug design and discovery
24. A geometric approach to macromolecule-ligand interactions
25. Structure-based molecular design
26. Substrate and temperature dependence of DNA photolyase repair activity examined with ultrafast spectroscopy
27. Active site of DNA photolyase: Tryptophan-306 is the intrinsic hydrogen atom donor essential for flavin radical photoreduction and DNA repair in vitro
28. Active site of Escherichia coli DNA photolyase: Mutations of Trp277 alter the selectivity of the enzyme without affecting the quantum yield of photorepair
29. Electron transfers in chemistry and biology
30. Computational simulations of DNA distortions by a cis,syn-cyclobutane thymine dimer lesion
31. Nature of biological electron transfer
32. Quantum chemical probes of electron-transfer kinetics: The nature of donor-acceptor interactions
33. Picosecond laser photolysis studies on the photorepair of pyrimidine dimers by DNA photolyase. 1. Laser photolysis of photolyase-2-deoxyuridine dinucleotide photodimer complex
34. Crystal structure of DNA photolyase from Escherichia coli
35. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
36. Structure and function of DNA photolyase
37. Binding of Escherichia coli DNA photolyase to UV-irradiated DNA
38. Effect of intervening medium in long-range biological electron transfer
39. Tunneling currents in electron transfer reactions in proteins
40. Tunneling currents in electron transfer reaction in proteins. II. Calculation of electronic superexchange matrix element and tunneling currents using nonorthogonal basis sets
41. Tunneling currents in proteins. Nonorthogonal atomic basis sets and Mulliken population analysis
42. Tunneling currents in long-distance electron transfer reactions in proteins
43. Crystal structure of DNA photolyase from Anacystis nidulans