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18. de Grotthuss CJT (1806) Sur la d´composition de l´eau et des corps qu´elle tient en dissolution
` l´aide de l´´lectricit´ galvanique. Ann Chim Paris 58:54-73
19. Agmon N (1995) The Grotthuss mechanism. Chem Phys Lett 244:456-462. doi:10.1016/
20. Shinobu A, Palm GJ, Schierbeek AJ, Agmon N (2010) Visualizing proton antenna in a high-
resolution green fluorescent protein structure. electronic version ahead of print. J Am Chem
Soc. doi:10.1021/ja1010652
21. Denisov VP, Peters J, H
orlein HD, Halle B (1996) Using buried water molecules to explore
the energy landscape of proteins. Nat Struct Biol 3:505-509. doi:10.1038/nsb0696-505
22. Agmon N (2005) Proton pathways in green fluorescence protein. Biophys J 88:2452-2461.
23. Shinobu A, Agmon N (2009) Mapping proton-wires in proteins: carbonic anhydrase and GFP
chromophore biosynthesis. J Phys Chem A 113:7253-7266. doi:10.1021/jp8102047
24. Garczarek F, Brown LS, Lanyi JK, Gerwert K (2005) Proton binding within a membrane
protein by a protonated water cluster. Proc Natl Acad Sci USA 102:3633-3638
25. Sham YY, Muegge I, Warshel A (1999) Simulating proton translocations in proteins: probing
proton transfer pathways in the rhodobacter sphaeroides reaction center. Protein Struct Funct
Genet 36:484-500. doi:10.1002/(SICI)1097-0134(19990901)36:4 < 484::AID-PROT13 > 3.0.
26. Taraphder S, Hummer G (2003) Protein side-chain motion and hydration in proton-transfer
pathways. Results for cytochrome P450cam. J Am Chem Soc 125:3931-3940. doi:10.1021/
27. Kunz K, Helms V (2007) QVADIS: a package to compute proton transfer pathways
in proteins. In: Falter C, Schliep A, Selbig J, Vingron M, Walther D (eds) GI-Edition -
Lecture notes in informatics (LNI) - Proceedings 115
28. Krammer EM, Till MS, Sebban P, Ullmann GM (2009) Proton transfer pathways in photo-
synthetic reaction centers analyzed by profile hidden Markov models and network calcula-
tions. J Mol Biol 388:631-643. doi:10.1016/j.jmb.2009.03.020
29. Karplus M, McCammon JA (2002) Molecular dynamics simulations of macromolecules: a
perspective. Nat Struct Biol 9:646-652. doi:10.1038/nsb0902-646
30. Helms V, Straatsma TP, McCammon JA (1999) Internal dynamics of green fluorescent
proteins. J Phys Chem B 103:3263-3269. doi:10.1021/jp983120q
31. Nifosi R, Tozzini V (2003) Molecular dynamics simulations of enhanced green fluorescent
proteins: effects of F64L, S65T and T203Y mutations on the ground-state proton equlibria.
Proteins 51:378-389. doi:10.1002/prot.10335
32. Vallverdu G, Demachy I, M´rola F, Pasquier H, Ridard J, L´vy B (2010) Relation between
pH, structure, and absorption spectrum of Cerulean: a study by molecular dynamics and TD
DFT calculations. Proteins 78:1040-1054. doi:10.1002/prot.22628
33. Gu W, Helms V (2007) Different protonation equilibria of 4-methylimidazole and acetic acid.
Chemphyschem 8:2445-2451. doi:10.1002/cphc.200700442
34. Gu W, Helms V (2009) Tightly connected water wires facilitate fast proton uptake at the
proton entrance of proton pumping proteins. J Am Chem Soc 131:2080-2081. doi:10.1021/
35. Schafer LV, Groenhof G, Klingen AR, Ullmann GM, Boggia-Pasqua M, Robb MA, Grubmul-
ler H (2007) Photoswitching of the fluorescent protein asFP595: mechanism, proton pathways,
and absorption spectra. Angew Chem Int Ed 46:530-536. doi:10.1002/anie.200602315
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