Skip to main content
SpringerLink
Log in

Proton Travel in Green Fluorescent Protein

  • Chapter
  • First Online:
Fluorescent Proteins I

Part of the book series: Springer Series on Fluorescence ((SS FLUOR,volume 11))

  • 1705 Accesses

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Marx D (2006) Proton transfer 200 years after van Grotthuss: insight from ab initio simulations. Chemphyschem 7:1848–1870. doi:10.1002/cphc.200600128

    Article  CAS  Google Scholar 

  2. Swanson JMJ, Maupin CM, Chen H, Petersen MK, Xu J, Wu Y, Voth GA (2007) Proton salvation and transport in aqueous and biomolecular systems: insight from computer simulations. J Phys Chem B 111:4300–4314. doi:10.1021/jp070104x

    Article  CAS  Google Scholar 

  3. Kemp DS (1995) How to promote proton transfer. Nature 373:196–197. doi:10.1038/373196a0

    Article  CAS  Google Scholar 

  4. Tuckerman ME, Marx D, Parrinello M (2002) The nature and transport mechanism of hydrated hydroxide ions in aqueous solution. Nature 417:925–929. doi:10.1038/nature00797

    Article  CAS  Google Scholar 

  5. Lu D, Voth GA (1998) Proton transfer in the enzyme carbonic anhydrase: an ab initio study. J Am Chem Soc 120:4006. doi:10.1021/ja973397o

    Article  CAS  Google Scholar 

  6. Warshel A, Naray-Szabo G, Sussman F, Hwang JK (1989) How do serine proteases really work? Biochemistry 28:3629–3637. doi:10.1021/bi00435a002

    Article  CAS  Google Scholar 

  7. Ädelroth P, Brzezinski P (2004) Surface-mediated proton-transfer reactions in membrane-bound proteins. Biochim Biophys Acta 1655:102–115. doi:10.1016/j.bbabio.2003.10.018

    Article  Google Scholar 

  8. Gutman M, Nachliel E (1997) Time-resolved dynamics of proton transfer in proteinous systems. Annu Rev Phys Chem 48:329–356. doi:10.1146/annurev.physchem.48.1.329

    Article  CAS  Google Scholar 

  9. Chattoraj M, King BA, Bublitz GU, Boxer SG (1996) Ultra-fast excited state dynamics in green fluorescent protein: multiple states and proton transfer. Proc Natl Acad Sci USA 93:8362–8367

    Article  CAS  Google Scholar 

  10. Kötting C, Gerwert K (2005) Proteins in action monitored by time resolved FTIR spectroscopy. Chemphyschem 6:881–888. doi:10.1002/cphc.200400504

    Article  Google Scholar 

  11. van Thor JJ, Pierik AJ, Nugteren-Roodzant I, Xie A, Hellingwerf KJ (1998) Characterization of the photoconversion of green fluorescent protein with FTIR spectroscopy. Biochemistry 37:16915–16921. doi:10.1021/bi981170f

    Article  Google Scholar 

  12. Haupts U, Maiti S, Schwille P, Webb WW (1998) Dynamics of fluorescence fluctuations in green fluorescent protein observed by fluorescence correlation spectroscopy. Proc Natl Acad Sci USA 95:13573–13578

    Article  CAS  Google Scholar 

  13. Widengren J, Terry B, Rigler R (1999) Protonation kinetics of GFP and FITC investigated by FCS – aspects of the use of fluorescent indicators for measuring pH. Chem Phys 249:259–271. doi:10.1016/S0301-0104(99)00256-6 DOI:dx.doi.org

    Article  CAS  Google Scholar 

  14. Schwille P, Kummer S, Heikal AA, Moerner WE, Webb WW (2000) Fluorescence correlation spectroscopy reveals fast optical excitation-driven intramolecular dynamics of yellow fluorescent proteins. Proc Natl Acad Sci USA 97:151–156

    Article  CAS  Google Scholar 

  15. Saxena AM, Udgaonkar JB, Krishnamoorthy G (2005) Protein dynamics control proton transfer from bulk solvent to protein interior: a case study with a green fluorescent protein. Prot Sci 14:1787–1799. doi:10.1110/ps.051391205

    Article  CAS  Google Scholar 

  16. Gu W, Frigato T, Straatsma TP, Helms V (2007) Dynamic protonation equilibrium of solvated acetic acid. Angew Chem Int Ed 46:2939–2943. doi:10.1002/anie.200603583

    Article  CAS  Google Scholar 

  17. Gutman M, Nachliel E, Kiryati S (1992) Dynamic studies of proton diffusion in mesoscopic heterogenous matrix II. The interbilayer space between phospholipid membranes. Biophys J 63:281–290. doi:10.1016/S0006-3495(92)81585-0

    Article  CAS  Google Scholar 

  18. de Grotthuss CJT (1806) Sur la décomposition de l´eau et des corps qu´elle tient en dissolution à l´aide de l´électricité galvanique. Ann Chim Paris 58:54–73

    Google Scholar 

  19. Agmon N (1995) The Grotthuss mechanism. Chem Phys Lett 244:456–462. doi:10.1016/0009-2614(95)00905-J

    Article  CAS  Google Scholar 

  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

    Google Scholar 

  21. Denisov VP, Peters J, Hörlein 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

    Article  CAS  Google Scholar 

  22. Agmon N (2005) Proton pathways in green fluorescence protein. Biophys J 88:2452–2461. doi:10.1529/biophysj.104.055541

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  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.CO;2-R

    Article  CAS  Google Scholar 

  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/ja016860c

    Article  CAS  Google Scholar 

  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

    Google Scholar 

  28. Krammer EM, Till MS, Sebban P, Ullmann GM (2009) Proton transfer pathways in photosynthetic reaction centers analyzed by profile hidden Markov models and network calculations. J Mol Biol 388:631–643. doi:10.1016/j.jmb.2009.03.020

    Article  CAS  Google Scholar 

  29. Karplus M, McCammon JA (2002) Molecular dynamics simulations of macromolecules: a perspective. Nat Struct Biol 9:646–652. doi:10.1038/nsb0902-646

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  32. Vallverdu G, Demachy I, Mérola F, Pasquier H, Ridard J, Lévy 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

    Article  CAS  Google Scholar 

  33. Gu W, Helms V (2007) Different protonation equilibria of 4-methylimidazole and acetic acid. Chemphyschem 8:2445–2451. doi:10.1002/cphc.200700442

    Article  CAS  Google Scholar 

  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/ja809301w

    Article  CAS  Google Scholar 

  35. Schäfer LV, Groenhof G, Klingen AR, Ullmann GM, Boggia-Pasqua M, Robb MA, Grubmüller 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

    Article  Google Scholar 

Download references

Acknowledgments

VH thanks Lars Schäfer (University of Groningen) for kindly making available Fig. 3 for this manuscript and Noam Agmon for a preprint of Shinobu et al. [20].

Author information

Authors and Affiliations

  1. Center for Bioinformatics, Saarland University, Campus C7.1, 66123, Saarbruecken, Germany

    Volkhard Helms & Wei Gu

Authors
  1. Volkhard Helms
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Wei Gu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Volkhard Helms .

Editor information

Editors and Affiliations

  1. , Campus B2 2, Saarland University, Saarbrücken, 66123, Saarland, Germany

    Gregor Jung

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Helms, V., Gu, W. (2011). Proton Travel in Green Fluorescent Protein. In: Jung, G. (eds) Fluorescent Proteins I. Springer Series on Fluorescence, vol 11. Springer, Berlin, Heidelberg. https://doi.org/10.1007/4243_2011_13

Download citation

Publish with us

Policies and ethics

Search

Navigation