Skip to main content
SpringerLink
Log in

Protonation/Deprotonation of Proteins by Neutron Diffraction Structure Analysis

  • Chapter
  • First Online:
The Role of Water in ATP Hydrolysis Energy Transduction by Protein Machinery

  • 600 Accesses

Abstract

Neutron protein crystallography can reveal nuclear position and it is very useful to find hydrogen or protonation/deprotonation of protein. It is, however, an intensity-limited experiment and requires large and good quality single protein crystal, so the user population has been so small. Recently, new intense neutron source makes ones to find several protonation states in proteins; PcyA complex (complex of Phycocyanobilin: Ferredoxin Oxidoreductase and Biliverdin IXα), cellulase and substrate complex and farnesyl pyrophosphate synthase (FPPS)-drug complex. At the same time, new techniques for neutron measurement such as high pressure freezing and dynamic nuclear polarization of protein have been also tried to be developed. Finally, a plan of new neutron facility to gain more S/N ratio is expected so that the sample crystal volume can be much small to find protonation/deprotonation.

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

Access this chapter

Log in via an institution
eBook
USD 16.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 129.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 179.99
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

  • Adams PD, Afonine PV et al (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Cryst D66:213–221

    Google Scholar 

  • Arai S et al (2004) More rapid evaluation of biomacromolecular crystals for diffraction experiments. Acta Cryst D 60:1032–1039

    Article  Google Scholar 

  • Blakely M (2009) Neutron macromolecular crystallography. Cryst Rev 15:157–218

    Article  Google Scholar 

  • Bunyatova EI (1995) New investigations of organic compounds for targets with polarized hydrogen nuclei. Nucl Instrum Methods Phys Res A 356:29–33

    Article  CAS  Google Scholar 

  • Casadei CM et al (2014) Neutron cryo-crystallography captures the protonation state of ferryl heme in a peroxidase. Science 345:193–197

    Article  CAS  Google Scholar 

  • Coates L, Stoica AD, Hoffmann C, Richards J, Cooper R (2010) The macromolecular neutron diffractometer (MaNDi) at the Spallation Neutron Source, Oak Ridge: enhanced optics design, high-resolution neutron detectors and simulated diffraction. J Appl Cryst 43:570–577

    Article  CAS  Google Scholar 

  • de Boer W (1973) High proton polarization in 1,2-propanediol at 3He temperatures. Nucl Instrum Methods 107:99–104

    Article  Google Scholar 

  • Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Cryst D60:2126–2132

    CAS  Google Scholar 

  • Helliwell JR (1997) Neutron Laue diffraction does it faster. Nat Struct Mol Biol 4:874–876

    Article  CAS  Google Scholar 

  • Hosoya T et al (2009) Development of a new detector and DAQ systems for iBIX. Nucl Instrum Methods Phys Res A 600:217–219

    Article  CAS  Google Scholar 

  • J-PARC Center, MLF (2010) Report of J-PARC materials and life science experimental facility future planning task (in Japanese). J-PARC 10-02

    Google Scholar 

  • Kabsch W (2010) XDS. Acta Cryst D66:125–132

    Google Scholar 

  • Kim CU, Kapfer R, Gruner SM (2005) High-pressure cooling of protein crystals without cryoprotectants. Acta Cryst D61:881–890

    CAS  Google Scholar 

  • Kim CU et al (2016) Tracking solvent and protein movement during CO2 release in carbonic anhydrase II crystals. Proc Nat Acad Sci USA 113:5257–5262

    Article  CAS  Google Scholar 

  • Kumada T, Noda Y, Ishikawa N (2012) Dynamic nuclear polarization of electron-beam irradiated polyethylene by pairs of alkyl free radicals. J Magn Reson 218:59–65

    Article  CAS  Google Scholar 

  • Kurihara K, Tanaka I et al (2004) A new neutron single crystal diffractometer dedicated for biological macromolecules (BIX-4). J Synchrotron Radiat 11:68–71

    Article  CAS  Google Scholar 

  • Kusaka K et al (2013) Evaluation of performance for IBARAKI biological crystal diffractometer iBIX with new detectors. J Synchrotron Radiat 20:994–998

    Article  CAS  Google Scholar 

  • Meilleur F et al (2013) The IMAGINE instrument: first neutron protein structure and new capabilities for neutron macromolecular crystallography. Acta Cryst D 69:2157–2160

    Article  CAS  Google Scholar 

  • Mishima O (1996) Relationship between melting and amorphization of ice. Nature 384:546–549

    Article  CAS  Google Scholar 

  • Nakamura A et al (2015) “Newton’s cradle” proton relay with amide imidic acid tautomerization in inverting cellulase visualized by neutron crystallography. Sci Adv 1:e1500263 (2015)

    Article  Google Scholar 

  • Niimura N, Bau R (2008) Neutron protein crystallography: beyond the folding structure of biological macromolecules. Acta Cryst A64:12–22

    Article  Google Scholar 

  • Niimura N, Podjarny A (2011) Neutron protein crystallography: hydrogen, protons, and hydration in bio-macromolecules. In: IUCr monographs on crystallography 25. Oxford University Press, Oxford

    Chapter  Google Scholar 

  • Niimura N, Karasawa Y, Tanaka I et al (1994) An imaging plate neutron detector. Nucl Instrum Methods A349:521–525

    Article  Google Scholar 

  • Niimura N, Minezaki Y et al (1997) Neutron Laue diffractometry with an imaging plate provides an effective data collection regime for neutron protein crystallography. Nat Struct Mol Biol 4:909–914

    Article  CAS  Google Scholar 

  • Niimura N, Takimoto-Kamimura M, Tanaka I (2016) Application of neutron diffraction in studies of protein dynamics and functions. In: Encyclopedia of analytical chemistry. Wiley, New York, pp 1–30

    Google Scholar 

  • NMX (Macromolecular Diffractometer) at ESS (European Spallation Source) (2017). https://europeanspallationsource.se/instruments/nmx. Accessed 20 Nov 2017

  • Ohhara T et al (2009) Development of data processing software for a new TOF single crystal neutron diffractometer at J-PARC. Nucl Instrum Methods A 600:195–197

    Article  CAS  Google Scholar 

  • Ostermann A, Schrader T (2015) BIODIFF: diffractometer for large unit cells. J Large-Scale Res Facil 1:A2

    Article  Google Scholar 

  • Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276:307–326

    Article  CAS  Google Scholar 

  • Piegsa FM et al (2013) Polarized neutron Laue diffraction on a crystal containing dynamically polarized proton spins. J Appl Cryst 46:30–34

    Article  CAS  Google Scholar 

  • Stuhrmann HB (2004) Unique aspects of neutron scattering for the study of biological systems. Rep Prog Phys 67:1073–1115

    Article  CAS  Google Scholar 

  • Tanaka I et al (2002) A high-performance neutron diffractometer for biological crystallography (BIX-3). J Appl Cryst 35:34–40

    Article  CAS  Google Scholar 

  • Tanaka I et al (2010) Neutron structure analysis by IBARAKI biological crystal diffractometer (iBIX) in J-PARC. Acta Cryst D66:1194–1197

    Google Scholar 

  • Tanaka I, Komatsuzaki N et al (2018) Cryoprotectant-free high-pressure freezing and dynamic nuclear polarization for more sensitive detection of hydrogen in neutron protein crystallography. Acta Cryst D. (submitted)

    Google Scholar 

  • Tanaka I, Kusaka K et al (2009) Overview of a new biological neutron diffractometer (iBIX) in J-PARC. Nucl Instrum Methods A 600:161–163

    Article  CAS  Google Scholar 

  • Tanaka I, Kusaka K, Chatake T, Niimura N (2013) Fundamental studies for the proton polarization technique in neutron protein crystallography. J Synchrotron Radiat 20:958–961

    Article  CAS  Google Scholar 

  • Unno M et al (2015) Insights into the proton transfer mechanism of a bilin reductase PcyA following neutron crystallography. J Am Chem Soc 137:5452–5460

    Article  CAS  Google Scholar 

  • Yano N et al (2016) Application of profile fitting method to neutron time-of-flight protein single crystal diffraction data collected at the iBIX. Sci Rep 6:36628

    Article  CAS  Google Scholar 

  • Yokoyama T et al (2015) Protonation state and hydration of bisphosphonate bound to farnesyl pyrophosphate synthase. J Med Chem 58:7549–7556

    Article  CAS  Google Scholar 

  • Zhao JK, Robertson L, Herwig K, Crabb D (2013) Polarized neutron in structural biology—present and future outlook. Phys Procedia 42:39–45

    Article  CAS  Google Scholar 

  • Zimmer O, Jouve HM, Stuhrmann HB (2016) Polarized proton spin density images the tyrosyl radical locations in bovine liver catalase. IUCr J 3:326–340

    Article  CAS  Google Scholar 

Download references

Acknowledgements

Authors would thank Profs. T. Iwata and Miyachi and their students in Yamagata University for conducting and discussing ESR and DNP measurements, Prof. Chatake in Kyoto University for preparation of protein crystals and discussion, Dr. T. Kumada in Japan Atomic Energy Agency (JAEA) for providing a radical concentration information, and Drs. H. Seto in High Energy Accelerator Research Organization (KEK) and Harada in JAEA for providing information of the second target station at MLF in J-PARC. Synchrotron radiation experiment was conducted at BL5A of the Photon Factory in KEK, Ibaraki, Japan [2014G650]. Finally, authors are profoundly grateful to iBIX users, Prof. T. Yamada, Dr. N. Yano, Mrs. S. Ninomiya and J. Hiroki, and all students in Tanaka laboratory in Ibaraki University.

Author information

Authors and Affiliations

  1. College of Engineering, Ibaraki University, Hitachi, Japan

    Ichiro Tanaka

  2. Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai, Japan

    Katsuhiro Kusaka & Nobuo Niimura

Authors
  1. Ichiro Tanaka
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Katsuhiro Kusaka
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nobuo Niimura
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ichiro Tanaka .

Editor information

Editors and Affiliations

  1. Institute of Engineering Education, Tohoku University, Sendai, Miyagi, Japan

    Makoto Suzuki

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Tanaka, I., Kusaka, K., Niimura, N. (2018). Protonation/Deprotonation of Proteins by Neutron Diffraction Structure Analysis. In: Suzuki, M. (eds) The Role of Water in ATP Hydrolysis Energy Transduction by Protein Machinery. Springer, Singapore. https://doi.org/10.1007/978-981-10-8459-1_9

Download citation

Publish with us

Policies and ethics

Search

Navigation