Skip to main content
Log in

Neutron Laue macromolecular crystallography

  • Article
  • Published:
European Biophysics Journal Aims and scope Submit manuscript

Abstract

Recent progress in neutron protein crystallography such as the use of the Laue technique and improved neutron optics and detector technologies have dramatically improved the speed and precision with which neutron protein structures can now be determined. These studies are providing unique and complementary insights on hydrogen and hydration in protein crystal structures that are not available from X-ray structures alone. Parallel improvements in modern molecular biology now allow fully (per)deuterated protein samples to be produced for neutron scattering that essentially eradicate the large—and ultimately limiting—hydrogen incoherent scattering background that has hampered such studies in the past. High quality neutron data can now be collected to near atomic resolution (∼2.0 Å) for proteins of up to ∼50 kDa molecular weight using crystals of volume ∼0.1 mm3 on the Laue diffractometer at ILL. The ability to flash-cool and collect high resolution neutron data from protein crystals at cryogenic temperature (15 K) has opened the way for kinetic crystallography on freeze trapped systems. Current instrument developments now promise to reduce crystal volume requirements by a further order of magnitude, making neutron protein crystallography a more accessible and routine technique.

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

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Arai S, Chatake T, Ohhara T, Kurihara K, Tanaka I, Suzuki N, Fujimoto Z, Mizuno H, Niimura N (2005) Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG)2 observed by neutron diffraction measurements. Nucleic Acids Res 33(9):3017–3024

    Article  Google Scholar 

  • Artero JB, Hartlein M, McSweeney S, Timmins P (2006) A comparison of refined X-ray structures of hydrogenated and perdeuterated rat gammaE-crystallin in H2O and D2O. Acta Crystallogr D Biol Crystallogr 61(Pt 11):1541–1549

    Google Scholar 

  • Bau R (2004) Neutron diffraction studies on rubredoxin from Pyrococcus furiosus. J Synchrotron Radiat 11(Pt 1):76–79

    Article  Google Scholar 

  • Bennett BC, Myles DA, Howell EE, Dealwis CG (2005) Preliminary neutron diffraction studies of Escherichia coli dihydrofolate reductase bound to the anticancer drug methotrexate. Acta Crystallogr D Biol Crystallogr 61(Pt 5):574–579

    Article  Google Scholar 

  • Blakeley MP, Mitschler A, Hazemann I, Meilleur F, Myles DA, Podjarny A (2006) Comparison of hydrogen determination with X-ray and neutron crystallography in a human aldose reductase-inhibitor complex. Eur Biophys J( this issue)

  • Blakeley MP, Kalb AJ, Helliwell JR, Myles DA (2004) The 15-K neutron structure of saccharide-free concanavalin A. Proc Natl Acad Sci USA 101(47):16405–16410

    Article  ADS  Google Scholar 

  • Bon C, Lehmann MS, Wilkinson C (1999) Quasi-Laue neutron-diffraction study of the water arrangement in crystals of triclinic hen egg-white lysozyme. Acta Crystallogr D Biol Crystallogr 55(Pt 5):978–987

    Article  Google Scholar 

  • Budayova-Spano M, Bonneté F, Ferté N, El Hajji M, Meilleur F, Blakeley MP, Castro B (2006) Acta Crystallogr F Biol Crystallogr 62:306–309

    Article  Google Scholar 

  • Budayova-Spano M, Fisher SZ, Dauvergne MT, Agbandje-McKenna M, Silverman DN, Myles DA, McKenna R (2006) Production and X-ray crystallographic analysis of fully deuterated human carbonic anhydrase II. Acta Crystallograph Sect F Struct Biol Crystallogr 62(Pt 1):6–9

    Google Scholar 

  • Chatake T, Tanaka I, Umino H, Arai S, Niimura N (2005) The hydration structure of a Z-DNA hexameric duplex determined by a neutron diffraction technique. Acta Crystallogr D Biol Crystallogr 61(Pt 8):1088–1098

    Article  Google Scholar 

  • Chatake T, Ostermann A, Kurihara K, Parak FG, Mizuno N, Voordouw G, Higuchi Y, Tanaka I, Niimura N (2004) Hydration structures in proteins and neutron diffraction experiment on dissimilatory sulfite reductase D (DsrD). J Synchrotron Radiat 11(Pt 1):72–75

    Google Scholar 

  • Chatake T, Ostermann A, Kurihara K, Parak FG, Niimura N (2003) Hydration in proteins observed by high-resolution neutron crystallography. Proteins 50(3):516–523

    Article  Google Scholar 

  • Cheng XD, Schoenborn BP (1991) Neutron diffraction study of carbonmonoxymyoglobin. J Mol Biol 220(2):381–399

    Article  Google Scholar 

  • Cipriani F, Dauvergne F, Gabriel A, Wilkinson C, Lehmann MS (1994) Image plate detectors for macromolecular neutron diffractometry. Biophys Chem 53:5–13

    Article  Google Scholar 

  • Cipriani F, Castagna JC, Wilkinson C, Lehmann MS, Buldt G (1996) A neutron image plate quasi-Laue diffractometer for protein crystallography. Basic Life Sci 64:423–431

    Google Scholar 

  • Coates L, Erskine PT, Wood SP, Myles DA, Cooper JB (2001) A neutron Laue diffraction study of endothiapepsin: implications for the aspartic proteinase mechanism. Biochemistry 40(44):13149–13157

    Article  Google Scholar 

  • Cooper JB, Myles DA (2000) A preliminary neutron Laue diffraction study of the aspartic proteinase endothiapepsin. Acta Crystallogr D Biol Crystallogr 56(Pt 2):246–248

    Article  Google Scholar 

  • Daniels BV, Myles DA, Forsyth VT, Lawson CL (2003) Crystals of Trp repressor suitable for high-resolution neutron Laue diffraction studies. Acta Crystallogr D Biol Crystallogr 59(Pt 1):136–138

    Google Scholar 

  • Dauter Z, Lamzin VS, Wilson KS (1997) The benefits of atomic resolution. Curr Opin Struct Biol 7(5):681–688

    Article  Google Scholar 

  • Engler N, Ostermann A, Niimura N, Parak FG (2003) Hydrogen atoms in proteins: positions and dynamics. Proc Natl Acad Sci USA 100(18):10243–10248

    Article  ADS  Google Scholar 

  • Habash J, Raftery J, Nuttall R, Price HJ, Wilkinson C, Kalb AJ, Helliwell JR (2000) Direct determination of the positions of the deuterium atoms of the bound water in-concanavalin A by neutron Laue crystallography. Acta Crystallogr D Biol Crystallogr 56 ( Pt 5):541–50

    Article  Google Scholar 

  • Hanson BL, Langan P, Katz AK, Li X, Harp JM, Glusker JP, Schoenborn BP, Bunick GJ (2004) A preliminary time-of-flight neutron diffraction study of Streptomyces rubiginosus D-xylose isomerase. Acta Crystallogr D Biol Crystallogr 60(Pt 2):241–249

    Article  Google Scholar 

  • Hazemann I, Dauvergne MT, Blakeley MP, Meilleur F, Haertlein M, Van Dorsselaer A, Mitschler A, Myles DA, Podjarny A (2005) High-resolution neutron protein crystallography with radically small crystal volumes: application of perdeuteration to human aldose reductase. Acta Crystallogr D Biol Crystallogr 61(Pt 10):1413–1417

    Article  Google Scholar 

  • Helliwell JR (1997) Neutron Laue diffraction does it faster. Nat Struct Biol 4(11):874–876

    Article  Google Scholar 

  • Høghøj P, Anderson IS, Ebisawa T, Takeda T (1996) Fabrication and performance of a large wavelength band multilayer monochromator. J Phys Soc Jpn 65:296–298

    Google Scholar 

  • Howard EI, Sanishvili R, Cachau RE, Mitschler A, Chevrier B, Barth P, Lamour V, Van Zandt M, Sibley E, Bon C, Moras D, Schneider TR, Joachimiak A, Podjarny A (2004) Ultrahigh resolution drug design I: details of interactions in human aldose reductase-inhibitor complex at 0.66 A. Proteins 55(4):792–804

    Article  Google Scholar 

  • Korszun ZR (1997) Neutron macromolecular crystallography. Methods Enzymol 276: 219–232

    Google Scholar 

  • Kossiakoff AA, Spencer SA (1981) Direct determination of the protonation states of aspartic acid-102 and histidine-57 in the tetrahedral intermediate of the serine proteases: neutron structure of trypsin. Biochemistry 20(22):6462–6474

    Article  Google Scholar 

  • Kurihara K, Tanaka I, Niimura N, Refai Muslih M, Ostermann A (2004) A new neutron single-crystal diffractometer dedicated for biological macromolecules (BIX-4). J Synchrotron Radiat 11:68–71

    Article  Google Scholar 

  • Langan P, Li X, Hanson BL, Coates L, Mustyakimov M (2006) Synthesis, capillary crystallization and preliminary joint X-ray and neutron crystallographic study of Z-DNA without polyamine at low pH. Acta Crystallogr F Biol Crystallogr 62

  • Lawson CL, Chin AS (2003) Analysis of neutron Laue diffraction from deuterium-exchanged Trp-repressor. Transactions ACA 38

  • Longhi S, Czjzek M, Cambillau C (1998) Messages from ultrahigh resolution crystal structures. Curr Opin Struct Biol 8(6):730–737

    Article  Google Scholar 

  • Li X, Langan P, Bau R, Tsyba I, Jenney FE Jr, Adams MW, Schoenborn BP (2004) W3Y single mutant of rubredoxin from Pyrococcus furiosus: a preliminary time-of-flight neutron study. Acta Crystallogr D Biol Crystallogr 60(Pt 1):200–202

    Google Scholar 

  • Maeda M, Chatake T, Tanaka I, Ostermann A, Niimura N (2004) Crystallization of a large single crystal of cubic insulin for neutron protein crystallography. J Synchrotron Radiat 11(Pt 1):41–44

    Article  Google Scholar 

  • Mason SA, Bentley GA, McIntyre GJ (1984) Deuterium exchange in lysozyme at 1.4-A resolution. Basic Life Sci 27:323–234

    Google Scholar 

  • Meilleur F, Snell EH, van der Woerd MJ, Judge RA, Myles DA (2006) A quasi-Laue neutron crystallographic study of D-xylose isomerase. Eur Biophys J (this issue)

  • Meilleur F, Blakeley MP, Myles DA (2005) Neutron Laue analysis of hydrogen and hydration in protein structure. In: Niimura N., Mizuno H., Helliwell J.R., Westhof E, (Eds) Hydrogen and hydration sensitive structural biology. pp 75–85

  • Meilleur F, Dauvergne MT, Schlichting I, Myles DA (2005) Production and X-ray crystallographic analysis of fully deuterated cytochrome P450cam. Acta Crystallogr D Biol Crystallogr 61(Pt5):539–544

    Article  Google Scholar 

  • Myles DA, Bon C, Langan P, Cipriani F, Castagna JC, Lehmann MS, Wilkinson C (1998) Neutron Laue diffraction in macromolecular crystallography. Physica B 241–243:1122–1130

    Google Scholar 

  • Myles DA, Timmins PA, Wilkinson C (2000) ILL Millenium Programme, Document ILL01CA01T, pages 42–45

  • Myles DA (2003) Recent trends and advances in neutron macromolecular crystallography. Transactions ACA 38

  • Niimura N, Minezaki Y, Nonaka T, Castagna JC, Cipriani F, Hoghoj P, Lehmann MS, Wilkinson C (1997a) Neutron Laue diffractometry with an imaging plate provides an effective data collection regime for neutron protein crystallography. Nat Struct Biol 4(11):909–914

    Article  Google Scholar 

  • Niimura N (1999) Neutrons expand the field of structural biology. Curr Opin Struct Biol 9(5):602–608

    Article  Google Scholar 

  • Niimura N, Minezaki Y, Nonaka T, Castagna JC, Cipriani F, Hoghoj P, Lehmann MS, Wilkinson C (1997b) Neutron Laue diffractometry with an imaging plate provides an effective data collection regime for neutron protein crystallography. Nat Struct Biol 4(11):909–914

    Article  Google Scholar 

  • Ostermann A, Tanaka I, Engler N, Niimura N, Parak FG (2002) Hydrogen and deuterium in myoglobin as seen by a neutron structure determination at 1.5 Å resolution. Biophys Chem 95(3):183–193

    Article  Google Scholar 

  • Phillips SE, Schoenborn BP (1981) Neutron diffraction reveals oxygen-histidine hydrogen bond in oxymyoglobin. Nature 292(5818):81–82

    Article  ADS  Google Scholar 

  • Podjarny A, Cachau RE, Schneider T, Van Zandt M, Joachimiak A (2004) Subatomic and atomic crystallographic studies of aldose reductase: implications for inhibitor binding. Cell Mol Life Sci 61(7–8):763–773

    Google Scholar 

  • Raghavan NV, Schoenborn BP (1984) The structure of bound water and refinement of acid metmyoglobin. Basic Life Sci 27:247–259

    Google Scholar 

  • Schmidt A, Lamzin VS (2002) Veni, vidi, vici - atomic resolution unravelling the mysteries of protein function. Curr Opin Struct Biol 12(6):698–703

    Article  Google Scholar 

  • Schmidt A, Jelsch C, Ostergaard P, Rypniewski W, Lamzin VS (2003) Trypsin revisited: crystallography AT (SUB) atomic resolution and quantum chemistry revealing details of catalysis. J Biol Chem 278(44):43357–43362

    Article  Google Scholar 

  • Schoenborn BP, Langan P (2004) Protein crystallography with spallation neutrons. J Synchrotron Radiat 11:80–82

    Article  Google Scholar 

  • Schultz AJ, Thiyagarajan P, Hodges JP, Rehm C, Myles DA, Langan P, Mesecar AD (2005) Design of the next generation neutron macromolecular diffractometer (MaNDi) at the Spallation Neutron Source. J Appl Cryst 38:964–974

    Article  Google Scholar 

  • Shu F, Ramakrishnan V, Schoenborn BP (2000) Enhanced visibility of hydrogen atoms by neutron crystallography on fully deuterated myoglobin. Proc Natl Acad Sci USA 97(8):3872–3877

    Article  ADS  Google Scholar 

  • Snell EH, van der Woerd MJ, Damon M, Judge RA, Myles DA, Meilleur F (2006) Optimizing crystal volume for neutron diffraction: Xylose Isomerase. Eur Biophys J, this issue

  • Sukumar N, Langan P, Mathews FS, Jones LH, Thiyagarajan P, Schoenborn BP, Davidson VL (2005) A preliminary time-of-flight neutron diffraction study on amicyanin from Paracoccus denitrificans. Acta Crystallogr D Biol Crystallogr 61(Pt 5):640–642

    Article  Google Scholar 

  • Teeter MM, Kossiakoff AA (1984) The neutron structure of the hydrophobic plant protein crambin. In: Schoenborn B (ed) Neutrons in Biology. Plenum Press, New York, pp 335–348

    Google Scholar 

  • Tuominen VU, Myles DA, Dauvergne MT, Lahti R, Heikinheimo P, Goldman A (2004) Production and preliminary analysis of perdeuterated yeast inorganic pyrophosphatase crystals suitable for neutron diffraction. Acta Crystallogr D Biol Crystallogr 60(Pt 3):606–609

    Article  Google Scholar 

  • Wlodawer A, Savage H, Dodson G (1989) Structure of insulin: results of joint neutron and X-ray refinement. Acta Crystallogr B 45( Pt 1):99–107

    Article  Google Scholar 

  • Wlodawer A, Sjolin L (1984) Application of joint neutron and x-ray refinement to the investigation of the structure of ribonuclease A at 2.0-A resolution. Basic Life Sci 27:349–364

    Google Scholar 

Download references

Acknowledgments

DAAM acknowledges support in part under DOE contract No. DE-AC05-00OR22725 with Oak Ridge National Laboratory, managed and operated by UT-Batelle, LLC.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Flora Meilleur.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Meilleur, F., Myles, D.A.A. & Blakeley, M.P. Neutron Laue macromolecular crystallography. Eur Biophys J 35, 611–620 (2006). https://doi.org/10.1007/s00249-006-0074-6

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00249-006-0074-6

Keywords

Navigation