1
|
Baitan D, Schubert R, Meyer A, Dierks K, Perbandt M, Betzel C. Growing Protein Crystals with Distinct Dimensions Using Automated Crystallization Coupled with In Situ Dynamic Light Scattering. J Vis Exp 2018. [PMID: 30175998 PMCID: PMC6126796 DOI: 10.3791/57070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The automated crystallization device is a patented technique1 especially developed for monitoring protein crystallization experiments with the aim to precisely maneuver the nucleation and crystal growth towards desired sizes of protein crystals. The controlled crystallization is based on sample investigation with in situ Dynamic Light Scattering (DLS) while all visual changes in the droplet are monitored online with the help of a microscope coupled to a CCD camera, thus enabling a full investigation of the protein droplet during all stages of crystallization. The use of in situ DLS measurements throughout the entire experiment allows a precise identification of the highly supersaturated protein solution transitioning to a new phase – the formation of crystal nuclei. By identifying the protein nucleation stage, the crystallization can be optimized from large protein crystals to the production of protein microcrystals. The experimental protocol shows an interactive crystallization approach based on precise automated steps such as precipitant addition, water evaporation for inducing high supersaturation, and sample dilution for slowing induced homogeneous nucleation or reversing phase transitions.
Collapse
Affiliation(s)
- Daniela Baitan
- Xtal Concepts GmbH; Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation c/o DESY, University of Hamburg
| | - Robin Schubert
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation c/o DESY, University of Hamburg; The Hamburg Center for Ultrafast Imaging, University of Hamburg
| | | | | | - Markus Perbandt
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation c/o DESY, University of Hamburg; The Hamburg Center for Ultrafast Imaging, University of Hamburg
| | - Christian Betzel
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation c/o DESY, University of Hamburg; The Hamburg Center for Ultrafast Imaging, University of Hamburg;
| |
Collapse
|
2
|
Bommer M, Coates L, Dau H, Zouni A, Dobbek H. Protein crystallization and initial neutron diffraction studies of the photosystem II subunit PsbO. Acta Crystallogr F Struct Biol Commun 2017; 73:525-531. [PMID: 28876232 PMCID: PMC5619745 DOI: 10.1107/s2053230x17012171] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/22/2017] [Indexed: 11/10/2022] Open
Abstract
The PsbO protein of photosystem II stabilizes the active-site manganese cluster and is thought to act as a proton antenna. To enable neutron diffraction studies, crystals of the β-barrel core of PsbO were grown in capillaries. The crystals were optimized by screening additives in a counter-diffusion setup in which the protein and reservoir solutions were separated by a 1% agarose plug. Crystals were cross-linked with glutaraldehyde. Initial neutron diffraction data were collected from a 0.25 mm3 crystal at room temperature using the MaNDi single-crystal diffractometer at the Spallation Neutron Source, Oak Ridge National Laboratory.
Collapse
Affiliation(s)
- Martin Bommer
- Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Leighton Coates
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Holger Dau
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Holger Dobbek
- Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| |
Collapse
|
3
|
Ng JD, Baird JK, Coates L, Garcia-Ruiz JM, Hodge TA, Huang S. Large-volume protein crystal growth for neutron macromolecular crystallography. Acta Crystallogr F Struct Biol Commun 2015; 71:358-70. [PMID: 25849493 PMCID: PMC4388167 DOI: 10.1107/s2053230x15005348] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/15/2015] [Indexed: 11/10/2022] Open
Abstract
Neutron macromolecular crystallography (NMC) is the prevailing method for the accurate determination of the positions of H atoms in macromolecules. As neutron sources are becoming more available to general users, finding means to optimize the growth of protein crystals to sizes suitable for NMC is extremely important. Historically, much has been learned about growing crystals for X-ray diffraction. However, owing to new-generation synchrotron X-ray facilities and sensitive detectors, protein crystal sizes as small as in the nano-range have become adequate for structure determination, lessening the necessity to grow large crystals. Here, some of the approaches, techniques and considerations for the growth of crystals to significant dimensions that are now relevant to NMC are revisited. These include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations.
Collapse
Affiliation(s)
- Joseph D. Ng
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL 35899, USA
- iXpressGenes Inc., Hudson Alpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - James K. Baird
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Leighton Coates
- Biology and Soft Matter Division, Oak Ridge National Laboratory, PO Box 2008, MS6475, Oak Ridge, TN 37831, USA
| | - Juan M. Garcia-Ruiz
- Laboratorio de Estudios Cristalográficos (IACT), CSIC–Universidad de Granada, Avenida de la Innovación s/n, Armilla (Granada), Spain
| | - Teresa A. Hodge
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Sijay Huang
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| |
Collapse
|
4
|
Giegé R. A historical perspective on protein crystallization from 1840 to the present day. FEBS J 2013; 280:6456-97. [DOI: 10.1111/febs.12580] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 08/30/2013] [Accepted: 09/27/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Richard Giegé
- Institut de Biologie Moléculaire et Cellulaire; Université de Strasourg et CNRS; France
| |
Collapse
|
5
|
Krauss IR, Merlino A, Vergara A, Sica F. An overview of biological macromolecule crystallization. Int J Mol Sci 2013; 14:11643-91. [PMID: 23727935 PMCID: PMC3709751 DOI: 10.3390/ijms140611643] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/08/2013] [Accepted: 05/20/2013] [Indexed: 12/11/2022] Open
Abstract
The elucidation of the three dimensional structure of biological macromolecules has provided an important contribution to our current understanding of many basic mechanisms involved in life processes. This enormous impact largely results from the ability of X-ray crystallography to provide accurate structural details at atomic resolution that are a prerequisite for a deeper insight on the way in which bio-macromolecules interact with each other to build up supramolecular nano-machines capable of performing specialized biological functions. With the advent of high-energy synchrotron sources and the development of sophisticated software to solve X-ray and neutron crystal structures of large molecules, the crystallization step has become even more the bottleneck of a successful structure determination. This review introduces the general aspects of protein crystallization, summarizes conventional and innovative crystallization methods and focuses on the new strategies utilized to improve the success rate of experiments and increase crystal diffraction quality.
Collapse
Affiliation(s)
- Irene Russo Krauss
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
| | - Alessandro Vergara
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +39-81-674-479; Fax: +39-81-674-090
| |
Collapse
|
6
|
Giegé R, Sauter C. Biocrystallography: past, present, future. HFSP JOURNAL 2010; 4:109-21. [PMID: 21119764 PMCID: PMC2929629 DOI: 10.2976/1.3369281] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 03/02/2010] [Indexed: 02/02/2023]
Abstract
The evolution of biocrystallography from the pioneers' time to the present era of global biology is presented in relation to the development of methodological and instrumental advances for molecular sample preparation and structure elucidation over the last 6 decades. The interdisciplinarity of the field that generated cross-fertilization between physics- and biology-focused themes is emphasized. In particular, strategies to circumvent the main bottlenecks of biocrystallography are discussed. They concern (i) the way macromolecular targets are selected, designed, and characterized, (ii) crystallogenesis and how to deal with physical and biological parameters that impact crystallization for growing and optimizing crystals, and (iii) the methods for crystal analysis and 3D structure determination. Milestones that have marked the history of biocrystallography illustrate the discussion. Finally, the future of the field is envisaged. Wide gaps of the structural space need to be filed and membrane proteins as well as intrinsically unstructured proteins still constitute challenging targets. Solving supramolecular assemblies of increasing complexity, developing a "4D biology" for decrypting the kinematic changes in macromolecular structures in action, integrating these structural data in the whole cell organization, and deciphering biomedical implications will represent the new frontiers.
Collapse
Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France
| | - Claude Sauter
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France
| |
Collapse
|
7
|
Niimura N, Bau R. Neutron protein crystallography: beyond the folding structure of biological macromolecules. Acta Crystallogr A 2007; 64:12-22. [DOI: 10.1107/s0108767307043498] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Accepted: 09/05/2007] [Indexed: 11/10/2022] Open
Abstract
Neutron diffraction provides an experimental method of directly locating H atoms in proteins, a technique complementary to ultra-high-resolution X-ray diffraction. Three different types of neutron diffractometers for biological macromolecules have been constructed in Japan, France and the USA, and they have been used to determine the crystal structures of proteins up to resolution limits of 1.5–2.5 Å. Results relating to H-atom positions and hydration patterns in proteins have been obtained from these studies. Examples include the geometrical details of hydrogen bonds, the role of H atoms in enzymatic activity, CH3configuration, H/D exchange in proteins and oligonucleotides, and the dynamical behavior of hydration structures, all of which have been extracted from these structural results and reviewed. Other techniques, such as the growth of large single crystals and a database of hydrogen and hydration in proteins, are described.
Collapse
|
8
|
Anderson MJ, Hansen CL, Quake SR. Phase knowledge enables rational screens for protein crystallization. Proc Natl Acad Sci U S A 2006; 103:16746-51. [PMID: 17075056 PMCID: PMC1636526 DOI: 10.1073/pnas.0605293103] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We show that knowledge of the phase behavior of a protein allows one to create a rational screen that increases the success rate of crystallizing challenging proteins. The strategy is based on using microfluidics to perform large numbers of protein solubility experiments across many different chemical conditions to identify reagents for crystallization experiments. Phase diagrams were generated for the identified reagents and used to design customized crystallization screens for every protein. This strategy was applied with a 75% success rate to the crystallization of 12 diverse proteins, most of which failed to crystallize when using traditional techniques. The overall diffraction success rate was 33%, about double what was achieved with conventional automation in large-scale protein structure consortia. The higher diffraction success rates are achieved by designing customized crystallization screens using the phase behavior information for each target. The identification of reagents based on an understanding of protein solubility and the use of phase diagrams in the design of individualized crystallization screens therefore promotes high crystallization rates and the production of diffraction-quality crystals.
Collapse
Affiliation(s)
- Megan J. Anderson
- *Department of Biochemistry and Molecular Biophysics, California Institute of Technology, MS 128-95, Pasadena, CA 91125
| | - Carl L. Hansen
- Departments of Physics and Astronomy and Electrical and Computer Engineering, Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, Canada V6T 1Z4; and
| | - Stephen R. Quake
- Department of Bioengineering, Stanford University and Howard Hughes Medical Institute, 318 Campus Drive, Room E300, Stanford, CA 94305
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
9
|
Sauter C, Lorber B, Cavarelli J, Moras D, Giegé R. The free yeast aspartyl-tRNA synthetase differs from the tRNA(Asp)-complexed enzyme by structural changes in the catalytic site, hinge region, and anticodon-binding domain. J Mol Biol 2000; 299:1313-24. [PMID: 10873455 DOI: 10.1006/jmbi.2000.3791] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aminoacyl-tRNA synthetases catalyze the specific charging of amino acid residues on tRNAs. Accurate recognition of a tRNA by its synthetase is achieved through sequence and structural signalling. It has been shown that tRNAs undergo large conformational changes upon binding to enzymes, but little is known about the conformational rearrangements in tRNA-bound synthetases. To address this issue the crystal structure of the dimeric class II aspartyl-tRNA synthetase (AspRS) from yeast was solved in its free form and compared to that of the protein associated to the cognate tRNA(Asp). The use of an enzyme truncated in N terminus improved the crystal quality and allowed us to solve and refine the structure of free AspRS at 2.3 A resolution. For the first time, snapshots are available for the different macromolecular states belonging to the same tRNA aminoacylation system, comprising the free forms for tRNA and enzyme, and their complex. Overall, the synthetase is less affected by the association than the tRNA, although significant local changes occur. They concern a rotation of the anticodon binding domain and a movement in the hinge region which connects the anticodon binding and active-site domains in the AspRS subunit. The most dramatic differences are observed in two evolutionary conserved loops. Both are in the neighborhood of the catalytic site and are of importance for ligand binding. The combination of this structural analysis with mutagenesis and enzymology data points to a tRNA binding process that starts by a recognition event between the tRNA anticodon loop and the synthetase anticodon binding module.
Collapse
MESH Headings
- Anticodon/chemistry
- Anticodon/genetics
- Anticodon/metabolism
- Aspartate-tRNA Ligase/chemistry
- Aspartate-tRNA Ligase/genetics
- Aspartate-tRNA Ligase/metabolism
- Binding Sites
- Catalytic Domain
- Conserved Sequence/genetics
- Crystallization
- Crystallography, X-Ray
- Models, Molecular
- Molecular Sequence Data
- Movement
- Nucleic Acid Conformation
- Protein Structure, Secondary
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Transfer, Asp/chemistry
- RNA, Transfer, Asp/genetics
- RNA, Transfer, Asp/metabolism
- Rotation
- Sequence Deletion/genetics
- Yeasts/enzymology
- Yeasts/genetics
Collapse
Affiliation(s)
- C Sauter
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 rue Laurent Fries, Illkirch Cedex, UPR 9004, France
| | | | | | | | | |
Collapse
|
10
|
Frugier M, Moulinier L, Giegé R. A domain in the N-terminal extension of class IIb eukaryotic aminoacyl-tRNA synthetases is important for tRNA binding. EMBO J 2000; 19:2371-80. [PMID: 10811628 PMCID: PMC384352 DOI: 10.1093/emboj/19.10.2371] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cytoplasmic aspartyl-tRNA synthetase (AspRS) from Saccharomyces cerevisiae is a homodimer of 64 kDa subunits. Previous studies have emphasized the high sensitivity of the N-terminal region to proteolytic cleavage, leading to truncated species that have lost the first 20-70 residues but that retain enzymatic activity and dimeric structure. In this work, we demonstrate that the N-terminal extension in yeast AspRS participates in tRNA binding and we generalize this finding to eukaryotic class IIb aminoacyl-tRNA synthetases. By gel retardation studies and footprinting experiments on yeast tRNA(Asp), we show that the extension, connected to the anticodon-binding module of the synthetase, contacts tRNA on the minor groove side of its anticodon stem. Sequence comparison of eukaryotic class IIb synthetases identifies a lysine-rich 11 residue sequence ((29)LSKKALKKLQK(39) in yeast AspRS with the consensus xSKxxLKKxxK in class IIb synthetases) that is important for this binding. Direct proof of the role of this sequence comes from a mutagenesis analysis and from binding studies using the isolated peptide.
Collapse
Affiliation(s)
- M Frugier
- Département 'Mécanismes et Macromolécules de la Synthèse Protéique et Cristallogenèse', UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, 67084 Strasbourg Cedex, France
| | | | | |
Collapse
|