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Amador VC, dos Santos-Silva CA, Vilela LMB, Oliveira-Lima M, de Santana Rêgo M, Roldan-Filho RS, de Oliveira-Silva RL, Lemos AB, de Oliveira WD, Ferreira-Neto JRC, Crovella S, Benko-Iseppon AM. Lipid Transfer Proteins (LTPs)-Structure, Diversity and Roles beyond Antimicrobial Activity. Antibiotics (Basel) 2021; 10:1281. [PMID: 34827219 PMCID: PMC8615156 DOI: 10.3390/antibiotics10111281] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/01/2021] [Accepted: 10/12/2021] [Indexed: 01/21/2023] Open
Abstract
Lipid transfer proteins (LTPs) are among the most promising plant-exclusive antimicrobial peptides (AMPs). They figure among the most challenging AMPs from the point of view of their structural diversity, functions and biotechnological applications. This review presents a current picture of the LTP research, addressing not only their structural, evolutionary and further predicted functional aspects. Traditionally, LTPs have been identified by their direct isolation by biochemical techniques, whereas omics data and bioinformatics deserve special attention for their potential to bring new insights. In this context, new possible functions have been identified revealing that LTPs are actually multipurpose, with many additional predicted roles. Despite some challenges due to the toxicity and allergenicity of LTPs, a systematic review and search in patent databases, indicate promising perspectives for the biotechnological use of LTPs in human health and also plant defense.
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Affiliation(s)
- Vinícius Costa Amador
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Carlos André dos Santos-Silva
- Department of Advanced Diagnostics, Institute for Maternal and Child Health-IRCCS, Burlo Garofolo, 34100 Trieste, Italy;
| | - Lívia Maria Batista Vilela
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Marx Oliveira-Lima
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Mireli de Santana Rêgo
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Ricardo Salas Roldan-Filho
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Roberta Lane de Oliveira-Silva
- General Microbiology Laboratory, Agricultural Science Campus, Universidade Federal do Vale do São Francisco, Petrolina 56300-990, Brazil;
| | - Ayug Bezerra Lemos
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Wilson Dias de Oliveira
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - José Ribamar Costa Ferreira-Neto
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Sérgio Crovella
- Department of Biological and Environmental Sciences, College of Arts and Science, Qatar University, Doha 1883, Qatar;
| | - Ana Maria Benko-Iseppon
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
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Yu J, Jiang L, Yan J, Li W. Microprocessing on Single Protein Crystals Using Femtosecond Pulse Laser. ACS Biomater Sci Eng 2020; 6:6445-6452. [PMID: 33449667 DOI: 10.1021/acsbiomaterials.0c01023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Proteins with different micropatterns have various applications in biosensing, structural analysis, and other biomedical fields. However, processing of micropatterns on single protein crystals remains a challenge due to the fragility of protein molecules. In this work, we studied femtosecond laser processing on single hen egg white lysozyme protein crystals. Optimized laser parameters were found to achieve micropatterning without cracking of protein crystals. The ablation morphology dependence on the laser fluence and the pulse number was discussed to control the processing results. Under a laser fluence higher than 1 J/cm2, the ablation hole was formed. While multipulses with fluence lower than the ablation threshold were applied, the foaming area was observed due to the denaturation of protein. The numerical simulation shows that the ablation results were influenced by the ionization and energy deposition process. Micropatterns including lines, areas, and microarrays can be processed with a minimum size of 2 μm. Processed patterns on the crystal surface can be used for biosensing microarrays and the enhancement of crystal growth. The microprocessing method proposed in this study has potential applications in different fields including biodevices and biomedicine.
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Affiliation(s)
- Jiachen Yu
- Key Laboratory for Advanced Materials Processing Technology, Ministry of Education of China, State Key Laboratory of Tribology, Department of Mechanical Engineering, Tsinghua University, Beijing 100084, China
| | - Lan Jiang
- Laser Micro/Nano Fabrication Laboratory, School of Mechanical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Jianfeng Yan
- Key Laboratory for Advanced Materials Processing Technology, Ministry of Education of China, State Key Laboratory of Tribology, Department of Mechanical Engineering, Tsinghua University, Beijing 100084, China
| | - Wenqi Li
- School of Life Sciences, Tsinghua University, Beijing 100084, China
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Rosenbach H, Victor J, Borggräfe J, Biehl R, Steger G, Etzkorn M, Span I. Expanding crystallization tools for nucleic acid complexes using U1A protein variants. J Struct Biol 2020; 210:107480. [PMID: 32070773 DOI: 10.1016/j.jsb.2020.107480] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/04/2020] [Accepted: 02/14/2020] [Indexed: 11/24/2022]
Abstract
The major bottlenecks in structure elucidation of nucleic acids are crystallization and phasing. Co-crystallization with proteins is a straight forward approach to overcome these challenges. The human RNA-binding protein U1A has previously been established as crystallization module, however, the absence of UV-active residues and the predetermined architecture in the asymmetric unit constitute clear limitations of the U1A system. Here, we report three crystal structures of tryptophan-containing U1A variants, which expand the crystallization toolbox for nucleic acids. Analysis of the structures complemented by SAXS, NMR spectroscopy, and optical spectroscopy allow for insights into the potential of the U1A variants to serve as crystallization modules for nucleic acids. In addition, we report a fast and efficient protocol for crystallization of RNA by soaking and present a fluorescence-based approach for detecting RNA-binding in crystallo. Our results provide a new tool set for the crystallization of RNA and RNA:DNA complexes.
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Affiliation(s)
- Hannah Rosenbach
- Institut für Physikalische Biologie, Heinrich-Heine-Universitaet Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany.
| | - Julian Victor
- Institut für Physikalische Biologie, Heinrich-Heine-Universitaet Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany.
| | - Jan Borggräfe
- Institut für Physikalische Biologie, Heinrich-Heine-Universitaet Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany.
| | - Ralf Biehl
- Jülich Centre for Neutron Science (JCNS-1/ICS-1), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany.
| | - Gerhard Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universitaet Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany.
| | - Manuel Etzkorn
- Institut für Physikalische Biologie, Heinrich-Heine-Universitaet Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany.
| | - Ingrid Span
- Institut für Physikalische Biologie, Heinrich-Heine-Universitaet Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany.
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de Wijn R, Hennig O, Roche J, Engilberge S, Rollet K, Fernandez-Millan P, Brillet K, Betat H, Mörl M, Roussel A, Girard E, Mueller-Dieckmann C, Fox GC, Olieric V, Gavira JA, Lorber B, Sauter C. A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography. IUCRJ 2019; 6:454-464. [PMID: 31098026 PMCID: PMC6503916 DOI: 10.1107/s2052252519003622] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/14/2019] [Indexed: 05/15/2023]
Abstract
Determining optimal conditions for the production of well diffracting crystals is a key step in every biocrystallography project. Here, a microfluidic device is described that enables the production of crystals by counter-diffusion and their direct on-chip analysis by serial crystallography at room temperature. Nine 'non-model' and diverse biomacromolecules, including seven soluble proteins, a membrane protein and an RNA duplex, were crystallized and treated on-chip with a variety of standard techniques including micro-seeding, crystal soaking with ligands and crystal detection by fluorescence. Furthermore, the crystal structures of four proteins and an RNA were determined based on serial data collected on four synchrotron beamlines, demonstrating the general applicability of this multipurpose chip concept.
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Affiliation(s)
- Raphaël de Wijn
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Oliver Hennig
- Institute for Biochemistry, Leipzig University, Bruederstrasse 34, 04103 Leipzig, Germany
| | - Jennifer Roche
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257 CNRS–Aix Marseille University, 163 Avenue de Luminy, 13288 Marseille, France
| | | | - Kevin Rollet
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Pablo Fernandez-Millan
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Karl Brillet
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Heike Betat
- Institute for Biochemistry, Leipzig University, Bruederstrasse 34, 04103 Leipzig, Germany
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Bruederstrasse 34, 04103 Leipzig, Germany
| | - Alain Roussel
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257 CNRS–Aix Marseille University, 163 Avenue de Luminy, 13288 Marseille, France
| | - Eric Girard
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | | | - Gavin C. Fox
- PROXIMA 2A beamline, Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, 91192 Gif-sur-Yvette, France
| | - Vincent Olieric
- Paul Scherrer Institute, Swiss Light Source, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - José A. Gavira
- Laboratorio de Estudios Cristalográficos, IACT, CSIC–Universidad de Granada, Avenida Las Palmeras 4, 18100 Armilla, Granada, Spain
| | - Bernard Lorber
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Claude Sauter
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
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Pichlo C, Toelzer C, Chojnacki K, Öcal S, Uthoff M, Ruegenberg S, Hermanns T, Schacherl M, Denzel MS, Hofmann K, Niefind K, Baumann U. Improved protein-crystal identification by using 2,2,2-trichloroethanol as a fluorescence enhancer. Acta Crystallogr F Struct Biol Commun 2018; 74:307-314. [PMID: 29717999 PMCID: PMC5931144 DOI: 10.1107/s2053230x18005253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 04/03/2018] [Indexed: 11/10/2022] Open
Abstract
The identification of initial lead conditions for successful protein crystallization is crucial for structural studies using X-ray crystallography. In order to reduce the number of false-negative conditions, an emerging number of fluorescence-based methods have been developed which allow more efficient identification of protein crystals and help to distinguish them from salt crystals. Detection of the native tryptophan fluorescence of protein crystals is one of the most widely used methods. However, this method can fail owing to the properties of the crystallized protein or the chemical composition of the crystallization trials. Here, a simple, fast and cost-efficient method employing 2,2,2-trichloroethanol (TCE) has been developed. It can be performed with a standard UV-light microscope and can be applied to cases in which detection of native tryptophan fluorescence fails. In four test cases this method had no effect on the diffraction properties of the crystals and no structural changes were observed. Further evidence is provided that TCE can be added to crystallization trials during their preparation, making this method compatible with high-throughput approaches.
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Affiliation(s)
- Christian Pichlo
- Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany
| | - Christine Toelzer
- Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany
| | - Konrad Chojnacki
- Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany
- Faculty of Chemistry, Warsaw University of Technology, ul. Noakowskiego 3, 00-664 Warsaw, Poland
| | - Sinan Öcal
- Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany
| | - Matthias Uthoff
- Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany
| | - Sabine Ruegenberg
- Max Planck Institute for Biology of Ageing, Research Institute, Joseph-Stelzmann-Strasse 9b, 50931 Cologne, Germany
| | - Thomas Hermanns
- Institute for Genetics, University of Cologne, Zülpicher Strasse 47a, 50674 Cologne, Germany
| | - Magdalena Schacherl
- Structural Dynamics of Proteins, Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Martin S. Denzel
- Max Planck Institute for Biology of Ageing, Research Institute, Joseph-Stelzmann-Strasse 9b, 50931 Cologne, Germany
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Zülpicher Strasse 47a, 50674 Cologne, Germany
| | - Karsten Niefind
- Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany
| | - Ulrich Baumann
- Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany
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Locating and Visualizing Crystals for X-Ray Diffraction Experiments. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2017; 1607:143-164. [PMID: 28573572 DOI: 10.1007/978-1-4939-7000-1_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Macromolecular crystallography has advanced from using macroscopic crystals, which might be >1 mm on a side, to crystals that are essentially invisible to the naked eye, or even under a standard laboratory microscope. As crystallography requires recognizing crystals when they are produced, and then placing them in an X-ray, electron, or neutron beam, this provides challenges, particularly in the case of advanced X-ray sources, where beams have very small cross sections and crystals may be vanishingly small. Methods for visualizing crystals are reviewed here, and examples of different types of cases are presented, including: standard crystals, crystals grown in mesophase, in situ crystallography, and crystals grown for X-ray Free Electron Laser or Micro Electron Diffraction experiments. As most techniques have limitations, it is desirable to have a range of complementary techniques available to identify and locate crystals. Ideally, a given technique should not cause sample damage, but sometimes it is necessary to use techniques where damage can only be minimized. For extreme circumstances, the act of probing location may be coincident with collecting X-ray diffraction data. Future challenges and directions are also discussed.
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Multivalent Interactions by the Set8 Histone Methyltransferase With Its Nucleosome Substrate. J Mol Biol 2016; 428:1531-43. [PMID: 26953260 DOI: 10.1016/j.jmb.2016.02.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 02/03/2016] [Accepted: 02/27/2016] [Indexed: 12/19/2022]
Abstract
Set8 is the only mammalian monomethyltransferase responsible for H4K20me1, a methyl mark critical for genomic integrity of eukaryotic cells. We present here a structural model for how Set8 uses multivalent interactions to bind and methylate the nucleosome based on crystallographic and solution studies of the Set8/nucleosome complex. Our studies indicate that Set8 employs its i-SET and c-SET domains to engage nucleosomal DNA 1 to 1.5 turns from the nucleosomal dyad and in doing so, it positions the SET domain for catalysis with H4 Lys20. Surprisingly, we find that a basic N-terminal extension to the SET domain plays an even more prominent role in nucleosome binding, possibly by making an arginine anchor interaction with the nucleosome H2A/H2B acidic patch. We further show that proliferating cell nuclear antigen and the nucleosome compete for binding to Set8 through this basic extension, suggesting a mechanism for how nucleosome binding protects Set8 from proliferating cell nuclear antigen-dependent degradation during the cell cycle.
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Dinç I, Pusey ML, Aygün RS. Optimizing Associative Experimental Design for Protein Crystallization Screening. IEEE Trans Nanobioscience 2016; 15:101-12. [PMID: 26955046 PMCID: PMC4898777 DOI: 10.1109/tnb.2016.2536030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The goal of protein crystallization screening is the determination of the main factors of importance to crystallizing the protein under investigation. One of the major issues about determining these factors is that screening is often expanded to many hundreds or thousands of conditions to maximize combinatorial chemical space coverage for maximizing the chances of a successful (crystalline) outcome. In this paper, we propose an experimental design method called "Associative Experimental Design (AED)" and an optimization method includes eliminating prohibited combinations and prioritizing reagents based on AED analysis of results from protein crystallization experiments. AED generates candidate cocktails based on these initial screening results. These results are analyzed to determine those screening factors in chemical space that are most likely to lead to higher scoring outcomes, crystals. We have tested AED on three proteins derived from the hyperthermophile Thermococcus thioreducens, and we applied an optimization method to these proteins. Our AED method generated novel cocktails (count provided in parentheses) leading to crystals for three proteins as follows: Nucleoside diphosphate kinase (4), HAD superfamily hydrolase (2), Nucleoside kinase (1). After getting promising results, we have tested our optimization method on four different proteins. The AED method with optimization yielded 4, 3, and 20 crystalline conditions for holo Human Transferrin, archaeal exosome protein, and Nucleoside diphosphate kinase, respectively.
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Affiliation(s)
- Imren Dinç
- DataMedia Research Lab, Computer Science Department, University of Alabama in Huntsville, Huntsville, Alabama 35899 USA
| | - Marc L. Pusey
- iXpressGenes, Inc., 601 Genome Way, Huntsville, Alabama 35806 USA
| | - Ramazan S. Aygün
- DataMedia Research Lab, Computer Science Department, University of Alabama in Huntsville, Huntsville, Alabama 35899 USA
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9
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Preparation, Crystallization, and Structure Determination of Chromatin Enzyme/Nucleosome Complexes. Methods Enzymol 2016; 573:43-65. [PMID: 27372748 DOI: 10.1016/bs.mie.2016.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Structural studies of chromatin complexes composed of chromatin factors or enzymes bound to the nucleosome have been constrained by the ability to produce high-quality complexes in the amounts appropriate for biophysical studies and by the difficulty of crystallizing these complexes. We describe here procedures and approaches to prepare chromatin complexes, to crystallize chromatin complexes, and to improve diffraction properties through postcrystallization soaks. Special attention is paid to evaluating the quality of the purified chromatin complexes as well as assessing the presence of the chromatin protein or enzyme in crystals. The methods described for preparing and purifying chromatin complexes should be applicable to biochemical, biophysical, and other structural approaches including cryoelectron microscopy.
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10
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Lukk T, Gillilan RE, Szebenyi DME, Zipfel WR. A visible-light-excited fluorescence method for imaging protein crystals without added dyes. J Appl Crystallogr 2016; 49:234-240. [PMID: 26937240 PMCID: PMC4762565 DOI: 10.1107/s160057671502419x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/16/2015] [Indexed: 11/10/2022] Open
Abstract
Fluorescence microscopy methods have seen an increase in popularity in recent years for detecting protein crystals in screening trays. The fluorescence-based crystal detection methods have thus far relied on intrinsic UV-inducible tryptophan fluorescence, nonlinear optics or fluorescence in the visible light range dependent on crystals soaked with fluorescent dyes. In this paper data are presented on a novel visible-light-inducible autofluorescence arising from protein crystals as a result of general stabilization of conjugated double-bond systems and increased charge delocalization due to crystal packing. The visible-light-inducible autofluorescence serves as a complementary method to bright-field microscopy in beamline applications where accurate crystal centering about the rotation axis is essential. Owing to temperature-dependent chromophore stabilization, protein crystals exhibit tenfold higher fluorescence intensity at cryogenic temperatures, making the method ideal for experiments where crystals are cooled to 100 K with a cryostream. In addition to the non-damaging excitation wavelength and low laser power required for imaging, the method can also serve a useful role for differentiating protein crystals from salt crystals in screening trays.
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Affiliation(s)
- Tiit Lukk
- MacCHESS (Macromolecular Diffraction Facility at CHESS), Cornell University, 161 Synchrotron Drive, Ithaca, NY 14853, USA
| | - Richard E. Gillilan
- MacCHESS (Macromolecular Diffraction Facility at CHESS), Cornell University, 161 Synchrotron Drive, Ithaca, NY 14853, USA
| | - Doletha M. E. Szebenyi
- MacCHESS (Macromolecular Diffraction Facility at CHESS), Cornell University, 161 Synchrotron Drive, Ithaca, NY 14853, USA
| | - Warren R. Zipfel
- Department of Biomedical Engineering, Cornell University, B41 Weill Hall, Ithaca, NY 14853, USA
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Sigdel M, Pusey ML, Aygun RS. CrystPro: Spatiotemporal Analysis of Protein Crystallization Images. CRYSTAL GROWTH & DESIGN 2015; 15:5254-5262. [PMID: 26640418 PMCID: PMC4669104 DOI: 10.1021/acs.cgd.5b00714] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Thousands of experiments corresponding to different combinations of conditions are set up to determine the relevant conditions for successful protein crystallization. In recent years, high throughput robotic set-ups have been developed to automate the protein crystallization experiments, and imaging techniques are used to monitor the crystallization progress. Images are collected multiple times during the course of an experiment. Huge number of collected images make manual review of images tedious and discouraging. In this paper, utilizing trace fluorescence labeling, we describe an automated system called CrystPro for monitoring the protein crystal growth in crystallization trial images by analyzing the time sequence images. Given the sets of image sequences, the objective is to develop an efficient and reliable system to detect crystal growth changes such as new crystal formation and increase of crystal size. CrystPro consists of three major steps- identification of crystallization trials proper for spatio-temporal analysis, spatio-temporal analysis of identified trials, and crystal growth analysis. We evaluated the performance of our system on 3 crystallization image datasets (PCP-ILopt-11, PCP-ILopt-12, and PCP-ILopt-13) and compared our results with expert scores. Our results indicate a) 98.3% accuracy and .896 sensitivity on identification of trials for spatio-temporal analysis, b) 77.4% accuracy and .986 sensitivity of identifying crystal pairs with new crystal formation, and c) 85.8% accuracy and 0.667 sensitivity on crystal size increase detection. The results show that our method is reliable and efficient for tracking growth of crystals and determining useful image sequences for further review by the crystallographers.
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