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Snell EH, Helliwell JR. Microgravity as an environment for macromolecular crystallization – an outlook in the era of space stations and commercial space flight. CRYSTALLOGR REV 2021. [DOI: 10.1080/0889311x.2021.1900833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- E. H. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
- Materials Design and Innovation Department, SUNY Buffalo, Buffalo, NY, USA
| | - J. R. Helliwell
- Chemistry Department, University of Manchester, Manchester, UK
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2
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On the Quality of Protein Crystals Grown under Diffusion Mass-transport Controlled Regime (I). CRYSTALS 2020. [DOI: 10.3390/cryst10020068] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
It has been previously shown that the diffraction quality of protein crystals strongly depends on mass transport during their growth. In fact, several studies support the idea that the higher the contribution of the diffusion during mass transport, the better the diffraction quality of the crystals. In this work, we have compared the crystal quality of two model (thaumatin and insulin) and two target (HBII and HBII-III) proteins grown by two different methods to reduce/eliminate convective mass transport: crystal growth in agarose gels and crystal growth in solution under microgravity. In both cases, we used identical counterdiffusion crystallization setups and the same data collection protocols. Additionally, critical parameters such as reactor geometry, stock batches of proteins and other chemicals, temperature, and duration of the experiments were carefully monitored. The diffraction datasets have been analyzed using a principal component analysis (PCA) to determine possible trends in quality indicators. The relevant indicators show that, for the purpose of structural crystallography, there are no obvious differences between crystals grown under reduced convective flow in space and convection-free conditions in agarose gel, indicating that the key factor contributing to crystal quality is the reduced convection environment and not how this reduced convection is achieved. This means that the possible detrimental effect on crystal quality due to the incorporation of gel fibers into the protein crystals is insignificant compared to the positive impact of an optimal convection-free environment provided by gels. Moreover, our results confirm that the counterdiffusion technique optimizes protein crystal quality and validates both environments in order to deliver high quality protein crystals, although other considerations, such as protein/gel interactions, must be considered when defining the optimal crystallization setup.
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3
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Caterino M, Herrmann M, Merlino A, Riccardi C, Montesarchio D, Mroginski MA, Musumeci D, Ruffo F, Paduano L, Hildebrandt P, Kozuch J, Vergara A. On the pH-Modulated Ru-Based Prodrug Activation Mechanism. Inorg Chem 2019; 58:1216-1223. [PMID: 30614697 DOI: 10.1021/acs.inorgchem.8b02667] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The RuIII-based prodrug AziRu efficiently binds to proteins, but the mechanism of its release is still disputed. Herein, in order to test the hypothesis of a reduction-mediated Ru release from proteins, a Raman-assisted crystallographic study on AziRu binding to a model protein (hen egg white lysozyme), in two different oxidation states, RuII and RuIII, was carried out. Our results indicate Ru reduction, but the Ru release upon reduction is dependent on the reducing agent. To better understand this process, a pH-dependent, spectroelectrochemical surface-enhanced Raman scattering (SERS) study was performed also on AziRu-functionalized Au electrodes as a surrogate and simplest model system of RuII- and RuIII-based drugs. This SERS study provided a p Ka of 6.0 ± 0.4 for aquated AziRu in the RuIII state, which falls in the watershed range of pH values separating most cancer environments from their physiological counterparts. These experiments also indicate a dramatic shift of the redox potential E0 by >600 mV of aquated AziRu toward more positive potentials upon acidification, suggesting a selective AziRu reduction in cancer lumen but not in healthy ones. It is expected that the nature of the ligands (e.g., pyridine vs imidazole, present in well-known RuIII complex NAMI-A) will modulate the p Ka and E0, without affecting the underlying reaction mechanism.
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Affiliation(s)
- Marco Caterino
- Department of Chemical Sciences , University of Naples Federico II , via Cinthia , Naples I-80126 , Italy
| | - Mona Herrmann
- Institut für Chemie , Technische Universität Berlin , Straße des 17 Juni 135 , Berlin 10623 , Germany
| | - Antonello Merlino
- Department of Chemical Sciences , University of Naples Federico II , via Cinthia , Naples I-80126 , Italy
| | - Claudia Riccardi
- Department of Chemical Sciences , University of Naples Federico II , via Cinthia , Naples I-80126 , Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences , University of Naples Federico II , via Cinthia , Naples I-80126 , Italy
| | - Maria A Mroginski
- Institut für Chemie , Technische Universität Berlin , Straße des 17 Juni 135 , Berlin 10623 , Germany
| | - Domenica Musumeci
- Department of Chemical Sciences , University of Naples Federico II , via Cinthia , Naples I-80126 , Italy
| | - Francesco Ruffo
- Department of Chemical Sciences , University of Naples Federico II , via Cinthia , Naples I-80126 , Italy
| | - Luigi Paduano
- Department of Chemical Sciences , University of Naples Federico II , via Cinthia , Naples I-80126 , Italy
| | - Peter Hildebrandt
- Institut für Chemie , Technische Universität Berlin , Straße des 17 Juni 135 , Berlin 10623 , Germany
| | - Jacek Kozuch
- Institut für Chemie , Technische Universität Berlin , Straße des 17 Juni 135 , Berlin 10623 , Germany
| | - Alessandro Vergara
- Department of Chemical Sciences , University of Naples Federico II , via Cinthia , Naples I-80126 , Italy.,CEINGE, Biotecnologie Avanzate s.c.a.r.l.m. , via G Salvatore , Naples I-80131 , Italy
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4
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The Study of the Mechanism of Protein Crystallization in Space by Using Microchannel to Simulate Microgravity Environment. CRYSTALS 2018. [DOI: 10.3390/cryst8110400] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Space is expected to be a convection-free, quiescent environment for the production of large-size and high-quality protein crystals. However, the mechanisms by which the diffusion environment in space improves the quality of the protein crystals are not fully understood. The interior of a microfluidic device can be used to simulate a microgravity environment to investigate the protein crystallization mechanism that occurs in space. In the present study, lysozyme crystals were grown in a prototype microchannel device with a height of 50 μm in a glass-polydimethylsiloxane (PDMS)-glass sandwich structure. Comparative experiments were also conducted in a sample pool with a height of 2 mm under the same growth conditions. We compared the crystal morphologies and growth rates of the grown crystals in the two sample pools. The experimental results showed that at very low initial supersaturation, the morphology and growth rates of lysozyme crystals under the simulated microgravity conditions is similar to that on Earth. With increasing initial supersaturation, a convection-free, quiescent environment is better for lysozyme crystal growth. When the initial supersaturation exceeded a threshold, the growth of the lysozyme crystal surface under the simulated microgravity conditions never completely transform from isotropic to anisotropic. The experimental results showed that the convection may have a dual effect on the crystal morphology. Convection can increase the roughness of the crystal surface and promote the transformation of the crystal form from circular to tetragonal during the crystallization process.
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5
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Environmental conditions shape the biofilm of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125. Microbiol Res 2018; 218:66-75. [PMID: 30454660 DOI: 10.1016/j.micres.2018.09.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/24/2018] [Accepted: 09/28/2018] [Indexed: 11/21/2022]
Abstract
Biofilms are the most widely distributed and successful microbial modes of life. The capacity of bacteria to colonize surfaces provides stability in the growth environment, allows the capturing of nutrients and affords protection from a range of environmental challenges and stress. Bacteria living in cold environments, like Antarctica, can be found as biofilms, even though the mechanisms of how this lifestyle is related to their environmental adaptation have been poorly investigated. In this paper, the biofilm of Pseudoalteromonas haloplanktis TAC125, one of the model organisms of cold-adapted bacteria, has been characterized in terms of biofilm typology and matrix composition. The characterization was performed on biofilms produced by the bacterium in response to different nutrient abundance and temperatures; in particular, this is the first report describing the structure of a biofilm formed at 0 °C. The results reported demonstrate that PhTAC125 produces biofilms in different amount and endowed with different physico-chemical properties, like hydrophobicity and roughness, by modulating the relative amount of the different macromolecules present in the biofilm matrix. The capability of PhTAC125 to adopt different biofilm structures in response to environment changes appears to be an interesting adaptation strategy and gives the first hints about the biofilm formation in cold environments.
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6
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Crystal structure of the ferric homotetrameric β 4 human hemoglobin. Biophys Chem 2018; 240:9-14. [DOI: 10.1016/j.bpc.2018.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/18/2018] [Accepted: 05/18/2018] [Indexed: 11/21/2022]
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7
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Wang L, He G, Ruan X, Zhang D, Xiao W, Li X, Wu X, Jiang X. Tailored Robust Hydrogel Composite Membranes for Continuous Protein Crystallization with Ultrahigh Morphology Selectivity. ACS APPLIED MATERIALS & INTERFACES 2018; 10:26653-26661. [PMID: 30009592 DOI: 10.1021/acsami.8b08381] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The tailored and robust hydrogel composite membranes (HCMs) with diverse ion adsorption and interfacial nucleation property are prepared and successfully used in the continuous lysozyme crystallization. Beyond the heterogeneous supporter, the HCMs functioning as an interface ion concentration controller and nucleation generator are demonstrated. By constructing accurately controlled nucleation and growth circumstances in the HCM-equipped membrane crystallizer, the target desired morphology (hexagon cube) and brand-new morphology (multiple flower shape) that differ from the ones created in the conventional crystallizer are continuously and repetitively generated with ultrahigh morphology selectivity. These tailored robust HCMs show great potential for improving current approaches to continuous protein crystallization with specific crystal targets from laboratorial research to actual engineering applications.
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Affiliation(s)
- Lin Wang
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Engineering Laboratory for Petrochemical Energy-efficient Separation Technology of Liaoning Province , Dalian University of Technology , Dalian , Liaoning 116024 , China
| | - Gaohong He
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Engineering Laboratory for Petrochemical Energy-efficient Separation Technology of Liaoning Province , Dalian University of Technology , Dalian , Liaoning 116024 , China
- School of Petroleum and Chemical Engineering , Dalian University of Technology at Panjin , Panjin 124221 , China
| | - Xuehua Ruan
- School of Petroleum and Chemical Engineering , Dalian University of Technology at Panjin , Panjin 124221 , China
| | - Daishuang Zhang
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Engineering Laboratory for Petrochemical Energy-efficient Separation Technology of Liaoning Province , Dalian University of Technology , Dalian , Liaoning 116024 , China
| | - Wu Xiao
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Engineering Laboratory for Petrochemical Energy-efficient Separation Technology of Liaoning Province , Dalian University of Technology , Dalian , Liaoning 116024 , China
| | - Xiangcun Li
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Engineering Laboratory for Petrochemical Energy-efficient Separation Technology of Liaoning Province , Dalian University of Technology , Dalian , Liaoning 116024 , China
| | - Xuemei Wu
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Engineering Laboratory for Petrochemical Energy-efficient Separation Technology of Liaoning Province , Dalian University of Technology , Dalian , Liaoning 116024 , China
| | - Xiaobin Jiang
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Engineering Laboratory for Petrochemical Energy-efficient Separation Technology of Liaoning Province , Dalian University of Technology , Dalian , Liaoning 116024 , China
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8
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Adawy A, Corbeek W, de Ronde E, van Enckevort WJP, de Grip WJ, Vlieg E. A practical kit for micro-scale application of the ceiling crystallisation method. CrystEngComm 2015. [DOI: 10.1039/c4ce01814a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a crystal growth kit for an easy micro-scale application of the ceiling crystallisation method. The kit provides a convenient means for effectuating lab-based microgravity crystallisation conditions.
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Affiliation(s)
- Alaa Adawy
- Radboud University Nijmegen
- Institute for Molecules and Materials
- Nijmegen, The Netherlands
| | - Wil Corbeek
- Radboud University Nijmegen
- Institute for Molecules and Materials
- Nijmegen, The Netherlands
| | - Erik de Ronde
- Radboud University Nijmegen
- Institute for Molecules and Materials
- Nijmegen, The Netherlands
| | | | - Willem J. de Grip
- Department of Biochemistry
- Radboud Institute for Molecular Life Sciences
- Radboud University Medical Center
- Nijmegen, The Netherlands
| | - Elias Vlieg
- Radboud University Nijmegen
- Institute for Molecules and Materials
- Nijmegen, The Netherlands
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9
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Roberge E. Crystal Clear: The ability to crystallize proteins in space is accelerating drug development on Earth. IEEE Pulse 2014; 5:30-4. [DOI: 10.1109/mpul.2014.2321427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Pechkova E, Bragazzi NL, Nicolini C. Advances in nanocrystallography as a proteomic tool. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 95:163-91. [PMID: 24985772 DOI: 10.1016/b978-0-12-800453-1.00005-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In order to overcome the difficulties and hurdles too much often encountered in crystallizing a protein with the conventional techniques, our group has introduced the innovative Langmuir-Blodgett (LB)-based crystallization, as a major advance in the field of both structural and functional proteomics, thus pioneering the emerging field of the so-called nanocrystallography or nanobiocrystallography. This approach uniquely combines protein crystallography and nanotechnologies within an integrated, coherent framework that allows one to obtain highly stable protein crystals and to fully characterize them at a nano- and subnanoscale. A variety of experimental techniques and theoretical/semi-theoretical approaches, ranging from atomic force microscopy, circular dichroism, Raman spectroscopy and other spectroscopic methods, microbeam grazing-incidence small-angle X-ray scattering to in silico simulations, bioinformatics, and molecular dynamics, has been exploited in order to study the LB-films and to investigate the kinetics and the main features of LB-grown crystals. When compared to classical hanging-drop crystallization, LB technique appears strikingly superior and yields results comparable with crystallization in microgravity environments. Therefore, the achievement of LB-based crystallography can have a tremendous impact in the field of industrial and clinical/therapeutic applications, opening new perspectives for personalized medicine. These implications are envisaged and discussed in the present contribution.
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Affiliation(s)
- Eugenia Pechkova
- Nanobiotechnology and Biophysics Laboratories (NBL), Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy; Nanoworld Institute Fondazione ELBA Nicolini (FEN), Pradalunga, Bergamo, Italy
| | - Nicola Luigi Bragazzi
- Nanobiotechnology and Biophysics Laboratories (NBL), Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy; Nanoworld Institute Fondazione ELBA Nicolini (FEN), Pradalunga, Bergamo, Italy; School of Public Health, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
| | - Claudio Nicolini
- Nanobiotechnology and Biophysics Laboratories (NBL), Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy; Nanoworld Institute Fondazione ELBA Nicolini (FEN), Pradalunga, Bergamo, Italy; Biodesign Institute, Arizona State University, Tempe, Arizona, USA.
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11
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Stability of silk and collagen protein materials in space. Sci Rep 2013; 3:3428. [PMID: 24305951 PMCID: PMC3851920 DOI: 10.1038/srep03428] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 11/19/2013] [Indexed: 11/08/2022] Open
Abstract
Collagen and silk materials, in neat forms and as silica composites, were flown for 18 months on the International Space Station [Materials International Space Station Experiment (MISSE)-6] to assess the impact of space radiation on structure and function. As natural biomaterials, the impact of the space environment on films of these proteins was investigated to understand fundamental changes in structure and function related to the future utility in materials and medicine in space environments. About 15% of the film surfaces were etched by heavy ionizing particles such as atomic oxygen, the major component of the low-Earth orbit space environment. Unexpectedly, more than 80% of the silk and collagen materials were chemically crosslinked by space radiation. These findings are critical for designing next-generation biocompatible materials for contact with living systems in space environments, where the effects of heavy ionizing particles and other cosmic radiation need to be considered.
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12
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Takahashi S, Ohta K, Furubayashi N, Yan B, Koga M, Wada Y, Yamada M, Inaka K, Tanaka H, Miyoshi H, Kobayashi T, Kamigaichi S. JAXA protein crystallization in space: ongoing improvements for growing high-quality crystals. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:968-73. [PMID: 24121350 PMCID: PMC3795566 DOI: 10.1107/s0909049513021596] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/02/2013] [Indexed: 05/08/2023]
Abstract
The Japan Aerospace Exploration Agency (JAXA) started a high-quality protein crystal growth project, now called JAXA PCG, on the International Space Station (ISS) in 2002. Using the counter-diffusion technique, 14 sessions of experiments have been performed as of 2012 with 580 proteins crystallized in total. Over the course of these experiments, a user-friendly interface framework for high accessibility has been constructed and crystallization techniques improved; devices to maximize the use of the microgravity environment have been designed, resulting in some high-resolution crystal growth. If crystallization conditions were carefully fixed in ground-based experiments, high-quality protein crystals grew in microgravity in many experiments on the ISS, especially when a highly homogeneous protein sample and a viscous crystallization solution were employed. In this article, the current status of JAXA PCG is discussed, and a rational approach to high-quality protein crystal growth in microgravity based on numerical analyses is explained.
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Affiliation(s)
- Sachiko Takahashi
- Confocal Science Inc., Hayakawa 2nd Building 7F, 2-12-2 Iwamoto-cho, Chiyoda-ku, Tokyo 101-0032, Japan
| | - Kazunori Ohta
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Naoki Furubayashi
- Maruwa Foods and Biosciences Inc., 170-1 Tsutsui-cho, Yamatokoriyama, Nara 639-1123, Japan
| | - Bin Yan
- Confocal Science Inc., Hayakawa 2nd Building 7F, 2-12-2 Iwamoto-cho, Chiyoda-ku, Tokyo 101-0032, Japan
| | - Misako Koga
- Confocal Science Inc., Hayakawa 2nd Building 7F, 2-12-2 Iwamoto-cho, Chiyoda-ku, Tokyo 101-0032, Japan
| | - Yoshio Wada
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Mitsugu Yamada
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Koji Inaka
- Maruwa Foods and Biosciences Inc., 170-1 Tsutsui-cho, Yamatokoriyama, Nara 639-1123, Japan
| | - Hiroaki Tanaka
- Confocal Science Inc., Hayakawa 2nd Building 7F, 2-12-2 Iwamoto-cho, Chiyoda-ku, Tokyo 101-0032, Japan
- Correspondence e-mail:
| | - Hiroshi Miyoshi
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Tomoyuki Kobayashi
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Shigeki Kamigaichi
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
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Cao HL, Sun LH, Li J, Tang L, Lu HM, Guo YZ, He J, Liu YM, Xie XZ, Shen HF, Zhang CY, Guo WH, Huang LJ, Shang P, He JH, Yin DC. A quality comparison of protein crystals grown under containerless conditions generated by diamagnetic levitation, silicone oil and agarose gel. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1901-10. [DOI: 10.1107/s0907444913016296] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Accepted: 06/11/2013] [Indexed: 11/10/2022]
Abstract
High-quality crystals are key to obtaining accurate three-dimensional structures of proteins using X-ray diffraction techniques. However, obtaining such protein crystals is often a challenge. Several containerless crystallization techniques have been reported to have the ability to improve crystal quality, but it is unknown which is the most favourable way to grow high-quality protein crystals. In this paper, a quality comparison of protein crystals which were grown under three containerless conditions provided by diamagnetic levitation, silicone oil and agarose gel was conducted. A control experiment on a vessel wall was also simultaneously carried out. Seven different proteins were crystallized under the four conditions, and the crystal quality was assessed in terms of the resolution limit, the mosaicity and theRmerge. It was found that the crystals grown under the three containerless conditions demonstrated better morphology than those of the control. X-ray diffraction data indicated that the quality of the crystals grown under the three containerless conditions was better than that of the control. Of the three containerless crystallization techniques, the diamagnetic levitation technique exhibited the best performance in enhancing crystal quality. This paper is to our knowledge the first report of improvement of crystal quality using a diamagnetic levitation technique. Crystals obtained from agarose gel demonstrated the second best improvement in crystal quality. The study indicated that the diamagnetic levitation technique is indeed a favourable method for growing high-quality protein crystals, and its utilization is thus potentially useful in practical efforts to obtain well diffracting protein crystals.
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14
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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: 78] [Impact Index Per Article: 7.1] [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.
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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
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15
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Ellisman MH, Deerinck TJ, Shu X, Sosinsky GE. Picking faces out of a crowd: genetic labels for identification of proteins in correlated light and electron microscopy imaging. Methods Cell Biol 2012; 111:139-55. [PMID: 22857927 DOI: 10.1016/b978-0-12-416026-2.00008-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Correlated light and electron microscopic (CLEM) imaging is a powerful method for dissecting cell and tissue function at high resolution. Each imaging mode provides unique information, and the combination of the two can contribute to a better understanding of the spatiotemporal patterns of protein expression, trafficking, and function. Critical to these methods is the use of genetically appended tags that highlight specific proteins of interest in order to be able to pick them out of their complex cellular environment. Here we review and discuss the current generation of genetic labels for direct protein identification by CLEM, addressing their relative strengths and weaknesses and in what experiments they would be most useful.
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Affiliation(s)
- Mark H Ellisman
- National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA 92093-0608, USA
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16
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Stojanoff V, Jakoncic J, Oren DA, Nagarajan V, Navarro Poulsen JC, Adams-Cioaba MA, Bergfors T, Sommer MOA. From screen to structure with a harvestable microfluidic device. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:971-5. [PMID: 21821908 PMCID: PMC3151141 DOI: 10.1107/s1744309111024456] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 06/21/2011] [Indexed: 11/11/2022]
Abstract
Advances in automation have facilitated the widespread adoption of high-throughput vapour-diffusion methods for initial crystallization screening. However, for many proteins, screening thousands of crystallization conditions fails to yield crystals of sufficient quality for structural characterization. Here, the rates of crystal identification for thaumatin, catalase and myoglobin using microfluidic Crystal Former devices and sitting-drop vapour-diffusion plates are compared. It is shown that the Crystal Former results in a greater number of identified initial crystallization conditions compared with vapour diffusion. Furthermore, crystals of thaumatin and lysozyme obtained in the Crystal Former were used directly for structure determination both in situ and upon harvesting and cryocooling. On the basis of these results, a crystallization strategy is proposed that uses multiple methods with distinct kinetic trajectories through the protein phase diagram to increase the output of crystallization pipelines.
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Affiliation(s)
- Vivian Stojanoff
- National Synchrotron Light Source, Brookhaven National Laboratories, Upton, NY 11973, USA
| | - Jean Jakoncic
- National Synchrotron Light Source, Brookhaven National Laboratories, Upton, NY 11973, USA
| | - Deena A. Oren
- Structural Biology Resource Center, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - V. Nagarajan
- JAN Scientific Inc., 4726 Eleventh Avenue NE, Suite 101, Seattle, WA 98105, USA
| | - Jens-Christian Navarro Poulsen
- Department of Chemistry, Biophysical Chemistry Group, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | | | - Terese Bergfors
- Department of Cell and Molecular Biology, Uppsala University, SE-75 124 Uppsala, Sweden
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17
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Dhouib K, Khan Malek C, Pfleging W, Gauthier-Manuel B, Duffait R, Thuillier G, Ferrigno R, Jacquamet L, Ohana J, Ferrer JL, Théobald-Dietrich A, Giegé R, Lorber B, Sauter C. Microfluidic chips for the crystallization of biomacromolecules by counter-diffusion and on-chip crystal X-ray analysis. LAB ON A CHIP 2009; 9:1412-21. [PMID: 19417908 DOI: 10.1039/b819362b] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Microfluidic devices were designed to perform on micromoles of biological macromolecules and viruses the search and the optimization of crystallization conditions by counter-diffusion, as well as the on-chip analysis of crystals by X-ray diffraction. Chips composed of microchannels were fabricated in poly-dimethylsiloxane (PDMS), poly-methyl-methacrylate (PMMA) and cyclo-olefin-copolymer (COC) by three distinct methods, namely replica casting, laser ablation and hot embossing. The geometry of the channels was chosen to ensure that crystallization occurs in a convection-free environment. The transparency of the materials is compatible with crystal growth monitoring by optical microscopy. The quality of the protein 3D structures derived from on-chip crystal analysis by X-ray diffraction using a synchrotron radiation was used to identify the most appropriate polymers. Altogether the results demonstrate that for a novel biomolecule, all steps from the initial search of crystallization conditions to X-ray diffraction data collection for 3D structure determination can be performed in a single chip.
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Affiliation(s)
- Kaouthar Dhouib
- Architecture et réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084, Strasbourg, France
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18
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Meyer A, Rypniewski W, Szymański M, Voelter W, Barciszewski J, Betzel C. Structure of mistletoe lectin I from Viscum album in complex with the phytohormone zeatin. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1590-5. [DOI: 10.1016/j.bbapap.2008.07.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 07/18/2008] [Accepted: 07/18/2008] [Indexed: 10/21/2022]
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19
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Vergara A, Capuano F, Paduano L, Sartorio R. Lysozyme Mutual Diffusion in Solutions Crowded by Poly(ethylene glycol). Macromolecules 2006. [DOI: 10.1021/ma0605705] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alessandro Vergara
- Department of Chemistry, University of Naples “Federico II”, Via Cinthia, Complesso Monte S. Angelo, 80126 Naples, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone, 16, 80134, Naples, Italy
| | - Fabio Capuano
- Department of Chemistry, University of Naples “Federico II”, Via Cinthia, Complesso Monte S. Angelo, 80126 Naples, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone, 16, 80134, Naples, Italy
| | - Luigi Paduano
- Department of Chemistry, University of Naples “Federico II”, Via Cinthia, Complesso Monte S. Angelo, 80126 Naples, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone, 16, 80134, Naples, Italy
| | - Roberto Sartorio
- Department of Chemistry, University of Naples “Federico II”, Via Cinthia, Complesso Monte S. Angelo, 80126 Naples, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone, 16, 80134, Naples, Italy
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