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Yang Z, Zuo Y, Dai L, Zhang L, Yu Y, Zhou L. Effect of ultrasonic-induced selenium crystallization behavior during selenium reduction. ULTRASONICS SONOCHEMISTRY 2023; 95:106392. [PMID: 37011518 PMCID: PMC10457590 DOI: 10.1016/j.ultsonch.2023.106392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/17/2023] [Accepted: 03/28/2023] [Indexed: 06/19/2023]
Abstract
In this work, the crystallization process of selenium was accelerated by ultrasonic wave. The effects of ultrasonic waves and conventional conditions of selenium crystallization were compared to understand the effects of different conditions on crystallization, including ultrasonic time, ultrasonic power, reduction temperature, and H2SeO3 concentration. The mechanism of ultrasound affecting selenium crystallization was also investigated by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The experimental results showed that ultrasonic time, ultrasonic power, and reduction temperature significantly influenced the crystallization process and morphology of selenium. Ultrasonic time had a large effect on the completeness (all products have been crystallized) and integrity of the crystallization of the products. Meanwhile, ultrasonic power and reduction temperature had no effect on the completeness of crystallization. However, it had a significant effect on the morphology and integrity of the crystallized products, and different morphologies of the nano-selenium materials could be obtained by changing the ultrasonic parameters. Both primary and secondary nucleation are important in the process of ultrasound-accelerated selenium crystallization. The cavitation effect and mechanical fluctuant effects generated by ultrasound could reduce the crystallization induction time and accelerate the primary nucleation rate. The high-speed micro-jet formed in the rupture of the cavitation bubble generated is the most important reason to influence the secondary nucleation of the system.
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Affiliation(s)
- Zheng Yang
- Faculty of Metallurgical and Energy Engineering, Kunming University of Science and Technology, Kunming 650093, Yunnan, China; Key Laboratory of Unconventional Metallurgy Ministry of Education, Kunming University of Science and Technology, Kunming 650093, Yunnan, China; Key Laboratory of Special Metallurgy of Yunnan Province, Kunming University of Science and Technology, Kunming 650093, Yunnan, China
| | - Yonggang Zuo
- Faculty of Metallurgical and Energy Engineering, Kunming University of Science and Technology, Kunming 650093, Yunnan, China; Key Laboratory of Unconventional Metallurgy Ministry of Education, Kunming University of Science and Technology, Kunming 650093, Yunnan, China; Key Laboratory of Special Metallurgy of Yunnan Province, Kunming University of Science and Technology, Kunming 650093, Yunnan, China
| | - Linqing Dai
- Faculty of Metallurgical and Energy Engineering, Kunming University of Science and Technology, Kunming 650093, Yunnan, China; Key Laboratory of Unconventional Metallurgy Ministry of Education, Kunming University of Science and Technology, Kunming 650093, Yunnan, China; Key Laboratory of Special Metallurgy of Yunnan Province, Kunming University of Science and Technology, Kunming 650093, Yunnan, China.
| | - Libo Zhang
- Faculty of Metallurgical and Energy Engineering, Kunming University of Science and Technology, Kunming 650093, Yunnan, China; Key Laboratory of Unconventional Metallurgy Ministry of Education, Kunming University of Science and Technology, Kunming 650093, Yunnan, China; Key Laboratory of Special Metallurgy of Yunnan Province, Kunming University of Science and Technology, Kunming 650093, Yunnan, China.
| | - Yusen Yu
- Faculty of Metallurgical and Energy Engineering, Kunming University of Science and Technology, Kunming 650093, Yunnan, China; Key Laboratory of Unconventional Metallurgy Ministry of Education, Kunming University of Science and Technology, Kunming 650093, Yunnan, China; Key Laboratory of Special Metallurgy of Yunnan Province, Kunming University of Science and Technology, Kunming 650093, Yunnan, China
| | - Liang Zhou
- Faculty of Metallurgical and Energy Engineering, Kunming University of Science and Technology, Kunming 650093, Yunnan, China; Key Laboratory of Unconventional Metallurgy Ministry of Education, Kunming University of Science and Technology, Kunming 650093, Yunnan, China; Key Laboratory of Special Metallurgy of Yunnan Province, Kunming University of Science and Technology, Kunming 650093, Yunnan, China
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Lynch ML, Snell ME, Potter SA, Snell EH, Bowman SEJ. 20 years of crystal hits: progress and promise in ultrahigh-throughput crystallization screening. Acta Crystallogr D Struct Biol 2023; 79:198-205. [PMID: 36876429 PMCID: PMC9986797 DOI: 10.1107/s2059798323001274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 02/11/2023] [Indexed: 03/01/2023] Open
Abstract
Diffraction-based structural methods contribute a large fraction of the biomolecular structural models available, providing a critical understanding of macromolecular architecture. These methods require crystallization of the target molecule, which remains a primary bottleneck in crystal-based structure determination. The National High-Throughput Crystallization Center at Hauptman-Woodward Medical Research Institute has focused on overcoming obstacles to crystallization through a combination of robotics-enabled high-throughput screening and advanced imaging to increase the success of finding crystallization conditions. This paper will describe the lessons learned from over 20 years of operation of our high-throughput crystallization services. The current experimental pipelines, instrumentation, imaging capabilities and software for image viewing and crystal scoring are detailed. New developments in the field and opportunities for further improvements in biomolecular crystallization are reflected on.
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Affiliation(s)
- Miranda L Lynch
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - M Elizabeth Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Stephen A Potter
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Edward H Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Sarah E J Bowman
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
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Bruno AE, Charbonneau P, Newman J, Snell EH, So DR, Vanhoucke V, Watkins CJ, Williams S, Wilson J. Classification of crystallization outcomes using deep convolutional neural networks. PLoS One 2018; 13:e0198883. [PMID: 29924841 PMCID: PMC6010233 DOI: 10.1371/journal.pone.0198883] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/25/2018] [Indexed: 11/19/2022] Open
Abstract
The Machine Recognition of Crystallization Outcomes (MARCO) initiative has assembled roughly half a million annotated images of macromolecular crystallization experiments from various sources and setups. Here, state-of-the-art machine learning algorithms are trained and tested on different parts of this data set. We find that more than 94% of the test images can be correctly labeled, irrespective of their experimental origin. Because crystal recognition is key to high-density screening and the systematic analysis of crystallization experiments, this approach opens the door to both industrial and fundamental research applications.
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Affiliation(s)
- Andrew E. Bruno
- Center for Computational Research, University at Buffalo, Buffalo, New York, United States of America
| | - Patrick Charbonneau
- Department of Chemistry, Duke University, Durham, North Carolina, United States of America
- Department of Physics, Duke University, Durham, North Carolina, United States of America
| | - Janet Newman
- Collaborative Crystallisation Centre, CSIRO, Parkville, Victoria, Australia
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
- SUNY Buffalo, Department of Materials, Design, and Innovation, Buffalo, New York, United States of America
| | - David R. So
- Google Brain, Google Inc., Mountain View, California, United States of America
| | - Vincent Vanhoucke
- Google Brain, Google Inc., Mountain View, California, United States of America
| | | | - Shawn Williams
- Platform Technology and Sciences, GlaxoSmithKline Inc., Collegeville, Pennsylvania, United States of America
| | - Julie Wilson
- Department of Mathematics, University of York, York, United Kingdom
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Lin Y. What's happened over the last five years with high-throughput protein crystallization screening? Expert Opin Drug Discov 2018; 13:691-695. [PMID: 29676184 DOI: 10.1080/17460441.2018.1465924] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yibin Lin
- a Department of Pediatrics, Center for Antimicrobial Resistance and Microbial Genomics , McGovern Medical School, The University of Texas Health Science Center at Houston , Houston , TX , USA
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Altan I, Fusco D, Afonine PV, Charbonneau P. Learning about Biomolecular Solvation from Water in Protein Crystals. J Phys Chem B 2018; 122:2475-2486. [DOI: 10.1021/acs.jpcb.7b09898] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Diana Fusco
- Department of Physics, University of California, Berkeley, California 94720, United States
| | - Pavel V. Afonine
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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Giegé R. What macromolecular crystallogenesis tells us - what is needed in the future. IUCRJ 2017; 4:340-349. [PMID: 28875021 PMCID: PMC5571797 DOI: 10.1107/s2052252517006595] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 05/02/2017] [Indexed: 05/05/2023]
Abstract
Crystallogenesis is a longstanding topic that has transformed into a discipline that is mainly focused on the preparation of crystals for practising crystallo-graphers. Although the idiosyncratic features of proteins have to be taken into account, the crystallization of proteins is governed by the same physics as the crystallization of inorganic materials. At present, a diversified panel of crystallization methods adapted to proteins has been validated, and although only a few methods are in current practice, the success rate of crystallization has increased constantly, leading to the determination of ∼105 X-ray structures. These structures reveal a huge repertoire of protein folds, but they only cover a restricted part of macromolecular diversity across the tree of life. In the future, crystals representative of missing structures or that will better document the structural dynamics and functional steps underlying biological processes need to be grown. For the pertinent choice of biologically relevant targets, computer-guided analysis of structural databases is needed. From another perspective, crystallization is a self-assembly process that can occur in the bulk of crowded fluids, with crystals being supramolecular assemblies. Life also uses self-assembly and supramolecular processes leading to transient, or less often stable, complexes. An integrated view of supramolecularity implies that proteins crystallizing either in vitro or in vivo or participating in cellular processes share common attributes, notably determinants and antideterminants that favour or disfavour their correct or incorrect associations. As a result, under in vivo conditions proteins show a balance between features that favour or disfavour association. If this balance is broken, disorders/diseases occur. Understanding crystallization under in vivo conditions is a challenge for the future. In this quest, the analysis of packing contacts and contacts within oligomers will be crucial in order to decipher the rules governing protein self-assembly and will guide the engineering of novel biomaterials. In a wider perspective, understanding such contacts will open the route towards supramolecular biology and generalized crystallogenesis.
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Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l’ARN, UPR 9002, Université de Strasbourg and CNRS, F-67084 Strasbourg, France
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The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability. Methods Mol Biol 2017; 1607:77-115. [PMID: 28573570 DOI: 10.1007/978-1-4939-7000-1_4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Crystallization of macromolecules has long been perceived as a stochastic process, which cannot be predicted or controlled. This is consistent with another popular notion that the interactions of molecules within the crystal, i.e., crystal contacts, are essentially random and devoid of specific physicochemical features. In contrast, functionally relevant surfaces, such as oligomerization interfaces and specific protein-protein interaction sites, are under evolutionary pressures so their amino acid composition, structure, and topology are distinct. However, current theoretical and experimental studies are significantly changing our understanding of the nature of crystallization. The increasingly popular "sticky patch" model, derived from soft matter physics, describes crystallization as a process driven by interactions between select, specific surface patches, with properties thermodynamically favorable for cohesive interactions. Independent support for this model comes from various sources including structural studies and bioinformatics. Proteins that are recalcitrant to crystallization can be modified for enhanced crystallizability through chemical or mutational modification of their surface to effectively engineer "sticky patches" which would drive crystallization. Here, we discuss the current state of knowledge of the relationship between the microscopic properties of the target macromolecule and its crystallizability, focusing on the "sticky patch" model. We discuss state-of-the-art in silico methods that evaluate the propensity of a given target protein to form crystals based on these relationships, with the objective to design variants with modified molecular surface properties and enhanced crystallization propensity. We illustrate this discussion with specific cases where these approaches allowed to generate crystals suitable for structural analysis.
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Renaissance of protein crystallization and precipitation in biopharmaceuticals purification. Biotechnol Adv 2017; 35:41-50. [DOI: 10.1016/j.biotechadv.2016.11.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 11/15/2016] [Accepted: 11/23/2016] [Indexed: 12/13/2022]
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McManus JJ, Charbonneau P, Zaccarelli E, Asherie N. The physics of protein self-assembly. Curr Opin Colloid Interface Sci 2016. [DOI: 10.1016/j.cocis.2016.02.011] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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