1
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Larpent P, Codan L, Bothe JR, Iuzzolino L, Pabit S, Gupta S, Fischmann T, Su Y, Reichert P, Stueber D, Cote A. Small-Angle X-ray Scattering as a Powerful Tool for Phase and Crystallinity Assessment of Monoclonal Antibody Crystallites in Support of Batch Crystallization. Mol Pharm 2024; 21:4024-4037. [PMID: 38958508 DOI: 10.1021/acs.molpharmaceut.4c00418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Crystalline suspensions of monoclonal antibodies (mAbs) have great potential to improve drug substance isolation and purification on a large scale and to be used for drug delivery via high-concentration formulations. Crystalline mAb suspensions are expected to have enhanced chemical and physical properties relative to mAb solutions delivered intravenously, making them attractive candidates for subcutaneous delivery. In contrast to small molecules, the development of protein crystalline suspensions is not a widely used approach in the pharmaceutical industry. This is mainly due to the challenges in finding crystalline hits and the suboptimal physical properties of the resulting crystallites when hits are found. Modern advances in instrumentation and increased knowledge of mAb crystallization have, however, resulted in higher probabilities of discovering crystal forms and improving their particle properties and characterization. In this regard, physical, analytical characterization plays a central role in the initial steps of understanding and later optimizing the crystallization of mAbs and requires careful selection of the appropriate tools. This contribution describes a novel crystal structure of the antibody pembrolizumab and demonstrates the usefulness of small-angle X-ray scattering (SAXS) for characterizing its crystalline suspensions. It illustrates the advantages of SAXS when used to (i) confirm crystallinity and crystal phase of crystallites produced in batch mode; (ii) confirm crystallinity under various conditions and detect variations in crystal phases, enabling fine-tuning of the crystallizations for phase control across multiple batches; (iii) monitor the physical response and stability of the crystallites in suspension with regard to filtration and washing; and (iv) monitor the physical stability of the crystallites upon drying. Overall, this work highlights how SAXS is an essential tool for mAb crystallization characterization.
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Affiliation(s)
- Patrick Larpent
- Department of Analytical Research and Development, MSD Werthenstein BioPharma GmbH, Industrie Nord 1, 6105 Schachen, Switzerland
| | - Lorenzo Codan
- Department of Process Research and Development, MSD Werthenstein BioPharma GmbH, Industrie Nord 1, 6105 Schachen, Switzerland
| | - Jameson R Bothe
- Department of Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Luca Iuzzolino
- Department of Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Suzette Pabit
- Department of Analytical Research and Development, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Sudipta Gupta
- Department of Analytical Research and Development, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Thierry Fischmann
- Department of Protein and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Yongchao Su
- Department of Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Paul Reichert
- Department of Protein and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Dirk Stueber
- Department of Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Aaron Cote
- Department of Biologics Process Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
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2
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Chavas LMG, Coulibaly F, Garriga D. Bridging the microscopic divide: a comprehensive overview of micro-crystallization and in vivo crystallography. IUCRJ 2024; 11:476-485. [PMID: 38958014 PMCID: PMC11220871 DOI: 10.1107/s205225252400513x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/30/2024] [Indexed: 07/04/2024]
Abstract
A series of events underscoring the significant advancements in micro-crystallization and in vivo crystallography were held during the 26th IUCr Congress in Melbourne, positioning microcrystallography as a pivotal field within structural biology. Through collaborative discussions and the sharing of innovative methodologies, these sessions outlined frontier approaches in macromolecular crystallography. This review provides an overview of this rapidly moving field in light of the rich dialogues and forward-thinking proposals explored during the congress workshop and microsymposium. These advances in microcrystallography shed light on the potential to reshape current research paradigms and enhance our comprehension of biological mechanisms at the molecular scale.
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Affiliation(s)
| | - Fasséli Coulibaly
- Biomedicine Discovery Institute & Department of Biochemistry and Molecular BiologyMonash UniversityClaytonAustralia
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3
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Cardona-Echavarría MC, Santillán C, Miranda-Blancas R, Stojanoff V, Rudiño-Piñera E. Unveiling success determinants for AMB-assisted phase expansion of fusion proteins in ARP/wARP. J Struct Biol 2024; 216:108089. [PMID: 38537893 DOI: 10.1016/j.jsb.2024.108089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/12/2024] [Accepted: 03/23/2024] [Indexed: 04/04/2024]
Abstract
Fusion proteins (FPs) are frequently utilized as a biotechnological tool in the determination of macromolecular structures using X-ray methods. Here, we explore the use of different protein tags in various FP, to obtain initial phases by using them in a partial molecular replacement (MR) and constructing the remaining FP structure with ARP/wARP. Usually, the tag is removed prior to crystallization, however leaving the tag on may facilitate crystal formation, and structural determination by expanding phases from known to unknown segments of the complex. In this study, the Protein Data Bank was mined for an up-to-date list of FPs with the most used protein tags, Maltose Binding Protein (MBP), Green Fluorescent Protein (GFP), Thioredoxin (TRX), Glutathione transferase (GST) and the Small Ubiquitin-like Modifier Protein (SUMO). Partial MR using the protein tag, followed by automatic model building, was tested on a subset of 116 FP. The efficiency of this method was analyzed and factors that influence the coordinate construction of a substantial portions of the fused protein were identified. Using MBP, GFP, and SUMO as phase generators it was possible to build at least 75 % of the protein of interest in 36 of the 116 cases tested. Our results reveal that tag selection has a significant impact; tags with greater structural stability, such as GFP, increase the success rate. Further statistical analysis identifies that resolution, Wilson B factor, solvent percentage, completeness, multiplicity, protein tag percentage in the FP (considering amino acids), and the linker length play pivotal roles using our approach. In cases where a structural homologous is absent, this method merits inclusion in the toolkit of protein crystallographers.
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Affiliation(s)
- María C Cardona-Echavarría
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos C.P. 62210, Mexico; Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos C.P. 62209, Mexico.
| | | | - Ricardo Miranda-Blancas
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México C.P. 04510, Mexico
| | - Vivian Stojanoff
- Brookhaven National Laboratory, Upton, NY 11973-5000, United States
| | - Enrique Rudiño-Piñera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos C.P. 62210, Mexico.
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4
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Lyu J, Zhu T, Zhou Y, Zhao T, Fei M, Zhong X, He H. Controlling the Crystal Growth of DNA Molecules via Strategic Chemical Modifications. Chemistry 2024; 30:e202400012. [PMID: 38477176 DOI: 10.1002/chem.202400012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/14/2024]
Abstract
Intermolecular interactions are critical to the crystallization of biomolecules, yet the precise control of biomolecular crystal growth based on these interactions remains elusive. To understand the connections between the crystallization kinetics and the strength of intermolecular interactions, herein we have employed DNA triangular crystals and modified ones as a versatile tool to investigate how the strength of intermolecular interaction affects crystal growth. Interestingly, we have found that the 2'-O-methylation at sticky ends of the DNA triangle could strengthen its intermolecular interaction, resulting in the accelerated formation of smaller crystals. Conversely, phosphorothioate modification could weaken the sticky-end cohesion and delay the nucleation, resulting in formation of fewer but larger crystals. In addition, these modification effects were consistently observed in the crystallization of a DNA decamer. In one word, our experimental results demonstrate that the strength of intermolecular interaction directly impacts crystal growth. It suggests that 2'-O-methylation and phosphorothioate modification represents a rational strategy for controlling DNA molecules grow into desired crystals and it also facilitates structural determination.
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Affiliation(s)
- Jiazhen Lyu
- School of Laboratory Medicine, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Tingyu Zhu
- School of Stomatology, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Yan Zhou
- School of Pharmacy, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Ting Zhao
- School of Laboratory Medicine, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Meiling Fei
- School of Laboratory Medicine, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Xiaowu Zhong
- School of Laboratory Medicine, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Hongfei He
- School of Laboratory Medicine, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
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5
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Athukorala A, Helbig KJ, McSharry BP, Forwood JK, Sarker S. An optimised protocol for the expression and purification of adenovirus core protein VII. J Virol Methods 2024; 326:114907. [PMID: 38432358 DOI: 10.1016/j.jviromet.2024.114907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Adenovirus protein VII (pVII) is a highly basic core protein, bearing resemblance to mammalian histones. Despite its diverse functions, a comprehensive understanding of its structural intricacies and the mechanisms underlying its functions remain elusive, primarily due to the complexity of producing a good amount of soluble pVII. This study aimed to optimise the expression and purification of recombinant pVII from four different adenoviruses with a simple vector construct. This study successfully determined the optimal conditions for efficiently purifying pVII across four adenovirus species, revealing the differential preference for bacterial expression systems. The One Shot BL21 Star (DE3) proved favourable over Rosetta 2 (DE3) pLysS with consistent levels of expression between IPTG-induced and auto-induction. We demonstrated that combining chemical and mechanical cell lysis is possible and highly effective. Other noteworthy benefits were observed in using RNase during sample processing. The addition of RNase has significantly improved the quality and quantity of the purified protein as confirmed by chromatographic and western blot analyses. These findings established a solid groundwork for pVII purification methodologies and carry the significant potential to assist in unveiling the core structure of pVII, its arrangement within the core, DNA condensation intricacies, and potential pathways for nuclear transport.
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Affiliation(s)
- Ajani Athukorala
- Department of Microbiology, Anatomy, Physiology, and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3086, Australia
| | - Karla J Helbig
- Department of Microbiology, Anatomy, Physiology, and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3086, Australia
| | - Brian P McSharry
- School of Dentistry and Medical Sciences Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Jade K Forwood
- School of Dentistry and Medical Sciences Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Subir Sarker
- Biomedical Sciences and Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia.
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6
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Oszajca M, Flejszar M, Szura A, Dróżdż P, Brindell M, Kurpiewska K. Exploring the coordination chemistry of ruthenium complexes with lysozymes: structural and in-solution studies. Front Chem 2024; 12:1371637. [PMID: 38638879 PMCID: PMC11024358 DOI: 10.3389/fchem.2024.1371637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/06/2024] [Indexed: 04/20/2024] Open
Abstract
This study presents a comprehensive structural analysis of the adducts formed upon the reaction of two Ru(III) complexes [HIsq][trans-RuIIICl4(dmso)(Isq)] (1) and [H2Ind][trans-RuIIICl4(dmso)(HInd)] (2) (where HInd-indazole, Isq-isoquinoline, analogs of NAMI-A) and two Ru(II) complexes, cis-[RuCl2(dmso)4] (c) and trans-[RuCl2(dmso)4] (t), with hen-egg white lysozyme (HEWL). Additionally, the crystal structure of an adduct of human lysozyme (HL) with ruthenium complex, [H2Ind][trans-RuCl4(dmso)(HInd)] was solved. X-ray crystallographic data analysis revealed that all studied Ru complexes, regardless of coordination surroundings and metal center charge, coordinate to the same amino acids (His15, Arg14, and Asp101) of HEWL, losing most of their original ligands. In the case of the 2-HL adduct, two distinct metalation sites: (i) Arg107, Arg113 and (ii) Gln127, Gln129, were identified. Crystallographic data were supported by studies of the interaction of 1 and 2 with HEWL in an aqueous solution. Hydrolytic stability studies revealed that both complexes 1 and 2 liberate the N-heterocyclic ligand under crystallization-like conditions (pH 4.5) as well as under physiological pH conditions, and this process is not significantly affected by the presence of HEWL. A comparative examination of nine crystal structures of Ru complexes with lysozyme, obtained through soaking and co-crystallization experiments, together with in-solution studies of the interaction between 1 and 2 with HEWL, indicates that the hydrolytic release of the N-heterocyclic ligand is one of the critical factors in the interaction between Ru complexes and lysozyme. This understanding is crucial in shedding light on the tendency of Ru complexes to target diverse metalation sites during the formation and in the final forms of the adducts with proteins.
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Affiliation(s)
- Maria Oszajca
- Department of Inorganic Chemistry, Faculty of Chemistry, Jagiellonian University, Kraków, Poland
| | - Monika Flejszar
- Department of Inorganic Chemistry, Faculty of Chemistry, Jagiellonian University, Kraków, Poland
- Department of Physical Chemistry, Faculty of Chemistry, Rzeszów University of Technology, Rzeszów, Poland
| | - Arkadiusz Szura
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Kraków, Poland
| | - Patrycja Dróżdż
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Kraków, Poland
| | - Małgorzata Brindell
- Department of Inorganic Chemistry, Faculty of Chemistry, Jagiellonian University, Kraków, Poland
| | - Katarzyna Kurpiewska
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Kraków, Poland
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7
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Bhalla N, Payam AF. Addressing the Silent Spread of Monkeypox Disease with Advanced Analytical Tools. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206633. [PMID: 36517107 DOI: 10.1002/smll.202206633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Monkeypox disease is caused by a virus which belongs to the orthopoxvirus genus of the poxviridae family. This disease has recently spread out to several non-endemic countries. While some cases have been linked to travel from endemic regions, more recent infections are thought to have spread in the community without any travel links, raising the risks of a wider outbreak. This state of public health represents a highly unusual event which requires urgent surveillance. In this context, the opportunities and technological challenges of current bio/chemical sensors, nanomaterials, nanomaterial characterization instruments, and artificially intelligent biosystems collectively called "advanced analytical tools" are reviewed here, which will allow early detection, characterization, and inhibition of the monkeypox virus (MPXV) in the community and limit its expansion from endemic to pandemic. A summary of background information is also provided from biological and epidemiological perspective of monkeypox to support the scientific case for its holistic management using advanced analytical tools.
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Affiliation(s)
- Nikhil Bhalla
- Nanotechnology and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, York St., BT15 1ED Belfast, Northern Ireland, UK
- Healthcare Technology Hub, Ulster University, York St., BT15 1ED Belfast, Northern Ireland, UK
| | - Amir Farokh Payam
- Nanotechnology and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, York St., BT15 1ED Belfast, Northern Ireland, UK
- Healthcare Technology Hub, Ulster University, York St., BT15 1ED Belfast, Northern Ireland, UK
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8
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Liberti D, Imbimbo P, Giustino E, D’Elia L, Ferraro G, Casillo A, Illiano A, Pinto G, Di Meo MC, Alvarez-Rivera G, Corsaro MM, Amoresano A, Zarrelli A, Ibáñez E, Merlino A, Monti DM. Inside out Porphyridium cruentum: Beyond the Conventional Biorefinery Concept. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2023; 11:381-389. [PMID: 36643001 PMCID: PMC9832536 DOI: 10.1021/acssuschemeng.2c05869] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/10/2022] [Indexed: 05/31/2023]
Abstract
Here, an unprecedented biorefinery approach has been designed to recover high-added value bioproducts starting from the culture ofPorphyridium cruentum. This unicellular marine red alga can secrete and accumulate high-value compounds that can find applications in a wide variety of industrial fields. 300 ± 67 mg/L of exopolysaccharides were obtained from cell culture medium; phycoerythrin was efficiently extracted (40% of total extract) and isolated by single chromatography, with a purity grade that allowed the crystal structure determination at 1.60 Å; a twofold increase in β-carotene yield was obtained from the residual biomass; the final residual biomass was found to be enriched in saturated fatty acids. Thus, for the first time, a complete exploitation ofP. cruentumculture was set up.
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Affiliation(s)
- Davide Liberti
- Department
of Chemical Sciences, University of Naples
Federico II, via Cinthia 4, Naples80126, Italy
| | - Paola Imbimbo
- Department
of Chemical Sciences, University of Naples
Federico II, via Cinthia 4, Naples80126, Italy
| | - Enrica Giustino
- Department
of Chemical Sciences, University of Naples
Federico II, via Cinthia 4, Naples80126, Italy
| | - Luigi D’Elia
- Department
of Chemical Sciences, University of Naples
Federico II, via Cinthia 4, Naples80126, Italy
| | - Giarita Ferraro
- Department
of Chemical Sciences, University of Naples
Federico II, via Cinthia 4, Naples80126, Italy
| | - Angela Casillo
- Department
of Chemical Sciences, University of Naples
Federico II, via Cinthia 4, Naples80126, Italy
| | - Anna Illiano
- Department
of Chemical Sciences, University of Naples
Federico II, via Cinthia 4, Naples80126, Italy
| | - Gabriella Pinto
- Department
of Chemical Sciences, University of Naples
Federico II, via Cinthia 4, Naples80126, Italy
| | - Maria Chiara Di Meo
- Department
of Sciences and Technologies (DST), University
of Sannio, Benevento82100, Italy
| | - Gerardo Alvarez-Rivera
- Laboratory
of Foodomics, Institute of Food Science
Research, CIAL, CSIC, Nicolás Cabrera 9, Madrid28049, Spain
| | - Maria Michela Corsaro
- Department
of Chemical Sciences, University of Naples
Federico II, via Cinthia 4, Naples80126, Italy
| | - Angela Amoresano
- Department
of Chemical Sciences, University of Naples
Federico II, via Cinthia 4, Naples80126, Italy
| | - Armando Zarrelli
- Department
of Chemical Sciences, University of Naples
Federico II, via Cinthia 4, Naples80126, Italy
| | - Elena Ibáñez
- Laboratory
of Foodomics, Institute of Food Science
Research, CIAL, CSIC, Nicolás Cabrera 9, Madrid28049, Spain
| | - Antonello Merlino
- Department
of Chemical Sciences, University of Naples
Federico II, via Cinthia 4, Naples80126, Italy
| | - Daria Maria Monti
- Department
of Chemical Sciences, University of Naples
Federico II, via Cinthia 4, Naples80126, Italy
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9
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Martin J, Robert X, Gouet P, Falson P, Chaptal V. Specific Xray diffraction patterns of membrane proteins caused by secondary structure collinearity. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184065. [PMID: 36206830 DOI: 10.1016/j.bbamem.2022.184065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/12/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022]
Abstract
Diffraction anisotropy is a phenomenon that impacts more specifically membrane proteins, compared to soluble ones, but the reasons for this discrepancy remained unclear. Often, it is referred to a difference in resolution limits between highest and lowest diffraction limits as a signature for anisotropy. We show in this article that there is no single correlation between anisotropy and difference in resolution limits, with notably a substantial number of structures displaying various anisotropy with no difference in resolution limits. We further investigated diffraction intensity profiles, and observed a peak centred on 4.9 Å resolution more predominant in membrane proteins. Since this peak is in the region corresponding to secondary structures, we investigated the influence of secondary structure ratio. We showed that secondary structure content has little influence on this profile, while secondary structure collinearity in membrane proteins correlate with a stronger peak. Finally, we could further show that the presence of this peak is linked to higher diffraction anisotropy. These results bring to light a specific diffraction of membrane protein crystals, which calls for a specific handling by crystallographic software. It also brings an explanation for investigators struggling with their anisotropic data.
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Affiliation(s)
- Juliette Martin
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Xavier Robert
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Patrice Gouet
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Pierre Falson
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Vincent Chaptal
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France.
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10
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Marchenkova MA, Boikova AS, Ilina KB, Konarev PV, Pisarevsky YV, Dyakova YA, Kovalchuk MV. The Relationship of Precursor Cluster Concentration in a Saturated Crystallization Solution to Long-Range Order During the Transition to the Solid Phase. Acta Naturae 2023; 15:58-68. [PMID: 37153505 PMCID: PMC10154781 DOI: 10.32607/actanaturae.11815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 01/11/2023] [Indexed: 05/09/2023] Open
Abstract
A model for the transition from disordered liquid state to the solid phase has been proposed based on establishing a correlation between the concentration of precursor clusters in a saturated solution and the features of solid phase formation. The validity of the model has been verified experimentally by simultaneously studying the oligomeric structure of lysozyme protein solutions and the peculiarities of solid phase formation from these solutions. It was shown that no solid phase is formed in the absence of precursor clusters (octamers) in solution; perfect monocrystals are formed at a small concentration of octamers; mass crystallization is observed with an increasing degree of supersaturation (and concentration of octamers); further increase in octamer concentration leads to the formation of an amorphous phase.
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Affiliation(s)
- M. A. Marchenkova
- Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences, Moscow, 119333 Russian Federation
| | - A. S. Boikova
- Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences, Moscow, 119333 Russian Federation
| | - K. B. Ilina
- Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences, Moscow, 119333 Russian Federation
| | - P. V. Konarev
- Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences, Moscow, 119333 Russian Federation
| | - Yu. V. Pisarevsky
- Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences, Moscow, 119333 Russian Federation
| | - Yu. A. Dyakova
- National Research Centre “Kurchatov Institute”, Moscow, 123182 Russian Federation
| | - M. V. Kovalchuk
- Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences, Moscow, 119333 Russian Federation
- National Research Centre “Kurchatov Institute”, Moscow, 123182 Russian Federation
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11
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Volpi S, Doolan A, Baldini L, Casnati A, Crowley PB, Sansone F. Complex Formation between Cytochrome c and a Tetra-alanino-calix[4]arene. Int J Mol Sci 2022; 23:ijms232315391. [PMID: 36499717 PMCID: PMC9737847 DOI: 10.3390/ijms232315391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Owing to their remarkable features, calix[n]arenes are being exploited to study different aspects of molecular recognition, including protein complexation. Different complexation modes have been described, depending on the moieties that complement the aromatic cavity, allowing for function regulation and/or controlled assembly of the protein target. Here, a rigid cone calix[4]arene, bearing four anionic alanine units at the upper rim, was tested as a ligand for cytochrome c. Cocrystallization attempts were unfruitful, preventing a solid-state study of the system. Next, the complex was studied using NMR spectroscopy, which revealed the presence of two binding sites at lysine residues with dissociation constants (Kd) in the millimolar range.
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Affiliation(s)
- Stefano Volpi
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Viale delle Scienze, 17/A, 43124 Parma, Italy
| | - Aishling Doolan
- School of Biological and Chemical Sciences, University of Galway, University Road, H91 TK33 Galway, Ireland
| | - Laura Baldini
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Viale delle Scienze, 17/A, 43124 Parma, Italy
- Correspondence:
| | - Alessandro Casnati
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Viale delle Scienze, 17/A, 43124 Parma, Italy
| | - Peter B. Crowley
- School of Biological and Chemical Sciences, University of Galway, University Road, H91 TK33 Galway, Ireland
| | - Francesco Sansone
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Viale delle Scienze, 17/A, 43124 Parma, Italy
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12
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Lee S, Jo K, Jeong HG, Choi YS, Kyoung H, Jung S. Freezing-induced denaturation of myofibrillar proteins in frozen meat. Crit Rev Food Sci Nutr 2022; 64:1385-1402. [PMID: 36052640 DOI: 10.1080/10408398.2022.2116557] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Freezing is commonly used to extend the shelf life of meat and meat products but may impact the overall quality of those products by inducing structural changes in myofibrillar proteins (MPs) through denaturation, chemical modification, and encouraging protein aggregation. This review covers the effect of freezing on the denaturation of MPs in terms of the effects of ice crystallization on solute concentrations, cold denaturation, and protein oxidation. Freezing-induced denaturation of MPs begins with ice crystallization in extracellular spaces and changes in solute concentrations in the unfrozen water fraction. At typical temperatures for freezing meat (lower than -18 °C), cold denaturation of proteins occurs, accompanied by an alteration in their secondary and tertiary structure. Moreover, the disruption of muscle cells triggers the release of cellular enzymes, accelerating protein degradation and oxidation. To minimize severe deterioration during the freezing and frozen storage of meat, there is a vital need to use an appropriate freezing temperature below the glass transition temperature and to avoid temperature fluctuations during storage to prevent recrystallization. Such an understanding of MP denaturation can be applied to determine the optimum freezing conditions for meat products with highly retained sensory, nutritional, and functional qualities.
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Affiliation(s)
- Seonmin Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
| | - Kyung Jo
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
| | - Hyun Gyung Jeong
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
| | - Yun-Sang Choi
- Research Group of Food Processing, Korea Food Research Institute, Wanju, Korea
| | - Hyunjin Kyoung
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
| | - Samooel Jung
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
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13
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Bhatia I, Yadav S, Biswal BK. Identification, structure determination and analysis of Mycobacterium smegmatis acyl-carrier protein synthase (AcpS) crystallized serendipitously. Acta Crystallogr F Struct Biol Commun 2022; 78:252-264. [PMID: 35787552 PMCID: PMC9254898 DOI: 10.1107/s2053230x22005738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/26/2022] [Indexed: 11/11/2022] Open
Abstract
The unintended crystallization of proteins which generally originate from the expression host instead of the target recombinant proteins is periodically reported. Despite the massive technological advances in the field, assigning a structural model to the corresponding diffraction data is not a trivial task. Here, the structure of acyl-carrier protein synthase (AcpS) from Mycobacterium smegmatis (msAcpS), which crystallized inadvertently in an experimental setup to grow crystals of a Mycobacterium tuberculosis protein using M. smegmatis as an expression system, is reported. After numerous unsuccessful attempts to solve the structure of the target protein by the molecular-replacement method no convincing solutions were obtained, indicating that the diffraction data may correspond to a crystal of an artifactual protein, which was finally identified by the Sequence-Independent Molecular replacement Based on Available Databases (SIMBAD) server. The msAcpS structure was solved at 2.27 Å resolution and structural analysis showed an overall conserved fold. msAcpS formed a trimeric structure similar to those of other reported structures of AcpS from various organisms; however, the residues involved in trimer formation are not strictly conserved. An unrelated metal ion (Ni2+), which was possibly incorporated during protein purification, was observed in the proximity of His49 and His116. Structural and sequence differences were observed in the loop connecting the α3 and α4 helices that is responsible for the open and closed conformations of the enzyme. Moreover, the structural analysis of msAcpS augments the current understanding of this enzyme, which plays a crucial role in the functional activation of acyl-carrier proteins in the fatty-acid biosynthesis pathway.
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Affiliation(s)
- Indu Bhatia
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Savita Yadav
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Bichitra K. Biswal
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
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14
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Yuan Z, Wu M, Meng Y, Niu Y, Xiao W, Ruan X, He G, Jiang X. Protein crystal regulation and harvest via electric field-based method. Curr Opin Chem Eng 2022. [DOI: 10.1016/j.coche.2021.100744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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15
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Bacterial Transcriptional Regulators: A Road Map for Functional, Structural, and Biophysical Characterization. Int J Mol Sci 2022; 23:ijms23042179. [PMID: 35216300 PMCID: PMC8879271 DOI: 10.3390/ijms23042179] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/11/2022] [Accepted: 02/11/2022] [Indexed: 12/12/2022] Open
Abstract
The different niches through which bacteria move during their life cycle require a fast response to the many environmental queues they encounter. The sensing of these stimuli and their correct response is driven primarily by transcriptional regulators. This kind of protein is involved in sensing a wide array of chemical species, a process that ultimately leads to the regulation of gene transcription. The allosteric-coupling mechanism of sensing and regulation is a central aspect of biological systems and has become an important field of research during the last decades. In this review, we summarize the state-of-the-art techniques applied to unravel these complex mechanisms. We introduce a roadmap that may serve for experimental design, depending on the answers we seek and the initial information we have about the system of study. We also provide information on databases containing available structural information on each family of transcriptional regulators. Finally, we discuss the recent results of research about the allosteric mechanisms of sensing and regulation involving many transcriptional regulators of interest, highlighting multipronged strategies and novel experimental techniques. The aim of the experiments discussed here was to provide a better understanding at a molecular level of how bacteria adapt to the different environmental threats they face.
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16
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Li M, Reichert P, Narasimhan C, Sorman B, Xu W, Cote A, Su Y. Investigating Crystalline Protein Suspension Formulations of Pembrolizumab from MAS NMR Spectroscopy. Mol Pharm 2022; 19:936-952. [PMID: 35107019 DOI: 10.1021/acs.molpharmaceut.1c00915] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Developing biological formulations to maintain the chemical and structural integrity of therapeutic antibodies remains a significant challenge. Monoclonal antibody (mAb) crystalline suspension formulation is a promising alternative for high concentration subcutaneous drug delivery. It demonstrates many merits compared to the solution formulation to reach a high concentration at the reduced viscosity and enhanced stability. One main challenge in drug development is the lack of high-resolution characterization of the crystallinity and stability of mAb microcrystals in the native formulations. Conventional analytical techniques often cannot evaluate structural details of mAb microcrystals in the native suspension due to the presence of visible particles, relatively small crystal size, high protein concentration, and multicomponent nature of a liquid formulation. This study demonstrates the first high-resolution characterization of mAb microcrystalline suspension using magic angle spinning (MAS) NMR spectroscopy. Crystalline suspension formulation of pembrolizumab (Keytruda, Merck & Co., Inc., Kenilworth, NJ 07033, U.S.) is utilized as a model system. Remarkably narrow 13C spectral linewidth of approximately 29 Hz suggests a high order of crystallinity and conformational homogeneity of pembrolizumab crystals. The impact of thermal stress and dehydration on the structure, dynamics, and stability of these mAb crystals in the formulation environment is evaluated. Moreover, isotopic labeling and heteronuclear 13C and 15N spectroscopies have been utilized to identify the binding of caffeine in the pembrolizumab crystal lattice, providing molecular insights into the cocrystallization of the protein and ligand. Our study provides valuable structural details for facilitating the design of crystalline suspension formulation of Keytruda and demonstrates the high potential of MAS NMR as an advanced tool for biophysical characterization of biological therapeutics.
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Affiliation(s)
- Mingyue Li
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Paul Reichert
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | | | - Bradley Sorman
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Wei Xu
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Aaron Cote
- Biologics Process Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Yongchao Su
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
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17
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Bollati M, Gourlay LJ. Protein Crystallization of Two Recombinant Lpt Proteins. Methods Mol Biol 2022; 2548:249-263. [PMID: 36151502 DOI: 10.1007/978-1-0716-2581-1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The prerequisite for 3D structure determination of macromolecules via X-ray crystallography is well-ordered, diffracting crystals. Here, we report the recombinant production, biophysical/biochemical protein sample characterization, and vapor diffusion sitting drop crystallization protocols for two lipopolysaccharide transport proteins: LptH from Pseudomonas aeruginosa (Pa-LptH) and an inactive LptC mutant (G153R) from Escherichia coli (EcLptC24-191G153R).
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Affiliation(s)
- Michela Bollati
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
- Institute of Biophysics - CNR, Milan, Italy
| | - Louise J Gourlay
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy.
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18
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Seidi F, Yazdi MK, Jouyandeh M, Habibzadeh S, Munir MT, Vahabi H, Bagheri B, Rabiee N, Zarrintaj P, Saeb MR. Crystalline polysaccharides: A review. Carbohydr Polym 2022; 275:118624. [PMID: 34742405 DOI: 10.1016/j.carbpol.2021.118624] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022]
Abstract
The biodegradability and mechanical properties of polysaccharides are dependent on their architecture (linear or branched) as well as their crystallinity (size of crystals and crystallinity percent). The amount of crystalline zones in the polysaccharide significantly governs their ultimate properties and applications (from packaging to biomedicine). Although synthesis, characterization, and properties of polysaccharides have been the subject of several review papers, the effects of crystallization kinetics and crystalline domains on the properties and application have not been comprehensively addressed. This review places focus on different aspects of crystallization of polysaccharides as well as applications of crystalline polysaccharides. Crystallization of cellulose, chitin, chitosan, and starch, as the main members of this family, were discussed. Then, application of the aforementioned crystalline polysaccharides and nano-polysaccharides as well as their physical and chemical interactions were overviewed. This review attempts to provide a complete picture of crystallization-property relationship in polysaccharides.
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Affiliation(s)
- Farzad Seidi
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources and International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China
| | - Mohsen Khodadadi Yazdi
- Center of Excellence in Electrochemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Maryam Jouyandeh
- Center of Excellence in Electrochemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Sajjad Habibzadeh
- Department of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran
| | | | - Henri Vahabi
- Université de Lorraine, CentraleSupélec, LMOPS, F-57000 Metz, France
| | - Babak Bagheri
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Navid Rabiee
- Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran
| | - Payam Zarrintaj
- School of Chemical Engineering, Oklahoma State University, 420 Engineering North, Stillwater, OK 74078, United States
| | - Mohammad Reza Saeb
- Department of Polymer Technology, Faculty of Chemistry, Gdańsk University of Technology, G. Narutowicza 11/12, 80-233 Gdańsk, Poland.
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19
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Stabilizing DNA–Protein Co-Crystals via Intra-Crystal Chemical Ligation of the DNA. CRYSTALS 2021. [DOI: 10.3390/cryst12010049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein and DNA co-crystals are most commonly prepared to reveal structural and functional details of DNA-binding proteins when subjected to X-ray diffraction. However, biomolecular crystals are notoriously unstable in solution conditions other than their native growth solution. To achieve greater application utility beyond structural biology, biomolecular crystals should be made robust against harsh conditions. To overcome this challenge, we optimized chemical DNA ligation within a co-crystal. Co-crystals from two distinct DNA-binding proteins underwent DNA ligation with the carbodiimide crosslinking agent 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) under various optimization conditions: 5′ vs. 3′ terminal phosphate, EDC concentration, EDC incubation time, and repeated EDC dose. This crosslinking and DNA ligation route did not destroy crystal diffraction. In fact, the ligation of DNA across the DNA–DNA junctions was clearly revealed via X-ray diffraction structure determination. Furthermore, crystal macrostructure was fortified. Neither the loss of counterions in pure water, nor incubation in blood serum, nor incubation at low pH (2.0 or 4.5) led to apparent crystal degradation. These findings motivate the use of crosslinked biomolecular co-crystals for purposes beyond structural biology, including biomedical applications.
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20
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Zhao J, Xu H, Lebrette H, Carroni M, Taberman H, Högbom M, Zou X. A simple pressure-assisted method for MicroED specimen preparation. Nat Commun 2021; 12:5036. [PMID: 34413316 PMCID: PMC8377027 DOI: 10.1038/s41467-021-25335-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022] Open
Abstract
Micro-crystal electron diffraction (MicroED) has shown great potential for structure determination of macromolecular crystals too small for X-ray diffraction. However, specimen preparation remains a major bottleneck. Here, we report a simple method for preparing MicroED specimens, named Preassis, in which excess liquid is removed through an EM grid with the assistance of pressure. We show the ice thicknesses can be controlled by tuning the pressure in combination with EM grids with appropriate carbon hole sizes. Importantly, Preassis can handle a wide range of protein crystals grown in various buffer conditions including those with high viscosity, as well as samples with low crystal concentrations. Preassis is a simple and universal method for MicroED specimen preparation, and will significantly broaden the applications of MicroED.
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Affiliation(s)
- Jingjing Zhao
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Marta Carroni
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
- Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Helena Taberman
- Max Delbrück Centrum for Molecular Medicine, Berlin, Germany
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Berlin, Germany
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
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21
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Klijn ME, Hubbuch J. Application of ultraviolet, visible, and infrared light imaging in protein-based biopharmaceutical formulation characterization and development studies. Eur J Pharm Biopharm 2021; 165:319-336. [PMID: 34052429 DOI: 10.1016/j.ejpb.2021.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/29/2021] [Accepted: 05/12/2021] [Indexed: 01/10/2023]
Abstract
Imaging is increasingly more utilized as analytical technology in biopharmaceutical formulation research, with applications ranging from subvisible particle characterization to thermal stability screening and residual moisture analysis. This review offers a comprehensive overview of analytical imaging for scientists active in biopharmaceutical formulation research and development, where it presents the unique information provided by the ultraviolet (UV), visible (Vis), and infrared (IR) sections in the electromagnetic spectrum. The main body of this review consists of an outline of UV, Vis, and IR imaging techniques for several (bio)physical properties that are commonly determined during protein-based biopharmaceutical formulation characterization and development studies. The review concludes with a future perspective of applied imaging within the field of biopharmaceutical formulation research.
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Affiliation(s)
- Marieke E Klijn
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, the Netherlands.
| | - Jürgen Hubbuch
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
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22
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Yazdi MK, Seidi F, Jin Y, Zarrintaj P, Xiao H, Esmaeili A, Habibzadeh S, Saeb MR. Crystallization of Polysaccharides. POLYSACCHARIDES 2021. [DOI: 10.1002/9781119711414.ch13] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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23
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Mesa Restrepo A, Fernando Alzate J, Patiño Gonzalez EB. Bone morphogenetic protein 2: heterologous expression and potential in bone regeneration. ACTUALIDADES BIOLÓGICAS 2021. [DOI: 10.17533/udea.acbi.v43n114a01] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Currently, bone morphogenetic protein 2 (BMP-2) is one of the two osteoinductive growth factors used in medical devices to promote bone formation. Typically, this protein is bought from commercial houses at high rates and in small quantities that are not enough to cover clinical needs. Because of this, it has been proposed that research centers use their own heterologous expression systems to have a constant supply of BMP-2. The aim of this study was to standardize the heterologous expression of BMP-2 and evaluate its osteoinductive activity in vitro. Our procedure for expression and purification was based on recombinant DNA technology using the plasmid pET-28 and IPTG as inductor. After extracting the protein from inclusion bodies, folding it and modifying it via a redox system, we observed via electrophoresis a 26 kDa dimer. We evaluated its osteoinductive activity in myoblastic C2C12 by quantifying enzymatically the activity of alkaline phosphate (ALP) and staining mineralization nodules. ALP activity is proportional to BMP-2 concentration, increasing 90% at 3 µg/mL. These cells form calcium nodules, mineralizing 50% of the area.
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24
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Stohrer C, Horrell S, Meier S, Sans M, von Stetten D, Hough M, Goldman A, Monteiro DCF, Pearson AR. Homogeneous batch micro-crystallization of proteins from ammonium sulfate. Acta Crystallogr D Struct Biol 2021; 77:194-204. [PMID: 33559608 PMCID: PMC7869895 DOI: 10.1107/s2059798320015454] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/21/2020] [Indexed: 01/19/2023] Open
Abstract
The emergence of X-ray free-electron lasers has led to the development of serial macromolecular crystallography techniques, making it possible to study smaller and more challenging crystal systems and to perform time-resolved studies on fast time scales. For most of these studies the desired crystal size is limited to a few micrometres, and the generation of large amounts of nanocrystals or microcrystals of defined size has become a bottleneck for the wider implementation of these techniques. Despite this, methods to reliably generate microcrystals and fine-tune their size have been poorly explored. Working with three different enzymes, L-aspartate α-decarboxylase, copper nitrite reductase and copper amine oxidase, the precipitating properties of ammonium sulfate were exploited to quickly transition from known vapour-diffusion conditions to reproducible, large-scale batch crystallization, circumventing the tedious determination of phase diagrams. Furthermore, the specific ammonium sulfate concentration was used to fine-tune the crystal size and size distribution. Ammonium sulfate is a common precipitant in protein crystallography, making these findings applicable to many crystallization systems to facilitate the production of large amounts of microcrystals for serial macromolecular crystallography experiments.
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Affiliation(s)
- Claudia Stohrer
- Biomedical Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Sam Horrell
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg, CFEL, Building 99, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Susanne Meier
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg, CFEL, Building 99, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Marta Sans
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg, CFEL, Building 99, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - David von Stetten
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Michael Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Adrian Goldman
- Biomedical Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
- Biological and Environmental Sciences, University of Helsinki, Viikinkaari 5, FIN-00014 Helsinki, Finland
| | - Diana C. F. Monteiro
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg, CFEL, Building 99, Luruper Chaussee 149, 22761 Hamburg, Germany
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Arwen R. Pearson
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg, CFEL, Building 99, Luruper Chaussee 149, 22761 Hamburg, Germany
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25
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Mozdzierz NJ, Hong MS, Lee Y, Benisch MHP, Jiang M, Myerson AS, Braatz RD. Tunable protein crystal size distribution via continuous slug-flow crystallization with spatially varying temperature. CrystEngComm 2021. [DOI: 10.1039/d1ce00387a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Under appropriate buffer and pH conditions, the magnitude and dispersion of the product protein crystals were reproducibly manipulated by controlling the spatial temperature along the tube in a continuous tubular crystallizer.
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Affiliation(s)
- Nicholas J. Mozdzierz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Moo Sun Hong
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yongkyu Lee
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- School of Chemical & Biological Engineering, Seoul National University, Seoul, South Korea
| | - Moritz H. P. Benisch
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Chemical & Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Mo Jiang
- Department of Chemical & Life Science Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Allan S. Myerson
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Richard D. Braatz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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26
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Abstract
High-quality crystals are essential to ensure high-resolution structural information. Protein crystals are controlled by many factors, such as pH, temperature, and the ion concentration of crystalline solutions. We previously reported the development of a device dedicated to protein crystallization. In the current study, we have further modified and improved our device. Exposure to external magnetic field leads to alignment of the crystal toward a preferred direction depending on the magnetization energy. Each material has different magnetic susceptibilities depending on the individual direction of their unit crystal cells. One of the strategies to acquire a large crystal entails controlling the nucleation rate. Furthermore, exposure of a crystal to a magnetic field may lead to new morphologies by affecting the crystal volume, shape, and quality.
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27
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Bhalla N, Pan Y, Yang Z, Payam AF. Opportunities and Challenges for Biosensors and Nanoscale Analytical Tools for Pandemics: COVID-19. ACS NANO 2020; 14:7783-7807. [PMID: 32551559 PMCID: PMC7319134 DOI: 10.1021/acsnano.0c04421] [Citation(s) in RCA: 214] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/18/2020] [Indexed: 05/05/2023]
Abstract
Biosensors and nanoscale analytical tools have shown huge growth in literature in the past 20 years, with a large number of reports on the topic of 'ultrasensitive', 'cost-effective', and 'early detection' tools with a potential of 'mass-production' cited on the web of science. Yet none of these tools are commercially available in the market or practically viable for mass production and use in pandemic diseases such as coronavirus disease 2019 (COVID-19). In this context, we review the technological challenges and opportunities of current bio/chemical sensors and analytical tools by critically analyzing the bottlenecks which have hindered the implementation of advanced sensing technologies in pandemic diseases. We also describe in brief COVID-19 by comparing it with other pandemic strains such as that of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) for the identification of features that enable biosensing. Moreover, we discuss visualization and characterization tools that can potentially be used not only for sensing applications but also to assist in speeding up the drug discovery and vaccine development process. Furthermore, we discuss the emerging monitoring mechanism, namely wastewater-based epidemiology, for early warning of the outbreak, focusing on sensors for rapid and on-site analysis of SARS-CoV2 in sewage. To conclude, we provide holistic insights into challenges associated with the quick translation of sensing technologies, policies, ethical issues, technology adoption, and an overall outlook of the role of the sensing technologies in pandemics.
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Affiliation(s)
- Nikhil Bhalla
- Nanotechnology
and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, Shore Road, BT37
0QB Jordanstown, Northern Ireland, United Kingdom
- Healthcare
Technology Hub, Ulster University, Shore Road, BT37 0QB Jordanstown, Northern
Ireland, United Kingdom
| | - Yuwei Pan
- Cranfield
Water Science Institute, Cranfield University, Cranfield, Bedfordshire MK43 0AL, United Kingdom
| | - Zhugen Yang
- Cranfield
Water Science Institute, Cranfield University, Cranfield, Bedfordshire MK43 0AL, United Kingdom
| | - Amir Farokh Payam
- Nanotechnology
and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, Shore Road, BT37
0QB Jordanstown, Northern Ireland, United Kingdom
- Healthcare
Technology Hub, Ulster University, Shore Road, BT37 0QB Jordanstown, Northern
Ireland, United Kingdom
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28
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Jiang X, Han M, Xia Z, Li J, Ruan X, Yan X, Xiao W, He G. Interfacial microdroplet evaporative crystallization on 3D printed regular matrix platform. AIChE J 2020. [DOI: 10.1002/aic.16280] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Xiaobin Jiang
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Engineering Laboratory for Petrochemical Energy‐efficient Separation Technology of Liaoning ProvinceDalian University of Technology Dalian China
| | - Mingguang Han
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Engineering Laboratory for Petrochemical Energy‐efficient Separation Technology of Liaoning ProvinceDalian University of Technology Dalian China
| | - Zeqiu Xia
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Engineering Laboratory for Petrochemical Energy‐efficient Separation Technology of Liaoning ProvinceDalian University of Technology Dalian China
| | - Jin Li
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Engineering Laboratory for Petrochemical Energy‐efficient Separation Technology of Liaoning ProvinceDalian University of Technology Dalian China
| | - Xuehua Ruan
- School of Chemical Engineering at PanjinDalian University of Technology Panjin China
| | - Xiaoming Yan
- School of Chemical Engineering at PanjinDalian University of Technology Panjin China
| | - Wu Xiao
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Engineering Laboratory for Petrochemical Energy‐efficient Separation Technology of Liaoning ProvinceDalian University of Technology Dalian China
| | - Gaohong He
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Engineering Laboratory for Petrochemical Energy‐efficient Separation Technology of Liaoning ProvinceDalian University of Technology Dalian China
- School of Chemical Engineering at PanjinDalian University of Technology Panjin China
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29
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Petrenko DE, Nikolaeva AY, Lazarenko VA, Dorovatovskii PV, Timofeev VI, Vlaskina AV, Korzhenevskiy DA, Mikhailova AG, Rakitina TV. Screening of Conditions that Facilitate Crystallization of Oligopeptidase B from Serratia Proteamaculans by Differential Scanning Fluorimetry. CRYSTALLOGR REP+ 2020. [DOI: 10.1134/s1063774520020170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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Ding J, Zhou Y, Zhu H, Deng M, Gao Y, Yang Y, Huang Z. Characterization of EstZY: A new acetylesterase with 7-aminocephalosporanic acid deacetylase activity from Alicyclobacillus tengchongensis. Int J Biol Macromol 2020; 148:333-341. [DOI: 10.1016/j.ijbiomac.2020.01.151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 12/04/2019] [Accepted: 01/15/2020] [Indexed: 02/03/2023]
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31
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Winegar PH, Hayes OG, McMillan JR, Figg CA, Focia PJ, Mirkin CA. DNA-Directed Protein Packing within Single Crystals. Chem 2020; 6:1007-1017. [PMID: 33709040 DOI: 10.1016/j.chempr.2020.03.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Designed DNA-DNA interactions are investigated for their ability to modulate protein packing within single crystals of mutant green fluorescent proteins (mGFPs) functionalized with a single DNA strand (mGFP-DNA). We probe the effects of DNA sequence, length, and protein-attachment position on the formation and protein packing of mGFP-DNA crystals. Notably, when complementary mGFP-DNA conjugates are introduced to one another, crystals form with nearly identical packing parameters, regardless of sequence if the number of bases is equivalent. DNA complementarity is essential, because experiments with non-complementary sequences produce crystals with different protein arrangements. Importantly, the DNA length and its position of attachment on the protein markedly influence the formation of and protein packing within single crystals. This work shows how designed DNA interactions can be used to influence the growth and packing in X-ray diffraction quality protein single crystals and is thus an important step forward in protein crystal engineering.
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Affiliation(s)
- Peter H Winegar
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Oliver G Hayes
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Janet R McMillan
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - C Adrian Figg
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Pamela J Focia
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
| | - Chad A Mirkin
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,Lead Contact
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32
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Applications of X-ray Powder Diffraction in Protein Crystallography and Drug Screening. CRYSTALS 2020. [DOI: 10.3390/cryst10020054] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Providing fundamental information on intra/intermolecular interactions and physicochemical properties, the three-dimensional structural characterization of biological macromolecules is of extreme importance towards understanding their mechanism of action. Among other methods, X-ray powder diffraction (XRPD) has proved its applicability and efficiency in numerous studies of different materials. Owing to recent methodological advances, this method is now considered a respectable tool for identifying macromolecular phase transitions, quantitative analysis, and determining structural modifications of samples ranging from small organics to full-length proteins. An overview of the XRPD applications and recent improvements related to the study of challenging macromolecules and peptides toward structure-based drug design is discussed. This review congregates recent studies in the field of drug formulation and delivery processes, as well as in polymorph identification and the effect of ligands and environmental conditions upon crystal characteristics. These studies further manifest the efficiency of protein XRPD for quick and accurate preliminary structural characterization.
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33
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Zhang Y, Wang S, Jia Z. In Situ Proteolysis Condition-Induced Crystallization of the XcpVWX Complex in Different Lattices. Int J Mol Sci 2020; 21:ijms21010308. [PMID: 31906428 PMCID: PMC6981927 DOI: 10.3390/ijms21010308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 12/28/2019] [Accepted: 12/29/2019] [Indexed: 12/13/2022] Open
Abstract
Although prevalent in the determination of protein structures; crystallography always has the bottleneck of obtaining high-quality protein crystals for characterizing a wide range of proteins; especially large protein complexes. Stable fragments or domains of proteins are more readily to crystallize; which prompts the use of in situ proteolysis to remove flexible or unstable structures for improving crystallization and crystal quality. In this work; we investigated the effects of in situ proteolysis by chymotrypsin on the crystallization of the XcpVWX complex from the Type II secretion system of Pseudomonas aeruginosa. Different proteolysis conditions were found to result in two distinct lattices in the same crystallization solution. With a shorter chymotrypsin digestion at a lower concentration; the crystals exhibited a P3 hexagonal lattice that accommodates three complex molecules in one asymmetric unit. By contrast; a longer digestion with chymotrypsin of a 10-fold higher concentration facilitated the formation of a compact P212121 orthorhombic lattice with only one complex molecule in each asymmetric unit. The molecules in the hexagonal lattice have shown high atomic displacement parameter values compared with the ones in the orthorhombic lattice. Taken together; our results clearly demonstrate that different proteolysis conditions can result in the generation of distinct lattices in the same crystallization solution; which can be exploited in order to obtain different crystal forms of a better quality
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Affiliation(s)
- Yichen Zhang
- Department of Biomedical and Molecular Sciences, Queen’s University, 18 Stuart Street, Kingston, ON K7L 3N6, Canada;
| | - Shu Wang
- College of Chemistry, Beijing Normal University, 19 Xinjiekou Outer Street, Beijing 100875, China;
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen’s University, 18 Stuart Street, Kingston, ON K7L 3N6, Canada;
- Correspondence: ; Tel.: +86-1-613-533-6277
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34
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Zhu Z, Zhou Q, Sun DW. Measuring and controlling ice crystallization in frozen foods: A review of recent developments. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.05.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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35
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Ambaye ND. Noncovalent structure of SENP1 in complex with SUMO2. Acta Crystallogr F Struct Biol Commun 2019; 75:332-339. [PMID: 31045562 PMCID: PMC6497105 DOI: 10.1107/s2053230x19004266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/28/2019] [Indexed: 02/02/2023] Open
Abstract
SUMOylation is a post-translational modification in which a small ubiquitin-like molecule (SUMO) is appended to substrate proteins and is known to influence myriads of biological processes. A delicate interplay between several families of SUMOylation proteins and their substrates ensures the proper level of SUMOylation required for normal cell function. Among the SUMO proteins, SUMO2 is known to form mono-SUMOylated proteins and engage in poly-SUMO chain formation, while sentrin-specific protease 1 (SENP1) is a key enzyme in regulating both events. Determination of the SENP1-SUMO2 interaction is therefore necessary to better understand SUMOylation. In this regard, the current paper reports the noncovalent structure of SENP1 in complex with SUMO2, which was refined to a resolution of 2.62 Å with R and Rfree values of 22.92% and 27.66%, respectively. The structure shows that SENP1-SUMO2 complex formation is driven largely by polar interactions and limited hydrophobic contacts. The essential C-terminal motif (QQTGG) of SUMO2 is stabilized by a number of specific bonding interactions that enable it to protrude into the catalytic triad of SENP1 and provide the arrangement necessary for maturation of SUMO and deSUMOylation activity. Overall, the structure shows a number of structural details that pinpoint the basis of SENP1-SUMO2 complex formation.
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Affiliation(s)
- Nigus D. Ambaye
- Department of Immune-Oncology, Beckman Research Institute, City of Hope National Medical Center, 1500 East Duarte Road, Duarte, CA 91010, USA
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36
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Ly A, Carrigy NB, Wang H, Harrison M, Sauvageau D, Martin AR, Vehring R, Finlay WH. Atmospheric Spray Freeze Drying of Sugar Solution With Phage D29. Front Microbiol 2019; 10:488. [PMID: 30949139 PMCID: PMC6436606 DOI: 10.3389/fmicb.2019.00488] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/25/2019] [Indexed: 01/11/2023] Open
Abstract
Therapeutic bacteriophages offer a potential alternative approach in the treatment of drug resistant bacteria. In the present study, we examine the ability of atmospheric spray freeze-drying (ASFD) to process bacteriophage D29 into a solid dry formulation. Bacteriophage D29 is of particular interest due to its ability to infect Mycobacterium tuberculosis. A sugar solution containing bacteriophage D29 was sprayed and instantly frozen in a cold chamber. Cold drying gas was then passed through the chamber at a high flow rate and atmospheric pressure. Convective transport combined with the low temperature of the drying gas results in sublimation of ice, yielding a free-flowing, porous powder. The bacteriophages were atmospheric spray freeze-dried in solutions with varying concentrations of trehalose and mannitol. A solution of trehalose and mannitol at a mass ratio of 7:3 and a total mass concentration of 100 mg/mL led to powder with 4.9 ± 0.1% moisture content and an acceptable titer reduction of ∼0.6 logs. In comparison, a pure trehalose solution and a 1:1 ratio of trehalose and mannitol both had titer reductions of >1.5 logs. Spectroscopic analysis showed that trehalose in the powder was amorphous while mannitol completely crystallized during the drying process, both of which are desirable for preserving phage viability and storage in powders. The results highlight the potential for using ASFD as an alternative process in preserving biopharmaceutical products.
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Affiliation(s)
- Alvin Ly
- Department of Engineering, University of Alberta, Edmonton, AB, Canada
| | | | - Hui Wang
- Department of Engineering, University of Alberta, Edmonton, AB, Canada
| | - Melissa Harrison
- Department of Engineering, University of Alberta, Edmonton, AB, Canada
| | - Dominic Sauvageau
- Department of Engineering, University of Alberta, Edmonton, AB, Canada
| | - Andrew R Martin
- Department of Engineering, University of Alberta, Edmonton, AB, Canada
| | - Reinhard Vehring
- Department of Engineering, University of Alberta, Edmonton, AB, Canada
| | - Warren H Finlay
- Department of Engineering, University of Alberta, Edmonton, AB, Canada
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37
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D'Agostino VG, Sighel D, Zucal C, Bonomo I, Micaelli M, Lolli G, Provenzani A, Quattrone A, Adami V. Screening Approaches for Targeting Ribonucleoprotein Complexes: A New Dimension for Drug Discovery. SLAS DISCOVERY 2019; 24:314-331. [PMID: 30616427 DOI: 10.1177/2472555218818065] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNA-binding proteins (RBPs) are pleiotropic factors that control the processing and functional compartmentalization of transcripts by binding primarily to mRNA untranslated regions (UTRs). The competitive and/or cooperative interplay between RBPs and an array of coding and noncoding RNAs (ncRNAs) determines the posttranscriptional control of gene expression, influencing protein production. Recently, a variety of well-recognized and noncanonical RBP domains have been revealed by modern system-wide analyses, underlying an evolving classification of ribonucleoproteins (RNPs) and their importance in governing physiological RNA metabolism. The possibility of targeting selected RNA-protein interactions with small molecules is now expanding the concept of protein "druggability," with new implications for medicinal chemistry and for a deeper characterization of the mechanism of action of bioactive compounds. Here, taking SF3B1, HuR, LIN28, and Musashi proteins as paradigmatic case studies, we review the strategies applied for targeting RBPs, with emphasis on the technological advancements to study protein-RNA interactions and on the requirements of appropriate validation strategies to parallel high-throughput screening (HTS) efforts.
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Affiliation(s)
- Vito Giuseppe D'Agostino
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Denise Sighel
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Chiara Zucal
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Isabelle Bonomo
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Mariachiara Micaelli
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Graziano Lolli
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Alessandro Provenzani
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Alessandro Quattrone
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Valentina Adami
- 2 University of Trento, HTS Core Facility, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
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38
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Stiving AQ, VanAernum ZL, Busch F, Harvey SR, Sarni SH, Wysocki VH. Surface-Induced Dissociation: An Effective Method for Characterization of Protein Quaternary Structure. Anal Chem 2019; 91:190-209. [PMID: 30412666 PMCID: PMC6571034 DOI: 10.1021/acs.analchem.8b05071] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Alyssa Q. Stiving
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Zachary L. VanAernum
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Florian Busch
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Samantha H. Sarni
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
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39
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Microfluidic Technologies and Platforms for Protein Crystallography. Bioanalysis 2019. [DOI: 10.1007/978-981-13-6229-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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40
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Thippeshappa S, George SD, Bankapur A, Chidangil S, Mathur D, Abdul Salam AA. Effect of biocompatible nucleants in rapid crystallization of natural amino acids using a CW Nd:YAG laser. Sci Rep 2018; 8:16018. [PMID: 30375443 PMCID: PMC6207789 DOI: 10.1038/s41598-018-34356-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/12/2018] [Indexed: 11/15/2022] Open
Abstract
Laser-induced crystallization is emerging as an alternative technique to crystallize biomolecules. However, its applications are limited to specific small molecules and some simple proteins, possibly because of the need to use high-intensity, pulsed lasers and relatively long laser irradiation time. Both these factors tend to denature biological molecules. If the laser-intensity and time required to crystallize biomolecules were to be reduced, laser-induced crystallization may well become of widespread utility. We report here the crystallization of nineteen natural amino acids by a laser-induced method in combination with one of three nucleants: aluminum, coconut coir, and peacock feather barbule. We have utilized a low-power, continuous wave (CW) Nd:YAG laser (λ = 1064 nm). The advantages of our method are (i) the use of very small laser powers (60 mW), and (ii) the ability to obtain diffraction quality crystals within a mere few seconds. For most amino acids our method yields several orders of magnitude reduction in crystallization time. The use of biocompatible nucleants like coir fibres and peacock feather barbules are novel; their non-toxic nature may find broad applicability in rapid crystallization of diverse biological molecules.
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Affiliation(s)
- Shilpa Thippeshappa
- Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, 576 104, Karnataka, India
| | - Sajan D George
- Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, 576 104, Karnataka, India.,Centre for Applied Nanosciences, Manipal Academy of Higher Education, Manipal, 576 104, Karnataka, India
| | - Aseefhali Bankapur
- Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, 576 104, Karnataka, India
| | - Santhosh Chidangil
- Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, 576 104, Karnataka, India
| | - Deepak Mathur
- Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, 576 104, Karnataka, India
| | - Abdul Ajees Abdul Salam
- Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, 576 104, Karnataka, India.
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41
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Qi F, Yoneda T, Neya S, Hoshino T. Simulation Time Required for Diminishing the Initial Conformational Deviations among Protein Crystal Structures. J Phys Chem B 2018; 122:8503-8515. [PMID: 30125105 DOI: 10.1021/acs.jpcb.8b04800] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Multiple crystal structures of a single kind of protein can be generally separated into several groups from their conformational deviations. A major factor causing the structural separation is the space group of crystals, in which precipitating agents have a strong influence on the packing of proteins in a crystal. In this study, we examined whether the separated groups of protein crystal structures can be merged into one group by computer simulation without a precipitating agent. The crystal structures of hen egg-white lysozyme (HEWL), myoglobin (Mb), hemoglobin (Hb), and human serum albumin (HSA) were selected as samples for molecular dynamics (MD) simulation. For example, 25 MD simulations were performed for HEWL, with 25 computational models being built from different crystal structures. Cluster analysis was applied to 25 snapshot structures obtained at the same time point from the respective simulation trajectories and the cluster analysis was repeated every 5 ns during the simulations. As a result, the separated cluster groups were basically merged into one group with only a few exceptions. In HEWL, noticeable conformational changes from the crystal structures were observed after heating. The dependence of the simulated structures on the initial crystals was diminished, and all of the clusters were merged into one group at 20 ns of MD simulation. In Mb, all of the clusters were merged into one group at 10 ns. For Hb and HSA, the time necessary for merging the structures became longer. In Hb, the initial group separation gradually became ambiguous after pre-equilibration, and the time required for diminishing the dependence on the crystal structure was 130 ns except for one cluster group. In HSA, 160 ns was necessary for all of the clusters to be merged into one group. These times provide important index for judging the equilibration of protein simulations.
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Affiliation(s)
- Fei Qi
- Graduate School of Pharmaceutical Sciences , Chiba University , Inohana 1-8-1 , Chuo-ku , Chiba 260-8675 , Japan
| | - Tomoki Yoneda
- Graduate School of Pharmaceutical Sciences , Chiba University , Inohana 1-8-1 , Chuo-ku , Chiba 260-8675 , Japan
| | - Saburo Neya
- Graduate School of Pharmaceutical Sciences , Chiba University , Inohana 1-8-1 , Chuo-ku , Chiba 260-8675 , Japan
| | - Tyuji Hoshino
- Graduate School of Pharmaceutical Sciences , Chiba University , Inohana 1-8-1 , Chuo-ku , Chiba 260-8675 , Japan
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42
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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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43
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Russo Krauss I, Ferraro G, Pica A, Márquez JA, Helliwell JR, Merlino A. Principles and methods used to grow and optimize crystals of protein-metallodrug adducts, to determine metal binding sites and to assign metal ligands. Metallomics 2018; 9:1534-1547. [PMID: 28967006 DOI: 10.1039/c7mt00219j] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The characterization of the interactions between biological macromolecules (proteins and nucleic acids) and metal-based drugs is a fundamental prerequisite for understanding their mechanisms of action. X-ray crystallography enables the structural analysis of such complexes with atomic level detail. However, this approach requires the preparation of highly diffracting single crystals, the measurement of diffraction patterns and the structural analysis and interpretation of macromolecule-metal interactions from electron density maps. In this review, we describe principles and methods used to grow and optimize crystals of protein-metallodrug adducts, to determine metal binding sites and to assign and validate metal ligands. Examples from the literature and experience in our own laboratory are provided and key challenges are described, notably crystallization and molecular model refinement against the X-ray diffraction data.
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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, I-80126, Napoli, Italy.
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44
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Vergara A, Caterino M, Merlino A. Raman-markers of X-ray radiation damage of proteins. Int J Biol Macromol 2018; 111:1194-1205. [PMID: 29374529 DOI: 10.1016/j.ijbiomac.2018.01.135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/10/2018] [Accepted: 01/19/2018] [Indexed: 12/25/2022]
Abstract
Despite their high relevance, the mechanisms of X-ray radiation damage on protein structure yet have to be completely established. Here, we used Raman microspectrophotometry to follow X-ray-induced chemical modifications on the structure of the model protein bovine pancreatic ribonuclease (RNase A). The combination of dose-dependent Raman spectra and ultrahigh resolution (eight structures solved using data collected between 0.85 and 1.17 Å resolution on the same single crystal) allowed direct observation of several radiation damage events, including covalent bond breakages and formation of radicals. Our results are relevant for analytical photodamage detection and provide implications for a detailed understanding of the mechanisms of photoproduct formation.
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Affiliation(s)
- Alessandro Vergara
- Department of Chemical Sciences, University of Naples "Federico II", Via Cinthia, Naples I-80126, Italy; CEINGE Biotecnologie Avanzate Scarl, Via G. Salvatore, Napoli, Italy
| | - Marco Caterino
- Department of Chemical Sciences, University of Naples "Federico II", Via Cinthia, Naples I-80126, Italy
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples "Federico II", Via Cinthia, Naples I-80126, Italy.
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45
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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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46
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Abstract
Bovine heart cytochrome c (bCyt c) is an extensively studied hemoprotein of only 104 residues. Due to the existence of isoforms generated by non-enzymatic deaminidation, crystallization of bCyt c is difficult and involves extensive purification and the use of microseeding or the presence of an electric field. Taking advantage of the capacity of cytochrome c (cyt c) to bind anions on its protein surface, the commercially available bCyt c was crystallized without extra purifications, using ammonium sulfate as precipitant and nitrate ions as additives. The structure of the ferric bCyt c in a new crystal form is described and compared with that previously solved at low ionic strength and with those of human and horse cyt c. The overall structure of bCyt c is conserved, while the side chains of several residues that play a role in the interactions of cyt c with its partners have different rotamers in the two structures. The effect of the presence of nitrate ions on the structure of the protein is then evaluated and compared with that observed in the case of ferrous and ferric horse heart cyt c.
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47
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Ahmed H, Lee L, Darmanin C, Yeo LY. A Novel Acoustomicrofluidic Nebulization Technique Yielding New Crystallization Morphologies. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:1602040. [PMID: 29205527 DOI: 10.1002/adma.201602040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 10/13/2017] [Indexed: 05/27/2023]
Abstract
A novel acoustic microfluidic nebulization platform is demonstrated, which, due to its unique ability to access intermediate evaporation rate regimes-significantly faster than that in slow solvent evaporation but considerably below that achieved in spray drying, is capable of producing novel crystal morphologies that have yet to be reported in both model inorganic and organic systems. In addition, the potential for simultaneously encapsulating single crystals within a biodegradable polymeric coating in a single simultaneous step together with the crystallization process as the solvent evaporates during nebulization is briefly shown. The platform not only has the potential to be highly scalable by employing a large number of these low-cost miniature devices in parallel to achieve industrially relevant particle production rates, but could also be advantageous over conventional spray drying in terms of energy utilization, given the tremendous efficiency associated with the high-frequency ultrasonic microdevice as well as its ambient temperature operation.
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Affiliation(s)
- Heba Ahmed
- Micro/Nanophysics Research Laboratory, RMIT University, Melbourne, VIC, 3000, Australia
| | - Lillian Lee
- Micro/Nanophysics Research Laboratory, RMIT University, Melbourne, VIC, 3000, Australia
| | - Connie Darmanin
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, LaTrobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Leslie Y Yeo
- Micro/Nanophysics Research Laboratory, RMIT University, Melbourne, VIC, 3000, Australia
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48
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Ereño-Orbea J, Sicard T, Cui H, Carson J, Hermans P, Julien JP. Structural Basis of Enhanced Crystallizability Induced by a Molecular Chaperone for Antibody Antigen-Binding Fragments. J Mol Biol 2017; 430:322-336. [PMID: 29277294 DOI: 10.1016/j.jmb.2017.12.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 11/30/2017] [Accepted: 12/13/2017] [Indexed: 12/20/2022]
Abstract
Monoclonal antibodies constitute one of the largest groups of drugs to treat cancers and immune disorders, and are guiding the design of vaccines against infectious diseases. Fragments antigen-binding (Fabs) have been preferred over monoclonal antibodies for the structural characterization of antibody-antigen complexes due to their relatively low flexibility. Nonetheless, Fabs often remain challenging to crystallize because of the surface characteristics of complementary determining regions and the residual flexibility in the hinge region between the variable and constant domains. Here, we used a variable heavy-chain (VHH) domain specific for the human kappa light chain to assist in the structure determination of three therapeutic Fabs that were recalcitrant to crystallization on their own. We show that this ligand alters the surface properties of the antibody-ligand complex and lowers its aggregation temperature to favor crystallization. The VHH crystallization chaperone also restricts the flexible hinge of Fabs to a narrow range of angles, and so independently of the variable region. Our findings contribute a valuable approach to antibody structure determination and provide biophysical insight into the principles that govern the crystallization of macromolecules.
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Affiliation(s)
- June Ereño-Orbea
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4
| | - Taylor Sicard
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4; Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Hong Cui
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4
| | - Jacob Carson
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4
| | - Pim Hermans
- BAC, BV, part of Thermo Fisher Scientific, Leiden, the Netherlands
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4; Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8; Department of Immunology, University of Toronto, Toronto, ON, Canada M5S 1A8.
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49
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Poon GG, Lemke T, Peter C, Molinero V, Peters B. Soluble Oligomeric Nucleants: Simulations of Chain Length, Binding Strength, and Volume Fraction Effects. J Phys Chem Lett 2017; 8:5815-5820. [PMID: 29116791 DOI: 10.1021/acs.jpclett.7b02651] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Recent theories and simulations suggest that molecular additives can bind to the surfaces of nuclei, lower the surface energy, and accelerate nucleation. Experiments have shown that oligomeric and polymeric additives can also modify nucleation rates of proteins, ice, and minerals; however, general design principles for oligomeric or polymeric promoters do not yet exist. Here we investigate oligomeric additives for which each segment of the oligomer can bind to surfaces of nuclei. We use semigrand canonical Monte Carlo simulations in a Potts lattice gas model to study the effects of oligomer chain length, volume fraction, and binding strength. We find that increasing each of those parameters lowers the nucleation barrier. At extremely low oligomer concentrations, the nucleation kinetics can be modeled as though each oligomer is a heterogeneous nucleation site in solution.
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Affiliation(s)
- Geoffrey G Poon
- Department of Chemical Engineering, University of California , Santa Barbara, California 93106, United States
| | - Tobias Lemke
- Department of Chemistry, University of Konstanz , Konstanz 78457, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz , Konstanz 78457, Germany
| | - Valeria Molinero
- Department of Chemistry, The University of Utah , Salt Lake City, Utah 84112, United States
| | - Baron Peters
- Department of Chemical Engineering, University of California , Santa Barbara, California 93106, United States
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50
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X-ray diffraction reveals the intrinsic difference in the physical properties of membrane and soluble proteins. Sci Rep 2017; 7:17013. [PMID: 29208950 PMCID: PMC5717104 DOI: 10.1038/s41598-017-17216-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/23/2017] [Indexed: 12/13/2022] Open
Abstract
Membrane proteins are distinguished from soluble proteins by their insertion into biological membranes. This insertion is achieved via a noticeable arrangement of hydrophobic amino acids that are exposed at the surface of the protein, and renders the interaction with the aliphatic tails of lipids more energetically favorable. This important difference between these two categories of proteins is the source of the need for a specific handling of membrane proteins, which transpired in the creation of new tools for their recombinant expression, purification and even crystallization. Following this line, we show here that crystals of membrane proteins display systematically higher diffraction anisotropy than those of soluble proteins. This phenomenon dramatically hampers structure solution and refinement, and has a strong impact on the quality of electron-density maps. A farther search for origins of this phenomenon showed that the type of crystallization, and thus the crystal packing, has no impact on anisotropy, nor does the nature or function of the membrane protein. Membrane proteins fully embedded within the membrane display equal anisotropy compared to the ones with extra membranous domains or fusions with soluble proteins. Overall, these results overturn common beliefs and call for a specific handling of their diffraction data.
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