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Vance TDR. Ice Isn't the Only Crystal in Town: Structure Determination of Ice-Binding Proteins via X-Ray Crystallography. Methods Mol Biol 2024; 2730:35-62. [PMID: 37943449 DOI: 10.1007/978-1-0716-3503-2_3] [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: 11/10/2023]
Abstract
Ice-binding proteins (IBPs) are proteins that have the remarkable ability to bind to ice, and their study has intrigued researchers for decades. This chapter explores the importance of structural biology in understanding IBPs and highlights the significant contributions of IBPs to the field of structural biology. The structures of various IBPs from different organisms have been elucidated, revealing key elements involved in ice binding. Structural biology techniques, including nuclear magnetic resonance (NMR) spectroscopy, transmission electron cryo-microscopy (cryo-EM), and X-ray crystallography, play crucial roles in solving protein structures. This article focuses on X-ray crystallography as a tool for investigating IBP structures, providing insights into its theoretical and practical aspects, experimental workflows, and common pitfalls to avoid.
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Affiliation(s)
- Tyler D R Vance
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
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2
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Banna HA, Das NK, Ojha M, Koirala D. Advances in chaperone-assisted RNA crystallography using synthetic antibodies. BBA ADVANCES 2023; 4:100101. [PMID: 37655005 PMCID: PMC10466895 DOI: 10.1016/j.bbadva.2023.100101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/13/2023] [Accepted: 08/17/2023] [Indexed: 09/02/2023] Open
Abstract
RNA molecules play essential roles in many biological functions, from gene expression regulation, cellular growth, and metabolism to catalysis. They frequently fold into three-dimensional structures to perform their functions. Therefore, determining RNA structure represents a key step for understanding the structure-function relationships and developing RNA-targeted therapeutics. X-ray crystallography remains a method of choice for determining high-resolution RNA structures, but it has been challenging due to difficulties associated with RNA crystallization and phasing. Several natural and synthetic RNA binding proteins have been used to facilitate RNA crystallography. Having unique properties to help crystal packing and phasing, synthetic antibody fragments, specifically the Fabs, have emerged as promising RNA crystallization chaperones, and so far, over a dozen of RNA structures have been solved using this strategy. Nevertheless, multiple steps in this approach need to be improved, including the recombinant expression of these anti-RNA Fabs, to warrant the full potential of these synthetic Fabs as RNA crystallization chaperones. This review highlights the nuts and bolts and recent advances in the chaperone-assisted RNA crystallography approach, specifically emphasizing the Fab antibody fragments as RNA crystallization chaperones.
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Affiliation(s)
- Hasan Al Banna
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Naba Krishna Das
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Manju Ojha
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Deepak Koirala
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
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3
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Martinez NG, Thieker DF, Carey LM, Rasquinha JA, Kistler SK, Kuhlman BA, Campbell SL. Biophysical and Structural Characterization of Novel RAS-Binding Domains (RBDs) of PI3Kα and PI3Kγ. J Mol Biol 2021; 433:166838. [PMID: 33539876 PMCID: PMC8005443 DOI: 10.1016/j.jmb.2021.166838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/26/2020] [Accepted: 01/18/2021] [Indexed: 12/15/2022]
Abstract
Phosphatidylinositol-3-kinases (PI3Ks) are lipid kinases that phosphorylate phosphatidylinositol 4,5-bisphosphate to generate a key lipid second messenger, phosphatidylinositol 3,4,5-bisphosphate. PI3Kα and PI3Kγ require activation by RAS proteins to stimulate signaling pathways that control cellular growth, differentiation, motility and survival. Intriguingly, RAS binding to PI3K isoforms likely differ, as RAS mutations have been identified that discriminate between PI3Kα and PI3Kγ, consistent with low sequence homology (23%) between their RAS binding domains (RBDs). As disruption of the RAS/PI3Kα interaction reduces tumor growth in mice with RAS- and epidermal growth factor receptor driven skin and lung cancers, compounds that interfere with this key interaction may prove useful as anti-cancer agents. However, a structure of PI3Kα bound to RAS is lacking, limiting drug discovery efforts. Expression of full-length PI3K isoforms in insect cells has resulted in low yield and variable activity, limiting biophysical and structural studies of RAS/PI3K interactions. This led us to generate the first RBDs from PI3Kα and PI3Kγ that can be expressed at high yield in bacteria and bind to RAS with similar affinity to full-length PI3K. We also solved a 2.31 Å X-ray crystal structure of the PI3Kα-RBD, which aligns well to full-length PI3Kα. Structural differences between the PI3Kα and PI3Kγ RBDs are consistent with differences in thermal stability and may underly differential RAS recognition and RAS-mediated PI3K activation. These high expression, functional PI3K RBDs will aid in interrogating RAS interactions and could aid in identifying inhibitors of this key interaction.
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Affiliation(s)
- Nicholas G Martinez
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, United States
| | - David F Thieker
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, United States
| | - Leiah M Carey
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, United States
| | - Juhi A Rasquinha
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, United States
| | - Samantha K Kistler
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, United States
| | - Brian A Kuhlman
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, United States
| | - Sharon L Campbell
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, United States.
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4
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Wyatt JW, Korasick DA, Qureshi IA, Campbell AC, Gates KS, Tanner JJ. Inhibition, crystal structures, and in-solution oligomeric structure of aldehyde dehydrogenase 9A1. Arch Biochem Biophys 2020; 691:108477. [PMID: 32717224 DOI: 10.1016/j.abb.2020.108477] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 10/23/2022]
Abstract
Aldehyde dehydrogenase 9A1 (ALDH9A1) is a human enzyme that catalyzes the NAD+-dependent oxidation of the carnitine precursor 4-trimethylaminobutyraldehyde to 4-N-trimethylaminobutyrate. Here we show that the broad-spectrum ALDH inhibitor diethylaminobenzaldehyde (DEAB) reversibly inhibits ALDH9A1 in a time-dependent manner. Possible mechanisms of inhibition include covalent reversible inactivation involving the thiohemiacetal intermediate and slow, tight-binding inhibition. Two crystal structures of ALDH9A1 are reported, including the first of the enzyme complexed with NAD+. One of the structures reveals the active conformation of the enzyme, in which the Rossmann dinucleotide-binding domain is fully ordered and the inter-domain linker adopts the canonical β-hairpin observed in other ALDH structures. The oligomeric structure of ALDH9A1 was investigated using analytical ultracentrifugation, small-angle X-ray scattering, and negative stain electron microscopy. These data show that ALDH9A1 forms the classic ALDH superfamily dimer-of-dimers tetramer in solution. Our results suggest that the presence of an aldehyde substrate and NAD+ promotes isomerization of the enzyme into the active conformation.
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Affiliation(s)
- Jesse W Wyatt
- Department of Chemistry, University of Missouri, Columbia, MO, 65211, United States
| | - David A Korasick
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | - Insaf A Qureshi
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad, 500046, India
| | - Ashley C Campbell
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | - Kent S Gates
- Department of Chemistry, University of Missouri, Columbia, MO, 65211, United States; Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | - John J Tanner
- Department of Chemistry, University of Missouri, Columbia, MO, 65211, United States; Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States.
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5
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Laciak AR, Korasick DA, Gates KS, Tanner JJ. Structural analysis of pathogenic mutations targeting Glu427 of ALDH7A1, the hot spot residue of pyridoxine-dependent epilepsy. J Inherit Metab Dis 2020; 43:635-644. [PMID: 31652343 PMCID: PMC7182499 DOI: 10.1002/jimd.12184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/17/2019] [Accepted: 10/23/2019] [Indexed: 12/11/2022]
Abstract
Certain loss-of-function mutations in the gene encoding the lysine catabolic enzyme aldehyde dehydrogenase 7A1 (ALDH7A1) cause pyridoxine-dependent epilepsy (PDE). Missense mutations of Glu427, especially Glu427Gln, account for ~30% of the mutated alleles in PDE patients, and thus Glu427 has been referred to as a mutation hot spot of PDE. Glu427 is invariant in the ALDH superfamily and forms ionic hydrogen bonds with the nicotinamide ribose of the NAD+ cofactor. Here we report the first crystal structures of ALDH7A1 containing pathogenic mutations targeting Glu427. The mutant enzymes E427Q, Glu427Asp, and Glu427Gly were expressed in Escherichia coli and purified. The recombinant enzymes displayed negligible catalytic activity compared to the wild-type enzyme. The crystal structures of the mutant enzymes complexed with NAD+ were determined to understand how the mutations impact NAD+ binding. In the E427Q and E427G structures, the nicotinamide mononucleotide is highly flexible and lacks a defined binding pose. In E427D, the bound NAD+ adopts a "retracted" conformation in which the nicotinamide ring is too far from the catalytic Cys residue for hydride transfer. Thus, the structures revealed a shared mechanism for loss of function: none of the variants are able to stabilise the nicotinamide of NAD+ in the pose required for catalysis. We also show that these mutations reduce the amount of active tetrameric ALDH7A1 at the concentration of NAD+ tested. Altogether, our results provide the three-dimensional molecular structural basis of the most common pathogenic variants of PDE and implicate strong (ionic) hydrogen bonds in the aetiology of a human disease.
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Affiliation(s)
- Adrian R. Laciak
- Department of Chemistry, University of Missouri, Columbia, Missouri
| | - David A. Korasick
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Kent S. Gates
- Department of Chemistry, University of Missouri, Columbia, Missouri
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - John J. Tanner
- Department of Chemistry, University of Missouri, Columbia, Missouri
- Department of Biochemistry, University of Missouri, Columbia, Missouri
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Suresh V, Sundaram R, Dash P, Sabat SC, Mohapatra D, Mohanty S, Vasudevan D, Senapati S. Macrophage migration inhibitory factor of Syrian golden hamster shares structural and functional similarity with human counterpart and promotes pancreatic cancer. Sci Rep 2019; 9:15507. [PMID: 31664114 PMCID: PMC6820718 DOI: 10.1038/s41598-019-51947-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 10/07/2019] [Indexed: 12/12/2022] Open
Abstract
Macrophage migration inhibitory factor (MIF) is a pleiotropic cytokine that increasingly is being studied in cancers and inflammatory diseases. Though murine models have been instrumental in understanding the functional role of MIF in different pathological conditions, the information obtained from these models is biased towards a specific species. In experimental science, results obtained from multiple clinically relevant animal models always provide convincing data that might recapitulate in humans. Syrian golden hamster (Mesocricetus auratus), is a clinically relevant animal model for multiple human diseases. Hence, the major objectives of this study were to characterize the structure and function of Mesocricetus auratus MIF (MaMIF) and finally evaluate its effect on pancreatic tumor growth in vivo. Initially, the recombinant MaMIF was cloned, expressed and purified in a bacterial expression system. The MaMIF primary sequence, biochemical properties, and crystal structure analysis showed greater similarity with human MIF. The crystal structure of MaMIF illustrates that it forms a homotrimer as known in human and mouse. However, MaMIF exhibits some minor structural variations when compared to human and mouse MIF. The in vitro functional studies show that MaMIF has tautomerase activity and enhances activation and migration of hamster peripheral blood mononuclear cells (PBMCs). Interestingly, injection of MaMIF into HapT1 pancreatic tumor-bearing hamsters significantly enhanced the tumor growth and tumor-associated angiogenesis. Together, the current study shows a structural and functional similarity between the hamster and human MIF. Moreover, it has demonstrated that a high level of circulating MIF originating from non-tumor cells might also promote pancreatic tumor growth in vivo.
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Affiliation(s)
- Voddu Suresh
- Tumor Microenvironment and Animal Models Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India.,Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Rajivgandhi Sundaram
- Macromolecular Crystallography Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India.,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Pujarini Dash
- Tumor Microenvironment and Animal Models Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Surendra Chandra Sabat
- Molecular Biology of Abiotic Stress Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Debasish Mohapatra
- Tumor Microenvironment and Animal Models Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Sneha Mohanty
- Department of Microbiology, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Dileep Vasudevan
- Macromolecular Crystallography Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | - Shantibhusan Senapati
- Tumor Microenvironment and Animal Models Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India.
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Ereño-Orbea J, Sicard T, Cui H, Akula I, Julien JP. Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques. J Vis Exp 2018. [PMID: 30035760 PMCID: PMC6124603 DOI: 10.3791/57750] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Glycoproteins on the surface of cells play critical roles in cellular function, including signalling, adhesion and transport. On leukocytes, several of these glycoproteins possess immunoglobulin (Ig) folds and are central to immune recognition and regulation. Here, we present a platform for the design, expression and biophysical characterization of the extracellular domain of human B cell receptor CD22. We propose that these approaches are broadly applicable to the characterization of mammalian glycoprotein ectodomains containing Ig domains. Two suspension human embryonic kidney (HEK) cell lines, HEK293F and HEK293S, are used to express glycoproteins harbouring complex and high-mannose glycans, respectively. These recombinant glycoproteins with different glycoforms allow investigating the effect of glycan size and composition on ligand binding. We discuss protocols for studying the kinetics and thermodynamics of glycoprotein binding to biologically relevant ligands and therapeutic antibody candidates. Recombinant glycoproteins produced in HEK293S cells are amenable to crystallization due to glycan homogeneity, reduced flexibility and susceptibility to endoglycosidase H treatment. We present methods for soaking glycoprotein crystals with heavy atoms and small molecules for phase determination and analysis of ligand binding, respectively. The experimental protocols discussed here hold promise for the characterization of mammalian glycoproteins to give insight into their function and investigate the mechanism of action of therapeutics.
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Affiliation(s)
- June Ereño-Orbea
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute
| | - Taylor Sicard
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute; Department of Biochemistry, University of Toronto
| | - Hong Cui
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute
| | - Indira Akula
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute; Department of Biochemistry, University of Toronto; Department of Immunology, University of Toronto;
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8
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Handing KB, Niedzialkowska E, Shabalin IG, Kuhn ML, Zheng H, Minor W. Characterizing metal-binding sites in proteins with X-ray crystallography. Nat Protoc 2018; 13:1062-1090. [PMID: 29674755 PMCID: PMC6235626 DOI: 10.1038/nprot.2018.018] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Metals have crucial roles in many physiological, pathological, toxicological, pharmaceutical, and diagnostic processes. Proper handling of metal-containing macromolecule samples for structural studies is not trivial, and failure to handle them properly is often a source of irreproducibility caused by issues such as pH changes, incorporation of unexpected metals, or oxidization/reduction of the metal. This protocol outlines the guidelines and best practices for characterizing metal-binding sites in protein structures and alerts experimenters to potential pitfalls during the preparation and handling of metal-containing protein samples for X-ray crystallography studies. The protocol features strategies for controlling the sample pH and the metal oxidation state, recording X-ray fluorescence (XRF) spectra, and collecting diffraction data sets above and below the corresponding metal absorption edges. This protocol should allow experimenters to gather sufficient evidence to unambiguously determine the identity and location of the metal of interest, as well as to accurately characterize the coordinating ligands in the metal binding environment within the protein. Meticulous handling of metal-containing macromolecule samples as described in this protocol should enhance experimental reproducibility in biomedical sciences, especially in X-ray macromolecular crystallography. For most samples, the protocol can be completed within a period of 7-190 d, most of which (2-180 d) is devoted to growing the crystal. The protocol should be readily understandable to structural biologists, particularly protein crystallographers with an intermediate level of experience.
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Affiliation(s)
- Katarzyna B Handing
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
| | - Ewa Niedzialkowska
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - Heping Zheng
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
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9
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Gorrec F, Löwe J. Automated Protocols for Macromolecular Crystallization at the MRC Laboratory of Molecular Biology. J Vis Exp 2018:55790. [PMID: 29443035 PMCID: PMC5908693 DOI: 10.3791/55790] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
When high quality crystals are obtained that diffract X-rays, the crystal structure may be solved at near atomic resolution. The conditions to crystallize proteins, DNAs, RNAs, and their complexes can however not be predicted. Employing a broad variety of conditions is a way to increase the yield of quality diffraction crystals. Two fully automated systems have been developed at the MRC Laboratory of Molecular Biology (Cambridge, England, MRC-LMB) that facilitate crystallization screening against 1,920 initial conditions by vapor diffusion in nanoliter droplets. Semi-automated protocols have also been developed to optimize conditions by changing the concentrations of reagents, the pH, or by introducing additives that potentially enhance properties of the resulting crystals. All the corresponding protocols will be described in detail and briefly discussed. Taken together, they enable convenient and highly efficient macromolecular crystallization in a multi-user facility, while giving the users control over key parameters of their experiments.
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Affiliation(s)
- Fabrice Gorrec
- Laboratory of Molecular Biology, Medical Research Council;
| | - Jan Löwe
- Laboratory of Molecular Biology, Medical Research Council
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10
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Forneris F, Wu J, Xue X, Ricklin D, Lin Z, Sfyroera G, Tzekou A, Volokhina E, Granneman JC, Hauhart R, Bertram P, Liszewski MK, Atkinson JP, Lambris JD, Gros P. Regulators of complement activity mediate inhibitory mechanisms through a common C3b-binding mode. EMBO J 2016; 35:1133-49. [PMID: 27013439 PMCID: PMC4868954 DOI: 10.15252/embj.201593673] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/29/2016] [Indexed: 01/17/2023] Open
Abstract
Regulators of complement activation (RCA) inhibit complement‐induced immune responses on healthy host tissues. We present crystal structures of human RCA (MCP, DAF, and CR1) and a smallpox virus homolog (SPICE) bound to complement component C3b. Our structural data reveal that up to four consecutive homologous CCP domains (i–iv), responsible for inhibition, bind in the same orientation and extended arrangement at a shared binding platform on C3b. Large sequence variations in CCP domains explain the diverse C3b‐binding patterns, with limited or no contribution of some individual domains, while all regulators show extensive contacts with C3b for the domains at the third site. A variation of ~100° rotation around the longitudinal axis is observed for domains binding at the fourth site on C3b, without affecting the overall binding mode. The data suggest a common evolutionary origin for both inhibitory mechanisms, called decay acceleration and cofactor activity, with variable C3b binding through domains at sites ii, iii, and iv, and provide a framework for understanding RCA disease‐related mutations and immune evasion.
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Affiliation(s)
- Federico Forneris
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science Utrecht University, Utrecht, The Netherlands
| | - Jin Wu
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science Utrecht University, Utrecht, The Netherlands
| | - Xiaoguang Xue
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science Utrecht University, Utrecht, The Netherlands
| | - Daniel Ricklin
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhuoer Lin
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Georgia Sfyroera
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Apostolia Tzekou
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elena Volokhina
- Department of Pediatric Nephrology (830), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joke Cm Granneman
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science Utrecht University, Utrecht, The Netherlands
| | - Richard Hauhart
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO, USA
| | - Paula Bertram
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO, USA
| | - M Kathryn Liszewski
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO, USA
| | - John P Atkinson
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO, USA
| | - John D Lambris
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Piet Gros
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science Utrecht University, Utrecht, The Netherlands
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11
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Shaw Stewart P, Mueller-Dieckmann J. Automation in biological crystallization. Acta Crystallogr F Struct Biol Commun 2014; 70:686-96. [PMID: 24915074 PMCID: PMC4051518 DOI: 10.1107/s2053230x14011601] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 05/20/2014] [Indexed: 11/11/2022] Open
Abstract
Crystallization remains the bottleneck in the crystallographic process leading from a gene to a three-dimensional model of the encoded protein or RNA. Automation of the individual steps of a crystallization experiment, from the preparation of crystallization cocktails for initial or optimization screens to the imaging of the experiments, has been the response to address this issue. Today, large high-throughput crystallization facilities, many of them open to the general user community, are capable of setting up thousands of crystallization trials per day. It is thus possible to test multiple constructs of each target for their ability to form crystals on a production-line basis. This has improved success rates and made crystallization much more convenient. High-throughput crystallization, however, cannot relieve users of the task of producing samples of high quality. Moreover, the time gained from eliminating manual preparations must now be invested in the careful evaluation of the increased number of experiments. The latter requires a sophisticated data and laboratory information-management system. A review of the current state of automation at the individual steps of crystallization with specific attention to the automation of optimization is given.
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Affiliation(s)
- Patrick Shaw Stewart
- Douglas Instruments Ltd, Douglas House, East Garston, Hungerford, Berkshire RG17 7HD, England
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