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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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Guo F, Zhang Y, Howard A, Xu Y. Crystal structure of hetero hexameric 11S seed storage protein of hazelnut. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108653. [PMID: 38670029 DOI: 10.1016/j.plaphy.2024.108653] [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: 11/06/2023] [Revised: 04/11/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024]
Abstract
Edible plant seeds provide a relatively inexpensive source of protein and make up a large part of nutrients for humans. Plant seeds accumulate storage proteins during seed development. Seed storage proteins act as a reserve of nutrition for seed germination and seedling growth. However, seed storage proteins may be allergenic, and the prevalence of food allergy has increased rapidly in recent years. The 11S globulins account for a significant number of known major food allergens. They are of interest to the public and the agricultural industry because of food safety concerns and the need for crop enhancement. We sought to determine the crystal structure of Cor a 9, the 11 S storage protein of hazelnut and a food allergen. The structure was refined to 1.92 Å, and the R and Rfree for the refined structure are 17.6% and 22.5%, respectively. The structure of Cor a 9 showed a hetero hexamer of an 11S seed storage protein for the first time. The hexamer was two trimers associated back-to-back. Two long alpha helixes at the C-terminal end of the acidic domain of one of the Cor a 9 isoforms lay at the trimer-trimer interface's groove. These data provided much-needed information about the allergenicity of the 11S seed proteins. The information may also facilitate a better understanding of the folding and transportation of 11S seed storage proteins.
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Affiliation(s)
- Feng Guo
- Discover Biotherapeutics, Exelixis Inc. 1851 Harbor Bay Parkway, Alameda, CA 94502, USA
| | - Yuzhu Zhang
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA.
| | - Andrew Howard
- Department of Biology, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Yixiang Xu
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
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3
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Dowd S, Lagalante L, Rahlfs J, Sharo C, Opulente D, Lagalante A, Elmer J. Sequencing of the Lumbricus terrestris genome reveals degeneracy in its erythrocruorin genes. Biochimie 2024; 219:130-141. [PMID: 37981225 DOI: 10.1016/j.biochi.2023.11.007] [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: 09/27/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023]
Abstract
The erythrocruorin of Lumbricus terrestris (LtEc) is a relatively large macromolecular assembly that consists of at least four different hemoglobin subunits (A, B, C, and D) and four linker subunits (L1, L2, L3, and L4). The complexity and stability of this large structure make LtEc an attractive hemoglobin-based oxygen carrier that could potentially be used as a substitute for donated red blood cells. However, the sequences of the LtEc subunit sequences must be determined before a scalable recombinant expression platform can be developed. The goal of this study was to sequence the L. terrestris genome to identify the complete sequences of the LtEc subunit genes. Our results revealed multiple homologous genes for each subunit (e.g., two homologous A globin genes; A1 and A2), with the exception of the L4 linker. Some of the homologous genes encoded identical peptide sequences (C1 and C2, L1a and L1b), while cDNA and mass spectrometry experiments revealed that some of the homologs are not expressed (e.g., A2). In contrast, multiple sequences for the B, D, L2, and L4 subunits were detected in LtEc samples. These observations reveal novel degeneracy in LtEc and other annelids, along with some new revisions to its previously published peptide sequences.
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Affiliation(s)
- Sean Dowd
- Department of Chemical and Biological Engineering, Villanova University, 800 E Lancaster Avenue, Villanova, PA, 19085, USA
| | - Luke Lagalante
- Department of Chemical and Biological Engineering, Villanova University, 800 E Lancaster Avenue, Villanova, PA, 19085, USA
| | - Jack Rahlfs
- Department of Chemical and Biological Engineering, Villanova University, 800 E Lancaster Avenue, Villanova, PA, 19085, USA
| | - Catherine Sharo
- Department of Chemical and Biological Engineering, Villanova University, 800 E Lancaster Avenue, Villanova, PA, 19085, USA
| | - Dana Opulente
- Department of Biology, Villanova University, 800 E Lancaster Avenue, Villanova, PA, 19085, USA
| | - Anthony Lagalante
- Department of Chemistry, Villanova University, 800 E Lancaster Avenue, Villanova, PA, 19085, USA
| | - Jacob Elmer
- Department of Chemical and Biological Engineering, Villanova University, 800 E Lancaster Avenue, Villanova, PA, 19085, USA.
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4
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Ding Y, Xue X. Medicinal Chemistry Strategies for the Modification of Bioactive Natural Products. Molecules 2024; 29:689. [PMID: 38338433 PMCID: PMC10856770 DOI: 10.3390/molecules29030689] [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: 12/14/2023] [Revised: 01/17/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
Natural bioactive compounds are valuable resources for drug discovery due to their diverse and unique structures. However, these compounds often lack optimal drug-like properties. Therefore, structural optimization is a crucial step in the drug development process. By employing medicinal chemistry principles, targeted molecular operations can be applied to natural products while considering their size and complexity. Various strategies, including structural fragmentation, elimination of redundant atoms or groups, and exploration of structure-activity relationships, are utilized. Furthermore, improvements in physicochemical properties, chemical and metabolic stability, biophysical properties, and pharmacokinetic properties are sought after. This article provides a concise analysis of the process of modifying a few marketed drugs as illustrative examples.
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Affiliation(s)
- Yuyang Ding
- Shenzhen Borui Pharmaceutical Technology Co., Ltd., Shenzhen 518055, China;
| | - Xiaoqian Xue
- Medi-X Pingshan, Southern University of Science and Technology, Shenzhen 518055, China
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5
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Makita H, Zhang M, Yano J, Kern J. Room temperature crystallography and X-ray spectroscopy of metalloenzymes. Methods Enzymol 2023; 688:307-348. [PMID: 37748830 PMCID: PMC10799221 DOI: 10.1016/bs.mie.2023.07.009] [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] [Indexed: 09/27/2023]
Abstract
The ultrashort (10s of femtoseconds) X-ray pulses generated by X-ray free electron lasers enable the measurement of X-ray diffraction and spectroscopic data from radiation-sensitive metalloenzymes at room temperature while mostly avoiding the effects of radiation damage usually encountered when performing such experiments at synchrotron sources. Here we discuss an approach to measure both X-ray emission and X-ray crystallographic data at the same time from the same sample volume. The droplet-on-tape setup described allows for efficient sample use and the integration of different reaction triggering options in order to conduct time-resolved studies with limited sample amounts. The approach is illustrated by two examples, photosystem II that catalyzes the light-driven oxidation of water to oxygen, and isopenicillin N synthase, an enzyme that catalyzes the double ring cyclization of a tripeptide precursor into the β-lactam isopenicillin and can be activated by oxygen exposure. We describe the necessary steps to obtain microcrystals of both proteins as well as the operation procedure for the drop-on-tape setup and details of the data acquisition and processing involved in this experiment. At the end, we present how the combination of time-resolved X-ray emission spectra and diffraction data can be used to improve the knowledge about the enzyme reaction mechanism.
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Affiliation(s)
- Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Miao Zhang
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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6
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Massera C, Helliwell JR. Golden oldies: ten crystallography articles that we think must be read. Acta Crystallogr E Crystallogr Commun 2023; 79:580-591. [PMID: 37601583 PMCID: PMC10439429 DOI: 10.1107/s2056989023004619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/24/2023] [Indexed: 08/22/2023]
Abstract
We have selected a set of ten 'golden oldies', diverse crystallography articles to illustrate important moments in the development of our field of science and which form landmark papers in crystallography. They are a mixture of 'science pull and technology push'. For each of our choices, we firstly created a new title that emphasizes how the paper's importance worked out from today's perspective. Then we describe the core details and impacts of each paper, with some quotations and a selected figure or two. Ten is an arbitrary number of highlights and our choice is personal.
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Affiliation(s)
- Chiara Massera
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma - Viale delle Scienze 17/A, 43124 Parma, Italy
| | - John R. Helliwell
- Department of Chemistry, University of Manchester, M13 9PL, United Kingdom
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7
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Henkel A, Galchenkova M, Maracke J, Yefanov O, Klopprogge B, Hakanpää J, Mesters JR, Chapman HN, Oberthuer D. JINXED: just in time crystallization for easy structure determination of biological macromolecules. IUCRJ 2023; 10:253-260. [PMID: 36892542 PMCID: PMC10161778 DOI: 10.1107/s2052252523001653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/23/2023] [Indexed: 05/06/2023]
Abstract
Macromolecular crystallography is a well established method in the field of structural biology and has led to the majority of known protein structures to date. After focusing on static structures, the method is now under development towards the investigation of protein dynamics through time-resolved methods. These experiments often require multiple handling steps of the sensitive protein crystals, e.g. for ligand-soaking and cryo-protection. These handling steps can cause significant crystal damage, and hence reduce data quality. Furthermore, in time-resolved experiments based on serial crystallography, which use micrometre-sized crystals for short diffusion times of ligands, certain crystal morphologies with small solvent channels can prevent sufficient ligand diffusion. Described here is a method that combines protein crystallization and data collection in a novel one-step process. Corresponding experiments were successfully performed as a proof-of-principle using hen egg-white lysozyme and crystallization times of only a few seconds. This method, called JINXED (Just IN time Crystallization for Easy structure Determination), promises high-quality data due to the avoidance of crystal handling and has the potential to enable time-resolved experiments with crystals containing small solvent channels by adding potential ligands to the crystallization buffer, simulating traditional co-crystallization approaches.
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Affiliation(s)
- Alessandra Henkel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Julia Maracke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Bjarne Klopprogge
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Johanna Hakanpää
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Jeroen R Mesters
- Institut für Biochemie, Universität zu Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
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8
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Saha S, Özden C, Samkutty A, Russi S, Cohen A, Stratton MM, Perry SL. Polymer-based microfluidic device for on-chip counter-diffusive crystallization and in situ X-ray crystallography at room temperature. LAB ON A CHIP 2023; 23:2075-2090. [PMID: 36942575 PMCID: PMC10631519 DOI: 10.1039/d2lc01194h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Proteins are long chains of amino acid residues that perform a myriad of functions in living organisms, including enzymatic reactions, signalling, and maintaining structural integrity. Protein function is determined directly by the protein structure. X-ray crystallography is the primary technique for determining the 3D structure of proteins, and facilitates understanding the effects of protein structure on function. The first step towards structure determination is crystallizing the protein of interest. We have developed a centrifugally-actuated microfluidic device that incorporates the fluid handling and metering necessary for protein crystallization. Liquid handling takes advantage of surface forces to control fluid flow and enable metering, without the need for any fluidic or pump connections. Our approach requires only the simple steps of pipetting the crystallization reagents into the device followed by either spinning or shaking to set up counter-diffusive protein crystallization trials. The use of thin, UV-curable polymers with a high level of X-ray transparency allows for in situ X-ray crystallography, eliminating the manual handling of fragile protein crystals and streamlining the process of protein structure analysis. We demonstrate the utility of our device using hen egg white lysozyme as a model system, followed by the crystallization and in situ, room temperature structural analysis of the hub domain of calcium-calmodulin dependent kinase II (CaMKIIβ).
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Affiliation(s)
- Sarthak Saha
- Department of Chemical Engineering, University of Massachusetts Amherst, MA 01003, USA.
| | - Can Özden
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA 01003, USA
| | - Alfred Samkutty
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA 01003, USA
| | - Silvia Russi
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aina Cohen
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Margaret M Stratton
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA 01003, USA
| | - Sarah L Perry
- Department of Chemical Engineering, University of Massachusetts Amherst, MA 01003, USA.
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9
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Das D, Deniz AA. Topological Considerations in Biomolecular Condensation. Biomolecules 2023; 13:151. [PMID: 36671536 PMCID: PMC9855981 DOI: 10.3390/biom13010151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/07/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Biomolecular condensation and phase separation are increasingly understood to play crucial roles in cellular compartmentalization and spatiotemporal regulation of cell machinery implicated in function and pathology. A key aspect of current research is to gain insight into the underlying physical mechanisms of these processes. Accordingly, concepts of soft matter and polymer physics, the thermodynamics of mixing, and material science have been utilized for understanding condensation mechanisms of multivalent macromolecules resulting in viscoelastic mesoscopic supramolecular assemblies. Here, we focus on two topological concepts that have recently been providing key mechanistic understanding in the field. First, we will discuss how percolation provides a network-topology-related framework that offers an interesting paradigm to understand the complex networking of dense 'connected' condensate structures and, therefore, their phase behavior. Second, we will discuss the idea of entanglement as another topological concept that has deep roots in polymer physics and important implications for biomolecular condensates. We will first review some historical developments and fundamentals of these concepts, then we will discuss current advancements and recent examples. Our discussion ends with a few open questions and the challenges to address them, hinting at unveiling fresh possibilities for the modification of existing knowledge as well as the development of new concepts relevant to condensate science.
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Affiliation(s)
| | - Ashok A. Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA
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10
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Tessler M, Galen SC, DeSalle R, Schierwater B. Let’s end taxonomic blank slates with molecular morphology. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1016412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many known evolutionary lineages have yet to be described formally due to a lack of traditional morphological characters. This is true for genetically distinctive groups within the amoeboid Placozoa animals, the protists in ponds, and the bacteria that cover nearly everything. These taxonomic tabula rasae, or blank slates, are problematic; without names, communication is hampered and other scientific progress is slowed. We suggest that the morphology of molecules be used to help alleviate this issue. Molecules, such as proteins, have structure. Proteins are even visualizable with X-ray crystallography, albeit more easily detected by and easier to work with using genomic sequencing. Given their structured nature, we believe they should not be considered as anything less than traditional morphology. Protein-coding gene content (presence/absence) can also be used easily with genomic sequences, and is a convenient binary character set. With molecular morphology, we believe that each taxonomic tabula rasa can be solved.
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11
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Blake LI, Cann MJ. Carbon Dioxide and the Carbamate Post-Translational Modification. Front Mol Biosci 2022; 9:825706. [PMID: 35300111 PMCID: PMC8920986 DOI: 10.3389/fmolb.2022.825706] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/03/2022] [Indexed: 01/10/2023] Open
Abstract
Carbon dioxide is essential for life. It is at the beginning of every life process as a substrate of photosynthesis. It is at the end of every life process as the product of post-mortem decay. Therefore, it is not surprising that this gas regulates such diverse processes as cellular chemical reactions, transport, maintenance of the cellular environment, and behaviour. Carbon dioxide is a strategically important research target relevant to crop responses to environmental change, insect vector-borne disease and public health. However, we know little of carbon dioxide’s direct interactions with the cell. The carbamate post-translational modification, mediated by the nucleophilic attack by carbon dioxide on N-terminal α-amino groups or the lysine ɛ-amino groups, is one mechanism by which carbon dioxide might alter protein function to form part of a sensing and signalling mechanism. We detail known protein carbamates, including the history of their discovery. Further, we describe recent studies on new techniques to isolate this problematic post-translational modification.
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12
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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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13
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Helliwell JR. Collecting Experiments. Making Big Data Biology. By Bruno J. Strasser. Chicago University Press, 2019. Pp. 392. Price USD 45.00. ISBN 9780226635040. J Appl Crystallogr 2022. [DOI: 10.1107/s1600576721012140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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14
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Kojima M, Abe S, Ueno T. Engineering of protein crystals for use as solid biomaterials. Biomater Sci 2021; 10:354-367. [PMID: 34928275 DOI: 10.1039/d1bm01752g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein crystals have attracted a great deal of attention as solid biomaterials because they have porous structures created by regular assemblies of proteins. The lattice structures of protein crystals are controlled by designing molecular interfacial interactions via covalent bonds and non-covalent bonds. Protein crystals have been functionalized as templates to immobilize foreign molecules such as metal nanoparticles, metal complexes, and proteins. These hybrid crystals are used as functional materials for catalytic reactions and structural analysis. Furthermore, in-cell protein crystals have been studied extensively, providing progress in rapid protein crystallization and crystallography. This review highlights recent advances in crystal engineering for protein crystallization and generation of solid functional materials both in vitro and within cells.
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Affiliation(s)
- Mariko Kojima
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
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15
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Membrane protein crystallography in the era of modern structural biology. Biochem Soc Trans 2020; 48:2505-2524. [DOI: 10.1042/bst20200066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023]
Abstract
The aim of structural biology has been always the study of biological macromolecules structures and their mechanistic behaviour at molecular level. To achieve its goal, multiple biophysical methods and approaches have become part of the structural biology toolbox. Considered as one of the pillars of structural biology, X-ray crystallography has been the most successful method for solving three-dimensional protein structures at atomic level to date. It is however limited by the success in obtaining well-ordered protein crystals that diffract at high resolution. This is especially true for challenging targets such as membrane proteins (MPs). Understanding structure-function relationships of MPs at the biochemical level is vital for medicine and drug discovery as they play critical roles in many cellular processes. Though difficult, structure determination of MPs by X-ray crystallography has significantly improved in the last two decades, mainly due to many relevant technological and methodological developments. Today, numerous MP crystal structures have been solved, revealing many of their mechanisms of action. Yet the field of structural biology has also been through significant technological breakthroughs in recent years, particularly in the fields of single particle electron microscopy (cryo-EM) and X-ray free electron lasers (XFELs). Here we summarise the most important advancements in the field of MP crystallography and the significance of these developments in the present era of modern structural biology.
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Flandre TD, Hey AS, Spence FJ. Nonclinical Safety Assessment of an Inhaled Formulation of Serelaxin: A Recombinant Human Protein in Rats and Cynomolgus Monkeys ( Macaca fascicularis). Toxicol Pathol 2020; 49:286-295. [PMID: 32815455 DOI: 10.1177/0192623320943129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Serelaxin is a recombinant human relaxin-2 intended for cardiovascular indications. Inhalation was chosen as alternative route to intravenous to allow daily administration for chronic applications and home treatment. A total of 4 short-term studies were conducted in rats and cynomolgus monkeys with inhaled formulation of serelaxin at dose up to 10 mg/kg/d. All rats and cynomolgus macaques receiving serelaxin were exposed to the test item. One rat and approximately 50% of macaques developed immunogenicity, which did not appear to affect exposure. No adverse effect on respiratory function or systemic changes was noted. Both species developed similar microscopic lesions characterized by eosinophilic cell infiltration around bronchi; however, in the rat, this was more pronounced and extended to a perivascular location. In addition, in the rat, serelaxin showed eosinophilic crystalline material associated with macrophages in the alveoli and bronchioles. In macaques, serelaxin induced minimal macrophage infiltrates in alveoli and perivascular/peribronchiolar mononuclear cell infiltrations. The minimal airway eosinophilic/mononuclear inflammatory cell infiltrations were considered to be nonadverse in macaques due to the minimal severity and the lack of any other alterations in the lung parenchyma. In the rat, the presence of eosinophilic crystalline material and macrophage response, characterized as precipitated test article, was considered adverse.
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Affiliation(s)
- Thierry D Flandre
- 98560Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Adam S Hey
- 98560Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Fiona J Spence
- 33413Novartis Institutes for Biomedical Research, Cambridge, MA, USA. Hey is now with the Clinical Pharmacology and Safety Sciences, AstraZeneca, Royston, UK
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Methods for Obtaining Better Diffractive Protein Crystals: From Sample Evaluation to Space Crystallization. CRYSTALS 2020. [DOI: 10.3390/cryst10020078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In this paper, we present a summary on how to obtain protein crystals from which better diffraction images can be produced. In particular, we describe, in detail, quality evaluation of the protein sample, the crystallization conditions and methods, flash-cooling protection of the crystal, and crystallization under a microgravity environment. Our approach to protein crystallization relies on a theoretical understanding of the mechanisms of crystal growth. They are useful not only for space experiments, but also for crystallization in the laboratory.
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Alahuhta M, Himmel ME, Bomble YJ, Lunin VV. Crystallography of Metabolic Enzymes. Methods Mol Biol 2020; 2096:125-139. [PMID: 32720151 DOI: 10.1007/978-1-0716-0195-2_10] [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: 06/11/2023]
Abstract
The metabolic enzymes like any enzymes generally display globular architecture where secondary structure elements and interactions between them preserve the spatial organization of the protein. A typical enzyme features a well-defined active site, designed for selective binding of the reaction substrate and facilitating a chemical reaction converting the substrate into a product. While many chemical reactions could be facilitated using only the functional groups that are found in proteins, the large percentage or intracellular reactions require use of cofactors, varying from single metal ions to relatively large molecules like numerous coenzymes, nucleotides and their derivatives, dinucleotides or hemes. Quite often these large cofactors become important not only for the catalytic function of the enzyme but also for the structural stability of it, as those are buried deep in the enzyme.
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Jeliazkov JR, Robinson AC, García-Moreno E. B, Berger JM, Gray JJ. Toward the computational design of protein crystals with improved resolution. Acta Crystallogr D Struct Biol 2019; 75:1015-1027. [PMID: 31692475 PMCID: PMC6834074 DOI: 10.1107/s2059798319013226] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/26/2019] [Indexed: 11/10/2022] Open
Abstract
Substantial advances have been made in the computational design of protein interfaces over the last 20 years. However, the interfaces targeted by design have typically been stable and high-affinity. Here, we report the development of a generic computational design method to stabilize the weak interactions at crystallographic interfaces. Initially, we analyzed structures reported in the Protein Data Bank to determine whether crystals with more stable interfaces result in higher resolution structures. We found that for 22 variants of a single protein crystallized by a single individual, the Rosetta-calculated `crystal score' correlates with the reported diffraction resolution. We next developed and tested a computational design protocol, seeking to identify point mutations that would improve resolution in a highly stable variant of staphylococcal nuclease (SNase). Using a protocol based on fixed protein backbones, only one of the 11 initial designs crystallized, indicating modeling inaccuracies and forcing us to re-evaluate our strategy. To compensate for slight changes in the local backbone and side-chain environment, we subsequently designed on an ensemble of minimally perturbed protein backbones. Using this strategy, four of the seven designed proteins crystallized. By collecting diffraction data from multiple crystals per design and solving crystal structures, we found that the designed crystals improved the resolution modestly and in unpredictable ways, including altering the crystal space group. Post hoc, in silico analysis of the three observed space groups for SNase showed that the native space group was the lowest scoring for four of six variants (including the wild type), but that resolution did not correlate with crystal score, as it did in the preliminary results. Collectively, our results show that calculated crystal scores can correlate with reported resolution, but that the correlation is absent when the problem is inverted. This outcome suggests that more comprehensive modeling of the crystallographic state is necessary to design high-resolution protein crystals from poorly diffracting crystals.
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Affiliation(s)
| | - Aaron C. Robinson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Bertrand García-Moreno E.
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - James M. Berger
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, Maryland, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jeffrey J. Gray
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, USA
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Design of Experiments As a Tool for Optimization in Recombinant Protein Biotechnology: From Constructs to Crystals. Mol Biotechnol 2019; 61:873-891. [DOI: 10.1007/s12033-019-00218-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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21
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Phan TM, Whitelam S, Schmit JD. Catalystlike role of impurities in speeding layer-by-layer growth. Phys Rev E 2019; 100:042114. [PMID: 31770938 PMCID: PMC8194389 DOI: 10.1103/physreve.100.042114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Indexed: 06/10/2023]
Abstract
Molecular self-assembly is usually done at low supersaturation, leading to low rates of growth, in order to allow time for binding mistakes to anneal. However, such conditions can lead to prohibitively long assembly times where growth proceeds by the slow nucleation of successive layers. Here we use a lattice model of molecular self-assembly to show that growth in this regime can be sped up by impurities, which lower the free-energy cost of layer nucleation. Under certain conditions impurities behave almost as a catalyst in that they are present at high concentration at the surface of the assembling structure, but at low concentration in the bulk of the assembled structure. Extrapolation of our numerics using simple analytic arguments suggests that this mechanism can reduce growth times by orders of magnitude in parameter regimes applicable to molecular systems.
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Affiliation(s)
- Tien M. Phan
- Department of Physics, Kansas State University, Manhattan, KS 66506, USA
| | - Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Jeremy D. Schmit
- Department of Physics, Kansas State University, Manhattan, KS 66506, USA
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Microgravity protein crystallization for drug development: a bold example of public sector entrepreneurship. JOURNAL OF TECHNOLOGY TRANSFER 2019. [DOI: 10.1007/s10961-019-09743-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Salis C, Papakonstantinou E, Pierouli K, Mitsis A, Basdeki L, Megalooikonomou V, Vlachakis D, Hagidimitriou M. A genomic data mining pipeline for 15 species of the genus Olea. ACTA ACUST UNITED AC 2019; 24. [PMID: 31218210 DOI: 10.14806/ej.24.0.922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In the big data era, conventional bioinformatics seems to fail in managing the full extent of the available genomic information. The current study is focused on olive tree species and the collection and analysis of genetic and genomic data, which are fragmented in various depositories. Extra virgin olive oil is classified as a medical food, due to nutraceutical benefits and its protective properties against cancer, cardiovascular diseases, age-related diseases, neurodegenerative disorders, and many other diseases. Extensive studies have reported the benefits of olive oil on human health. However, available data at the nucleotide sequence level are highly unstructured. Towards this aim, we describe an in-silico approach that combines methods from data mining and machine learning pipelines to ontology classification and semantic annotation. Fusing and analysing all available olive tree data is a step of uttermost importance in classifying and characterising the various cultivars, towards a comprehensive approach under the context of food safety and public health.
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Affiliation(s)
- Constantinos Salis
- Laboratory of Genetics, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
| | - Katerina Pierouli
- Laboratory of Genetics, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
| | - Athanasios Mitsis
- Laboratory of Genetics, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
| | - Lia Basdeki
- Laboratory of Genetics, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
| | - Vasileios Megalooikonomou
- Computer Engineering and Informatics Department, School of Engineering, University of Patras, Patras, Greece
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece.,Lab of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.,Department of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, London, United Kingdom
| | - Marianna Hagidimitriou
- Laboratory of Genetics, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
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Safronov V, Krivonogova N, Bezbakh I, Strelov V. Temperature-induced nucleation and growth of protein single crystals. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.04.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Abstract
This study reports the first experimental evidence of using DNA as a polymeric additive to enhance protein crystallization. Using three kinds of DNA with different molecular weights—calf DNA, salmon DNA, and herring DNA—this study showed an improvement in the success rate of lysozyme crystallization, as compared to control experiments, especially at low lysozyme concentration. The improvement of crystallization is particularly significant in the presence of calf DNA with the highest molecular weight. Calf DNA also speeds up the induction time of lysozyme crystallization and increases the number of crystals per drop. We hypothesized the effect of DNA on protein crystallization may be due to the combination of excluded volume effect, change of water’s surface tension, and the water competition effect. This work confirms predications of the potential use of DNA as a polymeric additive to enhance protein crystallization, potentially applied to systems with limited protein available or difficult to crystallize.
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Leonarski F, D'Ascenzo L, Auffinger P. Nucleobase carbonyl groups are poor Mg 2+ inner-sphere binders but excellent monovalent ion binders-a critical PDB survey. RNA (NEW YORK, N.Y.) 2019; 25:173-192. [PMID: 30409785 PMCID: PMC6348993 DOI: 10.1261/rna.068437.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/16/2018] [Indexed: 05/04/2023]
Abstract
Precise knowledge of Mg2+ inner-sphere binding site properties is vital for understanding the structure and function of nucleic acid systems. Unfortunately, the PDB, which represents the main source of Mg2+ binding sites, contains a substantial number of assignment issues that blur our understanding of the functions of these ions. Here, following a previous study devoted to Mg2+ binding to nucleobase nitrogens, we surveyed nucleic acid X-ray structures from the PDB with resolutions ≤2.9 Å to classify the Mg2+ inner-sphere binding patterns to nucleotide carbonyl, ribose hydroxyl, cyclic ether, and phosphodiester oxygen atoms. From this classification, we derived a set of "prior-knowledge" nucleobase Mg2+ binding sites. We report that crystallographic examples of trustworthy nucleobase Mg2+ binding sites are fewer than expected since many of those are associated with misidentified Na+ or K+ We also emphasize that binding of Na+ and K+ to nucleic acids is much more frequent than anticipated. Overall, we provide evidence derived from X-ray structures that nucleobases are poor inner-sphere binders for Mg2+ but good binders for monovalent ions. Based on strict stereochemical criteria, we propose an extended set of guidelines designed to help in the assignment and validation of ions directly contacting nucleobase and ribose atoms. These guidelines should help in the interpretation of X-ray and cryo-EM solvent density maps. When borderline Mg2+ stereochemistry is observed, alternative placement of Na+, K+, or Ca2+ must be considered. We also critically examine the use of lanthanides (Yb3+, Tb3+) as Mg2+ substitutes in crystallography experiments.
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Affiliation(s)
- Filip Leonarski
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
| | - Luigi D'Ascenzo
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
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Kordonskaya YV, Timofeev VI, Dyakova YA, Marchenkova MA, Pisarevsky YV, Podshivalov DD, Kovalchuk MV. Study of the Behavior of Lysozyme Oligomers in Solutions by the Molecular Dynamics Method. CRYSTALLOGR REP+ 2018. [DOI: 10.1134/s1063774518060196] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Ferreira J, Castro F, Rocha F, Kuhn S. Protein crystallization in a droplet-based microfluidic device: Hydrodynamic analysis and study of the phase behaviour. Chem Eng Sci 2018. [DOI: 10.1016/j.ces.2018.06.066] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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30
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Abstract
This paper reviews investigations on protein crystallization. It aims to present a comprehensive rather than complete account of recent studies and efforts to elucidate the most intimate mechanisms of protein crystal nucleation. It is emphasized that both physical and biochemical factors are at play during this process. Recently-discovered molecular scale pathways for protein crystal nucleation are considered first. The bond selection during protein crystal lattice formation, which is a typical biochemically-conditioned peculiarity of the crystallization process, is revisited. Novel approaches allow us to quantitatively describe some protein crystallization cases. Additional light is shed on the protein crystal nucleation in pores and crevices by employing the so-called EBDE method (equilibration between crystal bond and destructive energies). Also, protein crystal nucleation in solution flow is considered.
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Srivastava A, Nagai T, Srivastava A, Miyashita O, Tama F. Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics. Int J Mol Sci 2018; 19:E3401. [PMID: 30380757 PMCID: PMC6274748 DOI: 10.3390/ijms19113401] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/20/2018] [Accepted: 10/27/2018] [Indexed: 12/13/2022] Open
Abstract
Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.
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Affiliation(s)
- Ashutosh Srivastava
- Institute of Transformative Bio-Molecules (WPI), Nagoya University, Nagoya, Aichi 464-8601, Japan.
| | - Tetsuro Nagai
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.
| | - Arpita Srivastava
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.
| | - Osamu Miyashita
- RIKEN-Center for Computational Science, Kobe, Hyogo 650-0047, Japan.
| | - Florence Tama
- Institute of Transformative Bio-Molecules (WPI), Nagoya University, Nagoya, Aichi 464-8601, Japan.
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.
- RIKEN-Center for Computational Science, Kobe, Hyogo 650-0047, Japan.
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Bifunctional cross-linking approaches for mass spectrometry-based investigation of nucleic acids and protein-nucleic acid assemblies. Methods 2018; 144:64-78. [PMID: 29753003 DOI: 10.1016/j.ymeth.2018.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/30/2018] [Accepted: 05/04/2018] [Indexed: 12/13/2022] Open
Abstract
With the goal of expanding the very limited toolkit of cross-linking agents available for nucleic acids and their protein complexes, we evaluated the merits of a wide range of bifunctional agents that may be capable of reacting with the functional groups characteristic of these types of biopolymers. The survey specifically focused on the ability of test reagents to produce desirable inter-molecular conjugates, which could reveal the identity of interacting components and the position of mutual contacts, while also considering a series of practical criteria for their utilization as viable nucleic acid probes. The survey employed models consisting of DNA, RNA, and corresponding protein complexes to mimic as close as possible typical applications. Denaturing polyacrylamide gel electrophoresis (PAGE) and mass spectrometric (MS) analyses were implemented in concert to monitor the formation of the desired conjugates. In particular, the former was used as a rapid and inexpensive tool for the efficient evaluation of cross-linker activity under a broad range of experimental conditions. The latter was applied after preliminary rounds of reaction optimization to enable full-fledged product characterization and, more significantly, differentiation between mono-functional and intra- versus inter-molecular conjugates. This information provided the feedback necessary to further optimize reaction conditions and explain possible outcomes. Among the reagents tested in the study, platinum complexes and nitrogen mustards manifested the most favorable characteristics for practical cross-linking applications, whereas other compounds provided inferior yields, or produced rather unstable conjugates that did not survive the selected analytical conditions. The observed outcomes will help guide the selection of the most appropriate cross-linking reagent for a specific task, whereas the experimental conditions described here will provide an excellent starting point for approaching these types of applications. As a whole, the results of the survey clearly emphasize that finding a universal reagent, which may afford excellent performance with all types of nucleic acid substrates, will require extending the exploration beyond the traditional chemistries employed to modify the constitutive functional groups of these vital biopolymers.
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Safronov VV, Krivonogova NV, Strelov VI. Temperature Control of Protein Crystal Nucleation. CRYSTALLOGR REP+ 2018. [DOI: 10.1134/s1063774518020232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Mirabelli V, Majidi Salehi S, Angiolillo L, Belviso BD, Conte A, Del Nobile MA, Di Profio G, Caliandro R. Enzyme Crystals and Hydrogel Composite Membranes as New Active Food Packaging Material. GLOBAL CHALLENGES (HOBOKEN, NJ) 2018; 2:1700089. [PMID: 31565305 PMCID: PMC6607345 DOI: 10.1002/gch2.201700089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/01/2017] [Indexed: 06/10/2023]
Abstract
The great antimicrobial and antioxidant potential of enzymes makes them prone to be used as active packaging materials to preserve food from contamination or degradation. Major drawbacks are connected to the use of enzymes freely dispersed in solution, due to reduced protein stability. The immobilization of enzymes on solid supports to create biocatalytic interfaces has instead been proven to increase their stability and efficiency. In this work, it is shown that enzymes crystallized on hydrogel composite membranes (HCMs) can exert an effective antimicrobial action, thus making the composite membrane and crystals biofilm a potential active substrate for food packaging applications. The antimicrobial hen egg white lysozyme is crystallized on the surface of the hydrogel layer of HCMs, and its activity is determined by measuring the decrease in absorbance of Micrococcus lysodeikticus culture incubated with the specimen. The overall catalytic efficiency of the antimicrobial HCMs increases by a factor of 2 compared to the pure enzyme dissolved in solution at the same quantity. Because the enzyme in crystalline form is present in higher concentration and purity than in the solution, both its overall catalytic efficiency and antimicrobial action increase. Moreover, the hydrogel environment allows a better protein stabilization and retention during crystals dissolution.
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Affiliation(s)
- Valentina Mirabelli
- Institute of Crystallography (IC)National Research Council of Italy (CNR)via G. Amendola 122/o70126BariItaly
- Department of EconomicsUniversity of FoggiaLargo Papa Giovanni Paolo II, 171121FoggiaItaly
| | - Shabnam Majidi Salehi
- National Research Council of Italy (CNR) – Institute on Membrane Technology (ITM)via P. Bucci Cubo 17/C87036Rende (CS)Italy
| | - Luisa Angiolillo
- Department of Agricultural SciencesUniversity of FoggiaFood and Environment – Via Napoli 2571121FoggiaItaly
| | - Benny Danilo Belviso
- Institute of Crystallography (IC)National Research Council of Italy (CNR)via G. Amendola 122/o70126BariItaly
| | - Amalia Conte
- Department of Agricultural SciencesUniversity of FoggiaFood and Environment – Via Napoli 2571121FoggiaItaly
| | | | - Gianluca Di Profio
- National Research Council of Italy (CNR) – Institute on Membrane Technology (ITM)via P. Bucci Cubo 17/C87036Rende (CS)Italy
| | - Rocco Caliandro
- Institute of Crystallography (IC)National Research Council of Italy (CNR)via G. Amendola 122/o70126BariItaly
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Islam MM, Kuroda Y. A hetero-micro-seeding strategy for readily crystallizing closely related protein variants. Biochem Biophys Res Commun 2017; 493:504-508. [DOI: 10.1016/j.bbrc.2017.08.161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 08/31/2017] [Indexed: 10/18/2022]
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Holcomb J, Spellmon N, Zhang Y, Doughan M, Li C, Yang Z. Protein crystallization: Eluding the bottleneck of X-ray crystallography. AIMS BIOPHYSICS 2017; 4:557-575. [PMID: 29051919 PMCID: PMC5645037 DOI: 10.3934/biophy.2017.4.557] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
To date, X-ray crystallography remains the gold standard for the determination of macromolecular structure and protein substrate interactions. However, the unpredictability of obtaining a protein crystal remains the limiting factor and continues to be the bottleneck in determining protein structures. A vast amount of research has been conducted in order to circumvent this issue with limited success. No single method has proven to guarantee the crystallization of all proteins. However, techniques using antibody fragments, lipids, carrier proteins, and even mutagenesis of crystal contacts have been implemented to increase the odds of obtaining a crystal with adequate diffraction. In addition, we review a new technique using the scaffolding ability of PDZ domains to facilitate nucleation and crystal lattice formation. Although in its infancy, such technology may be a valuable asset and another method in the crystallography toolbox to further the chances of crystallizing problematic proteins.
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Affiliation(s)
- Joshua Holcomb
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA
| | - Nicholas Spellmon
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA
| | - Yingxue Zhang
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA
| | - Maysaa Doughan
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA
| | - Chunying Li
- Center for Molecular and Translational Medicine, Georgia State University, Atlanta, GA, USA
| | - Zhe Yang
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA
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Safari MS, Byington MC, Conrad JC, Vekilov PG. Polymorphism of Lysozyme Condensates. J Phys Chem B 2017; 121:9091-9101. [DOI: 10.1021/acs.jpcb.7b05425] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mohammad S. Safari
- Department
of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, Texas 77204-4004, United States
| | - Michael C. Byington
- Department
of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, Texas 77204-4004, United States
| | - Jacinta C. Conrad
- Department
of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, Texas 77204-4004, United States
| | - Peter G. Vekilov
- Department
of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, Texas 77204-4004, United States
- Department
of Chemistry, University of Houston, 3585 Cullen Blvd., Houston, Texas 77204-5003, United States
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38
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Giegé R. What macromolecular crystallogenesis tells us - what is needed in the future. IUCRJ 2017; 4:340-349. [PMID: 28875021 PMCID: PMC5571797 DOI: 10.1107/s2052252517006595] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 05/02/2017] [Indexed: 05/05/2023]
Abstract
Crystallogenesis is a longstanding topic that has transformed into a discipline that is mainly focused on the preparation of crystals for practising crystallo-graphers. Although the idiosyncratic features of proteins have to be taken into account, the crystallization of proteins is governed by the same physics as the crystallization of inorganic materials. At present, a diversified panel of crystallization methods adapted to proteins has been validated, and although only a few methods are in current practice, the success rate of crystallization has increased constantly, leading to the determination of ∼105 X-ray structures. These structures reveal a huge repertoire of protein folds, but they only cover a restricted part of macromolecular diversity across the tree of life. In the future, crystals representative of missing structures or that will better document the structural dynamics and functional steps underlying biological processes need to be grown. For the pertinent choice of biologically relevant targets, computer-guided analysis of structural databases is needed. From another perspective, crystallization is a self-assembly process that can occur in the bulk of crowded fluids, with crystals being supramolecular assemblies. Life also uses self-assembly and supramolecular processes leading to transient, or less often stable, complexes. An integrated view of supramolecularity implies that proteins crystallizing either in vitro or in vivo or participating in cellular processes share common attributes, notably determinants and antideterminants that favour or disfavour their correct or incorrect associations. As a result, under in vivo conditions proteins show a balance between features that favour or disfavour association. If this balance is broken, disorders/diseases occur. Understanding crystallization under in vivo conditions is a challenge for the future. In this quest, the analysis of packing contacts and contacts within oligomers will be crucial in order to decipher the rules governing protein self-assembly and will guide the engineering of novel biomaterials. In a wider perspective, understanding such contacts will open the route towards supramolecular biology and generalized crystallogenesis.
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Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l’ARN, UPR 9002, Université de Strasbourg and CNRS, F-67084 Strasbourg, France
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39
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Hegde RP, Pavithra GC, Dey D, Almo SC, Ramakumar S, Ramagopal UA. Can the propensity of protein crystallization be increased by using systematic screening with metals? Protein Sci 2017. [PMID: 28643473 DOI: 10.1002/pro.3214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein crystallization is one of the major bottlenecks in protein structure elucidation with new strategies being constantly developed to improve the chances of crystallization. Generally, well-ordered epitopes possessing complementary surface and capable of producing stable inter-protein interactions generate a regular three-dimensional arrangement of protein molecules which eventually results in a crystal lattice. Metals, when used for crystallization, with their various coordination numbers and geometries, can generate such epitopes mediating protein oligomerization and/or establish crystal contacts. Some examples of metal-mediated oligomerization and crystallization together with our experience on metal-mediated crystallization of a putative rRNA methyltransferase from Sinorhizobium meliloti are presented. Analysis of crystal structures from protein data bank (PDB) using a non-redundant data set with a 90% identity cutoff, reveals that around 67% of proteins contain at least one metal ion, with ∼14% containing combination of metal ions. Interestingly, metal containing conditions in most commercially available and popular crystallization kits generally contain only a single metal ion, with combinations of metals only in a very few conditions. Based on the results presented in this review, it appears that the crystallization screens need expansion with systematic screening of metal ions that could be crucial for stabilizing the protein structure or for establishing crystal contact and thereby aiding protein crystallization.
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Affiliation(s)
- Raghurama P Hegde
- Division of Biological Sciences, Poornaprajna Institute of Scientific Research, Bangalore, 560080, India
| | - Gowribidanur C Pavithra
- Division of Biological Sciences, Poornaprajna Institute of Scientific Research, Bangalore, 560080, India
- Manipal University, Manipal, 576104, India
| | - Debayan Dey
- Division of Biological Sciences, Poornaprajna Institute of Scientific Research, Bangalore, 560080, India
- Department of Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, 10461
- Department of Physiology & Biophysics, Albert Einstein College of Medicine, Bronx, New York, 10461
| | - S Ramakumar
- Department of Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Udupi A Ramagopal
- Division of Biological Sciences, Poornaprajna Institute of Scientific Research, Bangalore, 560080, India
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, 10461
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40
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Jiang X, Tuo L, Lu D, Hou B, Chen W, He G. Progress in membrane distillation crystallization: Process models, crystallization control and innovative applications. Front Chem Sci Eng 2017. [DOI: 10.1007/s11705-017-1649-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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41
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Locating and Visualizing Crystals for X-Ray Diffraction Experiments. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2017; 1607:143-164. [PMID: 28573572 DOI: 10.1007/978-1-4939-7000-1_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Macromolecular crystallography has advanced from using macroscopic crystals, which might be >1 mm on a side, to crystals that are essentially invisible to the naked eye, or even under a standard laboratory microscope. As crystallography requires recognizing crystals when they are produced, and then placing them in an X-ray, electron, or neutron beam, this provides challenges, particularly in the case of advanced X-ray sources, where beams have very small cross sections and crystals may be vanishingly small. Methods for visualizing crystals are reviewed here, and examples of different types of cases are presented, including: standard crystals, crystals grown in mesophase, in situ crystallography, and crystals grown for X-ray Free Electron Laser or Micro Electron Diffraction experiments. As most techniques have limitations, it is desirable to have a range of complementary techniques available to identify and locate crystals. Ideally, a given technique should not cause sample damage, but sometimes it is necessary to use techniques where damage can only be minimized. For extreme circumstances, the act of probing location may be coincident with collecting X-ray diffraction data. Future challenges and directions are also discussed.
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42
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König N, Paulus M, Julius K, Schulze J, Voetz M, Tolan M. Antibodies under pressure: A Small-Angle X-ray Scattering study of Immunoglobulin G under high hydrostatic pressure. Biophys Chem 2017. [PMID: 28622937 DOI: 10.1016/j.bpc.2017.05.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
In the present work two subclasses of the human antibody Immunoglobulin G (IgG) have been investigated by Small-Angle X-ray Scattering under high hydrostatic pressures up to 5kbar. It is shown that IgG adopts a symmetric T-shape in solution which differs significantly from available crystal structures. Moreover, high-pressure experiments verify the high stability of the IgG molecule. It is not unfolded by hydrostatic pressures of up to 5kbar but a slight increase of the radius of gyration was observed at elevated pressures.
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Affiliation(s)
- Nico König
- Fakultät Physik/DELTA, TU Dortmund, Dortmund 44221, Germany; Bayer AG, Leverkusen 51368, Germany.
| | - Michael Paulus
- Fakultät Physik/DELTA, TU Dortmund, Dortmund 44221, Germany
| | - Karin Julius
- Fakultät Physik/DELTA, TU Dortmund, Dortmund 44221, Germany
| | - Julian Schulze
- Fakultät Physik/DELTA, TU Dortmund, Dortmund 44221, Germany
| | | | - Metin Tolan
- Fakultät Physik/DELTA, TU Dortmund, Dortmund 44221, Germany
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Liang YR, Zhu LN, Gao J, Zhao HX, Zhu Y, Ye S, Fang Q. 3D-Printed High-Density Droplet Array Chip for Miniaturized Protein Crystallization Screening under Vapor Diffusion Mode. ACS APPLIED MATERIALS & INTERFACES 2017; 9:11837-11845. [PMID: 28306245 DOI: 10.1021/acsami.6b15933] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Here we describe the combination of three-dimensional (3D) printed chip and automated microfluidic droplet-based screening techniques for achieving massively parallel, nanoliter-scale protein crystallization screening under vapor diffusion mode. We fabricated high-density microwell array chips for sitting-drop vapor diffusion crystallization utilizing the advantage of the 3D-printing technique in producing high-aspect-ratio chips. To overcome the obstacle of 3D-printed microchips in performing long-term reactions caused by their porousness and gas permeability properties in chip body, we developed a two-step postprocessing method, including paraffin filling and parylene coating, to achieve high sealability and stability. We also developed a simple method especially suitable for controlling the vapor diffusion speed of nanoliter-scale droplets by changing the layer thickness of covering oil. With the above methods, 84 tests of nanoliter-scale protein crystallization under vapor diffusion mode were successfully achieved in the 7 × 12 droplet array chip with a protein consumption of 10 nL for each test, which is 20-100 times lower than that in the conventional large-volume screening system. Such a nanoliter-scale vapor diffusion system was applied to two model proteins with commercial precipitants and displayed advantages over that under microbatch mode. It identified more crystallization conditions, especially for the protein samples with lower concentrations.
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Affiliation(s)
- Yi-Ran Liang
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network, and ‡Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University , Hangzhou, 310058, China
| | - Li-Na Zhu
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network, and ‡Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University , Hangzhou, 310058, China
| | - Jie Gao
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network, and ‡Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University , Hangzhou, 310058, China
| | - Hong-Xia Zhao
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network, and ‡Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University , Hangzhou, 310058, China
| | - Ying Zhu
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network, and ‡Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University , Hangzhou, 310058, China
| | - Sheng Ye
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network, and ‡Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University , Hangzhou, 310058, China
| | - Qun Fang
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network, and ‡Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University , Hangzhou, 310058, China
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44
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Leonarski F, D'Ascenzo L, Auffinger P. Mg2+ ions: do they bind to nucleobase nitrogens? Nucleic Acids Res 2017; 45:987-1004. [PMID: 27923930 PMCID: PMC5314772 DOI: 10.1093/nar/gkw1175] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 11/10/2016] [Accepted: 11/14/2016] [Indexed: 01/28/2023] Open
Abstract
Given the many roles proposed for Mg2+ in nucleic acids, it is essential to accurately determine their binding modes. Here, we surveyed the PDB to classify Mg2+ inner-sphere binding patterns to nucleobase imine N1/N3/N7 atoms. Among those, purine N7 atoms are considered to be the best nucleobase binding sites for divalent metals. Further, Mg2+ coordination to N7 has been implied in several ribozyme catalytic mechanisms. We report that Mg2+ assigned near imine nitrogens derive mostly from poor interpretations of electron density patterns and are most often misidentified Na+, K+, NH4+ ions, water molecules or spurious density peaks. Consequently, apart from few documented exceptions, Mg2+ ions do not bind to N7 atoms. Without much of a surprise, Mn2+, Zn2+ and Cd2+, which have a higher affinity for nitrogens, may contact N7 atoms when present in crystallization buffers. In this respect, we describe for the first time a potential Zn2+ ribosomal binding site involving two purine N7 atoms. Further, we provide a set of guidelines to help in the assignment of Mg2+ in crystallographic, cryo-EM, NMR and model building practices and discuss implications of our findings related to ion substitution experiments.
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Affiliation(s)
- Filip Leonarski
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Luigi D'Ascenzo
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France
| | - Pascal Auffinger
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France
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45
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Zalewski JK, Heber S, Mo JH, O'Conor K, Hildebrand JD, VanDemark AP. Combining Wet and Dry Lab Techniques to Guide the Crystallization of Large Coiled-coil Containing Proteins. J Vis Exp 2017. [PMID: 28117766 DOI: 10.3791/54886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Obtaining crystals for structure determination can be a difficult and time consuming proposition for any protein. Coiled-coil proteins and domains are found throughout nature, however, because of their physical properties and tendency to aggregate, they are traditionally viewed as being especially difficult to crystallize. Here, we utilize a variety of quick and simple techniques designed to identify a series of possible domain boundaries for a given coiled-coil protein, and then quickly characterize the behavior of these proteins in solution. With the addition of a strongly fluorescent tag (mRuby2), protein characterization is simple and straightforward. The target protein can be readily visualized under normal lighting and can be quantified with the use of an appropriate imager. The goal is to quickly identify candidates that can be removed from the crystallization pipeline because they are unlikely to succeed, affording more time for the best candidates and fewer funds expended on proteins that do not produce crystals. This process can be iterated to incorporate information gained from initial screening efforts, can be adapted for high-throughput expression and purification procedures, and is augmented by robotic screening for crystallization.
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Affiliation(s)
| | - Simone Heber
- Department of Biological Sciences, University of Pittsburgh; Institute of Structural Biology, German Research Center for Environmental Health
| | - Joshua H Mo
- Department of Biological Sciences, University of Pittsburgh
| | - Keith O'Conor
- Department of Biological Sciences, University of Pittsburgh
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46
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Zhou RB, Cao HL, Zhang CY, Yin DC. A review on recent advances for nucleants and nucleation in protein crystallization. CrystEngComm 2017. [DOI: 10.1039/c6ce02562e] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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47
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Abstract
This chapter provides a review of different advanced methods that help to increase the success rate of a crystallization project, by producing larger and higher quality single crystals for determination of macromolecular structures by crystallographic methods. For this purpose, the chapter is divided into three parts. The first part deals with the fundamentals for understanding the crystallization process through different strategies based on physical and chemical approaches. The second part presents new approaches involved in more sophisticated methods not only for growing protein crystals but also for controlling the size and orientation of crystals through utilization of electromagnetic fields and other advanced techniques. The last section deals with three different aspects: the importance of microgravity, the use of ligands to stabilize proteins, and the use of microfluidics to obtain protein crystals. All these advanced methods will allow the readers to obtain suitable crystalline samples for high-resolution X-ray and neutron crystallography.
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Affiliation(s)
- Abel Moreno
- Instituto de Química, Universidad Nacional Autónoma de Mexico, Av. Universidad 3000, Cd.Mx., Mexico City, 04510, Mexico.
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48
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Renaissance of protein crystallization and precipitation in biopharmaceuticals purification. Biotechnol Adv 2017; 35:41-50. [DOI: 10.1016/j.biotechadv.2016.11.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 11/15/2016] [Accepted: 11/23/2016] [Indexed: 12/13/2022]
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49
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Boyko KM, Timofeev VI, Samygina VR, Kuranova IP, Popov VO, Koval’chuk MV. Protein crystallization under microgravity conditions. Analysis of the results of Russian experiments performed on the International Space Station in 2005−2015. CRYSTALLOGR REP+ 2016. [DOI: 10.1134/s1063774516050059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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50
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Sugitani N, Sivley RM, Perry KE, Capra JA, Chazin WJ. XPA: A key scaffold for human nucleotide excision repair. DNA Repair (Amst) 2016; 44:123-135. [PMID: 27247238 DOI: 10.1016/j.dnarep.2016.05.018] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nucleotide excision repair (NER) is essential for removing many types of DNA lesions from the genome, yet the mechanisms of NER in humans remain poorly understood. This review summarizes our current understanding of the structure, biochemistry, interaction partners, mechanisms, and disease-associated mutations of one of the critical NER proteins, XPA.
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Affiliation(s)
- Norie Sugitani
- Departments of Biochemistry, Biological Sciences, Biomedical Informatics, Chemistry, and Computer Science, and Vanderbilt Genetics Institute and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-7917, United States
| | - Robert M Sivley
- Departments of Biochemistry, Biological Sciences, Biomedical Informatics, Chemistry, and Computer Science, and Vanderbilt Genetics Institute and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-7917, United States
| | - Kelly E Perry
- Departments of Biochemistry, Biological Sciences, Biomedical Informatics, Chemistry, and Computer Science, and Vanderbilt Genetics Institute and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-7917, United States
| | - John A Capra
- Departments of Biochemistry, Biological Sciences, Biomedical Informatics, Chemistry, and Computer Science, and Vanderbilt Genetics Institute and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-7917, United States
| | - Walter J Chazin
- Departments of Biochemistry, Biological Sciences, Biomedical Informatics, Chemistry, and Computer Science, and Vanderbilt Genetics Institute and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-7917, United States.
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