1
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Shelley KL, Garman EF. Identifying and avoiding radiation damage in macromolecular crystallography. Acta Crystallogr D Struct Biol 2024; 80:314-327. [PMID: 38700059 PMCID: PMC11066884 DOI: 10.1107/s2059798324003243] [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: 02/29/2024] [Accepted: 04/15/2024] [Indexed: 05/05/2024] Open
Abstract
Radiation damage remains one of the major impediments to accurate structure solution in macromolecular crystallography. The artefacts of radiation damage can manifest as structural changes that result in incorrect biological interpretations being drawn from a model, they can reduce the resolution to which data can be collected and they can even prevent structure solution entirely. In this article, we discuss how to identify and mitigate against the effects of radiation damage at each stage in the macromolecular crystal structure-solution pipeline.
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Affiliation(s)
- Kathryn L. Shelley
- Department of Biochemistry, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, Washington, USA
| | - Elspeth F. Garman
- Department of Biochemistry, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
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2
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Wei L, Liu L, Gong W. Structure of mycobacterial ergothioneine-biosynthesis C-S lyase EgtE. J Biol Chem 2024; 300:105539. [PMID: 38072054 PMCID: PMC10805701 DOI: 10.1016/j.jbc.2023.105539] [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: 03/29/2023] [Revised: 11/12/2023] [Accepted: 11/28/2023] [Indexed: 01/02/2024] Open
Abstract
L-ergothioneine is widely distributed among various microbes to regulate their physiology and pathogenicity within complex environments. One of the key steps in the ergothioneine-biosynthesis pathway, the C-S bond cleavage reaction, uses the pyridoxal 5'-phosphate dependent C-S lyase to produce the final product L-ergothioneine. Here, we present the crystallographic structure of the ergothioneine-biosynthesis C-S lyase EgtE from Mycobacterium smegmatis (MsEgtE) represents the first published structure of ergothioneine-biosynthesis C-S lyases in bacteria and shows the effects of active site residues on the enzymatic reaction. The MsEgtE and the previously reported ergothioneine-biosynthesis C-S lyase Egt2 from Neurospora crassa (NcEgt2) fold similarly. However, discrepancies arise in terms of substrate recognition, as observed through sequence and structure comparison of MsEgtE and NcEgt2. The structural-based sequence alignment of the ergothioneine-biosynthesis C-S lyase from fungi and bacteria shows clear distinctions among the recognized substrate residues, but Arg348 is critical and an extremely conserved residue for substrate recognition. The α14 helix is exclusively found in the bacteria EgtE, which represent the most significant difference between bacteria EgtE and fungi Egt2, possibly resulting from the convergent evolution of bacteria and fungi.
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Affiliation(s)
- Lili Wei
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Lei Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
| | - Weimin Gong
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
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3
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Garman EF, Weik M. Radiation damage to biological macromolecules∗. Curr Opin Struct Biol 2023; 82:102662. [PMID: 37573816 DOI: 10.1016/j.sbi.2023.102662] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/27/2023] [Accepted: 07/04/2023] [Indexed: 08/15/2023]
Abstract
In this review, we describe recent research developments into radiation damage effects in macromolecular X-ray crystallography observed at synchrotrons and X-ray free electron lasers. Radiation damage in small molecule X-ray crystallography, small angle X-ray scattering experiments, microelectron diffraction, and single particle cryo-electron microscopy is briefly covered.
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Affiliation(s)
- Elspeth F Garman
- Department of Biochemistry, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK.
| | - Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France.
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4
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Jang J, Chang JH. Molecular Structure of Phosphoserine Aminotransferase from Saccharomyces cerevisiae. Int J Mol Sci 2023; 24:ijms24065139. [PMID: 36982214 PMCID: PMC10049462 DOI: 10.3390/ijms24065139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/10/2023] Open
Abstract
Phosphoserine aminotransferase (PSAT) is a pyridoxal 5′-phosphate-dependent enzyme involved in the second step of the phosphorylated pathway of serine biosynthesis. PSAT catalyzes the transamination of 3-phosphohydroxypyruvate to 3-phosphoserine using L-glutamate as the amino donor. Although structural studies of PSAT have been performed from archaea and humans, no structural information is available from fungi. Therefore, to elucidate the structural features of fungal PSAT, we determined the crystal structure of Saccharomyces cerevisiae PSAT (ScPSAT) at a resolution of 2.8 Å. The results demonstrated that the ScPSAT protein was dimeric in its crystal structure. Moreover, the gate-keeping loop of ScPSAT exhibited a conformation similar to that of other species. Several distinct structural features in the halide-binding and active sites of ScPSAT were compared with its homologs. Overall, this study contributes to our current understanding of PSAT by identifying the structural features of fungal PSAT for the first time.
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Affiliation(s)
- Jiyeon Jang
- Department of Biology Education, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
- Department of Biomedical Convergence Science and Technology, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
- Correspondence: ; Tel.: +82-53-950-5913; Fax: +82-53-950-6809
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5
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Marchesani F, Zangelmi E, Murtas G, Costanzi E, Ullah R, Peracchi A, Bruno S, Pollegioni L, Mozzarelli A, Storici P, Campanini B. L-Serine Biosynthesis in The Human Central Nervous System: Structure and Function of Phosphoserine Aminotransferase. Protein Sci 2023; 32:e4609. [PMID: 36851825 PMCID: PMC10031235 DOI: 10.1002/pro.4609] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 01/12/2023] [Accepted: 02/23/2023] [Indexed: 03/01/2023]
Abstract
Organisms from all kingdoms of life synthesize L-serine from 3-phosphoglycerate through the phosphorylated pathway, a three-step diversion of glycolysis. Phosphoserine aminotransferase (PSAT) catalyzes the intermediate step, the pyridoxal 5'-phosphate-dependent transamination of 3-phosphohydroxypyruvate and L-glutamate to O-phosphoserine and α-ketoglutarate. PSAT is particularly relevant in the central nervous system of mammals because L-serine is the metabolic precursor of D-serine, cysteine, phospholipids, and nucleotides. Several mutations in the human psat gene have been linked to serine deficiency disorders, characterized by severe neurological symptoms. Furthermore, PSAT is overexpressed in many tumors and this overexpression has been associated with poor clinical outcomes. Here, we report the detailed functional and structural characterization of the recombinant human PSAT. The reaction catalyzed by PSAT is reversible, with an equilibrium constant of about 10, and the enzyme is very efficient, with a kcat /Km of 5.9 × 106 M-1 s-1 , thus contributing in driving the pathway towards the products despite the extremely unfavorable first step catalyzed by 3-phosphoglycerate dehydrogenase. The three-dimensional X-ray crystal structure of PSAT was solved in the substrate-free as well as in the O-phosphoserine-bound forms. Both structures contain eight protein molecules in the asymmetric unit, arranged in four dimers, with a bound cofactor in each subunit. In the substrate-free form, the active site of PSAT contains a sulfate ion that, in the substrate-bound form, is replaced by the phosphate group of O-phosphoserine. Interestingly, fast crystal soaking used to produce the substrate-bound form allowed the trapping of different intermediates along the catalytic cycle. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Erika Zangelmi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Murtas
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Elisa Costanzi
- Protein Facility, Elettra Sincrotrone Trieste S.C.p.A., Trieste, Italy
| | - Raheem Ullah
- Protein Facility, Elettra Sincrotrone Trieste S.C.p.A., Trieste, Italy
- Present address: Structural Biology Lab, NIBGE, Faisalabad, Pakistan
| | - Alessio Peracchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | | | - Paola Storici
- Protein Facility, Elettra Sincrotrone Trieste S.C.p.A., Trieste, Italy
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6
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Shelley KL, Garman EF. Quantifying and comparing radiation damage in the Protein Data Bank. Nat Commun 2022; 13:1314. [PMID: 35288575 PMCID: PMC8921271 DOI: 10.1038/s41467-022-28934-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 02/18/2022] [Indexed: 11/09/2022] Open
Abstract
Radiation damage remains one of the major bottlenecks to accurate structure solution in protein crystallography. It can induce structural and chemical changes in protein crystals, and is hence an important consideration when assessing the quality and biological veracity of crystal structures in repositories like the Protein Data Bank (PDB). However, detection of radiation damage artefacts has traditionally proved very challenging. To address this, here we introduce the Bnet metric. Bnet summarises in a single value the extent of damage suffered by a crystal structure by comparing the B-factor values of damage-prone and non-damage-prone atoms in a similar local environment. After validating that Bnet successfully detects damage in 23 different crystal structures previously characterised as damaged, we calculate Bnet values for 93,978 PDB crystal structures. Our metric highlights a range of damage features, many of which would remain unidentified by the other summary statistics typically calculated for PDB structures.
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Affiliation(s)
- Kathryn L Shelley
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, United Kingdom.
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.
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7
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Tuieng RJ, Cartmell SH, Kirwan CC, Sherratt MJ. The Effects of Ionising and Non-Ionising Electromagnetic Radiation on Extracellular Matrix Proteins. Cells 2021; 10:3041. [PMID: 34831262 PMCID: PMC8616186 DOI: 10.3390/cells10113041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/28/2021] [Accepted: 10/30/2021] [Indexed: 02/07/2023] Open
Abstract
Exposure to sub-lethal doses of ionising and non-ionising electromagnetic radiation can impact human health and well-being as a consequence of, for example, the side effects of radiotherapy (therapeutic X-ray exposure) and accelerated skin ageing (chronic exposure to ultraviolet radiation: UVR). Whilst attention has focused primarily on the interaction of electromagnetic radiation with cells and cellular components, radiation-induced damage to long-lived extracellular matrix (ECM) proteins has the potential to profoundly affect tissue structure, composition and function. This review focuses on the current understanding of the biological effects of ionising and non-ionising radiation on the ECM of breast stroma and skin dermis, respectively. Although there is some experimental evidence for radiation-induced damage to ECM proteins, compared with the well-characterised impact of radiation exposure on cell biology, the structural, functional, and ultimately clinical consequences of ECM irradiation remain poorly defined.
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Affiliation(s)
- Ren Jie Tuieng
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK;
| | - Sarah H. Cartmell
- Department of Materials, School of Natural Sciences, Faculty of Science and Engineering and The Henry Royce Institute, Royce Hub Building, University of Manchester, Manchester M13 9PL, UK;
| | - Cliona C. Kirwan
- Division of Cancer Sciences and Manchester Breast Centre, Oglesby Cancer Research Building, Manchester Cancer Research Centre, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M20 4BX, UK;
| | - Michael J. Sherratt
- Division of Cell Matrix Biology & Regenerative Medicine and Manchester Breast Centre, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
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8
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Kandiah E, Carriel D, Garcia PS, Felix J, Banzhaf M, Kritikos G, Bacia-Verloop M, Brochier-Armanet C, Elsen S, Gutsche I. Structure, Function, and Evolution of the Pseudomonas aeruginosa Lysine Decarboxylase LdcA. Structure 2019; 27:1842-1854.e4. [PMID: 31653338 DOI: 10.1016/j.str.2019.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/09/2019] [Accepted: 10/01/2019] [Indexed: 11/28/2022]
Abstract
The only enzyme responsible for cadaverine production in the major multidrug-resistant human pathogen Pseudomonas aeruginosa is the lysine decarboxylase LdcA. This enzyme modulates the general polyamine homeostasis, promotes growth, and reduces bacterial persistence during carbenicillin treatment. Here we present a 3.7-Å resolution cryoelectron microscopy structure of LdcA. We introduce an original approach correlating phylogenetic signal with structural information and reveal possible recombination among LdcA and arginine decarboxylase subfamilies within structural domain boundaries. We show that LdcA is involved in full virulence in an insect pathogenesis model. Furthermore, unlike its enterobacterial counterparts, LdcA is regulated neither by the stringent response alarmone ppGpp nor by the AAA+ ATPase RavA. Instead, the P. aeruginosa ravA gene seems to play a defensive role. Altogether, our study identifies LdcA as an important player in P. aeruginosa physiology and virulence and as a potential drug target.
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Affiliation(s)
- Eaazhisai Kandiah
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Diego Carriel
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France; Biology of Cancer and Infection, U1036 INSERM, CEA, University of Grenoble Alpes, ERL5261 CNRS, Grenoble, France
| | - Pierre Simon Garcia
- Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France; MMSB Molecular Microbiology and Structural Biochemistry, Institut de Biologie et de Chimie des Protéines 7 Passage du Vercors, 69367 Lyon Cedex 07, France
| | - Jan Felix
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Manuel Banzhaf
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
| | - George Kritikos
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
| | - Maria Bacia-Verloop
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Céline Brochier-Armanet
- Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France; MMSB Molecular Microbiology and Structural Biochemistry, Institut de Biologie et de Chimie des Protéines 7 Passage du Vercors, 69367 Lyon Cedex 07, France
| | - Sylvie Elsen
- Biology of Cancer and Infection, U1036 INSERM, CEA, University of Grenoble Alpes, ERL5261 CNRS, Grenoble, France
| | - Irina Gutsche
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France.
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9
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N-terminal residues are crucial for quaternary structure and active site conformation for the phosphoserine aminotransferase from enteric human parasite E. histolytica. Int J Biol Macromol 2019; 132:1012-1023. [PMID: 30959130 DOI: 10.1016/j.ijbiomac.2019.04.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/04/2019] [Accepted: 04/04/2019] [Indexed: 11/24/2022]
Abstract
Phosphoserine aminotransferase (PSAT) is a pyridoxal-5'phosphate (PLP)-dependent enzyme that catalyzes the second reversible step in the phosphoserine biosynthetic pathway producing serine. The crystal structure of E. histolytica PSAT (EhPSAT) complexed with PLP was elucidated at 3.0 Å resolution and the structures of its mutants, EhPSAT_Δ45 and EhPSAT_Δ4, at 1.8 and 2.4 Å resolution respectively. Deletion of 45 N-terminal residues (EhPSAT_Δ45) resulted in an inactive protein, the structure showed a dimeric arrangement drastically different from that of the wild-type protein, with the two monomers translated and rotated by almost 180° with respect to each other; causing a rearrangement of the active site to which PLP was unable to bind. Deletion of first N-terminal 15 (EhPSAT_Δ15) and four 11th to 14th residues (EhPSAT_Δ4) yielded up to 98% and 90% decrease in the activity respectively. Absence of aldimine linkage between PLP-Lys in the crystal structure of EhPSAT_Δ4 mutant explains for such decrease in activity and describes the importance of these N-terminal residues. Furthermore, a halide-binding site was found in close proximity to the active site. A stretch of six amino acids (146-NNTIYG-151) only conserved in the Entamoeba genus, contributes to halide binding may explain that the halide inhibition could be specific to Entamoeba.
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10
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Phillips RS, Craig S. Crystal Structures of Wild-Type and F448A Mutant Citrobacter freundii Tyrosine Phenol-Lyase Complexed with a Substrate and Inhibitors: Implications for the Reaction Mechanism. Biochemistry 2018; 57:6166-6179. [PMID: 30260636 DOI: 10.1021/acs.biochem.8b00724] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tyrosine phenol-lyase (TPL; EC 4.1.99.2) is a pyridoxal 5'-phosphate-dependent enzyme that catalyzes the reversible hydrolytic cleavage of l-tyrosine to phenol and ammonium pyruvate. We have shown previously that F448A TPL has kcat and kcat/ Km values for l-tyrosine reduced by ∼104-fold [Phillips, R. S., Vita, A., Spivey, J. B., Rudloff, A. P., Driscoll, M. D., and Hay, S. (2016) ACS Catal. 6, 6770-6779]. We have now obtained crystal structures of F448A TPL and complexes with l-alanine, l-methionine, l-phenylalanine, and 3-F-l-tyrosine at 2.05-2.27 Å and the complex of wild-type TPL with l-phenylalanine at 1.8 Å. The small domain of F448A TPL, where Phe-448 is located, is more disordered in chain A than in wild-type TPL. The complexes of F448A TPL with l-alanine and l-phenylalanine are in an open conformation in both chains, while the complex with l-methionine is a 52:48 open:closed equilibrium mixture in chain A. Wild-type TPL with l-alanine is closed in chain A and open in chain B, and the complex with l-phenylalanine is a 56:44 open:closed mixture in chain A. Thus, the Phe-448 to alanine mutation affects the conformational equilibrium of open and closed active sites. The structure of the 3-F-l-tyrosine quinonoid complex of F448A TPL is unstrained and in an open conformation, with a hydrogen bond from the phenolic OH to Thr-124. These results support our previous conclusion that ground-state strain plays a critical role in the mechanism of TPL.
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11
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Abstract
An automated tool, RIDL (Radiation-Induced Density Loss), has been developed that enables user-independent detection and quantification of radiation-induced site-specific changes to macromolecular structures as a function of absorbed dose. RIDL has been designed to extract suitable per-atom descriptors of radiation damage, based on changes detectable in F
obs,n
− F
obs,1 Fourier difference maps between successive dose data sets. Subjective bias, which frequently plagues the interpretation of true damage signal versus noise, is thus eliminated. Metrics derived from RIDL have already proved beneficial for damage analysis on a range of protein and nucleic acid systems in the radiation damage literature. However, the tool is also sufficiently generalized for improving the rigour with which biologically relevant enzymatic changes can be probed and tracked during time-resolved crystallographic experiments.
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12
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Abstract
Radiation damage still remains a major limitation and challenge in macromolecular X-ray crystallography. Some of the high-intensity radiation used for diffraction data collection experiments is absorbed by the crystals, generating free radicals. These give rise to radiation damage even at cryotemperatures (~100 K), which can lead to incorrect biological conclusions being drawn from the resulting structure, or even prevent structure solution entirely. Investigation of mitigation strategies and the effects caused by radiation damage has been extensive over the past fifteen years. Here, recent understanding of the physical and chemical phenomena of radiation damage is described, along with the global effects inflicted on the collected data and the specific effects observed in the solved structure. Furthermore, this review aims to summarise the progress made in radiation damage studies in macromolecular crystallography from the experimentalist’s point of view and to give an introduction to the current literature.
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13
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Shelley KL, Dixon TPE, Brooks-Bartlett JC, Garman EF. RABDAM: quantifying specific radiation damage in individual protein crystal structures. J Appl Crystallogr 2018; 51:552-559. [PMID: 29657569 PMCID: PMC5884390 DOI: 10.1107/s1600576718002509] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 02/12/2018] [Indexed: 11/10/2022] Open
Abstract
Radiation damage remains one of the major limitations to accurate structure determination in protein crystallography (PX). Despite the use of cryo-cooling techniques, it is highly probable that a number of the structures deposited in the Protein Data Bank (PDB) have suffered substantial radiation damage as a result of the high flux densities of third generation synchrotron X-ray sources. Whereas the effects of global damage upon diffraction pattern reflection intensities are readily detectable, traditionally the (earlier onset) site-specific structural changes induced by radiation damage have proven difficult to identify within individual PX structures. More recently, however, development of the BDamage metric has helped to address this problem. BDamage is a quantitative, per-atom metric identifies potential sites of specific damage by comparing the atomic B-factor values of atoms that occupy a similar local packing density environment in the structure. Building upon this past work, this article presents a program, RABDAM, to calculate the BDamage metric for all selected atoms within any standard-format PDB or mmCIF file. RABDAM provides several useful outputs to assess the extent of damage suffered by an input PX structure. This free and open-source software will allow assessment and improvement of the quality of PX structures both previously and newly deposited in the PDB.
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Affiliation(s)
- Kathryn L. Shelley
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Thomas P. E. Dixon
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | - Elspeth F. Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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14
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Radiation damage at the active site of human alanine:glyoxylate aminotransferase reveals that the cofactor position is finely tuned during catalysis. Sci Rep 2017; 7:11704. [PMID: 28916765 PMCID: PMC5601474 DOI: 10.1038/s41598-017-11948-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/24/2017] [Indexed: 11/08/2022] Open
Abstract
The alanine:glyoxylate aminotransferase (AGT), a hepatocyte-specific pyridoxal-5'-phosphate (PLP) dependent enzyme, transaminates L-alanine and glyoxylate to glycine and pyruvate, thus detoxifying glyoxylate and preventing pathological oxalate precipitation in tissues. In the widely accepted catalytic mechanism of the aminotransferase family, the lysine binding to PLP acts as a catalyst in the stepwise 1,3-proton transfer, interconverting the external aldimine to ketimine. This step requires protonation by a conserved aspartate of the pyridine nitrogen of PLP to enhance its ability to stabilize the carbanionic intermediate. The aspartate residue is also responsible for a significant geometrical distortion of the internal aldimine, crucial for catalysis. We present the structure of human AGT in which complete X-ray photoreduction of the Schiff base has occurred. This result, together with two crystal structures of the conserved aspartate pathogenic variant (D183N) and the molecular modeling of the transaldimination step, led us to propose that an interplay of opposite forces, which we named spring mechanism, finely tunes PLP geometry during catalysis and is essential to move the external aldimine in the correct position in order for the 1,3-proton transfer to occur.
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15
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Rodrigues MJ, Windeisen V, Zhang Y, Guédez G, Weber S, Strohmeier M, Hanes JW, Royant A, Evans G, Sinning I, Ealick SE, Begley TP, Tews I. Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis. Nat Chem Biol 2017; 13:290-294. [PMID: 28092359 PMCID: PMC6078385 DOI: 10.1038/nchembio.2273] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/11/2016] [Indexed: 11/08/2022]
Abstract
Substrate channeling has emerged as a common mechanism for enzymatic intermediate transfer. A conspicuous gap in knowledge concerns the use of covalent lysine imines in the transfer of carbonyl-group-containing intermediates, despite their wideuse in enzymatic catalysis. Here we show how imine chemistry operates in the transfer of covalent intermediates in pyridoxal 5'-phosphate biosynthesis by the Arabidopsis thaliana enzyme Pdx1. An initial ribose 5-phosphate lysine imine is converted to the chromophoric I320 intermediate, simultaneously bound to two lysine residues and partially vacating the active site, which creates space for glyceraldehyde 3-phosphate to bind. Crystal structures show how substrate binding, catalysis and shuttling are coupled to conformational changes around strand β6 of the Pdx1 (βα)8-barrel. The dual-specificity active site and imine relay mechanism for migration of carbonyl intermediates provide elegant solutions to the challenge of coordinating a complex sequence of reactions that follow a path of over 20 Å between substrate- and product-binding sites.
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Affiliation(s)
- Matthew J Rodrigues
- Biological Sciences, University of Southampton, Southampton, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Volker Windeisen
- Biological Sciences, University of Southampton, Southampton, UK
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Yang Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Gabriela Guédez
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Stefan Weber
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Marco Strohmeier
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Jeremiah W Hanes
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
- Pacific Biosciences, Menlo Park, California, USA
| | - Antoine Royant
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
- European Synchrotron Radiation Facility, Grenoble, France
| | - Gwyndaf Evans
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Steven E Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Tadhg P Begley
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Ivo Tews
- Biological Sciences, University of Southampton, Southampton, UK
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
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16
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Abstract
Radiation damage inflicted on macromolecular crystals during X-ray diffraction experiments remains a limiting factor for structure solution, even when samples are cooled to cryotemperatures (~100 K). Efforts to establish mitigation strategies are ongoing and various approaches, summarized below, have been investigated over the last 15 years, resulting in a deeper understanding of the physical and chemical factors affecting damage rates. The recent advent of X-ray free electron lasers permits "diffraction-before-destruction" by providing highly brilliant and short (a few tens of fs) X-ray pulses. New fourth generation synchrotron sources now coming on line with higher X-ray flux densities than those available from third generation synchrotrons will bring the issue of radiation damage once more to the fore for structural biologists.
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Affiliation(s)
- Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| | - Martin Weik
- Institut de Biologie Structurale, University of Grenoble Alpes, CEA, CNRS, 71 Avenue des Martyrs, 38044, Grenoble, France.
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17
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Bury CS, Carmichael I, Garman EF. OH cleavage from tyrosine: debunking a myth. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:7-18. [PMID: 28009542 PMCID: PMC5182017 DOI: 10.1107/s1600577516016775] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/19/2016] [Indexed: 05/09/2023]
Abstract
During macromolecular X-ray crystallography experiments, protein crystals held at 100 K have been widely reported to exhibit reproducible bond scission events at doses on the order of several MGy. With the objective to mitigate the impact of radiation damage events on valid structure determination, it is essential to correctly understand the radiation chemistry mechanisms at play. OH-cleavage from tyrosine residues is regularly cited as amongst the most available damage pathways in protein crystals at 100 K, despite a lack of widespread reports of this phenomenon in protein crystal radiation damage studies. Furthermore, no clear mechanism for phenolic C-O bond cleavage in tyrosine has been reported, with the tyrosyl radical known to be relatively robust and long-lived in both aqueous solutions and the solid state. Here, the initial findings of Tyr -OH group damage in a myrosinase protein crystal have been reviewed. Consistent with that study, at increasing doses, clear electron density loss was detectable local to Tyr -OH groups. A systematic investigation performed on a range of protein crystal damage series deposited in the Protein Data Bank has established that Tyr -OH electron density loss is not generally a dominant damage pathway in protein crystals at 100 K. Full Tyr aromatic ring displacement is here proposed to account for instances of observable Tyr -OH electron density loss, with the original myrosinase data shown to be consistent with such a damage model. Systematic analysis of the effects of other environmental factors, including solvent accessibility and proximity to disulfide bonds or hydrogen bond interactions, is also presented. Residues in known active sites showed enhanced sensitivity to radiation-induced disordering, as has previously been reported.
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Affiliation(s)
- Charles S. Bury
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Ian Carmichael
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Elspeth F Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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18
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Correy GJ, Carr PD, Meirelles T, Mabbitt PD, Fraser NJ, Weik M, Jackson CJ. Mapping the Accessible Conformational Landscape of an Insect Carboxylesterase Using Conformational Ensemble Analysis and Kinetic Crystallography. Structure 2016; 24:977-87. [PMID: 27210287 DOI: 10.1016/j.str.2016.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 04/04/2016] [Accepted: 04/08/2016] [Indexed: 11/26/2022]
Abstract
The proper function of enzymes often depends upon their efficient interconversion between particular conformational sub-states on a free-energy landscape. Experimentally characterizing these sub-states is challenging, which has limited our understanding of the role of protein dynamics in many enzymes. Here, we have used a combination of kinetic crystallography and detailed analysis of crystallographic protein ensembles to map the accessible conformational landscape of an insect carboxylesterase (LcαE7) as it traverses all steps in its catalytic cycle. LcαE7 is of special interest because of its evolving role in organophosphate insecticide resistance. Our results reveal that a dynamically coupled network of residues extends from the substrate-binding site to a surface loop. Interestingly, the coupling of this network that is apparent in the apoenzyme appears to be reduced in the phosphorylated enzyme intermediate. Altogether, the results of this work highlight the importance of protein dynamics to enzyme function and the evolution of new activity.
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Affiliation(s)
- Galen J Correy
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Paul D Carr
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Tamara Meirelles
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Peter D Mabbitt
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Nicholas J Fraser
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Martin Weik
- Institut de Biologie Structurale Jean Pierre Ebel, Commisariat a l'Energie Atomique, Centre de National de la Recherche Scientifique, University Josef Fourier, 41 rue Jules Horowitz, 38027 Grenoble, France
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia.
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19
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Bury CS, McGeehan JE, Antson AA, Carmichael I, Gerstel M, Shevtsov MB, Garman EF. RNA protects a nucleoprotein complex against radiation damage. Acta Crystallogr D Struct Biol 2016; 72:648-57. [PMID: 27139628 PMCID: PMC4854314 DOI: 10.1107/s2059798316003351] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 02/26/2016] [Indexed: 11/10/2022] Open
Abstract
Radiation damage during macromolecular X-ray crystallographic data collection is still the main impediment for many macromolecular structure determinations. Even when an eventual model results from the crystallographic pipeline, the manifestations of radiation-induced structural and conformation changes, the so-called specific damage, within crystalline macromolecules can lead to false interpretations of biological mechanisms. Although this has been well characterized within protein crystals, far less is known about specific damage effects within the larger class of nucleoprotein complexes. Here, a methodology has been developed whereby per-atom density changes could be quantified with increasing dose over a wide (1.3-25.0 MGy) range and at higher resolution (1.98 Å) than the previous systematic specific damage study on a protein-DNA complex. Specific damage manifestations were determined within the large trp RNA-binding attenuation protein (TRAP) bound to a single-stranded RNA that forms a belt around the protein. Over a large dose range, the RNA was found to be far less susceptible to radiation-induced chemical changes than the protein. The availability of two TRAP molecules in the asymmetric unit, of which only one contained bound RNA, allowed a controlled investigation into the exact role of RNA binding in protein specific damage susceptibility. The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule. Additionally, the method enabled a quantification of the reduction in radiation-induced Lys and Phe disordering upon RNA binding directly from the electron density.
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Affiliation(s)
- Charles S. Bury
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
| | - John E. McGeehan
- Molecular Biophysics, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, King Henry I Street, Portsmouth PO1 2DY, England
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York Y010 5DD, England
| | - Ian Carmichael
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Markus Gerstel
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
| | - Mikhail B. Shevtsov
- Laboratory of Structural Biology of GPCRs, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russian Federation
| | - Elspeth F. Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
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20
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von Stetten D, Giraud T, Carpentier P, Sever F, Terrien M, Dobias F, Juers DH, Flot D, Mueller-Dieckmann C, Leonard GA, de Sanctis D, Royant A. In crystallo optical spectroscopy (icOS) as a complementary tool on the macromolecular crystallography beamlines of the ESRF. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:15-26. [PMID: 25615856 PMCID: PMC4304682 DOI: 10.1107/s139900471401517x] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 06/27/2014] [Indexed: 01/04/2023]
Abstract
The analysis of structural data obtained by X-ray crystallography benefits from information obtained from complementary techniques, especially as applied to the crystals themselves. As a consequence, optical spectroscopies in structural biology have become instrumental in assessing the relevance and context of many crystallographic results. Since the year 2000, it has been possible to record such data adjacent to, or directly on, the Structural Biology Group beamlines of the ESRF. A core laboratory featuring various spectrometers, named the Cryobench, is now in its third version and houses portable devices that can be directly mounted on beamlines. This paper reports the current status of the Cryobench, which is now located on the MAD beamline ID29 and is thus called the ID29S-Cryobench (where S stands for `spectroscopy'). It also reviews the diverse experiments that can be performed at the Cryobench, highlighting the various scientific questions that can be addressed.
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Affiliation(s)
| | - Thierry Giraud
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | | | - Franc Sever
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Maxime Terrien
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Fabien Dobias
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Douglas H. Juers
- Department of Physics, Whitman College, Walla Walla, WA 99362, USA
| | - David Flot
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | | | | | | | - Antoine Royant
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
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21
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Wickstrand C, Dods R, Royant A, Neutze R. Bacteriorhodopsin: Would the real structural intermediates please stand up? Biochim Biophys Acta Gen Subj 2014; 1850:536-53. [PMID: 24918316 DOI: 10.1016/j.bbagen.2014.05.021] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/23/2014] [Accepted: 05/29/2014] [Indexed: 11/18/2022]
Abstract
BACKGROUND Bacteriorhodopsin (bR) is the simplest known light driven proton pump and has been heavily studied using structural methods: eighty four X-ray diffraction, six electron diffraction and three NMR structures of bR are deposited within the protein data bank. Twenty one X-ray structures report light induced structural changes and changes induced by mutation, changes in pH, thermal annealing or X-ray induced photo-reduction have also been examined. SCOPE OF REVIEW We argue that light-induced structural changes that are replicated across several studies by independent research groups are those most likely to represent what is happening in reality. We present both internal distance matrix analyses that sort deposited bR structures into hierarchal trees, and difference Fourier analysis of deposited X-ray diffraction data. MAJOR CONCLUSIONS An internal distance matrix analysis separates most wild-type bR structures according to their different crystal forms, indicating how the protein's structure is influenced by crystallization conditions. A similar analysis clusters eleven studies of illuminated bR crystals as one branch of a hierarchal tree with reproducible movements of the extracellular portion of helix C towards helix G, and of the cytoplasmic portion of helix F away from helices A, B and G. All crystallographic data deposited for illuminated crystals show negative difference density on a water molecule (Wat402) that forms H-bonds to the retinal Schiff Base and two aspartate residues (Asp85, Asp212) in the bR resting state. Other recurring difference density features indicated reproducible side-chain, backbone and water molecule displacements. X-ray induced radiation damage also disorders Wat402 but acts via cleaving the head-groups of Asp85 and Asp212. GENERAL SIGNIFICANCE A remarkable level of agreement exists when deposited structures and crystallographic observations are viewed as a whole. From this agreement a unified picture of the structural mechanism of light-induced proton pumping by bR emerges. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.
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Affiliation(s)
- Cecilia Wickstrand
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Robert Dods
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Antoine Royant
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France; CNRS, IBS, F-38044 Grenoble, France; CEA, IBS, F-38044 Grenoble, France; European Synchrotron Radiation Facility, F-38043 Grenoble, France.
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden.
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22
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Thomsen M, Skalden L, Palm GJ, Höhne M, Bornscheuer UT, Hinrichs W. Crystallographic characterization of the (R)-selective amine transaminase from Aspergillus fumigatus. ACTA ACUST UNITED AC 2014; 70:1086-93. [PMID: 24699652 DOI: 10.1107/s1399004714001084] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 01/15/2014] [Indexed: 11/10/2022]
Abstract
The importance of amine transaminases for producing optically pure chiral precursors for pharmaceuticals and chemicals has substantially increased in recent years. The X-ray crystal structure of the (R)-selective amine transaminase from the fungus Aspergillus fumigatus was solved by S-SAD phasing to 1.84 Å resolution. The refined structure at 1.27 Å resolution provides detailed knowledge about the molecular basis of substrate recognition and conversion to facilitate protein-engineering approaches. The protein forms a homodimer and belongs to fold class IV of the pyridoxal-5'-phosphate-dependent enzymes. Both subunits contribute residues to form two active sites. The structure of the holoenzyme shows the catalytically important cofactor pyridoxal-5'-phosphate bound as an internal aldimine with the catalytically responsible amino-acid residue Lys179, as well as in its free form. A long N-terminal helix is an important feature for the stability of this fungal (R)-selective amine transaminase, but is missing in branched-chain amino-acid aminotransferases and D-amino-acid aminotransferases.
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Affiliation(s)
- Maren Thomsen
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany
| | - Lilly Skalden
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany
| | - Gottfried J Palm
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany
| | - Matthias Höhne
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany
| | - Uwe T Bornscheuer
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany
| | - Winfried Hinrichs
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany
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23
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Battula P, Dubnovitsky AP, Papageorgiou AC. Structural basis of L-phosphoserine binding to Bacillus alcalophilus phosphoserine aminotransferase. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:804-11. [PMID: 23633589 DOI: 10.1107/s0907444913002096] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 01/21/2013] [Indexed: 11/10/2022]
Abstract
Phosphoserine aminotransferase is a vitamin B6-dependent enzyme that catalyzes the reversible conversion of 3-phosphohydroxypyruvate to L-phosphoserine using glutamate as an amine donor. In an effort to gain insight into the substrate-recognition mechanism of the enzyme, crystal structures of Bacillus alcalophilus phosphoserine aminotransferase in the presence or absence of L-phosphoserine were determined to resolutions of 1.5 and 1.6 Å, respectively. Local conformational changes induced upon substrate binding were identified. However, in contrast to other aminotransferases, no domain or subunit movements were observed. Two Arg residues (Arg42 and Arg328) and two His residues (His41 and His327) were found to form a tight binding site for the phosphate group of L-phosphoserine. Comparison with Escherichia coli phosphoserine aminotransferase in complex with the substrate analogue α-methylglutamate revealed more extensive structural changes in the case of L-phosphoserine binding. Based on the structural analysis, the flexibility of Arg328 is proposed to be critical for substrate recognition.
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Affiliation(s)
- Pradeep Battula
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, BioCity, FIN-20521 Turku, Finland
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24
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Rausch C, Lerchner A, Schiefner A, Skerra A. Crystal structure of the ω-aminotransferase from Paracoccus denitrificans and its phylogenetic relationship with other class III aminotransferases that have biotechnological potential. Proteins 2013; 81:774-87. [PMID: 23239223 DOI: 10.1002/prot.24233] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 11/12/2012] [Accepted: 11/21/2012] [Indexed: 12/21/2022]
Abstract
Apart from their crucial role in metabolism, pyridoxal 5'-phosphate (PLP)-dependent aminotransferases (ATs) constitute a class of enzymes with increasing application in industrial biotechnology. To provide better insight into the structure-function relationships of ATs with biotechnological potential we performed a fundamental bioinformatics analysis of 330 representative sequences of pro- and eukaryotic Class III ATs using a structure-guided approach. The calculated phylogenetic maximum likelihood tree revealed six distinct clades of which the first segregates with a very high bootstrap value of 92%. Most enzymes in this first clade have been functionally well characterized, whereas knowledge about the natural functions and substrates of enzymes in the other branches is sparse. Notably, in those clades 2-6 members of the peculiar class of ω-ATs prevail, many of which have proven useful for the preparation of chiral amines or artificial amino acids. One representative is the ω-AT from Paracoccus denitrificans (PD ω-AT) which catalyzes, for example, the transamination in a novel biocatalytic process for the production of L-homoalanine from L-threonine. To gain structural insight into this important enzyme, its X-ray analysis was carried out at a resolution of 2.6 Å, including the covalently bound PLP as well as 5-aminopentanoate as a putative amino donor substrate. On the basis of this crystal structure in conjunction with our phylogenetic analysis, we have identified a generic set of active site residues of ω-ATs that are associated with a strong preference for aromatic substrates, thus guiding the discovery of novel promising enzymes for the biotechnological production of corresponding chiral amines.
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Affiliation(s)
- Christian Rausch
- Munich Center for integrated Protein Science (CiPSM) and Lehrstuhl für Biologische Chemie, Technische Universität München, Freising-Weihenstephan, Germany
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25
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Leal RMF, Bourenkov G, Russi S, Popov AN. A survey of global radiation damage to 15 different protein crystal types at room temperature: a new decay model. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:14-22. [PMID: 23254652 PMCID: PMC3943537 DOI: 10.1107/s0909049512049114] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 11/29/2012] [Indexed: 05/11/2023]
Abstract
The radiation damage rates to crystals of 15 model macromolecular structures were studied using an automated radiation sensitivity characterization procedure. The diffracted intensity variation with dose is described by a two-parameter model. This model includes a strong resolution-independent decay specific to room-temperature measurements along with a linear increase in overall Debye-Waller factors. An equivalent representation of sensitivity via a single parameter, normalized half-dose, is introduced. This parameter varies by an order of magnitude between the different structures studied. The data show a correlation of crystal radiation sensitivity with crystal solvent content but no dose-rate dependency was detected in the range 0.05-300 kGy s(-1). The results of the crystal characterization are suitable for either optimal planning of room-temperature data collection or in situ crystallization plate screening experiments.
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Affiliation(s)
| | - Gleb Bourenkov
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85b, Hamburg 22607, Germany
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26
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Crystal structures of complexes of the branched-chain aminotransferase from Deinococcus radiodurans with α-ketoisocaproate and L-glutamate suggest the radiation resistance of this enzyme for catalysis. J Bacteriol 2012; 194:6206-16. [PMID: 22984263 DOI: 10.1128/jb.01659-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Branched-chain aminotransferases (BCAT), which utilize pyridoxal 5'-phosphate (PLP) as a cofactor, reversibly catalyze the transfer of the α-amino groups of three of the most hydrophobic branched-chain amino acids (BCAA), leucine, isoleucine, and valine, to α-ketoglutarate to form the respective branched-chain α-keto acids and glutamate. The BCAT from Deinococcus radiodurans (DrBCAT), an extremophile, was cloned and expressed in Escherichia coli for structure and functional studies. The crystal structures of the native DrBCAT with PLP and its complexes with L-glutamate and α-ketoisocaproate (KIC), respectively, have been determined. The DrBCAT monomer, comprising 358 amino acids, contains large and small domains connected with an interdomain loop. The cofactor PLP is located at the bottom of the active site pocket between two domains and near the dimer interface. The substrate (L-glutamate or KIC) is bound with key residues through interactions of the hydrogen bond and the salt bridge near PLP inside the active site pocket. Mutations of some interaction residues, such as Tyr71, Arg145, and Lys202, result in loss of the specific activity of the enzymes. In the interdomain loop, a dynamic loop (Gly173 to Gly179) clearly exhibits open and close conformations in structures of DrBCAT without and with substrates, respectively. DrBCAT shows the highest specific activity both in nature and under ionizing radiation, but with lower thermal stability above 60 °C, than either BCAT from Escherichia coli (eBCAT) or from Thermus thermophilus (HB8BCAT). The dimeric molecular packing and the distribution of cysteine residues at the active site and the molecular surface might explain the resistance to radiation but small thermal stability of DrBCAT.
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27
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Schmidt M, Šrajer V, Purwar N, Tripathi S. The kinetic dose limit in room-temperature time-resolved macromolecular crystallography. JOURNAL OF SYNCHROTRON RADIATION 2012; 19:264-73. [PMID: 22338689 PMCID: PMC3284346 DOI: 10.1107/s090904951105549x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 12/23/2011] [Indexed: 05/16/2023]
Abstract
Protein X-ray structures are determined with ionizing radiation that damages the protein at high X-ray doses. As a result, diffraction patterns deteriorate with the increased absorbed dose. Several strategies such as sample freezing or scavenging of X-ray-generated free radicals are currently employed to minimize this damage. However, little is known about how the absorbed X-ray dose affects time-resolved Laue data collected at physiological temperatures where the protein is fully functional in the crystal, and how the kinetic analysis of such data depends on the absorbed dose. Here, direct evidence for the impact of radiation damage on the function of a protein is presented using time-resolved macromolecular crystallography. The effect of radiation damage on the kinetic analysis of time-resolved X-ray data is also explored.
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Affiliation(s)
- M Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA.
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28
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Mishra V, Kumar A, Ali V, Nozaki T, Zhang KYJ, Bhakuni V. Role of conserved active site tryptophan-101 in functional activity and stability of phosphoserine aminotransferase from an enteric human parasite. Amino Acids 2011; 43:483-91. [PMID: 22038178 DOI: 10.1007/s00726-011-1105-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 09/23/2011] [Indexed: 10/15/2022]
Abstract
Site-directed mutagenesis study was performed to elucidate the role of conserved tryptophan-101 present at the active site of phosphoserine aminotransferase from an enteric human parasite Entamoeba histolytica. Fluorescence resonance energy transfer and molecular dynamic simulation show that the indole ring of Trp101 stacks with the cofactor PLP. Loss of enzymatic activity and PLP polarization values suggest that Trp101 plays a major role in maintaining a defined PLP microenvironment essentially required for optimal enzymatic activity. Studies on W101F, W101H and W101A mutants show that only the indole ring of the conserved Trp101 forms most favorable stacking interaction with the pyridine ring of the cofactor PLP. Protein stability was compromised on substitution of Trp101 with Phe/His/Ala amino acids. A difference in conformational free energy of 1.65 kcal mol(-1) was observed between WT-protein and W101A mutant.
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Affiliation(s)
- Vibhor Mishra
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, 226001, India.
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29
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Juers DH, Weik M. Similarities and differences in radiation damage at 100 K versus 160 K in a crystal of thermolysin. JOURNAL OF SYNCHROTRON RADIATION 2011; 18:329-337. [PMID: 21525640 DOI: 10.1107/s0909049511007631] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Accepted: 03/01/2011] [Indexed: 05/30/2023]
Abstract
The temperature-dependence of radiation damage in macromolecular X-ray crystallography is currently much debated. Most protein crystallographic studies are based on data collected at 100 K. Data collection at temperatures below 100 K has been proposed to reduce radiation damage and above 100 K to be useful for kinetic crystallography that is aimed at the generation and trapping of protein intermediate states. Here the global and specific synchrotron-radiation sensitivity of crystalline thermolysin at 100 and 160 K are compared. Both types of damage are higher at 160 K than at 100 K. At 160 K more residue types are affected (Lys, Asp, Gln, Pro, Thr, Met, Asn) than at 100 K (Met, Asp, Glu, Lys). The X-ray-induced relative atomic B-factor increase is shown to correlate with the proximity of the atom to the nearest solvent channel at 160 K. Two models may explain the observed correlation: either an increase in static disorder or an increased attack of hydroxyl radicals from the solvent area of the crystal.
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Affiliation(s)
- Douglas H Juers
- Department of Physics, Whitman College, Walla Walla, WA 99362, USA
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Carpentier P, Royant A, Weik M, Bourgeois D. Raman-Assisted Crystallography Suggests a Mechanism of X-Ray-Induced Disulfide Radical Formation and Reparation. Structure 2010; 18:1410-9. [DOI: 10.1016/j.str.2010.09.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 08/27/2010] [Accepted: 09/23/2010] [Indexed: 11/24/2022]
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Petrova T, Ginell S, Mitschler A, Kim Y, Lunin VY, Joachimiak G, Cousido-Siah A, Hazemann I, Podjarny A, Lazarski K, Joachimiak A. X-ray-induced deterioration of disulfide bridges at atomic resolution. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:1075-91. [PMID: 20944241 DOI: 10.1107/s0907444910033986] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 08/23/2010] [Indexed: 11/10/2022]
Abstract
Overall and site-specific X-ray-induced damage to porcine pancreatic elastase was studied at atomic resolution at temperatures of 100 and 15 K. The experiments confirmed that irradiation causes small movements of protein domains and bound water molecules in protein crystals. These structural changes occur not only at 100 K but also at temperatures as low as 15 K. An investigation of the deterioration of disulfide bridges demonstrated the following. (i) A decrease in the occupancy of S(γ) atoms and the appearance of new cysteine rotamers occur simultaneously. (ii) The occupancy decrease is observed for all S(γ) atoms, while new rotamers arise for some of the cysteine residues; the appearance of new conformations correlates with the accessibility to solvent. (iii) The sum of the occupancies of the initial and new conformations of a cysteine residue is approximately equal to the occupancy of the second cysteine residue in the bridge. (iv) The most pronounced changes occur at doses below 1.4 × 10(7) Gy, with only small changes occurring at higher doses. Comparison of the radiation-induced changes in an elastase crystal at 100 and 15 K suggested that the dose needed to induce a similar level of deterioration of the disulfide bonds and atomic displacements at 15 K to those seen at 100 K is more than two times higher.
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Affiliation(s)
- Tatiana Petrova
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
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Ronda L, Bazhulina NP, Morozova EA, Revtovich SV, Chekhov VO, Nikulin AD, Demidkina TV, Mozzarelli A. Exploring methionine γ-lyase structure-function relationship via microspectrophotometry and X-ray crystallography. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:834-42. [PMID: 20601224 DOI: 10.1016/j.bbapap.2010.06.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 06/17/2010] [Accepted: 06/18/2010] [Indexed: 11/26/2022]
Abstract
Pyridoxal 5'-phosphate (PLP) dependent methionine γ-lyase catalyzes the breakdown of L-methionine to α-ketobutyric acid, methanethiol and ammonia. This enzyme, present in anaerobic microorganisms, has biomedical interest both for its activity as antitumor agent, depleting methionine supply in methionine-dependent cancers, and as target in the treatment of human pathogen infections, activating the pro-drug trifluoromethionine. To validate the structure of the enzyme from Citrobacter freundii, crystallized from monomethyl ether polyethylene glycol 2000, for the development of lead compounds, the reactivity of the crystalline enzyme towards L-methionine, substrate analogs and inhibitors was determined by polarized absorption microspectrophotometry. Spectral data were also collected for enzyme crystals, grown in monomethyl ether polyethylene glycol 2000 in the presence of ammonium sulfate. The three-dimensional structure of these enzyme crystals, solved at 1.65Å resolution with R(free) 23.2%, revealed the surprising absence of the aldimine bond between the active site Lys210 and PLP. Different hypothesis are proposed and discussed in the light of spectral and structural data, pointing out to the relevance of the complementarity between X-ray crystallography and single crystal spectroscopy for the understanding of biological mechanisms at molecular level. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.
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Affiliation(s)
- Luca Ronda
- Department of Biochemistry and Molecular Biology, University of Parma, Parma, Italy
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Bourenkov GP, Popov AN. Optimization of data collection taking radiation damage into account. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:409-19. [PMID: 20382994 PMCID: PMC2852305 DOI: 10.1107/s0907444909054961] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 12/21/2009] [Indexed: 11/20/2022]
Abstract
To take into account the effects of radiation damage, new algorithms for the optimization of data-collection strategies have been implemented in the software package BEST. The intensity variation related to radiation damage is approximated by log-linear functions of resolution and cumulative X-ray dose. Based on an accurate prediction of the basic characteristics of data yet to be collected, BEST establishes objective relationships between the accessible data completeness, resolution and signal-to-noise statistics that can be achieved in an experiment and designs an optimal plan for data collection.
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Affiliation(s)
- Gleb P Bourenkov
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85b, 22607 Hamburg, Germany
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Garman EF. Radiation damage in macromolecular crystallography: what is it and why should we care? ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:339-51. [PMID: 20382986 PMCID: PMC2852297 DOI: 10.1107/s0907444910008656] [Citation(s) in RCA: 240] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Accepted: 03/06/2010] [Indexed: 11/10/2022]
Abstract
Radiation damage inflicted during diffraction data collection in macromolecular crystallography has re-emerged in the last decade as a major experimental and computational challenge, as even for crystals held at 100 K it can result in severe data-quality degradation and the appearance in solved structures of artefacts which affect biological interpretations. Here, the observable symptoms and basic physical processes involved in radiation damage are described and the concept of absorbed dose as the basic metric against which to monitor the experimentally observed changes is outlined. Investigations into radiation damage in macromolecular crystallography are ongoing and the number of studies is rapidly increasing. The current literature on the subject is compiled as a resource for the interested researcher.
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Affiliation(s)
- Elspeth F Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England.
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Weik M, Colletier JP. Temperature-dependent macromolecular X-ray crystallography. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:437-46. [PMID: 20382997 PMCID: PMC2852308 DOI: 10.1107/s0907444910002702] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Accepted: 01/21/2010] [Indexed: 11/10/2022]
Abstract
X-ray crystallography provides structural details of biological macromolecules. Whereas routine data are collected close to 100 K in order to mitigate radiation damage, more exotic temperature-controlled experiments in a broader temperature range from 15 K to room temperature can provide both dynamical and structural insights. Here, the dynamical behaviour of crystalline macromolecules and their surrounding solvent as a function of cryo-temperature is reviewed. Experimental strategies of kinetic crystallography are discussed that have allowed the generation and trapping of macromolecular intermediate states by combining reaction initiation in the crystalline state with appropriate temperature profiles. A particular focus is on recruiting X-ray-induced changes for reaction initiation, thus unveiling useful aspects of radiation damage, which otherwise has to be minimized in macromolecular crystallography.
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Affiliation(s)
- Martin Weik
- CEA, IBS, Laboratoire de Biophysique Moléculaire, F-38054 Grenoble, France.
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Mishra V, Ali V, Nozaki T, Bhakuni V. Entamoeba histolytica Phosphoserine aminotransferase (EhPSAT): insights into the structure-function relationship. BMC Res Notes 2010; 3:52. [PMID: 20199659 PMCID: PMC2850911 DOI: 10.1186/1756-0500-3-52] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 03/03/2010] [Indexed: 11/29/2022] Open
Abstract
Background Presence of phosphorylated Serine biosynthesis pathway upstream to the de novo cysteine biosynthesis pathway makes PSAT a crucial enzyme. Besides this, phoshoserine produced by the enzyme can also be taken up directly by cysteine synthase as a substrate. PSAT is a PLP dependent enzyme where the cofactor serves as an epicenter for functional catalysis with the active site architecture playing crucial role in optimum function of the enzyme. Findings EhPSAT is a homodimer of molecular mass 86 kDa. To understand the structural modulations associated with pH dependent changes in functional activity of EhPSAT detailed biophysical studies were carried out. pH alterations had no significant effect on the secondary structure, cofactor orientation and oligomeric configuration of the enzyme however, pH dependent compaction in molecular dimensions was observed. Most interestingly, a direct correlation between pH induced modulation of functional activity and orientation of Trp 101 present in the active site of the enzyme was observed. Sodium halides nullified the pH induced global changes in the enzyme, however differential effect of these salts on the active site microenvironment and functional activity of the enzyme was observed. Conclusions The study unequivocally demonstrates that pH induced selective modification of active site microenvironment and not global change in structure or oligomeric status of the enzyme is responsible for the pH dependent change in enzymatic activity of PSAT.
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Affiliation(s)
- Vibhor Mishra
- Division of Molecular and Structural Biology, Central Drug Research Institute, Chattar Manzil Palace, Council of scientific and industrial research (CSIR), Lucknow 226001, India.
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Abstract
Carbonic anhydrase, a zinc metalloenzyme, catalyzes the reversible hydration of carbon dioxide to bicarbonate. It is involved in processes connected with acid-base homeostasis, respiration, and photosynthesis. More than 100 distinct human carbonic anhydrase II (HCAII) 3D structures have been generated in last 3 decades [Liljas A, et al. (1972) Nat New Biol 235:131-137], but a structure of an HCAII in complex with CO(2) or HCO(3)(-) has remained elusive. Here, we report previously undescribed structures of HCAII:CO(2) and HCAII:HCO(3)(-) complexes, together with a 3D molecular film of the enzymatic reaction observed successively in the same crystal after extended exposure to X-ray. We demonstrate that the unexpected enzyme activation was caused in an X-ray dose-dependent manner. Although X-ray damage to macromolecular samples has long been recognized [Ravelli RB, Garman EF (2006) Curr Opin Struct Biol 16:624-629], the detailed structural analysis reports on X-ray-driven reactions have been very rare in literature to date. Here, we report on enzyme activation and the associated chemical reaction in a crystal at 100 K. We propose mechanisms based on water photoradiolysis and/or electron radiolysis as the main cause of enzyme activation.
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Bourgeois D, Weik M. Kinetic protein crystallography: a tool to watch proteins in action. CRYSTALLOGR REV 2009. [DOI: 10.1080/08893110802604868] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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McGeehan J, Ravelli RBG, Murray JW, Owen RL, Cipriani F, McSweeney S, Weik M, Garman EF. Colouring cryo-cooled crystals: online microspectrophotometry. JOURNAL OF SYNCHROTRON RADIATION 2009; 16:163-72. [PMID: 19240328 PMCID: PMC2651762 DOI: 10.1107/s0909049509001629] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Accepted: 01/13/2009] [Indexed: 05/17/2023]
Abstract
X-rays can produce a high concentration of radicals within cryo-cooled macromolecular crystals. Some radicals have large extinction coefficients in the visible (VIS) range of the electromagnetic spectrum, and can be observed optically and spectrally. An online microspectrophotometer with high temporal resolution has been constructed that is capable of measuring UV/VIS absorption spectra (200-1100 nm) during X-ray data collection. The typical X-ray-induced blue colour that is characteristic of a wide range of cryo-conditions has been identified as trapped solvated electrons. Disulphide-containing proteins are shown to form disulphide radicals at millimolar concentrations, with absorption maxima around 400 nm. The solvated electrons and the disulphide radicals seem to have a lifetime in the range of seconds up to minutes at 100 K. The temperature dependence of the kinetics of X-ray-induced radical formation is different for the solvated electrons compared with the disulphide radicals. The online microspectrophotometer provides a technique complementary to X-ray diffraction for analysing and characterizing intermediates and redox states of proteins and enzymes.
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Affiliation(s)
- John McGeehan
- EMBL, 6 rue Jules Horowitz, 38042 Grenoble, France
- Biophysics Laboratories, School of Biological Sciences, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Raimond B. G. Ravelli
- EMBL, 6 rue Jules Horowitz, 38042 Grenoble, France
- Section Electron Microscopy, Department of Molecular Cell Biology, Leiden University Medical Center (LUMC), PO Box 9600, 2300RC Leiden, The Netherlands
- Correspondence e-mail: ,
| | - James W. Murray
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Imperial College, Exhibition Road, London SW7 2AZ, UK
| | - Robin Leslie Owen
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | | | - Martin Weik
- Laboratoire de Biophysique Moléculaire, Institut de Biologie Structurale, Jean Pierre EBEL, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
| | - Elspeth F. Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Correspondence e-mail: ,
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Holton JM. A beginner's guide to radiation damage. JOURNAL OF SYNCHROTRON RADIATION 2009; 16:133-42. [PMID: 19240325 PMCID: PMC2651760 DOI: 10.1107/s0909049509004361] [Citation(s) in RCA: 173] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Accepted: 02/06/2009] [Indexed: 05/04/2023]
Abstract
Many advances in the understanding of radiation damage to protein crystals, particularly at cryogenic temperatures, have been made in recent years, but with this comes an expanding literature, and, to the new breed of protein crystallographer who is not really interested in X-ray physics or radiation chemistry but just wants to solve a biologically relevant structure, the technical nature and breadth of this literature can be daunting. The purpose of this paper is to serve as a rough guide to radiation damage issues, and to provide references to the more exacting and detailed work. No attempt has been made to report precise numbers (a factor of two is considered satisfactory), and, since there are aspects of radiation damage that are demonstrably unpredictable, the 'worst case scenario' as well as the 'average crystal' are discussed in terms of the practicalities of data collection.
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Affiliation(s)
- James M Holton
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2330, USA.
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Owen RL, Pearson AR, Meents A, Boehler P, Thominet V, Schulze-Briese C. A new on-axis multimode spectrometer for the macromolecular crystallography beamlines of the Swiss Light Source. JOURNAL OF SYNCHROTRON RADIATION 2009; 16:173-82. [PMID: 19240329 PMCID: PMC2651763 DOI: 10.1107/s0909049508040120] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2008] [Accepted: 11/27/2008] [Indexed: 05/05/2023]
Abstract
X-ray crystallography at third-generation synchrotron sources permits tremendous insight into the three-dimensional structure of macromolecules. Additional information is, however, often required to aid the transition from structure to function. In situ spectroscopic methods such as UV-Vis absorption and (resonance) Raman can provide this, and can also provide a means of detecting X-ray-induced changes. Here, preliminary results are introduced from an on-axis UV-Vis absorption and Raman multimode spectrometer currently being integrated into the beamline environment at X10SA of the Swiss Light Source. The continuing development of the spectrometer is also outlined.
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Affiliation(s)
- Robin L. Owen
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Arwen R. Pearson
- Astbury Centre for Structural Molecular Biology, Astbury Building, The University of Leeds, Leeds LS2 9JT, UK
| | - Alke Meents
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Pirmin Boehler
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Vincent Thominet
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
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Petrova T, Lunin VY, Ginell S, Hazemann I, Lazarski K, Mitschler A, Podjarny A, Joachimiak A. X-ray-radiation-induced cooperative atomic movements in protein. J Mol Biol 2009; 387:1092-105. [PMID: 19233199 DOI: 10.1016/j.jmb.2009.02.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Revised: 02/06/2009] [Accepted: 02/10/2009] [Indexed: 11/25/2022]
Abstract
X-rays interact with biological matter and cause damage. Proteins and other macromolecules are damaged primarily by ionizing X-ray photons and secondarily by reactive radiolytic chemical species. In particular, protein molecules are damaged during X-ray diffraction experiments with protein crystals, which is, in many cases, a serious hindrance to structure solution. The local X-ray-induced structural changes of the protein molecule have been studied using a number of model systems. However, it is still not well understood whether these local chemical changes lead to global structural changes in protein and what the mechanism is. We present experimental evidence at atomic resolution indicating the movement of large parts of the protein globule together with bound water molecules in the early stages of radiation damage to the protein crystal. The data were obtained from a crystal cryocooled to approximately 100 K and diffracting to 1 A. The movement of the protein structural elements occurs simultaneously with the decarboxylation of several glutamate and aspartate residues that mediate contacts between moving protein structural elements and with the rearrangement of the water network. The analysis of the anisotropy of atomic displacement parameters reveals that the observed atomic movements occur at different rates in different unit cells of the crystal. Thus, the examination of the cooperative atomic movement enables us to better understand how radiation-induced local chemical and structural changes of the protein molecule eventually lead to disorder in protein crystals.
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Affiliation(s)
- Tatiana Petrova
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
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Shoot-and-Trap: use of specific x-ray damage to study structural protein dynamics by temperature-controlled cryo-crystallography. Proc Natl Acad Sci U S A 2008; 105:11742-7. [PMID: 18701720 DOI: 10.1073/pnas.0804828105] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although x-ray crystallography is the most widely used method for macromolecular structure determination, it does not provide dynamical information, and either experimental tricks or complementary experiments must be used to overcome the inherently static nature of crystallographic structures. Here we used specific x-ray damage during temperature-controlled crystallographic experiments at a third-generation synchrotron source to trigger and monitor (Shoot-and-Trap) structural changes putatively involved in an enzymatic reaction. In particular, a nonhydrolyzable substrate analogue of acetylcholinesterase, the "off-switch" at cholinergic synapses, was radiocleaved within the buried enzymatic active site. Subsequent product clearance, observed at 150 K but not at 100 K, indicated exit from the active site possibly via a "backdoor." The simple strategy described here is, in principle, applicable to any enzyme whose structure in complex with a substrate analogue is available and, therefore, could serve as a standard procedure in kinetic crystallography studies.
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De la Mora-Rey T, Wilmot CM. Synergy within structural biology of single crystal optical spectroscopy and X-ray crystallography. Curr Opin Struct Biol 2007; 17:580-6. [PMID: 17959373 DOI: 10.1016/j.sbi.2007.09.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Accepted: 09/11/2007] [Indexed: 11/30/2022]
Abstract
Advances in the adaptation of optical spectroscopy to monitor photo-induced or enzyme-catalyzed reactions in the crystalline state have enabled X-ray crystal structures to be accurately linked with spectroscopically defined intermediates. This, in turn, has led to a deeper understanding of the role protein structural changes play in function. The integration of optical spectroscopy with X-ray crystallography is growing and now extends beyond linking crystal structure to reaction intermediate. Recent examples of this synergy include applications in protein crystallization, X-ray data acquisition, radiation damage, and acquisition of phase information important for structure determination.
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Affiliation(s)
- Teresa De la Mora-Rey
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis 55455, USA
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Watanabe N, Cherney MM, van Belkum MJ, Marcus SL, Flegel MD, Clay MD, Deyholos MK, Vederas JC, James MNG. Crystal Structure of ll-Diaminopimelate Aminotransferase from Arabidopsis thaliana: A Recently Discovered Enzyme in the Biosynthesis of l-Lysine by Plants and Chlamydia. J Mol Biol 2007; 371:685-702. [PMID: 17583737 DOI: 10.1016/j.jmb.2007.05.061] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2007] [Revised: 05/21/2007] [Accepted: 05/22/2007] [Indexed: 11/18/2022]
Abstract
The essential biosynthetic pathway to l-Lysine in bacteria and plants is an attractive target for the development of new antibiotics or herbicides because it is absent in humans, who must acquire this amino acid in their diet. Plants use a shortcut of a bacterial pathway to l-Lysine in which the pyridoxal-5'-phosphate (PLP)-dependent enzyme ll-diaminopimelate aminotransferase (LL-DAP-AT) transforms l-tetrahydrodipicolinic acid (L-THDP) directly to LL-DAP. In addition, LL-DAP-AT was recently found in Chlamydia sp., suggesting that inhibitors of this enzyme may also be effective against such organisms. In order to understand the mechanism of this enzyme and to assist in the design of inhibitors, the three-dimensional crystal structure of LL-DAP-AT was determined at 1.95 A resolution. The cDNA sequence of LL-DAP-AT from Arabidopsis thaliana (AtDAP-AT) was optimized for expression in bacteria and cloned in Escherichia coli without its leader sequence but with a C-terminal hexahistidine affinity tag to aid protein purification. The structure of AtDAP-AT was determined using the multiple-wavelength anomalous dispersion (MAD) method with a seleno-methionine derivative. AtDAP-AT is active as a homodimer with each subunit having PLP in the active site. It belongs to the family of type I fold PLP-dependent enzymes. Comparison of the active site residues of AtDAP-AT and aspartate aminotransferases revealed that the PLP binding residues in AtDAP-AT are well conserved in both enzymes. However, Glu97* and Asn309* in the active site of AtDAP-AT are not found at similar positions in aspartate aminotransferases, suggesting that specific substrate recognition may require these residues from the other monomer. A malate-bound structure of AtDAP-AT allowed LL-DAP and L-glutamate to be modelled into the active site. These initial three-dimensional structures of LL-DAP-AT provide insight into its substrate specificity and catalytic mechanism.
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Affiliation(s)
- Nobuhiko Watanabe
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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Holton JM. XANES measurements of the rate of radiation damage to selenomethionine side chains. JOURNAL OF SYNCHROTRON RADIATION 2007; 14:51-72. [PMID: 17211072 PMCID: PMC2806430 DOI: 10.1107/s0909049506048898] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2006] [Accepted: 11/15/2006] [Indexed: 05/13/2023]
Abstract
The radiation-induced disordering of selenomethionine (SeMet) side chains represents a significant impediment to protein structure solution. Not only does the increased B-factor of these sites result in a serious drop in phasing power, but some sites decay much faster than others in the same unit cell. These radio-labile SeMet side chains decay faster than high-order diffraction spots with dose, making it difficult to detect this kind of damage by inspection of the diffraction pattern. The selenium X-ray absorbance near-edge spectrum (XANES) from samples containing SeMet was found to change significantly after application of X-ray doses of 10-100 MGy. Most notably, the sharp ;white line' feature near the canonical Se edge disappears. The change was attributed to breakage of the Cgamma-Se bond in SeMet. This spectral change was used as a probe to measure the decay rate of SeMet with X-ray dose in cryo-cooled samples. Two protein crystal types and 15 solutions containing free SeMet amino acid were examined. The damage rate was influenced by the chemical and physical condition of the sample, and the half-decaying dose for the selenium XANES signal ranged from 5 to 43 MGy. These decay rates were 34- to 3.8-fold higher than the rate at which the Se atoms interacted directly with X-ray photons, so the damage mechanism must be a secondary effect. Samples that cooled to a more crystalline state generally decayed faster than samples that cooled to an amorphous solid. The single exception was a protein crystal where a nanocrystalline cryoprotectant had a protective effect. Lowering the pH, especially with ascorbic or nitric acids, had a protective effect, and SeMet lifetime increased monotonically with decreasing sample temperature (down to 93 K). The SeMet lifetime in one protein crystal was the same as that of the free amino acid, and the longest SeMet lifetime measured was found in the other protein crystal type. This protection was found to arise from the folded structure of the protein molecule. A mechanism to explain observed decay rates involving the damaging species following the electric field lines around protein molecules is proposed.
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Affiliation(s)
- James M Holton
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2330, USA.
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