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Fobe TL, Kazakov A, Riccardi D. Cys.sqlite: A Structured-Information Approach to the Comprehensive Analysis of Cysteine Disulfide Bonds in the Protein Databank. J Chem Inf Model 2019; 59:931-943. [PMID: 30694665 PMCID: PMC6999612 DOI: 10.1021/acs.jcim.8b00950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cysteine is a multifaceted amino acid that is central to the structure and function of many proteins. A disulfide bond formed between two cysteines restrains protein conformations through the strong covalent bond and torsions about the bond that prefer, energetically, ±90°. In this study, we transform over 30 000 Protein Databank files (PDBx/mmCIFs) into a single file, the SQLite database (Cys.sqlite). The database schema is designed to accommodate the structural information on both oxidized and reduced cysteines and to retain essential protein metadata to establish informational and biological provenance. Cys.sqlite contains over 95 000 peptide chains and 500 000 cysteines (700 000 structural conformers); there are over 265 000 cysteine disulfide bond conformations from structures solved with all available experimental methods. The structural information is analyzed with respect to sequence identity cutoff, the experimental method, and energetics of the disulfide. We find that as the experimental information becomes limiting and the influence of modeling becomes more pronounced, the observed average strain increases artificially. The database and analyses presented here can be used to improve the refinement of biological structures from experiments that are known to contain one or more disulfide bonds.
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Affiliation(s)
- Theodore L Fobe
- University of Maryland , Department of Chemical and Biomolecular Engineering , College Park , Maryland 20742 , United States
- Summer Undergraduate Research Fellowship , National Institute of Standards and Technology , Boulder , Colorado 80305 , United States
| | - Andrei Kazakov
- Applied Chemicals and Materials Division , National Institute of Standards and Technology , Boulder , Colorado 80305 , United States
| | - Demian Riccardi
- Applied Chemicals and Materials Division , National Institute of Standards and Technology , Boulder , Colorado 80305 , United States
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Haworth NL, Wouters MJ, Hunter MO, Ma L, Wouters MA. Cross-strand disulfides in the hydrogen bonding site of antiparallel β-sheet (aCSDhs): Forbidden disulfides that are highly strained, easily broken. Protein Sci 2018; 28:239-256. [PMID: 30383331 DOI: 10.1002/pro.3545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/30/2018] [Accepted: 10/30/2018] [Indexed: 12/16/2022]
Abstract
Some disulfide bonds perform important structural roles in proteins, but another group has functional roles via redox reactions. Forbidden disulfides are stressed disulfides found in recognizable protein contexts, which currently constitute more than 10% of all disulfides in the PDB. They likely have functional redox roles and constitute a major subset of all redox-active disulfides. The torsional strain of forbidden disulfides is typically higher than for structural disulfides, but not so high as to render them immediately susceptible to reduction under physionormal conditions. Previously we characterized the most abundant forbidden disulfide in the Protein Data Bank, the aCSDn: a canonical motif in which disulfide-bonded cysteine residues are positioned directly opposite each other on adjacent anti-parallel β-strands such that the backbone hydrogen-bonded moieties are directed away from each other. Here we perform a similar analysis for the aCSDh, a less common motif in which the opposed cysteine residues are backbone hydrogen bonded. Oxidation of two Cys in this context places significant strain on the protein system, with the β-chains tilting toward each other to allow disulfide formation. Only left-handed aCSDh conformations are compatible with the inherent right-handed twist of β-sheets. aCSDhs tend to be more highly strained than aCSDns, particularly when both hydrogen bonds are formed. We discuss characterized roles of aCSDh motifs in proteins of the dataset, which include catalytic disulfides in ribonucleotide reductase and ahpC peroxidase as well as a redox-active disulfide in P1 lysozyme, involved in a major conformation change. The dataset also includes many binding proteins.
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Affiliation(s)
- Naomi L Haworth
- Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia.,Structural & Computational Biology Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Michael J Wouters
- Electricity Section, National Measurement Institute, Lindfield, New South Wales, Australia
| | - Morgan O Hunter
- Bioinformatics, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Lixia Ma
- School of Statistics, Henan University of Economics and Law, Henan Province, China
| | - Merridee A Wouters
- Bioinformatics, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia.,Cancer Data Science, Children's Medical Research Institute, Westmead, New South Wales, Australia
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Zheng L, Yu C, Zhan Y, Deng X, Wang Y, Jiang H. Locking Interconversion of Aromatic Oligoamide Foldamers by Intramolecular Side-chain Crosslinking: toward Absolute Control of Helicity in Synthetic Aromatic Foldamers. Chemistry 2017; 23:5361-5367. [DOI: 10.1002/chem.201700134] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Lu Zheng
- Key Laboratory of Theoretical and Computational Photochemistry, and Key Laboratory of Radiopharmaceuticals; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 P. R. China
| | - Chengyuan Yu
- Key Laboratory of Theoretical and Computational Photochemistry, and Key Laboratory of Radiopharmaceuticals; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 P. R. China
| | - Yulin Zhan
- Key Laboratory of Theoretical and Computational Photochemistry, and Key Laboratory of Radiopharmaceuticals; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 P. R. China
| | - Xuebin Deng
- Key Laboratory of Theoretical and Computational Photochemistry, and Key Laboratory of Radiopharmaceuticals; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 P. R. China
| | - Ying Wang
- Key Laboratory of Theoretical and Computational Photochemistry, and Key Laboratory of Radiopharmaceuticals; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 P. R. China
| | - Hua Jiang
- Key Laboratory of Theoretical and Computational Photochemistry, and Key Laboratory of Radiopharmaceuticals; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 P. R. China
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Wen J, Yang K, Liu F, Li H, Xu Y, Sun S. Diverse gatekeepers for mesoporous silica nanoparticle based drug delivery systems. Chem Soc Rev 2017; 46:6024-6045. [DOI: 10.1039/c7cs00219j] [Citation(s) in RCA: 312] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Progress on the design of diverse gatekeepers for mesoporous silica nanoparticle based drug delivery systems is summarized.
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Affiliation(s)
- Jia Wen
- Shaanxi Key Laboratory of Natural Products & Chemical Biology
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling
- P. R. China
| | - Kui Yang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling
- P. R. China
| | - Fengyu Liu
- State Key Laboratory of Fine Chemicals
- School of Chemistry
- Dalian University of Technology
- Dalian 116023
- China
| | - Hongjuan Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling
- P. R. China
| | - Yongqian Xu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling
- P. R. China
| | - Shiguo Sun
- Shaanxi Key Laboratory of Natural Products & Chemical Biology
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling
- P. R. China
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