1
|
Zhang X, Blumenthal RM, Cheng X. Updated understanding of the protein-DNA recognition code used by C2H2 zinc finger proteins. Curr Opin Struct Biol 2024; 87:102836. [PMID: 38754172 DOI: 10.1016/j.sbi.2024.102836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024]
Abstract
C2H2 zinc-finger (ZF) proteins form the largest family of DNA-binding transcription factors coded by mammalian genomes. In a typical DNA-binding ZF module, there are twelve residues (numbered from -1 to -12) between the last zinc-coordinating cysteine and the first zinc-coordinating histidine. The established C2H2-ZF "recognition code" suggests that residues at positions -1, -4, and -7 recognize the 5', central, and 3' bases of a DNA base-pair triplet, respectively. Structural studies have highlighted that additional residues at positions -5 and -8 also play roles in specific DNA recognition. The presence of bulky and either charged or polar residues at these five positions determines specificity for given DNA bases: guanine is recognized by arginine, lysine, or histidine; adenine by asparagine or glutamine; thymine or 5-methylcytosine by glutamate; and unmodified cytosine by aspartate. This review discusses recent structural characterizations of C2H2-ZFs that add to our understanding of the principles underlying the C2H2-ZF recognition code.
Collapse
Affiliation(s)
- Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA.
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| |
Collapse
|
2
|
Nishito Y, Kamimura Y, Nagamatsu S, Yamamoto N, Yasui H, Kambe T. Zinc and manganese homeostasis closely interact in mammalian cells. FASEB J 2024; 38:e23605. [PMID: 38597508 DOI: 10.1096/fj.202400181r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 03/13/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024]
Abstract
Understanding the homeostatic interactions among essential trace metals is important for explaining their roles in cellular systems. Recent studies in vertebrates suggest that cellular Mn metabolism is related to Zn metabolism in multifarious cellular processes. However, the underlying mechanism remains unclear. In this study, we examined the changes in the expression of proteins involved in cellular Zn and/or Mn homeostatic control and measured the Mn as well as Zn contents and Zn enzyme activities to elucidate the effects of Mn and Zn homeostasis on each other. Mn treatment decreased the expression of the Zn homeostatic proteins metallothionein (MT) and ZNT1 and reduced Zn enzyme activities, which were attributed to the decreased Zn content. Moreover, loss of Mn efflux transport protein decreased MT and ZNT1 expression and Zn enzyme activity without changing extracellular Mn content. This reduction was not observed when supplementing with the same Cu concentrations and in cells lacking Cu efflux proteins. Furthermore, cellular Zn homeostasis was oppositely regulated in cells expressing Zn and Mn importer ZIP8, depending on whether Zn or Mn concentration was elevated in the extracellular milieu. Our results provide novel insights into the intricate interactions between Mn and Zn homeostasis in mammalian cells and facilitate our understanding of the physiopathology of Mn, which may lead to the development of treatment strategies for Mn-related diseases in the future.
Collapse
Affiliation(s)
- Yukina Nishito
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Yoshiki Kamimura
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Shino Nagamatsu
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Nao Yamamoto
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Hiroyuki Yasui
- Department of Analytical and Bioinorganic Chemistry, Division of Analytical and Physical Sciences, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Taiho Kambe
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| |
Collapse
|
3
|
Zheng H, Zhang H, Zhong J, Gucwa M, Zhang Y, Ma H, Deng L, Mao L, Minor W, Wang N. PinMyMetal: A hybrid learning system to accurately model metal binding sites in macromolecules. RESEARCH SQUARE 2024:rs.3.rs-3908734. [PMID: 38463967 PMCID: PMC10925427 DOI: 10.21203/rs.3.rs-3908734/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Metal ions are vital components in many proteins for the inference and engineering of protein function, with coordination complexity linked to structural (4-residue predominate), catalytic (3-residue predominate), or regulatory (2-residue predominate) roles. Computational tools for modeling metal ions in protein structures, especially for transient, reversible, and concentration-dependent regulatory sites, remain immature. We present PinMyMetal (PMM), a sophisticated hybrid machine learning system for predicting zinc ion localization and environment in macromolecular structures. Compared to other predictors, PMM excels in predicting regulatory sites (median deviation of 0.34 Å), demonstrating superior accuracy in locating catalytic sites (median deviation of 0.27 Å) and structural sites (median deviation of 0.14 Å). PMM assigns a certainty score to each predicted site based on local structural and physicochemical features independent of homolog presence. Interactive validation through our server, CheckMyMetal, expands PMM's scope, enabling it to pinpoint and validates diverse functional zinc sites from different structure sources (predicted structures, cryo-EM and crystallography). This facilitates residue-wise assessment and robust metal binding site design. The lightweight PMM system demands minimal computing resources and is available at https://PMM.biocloud.top. While currently trained on zinc, the PMM workflow can easily adapt to other metals through expanded training data.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Lei Deng
- Hunan University College of Biology
| | | | | | - Nasui Wang
- Division of Endocrinology and Metabolism, The First Affiliated Hospital of Shantou University Medical College
| |
Collapse
|
4
|
Lan Y, Kuktaite R, Chawade A, Johansson E. Chasing high and stable wheat grain mineral content: Mining diverse spring genotypes under induced drought stress. PLoS One 2024; 19:e0298350. [PMID: 38359024 PMCID: PMC10868752 DOI: 10.1371/journal.pone.0298350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
Climate change-induced drought has an effect on the nutritional quality of wheat. Here, the impact of drought at different plant stages on mineral content in mature wheat was evaluated in 30 spring-wheat lines of diverse backgrounds (modern, old and wheat-rye-introgressions). Genotypes with rye chromosome 3R introgression showed a high accumulation of several important minerals, including Zn and Fe, and these also showed stability across drought conditions. High Se content was found in genotypes with chromosome 1R. Old cultivars (K, Mg, Na, P and S) and 2R introgression lines (Fe, Ca, Mn, Mg and Na) demonstrated high mineral yield at early and late drought, respectively. Based on the low nutritional value often reported for modern wheat and negative climate effects on the stability of mineral content and yield, genes conferring high Zn/Fe, Se, and stable mineral yield under drought at various plant stages should be explicitly explored among 3R, 1R, old and 2R genotypes, respectively.
Collapse
Affiliation(s)
- Yuzhou Lan
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Ramune Kuktaite
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Aakash Chawade
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Eva Johansson
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, Lomma, Sweden
| |
Collapse
|
5
|
Aboelnga MM, Gauld JW. Screening a library of potential competitive inhibitors against bacterial threonyl-tRNA synthetase: DFT calculations. J Biomol Struct Dyn 2023:1-9. [PMID: 37909495 DOI: 10.1080/07391102.2023.2276878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/24/2023] [Indexed: 11/03/2023]
Abstract
Due to the growing interest in directing aminoacyl-tRNA synthetases for antimicrobial therapies, evaluating the binding proficiency of potential inhibitors against this target holds significant importance. In this work, we proposed potential ligands that could properly bind to the crucial Zn(II) cofactor located in the active site of Threonyl-tRNA synthetases (ThrRS), potentially functioning as competitive inhibitors. Initially, detailed DFT quantum chemical study was conducted to examine the binding ability of threonine against unnatural amino acids to cofactor Zn(II). Then, the binding energy value for each suggested ligand has been determined and compared to the value determined for the native substrate, threonine. Our screening investigation showed that the native threonine should coordinate in a bidentate fashion to this Zn(II) which lead to the highest (binding energy) BE Thereby, the synthetic site of ThrRS rejects unnatural amino acids that cannot afford this type of coordination to Zn(II) ion which has been supported by our calculations. Moreover, based on their binding to the Zn(II) and the obtained BE values compared to the cognate threonine, many potent ligands have been suggested. Importantly, ligands with deprotonated warheads showed the highest binding ability amongst a list of potential hits. Further investigation on the selected ligands using molecular docking and QM/MM calculations confirmed our findings of the suggested ligands being able to bind efficiently in the active site of ThrRS. The suggested hits from this study should be valuable in paving routs for developing candidates as competitive inhibitors against the bacterial ThrRS.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Mohamed M Aboelnga
- Department of Chemistry, Faculty of Science, Damietta University, New Damietta, Egypt
| | - James W Gauld
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Canada
| |
Collapse
|
6
|
Suh JM, Kim M, Yoo J, Han J, Paulina C, Lim MH. Intercommunication between metal ions and amyloidogenic peptides or proteins in protein misfolding disorders. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
7
|
Ghosh MK, Tamang AM, Chandraker SK, Sikdar S, Jana B, Ghorai TK. Zn(II)-formate Framework of mab topology: Synthesis from tea extract, electronic structure, and DNA-binding. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
|
8
|
Mazmanian K, Chen T, Sargsyan K, Lim C. From quantum-derived principles underlying cysteine reactivity to combating the COVID-19 pandemic. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2022; 12:e1607. [PMID: 35600063 PMCID: PMC9111396 DOI: 10.1002/wcms.1607] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/31/2022] [Accepted: 02/13/2022] [Indexed: 12/20/2022]
Abstract
The COVID‐19 pandemic poses a challenge in coming up with quick and effective means to counter its cause, the SARS‐CoV‐2. Here, we show how the key factors governing cysteine reactivity in proteins derived from combined quantum mechanical/continuum calculations led to a novel multi‐targeting strategy against SARS‐CoV‐2, in contrast to developing potent drugs/vaccines against a single viral target such as the spike protein. Specifically, they led to the discovery of reactive cysteines in evolutionary conserved Zn2+‐sites in several SARS‐CoV‐2 proteins that are crucial for viral polypeptide proteolysis as well as viral RNA synthesis, proofreading, and modification. These conserved, reactive cysteines, both free and Zn2+‐bound, can be targeted using the same Zn‐ejector drug (disulfiram/ebselen), which enables the use of broad‐spectrum anti‐virals that would otherwise be removed by the virus's proofreading mechanism. Our strategy of targeting multiple, conserved viral proteins that operate at different stages of the virus life cycle using a Zn‐ejector drug combined with other broad‐spectrum anti‐viral drug(s) could enhance the barrier to drug resistance and antiviral effects, as compared to each drug alone. Since these functionally important nonstructural proteins containing reactive cysteines are highly conserved among coronaviruses, our proposed strategy has the potential to tackle future coronaviruses. This article is categorized under:Structure and Mechanism > Reaction Mechanisms and Catalysis Structure and Mechanism > Computational Biochemistry and Biophysics Electronic Structure Theory > Density Functional Theory
Collapse
Affiliation(s)
| | - Ting Chen
- Institute of Biomedical Sciences Academia Sinica Taipei Taiwan
| | - Karen Sargsyan
- Institute of Biomedical Sciences Academia Sinica Taipei Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences Academia Sinica Taipei Taiwan.,Department of Chemistry National Tsing Hua University Hsinchu Taiwan
| |
Collapse
|
9
|
Natasha N, Shahid M, Bibi I, Iqbal J, Khalid S, Murtaza B, Bakhat HF, Farooq ABU, Amjad M, Hammad HM, Niazi NK, Arshad M. Zinc in soil-plant-human system: A data-analysis review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:152024. [PMID: 34871690 DOI: 10.1016/j.scitotenv.2021.152024] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 05/27/2023]
Abstract
Zinc (Zn) plays an important role in the physiology and biochemistry of plants due to its established essentiality and toxicity for living beings at certain Zn concentration i.e., deficient or toxic over the optimum range. Being a vital cofactor of important enzymes, Zn participates in plant metabolic processes therefore, alters the biophysicochemical processes mediated by Zn-related enzymes/proteins. Excess Zn can provoke oxidative damage by enhancing the levels of reactive radicals. Hence, it is imperative to monitor Zn levels and associated biophysicochemical roles, essential or toxic, in the soil-plant interactions. This data-analysis review has critically summarized the recent literature of (i) Zn mobility/phytoavailability in soil (ii) molecular understanding of Zn phytouptake, (iii) uptake and distribution in the plants, (iv) essential roles in plants, (v) phyto-deficiency and phytotoxicity, (vi) detoxification processes to scavenge Zn phytotoxicity inside plants, and (vii) associated health hazards. The review especially compares the essential, deficient and toxic roles of Zn in biophysicochemical and detoxification processes inside the plants. To conclude, this review recommends some Zn-related research perspectives. Overall, this review reveals a thorough representation of Zn bio-geo-physicochemical interactions in soil-plant system using recent data.
Collapse
Affiliation(s)
- Natasha Natasha
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari 61100, Pakistan
| | - Muhammad Shahid
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari 61100, Pakistan.
| | - Irshad Bibi
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Jibran Iqbal
- College of Natural and Health Sciences, Zayed University, Abu Dhabi, United Arab Emirates
| | - Sana Khalid
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari 61100, Pakistan
| | - Behzad Murtaza
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari 61100, Pakistan
| | - Hafiz Faiq Bakhat
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari 61100, Pakistan
| | - Abu Bakr Umer Farooq
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari 61100, Pakistan
| | - Muhammad Amjad
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari 61100, Pakistan
| | - Hafiz Mohkum Hammad
- Department of Agronomy, Muhammad Nawaz Shreef University of Agriculture, Multan 66000, Pakistan
| | - Nabeel Khan Niazi
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Muhammad Arshad
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology, Sector H-12, Islamabad, 44000, Pakistan
| |
Collapse
|
10
|
Sousa SF, Calixto AR, Ferreira P, Ramos MJ, Lim C, Fernandes PA. Activation Free Energy, Substrate Binding Free Energy, and Enzyme Efficiency Fall in a Very Narrow Range of Values for Most Enzymes. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01947] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sérgio F. Sousa
- UCIBIO, REQUIMTE, Departamento de Quı́mica e Bioquı́mica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Ana R. Calixto
- UCIBIO, REQUIMTE, Departamento de Quı́mica e Bioquı́mica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro Ferreira
- UCIBIO, REQUIMTE, Departamento de Quı́mica e Bioquı́mica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO, REQUIMTE, Departamento de Quı́mica e Bioquı́mica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Pedro A. Fernandes
- UCIBIO, REQUIMTE, Departamento de Quı́mica e Bioquı́mica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| |
Collapse
|
11
|
Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview. Molecules 2019; 24:molecules24132462. [PMID: 31277490 PMCID: PMC6651669 DOI: 10.3390/molecules24132462] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 11/16/2022] Open
Abstract
Nature has tailored a wide range of metalloenzymes that play a vast array of functions in all living organisms and from which their survival and evolution depends on. These enzymes catalyze some of the most important biological processes in nature, such as photosynthesis, respiration, water oxidation, molecular oxygen reduction, and nitrogen fixation. They are also among the most proficient catalysts in terms of their activity, selectivity, and ability to operate at mild conditions of temperature, pH, and pressure. In the absence of these enzymes, these reactions would proceed very slowly, if at all, suggesting that these enzymes made the way for the emergence of life as we know today. In this review, the structure and catalytic mechanism of a selection of diverse metalloenzymes that are involved in the production of highly reactive and unstable species, such as hydroxide anions, hydrides, radical species, and superoxide molecules are analyzed. The formation of such reaction intermediates is very difficult to occur under biological conditions and only a rationalized selection of a particular metal ion, coordinated to a very specific group of ligands, and immersed in specific proteins allows these reactions to proceed. Interestingly, different metal coordination spheres can be used to produce the same reactive and unstable species, although through a different chemistry. A selection of hand-picked examples of different metalloenzymes illustrating this diversity is provided and the participation of different metal ions in similar reactions (but involving different mechanism) is discussed.
Collapse
|
12
|
|
13
|
|
14
|
Akhtar M, Georgieva I, Zahariev T, Trendafilova N, Ahmad T, Noor A, Tahir MN, Mazhar M, Isab AA, Ahmad S. Synthesis, X-ray structure, and DFT modeling of a new polymeric zinc(II) complex of 2-mercaptonicotinic acid (MntH), {[Zn(Mnt–Mnt)(en)]·H2O}n. MONATSHEFTE FUR CHEMIE 2019. [DOI: 10.1007/s00706-018-2330-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
15
|
The inhibitory effect of the amino acid complexes of Zn(II) on the growth of Aspergillus flavus and aflatoxin B1 production. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2019. [DOI: 10.1007/s13738-018-01581-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
16
|
|
17
|
DNA-BSA interaction, cytotoxicity and molecular docking of mononuclear zinc complexes with reductively cleaved N2S2 Schiff base ligands. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2018.08.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
18
|
Mazmanian K, Dudev T, Lim C. How First Shell–Second Shell Interactions and Metal Substitution Modulate Protein Function. Inorg Chem 2018; 57:14052-14061. [DOI: 10.1021/acs.inorgchem.8b01029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Karine Mazmanian
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 10617, Taiwan
- Taiwan and Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University, Sofia 1164, Bulgaria
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| |
Collapse
|
19
|
Crystal Chemistry of Zinc Quinaldinate Complexes with Pyridine-Based Ligands. CRYSTALS 2018. [DOI: 10.3390/cryst8010052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
20
|
Bellotti D, Łoboda D, Rowińska-Żyrek M, Remelli M. Investigation on the metal binding sites of a putative Zn(ii) transporter in opportunistic yeast species Candida albicans. NEW J CHEM 2018. [DOI: 10.1039/c8nj00533h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The protein fragment C4YJH2 of Candida albicans has the ability to tightly coordinate Zn(ii) at its C-terminal region by means of an evolutionarily well-conserved histidine-rich sequence.
Collapse
Affiliation(s)
- Denise Bellotti
- Department of Chemical and Pharmaceutical Sciences
- University of Ferrara
- I-44121 Ferrara
- Italy
| | - Dorota Łoboda
- Faculty of Chemistry
- University of Wroclaw
- 50-383 Wroclaw
- Poland
| | | | - Maurizio Remelli
- Department of Chemical and Pharmaceutical Sciences
- University of Ferrara
- I-44121 Ferrara
- Italy
| |
Collapse
|
21
|
Linder DP, Baker BE, Rodgers KR. [(H2O)Zn(Imidazole)n]2+: the vital roles of coordination number and geometry in Zn–OH2 acidity and catalytic hydrolysis. Phys Chem Chem Phys 2018; 20:24979-24991. [DOI: 10.1039/c8cp03121e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Zn(ii)–(Imidazole(ate))n coordination motif occurs in numerous biochemical systems, including carbonic anhydrase and the matrix metalloproteinases (MMPs).
Collapse
Affiliation(s)
- Douglas P. Linder
- Department of Chemistry and Physics
- Southwestern Oklahoma State University
- Weatherford
- USA
| | - Brett E. Baker
- Department of Chemistry and Physics
- Southwestern Oklahoma State University
- Weatherford
- USA
| | - Kenton R. Rodgers
- Department of Chemistry and Biochemistry
- North Dakota State University
- Fargo
- USA
| |
Collapse
|
22
|
Zborovsky L, Smolyakova A, Baskin M, Maayan G. A Pure Polyproline Type I-like Peptoid Helix by Metal Coordination. Chemistry 2017; 24:1159-1167. [DOI: 10.1002/chem.201704497] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Lieby Zborovsky
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 32000 Israel
| | - Alisa Smolyakova
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 32000 Israel
| | - Maria Baskin
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 32000 Israel
| | - Galia Maayan
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 32000 Israel
| |
Collapse
|
23
|
Maiti BK, Almeida RM, Moura I, Moura JJ. Rubredoxins derivatives: Simple sulphur-rich coordination metal sites and its relevance for biology and chemistry. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
24
|
Aboelnga MM, Gauld JW. Roles of the Active Site Zn(II) and Residues in Substrate Discrimination by Threonyl-tRNA Synthetase: An MD and QM/MM Investigation. J Phys Chem B 2017; 121:6163-6174. [PMID: 28592109 DOI: 10.1021/acs.jpcb.7b03782] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Threonyl-tRNA synthetase (ThrRS) is a Zn(II) containing enzyme that catalyzes the activation of threonine and its subsequent transfer to the cognate tRNA. This process is accomplished with remarkable fidelity, with ThrRS being able to discriminate its cognate substrate from similar analogues such as serine and valine. Molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) methods have been used to elucidate the role of Zn(II) in the aminoacylation mechanism of ThrRS. More specifically, the role of Zn(II) and active site residues in ThrRS's ability to discriminate between its cognate substrate l-threonine and the noncognate l-serine, l-valine, and d-threonine has been examined. The present results suggest that a role of the Zn(II) ion, with its Lewis acidity, is to facilitate deprotonation of the side chain hydroxyl groups of the aminoacyl moieties of cognate Thr-AMP and noncognate Ser-AMP substrates. In their deprotonated forms, these substrates are able to adopt a conformation preferable for aminoacyl transfer from aa-AMP onto the Ado-3'OH of the tRNAThr cosubstrate. Relative to the neutral substrates, when the substrates are first deprotonated with the assistance of the Zn(II) ion, the barrier for the rate-limiting step is decreased significantly by 42.0 and 39.2 kJ mol-1 for l-Thr-AMP and l-Ser-AMP, respectively. An active site arginyl also plays a key role in stabilizing the buildup of negative charge on the substrate's bridging phosphate oxygen during the mechanism. For the enantiomeric substrate analogue d-Thr-AMP, product formation is highly disfavored, and as a result, the reverse reaction has a very low barrier of 16.0 kJ mol-1.
Collapse
Affiliation(s)
- Mohamed M Aboelnga
- Department of Chemistry and Biochemistry, University of Windsor , Windsor, Ontario, N9B 3P4, Canada.,Department of Chemistry, Faculty of Science, University of Damietta , New Damietta, Damietta Governorate 34511, Egypt
| | - James W Gauld
- Department of Chemistry and Biochemistry, University of Windsor , Windsor, Ontario, N9B 3P4, Canada
| |
Collapse
|
25
|
Synthesis, crystal structure and DFT studies of a Zinc(II) complex of 1,3-diaminopropane (Dap), [Zn(Dap)(NCS)2][Zn(Dap)(NCS)2]n. The additional stabilizing role of S⋯π chalcogen bond. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.11.085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
26
|
Ahlstrand E, Hermansson K, Friedman R. Interaction Energies in Complexes of Zn and Amino Acids: A Comparison of Ab Initio and Force Field Based Calculations. J Phys Chem A 2017; 121:2643-2654. [DOI: 10.1021/acs.jpca.6b12969] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Emma Ahlstrand
- Department of Chemistry
and Biomedical Sciences, Linnæus University, 391 82 Kalmar, Sweden
- Linnæus University Centre for Biomaterials Chemistry, 391 82 Kalmar, Sweden
| | - Kersti Hermansson
- Department of Chemistry, Ångström Laboratory, Uppsala University, Box 538, 751 21 Uppsala, Sweden
| | - Ran Friedman
- Department of Chemistry
and Biomedical Sciences, Linnæus University, 391 82 Kalmar, Sweden
- Linnæus University Centre for Biomaterials Chemistry, 391 82 Kalmar, Sweden
| |
Collapse
|
27
|
Baskin M, Fridman N, Kosa M, Maayan G. Heteroleptic complexesviasolubility control: examples of Cu(ii), Co(ii), Ni(ii) and Mn(ii) complexes based on the derivatives of terpyridine and hydroxyquinoline. Dalton Trans 2017; 46:15330-15339. [DOI: 10.1039/c7dt03387g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We describe the preparation of synthetically challenging heteroleptic complexes by considering the solubility properties of their corresponding favored homoleptic complexes.
Collapse
Affiliation(s)
- Maria Baskin
- Schulich Faculty of Chemistry
- Technion-Israel Institute of Technology
- Haifa
- Israel
| | - Natalia Fridman
- Schulich Faculty of Chemistry
- Technion-Israel Institute of Technology
- Haifa
- Israel
| | - Monica Kosa
- Schulich Faculty of Chemistry
- Technion-Israel Institute of Technology
- Haifa
- Israel
| | - Galia Maayan
- Schulich Faculty of Chemistry
- Technion-Israel Institute of Technology
- Haifa
- Israel
| |
Collapse
|
28
|
Ferranco A, Basak S, Lough A, Kraatz HB. Metal coordination of ferrocene–histidine conjugates. Dalton Trans 2017; 46:4844-4859. [PMID: 28349138 DOI: 10.1039/c7dt00456g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Synthesis and complete structural characterization of ferrocene–histidine dipeptides including detailed analysis of the ligand–metal complexation.
Collapse
Affiliation(s)
- Annaleizle Ferranco
- Department of Physical and Environmental Sciences
- University of Toronto
- Toronto
- M1C 1A4 Canada
- Department of Chemistry
| | - Shibaji Basak
- Department of Physical and Environmental Sciences
- University of Toronto
- Toronto
- M1C 1A4 Canada
- Department of Chemistry
| | - Alan Lough
- Department of Chemistry
- University of Toronto
- Toronto
- M5S 3H6 Canada
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences
- University of Toronto
- Toronto
- M1C 1A4 Canada
- Department of Chemistry
| |
Collapse
|
29
|
Touw WG, van Beusekom B, Evers JMG, Vriend G, Joosten RP. Validation and correction of Zn-Cys xHis y complexes. Acta Crystallogr D Struct Biol 2016; 72:1110-1118. [PMID: 27710932 PMCID: PMC5053137 DOI: 10.1107/s2059798316013036] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 08/12/2016] [Indexed: 11/10/2022] Open
Abstract
Many crystal structures in the Protein Data Bank contain zinc ions in a geometrically distorted tetrahedral complex with four Cys and/or His ligands. A method is presented to automatically validate and correct these zinc complexes. Analysis of the corrected zinc complexes shows that the average Zn-Cys distances and Cys-Zn-Cys angles are a function of the number of cysteines and histidines involved. The observed trends can be used to develop more context-sensitive targets for model validation and refinement.
Collapse
Affiliation(s)
- Wouter G. Touw
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein-Zuid 26-28, 6525 GA Nijmegen, The Netherlands
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Bart van Beusekom
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Jochem M. G. Evers
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein-Zuid 26-28, 6525 GA Nijmegen, The Netherlands
| | - Gert Vriend
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein-Zuid 26-28, 6525 GA Nijmegen, The Netherlands
| | - Robbie P. Joosten
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| |
Collapse
|
30
|
Nakashige TG, Stephan JR, Cunden LS, Brophy MB, Wommack AJ, Keegan BC, Shearer JM, Nolan EM. The Hexahistidine Motif of Host-Defense Protein Human Calprotectin Contributes to Zinc Withholding and Its Functional Versatility. J Am Chem Soc 2016; 138:12243-51. [PMID: 27541598 PMCID: PMC5038136 DOI: 10.1021/jacs.6b06845] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Human calprotectin (CP, S100A8/S100A9 oligomer, MRP-8/MRP-14 oligomer) is an abundant host-defense protein that is involved in the metal-withholding innate immune response. CP coordinates a variety of divalent first-row transition metal ions, which is implicated in its antimicrobial function, and its ability to sequester nutrient Zn(II) ions from microbial pathogens has been recognized for over two decades. CP has two distinct transition-metal-binding sites formed at the S100A8/S100A9 dimer interface, including a histidine-rich site composed of S100A8 residues His17 and His27 and S100A9 residues His91 and His95. In this study, we report that CP binds Zn(II) at this site using a hexahistidine motif, completed by His103 and His105 of the S100A9 C-terminal tail and previously identified as the high-affinity Mn(II) and Fe(II) coordination site. Zn(II) binding at this unique site shields the S100A9 C-terminal tail from proteolytic degradation by proteinase K. X-ray absorption spectroscopy and Zn(II) competition titrations support the formation of a Zn(II)-His6 motif. Microbial growth studies indicate that the hexahistidine motif is important for preventing microbial Zn(II) acquisition from CP by the probiotic Lactobacillus plantarum and the opportunistic human pathogen Candida albicans. The Zn(II)-His6 site of CP expands the known biological coordination chemistry of Zn(II) and provides new insight into how the human innate immune system starves microbes of essential metal nutrients.
Collapse
Affiliation(s)
- Toshiki G. Nakashige
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jules R. Stephan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Lisa S. Cunden
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Megan Brunjes Brophy
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Andrew J. Wommack
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | | | - Elizabeth M. Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| |
Collapse
|
31
|
Peralta FA, Huidobro-Toro JP. Zinc as Allosteric Ion Channel Modulator: Ionotropic Receptors as Metalloproteins. Int J Mol Sci 2016; 17:E1059. [PMID: 27384555 PMCID: PMC4964435 DOI: 10.3390/ijms17071059] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 12/20/2022] Open
Abstract
Zinc is an essential metal to life. This transition metal is a structural component of many proteins and is actively involved in the catalytic activity of cell enzymes. In either case, these zinc-containing proteins are metalloproteins. However, the amino acid residues that serve as ligands for metal coordination are not necessarily the same in structural proteins compared to enzymes. While crystals of structural proteins that bind zinc reveal a higher preference for cysteine sulfhydryls rather than histidine imidazole rings, catalytic enzymes reveal the opposite, i.e., a greater preference for the histidines over cysteines for catalysis, plus the influence of carboxylic acids. Based on this paradigm, we reviewed the putative ligands of zinc in ionotropic receptors, where zinc has been described as an allosteric modulator of channel receptors. Although these receptors do not strictly qualify as metalloproteins since they do not normally bind zinc in structural domains, they do transitorily bind zinc at allosteric sites, modifying transiently the receptor channel's ion permeability. The present contribution summarizes current information showing that zinc allosteric modulation of receptor channels occurs by the preferential metal coordination to imidazole rings as well as to the sulfhydryl groups of cysteine in addition to the carboxyl group of acid residues, as with enzymes and catalysis. It is remarkable that most channels, either voltage-sensitive or transmitter-gated receptor channels, are susceptible to zinc modulation either as positive or negative regulators.
Collapse
Affiliation(s)
- Francisco Andrés Peralta
- Laboratorio de Farmacología de Nucleótidos, Laboratorio de Farmacología, Departamento de Biología, Facultad de Química y Biología, y Centro para el Desarrollo de Nanociencias y Nanotecnología (CEDENNA), Universidad de Santiago de Chile, Alameda Libertador B. O'Higgins, 3363 Santiago, Chile.
| | - Juan Pablo Huidobro-Toro
- Laboratorio de Farmacología de Nucleótidos, Laboratorio de Farmacología, Departamento de Biología, Facultad de Química y Biología, y Centro para el Desarrollo de Nanociencias y Nanotecnología (CEDENNA), Universidad de Santiago de Chile, Alameda Libertador B. O'Higgins, 3363 Santiago, Chile.
| |
Collapse
|
32
|
Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics. Int J Mol Sci 2016; 17:ijms17050671. [PMID: 27153067 PMCID: PMC4881497 DOI: 10.3390/ijms17050671] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 04/18/2016] [Accepted: 04/28/2016] [Indexed: 12/12/2022] Open
Abstract
Metal ions play a functional role in numerous biochemical processes and cellular pathways. Indeed, about 40% of all enzymes of known 3D structure require a metal ion to be able to perform catalysis. The interactions of the metals with the macromolecular framework determine their chemical properties and reactivity. The relevant interactions involve both the coordination sphere of the metal ion and the more distant interactions of the so-called second sphere, i.e., the non-bonded interactions between the macromolecule and the residues coordinating the metal (metal ligands). The metal ligands and the residues in their close spatial proximity define what we call a minimal functional site (MFS). MFSs can be automatically extracted from the 3D structures of metal-binding biological macromolecules deposited in the Protein Data Bank (PDB). They are 3D templates that describe the local environment around a metal ion or metal cofactor and do not depend on the overall macromolecular structure. MFSs provide a different view on metal-binding proteins and nucleic acids, completely focused on the metal. Here we present different protocols and tools based upon the concept of MFS to obtain deeper insight into the structural and functional properties of metal-binding macromolecules. We also show that structure conservation of MFSs in metalloproteins relates to local sequence similarity more strongly than to overall protein similarity.
Collapse
|
33
|
Baskin M, Maayan G. A rationally designed metal-binding helical peptoid for selective recognition processes. Chem Sci 2016; 7:2809-2820. [PMID: 28660058 PMCID: PMC5477017 DOI: 10.1039/c5sc04358a] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 01/08/2016] [Indexed: 12/13/2022] Open
Abstract
A helical peptoid bearing two distinct metal binding ligands at positions i and i+3 (Helix HQT i+3) enables the selective recognition of one or two metal ions depending on its environment, thus mimicking the unique recognition abilities of natural biopolymers.
Metal-binding biopolymers play a significant role in processes, such as regulation, recognition and catalysis, due to their high affinity towards specific metal ions, which they bind selectively from the cellular pool. Many enzymes can bind two or more metal ions, each at a specific binding site, to enable efficient cooperative function. Imitating these recognition abilities might lead to the production of biomimetic materials such as unique chelators and catalysts. Herein, we report a rationally designed helical peptoid bearing two distinct metal binding ligands at positions i and i + 3 (Helix HQT i + 3), which enables the selective recognition of one or two metal ions depending on its environment. Using various spectroscopic techniques, we describe (1) the selective intramolecular binding of Cu2+ and its extraction from a mixture of neighboring metal ions in high concentrations, and (2) the selective intermolecular binding of two different metal ions, including the pair Cu2+ and Zn2+, one at each binding site, for the generation of hetero-bimetallic peptoid duplexes. Thorough analysis and comparison between the spectroscopic data and association constants of the metal complexes formed by Helix HQT i + 3 and those formed by non-helical peptoids, or helical peptoids in which the two metal binding ligands are not pre-organized, revealed that the unique recognition processes performed by Helix HQT i + 3 are controlled by both the sequence and the structure of the peptoid.
Collapse
Affiliation(s)
- Maria Baskin
- Schulich Faculty of Chemistry , Technion-Israel Institute of Technology , Technion City , Hailfa 32000 , Israel .
| | - Galia Maayan
- Schulich Faculty of Chemistry , Technion-Israel Institute of Technology , Technion City , Hailfa 32000 , Israel .
| |
Collapse
|
34
|
Linder DP, Rodgers KR. Methanethiol Binding Strengths and Deprotonation Energies in Zn(II)-Imidazole Complexes from M05-2X and MP2 Theories: Coordination Number and Geometry Influences Relevant to Zinc Enzymes. J Phys Chem B 2015; 119:12182-92. [PMID: 26317178 DOI: 10.1021/acs.jpcb.5b07115] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Zn(II) is used in nature as a biocatalyst in hundreds of enzymes, and the structure and dynamics of its catalytic activity are subjects of considerable interest. Many of the Zn(II)-based enzymes are classified as hydrolytic enzymes, in which the Lewis acidic Zn(II) center facilitates proton transfer(s) to a Lewis base, from proton donors such as water or thiol. This report presents the results of a quantum computational study quantifying the dynamic relationship between the zinc coordination number (CN), its coordination geometry, and the thermodynamic driving force behind these proton transfers originating from a charge-neutral methylthiol ligand. Specifically, density functional theory (DFT) and second-order perturbation theory (MP2) calculations have been performed on a series of [(imidazole)nZn-S(H)CH3](2+) and [(imidazole)nZn-SCH3](+) complexes with the CN varied from 1 to 6, n = 0-5. As the number of imidazole ligands coordinated to zinc increases, the S-H proton dissociation energy also increases, (i.e., -S(H)CH3 becomes less acidic), and the Zn-S bond energy decreases. Furthermore, at a constant CN, the S-H proton dissociation energy decreases as the S-Zn-(ImH)n angles increase about their equilibrium position. The zinc-coordinated thiol can become more or less acidic depending upon the position of the coordinated imidazole ligands. The bonding and thermodynamic relationships discussed may apply to larger systems that utilize the [(His)3Zn(II)-L] complex as the catalytic site, including carbonic anhydrase, carboxypeptidase, β-lactamase, the tumor necrosis factor-α-converting enzyme, and the matrix metalloproteinases.
Collapse
Affiliation(s)
- Douglas P Linder
- Department of Chemistry and Physics, Southwestern Oklahoma State University , Weatherford, Oklahoma 73096, United States
| | - Kenton R Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58108, United States
| |
Collapse
|
35
|
Sousa SF, Ramos MJ, Lim C, Fernandes PA. Relationship between Enzyme/Substrate Properties and Enzyme Efficiency in Hydrolases. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00923] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sérgio F. Sousa
- UCIBIO,
REQUIMTE, Departamento de Química e Bioquímica, Faculdade
de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO,
REQUIMTE, Departamento de Química e Bioquímica, Faculdade
de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Carmay Lim
- Institute
of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Pedro A. Fernandes
- UCIBIO,
REQUIMTE, Departamento de Química e Bioquímica, Faculdade
de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| |
Collapse
|
36
|
Abstract
Zinc fingers are highly ubiquitous structural motifs that provide stability to proteins, thus contributing to their correct folding. Despite the high thermodynamic stability of the ZnCys4 centers, their kinetic properties display remarkable lability. Here, we use a combination of protein engineering with single molecule force spectroscopy atomic force microscopy (AFM) to uncover the surprising mechanical lability (∼90 pN) of the individual Zn-S bonds that form the two equivalent zinc finger motifs embedded in the structure of the multidomain DnaJ chaperone. Rational mutations within the zinc coordinating residues enable direct identification of the chemical determinants that regulate the interplay between zinc binding-requiring the presence of all four cysteines-and disulfide bond formation. Finally, our observations show that binding to hydrophobic short peptides drastically increases the mechanical stability of DnaJ. Altogether, our experimental approach offers a detailed, atomistic vista on the fine chemical mechanisms that govern the nanomechanics of individual, naturally occurring zinc finger.
Collapse
Affiliation(s)
- Judit Perales-Calvo
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London , Strand, WC2R 2LS, London, United Kingdom
| | - Ainhoa Lezamiz
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London , Strand, WC2R 2LS, London, United Kingdom
| | - Sergi Garcia-Manyes
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London , Strand, WC2R 2LS, London, United Kingdom
| |
Collapse
|
37
|
Chan ACK, Blair KM, Liu Y, Frirdich E, Gaynor EC, Tanner ME, Salama NR, Murphy MEP. Helical shape of Helicobacter pylori requires an atypical glutamine as a zinc ligand in the carboxypeptidase Csd4. J Biol Chem 2014; 290:3622-38. [PMID: 25505267 DOI: 10.1074/jbc.m114.624734] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Peptidoglycan modifying carboxypeptidases (CPs) are important determinants of bacterial cell shape. Here, we report crystal structures of Csd4, a three-domain protein from the human gastric pathogen Helicobacter pylori. The catalytic zinc in Csd4 is coordinated by a rare His-Glu-Gln configuration that is conserved among most Csd4 homologs, which form a distinct subfamily of CPs. Substitution of the glutamine to histidine, the residue found in prototypical zinc carboxypeptidases, resulted in decreased enzyme activity and inhibition by phosphate. Expression of the histidine variant at the native locus in a H. pylori csd4 deletion strain did not restore the wild-type helical morphology. Biochemical assays show that Csd4 can cleave a tripeptide peptidoglycan substrate analog to release m-DAP. Structures of Csd4 with this substrate analog or product bound at the active site reveal determinants of peptidoglycan specificity and the mechanism to cleave an isopeptide bond to release m-DAP. Our data suggest that Csd4 is the archetype of a new CP subfamily with a domain scheme that differs from this large family of peptide-cleaving enzymes.
Collapse
Affiliation(s)
- Anson C K Chan
- From the Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Kris M Blair
- the Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, the Program in Molecular and Cellular Biology, University of Washington, Seattle, Washington 98195, and
| | - Yanjie Liu
- the Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Emilisa Frirdich
- From the Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Erin C Gaynor
- From the Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Martin E Tanner
- the Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Nina R Salama
- the Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, the Program in Molecular and Cellular Biology, University of Washington, Seattle, Washington 98195, and
| | - Michael E P Murphy
- From the Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada,
| |
Collapse
|
38
|
Daniel AG, Farrell NP. The dynamics of zinc sites in proteins: electronic basis for coordination sphere expansion at structural sites. Metallomics 2014; 6:2230-41. [PMID: 25329367 DOI: 10.1039/c4mt00213j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The functional role assumed by zinc in proteins is closely tied to the variable dynamics around its coordination sphere arising by virtue of its flexibility in bonding. Modern experimental and computational methods allow the detection and study of previously unknown features of bonding between zinc and its ligands in protein environment. These discoveries are occurring just in time as novel biological functions of zinc, which involve rather unconventional coordination trends, are emerging. In this sense coordination sphere expansion of structural zinc sites, as observed in our previous experiments, is a novel phenomenon. Here we explore the electronic and structural requirements by simulating this phenomenon in structural zinc sites using DFT computations. For this purpose, we have chosen MPW1PW91 and a mixed basis set combination as the DFT method through benchmarking, because it accurately reproduces structural parameters of experimentally characterized zinc compounds. Using appropriate models, we show that the greater ionic character of zinc coordination would allow for coordination sphere expansion if the steric and electrostatic repulsions of the ligands are attenuated properly. Importantly, through the study of electronic and structural aspects of the models used, we arrive at a comprehensive bonding model, explaining the factors that influence coordination of zinc in proteins. The proposed model along with the existing knowledge would enhance our ability to predict zinc binding sites in proteins, which is today of growing importance given the predicted enormity of the zinc proteome.
Collapse
Affiliation(s)
- A Gerard Daniel
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA.
| | | |
Collapse
|
39
|
Göksu S, Naderi A, Akbaba Y, Kalın P, Akıncıoğlu A, Gülçin İ, Durdagi S, Salmas RE. Carbonic anhydrase inhibitory properties of novel benzylsulfamides using molecular modeling and experimental studies. Bioorg Chem 2014; 56:75-82. [DOI: 10.1016/j.bioorg.2014.07.009] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 07/19/2014] [Accepted: 07/23/2014] [Indexed: 12/15/2022]
|
40
|
Friedman R. Structural and computational insights into the versatility of cadmium binding to proteins. Dalton Trans 2014; 43:2878-87. [PMID: 24346117 DOI: 10.1039/c3dt52810c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cadmium is a highly toxic group XII metal, similar to zinc and mercury. Unlike zinc, which is one of the most common metal cofactors in biology, cadmium is highly toxic. Many Zn(2+)-binding proteins can bind Cd(2+)-ions without significantly affecting their structures. Here, the protein data bank is analysed with regard to protein-cadmium interactions, which shows that cadmium can bind to a variety of ion binding sites in proteins. Statistical analysis of Cd(2+)-side chain interactions is compared with a similar analysis of other ions. This analysis reveals that with regard to amino acid side-chain preference, Cd(2+) is more similar to Mn(2+) than to Zn(2+) or Hg(2+). Finally, the interaction energies of three native metal binding proteins are calculated where Cd(2+) binds instead of Zn(2+), Ca(2+) or Cu(2+). The interaction energies are decomposed into individual components whose contributions are discussed.
Collapse
Affiliation(s)
- Ran Friedman
- Computational Chemistry and Biochemistry Research Group, Department of Chemistry and Biomedical Sciences, Linnæus University, 391 82 Kalmar, Sweden
| |
Collapse
|
41
|
Santos-Martins D, Forli S, Ramos MJ, Olson AJ. AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins. J Chem Inf Model 2014; 54:2371-9. [PMID: 24931227 PMCID: PMC4144784 DOI: 10.1021/ci500209e] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Indexed: 12/14/2022]
Abstract
Zinc is present in a wide variety of proteins and is important in the metabolism of most organisms. Zinc metalloenzymes are therapeutically relevant targets in diseases such as cancer, heart disease, bacterial infection, and Alzheimer's disease. In most cases a drug molecule targeting such enzymes establishes an interaction that coordinates with the zinc ion. Thus, accurate prediction of the interaction of ligands with zinc is an important aspect of computational docking and virtual screening against zinc containing proteins. We have extended the AutoDock force field to include a specialized potential describing the interactions of zinc-coordinating ligands. This potential describes both the energetic and geometric components of the interaction. The new force field, named AutoDock4Zn, was calibrated on a data set of 292 crystal complexes containing zinc. Redocking experiments show that the force field provides significant improvement in performance in both free energy of binding estimation as well as in root-mean-square deviation from the crystal structure pose. The new force field has been implemented in AutoDock without modification to the source code.
Collapse
Affiliation(s)
- Diogo Santos-Martins
- Department of Integrative Structural and Computational
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
- REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Stefano Forli
- Department of Integrative Structural and Computational
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Maria João Ramos
- REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Arthur J. Olson
- Department of Integrative Structural and Computational
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| |
Collapse
|
42
|
Guzzo CM, Ringel A, Cox E, Uzoma I, Zhu H, Blackshaw S, Wolberger C, Matunis MJ. Characterization of the SUMO-binding activity of the myeloproliferative and mental retardation (MYM)-type zinc fingers in ZNF261 and ZNF198. PLoS One 2014; 9:e105271. [PMID: 25133527 PMCID: PMC4136804 DOI: 10.1371/journal.pone.0105271] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/20/2014] [Indexed: 02/03/2023] Open
Abstract
SUMO-binding proteins interact with SUMO modified proteins to mediate a wide range of functional consequences. Here, we report the identification of a new SUMO-binding protein, ZNF261. Four human proteins including ZNF261, ZNF198, ZNF262, and ZNF258 contain a stretch of tandem zinc fingers called myeloproliferative and mental retardation (MYM)-type zinc fingers. We demonstrated that MYM-type zinc fingers from ZNF261 and ZNF198 are necessary and sufficient for SUMO-binding and that individual MYM-type zinc fingers function as SUMO-interacting motifs (SIMs). Our binding studies revealed that the MYM-type zinc fingers from ZNF261 and ZNF198 interact with the same surface on SUMO-2 recognized by the archetypal consensus SIM. We also present evidence that MYM-type zinc fingers in ZNF261 contain zinc, but that zinc is not required for SUMO-binding. Immunofluorescence microscopy studies using truncated fragments of ZNF198 revealed that MYM-type zinc fingers of ZNF198 are necessary for localization to PML-nuclear bodies (PML-NBs). In summary, our studies have identified and characterized the SUMO-binding activity of the MYM-type zinc fingers in ZNF261 and ZNF198.
Collapse
Affiliation(s)
- Catherine M. Guzzo
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Alison Ringel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Eric Cox
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Ijeoma Uzoma
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Seth Blackshaw
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Michael J. Matunis
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
| |
Collapse
|
43
|
DalCorso G, Manara A, Piasentin S, Furini A. Nutrient metal elements in plants. Metallomics 2014; 6:1770-88. [DOI: 10.1039/c4mt00173g] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
44
|
Analyses of cobalt-ligand and potassium-ligand bond lengths in metalloproteins: trends and patterns. J Mol Model 2014; 20:2271. [PMID: 24850495 DOI: 10.1007/s00894-014-2271-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 04/23/2014] [Indexed: 10/25/2022]
Abstract
Cobalt and potassium are biologically important metal elements that are present in a large array of proteins. Cobalt is mostly found in vivo associated with a corrin ring, which represents the core of the vitamin B12 molecule. Potassium is the most abundant metal in the cytosol, and it plays a crucial role in maintaining membrane potential as well as correct protein function. Here, we report a thorough analysis of the geometric properties of cobalt and potassium coordination spheres that was performed with high resolution on a representative set of structures from the Protein Data Bank and complemented by quantum mechanical calculations realized at the DFT level of theory (B3LYP/ SDD) on mononuclear model systems. The results allowed us to draw interesting conclusions on the structural characteristics of both Co and K centers, and to evaluate the importance of effects such as their association energies and intrinsic thermodynamic stabilities. Overall, the results obtained provide useful data for enhancing the atomic models normally applied in theoretical and computational studies of Co or K proteins performed at the quantum mechanical level, and for developing molecular mechanical parameters for treating Co or K coordination spheres in molecular mechanics or molecular dynamics studies.
Collapse
|
45
|
Zastrow M, Pecoraro VL. Designing hydrolytic zinc metalloenzymes. Biochemistry 2014; 53:957-78. [PMID: 24506795 PMCID: PMC3985962 DOI: 10.1021/bi4016617] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 01/23/2014] [Indexed: 12/15/2022]
Abstract
Zinc is an essential element required for the function of more than 300 enzymes spanning all classes. Despite years of dedicated study, questions regarding the connections between primary and secondary metal ligands and protein structure and function remain unanswered, despite numerous mechanistic, structural, biochemical, and synthetic model studies. Protein design is a powerful strategy for reproducing native metal sites that may be applied to answering some of these questions and subsequently generating novel zinc enzymes. From examination of the earliest design studies introducing simple Zn(II)-binding sites into de novo and natural protein scaffolds to current studies involving the preparation of efficient hydrolytic zinc sites, it is increasingly likely that protein design will achieve reaction rates previously thought possible only for native enzymes. This Current Topic will review the design and redesign of Zn(II)-binding sites in de novo-designed proteins and native protein scaffolds toward the preparation of catalytic hydrolytic sites. After discussing the preparation of Zn(II)-binding sites in various scaffolds, we will describe relevant examples for reengineering existing zinc sites to generate new or altered catalytic activities. Then, we will describe our work on the preparation of a de novo-designed hydrolytic zinc site in detail and present comparisons to related designed zinc sites. Collectively, these studies demonstrate the significant progress being made toward building zinc metalloenzymes from the bottom up.
Collapse
Affiliation(s)
| | - Vincent L. Pecoraro
- Department of Chemistry, University
of Michigan, Ann Arbor, Michigan 48109, United
States
| |
Collapse
|
46
|
Karsisiotis AI, Damblon CF, Roberts GCK. A variety of roles for versatile zinc in metallo-β-lactamases. Metallomics 2014; 6:1181-97. [DOI: 10.1039/c4mt00066h] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
β-Lactamases inactivate the important β-lactam antibiotics by catalysing the hydrolysis of the β-lactam ring, thus. One class of these enzymes, the metallo-β-lactamases, bind two zinc ions at the active site and these play important roles in the catalytic mechanism.
Collapse
Affiliation(s)
| | - C. F. Damblon
- Chimie Biologique Structurale
- Institut de Chimie
- Université de Liège
- 4000 Liège, Belgium
| | - G. C. K. Roberts
- The Henry Wellcome Laboratories of Structural Biology
- Department of Biochemistry
- University of Leicester
- Leicester LE1 9HN, UK
| |
Collapse
|
47
|
Dong J, Callahan KL, Borotto NB, Vachet RW. Identifying Zn-bound histidine residues in metalloproteins using hydrogen-deuterium exchange mass spectrometry. Anal Chem 2013; 86:766-73. [PMID: 24313328 DOI: 10.1021/ac4032719] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In this work, we have developed a method that uses hydrogen-deuterium exchange (HDX) of C2-hydrogens of histidines coupled with mass spectrometry (MS) to identify Zn-bound histidines in metalloproteins. This method relies on differences in HDX reaction rates of Zn-bound and Zn-free His residues. Using several model peptides and proteins, we find that all Zn-bound His residues have substantially lower HDX reaction rates in the presence of the metal. The vast majority of non-Zn-binding His residues undergo no significant changes in HDX reaction rates when their reactivity is compared in the presence and absence of Zn. Using this new approach, we then determined the Zn binding site of β-2-microglobulin, a protein associated with metal-induced amyloidosis. Together, these results suggest that HDX-MS of His C2-hydrogens is a promising new method for identifying Zn-bound histidines in metalloproteins.
Collapse
Affiliation(s)
- Jia Dong
- Department of Chemistry, University of Massachusetts Amherst , LGRT, 710 North Pleasant Street, Amherst, MA 01003, United States
| | | | | | | |
Collapse
|
48
|
Marcial B, Sousa S, Santos HD, Ramos M. Structural and dynamics analysis of matrix metalloproteinases MMP-2 complexed with chemically modified tetracyclines (CMTs). J Biomol Struct Dyn 2013; 32:1907-18. [DOI: 10.1080/07391102.2013.842186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
49
|
Abstract
The aggregation of Aβ-peptide (Aβ) is widely considered to be the critical step in the pathology of Alzheimer's disease. Small, soluble Aβ oligomers have been shown to be more neurotoxic than large, insoluble aggregates and fibrils. Recent studies suggest that biometal ions, including Zn(II), may play an important role in the aggregation process. Experimentally determining the details of the binding process is complicated by the kinetic lability of zinc. To study the dynamic nature of the zinc-bound Aβ complexes and the potential mechanisms by which Zn(II) affects Aβ oligomerization we have performed atomistic molecular dynamics (MD) simulations of Zn(Aβ) and Zn(Aβ)2. The models were based on NMR data and predicted coordination environments from previous density functional theory calculations. When modeled as 4-coordinate covalently bound Zn(Aβ) n complexes (where n = 1 or 2), zinc imposes conformational changes in the surrounding Aβ residues. Moreover, zinc reduces the helix content and increases the random coil content of the full peptide. Although zinc binds at the N-terminus of Aβ, β-sheet formation is observed exclusively at the C-terminus in the Zn(Aβ) and most of the Zn(Aβ)2 complexes. Furthermore, initial binding to zinc promotes the formation of intra-chain salt-bridges, while subsequent dissociation promotes the formation of inter-chain salt-bridges. These results suggest that Zn-binding to Aβ accelerates the aggregation of Aβ by unfolding the helical structure in Aβ peptide and stabilizing the formation of vital salt-bridges within and between Aβ peptides.
Collapse
Affiliation(s)
- Lurong Pan
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - James C. Patterson
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| |
Collapse
|
50
|
Laitaoja M, Valjakka J, Jänis J. Zinc coordination spheres in protein structures. Inorg Chem 2013; 52:10983-91. [PMID: 24059258 DOI: 10.1021/ic401072d] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Zinc metalloproteins are one of the most abundant and structurally diverse proteins in nature. In these proteins, the Zn(II) ion possesses a multifunctional role as it stabilizes the fold of small zinc fingers, catalyzes essential reactions in enzymes of all six classes, or assists in the formation of biological oligomers. Previously, a number of database surveys have been conducted on zinc proteins to gain broader insights into their rich coordination chemistry. However, many of these surveys suffer from severe flaws and misinterpretations or are otherwise limited. To provide a more comprehensive, up-to-date picture on zinc coordination environments in proteins, zinc containing protein structures deposited in the Protein Data Bank (PDB) were analyzed in detail. A statistical analysis in terms of zinc coordinating amino acids, metal-to-ligand bond lengths, coordination number, and structural classification was performed, revealing coordination spheres from classical tetrahedral cysteine/histidine binding sites to more complex binuclear sites with carboxylated lysine residues. According to the results, coordination spheres of hundreds of crystal structures in the PDB could be misinterpreted due to symmetry-related molecules or missing electron densities for ligands. The analysis also revealed increasing average metal-to-ligand bond length as a function of crystallographic resolution, which should be taken into account when interrogating metal ion binding sites. Moreover, one-third of the zinc ions present in crystal structures are artifacts, merely aiding crystal formation and packing with no biological significance. Our analysis provides solid evidence that a minimal stable zinc coordination sphere is made up by four ligands and adopts a tetrahedral coordination geometry.
Collapse
Affiliation(s)
- Mikko Laitaoja
- University of Eastern Finland , Department of Chemistry, P.O. Box 111, FI-80101 Joensuu, Finland
| | | | | |
Collapse
|