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Li XY, Zhou XD, Hu JM. Peptides in the detection of metal ions. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:6589-6598. [PMID: 39269217 DOI: 10.1039/d4ay01232a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/15/2024]
Abstract
By means of their specific interactions with different metal ions, naturally occurring proteins control structures and functions of many biological processes and functions in organisms. In view of natural metallopeptides, scientists have proposed artificial peptides which coordinate with metal ions through their functional groups either for introducing a special reactivity or for constructing various sensors. However, the design of new peptide ligands requires a deep understanding of the structures, assembly properties, and dynamic behaviors of such peptides. This review briefly describes detection strategies of metal ions via coordination to the binding sites in peptides. The principles and functions of sensing systems are described as well. We also highlight some examples of a metal-induced peptide self-assembly with relevance to biotechnology applications.
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Affiliation(s)
- Xin-Yi Li
- Core Facility of Wuhan University, Wuhan University, Wuhan 430072, PR China
| | - Xiao-Dong Zhou
- Core Facility of Wuhan University, Wuhan University, Wuhan 430072, PR China
| | - Ji-Ming Hu
- Core Facility of Wuhan University, Wuhan University, Wuhan 430072, PR China
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2
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Kircheva N, Angelova S, Dudev T. Carbonic Anhydrases: Different Active Sites, Same Metal Selectivity Rules. Molecules 2024; 29:1995. [PMID: 38731486 PMCID: PMC11085502 DOI: 10.3390/molecules29091995] [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: 04/06/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
Carbonic anhydrases are mononuclear metalloenzymes catalyzing the reversible hydration of carbon dioxide in organisms belonging to all three domains of life. Although the mechanism of the catalytic reaction is similar, different families of carbonic anhydrases do not have a common ancestor nor do they exhibit significant resemblance in the amino acid sequence or the structure and composition of the metal-binding sites. Little is known about the physical principles determining the metal affinity and selectivity of the catalytic centers, and how well the native metal is protected from being dislodged by other metal species from the local environment. Here, we endeavor to shed light on these issues by studying (via a combination of density functional theory calculations and polarizable continuum model computations) the thermodynamic outcome of the competition between the native metal cation and its noncognate competitor in various metal-binding sites. Typical representatives of the competing cations from the cellular environments of the respective classes of carbonic anhydrases are considered. The calculations reveal how the Gibbs energy of the metal competition changes when varying the metal type, structure, composition, and solvent exposure of the active center. Physical principles governing metal competition in different carbonic anhydrase metal-binding sites are delineated.
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Affiliation(s)
- Nikoleta Kircheva
- Institute of Optical Materials and Technologies “Acad. J. Malinowski”, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (N.K.); (S.A.)
| | - Silvia Angelova
- Institute of Optical Materials and Technologies “Acad. J. Malinowski”, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (N.K.); (S.A.)
- University of Chemical Technology and Metallurgy, 8 St. Kliment Ohridski Blvd, 1756 Sofia, Bulgaria
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University “St. Kliment Ohridski”, 1164 Sofia, Bulgaria
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Burger N, Mittenbühler MJ, Xiao H, Shin S, Bozi LHM, Wei S, Sprenger HG, Sun Y, Zhu Y, Darabedian N, Petrocelli JJ, Muro PL, Che J, Chouchani ET. A comprehensive landscape of the zinc-regulated human proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.04.574225. [PMID: 38260676 PMCID: PMC10802333 DOI: 10.1101/2024.01.04.574225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Zinc is an essential micronutrient that regulates a wide range of physiological processes, principally through Zn 2+ binding to protein cysteine residues. Despite being critical for modulation of protein function, for the vast majority of the human proteome the cysteine sites subject to regulation by Zn 2+ binding remain undefined. Here we develop ZnCPT, a comprehensive and quantitative mapping of the zinc-regulated cysteine proteome. We define 4807 zinc-regulated protein cysteines, uncovering protein families across major domains of biology that are subject to either constitutive or inducible modification by zinc. ZnCPT enables systematic discovery of zinc-regulated structural, enzymatic, and allosteric functional domains. On this basis, we identify 52 cancer genetic dependencies subject to zinc regulation, and nominate malignancies sensitive to zinc-induced cytotoxicity. In doing so, we discover a mechanism of zinc regulation over Glutathione Reductase (GSR) that drives cell death in GSR-dependent lung cancers. We provide ZnCPT as a resource for understanding mechanisms of zinc regulation over protein function.
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Angelova S, Kircheva N, Nikolova V, Dobrev S, Dudev T. Electrostatic interactions - key determinants of the metal selectivity in La 3+ and Ca 2+ binding proteins. Phys Chem Chem Phys 2023. [PMID: 37386862 DOI: 10.1039/d3cp01978k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Nearly half of all known proteins contain metal co-factors. In the course of evolution two dozen metal cations (mostly monovalent and divalent species) have been selected to participate in processes of vital importance for living organisms. Trivalent metal cations have also been selected, although to a lesser extent as compared with their mono- and divalent counterparts. Notably, factors governing the metal selectivity in trivalent metal centers in proteins are less well understood than those in the respective divalent metal centers. Thus, the source of high La3+/Ca2+ selectivity in lanthanum-binding proteins, as compared with that of calcium-binding proteins (i.e., calmodulin), is still shrouded in mystery. The well-calibrated thermochemical calculations, performed here, reveal the dominating role of electrostatic interactions in shaping the metal selectivity in La3+-binding centers. The calculations also disclose other (second-order) determinants of metal selectivity in these systems, such as the rigidity and extent of solvent exposure of the binding site. All these factors are also implicated in shaping the metal selectivity in Ca2+-binding proteins.
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Affiliation(s)
- Silvia Angelova
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria.
| | - Nikoleta Kircheva
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria.
| | - Valya Nikolova
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1164 Sofia, Bulgaria.
| | - Stefan Dobrev
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria.
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1164 Sofia, Bulgaria.
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5
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Cao X, Wu M, Zhang G, Lin L, Tu M, Xiao D, Zhong C, Zhang H, Yang S, Liu J, Zhang X, Chen X, Wang X, Zhang Y, Xu S, Zhou X, Yang X, Hao L, Yang N. Longitudinal plasma magnesium status during pregnancy and the risk of gestational diabetes mellitus: a prospective cohort study. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:65392-65400. [PMID: 37084048 DOI: 10.1007/s11356-023-26855-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/03/2023] [Indexed: 05/03/2023]
Abstract
Emerging evidence has shown that magnesium (Mg) was associated with type 2 diabetes while few focused on abnormal glucose metabolism during pregnancy. The study is aimed at investigating the association between longitudinal changes in plasma Mg during pregnancy and subsequent risk of gestational diabetes (GDM) and exploring the possible influence of iron supplementation on the changes of plasma Mg levels. One thousand seven hundred fifty-six pregnant women from Tongji Maternal and Child Health Cohort (TMCHC) were involved. Blood samples were collected at gestational weeks 17.0 ± 0.9 and later 26.2 ± 1.4. Plasma Mg was measured by inductively coupled plasma mass spectrometry (ICP-MS) with decline rates calculated. Information on general characteristics and iron supplementation was collected by questionnaires. Oral glucose tolerance test (OGTT) was conducted at 24-28 gestational weeks to diagnose GDM. Poisson regression with robust error variance was used to estimate relative risks (RR) of GDM. Median concentrations of plasma Mg were 0.69 mmol/L and 0.63 mmol/L respectively at two collections. The prevalence of hypomagnesemia at the first collection was 73% and associated with a 1.59 (95%CI: 1.07, 2.37) fold risk of GDM. Adjusted RRs were 1.74 (95%CI: 1.06, 2.83) and 2.44 (95%CI: 1.54, 3.85) for women with hypomagnesemia and followed more tertile (T2 and T3 vs. T1) of Mg decrement. Iron supplementation above 30 mg/day was found associated with more Mg decrement (25.5% and 27.5% in T2 and T3 vs. 19.5% in T1). In conclusion, hypomagnesemia during pregnancy is prevalent and associated with increased GDM risk, especially in women followed by more plasma Mg decrement during pregnancy. High-dose iron supplementation may involve more plasma Mg decrement.
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Affiliation(s)
- Xiyu Cao
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, China
| | - Meng Wu
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, China
| | - Guofu Zhang
- School of Public Health, Xinxiang Medical University, Xinxiang, 453003, Henan, China
| | - Lixia Lin
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, China
| | - Menghan Tu
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, China
| | - Daxiang Xiao
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, China
| | - Chunrong Zhong
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, China
| | - Huaqi Zhang
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, China
| | - Siyu Yang
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, China
| | - Jin Liu
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, China
| | - Xu Zhang
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, China
| | - Xi Chen
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, China
| | - Xiaoyi Wang
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, China
| | - Yu Zhang
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, China
| | - Shangzhi Xu
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, China
| | - Xuezhen Zhou
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, China
| | - Xuefeng Yang
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, China
| | - Liping Hao
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, China
| | - Nianhong Yang
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, China.
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Nikolova V, Kircheva N, Dobrev S, Angelova S, Dudev T. Lanthanides as Calcium Mimetic Species in Calcium-Signaling/Buffering Proteins: The Effect of Lanthanide Type on the Ca2+/Ln3+ Competition. Int J Mol Sci 2023; 24:ijms24076297. [PMID: 37047269 PMCID: PMC10094714 DOI: 10.3390/ijms24076297] [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: 02/23/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
Lanthanides, the 14 4f-block elements plus Lanthanum, have been extensively used to study the structure and biochemical properties of metalloproteins. The characteristics of lanthanides within the lanthanide series are similar, but not identical. The present research offers a systematic investigation of the ability of the entire Ln3+ series to substitute for Ca2+ in biological systems. A well-calibrated DFT/PCM protocol is employed in studying the factors that control the metal selectivity in biological systems by modeling typical calcium signaling/buffering binding sites and elucidating the thermodynamic outcome of the competition between the “alien” La3+/Ln3+ and “native” Ca2+, and La3+ − Ln3+ within the lanthanide series. The calculations performed reveal that the major determinant of the Ca2+/Ln3+ selectivity in calcium proteins is the net charge of the calcium binding pocket; the more negative the charge, the higher the competitiveness of the trivalent Ln3+ with respect to its Ca2+ contender. Solvent exposure of the binding site also influences the process; buried active centers with net charge of −4 or −3 are characterized by higher Ln3+ over Ca2+ selectivity, whereas it is the opposite for sites with overall charge of −1. Within the series, the competition between La3+ and its fellow lanthanides is determined by the balance between two competing effects: electronic (favoring heavier lanthanides) and solvation (generally favoring the lighter lanthanides).
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Affiliation(s)
- Valya Nikolova
- Faculty of Chemistry and Pharmacy, Sofia University “St. Kliment Ohridski”, 1164 Sofia, Bulgaria
| | - Nikoleta Kircheva
- Institute of Optical Materials and Technologies “Acad. J. Malinowski”, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Stefan Dobrev
- Institute of Optical Materials and Technologies “Acad. J. Malinowski”, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Silvia Angelova
- Institute of Optical Materials and Technologies “Acad. J. Malinowski”, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University “St. Kliment Ohridski”, 1164 Sofia, Bulgaria
- Correspondence:
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7
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How Theoretical Evaluations Can Generate Guidelines for Designing/Engineering Metalloproteins with Desired Metal Affinity and Selectivity. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010249. [PMID: 36615442 PMCID: PMC9822464 DOI: 10.3390/molecules28010249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 12/29/2022]
Abstract
Almost half of all known proteins contain metal co-factors. Crucial for the flawless performance of a metalloprotein is the selection with high fidelity of the cognate metal cation from the surrounding biological fluids. Therefore, elucidating the factors controlling the metal binding and selectivity in metalloproteins is of particular significance. The knowledge thus acquired not only contributes to better understanding of the intimate mechanism of these events but, also, significantly enriches the researcher's toolbox that could be used in designing/engineering novel metalloprotein structures with pre-programmed properties. A powerful tool in aid of deciphering the physical principles behind the processes of metal recognition and selectivity is theoretical modeling of metal-containing biological structures. This review summarizes recent findings in the field with an emphasis on elucidating the major factors governing these processes. The results from theoretical evaluations are discussed. It is the hope that the physical principles evaluated can serve as guidelines in designing/engineering of novel metalloproteins of interest to both science and industry.
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8
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Competition between Ag+ and Ni2+ in nickel enzymes: Implications for the Ag+ antibacterial activity. Comput Biol Chem 2022; 101:107785. [DOI: 10.1016/j.compbiolchem.2022.107785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/24/2022] [Accepted: 11/05/2022] [Indexed: 11/09/2022]
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Hu Frisk J, Pejler G, Eriksson S, Wang L. Heavy metal tolerance of Mesorhizobium delmotii thymidylate kinase. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:1305-1317. [PMID: 35345982 DOI: 10.1080/15257770.2022.2055059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Metal ions play an important role in many metabolic processes in all living organisms. At low concentrations, heavy metals such as Fe2+, Cu2+ and Zn2+ are essential cofactors for many enzymes. However, at high concentrations they are toxic. Mesorhizobium species belong to the class α-proteobacteria and have high tolerance to soil acidity, salinity, temperature extremes, and metallicolous conditions. To identify factors responsible for this tolerance we have studied the effects of metal ions on Mesorhizobium delmotii thymidylate kinase (MdTMPK), an essential enzyme in the synthesis of dTTP, thus being vital for cell growth. We show that Mg2+ and Mn2+ are the divalent metal ions required for catalysis and that Mn2+ gives the highest catalytic efficiency. MdTMPK activity in the presence of Mg2+ was strongly inhibited by the co-presence of Zn2+, Ni2+ and Co2+. However, the addition of Cs+ caused >2-fold enhanced MdTMPK activity. For TMPK from Bacilus anthracis and humans, the effects of Mg2+ and Mn2+ were similar, whereas the effects of other divalent metal ions were different, and no stimulatory effect of Cs+ was observed. Together, our results demonstrate that MdTMPK and BaTMPK function well in the presence of high concentrations of heavy metal ions, introducing a potential contribution of these enzymes to the heavy metal tolerance of Mesorhizobium delmotii and Bacillus anthracis.
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Affiliation(s)
- Junmei Hu Frisk
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gunnar Pejler
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Staffan Eriksson
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Liya Wang
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
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10
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Cheshmedzhieva D, Ilieva S, Permyakov EA, Permyakov SE, Dudev T. Ca 2+/Sr 2+ Selectivity in Calcium-Sensing Receptor (CaSR): Implications for Strontium's Anti-Osteoporosis Effect. Biomolecules 2021; 11:1576. [PMID: 34827574 PMCID: PMC8615369 DOI: 10.3390/biom11111576] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/07/2021] [Accepted: 10/19/2021] [Indexed: 11/21/2022] Open
Abstract
The extracellular calcium-sensing receptor (CaSR) controls vital bone cell functions such as cell growth, differentiation and apoptosis. The binding of the native agonist (Ca2+) to CaSR activates the receptor, which undergoes structural changes that trigger a cascade of events along the cellular signaling pathways. Strontium (in the form of soluble salts) has been found to also be a CaSR agonist. The activation of the receptor by Sr2+ is considered to be the major mechanism through which strontium exerts its anti-osteoporosis effect, mostly in postmenopausal women. Strontium-activated CaSR initiates a series of signal transduction events resulting in both osteoclast apoptosis and osteoblast differentiation, thus strengthening the bone tissue. The intimate mechanism of Sr2+ activation of CaSR is still enigmatic. Herewith, by employing a combination of density functional theory (DFT) calculations and polarizable continuum model (PCM) computations, we have found that the Ca2+ binding sites 1, 3, and 4 in the activated CaSR, although possessing a different number and type of protein ligands, overall structure and charge state, are all selective for Ca2+ over Sr2+. The three binding sites, regardless of their structural differences, exhibit almost equal metal selectivity if they are flexible and have no geometrical constraints on the incoming Sr2+. In contrast to Ca2+ and Sr2+, Mg2+ constructs, when allowed to fully relax during the optimization process, adopt their stringent six-coordinated octahedral structure at the expense of detaching a one-backbone carbonyl ligand and shifting it to the second coordination layer of the metal. The binding of Mg2+ and Sr2+ to a rigid/inflexible calcium-designed binding pocket requires an additional energy penalty for the binding ion; however, the price for doing so (to be paid by Sr2+) is much less than that of Mg2+. The results obtained delineate the key factors controlling the competition between metal cations for the receptor and shed light on some aspects of strontium's therapeutic effects.
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Affiliation(s)
- Diana Cheshmedzhieva
- Faculty of Chemistry and Pharmacy, Sofia University “St. Kl. Ohridski”, 1164 Sofia, Bulgaria; (D.C.); (S.I.)
| | - Sonia Ilieva
- Faculty of Chemistry and Pharmacy, Sofia University “St. Kl. Ohridski”, 1164 Sofia, Bulgaria; (D.C.); (S.I.)
| | - Eugene A. Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center ‘Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences’, 142290 Pushchino, Russia;
| | - Sergei E. Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center ‘Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences’, 142290 Pushchino, Russia;
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University “St. Kl. Ohridski”, 1164 Sofia, Bulgaria; (D.C.); (S.I.)
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11
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Vologzhannikova AA, Shevelyova MP, Kazakov AS, Sokolov AS, Borisova NI, Permyakov EA, Kircheva N, Nikolova V, Dudev T, Permyakov SE. Strontium Binding to α-Parvalbumin, a Canonical Calcium-Binding Protein of the "EF-Hand" Family. Biomolecules 2021; 11:biom11081158. [PMID: 34439824 PMCID: PMC8392015 DOI: 10.3390/biom11081158] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 07/30/2021] [Accepted: 07/31/2021] [Indexed: 02/07/2023] Open
Abstract
Strontium salts are used for treatment of osteoporosis and bone cancer, but their impact on calcium-mediated physiological processes remains obscure. To explore Sr2+ interference with Ca2+ binding to proteins of the EF-hand family, we studied Sr2+/Ca2+ interaction with a canonical EF-hand protein, α-parvalbumin (α-PA). Evaluation of the equilibrium metal association constants for the active Ca2+ binding sites of recombinant human α-PA (‘CD’ and ‘EF’ sites) from fluorimetric titration experiments and isothermal titration calorimetry data gave 4 × 109 M−1 and 4 × 109 M−1 for Ca2+, and 2 × 107 M−1 and 2 × 106 M−1 for Sr2+. Inactivation of the EF site by homologous substitution of the Ca2+-coordinating Glu in position 12 of the EF-loop by Gln decreased Ca2+/Sr2+ affinity of the protein by an order of magnitude, whereas the analogous inactivation of the CD site induced much deeper suppression of the Ca2+/Sr2+ affinity. These results suggest that Sr2+ and Ca2+ bind to CD/EF sites of α-PA and the Ca2+/Sr2+ binding are sequential processes with the CD site being occupied first. Spectrofluorimetric Sr2+ titration of the Ca2+-loaded α-PA revealed presence of secondary Sr2+ binding site(s) with an apparent equilibrium association constant of 4 × 105 M−1. Fourier-transform infrared spectroscopy data evidence that Ca2+/Sr2+-loaded forms of α-PA exhibit similar states of their COO− groups. Near-UV circular dichroism (CD) data show that Ca2+/Sr2+ binding to α-PA induce similar changes in symmetry of microenvironment of its Phe residues. Far-UV CD experiments reveal that Ca2+/Sr2+ binding are accompanied by nearly identical changes in secondary structure of α-PA. Meanwhile, scanning calorimetry measurements show markedly lower Sr2+-induced increase in stability of tertiary structure of α-PA, compared to the Ca2+-induced effect. Theoretical modeling using Density Functional Theory computations with Polarizable Continuum Model calculations confirms that Ca2+-binding sites of α-PA are well protected against exchange of Ca2+ for Sr2+ regardless of coordination number of Sr2+, solvent exposure or rigidity of sites. The latter appears to be a key determinant of the Ca2+/Sr2+ selectivity. Overall, despite lowered affinity of α-PA to Sr2+, the latter competes with Ca2+ for the same EF-hands and induces similar structural rearrangements. The presence of a secondary Sr2+ binding site(s) could be a factor contributing to Sr2+ impact on the functional activity of proteins.
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Affiliation(s)
- Alisa A. Vologzhannikova
- Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia; (A.A.V.); (M.P.S.); (A.S.K.); (A.S.S.); (N.I.B.); (E.A.P.)
| | - Marina P. Shevelyova
- Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia; (A.A.V.); (M.P.S.); (A.S.K.); (A.S.S.); (N.I.B.); (E.A.P.)
| | - Alexey S. Kazakov
- Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia; (A.A.V.); (M.P.S.); (A.S.K.); (A.S.S.); (N.I.B.); (E.A.P.)
| | - Andrey S. Sokolov
- Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia; (A.A.V.); (M.P.S.); (A.S.K.); (A.S.S.); (N.I.B.); (E.A.P.)
| | - Nadezhda I. Borisova
- Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia; (A.A.V.); (M.P.S.); (A.S.K.); (A.S.S.); (N.I.B.); (E.A.P.)
| | - Eugene A. Permyakov
- Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia; (A.A.V.); (M.P.S.); (A.S.K.); (A.S.S.); (N.I.B.); (E.A.P.)
| | - Nikoleta Kircheva
- Institute of Optical Materials and Technologies “Acad. J. Malinowski”, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria;
| | - Valya Nikolova
- Faculty of Chemistry and Pharmacy, Sofia University “St. Kl. Ohridski”, 1164 Sofia, Bulgaria; (V.N.); (T.D.)
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University “St. Kl. Ohridski”, 1164 Sofia, Bulgaria; (V.N.); (T.D.)
| | - Sergei E. Permyakov
- Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia; (A.A.V.); (M.P.S.); (A.S.K.); (A.S.S.); (N.I.B.); (E.A.P.)
- Correspondence: ; Tel.: +7-(4967)-143-7741
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12
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Dudev T, Frutos LM, Castaño O. How mechanical forces can modulate the metal affinity and selectivity of metal binding sites in proteins. Metallomics 2020; 12:363-370. [DOI: 10.1039/c9mt00283a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The results obtained reveal that applying mechanical forces with a given strength and directionality can modulate the metal affinity and selectivity of metal binding sites in metalloproteins.
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Affiliation(s)
- Todor Dudev
- Faculty of Chemistry and Pharmacy
- Sofia University
- 1164 Sofia
- Bulgaria
| | - Luis Manuel Frutos
- Departamento de Química Analítica
- Química Física e Ingeniería Química
- Universidad de Alcala
- Madrid
- Spain
| | - Obis Castaño
- Departamento de Química Analítica
- Química Física e Ingeniería Química
- Universidad de Alcala
- Madrid
- Spain
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13
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Chen X, Song J, Chen ZN, Jin T, Long F, Xie H, Zheng Y, Zhuang W, Zhang L. Rational designing of 8-hydroxyquinolin-imidazolinone-based fluorescent protein mutants with dramatically red shifted emission: A computational study. J Comput Chem 2018; 39:2307-2315. [PMID: 30318750 DOI: 10.1002/jcc.25552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/11/2018] [Accepted: 07/16/2018] [Indexed: 01/17/2023]
Abstract
Engineering fluorescent proteins to be the customized in vivo labels for monitoring cellular dynamic events is critical in biochemical and biomedical studies. The design and development of novel red fluorescent proteins is one of the most important fronts in this field due to their potential of imaging the entire organism. A recent fluorescent protein mutant eqFP650-67-HqAla with the 8-hydroxyquinolin-imidazolinone (HQI) chromophore has the plausible bathochromic shift of ~30 nm in its emission spectrum wavelength comparing to the parent fluorescent protein eqFP650. However, molecular mechanism of this significant shift remains somewhat obscure. In this study, we carefully benchmarked our computational methods and performed extensive calculations to investigate various structural components' effect on the chromophore's emission energy and decipher the molecular origin of the spectral shift. The influences of conjugation size, substituent group, substituent site as well as the number of substituents have been examined by elaborately designed chromophore derivatives. Accordingly, we proposed several chromophore mutants with dramatic bathochromic shift of up to ~60 nm in their emission spectra. We further evaluated their structural stability in the protein using molecular dynamics simulations. Present theoretical study connects the structural feature of chromophore derivatives in red fluorescent proteins with their splendid performances in shifting the emission frequency and offer the molecular insight. The computational protocol and successive examination procedure to extract the structural effect utilized herein can also be widely applied to other fluorescent proteins in general. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Xian Chen
- Key Laboratory of Physics and Technology for Advanced Batteries (Ministry of Education), Department of Physics, Jilin University, Changchun, Jilin, 130012, People's Republic of China
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, People's Republic of China
| | - Jian Song
- College of Physics and Materials Science, Henan Normal University, Xin Xiang, Henan, 453007, People's Republic of China
| | - Zhe-Ning Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, People's Republic of China
| | - Tan Jin
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, People's Republic of China
| | - Fengqin Long
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, People's Republic of China
| | - Hua Xie
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, People's Republic of China
| | - Yisong Zheng
- Key Laboratory of Physics and Technology for Advanced Batteries (Ministry of Education), Department of Physics, Jilin University, Changchun, Jilin, 130012, People's Republic of China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, People's Republic of China
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, People's Republic of China
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14
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Dudev T, Cheshmedzhieva D, Doudeva L. Competition between abiogenic Al3+ and native Mg2+, Fe2+ and Zn2+ ions in protein binding sites: implications for aluminum toxicity. J Mol Model 2018; 24:55. [DOI: 10.1007/s00894-018-3592-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/24/2018] [Indexed: 11/24/2022]
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15
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Dudev T, Ilieva S, Doudeva L. How an electric field can modulate the metal ion selectivity of protein binding sites: insights from DFT/PCM calculations. Phys Chem Chem Phys 2018; 20:24633-24640. [DOI: 10.1039/c8cp04050h] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
An electric field (internal or external) is a potent force that can modulate the metal selectivity of a protein binding site.
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Affiliation(s)
- Todor Dudev
- Faculty of Chemistry and Pharmacy
- Sofia University
- Sofia 1164
- Bulgaria
| | - Sonia Ilieva
- Faculty of Chemistry and Pharmacy
- Sofia University
- Sofia 1164
- Bulgaria
| | - Lyudmila Doudeva
- Faculty of Chemistry and Pharmacy
- Sofia University
- Sofia 1164
- Bulgaria
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16
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Belmonte L, Mansy SS. Patterns of Ligands Coordinated to Metallocofactors Extracted from the Protein Data Bank. J Chem Inf Model 2017; 57:3162-3171. [PMID: 29116779 DOI: 10.1021/acs.jcim.7b00468] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A new R tool is described that rapidly identifies, ranks, and clusters sequence patterns coordinated to metallocofactors. This tool, PdPDB, fills a void because, unlike currently available tools, PdPDB searches through sequences with metal coordination as the primary determinant and can identify patterns consisting of amino acids, nucleotides, and small molecule ligands at once. PdPDB was tested by analyzing structures that coordinate Fe2+/3+, [2Fe-2S], [4Fe-4S], Zn2+, and Mg2+ cofactors. PdPDB confirmed previously identified sequence motifs and revealed which residues are enriched (e.g., glycine) and are under-represented (e.g., glutamine) near ligands to metal centers. The data show the similarities and differences between different metal-binding sites. The patterns that coordinate metallocofactors vary, depending upon whether the metal ions play a structural or catalytic role, with catalytic metal centers exhibiting partial coordination by small molecule ligands. PdPDB 2.0.1 is freely available as a CRAN package.
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Affiliation(s)
- Luca Belmonte
- CIBIO, University of Trento , Via Sommarive 9, 38123 Povo, Italy
| | - Sheref S Mansy
- CIBIO, University of Trento , Via Sommarive 9, 38123 Povo, Italy
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