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The Advantages of EPR Spectroscopy in Exploring Diamagnetic Metal Ion Binding and Transfer Mechanisms in Biological Systems. MAGNETOCHEMISTRY 2021. [DOI: 10.3390/magnetochemistry8010003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy has emerged as an ideal biophysical tool to study complex biological processes. EPR spectroscopy can follow minor conformational changes in various proteins as a function of ligand or protein binding or interactions with high resolution and sensitivity. Resolving cellular mechanisms, involving small ligand binding or metal ion transfer, is not trivial and cannot be studied using conventional biophysical tools. In recent years, our group has been using EPR spectroscopy to study the mechanism underlying copper ion transfer in eukaryotic and prokaryotic systems. This mini-review focuses on our achievements following copper metal coordination in the diamagnetic oxidation state, Cu(I), between biomolecules. We discuss the conformational changes induced in proteins upon Cu(I) binding, as well as the conformational changes induced in two proteins involved in Cu(I) transfer. We also consider how EPR spectroscopy, together with other biophysical and computational tools, can identify the Cu(I)-binding sites. This work describes the advantages of EPR spectroscopy for studying biological processes that involve small ligand binding and transfer between intracellular proteins.
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Colaneri MJ, Vitali J. Probing Axial Water Bound to Copper in Tutton Salt Using Single Crystal 17O-ESEEM Spectroscopy. J Phys Chem A 2018; 122:6214-6224. [PMID: 29989412 DOI: 10.1021/acs.jpca.8b04075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Electron spin-echo envelope modulation (ESEEM) signals attributed to axial water bound to Cu2+ have been detected and analyzed in Cu(II)-doped 17O-water-enriched potassium zinc sulfate hexahydrate (Tutton salt) crystals. The magnetic field orientation dependences of low frequency modulations were measured to fit hyperfine and quadrupole coupling tensors of a 17O ( I = 5/2) nucleus. The hyperfine tensor ( A xx, A yy, A zz: 0.13, 0.23, -3.81 MHz) exhibits almost axial symmetry with the largest value directed normal to the metal equatorial plane in the host structure. Comparisons with quantum chemical calculations position this nucleus about 2.3 Å from the copper. The isotropic coupling (-1.15 MHz) is small and reflects the weak axial water interaction with a dx2-y2 unshared orbital of copper. The 17O-water quadrupole interaction parameters ( e2 qQ/ h = 6.4 MHz and η = 0.93) are close to the average of those found in a variety of solid hydrates. In addition, the coupling tensor directions correlate very closely with the O8 water geometry, with the maximum quadrupole direction 3° from the water plane normal, and its minimum coupling about 2° from the H-H direction. In almost all previous magnetic resonance 17O-water studies, the quadrupole tensor orientation was based on theoretical considerations. This work represents one of the few experimental confirmations of its principal axis frame. When Cu2+ dopes into the Tutton salt, a Jahn-Teller distortion interchanges the relative long and intermediate metal O7 and O8 bond lengths of the zinc host. Therefore, only those unit cells containing the impurity conform to the pure copper Tutton structure. This study provides further support for this model. Moreover, coupling interactions from distant H217O such as in the present case have important implications in studies of copper enzymes and proteins where substrates have been proposed to displace weakly bound water in the active site.
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Affiliation(s)
- Michael J Colaneri
- Department of Chemistry and Physics , State University of New York at Old Westbury , Old Westbury , New York 11568 , United States
| | - Jacqueline Vitali
- Department of Physics and Department of Biological, Geological and Environmental Sciences , Cleveland State University , Cleveland , Ohio 44115 , United States
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Khan M, Hayat M, Khan SA, Iqbal N. Unb-DPC: Identify mycobacterial membrane protein types by incorporating un-biased dipeptide composition into Chou's general PseAAC. J Theor Biol 2017; 415:13-19. [DOI: 10.1016/j.jtbi.2016.12.004] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/24/2016] [Accepted: 12/07/2016] [Indexed: 01/22/2023]
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Giesche R, John H, Kehe K, Schmidt A, Popp T, Balzuweit F, Thiermann H, Gudermann T, Steinritz D. S - and N-alkylating agents diminish the fluorescence of fluorescent dye-stained DNA. Chem Biol Interact 2016; 262:12-18. [PMID: 27923644 DOI: 10.1016/j.cbi.2016.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 11/21/2016] [Accepted: 12/02/2016] [Indexed: 01/27/2023]
Abstract
Sulfur mustard (SM), a chemical warfare agent, causes DNA alkylation, which is believed to be the main cause of its toxicity. SM DNA adducts are commonly used to verify exposure to this vesicant. However, the required analytical state-of-the-art mass-spectrometry methods are complex, use delicate instruments, are not mobile, and require laboratory infrastructure that is most likely not available in conflict zones. Attempts have thus been made to develop rapid detection methods that can be used in the field. The analysis of SM DNA adducts (HETE-G) by immunodetection is a convenient and suitable method. For a diagnostic assessment, HETE-G levels must be determined in relation to the total DNA in the sample. Total DNA can be easily visualized by the use of fluorescent DNA dyes. This study examines whether SM and related compounds affect total DNA staining, an issue that has not been investigated before. After pure DNA was extracted from human keratinocytes (HaCaT cells), DNA was exposed to different S- and N-alkylating agents. Our experiments revealed a significant, dose-dependent decrease in the fluorescence signal of fluorescent dye-stained DNA after exposure to alkylating agents. After mass spectrometry and additional fluorescence measurements ruled out covalent modifications of ethidium bromide (EthBr) by SM, we assumed that DNA crosslinks caused DNA condensation and thereby impaired access of the fluorescent dyes to the DNA. DNA digestion by restriction enzymes restored fluorescence, a fact that strengthened our hypothesis. However, monofunctional agents, which are unable to crosslink DNA, also decreased the fluorescence signal. In subsequent experiments, we demonstrated that protons produced during DNA alkylation caused a pH decrease that was found responsible for the reduction in fluorescence. The use of an appropriate buffer system eliminated the adverse effect of alkylating agents on DNA staining with fluorescent dyes. An appropriate buffer system is thus crucial for DNA quantification with fluorescent dyes in the presence of alkylating compounds.
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Affiliation(s)
- Robert Giesche
- Bundeswehr Institute of Pharmacology and Toxicology, 80937 Munich, Germany
| | - Harald John
- Bundeswehr Institute of Pharmacology and Toxicology, 80937 Munich, Germany
| | - Kai Kehe
- Walther Straub Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universität München, 80336 Munich, Germany; Bundeswehr Medical Academy, 80937 Munich, Germany
| | - Annette Schmidt
- Bundeswehr Institute of Pharmacology and Toxicology, 80937 Munich, Germany
| | - Tanja Popp
- Bundeswehr Institute of Pharmacology and Toxicology, 80937 Munich, Germany; Walther Straub Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Frank Balzuweit
- Comprehensive Pneumology Center Munich (CPCM), German Center for Lung Research, 81377 Munich, Germany; Bundeswehr Medical Command, 56070 Koblenz, Germany
| | - Horst Thiermann
- Bundeswehr Institute of Pharmacology and Toxicology, 80937 Munich, Germany
| | - Thomas Gudermann
- Walther Straub Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universität München, 80336 Munich, Germany; Comprehensive Pneumology Center Munich (CPCM), German Center for Lung Research, 81377 Munich, Germany
| | - Dirk Steinritz
- Bundeswehr Institute of Pharmacology and Toxicology, 80937 Munich, Germany; Walther Straub Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universität München, 80336 Munich, Germany.
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Yang L, Wang S, Zhou M, Chen X, Zuo Y, Lv Y. Characterization of BioPlex network by topological properties. J Theor Biol 2016; 409:148-154. [PMID: 27552850 DOI: 10.1016/j.jtbi.2016.08.028] [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: 05/26/2016] [Revised: 07/28/2016] [Accepted: 08/20/2016] [Indexed: 11/16/2022]
Abstract
Protein-protein interaction (PPI) networks are emerging as valuable prototypes to study important problems in molecular cellular biology and systems biomedicine. An analysis of the topological properties of a PPI network is very helpful for understanding the function and structure of networks. In this study, we analyzed the topological patterns in the BioPlex network containing interactions among 10,961 proteins; most interactions were previously undocumented. The BioPlex network is a comprehensive map of human protein interactions and represents the first phase of a long-term effort to profile the entire human ORFEOME collection. Similar to other biological networks, we observed that the BioPlex network has several topological properties. We also quantified correlations profiles for the BioPlex network and compared them to randomized versions of the same network. We found that for the BioPlex network, edges between proteins with intermediate degrees were strongly suppressed, whereas edges between low-connected proteins were favored. Finally, the degrees of essential genes were compared with the degrees of non-essential genes and randomly selected proteins. There were no significant differences between the groups.
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Affiliation(s)
- Lei Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shiyuan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Meng Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xiaowen Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yongchun Zuo
- The National Research Center for Animal Transgenic Biotechnology, Inner Mongolia University, Hohhot 010021, China
| | - Yingli Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
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