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Chen K, Li W, Wang J, Wang W. Binding of Copper Ions with Octapeptide Region in Prion Protein: Simulations with Charge Transfer Model. J Phys Chem B 2019; 123:5216-5228. [PMID: 31242743 DOI: 10.1021/acs.jpcb.9b02457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Copper ions are important cofactors of many metalloproteins. The binding dynamics of proteins to the copper ion is important for biological functions but is less understood at the microscopic level. What are the key factors determining the recognition and the stabilization of the copper ion during the binding? Our work investigates the binding dynamics of the copper ion with a simple system (the N-terminus of PrP) using simulation methods. To precisely characterize the protein?ion interaction, we build up an effective copper?peptide force field based on quantum chemistry calculations. In our model, the effects of charge transfer, protonation/deprotonation, and induced polarization are considered. With this force field, we successfully characterize the local structures and the complex interactions of the octapeptide around the copper ion. Furthermore, using an enhanced sampling method, the binding/unbinding processes of the copper ion with the octapeptide are simulated. Free-energy landscapes are generated in consequence, and multiple binding pathways are characterized. It is observed that various native ligands contribute differently to the binding processes. Some residues are related to the capture of the ion (behaving like ?arm?s), and some others contribute to the stabilization of the coordination structure (acting like ?core?s). These different interactions induce various pathways. Besides, a nonnative binding ligand is determined, and it has essential contributions and modulations to the binding pathways. With all these results, the picture of copper?octapeptide binding is outlined. These features are believed to happen in many ion?peptide interactions, such as the cooperative stabilization between the coordinations with neighboring backbone nitrogens and an auxiliary intermediate coordination with the neighboring oxygen from the N-terminal direction. We believe that our studies are valuable to understand the complicated ion?peptide binding processes.
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Affiliation(s)
- Ke Chen
- National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, and School of Physics , Nanjing University , Nanjing 210093 , P.R. China
| | - Wenfei Li
- National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, and School of Physics , Nanjing University , Nanjing 210093 , P.R. China
| | - Jun Wang
- National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, and School of Physics , Nanjing University , Nanjing 210093 , P.R. China
| | - Wei Wang
- National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, and School of Physics , Nanjing University , Nanjing 210093 , P.R. China
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Bruschi M, Bertini L, Bonačić-Koutecký V, De Gioia L, Mitrić R, Zampella G, Fantucci P. Speciation of Copper–Peptide Complexes in Water Solution Using DFTB and DFT Approaches: Case of the [Cu(HGGG)(Py)] Complex. J Phys Chem B 2012; 116:6250-60. [DOI: 10.1021/jp210409c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Maurizio Bruschi
- Department of Environmental Science, University of Milano-Bicocca, Piazza della Scienza
1, I-20126 Milano, Italy
| | - Luca Bertini
- Department of Biotechnologies
and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy
| | - Vlasta Bonačić-Koutecký
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse
2, D-12489 Berlin, Germany
| | - Luca De Gioia
- Department of Biotechnologies
and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy
| | - Roland Mitrić
- Fachbereich Physik, Freie Universität zu Berlin, Arnimallee 14,
D-14195 Berlin, Germany
| | - Giuseppe Zampella
- Department of Biotechnologies
and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy
| | - Piercarlo Fantucci
- Department of Biotechnologies
and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy
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Structural characterization of Cu2+, Ni2+ and Zn2+ binding sites of model peptides associated with neurodegenerative diseases. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2011.07.004] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Ling Y, Khade RL, Zhang Y. Structural, EPR Superhyperfine, and NMR Hyperfine Properties of the Cu−Octarepeat Binding Site in the Prion Protein. J Phys Chem B 2011; 115:2663-70. [DOI: 10.1021/jp1119298] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yan Ling
- Department of Chemistry and Biochemistry, University of Southern Mississippi, 118 College Drive #5043, Hattiesburg, Mississippi 39406, United States
| | - Rahul L. Khade
- Department of Chemistry and Biochemistry, University of Southern Mississippi, 118 College Drive #5043, Hattiesburg, Mississippi 39406, United States
| | - Yong Zhang
- Department of Chemistry and Biochemistry, University of Southern Mississippi, 118 College Drive #5043, Hattiesburg, Mississippi 39406, United States
- Department of Chemistry, Chemical Biology, and Biomedical Engineering, Stevens Institute of Technology, Castle Point on Hudson, Hoboken, New Jersey 07030, United States
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Rivillas-Acevedo L, Grande-Aztatzi R, Lomelí I, García JE, Barrios E, Teloxa S, Vela A, Quintanar L. Spectroscopic and Electronic Structure Studies of Copper(II) Binding to His111 in the Human Prion Protein Fragment 106−115: Evaluating the Role of Protons and Methionine Residues. Inorg Chem 2011; 50:1956-72. [DOI: 10.1021/ic102381j] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lina Rivillas-Acevedo
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav), 07360, D.F., Mexico
| | - Rafael Grande-Aztatzi
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav), 07360, D.F., Mexico
| | - Italia Lomelí
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav), 07360, D.F., Mexico
| | - Javier E. García
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav), 07360, D.F., Mexico
| | - Erika Barrios
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav), 07360, D.F., Mexico
| | - Sarai Teloxa
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav), 07360, D.F., Mexico
| | - Alberto Vela
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav), 07360, D.F., Mexico
| | - Liliana Quintanar
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav), 07360, D.F., Mexico
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Qiao Y, Zhao J, Li P, Wang J, Feng J, Wang W, Sun H, Ma Y, Yuan Z. Adsorbents with high selectivity for uremic middle molecular peptides containing the Asp-Phe-Leu-Ala-Glu sequence. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:7181-7187. [PMID: 20201581 DOI: 10.1021/la904272e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Asp-Phe-Leu-Ala-Glu (DE5) is a frequent sequence of many toxic middle molecular peptides that accumulate in uremic patients. To eliminate these peptides by hemoperfusion, three adsorbents (CP1-Zn(2+), CP2-Zn(2+), and CP3-Zn(2+)) were designed on the basis of coordination and hydrophobic interactions. Adsorption experiments indicated that CP2-Zn(2+) had the highest affinity for DE5 among these three adsorbents. Also, the adsorption capacity of CP2-Zn(2+) in DE5 and DE5-containing peptides was about 2-6 times higher than that of peptides without the DE5 sequence. Linear polymers bearing the same functional groups of the adsorbents were used as models to study the adsorption mechanism via isothermal titration calorimetry (ITC) and computer-aided analyses. The results indicated that coordination and hydrophobic interactions played the most important roles in their affinity. When two carboxyl moieties on Asp and Glu residues coordinated to CP2-Zn(2+), the hydrophobic interaction took place by the aggregation of the hydrophobic amino acid residues with phenyl group on CP2-Zn(2+). The optimal collaboration of these interactions led to the tight binding and selective adsorption of DE5-containing peptides onto CP2-Zn(2+). These results may provide new insight into the design of affinity adsorbents for peptides containing DE5-like sequences.
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Affiliation(s)
- Yitao Qiao
- Key Laboratory of Functional Polymer Materials, Ministry of Education, College of Chemistry, Nankai University, Tianjin 300071, PR China
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Pandey KK, Snyder JP, Liotta DC, Musaev DG. Computational Studies of Transition Metal Selectivity of Octapeptide Repeat Region of Prion Protein (PrP). J Phys Chem B 2009; 114:1127-35. [PMID: 20020721 DOI: 10.1021/jp909945e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Krishna K. Pandey
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, and School of Chemical Sciences, Devi Ahilya University Indore, Indore 452001, India
| | - James P. Snyder
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, and School of Chemical Sciences, Devi Ahilya University Indore, Indore 452001, India
| | - Dennis C. Liotta
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, and School of Chemical Sciences, Devi Ahilya University Indore, Indore 452001, India
| | - Djamaladdin G. Musaev
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, and School of Chemical Sciences, Devi Ahilya University Indore, Indore 452001, India
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Insight into the copper coordination environment in the prion protein through density functional theory calculations of EPR parameters. J Biol Inorg Chem 2009; 14:547-57. [DOI: 10.1007/s00775-009-0469-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Accepted: 01/16/2009] [Indexed: 10/21/2022]
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Bruschi M, De Gioia L, Mitrić R, Bonačić-Koutecký V, Fantucci P. A DFT study of EPR parameters in Cu(ii) complexes of the octarepeat region of the prion protein. Phys Chem Chem Phys 2008; 10:4573-83. [DOI: 10.1039/b718603g] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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