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Pushie MJ, George G. Informing our Understanding of the Copper-Cuprizone Reaction with Computational Chemistry. Dalton Trans 2022; 51:10377-10391. [DOI: 10.1039/d2dt01476a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reaction of copper with bis(cyclohexanone)oxaldihydrazone (cuprizone) is a challenging coordination chemistry problem that has confounded attempts at elucidation for the past 70 years. The product of the reaction, a...
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Pushie MJ, Stefaniak E, Sendzik MR, Sokaras D, Kroll T, Haas KL. Using N-Terminal Coordination of Cu(II) and Ni(II) to Isolate the Coordination Environment of Cu(I) and Cu(II) Bound to His13 and His14 in Amyloid-β(4-16). Inorg Chem 2019; 58:15138-15154. [PMID: 31657204 DOI: 10.1021/acs.inorgchem.9b01940] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The amyloid-β (Aβ) peptide is a cleavage product of the amyloid precursor protein and has been implicated as a central player in Alzheimer's disease. The N-terminal end of Aβ is variable, and different proportions of these variable-length Aβ peptides are present in healthy individuals and those with the disease. The N-terminally truncated form of Aβ starting at position 4 (Aβ4-x) has a His residue as the third amino acid (His6 using the formal Aβ numbering). The N-terminal sequence Xaa-Xaa-His is known as an amino terminal copper and nickel binding motif (ATCUN), which avidly binds Cu(II). This motif is not present in the commonly studied Aβ1-x peptides. In addition to the ATCUN site, Aβ4-x contains an additional metal binding site located at the tandem His residues (bis-His at His13 and 14) which is also found in other isoforms of Aβ. Using the ATCUN and bis-His motifs, the Aβ4-x peptide is capable of binding multiple metal ions simultaneously. We confirm that Cu(II) bound to this particular ATCUN site is redox silent, but the second Cu(II) site is redox active and can be readily reduced with ascorbate. We have employed surrogate metal ions to block copper coordination at the ATCUN or the tandem His site in order to isolate spectral features of the copper coordination environment for structural characterization using extended X-ray absorption fine structure (EXAFS) spectroscopy. This approach reveals that each copper coordination environment is independent in the Cu2Aβ4-x state. The identification of two functionally different copper binding environments within the Aβ4-x sequence may have important implications for this peptide in vivo.
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Affiliation(s)
- M Jake Pushie
- Department of Surgery , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5E5 , Canada
| | - Ewelina Stefaniak
- Department of Chemistry and Physics , Saint Mary's College , Notre Dame , Indiana 46556 , United States.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Pawińskiego 5a , 02-106 Warsaw , Poland
| | - Madison R Sendzik
- Department of Chemistry and Physics , Saint Mary's College , Notre Dame , Indiana 46556 , United States
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource , SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource , SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| | - Kathryn L Haas
- Department of Chemistry and Physics , Saint Mary's College , Notre Dame , Indiana 46556 , United States
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Structural Consequences of Copper Binding to the Prion Protein. Cells 2019; 8:cells8080770. [PMID: 31349611 PMCID: PMC6721516 DOI: 10.3390/cells8080770] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 12/24/2022] Open
Abstract
Prion, or PrPSc, is the pathological isoform of the cellular prion protein (PrPC) and it is the etiological agent of transmissible spongiform encephalopathies (TSE) affecting humans and animal species. The most relevant function of PrPC is its ability to bind copper ions through its flexible N-terminal moiety. This review includes an overview of the structure and function of PrPC with a focus on its ability to bind copper ions. The state-of-the-art of the role of copper in both PrPC physiology and in prion pathogenesis is also discussed. Finally, we describe the structural consequences of copper binding to the PrPC structure.
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Kadej A, Kuczer M, Czarniewska E, Urbański A, Rosiński G, Kowalik-Jankowska T. High stability and biological activity of the copper(II) complexes of alloferon 1 analogues containing tryptophan. J Inorg Biochem 2016; 163:147-161. [PMID: 27453534 DOI: 10.1016/j.jinorgbio.2016.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/21/2016] [Accepted: 07/07/2016] [Indexed: 11/28/2022]
Abstract
Copper(II) complex formation processes between the alloferon 1 (Allo1) (HGVSGHGQHGVHG) analogues where the tryptophan residue is introducing in the place His residue H1W, H6W, H9W and H12W have been studied by potentiometric, UV-visible, CD and EPR spectroscopic, and MS methods. For all analogues of alloferon 1 complex speciation have been obtained for a 1:1 metal-to-ligand molar ratio and 2:1 of H1W because of precipitation at higher (2:1, 3:1 and 4:1) ratios. At physiological pH7.4 and a 1:1 metal-to-ligand molar ratio the tryptophan analogues of alloferon 1 form the CuH-1L and/or CuH-2L complexes with the 4N binding mode. The introduction of tryptophan in place of histidine residues changes the distribution diagram of the complexes formed with the change of pH and their stability constants compared to the respective substituted alanine analogues of alloferon 1. The CuH-1L, CuH-2L and CuH-3L complexes of the tryptophan analogues are more stable from 1 to 5 log units in comparison to those of the alanine analogues. This stabilization of the complexes may result from cation(Cu(II))-π and indole/imidazole ring interactions. The induction of apoptosis in vivo, in Tenebrio molitor cells by the ligands and their copper(II) complexes at pH7.4 was studied. The biological results show that copper(II) ions in vivo did not cause any apparent apoptotic features. The most active were the H12W peptide and Cu(II)-H12W complex formed at pH7.4.
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Affiliation(s)
- Agnieszka Kadej
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Mariola Kuczer
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Elżbieta Czarniewska
- Department of Animal Physiology and Development, Institute of Experimental Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Arkadiusz Urbański
- Department of Animal Physiology and Development, Institute of Experimental Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland; Department of Systematic Zoology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Grzegorz Rosiński
- Department of Animal Physiology and Development, Institute of Experimental Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
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Di Natale G, Turi I, Pappalardo G, Sóvágó I, Rizzarelli E. Cross-Talk Between the Octarepeat Domain and the Fifth Binding Site of Prion Protein Driven by the Interaction of Copper(II) with the N-terminus. Chemistry 2015; 21:4071-84. [DOI: 10.1002/chem.201405502] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Indexed: 12/21/2022]
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Pushie MJ, Nienaber KH, McDonald A, Millhauser GL, George GN. Combined EXAFS and DFT structure calculations provide structural insights into the 1:1 multi-histidine complexes of Cu(II) , Cu(I) , and Zn(II) with the tandem octarepeats of the mammalian prion protein. Chemistry 2014; 20:9770-83. [PMID: 25042361 DOI: 10.1002/chem.201304201] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 04/06/2014] [Indexed: 02/01/2023]
Abstract
The metal-coordinating properties of the prion protein (PrP) have been the subject of intense focus and debate since the first reports of its interaction with copper just before the turn of the century. The picture of metal coordination to PrP has been improved and refined over the past decade, but structural details of the various metal coordination modes have not been fully elucidated in some cases. In the present study, we have employed X-ray absorption near-edge spectroscopy as well as extended X-ray absorption fine structure (EXAFS) spectroscopy to structurally characterize the dominant 1:1 coordination modes for Cu(II) , Cu(I) , and Zn(II) with an N-terminal fragment of PrP. The PrP fragment corresponds to four tandem repeats representative of the mammalian octarepeat domain, designated as OR4 , which is also the most studied PrP fragment for metal interactions, making our findings applicable to a large body of previous work. Density functional theory (DFT) calculations have provided additional structural and thermodynamic data, and candidate structures have been used to inform EXAFS data analysis. The optimized geometries from DFT calculations have been used to identify potential coordination complexes for multi-histidine coordination of Cu(II) , Cu(I) , and Zn(II) in an aqueous medium, modelled using 4-methylimidazole to represent the histidine side chain. Through a combination of in silico coordination chemistry as well as rigorous EXAFS curve-fitting, using full multiple scattering on candidate structures derived from DFT calculations, we have characterized the predominant coordination modes for the 1:1 complexes of Cu(II) , Cu(I) , and Zn(II) with the OR4 peptide at pH 7.4 at atomic resolution, which are best represented as square-planar [Cu(II) (His)4 ](2+) , digonal [Cu(I) (His)2 ](+) , and tetrahedral [Zn(II) (His)3 (OH2 )](2+) , respectively.
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Affiliation(s)
- M Jake Pushie
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK, S7N 5E2 (Canada), Fax: (+1) 306-966-8593.
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Copper-induced structural propensities of the amyloidogenic region of human prion protein. J Biol Inorg Chem 2014; 19:635-45. [DOI: 10.1007/s00775-014-1132-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 04/02/2014] [Indexed: 12/15/2022]
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McDonald A, Pushie MJ, Millhauser GL, George GN. New insights into metal interactions with the prion protein: EXAFS analysis and structure calculations of copper binding to a single octarepeat from the prion protein. J Phys Chem B 2013; 117:13822-41. [PMID: 24102071 PMCID: PMC3890359 DOI: 10.1021/jp408239h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Copper coordination to the prion protein (PrP) has garnered considerable interest for almost 20 years, due in part to the possibility that this interaction may be part of the normal function of PrP. The most characterized form of copper binding to PrP has been Cu(2+) interaction with the conserved tandem repeats in the N-terminal domain of PrP, termed the octarepeats, with many studies focusing on single and multiple repeats of PHGGGWGQ. Extended X-ray absorption fine structure (EXAFS) spectroscopy has been used in several previous instances to characterize the solution structure of Cu(2+) binding into the peptide backbone in the HGGG portion of the octarepeats. All previous EXAFS studies, however, have benefitted from crystallographic structure information for [Cu(II) (Ac-HGGGW-NH2)(-2H)] but have not conclusively demonstrated that the complex EXAFS spectrum represents the same coordination environment for Cu(2+) bound to the peptide backbone. Density functional structure calculations as well as full multiple scattering EXAFS curve fitting analysis are brought to bear on the predominant coordination mode for Cu(2+) with the Ac-PHGGGWGQ-NH2 peptide at physiological pH, under high Cu(2+) occupancy conditions. In addition to the structure calculations, which provide a thermodynamic link to structural information, methods are also presented for extensive deconvolution of the EXAFS spectrum. We demonstrate how the EXAFS data can be analyzed to extract the maximum structural information and arrive at a structural model that is significantly improved over previous EXAFS characterizations. The EXAFS spectrum for the chemically reduced form of copper binding to the Ac-PHGGGWGQ-NH2 peptide is presented, which is best modeled as a linear two-coordinate species with a single His imidazole ligand and a water molecule. The extent of in situ photoreduction of the copper center during standard data collection is also presented, and EXAFS curve fitting of the photoreduced species reveals an intermediate structure that is similar to the Cu(2+) form with reduced coordination number.
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Affiliation(s)
- Alex McDonald
- Department of Geological Sciences, University of Saskatchewan , Saskatoon, Saskatchewan S7N 5E2, Canada
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Insertion of beta-alanine in model peptides for copper binding to His96 and His111 of the human prion protein. J Inorg Biochem 2013; 126:104-10. [DOI: 10.1016/j.jinorgbio.2013.05.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 05/29/2013] [Accepted: 05/29/2013] [Indexed: 12/30/2022]
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10
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Emwas AHM, Al-Talla ZA, Guo X, Al-Ghamdi S, Al-Masri HT. Utilizing NMR and EPR spectroscopy to probe the role of copper in prion diseases. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:255-268. [PMID: 23436479 DOI: 10.1002/mrc.3936] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 12/19/2012] [Accepted: 01/11/2013] [Indexed: 06/01/2023]
Abstract
Copper is an essential nutrient for the normal development of the brain and nervous system, although the hallmark of several neurological diseases is a change in copper concentrations in the brain and central nervous system. Prion protein (PrP) is a copper-binding, cell-surface glycoprotein that exists in two alternatively folded conformations: a normal isoform (PrP(C)) and a disease-associated isoform (PrP(Sc)). Prion diseases are a group of lethal neurodegenerative disorders that develop as a result of conformational conversion of PrP(C) into PrP(Sc). The pathogenic mechanism that triggers this conformational transformation with the subsequent development of prion diseases remains unclear. It has, however, been shown repeatedly that copper plays a significant functional role in the conformational conversion of prion proteins. In this review, we focus on current research that seeks to clarify the conformational changes associated with prion diseases and the role of copper in this mechanism, with emphasis on the latest applications of NMR and EPR spectroscopy to probe the interactions of copper with prion proteins.
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Affiliation(s)
- Abdul-Hamid M Emwas
- NMR Core Lab, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
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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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Bertini L, Bruschi M, Romaniello M, Zampella G, Tiberti M, Barbieri V, Greco C, La Mendola D, Bonomo RP, Fantucci P, De Gioia L. Copper coordination to the putative cell binding site of angiogenin: a DFT investigation. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1186-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Mechanism of copper(II)-induced misfolding of Parkinson's disease protein. Sci Rep 2011; 1:11. [PMID: 22355530 PMCID: PMC3216499 DOI: 10.1038/srep00011] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 04/28/2011] [Accepted: 05/06/2011] [Indexed: 01/20/2023] Open
Abstract
α-synuclein (aS) is a natively unfolded pre-synaptic protein found in all Parkinson's disease patients as the major component of fibrillar plaques. Metal ions, and especially Cu(II), have been demonstrated to accelerate aggregation of aS into fibrillar plaques, the precursors to Lewy bodies. In this work, copper binding to aS is investigated by a combination of quantum and molecular mechanics simulations. Starting from the experimentally observed attachment site, several optimized structures of Cu-binding geometries are examined. The most energetically favorable attachment results in significant allosteric changes, making aS more susceptible to misfolding. Indeed, an inverse kinematics investigation of the configuration space uncovers a dynamically stable β-sheet conformation of Cu-aS that serves as a nucleation point for a second β-strand. Based on these findings, we propose an atomistic mechanism of copper-induced misfolding of aS as an initial event in the formation of Lewy bodies and thus in PD pathogenesis.
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Yi HB, Xia FF, Zhou Q, Zeng D. [CuCl3]− and [CuCl4]2− Hydrates in Concentrated Aqueous Solution: A Density Functional Theory and ab Initio Study. J Phys Chem A 2011; 115:4416-26. [DOI: 10.1021/jp109723v] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Hai-Bo Yi
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, China.
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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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Mhidia R, Melnyk O. Selective cleavage of an azaGly peptide bond by copper(II). Long-range effect of histidine residue. J Pept Sci 2010; 16:141-7. [DOI: 10.1002/psc.1211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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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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Prion metal interaction: Is prion pathogenesis a cause or a consequence of metal imbalance? Chem Biol Interact 2009; 181:282-91. [PMID: 19660443 DOI: 10.1016/j.cbi.2009.07.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Revised: 07/22/2009] [Accepted: 07/27/2009] [Indexed: 12/14/2022]
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Bryantsev VS, Diallo MS, Goddard WA. Computational Study of Copper(II) Complexation and Hydrolysis in Aqueous Solutions Using Mixed Cluster/Continuum Models. J Phys Chem A 2009; 113:9559-67. [DOI: 10.1021/jp904816d] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Vyacheslav S. Bryantsev
- Materials and Process Simulation Center, Beckman Institute 139-74, California Institute of Technology, Pasadena, California 91125
| | - Mamadou S. Diallo
- Materials and Process Simulation Center, Beckman Institute 139-74, California Institute of Technology, Pasadena, California 91125
| | - William A. Goddard
- Materials and Process Simulation Center, Beckman Institute 139-74, California Institute of Technology, Pasadena, California 91125
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Barry SD, Rickard GA, Pushie MJ, Rauk A. The affinity of HGGG, GHGG, GGHG, and GGGH peptides for copper(II) and the structures of their complexes — An ab initio study. CAN J CHEM 2009. [DOI: 10.1139/v09-034] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structures and relative free energies in aqueous solution of the Cu(II) complexes of the “histidine walk” peptides, AcHGGGNH2, AcGHGGNH2, AcGGHGNH2, and AcGGGHNH2, were determined as a function of pH. Numerous structures of each species were found by gaseous- and solution-phase geometry optimization at the B3LYP/6–31G(d) level, and the effect of solvation estimated by the IEFPCM continuum solvation model. Free energies of solvation of the ionic species are large and favour structures with an extended peptide chain. In all Cu(II)–peptide complexes, deprotonation of two amide groups occurs readily at or below pH 7. In each system, the most abundant species at pH 7 is a neutral 1:1 complex with N3O1 coordination pattern. Binding in the forward direction toward the C terminus is preferred. The results are compared to recent experimental spectroscopic and potentiometric studies on related systems. Alternative explanations are offered for some of the experimental observations.
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Affiliation(s)
- Stephen D. Barry
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Gail A. Rickard
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - M. Jake Pushie
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Arvi Rauk
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
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Functional implications of multistage copper binding to the prion protein. Proc Natl Acad Sci U S A 2009; 106:11576-81. [PMID: 19561303 DOI: 10.1073/pnas.0903807106] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The prion protein (PrP) is responsible for a group of neurodegenerative diseases called the transmissible spongiform encephalopathies. The normal function of PrP has not yet been discovered, but indirect evidence suggests a linkage to its ability to bind copper. In this article, low-copper-concentration bindings of Cu(2+) to PrP are investigated by using a recently developed hybrid density functional theory (DFT)/DFT method. It is found that at the lowest copper concentrations, the binding site consists of 4 histidine residues coordinating the copper through epsilon imidazole nitrogens. At higher concentrations, 2 histidines are involved in the binding, one of them in the axial position. These results are in good agreement with existing experimental data. Comparison of free energies for all modes of coordination shows that when enough copper is available, the binding sites will spontaneously rearrange to accommodate more copper ions, despite the fact that binding energy per copper ion decreases with concentration. These findings support the hypothesis that PrP acts as a copper buffer in vivo, protecting other proteins from the attachment of copper ions. Using large-scale classical molecular dynamics, we also probe the structure of full-length copper-bound PrP, including its unfolded N-terminal domain. The results show that copper attachment leads to rearrangement of the structure of the Cu-bonded octarepeat region and to development of turns in areas separating copper-bound residues. These turns make the flexible N-terminal domain more rigid and thus more resistant to misfolding. The last result suggests that copper binding plays a beneficial role in the initial stages of prion diseases.
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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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Can copper binding to the prion protein generate a misfolded form of the protein? Biometals 2009; 22:159-75. [PMID: 19140013 DOI: 10.1007/s10534-008-9196-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Accepted: 12/07/2008] [Indexed: 10/21/2022]
Abstract
The native prion protein (PrP) has a two domain structure, with a globular folded alpha-helical C-terminal domain and a flexible extended N-terminal region. The latter can selectively bind Cu(2+) via four His residues in the octarepeat (OR) region, as well as two sites (His96 and His111) outside this region. In the disease state, the folded C-terminal domain of PrP undergoes a conformational change, forming amorphous aggregates high in beta-sheet content. Cu(2+) bound to the ORs can be redox active and has been shown to induce cleavage within the OR region, a process requiring conserved Trp residues. Using computational modeling, we have observed that electron transfer from Trp residues to copper can be favorable. These models also reveal that an indole-based radical cation or Cu(+) can initiate reactions leading to protein backbone cleavage. We have also demonstrated, by molecular dynamics simulations, that Cu(2+) binding to the His96 and His111 residues in the remaining PrP N-terminal fragment can induce localized beta-sheet structure, allowing us to suggest a potential mechanism for the initiation of beta-sheet misfolding in the C-terminal domain by Cu(2+).
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26
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Pushie MJ, Vogel HJ. A potential mechanism for Cu2+ reduction, beta-cleavage, and beta-sheet initiation within the N-terminal domain of the prion protein: insights from density functional theory and molecular dynamics calculations. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2009; 72:1040-1059. [PMID: 19697239 DOI: 10.1080/15287390903084389] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The N-terminal region of the native human prion protein encompasses four highly conserved octarepeats that each contain a single His, Pro, Gln, and Trp residue as well as several Gly residues. At neutral pH these repeats are capable of individually binding copper (Cu(2+)) ions, involving the His side chain and the backbone amide of the Gly residues. In addition, the two His residues at positions 96 and 111 are also capable of binding Cu(2+). At low concentrations of the metal ion or at low pH, one Cu(2+) may be bound by multiple His residues of the four octarepeats. This complex is known to be redox active, while none of the other Cu(2+)-bound complexes are. Using density functional theory and molecular dynamics calculations data demonstrated how this form of the protein could reduce Cu(2+), through a process involving electron transfer from the Trp side chain. The reduced Cu gives rise to reactive oxygen species (ROS), which can lead to beta-cleavage of the prion protein chain at any of the Gly residues around position 90. Protein fragments of lengths similar to those arising from beta-cleavage are predominantly found in both healthy and Creutzfeldt-Jakob disease (CJD)-affected brains. Models of Cu binding to the His96 and His111 residues also indicate that different modes of Cu(2+) binding result in formation of stable beta-hairpin structures in this region of the protein. It is postulated that through interactions with the C-terminal part of the protein these hairpins may initiate misfolding and yield more stable beta-sheet structures that might associate in the same fashion with additional prion proteins.
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Affiliation(s)
- M Jake Pushie
- Structural Biology Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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27
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Bryantsev VS, Diallo MS, van Duin ACT, Goddard III WA. Hydration of Copper(II): New Insights from Density Functional Theory and the COSMO Solvation Model. J Phys Chem A 2008; 112:9104-12. [DOI: 10.1021/jp804373p] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vyacheslav S. Bryantsev
- Materials and Process Simulation Center, Beckman Institute 139-74, California Institute of Technology, Pasadena, California 91125, and Department of Civil Engineering, Howard University, Washington, D.C. 20059
| | - Mamadou S. Diallo
- Materials and Process Simulation Center, Beckman Institute 139-74, California Institute of Technology, Pasadena, California 91125, and Department of Civil Engineering, Howard University, Washington, D.C. 20059
| | - Adri C. T. van Duin
- Materials and Process Simulation Center, Beckman Institute 139-74, California Institute of Technology, Pasadena, California 91125, and Department of Civil Engineering, Howard University, Washington, D.C. 20059
| | - William A. Goddard III
- Materials and Process Simulation Center, Beckman Institute 139-74, California Institute of Technology, Pasadena, California 91125, and Department of Civil Engineering, Howard University, Washington, D.C. 20059
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28
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Hureau C, Mathé C, Faller P, Mattioli TA, Dorlet P. Folding of the prion peptide GGGTHSQW around the copper(II) ion: identifying the oxygen donor ligand at neutral pH and probing the proximity of the tryptophan residue to the copper ion. J Biol Inorg Chem 2008; 13:1055-64. [DOI: 10.1007/s00775-008-0389-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Accepted: 05/13/2008] [Indexed: 10/22/2022]
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29
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Rimola A, Constantino E, Rodríguez-Santiago L, Sodupe M. Binding Properties of Cu+/2+-(glycyl)nglycine Complexes (n = 1−3). J Phys Chem A 2008; 112:3444-53. [DOI: 10.1021/jp711189s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Erika Constantino
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | | | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
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30
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Hodak M, Lu W, Bernholc J. Hybridab initioKohn-Sham density functional theory/frozen-density orbital-free density functional theory simulation method suitable for biological systems. J Chem Phys 2008; 128:014101. [DOI: 10.1063/1.2814165] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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31
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Riihimäki ES, Martínez JM, Kloo L. Structural effects of Cu(ii)-coordination in the octapeptide region of the human prion protein. Phys Chem Chem Phys 2008; 10:2488-95. [DOI: 10.1039/b717988j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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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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33
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Ke Y, Zhao J, Verkerk UH, Hopkinson AC, Siu KWM. Histidine, Lysine, and Arginine Radical Cations: Isomer Control via the Choice of Auxiliary Ligand (L) in the Dissociation of [CuII(L)(amino acid)]•2+ Complexes. J Phys Chem B 2007; 111:14318-28. [DOI: 10.1021/jp0746648] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuyong Ke
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
| | - Junfang Zhao
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
| | - Udo H. Verkerk
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
| | - Alan C. Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
| | - K. W. Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
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34
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Pushie MJ, Vogel HJ. Molecular dynamics simulations of two tandem octarepeats from the mammalian prion protein: fully Cu2+-bound and metal-free forms. Biophys J 2007; 93:3762-74. [PMID: 17704169 PMCID: PMC2084230 DOI: 10.1529/biophysj.107.109512] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular dynamics simulations have been conducted on a model fragment (Ac-PHGGGWGQPHGGGW-NH(2)) of the prion protein octarepeat domain, both in the Cu(2+)-bound and metal-free forms. The copper-bound models are based on the consensus structure of the core Cu(2+)-binding site of an individual octarepeat, relevant to the fully Cu(2+)-occupied prion protein octarepeat region. The model peptides contain Cu(2+) bound through a His imidazole ring and two deprotonated amide N-atoms in the peptide backbone supplied by the following two Gly residues. Both the copper-bound and metal-free models have been simulated with the OPLS all-atom force field with the GROMACS molecular dynamics package. These simulations, with two tandem copper-binding sites, represent the minimum model necessary to observe potential structuring between the copper-binding sites in the octarepeat region. The GWGQ residues constitute a flexible linker region that predominantly adopts a turn, serving to bring adjacent His residues into close proximity. The consequent formation of stable structures demonstrates that the copper-bound octarepeat region allows the copper-coordinating sites to come into van der Waals contact, packing into particular orientations to further stabilize the bend in the GWGQ linker region.
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Affiliation(s)
- M Jake Pushie
- Structural Biology Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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35
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Riihimäki ES, Martínez JM, Kloo L. Molecular Dynamics Simulations of Cu(II) and the PHGGGWGQ Octapeptide. J Phys Chem B 2007; 111:10529-37. [PMID: 17696524 DOI: 10.1021/jp072672i] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interaction between Cu2+ and the copper-binding octapeptide region in the human prion protein has been investigated by molecular dynamics simulations. In total four different nonbonded and bonded models were used in the study. Charge sets containing atomic partial charges were developed for these models. Out of the considered models, the bonded model performed physically in the most correct way. The simulations with the bonded model showed that the water molecules in the axial position are very labile. The tryptophan indole ring can remain in a stable position on top of the equatorial coordination plane of copper without water mediation. Strong aromatic interaction was observed between the imidazole and indole rings. The nonbonded models showed a tendency for water-mediated interaction between the copper ion and different carbonyl oxygen atoms. In the case of the bonded model, a carbonyl group could also interact directly with the copper ion in one of the apical position.
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Affiliation(s)
- Eva-Stina Riihimäki
- Inorganic Chemistry, Department of Chemistry, Royal Institute of Technology, 100 44 Stockholm, Sweden
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36
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Abstract
The transmissible spongiform encephalopathies (TSEs) arise from conversion of the membrane-bound prion protein from PrP(C) to PrP(Sc). Examples of the TSEs include mad cow disease, chronic wasting disease in deer and elk, scrapie in goats and sheep, and kuru and Creutzfeldt-Jakob disease in humans. Although the precise function of PrP(C) in healthy tissues is not known, recent research demonstrates that it binds Cu(II) in an unusual and highly conserved region of the protein termed the octarepeat domain. This review describes recent connections between copper and PrP(C), with an emphasis on the electron paramagnetic resonance elucidation of the specific copper-binding sites, insights into PrP(C) function, and emerging connections between copper and prion disease.
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Affiliation(s)
- Glenn L Millhauser
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA.
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37
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Pushie MJ, Ross ARS, Vogel HJ. Mass spectrometric determination of the coordination geometry of potential copper(II) surrogates for the mammalian prion protein octarepeat region. Anal Chem 2007; 79:5659-67. [PMID: 17608450 DOI: 10.1021/ac070312l] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The N-terminal domain of mammalian prion proteins contains several tandem repeats of the octapeptide PHGGGWGQ, each one capable of selectively binding up to 1 equiv of Cu2+. Under saturating conditions Cu2+ is known to coordinate the HGG portion of the repeat sequence via the histidine imidazole side chain, two deprotonated amide N-atoms, and a backbone carbonyl O-atom. Using appropriate selection criteria, we have generated a short list of candidate metal ions (Co3+, Ni2+, Pd2+, Pt2+) that can serve as potential surrogates for Cu2+. The selected metal ions were screened for binding interactions with the OR-derived peptide fragment AcHGGGWNH2 (Ac = acetyl, amino acid residues in italics) using electrospray ionization mass spectrometry. The coordination geometries of these metal ions with the synthetic OR peptide were subsequently determined from fragment analysis using collision-induced dissociation tandem mass spectrometry. Our results indicate that, although Co3+, Pd2+, and Pt2+ all bind to the OR fragment via the peptide backbone to varying extents, each of these metal ions appears to associate with the peptide in a unique manner, which is distinct from the way in which Cu2+ is coordinated. This work illustrates the extremely strong selectivity for Cu2+ of this highly conserved region of the mammalian prion protein.
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Affiliation(s)
- M Jake Pushie
- Structural Biology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
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38
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Furlan S, La Penna G, Guerrieri F, Morante S, Rossi GC. Studying the Cu binding sites in the PrP N-terminal region: a test case for ab initio simulations. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:841-5. [PMID: 17492282 DOI: 10.1007/s00249-007-0162-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Revised: 03/09/2007] [Accepted: 03/20/2007] [Indexed: 11/25/2022]
Abstract
First principle ab initio molecular dynamics simulations of the Car-Parrinello type have proved to be of invaluable help in understanding the microscopic mechanisms of chemical bonding both in solid state physics and in structural biophysics. In this work we present as a test case a study of the Cu coordination mode at the Prion Protein binding sites localized in the N-terminal octarepeat region. Using medium size PC-clusters, we are able to deal with systems with up to about 350 atoms and 10(3) electrons for as long as approximately 2 ps. With a foreseeable forthcoming scaling up of the available CPU times by a factor 10(3), one can hope to be soon able to simulate systems of biological interest of realistic size and for physical times of the order of the nanosecond.
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Affiliation(s)
- S Furlan
- Consiglio Nazionale delle Ricerche, ISMAC, Via De Marini 6, Genoa, Italy.
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39
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Furlan S, La Penna G, Guerrieri F, Morante S, Rossi GC. Ab initio simulations of Cu binding sites on the N-terminal region of prion protein. J Biol Inorg Chem 2007; 12:571-83. [PMID: 17333299 DOI: 10.1007/s00775-007-0218-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Accepted: 01/29/2007] [Indexed: 11/29/2022]
Abstract
The human prion protein binds Cu2+ ions in the octarepeat domain of the N-terminal tail up to full occupancy at pH 7.4. Recent experiments have shown that the HGGG octarepeat subdomain is responsible for holding the metal bound in a square-planar configuration. By using first principle ab initio molecular dynamics simulations of the Car-Parrinello type, the coordination of copper to the binding sites of the prion protein octarepeat region is investigated. Simulations are carried out for a number of structured binding sites. Results for the complexes Cu(HGGGW)(wat), Cu(HGGG), and [Cu(HGGG)]2 are presented. While the presence of a Trp residue and a water molecule does not seem to affect the nature of the copper coordination, high stability of the bond between copper and the amide nitrogen of deprotonated Gly residues is confirmed in all cases. For the more interesting [Cu(HGGG)]2 complex, a dynamically entangled arrangement of the two domains with exchange of amide nitrogen bonds between the two copper centers emerges, which is consistent with the short Cu-Cu distance observed in experiments at full copper occupancy.
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Affiliation(s)
- Sara Furlan
- National Research Council, Institute for Chemistry of Organo-metallic Compounds, Via Madonna Del Piano, 50019, Sesto Fiorentino (Florence), Italy
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Ronga L, Tizzano B, Palladino P, Ragone R, Urso E, Maffia M, Ruvo M, Benedetti E, Rossi F. The prion protein: Structural features and related toxic peptides. Chem Biol Drug Des 2007; 68:139-47. [PMID: 17062011 DOI: 10.1111/j.1747-0285.2006.00427.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Prion diseases are characterized by the conversion of the physiological cellular form of the prion protein (PrP(C)) into an insoluble, partially protease-resistant abnormal scrapie form (PrP(Sc)). PrP(C) is normally expressed in mammalian cell and is highly conserved among species, although its role in cellular function remains elusive. The conversion of PrP(C) to PrP(Sc) parallels a conformational change of the polypeptide from a predominantly alpha-helical to a highly beta-sheet secondary structure. The pathogenesis and molecular basis of the consequent nerve cell loss are not understood. Limited structural information is available on aggregate formation by this protein as the possible cause of these diseases and on its toxicity. This brief overview focuses on the large amount of structure-activity studies based on the prion fragment approach, hinging on peptides derived from the unstructured N-terminal and globular C-terminal domains. It is well documented that most of the fragments with regular secondary structure, with the exception of helices 1 and 3, possess a high beta-sheet propensity and tendency to form beta-sheet-like aggregates. In this context, helix 2 plays a crucial role because it is able to adopt both misfolded and partially helical conformation. However, only a few mutants are able to display its intrinsic neurotoxicity.
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Affiliation(s)
- Luisa Ronga
- Dipartimento delle Scienze Biologiche, C I R Pe B, Università Federico II di Napoli and Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
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Marino T, Russo N, Toscano M. On the Copper(II) Ion Coordination by Prion Protein HGGGW Pentapeptide Model. J Phys Chem B 2007; 111:635-40. [PMID: 17228921 DOI: 10.1021/jp065296v] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The interaction of the octapeptide domain of the prion protein with the transition-metal-ion Cu2+ was studied at the DFT level by using the HGGGW pentapeptide as a model to mimic the PHGGGWGQ octarepeat sequence. Ten complexes, in which the metal ion exhibits different coordinations, were considered. Our results indicate that the lowest-energy structure is characterized by a tetracoordinated metal center and that this tendency of the ion to assume the square planar geometry is strong enough to prevent the addition of a further water molecule in its coordination sphere. The role of tryptophan was found to cause a lowering of the system energy due to the stabilizing effect of the electrostatic interaction between the Trp aromatic indole and histidine imidazole rings.
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Affiliation(s)
- T Marino
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MIUR, Università della Calabria, I-87030 Arcavacata di Rende (CS), Italy
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42
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Riihimäki ES, Kloo L. Computational Comparison of Cation Coordination to Human Prion Peptide Models. Inorg Chem 2006; 45:8509-16. [PMID: 17029361 DOI: 10.1021/ic052079k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The coordination of the cations Cu(II), Co(II), Rh(III), Ir(III), Ni(II), Pd(II), Pt(II), and Zn(II) to the copper-binding octapeptide region in the human prion protein has been compared through structural optimization. The initial coordination mode used in the calculations is a five-coordinated mode obtained from previously published crystallographic data for Cu(II). The computational results show that, among these cations, the coordinations of Co(II) and Rh(III) are the most similar to that of Cu(II). The cations Ni(II), Pd(II), and Pt(II) prefer a four-coordinate square-planar coordination by the peptide ligand. The paramagnetic Co(II) ion with its large quadrupole moment is not a good substitute for Cu(II) to be used in NMR spectroscopic studies of the coordinated peptide region. Rh(III) has more attractive NMR spectroscopic characteristics than Cu(II) and Co(II) and may represent a suitable substitute for Cu(II) in these types of studies. Some preliminary experimental studies using NMR spectroscopic methods indicate that Rh(III) coordinates the copper-binding octapeptide region of the human prion protein, although further studies are required to determine the mode of interaction in detail.
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Affiliation(s)
- Eva-Stina Riihimäki
- Inorganic Chemistry, Royal Institute of Technology, S-100 44 Stockholm, Sweden
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43
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Conradie MM, Conradie J, Ghosh A. A DFT overview of high-valent iron, cobalt and nickel tetraamidomacrocyclic ligand (TAML) complexes: The end of innocence? J Inorg Biochem 2006; 100:620-6. [PMID: 16504297 DOI: 10.1016/j.jinorgbio.2006.01.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2005] [Revised: 01/10/2006] [Accepted: 01/10/2006] [Indexed: 11/26/2022]
Abstract
Amidato-N ligands are normally viewed as classic, strongly sigma-donating, innocent ligands. However, when coordinated to high-valent transition metal centers, tetraamidomacrocyclic ligands are often substantially non-innocent, i.e., exhibit radical character involving the amido pi-systems. Even the so-called MAC* ligand, generally considered to be an innocent ligand, is non-innocent in several of its known complexes.
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44
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ATCUN-like metal-binding motifs in proteins: identification and characterization by crystal structure and sequence analysis. Proteins 2006; 58:211-21. [PMID: 15508143 DOI: 10.1002/prot.20265] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The amino terminal Cu(II)- and Ni(II)-binding (ATCUN) motif is a small metal-binding site found in the N-terminus of many naturally occurring proteins. The ATCUN motif has been implicated in DNA cleavage and has been shown to have antitumor activity. In proteins, the ATCUN motif is formed from a histidine in the third position, its preceding residue and the free N-terminus. Four nitrogen atoms from these three residues act as metal ligands. Knowledge of metal-binding geometry helps in the design of metal-binding peptides and in understanding of the mechanisms of metal-mediated functions. Since the N-terminus region of ATCUN-containing proteins is highly disordered, no geometrical features can be derived from the protein structures. However, the crystal structure of a small metal-bound ATCUN peptide shows that the nitrogen ligands form a distorted square planar geometry. Distance constraints derived from this designed peptide were used to search 1949 polypeptide chains to find ATCUN-like motifs in any position along the polypeptide chain. Only approximately 1.9% and approximately 0.3% of histidines are involved in partial and full ATCUN-like geometric features, respectively. These two datasets were compared with the dataset of all histidines. None of the ATCUN-like motifs occur in the middle of an alpha-helix or a beta-strand. Further sequence analysis revealed total conservation of ATCUN histidines in four proteins including the transcription factor TBX3, implicated in Ulnar-Mammary Syndrome. Our analysis suggests that the ATCUN-like motif in TBX3 is a potential metal-binding site, although a structural role was not completely ruled out. Metal-binding activity in TBX3, if confirmed, will help us to understand the role of metals in transcriptional regulation and is likely to cast light on the causes of some serious genetic disorders. A conformational role is suggested for ATCUN-like motifs in other proteins.
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Raffa DF, Gómez-Balderas R, Brunelle P, Rickard GA, Rauk A. Ab initio model studies of copper binding to peptides containing a His–His sequence: relevance to the β-amyloid peptide of Alzheimer’s disease. J Biol Inorg Chem 2005; 10:887-902. [PMID: 16267663 DOI: 10.1007/s00775-005-0038-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2005] [Accepted: 09/15/2005] [Indexed: 10/25/2022]
Abstract
Two of the defining hallmarks of Alzheimer's disease (AD) are deposits of the beta-amyloid peptide, Abeta, and the generation of reactive oxygen species, both of which may be due to the Abeta peptide coordinating metal ions. The Cu2+ concentrations in cores of senile plaques are significantly elevated in AD patients. Experimental results indicate that Abeta1-42 in particular has a very high affinity for Cu2+, and that His13 and His14 are the two most firmly established ligands in the coordination sphere of the copper ion. Quantum chemical calculations using the unrestricted B3LYP hybrid density functional method with the 6-31G(d) basis set were performed for geometries, zero point energies and thermochemistry. The effects of solvation were accommodated using the CPCM method. The enthalpies were calculated with the 6-311+G(2df,2p) basis set. Calculations show that when Cu(H2O)(4)2+ combines with the model compound 1 (3-(1H-imidazol-5-yl)-N-[2-(1H-imidazol-5-yl)ethyl] propanamide) in the aqueous phase, the most stable binding site involves the Npi atoms of His13 and His14 as well as the carbonyl of the intervening backbone amide group. These structures are fairly rigid and the implications for conformational changes to the Abeta backbone are discussed. In solution at pH=7, Cu2+ promotes the deprotonation and involvement in the binding of the backbone amide nitrogen in a beta-sheet like structure. This geometry does not induce strain in the peptide backbone, making it the most likely representation of that portion of the Cu2+-Abeta complex monomer in aqueous solution.
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Affiliation(s)
- Duilio F Raffa
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, AB, Canada
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Chattopadhyay M, Walter ED, Newell DJ, Jackson PJ, Aronoff-Spencer E, Peisach J, Gerfen GJ, Bennett B, Antholine WE, Millhauser GL. The octarepeat domain of the prion protein binds Cu(II) with three distinct coordination modes at pH 7.4. J Am Chem Soc 2005; 127:12647-56. [PMID: 16144413 PMCID: PMC2909831 DOI: 10.1021/ja053254z] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The prion protein (PrP) binds Cu2+ in its N-terminal octarepeat domain. This unusual domain is comprised of four or more tandem repeats of the fundamental sequence PHGGGWGQ. Previous work from our laboratories demonstrates that at full copper occupancy, each HGGGW segment binds a single Cu2+. However, several recent studies suggest that low copper occupancy favors different coordination modes, possibly involving imidazoles from histidines in adjacent octapeptide segments. This is investigated here using a combination of X-band EPR, S-band EPR, and ESEEM, along with a library of modified peptides designed to favor different coordination interactions. At pH 7.4, three distinct coordination modes are identified. Each mode is fully characterized to reveal a series of copper-dependent octarepeat domain structures. Multiple His coordination is clearly identified at low copper stoichiometry. In addition, EPR detected copper-copper interactions at full occupancy suggest that the octarepeat domain partially collapses, perhaps stabilizing this specific binding mode and facilitating cooperative copper uptake. This work provides the first complete characterization of all dominant copper coordination modes at pH 7.4.
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Bonomo RP, Cucinotta V, Giuffrida A, Impellizzeri G, Magri A, Pappalardo G, Rizzarelli E, Santoro AM, Tabbi G, Vagliasindi LI. A re-investigation of copper coordination in the octa-repeats region of the prion protein. Dalton Trans 2005:150-8. [PMID: 15605159 DOI: 10.1039/b415727c] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An aqueous solution spectroscopic (Vis and EPR) study of the copper(II) complexes with the Ac-HGGG-NH2 and Ac-PHGGGWGQ-NH2 polypeptides (generically designated as L) suggests square base pyramids ascribable to [Cu(L)H(-2)] complex species, which contain three nitrogen donor atoms, arising from imidazole and peptide groups, in the equatorial plane and for a pseudo-octahedral geometry in the case of [CuLH-3]- and [Cu(L)H-4]2- which have four nitrogen donor atoms in their equatorial plane. The coordination sphere of the copper complex in the [Cu(L)H(-2)] species, which is present at neutral pH values, is completed by two oxygen donor atoms. ESI-MS spectra ascertained that water molecules are not present in the coordination equatorial plane of this latter species, in comparison with other copper(II) complexes with ligands bearing nitrogen and oxygen donor atoms and surely having equatorial water molecules. This indicates the coordination of a carbonyl oxygen atom in the equatorial plane has to be invoked. However, no direct proof about the involvement of a carbonyl group oxygen donor atom apically linked to copper was obtained, due to the flexibility of these structures at room temperature. Additionally, the low A(ll) value leads one to consider another oxygen atom of a carbonyl group being involved in the apical bond to copper in a fast exchange fashion. This apical interaction, which may also involve a water molecule, is more pronounced in the Cu-Ac-HGGG-NH2 than in the analogous Cu-Ac-PHGGGWGQ-NH2 system, probably because of the presence of tryptophan and proline in the polypeptide sequence.
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Affiliation(s)
- Raffaele P Bonomo
- Dipartimento di Scienze Chimiche, Universita di Catania, Viale A. Doria 6, 95125 Catania, Italy.
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Constantino E, Rimola A, Rodríguez-Santiago L, Sodupe M. Coordination properties of glycylglycine to Cu+, Ni+ and Co+. Influence of metal cation electronic configuration. NEW J CHEM 2005. [DOI: 10.1039/b512618e] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mirosavljević K, Sabolović J, Noethig-Laslo V. Conformational Analysis of Bis(L-N,N-dimethylvalinato)copper(II) and Bis(L-N,N-dimethylleucinato)copper(II) in Different Solvents by EPR Spectroscopy and a Molecular Mechanics Study. Eur J Inorg Chem 2004. [DOI: 10.1002/ejic.200300781] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Bennion BJ, DeMarco ML, Daggett V. Preventing Misfolding of the Prion Protein by TrimethylamineN-Oxide†. Biochemistry 2004; 43:12955-63. [PMID: 15476389 DOI: 10.1021/bi0486379] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Transmissible spongiform encephalopathies are a class of fatal neurodegenerative diseases linked to the prion protein. The prion protein normally exists in a soluble, globular state (PrP(C)) that appears to participate in copper metabolism in the central nervous system and/or signal transduction. Infection or disease occurs when an alternatively folded form of the prion protein (PrP(Sc)) converts soluble and predominantly alpha-helical PrP(C) into aggregates rich in beta-structure. The structurally disordered N-terminus adopts beta-structure upon conversion to PrP(Sc) at low pH. Chemical chaperones, such as trimethylamine N-oxide (TMAO), can prevent formation of PrP(Sc) in scrapie-infected mouse neuroblastoma cells [Tatzelt, J., et al. (1996) EMBO J. 15, 6363-6373]. To explore the mechanism of TMAO protection of PrP(C) at the atomic level, molecular dynamics simulations were performed under conditions normally leading to conversion (low pH) with and without 1 M TMAO. In PrP(C) simulations at low pH, the helix content drops and the N-terminus is brought into the small native beta-sheet, yielding a PrP(Sc)-like state. Addition of 1 M TMAO leads to a decreased radius of gyration, a greater number of protein-protein hydrogen bonds, and a greater number of tertiary contacts due to the N-terminus forming an Omega-loop and packing against the structured core of the protein, not due to an increase in the level of extended structure as with the PrP(C) to PrP(Sc) simulation. In simulations beginning with the "PrP(Sc)-like" structure (derived from PrP(C) simulated at low pH in pure water) in 1 M TMAO, similar structural reorganization at the N-terminus occurred, disrupting the extended sheet. The mechanism of protection by TMAO appears to be exclusionary in nature, consistent with previous theoretical and experimental studies. The TMAO-induced N-terminal conformational change prevents residues that are important in the conversion of PrP(C) to PrP(Sc) from assuming extended sheet structure at low pH.
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Affiliation(s)
- Brian J Bennion
- Department of Medicinal Chemistry and Biomolecular Structure and Design Program, University of Washington, Seattle, Washington 98195-7610, USA
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