1
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Pei R, Zhang J, Tan J, Luo Y, Ye S. Fermi Resonance of the N-D Stretching Mode Probing the Local Hydrogen-Bonding Environment in Proteins. J Phys Chem B 2024; 128:5658-5666. [PMID: 38836292 DOI: 10.1021/acs.jpcb.4c00390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Local H-bonding interactions are crucial for proteins to undergo various structural transitions and form different secondary structures. However, identifying slight distinctions in the local H-bonding of proteins is rather challenging. Here, we demonstrate that the Fermi resonance of the N-D stretching mode can provide an effective probe for the localized H-bonding environment of proteins both at the surface/interface and in the bulk. Using sum frequency generation vibrational spectroscopy and infrared spectroscopy, we established a correlation between the Fermi resonance of the N-D mode and protein secondary structures. The H-bond of N-D···C═O splits the N-D modes into two peaks (∼2410 and ∼2470 cm-1). The relative strength ratio (R) between the ∼2410 cm-1 peak and the ∼2470 cm-1 peak is very sensitive to H-bond strength and protein secondary structure. R is less than 1 for α-helical peptides, while R is greater than 1 for β-sheet peptides. For R < 2.5, both α-helical/loop structures and β-sheet structures exhibit almost identical Fermi coupling strengths (W = 28 cm-1). For R > 2.5, W decreases from 28 to 14 cm-1 and depends on the aggregation degree of the β-sheet oligomers or fibrils. The initial local H-bonding status impacts the misfolding dynamics of proteins at the lipid bilayer interface.
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Affiliation(s)
- Ruoqi Pei
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Jiahui Zhang
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Junjun Tan
- Hefei National Laboratory, University of Science and Technology of China, Hefei, Anhui 230088, China
| | - Yi Luo
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei, Anhui 230088, China
| | - Shuji Ye
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei, Anhui 230088, China
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2
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Näsström T, Ådén J, Shibata F, Andersson PO, Karlsson BC. A Capped Peptide of the Aggregation Prone NAC 71-82 Amino Acid Stretch of α-Synuclein Folds into Soluble β-Sheet Oligomers at Low and Elevated Peptide Concentrations. Int J Mol Sci 2020; 21:ijms21051629. [PMID: 32120928 PMCID: PMC7084662 DOI: 10.3390/ijms21051629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/25/2020] [Accepted: 02/25/2020] [Indexed: 12/13/2022] Open
Abstract
Although Lewy bodies and Lewy neurites are hallmarks of Parkinson's disease (PD) and dementia with Lewy bodies (DLB), misfolded α-synuclein oligomers are nowadays believed to be key for the development of these diseases. Attempts to target soluble misfolded species of the full-length protein have been limited so far, probably due to the fast aggregation kinetics and burial of aggregation prone segments in final cross-β-sheet fibrils. A previous characterisation study of fibrils prepared from a capped peptide of the non-amyloid β-component (NAC) 71-82 amino acid stretch of α-synuclein demonstrated an increased aggregation propensity resulting in a cross-β-structure that is also found in prion proteins. From this, it was suggested that capped NAC 71-82 peptide oligomers would provide interesting motifs with a capacity to regulate disease development. Here, we demonstrated, from a series of circular dichroism spectroscopic measurements and molecular dynamics simulations, the molecular-environment-sensitive behaviour of the capped NAC 71-82 peptide in a solution phase and the formation of β-sheet oligomeric structures in the supernatant of a fibrillisation mixture. These results highlighted the use of the capped NAC 71-82 peptide as a motif in the preparation of oligomeric β-sheet structures that potentially could be used in therapeutic strategies in the fight against progressive neurodegenerative disorders, such as PD and DLB.
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Affiliation(s)
- Thomas Näsström
- Physical Pharmacy Laboratory, Linnaeus University Centre for Biomaterials Chemistry, Linnaeus University, SE-392 31 Kalmar, Sweden;
- Correspondence: (T.N.); (B.C.G.K.); Tel.: +46-480-446329 (T.N.); +46-480-446740 (B.C.G.K.)
| | - Jörgen Ådén
- Department of Chemistry, University of Umeå, SE-901 87 Umeå, Sweden;
| | - Fumina Shibata
- Physical Pharmacy Laboratory, Linnaeus University Centre for Biomaterials Chemistry, Linnaeus University, SE-392 31 Kalmar, Sweden;
| | - Per Ola Andersson
- Department of Engineering Sciences: Applied Material Science, Uppsala University, SE-751 21 Uppsala, Sweden;
| | - Björn C.G. Karlsson
- Physical Pharmacy Laboratory, Linnaeus University Centre for Biomaterials Chemistry, Linnaeus University, SE-392 31 Kalmar, Sweden;
- Correspondence: (T.N.); (B.C.G.K.); Tel.: +46-480-446329 (T.N.); +46-480-446740 (B.C.G.K.)
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3
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Hecel A, Draghi S, Valensin D, Kozlowski H. The effect of a membrane-mimicking environment on the interactions of Cu 2+ with an amyloidogenic fragment of chicken prion protein. Dalton Trans 2018; 46:7758-7769. [PMID: 28589973 DOI: 10.1039/c7dt01069a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Prion proteins (PrP) from different species have the ability to tightly bind Cu2+ ions. Copper coordination sites are located in the disordered and flexible N-terminal region which contains several His anchoring sites. Among them, two His residues are found in the so called amyloidogenic PrP region which is believed to play a key role in the process leading to oligomer and fibril formation. Both chicken and human amyloidogenic regions have a hydrophobic C-terminal region rich in Ala and Val amino acids. Recent findings revealed that this domain undergoes random coil to α-helix structuring upon interaction with membrane models. This interaction might strongly impact metal binding abilities either in terms of donor sets or affinity. In this study we investigated Cu2+ interaction with an amyloidogenic fragment, chPrP105-140, derived from chicken prion protein (chPrP), in different solution environments. The behavior of the peptide and its metal complexes was analyzed in water and in the presence of negative and positive charged membrane mimicking environments formed by sodium dodecyl sulfate (SDS) and dodecyl trimethyl ammonium chloride (DTAC) micelles. The metal coordination sphere, the metal binding affinity and stoichiometry were evaluated by combining spectroscopic and potentiometric methods. Finally we compare copper(ii) interactions with human and chicken amyloidogenic fragments. Our results indicate that the chicken amyloidogenic fragment is a stronger copper ligand than the human amyloidogenic fragment.
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Affiliation(s)
- Aleksandra Hecel
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14., 50-383 Wroclaw, Poland
| | - Sara Draghi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Daniela Valensin
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Henryk Kozlowski
- Public Higher Medical Professional School in Opole, Katowicka 68, 45060 Opole, Poland
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4
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Hecel A, De Ricco R, Valensin D. Influence of membrane environments and copper ions on the structural features of amyloidogenic proteins correlated to neurodegeneration. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.06.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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5
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Inayathullah M, Rajadas J. Conformational dynamics of a hydrophobic prion fragment (113-127) in different pH and osmolyte solutions. Neuropeptides 2016; 57:9-14. [PMID: 26919915 DOI: 10.1016/j.npep.2016.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 02/09/2016] [Accepted: 02/14/2016] [Indexed: 01/17/2023]
Abstract
Prion diseases are characterized by a conformational change in prion protein from its native state into beta-sheet rich aggregates that are neurotoxic. The central domain that contain a highly conserved hydrophobic region of the protein play an important role in the toxicity. The conformation of the proteins is largely influenced by various solvent environments. Here we report results of study of hydrophobic prion fragment peptide PrP(113-127) under different pH and osmolytes solution conditions. The secondary structure and the folding of PrP(113-127) was determined using circular dichroism and fluorescence spectroscopic methods. The results indicate that PrP(113-127) adopts a random coil conformation in aqueous buffer at neutral pH and that converted into beta sheet on aging. Even though the initial random coil conformation was similar in different pH conditions, the acidic as well as basic pH conditions delays the conformational transition to beta sheet. FRET results indicate that the distance between N and C-terminal regions increased on aging due to unfolding by self-assembly of the peptide into an organized beta sheet structure. Presence of osmolytes, prevented or decelerated the aggregation process of PrP(113-127) peptide.
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Affiliation(s)
- Mohammed Inayathullah
- Biomaterials and Advanced Drug Delivery Laboratory, School of Medicine, Stanford University, Palo Alto, CA 94304, USA; Bioorganic and Neurochemistry Laboratory, Central Leather Research Institute, Adyar, Chennai, Tamil Nadu 600020, India; Cardiovascular Pharmacology Division, Cardiovascular Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jayakumar Rajadas
- Biomaterials and Advanced Drug Delivery Laboratory, School of Medicine, Stanford University, Palo Alto, CA 94304, USA; Cardiovascular Pharmacology Division, Cardiovascular Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA.
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6
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Chua KP, Chew LY, Mu Y. Replica exchange molecular dynamics simulation of cross-fibrillation of IAPP and PrP106-126. Proteins 2016; 84:1134-46. [DOI: 10.1002/prot.25060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/14/2016] [Accepted: 04/28/2016] [Indexed: 12/24/2022]
Affiliation(s)
- Khi Pin Chua
- Interdisciplinary Graduate School; Nanyang Technological University; 637551 Singapore
- Complexity Institute, Nanyang Technological University; 637551 Singapore
| | - Lock Yue Chew
- Interdisciplinary Graduate School; Nanyang Technological University; 637551 Singapore
- Complexity Institute, Nanyang Technological University; 637551 Singapore
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences; Nanyang Technological University; 637551 Singapore
| | - Yuguang Mu
- School of Biological Sciences; Nanyang Technological University; 637551 Singapore
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7
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Ning L, Pan D, Zhang Y, Wang S, Liu H, Yao X. Effects of the Pathogenic Mutation A117V and the Protective Mutation H111S on the Folding and Aggregation of PrP106-126: Insights from Replica Exchange Molecular Dynamics Simulations. PLoS One 2015; 10:e0125899. [PMID: 25993001 PMCID: PMC4439087 DOI: 10.1371/journal.pone.0125899] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 03/24/2015] [Indexed: 11/19/2022] Open
Abstract
The fragment 106-126 of prion protein exhibits similar properties to full-length prion. Experiments have shown that the A117V mutation enhances the aggregation of PrP106-126, while the H111S mutation abolishes the assembly. However, the mechanism of the change in the aggregation behavior of PrP106-126 upon the two mutations is not fully understood. In this study, replica exchange molecular dynamics simulations were performed to investigate the conformational ensemble of the WT PrP106-126 and its two mutants A117V and H111S. The obtained results indicate that the three species are all intrinsically disordered but they have distinct morphological differences. The A117V mutant has a higher propensity to form β-hairpin structures than the WT, while the H111S mutant has a higher population of helical structures. Furthermore, the A117V mutation increases the hydrophobic solvent accessible surface areas of PrP106-126 and the H111S mutation reduces the exposure of hydrophobic residues. It can be concluded that the difference in populations of β-hairpin structures and the change of hydrophobic solvent accessible areas may induce the different aggregation behaviors of the A117V and the H111S mutated PrP106-126. Understanding why the two mutations have contrary effects on the aggregation of PrP106-126 is very meaningful for further elucidation of the mechanism underlying aggregation and design of inhibitor against aggregation process.
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Affiliation(s)
- Lulu Ning
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Dabo Pan
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
- School of pharmaceutical technology, Qiandongnan National Polytechnic, Kaili, China
| | - Yan Zhang
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Shaopeng Wang
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
- * E-mail: (HL); (XY)
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
- * E-mail: (HL); (XY)
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8
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Ning L, Guo J, Bai Q, Jin N, Liu H, Yao X. Structural diversity and initial oligomerization of PrP106-126 studied by replica-exchange and conventional molecular dynamics simulations. PLoS One 2014; 9:e87266. [PMID: 24586266 PMCID: PMC3929351 DOI: 10.1371/journal.pone.0087266] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 12/24/2013] [Indexed: 12/15/2022] Open
Abstract
Prion diseases are marked by cerebral accumulation of the abnormal isoform of the prion protein. A fragment of prion protein composed of residues 106–126 (PrP106–126) exhibits similar properties to full length prion and plays a key role in the conformational conversion from cellular prion to its pathogenic pattern. Soluble oligomers of PrP106–126 have been proposed to be responsible for neurotoxicity. However, the monomeric conformational space and initial oligomerization of PrP106–126 are still obscure, which are very important for understanding the conformational conversion of PrP106–126. In this study, replica exchange molecular dynamics simulations were performed to investigate monomeric and dimeric states of PrP106–126 in implicit solvent. The structural diversity of PrP106–126 was observed and this peptide did not acquire stable structure. The dimeric PrP106–126 also displayed structural diversity and hydrophobic interaction drove the dimerization. To further study initial oligomerization of PrP106–126, 1 µs conventional molecular dynamics simulations of trimer and tetramer formation were carried out in implicit solvent. We have observed the spontaneous formation of several basic oligomers and stable oligomers with high β-sheet contents were sampled in the simulations of trimer and tetramer formation. The β-hairpin formed in hydrophobic tail of PrP106–126 with residues 118–120 in turn may stabilize these oligomers and seed the formation oligomers. This study can provide insight into the detailed information about the structure of PrP106–126 and the dynamics of aggregation of monomeric PrP106–126 into oligomers in atomic level.
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Affiliation(s)
- Lulu Ning
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Jingjing Guo
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Qifeng Bai
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | | | - Huanxiang Liu
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
- School of Pharmacy, Lanzhou University, Lanzhou, China
- * E-mail: (HL); (XY)
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
- State Key Lab for Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
- * E-mail: (HL); (XY)
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9
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Gill AC. β-hairpin-mediated formation of structurally distinct multimers of neurotoxic prion peptides. PLoS One 2014; 9:e87354. [PMID: 24498083 PMCID: PMC3909104 DOI: 10.1371/journal.pone.0087354] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 12/19/2013] [Indexed: 01/09/2023] Open
Abstract
Protein misfolding disorders are associated with conformational changes in specific proteins, leading to the formation of potentially neurotoxic amyloid fibrils. During pathogenesis of prion disease, the prion protein misfolds into β-sheet rich, protease-resistant isoforms. A key, hydrophobic domain within the prion protein, comprising residues 109-122, recapitulates many properties of the full protein, such as helix-to-sheet structural transition, formation of fibrils and cytotoxicity of the misfolded isoform. Using all-atom, molecular simulations, it is demonstrated that the monomeric 109-122 peptide has a preference for α-helical conformations, but that this peptide can also form β-hairpin structures resulting from turns around specific glycine residues of the peptide. Altering a single amino acid within the 109-122 peptide (A117V, associated with familial prion disease) increases the prevalence of β-hairpin formation and these observations are replicated in a longer peptide, comprising residues 106-126. Multi-molecule simulations of aggregation yield different assemblies of peptide molecules composed of conformationally-distinct monomer units. Small molecular assemblies, consistent with oligomers, comprise peptide monomers in a β-hairpin-like conformation and in many simulations appear to exist only transiently. Conversely, larger assemblies are comprised of extended peptides in predominately antiparallel β-sheets and are stable relative to the length of the simulations. These larger assemblies are consistent with amyloid fibrils, show cross-β structure and can form through elongation of monomer units within pre-existing oligomers. In some simulations, assemblies containing both β-hairpin and linear peptides are evident. Thus, in this work oligomers are on pathway to fibril formation and a preference for β-hairpin structure should enhance oligomer formation whilst inhibiting maturation into fibrils. These simulations provide an important new atomic-level model for the formation of oligomers and fibrils of the prion protein and suggest that stabilization of β-hairpin structure may enhance cellular toxicity by altering the balance between oligomeric and fibrillar protein assemblies.
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Affiliation(s)
- Andrew C. Gill
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush Campus, University of Edinburgh, Roslin, Edinburgh, United Kingdom
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10
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Inayathullah M, Satheeshkumar KS, Malkovskiy AV, Carre AL, Sivanesan S, Hardesty JO, Rajadas J. Solvent microenvironments and copper binding alters the conformation and toxicity of a prion fragment. PLoS One 2013; 8:e85160. [PMID: 24386462 PMCID: PMC3874036 DOI: 10.1371/journal.pone.0085160] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 11/22/2013] [Indexed: 11/19/2022] Open
Abstract
The secondary structures of amyloidogenic proteins are largely influenced by various intra and extra cellular microenvironments and metal ions that govern cytotoxicity. The secondary structure of a prion fragment, PrP(111-126), was determined using circular dichroism (CD) spectroscopy in various microenvironments. The conformational preferences of the prion peptide fragment were examined by changing solvent conditions and pH, and by introducing external stress (sonication). These physical and chemical environments simulate various cellular components at the water-membrane interface, namely differing aqueous environments and metal chelating ions. The results show that PrP(111-126) adopts different conformations in assembled and non-assembled forms. Aging studies on the PrP(111-126) peptide fragment in aqueous buffer demonstrated a structural transition from random coil to a stable β-sheet structure. A similar, but significantly accelerated structural transition was observed upon sonication in aqueous environment. With increasing TFE concentrations, the helical content of PrP(111-126) increased persistently during the structural transition process from random coil. In aqueous SDS solution, PrP(111-126) exhibited β-sheet conformation with greater α-helical content. No significant conformational changes were observed under various pH conditions. Addition of Cu2+ ions inhibited the structural transition and fibril formation of the peptide in a cell free in vitro system. The fact that Cu2+ supplementation attenuates the fibrillar assemblies and cytotoxicity of PrP(111-126) was witnessed through structural morphology studies using AFM as well as cytotoxicity using MTT measurements. We observed negligible effects during both physical and chemical stimulation on conformation of the prion fragment in the presence of Cu2+ ions. The toxicity of PrP(111-126) to cultured astrocytes was reduced following the addition of Cu2+ ions, owing to binding affinity of copper towards histidine moiety present in the peptide.
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Affiliation(s)
- Mohammed Inayathullah
- Biomaterials and Advanced Drug Delivery Laboratory, Stanford University School of Medicine, Stanford, California, United States of America
| | - K. S. Satheeshkumar
- Bioorganic and Neurochemistry Laboratory, Central Leather Research Institute, Adyar, Chennai, India
| | - Andrey V. Malkovskiy
- Biomaterials and Advanced Drug Delivery Laboratory, Stanford University School of Medicine, Stanford, California, United States of America
| | - Antoine L. Carre
- Department of Surgery, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Senthilkumar Sivanesan
- Biomaterials and Advanced Drug Delivery Laboratory, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jasper O. Hardesty
- Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
| | - Jayakumar Rajadas
- Biomaterials and Advanced Drug Delivery Laboratory, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Neurology and Neurological Science, Stanford University School of Medicine, Stanford, California, United States of America
- Cardiovascular Pharmacology Division, Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
- *
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11
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Wang X, He L, Zhao C, Du W, Lin J. Gold complexes inhibit the aggregation of prion neuropeptides. J Biol Inorg Chem 2013; 18:767-78. [DOI: 10.1007/s00775-013-1030-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 08/05/2013] [Indexed: 12/19/2022]
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12
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Hirata A, Yajima S, Yasuhara T, Nokihara K. Structural Conversion Rate Changes of Recombinant Bovine Prion by Designed Synthetic Peptides. Int J Pept Res Ther 2012. [DOI: 10.1007/s10989-012-9294-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Sauvé S, Buijs D, Gingras G, Aubin Y. Interactions between the conserved hydrophobic region of the prion protein and dodecylphosphocholine micelles. J Biol Chem 2011; 287:1915-22. [PMID: 22128151 DOI: 10.1074/jbc.m111.279364] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The three-dimensional structure of PrP110-136, a peptide encompassing the conserved hydrophobic region of the human prion protein, has been determined at high resolution in dodecylphosphocholine micelles by NMR. The results support the conclusion that the (Ctm)PrP, a transmembrane form of the prion protein, adopts a different conformation than the reported structures of the normal prion protein determined in solution. Paramagnetic relaxation enhancement studies with gadolinium-diethylenetriaminepentaacetic acid indicated that the conserved hydrophobic region peptide is not inserted symmetrically in the micelle, thus suggesting the presence of a guanidium-phosphate ion pair involving the side chain of the terminal arginine and the detergent headgroup. Titration of dodecylphosphocholine into a solution of PrP110-136 revealed the presence of a surface-bound species. In addition, paramagnetic probes located the surface-bound peptide somewhere below the micelle-water interface when using the inserted helix as a positional reference. This localization of the unknown population would allow a similar ion pair interaction.
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Affiliation(s)
- Simon Sauvé
- Centre for Vaccine Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, Ontario K1A 0K9, Canada
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14
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Kawahara M, Koyama H, Nagata T, Sadakane Y. Zinc, copper, and carnosine attenuate neurotoxicity of prion fragment PrP106-126. Metallomics 2011; 3:726-34. [PMID: 21442127 DOI: 10.1039/c1mt00015b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Prion diseases are progressive neurodegenerative diseases that are associated with the conversion of normal cellular prion protein (PrP(C)) to abnormal pathogenic prion protein (PrP(SC)) by conformational changes. Prion protein is a metal-binding protein that is suggested to be involved in metal homeostasis. We investigated here the effects of trace elements on the conformational changes and neurotoxicity of synthetic prion peptide (PrP106-126). PrP106-126 exhibited the formation of β-sheet structures and enhanced neurotoxicity during the aging process. The co-existence of Zn(2+) or Cu(2+) during aging inhibited β-sheet formation by PrP106-126 and attenuated its neurotoxicity on primary cultured rat hippocampal neurons. Although PrP106-126 formed amyloid-like fibrils as observed by atomic force microscopy, the height of the fibers was decreased in the presence of Zn(2+) or Cu(2+). Carnosine (β-alanyl histidine) significantly inhibited both the β-sheet formation and the neurotoxicity of PrP106-126. Our results suggested that Zn(2+) and Cu(2+) might be involved in the pathogenesis of prion diseases. It is also possible that carnosine might become a candidate for therapeutic treatments for prion diseases.
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Affiliation(s)
- Masahiro Kawahara
- Department of Analytical Chemistry, School of Pharmaceutical Sciences Kyushu University of Health and Welfare, 1714-1 Yoshino-cho, Nobeoka-shi, Miyazaki. Japan.
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15
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Di Natale G, Pappalardo G, Milardi D, Sciacca MFM, Attanasio F, La Mendola D, Rizzarelli E. Membrane Interactions and Conformational Preferences of Human and Avian Prion N-Terminal Tandem Repeats: The Role of Copper(II) Ions, pH, and Membrane Mimicking Environments. J Phys Chem B 2010; 114:13830-8. [DOI: 10.1021/jp1033036] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Giuseppe Di Natale
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy, and Istituto di Biostrutture e Bioimmagini - Catania, Consiglio Nazionale delle Ricerche, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Giuseppe Pappalardo
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy, and Istituto di Biostrutture e Bioimmagini - Catania, Consiglio Nazionale delle Ricerche, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Danilo Milardi
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy, and Istituto di Biostrutture e Bioimmagini - Catania, Consiglio Nazionale delle Ricerche, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Michele F. M. Sciacca
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy, and Istituto di Biostrutture e Bioimmagini - Catania, Consiglio Nazionale delle Ricerche, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Francesco Attanasio
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy, and Istituto di Biostrutture e Bioimmagini - Catania, Consiglio Nazionale delle Ricerche, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Diego La Mendola
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy, and Istituto di Biostrutture e Bioimmagini - Catania, Consiglio Nazionale delle Ricerche, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Enrico Rizzarelli
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy, and Istituto di Biostrutture e Bioimmagini - Catania, Consiglio Nazionale delle Ricerche, Viale Andrea Doria 6, 95125 Catania, Italy
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16
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Kojima A, Konishi M, Akizawa T. Metal-Binding Ability of His-Containing Fragment Peptides Originating from Prion Protein Studied by Column Switch HPLC. BUNSEKI KAGAKU 2010. [DOI: 10.2116/bunsekikagaku.59.701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Aya Kojima
- Faculty of Pharmaceutical Sciences, Setsunan University
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17
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Grabenauer M, Wu C, Soto P, Shea JE, Bowers MT. Oligomers of the Prion Protein Fragment 106−126 Are Likely Assembled from β-Hairpins in Solution, and Methionine Oxidation Inhibits Assembly without Altering the Peptide’s Monomeric Conformation. J Am Chem Soc 2009; 132:532-9. [DOI: 10.1021/ja905595k] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Megan Grabenauer
- Departments of Chemistry and Biochemistry and of Physics, University of California, Santa Barbara, California 93106, and Department of Physics, Creighton University, Omaha, Nebraska 68178
| | - Chun Wu
- Departments of Chemistry and Biochemistry and of Physics, University of California, Santa Barbara, California 93106, and Department of Physics, Creighton University, Omaha, Nebraska 68178
| | - Patricia Soto
- Departments of Chemistry and Biochemistry and of Physics, University of California, Santa Barbara, California 93106, and Department of Physics, Creighton University, Omaha, Nebraska 68178
| | - Joan-Emma Shea
- Departments of Chemistry and Biochemistry and of Physics, University of California, Santa Barbara, California 93106, and Department of Physics, Creighton University, Omaha, Nebraska 68178
| | - Michael T. Bowers
- Departments of Chemistry and Biochemistry and of Physics, University of California, Santa Barbara, California 93106, and Department of Physics, Creighton University, Omaha, Nebraska 68178
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18
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Bonomo RP, Di Natale G, Rizzarelli E, Tabbì G, Vagliasindi LI. Copper(ii) complexes of prion protein PEG11-tetraoctarepeat fragment: spectroscopic and voltammetric studies. Dalton Trans 2009:2637-46. [DOI: 10.1039/b821727k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Villa A, Mark AE, Saracino GAA, Cosentino U, Pitea D, Moro G, Salmona M. Conformational polymorphism of the PrP106-126 peptide in different environments: a molecular dynamics study. J Phys Chem B 2006; 110:1423-8. [PMID: 16471693 DOI: 10.1021/jp052722o] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Extensive molecular dynamic simulations (approximately 240 ns) have been used to investigate the conformational behavior of PrP106-126 prion peptide in four different environments (water, dimethyl sulfoxide, hexane, and trifluoroethanol) and under both neutral and acidic conditions. The conformational polymorphism of PrP106-126 in solution observed in the simulations supports the role of this fragment in the structural transition of the native to the abnormal form of prion protein in response to changes in the local environmental conditions. The peptide in solution is primarily unstructured. The simulations show an increased presence of helical structure in an apolar solvent, in agreement with the results from circular dichroism spectroscopy. In water solution, beta-sheet elements were observed between residues 108-112 and either residues 115-121 or 121-126. An alpha-beta transition was observed under neutral conditions. In DMSO, the peptide adopted an extended conformation, in agreement with nuclear magnetic resonance experiments.
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Affiliation(s)
- Alessandra Villa
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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20
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Di Natale G, Grasso G, Impellizzeri G, La Mendola D, Micera G, Mihala N, Nagy Z, Osz K, Pappalardo G, Rigó V, Rizzarelli E, Sanna D, Sóvágó I. Copper(II) interaction with unstructured prion domain outside the octarepeat region: speciation, stability, and binding details of copper(II) complexes with PrP106-126 peptides. Inorg Chem 2006; 44:7214-25. [PMID: 16180886 DOI: 10.1021/ic050754k] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Copper(II) complexes of the neurotoxic peptide fragments of human and chicken prion proteins were studied by potentiometric, UV-vis, CD, and EPR spectroscopic and ESI-MS methods. The peptides included the terminally blocked native and scrambled sequences of HuPrP106-126 (HuPrPAc106-126NH2 and ScrHuPrPAc106-126NH2) and also the nona- and tetrapeptide fragments of both the human and chicken prion proteins (HuPrPAc106-114NH2, ChPrPAc119-127NH2, HuPrPAc109-112NH2, and ChPrPAc122-125NH2). The histidyl imidazole-N donor atoms were found to be the major copper(II) binding sites of all peptides; 3N and 4N complexes containing additional 2 and 3 deprotonated amide-N donors, respectively, are the major species in the physiological pH range. The complex formation processes for nona- and tetrapeptides are very similar, supporting the fact that successive deprotonation and metal ion coordination of amide functions go toward the N-termini in the form of joined six- and five-membered chelates. As a consequence, the peptide sequences investigated here, related to the neurotoxic region of the human PrP106-126 sequence, show a higher metal-binding affinity than the octarepeat fragments. In the case of the HuPrP peptide sequences, a weak pH-dependent binding of the Met109 residue was also detected in the 3N-coordinated complexes.
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21
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Hureau C, Charlet L, Dorlet P, Gonnet F, Spadini L, Anxolabéhère-Mallart E, Girerd JJ. A spectroscopic and voltammetric study of the pH-dependent Cu(II) coordination to the peptide GGGTH: relevance to the fifth Cu(II) site in the prion protein. J Biol Inorg Chem 2006; 11:735-44. [PMID: 16758168 DOI: 10.1007/s00775-006-0118-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2006] [Accepted: 05/05/2006] [Indexed: 11/24/2022]
Abstract
The GGGTH sequence has been proposed to be the minimal sequence involved in the binding of a fifth Cu(II) ion in addition to the octarepeat region of the prion protein (PrP) which binds four Cu(II) ions. Coordination of Cu(II) by the N- and C-protected Ac-GGGTH-NH(2) pentapeptide (P(5)) was investigated by using potentiometric titration, electrospray ionization mass spectrometry, UV-vis spectroscopy, electron paramagnetic resonance (EPR) spectroscopy and cyclic voltammetry experiments. Four different Cu(II) complexes were identified and characterized as a function of pH. The Cu(II) binding mode switches from NO(3) to N(4) for pH values ranging from 6.0 to 10.0. Quasi-reversible reduction of the [Cu(II)(P(5))H(-2)] complex formed at pH 6.7 occurs at E (1/2)=0.04 V versus Ag/AgCl, whereas reversible oxidation of the [Cu(II)(P(5))H(-3)](-) complex formed at pH 10.0 occurs at E (1/2)=0.66 V versus Ag/AgCl. Comparison of our EPR data with those of the rSHaPrP(90-231) (Burns et al. in Biochemistry 42:6794-6803, 2003) strongly suggests an N(3)O binding mode at physiological pH for the fifth Cu(II) site in the protein.
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Affiliation(s)
- Christelle Hureau
- Laboratoire de Géophysique Interne et Tectonophysique, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France.
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