1
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Chakraborty D, Chebaro Y, Wales DJ. A multifunnel energy landscape encodes the competing α-helix and β-hairpin conformations for a designed peptide. Phys Chem Chem Phys 2020; 22:1359-1370. [PMID: 31854397 DOI: 10.1039/c9cp04778f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Depending on the amino acid sequence, as well as the local environment, some peptides have the capability to fold into multiple secondary structures. Conformational switching between such structures is a key element of protein folding and aggregation. Specifically, understanding the molecular mechanism underlying the transition from an α-helix to a β-hairpin is critical because it is thought to be a harbinger of amyloid assembly. In this study, we explore the energy landscape for an 18-residue peptide (DP5), designed by Araki and Tamura to exhibit equal propensities for the α-helical and β-hairpin forms. We find that the degeneracy is encoded in the multifunnel nature of the underlying free energy landscape. In agreement with experiment, we also observe that mutation of tyrosine at position 12 to serine shifts the equilibrium in favor of the α-helix conformation, by altering the landscape topography. The transition from the α-helix to the β-hairpin is a complex stepwise process, and occurs via collapsed coil-like intermediates. Our findings suggest that even a single mutation can tune the emergent features of the landscape, providing an efficient route to protein design. Interestingly, the transition pathways for the conformational switch seem to be minimally perturbed upon mutation, suggesting that there could be universal microscopic features that are conserved among different switch-competent protein sequences.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, UK.
| | - Yassmine Chebaro
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67404 Illkirch, France
| | - David J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, UK.
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2
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Lin Y, Sahoo BR, Ozawa D, Kinoshita M, Kang J, Lim MH, Okumura M, Huh YH, Moon E, Jang JH, Lee HJ, Ryu KY, Ham S, Won HS, Ryu KS, Sugiki T, Bang JK, Hoe HS, Fujiwara T, Ramamoorthy A, Lee YH. Diverse Structural Conversion and Aggregation Pathways of Alzheimer's Amyloid-β (1-40). ACS NANO 2019; 13:8766-8783. [PMID: 31310506 DOI: 10.1021/acsnano.9b01578] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Complex amyloid aggregation of amyloid-β (1-40) (Aβ1-40) in terms of monomer structures has not been fully understood. Herein, we report the microscopic mechanism and pathways of Aβ1-40 aggregation with macroscopic viewpoints through tuning its initial structure and solubility. Partial helical structures of Aβ1-40 induced by low solvent polarity accelerated cytotoxic Aβ1-40 amyloid fibrillation, while predominantly helical folds did not aggregate. Changes in the solvent polarity caused a rapid formation of β-structure-rich protofibrils or oligomers via aggregation-prone helical structures. Modulation of the pH and salt concentration transformed oligomers to protofibrils, which proceeded to amyloid formation. We reveal diverse molecular mechanisms underlying Aβ1-40 aggregation with conceptual energy diagrams and propose that aggregation-prone partial helical structures are key to inducing amyloidogenesis. We demonstrate that context-dependent protein aggregation is comprehensively understood using the macroscopic phase diagram, which provides general insights into differentiation of amyloid formation and phase separation from unfolded and folded structures.
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Affiliation(s)
- Yuxi Lin
- Department of Chemistry , Sookmyung Women's University , Cheongpa-ro 47-gil 100 , Yongsan-gu, Seoul 04310 , South Korea
| | - Bikash R Sahoo
- Biophysics Program and Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Daisaku Ozawa
- Department of Neurotherapeutics , Osaka University Graduate School of Medicine , 2-2 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Misaki Kinoshita
- Frontier Research Institute for Interdisciplinary Sciences , Tohoku University , 6-3 Aramaki-Aza-Aoba , Aoba-ku, Sendai 980-8578 , Japan
| | - Juhye Kang
- Department of Chemistry , Korea Advanced Institute of Science and Technology , Daejeon 34141 , South Korea
- Department of Chemistry , Ulsan National Institute of Science and Technology , Ulsan 44919 , South Korea
| | - Mi Hee Lim
- Department of Chemistry , Korea Advanced Institute of Science and Technology , Daejeon 34141 , South Korea
| | - Masaki Okumura
- Frontier Research Institute for Interdisciplinary Sciences , Tohoku University , 6-3 Aramaki-Aza-Aoba , Aoba-ku, Sendai 980-8578 , Japan
| | | | | | | | - Hyun-Ju Lee
- Department of Neural Development and Disease , Korea Brain Research Institute , 61 Cheomdan-ro , Dong-gu, Daegu 41068 , South Korea
| | - Ka-Young Ryu
- Department of Neural Development and Disease , Korea Brain Research Institute , 61 Cheomdan-ro , Dong-gu, Daegu 41068 , South Korea
| | - Sihyun Ham
- Department of Chemistry , Sookmyung Women's University , Cheongpa-ro 47-gil 100 , Yongsan-gu, Seoul 04310 , South Korea
| | - Hyung-Sik Won
- Department of Biotechnology, Research Institute and College of Biomedical and Health Science , Konkuk University , Chungju , Chungbuk 27478 , South Korea
| | | | - Toshihiko Sugiki
- Institute for Protein Research , Osaka University , Yamadaoka 3-2 , Suita , Osaka 565-0871 , Japan
| | | | - Hyang-Sook Hoe
- Department of Neural Development and Disease , Korea Brain Research Institute , 61 Cheomdan-ro , Dong-gu, Daegu 41068 , South Korea
| | - Toshimichi Fujiwara
- Institute for Protein Research , Osaka University , Yamadaoka 3-2 , Suita , Osaka 565-0871 , Japan
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Young-Ho Lee
- Institute for Protein Research , Osaka University , Yamadaoka 3-2 , Suita , Osaka 565-0871 , Japan
- Bio-Analytical Science , University of Science and Technology , Daejeon 34113 , South Korea
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3
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Karimi H, Heydari Dokoohaki M, Zolghadr AR, Ghatee MH. The interactions of an Aβ protofibril with a cholesterol-enriched membrane and involvement of neuroprotective carbazolium-based substances. Phys Chem Chem Phys 2019; 21:11066-11078. [PMID: 31090756 DOI: 10.1039/c9cp00859d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Recent studies have shown that the aggregation of the amyloid-beta peptide (Aβ) in the brain cell membrane is responsible for the emergence of Alzheimer's disease (AD); the exploration of effective factors involved in the extension of the aggregation process and alternatively the examination of an effective inhibitor via theoretical and experimental tools are among the main research topics in the field of AD treatment. Therefore, in this study, we used all-atom molecular dynamics (MD) simulations to clarify the impact of cell membrane cholesterol on the interaction of Aβ with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) as a membrane model. Moreover, the effect of the P7C3-S243 molecule on the abovementioned process was investigated. The simulation results disclosed the neuroprotective property of the P7C3-S243 molecule. The MD simulation results indicate that the interaction of cholesterol molecules with the Aβ oligomer is negligible and cannot enhance membrane rupture. However, strong hydrogen bonding between the POPC molecules and the oligomers led to membrane perturbation. According to our modellings, the P7C3-S243 molecular layer can protect the cell membrane by inhibiting the direct interaction between the bilayer and Aβ. In addition, free-energy calculations were conducted to determine the possible penetration of Aβ fibrils into the cholesterol-enriched membrane.
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Affiliation(s)
- Hedayat Karimi
- Department of Chemistry, Shiraz University, Shiraz, 71946-84795, Iran.
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4
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Poojari C, Strodel B. Stability of transmembrane amyloid β-peptide and membrane integrity tested by molecular modeling of site-specific Aβ42 mutations. PLoS One 2013; 8:e78399. [PMID: 24244308 PMCID: PMC3820573 DOI: 10.1371/journal.pone.0078399] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 09/11/2013] [Indexed: 11/20/2022] Open
Abstract
Interactions of the amyloid β-protein (Aβ) with neuronal cell membranes, leading to the disruption of membrane integrity, are considered to play a key role in the development of Alzheimer’s disease. Natural mutations in Aβ42, such as the Arctic mutation (E22G) have been shown to increase Aβ42 aggregation and neurotoxicity, leading to the early-onset of Alzheimer’s disease. A correlation between the propensity of Aβ42 to form protofibrils and its effect on neuronal dysfunction and degeneration has been established. Using rational mutagenesis of the Aβ42 peptide it was further revealed that the aggregation of different Aβ42 mutants in lipid membranes results in a variety of polymorphic aggregates in a mutation dependent manner. The mutant peptides also have a variable ability to disrupt bilayer integrity. To further test the connection between Aβ42 mutation and peptide–membrane interactions, we perform molecular dynamics simulations of membrane-inserted Aβ42 variants (wild-type and E22G, D23G, E22G/D23G, K16M/K28M and K16M/E22G/D23G/K28M mutants) as β-sheet monomers and tetramers. The effects of charged residues on transmembrane Aβ42 stability and membrane integrity are analyzed at atomistic level. We observe an increased stability for the E22G Aβ42 peptide and a decreased stability for D23G compared to wild-type Aβ42, while D23G has the largest membrane-disruptive effect. These results support the experimental observation that the altered toxicity arising from mutations in Aβ is not only a result of the altered aggregation propensity, but also originates from modified Aβ interactions with neuronal membranes.
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Affiliation(s)
- Chetan Poojari
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- * E-mail:
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5
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Gal N, Morag A, Kolusheva S, Winter R, Landau M, Jelinek R. Lipid Bilayers Significantly Modulate Cross-Fibrillation of Two Distinct Amyloidogenic Peptides. J Am Chem Soc 2013; 135:13582-9. [DOI: 10.1021/ja4070427] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Noga Gal
- Department
of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel 84105
| | - Ahiud Morag
- Department
of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel 84105
| | - Sofiya Kolusheva
- Ilse
Katz Institute for Nanotechnology, Ben Gurion University Beer Sheva, Israel 84105
| | - Roland Winter
- Technische Universität Dortmund Physikalische Chemie − Biophysikalische Chemie, Otto-Hahn-Straße
6, 44227 Dortmund, Germany
| | - Meytal Landau
- Department
of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Raz Jelinek
- Department
of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel 84105
- Ilse
Katz Institute for Nanotechnology, Ben Gurion University Beer Sheva, Israel 84105
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6
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Chandrakesan M, Sarkar B, Mithu VS, Abhyankar R, Bhowmik D, Nag S, Sahoo B, Shah R, Gurav S, Banerjee R, Dandekar S, Jose JC, Sengupta N, Madhu PK, Maiti S. The basic structural motif and major biophysical properties of Amyloid-β are encoded in the fragment 18–35. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.01.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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7
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Sarkar B, Das AK, Maiti S. Thermodynamically stable amyloid-β monomers have much lower membrane affinity than the small oligomers. Front Physiol 2013; 4:84. [PMID: 23781202 PMCID: PMC3681284 DOI: 10.3389/fphys.2013.00084] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 04/02/2013] [Indexed: 12/23/2022] Open
Abstract
Amyloid beta (Aβ) is an extracellular 39–43 residue long peptide present in the mammalian cerebrospinal fluid, whose aggregation is associated with Alzheimer's disease (AD). Small oligomers of Aβ are currently thought to be the key to toxicity. However, it is not clear why the monomers of Aβ are non-toxic, and at what stage of aggregation toxicity emerges. Interactions of Aβ with cell membranes is thought to be the initiator of toxicity, but membrane binding studies with different preparations of monomers and oligomers have not settled this issue. We have earlier found that thermodynamically stable Aβ monomers emerge spontaneously from oligomeric mixtures upon long term incubation in physiological solutions (Nag et al., 2011). Here we show that the membrane-affinity of these stable Aβ monomers is much lower than that of a mixture of monomers and small oligomers (containing dimers to decamers), providing a clue to the emergence of toxicity. Fluorescently labeled Aβ40 monomers show negligible binding to cell membranes of a neuronal cell line (RN46A) at physiological concentrations (250 nM), while oligomers at the same concentrations show strong binding within 30 min of incubation. The increased affinity most likely does not require any specific neuronal receptor, since this difference in membrane-affinity was also observed in a somatic cell-line (HEK 293T). Similar results are also obtained for Aβ42 monomers and oligomers. Minimal amount of cell death is observed at these concentrations even after 36 h of incubation. It is likely that membrane binding precedes subsequent slower toxic events induced by Aβ. Our results (a) provide an explanation for the non-toxic nature of Aβ monomers, (b) suggest that Aβ toxicity emerges at the initial oligomeric phase, and (c) provide a quick assay for monitoring the benign-to-toxic transformation of Aβ.
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Affiliation(s)
- Bidyut Sarkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research Colaba, Mumbai, India
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8
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Poojari C, Kukol A, Strodel B. How the amyloid-β peptide and membranes affect each other: An extensive simulation study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:327-39. [DOI: 10.1016/j.bbamem.2012.09.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 09/03/2012] [Accepted: 09/04/2012] [Indexed: 11/24/2022]
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9
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Scherzer-Attali R, Convertino M, Pellarin R, Gazit E, Segal D, Caflisch A. Methylations of tryptophan-modified naphthoquinone affect its inhibitory potential toward Aβ aggregation. J Phys Chem B 2013; 117:1780-9. [PMID: 23259849 DOI: 10.1021/jp309066p] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aggregation of amyloid beta (Aβ) is the hallmark of Alzheimer's disease (AD). Small molecules inhibiting Aβ can be valuable therapeutics for AD. We have previously reported that 1,4-naphthoquinon-2-yl-l-tryptophan (NQTrp), reduces aggregation and oligomerization of Aβ in vitro and in vivo. In silico analysis further showed that certain functional groups of NQTrp, not in the aromatic rings, are also involved in binding and inhibiting Aβ. To better understand the exact mode of action and identify the groups crucial for NQTrp inhibitory activity, we conducted structure-activity analysis. Four derivatives of NQTrp were studied in silico: a D-isomer, two single-methylated and one double-methylated derivative. In silico results showed that the NQTrp groups involved in hydrogen bonds are the anilinic NH (i.e., the NH linker between the quinone and tryptophan moieties), the quinonic carbonyls, and the carboxylic acid. These predictions were supported by in vitro results. Our results should aid in designing improved small-molecule inhibitors of Aβ aggregation for treating AD.
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Affiliation(s)
- Roni Scherzer-Attali
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel-Aviv 69978, Israel
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10
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Convertino M, Vitalis A, Caflisch A. Disordered binding of small molecules to Aβ(12-28). J Biol Chem 2011; 286:41578-41588. [PMID: 21969380 PMCID: PMC3308868 DOI: 10.1074/jbc.m111.285957] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 09/23/2011] [Indexed: 11/06/2022] Open
Abstract
In recent years, an increasing number of small molecules and short peptides have been identified that interfere with aggregation and/or oligomerization of the Alzheimer β-amyloid peptide (Aβ). Many of them possess aromatic moieties, suggesting a dominant role for those in interacting with Aβ along various stages of the aggregation process. In this study, we attempt to elucidate whether interactions of such aromatic inhibitors with monomeric Aβ(12-28) point to a common mechanism of action by performing atomistic molecular dynamics simulations at equilibrium. Our results suggest that, independently of the presence of inhibitors, monomeric Aβ(12-28) populates a partially collapsed ensemble that is largely devoid of canonical secondary structure at 300 K and neutral pH. The small molecules have different affinities for Aβ(12-28) that can be partially rationalized by the balance of aromatic and charged moieties constituting the molecules. There are no predominant binding modes, although aggregation inhibitors preferentially interact with the N-terminal portion of the fragment (residues 13-20). Analysis of the free energy landscape of Aβ(12-28) reveals differences highlighted by altered populations of a looplike conformer in the presence of inhibitors. We conclude that intrinsic disorder of Aβ persists at the level of binding small molecules and that inhibitors can significantly alter properties of monomeric Aβ via multiple routes of differing specificity.
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Affiliation(s)
- Marino Convertino
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Andreas Vitalis
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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11
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Observation of two families of folding pathways of BBL. Biophys J 2011; 100:2457-65. [PMID: 21575580 DOI: 10.1016/j.bpj.2011.03.058] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Revised: 03/11/2011] [Accepted: 03/21/2011] [Indexed: 11/23/2022] Open
Abstract
BBL is an independent folding domain of a large multienzyme complex, 2-oxoglutarate dehydrogenase. The folding mechanism of BBL is under debate between the views of noncooperative downhill-type and classical two-state. Extensive replica exchange molecular dynamics simulations of BBL in explicit solvent have shown some non-two-state behaviors despite no definitive evidence of downhill folding. In this work, we postprocess the replica exchange data using our roadmap-based MaxFlux reaction path algorithm to reveal atomically detailed folding pathways. A connected graph is used to organize and visualize the folding pathways initiated from random coils. High structural and transition heterogeneity is seen in the early stage of folding. Two main parallel folding pathways emerge in the later stage; one path shows that tertiary contact and helix formation develop at different stages of folding, whereas the other path exhibits concurrence of secondary and tertiary structure formation to some extent. Because the native state of BBL is sensitive to experimental conditions, we speculate that the relative predominance of the two pathways may vary with the protein construct and solvent conditions, possibly leading to the seeming discrepancy of experimental results. Our roadmap-based reaction path algorithm is a general tool to extract path information from replica exchange.
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12
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Fuchigami S, Fujisaki H, Matsunaga Y, Kidera A. Protein Functional Motions: Basic Concepts and Computational Methodologies. ADVANCING THEORY FOR KINETICS AND DYNAMICS OF COMPLEX, MANY-DIMENSIONAL SYSTEMS: CLUSTERS AND PROTEINS 2011. [DOI: 10.1002/9781118087817.ch2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Straub JE, Thirumalai D. Toward a molecular theory of early and late events in monomer to amyloid fibril formation. Annu Rev Phys Chem 2011; 62:437-63. [PMID: 21219143 PMCID: PMC11237996 DOI: 10.1146/annurev-physchem-032210-103526] [Citation(s) in RCA: 209] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Quantitative understanding of the kinetics of fibril formation and the molecular mechanism of transition from monomers to fibrils is needed to obtain insights into the growth of amyloid fibrils and more generally self-assembly multisubunit protein complexes. Significant advances using computations of protein aggregation in a number of systems have established generic and sequence-specific aspects of the early steps in oligomer formation. Theoretical considerations, which view oligomer and fibril growth as diffusion in a complex energy landscape, and computational studies, involving minimal lattice and coarse-grained models, have revealed general principles governing the transition from monomeric protein to ordered fibrillar aggregates. Detailed atomistic calculations have explored the early stages of the protein aggregation pathway for a number of amyloidogenic proteins, most notably amyloid β- (Aβ-) protein and fragments from proteins linked to various diseases. These computational studies have provided insights into the role of sequence, role of water, and specific interatomic interactions underlying the thermodynamics and dynamics of elementary kinetic steps in the aggregation pathway. Novel methods are beginning to illustrate the structural basis for the production of Aβ-peptides through interactions with secretases in the presence of membranes. We show that a variety of theoretical approaches, ranging from scaling arguments to minimal models to atomistic simulations, are needed as a complement to experimental studies probing the principles governing protein aggregation.
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Affiliation(s)
- John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.
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14
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Reddy AS, Izmitli A, de Pablo JJ. Effect of trehalose on amyloid β (29–40)-membrane interaction. J Chem Phys 2009; 131:085101. [DOI: 10.1063/1.3193726] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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Sequence and crowding effects in the aggregation of a 10-residue fragment derived from islet amyloid polypeptide. Biophys J 2009; 96:4552-60. [PMID: 19486677 DOI: 10.1016/j.bpj.2009.03.039] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 03/19/2009] [Accepted: 03/20/2009] [Indexed: 11/21/2022] Open
Abstract
Fibril formation from amyloidogenic peptides is a hallmark of a wide range of diseases, including Alzheimer's disease and type II diabetes. Characterization of the aggregation process should include intrinsic factors, such as sequence variation, and extrinsic factors, such as crowding effects. To this end, we examined the interactions of dimers composed of residues 20-29 of human islet amyloid polypeptide (hIAPP), which form fibrils in vitro, and the nonamyloidogenic rat IAPP (rIAPP) using molecular dynamics simulations modeled at different peptide concentrations. There is a substantial free energy barrier to unbind the hIAPP dimer whereas no barrier exists for separating the rIAPP dimer. The profound differences in the free energy landscapes of the rIAPP and hIAPP dimers explains the lack of fibril formation in hIAPP upon substitution of the C-terminal residues by proline. Enhancing the extent of crowding has a substantial effect on both the barrier for separating a hIAPP beta-sheet dimer and the formation of potential beta-sheet nucleation sites. Our results show that the propensity for forming nucleation sites is dependent not only on the amino-acid sequence but also on the context in which it is found.
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16
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17
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Kent A, Jha AK, Fitzgerald JE, Freed KF. Benchmarking implicit solvent folding simulations of the amyloid beta(10-35) fragment. J Phys Chem B 2008; 112:6175-86. [PMID: 18348560 PMCID: PMC2719849 DOI: 10.1021/jp077099h] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A pathogenetic feature of Alzhemier disease is the aggregation of monomeric beta-amyloid proteins (Abeta) to form oligomers. Usually these oligomers of long peptides aggregate on time scales of microseconds or longer, making computational studies using atomistic molecular dynamics models prohibitively expensive and making it essential to develop computational models that are cheaper and at the same time faithful to physical features of the process. We benchmark the ability of our implicit solvent model to describe equilibrium and dynamic properties of monomeric Abeta(10-35) using all-atom Langevin dynamics (LD) simulations, since Alphabeta(10-35) is the only fragment whose monomeric properties have been measured. The accuracy of the implicit solvent model is tested by comparing its predictions with experiment and with those from a new explicit water MD simulation, (performed using CHARMM and the TIP3P water model) which is approximately 200 times slower than the implicit water simulations. The dependence on force field is investigated by running multiple trajectories for Alphabeta(10-35) using the CHARMM, OPLS-aal, and GS-AMBER94 force fields, whereas the convergence to equilibrium is tested for each force field by beginning separate trajectories from the native NMR structure, a completely stretched structure, and from unfolded initial structures. The NMR order parameter, S2, is computed for each trajectory and is compared with experimental data to assess the best choice for treating aggregates of Alphabeta. The computed order parameters vary significantly with force field. Explicit and implicit solvent simulations using the CHARMM force fields display excellent agreement with each other and once again support the accuracy of the implicit solvent model. Alphabeta(10-35) exhibits great flexibility, consistent with experiment data for the monomer in solution, while maintaining a general strand-loop-strand motif with a solvent-exposed hydrophobic patch that is believed to be important for aggregation. Finally, equilibration of the peptide structure requires an implicit solvent LD simulation as long as 30 ns.
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Affiliation(s)
- Andrew Kent
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
- The James Franck Institute, The University of Chicago, Chicago, IL 60637
| | - Abhishek K Jha
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
- Institute of Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- The James Franck Institute, The University of Chicago, Chicago, IL 60637
| | - James E Fitzgerald
- Institute of Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- Department of Mathematics, The University of Chicago, Chicago, IL 60637
- Department of Physics, The University of Chicago, Chicago, IL 60637
| | - Karl F Freed
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
- The James Franck Institute, The University of Chicago, Chicago, IL 60637
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18
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Predicting the folding pathway of engrailed homeodomain with a probabilistic roadmap enhanced reaction-path algorithm. Biophys J 2008; 94:1622-9. [PMID: 18024496 DOI: 10.1529/biophysj.107.119214] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To predict a protein-folding pathway, we present an alternative to the time-consuming dynamic simulation of atomistic models. We replace the actual dynamic simulation with variational optimization of a reaction path connecting known initial and final protein conformations in such a way as to maximize an estimate of the reactive flux or minimize the mean first passage time at a given temperature, referred to as MaxFlux. We solve the MaxFlux global optimization problem with an efficient graph-theoretic approach, the probabilistic roadmap method (PRM). We employed CHARMM19 and the EEF1 implicit solvation model to describe the protein solution. The effectiveness of our MaxFlux-PRM is demonstrated in our promising simulation results on the folding pathway of the engrailed homeodomain. Our MaxFlux-PRM approach provides the direct evidence to support that the previously reported intermediate state is a genuine on-pathway intermediate, and the demand of CPU power is moderate.
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19
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Li W, Zhang J, Su Y, Wang J, Qin M, Wang W. Effects of Zinc Binding on the Conformational Distribution of the Amyloid-β Peptide Based on Molecular Dynamics Simulations. J Phys Chem B 2007; 111:13814-21. [DOI: 10.1021/jp076213t] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wenfei Li
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing 210093, China
| | - Jian Zhang
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing 210093, China
| | - Yu Su
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing 210093, China
| | - Jun Wang
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing 210093, China
| | - Meng Qin
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing 210093, China
| | - Wei Wang
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing 210093, China
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20
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Grant MA, Lazo ND, Lomakin A, Condron MM, Arai H, Yamin G, Rigby AC, Teplow DB. Familial Alzheimer's disease mutations alter the stability of the amyloid beta-protein monomer folding nucleus. Proc Natl Acad Sci U S A 2007; 104:16522-7. [PMID: 17940047 PMCID: PMC2034231 DOI: 10.1073/pnas.0705197104] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2007] [Indexed: 12/26/2022] Open
Abstract
Amyloid beta-protein (Abeta) oligomers may be the proximate neurotoxins in Alzheimer's disease (AD). Recently, to elucidate the oligomerization pathway, we studied Abeta monomer folding and identified a decapeptide segment of Abeta, (21)Ala-(22)Glu-(23)Asp-(24)Val-(25)Gly-(26)Ser-(27)Asn-(28)Lys-(29)Gly-(30)Ala, within which turn formation appears to nucleate monomer folding. The turn is stabilized by hydrophobic interactions between Val-24 and Lys-28 and by long-range electrostatic interactions between Lys-28 and either Glu-22 or Asp-23. We hypothesized that turn destabilization might explain the effects of amino acid substitutions at Glu-22 and Asp-23 that cause familial forms of AD and cerebral amyloid angiopathy. To test this hypothesis, limited proteolysis, mass spectrometry, and solution-state NMR spectroscopy were used here to determine and compare the structure and stability of the Abeta(21-30) turn within wild-type Abeta and seven clinically relevant homologues. In addition, we determined the relative differences in folding free energies (DeltaDeltaG(f)) among the mutant peptides. We observed that all of the disease-associated amino acid substitutions at Glu-22 or Asp-23 destabilized the turn and that the magnitude of the destabilization correlated with oligomerization propensity. The Ala21Gly (Flemish) substitution, outside the turn proper (Glu-22-Lys-28), displayed a stability similar to that of the wild-type peptide. The implications of these findings for understanding Abeta monomer folding and disease causation are discussed.
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Affiliation(s)
- Marianne A. Grant
- *Division of Molecular and Vascular Medicine, Beth Israel Deaconess Medical Center, and Department of Medicine, Harvard Medical School, Boston, MA 02215
| | - Noel D. Lazo
- Gustaf A. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, MA 01610
| | - Aleksey Lomakin
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139; and
| | | | - Hiromi Arai
- Department of Neurology, David Geffen School of Medicine, and
| | - Ghiam Yamin
- Department of Neurology, David Geffen School of Medicine, and
| | - Alan C. Rigby
- *Division of Molecular and Vascular Medicine, Beth Israel Deaconess Medical Center, and Department of Medicine, Harvard Medical School, Boston, MA 02215
| | - David B. Teplow
- Department of Neurology, David Geffen School of Medicine, and
- Molecular Biology Institute and Brain Research Institute, University of California, Los Angeles, CA 90095
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21
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Jiao Y, Yang P. Mechanism of Copper(II) Inhibiting Alzheimer's Amyloid β-Peptide from Aggregation: A Molecular Dynamics Investigation. J Phys Chem B 2007; 111:7646-55. [PMID: 17564430 DOI: 10.1021/jp0673359] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The aggregation of an amyloid beta peptide (Abeta) into fibrils is a key pathological event in Alzheimer's disease (AD). Under certain conditions, Cu2+ markedly inhibits Abeta from aggregation and is considered as a potential factor in the normal brain preventing Abeta from aggregation. The possible mechanism of the inhibitory effect of Cu2+ was investigated for the first time by molecular dynamics (MD) simulations. On the basis of the radial distribution function analysis of the MD data, a novel strategy, the Q function, was proposed to explore the binding sites of Cu2+ by evaluating the coordination priority of atoms in Abeta, and the [6-5-5] tri-ring 4N binding mode of the Cu2+-Abeta complexes was found. The mechanism of the conformational transition of Abeta from the beta conformation to distorted beta conformations, which destabilizes the aggregation of Abeta into fibrils, was also revealed. All the results provide helpful clues for an improved understanding of the role of Cu2+ in the pathogenesis of AD and contribute to the development of an anti-amyloid therapeutic strategy.
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Affiliation(s)
- Yong Jiao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
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22
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van Gestel J, de Leeuw SW. A statistical-mechanical theory of fibril formation in dilute protein solutions. Biophys J 2007; 90:3134-45. [PMID: 16603504 PMCID: PMC1432121 DOI: 10.1529/biophysj.105.076000] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We outline a theoretical treatment that describes fibril formation in dilute protein solutions. For this, we combine a theory describing self-assembly and conformational transition with a description of the lateral association of linear chains. Our statistical-mechanical model is able to predict the mean degree of polymerization and the length of the fibrils and their precursors, as well as the weight fractions of the different aggregated species in solution. We find that there appear to exist two regimes as a function of concentration, and as a function of the free energies of protein association: one in which low-molecular weight compounds dominate and one in which the fibrils do. The transition between these regimes can be quite sharp, and becomes sharper as more filaments are allowed to associate into a single fibril. The fraction of fibrils consisting of less than the maximum allowed number of filaments turns out to be negligible, in agreement with experimental studies, where the fibril thickness is found to be practically monodisperse. In addition, we find that the description of the fibril ends has a large effect on the predicted fibril length.
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Affiliation(s)
- Jeroen van Gestel
- Physical Chemistry and Molecular Thermodynamics Group, DelftChemTech, Technische Universiteit Delft, 2628 BL Delft, The Netherlands.
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23
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Baumketner A, Shea JE. The Structure of the Alzheimer Amyloid β 10-35 Peptide Probed through Replica-Exchange Molecular Dynamics Simulations in Explicit Solvent. J Mol Biol 2007; 366:275-85. [PMID: 17166516 DOI: 10.1016/j.jmb.2006.11.015] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Revised: 10/29/2006] [Accepted: 11/03/2006] [Indexed: 11/28/2022]
Abstract
The conformational states sampled by the Alzheimer amyloid beta (10-35) (Abeta 10-35) peptide were probed using replica-exchange molecular dynamics (REMD) simulations in explicit solvent. The Abeta 10-35 peptide is a fragment of the full-length Abeta 40/42 peptide that possesses many of the amyloidogenic properties of its full-length counterpart. Under physiological temperature and pressure, our simulations reveal that the Abeta 10-35 peptide does not possess a single unique folded state. Rather, this peptide exists as a mixture of collapsed globular states that remain in rapid dynamic equilibrium with each other. This conformational ensemble is dominated by random coil and bend structures with insignificant presence of an alpha-helical or beta-sheet structure. The 3D structure of Abeta 10-35 is seen to be defined by a salt bridge formed between the side-chains of K28 and D23. This salt bridge is also observed in Abeta fibrils and our simulations suggest that monomeric conformations of Abeta 10-35 contain pre-folded structural motifs that promote rapid aggregation of this peptide.
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Affiliation(s)
- Andrij Baumketner
- Department of Physics and Optical Science, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
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24
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Nguyen PH, Li MS, Stock G, Straub JE, Thirumalai D. Monomer adds to preformed structured oligomers of Abeta-peptides by a two-stage dock-lock mechanism. Proc Natl Acad Sci U S A 2007; 104:111-6. [PMID: 17190811 PMCID: PMC1766316 DOI: 10.1073/pnas.0607440104] [Citation(s) in RCA: 310] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2006] [Indexed: 11/18/2022] Open
Abstract
Nonfibrillar soluble oligomers, which are intermediates in the transition from monomers to amyloid fibrils, may be the toxic species in Alzheimer's disease. To monitor the early events that direct assembly of amyloidogenic peptides we probe the dynamics of formation of (Abeta(16-22))(n) by adding a monomer to a preformed (Abeta(16-22))(n-1) (n = 4-6) oligomer in which the peptides are arranged in an antiparallel beta-sheet conformation. All atom molecular dynamics simulations in water and multiple long trajectories, for a cumulative time of 6.9 mus, show that the oligomer grows by a two-stage dock-lock mechanism. The largest conformational change in the added disordered monomer occurs during the rapid ( approximately 50 ns) first dock stage in which the beta-strand content of the monomer increases substantially from a low initial value. In the second slow-lock phase, the monomer rearranges to form in register antiparallel structures. Surprisingly, the mobile structured oligomers undergo large conformational changes in order to accommodate the added monomer. The time needed to incorporate the monomer into the fluid-like oligomer grows even when n = 6, which suggests that the critical nucleus size must exceed six. Stable antiparallel structure formation exceeds hundreds of nanoseconds even though frequent interpeptide collisions occur at elevated monomer concentrations used in the simulations. The dock-lock mechanism should be a generic mechanism for growth of oligomers of amyloidogenic peptides.
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Affiliation(s)
- Phuong H. Nguyen
- *Institute of Physical and Theoretical Chemistry, J. W. Goethe University, Marie-Curie-Strasse 11, D-60439 Frankfurt, Germany
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Gerhard Stock
- *Institute of Physical and Theoretical Chemistry, J. W. Goethe University, Marie-Curie-Strasse 11, D-60439 Frankfurt, Germany
| | - John E. Straub
- Department of Chemistry, Boston University, Boston, MA 02215; and
| | - D. Thirumalai
- Biophysics Program, Institute for Physical Science and Technology, and
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742
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25
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Chapter 2 Extending Atomistic Time Scale Simulations by Optimization of the Action. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/s1574-1400(07)03002-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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26
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Yang H, Wu H, Li D, Han L, Huo S. Temperature-Dependent Probabilistic Roadmap Algorithm for Calculating Variationally Optimized Conformational Transition Pathways. J Chem Theory Comput 2006; 3:17-25. [DOI: 10.1021/ct0502054] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Haijun Yang
- Gustaf H. Carlson School of Chemistry and Biochemistry and Department of Mathematics and Computer Science, Clark University, 950 Main Street, Worcester, Massachusetts 01610
| | - Hao Wu
- Gustaf H. Carlson School of Chemistry and Biochemistry and Department of Mathematics and Computer Science, Clark University, 950 Main Street, Worcester, Massachusetts 01610
| | - Dawei Li
- Gustaf H. Carlson School of Chemistry and Biochemistry and Department of Mathematics and Computer Science, Clark University, 950 Main Street, Worcester, Massachusetts 01610
| | - Li Han
- Gustaf H. Carlson School of Chemistry and Biochemistry and Department of Mathematics and Computer Science, Clark University, 950 Main Street, Worcester, Massachusetts 01610
| | - Shuanghong Huo
- Gustaf H. Carlson School of Chemistry and Biochemistry and Department of Mathematics and Computer Science, Clark University, 950 Main Street, Worcester, Massachusetts 01610
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27
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Masu H, Mizutani I, Kato T, Azumaya I, Yamaguchi K, Kishikawa K, Kohmoto S. Naphthalene- and Anthracene-Based Aromatic Foldamers with Iminodicarbonyl Linkers: Their Stabilities and Application to a Chiral Photochromic System Using Retro [4 + 4] Cycloaddition. J Org Chem 2006; 71:8037-44. [PMID: 17025292 DOI: 10.1021/jo0611317] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A circular dichroism (CD) spectral study on chiral aromatic chain imides possessing anthracene and naphthalene moieties with bulky N substituents showed that their helical chirality based on folding remained for a reasonably long time without racemization in solution. Racemization due to conformational equilibration occurred very slowly, requiring over 1 week at ambient temperature. Their CD spectra both in solution and in the solid state gave similar CD signals, suggesting retention of helicity observed in the solid state even after dissolving. As an application of this novel chiral folding of aromatic chain imides, a chiral photochromic system was investigated based on the photo [4 + 4] cycloaddition and its thermal cycloreversion of an anthracene-naphthalene system. The foldamer possessing an anthracene moiety in the center connected with two naphthalene moieties below and above it by iminodicarbonyl linkers was prepared for this purpose. Induced CD was observed for the foldamer with (S)-1-(1-naphthyl)ethyl substituents at the imide nitrogen atoms. Chiral photochromic cycles were monitored by CD spectral measurement.
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Affiliation(s)
- Hyuma Masu
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, Sanuki, Kagawa 769-2193, Japan
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28
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Mukherjee A, Bagchi B. Contact pair dynamics during folding of two small proteins: chicken villin head piece and the Alzheimer protein beta-amyloid. J Chem Phys 2006; 120:1602-12. [PMID: 15268287 DOI: 10.1063/1.1633253] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The folding of an extended protein to its unique native state requires establishment of specific, predetermined, often distant, contacts between amino acid residue pairs. The dynamics of contact pair formation between various hydrophobic residues during folding of two different small proteins, the chicken villin head piece (HP-36) and the Alzheimer protein beta-amyloid (betaA-40), are investigated by Brownian dynamics (BD) simulations. These two proteins represent two very different classes-HP-36 being globular while betaA-40 is nonglobular, stringlike. Hydropathy scale and nonlocal helix propensity of amino acids are used to model the complex interaction potential among the various amino acid residues. The minimalistic model we use here employs a connected backbone chain of atoms of equal size while an amino acid is attached to each backbone atom as an additional atom of differing sizes and interaction parameters, determined by the characteristics of each amino acid. Even for such simple models, we find that the low-energy structures obtained by BD simulations of both the model proteins mimic the native state of the real protein rather well, with a best root-mean-square deviation of 4.5 A for HP-36. For betaA-40 (where a single well-defined structure is not available), the simulated structures resemble the reported ensemble rather well, with the well-known beta-bend correctly reproduced. We introduce and calculate a contact pair distance time correlation function, C(P) (ij)(t), to quantify the dynamical evolution of the pair contact formation between the amino acid residue pairs i and j. The contact pair time correlation function exhibits multistage dynamics, including a two stage fast collapse, followed by a slow (microsecond long) late stage dynamics for several specific pairs. The slow late stage dynamics is in accordance with the findings of Sali et al. Analysis of the individual trajectories shows that the slow decay is due to the attempt of the protein to form energetically more favorable pair contacts to replace the less favorable ones. This late stage contact formation is a highly cooperative process, involving participation of several pairs and thus entropically unfavorable and expected to face a large free energy barrier. This is because any new pair contact formation among hydrophobic pairs will require breaking of several contacts, before the favorable ones can be formed. This aspect of protein folding dynamics is similar to relaxation in glassy liquids, where also alpha relaxation requires highly cooperative process of hopping. The present analysis suggests that waiting time for the necessary pair contact formation may obey the Poissonian distribution. We also study the dynamics of Forster energy transfer during folding between two tagged amino acid pairs. This dynamics can be studied by fluorescence resonance energy transfer (FRET). It is found that suitably placed donor-acceptor pairs can capture the slow dynamics during folding. The dynamics probed by FRET is predicted to be nonexponential.
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Affiliation(s)
- Arnab Mukherjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, India 560 012
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29
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30
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Nguyen HD, Hall CK. Spontaneous fibril formation by polyalanines; discontinuous molecular dynamics simulations. J Am Chem Soc 2006; 128:1890-901. [PMID: 16464090 PMCID: PMC3215763 DOI: 10.1021/ja0539140] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fibrillary protein aggregates rich in beta-sheet structure have been implicated in the pathology of several neurodegenerative diseases. In this work, we investigate the formation of fibrils by performing discontinuous molecular dynamics simulations on systems containing 12 to 96 model Ac-KA(14)K-NH(2) peptides using our newly developed off-lattice, implicit-solvent, intermediate-resolution model, PRIME. We find that, at a low concentration, random-coil peptides assemble into alpha-helices at low temperatures. At intermediate concentrations, random-coil peptides assemble into alpha-helices at low temperatures and large beta-sheet structures at high temperatures. At high concentrations, the system forms beta-sheets over a wide range of temperatures. These assemble into fibrils above a critical temperature which decreases with concentration and exceeds the isolated peptide's folding temperature. At very high temperatures and all concentrations, the system is in a random-coil state. All of these results are in good qualitative agreement with those by Blondelle and co-workers on Ac-KA(14)K-NH(2) peptides. The fibrils observed in our simulations mimic the structural characteristics observed in experiments in terms of the number of sheets formed, the values of the intra- and intersheet separations, and the parallel peptide arrangement within each beta-sheet. Finally, we find that when the strength of the hydrophobic interaction between nonpolar side chains is high compared to the strength of hydrogen bonding, amorphous aggregates, rather than fibrillar aggregates, are formed.
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Affiliation(s)
- Hung D Nguyen
- Department of Chemical Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
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31
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32
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Abstract
Thermodynamic and dynamic properties of biomolecules can be calculated using a coarse-grained approach based upon sampling stationary points of the underlying potential energy surface. The superposition approximation provides an overall partition function as a sum of contributions from the local minima, and hence functions such as internal energy, entropy, free energy and the heat capacity. To obtain rates we must also sample transition states that link the local minima, and the discrete path sampling method provides a systematic means to achieve this goal. A coarse-grained picture is also helpful in locating the global minimum using the basin-hopping approach. Here we can exploit a fictitious dynamics between the basins of attraction of local minima, since the objective is to find the lowest minimum, rather than to reproduce the thermodynamics or dynamics.
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Affiliation(s)
- David J Wales
- Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK.
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33
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Buchete NV, Tycko R, Hummer G. Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments. J Mol Biol 2005; 353:804-21. [PMID: 16213524 DOI: 10.1016/j.jmb.2005.08.066] [Citation(s) in RCA: 221] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2005] [Revised: 08/25/2005] [Accepted: 08/26/2005] [Indexed: 01/09/2023]
Abstract
Filamentous amyloid aggregates are central to the pathology of Alzheimer's disease. We use all-atom molecular dynamics (MD) simulations with explicit solvent and multiple force fields to probe the structural stability and the conformational dynamics of several models of Alzheimer's beta-amyloid fibril structures, for both wild-type and mutated amino acid sequences. The structural models are based on recent solid state NMR data. In these models, the peptides form in-register parallel beta-sheets along the fibril axis, with dimers of two U-shaped peptides located in layers normal to the fibril axis. Four different topologies are explored for stacking the beta-strand regions against each other to form a hydrophobic core. Our MD results suggest that all four NMR-based models are structurally stable, and we find good agreement with dihedral angles estimated from solid-state NMR experiments. Asp23 and Lys28 form buried salt-bridges, resulting in an alternating arrangement of the negatively and positively charged residues along the fibril axis that is reminiscent of a one-dimensional ionic crystal. Interior water molecules are solvating the buried salt-bridges. Based on data from NMR measurements and MD simulations of short amyloid fibrils, we constructed structural models of long fibrils. Calculated X-ray fiber diffraction patterns show the characteristics of packed beta-sheets seen in experiments, and suggest new experiments that could discriminate between various fibril topologies.
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Affiliation(s)
- Nicolae-Viorel Buchete
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
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34
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Qiu W, Zhang L, Kao YT, Lu W, Li T, Kim J, Sollenberger GM, Wang L, Zhong D. Ultrafast Hydration Dynamics in Melittin Folding and Aggregation: Helix Formation and Tetramer Self-Assembly. J Phys Chem B 2005; 109:16901-10. [PMID: 16853151 DOI: 10.1021/jp0511754] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Melittin, an amphipathic peptide from honeybee venom, consists of 26 amino acid residues and adopts different conformations from a random coil, to an alpha-helix, and to a self-assembled tetramer under certain aqueous environments. We report here our systematic studies of the hydration dynamics in these conformations using single intrinsic tryptophan (W19) as a molecular probe. With femtosecond resolution, we observed the solvation dynamics occurring in 0.62 and 14.7 ps in a random-coiled primary structure. The former represents bulklike water motion, and the latter reflects surface-type hydration dynamics of proteins. As a comparison, a model tripeptide (KWK) was also studied. At a membrane-water interface, melittin folds into a secondary alpha-helical structure, and the interfacial water motion was found to take as long as 114 ps, indicating a well-ordered water structure along the membrane surface. In high-salt aqueous solution, the dielectric screening and ionic solvation promote the hydrophobic core collapse in melittin aggregation and facilitate the tetramer formation. This self-assembled tertiary structure is also stabilized by the strong hydrophilic interactions of charged C-terminal residues and associated ions with water molecules in the two assembled regions. The hydration dynamics was observed to occur in 87 ps, significantly slower than typical water relaxation at protein surfaces but similar to water motion at membrane interfaces. Thus, the observed time scale of approximately 100 ps probably implies appropriate water mobility for mediating the formation of high-order structures of melittin in an alpha-helix and a self-assembled tetramer. These results elucidate the critical role of hydration dynamics in peptide conformational transitions and protein structural stability and integrity.
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Affiliation(s)
- Weihong Qiu
- Departmens of Physics, OSU Biophysics, Chemical Physics, and Biochemistry Programs, 191 West Woodruff Avenue, The Ohio State University, Columbus, Ohio 43210, USA
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35
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Xu Y, Shen J, Luo X, Zhu W, Chen K, Ma J, Jiang H. Conformational transition of amyloid beta-peptide. Proc Natl Acad Sci U S A 2005; 102:5403-7. [PMID: 15800039 PMCID: PMC556260 DOI: 10.1073/pnas.0501218102] [Citation(s) in RCA: 206] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Indexed: 12/19/2022] Open
Abstract
The amyloid beta-peptides (Abetas), containing 39-43 residues, are the key protein components of amyloid deposits in Alzheimer's disease. To structurally characterize the dynamic behavior of Abeta(40), 12 independent long-time molecular dynamics (MD) simulations for a total of 850 ns were performed on both the wide-type peptide and its mutant in both aqueous solution and a biomembrane environment. In aqueous solution, an alpha-helix to beta-sheet conformational transition for Abeta(40) was observed, and an entire unfolding process from helix to coil was traced by MD simulation. Structures with beta-sheet components were observed as intermediates in the unfolding pathway of Abeta(40). Four glycines (G(25), G(29), G(33), and G(37)) are important for Abeta(40) to form beta-sheet in aqueous solution; mutations of these glycines to alanines almost abolished the beta-sheet formation and increased the content of the helix component. In the dipalmitoyl phosphatidylcholine (DPPC) bilayer, the major secondary structure of Abeta(40) is a helix; however, the peptide tends to exit the membrane environment and lie down on the surface of the bilayer. The dynamic feature revealed by our MD simulations rationalized several experimental observations for Abeta(40) aggregation and amyloid fibril formation. The results of MD simulations are beneficial to understanding the mechanism of amyloid formation and designing the compounds for inhibiting the aggregation of Abeta and amyloid fibril formation.
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Affiliation(s)
- Yechun Xu
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Graduate School of Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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36
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Masu H, Sakai M, Kishikawa K, Yamamoto M, Yamaguchi K, Kohmoto S. Aromatic Foldamers with Iminodicarbonyl Linkers: Their Structures and Optical Properties. J Org Chem 2005; 70:1423-31. [PMID: 15704979 DOI: 10.1021/jo048233m] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[structure: see text] Carboxamides possessing naphthalene rings connected by multiple iminodicarbonyl linkers were synthesized. These molecules forced the naphthalene rings to be placed in the positions facing each other, and they form helical foldamers both in solution and in the crystalline state. Their folding structures were investigated by single-crystal X-ray analysis and (1)H NMR spectroscopy. Their absorption and fluorescence spectra showed a red shift as the number of naphthalene moieties increased. This remarkable change is based on the intramolecular interaction between naphthalene moieties. Helicity of the foldamer can be controlled by the introduction of chiral auxiliaries at imide nitrogen atoms, which results in an observation of induced circular dichroism.
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Affiliation(s)
- Hyuma Masu
- Graduate School of Science and Technology, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
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37
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Abstract
The determination of the folding mechanisms of proteins is critical to understand the topological change that can propagate Alzheimer and Creutzfeld-Jakobs diseases, among others. The computational community has paid considerable attention to this problem; however, the associated time scale, typically on the order of milliseconds or more, represents a formidable challenge. Ab initio protein folding from long molecular dynamics simulations or ensemble dynamics is not feasible with ordinary computing facilities and new techniques must be introduced. Here we present a detailed study of the folding of a 16-residue beta-hairpin, described by a generic energy model and using the activation-relaxation technique. From a total of 90 trajectories at 300 K, three folding pathways emerge. All involve a simultaneous optimization of the complete hydrophobic and hydrogen bonding interactions. The first two pathways follow closely those observed by previous theoretical studies (folding starting at the turn or by interactions between the termini). The third pathway, never observed by previous all-atom folding, unfolding, and equilibrium simulations, can be described as a reptation move of one strand of the beta-sheet with respect to the other. This reptation move indicates that non-native interactions can play a dominant role in the folding of secondary structures. Furthermore, such a mechanism mediated by non-native hydrogen bonds is not available for study by unfolding and Gō model simulations. The exact folding path followed by a given beta-hairpin is likely to be influenced by its sequence and the solvent conditions. Taken together, these results point to a more complex folding picture than expected for a simple beta-hairpin.
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Affiliation(s)
- Guanghong Wei
- Département de physique and Regroupement québécois sur les matériaux de pointe, Université de Montréal, Montréal, Québec, Canada
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38
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Abstract
Ordered beta-sheet complexes, termed amyloid fibrils, are the underlying structural components of the intra- and extracellular fibrillar protein deposits that are associated with a variety of human diseases, including Alzheimer's, Parkinson's, and the prion diseases. In this work, we investigated the kinetics of fibril formation using our newly developed off-lattice intermediate resolution model, PRIME. The model is simple enough to allow the treatment of large multichain systems while maintaining a fairly realistic description of protein dynamics without built-in bias toward any conformation when used in conjunction with constant temperature discontinuous molecular dynamics, a fast alternative to conventional molecular dynamics. Simulations were performed on systems containing 48-96 model Ac-KA14K-NH2 peptides. We found that fibril formation for polyalanines incorporate features that are characteristic of three models, the templated assembly, nucleated polymerization, and nucleated conformational conversion models, but that none of them gave a completely satisfactory description of the simulation kinetics. Fibril formation was nucleation-dependent, occurring after a lag time that decreased with increasing peptide concentration and increased with increasing temperature. Fibril formation appeared to be a conformational conversion process in which small amorphous aggregates --> beta-sheets --> ordered nucleus --> subsequent rapid growth of a small stable fibril or protofilament. Fibril growth in our simulations involved both beta-sheet elongation, in which the fibril grew by adding individual peptides to the end of each beta-sheet, and lateral addition, in which the fibril grew by adding already formed beta-sheets to its side. The initial rate of fibril formation increased with increasing concentration and decreased with increasing temperature.
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Affiliation(s)
- Hung D Nguyen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, USA
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Simona F, Tiana G, Broglia RA, Colombo G. Modeling the α-helix to β-hairpin transition mechanism and the formation of oligomeric aggregates of the fibrillogenic peptide A(12–28): insights from all-atom molecular dynamics simulations. J Mol Graph Model 2004; 23:263-73. [PMID: 15530822 DOI: 10.1016/j.jmgm.2004.07.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2004] [Revised: 07/26/2004] [Accepted: 07/26/2004] [Indexed: 11/25/2022]
Abstract
In this paper, all-atom molecular dynamics simulations in explicit solvent are used to investigate the structural and dynamical determinants of the alpha-helical to beta-hairpin conformational transition of the 12-28 fragment from the full length Abeta Alzheimer's peptide. The transition from alpha-helical to beta-structure requires the peptide to populate intermediate beta-bend geometries in which several mainly hydrophobic interactions are partially formed. This is followed by the sudden collapse to ordered beta-hairpin structures and the simultaneous disruption of the hydrophobic side-chain interactions with a consequent increase in solvent exposure. The solvent exposure of hydrophobic side-chains belonging to a sequence of five consecutive residues in the beta-hairpin defines a possible starting point for the onset of the aggregation mechanisms. Several different conformations of model oligomeric (dimeric and tetrameric) aggregates are then investigated. These simulations show that while hydrophobic contacts are important to bring together different monomers with a beta-hairpin like conformation, more specific interactions such as hydrogen-bonding and coulombic interactions, should be considered necessary to provide further stabilization and ordering to the nascent fibrillar aggregates.
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Affiliation(s)
- Fabio Simona
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
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40
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Abstract
Amyloid fibrils are the structural components underlying the intra- and extracellular protein deposits that are associated with a variety of human diseases, including Alzheimer's, Parkinson's, and the prion diseases. In this work, we examine the thermodynamics of fibril formation using our newly-developed off-lattice intermediate-resolution protein model, PRIME. The model is simple enough to allow the treatment of large multichain systems while maintaining a fairly realistic description of protein dynamics when used in conjunction with constant-temperature discontinuous molecular dynamics, a fast alternative to conventional molecular dynamics. We conduct equilibrium simulations on systems containing 96 Ac-KA14K-NH2 peptides over a wide range of temperatures and peptide concentrations using the replica-exchange method. Based on measured values of the heat capacity, radius of gyration, and percentage of peptides that form the various structures, a phase diagram in the temperature-concentration plane is constructed delineating the regions where each structure is stable. There are four distinct single-phase regions: alpha-helices, fibrils, nonfibrillar beta-sheets, and random coils; and four two-phase regions: random coils/nonfibrillar beta-sheets, random coils/fibrils, fibrils/nonfibrillar beta-sheets, and alpha-helices/nonfibrillar beta-sheets. The alpha-helical region is at low temperature and low concentration. The nonfibrillar beta-sheet region is at intermediate temperatures and low concentrations and expands to higher temperatures as concentration is increased. The fibril region occurs at intermediate temperatures and intermediate concentrations and expands to lower as the peptide concentration is increased. The random-coil region is at high temperatures and all concentrations; this region shifts to higher temperatures as the concentration is increased.
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Affiliation(s)
- Hung D Nguyen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, USA
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41
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Paci E, Gsponer J, Salvatella X, Vendruscolo M. Molecular dynamics studies of the process of amyloid aggregation of peptide fragments of transthyretin. J Mol Biol 2004; 340:555-69. [PMID: 15210354 DOI: 10.1016/j.jmb.2004.05.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2003] [Revised: 04/21/2004] [Accepted: 05/03/2004] [Indexed: 10/26/2022]
Abstract
It has been shown recently that an 11-residue peptide fragment of transthyretin, TTR(105-115), can form amyloid fibrils in vitro by adopting an extended beta-strand conformation. We used molecular dynamics simulations on systems of TTR(105-115) peptides, for a total length of about 5 micros, to explore the process of self-assembly and the structures of the resulting aggregates. Our results suggest that an antiparallel association of the beta-strands is more probable than a parallel one and that the central residues (T106-L111) in a beta-strand have a high propensity to form inter-peptide hydrogen bonds. The study of the dynamics of self-association indicated that, for this peptide, trajectories leading to conformations with high alpha-helical content are off-pathway from those leading to aggregates with high beta-structure content. We also show that the diverse oligomeric structures that form spontaneously in the molecular dynamics simulations are, to a large extent, compatible with solid-state NMR experimental measurements, including chemical shifts, on fully formed fibrils. The strategy that we present may therefore be used in the design of new experiments to determine the structure of amyloid fibrils, such as those involving site-specific isotope labelling schemes to measure key inter-atomic distances.
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Affiliation(s)
- Emanuele Paci
- Biochemisches Institut der Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
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42
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Cárdenas AE, Elber R. Atomically detailed simulations of helix formation with the stochastic difference equation. Biophys J 2004; 85:2919-39. [PMID: 14581195 PMCID: PMC1303571 DOI: 10.1016/s0006-3495(03)74713-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
An algorithm is described to compute approximate classical trajectories as a boundary value problem with an integration step in the arc length. High-frequency motions are filtered out when a large integration step is used, maintaining the stability of the algorithm. At the limit of high filtering (large steps), but still offering an accurate description of the continuous path, the trajectory approaches the steepest descent path (SDP). The steepest descent path is widely used as a reaction coordinate in chemical systems. At intermediate step sizes, some inertial motions remain, interpolating between reaction coordinates and exact classical trajectories. Numerical studies of spatial and energetic properties of meta-trajectories are carried out. Two systems are considered here: valine dipeptide and the folding of a small helical protein. Although thermodynamic properties of meta-trajectories are affected by the filtering, the ordering of events remains similar for substantial differences in trajectory resolution.
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Affiliation(s)
- Alfredo E Cárdenas
- Department of Computer Science, Cornell University, Ithaca, New York 14850, USA
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43
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Daidone I, Simona F, Roccatano D, Broglia RA, Tiana G, Colombo G, Di Nola A. β-Hairpin conformation of fibrillogenic peptides: Structure and α-β transition mechanism revealed by molecular dynamics simulations. Proteins 2004; 57:198-204. [PMID: 15326604 DOI: 10.1002/prot.20178] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Understanding the conformational transitions that trigger the aggregation and amyloidogenesis of otherwise soluble peptides at atomic resolution is of fundamental relevance for the design of effective therapeutic agents against amyloid-related disorders. In the present study the transition from ideal alpha-helical to beta-hairpin conformations is revealed by long timescale molecular dynamics simulations in explicit water solvent, for two well-known amyloidogenic peptides: the H1 peptide from prion protein and the Abeta(12-28) fragment from the Abeta(1-42) peptide responsible for Alzheimer's disease. The simulations highlight the unfolding of alpha-helices, followed by the formation of bent conformations and a final convergence to ordered in register beta-hairpin conformations. The beta-hairpins observed, despite different sequences, exhibit a common dynamic behavior and the presence of a peculiar pattern of the hydrophobic side-chains, in particular in the region of the turns. These observations hint at a possible common aggregation mechanism for the onset of different amyloid diseases and a common mechanism in the transition to the beta-hairpin structures. Furthermore the simulations presented herein evidence the stabilization of the alpha-helical conformations induced by the presence of an organic fluorinated cosolvent. The results of MD simulation in 2,2,2-trifluoroethanol (TFE)/water mixture provide further evidence that the peptide coating effect of TFE molecules is responsible for the stabilization of the soluble helical conformation.
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Affiliation(s)
- Isabella Daidone
- Department of Chemistry, University of Rome La Sapienza, Rome, Italy
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44
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Lim J, Vachet RW. Using Mass Spectrometry To Study Copper−Protein Binding under Native and Non-Native Conditions: β-2-Microglobulin. Anal Chem 2004; 76:3498-504. [PMID: 15228316 DOI: 10.1021/ac049716t] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A method based on metal-catalyzed oxidation (MCO) reactions and mass spectrometry (MS) has been used to determine the Cu(II) binding sites in both native and unfolded conformations of beta-2-microglobulin (beta2m). Recent studies have shown that beta2m is destabilized and can form amyloid fibers in the presence of Cu(II). An increased affinity for Cu in unfolded states compared to that of the native state is suspected to facilitate overall protein destabilization. Cu-binding site information for native beta2m is difficult to obtain using traditional techniques because of its propensity to form amyloid fibers at relatively high protein concentrations in the presence of Cu and because of the nonspecific paramagnetic peak broadening observed in NMR analyses. In addition, Cu-binding information of unfolded beta2m is complicated by the high concentrations of denaturants (e.g., 8 M urea) needed to ensure protein unfolding. The MCO/MS approach has been successfully employed in this work to overcome these difficulties. The sensitivity of MS allowed the Cu-binding site of the native protein to be determined at the low concentrations of beta2m necessary to avoid amyloid fiber formation. Results indicate that the N-terminus of the protein and His31 are responsible for Cu(II) coordination in the native state. The MCO/MS method was also successful at determining the Cu-binding site in the presence of 8 M urea with the N-terminus, His31, His51, and His81 found to be Cu-bound in the unfolded state. This result supports the existence of a well-defined but different coordination structure in the unfolded state, which leads to the greater affinity for Cu(II) observed in the unfolded state of the protein. In general, it appears that the MCO/MS method is capable of providing Cu-binding site information for proteins that are difficult to study by traditional means.
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Affiliation(s)
- Jihyeon Lim
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA 01003, USA
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46
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47
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LeVine H. Y10W beta(1-40) fluorescence reflects epitope exposure in conformers of Alzheimer's beta-peptide. Arch Biochem Biophys 2003; 417:112-22. [PMID: 12921787 DOI: 10.1016/s0003-9861(03)00322-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The Alzheimer's beta-peptide in neutral aqueous solution is characterized variously as a random coil or a heterogeneous mixture of conformers. Under conditions of lowered pH characteristic of intracellular compartments such as endosomes or lysosomes, a different conformation is favored, which is reflected in the biophysical and biological properties of the peptide. The reactivity of the epitope of the monoclonal antibody 6F/3D, encompassing residues 9-14, is drastically reduced. The fluorescence of human sequence beta(1-40) with the tyrosine at position 10 substituted with tryptophan (Y10W beta(1-40)) is quenched nearly 50% when the peptide is shifted to pH 4.6. The exposure of the 6F/3D epitope parallels Y10W beta(1-40) fluorescence changes induced by a variety of perturbations. The linkage of the sensitivity of immunological detection with the potential for monitoring rapid changes by fluorescence offers convergence of biology and biophysics in the study of beta-amyloid peptide conformation.
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Affiliation(s)
- Harry LeVine
- Department of Molecular and Cellular Biochemistry, Chandler School of Medicine, University of Kentucky, 209 Sanders-Brown Building, 800 S. Limestone Street, Lexington, KY 40536-0230, USA.
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