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Abstract
Protein aggregation and amyloid formation are pathogenic events underlying the development of an increasingly large number of human diseases named “proteinopathies”. Abnormal accumulation in affected tissues of amyloid β (Aβ) peptide, islet amyloid polypeptide (IAPP), and the prion protein, to mention a few, are involved in the occurrence of Alzheimer’s (AD), type 2 diabetes mellitus (T2DM) and prion diseases, respectively. Many reports suggest that the toxic properties of amyloid aggregates are correlated with their ability to damage cell membranes. However, the molecular mechanisms causing toxic amyloid/membrane interactions are still far to be completely elucidated. This review aims at describing the mutual relationships linking abnormal protein conformational transition and self-assembly into amyloid aggregates with membrane damage. A cross-correlated analysis of all these closely intertwined factors is thought to provide valuable insights for a comprehensive molecular description of amyloid diseases and, in turn, the design of effective therapies.
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Amyloidogenic Intrinsically Disordered Proteins: New Insights into Their Self-Assembly and Their Interaction with Membranes. Life (Basel) 2020; 10:life10080144. [PMID: 32784399 PMCID: PMC7459996 DOI: 10.3390/life10080144] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/02/2020] [Accepted: 08/06/2020] [Indexed: 12/21/2022] Open
Abstract
Aβ, IAPP, α-synuclein, and prion proteins belong to the amyloidogenic intrinsically disordered proteins’ family; indeed, they lack well defined secondary and tertiary structures. It is generally acknowledged that they are involved, respectively, in Alzheimer’s, Type II Diabetes Mellitus, Parkinson’s, and Creutzfeldt–Jakob’s diseases. The molecular mechanism of toxicity is under intense debate, as many hypotheses concerning the involvement of the amyloid and the toxic oligomers have been proposed. However, the main role is represented by the interplay of protein and the cell membrane. Thus, the understanding of the interaction mechanism at the molecular level is crucial to shed light on the dynamics driving this phenomenon. There are plenty of factors influencing the interaction as mentioned above, however, the overall view is made trickier by the apparent irreproducibility and inconsistency of the data reported in the literature. Here, we contextualized this topic in a historical, and even more importantly, in a future perspective. We introduce two novel insights: the chemical equilibrium, always established in the aqueous phase between the free and the membrane phospholipids, as mediators of protein-transport into the core of the bilayer, and the symmetry-breaking of oligomeric aggregates forming an alternating array of partially ordered and disordered monomers.
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Symmetry-breaking transitions in the early steps of protein self-assembly. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:175-191. [PMID: 32123956 DOI: 10.1007/s00249-020-01424-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 01/22/2020] [Accepted: 02/10/2020] [Indexed: 10/24/2022]
Abstract
Protein misfolding and subsequent self-association are complex, intertwined processes, resulting in development of a heterogeneous population of aggregates closely related to many chronic pathological conditions including Type 2 Diabetes Mellitus and Alzheimer's disease. To address this issue, here, we develop a theoretical model in the general framework of linear stability analysis. According to this model, self-assemblies of peptides with pronounced conformational flexibility may become, under particular conditions, unstable and spontaneously evolve toward an alternating array of partially ordered and disordered monomers. The predictions of the theory were verified by atomistic molecular dynamics (MD) simulations of islet amyloid polypeptide (IAPP) used as a paradigm of aggregation-prone polypeptides (proteins). Simulations of dimeric, tetrameric, and hexameric human-IAPP self-assemblies at physiological electrolyte concentration reveal an alternating distribution of the smallest domains (of the order of the peptide mean length) formed by partially ordered (mainly β-strands) and disordered (turns and coil) arrays. Periodicity disappears upon weakening of the inter-peptide binding, a result in line with the predictions of the theory. To further probe the general validity of our hypothesis, we extended the simulations to other peptides, the Aβ(1-40) amyloid peptide, and the ovine prion peptide as well as to other proteins (SOD1 dimer) that do not belong to the broad class of intrinsically disordered proteins. In all cases, the oligomeric aggregates show an alternate distribution of partially ordered and disordered monomers. We also carried out Surface Enhanced Raman Scattering (SERS) measurements of hIAPP as an experimental validation of both the theory and in silico simulations.
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Do PC, Lee EH, Le L. Steered Molecular Dynamics Simulation in Rational Drug Design. J Chem Inf Model 2018; 58:1473-1482. [DOI: 10.1021/acs.jcim.8b00261] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Phuc-Chau Do
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Eric H. Lee
- Department of Medicine and Division of Hematology and Oncology, Loma Linda University Medical Center, Loma Linda, California 92350, United States
| | - Ly Le
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City 700000, Vietnam
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Martin LL, Kubeil C, Piantavigna S, Tikkoo T, Gray NP, John T, Calabrese AN, Liu Y, Hong Y, Hossain MA, Patil N, Abel B, Hoffmann R, Bowie JH, Carver JA. Amyloid aggregation and membrane activity of the antimicrobial peptide uperin 3.5. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24052] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | - Clemens Kubeil
- School of Chemistry; Monash University; Clayton Victoria 3800 Australia
| | | | - Tarun Tikkoo
- School of Chemistry; Monash University; Clayton Victoria 3800 Australia
| | - Nicholas P. Gray
- School of Chemistry; Monash University; Clayton Victoria 3800 Australia
| | - Torsten John
- School of Chemistry; Monash University; Clayton Victoria 3800 Australia
- Leibniz Institute of Surface Engineering (IOM) and Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry; Leipzig University; Leipzig 04318 Germany
| | - Antonio N. Calabrese
- Department of Chemistry and School of Physical Sciences; The University of Adelaide; Adelaide South Australia 5005 Australia
| | - Yanqin Liu
- Department of Chemistry and School of Physical Sciences; The University of Adelaide; Adelaide South Australia 5005 Australia
| | - Yuning Hong
- Department of Chemistry and Physics; La Trobe Institute for Molecular Science, La Trobe University; Melbourne Victoria 3086 Australia
| | - Mohammed A. Hossain
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne; Parkville Victoria 3010 Australia
| | - Nitin Patil
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne; Parkville Victoria 3010 Australia
| | - Bernd Abel
- Leibniz Institute of Surface Engineering (IOM) and Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry; Leipzig University; Leipzig 04318 Germany
| | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, and Center for Biotechnology and Biomedicine (BBZ), Universität Leipzig; Leipzig 04103 Germany
| | - John H. Bowie
- Department of Chemistry and School of Physical Sciences; The University of Adelaide; Adelaide South Australia 5005 Australia
| | - John A. Carver
- Research School of Chemistry; The Australian National University; Acton Australian Capital Territory 2601 Australia
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Molecular Modeling and Its Applications in Protein Engineering. Synth Biol (Oxf) 2016. [DOI: 10.1007/978-3-319-22708-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Tao W, Yoon G, Cao P, Eom K, Park HS. β-sheet-like formation during the mechanical unfolding of prion protein. J Chem Phys 2015; 143:125101. [DOI: 10.1063/1.4931819] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Weiwei Tao
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Gwonchan Yoon
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts 02215, USA
- Department of Mechanical Engineering, Korea University, Seoul 136-701, South Korea
| | - Penghui Cao
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Kilho Eom
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Harold S. Park
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts 02215, USA
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Valente M, Sousa SF, Magalhães AL, Freire C. Decomplexation and complexation of alkali metal cations by a crown-ether-type podand in dichloromethane: a steered molecular dynamics study. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1171-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Valente M, Sousa SF, Magalhães AL, Freire C. Transfer of the K+ cation across a water/dichloromethane interface: a steered molecular dynamics study with implications in cation extraction. J Phys Chem B 2012; 116:1843-9. [PMID: 22260719 DOI: 10.1021/jp210786j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this paper we report the characterization of the dichloromethane (DCM)/water interface in terms of density profile, width, and surface structure. The use of steered molecular dynamics (SMD) to study the transfer of the K(+) cation from the organic layer to the water layer is also described. The corresponding free energy is in semiquantitative agreement with published experimental and theoretical results. The transference of the K(+) cation from the water layer toward the DCM layer occurs with concomitant water transport as a water microdroplet that detaches itself from the water layer after ca. 16 Å of penetration into the organic layer by breaking the thin water thread that unites both. Complexation of the water microdroplet by a polyethylene-glycol type podand induces the loss of water molecules from the water microdroplet to bulk DCM and, eventually, to the water layer.
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Affiliation(s)
- Mário Valente
- REQUIMTE-Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre s/n, 4169-007, Porto, Portugal
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Rossetti G, Cong X, Caliandro R, Legname G, Carloni P. Common Structural Traits across Pathogenic Mutants of the Human Prion Protein and Their Implications for Familial Prion Diseases. J Mol Biol 2011; 411:700-12. [DOI: 10.1016/j.jmb.2011.06.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 06/01/2011] [Accepted: 06/06/2011] [Indexed: 10/18/2022]
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Computational study on the interaction of a ring-hydroxylating dioxygenase from Sphingomonas CHY-1 with PAHs. J Mol Graph Model 2011; 29:915-9. [DOI: 10.1016/j.jmgm.2011.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 01/19/2011] [Accepted: 03/02/2011] [Indexed: 11/20/2022]
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Lingenheil M, Denschlag R, Tavan P. Highly polar environments catalyze the unfolding of PrP C helix 1. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2010; 39:1177-1192. [PMID: 20049591 DOI: 10.1007/s00249-009-0570-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2009] [Revised: 10/21/2009] [Accepted: 12/14/2009] [Indexed: 05/28/2023]
Abstract
The first alpha-helix (H1) likely plays an important role in the conversion of the cellular prion protein (PrP(C)) into its pathogenic isoform (PrP(Sc)). In this conversion, H1 may either have to unfold or may represent a site of intermolecular contact. A recent molecular dynamics simulation suggested that H1 can unfold if it is detached from the protein core (Hirschberger et al. in Biophys J 90:3908, 2006). It has been hypothesized that the high dielectric constant epsilon (S) of the bulk water environment facilitates the unfolding of H1. To check this hypothesis, we performed a number of replica exchange molecular dynamics simulations of an H1 peptide in solvents of different epsilon (S). We found that the equilibrium helix fraction in water is less than 40%, in agreement with previous experimental findings, and that the helix unfolds much faster in water than in less polar solvents. The kinetically stabilizing effect of the organic solvents is largely unspecific and correlates well with their dielectric constant epsilon (S).
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Affiliation(s)
- Martin Lingenheil
- Department für Physik, LMU München, Oettingenstrasse 67, 80538, Munich, Germany
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Milardi D, Pappalardo M, Grasso DM, La Rosa C. Unveiling the unfolding pathway of FALS associated G37R SOD1 mutant: a computational study. MOLECULAR BIOSYSTEMS 2010; 6:1032-9. [PMID: 20485746 DOI: 10.1039/b918662j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Although the molecular determinants of Familial Amyotrophic Lateral Sclerosis (FALS) are still largely unknown, previous studies have demonstrated that aggregation of Cu, Zn superoxide dismutase (SOD1) mutants may play a causative role in FALS. It has been proposed that this pathogenic process occurs via a multi-step pathway involving metal loss, dimer dissociation and assembly of misfolded apo-monomers. The G37R, one of the many SOD1 mutations known to be associated to FALS, is difficult to be reconciled with this model because it is located far from the metal sites and the monomer-monomer interface. Consequently, an inspection of all the steps involved in G37R SOD1 misfolding is expected to provide hints in the understanding of the molecular basis of the disease. To this aim, an array of different computational strategies--i.e. Thermodynamic Integration (TI), implicit solvent Constant Temperature Molecular Dynamics (CTMD) and Steered Molecular Dynamics (SMD)--have been applied on the G37R SOD1 mutant. A comparison with parallel studies carried out for the Wild Type (WT) SOD1 pointed out that the mutation decreases the affinity of the protein for the Cu(ii) ion. Implicit solvents MD simulations performed on the two apo proteins revealed that in the mutant SOD1 a novel, stable H-bond network involving Arg37, Lys91, Lys36 and Leu38 is created thus confirming a pivotal role of this region in driving the biophysical properties of the entire protein. Finally, the presence of energetic "traps" in the force vs. elongation curves of G37R SOD1 is an indicator of the existence of intermediate states along the unfolding pathway which may lead to abnormal conformers. Our results support a general theory suggesting that the two major hypotheses regarding mutant SOD1 toxicity, i.e. aberrant copper redox chemistry and SOD1 misfolding are causally linked. In fact it is shown that the G37R mutation, although located far away the active site, may induce subtle modification in SOD1 leading to the loosening of metal binding and to the formation of metastable intermediate states along the unfolding pathway.
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Affiliation(s)
- Danilo Milardi
- Istituto CNR di Biostrutture e Bioimmagini-Unità Organizzativa e di Supporto di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
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Pietropaolo A, Muccioli L, Zannoni C, Rizzarelli E. Conformational Preferences of the Full Chicken Prion Protein in Solution and Its Differences with Respect to Mammals. Chemphyschem 2009; 10:1500-10. [DOI: 10.1002/cphc.200900078] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Kedarisetti KD, Dick S, Kurgan L. Searching for factors that distinguish disease-prone and disease-resistant prions via sequence analysis. Bioinform Biol Insights 2008; 2:133-44. [PMID: 19812771 DOI: 10.4137/bbi.s550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The exact mechanisms of prion misfolding and factors that predispose an individual to prion diseases are largely unknown. Our approach to identifying candidate factors in-silico relies on contrasting the C-terminal domain of PrP(C) sequences from two groups of vertebrate species: those that have been found to suffer from prion diseases, and those that have not. We propose that any significant differences between the two groups are candidate factors that may predispose individuals to develop prion disease, which should be further analyzed by wet-lab investigations. Using an array of computational methods we identified possible point mutations that could predispose PrP(C) to misfold into PrP(Sc). Our results include confirmatory findings such as the V210I mutation, and new findings including P137M, G142D, G142N, D144P, K185T, V189I, H187Y and T191P mutations, which could impact structural stability. We also propose new hypotheses that give insights into the stability of helix-2 and -3. These include destabilizing effects of Histidine and T188-T193 segment in helix-2 in the disease-prone prions, and a stabilizing effect of Leucine on helix-3 in the disease-resistant prions.
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Affiliation(s)
- Kanaka Durga Kedarisetti
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada
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