1
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Kumar N, Khatua P, Sinha SK. Can local heating and molecular crowders disintegrate amyloid aggregates? Chem Sci 2024; 15:6095-6105. [PMID: 38665536 PMCID: PMC11040654 DOI: 10.1039/d4sc00103f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024] Open
Abstract
The present study employs a blend of molecular dynamics simulations and a theoretical model to explore the potential disintegration mechanism of a matured Aβ octamer, aiming to offer a strategy to combat Alzheimer's disease. We investigate local heating and crowding effects on Aβ disintegration by selectively heating key Aβ segments and varying the concentration of sodium dodecyl sulphate (SDS), respectively. Despite initiation of disruption, Aβ aggregates resist complete disintegration during local heating due to rapid thermal energy distribution to the surrounding water. Conversely, although SDS molecules effectively inhibit Aβ aggregation at higher concentration through micelle formation, they fail to completely disintegrate the aggregate due to the exceedingly high energy barrier. To address the sampling challenge posed by the formidable energy barrier, we have performed well-tempered metadynamics simulations. Simulations reveal a multi-step disintegration mechanism for the Aβ octamer, suggesting a probable sequence: octamer → pentamer/hexamer ⇌ tetramer → monomer, with a rate-determining step constituting 45 kJ mol-1 barrier during the octamer to pentamer/hexamer transition. Additionally, we have proposed a novel two-state mean-field model based on Ising spins that offers an insight into the kinetics of the Aβ growth process and external perturbation effects on disintegration. Thus, the current simulation study, coupled with the newly introduced mean-field model, offers an insight into the detailed mechanisms underlying the Aβ aggregation process, guiding potential strategies for effective disintegration of Aβ aggregates.
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Affiliation(s)
- Naresh Kumar
- Department of Chemistry, Theoretical and Computational Biophysical Chemistry Group, Indian Institute of Technology Ropar Rupnagar Punjab 140001 India +91-01881-232066
| | - Prabir Khatua
- Department of Chemistry, GITAM School of Science, GITAM (Deemed to be University) Bengaluru 562163 India
| | - Sudipta Kumar Sinha
- Department of Chemistry, Theoretical and Computational Biophysical Chemistry Group, Indian Institute of Technology Ropar Rupnagar Punjab 140001 India +91-01881-232066
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2
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Li J, Guo M, Chen L, Chen Z, Fu Y, Chen Y. p53 amyloid aggregation in cancer: function, mechanism, and therapy. Exp Hematol Oncol 2022; 11:66. [PMID: 36171607 PMCID: PMC9520902 DOI: 10.1186/s40164-022-00317-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/13/2022] [Indexed: 11/28/2022] Open
Abstract
Similar to neurodegenerative diseases, the concept that tumors are prion like diseases has been proposed in recent years. p53, the most well-known tumor suppressor, has been extensively studied for its expression, mutation, and function in various tumors. Currently, an interesting phenomenon of p53 prion-like aggregation has been found in several tumors, and studies have found that its pathological aggregation may lead to functional alterations and ultimately affect tumor progression. It has been demonstrated that the mechanism of p53 aggregation involves its mutation, domains, isoform, etc. In addition to p53 itself, some other factors, including Zn2+ concentration, pH, temperature and chaperone abnormalities, can also contribute to p53 aggregation. Although there are some studies about the mechanism and role of p53 aggregation and amyloidosis in tumors, there still exist some controversies. In this paper, we review the mechanism of p53 amyloid fibril structure and discuss the characteristics and effects of p53 amyloid aggregation, as well as the pathogenic mechanism leading to the occurrence of aggregation in tumors. Finally, we summarize the various inhibitors targeting p53 aggregation and prion-like behavior. In conclusion, a comprehensive understanding of p53 aggregation can expand our understanding of the causes leading its loss of physiological function and that targeting p53 aggregation might be a promising therapeutic strategy for tumor therapy.
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Affiliation(s)
- Jingzhi Li
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.,Department of Obstetrics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Ming Guo
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Lin Chen
- Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Zhuchu Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Ying Fu
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China. .,Department of Obstetrics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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3
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Pilkington AW, Schupp J, Nyman M, Valentine SJ, Smith DM, Legleiter J. Acetylation of Aβ 40 Alters Aggregation in the Presence and Absence of Lipid Membranes. ACS Chem Neurosci 2020; 11:146-161. [PMID: 31834770 DOI: 10.1021/acschemneuro.9b00483] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A hallmark of Alzheimer's disease (AD) is the formation of senile plaques comprised of the β-amyloid (Aβ) peptide. Aβ fibrillization is a complex nucleation-dependent process involving a variety of metastable intermediate aggregates and features the formation of inter- and intramolecular salt bridges involving lysine residues, K16 and K28. Cationic lysine residues also mediate protein-lipid interactions via association with anionic lipid headgroups. As several toxic mechanisms attributed to Aβ involve membrane interactions, the impact of acetylation on Aβ40 aggregation in the presence and absence of membranes was determined. Using chemical acetylation, varying mixtures of acetylated and nonacetylated Aβ40 were produced. With increasing acetylation, fibril and oligomer formation decreased, eventually completely arresting fibrillization. In the presence of total brain lipid extract (TBLE) vesicles, acetylation reduced the interaction of Aβ40 with membranes; however, fibrils still formed at near complete levels of acetylation. Additionally, the combination of TBLE and acetylated Aβ promoted annular aggregates. Finally, toxicity associated with Aβ40 was reduced with increasing acetylation in a cell culture assay. These results suggest that in the absence of membranes that the cationic character of lysine plays a major role in fibril formation. However, acetylation promotes unique aggregation pathways in the presence of lipid membranes.
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Affiliation(s)
- Albert W. Pilkington
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - Jane Schupp
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Morgan Nyman
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - Stephen J. Valentine
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - David M. Smith
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia 26506, United States
- Rockefeller Neurosciences Institutes, West Virginia University, 1 Medical Center Drive, P.O. Box 9303, Morgantown, West Virginia 26505, United States
- Department of Neuroscience, West Virginia University, 1 Medical Center Drive, P.O. Box
9303, Morgantown, West Virginia 26505, United States
| | - Justin Legleiter
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
- Rockefeller Neurosciences Institutes, West Virginia University, 1 Medical Center Drive, P.O. Box 9303, Morgantown, West Virginia 26505, United States
- Department of Neuroscience, West Virginia University, 1 Medical Center Drive, P.O. Box
9303, Morgantown, West Virginia 26505, United States
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4
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Zbacnik NJ, Henry CS, Manning MC. A Chemometric Approach Toward Predicting the Relative Aggregation Propensity: Aβ(1-42). J Pharm Sci 2019; 109:624-632. [PMID: 31606543 DOI: 10.1016/j.xphs.2019.10.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 01/19/2023]
Abstract
A number of algorithms have been developed to predict the aggregation propensity of peptides and proteins, but virtually none have the ability to provide sequence-specific information on what physicochemical properties are most important in altering aggregation propensity. In this study, a chemometric approach using reduced amino acid properties is used to examine the aggregation behavior of a highly amyloidogenic peptide, Aβ(1-42). Specific residues are identified as being critical to the aggregation process. At each of these positions, the important physicochemical properties are identified that would either accelerate or inhibit fibril formation.
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Affiliation(s)
| | - Charles S Henry
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Mark Cornell Manning
- Legacy BioDesign LLC, Johnstown, Colorado 80534; Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523.
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5
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Ryan P, Patel B, Makwana V, Jadhav HR, Kiefel M, Davey A, Reekie TA, Rudrawar S, Kassiou M. Peptides, Peptidomimetics, and Carbohydrate-Peptide Conjugates as Amyloidogenic Aggregation Inhibitors for Alzheimer's Disease. ACS Chem Neurosci 2018; 9:1530-1551. [PMID: 29782794 DOI: 10.1021/acschemneuro.8b00185] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder accounting for 60-80% of dementia cases. For many years, AD causality was attributed to amyloid-β (Aβ) aggregated species. Recently, multiple therapies that target Aβ aggregation have failed in clinical trials, since Aβ aggregation is found in AD and healthy patients. Attention has therefore shifted toward the aggregation of the tau protein as a major driver of AD. Numerous inhibitors of tau-based pathology have recently been developed. Diagnosis of AD has shifted from measuring late stage senile plaques to early stage biomarkers, amyloid-β and tau monomers and oligomeric assemblies. Synthetic peptides and some derivative structures are being explored for use as theranostic tools as they possess the capacity both to bind the biomarkers and to inhibit their pathological self-assembly. Several studies have demonstrated that O-linked glycoside addition can significantly alter amyloid aggregation kinetics. Furthermore, natural O-glycosylation of amyloid-forming proteins, including amyloid precursor protein (APP), tau, and α-synuclein, promotes alternative nonamyloidogenic processing pathways. As such, glycopeptides and related peptidomimetics are being investigated within the AD field. Here we review advancements made in the last 5 years, as well as the arrival of sugar-based derivatives.
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Affiliation(s)
- Philip Ryan
- School of Pharmacy and Pharmacology, Griffith University, Gold Coast 4222, Australia
| | - Bhautikkumar Patel
- School of Pharmacy and Pharmacology, Griffith University, Gold Coast 4222, Australia
| | - Vivek Makwana
- School of Pharmacy and Pharmacology, Griffith University, Gold Coast 4222, Australia
| | - Hemant R. Jadhav
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani Campus, Pilani-333031, Rajasthan, India
| | - Milton Kiefel
- Institute for Glycomics, Griffith University, Gold Coast 4222, Australia
| | - Andrew Davey
- School of Pharmacy and Pharmacology, Griffith University, Gold Coast 4222, Australia
- Menzies Health Institute Queensland, Griffith University, Gold Coast 4222, Australia
- Quality Use of Medicines Network, Griffith University, Gold Coast 4222, Australia
| | | | - Santosh Rudrawar
- School of Pharmacy and Pharmacology, Griffith University, Gold Coast 4222, Australia
- Menzies Health Institute Queensland, Griffith University, Gold Coast 4222, Australia
- Quality Use of Medicines Network, Griffith University, Gold Coast 4222, Australia
- School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Michael Kassiou
- School of Chemistry, The University of Sydney, NSW 2006, Australia
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6
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Jamasbi E, Hossain MA, Tan M, Separovic F, Ciccotosto GD. Fluorescence imaging of the interaction of amyloid beta 40 peptides with live cells and model membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1609-1615. [PMID: 29408451 DOI: 10.1016/j.bbamem.2018.01.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/23/2018] [Accepted: 01/27/2018] [Indexed: 11/30/2022]
Abstract
Amyloid beta peptides (Aβ) found in plaques in the brain have been widely recognised as a hallmark of Alzheimer's disease although the underlying mechanism is still unknown. Aβ40 and Aβ40(A2T) peptides were synthesized and their effects on neuronal cells are reported together with the effect of tetramer forms of the peptides. ThT assay revealed that mutation affected the lag time and aggregation and the presence of lipid vesicles changed the fibril formation profile for both peptides. The A2T mutation appeared to reduce cytotoxicity and lessen binding of Aβ40 peptides to neuronal cells. Fluorescence microscopy of the interaction between Aβ40 peptides and giant unilamellar vesicles revealed that both peptides led to formation of smaller vesicles although the tetramer of Aβ(A2T) appeared to promote vesicle aggregation. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Affiliation(s)
- Elaheh Jamasbi
- School of Chemistry, Bio21 Institute, The University of Melbourne, VIC 3010, Australia
| | - Mohammed Akhter Hossain
- School of Chemistry, Bio21 Institute, The University of Melbourne, VIC 3010, Australia; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, VIC 3010, Australia
| | - Marsha Tan
- Department of Pathology, The University of Melbourne, VIC 3010, Australia
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, The University of Melbourne, VIC 3010, Australia.
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7
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Ribarič S. Peptides as Potential Therapeutics for Alzheimer's Disease. Molecules 2018; 23:E283. [PMID: 29385735 PMCID: PMC6017258 DOI: 10.3390/molecules23020283] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 01/26/2018] [Accepted: 01/28/2018] [Indexed: 12/22/2022] Open
Abstract
Intracellular synthesis, folding, trafficking and degradation of proteins are controlled and integrated by proteostasis. The frequency of protein misfolding disorders in the human population, e.g., in Alzheimer's disease (AD), is increasing due to the aging population. AD treatment options are limited to symptomatic interventions that at best slow-down disease progression. The key biochemical change in AD is the excessive accumulation of per-se non-toxic and soluble amyloid peptides (Aβ(1-37/44), in the intracellular and extracellular space, that alters proteostasis and triggers Aβ modification (e.g., by reactive oxygen species (ROS)) into toxic intermediate, misfolded soluble Aβ peptides, Aβ dimers and Aβ oligomers. The toxic intermediate Aβ products aggregate into progressively less toxic and less soluble protofibrils, fibrils and senile plaques. This review focuses on peptides that inhibit toxic Aβ oligomerization, Aβ aggregation into fibrils, or stabilize Aβ peptides in non-toxic oligomers, and discusses their potential for AD treatment.
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Affiliation(s)
- Samo Ribarič
- Institute of Pathophysiology, Faculty of Medicine, Zaloška 4, SI-1000 Ljubljana, Slovenia.
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8
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Khatua P, Sinha SK, Bandyopadhyay S. Size-Dependent Conformational Features of Aβ17–42 Protofilaments from Molecular Simulation Studies. J Chem Inf Model 2017; 57:2378-2392. [DOI: 10.1021/acs.jcim.7b00407] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Prabir Khatua
- Molecular
Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sudipta Kumar Sinha
- Department
of Chemistry, Indian Institute of Technology Ropar, Ropar 140001, India
| | - Sanjoy Bandyopadhyay
- Molecular
Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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9
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Das P, Chacko AR, Belfort G. Alzheimer's Protective Cross-Interaction between Wild-Type and A2T Variants Alters Aβ 42 Dimer Structure. ACS Chem Neurosci 2017; 8:606-618. [PMID: 28292185 DOI: 10.1021/acschemneuro.6b00357] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Whole genome sequencing has recently revealed the protective effect of a single A2T mutation in heterozygous carriers against Alzheimer's disease (AD) and age-related cognitive decline. The impact of the protective cross-interaction between the wild-type (WT) and A2T variants on the dimer structure is therefore of high interest, as the Aβ dimers are the smallest known neurotoxic species. Toward this goal, extensive atomistic replica exchange molecular dynamics simulations of the solvated WT homo- and A2T hetero- Aβ1-42 dimers have been performed, resulting into a total of 51 μs of sampling for each system. Weakening of a set of transient, intrachain contacts formed between the central and C-terminal hydrophobic residues is observed in the heterodimeric system. The majority of the heterodimers with reduced interaction between central and C-terminal regions lack any significant secondary structure and display a weak interchain interface. Interestingly, the A2T N-terminus, particularly residue F4, is frequently engaged in tertiary and quaternary interactions with central and C-terminal hydrophobic residues in those distinct structures, leading to hydrophobic burial. This atypical involvement of the N-terminus within A2T heterodimer revealed in our simulations implies possible interference on Aβ42 aggregation and toxic oligomer formation, which is consistent with experiments. In conclusion, the present study provides detailed structural insights onto A2T Aβ42 heterodimer, which might provide molecular insights onto the AD protective effect of the A2T mutation in the heterozygous state.
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Affiliation(s)
- Payel Das
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Anita R. Chacko
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Georges Belfort
- Howard
P. Isermann Department of Chemical and Biological Engineering, and
Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180-3590, United States
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10
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Nguyen PH, Sterpone F, Pouplana R, Derreumaux P, Campanera JM. Dimerization Mechanism of Alzheimer Aβ 40 Peptides: The High Content of Intrapeptide-Stabilized Conformations in A2V and A2T Heterozygous Dimers Retards Amyloid Fibril Formation. J Phys Chem B 2016; 120:12111-12126. [PMID: 27933940 DOI: 10.1021/acs.jpcb.6b10722] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Amyloid beta (Aβ) oligomerization is associated with the origin and progression of Alzheimer's disease (AD). While the A2V mutation enhances aggregation kinetics and toxicity, mixtures of wild-type (WT) and A2V, and also WT and A2T, peptides retard fibril formation and protect against AD. In this study, we simulate the equilibrium ensemble of WT:A2T Aβ40 dimer by means of extensive atomistic replica exchange molecular dynamics and compare our results with previous equivalent simulations of A2V:A2V, WT:WT, and WT:A2V Aβ40 dimers for a total time scale of nearly 0.1 ms. Qualitative comparison of the resulting thermodynamic properties, such as the relative binding free energies, with the reported experimental kinetic and thermodynamic data affords us important insight into the conversion from slow-pathway to fast-pathway dimer conformations. The crucial reaction coordinate or driving force of such transformation turns out to be related to hydrophobic interpeptide interactions. Analysis of the equilibrium ensembles shows that the fast-pathway conformations contain interpeptide out-of-register antiparallel β-sheet structures at short interpeptide distances. In contrast, the slow-pathway conformations are formed by the association of peptides at large interpeptide distances and high intrapeptide compactness, such as conformations containing intramolecular three-stranded β-sheets which sharply distinguish fast (A2V:A2V and WT:WT) and slow (WT:A2T and WT:A2V) amyloid-forming sequences. Also, this analysis leads us to predict that a molecule stabilizing the intramolecular three-stranded β-sheet or inhibiting the formation of an interpeptide β-sheet spanning residues 17-20 and 31-37 would further reduce fibril formation and probably the cytotoxicity of Aβ species.
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Affiliation(s)
- Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, IBPC, Université Paris Diderot, Sorbonne Paris Cité , 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, IBPC, Université Paris Diderot, Sorbonne Paris Cité , 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Ramon Pouplana
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona , 08028 Barcelona, Catalonia, Spain
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, IBPC, Université Paris Diderot, Sorbonne Paris Cité , 13 Rue Pierre et Marie Curie, 75005 Paris, France.,IUF (Institut Universitaire de France) , 103 Boulevard Michel, 75005 Paris, France
| | - Josep M Campanera
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona , 08028 Barcelona, Catalonia, Spain
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11
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Yagi-Utsumi M, Dobson CM. Conformational Effects of the A21G Flemish Mutation on the Aggregation of Amyloid β Peptide. Biol Pharm Bull 2016; 38:1668-72. [PMID: 26424029 DOI: 10.1248/bpb.b15-00466] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Among the various hereditary mutants of amyloid β (Aβ) in familial Alzheimer's disease (AD), the A21G Flemish-type mutant has unique properties showing a low aggregation propensity but progressive deposition in vascular walls. Moreover, in contrast to other familial AD cases that show extensive Aβ1-42 deposition in the brain, patients with Flemish AD predominantly exhibit the deposition of the Aβ1-40 isoform. Here we report the structural characterization of the Flemish-type mutant (A21G) in comparison with the wild-type Aβ1-40 peptide to examine the possible effects of the A21G mutation on the conformation of the Aβ1-40 isoform. The kinetic analysis of the aggregation of the peptides monitored by thioflavin T fluorescence measurement indicates that the mutation precludes the initial nucleation process of amyloid fibril formation by Aβ1-40. Spectroscopic data indicate that the Flemish-type mutant bound to aqueous micelles composed of lyso-GM1, in which the mobile N-terminal segment is tethered through the C-terminal helical segment, has reduced α-helical structure compared to the wild-type peptide. Our findings suggest that the mutational perturbation to the membrane binding properties is coupled with the changes in nucleation behavior of Aβ during its fibril formation.
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12
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Macdonald B, McCarley S, Noeen S, van Giessen AE. β-Hairpin Crowding Agents Affect α-Helix Stability in Crowded Environments. J Phys Chem B 2016; 120:650-9. [DOI: 10.1021/acs.jpcb.5b10575] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Bryanne Macdonald
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, United States
| | - Shannon McCarley
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, United States
| | - Sundus Noeen
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, United States
| | - Alan E. van Giessen
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, United States
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13
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Rosenman DJ, Wang C, García AE. Characterization of Aβ Monomers through the Convergence of Ensemble Properties among Simulations with Multiple Force Fields. J Phys Chem B 2015; 120:259-77. [PMID: 26562747 DOI: 10.1021/acs.jpcb.5b09379] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amyloid β (Aβ) monomers represent a base state in the pathways of aggregation that result in the fibrils and oligomers implicated in the pathogenesis of Alzheimer's disease (AD). The structural properties of these intrinsically disordered peptides remain unclear despite extensive experimental and computational investigations. Further, there are mutations within Aβ that change the way the peptide aggregates and are known to cause familial AD (FAD). Here, we analyze the ensembles of different isoforms (Aβ42 and Aβ40) and mutants (E22Δ, D23N, E22K, E22G, and A2T in Aβ40) of Aβ generated with all-atom replica exchange molecular dynamics (REMD) simulations on the μs/replica time scale. These were run using three different force field/water model combinations: OPLS-AA/L and TIP3P ("OPLS"), AMBER99sb-ILDN and TIP4P-Ew ("ILDN"), as well as CHARMM22* and TIP3SP ("CHARMM"). Despite fundamental changes in simulation parameters, we find that the resulting ensembles demonstrate a strong convergence in structural properties. In particular, antiparallel contacts between L17-A21 and A30-L34 are prevalent in ensembles of Aβ40, directly forming β sheets in the OPLS and ILDN combinations. A21-A30 commonly forms an interceding region that rarely interacts with the rest of the peptide. Further, Aβ42 contributes new β hairpin motifs involving V40-I41 in both OPLS and ILDN. However, the structural flexibility of the central region and the electrostatic interactions that characterize it are notably different between the different conditions. Further, for OPLS, each of the FAD mutations disrupts central bend character and increases the polymorphism of antiparallel contacts across the central region. However, the studied mutations in the ILDN set primarily encourage more global contacts involving the N-terminus and the central region, and promote the formation of new β topologies that may seed different aggregates involved in disease phenotypes. These differences aside, the large degree of agreement between simulation sets across multiple force fields provides a generalizable characterization of Aβ that is also consistent with experimental data and models.
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Affiliation(s)
- David J Rosenman
- Department of Biology, Rensselaer Polytechnic Institute , 110 Eighth Street, Troy, New York 12180, United States.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , 110 Eighth Street, Troy, New York 12180, United States
| | - Chunyu Wang
- Department of Biology, Rensselaer Polytechnic Institute , 110 Eighth Street, Troy, New York 12180, United States.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , 110 Eighth Street, Troy, New York 12180, United States.,Graduate Program in Biochemistry and Biophysics, Rensselaer Polytechnic Institute , 110 Eighth Street, Troy, New York 12180, United States
| | - Angel E García
- Department of Biology, Rensselaer Polytechnic Institute , 110 Eighth Street, Troy, New York 12180, United States.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , 110 Eighth Street, Troy, New York 12180, United States.,Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute , 110 Eighth Street, Troy, New York 12180, United States.,Center for Non Linear Studies, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States
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14
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Das P, Murray B, Belfort G. Alzheimer's protective A2T mutation changes the conformational landscape of the Aβ₁₋₄₂ monomer differently than does the A2V mutation. Biophys J 2015; 108:738-47. [PMID: 25650940 DOI: 10.1016/j.bpj.2014.12.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/01/2014] [Accepted: 12/04/2014] [Indexed: 12/20/2022] Open
Abstract
The aggregation of amyloid-β (Aβ) peptides plays a crucial role in the etiology of Alzheimer's disease (AD). Recently, it has been reported that an A2T mutation in Aβ can protect against AD. Interestingly, a nonpolar A2V mutation also has been found to offer protection against AD in the heterozygous state, although it causes early-onset AD in homozygous carriers. Since the conformational landscape of the Aβ monomer is known to directly contribute to the early-stage aggregation mechanism, it is important to characterize the effects of the A2T and A2V mutations on Aβ₁₋₄₂ monomer structure. Here, we have performed extensive atomistic replica-exchange molecular dynamics simulations of the solvated wild-type (WT), A2V, and A2T Aβ₁₋₄₂ monomers. Our simulations reveal that although all three variants remain as collapsed coils in solution, there exist significant structural differences among them at shorter timescales. A2V exhibits an enhanced double-hairpin population in comparison to the WT, similar to those reported in toxic WT Aβ₁₋₄₂ oligomers. Such double-hairpin formation is caused by hydrophobic clustering between the N-terminus and the central and C-terminal hydrophobic patches. In contrast, the A2T mutation causes the N-terminus to engage in unusual electrostatic interactions with distant residues, such as K16 and E22, resulting in a unique population comprising only the C-terminal hairpin. These findings imply that a single A2X (where X = V or T) mutation in the primarily disordered N-terminus of the Aβ₁₋₄₂ monomer can dramatically alter the β-hairpin population and switch the equilibrium toward alternative structures. The atomistically detailed, comparative view of the structural landscapes of A2V and A2T variant monomers obtained in this study can enhance our understanding of the mechanistic differences in their early-stage aggregation.
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Affiliation(s)
- Payel Das
- Soft Matter Theory and Simulations Group, Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York.
| | - Brian Murray
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| | - Georges Belfort
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
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15
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Yates EA, Legleiter J. Preparation protocols of aβ(1-40) promote the formation of polymorphic aggregates and altered interactions with lipid bilayers. Biochemistry 2014; 53:7038-50. [PMID: 25349919 DOI: 10.1021/bi500792f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The appearance of neuritic amyloid plaques comprised of β-amyloid peptide (Aβ) in the brain is a predominant feature in Alzheimer's disease (AD). In the aggregation process, Aβ samples a variety of potentially toxic aggregate species, ranging from small oligomers to fibrils. Aβ has the ability to form a variety of morphologically distinct and stable amyloid fibrils. Commonly termed polymorphs, such distinct aggregate species may play a role in variations of AD pathology. It has been well documented that polymorphic aggregates of Aβ can be produced by changes in the chemical environment and peptide preparations. As Aβ and several of its aggregated forms are known to interact directly with lipid membranes and this interaction may play a role in a variety of potential toxic mechanisms associated with AD, we determine how different Aβ(1-40) preparation protocols that lead to distinct polymorphic fibril aggregates influence the interaction of Aβ(1-40) with model lipid membranes. Using three distinct protocols for preparing Aβ(1-40), the aggregate species formed in the absence and presence of a lipid bilayers were investigated using a variety of scanning probe microscopy techniques. The three preparations of Aβ(1-40) promoted distinct oligomeric and fibrillar aggregates in the absence of bilayers that formed at different rates. Despite these differences in aggregation properties, all Aβ(1-40) preparations were able to disrupt supported total brain lipid extract bilayers, altering the bilayer's morphological and mechanical properties.
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Affiliation(s)
- Elizabeth A Yates
- The C. Eugene Bennett Department of Chemistry, West Virginia University , 217 Clark Hall, Morgantown, West Virginia 26506, United States
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16
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Benilova I, Gallardo R, Ungureanu AA, Castillo Cano V, Snellinx A, Ramakers M, Bartic C, Rousseau F, Schymkowitz J, De Strooper B. The Alzheimer disease protective mutation A2T modulates kinetic and thermodynamic properties of amyloid-β (Aβ) aggregation. J Biol Chem 2014; 289:30977-89. [PMID: 25253695 DOI: 10.1074/jbc.m114.599027] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Missense mutations in alanine 673 of the amyloid precursor protein (APP), which corresponds to the second alanine of the amyloid β (Aβ) sequence, have dramatic impact on the risk for Alzheimer disease; A2V is causative, and A2T is protective. Assuming a crucial role of amyloid-Aβ in neurodegeneration, we hypothesized that both A2V and A2T mutations cause distinct changes in Aβ properties that may at least partially explain these completely different phenotypes. Using human APP-overexpressing primary neurons, we observed significantly decreased Aβ production in the A2T mutant along with an enhanced Aβ generation in the A2V mutant confirming earlier data from non-neuronal cell lines. More importantly, thioflavin T fluorescence assays revealed that the mutations, while having little effect on Aβ42 peptide aggregation, dramatically change the properties of the Aβ40 pool with A2V accelerating and A2T delaying aggregation of the Aβ peptides. In line with the kinetic data, Aβ A2T demonstrated an increase in the solubility at equilibrium, an effect that was also observed in all mixtures of the A2T mutant with the wild type Aβ40. We propose that in addition to the reduced β-secretase cleavage of APP, the impaired propensity to aggregate may be part of the protective effect conferred by A2T substitution. The interpretation of the protective effect of this mutation is thus much more complicated than proposed previously.
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Affiliation(s)
- Iryna Benilova
- From the VIB Center for the Biology of Disease, the Center for Human Genetics and Leuven Institute for Neurodegenerative Diseases, University of Leuven
| | - Rodrigo Gallardo
- the VIB Switch Laboratory, the Switch Laboratory, Department of Cellular and Molecular Medicine
| | - Andreea-Alexandra Ungureanu
- Laboratory of Solid State Physics and Magnetism, University of Leuven, 3000 Leuven, and Imec, 3001 Leuven, Belgium
| | - Virginia Castillo Cano
- the VIB Switch Laboratory, the Switch Laboratory, Department of Cellular and Molecular Medicine
| | - An Snellinx
- From the VIB Center for the Biology of Disease, the Center for Human Genetics and Leuven Institute for Neurodegenerative Diseases, University of Leuven
| | - Meine Ramakers
- the VIB Switch Laboratory, the Switch Laboratory, Department of Cellular and Molecular Medicine
| | - Carmen Bartic
- Laboratory of Solid State Physics and Magnetism, University of Leuven, 3000 Leuven, and Imec, 3001 Leuven, Belgium
| | - Frederic Rousseau
- the VIB Switch Laboratory, the Switch Laboratory, Department of Cellular and Molecular Medicine
| | - Joost Schymkowitz
- the VIB Switch Laboratory, the Switch Laboratory, Department of Cellular and Molecular Medicine
| | - Bart De Strooper
- From the VIB Center for the Biology of Disease, the Center for Human Genetics and Leuven Institute for Neurodegenerative Diseases, University of Leuven,
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17
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Relationship between the initial rate of protein aggregation and the lag period for amorphous aggregation. Int J Biol Macromol 2014; 68:144-50. [PMID: 24794200 DOI: 10.1016/j.ijbiomac.2014.04.046] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/22/2014] [Accepted: 04/22/2014] [Indexed: 01/21/2023]
Abstract
Lag period is an inherent characteristic of the kinetic curves registered for protein aggregation. The appearance of a lag period is connected with the nucleation stage and the stages of the formation of folding or unfolding intermediates prone to aggregation (for example, the stage of protein unfolding under stress conditions). Discovering the kinetic regularities essential for elucidation of the protein aggregation mechanism comprises deducing the relationship between the lag period and aggregation rate. Fändrich proposed the following equation connecting the duration of the lag phase (tlag) and the aggregate growth rate (kg) in the amyloid fibrillation: kg=const/tlag. To establish the relationship between the initial rate of protein aggregation (v) and the lag period (t0) in the case of amorphous aggregation, the kinetics of dithithreitol-induced aggregation of holo-α-lactalbumin from bovine milk was studied (0.1M Na-phosphate buffer, pH 6.8; 37°C). The order of aggregation with respect to protein (n) was calculated from the dependence of the initial rate of protein aggregation on the α-lactalbumin concentration (n=5.3). The following equation connecting v and t0 has been proposed: v(1/n)=const/(t0-t0,lim), where t0,lim is the limiting value of t0 at high concentrations of the protein.
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18
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Gillam JE, MacPhee CE. Modelling amyloid fibril formation kinetics: mechanisms of nucleation and growth. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:373101. [PMID: 23941964 DOI: 10.1088/0953-8984/25/37/373101] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Amyloid and amyloid-like fibrils are self-assembling protein nanostructures, of interest for their robust material properties and inherent biological compatibility as well as their putative role in a number of debilitating mammalian disorders. Understanding fibril formation is essential to the development of strategies to control, manipulate or prevent fibril growth. As such, this area of research has attracted significant attention over the last half century. This review describes a number of different models that have been formulated to describe the kinetics of fibril assembly. We describe the macroscopic implications of mechanisms in which secondary processes such as secondary nucleation, fragmentation or branching dominate the assembly pathway, compared to mechanisms dominated by the influence of primary nucleation. We further describe how experimental data can be analysed with respect to the predictions of kinetic models.
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Affiliation(s)
- J E Gillam
- School of Physics and Astronomy, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, UK
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19
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Good gene, bad gene: New APP variant may be both. Prog Neurobiol 2012; 99:281-92. [DOI: 10.1016/j.pneurobio.2012.06.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/23/2012] [Accepted: 06/11/2012] [Indexed: 01/01/2023]
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20
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21
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Cohen SIA, Vendruscolo M, Welland ME, Dobson CM, Terentjev EM, Knowles TPJ. Nucleated polymerization with secondary pathways. I. Time evolution of the principal moments. J Chem Phys 2012; 135:065105. [PMID: 21842954 DOI: 10.1063/1.3608916] [Citation(s) in RCA: 229] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Self-assembly processes resulting in linear structures are often observed in molecular biology, and include the formation of functional filaments such as actin and tubulin, as well as generally dysfunctional ones such as amyloid aggregates. Although the basic kinetic equations describing these phenomena are well-established, it has proved to be challenging, due to their non-linear nature, to derive solutions to these equations except for special cases. The availability of general analytical solutions provides a route for determining the rates of molecular level processes from the analysis of macroscopic experimental measurements of the growth kinetics, in addition to the phenomenological parameters, such as lag times and maximal growth rates that are already obtainable from standard fitting procedures. We describe here an analytical approach based on fixed-point analysis, which provides self-consistent solutions for the growth of filamentous structures that can, in addition to elongation, undergo internal fracturing and monomer-dependent nucleation as mechanisms for generating new free ends acting as growth sites. Our results generalise the analytical expression for sigmoidal growth kinetics from the Oosawa theory for nucleated polymerisation to the case of fragmenting filaments. We determine the corresponding growth laws in closed form and derive from first principles a number of relationships which have been empirically established for the kinetics of the self-assembly of amyloid fibrils.
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Affiliation(s)
- Samuel I A Cohen
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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22
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Malavolta L, Nakaie CR. Comparative fibril formation of analogs corresponding to the (12-24) segment of the β-amyloid peptide. Neurol Sci 2011; 32:1123-7. [PMID: 21904866 DOI: 10.1007/s10072-011-0749-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 08/23/2011] [Indexed: 11/24/2022]
Abstract
The (1-42) β-amyloid peptide is a main component of the plaques found in the brain of patients suffering from the Alzheimer's disease. As the single substitution of Glu for Gln at position 22 of this peptide seems to be responsible for the manifestation of the more severe amyloidosis (Dutch-type), we decided to evaluate the aggregation characteristics of peptide analogs interchanging Glu and Gln residues at positions 22 and also 15 in the minor (12-24) (VHHQ(15)KLVFFAE(22)DV) fragment. The Q15Q22, E15E22, E15Q22 and the native Q15E22 were compared to the (1-42) β-amyloid peptide in terms of fibril or structured aggregates formation propensity. In contrast to a rather similar solubility data measured of all analogs, fluorescence and light scattering methods indicated that only Q15E22 and Q15Q22 displayed relevant fibril formation capacity. Conversely, E15E22 and E15Q22 were not capable of the formation of this type of structure thus suggesting a key role for the Q(15) residue in the unique aggregation characteristic of the β-amyloid peptide.
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Affiliation(s)
- Luciana Malavolta
- Instituto Israelita de Ensino e Pesquisa Albert Einstein, Av. Albert Einstein, 627, São Paulo, SP CEP 05652-000, Brazil
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23
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Cohen SIA, Vendruscolo M, Dobson CM, Knowles TPJ. Nucleated polymerisation in the presence of pre-formed seed filaments. Int J Mol Sci 2011; 12:5844-52. [PMID: 22016630 PMCID: PMC3189754 DOI: 10.3390/ijms12095844] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 08/30/2011] [Accepted: 08/30/2011] [Indexed: 11/20/2022] Open
Abstract
We revisit the classical problem of nucleated polymerisation and derive a range of exact results describing polymerisation in systems intermediate between the well-known limiting cases of a reaction starting from purely soluble material and for a reaction where no new growth nuclei are formed.
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Affiliation(s)
| | | | | | - Tuomas P. J. Knowles
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +44-0-1223-336300; Fax.: +44-0-1223-336362
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24
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Yates EA, Cucco EM, Legleiter J. Point mutations in Aβ induce polymorphic aggregates at liquid/solid interfaces. ACS Chem Neurosci 2011; 2:294-307. [PMID: 22778873 DOI: 10.1021/cn200001k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 04/11/2011] [Indexed: 11/30/2022] Open
Abstract
A pathological hallmark of Alzheimer's disease (AD), a late onset neurodegenerative disease, is the development of neuritic amyloid plaques, composed predominantly of aggregates of the β-amyloid (Aβ) peptide. It has been demonstrated that Aβ can aggregate into a variety of polymorphic aggregate structures under different chemical environments, and a potentially important environmental factor in dictating aggregate structure is the presence of surfaces. There are also several mutations clustered around the central hydrophobic core of Aβ (E22G Arctic mutation, E22K Italian mutation, D23N Iowa mutation, and A21G Flemish mutation). These mutations are associated with hereditary diseases ranging from almost pure cerebral amyloid angiopathy (CAA) to typical Alzheimer's disease pathology. The goal of this study was to determine how these mutations influence the morphology of Aβ aggregates under free solution conditions and at an anionic surface/liquid interface. While the rate of formation of specific aggregates was altered by mutations in Aβ under free solution conditions, the respective aggregate morphologies were similar. However, aggregation occurring directly on a negatively charged mica surface resulted in distinct aggregate morphologies formed by different mutant forms of Aβ. These studies provide insight into the potential role anionic surfaces play in dictating the formation of Aβ polymorphic aggregate structures.
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Affiliation(s)
- Elizabeth A. Yates
- The C. Eugene Bennett Department of Chemistry, ‡WVnano Initiative, §the Center for Neurosciences, West Virginia University, 217 Clark Hall, P.O. Box 6045, Morgantown, West Virginia 26506, United States
| | - Elena M. Cucco
- The C. Eugene Bennett Department of Chemistry, ‡WVnano Initiative, §the Center for Neurosciences, West Virginia University, 217 Clark Hall, P.O. Box 6045, Morgantown, West Virginia 26506, United States
| | - Justin Legleiter
- The C. Eugene Bennett Department of Chemistry, ‡WVnano Initiative, §the Center for Neurosciences, West Virginia University, 217 Clark Hall, P.O. Box 6045, Morgantown, West Virginia 26506, United States
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25
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Scheidt HA, Morgado I, Rothemund S, Huster D, Fändrich M. Solid‐State NMR Spectroscopic Investigation of Aβ Protofibrils: Implication of a β‐Sheet Remodeling upon Maturation into Terminal Amyloid Fibrils. Angew Chem Int Ed Engl 2011; 50:2837-40. [DOI: 10.1002/anie.201007265] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Indexed: 11/06/2022]
Affiliation(s)
- Holger A. Scheidt
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstrasse 16–18, 04107 Leipzig (Germany)
- Institute of Biochemistry and Biotechnology, Martin‐Luther University Halle‐Wittenberg (MLU) (Germany)
| | - Isabel Morgado
- Institute of Biochemistry and Biotechnology, Martin‐Luther University Halle‐Wittenberg (MLU) (Germany)
| | - Sven Rothemund
- Interdisciplinary Center for Clinical Research, University of Leipzig (Germany)
| | - Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstrasse 16–18, 04107 Leipzig (Germany)
| | - Marcus Fändrich
- Max‐Planck Research Unit for Enzymology of Protein Folding and MLU, Weinbergweg 22, 06120 Halle (Germany)
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26
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Scheidt HA, Morgado I, Rothemund S, Huster D, Fändrich M. Festkörper‐NMR‐spektroskopische Untersuchungen an Aβ‐Protofibrillen: Nachweis einer Umgestaltung der β‐Faltblätter bei der Ausreifung von Amyloidfibrillen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007265] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Holger A. Scheidt
- Institut für Medizinische Physik und Biophysik, Universität Leipzig, Härtelstraße 16–18, 04107 Leipzig (Deutschland)
- Institut für Biochemie und Biotechnologie, Martin‐Luther Universität Halle‐Wittenberg (Deutschland)
| | - Isabel Morgado
- Institut für Biochemie und Biotechnologie, Martin‐Luther Universität Halle‐Wittenberg (Deutschland)
| | - Sven Rothemund
- Interdisziplinäres Zentrum für Klinische Forschung, Universität Leipzig (Deutschland)
| | - Daniel Huster
- Institut für Medizinische Physik und Biophysik, Universität Leipzig, Härtelstraße 16–18, 04107 Leipzig (Deutschland)
| | - Marcus Fändrich
- Max‐Planck‐Forschungsstelle für Enzymologie der Proteinfaltung und MLU, Weinbergweg 22, 06120 Halle (Deutschland)
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27
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Micelle-like architecture of the monomer ensemble of Alzheimer's amyloid-β peptide in aqueous solution and its implications for Aβ aggregation. J Mol Biol 2010; 403:148-165. [PMID: 20709081 DOI: 10.1016/j.jmb.2010.08.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 07/27/2010] [Accepted: 08/02/2010] [Indexed: 01/05/2023]
Abstract
Aggregation of amyloid-β (Aβ) peptide, a 39- to 43-residue fragment of the amyloid precursor protein, is associated with Alzheimer's disease, the most common form of dementia in the elderly population. Several experimental studies have tried to characterize the atomic details of amyloid fibrils, which are the final product of Aβ aggregation. Much less is known about species forming during the early stages of aggregation, in particular about the monomeric state of the Aβ peptide that may be viewed as the product of the very first step in the hypothesized amyloid cascade. Here, the equilibrium ensembles of monomeric Aβ alloforms Aβ(1-40) and Aβ(1-42) are investigated by Monte Carlo simulations using an atomistic force field and implicit solvent model that have been shown previously to correctly reproduce the ensemble properties of other intrinsically disordered polypeptides. Our simulation results indicate that at physiological temperatures, both alloforms of Aβ assume a largely collapsed globular structure. Conformations feature a fluid hydrophobic core formed, on average, by contacts both within and between the two segments comprising residues 12-21 and 24-40/42, respectively. Furthermore, the 11 N-terminal residues are completely unstructured, and all charged side chains, in particular those of Glu22 and Asp23, remain exposed to solvent. Taken together, these observations indicate a micelle-like† architecture at the monomer level whose implications for oligomerization, as well as fibril formation and elongation, are discussed. We establish quantitatively the intrinsic disorder of Aβ and find the propensity to form regular secondary structure to be low but sequence specific. In the presence of a global and unspecific bias for backbone conformations to populate the β-basin, the β-sheet propensity along the sequence is consistent with the arrangement of the monomer within the fibril, as derived from solid-state NMR data. These observations indicate that the primary sequence partially encodes fibril structure, but that fibril elongation must be thought of as a templated assembly step.
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28
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Blinov N, Dorosh L, Wishart D, Kovalenko A. Association thermodynamics and conformational stability of beta-sheet amyloid beta(17-42) oligomers: effects of E22Q (Dutch) mutation and charge neutralization. Biophys J 2010; 98:282-96. [PMID: 20338850 DOI: 10.1016/j.bpj.2009.09.062] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Revised: 09/16/2009] [Accepted: 09/17/2009] [Indexed: 12/21/2022] Open
Abstract
Amyloid fibrils are associated with many neurodegenerative diseases. It was found that amyloidogenic oligomers, not mature fibrils, are neurotoxic agents related to these diseases. Molecular mechanisms of infectivity, pathways of aggregation, and molecular structure of these oligomers remain elusive. Here, we use all-atom molecular dynamics, molecular mechanics combined with solvation analysis by statistical-mechanical, three-dimensional molecular theory of solvation (also known as 3D-RISM-KH) in a new MM-3D-RISM-KH method to study conformational stability, and association thermodynamics of small wild-type Abeta(17-42) oligomers with different protonation states of Glu(22), as well the E22Q (Dutch) mutants. The association free energy of small beta-sheet oligomers shows near-linear trend with the dimers being thermodynamically more stable relative to the larger constructs. The linear (within statistical uncertainty) dependence of the association free energy on complex size is a consequence of the unilateral stacking of monomers in the beta-sheet oligomers. The charge reduction of the wild-type Abeta(17-42) oligomers upon protonation of the solvent-exposed Glu(22) at acidic conditions results in lowering the association free energy compared to the wild-type oligomers at neutral pH and the E22Q mutants. The neutralization of the peptides because of the E22Q mutation only marginally affects the association free energy, with the reduction of the direct electrostatic interactions mostly compensated by the unfavorable electrostatic solvation effects. For the wild-type oligomers at acidic conditions such compensation is not complete, and the electrostatic interactions, along with the gas-phase nonpolar energetic and the overall entropic effects, contribute to the lowering of the association free energy. The differences in the association thermodynamics between the wild-type Abeta(17-42) oligomers at neutral pH and the Dutch mutants, on the one hand, and the Abeta(17-42) oligomers with protonated Glu(22), on the other, may be explained by destabilization of the inter- and intrapeptide salt bridges between Asp(23) and Lys(28). Peculiarities in the conformational stability and the association thermodynamics for the different models of the Abeta(17-42) oligomers are rationalized based on the analysis of the local physical interactions and the microscopic solvation structure.
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Affiliation(s)
- Nikolay Blinov
- National Institute for Nanotechnology, National Research Council of Canada, Edmonton, Alberta, Canada
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29
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Role of small oligomers on the amyloidogenic aggregation free-energy landscape. J Mol Biol 2009; 395:134-54. [PMID: 19837085 DOI: 10.1016/j.jmb.2009.10.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 10/07/2009] [Accepted: 10/12/2009] [Indexed: 11/20/2022]
Abstract
We combine atomic-force-microscopy particle-size-distribution measurements with earlier measurements on 1-anilino-8-naphthalene sulfonate, thioflavin T, and dynamic light scattering to develop a quantitative kinetic model for the aggregation of beta-lactoglobulin into amyloid. We directly compare our simulations to the population distributions provided by dynamic light scattering and atomic force microscopy. We combine species in the simulation according to structural type for comparison with fluorescence fingerprint results. The kinetic model of amyloidogenesis leads to an aggregation free-energy landscape. We define the roles of and propose a classification scheme for different oligomeric species based on their location in the aggregation free-energy landscape. We relate the different types of oligomers to the amyloid cascade hypothesis and the toxic oligomer hypothesis for amyloid-related diseases. We discuss existing kinetic mechanisms in terms of the different types of oligomers. We provide a possible resolution to the toxic oligomer-amyloid coincidence.
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30
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Takeda T, Klimov DK. Side chain interactions can impede amyloid fibril growth: replica exchange simulations of Abeta peptide mutant. J Phys Chem B 2009; 113:11848-57. [PMID: 19708712 PMCID: PMC2765228 DOI: 10.1021/jp904070w] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Using replica exchange molecular dynamics, we study the effect of Asp23Tyr mutation on Abeta(10-40) fibril growth. The effect of this mutation is revealed through the computation of free energy landscapes, the distributions of peptide-fibril interactions, and by comparison with the wild-type Abeta(10-40) peptide. Asp23Tyr mutation has a relatively minor influence on the docking of Abeta peptides to the fibril. However, it has a strong impact on the locking stage due to profound stabilization of the parallel in-registry beta-sheets formed by the peptides on the fibril edge. The enhanced stability of parallel beta-sheets results from the deletion of side chain interactions formed by Asp23, which are incompatible with the fibril-like conformers. Consequently, Asp23Tyr mutation is expected to promote fibril growth. We argue that strong off-registry side chain interactions may slow down fibril assembly as it occurs for the wild-type Abeta peptide. The analysis of experimental data offers support to our in silico conclusions.
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Affiliation(s)
- Takako Takeda
- Department of Bioinformatics and Computational Biology, George Mason University, Manassas, VA 20110
| | - Dmitri K. Klimov
- Department of Bioinformatics and Computational Biology, George Mason University, Manassas, VA 20110
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31
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Takeda T, Klimov DK. Probing energetics of Abeta fibril elongation by molecular dynamics simulations. Biophys J 2009; 96:4428-37. [PMID: 19486667 DOI: 10.1016/j.bpj.2009.03.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Revised: 02/23/2009] [Accepted: 03/03/2009] [Indexed: 11/30/2022] Open
Abstract
Using replica exchange molecular dynamics simulations and an all-atom implicit solvent model, we probed the energetics of Abeta(10-40) fibril growth. The analysis of the interactions between incoming Abeta peptides and the fibril led us to two conclusions. First, considerable variations in fibril binding propensities are observed along the Abeta sequence. The peptides in the fibril and those binding to its edge interact primarily through their N-termini. Therefore, the mutations affecting the Abeta positions 10-23 are expected to have the largest impact on fibril elongation compared with those occurring in the C-terminus and turn. Second, we performed weak perturbations of the binding free energy landscape by scanning partial deletions of side-chain interactions at various Abeta sequence positions. The results imply that strong side-chain interactions--in particular, hydrophobic contacts--impede fibril growth by favoring disordered docking of incoming peptides. Therefore, fibril elongation may be promoted by moderate reduction of Abeta hydrophobicity. The comparison with available experimental data is presented.
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Affiliation(s)
- Takako Takeda
- Department of Bioinformatics and Computational Biology, George Mason University, Manassas, Virginia, USA
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Takeda T, Klimov DK. Probing the effect of amino-terminal truncation for Abeta1-40 peptides. J Phys Chem B 2009; 113:6692-702. [PMID: 19419218 DOI: 10.1021/jp9016773] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We examine the effect of deletion of the amino-terminal (residues 1-9) on the structure and energetics of Abeta1-40 peptides. To this end, we use replica exchange molecular dynamics to compare the conformational ensembles of Abeta1-40 and amino-truncated Abeta10-40 monomers and dimers. Overall, the deletion of the amino-terminal appears to cause minor structural and energetic changes in Abeta monomers and dimers. More specifically, our findings are as follows: (1) there is a small but discernible conversion of beta-strand structure into helix upon amino-terminal deletion, (2) secondary structure changes due to truncation are caused by missing side chain interactions formed by the amino-terminal, and (3) the amino-terminal together with the central sequence region (residues 10-23) represents the primary aggregation interface in Abeta1-40 dimers. The amino-truncated Abeta10-40 retains this aggregation interface, which is reduced to the central sequence region. We argue that the analysis of available experimental data supports our conclusions. Our findings also suggest that amino-truncated Abeta10-40 peptide is an adequate model for studying Abeta1-40 aggregation.
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Affiliation(s)
- Takako Takeda
- Department of Bioinformatics and Computational Biology, George Mason University, Manassas, Virginia 20110, USA
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33
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Langkilde AE, Vestergaard B. Methods for structural characterization of prefibrillar intermediates and amyloid fibrils. FEBS Lett 2009; 583:2600-9. [PMID: 19481541 DOI: 10.1016/j.febslet.2009.05.040] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 05/20/2009] [Accepted: 05/22/2009] [Indexed: 11/15/2022]
Abstract
Protein fibrillation is first and foremost a structural phenomenon. Adequate structural investigation of the central conformational individuals of the fibrillation process is however exceedingly difficult. This is due to the nature of the process, which may be described as a dynamically evolving equilibrium between a large number of structural species. These are furthermore of highly diverging sizes and present in very uneven amounts and timeframes. Different structural methods have different strengths and limitations. These, and in particular recent advances within solution analysis of the undisturbed equilibrium using small angle X-ray scattering, are reviewed here.
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Affiliation(s)
- Annette Eva Langkilde
- Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Copenhagen, Denmark
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35
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Di Fede G, Catania M, Morbin M, Rossi G, Suardi S, Mazzoleni G, Merlin M, Giovagnoli AR, Prioni S, Erbetta A, Falcone C, Gobbi M, Colombo L, Bastone A, Beeg M, Manzoni C, Francescucci B, Spagnoli A, Cantù L, Del Favero E, Levy E, Salmona M, Tagliavini F. A recessive mutation in the APP gene with dominant-negative effect on amyloidogenesis. Science 2009; 323:1473-7. [PMID: 19286555 PMCID: PMC2728497 DOI: 10.1126/science.1168979] [Citation(s) in RCA: 308] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
beta-Amyloid precursor protein (APP) mutations cause familial Alzheimer's disease with nearly complete penetrance. We found an APP mutation [alanine-673-->valine-673 (A673V)] that causes disease only in the homozygous state, whereas heterozygous carriers were unaffected, consistent with a recessive Mendelian trait of inheritance. The A673V mutation affected APP processing, resulting in enhanced beta-amyloid (Abeta) production and formation of amyloid fibrils in vitro. Co-incubation of mutated and wild-type peptides conferred instability on Abeta aggregates and inhibited amyloidogenesis and neurotoxicity. The highly amyloidogenic effect of the A673V mutation in the homozygous state and its anti-amyloidogenic effect in the heterozygous state account for the autosomal recessive pattern of inheritance and have implications for genetic screening and the potential treatment of Alzheimer's disease.
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Affiliation(s)
- Giuseppe Di Fede
- Division of Neurology and Neuropathology, “Carlo Besta” National Neurological Institute, 20133 Milan, Italy
| | - Marcella Catania
- Division of Neurology and Neuropathology, “Carlo Besta” National Neurological Institute, 20133 Milan, Italy
| | - Michela Morbin
- Division of Neurology and Neuropathology, “Carlo Besta” National Neurological Institute, 20133 Milan, Italy
| | - Giacomina Rossi
- Division of Neurology and Neuropathology, “Carlo Besta” National Neurological Institute, 20133 Milan, Italy
| | - Silvia Suardi
- Division of Neurology and Neuropathology, “Carlo Besta” National Neurological Institute, 20133 Milan, Italy
| | - Giulia Mazzoleni
- Division of Neurology and Neuropathology, “Carlo Besta” National Neurological Institute, 20133 Milan, Italy
| | - Marco Merlin
- Division of Neurology and Neuropathology, “Carlo Besta” National Neurological Institute, 20133 Milan, Italy
| | - Anna Rita Giovagnoli
- Division of Neurology and Neuropathology, “Carlo Besta” National Neurological Institute, 20133 Milan, Italy
| | - Sara Prioni
- Division of Neurology and Neuropathology, “Carlo Besta” National Neurological Institute, 20133 Milan, Italy
| | - Alessandra Erbetta
- Division of Neuroradiology, “Carlo Besta” National Neurological Institute, 20133 Milan, Italy
| | - Chiara Falcone
- Division of Neuroepidemiology, “Carlo Besta” National Neurological Institute, 20133 Milan, Italy
| | - Marco Gobbi
- Department of Molecular Biochemistry and Pharmachology, Istituto di Ricerche Farmacologiche “Mario Negri,” 20156 Milan, Italy
| | - Laura Colombo
- Department of Molecular Biochemistry and Pharmachology, Istituto di Ricerche Farmacologiche “Mario Negri,” 20156 Milan, Italy
| | - Antonio Bastone
- Department of Molecular Biochemistry and Pharmachology, Istituto di Ricerche Farmacologiche “Mario Negri,” 20156 Milan, Italy
| | - Marten Beeg
- Department of Molecular Biochemistry and Pharmachology, Istituto di Ricerche Farmacologiche “Mario Negri,” 20156 Milan, Italy
| | - Claudia Manzoni
- Department of Molecular Biochemistry and Pharmachology, Istituto di Ricerche Farmacologiche “Mario Negri,” 20156 Milan, Italy
| | - Bruna Francescucci
- Division of Cognitive Disorders, Centro Sant’Ambrogio Fatebenefratelli, Cernusco sul Naviglio, 20063 Milan, Italy
| | - Alberto Spagnoli
- Division of Cognitive Disorders, Centro Sant’Ambrogio Fatebenefratelli, Cernusco sul Naviglio, 20063 Milan, Italy
| | - Laura Cantù
- Department of Medical Chemistry, Biochemistry, and Biotechnology, University of Milan, Segrate, 20090 Milan, Italy
| | - Elena Del Favero
- Department of Medical Chemistry, Biochemistry, and Biotechnology, University of Milan, Segrate, 20090 Milan, Italy
| | - Efrat Levy
- Departments of Pharmacology and Psychiatry, New York University School of Medicine, and Nathan S. Kline Institute, Orangeburg, NY 10962, USA
| | - Mario Salmona
- Department of Molecular Biochemistry and Pharmachology, Istituto di Ricerche Farmacologiche “Mario Negri,” 20156 Milan, Italy
| | - Fabrizio Tagliavini
- Division of Neurology and Neuropathology, “Carlo Besta” National Neurological Institute, 20133 Milan, Italy
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36
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Clarke OJ, Parker MJ. Identification of amyloidogenic peptide sequences using a coarse-grained physicochemical model. J Comput Chem 2009; 30:621-30. [PMID: 18711722 DOI: 10.1002/jcc.21085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cross-beta amyloid is implicated in over 20 human diseases. Experiments suggest that specific sequence elements within amyloidogenic proteins play a major role in seeding amyloid formation. Identifying these seeding sequences is important for rationalizing the molecular mechanisms of amyloid formation and for elaborating therapeutic strategies that target amyloid. Theoretical techniques play an important role in facilitating the identification and structural characterization of putative seeding sequences; most amyloid species are not amenable to high resolution experimental structure techniques. In this study we have combined a coarse-grained physicochemical protein model with a highly efficient Monte Carlo sampling technique to identify amyloidogenic sequences in four proteins for which respective experimental peptide fragmentation data exist. Peptide sequences were defined as amyloidogenic if the ensemble structure predicted for three interacting peptides described a stable and regular three-stranded beta-sheet. For such peptides, free energies were calculated to provide a measure of amyloid propensity. The overall agreement between the experimental and predicted data is good, and we correctly identify several self-recognition motifs proposed to define the cross-beta amyloid fibril architectures of two of the proteins. Our results compare very favorably with those obtained using atomistic molecular dynamics methods, though our simulations are 30-40 times faster.
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Affiliation(s)
- Oliver J Clarke
- Institute of Molecular and Cellular Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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37
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Macao B, Hoyer W, Sandberg A, Brorsson AC, Dobson CM, Härd T. Recombinant amyloid beta-peptide production by coexpression with an affibody ligand. BMC Biotechnol 2008; 8:82. [PMID: 18973685 PMCID: PMC2606684 DOI: 10.1186/1472-6750-8-82] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Accepted: 10/30/2008] [Indexed: 12/02/2022] Open
Abstract
Background Oligomeric and fibrillar aggregates of the amyloid β-peptide (Aβ) have been implicated in the pathogenesis of Alzheimer's disease (AD). The characterization of Aβ assemblies is essential for the elucidation of the mechanisms of Aβ neurotoxicity, but requires large quantities of pure peptide. Here we describe a novel approach to the recombinant production of Aβ. The method is based on the coexpression of the affibody protein ZAβ3, a selected affinity ligand derived from the Z domain three-helix bundle scaffold. ZAβ3 binds to the amyloidogenic central and C-terminal part of Aβ with nanomolar affinity and consequently inhibits aggregation. Results Coexpression of ZAβ3 affords the overexpression of both major Aβ isoforms, Aβ(1–40) and Aβ(1–42), yielding 4 or 3 mg, respectively, of pure 15N-labeled peptide per liter of culture. The method does not rely on a protein-fusion or -tag and thus does not require a cleavage reaction. The purified peptides were characterized by NMR, circular dichroism, SDS-PAGE and size exclusion chromatography, and their aggregation propensities were assessed by thioflavin T fluorescence and electron microscopy. The data coincide with those reported previously for monomeric, largely unstructured Aβ. ZAβ3 coexpression moreover permits the recombinant production of Aβ(1–42) carrying the Arctic (E22G) mutation, which causes early onset familial AD. Aβ(1–42)E22G is obtained in predominantly monomeric form and suitable, e.g., for NMR studies. Conclusion The coexpression of an engineered aggregation-inhibiting binding protein offers a novel route to the recombinant production of amyloidogenic Aβ peptides that can be advantageously employed to study the molecular basis of AD. The presented expression system is the first for which expression and purification of the aggregation-prone Arctic variant (E22G) of Aβ(1–42) is reported.
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Affiliation(s)
- Bertil Macao
- Department of Medical Biochemistry, University of Gothenburg, Göeborg, Sweden.
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38
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Vendruscolo M, Tartaglia GG. Towards quantitative predictions in cell biology using chemical properties of proteins. MOLECULAR BIOSYSTEMS 2008; 4:1170-5. [PMID: 19396379 DOI: 10.1039/b805710a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It has recently been suggested that the concentrations of proteins in the cell are tuned towards their critical values, and that the alteration of this balance often results in misfolding diseases. This concept is intriguing because the in vivo concentrations of proteins are closely regulated by complex cellular processes, while their critical concentrations are primarily determined by the chemical characters of their amino acid sequences. We discuss here how the presence of a link between the upper levels of in vivo concentrations and critical concentrations offers an opportunity to make quantitative predictions in cell biology based on the chemical properties of proteins.
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Affiliation(s)
- Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB21EW, UK
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39
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Hydration effects on the HET-s prion and amyloid-beta fibrillous aggregates, studied with three-dimensional molecular theory of solvation. Biophys J 2008; 95:4540-8. [PMID: 18689456 DOI: 10.1529/biophysj.107.123000] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We study the thermodynamic properties of the experimental fragments of the amyloid fibril made of the HET-s prion proteins (the infectious element of the filamentous fungus Podospora anserina) and of amyloid-beta proteins (the major component of Alzheimer's disease-associated plaques) by using the three-dimensional molecular theory of solvation. The full quantitative picture of hydration effects, including the hydration thermodynamics and hydration structure around the fragments, is presented. For both the complexes, the hydration entropic effects dominate, which results in the entropic part offsetting the unfavorable energetic part of the free energy change upon the association. This is in accord with the fact that the hydrophobic cooperativity plays an essential role in the formation of amyloid fibrils. By calculating the partial molar volume of the proteins, we found that the volume change upon the association in both the systems is large and positive, with the implication that high pressure causes destabilization of the fibril. This observation is in good agreement with the recent experimental results. We also found that both the HET-s and amyloid-beta pentamers have loose intermolecular packing with voids. The three-dimensional molecular theory of solvation predicts that water molecules can be locked in the interior cavities along the fibril axis for both the HET-s and amyloid-beta proteins. We provide a detailed molecular picture of the structural water localized in the interior of the fibrils. Our results suggest that the interior hydration plays an important role in the structural stability of fibrils.
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40
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Tartaglia GG, Pawar AP, Campioni S, Dobson CM, Chiti F, Vendruscolo M. Prediction of Aggregation-Prone Regions in Structured Proteins. J Mol Biol 2008; 380:425-36. [DOI: 10.1016/j.jmb.2008.05.013] [Citation(s) in RCA: 378] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Revised: 05/02/2008] [Accepted: 05/08/2008] [Indexed: 11/17/2022]
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41
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Zheng J, Ma B, Chang Y, Nussinov R. Molecular dynamics simulations of Alzheimer Abeta40 elongation and lateral association. FRONT BIOSCI-LANDMRK 2008; 13:3919-30. [PMID: 18508486 DOI: 10.2741/2980] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Amyloid-beta (Abeta) peptides can elongate in the fibril axis and associate in the lateral direction. We present detailed atomic Abeta models with different in-register intermolecular beta-sheet-beta-sheet associations. We probe structural stability, conformational dynamics, and association force of Abeta oligomers with various sizes and structures for both wild-type and mutated sequences using molecular dynamics (MD) simulations. MD simulations show that an Abeta oligomer that is laterally associated through the C-terminal-C-terminal interface is energetically more favorable than other oligomers with the N-terminal-N-terminal and C-terminal-N-terminal interfaces. We further develop a simple numerical model to describe the kinetics of Abeta aggregation process by considering fibril elongation and lateral association using a Monte Carlo algorithm. Kinetic data suggest that fibril elongation and lateral association are mutually competitive. Single-point mutations of Glu22 or Met35 at the interfaces have profound negative effects on intermolecular beta-sheet-beta-sheet association. These disease-related mutants (E22K, E22Q, and M35O) display more flexible structures, weaker lateral association, and stronger elongation tendencies than the wild type, suggesting that amyloid oligomerization and neurotoxicity might be linked to fibril longitudinal growth.
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Affiliation(s)
- Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA.
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42
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Monitoring fibril formation of the N-terminal domain of PABPN1 carrying an alanine repeat by tryptophan fluorescence and real-time NMR. FEBS Lett 2008; 582:1587-92. [PMID: 18406354 DOI: 10.1016/j.febslet.2008.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Revised: 04/02/2008] [Accepted: 04/02/2008] [Indexed: 11/21/2022]
Abstract
Intranuclear fibrils due to poly-alanine expansions in the N-terminal domain of the poly(A) binding protein PABPN1 correlate with the disease oculopharyngeal muscular dystrophy (OPMD). For monitoring fibril formation by fluorescence and real-time NMR spectroscopy, tryptophans were introduced either into the middle or C-terminal of the poly-alanine segment. The kinetics of fibril formation which were monitored by fluorescence spectroscopy were matched by real-time NMR kinetics. Our results show that fibril formation is concomitant with the burial of the tryptophans in the fibrillar core. Since no soluble pre-fibrillar intermediate(s) was detected, fibril formation of this domain may be regarded as a two state conversion from an unfolded soluble into folded insoluble species.
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43
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Luheshi LM, Crowther DC, Dobson CM. Protein misfolding and disease: from the test tube to the organism. Curr Opin Chem Biol 2008; 12:25-31. [DOI: 10.1016/j.cbpa.2008.02.011] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2008] [Revised: 02/06/2008] [Accepted: 02/06/2008] [Indexed: 10/22/2022]
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44
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Garai K, Sahoo B, Sengupta P, Maiti S. Quasihomogeneous nucleation of amyloid beta yields numerical bounds for the critical radius, the surface tension, and the free energy barrier for nucleus formation. J Chem Phys 2008; 128:045102. [DOI: 10.1063/1.2822322] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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45
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Bradford VJ, Iverson BL. Amyloid-like Behavior in Abiotic, Amphiphilic Foldamers. J Am Chem Soc 2008; 130:1517-24. [DOI: 10.1021/ja0780840] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Valerie J. Bradford
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Texas 78712
| | - Brent L. Iverson
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Texas 78712
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46
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Tartaglia GG, Vendruscolo M. The Zyggregator method for predicting protein aggregation propensities. Chem Soc Rev 2008; 37:1395-401. [DOI: 10.1039/b706784b] [Citation(s) in RCA: 267] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Gaggelli E, Janicka-Klos A, Jankowska E, Kozlowski H, Migliorini C, Molteni E, Valensin D, Valensin G, Wieczerzak E. NMR studies of the Zn2+ interactions with rat and human beta-amyloid (1-28) peptides in water-micelle environment. J Phys Chem B 2007; 112:100-9. [PMID: 18072760 DOI: 10.1021/jp075168m] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alzheimer's disease is a fatal neurodegenerative disorder involving the abnormal accumulation and deposition of peptides (amyloid-beta, Abeta) derived from the amyloid precursor protein. Here, we present the structure and the Zn2+ binding sites of human and rat Abeta(1-28) fragments in water/sodium dodecyl sulfate (SDS) micelles by using 1H NMR spectroscopy. The chemical shift variations measured after Zn2+ addition at T>310 K allowed us to assign the binding donor atoms in both rat and human zinc complexes. The Asp-1 amine, His-6 Ndelta, Glu-11 COO-, and His-13 Nepsilon of rat Abeta28 all enter the metal coordination sphere, while His-6 Ndelta, His-13, His-14 Nepsilon, Asp-1 amine, and/or Glu-11 COO- are all bound to Zn2+ in the case of human Abeta28. Finally, a comparison between the rat and human binding abilities was discussed.
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Affiliation(s)
- Elena Gaggelli
- Department of Chemistry, University of Siena, via Aldo Moro, 53-100 Siena, Italy
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48
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Protofibril assemblies of the arctic, Dutch, and Flemish mutants of the Alzheimer's Abeta1-40 peptide. Biophys J 2007; 94:2007-16. [PMID: 18032553 DOI: 10.1529/biophysj.107.121467] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Using a coarse-grained model of the Abeta peptide, we analyze the Arctic (E22G), Dutch (E22Q), and Flemish (A21G) familial Alzheimer's disease (FAD) mutants for any changes in the stability of amyloid assemblies with respect to the wild-type (WT) sequence. Based on a structural reference state of two protofilaments aligned to create the "agitated" protofibril as determined by solid-state NMR, we determine free energy trends for Abeta assemblies for the WT and FAD familial sequences. We find that the structural characteristics and oligomer size of the critical nucleus vary dramatically among the hereditary mutants. The Arctic mutant's disorder in the turn region introduces new stabilizing interactions that better align the two protofilaments, yielding a well-defined protofibril axis at relatively small oligomer sizes with respect to WT. By contrast, the critical nucleus for the Flemish mutant is beyond the 20 chains characterized in this study, thereby showing a strong shift in the equilibrium toward monomers with respect to larger protofibril assemblies. The Dutch mutant forms more ordered protofilaments than WT, but exhibits greater disorder in protofibril structure that includes an alternative polymorph of the WT fibril. An important conclusion of this work is that the Dutch mutant does not support the agitated protofibril assembly. We discuss the implications of the structural ensembles and free energy profiles for the FAD mutants in regards to interpretation of the kinetics of fibril assembly using chromatography and dye-binding experiments.
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49
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Klement K, Wieligmann K, Meinhardt J, Hortschansky P, Richter W, Fändrich M. Effect of Different Salt Ions on the Propensity of Aggregation and on the Structure of Alzheimer’s Aβ(1-40) Amyloid Fibrils. J Mol Biol 2007; 373:1321-33. [PMID: 17905305 DOI: 10.1016/j.jmb.2007.08.068] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Revised: 08/21/2007] [Accepted: 08/31/2007] [Indexed: 10/22/2022]
Abstract
The formation of amyloid fibrils and other polypeptide aggregates depends strongly on the physico-chemical environment. One such factor affecting aggregation is the presence and concentration of salt ions. We have examined the effects of salt ions on the aggregation propensity of Alzheimer's Abeta(1-40) peptide and on the structure of the dissolved and of the fibrillar peptide. All salts examined promote aggregation strongly. The most pronounced effect is seen within the cationic series, i.e. for MgCl2. Evaluation of different possible explanations suggests that Abeta(1-40) aggregation depends on direct interaction between ions and Abeta(1-40) peptide, and correlates with ion-induced changes of the surface tension. Salts have profound effects on the fibril structure. In the presence of salts, fibrils are associated with smaller diameters, narrower crossover distances and lower amide I maxima. Since Abeta(1-40) aggregation responds to salts in a manner unlike that for other polypeptides, such as glucagon, beta2-microglobulin or alpha-synuclein; these data argue that there is no fully uniform way in which salts affect aggregation of different polypeptide chains. These observations are important for understanding and predicting aggregation on the basis of simple physico-chemical properties.
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Affiliation(s)
- Karolin Klement
- Leibniz-Institut für Altersforschung, Beutenbergstrasse 11, D-07745 Jena, Germany
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