1
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Ruttenberg SM, Nowick JS. A turn for the worse: Aβ β-hairpins in Alzheimer's disease. Bioorg Med Chem 2024; 105:117715. [PMID: 38615460 DOI: 10.1016/j.bmc.2024.117715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/16/2024]
Abstract
Amyloid-β (Aβ) oligomers are a cause of neurodegeneration in Alzheimer's disease (AD). These soluble aggregates of the Aβ peptide have proven difficult to study due to their inherent metastability and heterogeneity. Strategies to isolate and stabilize homogenous Aβ oligomer populations have emerged such as mutations, covalent cross-linking, and protein fusions. These strategies along with molecular dynamics simulations have provided a variety of proposed structures of Aβ oligomers, many of which consist of molecules of Aβ in β-hairpin conformations. β-Hairpins are intramolecular antiparallel β-sheets composed of two β-strands connected by a loop or turn. Three decades of research suggests that Aβ peptides form several different β-hairpin conformations, some of which are building blocks of toxic Aβ oligomers. The insights from these studies are currently being used to design anti-Aβ antibodies and vaccines to treat AD. Research suggests that antibody therapies designed to target oligomeric Aβ may be more successful at treating AD than antibodies designed to target linear epitopes of Aβ or fibrillar Aβ. Aβ β-hairpins are good epitopes to use in antibody development to selectively target oligomeric Aβ. This review summarizes the research on β-hairpins in Aβ peptides and discusses the relevance of this conformation in AD pathogenesis and drug development.
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Affiliation(s)
- Sarah M Ruttenberg
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, United States
| | - James S Nowick
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, United States.
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2
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Devaurs D, Antunes DA, Borysik AJ. Computational Modeling of Molecular Structures Guided by Hydrogen-Exchange Data. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:215-237. [PMID: 35077179 DOI: 10.1021/jasms.1c00328] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Data produced by hydrogen-exchange monitoring experiments have been used in structural studies of molecules for several decades. Despite uncertainties about the structural determinants of hydrogen exchange itself, such data have successfully helped guide the structural modeling of challenging molecular systems, such as membrane proteins or large macromolecular complexes. As hydrogen-exchange monitoring provides information on the dynamics of molecules in solution, it can complement other experimental techniques in so-called integrative modeling approaches. However, hydrogen-exchange data have often only been used to qualitatively assess molecular structures produced by computational modeling tools. In this paper, we look beyond qualitative approaches and survey the various paradigms under which hydrogen-exchange data have been used to quantitatively guide the computational modeling of molecular structures. Although numerous prediction models have been proposed to link molecular structure and hydrogen exchange, none of them has been widely accepted by the structural biology community. Here, we present as many hydrogen-exchange prediction models as we could find in the literature, with the aim of providing the first exhaustive list of its kind. From purely structure-based models to so-called fractional-population models or knowledge-based models, the field is quite vast. We aspire for this paper to become a resource for practitioners to gain a broader perspective on the field and guide research toward the definition of better prediction models. This will eventually improve synergies between hydrogen-exchange monitoring and molecular modeling.
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Affiliation(s)
- Didier Devaurs
- MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, U.K
| | - Dinler A Antunes
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77005, United States
| | - Antoni J Borysik
- Department of Chemistry, King's College London, London SE1 1DB, U.K
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3
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Zhdanova PV, Ishchenko AA, Chernonosov AA, Zharkov DO, Koval VV. Dynamics and Conformational Changes in Human NEIL2 DNA Glycosylase Analyzed by Hydrogen/Deuterium Exchange Mass Spectrometry. J Mol Biol 2021; 434:167334. [PMID: 34757057 DOI: 10.1016/j.jmb.2021.167334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/18/2021] [Accepted: 10/25/2021] [Indexed: 12/31/2022]
Abstract
Base excision DNA repair (BER) is necessary for removal of damaged nucleobases from the genome and their replacement with normal nucleobases. BER is initiated by DNA glycosylases, the enzymes that cleave the N-glycosidic bonds of damaged deoxynucleotides. Human endonuclease VIII-like protein 2 (hNEIL2), belonging to the helix-two-turn-helix structural superfamily of DNA glycosylases, is an enzyme uniquely specific for oxidized pyrimidines in non-canonical DNA substrates such as bubbles and loops. The structure of hNEIL2 has not been solved; its closest homologs with known structures are NEIL2 from opossum and from giant mimivirus. Here we analyze the conformational dynamics of free hNEIL2 using a combination of hydrogen/deuterium exchange mass spectrometry, homology modeling and molecular dynamics simulations. We show that a prominent feature of vertebrate NEIL2 - a large insert in its N-terminal domain absent from other DNA glycosylases - is unstructured in solution. It was suggested that helix-two-turn-helix DNA glycosylases undergo open-close transition upon DNA binding, with the large movement of their N- and C-terminal domains, but the open conformation has been elusive to capture. Our data point to the open conformation as favorable for free hNEIL2 in solution. Overall, our results are consistent with the view of hNEIL2 as a conformationally flexible protein, which may be due to its participation in the repair of non-canonical DNA structures and/or to the involvement in functional and regulatory protein-protein interactions.
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Affiliation(s)
- Polina V Zhdanova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibisk, Russia; Novosibirsk State University, Novosibisk, Russia
| | - Alexander A Ishchenko
- Groupe "Réparation de lADN", Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, Villejuif F-94805, France; Gustave Roussy, Université Paris-Saclay, Villejuif F-94805, France
| | | | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibisk, Russia; Novosibirsk State University, Novosibisk, Russia
| | - Vladimir V Koval
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibisk, Russia; Novosibirsk State University, Novosibisk, Russia.
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4
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Wong KM, Shao Q, Wang Y, Seroski DT, Liu R, Lint AH, Hudalla GA, Hall CK, Paravastu AK. CATCH Peptides Coassemble into Structurally Heterogeneous β-Sheet Nanofibers with Little Preference to β-Strand Alignment. J Phys Chem B 2021; 125:4004-4015. [PMID: 33876641 DOI: 10.1021/acs.jpcb.0c11645] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Coassembling peptides offer an additional degree of freedom in the design of nanostructured biomaterials when compared to analogous self-assembling peptides. Yet, our understanding of how amino acid sequences encodes coassembled nanofiber structure is limited. Prior work on a charge-complementary pair, CATCH+ and CATCH- peptides, detected like-peptide nearest neighbors (CATCH+:CATCH+ and CATCH-:CATCH-) within coassembled β-sheet nanofibers; these self-associated peptide pairs marked a departure from an "ideal" coassembled structure. In this work, we employ solid-state NMR, isotope-edited FTIR, and coarse-grained molecular dynamics simulations to evaluate the alignment of β-strands within CATCH peptide nanofibers. Both experimental and computational results suggest that CATCH molecules coassemble into structurally heterogeneous nanofibers, which is consistent with our observations in another coassembling system, the King-Webb peptides. Within β-sheet nanofibers, β-strands were found to have nearest neighbors aligned in-register parallel, in-register antiparallel, and out-of-register. In comparison to the King-Webb peptides, CATCH nanofibers exhibit a greater degree of structural heterogeneity. By comparing the amino acid sequences of CATCH and King-Webb peptides, we can begin to unravel sequence-to-structure relationships, which may encode more precise coassembled β-sheet nanostructures.
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Affiliation(s)
- Kong M Wong
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Qing Shao
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Dillon T Seroski
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, 1275 Center Drive, Biomedical Sciences J293, P.O. Box 116131, Gainesville, Florida 32611, United States
| | - Renjie Liu
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, 1275 Center Drive, Biomedical Sciences J293, P.O. Box 116131, Gainesville, Florida 32611, United States
| | - Annabelle H Lint
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Gregory A Hudalla
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, 1275 Center Drive, Biomedical Sciences J293, P.O. Box 116131, Gainesville, Florida 32611, United States
| | - Carol K Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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5
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Lee PS, Bradshaw RT, Marinelli F, Kihn K, Smith A, Wintrode PL, Deredge DJ, Faraldo-Gómez JD, Forrest LR. Interpreting Hydrogen-Deuterium Exchange Experiments with Molecular Simulations: Tutorials and Applications of the HDXer Ensemble Reweighting Software [Article v1.0]. LIVING JOURNAL OF COMPUTATIONAL MOLECULAR SCIENCE 2021; 3:1521. [PMID: 36644498 PMCID: PMC9835200 DOI: 10.33011/livecoms.3.1.1521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Hydrogen-deuterium exchange (HDX) is a comprehensive yet detailed probe of protein structure and dynamics and, coupled to mass spectrometry, has become a powerful tool for investigating an increasingly large array of systems. Computer simulations are often used to help rationalize experimental observations of exchange, but interpretations have frequently been limited to simple, subjective correlations between microscopic dynamical fluctuations and the observed macroscopic exchange behavior. With this in mind, we previously developed the HDX ensemble reweighting approach and associated software, HDXer, to aid the objective interpretation of HDX data using molecular simulations. HDXer has two main functions; first, to compute H-D exchange rates that describe each structure in a candidate ensemble of protein structures, for example from molecular simulations, and second, to objectively reweight the conformational populations present in a candidate ensemble to conform to experimental exchange data. In this article, we first describe the HDXer approach, theory, and implementation. We then guide users through a suite of tutorials that demonstrate the practical aspects of preparing experimental data, computing HDX levels from molecular simulations, and performing ensemble reweighting analyses. Finally we provide a practical discussion of the capabilities and limitations of the HDXer methods including recommendations for a user's own analyses. Overall, this article is intended to provide an up-to-date, pedagogical counterpart to the software, which is freely available at https://github.com/Lucy-Forrest-Lab/HDXer.
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Affiliation(s)
- Paul Suhwan Lee
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Richard T. Bradshaw
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA,For correspondence: (RTB); (LRF)
| | - Fabrizio Marinelli
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kyle Kihn
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - Ally Smith
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - Patrick L. Wintrode
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - Daniel J. Deredge
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - José D. Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lucy R. Forrest
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA,For correspondence: (RTB); (LRF)
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6
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Khorvash M, Blinov N, Ladner-Keay C, Lu J, Silverman JM, Gibbs E, Wang YT, Kovalenko A, Wishart D, Cashman NR. Molecular interactions between monoclonal oligomer-specific antibody 5E3 and its amyloid beta cognates. PLoS One 2020; 15:e0232266. [PMID: 32469918 PMCID: PMC7259632 DOI: 10.1371/journal.pone.0232266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 04/12/2020] [Indexed: 11/30/2022] Open
Abstract
Oligomeric amyloid β (Aβ) is currently considered the most neurotoxic form of the Aβ peptide implicated in Alzheimer’s disease (AD). The molecular structures of the oligomers have remained mostly unknown due to their transient nature. As a result, the molecular mechanisms of interactions between conformation-specific antibodies and their Aβ oligomer (AβO) cognates are not well understood. A monoclonal conformation-specific antibody, m5E3, was raised against a structural epitope of Aβ oligomers. m5E3 binds to AβOs with high affinity, but not to Aβ monomers or fibrils. In this study, a computational model of the variable fragment (Fv) of the m5E3 antibody (Fv5E3) is introduced. We further employ docking and molecular dynamics simulations to determine the molecular details of the antibody-oligomer interactions, and to classify the AβOs as Fv5E3-positives and negatives, and to provide a rationale for the low affinity of Fv5E3 for fibrils. This information will help us to perform site-directed mutagenesis on the m5E3 antibody to improve its specificity and affinity toward oligomeric Aβ species. We also provide evidence for the possible capability of the m5E3 antibody to disaggregate AβOs and to fragment protofilaments.
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Affiliation(s)
- Massih Khorvash
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, British Columbia, Canada
| | - Nick Blinov
- Department of Mechanical Engineering, Edmonton, Alberta, Canada
- National Research Council of Canada, Edmonton, Alberta, Canada
| | - Carol Ladner-Keay
- National Research Council of Canada, Edmonton, Alberta, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Jie Lu
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, British Columbia, Canada
| | - Judith M. Silverman
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, British Columbia, Canada
| | - Ebrima Gibbs
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, British Columbia, Canada
| | - Yu Tian Wang
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, British Columbia, Canada
| | - Andriy Kovalenko
- Department of Mechanical Engineering, Edmonton, Alberta, Canada
- National Research Council of Canada, Edmonton, Alberta, Canada
| | - David Wishart
- National Research Council of Canada, Edmonton, Alberta, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
| | - Neil R. Cashman
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, British Columbia, Canada
- * E-mail:
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7
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Bradshaw RT, Marinelli F, Faraldo-Gómez JD, Forrest LR. Interpretation of HDX Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles. Biophys J 2020; 118:1649-1664. [PMID: 32105651 PMCID: PMC7136279 DOI: 10.1016/j.bpj.2020.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/28/2020] [Accepted: 02/05/2020] [Indexed: 01/12/2023] Open
Abstract
Hydrogen-deuterium exchange combined with mass spectrometry (HDX-MS) is a widely applied biophysical technique that probes the structure and dynamics of biomolecules without the need for site-directed modifications or bio-orthogonal labels. The mechanistic interpretation of HDX data, however, is often qualitative and subjective, owing to a lack of quantitative methods to rigorously translate observed deuteration levels into atomistic structural information. To help address this problem, we have developed a methodology to generate structural ensembles that faithfully reproduce HDX-MS measurements. In this approach, an ensemble of protein conformations is first generated, typically using molecular dynamics simulations. A maximum-entropy bias is then applied post hoc to the resulting ensemble such that averaged peptide-deuteration levels, as predicted by an empirical model, agree with target values within a given level of uncertainty. We evaluate this approach, referred to as HDX ensemble reweighting (HDXer), for artificial target data reflecting the two major conformational states of a binding protein. We demonstrate that the information provided by HDX-MS experiments and by the model of exchange are sufficient to recover correctly weighted structural ensembles from simulations, even when the relevant conformations are rarely observed. Degrading the information content of the target data—e.g., by reducing sequence coverage, by averaging exchange levels over longer peptide segments, or by incorporating different sources of uncertainty—reduces the structural accuracy of the reweighted ensemble but still allows for useful insights into the distinctive structural features reflected by the target data. Finally, we describe a quantitative metric to rank candidate structural ensembles according to their correspondence with target data and illustrate the use of HDXer to describe changes in the conformational ensemble of the membrane protein LeuT. In summary, HDXer is designed to facilitate objective structural interpretations of HDX-MS data and to inform experimental approaches and further developments of theoretical exchange models.
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Affiliation(s)
- Richard T Bradshaw
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Fabrizio Marinelli
- Theoretical Molecular Biophysics Unit, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Unit, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland.
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland.
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8
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Wan H, Ge Y, Razavi A, Voelz VA. Reconciling Simulated Ensembles of Apomyoglobin with Experimental Hydrogen/Deuterium Exchange Data Using Bayesian Inference and Multiensemble Markov State Models. J Chem Theory Comput 2020; 16:1333-1348. [PMID: 31917926 DOI: 10.1021/acs.jctc.9b01240] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Hydrogen/deuterium exchange (HDX) is a powerful technique to investigate protein conformational dynamics at amino acid resolution. Because HDX provides a measurement of solvent exposure of backbone hydrogens, ensemble-averaged over potentially slow kinetic processes, it has been challenging to use HDX protection factors to refine structural ensembles obtained from molecular dynamics simulations. This entails dual challenges: (1) identifying structural observables that best correlate with backbone amide protection from exchange and (2) restraining these observables in molecular simulations to model ensembles consistent with experimental measurements. Here, we make significant progress on both fronts. First, we describe an improved predictor of HDX protection factors from structural observables in simulated ensembles, parametrized from ultralong molecular dynamics simulation trajectory data, with a Bayesian inference approach used to retain the full posterior distribution of model parameters. We next present a new method for obtaining simulated ensembles in agreement with experimental HDX protection factors, in which molecular simulations are performed at various temperatures and restraint biases and used to construct multiensemble Markov State Models (MSMs). Finally, the BICePs (Bayesian Inference of Conformational Populations) algorithm is then used with our HDX protection factor predictor to infer which thermodynamic ensemble agrees best with the experiment and estimate populations of each conformational state in the MSM. To illustrate the approach, we use a combination of HDX protection factor restraints and chemical shift restraints to model the conformational ensemble of apomyoglobin at pH 6. The resulting ensemble agrees well with the experiment and gives insight into the all-atom structure of disordered helices F and H in the absence of heme.
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Affiliation(s)
- Hongbin Wan
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Yunhui Ge
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Asghar Razavi
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Vincent A Voelz
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
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9
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Claesen J, Politis A. POPPeT: a New Method to Predict the Protection Factor of Backbone Amide Hydrogens. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:67-76. [PMID: 30338451 PMCID: PMC6318252 DOI: 10.1007/s13361-018-2068-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 08/13/2018] [Accepted: 08/28/2018] [Indexed: 05/29/2023]
Abstract
Hydrogen exchange (HX) has become an important tool to monitor protein structure and dynamics. The interpretation of HX data with respect to protein structure requires understanding of the factors that influence exchange. Simulated protein structures can be validated by comparing experimental deuteration profiles with the profiles derived from the modeled protein structure. To do this, we propose here a new method, POPPeT, for protection factor prediction based on protein motions that enable HX. By comparing POPPeT with two existing methods, the phenomenological approximation and COREX, we show enhanced predictability measured at both protection factor and deuteration level. This method can be subsequently used by modeling strategies for protein structure prediction. Graphical Abstract ᅟ.
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Affiliation(s)
| | - Argyris Politis
- Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK.
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10
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Mohammadiarani H, Shaw VS, Neubig RR, Vashisth H. Interpreting Hydrogen-Deuterium Exchange Events in Proteins Using Atomistic Simulations: Case Studies on Regulators of G-Protein Signaling Proteins. J Phys Chem B 2018; 122:9314-9323. [PMID: 30222348 PMCID: PMC6430106 DOI: 10.1021/acs.jpcb.8b07494] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Hydrogen-deuterium exchange (HDX) experiments are widely used in studies of protein dynamics. To predict the propensity of amide hydrogens for exchange with deuterium, several models have been reported in which computations of amide-hydrogen protection factors are carried out using molecular dynamics (MD) simulations. Given significant variation in the criteria used in different models, the robustness and broader applicability of these models to other proteins, especially homologous proteins showing distinct amide-exchange patterns, remains unknown. The sensitivity of the predictions when MD simulations are conducted with different force-fields is yet to tested and quantified. Using MD simulations and experimental HDX data on three homologous signaling proteins, we report detailed studies quantifying the performance of seven previously reported models (M1-M7) of two general types: empirical and fractional-population models. We find that the empirical models show inconsistent predictions but predictions of the fractional population models are robust. Contrary to previously reported work, we find that the solvent-accessible surface area of amide hydrogens is a useful metric when combined with a new metric defining the distances of amide hydrogens from the first polar atoms in proteins. On the basis of this, we report two new models, one empirical (M8) and one population-based (M9). We find strong protection of amide hydrogens from solvent exchange both within the stable helical motifs and also in the interhelical loops. We further observe that the exchange-competent states of amide hydrogens occur on the sub 100 ps time-scale via localized fluctuations, and such states among amides of a given protein do not appear to show any cooperativity or allosteric coupling.
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Affiliation(s)
- Hossein Mohammadiarani
- Department of Chemical Engineering , University of New Hampshire , Durham , New Hampshire 03824 , United States
| | - Vincent S Shaw
- Department of Pharmacology and Toxicology , Michigan State University , East Lansing , Michigan 48825 , United States
| | - Richard R Neubig
- Department of Pharmacology and Toxicology , Michigan State University , East Lansing , Michigan 48825 , United States
| | - Harish Vashisth
- Department of Chemical Engineering , University of New Hampshire , Durham , New Hampshire 03824 , United States
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11
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Xiao Y, McElheny D, Hoshi M, Ishii Y. Solid-State NMR Studies of Amyloid Materials: A Protocol to Define an Atomic Model of Aβ(1-42) in Amyloid Fibrils. Methods Mol Biol 2018; 1777:407-428. [PMID: 29744851 DOI: 10.1007/978-1-4939-7811-3_26] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Intense efforts have been made to understand the molecular structures of misfolded amyloid β (Aβ) in order to gain insight into the pathological mechanism of Alzheimer's disease. Solid-state NMR spectroscopy (SSNMR) is considered a primary tool for elucidating the structures of insoluble and noncrystalline amyloid fibrils and other amyloid assemblies. In this chapter, we describe a detailed protocol to obtain the first atomic model of the 42-residue human Aβ peptide Aβ(1-42) in structurally homogeneous amyloid fibrils from our recent SSNMR study (Nat Struct Mol Biol 22:499-505, 2015). Despite great biological and clinical interest in Aβ(1-42) fibrils, their structural details have been long-elusive until this study. The protocol is divided into four sections. First, the solid-phase peptide synthesis (SPPS) and purification of monomeric Aβ(1-42) is described. We illustrate a controlled incubation method to prompt misfolding of Aβ(1-42) into homogeneous amyloid fibrils in an aqueous solution with fragmented Aβ(1-42) fibrils as seeds. Next, we detail analysis of Aβ(1-42) fibrils by SSNMR to obtain structural restraints. Finally, we describe methods to construct atomic models of Aβ(1-42) fibrils based on SSNMR results through two-stage molecular dynamics calculations.
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Affiliation(s)
- Yiling Xiao
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Dan McElheny
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Minako Hoshi
- Institute of Biomedical Research and Innovation, FBRI, Kobe, Japan
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshitaka Ishii
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA.
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.
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12
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Roberts VA, Pique ME, Hsu S, Li S. Combining H/D Exchange Mass Spectrometry and Computational Docking To Derive the Structure of Protein-Protein Complexes. Biochemistry 2017; 56:6329-6342. [PMID: 29099587 DOI: 10.1021/acs.biochem.7b00643] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein-protein interactions are essential for biological function, but structures of protein-protein complexes are difficult to obtain experimentally. To derive the protein complex of the DNA-repair enzyme human uracil-DNA-glycosylase (hUNG) with its protein inhibitor (UGI), we combined rigid-body computational docking with hydrogen/deuterium exchange mass spectrometry (DXMS). Computational docking of the unbound protein structures provides a list of possible three-dimensional models of the complex; DXMS identifies solvent-protected protein residues. DXMS showed that unbound hUNG is compactly folded, but unbound UGI is loosely packed. An increased level of solvent protection of hUNG in the complex was localized to four regions on the same face. The decrease in the number of incorporated deuterons was quantitatively interpreted as the minimum number of main-chain hUNG amides buried in the protein-protein interface. The level of deuteration of complexed UGI decreased throughout the protein chain, indicating both tighter packing and direct solvent protection by hUNG. Three UGI regions showing the greatest decreases were best interpreted leniently, requiring just one main-chain amide from each in the interface. Applying the DXMS constraints as filters to a list of docked complexes gave the correct complex as the largest favorable energy cluster. Thus, identification of approximate protein interfaces was sufficient to distinguish the protein complex. Surprisingly, incorporating the DXMS data as added favorable potentials in the docking calculation was less effective in finding the correct complex. The filtering method has greater flexibility, with the capability to test each constraint and enforce simultaneous contact by multiple regions, but with the caveat that the list from the unbiased docking must include correct complexes.
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Affiliation(s)
- Victoria A Roberts
- San Diego Supercomputer Center, University of California, San Diego , La Jolla, California 92093, United States
| | - Michael E Pique
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Simon Hsu
- School of Medicine, University of California, San Diego , La Jolla, California 92093, United States
| | - Sheng Li
- School of Medicine, University of California, San Diego , La Jolla, California 92093, United States
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13
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Söldner CA, Sticht H, Horn AHC. Role of the N-terminus for the stability of an amyloid-β fibril with three-fold symmetry. PLoS One 2017; 12:e0186347. [PMID: 29023579 PMCID: PMC5638522 DOI: 10.1371/journal.pone.0186347] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/01/2017] [Indexed: 12/28/2022] Open
Abstract
A key player in Alzheimer’s disease is the peptide amyloid-beta (Aβ), whose aggregation into small soluble oligomers, protofilaments, and fibrils finally leads to plaque deposits in human brains. The aggregation behavior of Aβ is strongly modulated by the nature and composition of the peptide’s environment and by its primary sequence properties. The N-terminal residues of Aβ play an important role, because they are known to change the peptide’s aggregation propensity. Since these residues are for the first time completely resolved at the molecular level in a three-fold symmetric fibril structure derived from a patient, we chose that system as template for a systematic investigation of the influence of the N-terminus upon structural stability. Using atomistic molecular dynamics simulations, we examined several fibrillar systems comprising three, six, twelve and an infinite number of layers, both with and without the first eight residues. First, we found that three layers are not sufficient to stabilize the respective Aβ topology. Second, we observed a clear stabilizing effect of the N-terminal residues upon the overall fibril fold: truncated Aβ systems were less stable than their full-length counterparts. The N-terminal residues Arg5, Asp7, and Ser8 were found to form important interfilament contacts stabilizing the overall fibril structure of three-fold symmetry. Finally, similar structural rearrangements of the truncated Aβ species in different simulations prompted us to suggest a potential mechanism involved in the formation of amyloid fibrils with three-fold symmetry.
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Affiliation(s)
- Christian A. Söldner
- Bioinformatik, Institut für Biochemie, Emil-Fischer-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Heinrich Sticht
- Bioinformatik, Institut für Biochemie, Emil-Fischer-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Anselm H. C. Horn
- Bioinformatik, Institut für Biochemie, Emil-Fischer-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- * E-mail:
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14
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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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15
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Devaurs D, Antunes DA, Papanastasiou M, Moll M, Ricklin D, Lambris JD, Kavraki LE. Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data. Front Mol Biosci 2017; 4:13. [PMID: 28344973 PMCID: PMC5344923 DOI: 10.3389/fmolb.2017.00013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/24/2017] [Indexed: 11/13/2022] Open
Abstract
Monitoring hydrogen/deuterium exchange (HDX) undergone by a protein in solution produces experimental data that translates into valuable information about the protein's structure. Data produced by HDX experiments is often interpreted using a crystal structure of the protein, when available. However, it has been shown that the correspondence between experimental HDX data and crystal structures is often not satisfactory. This creates difficulties when trying to perform a structural analysis of the HDX data. In this paper, we evaluate several strategies to obtain a conformation providing a good fit to the experimental HDX data, which is a premise of an accurate structural analysis. We show that performing molecular dynamics simulations can be inadequate to obtain such conformations, and we propose a novel methodology involving a coarse-grained conformational sampling approach instead. By extensively exploring the intrinsic flexibility of a protein with this approach, we produce a conformational ensemble from which we extract a single conformation providing a good fit to the experimental HDX data. We successfully demonstrate the applicability of our method to four small and medium-sized proteins.
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Affiliation(s)
- Didier Devaurs
- Department of Computer Science, Rice UniversityHouston, TX, USA
| | | | - Malvina Papanastasiou
- Department of Pathology and Laboratory Medicine, University of PennsylvaniaPhiladelphia, PA, USA
- Broad Institute of MIT & HarvardCambridge, MA, USA
| | - Mark Moll
- Department of Computer Science, Rice UniversityHouston, TX, USA
| | - Daniel Ricklin
- Department of Pathology and Laboratory Medicine, University of PennsylvaniaPhiladelphia, PA, USA
- Department of Pharmaceutical Sciences, University of BaselBasel, Switzerland
| | - John D. Lambris
- Department of Pathology and Laboratory Medicine, University of PennsylvaniaPhiladelphia, PA, USA
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16
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Ma B, Zhao J, Nussinov R. Conformational selection in amyloid-based immunotherapy: Survey of crystal structures of antibody-amyloid complexes. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1860:2672-81. [PMID: 27266343 PMCID: PMC5610039 DOI: 10.1016/j.bbagen.2016.05.040] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/05/2016] [Accepted: 05/31/2016] [Indexed: 11/27/2022]
Abstract
BACKGROUND The dominant feature in neurodegenerative diseases is protein aggregations that lead to neuronal loss. Immunotherapies using antibodies or antibody fragments to target the aggregations are a highly perused approach. The molecular mechanisms underlying the amyloid-based immunotherapy are complex. Deciphering the properties of amyloidogenic proteins responsible for these diseases is essential to obtain insights into antibody recognition of the amyloid antigens. SCOPE OF REVIEW We systematically explore all available crystal structures of antibody-amyloid complexes related to neurodegenerative diseases, including antibodies that recognize the Aβ peptide, tau protein, prion protein, alpha-synuclein, huntingtin protein (mHTT), and polyglutamine. MAJOR CONCLUSIONS We found that antibodies mostly use the conformational selection mechanism to recognize the highly flexible amyloid antigens. In particular, solanezumab bound to Aβ12-28 tripeptide motif conformation (F19F20A21), which is shared with the Aβ42 fibril. This motif, which is trapped by the antibody, may provide the missing link in amyloid formation. Water molecules often bridge between the antibody and amyloid, contributing to the recognition. GENERAL SIGNIFICANCE This paper provides the structural basis for antibody recognition of amyloidogenic proteins. The analysis and discussion of known structures are expected to help in the design and optimization of antibodies in neurodegenerative diseases. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.
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Affiliation(s)
- Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, United States.
| | - Jun Zhao
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, United States
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, United States; Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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17
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Tran L, Basdevant N, Prévost C, Ha-Duong T. Structure of ring-shaped Aβ₄₂ oligomers determined by conformational selection. Sci Rep 2016; 6:21429. [PMID: 26868929 PMCID: PMC4751476 DOI: 10.1038/srep21429] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/22/2016] [Indexed: 11/28/2022] Open
Abstract
The oligomerization of amyloid beta (Aβ) peptides into soluble non-fibrillar species plays a critical role in the pathogenesis of Alzheimer’s disease. However, it has been challenging to characterize the tertiary and quaternary structures of Aβ peptides due to their disordered nature and high aggregation propensity. In this work, replica exchange molecular dynamics simulations were used to explore the conformational space of Aβ42 monomer. Among the most populated transient states, we identified a particular conformation which was able to generate ring-shaped pentamers and hexamers, when docked onto itself. The structures of these aggregates were stable during microsecond all-atom MD simulations in explicit solvent. In addition to high resolution models of these oligomers, this study provides support for the conformational selection mechanism of Aβ peptide self-assembly.
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Affiliation(s)
- Linh Tran
- BIOCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, Châtenay-Malabry, 92290, France
| | | | - Chantal Prévost
- LBT, Univ. Paris-Diderot, CNRS, Sorbonne Paris-Cité, Paris, 75005 France
| | - Tâp Ha-Duong
- BIOCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, Châtenay-Malabry, 92290, France
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18
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Gu L, Tran J, Jiang L, Guo Z. A new structural model of Alzheimer's Aβ42 fibrils based on electron paramagnetic resonance data and Rosetta modeling. J Struct Biol 2016; 194:61-7. [PMID: 26827680 DOI: 10.1016/j.jsb.2016.01.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/24/2016] [Accepted: 01/27/2016] [Indexed: 10/22/2022]
Abstract
Brain deposition of Aβ in the form of amyloid plaques is a pathological hallmark of Alzheimer's disease. There are two major species of Aβ in the brain: Aβ42 and Aβ40. Although Aβ40 is several-fold more abundant than Aβ42 in soluble form, Aβ42 is the major component of amyloid plaques. Structural knowledge of Aβ42 fibrils is important both for understanding the process of Aβ aggregation and for designing fibril-targeting drugs. Here we report site-specific structural information of Aβ42 fibrils at 22 residue positions based on electron paramagnetic resonance data. In combination with structure prediction program Rosetta, we modeled Aβ42 fibril structure at atomic resolution. Our Aβ42 fibril model consists of four parallel in-register β-sheets: βN (residues ∼7-13), β1 (residues ∼17-20), β2 (residues ∼32-36), and βC (residues 39-41). The region of β1-loop-β2 in Aβ42 fibrils adopts similar structure as that in Aβ40 fibrils. This is consistent with our cross seeding data that Aβ42 fibril seeds shortened the lag phase of Aβ40 fibrillization. On the other hand, Aβ42 fibrils contain a C-terminal β-arc-β motif with a special turn, termed "arc", at residues 37-38, which is absent in Aβ40 fibrils. Our results can explain both the higher aggregation propensity of Aβ42 and the importance of Aβ42 to Aβ40 ratio in the pathogenesis of Alzheimer's disease.
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Affiliation(s)
- Lei Gu
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Joyce Tran
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Lin Jiang
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Zhefeng Guo
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
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19
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Baram M, Atsmon-Raz Y, Ma B, Nussinov R, Miller Y. Amylin-Aβ oligomers at atomic resolution using molecular dynamics simulations: a link between Type 2 diabetes and Alzheimer's disease. Phys Chem Chem Phys 2016; 18:2330-8. [PMID: 26349542 PMCID: PMC4720542 DOI: 10.1039/c5cp03338a] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Clinical studies have identified Type 2 diabetes (T2D) as a risk factor of Alzheimer's disease (AD). One of the potential mechanisms that link T2D and AD is the loss of cells associated with degenerative changes. Amylin1-37 aggregates (the pathological species in T2D) were found to be co-localized with those of Aβ1-42 (the pathological species in AD) to form the Amylin1-37-Aβ1-42 plaques, promoting aggregation and thus contributing to the etiology of AD. However, the mechanisms by which Amylin1-37 co-aggregates with Aβ1-42 are still elusive. This work presents the interactions between Amylin1-37 oligomers and Aβ1-42 oligomers at atomic resolution applying extensive molecular dynamics simulations for relatively large ensemble of cross-seeding Amylin1-37-Aβ1-42 oligomers. The main conclusions of this study are first, Aβ1-42 oligomers prefer to interact with Amylin1-37 oligomers to form single layer conformations (in-register interactions) rather than double layer conformations; and second, in some double layer conformations of the cross-seeding Amylin1-37-Aβ1-42 oligomers, the Amylin1-37 oligomers destabilize the Aβ1-42 oligomers and thus inhibit Aβ1-42 aggregation, while in other double layer conformations, the Amylin1-37 oligomers stabilize Aβ1-42 oligomers and thus promote Aβ1-42 aggregation.
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Affiliation(s)
- Michal Baram
- Department of Chemistry, Ben-Gurion University of the Negev, Beér-Sheva 84105, Israel and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beér-Sheva 84105, Israel.
| | - Yoav Atsmon-Raz
- Department of Chemistry, Ben-Gurion University of the Negev, Beér-Sheva 84105, Israel and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beér-Sheva 84105, Israel.
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA.
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA. and Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yifat Miller
- Department of Chemistry, Ben-Gurion University of the Negev, Beér-Sheva 84105, Israel and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beér-Sheva 84105, Israel.
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20
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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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21
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Park IH, Venable JD, Steckler C, Cellitti SE, Lesley SA, Spraggon G, Brock A. Estimation of Hydrogen-Exchange Protection Factors from MD Simulation Based on Amide Hydrogen Bonding Analysis. J Chem Inf Model 2015; 55:1914-25. [PMID: 26241692 DOI: 10.1021/acs.jcim.5b00185] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydrogen exchange (HX) studies have provided critical insight into our understanding of protein folding, structure, and dynamics. More recently, hydrogen exchange mass spectrometry (HX-MS) has become a widely applicable tool for HX studies. The interpretation of the wealth of data generated by HX-MS experiments as well as other HX methods would greatly benefit from the availability of exchange predictions derived from structures or models for comparison with experiment. Most reported computational HX modeling studies have employed solvent-accessible-surface-area based metrics in attempts to interpret HX data on the basis of structures or models. In this study, a computational HX-MS prediction method based on classification of the amide hydrogen bonding modes mimicking the local unfolding model is demonstrated. Analysis of the NH bonding configurations from molecular dynamics (MD) simulation snapshots is used to determine partitioning over bonded and nonbonded NH states and is directly mapped into a protection factor (PF) using a logistics growth function. Predicted PFs are then used for calculating deuteration values of peptides and compared with experimental data. Hydrogen exchange MS data for fatty acid synthase thioesterase (FAS-TE) collected for a range of pHs and temperatures was used for detailed evaluation of the approach. High correlation between prediction and experiment for observable fragment peptides is observed in the FAS-TE and additional benchmarking systems that included various apo/holo proteins for which literature data were available. In addition, it is shown that HX modeling can improve experimental resolution through decomposition of in-exchange curves into rate classes, which correlate with prediction from MD. Successful rate class decompositions provide further evidence that the presented approach captures the underlying physical processes correctly at the single residue level. This assessment is further strengthened in a comparison of residue resolved protection factor predictions for staphylococcal nuclease with NMR data, which was also used to compare prediction performance with other algorithms described in the literature. The demonstrated transferable and scalable MD based HX prediction approach adds significantly to the available tools for HX-MS data interpretation based on available structures and models.
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Affiliation(s)
- In-Hee Park
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - John D Venable
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Caitlin Steckler
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive, San Diego, California 92121, United States.,Joint Center for Structural Genomics , La Jolla, California 92037, United States
| | - Susan E Cellitti
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Scott A Lesley
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive, San Diego, California 92121, United States.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute , La Jolla, California 92037, United States.,Joint Center for Structural Genomics , La Jolla, California 92037, United States
| | - Glen Spraggon
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Ansgar Brock
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
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22
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Xiao Y, Ma B, McElheny D, Parthasarathy S, Long F, Hoshi M, Nussinov R, Ishii Y. Aβ(1-42) fibril structure illuminates self-recognition and replication of amyloid in Alzheimer's disease. Nat Struct Mol Biol 2015; 22:499-505. [PMID: 25938662 PMCID: PMC4476499 DOI: 10.1038/nsmb.2991] [Citation(s) in RCA: 620] [Impact Index Per Article: 68.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 04/15/2015] [Indexed: 12/19/2022]
Abstract
Increasing evidence has suggested that formation and propagation of misfolded aggregates of 42-residue human amyloid β (Aβ(1-42)), rather than of the more abundant Aβ(1-40), provokes the Alzheimer's disease cascade. However, structural details of misfolded Aβ(1-42) have remained elusive. Here we present the atomic model of an Aβ(1-42) amyloid fibril, from solid-state NMR (ssNMR) data. It displays triple parallel-β-sheet segments that differ from reported structures of Aβ(1-40) fibrils. Remarkably, Aβ(1-40) is incompatible with the triple-β-motif, because seeding with Aβ(1-42) fibrils does not promote conversion of monomeric Aβ(1-40) into fibrils via cross-replication. ssNMR experiments suggest that C-terminal Ala42, absent in Aβ(1-40), forms a salt bridge with Lys28 to create a self-recognition molecular switch that excludes Aβ(1-40). The results provide insight into the Aβ(1-42)-selective self-replicating amyloid-propagation machinery in early-stage Alzheimer's disease.
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Affiliation(s)
- Yiling Xiao
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Buyong Ma
- Cancer and Inflammation Program, Leidos Biomedical Research, National Cancer Institute at Frederick, Frederick, Maryland, USA
| | - Dan McElheny
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, USA
| | | | - Fei Long
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Minako Hoshi
- 1] Institute of Biomedical Research and Innovation, Kobe, Japan. [2] Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ruth Nussinov
- 1] Cancer and Inflammation Program, Leidos Biomedical Research, National Cancer Institute at Frederick, Frederick, Maryland, USA. [2] Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yoshitaka Ishii
- 1] Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, USA. [2] Center for Structural Biology, University of Illinois at Chicago, Chicago, Illinois, USA
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23
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Nasica-Labouze J, Nguyen PH, Sterpone F, Berthoumieu O, Buchete NV, Coté S, De Simone A, Doig AJ, Faller P, Garcia A, Laio A, Li MS, Melchionna S, Mousseau N, Mu Y, Paravastu A, Pasquali S, Rosenman DJ, Strodel B, Tarus B, Viles JH, Zhang T, Wang C, Derreumaux P. Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies. Chem Rev 2015; 115:3518-63. [PMID: 25789869 DOI: 10.1021/cr500638n] [Citation(s) in RCA: 475] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jessica Nasica-Labouze
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Phuong H Nguyen
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabio Sterpone
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Olivia Berthoumieu
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Sébastien Coté
- ∥Département de Physique and Groupe de recherche sur les protéines membranaires (GEPROM), Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Québec H3C 3T5, Canada
| | - Alfonso De Simone
- ⊥Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Andrew J Doig
- #Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Peter Faller
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Alessandro Laio
- ○The International School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Mai Suan Li
- ◆Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.,¶Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Simone Melchionna
- ⬠Instituto Processi Chimico-Fisici, CNR-IPCF, Consiglio Nazionale delle Ricerche, 00185 Roma, Italy
| | | | - Yuguang Mu
- ▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Anant Paravastu
- ⊕National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Samuela Pasquali
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | | | - Birgit Strodel
- △Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Bogdan Tarus
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - John H Viles
- ▼School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Tong Zhang
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | | | - Philippe Derreumaux
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,□Institut Universitaire de France, 75005 Paris, France
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24
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Piazza M, Guillemette JG, Dieckmann T. Dynamics of nitric oxide synthase-calmodulin interactions at physiological calcium concentrations. Biochemistry 2015; 54:1989-2000. [PMID: 25751535 DOI: 10.1021/bi501353s] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The intracellular Ca²⁺ concentration is an important regulator of many cellular functions. The small acidic protein calmodulin (CaM) serves as a Ca²⁺ sensor and control element for many enzymes. Nitric oxide synthase (NOS) is one of the proteins that is activated by CaM and plays a major role in a number of key physiological and pathological processes. Previous studies have shown CaM to act like a switch that causes a conformational change in NOS to allow for the electron transfer between the reductase and oxygenase domains through a process that is thought to be highly dynamic. We have analyzed the structure and dynamics of complexes formed by peptides based on inducible NOS (iNOS) and endothelial NOS (eNOS) with CaM at Ca²⁺ concentrations that mimic the physiological basal (17 and 100 nM) and elevated levels (225 nM) found in mammalian cells using fluorescence techniques and nuclear magnetic resonance spectroscopy. The results show the CaM-NOS complexes have similar structures at physiological and fully saturated Ca²⁺ levels; however, their dynamics are remarkably different. At 225 nM Ca²⁺, the CaM-NOS complexes show overall an increase in backbone dynamics, when compared to the dynamics of the complexes at saturating Ca²⁺ concentrations. Specifically, the N-lobe of CaM in the CaM-iNOS complex displays a lower internal mobility (higher S²) and higher exchange protection compared to those of the CaM-eNOS complex. In contrast, the C-lobe of CaM in the CaM-eNOS complex is less dynamic. These results illustrate that structures of CaM-NOS complexes determined at saturated Ca²⁺ concentrations cannot provide a complete picture because the differences in intramolecular dynamics become visible only at physiological Ca²⁺ levels.
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Affiliation(s)
- Michael Piazza
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - J Guy Guillemette
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Thorsten Dieckmann
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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25
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Gu L, Liu C, Stroud JC, Ngo S, Jiang L, Guo Z. Antiparallel triple-strand architecture for prefibrillar Aβ42 oligomers. J Biol Chem 2014; 289:27300-27313. [PMID: 25118290 PMCID: PMC4175361 DOI: 10.1074/jbc.m114.569004] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 08/05/2014] [Indexed: 12/21/2022] Open
Abstract
Aβ42 oligomers play key roles in the pathogenesis of Alzheimer disease, but their structures remain elusive partly due to their transient nature. Here, we show that Aβ42 in a fusion construct can be trapped in a stable oligomer state, which recapitulates characteristics of prefibrillar Aβ42 oligomers and enables us to establish their detailed structures. Site-directed spin labeling and electron paramagnetic resonance studies provide structural restraints in terms of side chain mobility and intermolecular distances at all 42 residue positions. Using these restraints and other biophysical data, we present a novel atomic-level oligomer model. In our model, each Aβ42 protein forms a single β-sheet with three β-strands in an antiparallel arrangement. Each β-sheet consists of four Aβ42 molecules in a head-to-tail arrangement. Four β-sheets are packed together in a face-to-back fashion. The stacking of identical segments between different β-sheets within an oligomer suggests that prefibrillar oligomers may interconvert with fibrils via strand rotation, wherein β-strands undergo an ∼90° rotation along the strand direction. This work provides insights into rational design of therapeutics targeting the process of interconversion between toxic oligomers and non-toxic fibrils.
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Affiliation(s)
- Lei Gu
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Cong Liu
- Departments of Chemistry and Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095,; Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China, and
| | - James C Stroud
- Department of Chemistry and Chemical Biology, Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131
| | - Sam Ngo
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Lin Jiang
- Departments of Chemistry and Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Zhefeng Guo
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095.
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26
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Nguyen PH, Li MS, Derreumaux P. Amyloid oligomer structure characterization from simulations: A general method. J Chem Phys 2014; 140:094105. [DOI: 10.1063/1.4866902] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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27
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Nguyen PH, Tarus B, Derreumaux P. Familial Alzheimer A2 V Mutation Reduces the Intrinsic Disorder and Completely Changes the Free Energy Landscape of the Aβ1–28 Monomer. J Phys Chem B 2014; 118:501-10. [DOI: 10.1021/jp4115404] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Phuong H. Nguyen
- Laboratoire
de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Bogdan Tarus
- Laboratoire
de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratoire
de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France, IUF, 103 Boulevard Saint-Michel, 75005 Paris, France
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28
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Wang FN, Peng SL, Lu CT, Peng HH, Yeh TC. Water signal attenuation by D2O infusion as a novel contrast mechanism for 1H perfusion MRI. NMR IN BIOMEDICINE 2013; 26:692-698. [PMID: 23355425 DOI: 10.1002/nbm.2914] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 12/06/2012] [Accepted: 12/06/2012] [Indexed: 06/01/2023]
Abstract
Deuterium oxide (D2 O), which is commercially available and nonradioactive, was proposed as a perfusion tracer before the clinical usage of conventional gadolinium-based MRI contrast agents. However, the sensitivity of direct deuterium detection is the major challenge for its application. In this study, we propose a contrast-enhanced strategy to indirectly trace administered D2 O by monitoring the signal attenuation of (1) H MRI. Experiments on D2 O concentration phantoms and in vivo rat brains were conducted to prove the concept of the proposed contrast mechanism. An average maximum signal drop ratio of 5.25 ± 0.91% was detected on (1) H MR images of rat brains with 2 mL of D2 O administered per 100 g of body weight. As a diffusible tracer for perfusion, D2 O infusion is a practicable method for the assessment of tissue perfusion and has the potential to provide different information from gadolinium-based contrast agents, which have limited permeability for blood vessels. Furthermore, the observed negative relaxivities of D2 O reveal the (1) H-D exchange effect. Therefore, applications of perfusion MRI with D2 O as a contrast agent are worthy of further investigation.
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Affiliation(s)
- Fu-Nien Wang
- Department of Biomedical Engineering and Environmental Sciences, College of Nuclear Science, National Tsing Hua University, Hsinchu, Taiwan.
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29
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Gu L, Liu C, Guo Z. Structural insights into Aβ42 oligomers using site-directed spin labeling. J Biol Chem 2013; 288:18673-83. [PMID: 23687299 DOI: 10.1074/jbc.m113.457739] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Oligomerization of the 42-residue peptide Aβ42 plays a key role in the pathogenesis of Alzheimer disease. Despite great academic and medical interest, the structures of these oligomers have not been well characterized. Site-directed spin labeling combined with electron paramagnetic resonance spectroscopy is a powerful approach for studying structurally ill-defined systems, but its application in amyloid oligomer structure study has not been systematically explored. Here we report a comprehensive structural study on a toxic Aβ42 oligomer, called globulomer, using site-directed spin labeling complemented by other techniques. Transmission electron microscopy shows that these oligomers are globular structures with diameters of ∼7-8 nm. Circular dichroism shows primarily β-structures. X-ray powder diffraction suggests a highly ordered intrasheet hydrogen-bonding network and a heterogeneous intersheet packing. Residue-level mobility analysis on spin labels introduced at 14 different positions shows a structured state and a disordered state at all labeling sites. Side chain mobility analysis suggests that structural order increases from N- to C-terminal regions. Intermolecular distance measurements at 14 residue positions suggest that C-terminal residues Gly-29-Val-40 form a tightly packed core with intermolecular distances in a narrow range of 11.5-12.5 Å. These intermolecular distances rule out the existence of fibril-like parallel in-register β-structures and strongly suggest an antiparallel β-sheet arrangement in Aβ42 globulomers.
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Affiliation(s)
- Lei Gu
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, UCLA, Los Angeles, California 90095, USA
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30
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Lindgren J, Segerfeldt P, Sholts SB, Gräslund A, Karlström AE, Wärmländer SKTS. Engineered non-fluorescent Affibody molecules facilitate studies of the amyloid-beta (Aβ) peptide in monomeric form: low pH was found to reduce Aβ/Cu(II) binding affinity. J Inorg Biochem 2012; 120:18-23. [PMID: 23262458 DOI: 10.1016/j.jinorgbio.2012.11.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 11/23/2012] [Accepted: 11/23/2012] [Indexed: 11/17/2022]
Abstract
Aggregation of amyloid-beta (Aβ) peptides into oligomers and amyloid plaques in the human brain is considered a causative factor in Alzheimer's disease (AD). As metal ions are over-represented in AD patient brains, and as distinct Aβ aggregation pathways in presence of Cu(II) have been demonstrated, metal binding to Aβ likely affects AD progression. Aβ aggregation is moreover pH-dependent, and AD appears to involve inflammatory conditions leading to physiological acidosis. Although metal binding specificity to Aβ varies at different pH's, metal binding affinity to Aβ has so far not been quantitatively investigated at sub-neutral pH levels. This may be explained by the difficulties involved in studying monomeric peptide properties under aggregation-promoting conditions. We have recently devised a modified Affibody molecule, Z(Aβ3)(12-58), that binds Aβ with sub-nanomolar affinity, thereby locking the peptide in monomeric form without affecting the N-terminal region where metal ions bind. Here, we introduce non-fluorescent Aβ-binding Affibody variants that keep Aβ monomeric while only slightly affecting the Aβ peptide's metal binding properties. Using fluorescence spectroscopy, we demonstrate that Cu(II)/Aβ(1-40) binding is almost two orders of magnitude weaker at pH 5.0 (apparent K(D)=51 μM) than at pH 7.3 (apparent K(D)=0.86 μM). This effect is arguably caused by protonation of the histidines involved in the metal ligandation. Our results indicate that engineered variants of Affibody molecules are useful for studying metal-binding and other properties of monomeric Aβ under various physiological conditions, which will improve our understanding of the molecular mechanisms involved in AD.
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Affiliation(s)
- Joel Lindgren
- Division of Molecular Biotechnology, School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91 Stockholm, Sweden
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31
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Gallion SL. Modeling amyloid-beta as homogeneous dodecamers and in complex with cellular prion protein. PLoS One 2012; 7:e49375. [PMID: 23145167 PMCID: PMC3493521 DOI: 10.1371/journal.pone.0049375] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 10/11/2012] [Indexed: 12/16/2022] Open
Abstract
Soluble amyloid beta (Aβ) peptide has been linked to the pathology of Alzheimer's disease. A variety of soluble oligomers have been observed to be toxic, ranging from dimers to protofibrils. No tertiary structure has been identified as a single biologically relevant form, though many models are comprised of highly ordered β-sheets. Evidence exists for much less ordered toxic oligomers. The mechanism of toxicity remains highly debated and probably involves multiple pathways. Interaction of Aβ oligomers with the N-terminus of the cellular form of the prion protein (PrP(c)) has recently been proposed. The intrinsically disordered nature of this protein and the highly polymorphic nature of Aβ oligomers make structural resolution of the complex exceptionally challenging. In this study, molecular dynamics simulations are performed for dodecameric assemblies of Aβ comprised of monomers having a single, short antiparallel β-hairpin at the C-terminus. The resulting models, devoid of any intermolecular hydrogen bonds, are shown to correlate well with experimental data and are found to be quite stable within the hydrophobic core, whereas the α-helical N-termini transform to a random coil state. This indicates that highly ordered assemblies are not required for stability and less ordered oligomers are a viable component in the population of soluble oligomers. In addition, a tentative model is proposed for the association of Aβ dimers with a double deletion mutant of the intrinsically disordered N-terminus of PrP(c). This may be useful as a conceptual working model for the binding of higher order oligomers and in the design of further experiments.
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32
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Ma B, Nussinov R. Selective molecular recognition in amyloid growth and transmission and cross-species barriers. J Mol Biol 2012; 421:172-84. [PMID: 22119878 PMCID: PMC6407624 DOI: 10.1016/j.jmb.2011.11.023] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 11/10/2011] [Accepted: 11/13/2011] [Indexed: 11/23/2022]
Abstract
Mutual conformational selection and population shift followed by minor induced-fit optimization is the key mechanism in biomolecular recognition, and monomers and small oligomers binding to amyloid seeds in fibril growth is a molecular recognition event. Here, we describe amyloid aggregation, preferred species, cross-species barriers and transmission within the broad framework of molecular recognition. Cross-seeding of amyloid species is governed by conformational selection of compatible (complementary) states. If the dominant conformations of two species are similar, they can cross-seed each other; on the other hand, if they are sufficiently different, they will grow into different fibrils, reflecting species barriers. Such a scenario has recently been observed for the tau protein, which has four repeats. While a construct consisting of repeats 1, 3 and 4 can serve as a seed for the entire four-repeat tau segment, the inverse does not hold. On the other hand, the tau protein repeats with the characteristic U-turn shape can cross-seed Alzheimer's amyloid β and, similarly, the islet amyloid polypeptide. Within this framework, we suggest that the so-called "central dogma" of amyloid formation, where aggregation takes place through nonspecific backbone hydrogen bonding interactions, which are common to all peptides and proteins, is a simple reflection of the heterogeneous, polymorphic free-energy landscape of amyloid species. Here, we review available data and make some propositions addressing this key problem. In particular, we argue that recent theoretical and experimental observations support the key role of selective molecular recognition in amyloidosis and in determining cross-species barriers and transmission.
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Affiliation(s)
- Buyong Ma
- Basic Science Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program NCI-Frederick, Frederick, MD 21702
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program NCI-Frederick, Frederick, MD 21702
- Sackler Inst. of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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33
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Roberts VA, Pique ME, Hsu S, Li S, Slupphaug G, Rambo RP, Jamison JW, Liu T, Lee JH, Tainer JA, Ten Eyck LF, Woods VL. Combining H/D exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil-DNA glycosylase. Nucleic Acids Res 2012; 40:6070-81. [PMID: 22492624 PMCID: PMC3401472 DOI: 10.1093/nar/gks291] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 02/21/2012] [Accepted: 03/15/2012] [Indexed: 12/21/2022] Open
Abstract
X-ray crystallography provides excellent structural data on protein-DNA interfaces, but crystallographic complexes typically contain only small fragments of large DNA molecules. We present a new approach that can use longer DNA substrates and reveal new protein-DNA interactions even in extensively studied systems. Our approach combines rigid-body computational docking with hydrogen/deuterium exchange mass spectrometry (DXMS). DXMS identifies solvent-exposed protein surfaces; docking is used to create a 3-dimensional model of the protein-DNA interaction. We investigated the enzyme uracil-DNA glycosylase (UNG), which detects and cleaves uracil from DNA. UNG was incubated with a 30 bp DNA fragment containing a single uracil, giving the complex with the abasic DNA product. Compared with free UNG, the UNG-DNA complex showed increased solvent protection at the UNG active site and at two regions outside the active site: residues 210-220 and 251-264. Computational docking also identified these two DNA-binding surfaces, but neither shows DNA contact in UNG-DNA crystallographic structures. Our results can be explained by separation of the two DNA strands on one side of the active site. These non-sequence-specific DNA-binding surfaces may aid local uracil search, contribute to binding the abasic DNA product and help present the DNA product to APE-1, the next enzyme on the DNA-repair pathway.
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Affiliation(s)
- Victoria A Roberts
- San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, MC 0505, La Jolla, CA 92093, USA.
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34
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Yu X, Luo Y, Dinkel P, Zheng J, Wei G, Margittai M, Nussinov R, Ma B. Cross-seeding and conformational selection between three- and four-repeat human Tau proteins. J Biol Chem 2012; 287:14950-9. [PMID: 22393063 PMCID: PMC3340261 DOI: 10.1074/jbc.m112.340794] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2012] [Revised: 02/21/2012] [Indexed: 11/06/2022] Open
Abstract
In Alzheimer's disease and frontotemporal dementias, the microtubule-associated protein Tau forms intracellular paired helical filaments. The filaments can form not only by the full-length human Tau protein, but also by the three repeated (K19) or four repeated (K18) Tau segments. However, of interest, experimentally, K19 can seed K18, but not vice versa. To obtain insight into the cross-seeding between K18 and K19 aggregates, here, K18 and K19 octamers with repeat 3 (R3) in U-shaped, L-shaped, and long straight line-shaped (SL-shape) conformations are assembled into different structures. The simulation results show that K18-8/K19-8 (K18 and K19 assemblies number 8) with R3 in an L shape and K18-9/K19-9 with R3 in an SL shape are highly populated and present the highest structural similarity among all simulated K18 and K19 octamers, suggesting that similar folding of K18/K19 may serve as structural core for the K18-K19 co-assembled heterogeneous filament. We demonstrate that formation of stable R2 and R3 conformations is the critical step for K18 aggregation, and R3 is critical for K19 fibrillization. The different core units in K18 and K19 may create a cross-seeding barrier for the K18 seed to trigger K19 fibril growth because R2 is not available for K19. Our study provides insights into cross-seeding involving heterogeneous structures. The polymorphic nature of protein aggregation could be magnified in the cross-seeding process. If the seeding conformations lead to too much divergence in the energy landscape, it could impede fibril formation. Such an effect could also contribute to the asymmetric barrier between K18 and K19.
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Affiliation(s)
- Xiang Yu
- From the Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325
| | - Yin Luo
- From the Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325
- the State Key Laboratory of Surface Physics, the Key Laboratory for Computational Physical Sciences (Ministry of Education), and the Department of Physics, Fudan University, Shanghai, China
| | - Paul Dinkel
- the Department of Chemistry & Biochemistry, University of Denver, Denver, Colorado 80208
| | - Jie Zheng
- From the Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325
| | - Guanghong Wei
- the State Key Laboratory of Surface Physics, the Key Laboratory for Computational Physical Sciences (Ministry of Education), and the Department of Physics, Fudan University, Shanghai, China
| | - Martin Margittai
- the Department of Chemistry & Biochemistry, University of Denver, Denver, Colorado 80208
| | - Ruth Nussinov
- the Basic Research Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, Maryland 21702, and
- the Department of Human Genetics and Molecular Medicine, Sackler Institute of Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Buyong Ma
- the Basic Research Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, Maryland 21702, and
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