51
|
Rationally designed turn promoting mutation in the amyloid-β peptide sequence stabilizes oligomers in solution. PLoS One 2011; 6:e21776. [PMID: 21799748 PMCID: PMC3142112 DOI: 10.1371/journal.pone.0021776] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 06/12/2011] [Indexed: 11/20/2022] Open
Abstract
Enhanced production of a 42-residue beta amyloid peptide (Aβ42) in affected parts of the brain has been suggested to be the main causative factor for the development of Alzheimer's Disease (AD). The severity of the disease depends not only on the amount of the peptide but also its conformational transition leading to the formation of oligomeric amyloid-derived diffusible ligands (ADDLs) in the brain of AD patients. Despite being significant to the understanding of AD mechanism, no atomic-resolution structures are available for these species due to the evanescent nature of ADDLs that hinders most structural biophysical investigations. Based on our molecular modeling and computational studies, we have designed Met35Nle and G37p mutations in the Aβ42 peptide (Aβ42Nle35p37) that appear to organize Aβ42 into stable oligomers. 2D NMR on the Aβ42Nle35p37 peptide revealed the occurrence of two β-turns in the V24-N27 and V36-V39 stretches that could be the possible cause for the oligomer stability. We did not observe corresponding NOEs for the V24-N27 turn in the Aβ21–43Nle35p37 fragment suggesting the need for the longer length amyloid peptide to form the stable oligomer promoting conformation. Because of the presence of two turns in the mutant peptide which were absent in solid state NMR structures for the fibrils, we propose, fibril formation might be hindered. The biophysical information obtained in this work could aid in the development of structural models for toxic oligomer formation that could facilitate the development of therapeutic approaches to AD.
Collapse
|
52
|
Harvey SR, Macphee CE, Barran PE. Ion mobility mass spectrometry for peptide analysis. Methods 2011; 54:454-61. [PMID: 21669288 DOI: 10.1016/j.ymeth.2011.05.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 05/04/2011] [Accepted: 05/22/2011] [Indexed: 02/03/2023] Open
Abstract
The use of ion mobility mass spectrometry has grown rapidly over the last two decades. This powerful analytical platform now forms an attractive prospect for comprehensive analysis of many different molecular species, including chemically complex biological molecules. This paper describes the application of IM-MS to the study of peptides. We focus on three different ion mobility devices that are most frequently found in tandem with mass spectrometers. These are instruments using linear drift tubes (LDT), those using travelling wave ion guides (TWIGS) and those employing high field asymmetric ion mobility spectrometry (FAIMS). Each technique is described. Examples are given on the use of IM-MS for the determination of peptide structure, the study of peptides that form amyloid fibrils, and the study of complex peptide mixtures in proteomic investigations. We describe and comment on the methodologies used and the outlook for this developing analytical technique.
Collapse
Affiliation(s)
- Sophie R Harvey
- The School of Chemistry, The University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | | | | |
Collapse
|
53
|
Urbanc B, Betnel M, Cruz L, Li H, Fradinger EA, Monien BH, Bitan G. Structural basis for Aβ1–42 toxicity inhibition by Aβ C-terminal fragments: discrete molecular dynamics study. J Mol Biol 2011; 410:316-28. [PMID: 21621545 DOI: 10.1016/j.jmb.2011.05.021] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 04/12/2011] [Accepted: 05/14/2011] [Indexed: 11/16/2022]
Abstract
Amyloid β-protein (Aβ) is central to the pathology of Alzheimer's disease. Of the two predominant Aβ alloforms, Aβ(1-40) and Aβ(1-42), the latter forms more toxic oligomers. C-terminal fragments (CTFs) of Aβ were recently shown to inhibit Aβ(1-42) toxicity in vitro. Here, we studied Aβ(1-42) assembly in the presence of three effective CTF inhibitors and an ineffective fragment, Aβ(21-30). Using a discrete molecular dynamics approach that recently was shown to capture key differences between Aβ(1-40) and Aβ(1-42) oligomerization, we compared Aβ(1-42) oligomer formation in the absence and presence of CTFs or Aβ(21-30) and identified structural elements of Aβ(1-42) that correlated with Aβ(1-42) toxicity. CTFs co-assembled with Aβ(1-42) into large heterooligomers containing multiple Aβ(1-42) and inhibitor fragments. In contrast, Aβ(21-30) co-assembled with Aβ(1-42) into heterooligomers containing mostly a single Aβ(1-42) and multiple Aβ(21-30) fragments. The CTFs, but not Aβ(21-30), decreased the β-strand propensity of Aβ(1-42) in a concentration-dependent manner. CTFs and Aβ(21-30) had a high binding propensity to the hydrophobic regions of Aβ(1-42), but only CTFs were found to bind the Aβ(1-42) region A2-F4. Consequently, only CTFs but not Aβ(21-30) reduced the solvent accessibility of Aβ(1-42) in region D1-R5. The reduced solvent accessibility of Aβ(1-42) in the presence of CTFs was comparable to the solvent accessibility of Aβ(1-40) oligomers formed in the absence of Aβ fragments. These findings suggest that region D1-R5, which was more exposed to the solvent in Aβ(1-42) than in Aβ(1-40) oligomers, is involved in mediating Aβ(1-42) oligomer neurotoxicity.
Collapse
Affiliation(s)
- B Urbanc
- Department of Physics, Drexel University, Philadelphia, PA 19104, USA.
| | | | | | | | | | | | | |
Collapse
|
54
|
Viet MH, Ngo ST, Lam NS, Li MS. Inhibition of Aggregation of Amyloid Peptides by Beta-Sheet Breaker Peptides and Their Binding Affinity. J Phys Chem B 2011; 115:7433-46. [DOI: 10.1021/jp1116728] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Man Hoang Viet
- Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Son Tung Ngo
- Institute for Computational Science and Technology, 6 Quarter, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Nguyen Sy Lam
- Computational Physics Laboratory, Vietnam National University, Ho Chi Minh City, 227 Nguyen Van Cu, District 5, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, 02-668 Warsaw, Poland
| |
Collapse
|
55
|
Grasso G. The use of mass spectrometry to study amyloid-β peptides. MASS SPECTROMETRY REVIEWS 2011; 30:347-365. [PMID: 21500241 DOI: 10.1002/mas.20281] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 11/06/2009] [Accepted: 11/06/2009] [Indexed: 05/30/2023]
Abstract
Amyloid-β peptide (Aβ) varies in size from 39 to 43 amino acids and arises from sequential β- and γ-secretase processing of the amyloid precursor protein. Whereas the non-pathological role for Aβ is yet to be established, there is no disputing that Aβ is now widely regarded as central to the development of Alzheimer's disease (AD). The so named "amyloid cascade hypothesis" states that disease progression is the result of an increased Aβ burden in affected areas of the brain. To elucidate the Aβ role in AD, many analytical approaches have been proposed as suitable tools to investigate not only the total Aβ load but also many other issues that are considered crucial for AD, such as: (i) the aggregation state in which Aβ is present; (ii) its interaction with other species or metals; (iii) its ability to induce oxidative stress; and (iv) its degradative pathways. This review provides an insight into the use of mass spectrometry (MS) in the field of Aβ investigation aimed to assess its role in AD. In particular, the different MS-based approaches applied in vitro and in vivo that can provide detailed information on the above-mentioned issues are reviewed. Moreover, the advantages offered by the MS methods over all the other techniques are highlighted, together with the recent developments and uses of combined analytical approaches to detect and characterize Aβ.
Collapse
Affiliation(s)
- Giuseppe Grasso
- Chemistry Department, Università di Catania, Viale Andrea Doria 6, Catania 95125, Italy.
| |
Collapse
|
56
|
Velez-Vega C, Escobedo FA. Characterizing the structural behavior of selected Aβ-42 monomers with different solubilities. J Phys Chem B 2011; 115:4900-10. [PMID: 21486050 DOI: 10.1021/jp1086575] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The conformational behavior of the wild-type amyloid β-42 (Aβ-42) monomer and two of its mutants was explored via all-atom replica exchange molecular dynamics simulations in explicit solvent, to identify structural features that may promote or deter early-stage oligomerization. The markers used for this purpose indicate that while the three peptides are relatively flexible they have distinct preferential structures and degree of rigidity. In particular, we found that one mutant that remains in the monomeric state in experiments displays a characteristic N-terminal structure that significantly enhances its rigidity. This finding is consistent with various studies that have detected a reduction in oligomerization frequency and Aβ-related toxicity upon sequence-specific antibody or ligand binding to the N-terminal tail of wild-type monomers, likely leading to the stabilization of this region. In general, our results highlight a potential role of the N-terminal segment on Aβ oligomerization and give insights into specific interactions that may be responsible for promoting the pronounced structural changes observed upon introducing point mutations on the wild-type Aβ-42 peptide.
Collapse
Affiliation(s)
- Camilo Velez-Vega
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, USA
| | | |
Collapse
|
57
|
Chen L, Shao Q, Gao YQ, Russell DH. Molecular Dynamics and Ion Mobility Spectrometry Study of Model β-Hairpin Peptide, Trpzip1. J Phys Chem A 2011; 115:4427-35. [DOI: 10.1021/jp110014j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Liuxi Chen
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Qiang Shao
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yi-Qin Gao
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H. Russell
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| |
Collapse
|
58
|
Lu Y, Wei G, Derreumaux P. Effects of G33A and G33I mutations on the structures of monomer and dimer of the amyloid-β fragment 29-42 by replica exchange molecular dynamics simulations. J Phys Chem B 2010; 115:1282-8. [PMID: 21186801 DOI: 10.1021/jp110269a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The early formed oligomers of amyloid-β proteins with 40 and 42 amino acids are believed to be the culprits of Alzheimer's disease. Aβ1-42 peptides with alanine and isoleucine mutations of glycine 33 are known to be much less toxic than the wild-type Aβ1-42 and promote the aggregation process in vitro. The fragment Aβ29-42 has also been shown to form fibrils, disrupt Aβ1-42 oligomerization, and inhibit Aβ1-42-induced neurotoxicity. As a first step toward understanding the impact of G33A and G33I mutations on the earliest steps along the Aβ1-42 aggregation pathway, we have studied the structures of the monomer and dimer of Aβ29-42 and its two G33 variants using coarse-grained replica exchange molecular dynamics simulations. These simulations, totaling 15 μs, indicate that both substitutions impact the conformational ensemble of Aβ29-42. For the monomer, the population of the β-hairpin is high for wild-type Aβ29-42, but marginal for Aβ29-42 G33I mutant. The three dimers are also stabilized by different patterns of interaction. The data are discussed in terms of the differences in the aggregation characteristics between wild-type Aβ1-42 and its two G33A and G33I variants.
Collapse
Affiliation(s)
- Yan Lu
- State Key Laboratory of Surface Physics, Department of Physics, Fudan University, Shanghai, China
| | | | | |
Collapse
|
59
|
On the origins of the weak folding cooperativity of a designed ββα ultrafast protein FSD-1. PLoS Comput Biol 2010; 6:e1000998. [PMID: 21124953 PMCID: PMC2987907 DOI: 10.1371/journal.pcbi.1000998] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 10/14/2010] [Indexed: 11/19/2022] Open
Abstract
FSD-1, a designed small ultrafast folder with a ββα fold, has been actively studied in the last few years as a model system for studying protein folding mechanisms and for testing of the accuracy of computational models. The suitability of this protein to describe the folding of naturally occurring α/β proteins has recently been challenged based on the observation that the melting transition is very broad, with ill-resolved baselines. Using molecular dynamics simulations with the AMBER protein force field (ff96) coupled with the implicit solvent model (IGB = 5), we shed new light into the nature of this transition and resolve the experimental controversies. We show that the melting transition corresponds to the melting of the protein as a whole, and not solely to the helix-coil transition. The breadth of the folding transition arises from the spread in the melting temperatures (from ∼325 K to ∼302 K) of the individual transitions: formation of the hydrophobic core, β-hairpin and tertiary fold, with the helix formed earlier. Our simulations initiated from an extended chain accurately predict the native structure, provide a reasonable estimate of the transition barrier height, and explicitly demonstrate the existence of multiple pathways and multiple transition states for folding. Our exhaustive sampling enables us to assess the quality of the Amber ff96/igb5 combination and reveals that while this force field can predict the correct native fold, it nonetheless overstabilizes the α-helix portion of the protein (Tm = ∼387K) as well as the denatured structures. The protein folding process, in which a linear chain of amino acids reaches its biologically active three-dimensional shape, is fundamental to life. Small “ultrafast” folders, proteins that fold in microseconds, have received considerable attention, because these proteins serve as model systems for the folding of larger proteins, and thus permit a testing of the accuracy of computational models as well as an assessment of protein folding theories. FSD-1, a designed small ultrafast folder with a ββα fold, has been actively studied in the last few years as a model system for mixed α/β fold proteins. The suitability of this protein to describe the folding of naturally occurring proteins has however recently been challenged based on the observation that the melting transition is very broad, with ill-resolved baselines. Prior simulations have not been successful in providing an interpretation of this broad melting transition. In the present study, our extensive molecular dynamics simulations using the AMBER protein force field (ff96) coupled with the implicit solvent model (IGB = 5) shed new light on the nature of the folding transition of this protein, as well as reveal the strengths and weaknesses of the force field in predicting the thermodynamics and kinetics of folding.
Collapse
|
60
|
Sgourakis NG, Merced-Serrano M, Boutsidis C, Drineas P, Du Z, Wang C, Garcia AE. Atomic-level characterization of the ensemble of the Aβ(1-42) monomer in water using unbiased molecular dynamics simulations and spectral algorithms. J Mol Biol 2010; 405:570-83. [PMID: 21056574 DOI: 10.1016/j.jmb.2010.10.015] [Citation(s) in RCA: 186] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 10/06/2010] [Accepted: 10/13/2010] [Indexed: 01/05/2023]
Abstract
Aβ(1-42) is the highly pathologic isoform of amyloid-β, the peptide constituent of fibrils and neurotoxic oligomers involved in Alzheimer's disease. Recent studies on the structural features of Aβ in water have suggested that the system can be described as an ensemble of distinct conformational species in fast exchange. Here, we use replica exchange molecular dynamics (REMD) simulations to characterize the conformations accessible to Aβ42 in explicit water solvent, under the ff99SB force field. Monitoring the correlation between J-coupling((3)J(H(N))(H(α))) and residual dipolar coupling (RDC) data calculated from the REMD trajectories to their experimental values, as determined by NMR, indicates that the simulations converge towards sampling an ensemble that is representative of the experimental data after 60 ns/replica of simulation time. We further validate the converged MD-derived ensemble through direct comparison with (3)J(H(N))(H(α)) and RDC experimental data. Our analysis indicates that the ff99SB-derived REMD ensemble can reproduce the experimental J-coupling values with high accuracy and further provide good agreement with the RDC data. Our results indicate that the peptide is sampling a highly diverse range of conformations: by implementing statistical learning techniques (Laplacian eigenmaps, spectral clustering, and Laplacian scores), we are able to obtain an otherwise hidden structure in the complex conformational space of the peptide. Using these methods, we characterize the peptide conformations and extract their intrinsic characteristics, identify a small number of different conformations that characterize the whole ensemble, and identify a small number of protein interactions (such as contacts between the peptide termini) that are the most discriminative of the different conformations and thus can be used in designing experimental probes of transitions between such molecular states. This is a study of an important intrinsically disordered peptide system that provides an atomic-level description of structural features and interactions that are relevant during the early stages of the oligomerization and fibril nucleation pathways.
Collapse
Affiliation(s)
- Nikolaos G Sgourakis
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, NY 12180, USA
| | | | | | | | | | | | | |
Collapse
|
61
|
Davis CH, Berkowitz ML. A molecular dynamics study of the early stages of amyloid-beta(1-42) oligomerization: the role of lipid membranes. Proteins 2010; 78:2533-45. [PMID: 20602359 DOI: 10.1002/prot.22763] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
As research progresses toward understanding the role of the amyloid-beta (Abeta) peptide in Alzheimer's disease, certain aspects of the aggregation process for Abeta are still not clear. In particular, the accepted constitution of toxic aggregates in neurons has shifted toward small oligomers. However, the process of forming these oligomers in cells is also not full clear. Even more interestingly, it has been implied that cell membranes, and, in particular, anionic lipids within those membranes, play a key role in the progression of Abeta aggregation, but the exact nature of the Abeta-membrane interaction in this process is unknown. In this work, we use a thermodynamic cycle and umbrella sampling molecular dynamics to investigate dimerization of the 42-residue Abeta peptide on model zwitterionic dipalmitoylphosphatidylcholine (DPPC) or model anionic dioleoylphosphatidylserine (DOPS) bilayer surfaces. We determined that Abeta dimerization was strongly favored through interactions with the DOPS bilayer. Further, our calculations showed that the DOPS bilayer promoted strong protein-protein interactions within the Abeta dimer, whereas DPPC favored strong protein-lipid interactions. By promoting dimer formation and subsequent dimer release into the solvent, the DOPS bilayer acts as a catalyst in Abeta aggregation.
Collapse
Affiliation(s)
- Charles H Davis
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | | |
Collapse
|
62
|
Li H, Monien BH, Lomakin A, Zemel R, Fradinger EA, Tan M, Spring SM, Urbanc B, Xie CW, Benedek GB, Bitan G. Mechanistic investigation of the inhibition of Abeta42 assembly and neurotoxicity by Abeta42 C-terminal fragments. Biochemistry 2010; 49:6358-64. [PMID: 20568734 DOI: 10.1021/bi100773g] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Oligomeric forms of amyloid beta-protein (Abeta) are key neurotoxins in Alzheimer's disease (AD). Previously, we found that C-terminal fragments (CTFs) of Abeta42 interfered with assembly of full-length Abeta42 and inhibited Abeta42-induced toxicity. To decipher the mechanism(s) by which CTFs affect Abeta42 assembly and neurotoxicity, here, we investigated the interaction between Abeta42 and CTFs using photoinduced cross-linking and dynamic light scattering. The results demonstrate that distinct parameters control CTF inhibition of Abeta42 assembly and Abeta42-induced toxicity. Inhibition of Abeta42-induced toxicity was found to correlate with stabilization of oligomers with a hydrodynamic radius (R(H)) of 8-12 nm and attenuation of formation of oligomers with an R(H) of 20-60 nm. In contrast, inhibition of Abeta42 paranucleus formation correlated with CTF solubility and the degree to which CTFs formed amyloid fibrils themselves but did not correlate with inhibition of Abeta42-induced toxicity. Our findings provide important insight into the mechanisms by which different CTFs inhibit the toxic effect of Abeta42 and suggest that stabilization of nontoxic Abeta42 oligomers is a promising strategy for designing inhibitors of Abeta42 neurotoxicity.
Collapse
Affiliation(s)
- Huiyuan Li
- Department of Neurology, David Geffen School of Medicine, University of California-Los Angeles, 635 Charles E.Young Drive S., Los Angeles, CA 90095, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
63
|
Miller Y, Ma B, Nussinov R. Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in a rugged energy landscape. Chem Rev 2010; 110:4820-38. [PMID: 20402519 PMCID: PMC2920034 DOI: 10.1021/cr900377t] [Citation(s) in RCA: 234] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Indexed: 01/13/2023]
Affiliation(s)
| | | | - Ruth Nussinov
- To whom correspondence should be addressed. Tel.: (301) 846-5579. Fax: (301) 846-5598. E-mail:
| |
Collapse
|
64
|
Ly T, Julian RR. Elucidating the tertiary structure of protein ions in vacuo with site specific photoinitiated radical reactions. J Am Chem Soc 2010; 132:8602-9. [PMID: 20524634 PMCID: PMC2907658 DOI: 10.1021/ja910665d] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new method for identifying residue specific through space contacts as a function of protein secondary and tertiary structure in the gas phase is presented. Photodissociation of a non-native carbon-iodine bond incorporated into Tyr59 of ubiquitin yields a radical site specifically at that residue. The subsequent radical migration is shown to be highly dependent on the structure of the protein. Radical-directed dissociation (RDD) of low charge states, which adopt compact structures, generates backbone fragmentation that is prominently distributed throughout the protein sequence, including residues that are distant in sequence from Tyr59. Higher charge states of ubiquitin, which adopt elongated, unfolded structures, yield RDD that is primarily nearby in sequence to Tyr59. Regardless of which structure is probed, information at the residue-level is obtained by examining specific radical-donor and radical-acceptor pairs. The relative importance of a particular interaction pair for a specific conformation can be revealed by tracking the charge state dependence of the dissociation. Structurally important contact pairs exhibit strong and concerted changes in relative intensities as a function of charge state and can also be used to reveal structural features which persist among different protein structures. Moreover, incorporation of distance constraint information into molecular mechanics conformational searches can be used to drive the search toward relevant conformational space. Implementation of this approach has revealed highly stable, previously undiscovered structures for the +4 and +6 charge states of ubiquitin, which bear little resemblance to the crystal structure.
Collapse
Affiliation(s)
- Tony Ly
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Ryan R. Julian
- Department of Chemistry, University of California, Riverside, CA 92521
| |
Collapse
|
65
|
Li H, Monien BH, Fradinger EA, Urbanc B, Bitan G. Biophysical characterization of Abeta42 C-terminal fragments: inhibitors of Abeta42 neurotoxicity. Biochemistry 2010; 49:1259-67. [PMID: 20050679 DOI: 10.1021/bi902075h] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A key event in Alzheimer's disease (AD) is age-dependent, brain accumulation of amyloid beta-protein (Abeta) leading to Abeta self-association into neurotoxic oligomers. Previously, we showed that Abeta oligomerization and neurotoxicity could be inhibited by C-terminal fragments (CTFs) of Abeta42. Because these CTFs are highly hydrophobic, we asked if they themselves aggregated and, if so, what parameters regulated their aggregation. To answer these questions, we investigated the dependence of CTF aqueous solubility, aggregation kinetics, and morphology on peptide length and sequence and the correlation between these characteristics and inhibition of Abeta42-induced toxicity. We found that CTFs up to 8 residues long were soluble at concentrations >100 microM and had a low propensity to aggregate. Longer CTFs were soluble at approximately 1-80 microM, and most, but not all, readily formed beta-sheet-rich fibrils. Comparison to Abeta40-derived CTFs showed that the C-terminal dipeptide I41-A42 strongly promoted aggregation. Aggregation propensity correlated with the previously reported tendency to form beta-hairpin conformation but not with inhibition of Abeta42-induced neurotoxicity. The data enhance our understanding of the physical characteristics that affect CTF activity and advance our ability to design, synthesize, and test future generations of inhibitors.
Collapse
Affiliation(s)
- Huiyuan Li
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, 635 Charles E. Young Drive, Los Angeles, California 90095, USA
| | | | | | | | | |
Collapse
|
66
|
Miyashita N, Straub JE, Thirumalai D. Structures of beta-amyloid peptide 1-40, 1-42, and 1-55-the 672-726 fragment of APP-in a membrane environment with implications for interactions with gamma-secretase. J Am Chem Soc 2010; 131:17843-52. [PMID: 19995075 DOI: 10.1021/ja905457d] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Aggregation of Amyloid beta (Abeta) peptide has been linked to the neurodegenerative Alzheimer's Disease and implicated in other amyloid diseases including cerebral amyloid angiopathy. Abeta peptide is generated by cleavage of the amyloid precursor protein (APP) by transmembrane proteases. It is crucial to determine the structures of beta-amyloid peptides in a membrane to provide a molecular basis for the cleavage mechanism. We report the structures of amyloid beta peptide (Abeta(1-40) and Abeta(1-42)) as well as the 672-726 fragment of APP (referred to as Abeta(1-55)) in a membrane environment determined by replica-exchange molecular dynamics simulation. Abeta(1-40) is found to have two helical domains A (13-22) and B(30-35) and a type I beta-turn at 23-27. The peptide is localized at the interface between membrane and solvent. Substantial fluctuations in domain A are observed. The dominant simulated tertiary structure of Abeta(1-40) is observed to be similar to the simulated Abeta(1-42) structure. However, there are differences observed in the overall conformational ensemble, as characterized by the two-dimensional free energy surfaces. The fragment of APP (Abeta(1-55)) is observed to have a long transmembrane helix. The position of the transmembrane region and ensemble of membrane structures are elucidated. The conformational transition between the transmembrane Abeta(1-55) structure, prior to cleavage, and the Abeta(1-40) structure, following cleavage, is proposed.
Collapse
Affiliation(s)
- Naoyuki Miyashita
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | | | | |
Collapse
|
67
|
Dupuis NF, Wu C, Shea JE, Bowers MT. Human islet amyloid polypeptide monomers form ordered beta-hairpins: a possible direct amyloidogenic precursor. J Am Chem Soc 2010; 131:18283-92. [PMID: 19950949 DOI: 10.1021/ja903814q] [Citation(s) in RCA: 190] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Oligomerization of human islet amyloid polypeptide (IAPP) has been increasingly considered a pathogenic process in type II diabetes. Here structural features of the IAPP monomer have been probed using a combination of ion mobility mass spectrometry (IMS-MS) and all-atom replica exchange molecular dynamics (REMD) simulations. Three distinct conformational families of human IAPP monomer are observed in IMS experiments, and two of them are identified as dehydrated solution structures on the basis of our simulation results: one is an extended beta-hairpin structural family, and the second is a compact helix-coil structural family. The extended beta-hairpin family is topologically similar to the peptide conformation in the solid-state NMR fibril structure published by Tycko and co-workers. It is absent in both experiments and simulations performed on the non-amyloidogenic rat IAPP, suggesting it may play an important role in the fibrillation pathway of human IAPP. In addition, pH dependence studies show that the relative abundance of the beta-hairpin structural family is significantly enhanced at pH 8.0. This observation is consistent with the increased rate of fibrillation at high pH in vitro and offers a possible explanation of the pH dependent fibrillation in vivo. This paper, to the best of our knowledge, presents the first experimental evidence of a significant population of beta-hairpin conformers for the IAPP peptide. It is consistent with a previous suggestion in the literature that beta-sheet-rich oligomers are assembled from ordered beta-hairpins rather than from coiled structures.
Collapse
Affiliation(s)
- Nicholas F Dupuis
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | | | | | | |
Collapse
|
68
|
Davis CH, Berkowitz ML. Structure of the amyloid-beta (1-42) monomer absorbed to model phospholipid bilayers: a molecular dynamics study. J Phys Chem B 2010; 113:14480-6. [PMID: 19807060 DOI: 10.1021/jp905889z] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The amyloid-beta (Abeta) peptide, the 39 to 43 amino acid peptide that plays a substantial role in Alzheimer's disease, has been shown to interact strongly with lipids both in vitro and in vivo. Abeta-lipid interactions have been proposed as a considerable factor in accelerating Abeta aggregation through the templating role of membranes in aggregation disorders. Previous work has shown that anionic lipids are able to significantly increase Abeta aggregation rate and induce a structural conversion in Abeta from a random coil to a beta-structure that is similar to the monomer structure observed in mature fibrils. However, it is unclear if this structural change occurs with the Abeta monomer because of direct interactions with the lipids or if the structural change results from protein-protein interactions during oligomerization. We use extensive replica exchange molecular dynamics simulations of an Abeta monomer bound to a homogeneous model zwitterionic or anionic lipid bilayer. From these simulations, we do not observe any significant beta-structure formation except for a small, unstable beta-hairpin formed on the anionic dioleylphosphatidylserine bilayer. Further, we see that the Asp23-Lys28 salt bridge that plays a role in beta-hairpin formation is not substantially formed on the bilayer surface and that Lys28 preferentially interacts with lipids when bound to the bilayer. These results suggest that the structural conversion seen in experiments are not due to the ordering of monomeric Abeta on the bilayer surface but are a result of protein-protein interactions enhanced by Abeta binding to the cell membrane.
Collapse
Affiliation(s)
- Charles H Davis
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | | |
Collapse
|
69
|
Siu CK, Guo Y, Saminathan IS, Hopkinson AC, Siu KWM. Optimization of Parameters Used in Algorithms of Ion-Mobility Calculation for Conformational Analyses. J Phys Chem B 2009; 114:1204-12. [DOI: 10.1021/jp910858z] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Chi-Kit Siu
- Department of Biology and Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, China
| | - Yuzhu Guo
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto M3J 1P3, Canada
| | - Irine S. Saminathan
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto M3J 1P3, Canada
| | - Alan C. Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto M3J 1P3, Canada
| | - K. W. Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto M3J 1P3, Canada
| |
Collapse
|
70
|
Grabenauer M, Wu C, Soto P, Shea JE, Bowers MT. Oligomers of the Prion Protein Fragment 106−126 Are Likely Assembled from β-Hairpins in Solution, and Methionine Oxidation Inhibits Assembly without Altering the Peptide’s Monomeric Conformation. J Am Chem Soc 2009; 132:532-9. [DOI: 10.1021/ja905595k] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Megan Grabenauer
- Departments of Chemistry and Biochemistry and of Physics, University of California, Santa Barbara, California 93106, and Department of Physics, Creighton University, Omaha, Nebraska 68178
| | - Chun Wu
- Departments of Chemistry and Biochemistry and of Physics, University of California, Santa Barbara, California 93106, and Department of Physics, Creighton University, Omaha, Nebraska 68178
| | - Patricia Soto
- Departments of Chemistry and Biochemistry and of Physics, University of California, Santa Barbara, California 93106, and Department of Physics, Creighton University, Omaha, Nebraska 68178
| | - Joan-Emma Shea
- Departments of Chemistry and Biochemistry and of Physics, University of California, Santa Barbara, California 93106, and Department of Physics, Creighton University, Omaha, Nebraska 68178
| | - Michael T. Bowers
- Departments of Chemistry and Biochemistry and of Physics, University of California, Santa Barbara, California 93106, and Department of Physics, Creighton University, Omaha, Nebraska 68178
| |
Collapse
|
71
|
McLean JA. The mass-mobility correlation redux: the conformational landscape of anhydrous biomolecules. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1775-81. [PMID: 19646898 DOI: 10.1016/j.jasms.2009.06.016] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Revised: 06/24/2009] [Accepted: 06/25/2009] [Indexed: 05/09/2023]
Abstract
Structural separations on the basis of gas-phase ion mobility-mass spectrometry are increasingly used for the analysis of complex biological samples. As a tool to elucidate biomolecular structure, ion mobility-mass spectrometry methods are unique in that direct molecular structural information is obtained for all resolved species, largely irrespective of the complexity of the sample. Computational approaches are used to interpret and discern structural details consistent with the empirical results. To a first approximation, correlations of mobility with mass allow for qualitative identification of the molecular class to which a particular species belongs. These correlations allow simultaneous characterization of different classes of biomolecules, which provides a means for combining omics measurements, such as lipidomics, proteomics, glycomics, and metabolomics, in the same analysis. Examination of the correlation of fine structure reveals that specific structural motifs, chemical functionality, chemical connectivity, and composition may also be determined, depending on the specific biomolecular class. Mapping the coarse and fine structure in ion mobility-mass spectrometry conformation space measurements provides an atlas for interpretation and discovery in complicated spectra.
Collapse
Affiliation(s)
- John A McLean
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee 37215, USA.
| |
Collapse
|
72
|
Drayβ MK, Blunk D, Oomens J, Gao B, Wyttenbach T, Bowers MT, Schäfer M. Systematic Study of the Structures of Potassiated Tertiary Amino Acids: Salt Bridge Structures Dominate. J Phys Chem A 2009; 113:9543-50. [DOI: 10.1021/jp903036t] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Miriam K. Drayβ
- Department of Chemistry, University of Cologne, Greinstraβe 4, 50939 Köln, Germany, FOM Institute for Plasmaphysics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands,University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands, and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Dirk Blunk
- Department of Chemistry, University of Cologne, Greinstraβe 4, 50939 Köln, Germany, FOM Institute for Plasmaphysics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands,University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands, and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Jos Oomens
- Department of Chemistry, University of Cologne, Greinstraβe 4, 50939 Köln, Germany, FOM Institute for Plasmaphysics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands,University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands, and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Bing Gao
- Department of Chemistry, University of Cologne, Greinstraβe 4, 50939 Köln, Germany, FOM Institute for Plasmaphysics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands,University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands, and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Thomas Wyttenbach
- Department of Chemistry, University of Cologne, Greinstraβe 4, 50939 Köln, Germany, FOM Institute for Plasmaphysics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands,University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands, and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Michael T. Bowers
- Department of Chemistry, University of Cologne, Greinstraβe 4, 50939 Köln, Germany, FOM Institute for Plasmaphysics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands,University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands, and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Mathias Schäfer
- Department of Chemistry, University of Cologne, Greinstraβe 4, 50939 Köln, Germany, FOM Institute for Plasmaphysics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands,University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands, and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| |
Collapse
|
73
|
Murray MM, Bernstein SL, Nyugen V, Condron MM, Teplow DB, Bowers MT. Amyloid beta protein: Abeta40 inhibits Abeta42 oligomerization. J Am Chem Soc 2009; 131:6316-7. [PMID: 19385598 PMCID: PMC2697393 DOI: 10.1021/ja8092604] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Abeta40 and Abeta42 are peptides that adopt similar random-coil structures in solution. Abeta42, however, is significantly more neurotoxic than Abeta40 and forms amyloid fibrils much more rapidly than Abeta40. Here, mass spectrometry and ion mobility spectrometry are used to investigate a mixture of Abeta40 and Abeta42. The mass spectrum for the mixed solution shows the presence of a heterooligomer composed of equal parts of Abeta40 and Abeta42. Ion mobility results indicate that this mixed species comprises an oligomer distribution extending to tetramers. Abeta40 alone produces such a distribution, whereas Abeta42 alone produces oligomers as large as dodecamers. This indicates that Abeta40 inhibits Abeta42 oligomerization.
Collapse
Affiliation(s)
- Megan M. Murray
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-950
| | - Summer L. Bernstein
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-950
| | - Vy Nyugen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-950
| | - Margaret M. Condron
- Department of Neurology, David Geffen School of Medicine, and Molecular Biology Institute and Brain Research Institute, University of California, Los Angeles, CA 90095
| | - David B. Teplow
- Department of Neurology, David Geffen School of Medicine, and Molecular Biology Institute and Brain Research Institute, University of California, Los Angeles, CA 90095
| | - Michael T. Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-950
| |
Collapse
|