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Molecular dynamics simulations of copper binding to amyloid-β Glu22 mutants. Heliyon 2019; 6:e03071. [PMID: 31909253 PMCID: PMC6940626 DOI: 10.1016/j.heliyon.2019.e03071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 11/25/2019] [Accepted: 12/13/2019] [Indexed: 11/21/2022] Open
Abstract
We report microsecond timescale ligand field molecular dynamics simulations of the copper complexes of three known mutants of the amyloid-β peptide, E22G, E22Q and E22K, alongside the naturally occurring sequence. We find that all three mutants lead to formation of less compact structures than the wild-type: E22Q is the most similar to the native peptide, while E22G and especially E22K are markedly different in size, shape and stability. Turn and coil structures dominate all structures studied but subtle differences in helical and β-sheet distribution are noted, especially in the C-terminal region. The origin of these changes is traced to disruption of key salt bridges: in particular, the Asp23-Lys28 bridge that is prevalent in the wild-type is absent in E22G and E22K, while Lys22 in the latter mutant forms a strong association with Asp23. We surmise that the drastically different pattern of salt bridges in the mutants lead to adoption of a different structural ensemble of the peptide backbone, and speculate that this might affect the ability of the mutant peptides to aggregate in the same manner as known for the wild-type.
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Kepp KP, Squitti R. Copper imbalance in Alzheimer’s disease: Convergence of the chemistry and the clinic. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.06.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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Mehra R, Kepp KP. Cell size effects in the molecular dynamics of the intrinsically disordered Aβ peptide. J Chem Phys 2019; 151:085101. [DOI: 10.1063/1.5115085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Rukmankesh Mehra
- Technical University of Denmark, DTU Chemistry, Building 206, 2800 Kgs. Lyngby, Denmark
| | - Kasper P. Kepp
- Technical University of Denmark, DTU Chemistry, Building 206, 2800 Kgs. Lyngby, Denmark
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Tiwari MK, Hägglund PM, Møller IM, Davies MJ, Bjerrum MJ. Copper ion / H 2O 2 oxidation of Cu/Zn-Superoxide dismutase: Implications for enzymatic activity and antioxidant action. Redox Biol 2019; 26:101262. [PMID: 31284117 PMCID: PMC6614508 DOI: 10.1016/j.redox.2019.101262] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/18/2019] [Accepted: 06/26/2019] [Indexed: 01/25/2023] Open
Abstract
Copper ion-catalyzed oxidation of yeast SOD1 (ySOD1) was examined to determine early oxidative modifications, including oxidation of a crucial disulfide bond, and the structural and functional repercussions of these events. The study used distinct oxidative conditions: Cu2+/H2O2, Cu2+/H2O2/AscH− and Cu2+/H2O2/glucose. Capillary electrophoresis experiments and quantification of protein carbonyls indicate that ySOD1 is highly susceptible to oxidative modification and that changes can be detected within 0.1 min of the initiation of the reaction. Oxidation-induced structural perturbations, characterized by circular dichroism, revealed the formation of partially-unfolded ySOD1 species in a dose-dependent manner. Consistent with these structural changes, pyrogallol assay indicates a partial loss of enzymatic activity. ESI-MS analyses showed seven distinct oxidized ySOD1 species under mild oxidation within 0.1 min. LC/MS analysis after proteolytic digestion demonstrated that the copper-coordinating active site histidine residues, His47 and His49, were converted into 2-oxo-histidine. Furthermore, the Cu and Zn bridging residue, His64 is converted into aspartate/asparagine. Importantly, the disulfide-bond Cys58-Cys147 which is critical for the structural and functional integrity of ySOD1 was detected as being oxidized at Cys147. We propose, based on LC/MS analyses, that disulfide-bond oxidation occurs without disulfide bond cleavage. Modifications were also detected at Met85 and five surface-exposed Lys residues. Based on these data we propose that the Cys58-Cys147 bond may act as a sacrificial target for oxidants and protect ySOD1 from oxidative inactivation arising from exposure to Cu2+/H2O2 and auto-inactivation during extended enzymatic turnover. Oxidation of yeast superoxide dismutase (ySOD1) by Cu2+/H2O2 is examined. Rapid modification of His, Met, Cys and Lys residues detected by LC-MS methods. Oxidation of active site His residues and partial protein unfolding are early events. The Cys58-Cys147 disulfide bond is oxidized and may act as a sacrificial target. Excess exogenous Cu2+ decreases protein damage and can reverse loss of activity.
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Affiliation(s)
- Manish K Tiwari
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Per M Hägglund
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Slagelse, Denmark
| | - Michael J Davies
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten J Bjerrum
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
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Wilkens C, Tiwari MK, Webb H, Jam M, Czjzek M, Svensson B. Asp271 is critical for substrate interaction with the surface binding site in β-agarase a from Zobellia galactanivorans. Proteins 2018; 87:34-40. [PMID: 30315603 DOI: 10.1002/prot.25614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/11/2018] [Accepted: 10/08/2018] [Indexed: 11/10/2022]
Abstract
In the marine environment agar degradation is assured by bacteria that contain large agarolytic systems with enzymes acting in various endo- and exo-modes. Agarase A (AgaA) is an endo-glycoside hydrolase of family 16 considered to initiate degradation of agarose. Agaro-oligosaccharide binding at a unique surface binding site (SBS) in AgaA from Zobellia galactanivorans was investigated by computational methods in conjunction with a structure/sequence guided approach of site-directed mutagenesis probed by surface plasmon resonance binding analysis of agaro-oligosaccharides of DP 4-10. The crystal structure has shown that agaro-octaose interacts via H-bonds and aromatic stacking along 7 subsites (L through R) of the SBS in the inactive catalytic nucleophile mutant AgaA-E147S. D271 is centrally located in the extended SBS where it forms H-bonds to galactose and 3,6-anhydrogalactose residues of agaro-octaose at subsites O and P. We propose D271 is a key residue in ligand binding to the SBS. Thus AgaA-E147S/D271A gave slightly decreasing KD values from 625 ± 118 to 468 ± 13 μM for agaro-hexaose, -octaose, and -decaose, which represent 3- to 4-fold reduced affinity compared with AgaA-E147S. Molecular dynamics simulations and interaction analyses of AgaA-E147S/D271A indicated disruption of an extended H-bond network supporting that D271 is critical for the functional SBS. Notably, neither AgaA-E147S/W87A nor AgaA-E147S/W277A, designed to eliminate stacking with galactose residues at subsites O and Q, respectively, were produced in soluble form. W87 and W277 may thus control correct folding and structural integrity of AgaA.
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Affiliation(s)
- Casper Wilkens
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Manish K Tiwari
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Helen Webb
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Murielle Jam
- Laboratory for Integrative Biology of Marine Models, Station Biologique, Sorbonne University, Université Pierre et Marie Curie, Roscoff, France
| | - Mirjam Czjzek
- Laboratory for Integrative Biology of Marine Models, Station Biologique, Sorbonne University, Université Pierre et Marie Curie, Roscoff, France
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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Kepp KP. Ten Challenges of the Amyloid Hypothesis of Alzheimer’s Disease. J Alzheimers Dis 2016; 55:447-457. [DOI: 10.3233/jad-160550] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Kepp KP. Alzheimer's disease due to loss of function: A new synthesis of the available data. Prog Neurobiol 2016; 143:36-60. [PMID: 27327400 DOI: 10.1016/j.pneurobio.2016.06.004] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/10/2016] [Accepted: 06/11/2016] [Indexed: 12/11/2022]
Abstract
Alzheimer's Disease (AD) is a highly complex disease involving a broad range of clinical, cellular, and biochemical manifestations that are currently not understood in combination. This has led to many views of AD, e.g. the amyloid, tau, presenilin, oxidative stress, and metal hypotheses. The amyloid hypothesis has dominated the field with its assumption that buildup of pathogenic β-amyloid (Aβ) peptide causes disease. This paradigm has been criticized, yet most data suggest that Aβ plays a key role in the disease. Here, a new loss-of-function hypothesis is synthesized that accounts for the anomalies of the amyloid hypothesis, e.g. the curious pathogenicity of the Aβ42/Aβ40 ratio, the loss of Aβ caused by presenilin mutation, the mixed phenotypes of APP mutations, the poor clinical-biochemical correlations for genetic variant carriers, and the failure of Aβ reducing drugs. The amyloid-loss view accounts for recent findings on the structure and chemical features of Aβ variants and their coupling to human patient data. The lost normal function of APP/Aβ is argued to be metal transport across neuronal membranes, a view with no apparent anomalies and substantially more explanatory power than the gain-of-function amyloid hypothesis. In the loss-of-function scenario, the central event of Aβ aggregation is interpreted as a loss of soluble, functional monomer Aβ rather than toxic overload of oligomers. Accordingly, new research models and treatment strategies should focus on remediation of the functional amyloid balance, rather than strict containment of Aβ, which, for reasons rationalized in this review, has failed clinically.
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Affiliation(s)
- Kasper P Kepp
- Technical University of Denmark, DTU Chemistry, DK-2800 Kongens Lyngby, Denmark.
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Somavarapu AK, Kepp KP. Direct Correlation of Cell Toxicity to Conformational Ensembles of Genetic Aβ Variants. ACS Chem Neurosci 2015; 6:1990-6. [PMID: 26447342 DOI: 10.1021/acschemneuro.5b00238] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We report a systematic analysis of conformational ensembles generated from multiseed molecular dynamics simulations of all 15 known genetic variants of Aβ42. We show that experimentally determined variant toxicities are largely explained by random coil content of the amyloid ensembles (correlation with smaller EC50 values; R(2) = 0.54, p = 0.01), and to some extent the helix character (more helix-character is less toxic, R(2) = 0.32, p = 0.07) and hydrophobic surface (R(2) = 0.37, p = 0.04). Our findings suggest that qualitative structural features of the amyloids, rather than the quantitative levels, are fundamentally related to neurodegeneration. The data provide molecular explanations for the high toxicity of E22 variants and for the protective features of the recently characterized A2T variant. The identified conformational features, for example, the local helix-coil-strand transitions of the C-terminals of the peptides, are of likely interest in the direct targeting of amyloids by rational drug design.
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Affiliation(s)
- Arun Kumar Somavarapu
- DTU Chemistry, Technical University of Denmark, Kemiorvet 206, DK-2800 Kongens Lyngby, Denmark
| | - Kasper P. Kepp
- DTU Chemistry, Technical University of Denmark, Kemiorvet 206, DK-2800 Kongens Lyngby, Denmark
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Somavarapu AK, Kepp KP. The Dependence of Amyloid-β Dynamics on Protein Force Fields and Water Models. Chemphyschem 2015; 16:3278-89. [PMID: 26256268 DOI: 10.1002/cphc.201500415] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Indexed: 01/10/2023]
Abstract
We studied the dynamics of Aβ40 , involved in Alzheimer's disease, by using 21 methods combined from Amber03, Amber99sb-ILDN, Charmm27, Charmm22*, OPLS-2001, OPLS-2006, OPLS-2008, Gromos96-43a1, Gromos96-53a6, Gromos96-54a7, and the water models SPC, TIP3P, TIP4P. Major differences in the structural ensembles were systematized: Amber03, Charmm27, and Gromos96-54a7 stabilize the helices; Gromos96-43a1 and Gromos53a6 favor the β-strands (with Charmm22* and Amber99sb-ILDN in between), and OPLS produces unstructured ensembles. The accuracy of the NMR chemical shifts was in the order: Charmm22*>Amber99sb-ILDN>OPLS-2008≈Gromos96-43a1>Gromos96-54a7≈OPLS-2001>OPLS-2006>Gromos96-53a6>Charmm27>Amber03. The computed (3) JHNHα -coupling constants were sensitive to experiment type and Karplus parameterization. Overall, the ensembles of Charmm22* and Amber99sb-ILDN provided the best agreement with experimental NMR and circular dichroism data, providing a model for the real Aβ monomer ensemble. Also, the polar water model TIP3P significantly favored helix and compact conformations.
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Affiliation(s)
| | - Kasper P Kepp
- Technical University of Denmark, DTU Chemistry, DK-2800, Kongens Lyngby, Denmark.
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Affiliation(s)
- Manish K. Tiwari
- DTU Chemistry Technical University of Denmark Kongens Lyngby Denmark
| | - Kasper P. Kepp
- DTU Chemistry Technical University of Denmark Kongens Lyngby Denmark
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Tiwari MK, Kepp KP. Modeling the Aggregation Propensity and Toxicity of Amyloid-β Variants. J Alzheimers Dis 2015; 47:215-29. [DOI: 10.3233/jad-150046] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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