Interaction of Amyloid Inhibitor Proteins with Amyloid Beta Peptides: Insight from Molecular Dynamics Simulations
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{"title"=>"Interaction of amyloid inhibitor proteins with amyloid beta peptides: Insight from molecular dynamics simulations", "type"=>"journal", "authors"=>[{"first_name"=>"Payel", "last_name"=>"Das", "scopus_author_id"=>"8916011000"}, {"first_name"=>"Seung Gu", "last_name"=>"Kang", "scopus_author_id"=>"55613716300"}, {"first_name"=>"Sally", "last_name"=>"Temple", "scopus_author_id"=>"7004577083"}, {"first_name"=>"Georges", "last_name"=>"Belfort", "scopus_author_id"=>"7006331990"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"25422897", "sgr"=>"84912525082", "doi"=>"10.1371/journal.pone.0113041", "scopus"=>"2-s2.0-84912525082", "pui"=>"600596219", "isbn"=>"19326203 (ISSN)", "issn"=>"19326203"}, "id"=>"233093e3-0b94-38ff-a5a7-47f78ff38661", "abstract"=>"Knowledge of the detailed mechanism by which proteins such as human αB- crystallin and human lysozyme inhibit amyloid beta (Aβ) peptide aggregation is crucial for designing treatment for Alzheimer's disease. Thus, unconstrained, atomistic molecular dynamics simulations in explicit solvent have been performed to characterize the Aβ17-42 assembly in presence of the αB-crystallin core domain and of lysozyme. Simulations reveal that both inhibitor proteins compete with inter-peptide interaction by binding to the peptides during the early stage of aggregation, which is consistent with their inhibitory action reported in experiments. However, the Aβ binding dynamics appear different for each inhibitor. The binding between crystallin and the peptide monomer, dominated by electrostatics, is relatively weak and transient due to the heterogeneous amino acid distribution of the inhibitor surface. The crystallin-bound Aβ oligomers are relatively long-lived, as they form more extensive contact surface with the inhibitor protein. In contrast, a high local density of arginines from lysozyme allows strong binding with Aβ peptide monomers, resulting in stable complexes. Our findings not only illustrate, in atomic detail, how the amyloid inhibitory mechanism of human αB-crystallin, a natural chaperone, is different from that of human lysozyme, but also may aid de novo design of amyloid inhibitors.", "link"=>"http://www.mendeley.com/research/interaction-amyloid-inhibitor-proteins-amyloid-beta-peptides-insight-molecular-dynamics-simulations", "reader_count"=>34, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>9, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>10, "Student > Master"=>5, "Other"=>1, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>9, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>10, "Student > Master"=>5, "Other"=>1, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>10, "Agricultural and Biological Sciences"=>4, "Neuroscience"=>2, "Physics and Astronomy"=>1, "Chemistry"=>13, "Immunology and Microbiology"=>1, "Engineering"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Neuroscience"=>{"Neuroscience"=>2}, "Chemistry"=>{"Chemistry"=>13}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>10}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>1, "United Kingdom"=>1, "France"=>1, "India"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1806872"], "description"=>"<p>(a) Probability distributions of the number of heavy atom contacts formed between two Aβ peptides (black) in the control system (no inhibitor), between ACD and an Aβ monomer (red), between ACD and an Aβ oligomer (green), and between lysozyme and an Aβ monomer (blue). Lysozyme-bound Aβ oligomers were excluded from the analysis due to their minor population. At least five different ∼200 ns runs were used, in which multiple binding/unbinding events were observed. (b) Mean survival time correlation function, S(t), of peptides in the vicinity of the inhibitor: ACD-bound monomer (black), ACD-bound oligomer (red) and lysozyme-bound monomer (green). Each curve shows average of five independent runs. S(t = 0) measures the average number of peptide molecules bound with inhibitor, and S(t) gives the average number of peptide molecules that remain bound after a period of time, t, given that they were present at t = 0. A short escape of 1 ns was allowed during the calculation.</p>", "links"=>[], "tags"=>["binding", "inhibitor protein", "inhibitor proteins", "inhibitor surface", "amyloid inhibitors", "mechanism", "contact surface", "Molecular Dynamics Simulations Knowledge", "acid distribution", "aggregation", "α B", "Amyloid Beta Peptides", "Amyloid Inhibitor Proteins", "lysozyme", "crystallin", "dynamics simulations", "amyloid beta", "peptide monomer"], "article_id"=>1251751, "categories"=>["Biological Sciences"], "users"=>["Payel Das", "Seung-gu Kang", "Sally Temple", "Georges Belfort"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113041.g003", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Binding_and_lifetime_of_inhibitor_peptide_complexes_/1251751", "title"=>"Binding and lifetime of inhibitor-peptide complexes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-25 03:11:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1806871"], "description"=>"<p>2D potential of mean force PMF plots as a function of the number of contacts between a peptide and the inhibitor protein (x axis) and the number of inter-peptide contacts for a peptide (y axis): (a) ACD and (b) lysozyme. Each contour level represents 0.5 kcal/mol free energy difference. The color scale for the free energy (kcal/mol) is shown at the bottom. Presence of ACD-bound oligomers is apparent. A snapshot of a crystallin-bound oligomer is shown, in which one Aβ dimer (yellow and orange) is attached to one α-crystallin domain and one Aβ trimer (green, cyan, and violet) is complexed with another α-crystallin domain. Crystallin domains are shown in gray. In contrast, lysozyme-bound monomers are primarily populated. A snapshot of lysozyme (in gray) is shown, in which three Aβ monomers (green, cyan, and violet) are found complexed. (c) Evolution of number of different sized Aβ species averaged over at least five different runs for each system. (a): control system (no inhibitor); (b): ACD-bound peptides; (c): lysozyme-bound peptides. Data is averaged over every 50 ns. Colored bars represent: yellow: uncomplexed ACD or lysozyme; red: Aβ monomer; blue: small Aβ oligomer (n = 2–5); green: larger Aβ oligomer (n>5).</p>", "links"=>[], "tags"=>["binding", "inhibitor protein", "inhibitor proteins", "inhibitor surface", "amyloid inhibitors", "mechanism", "contact surface", "Molecular Dynamics Simulations Knowledge", "acid distribution", "aggregation", "α B", "Amyloid Beta Peptides", "Amyloid Inhibitor Proteins", "lysozyme", "crystallin", "dynamics simulations", "amyloid beta", "peptide monomer"], "article_id"=>1251750, "categories"=>["Biological Sciences"], "users"=>["Payel Das", "Seung-gu Kang", "Sally Temple", "Georges Belfort"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113041.g002", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Effect_of_amyloid_inhibitor_proteins_on_A_946_assembly_/1251750", "title"=>"Effect of amyloid inhibitor proteins on Aβ assembly.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-25 03:11:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1806849"], "description"=>"<p>(a) Structure of an ACD monomer in cartoon and of the ACD dimer in surface representation colored according to residue type. Color scheme used: red - acidic, blue - basic, green - polar, and white - hydrophobic. (b) Cartoon and surface representations of the human lysozyme protein colored according to the residue type. (c) Sequence and the secondary structure assignment of human α-crystallin domain (ACD, residues 66–150) and of human lysozyme using the secondary structure assignment program DSSP <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113041#pone.0113041-Kabsch1\" target=\"_blank\">[97]</a>. Yellow arrows indicate β-strands, purple indicates turn, blue indicates bend, red spirals indicate the alpha- helix, light pink spirals indicate the 3<sub>10</sub> helix, and black indicates coils. Sequence of the Aβ<sub>17–42</sub> peptide is also shown. (d) System set up with one ACD dimer (black cartoon) placed in the center of a cubic box of water (shown in red) that also contains 10 Aβ<sub>17–42</sub> peptides (green spheres, only backbone is shown). Sodium and Chloride ions are shown as cyan and yellow spheres, respectively.</p>", "links"=>[], "tags"=>["binding", "inhibitor protein", "inhibitor proteins", "inhibitor surface", "amyloid inhibitors", "mechanism", "contact surface", "Molecular Dynamics Simulations Knowledge", "acid distribution", "aggregation", "α B", "Amyloid Beta Peptides", "Amyloid Inhibitor Proteins", "lysozyme", "crystallin", "dynamics simulations", "amyloid beta", "peptide monomer"], "article_id"=>1251732, "categories"=>["Biological Sciences"], "users"=>["Payel Das", "Seung-gu Kang", "Sally Temple", "Georges Belfort"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113041.g001", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structure_and_sequence_of_the_simulated_proteins_/1251732", "title"=>"Structure and sequence of the simulated proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-25 03:11:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1806913"], "description"=>"<div><p>Knowledge of the detailed mechanism by which proteins such as human αB- crystallin and human lysozyme inhibit amyloid beta (Aβ) peptide aggregation is crucial for designing treatment for Alzheimer's disease. Thus, unconstrained, atomistic molecular dynamics simulations in explicit solvent have been performed to characterize the Aβ<sub>17–42</sub> assembly in presence of the αB-crystallin core domain and of lysozyme. Simulations reveal that both inhibitor proteins compete with inter-peptide interaction by binding to the peptides during the early stage of aggregation, which is consistent with their inhibitory action reported in experiments. However, the Aβ binding dynamics appear different for each inhibitor. The binding between crystallin and the peptide monomer, dominated by electrostatics, is relatively weak and transient due to the heterogeneous amino acid distribution of the inhibitor surface. The crystallin-bound Aβ oligomers are relatively long-lived, as they form more extensive contact surface with the inhibitor protein. In contrast, a high local density of arginines from lysozyme allows strong binding with Aβ peptide monomers, resulting in stable complexes. Our findings not only illustrate, in atomic detail, how the amyloid inhibitory mechanism of human αB-crystallin, a natural chaperone, is different from that of human lysozyme, but also may aid <i>de novo</i> design of amyloid inhibitors.</p></div>", "links"=>[], "tags"=>["binding", "inhibitor protein", "inhibitor proteins", "inhibitor surface", "amyloid inhibitors", "mechanism", "contact surface", "Molecular Dynamics Simulations Knowledge", "acid distribution", "aggregation", "α B", "Amyloid Beta Peptides", "Amyloid Inhibitor Proteins", "lysozyme", "crystallin", "dynamics simulations", "amyloid beta", "peptide monomer"], "article_id"=>1251792, "categories"=>["Biological Sciences"], "users"=>["Payel Das", "Seung-gu Kang", "Sally Temple", "Georges Belfort"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113041", "stats"=>{"downloads"=>3, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Interaction_of_Amyloid_Inhibitor_Proteins_with_Amyloid_Beta_Peptides_Insight_from_Molecular_Dynamics_Simulations_/1251792", "title"=>"Interaction of Amyloid Inhibitor Proteins with Amyloid Beta Peptides: Insight from Molecular Dynamics Simulations", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-11-25 03:11:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1806894"], "description"=>"<p>Ensemble-averaged pairwise contact maps (a) between ACD and Aβ and (c) between lysozyme and Aβ. Data shown is averaged over all ∼200 ns runs. X and Y axes show residues from the inhibitor protein and Aβ<sub>17–42</sub>, respectively. A contact between residue <i>i</i> from the inhibitor and residue <i>j</i> from Aβ is considered, if any heavy atom from residue <i>i</i> is within 5 Å of any heavy atom from residue <i>j</i>. The contacts are color-coded according to the color scale shown in right. The secondary structure assignment of the inhibitor is shown on top. The molecular surfaces of the inhibitor proteins ((b) ACD and (d) lysozyme) are also shown, which is color-coded red to blue (low to high) according to the probability of contact formation with Aβ. (e) Contact probabilities for each residue type of ACD (red) and lysozyme (blue). (d) Residue-based contact probabilities of the Aβ<sub>17–42</sub> peptide with ACD (red) and with lysozyme (blue).</p>", "links"=>[], "tags"=>["binding", "inhibitor protein", "inhibitor proteins", "inhibitor surface", "amyloid inhibitors", "mechanism", "contact surface", "Molecular Dynamics Simulations Knowledge", "acid distribution", "aggregation", "α B", "Amyloid Beta Peptides", "Amyloid Inhibitor Proteins", "lysozyme", "crystallin", "dynamics simulations", "amyloid beta", "peptide monomer"], "article_id"=>1251773, "categories"=>["Biological Sciences"], "users"=>["Payel Das", "Seung-gu Kang", "Sally Temple", "Georges Belfort"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113041.g004", "stats"=>{"downloads"=>2, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Probability_of_inhibitor_peptide_contact_formation_/1251773", "title"=>"Probability of inhibitor-peptide contact formation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-25 03:11:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1806907"], "description"=>"<p>Ensemble-averaged probabilities of (a) tertiary contact and (b) quaternary contact formation of Aβ peptides in the control system (left), ACD-bound (middle), or lysozyme-bound (right) obtained from an ensemble generated from at least five ∼200 ns runs. The size of the ensemble is>10000 conformations. The peptide is considered complexed, if it forms more than five contacts with ACD/lysozyme. Only the non-sequential tertiary contacts (that are not formed between neighboring residues (<i>i+1</i>, and <i>i+2</i>) in sequence) are shown. The contacts are color-coded according to the color scale shown on the right. Snapshots of the oligomeric conformations with prevalent inter-monomer contacts are shown at bottom. Peptides are colored in green, pink, or tan, whereas ACD/lysozyme is colored in white. The N– and C-termini of the peptides are colored in red and blue, respectively. For the ACD-bound oligomer, only the inter-peptide contacts that form with higher probability compared to the free oligomer are shown for clarity.</p>", "links"=>[], "tags"=>["binding", "inhibitor protein", "inhibitor proteins", "inhibitor surface", "amyloid inhibitors", "mechanism", "contact surface", "Molecular Dynamics Simulations Knowledge", "acid distribution", "aggregation", "α B", "Amyloid Beta Peptides", "Amyloid Inhibitor Proteins", "lysozyme", "crystallin", "dynamics simulations", "amyloid beta", "peptide monomer"], "article_id"=>1251786, "categories"=>["Biological Sciences"], "users"=>["Payel Das", "Seung-gu Kang", "Sally Temple", "Georges Belfort"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113041.g005", "stats"=>{"downloads"=>2, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Probability_of_peptide_peptide_contact_formation_/1251786", "title"=>"Probability of peptide-peptide contact formation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-25 03:11:11"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[291]}, {"subject_area"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[292, 461]}, {"subject_area"=>"/Computer and information sciences/Systems science", "average_usage"=>[289, 462]}, {"subject_area"=>"/Engineering and technology/Control engineering", "average_usage"=>[262, 455]}, {"subject_area"=>"/Medicine and health sciences/Pathology and laboratory medicine", "average_usage"=>[287]}, {"subject_area"=>"/Physical sciences", "average_usage"=>[271]}, {"subject_area"=>"/Physical sciences/Chemistry", "average_usage"=>[262]}, {"subject_area"=>"/Physical sciences/Materials science", "average_usage"=>[259]}]}
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