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{"title"=>"Insight into the stability of cross-β amyloid fibril from VEALYL short peptide with molecular dynamics simulation", "type"=>"journal", "authors"=>[{"first_name"=>"Wei", "last_name"=>"Ye", "scopus_author_id"=>"54794598000"}, {"first_name"=>"Yue", "last_name"=>"Chen", "scopus_author_id"=>"57196264260"}, {"first_name"=>"Wei", "last_name"=>"Wang", "scopus_author_id"=>"56948573300"}, {"first_name"=>"Qingfen", "last_name"=>"Yu", "scopus_author_id"=>"55216455600"}, {"first_name"=>"Yixue", "last_name"=>"Li", "scopus_author_id"=>"35227517800"}, {"first_name"=>"Jian", "last_name"=>"Zhang", "scopus_author_id"=>"7601341506"}, {"first_name"=>"Hai Feng", "last_name"=>"Chen", "scopus_author_id"=>"57192534806"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84861012177", "doi"=>"10.1371/journal.pone.0036382", "sgr"=>"84861012177", "isbn"=>"0006-3525 (Print)\\r0006-3525 (Linking)", "pmid"=>"22590535", "issn"=>"19326203", "pui"=>"364802809"}, "id"=>"7424b4de-ebf1-31d6-a4ba-28a5a927af1d", "abstract"=>"Amyloid fibrils are found in many fatal neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, type II diabetes, and prion disease. The VEALYL short peptide from insulin has been confirmed to aggregate amyloid-like fibrils. However, the aggregation mechanism of amyloid fibril is poorly understood. Here, we utilized molecular dynamics simulation to analyse the stability of VEALYL hexamer. The statistical results indicate that hydrophobic residues play key roles in stabilizing VEALYL hexamer. Single point and two linkage mutants confirmed that Val1, Leu4, and Tyr5 of VEALYL are key residues. The consistency of the results for the VEALYL oligomer suggests that the intermediate states might be trimer (3-0) and pentamer(3-2). These results can help us to obtain an insight into the aggregation mechanism of amyloid fibril. These methods can be used to study the stability of amyloid fibril from other short peptides.", "link"=>"http://www.mendeley.com/research/insight-stability-cross%CE%B2-amyloid-fibril-vealyl-short-peptide-molecular-dynamics-simulation", "reader_count"=>23, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>8, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>1, "Other"=>2, "Student > Master"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>8, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>1, "Other"=>2, "Student > Master"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>2, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>8, "Medicine and Dentistry"=>2, "Chemistry"=>4}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>4}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>8}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}}, "group_count"=>0}

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• http://doi.org/10.1039/c3cp53145g
• http://doi.org/10.1093/abbs/gmt026
• http://doi.org/10.3389/fmolb.2015.00061
• http://doi.org/10.1080/07391102.2017.1317666
• http://doi.org/10.1371/journal.pone.0059627
• http://doi.org/10.1021/acs.biochem.5b00061
• http://doi.org/10.1038/srep24587

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/330392", "https://ndownloader.figshare.com/files/330419", "https://ndownloader.figshare.com/files/330457", "https://ndownloader.figshare.com/files/330498"], "description"=>"<div><p>Amyloid fibrils are found in many fatal neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, type II diabetes, and prion disease. The VEALYL short peptide from insulin has been confirmed to aggregate amyloid-like fibrils. However, the aggregation mechanism of amyloid fibril is poorly understood. Here, we utilized molecular dynamics simulation to analyse the stability of VEALYL hexamer. The statistical results indicate that hydrophobic residues play key roles in stabilizing VEALYL hexamer. Single point and two linkage mutants confirmed that Val1, Leu4, and Tyr5 of VEALYL are key residues. The consistency of the results for the VEALYL oligomer suggests that the intermediate states might be trimer (3-0) and pentamer(3-2). These results can help us to obtain an insight into the aggregation mechanism of amyloid fibril. These methods can be used to study the stability of amyloid fibril from other short peptides.</p> </div>", "links"=>[], "tags"=>["amyloid", "fibril", "vealyl", "peptide", "molecular", "simulation"], "article_id"=>125244, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics", "Neuroscience"], "users"=>["Wei Ye", "Yue Chen", "Wei Wang", "Qingfen Yu", "Yixue Li", "Jian Zhang", "Hai-Feng Chen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0036382.s001", "https://dx.doi.org/10.1371/journal.pone.0036382.s002", "https://dx.doi.org/10.1371/journal.pone.0036382.s003", "https://dx.doi.org/10.1371/journal.pone.0036382.s004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Insight_into_the_Stability_of_Cross_Amyloid_Fibril_from_VEALYL_Short_Peptide_with_Molecular_Dynamics_Simulation/125244", "title"=>"Insight into the Stability of Cross-β Amyloid Fibril from VEALYL Short Peptide with Molecular Dynamics Simulation", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-05-10 01:27:24"}
• {"files"=>["https://ndownloader.figshare.com/files/639968"], "description"=>"<p>The schematic organization of dimer, trimer, tetramer, pentamer, and hexamer VEALYL model. The organization of strand is indicated.</p>", "links"=>[], "tags"=>["schematic", "hexamer", "vealyl", "strand"], "article_id"=>310452, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics", "Neuroscience"], "users"=>["Wei Ye", "Yue Chen", "Wei Wang", "Qingfen Yu", "Yixue Li", "Jian Zhang", "Hai-Feng Chen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0036382.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_schematic_organization_of_dimer_trimer_tetramer_pentamer_and_hexamer_VEALYL_model_The_organization_of_strand_is_indicated_/310452", "title"=>"The schematic organization of dimer, trimer, tetramer, pentamer, and hexamer VEALYL model. The organization of strand is indicated.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-10 00:07:32"}
• {"files"=>["https://ndownloader.figshare.com/files/640127"], "description"=>"<p>Cα variation of residues for VEALYL hexamer. Each short peptide is monitored, respectively. The fluctuations of six peptides are different.</p>", "links"=>[], "tags"=>["residues", "vealyl", "peptide", "fluctuations", "peptides"], "article_id"=>310612, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics", "Neuroscience"], "users"=>["Wei Ye", "Yue Chen", "Wei Wang", "Qingfen Yu", "Yixue Li", "Jian Zhang", "Hai-Feng Chen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0036382.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_C_945_variation_of_residues_for_VEALYL_hexamer_Each_short_peptide_is_monitored_respectively_The_fluctuations_of_six_peptides_are_different_/310612", "title"=>"Cα variation of residues for VEALYL hexamer. Each short peptide is monitored, respectively. The fluctuations of six peptides are different.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-10 00:10:12"}
• {"files"=>["https://ndownloader.figshare.com/files/640275"], "description"=>"<p>Hydrogen bond was arranged by descending order according to the population. The populations of 17 hydrogen bonds are larger than 40%.</p>", "links"=>[], "tags"=>["vealyl"], "article_id"=>310764, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics", "Neuroscience"], "users"=>["Wei Ye", "Yue Chen", "Wei Wang", "Qingfen Yu", "Yixue Li", "Jian Zhang", "Hai-Feng Chen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0036382.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hydrogen_bond_for_VEALYL_hexamer_/310764", "title"=>"Hydrogen bond for VEALYL hexamer.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-10 00:12:44"}
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• {"files"=>["https://ndownloader.figshare.com/files/640488"], "description"=>"<p>The color code of wild type and mutants (V1G, E2G, A3G, L4G, Y5G, L6G, and A3GL4G) was labeled in the caption.</p>", "links"=>[], "tags"=>["mutants", "20", "ns", "md"], "article_id"=>310974, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics", "Neuroscience"], "users"=>["Wei Ye", "Yue Chen", "Wei Wang", "Qingfen Yu", "Yixue Li", "Jian Zhang", "Hai-Feng Chen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0036382.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_fraction_of_native_contact_between_946_strands_for_wild_type_and_mutants_during_the_20_ns_MD_simulations_/310974", "title"=>"The fraction of native contact between β-strands for wild type and mutants during the 20 ns MD simulations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-10 00:16:14"}
• {"files"=>["https://ndownloader.figshare.com/files/640562"], "description"=>"<p>The interstrand distance was calculated by averaging pairwise residue Cα-Cα distances of strand1-strand2, strand2-strand3, strand4-strand5, and strand5-strand6 within the same β-sheet layer. The intersheet distance was calculated between the Cα center of sheet1 and sheet2.</p>", "links"=>[], "tags"=>["interstrand", "intersheet", "mutants", "10", "ns"], "article_id"=>311050, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics", "Neuroscience"], "users"=>["Wei Ye", "Yue Chen", "Wei Wang", "Qingfen Yu", "Yixue Li", "Jian Zhang", "Hai-Feng Chen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0036382.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_average_interstrand_and_intersheet_distance_between_946_strands_for_wild_type_and_mutants_during_10_ns_simulation_/311050", "title"=>"The average interstrand and intersheet distance between β-strands for wild type and mutants during 10 ns simulation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-10 00:17:30"}
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• {"files"=>["https://ndownloader.figshare.com/files/640722"], "description"=>"<p>Native contact between pairwise residues was calculated, then added according to the residue number of normalized peptides, and divided by the number of peptide. Hydrogen bond was calculated, then added according to the residue number of normalized peptides, and divided by the number of peptide.</p>", "links"=>[], "tags"=>["hydrogen", "residue"], "article_id"=>311208, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics", "Neuroscience"], "users"=>["Wei Ye", "Yue Chen", "Wei Wang", "Qingfen Yu", "Yixue Li", "Jian Zhang", "Hai-Feng Chen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0036382.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Average_number_of_native_contact_and_hydrogen_bond_for_each_residue_of_oligomer_/311208", "title"=>"Average number of native contact and hydrogen bond for each residue of oligomer.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-10 00:20:08"}
• {"files"=>["https://ndownloader.figshare.com/files/640814"], "description"=>"<p>Simulation condition of wild type and mutant for VEALYL peptides.</p>", "links"=>[], "tags"=>["mutant", "vealyl"], "article_id"=>311305, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics", "Neuroscience"], "users"=>["Wei Ye", "Yue Chen", "Wei Wang", "Qingfen Yu", "Yixue Li", "Jian Zhang", "Hai-Feng Chen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0036382.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Simulation_condition_of_wild_type_and_mutant_for_VEALYL_peptides_/311305", "title"=>"Simulation condition of wild type and mutant for VEALYL peptides.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-10 00:21:45"}

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Relative Metric

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F1000Prime