Disordered Flanks Prevent Peptide Aggregation
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Mendeley | Further Information

{"title"=>"Disordered flanks prevent peptide aggregation", "type"=>"journal", "authors"=>[{"first_name"=>"Sanne", "last_name"=>"Abeln", "scopus_author_id"=>"8727728500"}, {"first_name"=>"Daan", "last_name"=>"Frenkel", "scopus_author_id"=>"7005702293"}], "year"=>2008, "source"=>"PLoS Computational Biology", "identifiers"=>{"sgr"=>"58149147308", "doi"=>"10.1371/journal.pcbi.1000241", "issn"=>"1553734X", "pui"=>"354027881", "isbn"=>"1553-7358 (Electronic)", "pmid"=>"19096500", "scopus"=>"2-s2.0-58149147308"}, "id"=>"342f796d-52ad-3d0f-95bf-38994620c768", "abstract"=>"Natively unstructured or disordered regions appear to be abundant in eukaryotic proteins. Many such regions have been found alongside small linear binding motifs. We report a Monte Carlo study that aims to elucidate the role of disordered regions adjacent to such binding motifs. The coarse-grained simulations show that small hydrophobic peptides without disordered flanks tend to aggregate under conditions where peptides embedded in unstructured peptide sequences are stable as monomers or as part of small micelle-like clusters. Surprisingly, the binding free energy of the motif is barely decreased by the presence of disordered flanking regions, although it is sensitive to the loss of entropy of the motif itself upon binding. This latter effect allows for reversible binding of the signalling motif to the substrate. The work provides insights into a mechanism that prevents the aggregation of signalling peptides, distinct from the general mechanism of protein folding, and provides a testable hypothesis to explain the abundance of disordered regions in proteins.", "link"=>"http://www.mendeley.com/research/disordered-flanks-prevent-peptide-aggregation", "reader_count"=>55, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>17, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>3, "Student > Master"=>3, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>6}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>17, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>3, "Student > Master"=>3, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>6}, "reader_count_by_subject_area"=>{"Engineering"=>2, "Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>4, "Materials Science"=>1, "Agricultural and Biological Sciences"=>31, "Chemical Engineering"=>2, "Physics and Astronomy"=>7, "Chemistry"=>5}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Materials Science"=>{"Materials Science"=>1}, "Chemistry"=>{"Chemistry"=>5}, "Physics and Astronomy"=>{"Physics and Astronomy"=>7}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>31}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>2}, "Chemical Engineering"=>{"Chemical Engineering"=>2}}, "reader_count_by_country"=>{"Canada"=>1, "Netherlands"=>1, "Austria"=>1, "Korea (South)"=>1, "United States"=>2, "Denmark"=>1, "United Kingdom"=>1}, "group_count"=>7}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/913223"], "description"=>"<p>Free energy as a function of external contacts at T = 0.23. The free energy is defined as <i>F</i>(<i>C<sub>ext</sub></i>) = −<i>k<sub>B</sub>T</i> ln(<i>P</i>(<i>C<sub>ext</sub></i>)) where <i>P</i>(<i>C<sub>ext</sub></i>) is the probability of a configuration with <i>C<sub>ext</sub></i> external contacts. The number of peptide chains was kept constant at 10. Free energies for 0<<i>C<sub>ext</sub></i><55 are displayed; free energies for a higher number of external contacts are dominated by finite size effects (10 peptides) effect of the system.</p>", "links"=>[], "tags"=>["biophysics/biomacromolecule-ligand interactions", "biophysics/protein folding", "biophysics/theory and simulation", "chemical biology/protein chemistry and proteomics", "Computational biology"], "article_id"=>583683, "categories"=>["Biophysics", "Biological Sciences", "Biochemistry"], "users"=>["Sanne Abeln", "Daan Frenkel"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000241.g003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Aggregation_free_energy_/583683", "title"=>"Aggregation free energy.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-12-19 01:01:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/913099"], "description"=>"<p>Top: Example of a linear binding motif bound to its substrate. CtIP phosphopeptide is bound to BRCT repeats of BRCA1 (1Y98). Bottom: Model of a binding motif. The motif, with sequence RWWLY, is designed to bind specifically to the substrate. The yellow residues are hydrophobic, the blue negatively charged, the red positively charged and the grey hydrophilic.</p>", "links"=>[], "tags"=>["binding"], "article_id"=>583558, "categories"=>["Biophysics", "Biological Sciences", "Biochemistry"], "users"=>["Sanne Abeln", "Daan Frenkel"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000241.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Linear_binding_motifs_/583558", "title"=>"Linear binding motifs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-12-19 00:59:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/451023", "https://ndownloader.figshare.com/files/451048", "https://ndownloader.figshare.com/files/451076"], "description"=>"<div><p>Natively unstructured or disordered regions appear to be abundant in eukaryotic proteins. Many such regions have been found alongside small linear binding motifs. We report a Monte Carlo study that aims to elucidate the role of disordered regions adjacent to such binding motifs. The coarse-grained simulations show that small hydrophobic peptides without disordered flanks tend to aggregate under conditions where peptides embedded in unstructured peptide sequences are stable as monomers or as part of small micelle-like clusters. Surprisingly, the binding free energy of the motif is barely decreased by the presence of disordered flanking regions, although it is sensitive to the loss of entropy of the motif itself upon binding. This latter effect allows for reversible binding of the signalling motif to the substrate. The work provides insights into a mechanism that prevents the aggregation of signalling peptides, distinct from the general mechanism of protein folding, and provides a testable hypothesis to explain the abundance of disordered regions in proteins.</p></div>", "links"=>[], "tags"=>["disordered", "flanks", "peptide", "aggregation"], "article_id"=>148887, "categories"=>["Biophysics", "Biological Sciences", "Biochemistry"], "users"=>["Sanne Abeln", "Daan Frenkel"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000241.s001", "https://dx.doi.org/10.1371/journal.pcbi.1000241.s002", "https://dx.doi.org/10.1371/journal.pcbi.1000241.s003"], "stats"=>{"downloads"=>6, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Disordered_Flanks_Prevent_Peptide_Aggregation/148887", "title"=>"Disordered Flanks Prevent Peptide Aggregation", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-12-19 02:28:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/913325"], "description"=>"<p>Cluster size (<i>N</i>) versus melting temperatures (<i>T<sub>s</sub></i>) for different cluster sizes. The shaded area indicates the temperature range in which reversible binding is possible for the flexible binding motifs to the substrate (see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000241#pcbi-1000241-g002\" target=\"_blank\">Figure 2</a>). Stable aggregates exist in the regions below the melting curves.</p>", "links"=>[], "tags"=>["temperatures", "aggregated"], "article_id"=>583787, "categories"=>["Biophysics", "Biological Sciences", "Biochemistry"], "users"=>["Sanne Abeln", "Daan Frenkel"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000241.g005", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Melting_temperatures_of_aggregated_clusters_/583787", "title"=>"Melting temperatures of aggregated clusters.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-12-19 01:03:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/913280"], "description"=>"<p>Top: snapshot of 301 aggregated binding motifs. Bottom: snapshot of two micelles formed by 18 binding motifs embedded in Threonine flanks (grey). The binding motifs have been given a colour ranging from blue to red according to their order of appearance in the simulation box.</p>", "links"=>[], "tags"=>["binding"], "article_id"=>583740, "categories"=>["Biophysics", "Biological Sciences", "Biochemistry"], "users"=>["Sanne Abeln", "Daan Frenkel"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000241.g004", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Aggregation_of_binding_motifs_/583740", "title"=>"Aggregation of binding motifs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-12-19 01:02:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/913160"], "description"=>"<p>Average amount of binding (〈<i>P<sub>b</sub></i>〉, top) and heat capacity (<i>C<sub>v</sub></i>, bottom) as a function of temperature shown for an isolated binding motif (BM), a binding motif within disordered flanks (BM disorder) and a rigid binding motif embedded in a rigid structure (BM rigid).</p>", "links"=>[], "tags"=>["biophysics/biomacromolecule-ligand interactions", "biophysics/protein folding", "biophysics/theory and simulation", "chemical biology/protein chemistry and proteomics", "Computational biology"], "article_id"=>583615, "categories"=>["Biophysics", "Biological Sciences", "Biochemistry"], "users"=>["Sanne Abeln", "Daan Frenkel"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000241.g002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reversible_binding_/583615", "title"=>"Reversible binding.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-12-19 01:00:15"}

PMC Usage Stats | Further Information

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Relative Metric

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