Modelling the Self-Assembly of Elastomeric Proteins Provides Insights into the Evolution of Their Domain Architectures
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{"title"=>"Modelling the self-assembly of elastomeric proteins provides insights into the evolution of their domain architectures", "type"=>"journal", "authors"=>[{"first_name"=>"Hongyan", "last_name"=>"Song", "scopus_author_id"=>"38762159900"}, {"first_name"=>"John", "last_name"=>"Parkinson", "scopus_author_id"=>"18335998200"}], "year"=>2012, "source"=>"PLoS Computational Biology", "identifiers"=>{"scopus"=>"2-s2.0-84861162096", "pmid"=>"22396636", "sgr"=>"84861162096", "isbn"=>"1553-7358 (Electronic)\\r1553-734X (Linking)", "doi"=>"10.1371/journal.pcbi.1002406", "issn"=>"15537358", "pui"=>"364830945"}, "id"=>"2a1624ab-a03d-3bf4-a85c-ef252b4f4f93", "abstract"=>"Elastomeric proteins such as elastin, resilin, abductin and wheat gluten represent a remarkable class of self-assembling proteins that provide properties of extensibility and elastic recoil. Although unrelated from an evolutionary viewpoint, these proteins nonetheless share a common sequence design involving highly repetitive elastomeric regions interspersed with elements capable of forming cross-links that help stabilize the formation of polymers. Attempts to explore the influence of domain architecture on the self-assembly and mechanical properties of elastomeric proteins at the molecular level have largely been hindered by a general lack of detailed structural information. Here we introduce a novel theoretical study based on random walks to simulate the self-assembly of elastomeric proteins. Applying this model, we explored the impact of different configurations of elastomeric and cross-linking elements on the stability of the resultant polymer. Through exploring the complex relationships between elastomeric domains, required to drive self-assembly, and cross-linking domains, required for structural integrity, results from these simulations provide insights into the molecular basis for the evolution of elastomeric proteins as well as help guide the rational design of novel elastomeric-peptides.", "link"=>"http://www.mendeley.com/research/modelling-selfassembly-elastomeric-proteins-provides-insights-evolution-domain-architectures", "reader_count"=>33, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>6, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>8, "Student > Master"=>5, "Other"=>2, "Student > Bachelor"=>4, "Lecturer"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>6, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>8, "Student > Master"=>5, "Other"=>2, "Student > Bachelor"=>4, "Lecturer"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Agricultural and Biological Sciences"=>12, "Arts and Humanities"=>1, "Chemical Engineering"=>1, "Chemistry"=>1, "Engineering"=>5, "Biochemistry, Genetics and Molecular Biology"=>2, "Materials Science"=>2, "Medicine and Dentistry"=>1, "Neuroscience"=>1, "Physics and Astronomy"=>4, "Psychology"=>1, "Social Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>4}, "Psychology"=>{"Psychology"=>1}, "Unspecified"=>{"Unspecified"=>1}, "Chemical Engineering"=>{"Chemical Engineering"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Engineering"=>{"Engineering"=>5}, "Chemistry"=>{"Chemistry"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>12}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}}, "reader_count_by_country"=>{"United States"=>2, "United Kingdom"=>1, "Israel"=>1, "Germany"=>1, "India"=>1}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/672749"], "description"=>"<p>(A) Graphs showing the impact of increasing the relative number of domains while keeping rod length constant (20 units). Two conformations were examined: conformation 1 refers to rods in which the number of elastomeric domains (blue) exceeds the number of cross-linking domains (red); conformation 2 refers to rods in which the number if cross-linking domains exceeds the number of elastomeric domains. (B) Graphs showing the impact of adding additional domains. Here three conformations were investigated: conformation 1 consists of rods composed of domains of length one unit; conformation 2 consists of rods composed of elastomeric domains of length 4 units and cross-linking domains of length 1 unit; and conformation 3 is an asymmetrical rod consisting of two sets of: a elastomeric domain of length five units and a cross-linking domain of length two, between which are increasing numbers of elastomeric domains of length four and a cross-linking domain of length one. Error bars indicate standard deviations for ten replicates.</p>", "links"=>[], "tags"=>["aggregate", "morphology"], "article_id"=>343245, "categories"=>["Physics", "Biotechnology", "Biological Sciences", "Biochemistry"], "users"=>["Hongyan Song", "John Parkinson"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002406.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Quantitative_effects_of_domain_number_on_aggregate_morphology_and_stability_/343245", "title"=>"Quantitative effects of domain number on aggregate morphology and stability.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-01 00:54:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/672643"], "description"=>"<p>(A) Implementation of modified DLA algorithm. (I) Schematic showing the release of new rods from a release template defined as 30 units distant from the growing aggregate. (II) View of a section of an aggregate generated with rods composed of a single elastomeric domain of length 20 units and diameter 1 unit, using <i>KT</i> = 20 and <i>X</i> = 1,000. Orange arrows indicate the direction of lateral surface diffusion for a newly accreted rod (red) that drive the minimization of exposed hydrophobic surface. (B) Phase diagram showing a two dimensional cross-section through a central 60 unit section of representative aggregates grown under different values of <i>KT</i> and <i>X</i>. (C) Side views of 80 units of the central section of representative fibrils from (B). (D) Quantitative measures of morphological characteristics of aggregates represented in the phase diagram (B). Aggregates were grown using 10,000 rods, standard deviations are from 10 replicates.</p>", "links"=>[], "tags"=>["diffusion", "aggregate"], "article_id"=>343134, "categories"=>["Physics", "Biotechnology", "Biological Sciences", "Biochemistry"], "users"=>["Hongyan Song", "John Parkinson"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002406.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Impact_of_surface_diffusion_on_aggregate_morphology_/343134", "title"=>"Impact of surface diffusion on aggregate morphology.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-01 00:52:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/672860"], "description"=>"<p>Based on potential cross-links formed by neighbouring cross-linking domains, a network of rod connectivity can be generated (A). In this network nodes indicate individual rods and edges represent potential cross-links. (B) Graphs showing graph theoretical properties of networks generated for 32 different rod architectures composed of different numbers and sizes of elastomeric (blue) and cross-linking (red) domains. Domain architectures are indicated at the bottom. The arrow indicates architecture 28 used to construct the network in (A). Error bars indicate standard deviations for ten replicates. (C) Magnified section of the network presented in (A) highlighting a node (green) which has a high value of betweenness and low node degree and may therefore represent a weak point within the aggregate.</p>", "links"=>[], "tags"=>["aggregate"], "article_id"=>343355, "categories"=>["Physics", "Biotechnology", "Biological Sciences", "Biochemistry"], "users"=>["Hongyan Song", "John Parkinson"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002406.g003", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Network_analysis_of_aggregate_stability_/343355", "title"=>"Network analysis of aggregate stability.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-01 00:55:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/344366", "https://ndownloader.figshare.com/files/344425"], "description"=>"<div><p>Elastomeric proteins have evolved independently multiple times through evolution. Produced as monomers, they self-assemble into polymeric structures that impart properties of stretch and recoil. They are composed of an alternating domain architecture of elastomeric domains interspersed with cross-linking elements. While the former provide the elasticity as well as help drive the assembly process, the latter serve to stabilise the polymer. Changes in the number and arrangement of the elastomeric and cross-linking regions have been shown to significantly impact their assembly and mechanical properties. However, to date, such studies are relatively limited. Here we present a theoretical study that examines the impact of domain architecture on polymer assembly and integrity. At the core of this study is a novel simulation environment that uses a model of diffusion limited aggregation to simulate the self-assembly of rod-like particles with alternating domain architectures. Applying the model to different domain architectures, we generate a variety of aggregates which are subsequently analysed by graph-theoretic metrics to predict their structural integrity. Our results show that the relative length and number of elastomeric and cross-linking domains can significantly impact the morphology and structural integrity of the resultant polymeric structure. For example, the most highly connected polymers were those constructed from asymmetric rods consisting of relatively large cross-linking elements interspersed with smaller elastomeric domains. In addition to providing insights into the evolution of elastomeric proteins, simulations such as those presented here may prove valuable for the tuneable design of new molecules that may be exploited as useful biomaterials.</p> </div>", "links"=>[], "tags"=>["self-assembly", "elastomeric", "proteins", "provides", "insights", "architectures"], "article_id"=>128073, "categories"=>["Physics", "Biotechnology", "Biological Sciences", "Biochemistry"], "users"=>["Hongyan Song", "John Parkinson"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1002406.s001", "https://dx.doi.org/10.1371/journal.pcbi.1002406.s002"], "stats"=>{"downloads"=>2, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Modelling_the_Self_Assembly_of_Elastomeric_Proteins_Provides_Insights_into_the_Evolution_of_Their_Domain_Architectures/128073", "title"=>"Modelling the Self-Assembly of Elastomeric Proteins Provides Insights into the Evolution of Their Domain Architectures", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-03-01 02:14:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/673013"], "description"=>"<p>(A) Graphs showing distributions of node degree, betweenness and cluster coefficients for nodes generated from networks associated with the eight rod architectures leading to aggregates with the highest average node degree (domain architectures 25–32 in <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002406#pcbi-1002406-g003\" target=\"_blank\">Figure 3</a>). (B) Heatmaps showing the frequency of nodes (as a percentage) with specific values of betweenness and node degree. Rod architectures are indicated to the left of each heatmap. Aggregates composed of a large fraction of nodes which are both of high node degree and high betweenness are expected to be more resistant to mechanical failure. Standard deviations are provided for ten replicates.</p>", "links"=>[], "tags"=>["aggregates", "generated"], "article_id"=>343506, "categories"=>["Physics", "Biotechnology", "Biological Sciences", "Biochemistry"], "users"=>["Hongyan Song", "John Parkinson"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002406.g004", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detailed_network_statistics_for_aggregates_generated_from_a_select_set_of_eight_rod_architectures_/343506", "title"=>"Detailed network statistics for aggregates generated from a select set of eight rod architectures.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-01 00:58:26"}

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Relative Metric

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