Protein Dynamics Governed by Interfaces of High Polarity and Low Packing Density
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{"title"=>"Protein Dynamics Governed by Interfaces of High Polarity and Low Packing Density", "type"=>"journal", "authors"=>[{"first_name"=>"Vladimir Espinosa", "last_name"=>"Angarica", "scopus_author_id"=>"24334580000"}, {"first_name"=>"Javier", "last_name"=>"Sancho", "scopus_author_id"=>"7201937433"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84868117563", "doi"=>"10.1371/journal.pone.0048212", "pui"=>"365952322", "pmid"=>"23110216", "scopus"=>"2-s2.0-84868117563", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"78dee2c8-5883-37d0-8023-a38cf8c75ea5", "abstract"=>"The folding pathway, three-dimensional structure and intrinsic dynamics of proteins are governed by their amino acid sequences. Internal protein surfaces with physicochemical properties appropriate to modulate conformational fluctuations could play important roles in folding and dynamics. We show here that proteins contain buried interfaces of high polarity and low packing density, coined as LIPs: Light Interfaces of high Polarity, whose physicochemical properties make them unstable. The structures of well-characterized equilibrium and kinetic folding intermediates indicate that the LIPs of the corresponding native proteins fold late and are involved in local unfolding events. Importantly, LIPs can be identified using very fast and uncomplicated computational analysis of protein three-dimensional structures, which provides an easy way to delineate the protein segments involved in dynamics. Since LIPs can be retained while the sequences of the interacting segments diverge significantly, proteins could in principle evolve new functional features reusing pre-existing encoded dynamics. Large-scale identification of LIPS may contribute to understanding evolutionary constraints of proteins and the way protein intrinsic dynamics are encoded.", "link"=>"http://www.mendeley.com/research/protein-dynamics-governed-interfaces-high-polarity-low-packing-density", "reader_count"=>18, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Student > Doctoral Student"=>1, "Researcher"=>4, "Student > Ph. D. Student"=>5, "Student > Master"=>1, "Student > Bachelor"=>3, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Student > Doctoral Student"=>1, "Researcher"=>4, "Student > Ph. D. Student"=>5, "Student > Master"=>1, "Student > Bachelor"=>3, "Professor"=>2}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>6, "Materials Science"=>1, "Agricultural and Biological Sciences"=>7, "Pharmacology, Toxicology and Pharmaceutical Science"=>2, "Physics and Astronomy"=>1, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>7}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>2}}, "reader_count_by_country"=>{"United States"=>1, "United Kingdom"=>1, "Russia"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/295697", "https://ndownloader.figshare.com/files/295767", "https://ndownloader.figshare.com/files/295804", "https://ndownloader.figshare.com/files/295863", "https://ndownloader.figshare.com/files/295904", "https://ndownloader.figshare.com/files/295946", "https://ndownloader.figshare.com/files/296023", "https://ndownloader.figshare.com/files/296235"], "description"=>"<div><p>The folding pathway, three-dimensional structure and intrinsic dynamics of proteins are governed by their amino acid sequences. Internal protein surfaces with physicochemical properties appropriate to modulate conformational fluctuations could play important roles in folding and dynamics. We show here that proteins contain buried interfaces of high polarity and low packing density, coined as LIPs: Light Interfaces of high Polarity, whose physicochemical properties make them unstable. The structures of well-characterized equilibrium and kinetic folding intermediates indicate that the LIPs of the corresponding native proteins fold late and are involved in local unfolding events. Importantly, LIPs can be identified using very fast and uncomplicated computational analysis of protein three-dimensional structures, which provides an easy way to delineate the protein segments involved in dynamics. Since LIPs can be retained while the sequences of the interacting segments diverge significantly, proteins could in principle evolve new functional features reusing pre-existing encoded dynamics. Large-scale identification of LIPS may contribute to understanding evolutionary constraints of proteins and the way protein intrinsic dynamics are encoded.</p> </div>", "links"=>[], "tags"=>["governed", "interfaces", "polarity", "packing", "density"], "article_id"=>118247, "categories"=>["Information And Computing Sciences", "Biochemistry", "Chemistry", "Physics", "Biophysics"], "users"=>["Vladimir Espinosa Angarica", "Javier Sancho"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0048212.s001", "https://dx.doi.org/10.1371/journal.pone.0048212.s002", "https://dx.doi.org/10.1371/journal.pone.0048212.s003", "https://dx.doi.org/10.1371/journal.pone.0048212.s004", "https://dx.doi.org/10.1371/journal.pone.0048212.s005", "https://dx.doi.org/10.1371/journal.pone.0048212.s006", "https://dx.doi.org/10.1371/journal.pone.0048212.s007", "https://dx.doi.org/10.1371/journal.pone.0048212.s008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Protein_Dynamics_Governed_by_Interfaces_of_High_Polarity_and_Low_Packing_Density__/118247", "title"=>"Protein Dynamics Governed by Interfaces of High Polarity and Low Packing Density", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-10-26 02:17:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/552970"], "description"=>"<p><b>A</b>) Stacked-aligned profiles for polarity ratio and packing density in <i>Anabaena</i> PCC 71191 apoflavodoxin (PDB: 1FTG, Resolution  = 2.0 Å). The property values (see definitions in Materials and Methods) are plotted against the position of the fourth residue of an eight-residue probe fragment. The segments encompassing residues 87–108 and 118–152, which have been found to be unstructured in the equilibrium intermediate of this protein <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048212#pone.0048212-AyusoTejedor1\" target=\"_blank\">[31]</a>, are highlighted in grey. We also show in grey dashed lines the polarity and packing cutoffs. <b>B</b>) Surface representation of buried atoms at interfaces 87–107 (yellow) and 118–152 (red) and the associated interacting fragments (in cartoon representation) colored purple and blue, respectively. <b>C</b>) Surface representation of the buried atoms according to our characterization of polar light interfaces (LIPs). The LIPs 87–99 (yellow), 120–133 (red) and 140–155 (cyan) are shown and the associated interacting fragments are colored purple, blue and green and are depicted in cartoon representation.</p>", "links"=>[], "tags"=>["characterization", "lips"], "article_id"=>223470, "categories"=>["Information And Computing Sciences", "Biochemistry", "Chemistry", "Physics", "Biophysics"], "users"=>["Vladimir Espinosa Angarica", "Javier Sancho"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0048212.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_and_structural_characterization_of_LIPs_in_apoflavodoxin_/223470", "title"=>"Identification and structural characterization of LIPs in apoflavodoxin.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-26 00:57:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/553034"], "description"=>"<p>(A) Polarity ratio and packing density profiles of Cytochrome c (PDB: 1HRC, Resolution  = 1.9 Å). The segment shadowed in grey corresponds to the lowest stability region of the protein (infrared foldon: residues 40–57) according to equilibrium and kinetic H-exchange NMR experiments <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048212#pone.0048212-Krishna1\" target=\"_blank\">[39]</a>. The light blue bar indicates the only LIP in Cytochrome c, which includes residues 40–45 and is located in the unstable foldon. (B) Ribbons representation showing the unstable foldon in grey. In the charts, the polarity and packing cutoffs are indicated as grey dashed lines</p>", "links"=>[], "tags"=>["lowest", "foldon", "cytochrome"], "article_id"=>223536, "categories"=>["Information And Computing Sciences", "Biochemistry", "Chemistry", "Physics", "Biophysics"], "users"=>["Vladimir Espinosa Angarica", "Javier Sancho"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0048212.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_LIP_and_the_lowest_stability_foldon_in_Cytochrome_c_/223536", "title"=>"LIP and the lowest stability foldon in Cytochrome c.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-26 00:58:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/553093"], "description"=>"<p>(A) Polarity ratio and packing density profiles of α-Lactalbumine (PDB: 1HML, Resolution  = 1.7 Å). The segment shadowed in grey corresponds to the β-domain (residues 40–81), the one that lacks secondary structure in the molten globule intermediate <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048212#pone.0048212-Schulman1\" target=\"_blank\">[43]</a>. The light blue bars indicate the two LIPs in α-Lactalbumine, encompassing residues 35–51 and 64–70, and essentially defining the β-domain. (B) Ribbons representation showing the unstable β-domain in grey. In the charts, the polarity and packing cutoffs are indicated as grey dashed lines.</p>", "links"=>[], "tags"=>["unfolded", "molten"], "article_id"=>223593, "categories"=>["Information And Computing Sciences", "Biochemistry", "Chemistry", "Physics", "Biophysics"], "users"=>["Vladimir Espinosa Angarica", "Javier Sancho"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0048212.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_LIPs_and_the_unfolded_domain_of_the_945_Lactalbumine_Molten_globule_/223593", "title"=>"LIPs and the unfolded domain of the α-Lactalbumine Molten globule.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-26 00:59:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/553162"], "description"=>"<p>(A) Polarity ratio and packing density profiles of Indole-3-glycerol phosphate synthase (PDB: 2C3Z, Resolution  = 2.8 Å). The segments shadowed in grey correspond to the unfolded regions of the equilibrium intermediate of chemical unfolding (intermediate Ia), which coincides with the on-pathway kinetic folding intermediate <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048212#pone.0048212-Gu1\" target=\"_blank\">[44]</a>. The light blue bars indicate the five LIPs in Indole-3-glycerol phosphate synthase. LIPs 7-18 and 23–40 map onto the N-terminal unfolded region of the protein (1–47). The next LIP, 58–68, defines the loop that is unfolded even in the native state (59–68). Finally, LIPs 148–170 and 178–205 are located at the C-terminal unfolded segment of the protein (162–220). (B) Ribbons representation showing the unfolded regions of the intermediate in grey. In the charts, the polarity and packing cutoffs are indicated as grey dashed lines</p>", "links"=>[], "tags"=>["unfolded", "regions", "equilibrium", "intermediate", "indole-3-glycerol", "phosphate"], "article_id"=>223656, "categories"=>["Information And Computing Sciences", "Biochemistry", "Chemistry", "Physics", "Biophysics"], "users"=>["Vladimir Espinosa Angarica", "Javier Sancho"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0048212.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_LIPs_and_the_unfolded_regions_of_the_equilibrium_and_kinetic_intermediate_of_Indole_3_glycerol_phosphate_synthase_/223656", "title"=>"LIPs and the unfolded regions of the equilibrium (and kinetic) intermediate of Indole-3-glycerol phosphate synthase.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-26 01:00:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/553220"], "description"=>"<p>(A) Polarity ratio and packing density profiles of barnase (PDB: 1A2P, Resolution  = 1.5 Å). The segments shadowed in grey correspond to the regions displaying φ-values equal to or lower than 0.5 in the late transition state of barnase folding (TS2) <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048212#pone.0048212-Salvatella1\" target=\"_blank\">[47]</a>. The light blue bars indicate the three LIPs in barnase: 20–30, 44–57 and 65–89. They closely correspond to the segments exhibiting low φ-values in the transition state (19–37, 39–55 y 72–88). (B) Ribbons representation showing in grey the transition state regions with low φ-values. In the charts, the polarity and packing cutoffs are indicated as grey dashed lines.</p>", "links"=>[], "tags"=>["ensemble", "barnase"], "article_id"=>223718, "categories"=>["Information And Computing Sciences", "Biochemistry", "Chemistry", "Physics", "Biophysics"], "users"=>["Vladimir Espinosa Angarica", "Javier Sancho"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0048212.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_LIPs_in_the_late_transition_state_ensemble_of_barnase_folding_/223718", "title"=>"LIPs in the late transition state ensemble of barnase folding.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-26 01:01:58"}

PMC Usage Stats | Further Information

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Relative Metric

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