Conformational Preference of ‘CαNN’ Short Peptide Motif towards Recognition of Anions
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{"title"=>"Conformational Preference of 'CαNN' Short Peptide Motif towards Recognition of Anions", "type"=>"journal", "authors"=>[{"first_name"=>"Tridip", "last_name"=>"Sheet", "scopus_author_id"=>"36139131600"}, {"first_name"=>"Subhrangshu", "last_name"=>"Supakar", "scopus_author_id"=>"55620312300"}, {"first_name"=>"Raja", "last_name"=>"Banerjee", "scopus_author_id"=>"7201904983"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84874896018", "pmid"=>"23516403", "sgr"=>"84874896018", "doi"=>"10.1371/journal.pone.0057366", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"19326203", "pui"=>"368518521"}, "id"=>"5b1929af-f3f8-3b4b-b4ed-c7fe0f8e171d", "abstract"=>"Among several 'anion binding motifs', the recently described 'C(α)NN' motif occurring in the loop regions preceding a helix, is conserved through evolution both in sequence and its conformation. To establish the significance of the conserved sequence and their intrinsic affinity for anions, a series of peptides containing the naturally occurring 'C(α)NN' motif at the N-terminus of a designed helix, have been modeled and studied in a context free system using computational techniques. Appearance of a single interacting site with negative binding free-energy for both the sulfate and phosphate ions, as evidenced in docking experiments, establishes that the 'C(α)NN' segment has an intrinsic affinity for anions. Molecular Dynamics (MD) simulation studies reveal that interaction with anion triggers a conformational switch from non-helical to helical state at the 'C(α)NN' segment, which extends the length of the anchoring-helix by one turn at the N-terminus. Computational experiments substantiate the significance of sequence/structural context and justify the conserved nature of the 'C(α)NN' sequence for anion recognition through \"local\" interaction.", "link"=>"http://www.mendeley.com/research/conformational-preference-c%CE%B1nn-short-peptide-motif-towards-recognition-anions", "reader_count"=>10, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>1, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>3, "Student > Postgraduate"=>1, "Student > Master"=>1, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>1, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>3, "Student > Postgraduate"=>1, "Student > Master"=>1, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>2, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>1}}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1007049"], "description"=>"<p>The ranges of the parameters comply well with those obtained for respective crystal structures and described by Denessiouk et al., in 2005. The estimated binding free energy gives a measure of relative stability of interaction (relative affinity for the anion) which largely depends on the conformational status of the ‘C<sup>α</sup>NN’ segment.</p>", "links"=>[], "tags"=>["ion", "chimeric", "peptides", "docked", "structures", "h-bond"], "article_id"=>667670, "categories"=>["Biochemistry", "Biological Sciences", "Chemistry", "Physics", "Biophysics"], "users"=>["Tridip Sheet", "Subhrangshu Supakar", "Raja Banerjee"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057366.t002", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Interaction_parameters_between_the_sulfate_phosphate_ion_with_the_related_C_945_NN_8217_segment_of_the_chimeric_peptides_in_a_context_free_system_250_docked_structures_of_the_individual_conformation_are_described_in_terms_of_X_H_8212_O_where_X_8202_8202_/667670", "title"=>"Interaction parameters between the sulfate/phosphate ion with the related ‘C<sup>α</sup>NN’ segment of the chimeric peptides in a context free system (250 docked structures of the individual conformation) are described in terms of X-H—O (where X = C<sup>α</sup><sub>−1</sub>/N<sub>0</sub>/N<sub>+1</sub>) distances(<b>Å</b>) and angles(°) indicating the nature of H-bond formation (mean value of the parameters in parenthesis).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-13 02:07:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1007028"], "description"=>"a<p>PDB IDs from where the ‘C<sup>α</sup>NN’ motif segment residues are taken, residue number of PDB IDs are in parenthesis; the</p>b<p>‘C<sup>α</sup>NN’ motif segment is underlined;</p>c<p>anchor helix (ABGY) sequence: -Ala-Aib-Ala-Lys-Ala-Aib-Lys-Ala-Lys-Ala-Aib-Gly-Gly-Tyr-NH<sub>2</sub>.</p>", "links"=>[], "tags"=>["designed", "peptide", "sequences", "computational"], "article_id"=>667655, "categories"=>["Biochemistry", "Biological Sciences", "Chemistry", "Physics", "Biophysics"], "users"=>["Tridip Sheet", "Subhrangshu Supakar", "Raja Banerjee"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057366.t001", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Details_of_designed_peptide_sequences_used_for_computational_work_/667655", "title"=>"Details of designed peptide sequences used for computational work.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-13 02:07:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/986673"], "description"=>"<p>(a) Distribution of (X)H—O distance for interaction with sulfate ion; (b) distribution of α<sub>−1</sub>/N<sub>0</sub>/N<sub>+1</sub>). The mean (μ) value, standard deviation (σ) value and goodness of the fit (adjusted R<sup>2</sup>) of each distribution are mentioned. The ratio of σ/μ is shown to emphasize that there is very little spread about the mean value.</p>", "links"=>[], "tags"=>["h-bond", "constraints"], "article_id"=>651674, "categories"=>["Biochemistry", "Biological Sciences", "Chemistry", "Physics", "Biophysics"], "users"=>["Tridip Sheet", "Subhrangshu Supakar", "Raja Banerjee"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057366.g002", "stats"=>{"downloads"=>3, "page_views"=>39, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_H_bond_distance_and_angle_constraints_obtained_from_interaction_of_anion_s_and_8216_experimental_NMR_8217_structure_of_CPS224Ac_/651674", "title"=>"Distribution of H-bond distance and angle constraints obtained from interaction of anion(s) and ‘experimental NMR’ structure of CPS224Ac.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-14 12:02:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/986670"], "description"=>"<p>a) Lowest energy conformer of the 250 sulfate ion docked structures of ‘experimental NMR’ structure along with its detailed representation of interactions showing that ‘C<sup>α</sup>NN’ motif segment acts as the only recognition site for sulfate ion; b) lowest energy conformer of the 250 phosphate ion docked structures of ‘experimental NMR’ structure along with its detailed representation of interactions showing that ‘C<sup>α</sup>NN’ motif segment acts as the only recognition site for phosphate ion; c) ESI-MS result showing the binding of sulfate ion with CPS224Ac (Inset: isotopic distribution of m/z 926.5 showing the difference of 0.5, indicating doubly charged species); d) ESI-MS result showing the binding of phosphate ion with CPS224Ac (Inset: isotopic distribution of m/z 926.4 showing the difference of 0.5, indicating doubly charged species).</p>", "links"=>[], "tags"=>["anion", "motif"], "article_id"=>651671, "categories"=>["Biochemistry", "Biological Sciences", "Chemistry", "Physics", "Biophysics"], "users"=>["Tridip Sheet", "Subhrangshu Supakar", "Raja Banerjee"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057366.g001", "stats"=>{"downloads"=>0, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Representation_of_interaction_of_anion_with_C_945_NN_8217_motif_of_CPS224Ac_/651671", "title"=>"Representation of interaction of anion with ‘C<sup>α</sup>NN’ motif of CPS224Ac.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-14 12:02:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/986675"], "description"=>"<p>a) Partial representation (first 1 ns of total 40 ns simulation) of sulfate ion interaction with the C<sup>α</sup>NN′ motif segment of CPS224Ac (blue lines indicate weak interaction while red line indicate strong H-bond) along with the detail monitoring of backbone dihedral angles (φ, ψ) of Lys3 with respect to time in the MD trajectory; b) Ramachandran plot of the backbone dihedral angle distributions (φ, ψ) of all the residues during the MD simulation (40 ns) showing perturbation takes place only in the C<sup>α</sup>NN′ motif segment; c) Distribution of backbone dihedral angles (φ, ψ) of Lys3 residue as Ramachandran plot during the 40 ns MD-simulation, emphasizing its existence in helical conformation only during interaction of sulfate ion with C<sup>α</sup>NN′ motif segment peptide.</p>", "links"=>[], "tags"=>["simulations", "40", "ns", "sulfate", "ion-bound", "conformer", "nmr"], "article_id"=>651676, "categories"=>["Biochemistry", "Biological Sciences", "Chemistry", "Physics", "Biophysics"], "users"=>["Tridip Sheet", "Subhrangshu Supakar", "Raja Banerjee"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057366.g003", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_MD_simulations_for_40_ns_at_276K_of_the_sulfate_ion_bound_conformer_of_the_8216_experimental_NMR_structure_8217_of_CPS224Ac_/651676", "title"=>"MD simulations (for 40 ns at 276K) of the sulfate ion-bound conformer of the ‘experimental NMR structure’ of CPS224Ac.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-14 12:03:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/986676"], "description"=>"<p>a) For 40 ns and b) first 8 ns; showing the destabilization of helical conformation at the ‘C<sup>α</sup>NN’ segment in the MD trajectory.</p>", "links"=>[], "tags"=>["md"], "article_id"=>651677, "categories"=>["Biochemistry", "Biological Sciences", "Chemistry", "Physics", "Biophysics"], "users"=>["Tridip Sheet", "Subhrangshu Supakar", "Raja Banerjee"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057366.g004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Details_of_NH_NH_i_i_1_distance_s_around_the_8216_C_945_NN_8217_region_during_the_MD_simulation_/651677", "title"=>"Details of NH—NH<sub>(i,i+1)</sub> distance(s) around the ‘C<sup>α</sup>NN’ region during the MD simulation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-14 12:03:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/986678", "https://ndownloader.figshare.com/files/986679", "https://ndownloader.figshare.com/files/986680", "https://ndownloader.figshare.com/files/986682", "https://ndownloader.figshare.com/files/986683", "https://ndownloader.figshare.com/files/986685", "https://ndownloader.figshare.com/files/986686", "https://ndownloader.figshare.com/files/986687", "https://ndownloader.figshare.com/files/986688", "https://ndownloader.figshare.com/files/986689"], "description"=>"<div><p>Among several ‘anion binding motifs’, the recently described ‘C<sup>α</sup>NN’ motif occurring in the loop regions preceding a helix, is conserved through evolution both in sequence and its conformation. To establish the significance of the conserved sequence and their intrinsic affinity for anions, a series of peptides containing the naturally occurring ‘C<sup>α</sup>NN’ motif at the N-terminus of a designed helix, have been modeled and studied in a context free system using computational techniques. Appearance of a single interacting site with negative binding free-energy for both the sulfate and phosphate ions, as evidenced in docking experiments, establishes that the ‘C<sup>α</sup>NN’ segment has an intrinsic affinity for anions. Molecular Dynamics (MD) simulation studies reveal that interaction with anion triggers a conformational switch from non-helical to helical state at the ‘C<sup>α</sup>NN’ segment, which extends the length of the anchoring-helix by one turn at the N-terminus. Computational experiments substantiate the significance of sequence/structural context and justify the conserved nature of the ‘C<sup>α</sup>NN’ sequence for anion recognition through “local” interaction.</p> </div>", "links"=>[], "tags"=>["conformational", "peptide", "motif", "anions"], "article_id"=>651679, "categories"=>["Biochemistry", "Biological Sciences", "Chemistry", "Physics", "Biophysics"], "users"=>["Tridip Sheet", "Subhrangshu Supakar", "Raja Banerjee"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0057366.s001", "https://dx.doi.org/10.1371/journal.pone.0057366.s002", "https://dx.doi.org/10.1371/journal.pone.0057366.s003", "https://dx.doi.org/10.1371/journal.pone.0057366.s004", "https://dx.doi.org/10.1371/journal.pone.0057366.s005", "https://dx.doi.org/10.1371/journal.pone.0057366.s006", "https://dx.doi.org/10.1371/journal.pone.0057366.s007", "https://dx.doi.org/10.1371/journal.pone.0057366.s008", "https://dx.doi.org/10.1371/journal.pone.0057366.s009", "https://dx.doi.org/10.1371/journal.pone.0057366.s010"], "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Conformational_Preference_of_C_NN_Short_Peptide_Motif_towards_Recognition_of_Anions__/651679", "title"=>"Conformational Preference of ‘C<sup>α</sup>NN’ Short Peptide Motif towards Recognition of Anions", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-03-14 12:04:25"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"8", "full-text"=>"8", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"4", "full-text"=>"6", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"2", "full-text"=>"5", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"2", "full-text"=>"1", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"3", "full-text"=>"0", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}

Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Physical sciences", "average_usage"=>[254, 431, 547, 651, 748, 842, 932, 1017, 1098, 1178, 1259, 1336, 1404]}, {"subject_area"=>"/Physical sciences/Physics", "average_usage"=>[254, 421, 527, 626, 720, 813, 900, 983, 1063, 1136, 1210, 1283, 1342]}]}
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