Conformational preference of 'CαNN' short peptide motif towards recognition of anions

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...

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Published in:PloS one 2013-03, Vol.8 (3), p.e57366-e57366
Main Authors: Sheet, Tridip, Supakar, Subhrangshu, Banerjee, Raja
Format: Article
Language:English
Subjects:
Affinity
Amino Acid Motifs
Amino Acid Sequence
Anchoring
Anions
Anions - chemistry
Anions - metabolism
Binding
Bioinformatics
Biology
Chemistry
Computation
Computer applications
Computer simulation
Conformation
Conserved sequence
Docking
Free energy
Hydrogen Bonding
Magnetic Resonance Spectroscopy
Molecular Docking Simulation
Molecular dynamics
Molecular Dynamics Simulation
N-Terminus
NMR
Nuclear magnetic resonance
Peptides
Peptides - chemistry
Peptides - metabolism
Phosphates
Physics
Polypeptides
Preferences
Protein Binding
Protein Conformation
Proteins
Recognition
Sulfate
Sulfates - chemistry
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description 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.
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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.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0057366</identifier><identifier>PMID: 23516403</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Affinity ; Amino Acid Motifs ; Amino Acid Sequence ; Anchoring ; Anions ; Anions - chemistry ; Anions - metabolism ; Binding ; Bioinformatics ; Biology ; Chemistry ; Computation ; Computer applications ; Computer simulation ; Conformation ; Conserved sequence ; Docking ; Free energy ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy ; Molecular Docking Simulation ; Molecular dynamics ; Molecular Dynamics Simulation ; N-Terminus ; NMR ; Nuclear magnetic resonance ; Peptides ; Peptides - chemistry ; Peptides - metabolism ; Phosphates ; Physics ; Polypeptides ; Preferences ; Protein Binding ; Protein Conformation ; Proteins ; Recognition ; Sulfate ; Sulfates - chemistry</subject><ispartof>PloS one, 2013-03, Vol.8 (3), p.e57366-e57366</ispartof><rights>2013 Sheet et al. 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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. 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subjects Affinity
Amino Acid Motifs
Amino Acid Sequence
Anchoring
Anions
Anions - chemistry
Anions - metabolism
Binding
Bioinformatics
Biology
Chemistry
Computation
Computer applications
Computer simulation
Conformation
Conserved sequence
Docking
Free energy
Hydrogen Bonding
Magnetic Resonance Spectroscopy
Molecular Docking Simulation
Molecular dynamics
Molecular Dynamics Simulation
N-Terminus
NMR
Nuclear magnetic resonance
Peptides
Peptides - chemistry
Peptides - metabolism
Phosphates
Physics
Polypeptides
Preferences
Protein Binding
Protein Conformation
Proteins
Recognition
Sulfate
Sulfates - chemistry
title Conformational preference of 'CαNN' short peptide motif towards recognition of anions
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