title: Multifaceted analyses of the interactions between human heart type fatty acid binding protein and its specific aptamers.
abstract: Aptamer-protein interaction studies have been mainly confined to dissociation constant (Kd) determination. A combinatorial approach involving limited proteolysis mass spectroscopy, molecular docking and CD studies is reported here to elucidate the specific interactions involved.
  
  
  
  To generate aptamers specific for human FABP3, SELEX was performed incorporating counter SELEX cycles against control FABPs and GST tag, followed by their characterization by EMSA, CD and SVD analysis. Based on computationally obtained aptamer-protein complex models, the interacting aptamer, and protein residues were predicted and supported by limited proteolysis experiments.
  
  
  
  Two aptamers N13 and N53 specific for human fatty acid binding protein (FABP3) were isolated with corresponding Kdof 0.0743±0.0142μM and 0.3337±0.1485μM for FABP3 interactions. Both aptamers possess stable B-DNA structures at salt concentration of 100mM and pH range (6-9). The N13 aptamer led interaction involved 3 salt bridges and 2 hydrogen bonds, whereas N53 had 2 salt bridges with 8 hydrogen and 7 hydrophobic interactions.
  
  
  
  The aptamers generated are the first to be reported against human FABP3. The higher interaction footprint of N53 incited synergistic conformational changes in both N53 and FABP3 during interaction, leading to a decline in binding affinity in comparison to N13 which corroborated to the calculated Kdvalues.
  
  
  
  This combinatorial method may be used to retrieve the possible specific binding modes and interaction patterns involved in large aptamer-protein complexes. Thus the method can be exploited to identify the optimum aptamer length for in-depth structure-function studies and its tailored applications.
authors.affiliation: Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
authors.forename: Ankana
authors.initials: A
authors.lastname: Kakoti
authors.affiliation: Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India. Electronic address: pgoswami@iitg.ernet.in.
authors.forename: Pranab
authors.initials: P
authors.lastname: Goswami
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D002942:Circular Dichroism; D019295:Computational Biology; D024202:Electrophoretic Mobility Shift Assay; D000074026:Fatty Acid Binding Protein 3; D050556:Fatty Acid-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D062105:Molecular Docking Simulation; D009691:Nucleic Acid Denaturation; D009711:Nucleotides / Q000378:metabolism; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D059748:Proteolysis; D016415:Sequence Alignment
chemical_list: D000596:Amino Acids; D052157:Aptamers, Nucleotide; C493408:FABP3 protein, human; D000074026:Fatty Acid Binding Protein 3; D050556:Fatty Acid-Binding Proteins; D009711:Nucleotides; D010446:Peptide Fragments
keywords: Aptamer; Human heart type fatty acid binding protein; Limited proteolysis; MALDI