title: Characterization of aptamer-protein complexes by X-ray crystallography and alternative approaches.
abstract: Aptamers are oligonucleotide ligands, either RNA or ssDNA, selected for high-affinity binding to molecular targets, such as small organic molecules, proteins or whole microorganisms. While reports of new aptamers are numerous, characterization of their specific interaction is often restricted to the affinity of binding (K(D)). Over the years, crystal structures of aptamer-protein complexes have only scarcely become available. Here we describe some relevant technical issues about the process of crystallizing aptamer-protein complexes and highlight some biochemical details on the molecular basis of selected aptamer-protein interactions. In addition, alternative experimental and computational approaches are discussed to study aptamer-protein interactions.
authors.affiliation: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands.
authors.forename: Vincent J B
authors.initials: VJB
authors.lastname: Ruigrok
authors.affiliation: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands.
authors.forename: Mark
authors.initials: M
authors.lastname: Levisson
authors.affiliation: Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands.
authors.forename: Johan
authors.initials: J
authors.lastname: Hekelaar
authors.affiliation: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands.
authors.forename: Hauke
authors.identifier: 0000-0002-6138-5026
authors.initials: H
authors.lastname: Smidt
authors.affiliation: Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands.
authors.forename: Bauke W
authors.initials: BW
authors.lastname: Dijkstra
authors.affiliation: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands.
authors.forename: John
authors.initials: J
authors.lastname: Van der Oost
mesh_terms: D000818:Animals; D052157:Aptamers, Nucleotide / Q000737:chemistry* / Q000378:metabolism*; D018360:Crystallography, X-Ray; D006801:Humans; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D052157:Aptamers, Nucleotide; D011506:Proteins