Molecular dynamics simulation studies of a protein–RNA complex with a selectively modified binding interface

The RNA recognition motif (RRM) is one of the most common RNA binding domains. We have investigated the contribution of three highly conserved aromatic amino acids to RNA binding by the N‐terminal RRM of the U1A protein. Recently, we synthesized a modified base (A‐4CPh) in which a phenyl group is tethered to adenine using a linker of 4 methylene groups. The substitution of this base for adenine in the target RNA selectively stabilizes the complex formed with a U1A protein in which one of the conserved aromatic amino acids is replaced with Ala (Phe56Ala). In this article, we report molecular dynamics (MD) simulations that probe the structural consequences of the substitution of A‐4CPh for adenine in the wild type and Phe56Ala U1A–RNA complexes and in the free RNA. The simulations suggest that A‐4CPh stabilizes the complex formed with Phe56Ala by adopting a folded conformation in which the tethered phenyl group fills the site occupied by the phenyl group of Phe56 in the wild‐type complex. In contrast, an extended conformation of A‐4CPh is predicted to be most stable in the complex formed with the wild‐type protein. The calculations indicate A‐4CPh is in an extended conformation in the free RNA. Therefore, preorganizing the structure of the phenyl‐tethered base for binding may improve both the affinity and specificity of the RNA containing A‐4CPh for the Phe56Ala U1A protein. Taken together, the previous experimental work and the calculations reported here suggest a general design strategy for altering RRM–RNA complex stability. © 2005 Wiley Periodicals, Inc. Biopolymers 81: 256–269, 2006

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