RNA-LIM is a new procedure for coarse-grained estimation of the structure of single-stranded-RNA (ss-RNA) bound to the surface of a protein. Capable of utilizing any type of pseudo-potential describing the affinity between ss-RNA and surface amino acids, RNA-LIM evolves an ss-RNA chain, of known sequence, as a series of walks between fixed sites on a protein surface. The optimal routes are found by application of a set of minimal ‘limiting’ restraints derived jointly from (1) selective sampling of the ribonucleotide-amino acid affinity pseudo-potential data, and (2) RNA structural specification obtained from a statistical potential gathered from a library of ss-RNA-protein structures. We describe the general approach using a NAST-like approximation of the ss-RNA chain [Jonikas et al. 2009 Bioinformatics 15, 189-199] and a generalized pseudo-potential reflecting the location of a nucleic acid binding site. Minimum and maximum performance indicators of the methodology are established using synthetic data for which the pseudo-potential defining nucleic acid binding affinity is systematically degraded. Some potential uses and extensions of the routine are discussed.
References
Hall, D., Li, S., Yamashita, K., Azuma, R., Carver, J. A., & Standley, D. M. (2014). A novel protein distance matrix based on the minimum arc-length between two amino-acid residues on the surface of a globular protein. Biophysical chemistry.