Book of Abstracts: Albany 2011
June 14-18 2011
©Adenine Press (2010)
Energetically Favourable Communication Pathways in Pyrrolysyl-tRNA Synthetase
Aminoacyl-tRNA synthetases (aaRS) play a pivotal role in the protein biosynthetic machinery, ensuring the correct translation of the genetic code. The response to cognate tRNA binding is elicited in the release of the activated amino acid from the pre-transfer complex to the 3’ end of the tRNA. Such efficient communication across distant sites (1) underlies allostery, making the aaRS an excellent model for studying this phenomenon. Several studies at atomistic detail (2, 3), including investigations on aaRS (such as MetRS and TrpRS) from our own lab (4, 5), have elucidated allosteric communications. Here we have chosen an atypical aaRS, pyrrolysyl-tRNA synthetase (from D.hafniense [DhPylRS]), in its three different states of ligation (Sys1: native DhPylRS, Sys2: DhPylRS+2YLY, Sys3: DhPylRS+2YLY+2tRNA) for our study. Interestingly, in contrast to canonical aaRS, DhPylRS exhibits a diffused recognition of tRNA bases (not residing in the triplet codon). Recent crystal structure of DhPylRS [dimer] bound to tRNAPyl has given insights into the unique protein-tRNA interactions accounting for the orthogonality of this aaRS-tRNA pair (6).
In this study, we investigate the interaction energy weighted (7) protein-tRNA network and its dynamical properties to gain insight into the functioning of this non-canonical tRNA-synthetase and understand the mechanism of long-range communications. The concept of pre-existing paths of communication (8) and their manifestations at different liganded forms are probed in this study. Specifically, the ensemble derived interaction energy between residues is a parameter that regulates the transmission of perturbation upon ligand binding between distant functional sites in DhPylRS. Interaction energy based long-range residue coupling from the MD ensembles is found to contribute to global signal transfer. Our analysis reveals the importance of side-chain interactions while backbone conformational changes are not significant for Sys1-3. The ligand induced changes in conformation and communication pathways are efficiently captured by protein-tRNA energy networks for the three systems. We also probe different weighted network parameters (e.g. betweenness and funneling) to obtain the key residues for signal propagation across distant sites. The cost of communication between distant functional sites and pre-existence of the optimal and sub-optimal pathways in the MD ensemble is also investigated. Furthermore, asymmetry in terms of communication efficiency between the two subunits is clearly evident from all our studies for Sys1-3 to various extents, with Sys3 being maximally asymmetric. Interestingly, the concept of half-sites reactivity discussed in literature agrees well to this asymmetry between the two subunits. Additionally we find that the transfer of activated amino acid to the 3’ end of tRNA is co-ordinated by alternation of global rigidity/flexibility. Our results exhibit good correlation with mutagenesis experiments for DhPylRS. Based on these observations, a general mechanistic insight for allosteric communication and the relevance of asymmetry in the dimeric protein is presented.
Abbreviations: YLY- adenylated pyrrolysine, Pyl – pyrrolysine
Molecular Biophysics Unit