Paper Citing NAMD - Abstract
Mucic, Ivana D.; Nikolic, Milan R.; Stojanovic, Srdan D.
Contribution of cation-pi interactions to the stability of Sm/LSm oligomeric assemblies
PROTOPLASMA, 252:947-958, JUL 2015
In this work, we have analyzed the influence of cation-pi interactions to the stability of Sm/LSm assemblies and their environmental preferences. The number of interactions formed by arginine is higher than lysine in the cationic group, while histidine is comparatively higher than phenylalanine and tyrosine in the pi group. Arg-Tyr interactions are predominant among the various pairs analyzed. The furcation level of multiple cation-pi interactions is much higher than that of single cation-pi interactions in Sm/LSm interfaces. We have found hot spot residues forming cation-pi interactions, and hot spot composition is similar for all aromatic residues. The Arg-Phe pair has the strongest interaction energy of -8.81 kcal mol(-1) among all the possible pairs of amino acids. The extent of burial of the residue side-chain correlates with the Delta Delta G of binding for residues in the core and also for hot spot residues cation-pi bonded across the interface. Secondary structure of the cation-pi residues shows that Arg and Lys preferred to be in strand. Among the pi residues, His prefers to be in helix, Phe prefers to be in turn, and Tyr prefers to be in strand. Stabilization centers for these proteins showed that all the five residues found in cation-pi interactions are important in locating one or more of such centers. More than 50 % of the cation-pi interacting residues are highly conserved. It is likely that the cation-pi interactions contribute significantly to the overall stability of Sm/LSm proteins.
