Sulfate ion interaction with ‘anion recognition’ short peptide motif at the N-terminus of an isolated helix: A conformational landscape

Conformational Preference of ‘CαNN’ Short Peptide Motif towards Recognition of Anions

“…It is also found that out of these two interacting oxygen atoms, in each set of the respective 250 docked conformers, one oxygen atom is interacting concurrently with the C α -H atom of Gly2 and the main chain N-H atom of Lys3, while the other interacting oxygen atom has shared its contribution only to the main-chain N-H atom of Gln4, as observed in the crystal structure of 1MUG and proposed for the ‘C α NN’ motif [1], [13]. This result supports the observation of our earlier NMR study on CPS224Ac [25] which showed that upon interaction with the sulfate ion the chemical shift value of the main-chain N-H along with C α H atom of Lys3 and the main-chain N-H along with C α H atom of Gln4 were only altered (downfield shift observed for N-H, while upfield shift observed for C α H when compared to those individual in the absence of the sulfate ion), while others including ε-CH 2 and side chain NH 2 of Lys(s) remained unchanged (Figure S1). However, NMR results cannot locate the exact nature of the interaction of oxygen atoms of the sulfate ion, which could be acquired in details by this docking experiment.…”

“…Translating the αN and NN nuclear Overhauser effect (nOe) cross-peak intensities, obtained from the interaction between CPS224Ac and the sulfate ion in the 2D-NMR (nuclear magnetic resonance) experiments [25], into suitable distance upper limits (NOE ∝ (1/r) 6 ) [weak (w): 4.25 Å, medium (m): 3.5 Å, strong (s): 3.0 Å] and the 3 J Nα values of individual residues into the backbone dihedral angles (φ±10) using Karplus equation ( 3 J Nα  = 6.4Cos 2 θ−1.4Cosθ+1.9 where, θ = |φ−60 0 |) [31], 100 structures are generated by the programme DYANA (Dynamics Algorithm for NMR Application) [32]. Side chain conformation for the Lys residue(s) of the best ranked NMR derived structures is resolved by using the rotamer library of Swiss Pdb Viewer [33].…”

“…The ‘experimental NMR structure’. Molecular docking experiments, using AutoDock 4.2 software [38], [39], have been performed between the ‘experimental NMR structure’ of CPS224Ac [25] and the anion(s) (separately with the sulfate and the phosphate ion) using several grid size to identify the site for recognition of anion in the peptide and to get an idea about the associated parameters of interaction. The results show that, in all the respective 250 iteration for individual sulfate and phosphate ion, for all the grid size only the ‘C α NN’ motif segment, present at the N-terminus of the context free helical peptide, can recognize the sulfate/phosphate ion through non-covalent interaction mediated through H-bond (hydrogen bond) (Figure 1a, b).…”

“…Moreover, participation of the protein tertiary structure in affecting the N-terminal helix-extension upon anion binding has also to be corroborated. In a recent publication [25] using complementary spectroscopic techniques we have presented evidence for the interaction of a sulfate (SO 4 2− ) ion with a ‘C α NN motif’ segment (Gly-Lys-Gln from protein 1MUG) in an 18-residue designed chimeric peptide sequence in a context free system as reported in protein crystal structures.…”

Anion Recognition in Water: Recent Advances from a Supramolecular and Macromolecular Perspective

“…The system was initially put forward as a phosphate‐recognition unit (Figure 11 d), but by attaching Leu‐Gly‐Lys‐Gln, a C α NN fragment, to the N terminus of an anchor helix, Sheet and Banerjee observed sulfate recognition in water manifested as a change in the conformation that was typical of an “induced fit” system 62. Computational analysis confirmed earlier crystallographic studies showing that both sulfate and phosphate binding triggers a conformational switch from a nonhelical to a helical morphology 63…”