Computational design of model scaffold for anion recognition based on the 'Cα NN' motif

New facets of larger Nest motifs in proteins

The Nest is a concave-shaped structural motif in proteins formed by consecutive enantiomeric left-handed (L) and right-handed (R) helical conformation of the backbone. This important motif subsumes many turn and helix capping structures and binds electron-rich ligands. Simple Nests are either RL or LR. Larger Nests (>2 residues long) may be RLR, LRL, RLRL, and so forth, being considered as composed of overlapping simple Nests. The larger Nests remain under-explored despite their widely known contributions to protein function. In our study, we address whether the recurrence of enantiomeric geometry in the larger Nests constrains the peptide backbone such that distinct compositional and conformational preferences are seen compared to simple Nests. Our analysis reveals the critical role of the L helical torsion angle in the formation of larger Nests. This can be observed through the higher propensity of residue or secondary structure combinations in LR and LRL backbone conformation in comparison to RL or RLR, although LR/LRL is considerably lower by occurrence. We also find that the most abundant doublets and triplets in Nests have a propensity for particular secondary structures, suggesting a strong sequence-structure relationship in the larger Nest. Overall, our analysis corroborates distinct features of simple and the larger Nests. Such insights would be helpful towards in-vitro design of peptides and peptidomimetic studies.

Design of a Peptide-Based Model Leads for Scavenging Anions

Among several peptide-based anion recognition motifs, the "CαNN" motif containing C-1 α, N0, and N+1 of three consecutive residues is unique in its mode of interaction. Having a spatial geometry of βαα or βαβ, this motif occurs in the N terminus of a helix and often found at the functional interface of a protein, mediating crucial biological significance upon interaction with anion(s). The interaction of anion(s) with chimeric peptide sequences containing the naturally occurring "CαNN" motif (CPS224Ac, CPS226, and CPS228) reported in our previous attempts strongly confirms that the information regarding the interaction is embedded within the local sequences of the motif segment. At these prevailing circumstances, an effort has been pursued to design novel scaffolds based on the "CαNN" motif for achieving better recognition of anion(s). Exploring the existing data set of the "CαNN" motif available in the FSSP database, four novel peptide-based scaffolds have been designed (DS1, DS2, DS3, and DS4), and preliminary screenings have been performed using computational approaches. Our initial work suggests that two (DS1 and DS3) out of the four scaffolds are potential candidates for better anion recognition. By employing biophysical characterization using both qualitative and quantitative measures, in this present study, we report the interaction of sulfate and phosphate ions with these two designed scaffolds, in which there is much better recognition of anions by these scaffolds than the natural sequences, justifying their logical engineering. Our observation strongly suggests that these designed scaffolds are better potential candidates than those of the naturally occurring "CαNN" motif in terms of anion recognition and could be utilized for the scavenging of anion(s) for different purposes.

Interaction landscape of a 'CαNN' motif with arsenate and arsenite: a potential peptide-based scavenger of arsenic

Arsenic (As) is a toxic metalloid that has drawn immense attention from the scientific community recently due to its fatal effects through its unwanted occurrence in ground water around the globe. The presence of an excess amount of water soluble arsenate and/or arsenite salt (permissible limit 10 μg L-1 as recommended by the WHO) in water has been correlated with several human diseases. Although arsenate (HAsO4 2-) is a molecular analogue of phosphate (HPO4 2-), phosphate is indispensable for life, while arsenic and its salts are toxic. Therefore, it is worthwhile to focus on the removal of arsenic from water. Towards this end, the design of peptide-based scaffolds for the recognition of arsenate and arsenite would add a new dimension. Utilizing the stereochemical similarity between arsenate (HAsO4 2-) and phosphate (HPO4 2-), we successfully investigated the recognition of arsenate and arsenite with a naturally occurring novel phosphate binding 'CαNN' motif and its related designed analogues. Using computational as well as biophysical approaches, for the first time, we report here that a designed peptide-based scaffold based on the 'CαNN' motif can recognize anions of arsenic in a thermodynamically favorable manner in a context-free system. This peptide-based arsenic binding agent has the potential for future development as a scavenger of arsenic anions to obtain arsenic free water.

Quantum chemical studies on anion specificity of CαNN motif in functional proteins

Anion binding C^αNN motif is found in functionally important regions of protein structures. This motif based only on backbone atoms from three adjacent residues, recognizes free sulphate or phosphate ion as well as phosphate groups in nucleotides and in a variety of cofactors. The mode of anion recognition and microscopic picture of binding interaction remains unclear. Here we perform self-consistent quantum chemical calculations considering sulphate and phosphate bound C^αNN motif fragments from crystal structures of functional proteins in order to figure out microscopic basis of anion recognition. Our calculations indicate that stability and preference of the anion in the motif depends on the sequence of the motif. The stabilization energy is larger in case of polar residue containing motif fragment. Nitrogen atom of the polar residue of motif mainly participates in the coordination at the lowest energy levels. Anion replacement decreases stabilization energy along with coordination between motif atoms and oxygen atoms of anion shifted to higher energies, suggesting preference of the motif residues to specific anion. Our analysis may be helpful to understand microscopic basis of interaction between proteins and ionic species.

Anion induced conformational preference of Cα NN motif residues in functional proteins

Among different ligand binding motifs, anion binding C^α NN motif consisting of peptide backbone atoms of three consecutive residues are observed to be important for recognition of free anions, like sulphate or biphosphate and participate in different key functions. Here we study the interaction of sulphate and biphosphate with C^α NN motif present in different proteins. Instead of total protein, a peptide fragment has been studied keeping C^α NN motif flanked in between other residues. We use classical force field based molecular dynamics simulations to understand the stability of this motif. Our data indicate fluctuations in conformational preferences of the motif residues in absence of the anion. The anion gives stability to one of these conformations. However, the anion induced conformational preferences are highly sequence dependent and specific to the type of anion. In particular, the polar residues are more favourable compared to the other residues for recognising the anion.