Probing Backbone Hydrogen Bonds in Proteins by Amide-to-Ester Mutations

A facile approach for incorporating tyrosine esters to probe ion-binding sites and backbone hydrogen bonds

Amide-to-ester substitutions are used to study the role of the amide bonds of the protein backbone in protein structure, function, and folding. An amber suppressor tRNA/synthetase pair has been reported for incorporation of p-hydroxy-phenyl-L-lactic acid (HPLA), thereby introducing ester substitution at tyrosine residues. However, the application of this approach was limited due to the low yields of the modified proteins and the high cost of HPLA. Here we report the in vivo generation of HPLA from the significantly cheaper phenyl-L-lactic acid. We also construct an optimized plasmid with the HPLA suppressor tRNA/synthetase pair that provides higher yields of the modified proteins. The combination of the new plasmid and the in-situ generation of HPLA provides a facile and economical approach for introducing tyrosine ester substitutions. We demonstrate the utility of this approach by introducing tyrosine ester substitutions into the K+ channel KcsA and the integral membrane enzyme GlpG. We introduce the tyrosine ester in the selectivity filter of the M96V mutant of the KcsA to probe the role of the second ion binding site in the conformation of the selectivity filter and the process of inactivation. We use tyrosine ester substitutions in GlpG to perturb backbone H-bonds to investigate the contribution of these H-bonds to membrane protein stability. We anticipate that the approach developed in this study will facilitate further investigations using tyrosine ester substitutions.

Backbone amides are determinants of Cl- selectivity in CLC ion channels

Chloride homeostasis is regulated in all cellular compartments. CLC-type channels selectively transport Cl- across biological membranes. It is proposed that side-chains of pore-lining residues determine Cl- selectivity in CLC-type channels, but their spatial orientation and contributions to selectivity are not conserved. This suggests a possible role for mainchain amides in selectivity. We use nonsense suppression to insert α-hydroxy acids at pore-lining positions in two CLC-type channels, CLC-0 and bCLC-k, thus exchanging peptide-bond amides with ester-bond oxygens which are incapable of hydrogen-bonding. Backbone substitutions functionally degrade inter-anion discrimination in a site-specific manner. The presence of a pore-occupying glutamate side chain modulates these effects. Molecular dynamics simulations show backbone amides determine ion energetics within the bCLC-k pore and how insertion of an α-hydroxy acid alters selectivity. We propose that backbone-ion interactions are determinants of Cl- specificity in CLC channels in a mechanism reminiscent of that described for K+ channels.

Photoinduced carbamoylation reactions: unlocking new reactivities towards amide synthesis

The preparation of amide-containing compounds is among the most interesting and challenging topics for the synthetic community. Such relevance is given by their reactive aspects explored in the context of organic synthesis and by the direct application of these compounds as pharmaceuticals and useful materials, and their key roles in biological structures. A simple and straightforward strategy for the amide moiety installation is the use of carbamoyl radicals - this nucleophilic one-electron intermediate is prone to undergo a series of transformations, providing a range of structurally relevant derivatives. In this review, we summarize the latest advances in the field from the perspective of photoinduced protocols. To this end, their synthetic applications are organized accordingly to the nature of the radical precursor (formamides through HAT, 4-substituted-1,4-dihydropyridines, oxamic acids, and N-hydroxyphthalimido esters), the mechanistic aspects also being highlighted. The discussion also includes a recent approach proceeding via photolytic C-S cleavage of dithiocarbamate-carbamoyl intermediates. By exploring fundamental concepts, this material aims to offer an understanding of the topic, which will encourage and facilitate the design of new synthetic strategies applying the carbamoyl radical.

Water soluble PEGylated phenothiazines as valuable building blocks for bio-materials

The paper reports a series of three new PEGylated phenothiazine derivatives which keep the potential of valuable building blocks for preparing eco-materials addressed to a large realm of fields, from bio-medicine to opto-electronics. They were synthetized by connecting the hydrophilic poly(ethylene glycol) to the hydrophobic phenothiazine via an ether, ester, or amide linking group. The successful synthesis of the targeted polymers and their purity were demonstrated by NMR and FTIR spectroscopy methods. Their capacity to self-assembly in water was studied by DLS and UV-vis techniques and the particularities of the formed aggregates were investigated by fluorescence spectroscopy, SEM, AFM, POM and UV light microscopy. The biocompatibility was assessed on normal human dermal fibroblasts and human cervical cancer cells. The synthetized compounds showed the formation of luminescent aggregates and proved excellent biocompatibility on normal cells. In addition, a concentration dependent cytotoxicity against HeLa cancer cells was noticed for the PEGylated phenothiazine containing an ester unit.

Peptide Folding and Binding Probed by Systematic Non-canonical Mutagenesis

Many proteins and peptides fold upon binding another protein. Mutagenesis has proved an essential tool in the study of these multi-step molecular recognition processes. By comparing the biophysical behavior of carefully selected mutants, the concert of interactions and conformational changes that occur during folding and binding can be separated and assessed. Recently, this mutagenesis approach has been radically expanded by deep mutational scanning methods, which allow for many thousands of mutations to be examined in parallel. Furthermore, these high-throughput mutagenesis methods have been expanded to include mutations to non-canonical amino acids, returning peptide structure-activity relationships with unprecedented depth and detail. These developments are timely, as the insights they provide can guide the optimization of de novo cyclic peptides, a promising new modality for chemical probes and therapeutic agents.

How Strong is Hydrogen Bonding to Amide Nitrogen?

The protonation of the carboxamide nitrogen atom is an essential part of in vivo and in vitro processes (cis-trans isomerization, amides hydrolysis etc). This phenomenon is well studied in geometrically strongly distorted amides, although there is little data concerning the protonation of undistorted amides. In the latter case, the participation of amide nitrogen in hydrogen bonding (which can be regarded as the incipient state of a proton transfer process) is less well-studied. Thus, it would be a worthy goal to investigate the enthalpy of this interaction. We prepared and investigated a set of peri-substituted naphthalenes containing the protonated dimethylamino group next to the amide nitrogen atom ("amide proton sponges"), which could serve as models for the study of an intramolecular hydrogen bond with the amide nitrogen atom. X-Ray analysis, NMR spectra, basicity values as well as quantum chemical calculations revealed the existence of a hydrogen bond with the amide nitrogen, that should be attributed to the borderline between moderate and weak intramolecular hydrogen bonds (2-7 kcal ⋅ mol^-1 ).

Molecular determinants for agonist recognition and discrimination in P2X2 receptors

P2X receptors (P2XRs) are ligand-gated cation channels involved in pain and inflammation. Gasparri et al. show that the backbone carbonyl atoms of amino acid residue Thr184 are involved in ligand discrimination, while those of Lys69 contribute mostly to ligand recognition by rat P2X2Rs.

P2X receptors (P2XRs) are trimeric ligand-gated ion channels that open a cation-selective pore in response to ATP binding. P2XRs contribute to synaptic transmission and are involved in pain and inflammation, thus representing valuable drug targets. Recent crystal structures have confirmed the findings of previous studies with regards to the amino acid chains involved in ligand recognition, but they have also suggested that backbone carbonyl atoms contribute to ATP recognition and discrimination. Here we use a combination of site-directed mutagenesis, amide-to-ester substitutions, and a range of ATP analogues with subtle alterations to either base or sugar component to investigate the contributions of backbone carbonyl atoms toward ligand recognition and discrimination in rat P2X2Rs. Our findings demonstrate that while the Lys69 backbone carbonyl makes an important contribution to ligand recognition, the discrimination between different ligands is mediated by both the side chain and the backbone carbonyl oxygen of Thr184. Together, our data demonstrate how conserved elements in P2X2Rs recognize and discriminate agonists.