Urea-aromatic interactions in biology

Abstract

Noncovalent interactions are key determinants in both chemical and biological processes. Among such processes, the hydrophobic interactions play an eminent role in folding of proteins, nucleic acids, formation of membranes, protein-ligand recognition, etc.. Though this interaction is mediated through the aqueous solvent, the stability of the above biomolecules can be highly sensitive to any small external perturbations, such as temperature, pressure, pH, or even cosolvent additives, like, urea-a highly soluble small organic molecule utilized by various living organisms to regulate osmotic pressure. A plethora of detailed studies exist covering both experimental and theoretical regimes, to understand how urea modulates the stability of biological macromolecules. While experimentalists have been primarily focusing on the thermodynamic and kinetic aspects, theoretical modeling predominantly involves mechanistic information at the molecular level, calculating atomistic details applying the force field approach to the high level electronic details using the quantum mechanical methods. The review focuses mainly on examples with biological relevance, such as (1) urea-assisted protein unfolding, (2) ureaassisted RNA unfolding, (3) urea lesion interaction within damaged DNA, (4) urea conduction through membrane proteins, and (5) protein-ligand interactions those explicitly address the vitality of hydrophobic interactions involving exclusively the urea-aromatic moiety.

Biophysical Reviews: 2020—looking back, going forward

“…Issue 1 started off with equal parts hope and sadness with the respective announcement of the inaugural winner of the Michèle Auger winner (Dr. Alexandra Zidovska) (Hall 2020b ) and the obituary for Dr. Christopher M. Dobson (Dumoulin 2020 ). Some of the interesting review articles in Issue 1 included those on the topics of hybrid biosynthetic strategies (Alissandratos 2020 ), dramatic effects of proline substitution on protein structural propensities (Ganguly and Basu 2020 ), computational studies of the interaction of urea with protein interfaces (Raghunathan et al 2020 ) and the use of the differential scanning fluorimetry (DSF) for high throughput drug candidate screening (Gao et al 2020 ).…”

Supramolecular Hydrogels with Tunable Swelling by Host Complexation with Cyclobis(paraquat-p-phenylene)

“…Non-covalent interactions occupy a pivotal role in living systems by determining the structure and function of a plethora of biomolecules such as DNA, RNA and proteins. 16,17 They also enable specifical, transient recognition and binding of (macro)molecules, rendering adaptive supramolecular assemblies. [18][19][20] In particular, in the last past two decades, the marriage of supramolecular host-guest chemistry and hydrogel science has led to the development of materials featuring fascinating swelling, adhesive, shape-memory and self-healing properties.…”

“…Non-covalent interactions occupy a pivotal role in living systems by determining the structure and function of a plethora of biomolecules such as DNA, RNA, and proteins. , They also enable specific transient recognition and binding of (macro)­molecules, rendering adaptive supramolecular assemblies. − In particular, in the last 2 decades, the combination of supramolecular host–guest chemistry and hydrogel science has led to the development of materials featuring fascinating swelling, adhesive, shape-memory, and self-healing properties. , A large majority of these studies deal with supramolecular hydrogels in which host–guest interactions act as cross-link junctions to create single or double networks, while their stimuli-controlled dissociation results in a gel–sol transition. − Recently, host–guest interactions have also been exploited to tune the swelling–shrinking properties of covalently cross-linked hydrogels. For example, methylated β-cyclodextrin was used as a host entity to trigger the swelling of chemically cross-linked poly­( N , N -diethylacrylamide) hydrogels bearing complementary hydrophobic adamantyl modules .…”

Amide-π interactions in active centers of superoxide dismutase

“…10,11 Further investigations by various research groups established the role of these interactions in ligand recognition and stabilization of secondary structures, mainly -sheets and helix termini. [12][13][14][15] The Diederich lab has taken the lead in increasing our understanding of these interactions and the knowledge gained from this structure-activity relationship study and the detection of the binding mode has been continuing to inspire their use in rational design. [16][17][18][19][20][21][22] Planar residues, such as His, Tyr, Asp, Arg, Pro, etc.…”