Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less specific electrostatic interactions, impart important properties to proteins. Modulation of the charges on the amino acids, e.g., by pH and by phosphorylation and dephosphorylation, have significant effects such as protein denaturation and switch-like response of signal transduction networks. This review aims to present a unifying theme among the various effects of protein charges and polar groups. Simple models will be used to illustrate basic ideas about electrostatic interactions in proteins, and these ideas in turn will be used to elucidate the roles of electrostatic interactions in protein structure, folding, binding, condensation, and related biological functions. In particular, we will examine how charged side chains are spatially distributed in various types of proteins and how electrostatic interactions affect thermodynamic and kinetic properties of proteins. Our hope is to capture both important historical developments and recent experimental and theoretical advances in quantifying electrostatic contributions of proteins.
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http://dx.doi.org/10.1021/acs.chemrev.7b00305 | DOI Listing |
Phys Chem Chem Phys
January 2025
Institute of Science and Technology, Federal University of São Paulo, 12247-014, São José dos Campos, São Paulo, Brazil.
This study investigates the structural and dynamic properties of ternary mixtures composed of NaPF, ethylene carbonate (EC), and the ionic liquid choline glycine (ChGly), with a focus on their potential as electrolytes for supercapacitors. The combination of NaPF-EC, known for its high ionic conductivity, with the biodegradable and environmentally friendly ChGly offers a promising approach to enhancing electrolyte performance. Through molecular simulations, we analyze how the inclusion of small concentrations of ChGly affects key properties such as density, cohesive energy, and ion mobility.
View Article and Find Full Text PDFThe growing body of experimental and computational studies suggested that the cross-neutralization antibody activity against Omicron variants may be driven by balance and tradeoff of multiple energetic factors and interaction contributions of the evolving escape hotspots involved in antigenic drift and convergent evolution. However, the dynamic and energetic details quantifying the balance and contribution of these factors, particularly the balancing nature of specific interactions formed by antibodies with the epitope residues remain scarcely characterized. In this study, we performed molecular dynamics simulations, ensemble-based deep mutational scanning of SARS-CoV-2 spike residues and binding free energy computations for two distinct groups of broadly neutralizing antibodies : E1 group (BD55-3152, BD55-3546 and BD5-5840) and F3 group (BD55-3372, BD55-4637 and BD55-5514).
View Article and Find Full Text PDFTauopathies, a group of neurodegenerative disorders, are characterized by the abnormal aggregation of tau proteins into neurofibrillary tangles (NFTs), driving synaptic dysfunction, neuronal loss, and disease progression through tau aggregate propagation. Graphene quantum dots (GQDs) functionalized with - cysteine ( -GQDs) have shown promise in inhibiting tau aggregation and transmission π-π stacking and electrostatic interactions with tau proteins. However, the non-specific binding of GQDs to various proteins in the physiological environment, such as serum albumin, limits their clinical translation.
View Article and Find Full Text PDFBiomacromolecules
January 2025
Department of Chemical Engineering, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
Mussel byssi form a robust underwater adhesive system, anchoring to various surfaces in harsh marine environments. Central to byssus is foot protein type 4 (fp-4), a junction protein connecting collagenous threads to proteinaceous plaque. This study investigated an anionic plaque-binding domain of fp-4 (fp-4a) and its interactions with cationic foot proteins (fp-1, fp-5, and fp-151 as model substitutes for fp-2) and metal ions (Ca, Fe, and V).
View Article and Find Full Text PDFSci Rep
January 2025
Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia.
The modern world is facing the issue of emerging pollutants for its sustainable development. We report a detailed study on the abatement of ciprofloxacin (CIP) by BeO nanocage. Five different geometries of BeO nanocage with CIP i.
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