Path-metadynamics: A computational study of conformational transitions in proteins

Path-metadynamics: A computational study of conformational transitions in proteins

Systematic In Silico Analysis of Interhelical Electrostatic Interactions in Leucine Zippers

Energy decomposition showed that favorable solvation and van der Waals contributions outweighed the electrostatic penalty, indicating that leucine zipper stability reflects a balance of electrostatics, solvation, packing, and positional context.

Coil-helix transition in macromolecules. I. Minimal model.

This work presents a minimal coarse-grained molecular dynamics model for the coil-helix transition in polymers. We demonstrate that the addition of a Morse potential to a freely jointed chain with volume and bond potentials is sufficient to reproduce the essential thermodynamic features of the transition. From the simu...

Biomolecular Condensates Dictate the Folding Landscape of Protein Alpha-Helices.

This work investigates how protein folding landscapes are altered inside condensates, using the protein α-helix as a model folded domain and develops a chemically specific, residue-resolution model for quantification of α-helical folding and applies it to characterize diverse helices within condensates of varying physi...

Hydrophobic Patterns and Folding Thermodynamics-Kinetics in a 2D HP Model

Protein folding is a process in which the linear amino acid chain is transformed into a stable three-dimensional native structure which enables the protein to carry out its function. In several neurodegenerative diseases, including Alzheimer's disease (amyloid-β) and Huntington's disease (huntingtin), a pathological me...

Nucleotide-binding motifs nucleated folding of the first enzymes

It is concluded that the early emergence of the Rossmann fold reflects the chemical and physical constraints of protein folding, explaining both its profound antiquity and sustained longevity.