Hydrogen Bonds in Polymer Folding

Hydrogen bonds in polymer folding.

We studied the thermodynamics of a homopolymeric chain with both van der Waals and directed hydrogen bond interaction. The effect of hydrogen bonds is to reduce dramatically the entropy of low-lying states and to give rise to long-range order and to conformations displaying secondary structures. For compact polymers a transition is found between helix-rich states and low-entropy sheet-dominated...

Hydrogen Bonds

Short hydrogen bonds in proteins.

Short hydrogen bonds are present in many chemical and biological systems. It is well known that these short hydrogen bonds are found in the active site of enzymes and aid enzyme catalysis. This study aims to systematically characterize all short hydrogen bonds from a nonredundant dataset of protein structures. The study has revealed that short hydrogen bonds are commonly found in proteins and a...

Desolvation shell of hydrogen bonds in folded proteins, protein complexes and folding pathways.

A few backbone hydrogen bonds (HBS) in native protein folds are poorly protected from water attack: their desolvation shell contains an inordinately low number of hydrophobic residues. Thus, an approach by solvent-structuring moieties of a binding partner should contribute significantly to enhance their stability. This effect represents an important factor in the site specificity inherent to pr...

Polymer-based catch-bonds.

Catch-bonds refer to the counterintuitive notion that the average lifetime of a bond has a maximum at a nonzero applied force. They have been found in several ligand-receptor pairs and their origin is still a topic of debate. Here, we use coarse-grained simulations and kinetic theory to demonstrate that a multimeric protein, with self-interacting domain pairs, can display catch-bond behavior. O...