Helmholtz free energies of atom pair interactions in proteins

摘要: Backgound: Proteins fold to unique three-dimensional structures, but how they achieve this transition and maintain their native folds is controversial. Information on the functional form of molecular interactions required address these issues. The basic building blocks are free energies atom pair in dense protein solvent systems. In a medium, entropic effects often dominate over internal energy estimates notoriously difficult obtain. A prominent example peptide hydrogen bond (H-bond). It still unclear what extent H-bonds contribute folding stability structures. Results Radial distribution functions compiled from database known folds. transformed Helmholtz using recipe statistical mechanics interacting particular we concentrate features H-bonds. Differences correspond reversible work or gained when distance between two particles changed. Consequently, directly display energetic respective thermodynamic process, such as H-bond formation disruption. Conclusion potential, high barrier isolates deep narrow minimum at contact large distances, difference distances close zero. plays an intriguing role disruption: both processes require activation order 2 kT . opposes compact states, once formed, act locks network bonds keeps polypeptide chains precise spatial configuration. On other hand, do not folds, because balance