Development and Validation of a DFT-Based Force Field for a Hydrated Homoalanine Polypeptide
Ying Yuan, Zhonghua Ma, Feng Wang
Abstract
, the new force field shows about 15% helical conformations, 20% conformation in the β basin, and 65% polyproline II. The predicted helical population of short hydrated alanine is higher than previous estimates based on the same experimental data. Gas-phase simulations indicate that the force field developed by AFM solution-phase data is likely to produce a reasonable conformation distribution when hydration water is no longer present, such as the interior of a protein.
Topics & Concepts
Force field (fiction)Polyproline helixDispersion (optics)ChemistryChemical physicsField (mathematics)Computational chemistryLondon dispersion forceDensity functional theoryScalar (mathematics)MoleculeStatistical physicsThermodynamicsPhysicsMathematicsGeometryQuantum mechanicsOrganic chemistryPure mathematicsBiochemistryPeptidevan der Waals forceProtein Structure and DynamicsEnzyme Structure and FunctionDNA and Nucleic Acid Chemistry