A comprehensive test of the AMOEBA force field using spectroscopy, structures, and simulations of nitrile protein environments

Abstract

Local noncovalent interactions, including hydrogen bonds (H-bonds), generate electric fields that are essential for biological assembly and function. We recently demonstrated that a nitrile’s (–C≡N) infrared (IR) transition dipole moment and anomalous H-bond frequency blueshift can report on its environmental electric field and H-bond geometry and dynamics, respectively. Here, we expand on prior work with nitriles site-selectively incorporated into photoactive yellow protein by introducing mutations designed to alter nitrile H-bonding and local electrostatics. A comprehensive analysis combining IR data, high-resolution X-ray crystal structures, and extensive molecular dynamics simulations demonstrates that the multipolar, polarizable AMOEBA force field accurately models electrostatics and H-bond geometries in both fast and slow H-bond exchange regimes. This finding is reached by correlating experimentally and computationally derived –C≡N electric fields and H-bond blueshifts exhibiting different H-bond fluctuation timescales. This result implies that AMOEBA correctly models thermodynamic and kinetic aspects of noncovalent interactions. The diverse, thoroughly characterized collection of –C≡N protein environments reported herein provides a benchmark for next-generation molecular dynamics force fields that incorporate higher level descriptions of molecular electrostatics.