A distributed lattice of aligned atoms exists in a protein structure: A hierarchical clustering study of displacement parameters in bovine trypsin

Abstract

AbstractLow-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5 THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increases upon terahertz irradiation. Atomic displacement similarities develop between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arise from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. This method can ultimately reveal how the alignment of chemically related atoms and the underlying polar vibrational dynamics make a protein structure stable.