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

Abstract

Vibrational oscillations in amide and side chain groups are well studied in proteins, but these are not occupied at ambient temperatures and they have a short lifespan when infrared radiation is present. Active vibrational modes in proteins lie in the terahertz (THz) range at physiological temperatures, and their experimental descriptions of them in this range are lacking. In this paper, we present the effect of 0.5 THz irradiation on atomic displacement parameters (ADP) in bovine trypsin. The crystals were subjected to terahertz radiation in an alternating manner and two states of the crystals were recovered using X-ray crystallography. The clustering of ADPs uniquely identified atoms from the different crystals. The ADP similarities tended to develop between chemically similar atoms and between atoms of the catalytic triad. This pattern of ADP similarity is likely created by delocalized polar vibration modes rather than, as frequently assumed, elastic and rigid-body motions.