Direct observation of two distinct types of short hydrogen bond in photoactive yellow protein

Yamaguchi, Shigeo*; Kamikubo, Hironari*; Kurihara, Kazuo; Kuroki, Ryota; Niimura, Nobuo*; Shimizu, Nobutaka*; Yamazaki, Yoichi*; Kataoka, Mikio*

Hydrogen bond dominates various physical properties in biological molecules and biological chemical reactions including proton transfer, hydrolysis, and so on. A special type of hydrogen bonds, the short hydrogen bond (SHB), has been proposed to have an important role in protein structure and function. The physical properties of SHBs, however, are still under debate. In the photoactive yellow protein (PYP), a light sensor protein, two SHBs near the chromophore have been revealed by X-ray crystallographic studies. The bond distances of the SHBs are modulated during the photo-reaction, resulting in the local proton transfer. From these facts, it can be postulated that these SHBs play a crucial role in the local proton transfer. Using high-resolution neutron crystallography in combination with high-resolution X-ray crystallography, we identified two deuterium atoms involved in two SHBs in PYP. One SHB, between the chromophore and E46, is identified as a low-barrier hydrogen bond (LBHB); the other, between the chromophore and Y42, is a short ionic hydrogen bond (SIHB). This is the first direct evidence of the coexistence of two distinct SHBs in the ground state of a protein. At the conference, we will present the neutron crystallographic structure and discuss the two SHBs in PYP.