Proteins in Action Monitored by Time-Resolved FTIR Spectroscopy

Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy

Much progress has been made in our understanding of water molecule reactions on surfaces, proton solvation in gas-phase water clusters and proton transfer through liquids. Compared with our advanced understanding of these physico-chemical systems, much less is known about individual water molecules and their cooperative behaviour in heterogeneous proteins during enzymatic reactions. Here we use time-resolved Fourier transform infrared spectroscopy (trFTIR) and in situ H2(18)O/H2(16)O exchange FTIR to determine how the membrane protein bacteriorhodopsin uses the interplay among strongly hydrogen-bonded water molecules, a water molecule with a dangling hydroxyl group and a protonated water cluster to transfer protons. The precise arrangement of water molecules in the protein matrix results in a controlled Grotthuss proton transfer, in contrast to the random proton migration that occurs in liquid water. Our findings support the emerging paradigm that intraprotein water molecules are as essential for biological functions as amino acids.

Making light work of enzyme catalysis: protochlorophyllide oxidoreductase

In the chlorophyll biosynthetic pathway, the enzyme protochlorophyllide oxidoreductase (POR) catalyses a key light-driven reaction that triggers a profound transformation in plant development. Because POR is activated by light, it can provide information on the way in which light energy can be harnessed to power enzyme reactions and it presents us with a unique opportunity to study catalysis at low temperatures and on ultrafast timescales that are not accessible for most analyses of enzyme function. Recent advances in our understanding of the catalytic mechanism of POR illustrate why it is an important generic model for studying enzyme catalysis and reaction dynamics.

Theoretical IR spectroscopy based on QM/MM calculations provides changes in charge distribution, bond lengths, and bond angles of the GTP ligand induced by the Ras-protein

The GTPase Ras p21 is a crucial switch in cellular signal transduction. Fourier transform infrared (FTIR) spectra of the substrate guanosine triphosphate (GTP) show remarkable changes when it binds to the enzyme. The reduced band widths indicate that the flexible GTP molecule is guided by the protein into a preferred conformation. The delocalized phosphate vibrations of unbound GTP become localized. The frequency shifts show an electron movement toward beta-phosphate, which probably contributes to catalysis by reducing the free activation energy. To quantify these qualitative observations we performed QM/MM molecular dynamics simulations of Ras.GTP and GTP in water. The triphosphate part of GTP was treated quantum mechanically using density functional theory (DFT). Vibrational spectra were calculated in harmonic approximation with an average deviation of 3% from the experimental frequencies. This provides a high confidence in the computational results as vibrational spectra are highly sensitive to conformation and charge distribution. As compared to GTP in water, Ras-bound GTP shows a shift of negative charge of approximately 0.2 e toward the beta-phosphate from gamma-phosphate and from alpha-phosphate due to the positive charge of the magnesium ion, to a lesser extent of Lys-16, and surprisingly without any effect of the P-loop backbone. Magnesium and Gly-13 twist and bend the gamma-O-beta bonds such that the crucial bond is stretched before cleaving.