Photo-initiation of biochemical processes

The present Chapter concerns itself with the investigation of ultrafast biochemical processes with the Swiss- FEL. Since most such studies will be per formed in the optical pump – X-ray probe scheme, one needs to ask: which photo-initiated effects can be used as optical pump triggers? Well-known photo-excited biochemical processes in proteins can be classified as “natural” or “ar tificial” [1]. Natural photo-activated protein-components are: the photosynthetic reaction center of chlorophyll (causing light-harvesting and electron transfer), the retinal group in rhodopsin vision complexes (causing isomerization, proton pumping and membrane polarization), the flavin group in DNA photolyase (per forming DNA repair in plants by photocatalytically removing pyrimidine dimers) the cryptochrome and phototropin photoreceptors (causing electron transfer and covalent reactions), and the linear tetrapyrroles in phytochrome photoreceptors of plants and bacteria (causing photoisomerization). Artificial photo-activated components are: the flavin group in flavodoxin (causing electron transfer), and the heme group in hemoproteins (e.g., myoglobin) (causing redox chemistry and a so-called “protein quake” – see Fig. IV.2). A major theme in fast and ultrafast biochemistry, discussed below, is the folding of a protein to its native state. Several methods of photo-initiating the folding process have been developed, including: a) rapid temperature jumps, down to 50 ns, which cause, e.g., helix solvation [4], b) ns laser photolysis of folding-inhibiting ligands [5], c) photo-cleavable protein cross-linking reagents [6], and d) folding induced by electron transfer [7]. A fur ther possible fast per turbation of biomolecules in solution is via a ps teraher tz pulse. It is known that THz absorption disrupts the H2O network by breaking hydrogen bonds and that the function of a protein molecule is influenced by its surrounding solvation shell of up to 1000 water molecules [8]. Finally, it is possible to reversibly deactivate a biomolecule by the addition of a caging group [9, 10]. When this group is photocleaved away, by a visible or UV light pulse, the biomolecule becomes activated, via a rapid series of decaging reactions (see Fig. IV.3). A par ticularly attractive possibility is to rapidly decage the biological energy-carrier ATP [11], a feat which has been accomplished, using a Coumarin derivative, yielding a decaging time of 600 fs [12].