B, bathorhodopsin

BphP, bacteriophytochrome photoreceptor BR, bacteriorhodopsin BSI, blue-shifted intermediate BV, biliverdin IX-a

CCA, complementary chromatic adaption CD, circular dichroism spectroscopy cDNA, complementary DNA cFR, constant far-red light Chopl, channel opsin 1 Cop, chlamyopsin

CpHl, cyanobacterial phytochrome 1

Cry (or CRY), cryptochrome

E-PYP, PYP from Ectothiorhodospira halophila

FL, full length

FMN, flavin mononucleotide FR, far-red light

FTIR, Fourier-transform infrared

FTR, Fourier-transform Raman spectroscopy

GFP, green fluorescent protein

GPCR, G-protein-coupled receptor

Gtbc, be heterodimer subunit of Gt

Gta, a subunit of Gt

Gt, transducin (retinal G-protein)

GUS, (3-glucuronidase

HIR, high irradiance response

HOOP, hydrogen out-of-plane

HR, halorhodopsin

Htp, halobacterial transducer protein

L, lumirhodopsin

LADS, lifetime-associated difference spectra LFR, low fluence response MI, metarhodopsin I Mil, metarhodopsin II

NMR, nuclear magnetic resonance spectroscopy

P(])B, phytochromobilin

PAS, photoacoustic spectroscopy

PBD, photothermal beam deflection

PC, phosphatidylcholine

PCB, phycocyanobilin

PE, phosphatidylethanolamine

PEB, phycoerythrobilin

PEC, phycoerythrocyanin

Pfr (or Pfr), far-red-adsorbing state of phytochrome

Phot (or PHOT), phototropin

Phy (or PHY), phytochrome

Pr (or Pr), red-adsorbing state of phytochrome

PS, phosphatidylserine

PSB, protonated Schiff base

PYP, photoactive yellow protein

R*, light-activated rhodopsin

R, rhodopsin

RK, rhodopsin kinase

ROS, rod outer segment

RPE, retinal pigment epithelial cells

SB, Schiff base

SDM, site-directed mutagenesis

SPR, surface plasmon resonance spectroscopy

SR, sensory rhodopsin

TG, thermal grating

VLIR, very low fluence response

Vop, volvoxopin

Chapter 1

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