Density functional theory (DFT) calculations based on the self-consistent-charge tight-binding approximation have been performed to study the influence of the protein pocket on the 3-dimensional structure of the 11-cis-retinal Schiff base (SB) chromophore. Starting with an effectively planar chromophore embedded in a protein pocket consisting of the 27 next-nearest amino acids, the relaxed chro...

The unique ability of photoactive proteins to capture and use energy from a photon of light depends on the chromophore, its linkage to the protein, and the surrounding protein environment. To understand the molecular mechanisms by which a chromophore and protein interact to undergo a light cycle, we are studying photoactive yellow protein (PYP), a 14-kDa water-soluble photoreceptor from Ectothi...

When the nonprotein chromophore of neocarzinostatin was allowed to react with either calf thymus DNA or poly(dA-dT) . poly(dA-dT) in the presence of 2-mercaptoethanol and the DNA was precipitated with ethanol, 5% of the fluorescence attributable to the naphthalene rings of the chromophore coprecipitated with the DNA. Most of this fluorescence remained attached to DNA through successive reprecip...

A new series of donor-stabilized addition complexes of cobalt(II) with disubstituted diphenyldithiophosphates [{(ArO)2PS2}2CoL2] {Ar = 2,4-(CH3)2C6H3 [(1)-(3)] and 3,5-(CH3)2C6H3 [(4)-(6)]; L = C5H5N [(1), (4)], 3,4-(CH3)2C5H3N [(2), (5)] and 4-(C2H5)C5H4N [(3), (6)]} were successfully isolated and characterized by elemental analyses, magnetic moment measurements, IR and single-crystal X-ray an...

Samples of irradiated and control Avena sativa shoot tissue were homogenized together to determine whether, during homogenization phytochrome from irradiated tissue can bind to the particulate material simultaneously extracted from the control tissue. The level of phytochrome pelletability for such mixed tissue homogenizations is equal to: (a) the values obtained when the extracts from separate...

A new chromophore, 2-(4-nitrophenyl)benzofuran (NPBF), was designed for two-photon (TP) uncaging using near-IR light. The TP absorption (TPA) cross-sections of the newly designed NPBF chromophore were determined to be 18 GM at 720 nm and 54 GM at 740 nm in DMSO. The TP uncaging reaction of a caged benzoate with the NPBF chromophore quantitatively produced benzoic acid with an efficiency (δu) of...

Yamaguchi et al. have recently identified positions of hydrogen and deuterium atoms in photoactive yellow protein (PYP) using high-resolution neutron scattering. They reported that the hydrogen bond between the PYP chromophore and Glu46 was not a short ionic hydrogen bond (SIHB) but a low barrier hydrogen bond (LBHB). Furthermore, it was suggested that Arg52 close to the chromophore was deproto...

The methanol-extractable, nonprotein chromophore of the antitumor, protein antibiotic neocarzinostatin (NCS) has at least the full activity of the parent compound in inhibiting DNA synthesis and growth of HeLa cells and in causing DNA strand breaks in vivo and in vitro. In vitro DNA strand scission by the chromophore is markedly stimulated by 2-mercaptoethanol and is inhibited by guanidine hydr...

Dopamine and dobutamine have recently been shown to produce a negative interference in several biochemical tests that use peroxide and peroxidase to generate a chromophore. To define the chemical mechanism of this interference, we examined the effects of dopamine and dobutamine in various peroxidase-based biochemical tests. Dopamine interfered stoichiometrically with peroxidase-based tests that...

N-retinyl, the chromophore of bleached and reduced rhodopsin, N-retinyl-opsin, was used as a covalently attached fluorescence probe to examine the structure of N-retinyl-opsin and the rod outer segment. The efficiency of energy transfer from the protein part of N-retinyl-opsin to the chromophore is 12 +/- 5%. It is argued that this implies that the N-retinyl-opsin molecule is asymmetrical. Krop...