Conformational analysis of (4Z, 15Z)-bilirubin-IX(alpha) by molecular mechanics computations reveals a global energy minimum folded conformation. Powerful added stabilization is achieved through intramolecular hydrogen bonding. Theoretical treatment of bilirubin as a molecular exciton predicts an intense bisignate circular dichroism spectrum for the folded conformation: (Delta) (epsilon) is congruent to 270 L (DOT) mole-1 (DOT) cm-1 for the $OM450 nm electronic transition(s). Synthesis of bilirubin analogs with propionic acid groups methylated at the (alpha) or (beta) position introduces an allosteric effect that allows for an optical resolution of the pigments, with enantiomers exhibiting the theoretically predicted circular dichroism.

A recently developed ellipsometric technique for the nanosecond time-resolved measurement of natural and magnetic circular dichroism (TRCD and TRMCD) spectra is discussed and applications to dynamical studies of biologically important molecules, principally hemeproteins, are presented. Nanosecond TRCD spectra of the Soret band of hemoglobin and myoglobin have been measured after photolysis of the carbonmonoxy complex. The TRCD of the photoreduction of metmyoglobin has also been studied. Nanosecond TRMCD spectroscopy of cytochrome c oxidase (cytochrome aa3) gives information about the spin state of the iron in the heme a3 transient intermediate formed after photolysis of the CO complex. Applications of TRMCD spectroscopy to cytochromes ba3 and c3 are also discussed, as are TRCD studies of phytochrome proteins. Recent progress in characterizing and eliminating spectral artifacts arising from photoselection in photolyzed proteins is summarized.

The observation of Circular Dichroism (CD) in vibrational transitions in the infrared spectral region offers new possibilities to determine molecular solution conformation. The application of this technique, known as vibrational CD or VCD, to peptides and nucleic acids is described.

Recent advances have led to dramatic improvements in the measurement of Raman optical activity (ROA). These include the use of new scattering geometries and improvements in polarization modulation methodology and multichannel-detector technology. Several new ROA experimental configurations are selected to illustrate the capabilities of a new ROA instrument constructed recently at Syracuse University. Both general and simplified theoretical expressions are used to identify fundamental aspects of various ROA experiments and to determine preferred configurations for the measurement of ROA. The authors find for their instrument that the optimum configuration is in-phase dual circular polarization (DCPI) ROA in backscattering geometry, as illustrated using (+)-fenchone. DCPI- ROA backscattering spectra are presented for aqueous solutions of L-alanine, glycyl-L-alanine and D-mannose. The large couplet arising from the bands between 800 and 900 cm-1 in the ROA spectrum of alanine is interpreted in terms of coupled methyl rocking and the methyl carbon-carbon stretching internal coordinates. The feasibility of applying ROA to the study of biological molecules is demonstrated by the high quality of the ROA spectra obtained for these molecules.

The laser microscopic method of polarized fluorescence depletion (PFD) has permitted the rotational dynamics of functional membrane proteins to be measured on single cells under physiological conditions. This provides information comparable to that obtained by the older technique of time-resolved phosphorescence anisotropy (TPA) but with a greater than 1000- fold reduction in sample requirements. A new cuvette implementation of PFD methods, together with a data analysis model appropriate to this new experimental geometry, permits small volumes of dilute cell suspensions to be examined in their entirety. Data can thus be obtained at rates comparable to TPA. The instrument can also be used for TPA measurements and this permits direct comparison of PFD and TPA results obtained under otherwise identical conditions. In addition, a new photomultiplier gating device and system timing strategy reduce the minimum observable rotational correlation times to < 2 microsecond(s) ec, a 10-fold improvement over previous systems. These speed improvements have been examined in studies of BSA rotation in glycerol solution.

Fluorescence energy transfer can be used to investigate spatial distributions of acceptor molecules on surfaces or in membranes. In these applications energy transfer is observed from multiple donors to multiple acceptors. The fluorescence decay in such instances is non- exponential and is described by a 'stretched' exponential. This behavior is sometimes referred to as being fractal in time. A theoretical analysis of these decays is presented. Using this analysis the time-resolved fluorescence of the donor can be used to determine the fractal dimension of the surface distribution as well as the size of the acceptor domains. Application of these theoretical results to experimental data on the structure of membrane protein aggregates is described. A key problem is to determine the functional unit of membrane proteins. Two different proteins, bacteriorhodopsin and the calcium ATPase, have been investigated in model reconstituted vesicle systems. Energy transfer experiments can be devised that will measure two different fractal dimensions characterizing these aggregates. They are the fractal dimension associated with the density distribution and the one associated with the length of the 'coastline'. This information can be interpreted in terms of the number of proteins in the unit structure. In bacteriorhodopsin both hexagonal-packed and monomeric units are stable and the monomer is functional. The calcium ATPase results are consistent with a tetrameric functional unit.

The authors review three examples of how fluorescence spectroscopic techniques have been employed to elucidate structural features of the nicotinic acetylcholine receptor from the electric organ of Torpedo californica. The instrumentation and most relevant fluorescence methods utilized for these studies are briefly discussed. The examples reviewed are as follows: (1) the measurement of the average distance between the two acetylcholine binding sites on the receptor and the noncompetitive inhibitor binding site in the central ion channel, (2) the measurement of distance between fluorescently labeled snake (alpha) -toxins bound to the same membrane-associated receptor oligomer and bound to the adjacent receptor oligomers, and (3) the relative orientation of snake (alpha) -toxin with respect to the central ion channel and the plane of the lipid membrane into which the receptor is embedded.

The cell surface receptor for epidermal growth factor (EGFR) is one of the most studied integral membrane proteins. The receptor is widely distributed in cells and tissues of mammalian and avian tissues and plays an important role in growth control. Binding of the epidermal growth factor (EGF) to EGFR initiates a complex biological response, which includes self-phosphorylation of the receptor due to an intrinsic tyrosine kinase activity, phosphorylation of other membrane proteins, increased intake of metabolites, and increased proliferation. Complete amino acid sequence of EGFR revealed a high degree of homology with viral oncogenes and allowed tentative identification of an external hormone binding domain, a transmembrane domain, and a cytoplasmic domain that includes tyrosine kinase activity. EGF binding induces rapid aggregation of EGFR, a process which was also observed on other receptor systems. These and other observations led to a hypothesis that microaggregation of EGFR is a necessary prerequisite for the biological response of EGF. A direct approach to study the processes of oligomerization of cell membrane proteins is to measure their mobility under various conditions. The lateral mobility of the EGFR was studied on mouse 3T3 fibroblasts and on A431 cells. However, an examination of the equations for the lateral and rotational diffusion in membranes shows that only rotational diffusion is strongly dependent on the size of the diffusing entity. A method of measuring protein rotational diffusion by time-resolved phosphorescence has proved to be very useful in the analysis of both in vivo and in vitro systems. The authors apply this method to study the mobility of EGFR on living A431 cells and membrane preparations.

The authors report on the formation of an unusually stable As(III)-thiolate with a single 'high- affinity' cysteine (Cys) of E. coli RI methylase, monitored via its influence on a neighboring tryptophan (Trp) residue in the enzyme structure. The binding was studied by Trp fluorescence quenching, low temperature phosphorescence and triplet state optically detected magnetic resonance (ODMR) of the intrinsic Trp residue(s). The affected Trp is subject to an external heavy atom effect (HAE) from arsenic, quenching its fluorescence and reducing its phosphorescence lifetime from 6 sec to ca. 70 msec. The enzyme high affinity binding site has at least 27 times the affinity for As(III) as does a typical sulfhydryl reagent, HSCH2CONH2. The accessibility of the arsenical to this Cys site was reduced upon formation of the ternary complex methylase-DNA-sinefungin, suggesting a local conformational change in the enzyme when DNA is bound. The enzymatic activity assay of methylase is not affected by the addition of a 1:1 molar ratio of the arsenical to the methylase, but incubation with an excess of As(III) causes complete loss of enzymatic activity. This suggests that the high- affinity Cys residue is not a part of the active site of the enzyme, but the addition of a molar excess of arsenical to the enzyme derivatizes the Cys residue known to be located in the active site.

The third-order (pi) -electron polarizability, (gamma) (pi), of bacteriorhodopsin in the 0.0 - 1.2 eV optical region is assigned based on an analysis of the experimental two-photon properties of the low-lying singlet state manifold. The following selected values of (gamma) (pi) (units of 10-36 esu) are observed: (gamma) (0;0,0,0) equals 2482 +/- 327; (gamma) (-3(omega) ;(omega) ,(omega) ,(omega) ) equals 2976 +/- 385 ((omega) equals 0.25 eV), 5867 +/- 704 ((omega) = 0.5 eV), 14863 +/- 1614 ((omega) = 0.66 eV), 15817 +/- 2314 ((omega) equals 1.0 eV), 10755 +/- 1733 ((omega) equals 1.17 eV). The third-order polarizability of this protein which contains an all-trans retinyl protonated Schiff base chromophore with six double bonds, is comparable to that observed for much longer chain polyenes (for example, dodecapreno (beta) -carotene, a polyene with 19 double bonds, exhibits a third-order (pi) -electron polarizability at 0.66 eV of 17000 +/- 6000 X 10-36 esu. The authors attribute the enhanced third-order nonlinearity associated with the protein bound chromophore of bacteriorhodopsin to two mutually enhancing origins. First, the chromophore is protonated, and the resultant charge reorganization enhances the polarizability in a fashion that is similar to that known to occur for polaronic and bipolaronic chromophores. It is estimated that protonation generates a five-fold enhancement in (gamma) (pi). Second, the protein bound chromophore exhibits a large change in dipole moment upon excitation into the lowest-lying, strongly-allowed 1B*u+-like state ((Delta) (mu) = 13.5 D). The latter property is responsible for a Type III enhancement of the third-order polarizability, and yields at least a 20-fold increase in (gamma) (pi).

Absorption, fluorescence, and resonance Raman spectra of the membrane stain merocyanine- 540 (MC540) were measured. The aggregation of the dye, its binding to lipid membranes and its response to trans-membrane electric potential differences were studied. The dye was found to aggregate even at micromolar concentrations in water, but not in organic solvents. The binding constant to liposomes was determined by a titration method. Resonance Raman spectra of MC540 were measured for the first time. Distinct changes were observed in the vibrational spectrum upon the generation of a valinomycin-induced K+-diffusion potential on liposomes. The ratio of Raman band intensities which was found to be related to the membrane potential can be used to evaluate the potential's absolute value.

In nucleotid coumarin conjugates nucleic acid base specific quenching of the dye is observed. The lifetime of the coupled dye in aqueous solution decreases in the order: adenine (A)>cytosine(C)>thymine(T)>guanine(G). These differences in fluorescence properties of the label can be utilized to develop a new method for DNA sequencing with only one dye and one lane. The paper investigates whether quenching might result from photoinduced electron transfer. Thus redox potentials of several nucleosides and coumarin-120 were determined by cyclic voltammetry and polarography in dimethylformamide. It was found for the bases of 2'-deoxynucleosides, that G can be oxidized electrochemically (1,18 vs SCE), whereas A, C and T can be reduced (-2.69 V.-2.47 V and -2.38 V vs SCE). The correlation of the standard free energy ((Delta) G0) and log (kq) of intra- and intermolecular quenching constants, evaluated from Stern-Volmer plots, give an experimental hint, that the donor and acceptor properties of the fluorescent label are important for the specific quenching. Additional ground state interactions were found for some purine and pyrimidine bases.

The general characteristics of the resonance Raman (RR) scattering from the photophysically important, near-infrared absorption band of the primary electron donor (P) in photosynthetic reaction centers (RCs) are discussed within the context of spectra recently reported for RCs from Rhodobacter sphaeroides wild-type strain 2.4.1. The observed RR intensity enhancement patterns of the low-frequency modes are compared with those expected for various excited-state displacements. The influence of multimode scattering and vibrational lifetime effects is also discussed.

The kinetics of the photochemical ring openings of 1,3-cyclohexadiene (CHD), 1,3,5- cyclooctatriene (COT) and ((alpha) -PHE) were determined by picosecond, time-resolved UV resonance Raman spectroscopy. The time evolution of the photoproduct ethylenic intensity demonstrates that the photolysis of CHD produces ground state cis-hexatriene in 8 +/- 1 ps. Similarly, the photoproducts of COT and (alpha) -PHE appear in 12 +/- 2 ps and 11 +/- 2 ps, respectively. The similar ground state photoproduct formation times of these reactions indicates that the $OM10 ps timescale is a general feature of photochemical electrocyclic ring-opening reactions.

Picosecond resonance Raman spectroscopy has been used to obtain structural information on the primary photointermediates of bacteriorhodopsin. A synchronously pumped dye laser was amplified at 50 Hz to produce a probe pulse at 589 nm. A second, spectrally distinct, pump pulse at 550 nm was generated by amplification of a 10 nm portion of a continuum produced from the probe pulse. This apparatus was used to record spectra of the J, K, and KL intermediates. The J spectrum exhibits strong hydrogen out-of-plane (HOOP) intensity and the fingerprint region consists of a broad series of lines centered at 1180 cm-1. By 3 ps, K has formed and the relative HOOP intensity decreases while the fingerprint collapses to a single mode at 1190 cm-1, characteristic of a 13-cis chromophore. These results argue that J contains a highly twisted chromophore which relaxes upon conversion to K and that isomerization is complete within 3 ps. Between 3 ps and 3.7 ns there is a resurgence in HOOP intensity and the ethylenic frequency rises from 1518 to 1521 cm-1 indicating the conversion of K to KL.

Time-resolved electronic absorption, infrared, resonance Raman, and magnetic circular dichroism spectroscopies are applied to characterization of the intermediate which is formed within 20 ps after photodissociation of CO from cytochrome a3 of reduced cytochrome oxidase. This intermediate decays with the same halflife (ca. 1 microsecond(s)) as the post- photodissociation CuB+-CO species previously observed by time-resolved infrared. The transient UV-Vis spectra, kinetics, infrared, and Raman evidence suggest that an endogenous ligand is transferred from CuB to Fea3 when CO binds to CuB, forming a cytochrome a3 species with axial ligation which differs from the reduced unliganded enzyme. The time-resolved magnetic circular dichroism results suggest that this transient is high spin and therefore five coordinate. Thus it is inferred that the ligand from CuB binds on the distal side of cytochrome a3 and displaces the proximal histidine imidazole. This remarkable mechanistic feature is an additional aspect of the previously proposed 'ligand shuttle' activity of the CuB/Fea3 pair. The authors suggest that the ligand shuttle may play a functional role in redox-linked proton translocation by the enzyme. More detail on this work is presented elsewhere.

Picosecond absorption and circular dichroism (CD) studies of photosynthetic reaction centers (RC) from Rhodabacter Sphaeroides are reported. The transient absorption spectra obtained are consistent with previous studies and provide definitive evidence for the formation of the two charge transfer intermediates: (BChl2)+BPhL-QA and (BChl2)+BPhLQA+ with rate constants whose half lives are <10 picosecond and $OM200 picoseconds, respectively. The transient circular dichroism spectra of these two charge separated intermediates are characterized by a nonconservative CD band centered at 800 nm with similar shape and intensity. This result clearly demonstrates that the negative CD band at 814 nm arises from the exciton coupling of the bacteriochlorophyll dimer. This transient CD cannot be due to excitonic interactions between the pigments in the reaction center and suggest that the monomer bacteriochlorophyll is either intrinsically chiral through distortions induced by the surrounding protein structure or obtains rotational strength from coupled oscillator interactions with surrounding aromatic residues in the protein.

A strategy for DNA characterization was developed, which exploits the normally unwanted interactions of the dye with its environment. With a single suitable dye, acting as a sensitive probe, one can characterize the neighboring DNA-base by time-resolved fluorescence spectroscopy due to specific dynamic quenching reactions affecting the fluorescence lifetime. By specific coupling of the dye to a linker-group at the 3' terminus of DNA a one- label/one-lane concept for DNA sequencing seems to be possible and all problems with multiple dyes can be avoided. To study the feasibility of this concept, fluorescence lifetimes of various model phosphorothioate oligodeoxyribonucleotides, different in length and labelled with a specially synthesized coumarin derivative, were measured in different aqueous solutions with a DFDL-UV picosecond fluorescence spectrometer. The influence of nucleic acid-dye interactions on the lifetime and quantum yield of the coupled dye is investigated. In mononucleotides fluorescence lifetimes range between 5.3 and 1.4 ns. The order in the quenching efficiency of the bases is adenine (A) equals 0, cytosine (C) < thymine (T) < guanine (G). In labelled di- and oligonucleotides the order of quenching changes slightly: A equals 0, C < G.

This paper presents the results of experimental investigations of a series of conformationally inhomogeneous compounds with polarization sensitive coherent active (anti-Stokes) Raman scattering spectroscopy (PS CARS). Interpretation of vibrational spectra is refined and spectroscopic parameters are determined of resonances of complex spectral band of n-penthane (bands at 868 and 841 cm-1), 5,5-dimethyl, 2-ethinyle, 1,2-dioxane (bands at 949 and 910 cm-1) which were not resolved previously with the use of spontaneous Raman scattering spectroscopy (SRS). Thereby the principle of holographic spectroscopy was realized and tested in the full scale.

Time-resolved infrared spectroscopy (TRIRS) has been employed to study the reactions of small molecules with the cytochrome a3-CuB site of cytochrome c oxidase (CcO). All phases of these reactions have been investigated, from ultrafast phenomena (hundreds of femtoseconds) to relatively slow processes (milliseconds). The ligation dynamics immediately following photodissociation have been studied using a TRIRS technique with time resolution of less than 1 ps. The rate of photoinitiated transfer of CO from Fea32+ to CuB+ was measured directly by monitoring the development of the transient CuB+-CO absorption. The development of a stationary CuB+ spectrum which is constant until the CO dissociates from CuB+ occurs in less than 1 ps, indicating that the photoinitiated transfer of CO is remarkably fast. This unprecedented ligand transfer rate has profound implications with regard to the structure and dynamics of the cytochrome a3-CuB site, the functional architecture of the protein and coordination dynamics in general. The photodissociation and recombination of CN- has also been studied using a real-time TRIR technique. The CN- recombination rate of 430 s-1 is consistent with a recombination pathway similar to the one we have previously proposed for CO, in which a long-lived barrier to recombination is formed by the binding of an endogenous ligand L to Fea32+. The authors suggest the rate determining step for CN- recombination is the thermal dissociation of the Fea32+-L bond.

We have directly observed hot vibrations in photoexcited deoxyhemoglobin. The data quantitatively indicate a heme vibrational temperature of 20 K above room temperature within the time sampled by an 8ps laser pulse. The slow component of vibrational relaxation occurs with a rate constant of (2.5ps)1. Similar dynamics are observed in oxyhemoglobin. The initial stages of recombmation of 02 with the heme following photodissociation of oxyhemoglobin are observed in the transient vibrational spectrum. Contrary to previous work, we do not observe the influence of protein dynamics on 02 recombination.