Polarized absorption spectra of green fluorescent protein single crystals: transition dipole moment directions

Polarized absorption spectra of orthorhombic crystals of wild-type green fluorescent protein (GFP) were measured between 350 and 520 nm to obtain information on the directions of the electronic transition dipole moments ((-->)m) of the chromophore relative to the molecular axes. The transition dipole moment orientation is a basic spectroscopic parameter of relevance to biologists when interpreting F?rster-type fluorescence resonance energy transfer data and for comparing absorbance and fluorescence spectra of GFP with quantum chemical calculations. Maximal extinction was obtained throughout the spectrum when the polarization direction of the electric vector of incident light was parallel to the c-axis of the crystal. The transition dipole moments were assumed to be parallel to the plane of the chromophore. With this assumption and the measured dichroic ratios in the crystals, the transition dipole moments associated with the neutral (lambda(max) = 398 nm) and anionic (lambda(max) = 478 nm) forms of the chromophore were found to subtend angles of approximately 26 degrees and 13 degrees (counterclockwise), respectively, with the vector that joins the phenolic and imidazolinone oxygen atoms of the chromophore.     

Low frequency Raman spectra of Z-DNA

We have performed a Raman study of the low frequency modes in three oligo- and polynucleotides in Z-conformation, and we compare the spectra of these samples to those of two polynucleotides in B-conformation. In Z-DNA we find 5 intrahelical modes below 200 cm-1, in addition to the interhelical mode near 30 cm-1 which is only observed in crystalline samples. The most prominent intrahelical mode has a frequency of about 105 cm-1, close to the frequency of the strongest intrahelical mode in A-and B-DNA. The sequence dependence of the frequency of this mode is considerably larger than for the same mode in B-DNA. The other modes are less pronounced, and their frequency variations with base sequence are within the experimental accuracy.     

Optical spectra and electronic structure of flavine mononucleotide in flavodoxin crystals.

The polarized single-crystal absorption spectra of the oxidized and semiquinone forms of flavodoxin from Clostridium MP have been measured with a double beam recording microspectrophotometer. The spectra establish that the radical species in the crystal is the neutral (blue) falvine semiquinone. Combination of the spectra reported here with polarization data from previous fluorescence and stretched-film studies provides transition moment directions for the first two phi-phi transitions of the oxidized form. Predictions of molecular orbital theory are in good agreement with these experimental directions. The crystal spectra of the semiquinone indicate that the two lowest frequency transitions have the same detailed orbital origin as the corresponding transitions of the oxidized form; in the semiquinone these transitions appear at lower frequency, are closer together, and, as predicted from detailed considerations of transition probabilities, exhibit approximately half the absorption intensity. Our hypothesis of a common orbital origin suggests that semiquinone formation takes place by the addition of an electron to the lowest empty phi orbital of the oxidized form without any gross electronic rearrangement.     

Polarized infrared spectra of crystalline glycosaminoglycans

Polarized infrared spectra have been recorded for oriented, crystalline specimens of hyaluronates, chondroitin 4-sulfate and 6-sulfate, dermatan sulfate, and a cartilage proteoglycan, having different known chain conformations as determined by X-ray diffraction. The dichroism data for the vibrational modes of the amide and carboxyl groups have been interpreted with respect to the particular molecular structures.     

The high salt form of poly(dG-dC).poly(dG-dC) is left-handed Z-DNA: Raman spectra of crystals and solutions.

The laser-Raman spectra of crystalline d(CpGpCpGpCpG) and of aqueous poly(dG-dC).poly(dG-dC) in high salt (4M NaCl) and low salt (0.1M NaCl) solutions have been measured and compared. The spectra of the crystal and the high-salt solution show a striking congruence, which indicates clearly that the high-salt form of the aqueous polymer has the left-handed Z-DNA structure of the crystalline oligomer. These two spectra differ substantially from that of the low-salt form of the polymer, which has been found previously to have spectral characteristics of the B-form of DNA. The high salt spectrum shows a unique line due to guanine residues at 625 cm-1 which should be useful for qualitative and possibly quantitative assessment of the amount of Z-structure present in a sample of DNA.     

Polarized attenuated total reflectance spectra of oriented purple membranes

The technique of polarized Fourier transform infrared attenuated total reflectance spectroscopy has been applied to the study of oriented purple membranes of Halobacterium cutirubrum. This method offers a fast and simple approach for probing conformations of proteins in-situ and capable of obtaining polarized infrared spectra at an angle of incidence that is much greater than the Brewster angle.     

Structural variability and new intermolecular interactions of Z-DNA in crystals of d(pCpGpCpGpCpG).

We have determined the single crystal x-ray structure of the synthetic DNA hexamer d(pCpGpCpGpCpG) in two different crystal forms. The hexamer pCGCGCG has the Z-DNA conformation and in both cases the asymmetric unit contains more than one Z-DNA duplex. Crystals belong to the space group C222(1) with a = 69.73, b = 52.63, and c = 26.21 A, and to the space group P2(1) with a = 49.87, b = 41.26, c = 21.91 A, and gamma = 97.12 degrees. Both crystals show new crystal packing modes. The molecules also show striking new features when compared with previously determined Z-DNA structures: 1) the bases in one duplex have a large inclination with respect to the helical axis, which alters the overall shape of the molecule. 2) Some cytosine nitrogens interact by hydrogen bonding with phosphates in neighbor molecules. Similar base-phosphate interactions had been previously detected in some B-DNA crystals. 3) Basepair stacking between the ends of neighbor molecules is variable and no helical continuity is maintained between contiguous hexamer duplexes.     

Z-DNA功能研究的回顾和近况

自从Rich等在1979年首次发现左手螺旋的Z-DNA以后,人们对Z-DNA的研究不断深入,并推测它在基因转录、基因调控以及基因重组等方面有着重要的作用。最新研究表明Z-DNA与病毒的发病机制有关。这个研究结果可能蕴藏着关于这种另类DNA如何行使功能的答案,并可能由此成功研制能有效抗天花病毒的化合物。     

Electrical conductivity of single crystals of lysozyme

The dc electrical conductivity of large single crystals of hen egg-white lysozyme has been measured. The samples were grown from aqueous solution and dried in air with silica gel. The temperature dependence of the conductivity obeyed the relation σ = σ₀ exp(? ΔE/kT), with ΔE = 1.2 eV. The ΔE value agreed with most of the previous results for various proteins in the form of lyophilized powder. On the other hand, log σ₀, being between 7 and 11, was much larger than the previously reported values and differed among the samples. An irreversible decrease in σ₀, without affecting ΔE, was observed on heating the samples above 85°C. It was shown that the set of results can be explained if the charge carriers responsible for the observed conduction are regarded as protons, originating from residual water molecules. Photoresponse of the samples to uv radiation below 305–315 nm was also observed. Reproducible and reliable results were obtained relatively easily in the present experiments, which is thought to be the main advantage of using single-crystalline samples.     

Isotopic effects in the electronic spectra of tryptophan

Summary. No influence of isotopic substitution in deuterium-substituted tryptophan on the florescence excitation spectrum has previously been found out. Here, the isotopic effects of electronic excitation of deuterium-substituted tryptophan were experimentally and theoretically analyzed for first time. It was shown a short-wave shift of the UV-absorption maximum at 220 nm corresponding to the 360 cal/mol and short-wave shift for fluorescence spectrum corresponding to the 210 cal/mol. To account for this effect, the quantum chemical calculations of the geometric and electron structure, frequencies of normal vibrations and transition energies have been performed. The isotopic effects originate from the zero-point energies of ground and excited states. It was found that isotopic shifts depend on the position of isotope in the molecule and kind of transition. So, it can be utilized in the analysis of proteins structure and complexation.     

Radiolytic signature of Z-DNA.

Ionizing radiations induce various damages in DNA via the hydroxyl radical OH. generated by the radiolysis of water. We compare here the radiosensitivity of B- and Z-DNA, by using a Z-prone stretch included in a plasmid. In the supercoiled plasmid, the stretch is in the Z-form, whereas it is in the B-form when the plasmid is relaxed. Frank strand breaks (FSB) and alkali-revealed breaks (ARB) were located and quantified using sequencing gel electrophoresis. We show that B- and Z-DNA have the same mean sensitivity towards radiolytic attack, for both FSB and ARB. Nevertheless, the guanine sites are more sensitive, and the cytosine sites less sensitive in Z- than in B-DNA, leading to a characteristic signature of the Z-form. The comparison of experiments with the outcome of a Monte Carlo simulation of OH. radical attack suggests that transfer of initial damage from a guanine base to its attached sugar or the adjacent 3' cytosine is more important in Z-DNA than in B-DNA.     

Preparation of single crystals of a yolk lipoprotein

Single crystals of a yolk lipoprotein from two species of lamprey oocytes have been prepared and shown to belong to the monoclinic space group C2. The unit cell dimensions combined with molecular weight determinations support the idea that the lipoprotein is a symmetrical dimer centered on a crystallographic 2-fold symmetry axis. The lipid content is estimated to be about 15% (w/w) and the crystals are suitable for structural studies by single crystal X-ray analysis. The X-ray results are correlated with those obtained by electron diffraction.     

Enzymatic depolymerization of lamellar single crystals of nigeran

Lamellar single crystals of the α-glucan: nigeran have been subjected to controlled enzymic degradation as an approach to understanding polysaccharide organization in these crystals. Analysis of both reactant and products by various methods argues that a situation exists where the crystals are inaccessible at 20°C but become increasingly accessible as the temperature approaches that of solution for the crystals in water. One has to conclude that chain folds are inaccessible to enzymes at 20°C and become increasingly accessible as one approaches the “melting temperature.” This could be due to increased mobility of the surface chains as temperature is raised, which produces large dynamic loops and makes enzyme degradation possible. The general conclusion is that nigeran single-crystal surfaces are disordered and increasingly mobile close to their dissolution temperature in water.