Highlights of synchrotron radiation

The applications of the electromagnetic radiation generated by relativistic electrons circulating in synchrotrons and storage rings have rapidly extended into many scientific disciplines. This article first briefly reviews the history of synchrotron radiation, and recapitulates its properties. The available sources are listed, and some aspects of the facilities that are required to make use of the radiation are discussed, with particular emphasis on the optical elements. Several noteworthy examples of scientific research conducted with synchrotron radiation are described. These are drawn principally from the X-ray region, and comprise X-ray fluorescence, small-angle scattering, powder profile refinement, extended X-ray absorption fine structure, topography, time-resolved spectroscopy, and VUV and photoelectron spectroscopy of solids. In conclusion, a few topics are mentioned relating to the future expansion and application of synchrotron radiation research facilities.     

Noncausal time response in frustrated total internal reflection?

Tunneling of photons in frustrated total internal reflection has been studied in the time domain with single-cycle femtosecond pulses. It is seen that both the phase and energy of the pulse travel faster than the speed of light in vacuum. Theoretical analysis of the experiments shows that the time-response function for electromagnetic waves propagating in the air gap is noncausal. However, it is found that superluminal signal propagation is not possible in this case because of the inevitable diffractive spreading of the signal beam.     

Resonant phase patterns in a reaction-diffusion system

Resonance regions similar to the Arnol'd tongues found in single oscillator frequency locking are observed in experiments using a spatially extended periodically forced Belousov-Zhabotinsky system. We identify six distinct 2:1 subharmonic resonant patterns and describe them in terms of the position-dependent phase and magnitude of the oscillations. Some experimentally observed features are also found in numerical studies of a forced Brusselator reaction-diffusion model.     

Chirp response of an active-controlled thickness-drive tunable transducer

The chirp response of a thickness-drive tunable transducer for wide range time-bandwidth and sweep rates chirp signals is demonstrated experimentally and computationally. The computational evaluation uses recursive digital-filter model based on the z-transform method. The model is limited to simple lossless structure with no front and backing layers. The model and experimental results show that there is no limit on the maximum sweep rate of the chirp signal but practically the limit is determined by the limitation of the circuit that generates the control voltage that simulates a variable electric load.     

The case of the missing ring: radical cleavage of a carbon-carbon bond and implications for GFP chromophore biosynthesis

The green fluorescent protein (GFP) creates its fluorophore by promoting spontaneous peptide backbone cyclization and amino acid oxidation chemistry on its own Ser65, Tyr66, Gly67 tripeptide sequence. Here we use high-resolution crystallography and mutational analyses to characterize GFP variants that undergo backbone cyclization followed by either anticipated chromophore synthesis via Y66F Calpha-Cbeta double-bond formation or unprecedented loss of a Y66F benzyl moiety via Calpha-Cbeta bond cleavage. We discovered a Y66F cleavage variant that subsequently incorporates an oxygen atom, likely from molecular oxygen, at the Y66 Calpha position. The post-translational products identified from these Y66F GFP structures support a common intermediate that partitions between Calpha-Cbeta oxidation and homolytic cleavage pathways. Our data indicate that Glu222 is the branchpoint control for this partitioning step and also influences subsequent oxygen incorporation reactions. From these results, we propose mechanisms for Y66F Calpha-Cbeta cleavage, oxygen incorporation, and chromophore biosynthesis with shared features that include radical chemistry. By revealing how GFP and RFP protein environments steer chemistry to favor fluorophore biosynthesis and disfavor alternative reactivity, we identify strategies for protein design. The proposed, common, one-electron oxidized, radical intermediate for post-translation modifications in the GFP family has general implications for how proteins drive and control spontaneous post-translational chemical modifications in the absence of metal ions.     

Direct measurement of a pK(a) near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography

The hepatitis delta virus (HDV) ribozyme uses a cytosine to facilitate general acid-base catalysis. Biochemical studies suggest that C75 has a pKa perturbed to near neutrality. To measure this pKa directly, Raman spectra were recorded on single ribozyme crystals using a Raman microscope. A spectral feature arising from a single neutral cytosine was identified at 1528 cm(-1). At low pH, this mode was replaced with a new spectral feature. Monitoring these features as a function of pH revealed pKa values for the cytosine that couple anticooperatively with Mg2+ binding, with values of 6.15 and 6.40 in the presence of 20 and 2 mM Mg2+, respectively. These pKa values agree well with those obtained from ribozyme activity experiments in solution. To correlate the observed pKa with a specific nucleotide, crystals of C75U, which is catalytically inactive, were examined. The Raman difference spectra show that this mutation does not affect the conformation of the ribozyme. However, crystals of C75U did not produce a signal from a protonatable cytosine, providing strong evidence that protonation of C75 is being monitored in the wild-type ribozyme. These studies provide the first direct physical measurement of a pKa near neutrality for a catalytic residue in a ribozyme and show that ribozymes, like their protein enzyme counterparts, can optimize the pKa of their side chains for proton transfer.     

Tyrosyl rotamer interconversion rates and the fluorescence decays of N-acetyltyrosinamide and short tyrosyl peptides

It has long been recognized that the fluorescence lifetimes of amino acid residues such as tyrosine and tryptophan depend on the rotameric configuration of the aromatic side chain, but estimates of the rate of interchange of rotameric states have varied widely. We report measurements of the rotameric populations and interchange rates for tyrosine in N-acetyltyrosinamide (NATyrA), the tripeptide Tyr-Gly-Gly (YGG), and the pentapeptide Leu-enkephalin (YGGFL). The fluorescence lifetimes were analyzed to determine the rotameric interchange rates in the context of a model incorporating exchange among three rotameric states. Maximum entropy method analysis verified the presence of three fluorescence decay components for YGGFL and two for YGG and NATyrA. Rotameric exchange between the gauche(-) and trans states occurred on the nanosecond time scale, whereas exchange with the gauche(+) state occurred on a longer time scale. Good agreement was obtained with rotameric populations and exchange rates from molecular dynamics simulations. Quenching by iodide was used to vary the intrinsic fluorescence lifetimes, providing additional constraints on the determined interchange rates. The temperature dependence was measured to determine barriers to exchange of the two most populated rotamers of 3, 5, and 7 kcal/mol for NATyrA, YGG, and YGGFL, respectively.     

Syntheses of (2')3'-15N-amino-(2')3'-deoxyguanosine and determination of their pKa values by 15N NMR spectroscopy

2'-Amino-2'-deoxyguanosine and 3'-amino-3'-deoxyguanosine are valuable probes for investigating the metal ion interactions at the active site of the group I ribozyme. However, these experiments require a thorough understanding of the protonation state of the amino group at a specific pH. Here, we describe the first syntheses of 2'-15N-amino-2'-deoxyadenosine, 2'-15N-amino-2'-deoxyguanosine, and 3'-15N-amino-3'-deoxyguanosine. The 15N-enriched nucleus allows convenient and accurate determination of the amine pKa by 15N NMR.     

Assessing chiral self-recognition using chiral stationary phases

Chiral stationary phases were synthesized and their ability to separate racemic precursors from which they were derived was assessed. Taken in conjunction with homochiral recognition previously observed in the solid state, the results of this study reveal that a geometrically controlling π-π interaction has a profound influence on molecular recognition.