The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PDB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB.
High-resolution, mid-infrared spectra of methanol isotopologues (CH3OH, CH3OD, CD3OH, and CD3OD) embedded in superfluid helium nanodroplets have been obtained. For the normal isotopologue, we observed the CO stretching overtone band, the lines within which are 2× broader than in the fundamental for E species methanol and no different than the fundamental for A species methanol. For CH3OD, we observed the CO stretching overtone band for the first time, which was characterized by narrow line widths for both nuclear spin species. Spectra in the CD3 stretching bands were much broader, which is attributed to rapid relaxation to nearby anharmonically coupled vibrational state(s). Apparently the coupling is much stronger for CD3OD, for which the rotational substructure is completely washed out. Inertial analyses of the rotationally resolved fundamental and overtone bands reveal that the moment of inertia of helium, ΔI He, that couples to rotation decreases in going from the heavier (CD3OH) to lighter (CH3OH) isotopologues (i.e., with decreasing gas phase moment of inertia, I G). The dependence of ΔI He on I G is larger than that found for other molecules in regions approaching the heavy and light rotor limits, which suggests a relatively large breakdown in the adiabatic following of helium density for this moderately light rotor.
We report high-resolution infrared spectra of OCS isotopologues embedded in helium nanodroplets that were recorded with a newly built spectrometer. For the normal isotopologue, we observed the relatively weak third bending overtone band, in addition to new high J transitions in the C-O stretching fundamental, which has previously been investigated by diode laser spectroscopy [S. Grebenev et al., J. Chem. Phys. 112, 4485 (2000)]. Similar to the gas phase, the overtone band is (only) 45 cm higher in energy than the fundamental, and this leads to additional broadening due to rapid vibrational relaxation that is accompanied by the creation of real/virtual phonon excitations. We also observed spectra in the C-O stretching fundamental for several minor isotopologues of OCS, including OCS, OCS, and OCS, in addition to some new peaks for OCS. A rovibrational analysis allowed for determination of the moment of inertia of helium (ΔI) that couples to the rotation of OCS for each isotopologue. In the context of the adiabatic following approximation, the helium density structure that follows the rotation of OCS should essentially remain unchanged between the isotopologues, i.e., there should be no dependence of ΔI on the gas phase moment of inertia of OCS (I). While this behavior was expected for the "heavy" OCS rotor investigated here, we instead found an approximately linear 1:1 relation between ΔI and I, which suggests partial breakdown of the adiabatic following approximation, making OCS the heaviest molecule for which evidence for this effect has been obtained.
The far-infrared spectrum (100–500 cm–1) of a d 1 isotopologue of the astrophysically important molecule, vinyl alcohol, is reported. We observed several low energy (OD) torsional bands: the fundamental and first two hot bands of the syn rotamer and the fundamental and first hot band of the (higher energy) anti rotamer. While the bands corresponding to the anti rotamer are somewhat obscured by rotational lines of water (making a full spectroscopic analysis unfeasible at this stage), the syn-vinyl alcohol bands are not, and a global fit was performed that included 4404 distinct infrared lines assigned in this work, in addition to 59 previously reported microwave lines. This simultaneous analysis of the torsional fundamental, torsional hot band, and pure rotational band of syn-vinyl alcohol allowed for determination of spectroscopic parameters in the first two torsionally excited states and for refinement of them in the ground state. These parameters should be useful in searches for both cold and warm CH2CHOD in interstellar molecular clouds.
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