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Michael A. Clores,Joward B. Bautista,Jason B. Fernandez,Michael A. Cuesta,Rafe M. Brown 국립중앙과학관 2021 Journal of Asia-Pacific Biodiversity Vol.14 No.1
We report for the first time the herpetological biodiversity (amphibians and reptiles) of the Caramoan Island Group (CIG), Maqueda Channel, southern Luzon Island, the Philippines. Herpetofaunal biodiversity assessment, using the standard field-based methodology for survey work, was conducted at nine sites in the CIG, off the northeast coast of the Bicol Peninsula of southern Luzon. The overall species richness (s) in the CIG is 22 (three amphibians, 12 lizards, and seven snakes) represent new island records for a variety of the native species, ten of which are endemic to the Philippines. Beta diversity (β-diversity) of the CIG is 0.84 reflecting a relatively high degree of local area turnover of species when among-site comparisons were quantified; this finding most likely reflects habitat variability which is consistent with our observation emphasizing how a high proportion of faunal diversity is associated with, or confined, to very specific microhabitats (limestone areas, lower-montane forests, mangroves, beach coastal forests, etc.). The overall community similarity index of the archipelago was 0.545 implying that CIG has moderate overlap of amphibian and reptilian species composition. Our findings provide baseline information on the unique composition of herpetofauna in the CIG, which highlights a general paucity of knowledge about the Peninsula’s herpetofaunal diversity.
Ryu, Kyoung-Seok,Tugarinov, Vitali,Clore, G. Marius American Chemical Society 2014 JOURNAL OF THE AMERICAN CHEMICAL SOCIETY - Vol.136 No.41
<P/><P>The kinetics of translocation of the homeodomain transcription factor HoxD9 between specific sites of the same or opposite polarities on the same DNA molecule have been studied by <SUP>15</SUP>N<SUB><I>z</I></SUB>-exchange NMR spectroscopy. We show that exchange occurs by two facilitated diffusion mechanisms: a second-order intermolecular exchange reaction between specific sites located on different DNA molecules without the protein dissociating into free solution that predominates at high concentrations of free DNA, and a first-order intramolecular process involving direct transfer between specific sites located on the same DNA molecule. Control experiments using a mixture of two DNA molecules, each possessing only a single specific site, indicate that transfer between specific sites by full dissociation of HoxD9 into solution followed by reassociation is too slow to measure by <I>z</I>-exchange spectroscopy. Intramolecular transfer with comparable rate constants occurs between sites of the same and opposing polarity, indicating that both rotation-coupled sliding and hopping/flipping (analogous to geminate recombination) occur. The half-life for intramolecular transfer (0.5–1 s) is many orders of magnitude larger than the calculated transfer time (1–100 μs) by sliding, leading us to conclude that the intramolecular transfer rates measured by <I>z</I>-exchange spectroscopy represent the rate-limiting step for a one-base-pair shift from the specific site to the immediately adjacent nonspecific site. At zero concentration of added salt, the intramolecular transfer rate constants between sites of opposing polarity are smaller than those between sites of the same polarity, suggesting that hopping/flipping may become rate-limiting at very low salt concentrations.</P>
Schwieters, Charles D.,Suh, Jeong-Yong,Grishaev, Alexander,Ghirlando, Rodolfo,Takayama, Yuki,Clore, G. Marius American Chemical Society 2010 JOURNAL OF THE AMERICAN CHEMICAL SOCIETY - Vol.132 No.37
<P>The solution structures of free Enzyme I (EI, ∼128 kDa, 575 × 2 residues), the first enzyme in the bacterial phosphotransferase system, and its complex with HPr (∼146 kDa) have been solved using novel methodology that makes use of prior structural knowledge (namely, the structures of the dimeric EIC domain and the isolated EIN domain both free and complexed to HPr), combined with residual dipolar coupling (RDC), small- (SAXS) and wide- (WAXS) angle X-ray scattering and small-angle neutron scattering (SANS) data. The calculational strategy employs conjoined rigid body/torsion/Cartesian simulated annealing, and incorporates improvements in calculating and refining against SAXS/WAXS data that take into account complex molecular shapes in the description of the solvent layer resulting in a better representation of the SAXS/WAXS data. The RDC data orient the symmetrically related EIN domains relative to the <I>C</I><SUB>2</SUB> symmetry axis of the EIC dimer, while translational, shape, and size information is provided by SAXS/WAXS. The resulting structures are independently validated by SANS. Comparison of the structures of the free EI and the EI−HPr complex with that of the crystal structure of a trapped phosphorylated EI intermediate reveals large (∼70−90°) hinge body rotations of the two subdomains comprising the EIN domain, as well as of the EIN domain relative to the dimeric EIC domain. These large-scale interdomain motions shed light on the structural transitions that accompany the catalytic cycle of EI.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/2010/jacsat.2010.132.issue-37/ja105485b/production/images/medium/ja-2010-05485b_0014.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/ja105485b'>ACS Electronic Supporting Info</A></P>