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31.
Lemak A Gutmanas A Chitayat S Karra M Farès C Sunnerhagen M Arrowsmith CH 《Journal of biomolecular NMR》2011,49(1):27-38
The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number
and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein
NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1)
spectral resolution – especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on
a continuous network of weak scalar couplings as part of most common assignment protocols. In order to facilitate NMR structure
determination, we developed a semi-automated strategy that utilizes non-uniform sampling (NUS) and multidimensional decomposition
(MDD) for optimal data collection and processing of selected, high resolution multidimensional NMR experiments, combined it
with an ABACUS protocol for sequential and side chain resonance assignments, and streamlined this procedure to execute structure
and refinement calculations in CYANA and CNS, respectively. Two graphical user interfaces (GUIs) were developed to facilitate
efficient analysis and compilation of the data and to guide automated structure determination. This integrated method was
implemented and refined on over 30 high quality structures of proteins ranging from 5.5 to 16.5 kDa in size. 相似文献
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Gutiérrez P Osborne MJ Siddiqui N Trempe JF Arrowsmith C Gehring K 《Protein science : a publication of the Protein Society》2004,13(3):659-667
aIF2 beta is the archaeal homolog of eIF2 beta, a member of the eIF2 heterotrimeric complex, implicated in the delivery of Met-tRNA(i)(Met) to the 40S ribosomal subunit. We have determined the solution structure of the intact beta-subunit of aIF2 from Methanobacterium thermoautotrophicum. aIF2 beta is composed of an unfolded N terminus, a mixed alpha/beta core domain and a C-terminal zinc finger. NMR data shows the two folded domains display restricted mobility with respect to each other. Analysis of the aIF2 gamma structure docked to tRNA allowed the identification of a putative binding site for the beta-subunit in the ternary translation complex. Based on structural similarity and biochemical data, a role for the different secondary structure elements is suggested. 相似文献
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Kim Y Yakunin AF Kuznetsova E Xu X Pennycooke M Gu J Cheung F Proudfoot M Arrowsmith CH Joachimiak A Edwards AM Christendat D 《The Journal of biological chemistry》2004,279(1):517-526
The protein TA0175 has a large number of sequence homologues, most of which are annotated as unknown and a few as belonging to the haloacid dehalogenase superfamily, but has no known biological function. Using a combination of amino acid sequence analysis, three-dimensional crystal structure information, and kinetic analysis, we have characterized TA0175 as phosphoglycolate phosphatase from Thermoplasma acidophilum. The crystal structure of TA0175 revealed two distinct domains, a larger core domain and a smaller cap domain. The large domain is composed of a centrally located five-stranded parallel beta-sheet with strand order S10, S9, S8, S1, S2 and a small beta-hairpin, strands S3 and S4. This central sheet is flanked by a set of three alpha-helices on one side and two helices on the other. The smaller domain is composed of an open faced beta-sandwich represented by three antiparallel beta-strands, S5, S6, and S7, flanked by two oppositely oriented alpha-helices, H3 and H4. The topology of the large domain is conserved; however, structural variation is observed in the smaller domain among the different functional classes of the haloacid dehalogenase superfamily. Enzymatic assays on TA0175 revealed that this enzyme catalyzed the dephosphorylation of phosphoglycolate in vitro with similar kinetic properties seen for eukaryotic phosphoglycolate phosphatase. Activation by divalent cations, especially Mg2+, and competitive inhibition behavior with Cl- ions are similar between TA0175 and phosphoglycolate phosphatase. The experimental evidence presented for TA0175 is indicative of phosphoglycolate phosphatase. 相似文献
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BJÖRN ROGELL MARTIN EKLUND HANNA THÖRNGREN ANSSI LAURILA JACOB HÖGLUND 《Molecular ecology》2010,19(11):2229-2240
Although loss of genetic variation is frequently assumed to be associated with loss of adaptive potential, only few studies have examined adaptation in populations with little genetic variation. On the Swedish west coast, the northern fringe populations of the natterjack toad Bufo calamita inhabit an atypical habitat consisting of offshore rock islands. There are strong among‐population differences in the amount of neutral genetic variation, making this system suitable for studies on mechanisms of trait divergence along a gradient of within‐population genetic variation. In this study, we examined the mechanisms of population divergence using QST–FST comparisons and correlations between quantitative and neutral genetic variation. Our results suggest drift or weak stabilizing selection across the six populations included in this study, as indicated by low QST–FST values, lack of significant population × temperature interactions and lack of significant differences among the islands in breeding pond size. The six populations included in this study differed in both neutral and quantitative genetic variation. Also, the correlations between neutral and quantitative genetic variation tended to be positive, however, the relatively small number of populations prevents any strong conclusions based on these correlations. Contrary to the majority of QST–FST comparisons, our results suggest drift or weak stabilizing selection across the examined populations. Furthermore, the low heritability of fitness‐related traits may limit evolutionary responses in some of the populations. 相似文献
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In March 2009, we documented the death of one member of a triplet polar bear (Ursus maritimus) litter at its den site in the southern Beaufort Sea (SBS) of Alaska. We used a self-contained video camera unit to document
activity between den emergence and departure. All three cubs showed low activity levels relative to other cubs observed, and
one died within one week of den emergence. Necropsy confirmed that the dead cub had a low body weight and was malnourished.
Capture later confirmed that the two surviving cubs were also undersized. Polar bear cub survival is influenced by many factors
including litter size and sea ice conditions. Triplet litters are often smaller and suffer higher mortality rates than singletons
and twins. This cub was not only a triplet but also born following 2 years of record minimum sea ice extent, both of which
may have played a role in this cub’s demise. 相似文献