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1.
Described here is a set of three-dimensional (3D) NMR experiments that rely on CACA-TOCSY magnetization transfer via the weak
3 \textJ\textCa\textCa ^{ 3} {\text{J}}_{{{\text{C}}\alpha {\text{C}}\alpha }} coupling. These pulse sequences, which resemble recently described 13C detected CACA-TOCSY (Takeuchi et al. 2010) experiments, are recorded in 1H2O, and use 1H excitation and detection. These experiments require alternate 13C-12C labeling together with perdeuteration, which allows utilizing the small
3 \textJ\textCa\textCa ^{ 3} {\text{J}}_{{{\text{C}}\alpha {\text{C}}\alpha }} scalar coupling that is otherwise masked by the stronger 1JCC couplings in uniformly 13C labeled samples. These new experiments provide a unique assignment ladder-mark that yields bidirectional supra-sequential
information and can readily straddle proline residues. Unlike the conventional HNCA experiment, which contains only sequential
information to the
1 3 \textCa ^{ 1 3} {\text{C}}^{\alpha } of the preceding residue, the 3D hnCA-TOCSY-caNH experiment can yield sequential correlations to alpha carbons in positions
i−1, i + 1 and i−2. Furthermore, the 3D hNca-TOCSY-caNH and Hnca-TOCSY-caNH experiments, which share the same magnetization pathway but use
a different chemical shift encoding, directly couple the 15N-1H spin pair of residue i to adjacent amide protons and nitrogens at positions i−2, i−1, i + 1 and i + 2, respectively. These new experimental features make protein backbone assignments more robust by reducing the degeneracy problem
associated with the conventional 3D NMR experiments. 相似文献
2.
Following Petoukhov and his collaborators, we use two length n zero-one sequences, α and β, to represent a length n genetic sequence
((a) || (b)){\alpha\choose\beta}
so that the columns of
((a) || (b)){\alpha\choose\beta}
have the following correspondence with the nucleotides:
C ~ (0 || 0)C\sim{0\choose0}
,
U ~ (1 || 0)U\sim{1\choose0}
,
G ~ (1 || 1)G\sim{1\choose1}
,
A ~ (0 || 1)A\sim{0\choose1}
. Using the Gray code ordering to arrange α and β, we build a 2
n
×2
n
matrix C
n
including all the 4
n
length n genetic sequences. Furthermore, we use the Hamming distance of α and β to construct a 2
n
×2
n
matrix D
n
. We explore structures of these matrices, refine the results in earlier papers, and propose new directions for further research. 相似文献
3.
The temporal profile of the phosphorescence of singlet oxygen endogenously photosensitized by photosystem II (PSII) reaction
centre (RC) in an aqueous buffer has been recorded using laser excitation and a near infrared photomultiplier tube. A weak
emission signal was discernible, and could be fitted to the functional form a[exp( - t/t2 ) - exp( - t/t1 )] a[\exp ( - t/\tau_{2} ) - \exp ( - t/\tau_{1} )] , with $ a > 0 $ a > 0 and $ \tau_{2} > \tau_{1} $ \tau_{2} > \tau_{1} . The value of t2 \tau_{2} decreased from 11.6 ± 0.5 μs under aerobic conditions to 4.1 ± 0.2 μs in oxygen-saturated samples, due to enhanced bimolecular
quenching of the donor triplet by oxygen, whereas that of t1 \tau_{1} , identifiable with the lifetime of singlet oxygen, was close to 3 μs in both cases. Extrapolations based on the low amplitude
of the emission signal of singlet oxygen formed by PSII RC in the aqueous buffer and the expected values of t1 \tau_{1} and t2 \tau_{2} in chloroplasts indicate that attempts to analyse the temporal profile of singlet oxygen in chloroplasts are unlikely to
be rewarded with success without a significant advance in the sensitivity of the detection equipment. 相似文献
4.
The difference equation f
b
:[0,1]–[0,1] defined by f
b
(x)=b x(1–x) is studied. In particular complete qualitative information is obtained for the parameter value b=3.83. For example the number of fixed points of (f
b
)i is given by
Ni = 1 + ( \frac1 + ?5 2 )i + ( \frac1 - ?5 2 )iN_i = 1 + \left( {\frac{{1 + \sqrt 5 }}{2}} \right)^i + \left( {\frac{{1 - \sqrt 5 }}{2}} \right)^i 相似文献
5.
Hsieh JY Chiang TY Chen JL Chen YW Lin HC Hwang CC 《Journal of molecular modeling》2011,17(10):2455-2464
Molecular dynamics simulations of the biphalin molecule, (Tyr-D-Ala-Gly-Phe-NH)2, and the active tetrapeptide hydrazide, Tyr-D-Ala-Gly-Phe-NH-NH2 were performed to investigate the cause of the increased μ and δ receptor binding affinities of the former over the latter.
The simulation results demonstrate that the acylation of the two equal tetrapeptide fragments of biphalin produces the constrained
hydrazide bridges C4a - C4¢- N9 - N10 {\hbox{C}}_4^{\alpha } - {{\hbox{C}}_4}\prime - {{\hbox{N}}_9} - {{\hbox{N}}_{{10}}} and N9 - N10 - C5¢- C5a {{\hbox{N}}_9} - {{\hbox{N}}_{{10}}} - {{\hbox{C}}_5}\prime - {\hbox{C}}_5^{\alpha } , which in turn increase the opportunity of conformations for binding to μ or δ receptors. Meanwhile, the connection of the
two active tetrapeptide fragments of biphalin also results in the constrained side chain torsion angle χ2 at one of the two residues Phe. This constrained side chain torsion angle not only significantly increases the δ receptor
binding affinity but also makes most of the δ receptor binding conformations of biphalin bind to the δ receptor through the
fragment containing the mentioned residue Phe. 相似文献
6.
Mammalian metallothioneins (
\textM7\textIIMTs {\text{M}}_7^{\text{IIMTs}} ) show a clustered arrangement of the metal ions and a nonregular protein structure. The solution structures of Cd3-thiolate cluster containing β-domain of mouse β-MT-1 and rat β-MT-2 show high structural similarities, but widely differing
structure dynamics. Molecular dynamics simulations revealed a substantially increased number of
\textNH - \textSg {\text{NH - }}{{\text{S}}^\gamma } hydrogen bonds in β-MT-2, features likely responsible for the increased stability of the Cd3-thiolate cluster and the enfolding protein domain. Alterations in the
\textNH - \textSg {\text{NH - }}{{\text{S}}^\gamma } hydrogen-bonding network may provide a rationale for the differences in dynamic properties encountered in the β-domains of
MT-1, -2, and -3 isoforms, believed to be essential for their different biological function. 相似文献
7.
Yu. P. Fedonenko E. I. Katsy L. P. Petrova A. S. Boyko E. L. Zdorovenko V. V. Kachala A. S. Shashkov Yu. A. Knirel 《Russian Journal of Bioorganic Chemistry》2010,36(2):219-223
The rhizobacteria Azospirillum brasilense Sp245 produce immunochemically different lipopolysaccharides LPSI and LPSII, both
containing identical pentasaccharides built from D-rhamnose residues as the repeating units of O-specific polysaccharides (OPS). In this study, we report the structure of the
OPS from A. brasilense LPSI−LPSII− mutant Sp245.5, which spontaneously lost the p85 and p120 plasmids upon the formation of a new 300-MDa megaplasmid after
the long-term storage of the bacteria in a rich medium. The repeating unit of the OPS of A. brasilense Sp245.5 appeared to be a disaccharide consisting of residues of N-acetyl-D-galactosamine and N-acetyl-D-mannosaminuronic acid:
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