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101.
102.
Fast multidimensional NMR with a time resolution of a few seconds provides a new tool for high throughput screening and site-resolved
real-time studies of kinetic molecular processes by NMR. Recently we have demonstrated the feasibility to record protein 1H–15N correlation spectra in a few seconds of acquisition time using a new SOFAST-HMQC experiment (Schanda and Brutscher (2005)
J. Am. Chem. Soc. 127, 8014). Here, we investigate in detail the performance of SOFAST-HMQC to record 1H–15N and 1H−13C correlation spectra of proteins of different size and at different magnetic field strengths. Compared to standard 1H–15N correlation experiments SOFAST-HMQC provides a significant gain in sensitivity, especially for fast repetition rates. Guidelines
are provided on how to set up SOFAST-HMQC experiments for a given protein sample. In addition, an alternative pulse scheme,
IPAP-SOFAST-HMQC is presented that allows application on NMR spectrometers equipped with cryogenic probes, and fast measurement
of one-bond 1H–13C and 1H–15N scalar and residual dipolar coupling constants. 相似文献
103.
This study reports the sequence specific chemical shifts assignments for 76 residues of the 94 residues containing monomeric unit of the photosynthetic light-harvesting 2 transmembrane protein complex from Rhodopseudomonas acidophila strain 10050, using Magic Angle Spinning (MAS) NMR in combination with extensive and selective biosynthetic isotope labeling methods. The sequence specific chemical shifts assignment is an essential step for structure determination by MAS NMR. Assignments have been performed on the basis of 2-dimensional proton-driven spin diffusion 13C–13C correlation experiments with mixing times of 20 and 500 ms and band selective 13C–15N correlation spectroscopy on a series of site-specific biosynthetically labeled samples. The decreased line width and the reduced number of correlation signals of the selectively labeled samples with respect to the uniformly labeled samples enable to resolve the narrowly distributed correlation signals of the backbone carbons and nitrogens involved in the long -helical transmembrane segments. Inter-space correlations between nearby residues and between residues and the labeled BChl a cofactors, provided by the 13C–13C correlation experiments using a 500 ms spin diffusion period, are used to arrive at sequence specific chemical shift assignments for many residues in the protein complex. In this way it is demonstrated that MAS NMR methods combined with site-specific biosynthetic isotope labeling can be used for sequence specific assignment of the NMR response of transmembrane proteins. 相似文献
104.
New anatomical method of grain angles measurement using confocal microscopy and image cross-correlation 总被引:1,自引:0,他引:1
Some tropical trees with indistinct growth rings have a distinct interlocked grain that reveals their internal growth rhythm. To determine their growth rhythm, it is necessary to accurately measure the wood grain angle. The usual methods for grain angle measurement are radial splitting using wood disks, which occasionally provides inaccurate data, and serial tangential sectioning, which requires preparation and analysis of many sections. The present report proposes an easier but accurate method to measure grain angle using a single xylem transverse section. A confocal microscope was used to obtain two optical sections of different depths from a transverse section of a 7-year-old Hopea odorata Roxb. The tangential lag between the optical images was then calculated using image cross-correlation and transformed into grain angle. Radially consecutive sampling revealed distinct radial fluctuations in the grain angle. The fluctuation data were compared to data obtained by radial splitting and serial tangential sectioning. There was a strong correlation between grain angle using the three methods. In the region close to the cambium, however, the present method revealed an abrupt change in the grain angle, although radial splitting showed a smooth undulation throughout the radius. Using the present method, the analysis of a radial range of 5 cm required a single transverse section compared to 1,000 tangential sections 50-m thick. In conclusion, the present method using a single transverse section, confocal microscopy, and image cross-correlation analysis provides more accurate data than radial splitting, and is less time-consuming than serial tangential sectioning. 相似文献
105.
Lamellar organization of pigments in chlorosomes, the light harvesting complexes of green photosynthetic bacteria
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Psencík J Ikonen TP Laurinmäki P Merckel MC Butcher SJ Serimaa RE Tuma R 《Biophysical journal》2004,87(2):1165-1172
Chlorosomes of green photosynthetic bacteria constitute the most efficient light harvesting complexes found in nature. In addition, the chlorosome is the only known photosynthetic system where the majority of pigments (BChl) is not organized in pigment-protein complexes but instead is assembled into aggregates. Because of the unusual organization, the chlorosome structure has not been resolved and only models, in which BChl pigments were organized into large rods, were proposed on the basis of freeze-fracture electron microscopy and spectroscopic constraints. We have obtained the first high-resolution images of chlorosomes from the green sulfur bacterium Chlorobium tepidum by cryoelectron microscopy. Cryoelectron microscopy images revealed dense striations approximately 20 A apart. X-ray scattering from chlorosomes exhibited a feature with the same approximately 20 A spacing. No evidence for the rod models was obtained. The observed spacing and tilt-series cryoelectron microscopy projections are compatible with a lamellar model, in which BChl molecules aggregate into semicrystalline lateral arrays. The diffraction data further indicate that arrays are built from BChl dimers. The arrays form undulating lamellae, which, in turn, are held together by interdigitated esterifying alcohol tails, carotenoids, and lipids. The lamellar model is consistent with earlier spectroscopic data and provides insight into chlorosome self-assembly. 相似文献
106.
Viktor Hornak Markus Eilers Mordechai Sheves Steven O. Smith 《Journal of molecular biology》2010,396(3):510-527
Structural restraints provided by solid-state NMR measurements of the metarhodopsin II intermediate are combined with molecular dynamics simulations to help visualize structural changes in the light activation of rhodopsin. Since the timescale for the formation of the metarhodopsin II intermediate (> 1 ms) is beyond that readily accessible by molecular dynamics, we use NMR distance restraints derived from 13C dipolar recoupling measurements to guide the simulations. The simulations yield a working model for how photoisomerization of the 11-cis retinylidene chromophore bound within the interior of rhodopsin is coupled to transmembrane helix motion and receptor activation. The mechanism of activation that emerges is that multiple switches on the extracellular (or intradiscal) side of rhodopsin trigger structural changes that converge to disrupt the ionic lock between helices H3 and H6 on the intracellular side of the receptor. 相似文献
107.
We present a novel target function based on atomic coordinates that permits quaternary structural refinement of multi-domain
protein–protein or protein–RNA complexes. It requires that the high-resolution structures of the individual domains are known
and that small angle scattering (SAS) data as well as NMR orientational restraints from residual dipolar couplings (RDCs)
of the complex are available. We show that, when used in combination, the translational and rotational restraints contained
in SAS intensities and RDCs, respectively, define a target potential function that permits to determine the overall topology
of complexes made up of domains with low internal symmetry. We apply the target function on a modestly anisotropic model system,
the Barnase/Barstar complex, and discuss factors that influence the structural refinement such as data errors and the geometrical
properties of the individual domains. 相似文献
108.
Interfacial behavior of cytoplasmic and mitochondrial creatine kinase oligomeric states 总被引:1,自引:0,他引:1
Adsorption to the air/water interface of isoenzymes of creatine kinase was investigated using surface pressure-area isotherms and Brewster angle microscopy (BAM) observations. Octameric mitochondrial creatine kinase (mtCK) exhibits a significant affinity for the air/water interface. Whatever the mode of formation of the interfacial film, i.e., injection of the protein in the subphase or spreading onto the buffer surface, the final arrangement and conformation adopted by mtCK molecules lead to a similar result. In contrast, the dimeric isoenzymes mtCK and cytosolic MMCK do not induce any surface pressure variation. However, when the subphase contains 0.3M NaCl, both isoenzymes adsorb to the interface. When treated with 0.8 or 3M GdnHCl, muscle creatine kinase (MMCK) becomes surface active and occupies a greater surface than mtCK. This result contrasts with previous observations, often derived from monomeric proteins, that their surface activity is increased upon unfolding. It underlines the possible influence exerted by the protein oligomeric state on its interfacial activity. At a subphase pH of 8.8, which corresponds to the pI of octameric mtCK, the profiles of the isotherms obtained with dimeric and octameric states and the resistance to compression of the protein monolayers are significantly affected when compared to those recorded at pH 7.4. These data suggest that the octamer is more hydrophobic than the dimer and may contribute to explaining why octamers bind to the inner mitochondrial membrane while dimers do not. 相似文献
109.
Varga A Flachner B Konarev P Gráczer E Szabó J Svergun D Závodszky P Vas M 《FEBS letters》2006,580(11):2698-2706
Closure of the two domains of 3-phosphoglycerate kinase, upon substrate binding, is essential for the enzyme function. The available crystal structures cannot provide sufficient information about the mechanism of substrate assisted domain closure and about the requirement of only one or both substrates, since lattice forces may hinder the large scale domain movements. In this study the known X-ray data, obtained for the open and closed conformations, were probed by solution small-angle X-ray scattering experiments. The results prove that binding of both substrates is essential for domain closure. Molecular graphical analysis, indeed, reveals formation of a double-sided H-bond network, which affects substantially the shape of the main molecular hinge at beta-strand L, under the concerted action of both substrates. 相似文献
110.
The designed antimicrobial peptide KIGAKIKIGAKIKIGAKI possesses enhanced membrane selectivity for bacterial lipids, such as phosphatidylethanolamine and phosphatidylglycerol. The perturbation of the bilayer by the peptide was first monitored using oriented bilayer samples on glass plates. The alignment of POPE/POPG model membranes with respect to the bilayer normal was severely altered at 4 mol% KIGAKI while the alignment of POPC bilayers was retained. The interaction mechanism between the peptide and POPE/POPG bilayers was investigated by carefully comparing three bilayer MLV samples (POPE bilayers, POPG bilayers, and POPE/POPG 4/1 bilayers). KIGAKI induces the formation of an isotropic phase for POPE/POPG bilayers, but only a slight change in the 31P NMR CSA line shape for both POPE and POPG bilayers, indicating the synergistic roles of POPE and POPG lipids in the disruption of the membrane structure by KIGAKI. 2H NMR powder spectra show no reduction of the lipid chain order for both POPG and POPE/POPG bilayers upon peptide incorporation, supporting the evidence that the peptide acts as a surface peptide. 31P longitudinal relaxation studies confirmed that different dynamic changes occurred upon interaction of the peptide with the three different lipid bilayers, indicating that the strong electrostatic interaction between the cationic peptide KIGAKI and anionic POPG lipids is not the only factor in determining the antimicrobial activity. Furthermore, 31P and 2H NMR powder spectra demonstrated a change in membrane characteristics upon mixing of POPE and POPG lipids. The interaction between different lipids, such as POPE and POPG, in the mixed bilayers may provide the molecular basis for the KIGAKI carpet mechanism in the permeation of the membrane. 相似文献