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81.
Mazon H Marcillat O Forest E Vial C 《Protein science : a publication of the Protein Society》2004,13(2):476-486
Creatine kinase (CK) isoenzymes catalyse the reversible transfer of a phosphoryl group from ATP onto creatine. This reaction plays a very important role in the regulation of intracellular ATP concentrations in excitable tissues. CK isoenzymes are highly resistant to proteases in native conditions. To appreciate localized backbone dynamics, kinetics of amide hydrogen exchange with deuterium was measured by pulse-labeling the dimeric cytosolic muscle CK isoenzyme. Upon exchange, the protein was digested with pepsin, and the deuterium content of the resulting peptides was determined by liquid chromatography coupled to mass spectrometry (MS). The deuteration kinetics of 47 peptides identified by MS/MS and covering 96% of the CK backbone were analyzed. Four deuteration patterns have been recognized: The less deuterated peptides are located in the saddle-shaped core of CK, whereas most of the highly deuterated peptides are close to the surface and located around the entrance to the active site. Their exchange kinetics are discussed by comparison with the known secondary and tertiary structures of CK with the goal to reveal the conformational dynamics of the protein. Some of the observed dynamic motions may be linked to the conformational changes associated with substrate binding and catalytic mechanism. 相似文献
82.
Quantifying patterns of fine root dynamics is crucial to the understanding of ecosystem structure and function, and in predicting
how ecosystems respond to disturbance. Part of this understanding involves consideration of the carbon lost through root turnover.
In the context of the rainfall pattern in the tropics, it was hypothesised that rainfall would strongly influence fine root
biomass and longevity. A field study was conducted to determine root biomass, elemental composition and the influence of rainfall
on longevity of fine roots in a tropical lowland evergreen rainforest at Danum Valley, Sabah, Malaysia. A combination of root
coring, elemental analysis and rhizotron observation methods were used. Fine (less than 2 mm diameter) root biomass was relatively
low (1700 kg ha −1) compared with previously described rainforest data. Standing root biomass was positively correlated with
preceding rainfall, and the low fine root biomass in the dry season contained higher concentrations of N and lower concentrations
of P and K than at other times. Observations on rhizotrons demonstrated that the decrease in fine root biomass in the dry
season was a product of both a decrease in fine root length appearance and an increase in fine root length disappearance.
Fitting an overall model to root survival time showed significant effects of rainfall preceding root disappearance, with the
hazard of root disappearance decreasing by 8 for each 1 mm increase in the average daily (30 day) rainfall preceding root
disappearance. While it is acknowledged that other factors have a part to play, this work demonstrates the importance of rainfall
and soil moisture in influencing root biomass and root disappearance in this tropical rainforest. 相似文献
83.
Use of atomic force microscopy (AFM) has recently led to a better understanding of the molecular mechanisms of the unfolding process by mechanical forces; however, the rational design of novel proteins with specific mechanical strength remains challenging. We have approached this problem from a new perspective that generates linear physical–chemical properties (PCP) motifs from a limited AFM data set. Guided by our linear sequence analysis, we designed and analyzed four new mutants of the titin I1 domain with the goal of increasing the domain's mechanical strength. All four mutants could be cloned and expressed as soluble proteins. AFM data indicate that at least two of the mutants have increased molecular mechanical strength. This observation suggests that the PCP method is useful to graft sequences specific for high mechanical stability to weak proteins to increase their mechanical stability, and represents an additional tool in the design of novel proteins besides steered molecular dynamics calculations, coarse grained simulations, and ?‐value analysis of the transition state. Proteins 2012; © 2011 Wiley Periodicals, Inc. 相似文献
84.
Water dynamics clue to key residues in protein folding 总被引:1,自引:0,他引:1
Meng Gao Xin-Qiu Yao Zhen-Su She 《Biochemical and biophysical research communications》2010,392(1):95-10887
A computational method independent of experimental protein structure information is proposed to recognize key residues in protein folding, from the study of hydration water dynamics. Based on all-atom molecular dynamics simulation, two key residues are recognized with distinct water dynamical behavior in a folding process of the Trp-cage protein. The identified key residues are shown to play an essential role in both 3D structure and hydrophobic-induced collapse. With observations on hydration water dynamics around key residues, a dynamical pathway of folding can be interpreted. 相似文献
85.
DNA ligases are essential guardians of genome integrity by virtue of their ability to recognize and seal 3′-OH/5′-phosphate nicks in duplex DNA. The substrate binding and three chemical steps of the ligation pathway are coupled to global and local changes in ligase structure, involving both massive protein domain movements and subtle remodeling of atomic contacts in the active site. Here we applied solution NMR spectroscopy to study the conformational dynamics of the Chlorella virus DNA ligase (ChVLig), a minimized eukaryal ATP-dependent ligase consisting of nucleotidyltransferase, OB, and latch domains. Our analysis of backbone 15N spin relaxation and 15N,1H residual dipolar couplings of the covalent ChVLig-AMP intermediate revealed conformational sampling on fast (picosecond to nanosecond) and slow timescales (microsecond to millisecond), indicative of interdomain and intradomain flexibility. We identified local and global changes in ChVLig-AMP structure and dynamics induced by phosphate. In particular, the chemical shift perturbations elicited by phosphate were clustered in the peptide motifs that comprise the active site. We hypothesize that phosphate anion mimics some of the conformational transitions that occur when ligase-adenylate interacts with the nick 5′-phosphate. 相似文献
86.
Review of elevated atmospheric CO2 effects on agro-ecosystems: residue decomposition processes and soil C storage 总被引:15,自引:0,他引:15
A series of studies using major crops (cotton [Gossypium hirsutum L.], wheat [Triticum aestivum L.], grain sorghum [Sorghum bicolor (L.) Moench.] and soybean [Glycine max (L.) Merr.]) were reviewed to examine the impact of elevated atmospheric CO2 on crop residue decomposition within agro-ecosystems. Experiments evaluated utilized plant and soil material collected from
CO2 study sites using Free Air CO2 Enrichment (FACE) and open top chambers (OTC). A incubation study of FACE residue revealed that CO2-induced changes in cotton residue composition could alter decomposition processes, with a decrease in N mineralization observed
with FACE, which was dependent on plant organ and soil series. Incubation studies utilizing plant material grown in OTC considered
CO2-induced changes in relation to quantity and quality of crop residue for two species, soybean and grain sorghum. As with cotton,
N mineralization was reduced with elevated CO2 in both species, however, difference in both quantity and quality of residue impacted patterns of C mineralization. Over
the short-term (14 d), little difference was observed for CO2 treatments in soybean, but C mineralization was reduced with elevated CO2 in grain sorghum. For longer incubation periods (60 d), a significant reduction in CO2-C mineralized per g of residue added was observed with the elevated atmospheric CO2 treatment in both crop species. Results from incubation studies agreed with those from the OTC field observations for both
measurements of short-term CO2 efflux following spring tillage and the cumulative effect of elevated CO2 (> 2 years) in this study. Observations from field and laboratory studies indicate that with elevated atmospheric CO2, the rate of plant residue decomposition may be limited by N and the release of N from decomposing plant material may be
slowed. This indicates that understanding N cycling as affected by elevated CO2 is fundamental to understanding the potential for soil C storage on a global scale.
This revised version was published online in June 2006 with corrections to the Cover Date. 相似文献
87.
Stephen N. Floor Kendall J. Condon Deepak Sharma Eckhard Jankowsky Jennifer A. Doudna 《The Journal of biological chemistry》2016,291(5):2412-2421
DEAD-box proteins utilize ATP to bind and remodel RNA and RNA-protein complexes. All DEAD-box proteins share a conserved core that consists of two RecA-like domains. The core is flanked by subfamily-specific extensions of idiosyncratic function. The Ded1/DDX3 subfamily of DEAD-box proteins is of particular interest as members function during protein translation, are essential for viability, and are frequently altered in human malignancies. Here, we define the function of the subfamily-specific extensions of the human DEAD-box protein DDX3. We describe the crystal structure of the subfamily-specific core of wild-type DDX3 at 2.2 Å resolution, alone and in the presence of AMP or nonhydrolyzable ATP. These structures illustrate a unique interdomain interaction between the two ATPase domains in which the C-terminal domain clashes with the RNA-binding surface. Destabilizing this interaction accelerates RNA duplex unwinding, suggesting that it is present in solution and inhibitory for catalysis. We use this core fragment of DDX3 to test the function of two recurrent medulloblastoma variants of DDX3 and find that both inactivate the protein in vitro and in vivo. Taken together, these results redefine the structural and functional core of the DDX3 subfamily of DEAD-box proteins. 相似文献
88.
89.
A number of studies have examined the structural properties of late folding intermediates of (beta/alpha)8-barrel proteins involved in tryptophan biosynthesis, whereas there is little information available about the early folding events of these proteins. To identify the contiguous polypeptide segments important to the folding of the (beta/alpha)8-barrel protein Escherichia coli N-(5'-phosphoribosyl)anthranilate isomerase, we structurally characterized fragments and circularly permuted forms of the protein. We also simulated thermal unfolding of the protein using molecular dynamics. Our fragmentation experiments demonstrate that the isolated (beta/alpha)(1-4)beta5 fragment is almost as stable as the full-length protein. The far and near-UV CD spectra of this fragment are indicative of native-like secondary and tertiary structures. Structural analysis of the circularly permutated proteins shows that if the protein is cleaved within the two N-terminal betaalpha modules, the amount of secondary structure is unaffected, whereas, when cleaved within the central (beta/alpha)(3-4)beta5 segment, the protein simply cannot fold. An ensemble of the denatured structures produced by thermal unfolding simulations contains a persistent local structure comprised of beta3, beta4 and beta5. The presence of this three-stranded beta-barrel suggests that it may be an important early-stage folding intermediate. Interactions found in (beta/alpha)(3-4)beta5 may be essential for the early events of ePRAI folding if they provide a nucleation site that directs folding. 相似文献
90.
The flexibility of different regions of HIV-1 protease was examined by using a database consisting of 73 X-ray structures that differ in terms of sequence, ligands or both. The root-mean-square differences of the backbone for the set of structures were shown to have the same variation with residue number as those obtained from molecular dynamics simulations, normal mode analyses and X-ray B-factors. This supports the idea that observed structural changes provide a measure of the inherent flexibility of the protein, although specific interactions between the protease and the ligand play a secondary role. The results suggest that the potential energy surface of the HIV-1 protease is characterized by many local minima with small energetic differences, some of which are sampled by the different X-ray structures of the HIV-1 protease complexes. Interdomain correlated motions were calculated from the structural fluctuations and the results were also in agreement with molecular dynamics simulations and normal mode analyses. Implications of the results for the drug-resistance engendered by mutations are discussed briefly. 相似文献