The non-detectability of NH...N hydrogen bonds in nucleic acids due to exchange broadened imino/amino protons has recently been addressed via the use of non-exchangeable protons for detecting internucleotide 2hJ(NN) couplings. In these applications, the appropriate non-exchangeable proton is separated by two bonds from the NH...N bond. In this paper, we extend the scope of this approach to protons which are separated by four bonds from the NH...N moiety. Specifically, we consider the case of the commonly occurring sheared G x A mismatch alignment, in which we use the adenine H2 proton to report on the (A)N6H6(1.2)...N3(G) hydrogen bond, in the presence of undetectable, exchange broadened N6H6(1.2) protons. Two sequences, the 'straight-through' (H6)N6N3H2 and 'out-and-back' H2N6N3 experiments, are presented for observing these correlations in H2O and D2O solution, respectively. The sequences are demonstrated on two uniformly 15N,13C labelled DNA samples: d(G1G2G3T4T5C6A7G8G9)2, containing a G3 x (C6-A7) triad involving a sheared G3 x A7 mismatch, and d(G1G2G3C4A5G6G7T8)4, containing an A5 x (G3 x G6 x G3 x G6) x A5 hexad involving a sheared G3 x A5 mismatch. 相似文献
Programmers struggle to understand performance of task-based OpenMP programs since profiling tools only report thread-based performance. Performance tuning also requires task-based performance in order to balance per-task memory hierarchy utilization against exposed task parallelism. We provide a cost-effective method to extract detailed task-based performance information from OpenMP programs. We demonstrate the utility of our method by quickly diagnosing performance problems and characterizing exposed task parallelism and per-task instruction profiles of benchmarks in the widely-used Barcelona OpenMP Tasks Suite. Programmers can tune performance faster and understand performance tradeoffs more effectively than existing tools by using our method to characterize task-based performance. 相似文献
Mcm10 protein is essential for initiation and elongation phases of replication. Human cells proteolyze Mcm10 during mitosis,
presumably to ensure a single round of replication. It has been proposed that anaphase promoting complex ubiquitinates Mcm10
in late M and early G1 phases. 相似文献
TraI, the F plasmid-encoded nickase, is a 1,756 amino acid protein essential for conjugative transfer of F plasmid DNA from
one bacterium to another. While crystal structures of N- and C-terminal domains of F TraI have been determined, central domains
of the protein are structurally unexplored. These middle domains (between residues 306 and 1,500) are known to both bind single-stranded
DNA (ssDNA) and unwind DNA through a highly processive helicase activity. Of this central region, the more C-terminal portion
(~900–1500) appears related to helicase RecD of the E. coli RecBCD complex. The more N-terminal portion (306–900), however, shows limited sequence similarity to other proteins. In an
attempt to define the structure of well-folded domains of this middle region and discern their function, we have isolated
stable regions of TraI following limited proteolysis. One of these regions, TraI (381–569), was identified and a genetic construct
encoding it was engineered. The protein was expressed, purified, and the sequence-specific chemical shifts for it were assigned. 相似文献
CgtA is an essential OBG GTPase (Trach & Hoch, 1989) highly conserved from bacteria to eukaryotes. It is a multifunctional protein, involved in DNA replication, chromosome partitioning (Slominska et al., 2002), nutritional stress response, initiation of sporulation, ribosome maturation, etc. Despite being a multifunctional essential protein, its mode of action is not well- characterized and key question remains: how does this protein work in wide varieties of cellular function? The expression of cgtA-mRNA increases on the onset of nutritional stress. Purified CgtA protein shows increased GTPase activity in the presence of ribosome. Our experiment with thiostrepton reveals that, although ribosome is able to trigger the GTPase activity of CgtA, its probable site of GTPase inducing activity is different from other regular translation factors like EF-G, that uses GTP. For structure function study we have generated an energy minimized homology model of the Vibrio cholerae CgtA protein, which reveals two large domains, an OBG-fold and a GTP– hydrolysis domain, with an extended C-terminal part. We compared the amino acid sequence of CgtA across various species in the database, and found that its Glycine98 and the Tyrosine195 residues are 100% conserved in prokaryotes. These amino acids are highly conserved in eukaryotes as well. Gly98 and Tyr195 are located on the hinge region of CgtA comprising of portions of the OBG and the GTP–hydrolysis domains, respectively. To decipher the mode of actions of CgtA and the role of the conserved Gly98 residue, we have replaced the Gly with a relatively larger amino acid, i.e. Asp. Our study reveals that the mutant CgtA(G98D) shows a reduced GTPase activity in presence of ribosome compared to the wild type. This indicates a restricted inter-domain movement of CgtA due to the above point mutation. To understand this phenomenon we are using MD simulations. We will discuss results from MD simulations and other mutation studies as well. Our results indicate that ribosome acts as a modulator for increasing the GTPase activity of CgtA. The perfect conservation of G98 residue is important for the proper functionality of CgtA. 相似文献
The side chains of Lys66, Asp66, and Glu66 in staphylococcal nuclease are fully buried and surrounded mainly by hydrophobic matter, except for internal water molecules associated with carboxylic oxygen atoms. These ionizable side chains titrate with pKa values of 5.7, 8.8, and 8.9, respectively. To reproduce these pKa values with continuum electrostatics calculations, we treated the protein with high dielectric constants. We have examined the structural origins of these high apparent dielectric constants by using NMR spectroscopy to characterize the structural response to the ionization of these internal side chains. Substitution of Val66 with Lys66 and Asp66 led to increased conformational fluctuations of the microenvironments surrounding these groups, even under pH conditions where Lys66 and Asp66 are neutral. When Lys66, Asp66, and Glu66 are charged, the proteins remain almost fully folded, but resonances for a few backbone amides adjacent to the internal ionizable residues are broadened. This suggests that the ionization of the internal groups promotes a local increase in dynamics on the intermediate timescale, consistent with either partial unfolding or increased backbone fluctuations of helix 1 near residue 66, or, less likely, with increased fluctuations of the charged side chains at position 66. These experiments confirm that the high apparent dielectric constants reported by internal Lys66, Asp66, and Glu66 reflect localized changes in conformational fluctuations without incurring detectable global structural reorganization. To improve structure-based pKa calculations in proteins, we will need to learn how to treat this coupling between ionization of internal groups and local changes in conformational fluctuations explicitly. 相似文献
At present plants continuously exposed to salinity stress due to the challenging environment that has reduced the crop growth and productivity worldwide. Application of phytohormones by using seed priming method emerges as one of the most reliable and cost effective to alleviate the toxic effect of salinity stress. In this study, we evaluate the effect of seed-primed salicylic acid (SA) to reduce the adverse effect of different salt concentrations (0, 100, 200, and 300 mM NaCl) in pea (Pisum sativum L.) seedlings. After seedling emergence, percent seed germination was calculated; however, after 60 days; plants were sampled for studying the growth and photosynthetic traits, lipid peroxidation level, antioxidant activities, ions accumulation, and its sequestration. The results depicted that salinity treatments hampered overall growth performance and induced oxidative stress in a dose-dependent manner. Salinity also has negatively influence on ion accumulation as Na+ ion increased while K+ ion decreased. On the other hand, seed priming with SA significantly reduced the salinity-induced effects on the overall performance of plants, including growth and photosynthetic attributes. SA alleviated the adverse effect of salinity even at higher salinity level by inducing enzymatic and non-enzymatic antioxidant systems, soluble sugars, and proline accumulation, and regulating ion homeostasis along with up-regulation of Na+/H+ antiporters (SOS1 and NHX1). Thus, seed priming with SA shows a comprehensive role in mitigation of salinity stress and can be used as a model for promising salinity tolerant cultivation.