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排序方式: 共有2023条查询结果,搜索用时 15 毫秒
941.
942.
Kirpota OO Endutkin AV Ponomarenko MP Ponomarenko PM Zharkov DO Nevinsky GA 《Nucleic acids research》2011,39(11):4836-4850
We have used a stepwise increase in ligand complexity approach to estimate the relative contributions of the nucleotide units of DNA containing 7,8-dihydro-8-oxoguanine (oxoG) to its total affinity for human 8-oxoguanine DNA glycosylase (OGG1) and construct thermodynamic models of the enzyme interaction with cognate and non-cognate DNA. Non-specific OGG1 interactions with 10–13 nt pairs within its DNA-binding cleft provides approximately 5 orders of magnitude of its affinity for DNA (ΔG° approximately −6.7 kcal/mol). The relative contribution of the oxoG unit of DNA (ΔG° approximately −3.3 kcal/mol) together with other specific interactions (ΔG° approximately −0.7 kcal/mol) provide approximately 3 orders of magnitude of the affinity. Formation of the Michaelis complex of OGG1 with the cognate DNA cannot account for the major part of the enzyme specificity, which lies in the kcat term instead; the rate increases by 6–7 orders of magnitude for cognate DNA as compared with non-cognate one. The kcat values for substrates of different sequences correlate with the DNA twist, while the KM values correlate with ΔG° of the DNA fragments surrounding the lesion (position from −6 to +6). The functions for predicting the KM and kcat values for different sequences containing oxoG were found. 相似文献
943.
944.
945.
Zhao N Pang B Shyu CR Korkin D 《Protein science : a publication of the Protein Society》2011,20(7):1275-1284
Protein-protein interactions play an essential role in the functioning of cell. The importance of charged residues and their diverse role in protein-protein interactions have been well studied using experimental and computational methods. Often, charged residues located in protein interaction interfaces are conserved across the families of homologous proteins and protein complexes. However, on a large scale, it has been recently shown that charged residues are significantly less conserved than other residue types in protein interaction interfaces. The goal of this work is to understand the role of charged residues in the protein interaction interfaces through their conservation patterns. Here, we propose a simple approach where the structural conservation of the charged residue pairs is analyzed among the pairs of homologous binary complexes. Specifically, we determine a large set of homologous interactions using an interaction interface similarity measure and catalog the basic types of conservation patterns among the charged residue pairs. We find an unexpected conservation pattern, which we call the correlated reappearance, occurring among the pairs of homologous interfaces more frequently than the fully conserved pairs of charged residues. Furthermore, the analysis of the conservation patterns across different superkingdoms as well as structural classes of proteins has revealed that the correlated reappearance of charged residues is by far the most prevalent conservation pattern, often occurring more frequently than the unconserved charged residues. We discuss a possible role that the new conservation pattern may play in the long-range electrostatic steering effect. 相似文献
946.
Polyoxometalate/laccase-mediated oxidative polymerization of catechol for textile dyeing 总被引:1,自引:0,他引:1
Kim S Silva C Evtuguin DV Gamelas JA Cavaco-Paulo A 《Applied microbiology and biotechnology》2011,89(4):981-987
The synergistic effect between polyoxometalates (POMs), namely K5[SiW11VVO40]·11H2O and H5[PMo10VV
2O40]·13H2O and laccase from ascomycete Myceliophthora thermophila has been employed for the first time in oxidative polymerization of catechol. Such a laccase-mediator system allowed the
formation of a relatively high molecular weight polycatechol as confirmed by size exclusion chromatography and electrospray
ionization mass spectrometry (ESI-MS) (3990 Da when using K5[SiW11VVO40]·11H2O and 3600 Da with H5[PMo10VV
2O40]·13H2O). The synthesized polymers were applied as dyes for the dyeing of flax fabrics. The color intensity of flax fabrics colored
with polymer solutions was evaluated by diffuse reflectance spectrophotometry via k/s measurements (+10% of fixation ratio). A new synthetic process allowed a dyeing polymer, provided upon flax coloration, better
color fixation and color resistance when compared to that obtained by conventional synthesis with laccase solely or with addition
of organic mediator (1-hydroxybenzotriazole). 相似文献
947.
Temperature-dependence of protein dynamics can provide information on details of the free energy landscape by probing the
characteristics of the potential responsible for the fluctuations. We have investigated the temperature-dependence of picosecond
to nanosecond backbone dynamics at carbonyl carbon sites in chicken villin headpiece subdomain protein using a combination
of three NMR relaxation rates: 13C′ longitudinal rate, and two cross-correlated rates involving dipolar and chemical shift anisotropy (CSA) relaxation mechanisms,
13C′/13C′-13Cα CSA/dipolar and 13C′/13C′–15N CSA/dipolar. Order parameters have been extracted using the Lipari-Szabo model-free approach assuming a separation of the
time scales of internal and molecular motions in the 2–16°C temperature range. There is a gradual deviation from this assumption
from lower to higher temperatures, such that above 16°C the separation of the time scales is inconsistent with the experimental
data and, thus, the Lipari-Szabo formalism can not be applied. While there are variations among the residues, on the average
the order parameters indicate a markedly steeper temperature dependence at backbone carbonyl carbons compared to that probed
at amide nitrogens in an earlier study. This strongly advocates for probing sites other than amide nitrogen for accurate characterization
of the potential and other thermodynamics characteristics of protein backbone. 相似文献
948.
The capacity to polymerize into amyloid fibrils is common to many proteins. While some proteins naturally form these fibrils to serve functional roles, amyloid is usually associated with pathogenic processes in which specific proteins aberrantly aggregate within cells or tissues. Though the contribution of amyloid fibrils to actual disease pathogenesis is not always clear, one possibility is that the titration of essential proteins from solution into aggregates contributes to the cellular degeneration common to many amyloid diseases. Using mammalian and yeast model systems, we recently showed that the common biophysical properties of amyloid aggregates—including strong resistance to dissolution—enable stringent purification and identification of both amyloid-forming and amyloid-associated proteins directly from cells. Strikingly, many proteins that were previously implicated in formation or clearance of intracellular aggregates, including several stress granule components, were found to co-aggregate with amyloid formed by a polyglutamine-expanded huntingtin fragment. This direct evaluation of proteins within aggregates can help identify new amyloid-forming proteins, as well as proteins that can indirectly contribute to disease mechanisms. 相似文献
949.
950.
Elena Naimark Dmitry Kirpotin Natalia Boeva Vladimir Gmoshinskiy Maria Kalinina Yulia Lyupina Alexander Markov Michail Nikitin Alexander Shokurov Dmitry Volkov 《Ecology and evolution》2021,11(2):1037
The reliability of evolutionary reconstructions based on the fossil record critically depends on our knowledge of the factors affecting the fossilization of soft‐bodied organisms. Despite considerable research effort, these factors are still poorly understood. In order to elucidate the main prerequisites for the preservation of soft‐bodied organisms, we conducted long‐term (1–5 years) taphonomic experiments with the model crustacean Artemia salina buried in five different sediments. The subsequent analysis of the carcasses and sediments revealed that, in our experimental settings, better preservation was associated with the fast deposition of aluminum and silicon on organic tissues. Other elements such as calcium, magnesium, and iron, which can also accumulate quickly on the carcasses, appear to be much less efficient in preventing decay. Next, we asked if the carcasses of uni‐ and multicellular organisms differ in their ability to accumulate aluminum ions on their surface. The experiments with the flagellate Euglena gracilis and the sponge Spongilla lacustris showed that aluminum ions are more readily deposited onto a multicellular body. This was further confirmed by the experiments with uni‐ and multicellular stages of the social ameba Dictyostelium discoideum. The results lead us to speculate that the evolution of cell adhesion molecules, which provide efficient cell–cell and cell–substrate binding, probably can explain the rich fossil record of soft‐bodied animals, the comparatively poor fossil record of nonskeletal unicellular eukaryotes, and the explosive emergence of the Cambrian diversity of soft‐bodied fossils. 相似文献