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21.
Michael Shokhen Amnon Albeck 《Protein science : a publication of the Protein Society》2017,26(12):2355-2366
Rhomboid proteases constitute a family of intramembrane serine proteases ubiquitous in all forms of life. They differ in many aspects from their soluble counterparts. We applied molecular dynamics (MD) computational approach to address several challenging issues regarding their catalytic mechanism: How does the exosite of GlpG rhomboid protease control the kinetics efficiency of substrate hydrolysis? What is the mechanism of inhibition by the non‐competitive peptidyl aldehyde inhibitors bound to the GlpG rhomboid active site (AS)? What is the underlying mechanism that explains the hypothesis that GlpG rhomboid protease is not adopted for the hydrolysis of short peptides that do not contain a transmembrane domain (TMD)? Two fundamental features of rhomboid catalysis, the enzyme recognition and discrimination of substrates by TMD interactions in the exosite, and the concerted mechanism of non‐covalent pre‐catalytic complex to covalent tetrahedral complex (TC) conversion, provide answers to these mechanistic questions. 相似文献
22.
Endo peptidyl epoxides, in which the central epoxidic moiety replaces the scissile amide bond of a P(3)-P(3)' peptide, were designed as cysteine proteases inhibitors. The additional P'-S' interactions, relative to those of an exo peptidyl epoxide of the same P(3)-P(1) sequence, significantly improved affinity to the enzymes papain and cathepsin B, but also changed the mode of inhibition from active-site directed inactivation to reversible competitive inhibition. Computational models rationalize the binding affinity and the inhibition mechanism. 相似文献
23.
Pascale Simard Hugo Galarneau Sébastien Marois Daniel Rusu Caroline D Hoemann Patrice E Poubelle Hani El-Gabalawy Maria JG Fernandes 《Arthritis research & therapy》2009,11(3):R74-10
Introduction
Osteoarthritis is characterized by the progressive destruction of cartilage in the articular joints. Novel therapies that promote resurfacing of exposed bone in focal areas are of interest in osteoarthritis because they may delay the progression of this disabling disease in patients who develop focal lesions. Recently, the addition of 80% deacetylated chitosan to cartilage microfractures was shown to promote the regeneration of hyaline cartilage. The molecular mechanisms by which chitosan promotes cartilage regeneration remain unknown. Because neutrophils are transiently recruited to the microfracture site, the effect of 80% deacetylated chitosan on the function of neutrophils was investigated. Most studies on neutrophils use preparations of chitosan with an uncertain degree of deacetylation. For therapeutic purposes, it is of interest to determine whether the degree of deacetylation influences the response of neutrophils to chitosan. The effect of 95% deacetylated chitosan on the function of neutrophils was therefore also investigated and compared with that of 80% deacetylated chitosan. 相似文献24.
"Triple-negative" breast cancers are aggressive malignancies that respond poorly to treatments. Now Sun et al. (2011) find that the activity of the protein tyrosine phosphatase PTPN12 is lost in a large percentage of this breast cancer subtype, offering molecular drivers and possible therapeutic targets for this heterogeneous and intractable cancer. 相似文献
25.
Khersonsky O Röthlisberger D Wollacott AM Murphy P Dym O Albeck S Kiss G Houk KN Baker D Tawfik DS 《Journal of molecular biology》2011,407(3):391-1021
Although de novo computational enzyme design has been shown to be feasible, the field is still in its infancy: the kinetic parameters of designed enzymes are still orders of magnitude lower than those of naturally occurring ones. Nonetheless, designed enzymes can be improved by directed evolution, as recently exemplified for the designed Kemp eliminase KE07. Random mutagenesis and screening resulted in variants with > 200-fold higher catalytic efficiency and provided insights about features missing in the designed enzyme. Here we describe the optimization of KE70, another designed Kemp eliminase. Amino acid substitutions predicted to improve catalysis in design calculations involving extensive backbone sampling were individually tested. Those proven beneficial were combinatorially incorporated into the originally designed KE70 along with random mutations, and the resulting libraries were screened for improved eliminase activity. Nine rounds of mutation and selection resulted in > 400-fold improvement in the catalytic efficiency of the original KE70 design, reflected in both higher kcat values and lower Km values, with the best variants exhibiting kcat/Km values of > 5 × 104 s− 1 M− 1. The optimized KE70 variants were characterized structurally and biochemically, providing insights into the origins of the improvements in catalysis. Three primary contributions were identified: first, the reshaping of the active-site cavity to achieve tighter substrate binding; second, the fine-tuning of electrostatics around the catalytic His-Asp dyad; and, third, the stabilization of the active-site dyad in a conformation optimal for catalysis. 相似文献
26.
27.
Cecilia JG de Almeida Jean-Fran?ois Jasmin Francesco Del Galdo Michael P Lisanti 《Cell cycle (Georgetown, Tex.)》2013,12(14):2248-2254
Caveolar domains act as platforms for the organization of molecular complexes involved in signal transduction. Caveolin proteins, the principal structural components of caveolae, have been involved in many cellular processes. Caveolin-1 (Cav-1) and caveolin-2 (Cav-2) are highly expressed in the lung. Cav-1-deficient mice (Cav-1−/−) and Cav-2-deficient mice (Cav-2−/−) exhibit severe lung dysfunction attributed to a lack of Cav-2 expression. Recently, Cav-1 has been shown to regulate lung fibrosis in different models. Here, we show that Cav-2 is also involved in modulation of the fibrotic response, but through distinct mechanisms. Treatment of wild-type mice with the pulmonary fibrosis-inducer bleomycin reduced the expression of Cav-2 and its phosphorylation at tyrosine 19. Importantly, Cav-2−/− mice, but not Cav-1−/− mice, were more sensitive to bleomycin-induced lung injury in comparison to wild-type mice. Bleomycin-induced lung injury was characterized by alveolar thickening, increase in cell density, and extracellular matrix deposition. The lung injury observed in bleomycin-treated Cav-2−/− mice was not associated with alterations in the TGF-β signaling pathway and/or in the ability to produce collagen. However, apoptosis and proliferation were more prominent in lungs of bleomycin-treated Cav-2−/− mice. Since Cav-1−/− mice also lack Cav-2 expression and show a different outcome after bleomycin treatment, we conclude that Cav-1 and Cav-2 have distinct roles in bleomycin induced-lung fibrosis, and that the balance of both proteins determines the development of the fibrotic process. 相似文献
28.
Two distinct conformational states define the interaction of human RAD51‐ATP with single‐stranded DNA
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Andrea Candelli Edwige B Garcin Mauro Modesti Luca Pellegrini Gijs JL Wuite Erwin JG Peterman 《The EMBO journal》2018,37(7)
An essential mechanism for repairing DNA double‐strand breaks is homologous recombination (HR). One of its core catalysts is human RAD51 (hRAD51), which assembles as a helical nucleoprotein filament on single‐stranded DNA, promoting DNA‐strand exchange. Here, we study the interaction of hRAD51 with single‐stranded DNA using a single‐molecule approach. We show that ATP‐bound hRAD51 filaments can exist in two different states with different contour lengths and with a free‐energy difference of ~4 kBT per hRAD51 monomer. Upon ATP hydrolysis, the filaments convert into a disassembly‐competent ADP‐bound configuration. In agreement with the single‐molecule analysis, we demonstrate the presence of two distinct protomer interfaces in the crystal structure of a hRAD51‐ATP filament, providing a structural basis for the two conformational states of the filament. Together, our findings provide evidence that hRAD51‐ATP filaments can exist in two interconvertible conformational states, which might be functionally relevant for DNA homology recognition and strand exchange. 相似文献
29.
The alcohol dehydrogenase (Adh) region from five planitibia subgroup
species of Hawaiian picture-wing Drosophila has been cloned. A total of 15
kb of DNA in and around the Adh gene has been compared among the five
species. Genetic distances were calculated to determine evolutionary
relationships. These distances agree with previous distances determined by
protein polymorphism and DNA hybridization techniques and can be
interpreted in terms of specific island colonization and speciation
(founder) events over the past 5 Myr. Examination of the restriction maps
of the cloned Adh region from the five species shows many instances of
small deletions, insertion of a transposable element in D. heteroneura, and
the existence of a highly variable region on the 3' side of the Adh gene.
Clustering relationships and rates of DNA change are calculated and
compared with the relationship found for other species of Drosophila.
相似文献
30.
Okun E Dikshtein Y Carmely A Saida H Frei G Sela BA Varshavsky L Ofir A Levy E Albeck M Sredni B 《The FEBS journal》2007,274(12):3159-3170
Ammonium trichloro(dioxoethylene-o,o')tellurate (AS101) is an organotellurium compound with pleiotropic functions that has been associated with antitumoral, immunomodulatory and antineurodegenerative activities. Tellurium compounds with a +4 oxidation state, such as AS101, react uniquely with thiols, forming disulfide molecules. In light of this, we tested whether AS101 can react with the amino acid homocysteine both in vitro and in vivo. AS101 conferred protection against homocysteine-induced apoptosis of HL-60 cells. The protective mechanism of AS101 against homocysteine toxicity was directly mediated by its chemical reactivity, whereby AS101 reacted with homocysteine to form homocystine, the less toxic disulfide form of homocysteine. Moreover, AS101 was shown here to reduce the levels of total homocysteine in an in vivo model of hyperhomocysteinemia. As a result, AS101 also prevented sperm cells from undergoing homocysteine-induced DNA fragmentation. Taken together, our results suggest that the organotellurium compound AS101 may be of clinical value in reducing total circulatory homocysteine levels. 相似文献