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101.
Piia Kokkonen David Bednar Gaspar Pinto Zbynek Prokop Jiri Damborsky 《Biotechnology advances》2019,37(6):107386
Enzymes are efficient and specific catalysts for many essential reactions in biotechnological and pharmaceutical industries. Many times, the natural enzymes do not display the catalytic efficiency, stability or specificity required for these industrial processes. The current enzyme engineering methods offer solutions to this problem, but they mainly target the buried active site where the chemical reaction takes place. Despite being many times ignored, the tunnels and channels connecting the environment with the active site are equally important for the catalytic properties of enzymes. Changes in the enzymatic tunnels and channels affect enzyme activity, specificity, promiscuity, enantioselectivity and stability. This review provides an overview of the emerging field of enzyme access tunnel engineering with case studies describing design of all the aforementioned properties. The software tools for the analysis of geometry and function of the enzymatic tunnels and channels and for the rational design of tunnel modifications will also be discussed. The combination of new software tools and enzyme engineering strategies will provide enzymes with access tunnels and channels specifically tailored for individual industrial processes. 相似文献
102.
Novy RG Gillen AM Whitworth JL 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2007,114(7):1161-1172
Potato virus Y (PVY) and potato leafroll virus (PLRV) are two of the most important viral pathogens of potato. Infection of
potato by these viruses results in losses of yield and quality in commercial production and in the rejection of seed in certification
programs. Host plant resistance to these two viruses was identified in the backcross progeny of a Solanum etuberosum Lindl. somatic hybrid. Multiple years of field evaluations with high-virus inoculum and aphid populations have shown the
PVY and PLRV resistances of S. etuberosum to be stably expressed in two generations of progeny. However, while PLRV resistance was transmitted and expressed in the
third generation of backcrossing to cultivated potato (Solanum tuberosum L. subsp. tuberosum), PVY resistance was lost. PLRV resistance appears to be monogenic based on the inheritance of resistance in a BC3 population. Data from a previous evaluation of the BC2 progeny used in this study provides evidence that PLRV resistance was partly conferred by reduced PLRV accumulation in foliage.
The field and grafting data presented in this study suggests that resistance to the systemic spread of PLRV from infected
foliage to tubers also contributes to the observed resistance from S. etuberosum. The PLRV resistance contributed by S. etuberosum is stably transmitted and expressed through sexual generations and therefore would be useful to potato breeders for the development
of PLRV resistant potato cultivars. 相似文献
103.
Horak D Babic M Jendelová P Herynek V Trchová M Pientka Z Pollert E Hájek M Syková E 《Bioconjugate chemistry》2007,18(3):635-644
New surface-modified iron oxide nanoparticles were developed by precipitation of Fe(II) and Fe(III) salts with ammonium hydroxide according to two methods. In the first method, precipitation was done in the presence of D-mannose solution (in situ coating); the second method involved oxidation of precipitated magnetite with sodium hypochlorite followed by addition of D-mannose solution (postsynthesis coating). Selected nanoparticles were characterized by transmission electron microscopy (TEM), atomic force microscopy (AFM), elemental analysis, dynamic light scattering, infrared (IR), X-ray powder analysis, and ultrasonic spectrometry. While the first preparation method produced very fine nanoparticles ca. 2 nm in diameter, the second one yielded ca. 6 nm particles. Addition of D-mannose after synthesis did not affect the iron oxide particle size. UV-vis spectroscopy suggested that D-mannose suppresses the nonspecific sorption of serum proteins from DMEM culture medium on magnetic nanoparticles. Rat bone marrow stromal cells (rMSCs) were labeled with uncoated and d-mannose-modified iron oxide nanoparticles and with Endorem (Guerbet, France; control). Optical and transmission electron microscopy confirmed the presence of D-mannose-modified iron oxide nanoparticles inside the cells. D-mannose-modified nanoparticles crossed the cell membranes and were internalized well by the cells. Relaxivity measurements of labeled cells in gelatin revealed very high relaxivities only for postsynthesis D-mannose-coated iron oxide nanoparticles. 相似文献
104.
Gravett MG Thomas A Schneider KA Reddy AP Dasari S Jacob T Lu X Rodland M Pereira L Sadowsky DW Roberts CT Novy MJ Nagalla SR 《Journal of proteome research》2007,6(1):89-96
Intra-amniotic infection (IAI) is associated with preterm birth and perinatal mortality. To identify potential biomarkers, we performed a comprehensive survey of the cervical-vaginal fluid (CVF) proteome from a primate IAI model utilizing multidimensional protein identification technology (LC/LC-MS/MS) and MALDI-TOF-MS analyses. Analyses of CVF proteome identified 205 unique proteins and differential expression of 27 proteins in controls and IAI samples. Protein expression signatures and immunodetection of specific biomarkers identified can be employed for noninvasive detection of IAI. 相似文献
105.
Jan Frankovsky Barbora Keresztesov Jana Bellov Nina Kunov Nikola anigov Katerina Hanakova Jacob A. Bauer Gabriela Ondrovi
ov Veronika Luk
ov Barbara Sivkov Zbynek Zdrahal Vladimír Pevala Katarína Prochzkov Jozef Nosek Peter Barth Eva Kutejova Lubomir Tomaska 《The Journal of biological chemistry》2021,297(4)
Acylation modifications, such as the succinylation of lysine, are post-translational modifications and a powerful means of regulating protein activity. Some acylations occur nonenzymatically, driven by an increase in the concentration of acyl group donors. Lysine succinylation has a profound effect on the corresponding site within the protein, as it dramatically changes the charge of the residue. In eukaryotes, it predominantly affects mitochondrial proteins because the donor of succinate, succinyl-CoA, is primarily generated in the tricarboxylic acid cycle. Although numerous succinylated mitochondrial proteins have been identified in Saccharomyces cerevisiae, a more detailed characterization of the yeast mitochondrial succinylome is still lacking. Here, we performed a proteomic MS analysis of purified yeast mitochondria and detected 314 succinylated mitochondrial proteins with 1763 novel succinylation sites. The mitochondrial nucleoid, a complex of mitochondrial DNA and mitochondrial proteins, is one of the structures whose protein components are affected by succinylation. We found that Abf2p, the principal component of mitochondrial nucleoids responsible for compacting mitochondrial DNA in S. cerevisiae, can be succinylated in vivo on at least thirteen lysine residues. Abf2p succinylation in vitro inhibits its DNA-binding activity and reduces its sensitivity to digestion by the ATP-dependent ScLon protease. We conclude that changes in the metabolic state of a cell resulting in an increase in the concentration of tricarboxylic acid intermediates may affect mitochondrial functions. 相似文献
106.
Screwworms, Cochliomyia hominivorax (Fig. 1), have been eradicated from the USA and now have a tenuous hold only in the Yucatan peninsula of Mexico, where control programmes based on massive release of sterile males have recently been initiated. Sterile male release operations are now underway in Guatemala and proposals have been made to extend the eradication procedures south to the Darien Gap in Panama. It is planned to extend the barrier zone to Belize and Guatemala later this year. This article reviews the progress and operational obstacles of the screwworm eradication programme. 相似文献
107.
Vera Novy Leonor Vieira Carneiro Jae Ho Shin Johan Larsbrink Lisbeth Olsson 《The Journal of biological chemistry》2021,297(5)
Cutinases are esterases that release fatty acids from the apoplastic layer in plants. As they accept bulky and hydrophobic substrates, cutinases could be used in many applications, ranging from valorization of bark-rich side streams to plastic recycling. Advancement of these applications, however, requires deeper knowledge of cutinases’ biodiversity and structure–function relationships. Here, we mined over 3000 members from carbohydrate esterase family 5 for putative cutinases and condensed it to 151 genes from known or putative lignocellulose-targeting organisms. The 151 genes were subjected to a phylogenetic analysis, which showed that cutinases with available crystal structures were phylogenetically closely related. We then selected nine phylogenic diverse cutinases for recombinant production and characterized their kinetic activity against para-nitrophenol substrates esterified with consecutively longer alkyl chains (pNP-C2 to C16). Each investigated cutinase had a unique activity fingerprint against the tested pNP substrates. The five enzymes with the highest activity on pNP-C12 and C16, indicative of activity on bulky hydrophobic compounds, were selected for in-depth kinetic and structure–function analysis. All five enzymes showed a decrease in kcat values with increasing substrate chain length, whereas KM values and binding energies (calculated from in silico docking analysis) improved. Two cutinases from Fusarium solani and Cryptococcus sp. exhibited outstandingly low KM values, resulting in high catalytic efficiencies toward pNP-C16. Docking analysis suggested that different clades of the phylogenetic tree may harbor enzymes with different modes of substrate interaction, involving a solvent-exposed catalytic triad, a lipase-like lid, or a clamshell-like active site possibly formed by flexible loops. 相似文献
108.
Andrea T. Kramer Barbara Crane Jeff Downing J.L. Hamrick Kayri Havens Amy Highland Sarah K. Jacobi Thomas N. Kaye Eric V. Lonsdorf Jennifer Ramp Neale Ari Novy Peter E. Smouse Douglas W. Tallamy Abigail White Jacob Zeldin 《Restoration Ecology》2019,27(3):470-476
Current guidance on sourcing native plants to support ecosystem function focuses on the high risk of failure when unsuitable material is used in ecological restoration. However, there is growing recognition that risks may be lower and rewards higher at highly disturbed sites isolated from remnant populations, especially when considering support for pollinators, wildlife, and other ecosystem functions. We developed the first decision support tool using expert opinion to assess suitability of different native plant sources, including horticultural cultivars, in two different planting contexts. We assessed the suitability of 761 sources for 72 commonly sold native species in two different planting contexts (small, isolated, highly disturbed sites vs. large, undisturbed sites near remnant populations). Information on genetic and adaptive backgrounds of sources was strikingly lacking, forcing us to exclude one‐third of sources from our assessment. While only 3% of cultivars received high suitability scores for use in large, undisturbed sites near remnant populations, 52% received high suitability scores in small, isolated, highly disturbed sites. However, nearly 25% of cultivars had floral or leaf traits that differed from wild plants in ways that may compromise their ability to support pollinators and other wildlife. Forbs and cultivars lacking genetic diversity and source information were most likely to have altered traits. We recommend that native plant breeders and sellers work together to ensure ecosystem function, adaptation, and diversity information is available to consumers, that consumers request this information to drive demand, and that researchers further investigate how context influences risks and benefits of different sources. 相似文献
109.
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