Structure prediction and network analysis of chitinases from the Cape sundew, Drosera capensis

Unhelkar, Megha H.; Duong, Vy; Enendu, Kaosoluchi; Kelly, John; Tahir, S. Hasan; Butts, Carter T.; Martin, Rachel W.

doi:10.1016/j.bbagen.2016.12.007

Cited by 16 publications

(23 citation statements)

References 60 publications

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“… * Present. References: [1] Fukushima et al, 2017 ; [2] Schulze et al, 2012 ; [3] Pavlovic, Jaksova & Novak, 2017 ; [4] Pavlovic et al, 2013 ; [5] Butts, Bierma & Martin, 2016 ; [6] Unhelkar et al, 2017 ; [7] Matušíková et al, 2005 ; [8] Michalko et al, 2013 ; [9] Jopcik et al, 2017 ; [10] Morohoshi et al, 2011 ; [11] Amagase, 1972 ; [12] Sirova, Adamec & Vrba, 2003 ; [13] Płachno et al, 2006 ; [14] Luciano & Newell, 2017 ; [15] Porembski & Barthlott, 2006 ; [16] Adlassnig, Peroutka & Lendl, 2010 ; [17] Jaffe et al, 1992 ; [18] Mithöfer, 2011 ; [19] Srivastava et al, 2011 ; [20] Hatano & Hamada, 2008 ; [21] Rottloff et al, 2016 ; [22] Takeuchi et al, 2011 ; [23] Lee et al, 2016 ; [24] Schrader et al, 2017 ; [25] Kadek et al, 2014a ; Kadek et al, 2014b ; [26] Higashi et al, 1993 ; [27] Buch et al, 2015 ; [28] Stephenson & Hogan, 2006 ; [29] Athauda et al, 2004 ; [30] Yilamujiang et al, 2017 ; [31] Eilenberg et al, 2006 ; [32] Renner & Specht, 2013 ; [33] Tokes, Woon & Chambers, 1974 ; [34] Thornhill, Harper & Hallam, 2008 . …”

Section: Digestive Enzyme Discovery Identification and Characterisatmentioning

confidence: 99%

“…There are only a few reports on the structural characterisation of the digestive enzymes secreted by carnivorous plants. To date, proteases and chitinases are the most characterised in structural and enzymatic properties ( Ishisaki et al, 2012a ; Fukushima et al, 2017 ; Jopcik et al, 2017 ; Unhelkar et al, 2017 ). Athauda et al (2004) was the first to report a complete model of purified Nepenthesin from N. distillatoria .…”

Section: Digestive Enzyme Discovery Identification and Characterisatmentioning

confidence: 99%

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Discovery of digestive enzymes in carnivorous plants with focus on proteases

Ravee

Salleh

Goh

2018

PeerJ

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BackgroundCarnivorous plants have been fascinating researchers with their unique characters and bioinspired applications. These include medicinal trait of some carnivorous plants with potentials for pharmaceutical industry.MethodsThis review will cover recent progress based on current studies on digestive enzymes secreted by different genera of carnivorous plants: Drosera (sundews), Dionaea (Venus flytrap), Nepenthes (tropical pitcher plants), Sarracenia (North American pitcher plants), Cephalotus (Australian pitcher plants), Genlisea (corkscrew plants), and Utricularia (bladderworts).ResultsSince the discovery of secreted protease nepenthesin in Nepenthes pitcher, digestive enzymes from carnivorous plants have been the focus of many studies. Recent genomics approaches have accelerated digestive enzyme discovery. Furthermore, the advancement in recombinant technology and protein purification helped in the identification and characterisation of enzymes in carnivorous plants.DiscussionThese different aspects will be described and discussed in this review with focus on the role of secreted plant proteases and their potential industrial applications.

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Section: Digestive Enzyme Discovery Identification and Characterisatmentioning

confidence: 99%

Section: Digestive Enzyme Discovery Identification and Characterisatmentioning

confidence: 99%

Discovery of digestive enzymes in carnivorous plants with focus on proteases

Ravee

Salleh

Goh

2018

PeerJ

View full text Add to dashboard Cite

show abstract

“…Physically, these, respectively, indicate the total number of contacts associated with the chemical group (potentially impeding its motion), the number of truss-like, triangular structures in which the group is embedded (again, restricting mobility), and the extent of local cohesion around the chemical group, which is found to distinguish “tighter” and “looser” packing regimes. 55 To summarize the impact of each measure over the active site as a whole, values were averaged across active site vertices. As an additional constraint measure, the number of paths between each pair of active site vertices through neighboring (i.e., nonactive site) vertices was computed, and the log of the minimum of this value over the set of active site vertex pairs was employed as a measure of site cohesion.…”

Section: Methodsmentioning

confidence: 99%

Sequence Characterization and Molecular Modeling of Clinically Relevant Variants of the SARS-CoV-2 Main Protease

et al. 2020

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The SARS-CoV-2 main protease (M pro ) is essential to viral replication and cleaves highly specific substrate sequences, making it an obvious target for inhibitor design. However, as for any virus, SARS-CoV-2 is subject to constant neutral drift and selection pressure, with new M pro mutations arising over time. Identification and structural characterization of M pro variants is thus critical for robust inhibitor design. Here we report sequence analysis, structure predictions, and molecular modeling for seventy-nine M pro variants, constituting all clinically observed mutations in this protein as of April 29, 2020. Residue substitution is widely distributed, with some tendency toward larger and more hydrophobic residues. Modeling and protein structure network analysis suggest differences in cohesion and active site flexibility, revealing patterns in viral evolution that have relevance for drug discovery.

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“…There are only a few reports on the structural characterisation of the digestive enzymes secreted by carnivorous plants. To date, proteases and chitinases are the most characterised in structural and enzymatic properties (Ishisaki et al, 2012a;Fukushima et al, 2017;Jopcik et al, 2017;Unhelkar et al, 2017). Athauda et al (2004) was the first to report a complete model of purified Nepenthesin from N. distillatoria.…”

Section: Digestive Enzyme Discovery Identification and Characterisationmentioning

confidence: 99%

Discovery of digestive enzymes in carnivorous plants with focus on proteases

Ravee

Salleh

Goh

2018

Preprint

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Background. Carnivorous plants have been fascinating researchers with their unique characters and bioinspired applications. These include medicinal trait of some carnivorous plants with potentials for pharmaceutical industry. Methods. This review will cover recent progress based on current studies on digestive enzymes secreted by different genera of carnivorous plants: Drosera (sundews), Dionaea (Venus flytrap), Nepenthes (tropical pitcher plants), Sarracenia (North American pitcher plants), Cephalotus (Australian pitcher plants), Genlisea (corkscrew plants), and Utricularia (bladderworts). Results. Since the discovery of secreted protease nepenthesin in Nepenthes pitcher, digestive enzymes from carnivorous plants have been the focus of many studies. Recent genomics approaches have accelerated digestive enzyme discovery. Furthermore, the advancement in recombinant technology and protein purification helped in the identification and characterisation of enzymes in carnivorous plants. Discussion. These different aspects will be described and discussed in this review with focus on the role of secreted plant proteases and their potential industrial applications.

show abstract

Structure prediction and network analysis of chitinases from the Cape sundew, Drosera capensis

Cited by 16 publications

References 60 publications

Discovery of digestive enzymes in carnivorous plants with focus on proteases

Discovery of digestive enzymes in carnivorous plants with focus on proteases

Sequence Characterization and Molecular Modeling of Clinically Relevant Variants of the SARS-CoV-2 Main Protease

Discovery of digestive enzymes in carnivorous plants with focus on proteases

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