2017
DOI: 10.1016/j.bbagen.2016.12.007
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Structure prediction and network analysis of chitinases from the Cape sundew, Drosera capensis

Abstract: This work demonstrates how computational techniques can facilitate quickly moving from raw sequence data to refined structural models and comparative analysis, and to select promising candidates for subsequent biochemical characterization. This capability is increasingly important given the large and growing body of data from high-throughput genome sequencing, which makes experimental characterization of every target impractical.

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Cited by 16 publications
(23 citation statements)
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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%
See 1 more Smart Citation
“… * 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%
“…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%
“…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%