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Understanding the impacts of self-shuffling approach on structure and function of shuffled endoglucanase enzyme via MD simulations

Understanding the impacts of self-shuffling approach on structure and function of shuffled... AbstractObjectiveWe identify the impacts of structural differences on functionality of EG3_S2 endoglucanase enzyme with MD studies. The results of previous experimental studies have been explained in details with computational approach. The objective of this study is to explain the functional differences between shuffled enzyme (EG3_S2) and its native counterpart (EG3_nat) from Trichoderma reseei, via Molecular Dynamics approach.Materials and methodsFor this purpose, we performed MD simulations along 30 ns at three different reaction temperatures collected as NpT ensemble, and then monitored the backbone motion, flexibilities of residues, and intramolecular interactions of EG3_S2 and EG3_nat enzymes.ResultsAccording to MD results, we conclude that EG3_S2 and EG3_nat enzymes have unique RMSD patterns, e.g. RMSD pattern of EG3_S2 is more dynamic than that of EG3_nat at all temperatures. In addition to this dynamicity, EG3_S2 establishes more salt bridge interactions than EG3_nat.ConclusionBy taking these results into an account with the preservation of catalytic Glu residues in a proper manner, we explain the structural basis of differences between shuffled and native enzyme via molecular dynamic studies. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Turkish Journal of Biochemistry de Gruyter

Understanding the impacts of self-shuffling approach on structure and function of shuffled endoglucanase enzyme via MD simulations

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References (49)

Publisher
de Gruyter
Copyright
©2020 Walter de Gruyter GmbH, Berlin/Boston
ISSN
0250-4685
eISSN
1303-829X
DOI
10.1515/tjb-2018-0180
Publisher site
See Article on Publisher Site

Abstract

AbstractObjectiveWe identify the impacts of structural differences on functionality of EG3_S2 endoglucanase enzyme with MD studies. The results of previous experimental studies have been explained in details with computational approach. The objective of this study is to explain the functional differences between shuffled enzyme (EG3_S2) and its native counterpart (EG3_nat) from Trichoderma reseei, via Molecular Dynamics approach.Materials and methodsFor this purpose, we performed MD simulations along 30 ns at three different reaction temperatures collected as NpT ensemble, and then monitored the backbone motion, flexibilities of residues, and intramolecular interactions of EG3_S2 and EG3_nat enzymes.ResultsAccording to MD results, we conclude that EG3_S2 and EG3_nat enzymes have unique RMSD patterns, e.g. RMSD pattern of EG3_S2 is more dynamic than that of EG3_nat at all temperatures. In addition to this dynamicity, EG3_S2 establishes more salt bridge interactions than EG3_nat.ConclusionBy taking these results into an account with the preservation of catalytic Glu residues in a proper manner, we explain the structural basis of differences between shuffled and native enzyme via molecular dynamic studies.

Journal

Turkish Journal of Biochemistryde Gruyter

Published: Apr 1, 2020

Keywords: Molecular Dynamics (MD) simulations; Endoglucanase; Trichoderma reesei; DNA shuffling; EG3 (Cel12A); Moleküler Dinamik simülasyonları; Endoglukanaz; Trichoderma reesei; DNA karma metodu; EG3 (Cel12A)

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