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1 Electronic Supplementary Material (ESI) for RSC Advances. This journal is The Royal Society of Chemistry 2015 Supplementary Information Dynamics of the thumb-finger regions in GH11 xylanase Bacillus circulans: comparison between the Michaelis and covalent intermediate Ndumiso N. Mhlongo a, Mahasin Ebrahim a, Adam A. Skelton a, Hendrik G. Kruger b, Ian H. Williams c and Mahmoud E. S. Soliman a* a Molecular Modeling and Drug Design Research Group, School of Health Sciences University of KwaZulu-Natal, Durban 4001, South Africa b Catalysis and Peptide Research Unit, School of Health Sciences University of KwaZulu-Natal, Durban 4001, South Africa c Department of Chemistry, University of Bath, Bath, United Kingdom * Corresponding author: Mahmoud E. S. Soliman, soliman@ukzn.ac.za Telephone: , Fax: Webpage:
2 S1: Comparative RMSD for alpha carbon atoms of the respective free enzyme, noncovalently complex and covalent complex: T1, T2, T3, T4 & T avg are represent four distinctive 50 ns MD trajectories and overall average, respectively.
3 S2: The extent of opening and closing of the enzyme. A thumb-finger distance as a function of time for the free enzyme (blue), non-covalently bound (red) and covalently bound (green) systems: T1, T2, T3, T4 & T avg are represent four distinctive 50 ns MD trajectories and overall average, respectively.
4 S3: The Asp11-Glu172 distance as a function of time for the free enzyme (blue), noncovalently bound (red) and covalently bound (green) systems: T1, T2, T3, T4 & T avg are represent four distinctive 50 ns MD trajectories and overall average, respectively.
5 S4: Asp11-Glu78 distance as a function of time for the free enzyme (blue), noncovalently bound (red) and covalently bound (green) systems: T1, T2, T3, T4 & T avg are represent four distinctive 50 ns MD trajectories and overall average, respectively.
6 S5: The extent of compression on the thumb region of the enzyme for the free enzyme (blue), non-covalently (red) and covalently bound (green) systems: T1, T2, T3, T4 & T avg are represent four distinctive 50 ns MD trajectories and overall average, respectively.
7 S6: The extent of compression of the thumb region of the enzyme. Pro116-Glu172 cross-distance as a function of time for the free enzyme (blue), non-covalently (red) and covalently bonded (green) systems: T1, T2, T3, T4 & T avg are represent four distinctive 50 ns MD trajectories and overall average, respectively.
8 S7: The extent of opening of the enzyme active site. Glu78-Glu172 distance as a function of time for the free enzyme (blue), non-covalently (red) and covalently bonded (green) systems: T1, T2, T3, T4 & T avg are represent four distinctive 50 ns MD trajectories and overall average, respectively.
9 S8: Comparative Pro116-Glu172-Asp11 angle measured for the respective free enzyme, non-covalent and covalent intermediate systems: T1, T2, T3, T4 & T avg are represent four distinctive 50 ns MD trajectories and overall average, respectively.
10 S9: Comparative Asp11-Glu78-Pro116 angle measured for the respective free enzyme, non-covalent and covalent intermediate systems: T1, T2, T3, T4 & T avg are represent four distinctive 50 ns MD trajectories and overall average, respectively.
11 Table S1: Average distance measured for the respective free enzyme, non-covalent intermediate and covalent intermediate complex. Table S2: Average angle measured for the respective free enzyme, non-covalent intermediate and covalent intermediate complex. Table S3: Average H-bond distances between the substrate and active site residues monitored during MD simulation of the non-covalent intermediate complex. Table S4: Average H-bond distances between the substrate and active site residues monitored during MD simulation of the covalent intermediate complex.
12 Table S5: Average radius of gyration (Rg) monitored during MD simulation of the free enzyme, non-covalent complex and covalent complex. Table S6: Prominent residues contribution towards motions across distinctive modes of the free enzyme, non-covalent complex and covalent complex systems.
13 S10: Interaction of a non-covalently bound (A) and a covalently bound (B) xylobiose sugar with B. circulans endo-β-1,4-xylanase.
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