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Published on: January 16, 2016
Exploring unfolding pathway of CGTase: insight from molecular dynamics simulation
Yi Fu1, Yanrui Ding, Zhiguo Chen
1School of Information Technology, Jiangnam University, Wuxi 214122, China.
Protein thermostability, crucial for enzymes like Cyclodextrin glycosyltransferase (CGTase), is achieved through structural modifications. Molecular dynamics simulations reveal uneven stability distribution and key unfolding mechanisms in CGTase.
Area of Science:
- Biochemistry and Molecular Biology
- Protein Science
- Computational Biology
Background:
- Protein thermostability is vital for enzymes, particularly those from thermophilic organisms.
- Understanding protein stability mechanisms aids in protein engineering and biotechnology.
- Cyclodextrin glycosyltransferase (CGTase) is an industrially relevant enzyme with potential for enhanced stability.
Purpose of the Study:
- To investigate the thermal unfolding mechanisms of CGTase from Bacillus macerans.
- To elucidate the structure-stability relationship of CGTase using molecular dynamics simulations.
- To analyze the role of non-bonded interactions in protein stabilization.
Main Methods:
- Performed 1.5 ns molecular dynamics simulations of CGTase at five different temperatures.
- Analyzed thermal unfolding pathways, focusing on domain and secondary structure dynamics.
- Investigated the contribution of hydrogen bonds and salt bridges to protein stability.
Main Results:
- CGTase unfolding initiated simultaneously in the N-terminal and domain D; outer domains unfolded faster than the catalytic core.
- The catalytic center, protected by the (a/b)8 TIM-barrel, remained stable up to 600 K.
- Beta-sheet unfolding followed a random ordered mechanism, with specific sheets unfolding more rapidly; stability was not uniform across the structure.
Conclusions:
- CGTase stability is heterogeneously distributed, with the catalytic core being highly protected.
- Non-bonded interactions significantly influence protein stability and secondary structure.
- The findings provide insights into protein structure-stability relationships and folding mechanisms.
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