Exploring Solanum tuberosum Epoxide Hydrolase Internal Architecture by Water Molecules Tracking
Abstract
1. Introduction
2. Materials and Methods
2.1. Protein Preparation
2.2. Molecular Dynamics Simulations
2.3. Tunnel Identification
2.4. Water Tracking, Hot-Spot and Pocket Detection
2.5. Evolutionary Analysis
3. Results
3.1. Water Trajectories—Tunnels and Incidental Pathways
3.2. Cavities and Pockets
3.3. Trapped Water Molecules—Hot-Spot Identification
3.4. Evolutionary Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Cavity I | Cavity II | Cavity III | |
---|---|---|---|
MD1 | I180, T182, Y183, R184, F189, D265*, L266, A299, H300*, F301 | H31, G32, F33, E35 *, S39, W40, H104 *, D105 *, G107, H300 *, F301 | F33, P34, F158, F168, V176, L177, I180, F191, F223, G227, F228, T229, G230, A231, V232 |
MD2 | I180, T182, Y183, R184, F189, W210, L266, A299, H300*, F301, E305 | G32, F33, P34, E35*, H104*, D105*, H300*, F301 | F33, Y154*, F158, F168, I180, F189, F191, I200 |
MD3 | I180, L181, T182, Y183, R184, D185, P186, A187, F189, L207, W210, F264, D265*, L266, A299, H300*, F301, E305 | - | F33, P34, Y154*, F158, F168, V176, K179, I180, F189, L197, I200, F228 |
MD4 | I180, T182, Y183, R184, D185, F189, A203, L207, S208, W210, F264, D265*, L266, A299, H300*, F301, E305 | H31, G32, F33, E35*, S39, W40, H104*, D105*, L128, H300 *, F301, V302, S303 | F33, P34, Y154*, F158, F168, V176, L177, K179, I180, F189, F191, L197, I200, F228 |
MD5 | K179, I180, L181, T182, Y183, R184, D185, P186, A187, A203, P204, L207, S208, W210, F264, D265 *, L266, A298, A299, H300 *, F301, V302, Q304, E305 | G32, F33, P34, E35*, H104*, D105*, H300*, F301, | F33, Y154*, F158, F168, V176, K179, I180, F189, F191, L197, I200, F228, V232 |
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Mitusińska, K.; Magdziarz, T.; Bzówka, M.; Stańczak, A.; Góra, A. Exploring Solanum tuberosum Epoxide Hydrolase Internal Architecture by Water Molecules Tracking. Biomolecules 2018, 8, 143. https://doi.org/10.3390/biom8040143
Mitusińska K, Magdziarz T, Bzówka M, Stańczak A, Góra A. Exploring Solanum tuberosum Epoxide Hydrolase Internal Architecture by Water Molecules Tracking. Biomolecules. 2018; 8(4):143. https://doi.org/10.3390/biom8040143
Chicago/Turabian StyleMitusińska, Karolina, Tomasz Magdziarz, Maria Bzówka, Agnieszka Stańczak, and Artur Góra. 2018. "Exploring Solanum tuberosum Epoxide Hydrolase Internal Architecture by Water Molecules Tracking" Biomolecules 8, no. 4: 143. https://doi.org/10.3390/biom8040143
APA StyleMitusińska, K., Magdziarz, T., Bzówka, M., Stańczak, A., & Góra, A. (2018). Exploring Solanum tuberosum Epoxide Hydrolase Internal Architecture by Water Molecules Tracking. Biomolecules, 8(4), 143. https://doi.org/10.3390/biom8040143