Simple Selection Procedure to Distinguish between Static and Flexible Loops
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Tunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego 8, 44-100 Gliwice, Poland
2
Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego 8, 44-100 Gliwice, Poland
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2020, 21(7), 2293; https://doi.org/10.3390/ijms21072293
Received: 10 March 2020
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Revised: 22 March 2020
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Accepted: 24 March 2020
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Published: 26 March 2020
(This article belongs to the Section Macromolecules)
Loops are the most variable and unorganized elements of the secondary structure of proteins. Their ability to shift their shape can play a role in the binding of small ligands, enzymatic catalysis, or protein–protein interactions. Due to the loop flexibility, the positions of their residues in solved structures show the largest B-factors, or in a worst-case scenario can be unknown. Based on the loops’ movements’ timeline, they can be divided into slow (static) and fast (flexible). Although most of the loops that are missing in experimental structures belong to the flexible loops group, the computational tools for loop reconstruction use a set of static loop conformations to predict the missing part of the structure and evaluate the model. We believe that these two loop types can adopt different conformations and that using scoring functions appropriate for static loops is not sufficient for flexible loops. We showed that common model evaluation methods, are insufficient in the case of flexible solvent-exposed loops. Instead, we recommend using the potential energy to evaluate such loop models. We provide a novel model selection method based on a set of geometrical parameters to distinguish between flexible and static loops without the use of molecular dynamics simulations. We have also pointed out the importance of water network and interactions with the solvent for the flexible loop modeling.
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MDPI and ACS Style
Mitusińska, K.; Skalski, T.; Góra, A. Simple Selection Procedure to Distinguish between Static and Flexible Loops. Int. J. Mol. Sci. 2020, 21, 2293. https://doi.org/10.3390/ijms21072293
AMA Style
Mitusińska K, Skalski T, Góra A. Simple Selection Procedure to Distinguish between Static and Flexible Loops. International Journal of Molecular Sciences. 2020; 21(7):2293. https://doi.org/10.3390/ijms21072293
Chicago/Turabian StyleMitusińska, Karolina, Tomasz Skalski, and Artur Góra. 2020. "Simple Selection Procedure to Distinguish between Static and Flexible Loops" International Journal of Molecular Sciences 21, no. 7: 2293. https://doi.org/10.3390/ijms21072293
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