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Journal Articles Proteins - Structure, Function and Bioinformatics Year : 2022

Tripeptide loop closure: a detailed study of reconstructions based on Ramachandran distributions

Abstract

Tripeptide loop closure (TLC) is a standard procedure to reconstruct protein backbone conformations, by solving a zero dimensional polynomial system yielding up to 16 solutions. In this work, we first show that multiprecision is required in a TLC solver to guarantee the existence and the accuracy of solutions. We then compare solutions yielded by the TLC solver against tripeptides from the Protein Data Bank. We show that these solutions are geometrically diverse (up to 3Å RMSD with respect to the data), and sound in terms of potential energy. Finally, we compare Ramachandran distributions of data and reconstructions for the three amino acids. The distribution of reconstructions in the second angular space (φ2, ψ2) stands out, with a rather uniform distribution leaving a central void. We anticipate that these insights, coupled to our robust implementation in the Structural Bioinformatics Library (https://sbl.inria.fr/doc/Tripeptide_loop_closure-user-manual.html), will boost the interest of TLC for structural modeling in general, and the generation of conformations of flexible loops in particular.
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Dates and versions

hal-03232851 , version 1 (22-05-2021)

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Timothee O'Donnell, Charles H Robert, Frédéric Cazals. Tripeptide loop closure: a detailed study of reconstructions based on Ramachandran distributions. Proteins - Structure, Function and Bioinformatics, 2022, 90 (3), pp.858-868. ⟨10.1002/prot.26281⟩. ⟨hal-03232851⟩
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