Decoding Collagen Triple Helix Stability by Means of Hybrid DFT Simulations

The Journal of Physical Chemistry. B
Michele CutiniPiero Ugliengo

Abstract

Collagen is a protein family defined by a triple helix motif, which comprises roughly one-third of the total human protein content. Decoding the reasons underlying the stability of the collagen triple helix is of both fundamental and applicative relevance, for instance, to guide collagen protein engineering. In principle, full quantum mechanical approaches based on density functional theory (DFT) are ideal to study the subtle physicochemical features of collagen. Unfortunately, the huge size of the protein prevents the straightforward application of DFT to realistic collagen protein models. In this paper, we propose a new realistic model of the collagen protein based on a periodic approach. The protein model exploits the intrinsic symmetry of the collagen triple helix, dramatically lowering the cost of the simulations. This allows using accurate hybrid DFT simulations (B3LYP-D/TZP) for systematic studies of the collagen protein features. We have tested the proposed model/level-of-theory combination to analyze the well-known proline-conformation/collagen-stability relationship. For this purpose, we have performed an extensive conformational analysis of the proline ring within the protein, clarifying some of the reasons linking s...Continue Reading

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Citations

Jun 11, 2020·Journal of Materials Chemistry. B, Materials for Biology and Medicine·Chenxi ZhaiJingjie Yeo
Mar 24, 2021·Journal of Chemical Theory and Computation·Michele CutiniPiero Ugliengo
Nov 19, 2019·The Journal of Physical Chemistry Letters·Michele CutiniPiero Ugliengo
Aug 23, 2021·The Journal of Chemical Physics·Michele Cutini, Piero Ugliengo

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