A linker of the proline-threonine repeating motif sequence is bimodal

Abstract

The linker of the endoglucanase from Xanthomonas campestris pv. campestris ((PT)12) has a specific sequence, a repeating proline-threonine motif. In order to understand its role, it has been compared to a regular sequence linker, in this work—the cellobiohydrolase 2 from Trichoderma reesei (CBH2). Elastic properties of the two linkers have been estimated by calculating free energy profile along the linker length from an enhanced sampling molecular dynamics simulation. The (PT)12 exhibits more pronounced elastic behaviour than CBH2. The PT repeating motif results in a two-mode energy profile which could be very useful in the enzyme motions along the substrate during hydrolytic catalysis.

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Funding

This study was financially supported by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) via grants 08/56255-9, 09/54035-4 and 10/08680-2; Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) via grants 490022/2009-0 and 550985/2010-7.

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Correspondence to Ivana M. Stanković.

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Skaf, M.S., Polikarpov, I. & Stanković, I.M. A linker of the proline-threonine repeating motif sequence is bimodal. J Mol Model 26, 178 (2020). https://doi.org/10.1007/s00894-020-04434-0

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Keywords

  • Replica exchange molecular dynamics
  • Linker
  • Endoglucanase
  • Elasticity