Activation and friction in enzymatic loop opening and closing dynamics

Kirill Zinovjev, Paul Guénon, Carlos A. Ramos-Guzmán, J. Javier Ruiz-Pernía, Damien Laage and Iñaki Tuñón ()
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Kirill Zinovjev: Universidad de Valencia
Paul Guénon: Universidad de Valencia
Carlos A. Ramos-Guzmán: Universidad de Valencia
J. Javier Ruiz-Pernía: Universidad de Valencia
Damien Laage: CNRS
Iñaki Tuñón: Universidad de Valencia

Nature Communications, 2024, vol. 15, issue 1, 1-12

Abstract: Abstract Protein loop dynamics have recently been recognized as central to enzymatic activity, specificity and stability. However, the factors controlling loop opening and closing kinetics have remained elusive. Here, we combine molecular dynamics simulations with string-method determination of complex reaction coordinates to elucidate the molecular mechanism and rate-limiting step for WPD-loop dynamics in the PTP1B enzyme. While protein conformational dynamics is often represented as diffusive motion hindered by solvent viscosity and internal friction, we demonstrate that loop opening and closing is activated. It is governed by torsional rearrangement around a single loop peptide group and by significant friction caused by backbone adjustments, which can dynamically trap the loop. Considering both torsional barrier and time-dependent friction, our calculated rate constants exhibit very good agreement with experimental measurements, reproducing the change in loop opening kinetics between proteins. Furthermore, we demonstrate the applicability of our results to other enzymatic loops, including the M20 DHFR loop, thereby offering prospects for loop engineering potentially leading to enhanced designs.

Date: 2024
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DOI: 10.1038/s41467-024-46723-9

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