Issue 7, 2019

Evaluating rotation diffusion properties of molecules from short trajectories

Abstract

We show that under proper assumptions it is possible to estimate with good precision the principal values of the rotational diffusion tensor of proteins from the analysis of short (up to 2–3 ns) molecular dynamics trajectories. We apply this analysis to a few model cases: three polyalanine peptides (2, 5, and 10 aminoacids), the fragment B3 of protein G (GB3), the bovine pancreatic trypsin inhibitor (BPTI), the hen egg-white lysozyme (LYS), the B1 domain of plexin (PB1), and thrombin. The protocol is based on the analysis of the global angular momentum autocorrelation functions, complementing the standard approach based on rotational autocorrelation functions, which requires much longer trajectories. A comparison with values predicted by hydrodynamic modeling and available experimental data is presented.

Graphical abstract: Evaluating rotation diffusion properties of molecules from short trajectories

Supplementary files

Article information

Article type
Paper
Submitted
31 srp 2018
Accepted
06 stu 2018
First published
06 stu 2018

Phys. Chem. Chem. Phys., 2019,21, 3662-3668

Evaluating rotation diffusion properties of molecules from short trajectories

A. Polimeno and M. Zerbetto, Phys. Chem. Chem. Phys., 2019, 21, 3662 DOI: 10.1039/C8CP04879G

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