Observing reorientation dynamics with Time-Resolved fluorescence and molecular dynamics in varying periodic boundary conditions

Abstract

This work presents a combined study of time-resolved fluorescence spectroscopy and all-atom molecular dynamics simulation to investigate periodic boundary conditions’ and water models’ influence on the orientation dynamics and translational and rotational diffusion of peptides in solution. We have characterized the effects of solvent box size and water model choice on the dynamics of two peptide systems, NATA and WK5. Computationally, translational, and rotational diffusion and internal fluctuations are investigated through all-atom molecular dynamics simulation with two water models and different box sizes. These results are compared with time-resolved fluorescence anisotropy decay (FAD) measurements. The associated time constant and orientation dynamics from FAD measurement along the ¹L_b axis provided baseline data to validate molecular dynamics simulation. The modeling results show that diffusion rates vary roughly in inverse proportion to water model viscosity, as one would expect. Corrections for finite box size are significant for translational diffusion and insignificant for rotational diffusion. This study also finds that internal dynamics described by autocorrelation functions and kinetic network models are relatively insensitive to both box size and water model properties. Our observation suggests that different peptide properties respond differently to a change in simulation conditions.

Communicated by Ramaswamy H. Sarma

Keywords:

• Time-resolved fluorescence
• molecular dynamics simulations
• periodic boundary conditions
• kinetics
• optimum dimensionality reduction

Acknowledgements

We want to acknowledge XSEDE grant TG-MCB 16009 for computer time. Parts of the simulations described were conducted at the Center for Research Computing at the University of Kansas and on computer workstations supported by the General Research Fund at the University of Kansas. We would like to thank Prof. Carey K. Johnson for allowing access to the fluorescence apparatus. GSJ would like to thank Wade Burleson and Kyle Williams for the inspirational conversation. This project was supported in part by an NSF grant, CHE1807852.

Disclosure statement

No potential conflict of interest was reported by the author(s).