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Intermediate Scattering Functions of a Rigid Body Monoclonal Antibody Protein in Solution Studied by Dissipative Particle Dynamic Simulation

Published

Author(s)

Nicos Martys, William L. George, Joseph E. Curtis, Jannatun Nayem, Y. Z, Yun Liu

Abstract

In the past decade, there is increased research interest in studying internal motions of flexible proteins in solution using Neutron Spin Echo (NSE) as NSE can simultaneously probe the dynamics at the length and time scale comparable to protein domain motions. However, the collective intermediate scattering function (ISF) measured by NSE has the contribution from translational, rotational, and internal motions, which are rather complicated to be separated. Widely used NSE theories to interpret experimental data usually assume that the translational and rotational motions of a rigid particle is decoupled and independent to each other. To evaluate the accuracy of this approximation for monoclonal antibody (mAb) proteins in solution, dissipative particle dynamic computer simulation is used here to simulate a rigidbody mAb for up to about 200 nanoseconds. The total ISF together with the ISFs due to only the translational and rotational motions is calculated as well as their corresponding effective diffusion coefficients. The aforementioned approximation introduces appreciable errors to the calculated effective diffusion coefficients and the ISFs. For the effective diffusion coefficient, the error introduced by this approximation can be as large as about 10% even though the overall agreement is considered reasonable for many cases. Thus, it needs to be cautions when interpreting the data with a small signal change. In addition, the accuracy of the calculated ISFs due to the finite computer simulation time is also discussed.
Citation
Structural Dynamics
Volume
8
Issue
2

Keywords

neutron spin echo, protein, dynamics, diffusion, rigid body

Citation

Martys, N. , George, W. , Curtis, J. , Nayem, J. , Z, Y. and Liu, Y. (2021), Intermediate Scattering Functions of a Rigid Body Monoclonal Antibody Protein in Solution Studied by Dissipative Particle Dynamic Simulation, Structural Dynamics (Accessed December 9, 2021)
Created April 7, 2021, Updated September 9, 2021