Crowding-Induced Elongated Conformation of Urea-Unfolded Apoazurin: Investigating the Role of Crowder Shape in Silico
Journal article, 2019

American Chemical Society. Here, we show by solution nuclear magnetic resonance measurements that the urea-unfolded protein apoazurin becomes elongated when the synthetic crowding agent dextran 20 is present, in contrast to the prediction from the macromolecular crowding effect based on the argument of volume exclusion. To explore the complex interactions beyond volume exclusion, we employed coarse-grained molecular dynamics simulations to explore the conformational ensemble of apoazurin in a box of monodisperse crowders under strong chemically denaturing conditions. The elongated conformation of unfolded apoazurin appears to result from the interplay of the effective attraction between the protein and crowders and the shape of the crowders. With a volume-conserving crowder model, we show that the crowder shape provides an anisotropic direction of the depletion force, in which a bundle of surrounding rodlike crowders stabilize an elongated conformation of unfolded apoazurin in the presence of effective attraction between the protein and crowders.

Author

Fabio C. Zegarra

University of Houston

Dirar Homouz

University of Houston

Khalifa University of Science and Technology

Rice University

Andrei G. Gasic

University of Houston

Rice University

Lucas Babel

University of Houston

M. Kovermann

University of Konstanz

Pernilla Wittung Stafshede

Chalmers, Biology and Biological Engineering, Chemical Biology

Margaret S. Cheung

University of Houston

Rice University

Journal of Physical Chemistry B

1520-6106 (ISSN) 1520-5207 (eISSN)

Vol. 123 17 3607-3617

Subject Categories

Physical Chemistry

Biophysics

Structural Biology

DOI

10.1021/acs.jpcb.9b00782

More information

Latest update

5/24/2019