Vol. 32 No. 3 (2022)
Papers

Effects of macromolecular crowding on folding of small globular proteins

Nhung T. T. Nguyen
\(^1\)Institute of Physics, Vietnam Academy of Science and Technology, 10 Dao Tan, Ba Dinh, Hanoi 11108, Vietnam
\(^2\)Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 11307, Vietnam
Phuong Thuy Bui
\(^1\)Institute of Theoretical and Applied Research, Duy Tan University, Hanoi, 100000, Vietnam
\(^2\)Faculty of Pharmacy, Duy Tan University, Da Nang, 550000, Vietnam
Trinh Xuan Hoang
\(^1\)Institute of Physics, Vietnam Academy of Science and Technology, 10 Dao Tan, Ba Dinh, Hanoi 11108, Vietnam
\(^2\)Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 11307, Vietnam

Published 29-04-2022

Keywords

  • MD simulation,
  • folding stability,
  • scaled particle theory

How to Cite

Nguyen, N. T. T., Bui, P. T., & Hoang, T. X. (2022). Effects of macromolecular crowding on folding of small globular proteins. Communications in Physics, 32(3), 233. https://doi.org/10.15625/0868-3166/16830

Abstract

The effects of inert spherical crowders on the melting temperature and the folding stability of small globular proteins are investigated by using molecular dynamics simulations with a Gō-like model for the proteins. The energy parameter in the Gō-like model is obtained individually for each protein by matching the model’s melting temperature to the experimental melting
temperature in the absence of crowders. It is shown that both the melting temperature and the folding stability of protein increase in the presence of the crowders. Specifically, as the crowders’ volume fraction φc increases from 0 to 0.4 the melting temperature increases by more than 20 Kelvins, whereas the folding stability is enhanced by up to ∼3.6 kcal/mol depending on the protein and the temperature. At room temperature (300 K), the stability enhancement is 1.2–1.4 kcal/mol, which is close to prior experimental data. It is also shown that the dependence of the folding free energy change on φc can be fitted well to the scaled particle theory by assuming a linear dependence of the effective size of the unfolded state on φc .

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