Structural Stability Analysis of Proteins Using End-to-End Distance: A 3D-RISM Approach

Yutaka Maruyama and Ayori Mitsutake
Additional contact information
Yutaka Maruyama: Quemix Inc., 2-11-2 Nihombashi, Chuo-ku, Tokyo 103-0027, Japan
Ayori Mitsutake: Department of Physics, School of Science and Technology, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki-shi 214-8571, Japan

J, 2022, vol. 5, issue 1, 1-12

Abstract: The stability of a protein is determined from its properties and surrounding solvent. In our previous study, the total energy as a sum of the conformational and solvation free energies was demonstrated to be an appropriate energy function for evaluating the stability of a protein in a protein folding system. We plotted the various energies against the root mean square deviation, required as a reference structure. Herein, we replotted the various energies against the end-to-end distance between the N- and C-termini, which is not a required reference and is experimentally measurable. The solvation free energies for all proteins tend to be low as the end-to-end distance increases, whereas the conformational energies tend to be low as the end-to-end distance decreases. The end-to-end distance is one of interesting measures to study the behavior of proteins.

Keywords: molecular solvation theory; 3D-RISM; solvation-free energy; conformational energy; molecular dynamics; simulation; protein; structural stability; end-to-end distance (search for similar items in EconPapers)
JEL-codes: I1 I10 I12 I13 I14 I18 I19 (search for similar items in EconPapers)
Date: 2022
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.mdpi.com/2571-8800/5/1/9/pdf (application/pdf)
https://www.mdpi.com/2571-8800/5/1/9/ (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:gam:jjopen:v:5:y:2022:i:1:p:9-125:d:749109

Access Statistics for this article

J is currently edited by Ms. Angelia Su

More articles in J from MDPI
Bibliographic data for series maintained by MDPI Indexing Manager ().