Comparative mechanical unfolding studies of spectrin domains R15, R16 and R17

Anna V Glyakina; Ilya V Likhachev; Nikolay K Balabaev; Oxana V Galzitskaya

doi:10.1016/j.jsb.2017.12.003

Comparative mechanical unfolding studies of spectrin domains R15, R16 and R17

J Struct Biol. 2018 Feb;201(2):162-170. doi: 10.1016/j.jsb.2017.12.003. Epub 2017 Dec 5.

Authors

Anna V Glyakina¹, Ilya V Likhachev², Nikolay K Balabaev³, Oxana V Galzitskaya⁴

Affiliations

¹ Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia; Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.
² Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia; Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; Tula State University, Tula 300012, Russia.
³ Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.
⁴ Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia. Electronic address: ogalzit@vega.protres.ru.

PMID: 29221897
DOI: 10.1016/j.jsb.2017.12.003

Abstract

Spectrins belong to repetitive three-helix bundle proteins that have vital functions in multicellular organisms and are of potential value in nanotechnology. To reveal the unique physical features of repeat proteins we have studied the structural and mechanical properties of three repeats of chicken brain α-spectrin (R15, R16 and R17) at the atomic level under stretching at constant velocities (0.01, 0.05 and 0.1 Å·ps^-1) and constant forces (700 and 900 pN) using molecular dynamics (MD) simulations at T = 300 K. 114 independent MD simulations were performed and their analysis has been done. Despite structural similarity of these domains we have found that R15 is less mechanically stable than R16, which is less stable than R17. This result is in agreement with the thermal unfolding rates. Moreover, we have observed the relationship between mechanical stability, flexibility of the domains and the number of aromatic residues involved in aromatic clusters.

Keywords: Aromatic cluster; Disordered regions; Mechanical unfolding; Molecular dynamics; Spectrin repeats; Stability.

Publication types

Comparative Study
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Chickens
Molecular Dynamics Simulation
Protein Domains
Protein Folding
Protein Stability
Protein Unfolding
Repetitive Sequences, Amino Acid
Spectrin / chemistry*
Spectrin / metabolism

Substances

Spectrin