Phase transition from α-helices to β-sheets in supercoils of fibrillar proteins

 pdf (3492K)  / List of references

The transition from α-helices to β-strands under external mechanical force in fibrin molecule containing coiled-coils is studied and free energy landscape is resolved. The detailed theoretical modeling of each stage of coiled-coils fragment pulling process was performed. The plots of force (F) as a function of molecule expansion (X) for two symmetrical fibrin coiled-coils (each ∼17 nm in length) show three distinct modes of mechanical behaviour: (1) linear (elastic) mode when coiled-coils behave like entropic springs (F<100−125 pN and X<7−8 nm), (2) viscous (plastic) mode when molecule resistance force does not increase with increase in elongation length (F≈150 pN and X≈10−35 nm) and (3) nonlinear mode (F>175−200 pN and X>40−50 nm). In linear mode the coiled-coils unwind at 2π radian angle, but no structural transition occurs. Viscous mode is characterized by the phase transition from the triple α-spirals to three-stranded parallel β-sheet. The critical tension of α-helices is 0.25 nm per turn, and the characteristic energy change is equal to 4.9 kcal/mol. Changes in internal energy Δu, entropy Δs and force capacity cf per one helical turn for phase transition were also computed. The observed dynamic behavior of α-helices and phase transition from α-helices to β-sheets under tension might represent a universal mechanism of regulation of fibrillar protein structures subject to mechanical stresses due to biological forces.

Keywords: phase transition from α-helices to β-sheets, thermodynamics of transition from α-helices to β-sheets, molecular modeling, fibrinogen, fibrin fibers, Molecular Dynamics, GPU
Citation in English: Zhmurov A.A., Alekseenko A.E., Barsegov V.A., Kononova O.G., Kholodov Y.A. Phase transition from α-helices to β-sheets in supercoils of fibrillar proteins // Computer Research and Modeling, 2013, vol. 5, no. 4, pp. 705-725
Citation in English: Zhmurov A.A., Alekseenko A.E., Barsegov V.A., Kononova O.G., Kholodov Y.A. Phase transition from α-helices to β-sheets in supercoils of fibrillar proteins // Computer Research and Modeling, 2013, vol. 5, no. 4, pp. 705-725
DOI: 10.20537/2076-7633-2013-5-4-705-725
Views (last year): 6. Citations: 1 (RSCI).

Indexed in Scopus

Full-text version of the journal is also available on the web site of the scientific electronic library eLIBRARY.RU

The journal is included in the Russian Science Citation Index

The journal is included in the RSCI

International Interdisciplinary Conference "Mathematics. Computing. Education"