A structure-based model fails to probe the mechanical unfolding pathways of the titin I27 domain
PBN-AR
Instytucja
Instytut Fizyki Polskiej Akademii Nauk
Informacje podstawowe
Główny język publikacji
en
Czasopismo
JOURNAL OF CHEMICAL PHYSICS
ISSN
0021-9606
EISSN
1089-7690
Wydawca
AMER INST PHYSICS
DOI
URL
Rok publikacji
2013
Numer zeszytu
Strony od-do
1-10
Numer tomu
139
Identyfikator DOI
Liczba arkuszy
Autorzy
Słowa kluczowe
en
biochemistry biomechanics free energy mechanical stability molecular biophysics molecular configurations
Streszczenia
Język
en
Treść
We discuss the use of a structure based Cα-Go model and Langevin dynamics to study in detail the mechanical properties and unfolding pathway of the titin I27 domain. We show that a simple Go-model does detect correctly the origin of the mechanical stability of this domain. The unfolding free energy landscape parameters xu and ΔG‡, extracted from dependencies of unfolding forces on pulling speeds, are found to agree reasonably well with experiments. We predict that above v = 104 nm/s the additional force-induced intermediate state is populated at an end-to-end extension of about 75 Å. The force-induced switch in the unfolding pathway occurs at the critical pulling speed vcrit ≈ 106–107 nm/s. We argue that this critical pulling speed is an upper limit of the interval where Bell's theory works. However, our results suggest that the Go-model fails to reproduce the experimentally observed mechanical unfolding pathway properly, yielding an incomplete picture of the free energy landscape. Surprisingly, the experimentally observed intermediate state with the A strand detached is not populated in Go-model simulations over a wide range of pulling speeds. The discrepancy between simulation and experiment is clearly seen from the early stage of the unfolding process which shows the limitation of the Go model in reproducing unfolding pathways and deciphering the complete picture of the free energy landscape.
Cechy publikacji
Oryginalny artykuł naukowy
Oryginalny artykuł naukowy przedstawia rezultaty oryginalnych badań naukowych lub eksperymentu.
Original article
Original article presents the results of original research or experiment.
Inne
System-identifier
PBN-R:492673
CrossrefMetadata from Crossref logo
Cytowania
Liczba prac cytujących tę pracę
Brak danych
Referencje
Liczba prac cytowanych przez tę pracę
Brak danych