We present a computational study on the driven transport of the Maltose Binding Protein (MBP) across nanochannels in the framework of coarse-grained modeling. The work is motivated by recent experiments on voltage-driven transport of MBP across nanopores exploring the influence of denaturation on translocation pathways. Our simplified approach allows a statistical mechanical interpretation of the process which may be convenient also to the experiments. Specifically, we identify and characterize short and long channel blockades, associated to the translocation of denaturated and folded MBP conformations, respectively. We show that long blockades are related to long stall events where MBP undergoes specific and reproducible structural rearrangements. To clarify the origin of the stalls, the stick-and-slip translocation is compared to mechanical unfolding pathways obtained via steered molecular dynamics. This comparison clearly shows the translocation pathway to significantly differ from free-space unfolding dynamics and strongly suggests that stalling events are preferentially determined by the MBP regions with higher density of long-range native interactions. This result might constitute a possible criterion to predict a priori some statistical features of protein translocation from the structural analysis.

Bacci, M., Chinappi, M., Casciola, C.m., Cecconi, F. (2012). Role of denaturation in Maltose Binding Protein translocation dynamics. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, 116(14), 4255-4262 [10.1021/jp300143x].

Role of denaturation in Maltose Binding Protein translocation dynamics

Chinappi M.;
2012-01-01

Abstract

We present a computational study on the driven transport of the Maltose Binding Protein (MBP) across nanochannels in the framework of coarse-grained modeling. The work is motivated by recent experiments on voltage-driven transport of MBP across nanopores exploring the influence of denaturation on translocation pathways. Our simplified approach allows a statistical mechanical interpretation of the process which may be convenient also to the experiments. Specifically, we identify and characterize short and long channel blockades, associated to the translocation of denaturated and folded MBP conformations, respectively. We show that long blockades are related to long stall events where MBP undergoes specific and reproducible structural rearrangements. To clarify the origin of the stalls, the stick-and-slip translocation is compared to mechanical unfolding pathways obtained via steered molecular dynamics. This comparison clearly shows the translocation pathway to significantly differ from free-space unfolding dynamics and strongly suggests that stalling events are preferentially determined by the MBP regions with higher density of long-range native interactions. This result might constitute a possible criterion to predict a priori some statistical features of protein translocation from the structural analysis.
Pubblicato
Rilevanza internazionale
Articolo
Esperti anonimi
Settore ING-IND/34
Settore FIS/07
English
Bacci, M., Chinappi, M., Casciola, C.m., Cecconi, F. (2012). Role of denaturation in Maltose Binding Protein translocation dynamics. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, 116(14), 4255-4262 [10.1021/jp300143x].
Bacci, M; Chinappi, M; Casciola, Cm; Cecconi, F
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2108/247498
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