Table 1.
Detailed information of all the MD simulation systems.
Figure 1.
Representative NA structures together with root mean square deviation of 150-loop in three systems.
Root mean square deviation (RMSD) of the 150-loop calculated by fitting the whole protein excluding the loop in N1o (A), N1c (B) and N2 (C) systems. Black and red dots represent RMSD value that calculated by fitting to N1 structure with a closed and open conformation of the 150-loop respectively. N1 structure with a closed and open conformation of 150-loop were shown in (D). Closed and open conformation of 150-loop were colored by cyan and magenta respectively.
Figure 2.
Potential of mean force (PMF) based on volume of 150-cavity.
PMF calculated based on volume of 150-cavity. Structure representing two local minima together with 16 Å3 and 24 Å3 is shown as cartoon with green color. As a comparison, crystal structures with closed and open configuration of 150-loop are aligned together and colored cyan and green respectively.
Figure 3.
Open propensity of 150-cavity and backbone dihedral angle distribution of residue 149.
Open percentage for 150-cavity is calculated based on its volume in three systems (A). Lines with square, circle and triangle represents N1o, N1c and N2 system respectively. Distribution based on psi angle of residue 149 is shown in (B). Dash, dash-dot and solid line represents N1o, N1c and N2 system respectively.
Figure 4.
Top 4 dominant cluster center structures based on RMSD of 150-loop in three systems.
Cluster analysis was based on RMSD of the 150-loop. The structures of the top 4 dominant cluster centers are shown with their cluster size in N1o (A), N1c (B) and N2 system (C) respectively. The conformation of the initial open and closed 150-loop is colored magenta and cyan respectively. The structure of each cluster center is shown in green color.
Figure 5.
Dihedral PCA indicated turn A of 150-loop is dominant changing place.
Free energy landscape obtained from dihedral PCA analysis of N1o and N1c system is shown in panel (A) and (B) respectively. Four local minima were highlight and their representative structures were shown on its right panel by clustering analysis. Structure of cluster 1, 2, 3, 4 is shown in forest green, green, lemon and yellow color. Crystal structure with closed and open 150-loop is shown in cyan and magenta color respectively.
Figure 6.
Correlation between salt bridge forming propensity and open percentage of 150-cavity.
Correlation between the propensity of salt bridge forming and open percentage of the 150-loop based on volume calculation is shown in (A), both the open percentage based on volume calculation and salt bridge forming propensity were average at every 1 ns. Structures of cluster centers in the first 100 ns and the final 100 ns of N2 system are shown in panel (B) and (C). The crystal structure of N2 is shown in green color, and structure snapshots from simulations are shown in pink, yellow, orange and palecyan color.
Figure 7.
Correlation between open propensity of 150-cavity and contact number between 150 and 430 loops.
Correlation between open percentage based on volume and contact number between 150 and 430-loop of two strains is shown in (A), both the open propensity of 150-cavity and contact number between 150 and 430-loop were averaged at every 10 ns. Distribution of minimal distance between heavy atoms of 150 and 430-loop is shown in (B). Panel (C) and (D) represent structure of the highest peak in N1 and N2 in (D) respectively.
Figure 8.
Conformational transition doorway of 150-loop in 09N1.
Conformational transition doorway of 150-loop in 09N1 (A), only those with transition times larger than 100 are displayed. Symbols in yellow, orange, red and green color represent largely open, open, open-meta and close-meta conformation of 150-loop respectively; Structure snapshots with different conformation of 150-loop relating the symbols in the transition doorway (B). The initially open and closed 150-loop is colored magenta and cyan respectively. Each cluster center structure is shown in green color. ILE149 is shown as sticks.