3. Effect of I47V mutation on drug resistance of HIV-1 Protease against JE-
4.3. Results and Discussions
4.3.3. Secondary structure analysis
The secondary structural changes during the whole 30 ns MD simulation period was analyzed using the DSSP definitions and was calculated by the do_dssp program. A detailed comparative analysis of the secondary structural changes (Figure 4.4 upper and 4.4 lower) during the simulations is outlined below:
Figure 4.4. Secondary structure matrixes for the entire 1 bar (Upper) and 3 kbar (Lower) system simulation times of 30 ns. Color code may be interpreted from the legend.
Residues 1-4 (No secondary structure assigned by DSSP): Unchanged from 1 bar to 3 Kbar in the initial but appearance of β-bridge in later.
Residues 5-7 (Bend): Stable bend at 1 bar but fluctuate between bend, turn and coil for 3 Kbar.
Residues 8-9 (No secondary structure assigned by DSSP): Unchanged from 1 bar to 3 Kbar.
Residues 10-14 (Extended β-strand): Stable β-strand unchanged from 1 bar to 3 Kbar.
Residues 15-18 (Turn): Turn with intermittent bend properties from 1 bar changes to stable turn at 3 Kbar.
Residues 19-24 (β-sheet): Stable β-sheet unchanged from 1 bar to 3 Kbar.
Residue 25 (No secondary structure assigned by DSSP): Oscillates between coil, turn and sheet.
Residues 26-31 (Bend): Stable bend at 1 bar. Unchanged from 1 bar to 3 Kbar.
Residues 32-34: Oscillates between β-sheets and coil. Mostly unchanged from 1bar to 3 Kbar.
Residues 35-42 (Bend/loop): Oscillates between bend and coil. Coil is more prominent than bends. Mostly unchanged from 1bar to 3 Kbar.
Residues 43-48 (β-sheet): Stable β-sheet unchanged from 1 bar to 3 Kbar.
Residue 49 (β-sheet): Mostly replaced by coil from 1 bar to 3 Kbar.
Residue 50-51 (Bend): Oscillates between bends and turns and appearance of coil in between moving from 1 bar to 3 Kbar.
Residues 52-66 (β-sheet): Stable β-sheet unchanged from 1 bar to 3 Kbar.
Residues 67-69 (Bend): Oscillates between bends and sheet at the initial time, but formation of stable bends around 20-25 ns at 1 bar. But for 3 Kbar stable bends are seen in the initial up to 12 ns and later occupied by intermittent β-sheet.
Residues 70-78 (β-sheet): Stable β-sheet unchanged from 1 bar to 3 Kbar.
Residues 79-83: Same as that of 67-69 residues.
Residues 84-86 (β-sheet): Stable β-sheet unchanged from 1 bar to 3 Kbar.
Residues 87-90 (α-helix): Stable α-helix unchanged from 1 bar to 3 Kbar.
Residues 91-93: Oscillates between helix, turn and sheets at 1 bar. Unchanged at 3 Kbar but α-helix occurrence is prominent as compared to turns and sheets.
Residues 94-95: Oscillates between β-sheet and turn with prominence around 20-25 ns for 1 bar. Unchanged from 1 bar to 3 Kbar, but turn is seen throughout the simulation time with little intermittent β-sheet for 3 Kbar.
Residues 96-97: Stable β-sheet unchanged from 1 bar to 3 Kbar.
Residues 98-99: Same as that of 94-95 residues.
Residues 100-103: Same as that of 94-95 residues.
Residues 104-106: Same as that of 67-69 residues.
Residues 107-114 (β-sheet): Stable β-sheet unchanged from 1 bar to 3 Kbar.
Residues 115-116: Same as that of 94-95 residues.
Residues 117-123 (β-sheet): Stable β-sheet unchanged from 1 bar to 3 Kbar.
Residue 124: Oscillates between sheet and coil at 1 bar. Unchanged at 3 Kbar.
Residues 125-130: Same as that of 67-69 residues.
Residues 131-133: Same as that of 32-34 residues.
Residues 134-141: Oscillates between bends, sheets and coils. Bends and coils are prominent in 20-25 ns at 1 bar. At 3 Kbar bend, coil and sheet oscillates but coil and bend are prominent and seen throughout the simulation with intermittent β-sheets.
Residues 142-148 (β-sheet): Stable β-sheet unchanged from 1 bar to 3 Kbar.
Residues 149-151: Oscillates between bends, turns and coil. Turns is prominent at 1 bar and remain unchanged at 3 Kbar except the coil that seems prominent in the first 4 ns and 22-25 ns.
Residues 152-165: (β-sheet): Stable β-sheet unchanged from 1 bar to 3 Kbar except the residue 160 which oscillates between sheet and bend.
Residues 166-168: (Bend): Stable bend unchanged from 1 bar to 3 Kbar.
Residues 169-175 (β-sheet): Stable β-sheet unchanged from 1 bar to 3 Kbar.
Residues 176-181: Stable bends and coils unchanged from 1 bar to 3 Kbar.
Residues 182-183 (β-sheet): Stable β-sheet unchanged from 1 bar to 3 Kbar.
Residue 184: Coil at 1bar unchanged from 1 bar to 3 Kbar.
Residues 185-188 (α-helix): Stable α-helix at 1 bar. This part of the protein shows distinct differences between 1 bar and 3 Kbar by the occupancy of turns over helix from around 10-25 ns. The helix in the chain-B is lost during this period.
Residues 189-191: Oscillate between helix and turns throughout the simulation period at 1 bar. At 3 Kbar turns are mostly occupied with intermittent helices. Interestingly bends are seen around 8-10 ns.
Residue 192: Coil at 1bar unchanged from 1 bar to 3 Kbar.
Residues 193-196 (β-sheet): Stable β-sheet unchanged from 1 bar to 3 Kbar.
Residues 197-198: No secondary structure assigned by DSSP.
Shortening secondary structure observations:
Comparative analysis of the secondary structures from 30 ns for both the normal and high pressure conditions, it is observed that the global changes in the protein conformation remains unchanged. Marked specific local changes seen with the expense of β-sheets and α-helices to turns and bends.
Residues 49-99 (in chain A) and residues 100-140 (in chain B) regions: This part of the protein shows distinct differences between 1 bar and 3 Kbar. Bends, turns and coils are formed in the expense of β-sheets and are more prominent around 20-25 ns for 1 bar. But in 3 Kbar the changes in structure seems throughout the simulation period indicating the structural instability under high pressure correlating the RMSD shown in Figure 6.2.
Chain-B helix (Residues 185-191): The most notable difference seen here by the occupancy of turns over helices from around 10-25 ns where the α-helix is being disrupted under high pressure.