The residues which are involved in forming hydrophobic contacts belong to active-site, flaps and 80?s loop such as residues Ala28, Val32, Ile47, Ile50, Ile54, Ile84, Pro81, Val82 of both chain A and chain B (Fig.?S4D). flap region and the active site, which is similar to the decrease in flexibility observed by inhibitor binding to the protease. This suggests an allosteric mechanism to inhibit protease activity. Further, the protease mutants G40E and G40R are known to have decreased activity and were also subjected to MD simulations. We find that the loss of flexibility in the mutants is similar to that observed in the protease bound to the Ab/inhibitor. These insights spotlight the role played by dynamics in the function of the protease and how control of flexibility through Ab Alectinib Hydrochloride binding and site specific mutations can inhibit protease activity. or by mutant/Ab-bound protease with respect to WT-free protease. The hydrogen-bonding scores thus obtained (magnitudes), for the hydrogen-bonding interactions are outlined in Furniture?S3CS6 and for hydrogen-bonding interactions are listed in Furniture?S7CS10 (observe also figures Figs.?4, S2CS4A). The changes in the hydrogen-bonding networks and salt-bridges in the functionally important regions of HIV-1 protease are discussed in detail as follows. Open in a separate window Physique 3 Hydrogen-bonding map computed from your equilibrated region of the trajectories of (A) WT-free, (B) G40E, (C) G40R and (D) Ab-bound proteases. Only those hydrogen-bond pairs are shown, which are having a score more than 20 (refer to Methods). The functionally important regions of protease such as dimer interface (DI), active site (AS), elbow (E), flaps (F) and cantilever (C) are marked on axes of the maps. Note that the hydrogen-bonding map for RIT-bound protease is usually shown in supporting information Fig.?S4B. Open in a separate window Physique 4 The representative structure of the (A) WT-free and (B) G40E proteases are shown in trace representation, highlighting and comparing the hydrogen-bonds and salt-bridges that are and (as explained in Methods) for the functionally important regions individually (i) Elbow, (ii), Active site (iii) Cantilever, (iv) Dimer Alectinib Hydrochloride interface and (v) Flaps. The C atoms of the residues forming the hydrogen-bond are shown in spheres. The hydrogen-bonds within the monomers are shown as blue dashed collection, inter-chain hydrogen-bonds are shown in reddish dashed-line and the salt-bridges are shown in pink solid collection. Elbow (residues 36C46) The quenching in the fluctuations of HIV-1 PR is usually observed, upon binding of Alectinib Hydrochloride the elbow region of the protease to the F11.2.32 Ab (Fig.?2). Similarly, a single mutation in the elbow region of each monomer of the HIV-1 PR has decreased its fluctuations and made the structure rigid (Fig.?2). Mutations Rabbit polyclonal to AKAP7 at position 40 have resulted in the formation of the salt-bridges between the residues Glu40 and Arg41 in G40E; Arg40 and Asp60 in G40R in both the monomers of the protease as shown in Figs.?4B(i) and S2B(i) (salt-bridge percentages are outlined in Table?S2). In the case of bound protease, G40 of protease chain A (bound to Ab) forms strong mainchain-mainchain hydrogen-bonding conversation with Arg-31 of the heavy chain of Ab for more than 95% of the time12. Due to this strong mainchain-mainchain hydrogen-bonding conversation, the fluctuations in the elbow region of the chain A of Ab-bound protease are presumably reduced more as compared to mutant and WT-free protease (Fig.?2). We find that, in the case of WT-free protease, G40 does not form any conversation with the remaining part of Alectinib Hydrochloride the protease. Thus, it may be surmised that the new salt-bridges at the mutant site (Table?S2) and the interactions the elbow region of the Ab-bound protease forms with the Ab, may have resulted in a significant rearrangement of the interactions within the protease. Active site (residues 25C27) The number of salt-bridges and hydrogen-bonding interactions the active site residues (residues 25C27) and the residues near to the active site (Leu24, Asp29, Asp30, Thr31, Val32) are forming with rest of the protease or within themselves are increased in both mutants and Ab/RIT bound proteases (Figs.?4B(ii), S2B(ii), S3B(ii)), S4A(b)(i) and Furniture?S2CS6). For example, the propensity of the salt-bridges between the residues Asp29 and Arg87 is usually increased significantly in both the chains of the mutants and Ab/RIT bound protease (Table?S2). Many hydrogen-bonds are observed in mutants and Ab/RIT bound protease. Such as, the following hydrogen bonding pairs are observed between nearby active-site residues (Asp30 and Thr31) and Thr74 of cantilever and Asn88 of 80?s loop for most of the frames:.