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Mutational analysis and allosteric effects in the HIV-1 capsid protein carboxyl-terminal dimerization domain.

Yu X, Wang Q, Yang JC, Buch I, Tsai CJ, Ma B, Cheng SZ, Nussinov R, Zheng J - Biomacromolecules (2009)

Bottom Line: Here, we compare the structural stability, conformational dynamics, and association force of the CTD dimers for both wild-type and mutated sequences using all-atom explicit-solvent molecular dynamics (MD).The simulations show that Q155N and E159D at the major homology region (MHR) and W184A and M185A at the helix 2 region are energetically less favorable than the wild-type, imposing profound negative effects on intermolecular CA-CA dimerization.Most interestingly, the MHR that is far from the interacting dimeric interface is more sensitive to the mutations than the helix 2 region that is located at the CA-CA dimeric interface, indicating that structural changes in the distinct motif of the CA could similarly allosterically prevent the CA capsid formation.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA.

ABSTRACT
The carboxyl-terminal domain (CTD, residues 146-231) of the HIV-1 capsid (CA) protein plays an important role in the CA-CA dimerization and viral assembly of the human immunodeficiency virus type 1. Disrupting the native conformation of the CA is essential for blocking viral capsid formation and viral replication. Thus, it is important to identify the exact nature of the structural changes and driving forces of the CTD dimerization that take place in mutant forms. Here, we compare the structural stability, conformational dynamics, and association force of the CTD dimers for both wild-type and mutated sequences using all-atom explicit-solvent molecular dynamics (MD). The simulations show that Q155N and E159D at the major homology region (MHR) and W184A and M185A at the helix 2 region are energetically less favorable than the wild-type, imposing profound negative effects on intermolecular CA-CA dimerization. Detailed structural analysis shows that three mutants (Q155N, E159D, and W184A) display much more flexible local structures and weaker CA-CA association than the wildtype, primarily due to the loss of interactions (hydrogen bonds, side chain hydrophobic contacts, and pi-stacking) with their neighboring residues. Most interestingly, the MHR that is far from the interacting dimeric interface is more sensitive to the mutations than the helix 2 region that is located at the CA-CA dimeric interface, indicating that structural changes in the distinct motif of the CA could similarly allosterically prevent the CA capsid formation. In addition, the structural and free energy comparison of the five residues shorter CA (151-231) dimer with the CA (146-231) dimer further indicates that hydrophobic interactions, side chain packing, and hydrogen bonds are the major, dominant driving forces in stabilizing the CA interface.

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Variations of pairwise interface residue distances at the selected positions of 192I−192II, 185I−185II, 184I−184II, and 180I−180II between the helix2I−helix2II motifs for (a) wild-type, (b) W184A, and (c) M185A, where I and II indicate different CTD monomers. Variations of pairwise residue distances at the selected positions of 155−159, 155−194, and 155−195 within the same CTD monomer for (d) wild-type (146−231), (e) Q155N, and (f) E159D.
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fig6: Variations of pairwise interface residue distances at the selected positions of 192I−192II, 185I−185II, 184I−184II, and 180I−180II between the helix2I−helix2II motifs for (a) wild-type, (b) W184A, and (c) M185A, where I and II indicate different CTD monomers. Variations of pairwise residue distances at the selected positions of 155−159, 155−194, and 155−195 within the same CTD monomer for (d) wild-type (146−231), (e) Q155N, and (f) E159D.

Mentions: To quantitatively monitor specific interactions and relative motions of mutated residues and their neighboring residues, four residue-pair distances in the helix 2 region and three residue-pair distances in the MHR region were selected and measured as a function of simulation time. Figures 6a−c show the intermolecular distances of four identical residue pairs at the dimeric interface between E180I−E180II, Q192I−Q192II, W184I−W184II, or A184I−A184II, and M185I−M185II or A185I−A185II, where I and II represent different monomeric CTDs. Glu180 and Gln192 are located at the edges of the helix 2, while Trp184 and Met185 are located in the middle of the helix 2 with all sidechains pointing toward the dimeric interface. Positions 180, 184, 185, and 192, which are almost evenly distributed along helix 2, were selected to monitor the opening-closing motions between two CTDs. As can be seen in Figure 6a, all four residue pairs were able to maintain their initial contacts at the dimeric interface with small distance fluctuations, indicating that the dimeric interface is well preserved during the entire simulations. M185A displayed some distance fluctuation between Q192I−Q192II, but no significant difference was observed between the wild-type and the mutant M185A (Figure 6c), primarily due to that short Met185 did not involve many interactions with its neighboring residues. In contrast, for the mutant W184A, all four residue-pair distances experienced large fluctuations, quickly increasing within the first 10 ns, which indicated that they lost their original contacts at the helix2I−helix2II interface (Figure 6b). These results suggest that the most critical interaction at the dimeric interaction is W184I−W184II; whereas M185I−M185II interaction has little effect on stabilization of the dimer interface.


Mutational analysis and allosteric effects in the HIV-1 capsid protein carboxyl-terminal dimerization domain.

Yu X, Wang Q, Yang JC, Buch I, Tsai CJ, Ma B, Cheng SZ, Nussinov R, Zheng J - Biomacromolecules (2009)

Variations of pairwise interface residue distances at the selected positions of 192I−192II, 185I−185II, 184I−184II, and 180I−180II between the helix2I−helix2II motifs for (a) wild-type, (b) W184A, and (c) M185A, where I and II indicate different CTD monomers. Variations of pairwise residue distances at the selected positions of 155−159, 155−194, and 155−195 within the same CTD monomer for (d) wild-type (146−231), (e) Q155N, and (f) E159D.
© Copyright Policy - open-access - ccc-price
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651736&req=5

fig6: Variations of pairwise interface residue distances at the selected positions of 192I−192II, 185I−185II, 184I−184II, and 180I−180II between the helix2I−helix2II motifs for (a) wild-type, (b) W184A, and (c) M185A, where I and II indicate different CTD monomers. Variations of pairwise residue distances at the selected positions of 155−159, 155−194, and 155−195 within the same CTD monomer for (d) wild-type (146−231), (e) Q155N, and (f) E159D.
Mentions: To quantitatively monitor specific interactions and relative motions of mutated residues and their neighboring residues, four residue-pair distances in the helix 2 region and three residue-pair distances in the MHR region were selected and measured as a function of simulation time. Figures 6a−c show the intermolecular distances of four identical residue pairs at the dimeric interface between E180I−E180II, Q192I−Q192II, W184I−W184II, or A184I−A184II, and M185I−M185II or A185I−A185II, where I and II represent different monomeric CTDs. Glu180 and Gln192 are located at the edges of the helix 2, while Trp184 and Met185 are located in the middle of the helix 2 with all sidechains pointing toward the dimeric interface. Positions 180, 184, 185, and 192, which are almost evenly distributed along helix 2, were selected to monitor the opening-closing motions between two CTDs. As can be seen in Figure 6a, all four residue pairs were able to maintain their initial contacts at the dimeric interface with small distance fluctuations, indicating that the dimeric interface is well preserved during the entire simulations. M185A displayed some distance fluctuation between Q192I−Q192II, but no significant difference was observed between the wild-type and the mutant M185A (Figure 6c), primarily due to that short Met185 did not involve many interactions with its neighboring residues. In contrast, for the mutant W184A, all four residue-pair distances experienced large fluctuations, quickly increasing within the first 10 ns, which indicated that they lost their original contacts at the helix2I−helix2II interface (Figure 6b). These results suggest that the most critical interaction at the dimeric interaction is W184I−W184II; whereas M185I−M185II interaction has little effect on stabilization of the dimer interface.

Bottom Line: Here, we compare the structural stability, conformational dynamics, and association force of the CTD dimers for both wild-type and mutated sequences using all-atom explicit-solvent molecular dynamics (MD).The simulations show that Q155N and E159D at the major homology region (MHR) and W184A and M185A at the helix 2 region are energetically less favorable than the wild-type, imposing profound negative effects on intermolecular CA-CA dimerization.Most interestingly, the MHR that is far from the interacting dimeric interface is more sensitive to the mutations than the helix 2 region that is located at the CA-CA dimeric interface, indicating that structural changes in the distinct motif of the CA could similarly allosterically prevent the CA capsid formation.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA.

ABSTRACT
The carboxyl-terminal domain (CTD, residues 146-231) of the HIV-1 capsid (CA) protein plays an important role in the CA-CA dimerization and viral assembly of the human immunodeficiency virus type 1. Disrupting the native conformation of the CA is essential for blocking viral capsid formation and viral replication. Thus, it is important to identify the exact nature of the structural changes and driving forces of the CTD dimerization that take place in mutant forms. Here, we compare the structural stability, conformational dynamics, and association force of the CTD dimers for both wild-type and mutated sequences using all-atom explicit-solvent molecular dynamics (MD). The simulations show that Q155N and E159D at the major homology region (MHR) and W184A and M185A at the helix 2 region are energetically less favorable than the wild-type, imposing profound negative effects on intermolecular CA-CA dimerization. Detailed structural analysis shows that three mutants (Q155N, E159D, and W184A) display much more flexible local structures and weaker CA-CA association than the wildtype, primarily due to the loss of interactions (hydrogen bonds, side chain hydrophobic contacts, and pi-stacking) with their neighboring residues. Most interestingly, the MHR that is far from the interacting dimeric interface is more sensitive to the mutations than the helix 2 region that is located at the CA-CA dimeric interface, indicating that structural changes in the distinct motif of the CA could similarly allosterically prevent the CA capsid formation. In addition, the structural and free energy comparison of the five residues shorter CA (151-231) dimer with the CA (146-231) dimer further indicates that hydrophobic interactions, side chain packing, and hydrogen bonds are the major, dominant driving forces in stabilizing the CA interface.

Show MeSH
Related in: MedlinePlus