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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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Structural comparison and characterization of wild-type CA (146−231) and its mutants (Q155N and E159D) at the MHR region. (a) Backbone RMSD relative to the initial energy-minimized structure and (b) residue-based backbone RMSF relative to average structure for the wild-type and mutants.
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fig4: Structural comparison and characterization of wild-type CA (146−231) and its mutants (Q155N and E159D) at the MHR region. (a) Backbone RMSD relative to the initial energy-minimized structure and (b) residue-based backbone RMSF relative to average structure for the wild-type and mutants.

Mentions: The MHR region consisting of 20 amino acids (residues 153−172) forms a compact strand-turn-helix motif.(8) Gln155 and Glu159 are located at the edges of the turn and the interactions between Gln155 and Glu159 stabilize the turn structure and restrain the turn motion. It is generally accepted that a turn/loop region is very flexible and thus is vulnerable to mutations.33−35 To minimize the effect of the mutation residue size and hydrophobicity at the target position, Asn was selected to replace Gln155, while Asp was selected to replace Glu159; Gln versus Asn and Glu versus Asp have comparable size and hydrophobicity. Figure 4a clearly shows that both mutants occurring at the MHR region experienced much larger structural deviation than the wild-type, with the RMSD quickly rising to a plateau of ∼5.5 Å. As expected, the RMSF profile also showed a similar increased trend with three sharp peaks occurring at the MHR region (residues 155−159), the hinge connecting helix 1 and helix 2 (residues 174−178), and the hinge connecting helix 3 and helix 4 (residues 205−210; Figure 4b). As shown in Figure 5, Gln155 was closely packed against Ala194 and Asn195 at the helix 2 region bridging the MHR and helix 2 motifs. Between the MHR and helix 2 regions, Gln155 formed nine hydrogen bonds with Asn195 and Ala194, while within the MHR region, Gln55 formed three hydrogen bonds with Glu159 (Figure 5a). The Q155N substitution significantly disrupted the hydrogen-bond network of residue 155 with Ala194, Asn195, and Glu159, decreasing from nine (wild-type) to three (Q155N; Figure 5b). The loss of hydrogen bonding and side chain contacts between the MHR and helix 2 regions strongly affects the structural fluctuation of the local turn region (residues 155−159), as indicated by RMSF values rising from 1.81 Å (wild-type) to 4.47 Å (Q155N; Figure 4b). Interestingly, although residue Glu159 is far from the helix 2 region and is not involved in any contact with residues in the helix 2, E159D also led to the loss of two hydrogen bonds and potential van der Waals interactions within the MHR region (Figure 4c). As a consequence, the turn restricted by Gln155 and Asp159 become more flexible and free to move as compared to the turn initially restricted by Gln155 and Glu159 so that hydrogen bonds and side chain contacts between Gln155 and its neighboring Asn195 and Ala194 tend to break and form easily. Taken together, the substitution of Gln155 and Glu159 has a large destabilizing effect not only on the local structure and dynamics, but also on the overall organization of the CA dimer. The structural instability of Gln155 and Glu159 could be attributed to the loss of hydrogen bonds and van der Waal interactions. It is reasonable to expect that substitutions at positions of 155 and 159, other than Q155N and E159D, will lead to even larger structural perturbation in the loop due to the large differences of molecular size and hydrophobicity of sidechains.


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)

Structural comparison and characterization of wild-type CA (146−231) and its mutants (Q155N and E159D) at the MHR region. (a) Backbone RMSD relative to the initial energy-minimized structure and (b) residue-based backbone RMSF relative to average structure for the wild-type and mutants.
© Copyright Policy - open-access - ccc-price
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2651736&req=5

fig4: Structural comparison and characterization of wild-type CA (146−231) and its mutants (Q155N and E159D) at the MHR region. (a) Backbone RMSD relative to the initial energy-minimized structure and (b) residue-based backbone RMSF relative to average structure for the wild-type and mutants.
Mentions: The MHR region consisting of 20 amino acids (residues 153−172) forms a compact strand-turn-helix motif.(8) Gln155 and Glu159 are located at the edges of the turn and the interactions between Gln155 and Glu159 stabilize the turn structure and restrain the turn motion. It is generally accepted that a turn/loop region is very flexible and thus is vulnerable to mutations.33−35 To minimize the effect of the mutation residue size and hydrophobicity at the target position, Asn was selected to replace Gln155, while Asp was selected to replace Glu159; Gln versus Asn and Glu versus Asp have comparable size and hydrophobicity. Figure 4a clearly shows that both mutants occurring at the MHR region experienced much larger structural deviation than the wild-type, with the RMSD quickly rising to a plateau of ∼5.5 Å. As expected, the RMSF profile also showed a similar increased trend with three sharp peaks occurring at the MHR region (residues 155−159), the hinge connecting helix 1 and helix 2 (residues 174−178), and the hinge connecting helix 3 and helix 4 (residues 205−210; Figure 4b). As shown in Figure 5, Gln155 was closely packed against Ala194 and Asn195 at the helix 2 region bridging the MHR and helix 2 motifs. Between the MHR and helix 2 regions, Gln155 formed nine hydrogen bonds with Asn195 and Ala194, while within the MHR region, Gln55 formed three hydrogen bonds with Glu159 (Figure 5a). The Q155N substitution significantly disrupted the hydrogen-bond network of residue 155 with Ala194, Asn195, and Glu159, decreasing from nine (wild-type) to three (Q155N; Figure 5b). The loss of hydrogen bonding and side chain contacts between the MHR and helix 2 regions strongly affects the structural fluctuation of the local turn region (residues 155−159), as indicated by RMSF values rising from 1.81 Å (wild-type) to 4.47 Å (Q155N; Figure 4b). Interestingly, although residue Glu159 is far from the helix 2 region and is not involved in any contact with residues in the helix 2, E159D also led to the loss of two hydrogen bonds and potential van der Waals interactions within the MHR region (Figure 4c). As a consequence, the turn restricted by Gln155 and Asp159 become more flexible and free to move as compared to the turn initially restricted by Gln155 and Glu159 so that hydrogen bonds and side chain contacts between Gln155 and its neighboring Asn195 and Ala194 tend to break and form easily. Taken together, the substitution of Gln155 and Glu159 has a large destabilizing effect not only on the local structure and dynamics, but also on the overall organization of the CA dimer. The structural instability of Gln155 and Glu159 could be attributed to the loss of hydrogen bonds and van der Waal interactions. It is reasonable to expect that substitutions at positions of 155 and 159, other than Q155N and E159D, will lead to even larger structural perturbation in the loop due to the large differences of molecular size and hydrophobicity of sidechains.

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