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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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Crystal dimeric structure of the C-terminal domain of CA protein (146−231; PDB code 1A43). (a) Secondary structure of CA dimer in cartoon representation. Each monomer consists of four helixes: helix 1 (161−174; red), helix 2 (179−192; yellow), helix 3 (196−205; green), and helix 4 (211−217; purple). (b) Key residues in the helix 2 with all side chain orientations facing the interface in licorice representation (Glu180, Val181, Trp184, Met185, Thr188, Leu189, and Gln192). The images are generated by VMD.(47)
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fig1: Crystal dimeric structure of the C-terminal domain of CA protein (146−231; PDB code 1A43). (a) Secondary structure of CA dimer in cartoon representation. Each monomer consists of four helixes: helix 1 (161−174; red), helix 2 (179−192; yellow), helix 3 (196−205; green), and helix 4 (211−217; purple). (b) Key residues in the helix 2 with all side chain orientations facing the interface in licorice representation (Glu180, Val181, Trp184, Met185, Thr188, Leu189, and Gln192). The images are generated by VMD.(47)

Mentions: The X-ray crystal structure (resolution 2.6 Å, PDB code 1A43) of the C-terminal dimerization domain of the HIV-1 CA protein (146−231) was used as the starting point for all the MD simulations. In the native HIV capsid, two CTDs form a dimeric structure along a 2-fold screw axis. Each CTD monomer contains four helical structures: helix 1 (residues 161−174), helix 2 (residues 179−192), helix 3 (residues 196−205), and helix 4 (residues 211−217). Two CTDs form a dimeric interface via helix 2 packing along a C2 symmetry (Figure 1). All starting structures of the mutants were built from the wild-type by replacing the side chains of the targeted residues but without changing the backbone conformations and side-chain orientations. Four mutations were used in the simulations: W184A and M185A located in helix 2 region, and Q155N and E159D located in major homology region (MHR). The structure of the designed mutant was first minimized for 500 steps using the steepest decent algorithm with the backbone of the protein restrained before being subjected to the following system setup and production runs. The N- and C-termini were blocked by acetyl and amine groups, respectively.


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)

Crystal dimeric structure of the C-terminal domain of CA protein (146−231; PDB code 1A43). (a) Secondary structure of CA dimer in cartoon representation. Each monomer consists of four helixes: helix 1 (161−174; red), helix 2 (179−192; yellow), helix 3 (196−205; green), and helix 4 (211−217; purple). (b) Key residues in the helix 2 with all side chain orientations facing the interface in licorice representation (Glu180, Val181, Trp184, Met185, Thr188, Leu189, and Gln192). The images are generated by VMD.(47)
© Copyright Policy - open-access - ccc-price
Related In: Results  -  Collection

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

fig1: Crystal dimeric structure of the C-terminal domain of CA protein (146−231; PDB code 1A43). (a) Secondary structure of CA dimer in cartoon representation. Each monomer consists of four helixes: helix 1 (161−174; red), helix 2 (179−192; yellow), helix 3 (196−205; green), and helix 4 (211−217; purple). (b) Key residues in the helix 2 with all side chain orientations facing the interface in licorice representation (Glu180, Val181, Trp184, Met185, Thr188, Leu189, and Gln192). The images are generated by VMD.(47)
Mentions: The X-ray crystal structure (resolution 2.6 Å, PDB code 1A43) of the C-terminal dimerization domain of the HIV-1 CA protein (146−231) was used as the starting point for all the MD simulations. In the native HIV capsid, two CTDs form a dimeric structure along a 2-fold screw axis. Each CTD monomer contains four helical structures: helix 1 (residues 161−174), helix 2 (residues 179−192), helix 3 (residues 196−205), and helix 4 (residues 211−217). Two CTDs form a dimeric interface via helix 2 packing along a C2 symmetry (Figure 1). All starting structures of the mutants were built from the wild-type by replacing the side chains of the targeted residues but without changing the backbone conformations and side-chain orientations. Four mutations were used in the simulations: W184A and M185A located in helix 2 region, and Q155N and E159D located in major homology region (MHR). The structure of the designed mutant was first minimized for 500 steps using the steepest decent algorithm with the backbone of the protein restrained before being subjected to the following system setup and production runs. The N- and C-termini were blocked by acetyl and amine groups, respectively.

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