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Composite Sequence-Structure Stability Models as Screening Tools for Identifying Vulnerable Targets for HIV Drug and Vaccine Development.

Manocheewa S, Mittler JE, Samudrala R, Mullins JI - Viruses (2015)

Bottom Line: The destabilizing mutations predicted by these models were rarely found in a database of 5811 HIV-1 CA coding sequences, with none being present at a frequency greater than 2%.Furthermore, 90% of variants with the low predicted stability (from a set of 184 CA variants whose replication fitness or infectivity has been studied in vitro) had aberrant capsid structures and reduced viral infectivity.The CA regions enriched with these sites also overlap with peptides shown to induce cellular immune responses associated with lower viral loads in infected individuals.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, University ofWashington, Seattle,WA 98195-8070, USA. manocs@uw.edu.

ABSTRACT
Rapid evolution and high sequence diversity enable Human Immunodeficiency Virus (HIV) populations to acquire mutations to escape antiretroviral drugs and host immune responses, and thus are major obstacles for the control of the pandemic. One strategy to overcome this problem is to focus drugs and vaccines on regions of the viral genome in which mutations are likely to cripple function through destabilization of viral proteins. Studies relying on sequence conservation alone have had only limited success in determining critically important regions. We tested the ability of two structure-based computational models to assign sites in the HIV-1 capsid protein (CA) that would be refractory to mutational change. The destabilizing mutations predicted by these models were rarely found in a database of 5811 HIV-1 CA coding sequences, with none being present at a frequency greater than 2%. Furthermore, 90% of variants with the low predicted stability (from a set of 184 CA variants whose replication fitness or infectivity has been studied in vitro) had aberrant capsid structures and reduced viral infectivity. Based on the predicted stability, we identified 45 CA sites prone to destabilizing mutations. More than half of these sites are targets of one or more known CA inhibitors. The CA regions enriched with these sites also overlap with peptides shown to induce cellular immune responses associated with lower viral loads in infected individuals. Lastly, a joint scoring metric that takes into account both sequence conservation and protein structure stability performed better at identifying deleterious mutations than sequence conservation or structure stability information alone. The computational sequence-structure stability approach proposed here might therefore be useful for identifying immutable sites in a protein for experimental validation as potential targets for drug and vaccine development.

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HIV-1 capsid (CA) sites prone to destabilizing mutations. (A,B) The amino-terminal domain (NTD) is shown in cyan and the carboxy-terminal domain (CTDd) is in yellow with the sites prone to destabilizing mutations highlighted in blue and orange; (A,B) side-view of three CA chains and two additional CTD from a hexamer of the hexamer of hexamer (HOH); (B) showing the solvent accessible surfaces; and (C) the database frequency of the consensus amino acid (open circle) and the frequency of mutations that lower stability (“×”) at each CA residue. The dash line shows the frequency of 0.75. (D) There is no linear relationship between sequence conservation and the frequency of mutations that lower stability. Each dot represents a mutation.
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viruses-07-02901-f007: HIV-1 capsid (CA) sites prone to destabilizing mutations. (A,B) The amino-terminal domain (NTD) is shown in cyan and the carboxy-terminal domain (CTDd) is in yellow with the sites prone to destabilizing mutations highlighted in blue and orange; (A,B) side-view of three CA chains and two additional CTD from a hexamer of the hexamer of hexamer (HOH); (B) showing the solvent accessible surfaces; and (C) the database frequency of the consensus amino acid (open circle) and the frequency of mutations that lower stability (“×”) at each CA residue. The dash line shows the frequency of 0.75. (D) There is no linear relationship between sequence conservation and the frequency of mutations that lower stability. Each dot represents a mutation.

Mentions: As non-infectious mutants were more likely to be associated with lower stability, we speculated that a large proportion of destabilizing mutations at a site suggests low mutational tolerance. We identified 50 residues in the CA that were prone to destabilizing mutations (Figure 7 and Table S2). At least three-fourths of all possible mutations at these sites were predicted to lower protein stability by both scoring functions using the mature CA hexamer and the CTD of the HOH as templates. Most of these residues were located in secondary structure elements of the protein with small solvent accessible surface areas—many had side-chains almost completely buried. Exceptions were G8, located in the β-hairpin of the NTD, and L205, located in helix 10. These residues were either situated in the core of the CA, or at the CA intra-hexamer or inter-hexamer interfaces (Figure 7A,B and Table S2). These regions were shown to be genetically fragile, with low tolerance for amino acid substitutions [15,16,30]. All fifty residues were extremely highly conserved, with consensus amino acid frequencies ranging between 0.98 and 0.99. However, we did not observe a linear relationship between sequence conservation and the frequency of mutations that lower the stability (Pearson’s correlation r = 0.15, Figure 7D).


Composite Sequence-Structure Stability Models as Screening Tools for Identifying Vulnerable Targets for HIV Drug and Vaccine Development.

Manocheewa S, Mittler JE, Samudrala R, Mullins JI - Viruses (2015)

HIV-1 capsid (CA) sites prone to destabilizing mutations. (A,B) The amino-terminal domain (NTD) is shown in cyan and the carboxy-terminal domain (CTDd) is in yellow with the sites prone to destabilizing mutations highlighted in blue and orange; (A,B) side-view of three CA chains and two additional CTD from a hexamer of the hexamer of hexamer (HOH); (B) showing the solvent accessible surfaces; and (C) the database frequency of the consensus amino acid (open circle) and the frequency of mutations that lower stability (“×”) at each CA residue. The dash line shows the frequency of 0.75. (D) There is no linear relationship between sequence conservation and the frequency of mutations that lower stability. Each dot represents a mutation.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664974&req=5

viruses-07-02901-f007: HIV-1 capsid (CA) sites prone to destabilizing mutations. (A,B) The amino-terminal domain (NTD) is shown in cyan and the carboxy-terminal domain (CTDd) is in yellow with the sites prone to destabilizing mutations highlighted in blue and orange; (A,B) side-view of three CA chains and two additional CTD from a hexamer of the hexamer of hexamer (HOH); (B) showing the solvent accessible surfaces; and (C) the database frequency of the consensus amino acid (open circle) and the frequency of mutations that lower stability (“×”) at each CA residue. The dash line shows the frequency of 0.75. (D) There is no linear relationship between sequence conservation and the frequency of mutations that lower stability. Each dot represents a mutation.
Mentions: As non-infectious mutants were more likely to be associated with lower stability, we speculated that a large proportion of destabilizing mutations at a site suggests low mutational tolerance. We identified 50 residues in the CA that were prone to destabilizing mutations (Figure 7 and Table S2). At least three-fourths of all possible mutations at these sites were predicted to lower protein stability by both scoring functions using the mature CA hexamer and the CTD of the HOH as templates. Most of these residues were located in secondary structure elements of the protein with small solvent accessible surface areas—many had side-chains almost completely buried. Exceptions were G8, located in the β-hairpin of the NTD, and L205, located in helix 10. These residues were either situated in the core of the CA, or at the CA intra-hexamer or inter-hexamer interfaces (Figure 7A,B and Table S2). These regions were shown to be genetically fragile, with low tolerance for amino acid substitutions [15,16,30]. All fifty residues were extremely highly conserved, with consensus amino acid frequencies ranging between 0.98 and 0.99. However, we did not observe a linear relationship between sequence conservation and the frequency of mutations that lower the stability (Pearson’s correlation r = 0.15, Figure 7D).

Bottom Line: The destabilizing mutations predicted by these models were rarely found in a database of 5811 HIV-1 CA coding sequences, with none being present at a frequency greater than 2%.Furthermore, 90% of variants with the low predicted stability (from a set of 184 CA variants whose replication fitness or infectivity has been studied in vitro) had aberrant capsid structures and reduced viral infectivity.The CA regions enriched with these sites also overlap with peptides shown to induce cellular immune responses associated with lower viral loads in infected individuals.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, University ofWashington, Seattle,WA 98195-8070, USA. manocs@uw.edu.

ABSTRACT
Rapid evolution and high sequence diversity enable Human Immunodeficiency Virus (HIV) populations to acquire mutations to escape antiretroviral drugs and host immune responses, and thus are major obstacles for the control of the pandemic. One strategy to overcome this problem is to focus drugs and vaccines on regions of the viral genome in which mutations are likely to cripple function through destabilization of viral proteins. Studies relying on sequence conservation alone have had only limited success in determining critically important regions. We tested the ability of two structure-based computational models to assign sites in the HIV-1 capsid protein (CA) that would be refractory to mutational change. The destabilizing mutations predicted by these models were rarely found in a database of 5811 HIV-1 CA coding sequences, with none being present at a frequency greater than 2%. Furthermore, 90% of variants with the low predicted stability (from a set of 184 CA variants whose replication fitness or infectivity has been studied in vitro) had aberrant capsid structures and reduced viral infectivity. Based on the predicted stability, we identified 45 CA sites prone to destabilizing mutations. More than half of these sites are targets of one or more known CA inhibitors. The CA regions enriched with these sites also overlap with peptides shown to induce cellular immune responses associated with lower viral loads in infected individuals. Lastly, a joint scoring metric that takes into account both sequence conservation and protein structure stability performed better at identifying deleterious mutations than sequence conservation or structure stability information alone. The computational sequence-structure stability approach proposed here might therefore be useful for identifying immutable sites in a protein for experimental validation as potential targets for drug and vaccine development.

Show MeSH
Related in: MedlinePlus