Limits...
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.

Show MeSH

Related in: MedlinePlus

Clusters of sites prone to destabilizing mutations overlap with peptides shown to induce robust immune response and be associated with viral control. Positions prone to destabilizing mutations are underlined and bolded in HIV-1 Gag-p24 subtype B consensus sequence. Yellow regions depict four continuous stretches of sites found in three or more overlapping 15 amino acid windows with each window containing five or more destabilizing sites. CE peptides [3,14,41] and “Beneficial” peptides from [42] were previously shown to induce robust immune responses [43,44] and associated with viral control [42], respectively. * denote residues not included in all the template structures examined and, hence, excluded from the analysis.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4664974&req=5

viruses-07-02901-f008: Clusters of sites prone to destabilizing mutations overlap with peptides shown to induce robust immune response and be associated with viral control. Positions prone to destabilizing mutations are underlined and bolded in HIV-1 Gag-p24 subtype B consensus sequence. Yellow regions depict four continuous stretches of sites found in three or more overlapping 15 amino acid windows with each window containing five or more destabilizing sites. CE peptides [3,14,41] and “Beneficial” peptides from [42] were previously shown to induce robust immune responses [43,44] and associated with viral control [42], respectively. * denote residues not included in all the template structures examined and, hence, excluded from the analysis.

Mentions: To identify candidate regions for CTL vaccine immunogens design, we searched the CA by assessing sliding windows of 15 amino acids, one amino acid at a time, and counted the number of sites prone to destabilizing mutations within each window. The window of size 15 was selected to cover the length of known CTL epitopes [40]. We detected four linear regions in the CA that are enriched with sites prone to destabilizing mutations (Figure 8). These candidate regions were defined as a continuous stretch of sites found in three or more overlapping windows with each window having five or more destabilizing sites. These clusters of sites prone to destabilizing mutations were significantly associated with both “conserved elements” (CE) peptides [3,14,41] and ”beneficial” CA peptides [42] (p < 0.0001; Chi-square and Fisher’s exact test). As shown in Figure 8, all four regions overlap with four of seven previously identified CE peptides, which were shown to induce robust cellular and broad humoral immune responses in macaques [43,44]. Interestingly, the four regions also overlap with three CA peptides associated with viral control [42] (Figure 8). One of the CE peptides and one of the beneficial peptides are located at the carboxy-terminal end of the CA. This region is missing in the template protein structures and, hence, was excluded from our analyses (Figure 8).


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)

Clusters of sites prone to destabilizing mutations overlap with peptides shown to induce robust immune response and be associated with viral control. Positions prone to destabilizing mutations are underlined and bolded in HIV-1 Gag-p24 subtype B consensus sequence. Yellow regions depict four continuous stretches of sites found in three or more overlapping 15 amino acid windows with each window containing five or more destabilizing sites. CE peptides [3,14,41] and “Beneficial” peptides from [42] were previously shown to induce robust immune responses [43,44] and associated with viral control [42], respectively. * denote residues not included in all the template structures examined and, hence, excluded from the analysis.
© Copyright Policy
Related In: Results  -  Collection

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

viruses-07-02901-f008: Clusters of sites prone to destabilizing mutations overlap with peptides shown to induce robust immune response and be associated with viral control. Positions prone to destabilizing mutations are underlined and bolded in HIV-1 Gag-p24 subtype B consensus sequence. Yellow regions depict four continuous stretches of sites found in three or more overlapping 15 amino acid windows with each window containing five or more destabilizing sites. CE peptides [3,14,41] and “Beneficial” peptides from [42] were previously shown to induce robust immune responses [43,44] and associated with viral control [42], respectively. * denote residues not included in all the template structures examined and, hence, excluded from the analysis.
Mentions: To identify candidate regions for CTL vaccine immunogens design, we searched the CA by assessing sliding windows of 15 amino acids, one amino acid at a time, and counted the number of sites prone to destabilizing mutations within each window. The window of size 15 was selected to cover the length of known CTL epitopes [40]. We detected four linear regions in the CA that are enriched with sites prone to destabilizing mutations (Figure 8). These candidate regions were defined as a continuous stretch of sites found in three or more overlapping windows with each window having five or more destabilizing sites. These clusters of sites prone to destabilizing mutations were significantly associated with both “conserved elements” (CE) peptides [3,14,41] and ”beneficial” CA peptides [42] (p < 0.0001; Chi-square and Fisher’s exact test). As shown in Figure 8, all four regions overlap with four of seven previously identified CE peptides, which were shown to induce robust cellular and broad humoral immune responses in macaques [43,44]. Interestingly, the four regions also overlap with three CA peptides associated with viral control [42] (Figure 8). One of the CE peptides and one of the beneficial peptides are located at the carboxy-terminal end of the CA. This region is missing in the template protein structures and, hence, was excluded from our analyses (Figure 8).

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