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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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Genetic barrier influences the emergence of amino acid mutations but not impact of mutations on viral infectivity: (A) Number of nucleotide changes required for mutations observed and not observed in the HIV database of 5811 sequences; (B) Number of nucleotide changes required for mutations whose impact on infectivity was tested; amino acid mutations classified into three groups based on their frequency in the HIV database with stability predicted by DOPE (C) and FOLDEF (D) using the mature CA hexamer as the template.
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viruses-07-02901-f003: Genetic barrier influences the emergence of amino acid mutations but not impact of mutations on viral infectivity: (A) Number of nucleotide changes required for mutations observed and not observed in the HIV database of 5811 sequences; (B) Number of nucleotide changes required for mutations whose impact on infectivity was tested; amino acid mutations classified into three groups based on their frequency in the HIV database with stability predicted by DOPE (C) and FOLDEF (D) using the mature CA hexamer as the template.

Mentions: A considerable proportion of amino acid substitutions have not been observed despite having minimal impact on protein stability (Figure 1C,D and Figure S4). Fifty-nine percent of all possible amino acid substitutions from the consensus sequence required two or more nucleotide changes. However, this proportion increased to 72% for undetected mutations and decreased to 13% for observed mutations (Figure 3A), indicating that a genetic barrier plays a role in emergence of amino acid changes in the CA. However, substitutions requiring single nucleotide changes were not further enriched when considering mutations observed in 1% or more of the sequences, although there was an increase in the proportion of transition mutations compared to transversion mutations (Figure S6A). There was no association between genetic barrier, i.e., amino acid changes requiring an increased numbers of base changes, and effect of mutations on viral infectivity or protein stability (Figure 3B–D and Figure S6B).


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)

Genetic barrier influences the emergence of amino acid mutations but not impact of mutations on viral infectivity: (A) Number of nucleotide changes required for mutations observed and not observed in the HIV database of 5811 sequences; (B) Number of nucleotide changes required for mutations whose impact on infectivity was tested; amino acid mutations classified into three groups based on their frequency in the HIV database with stability predicted by DOPE (C) and FOLDEF (D) using the mature CA hexamer as the template.
© Copyright Policy
Related In: Results  -  Collection

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

viruses-07-02901-f003: Genetic barrier influences the emergence of amino acid mutations but not impact of mutations on viral infectivity: (A) Number of nucleotide changes required for mutations observed and not observed in the HIV database of 5811 sequences; (B) Number of nucleotide changes required for mutations whose impact on infectivity was tested; amino acid mutations classified into three groups based on their frequency in the HIV database with stability predicted by DOPE (C) and FOLDEF (D) using the mature CA hexamer as the template.
Mentions: A considerable proportion of amino acid substitutions have not been observed despite having minimal impact on protein stability (Figure 1C,D and Figure S4). Fifty-nine percent of all possible amino acid substitutions from the consensus sequence required two or more nucleotide changes. However, this proportion increased to 72% for undetected mutations and decreased to 13% for observed mutations (Figure 3A), indicating that a genetic barrier plays a role in emergence of amino acid changes in the CA. However, substitutions requiring single nucleotide changes were not further enriched when considering mutations observed in 1% or more of the sequences, although there was an increase in the proportion of transition mutations compared to transversion mutations (Figure S6A). There was no association between genetic barrier, i.e., amino acid changes requiring an increased numbers of base changes, and effect of mutations on viral infectivity or protein stability (Figure 3B–D and Figure S6B).

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