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A Functional Interplay between Human Immunodeficiency Virus Type 1 Protease Residues 77 and 93 Involved in Differential Regulation of Precursor Autoprocessing and Mature Protease Activity.

Counts CJ, Ho PS, Donlin MJ, Tavis JE, Chen C - PLoS ONE (2015)

Bottom Line: The free mature PR is liberated as a result of precursor autoprocessing upon virion release.Furthermore, the 77I93V covariant enhanced precursor autoprocessing and Gag polyprotein processing but decreased the mature PR activity.Our data also suggests that these covariance pairs differentially regulate precursor autoprocessing and the mature protease activity.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America.

ABSTRACT
HIV-1 protease (PR) is a viral enzyme vital to the production of infectious virions. It is initially synthesized as part of the Gag-Pol polyprotein precursor in the infected cell. The free mature PR is liberated as a result of precursor autoprocessing upon virion release. We previously described a model system to examine autoprocessing in transfected mammalian cells. Here, we report that a covariance analysis of miniprecursor (p6*-PR) sequences derived from drug naïve patients identified a series of amino acid pairs that vary together across independent viral isolates. These covariance pairs were used to build the first topology map of the miniprecursor that suggests high levels of interaction between the p6* peptide and the mature PR. Additionally, several PR-PR covariance pairs are located far from each other (>12 Å Cα to Cα) relative to their positions in the mature PR structure. Biochemical characterization of one such covariance pair (77-93) revealed that each residue shows distinct preference for one of three alkyl amino acids (V, I, and L) and that a polar or charged amino acid at either of these two positions abolishes precursor autoprocessing. The most commonly observed 77V is preferred by the most commonly observed 93I, but the 77I variant is preferred by other 93 variances (L, V, or M) in supporting precursor autoprocessing. Furthermore, the 77I93V covariant enhanced precursor autoprocessing and Gag polyprotein processing but decreased the mature PR activity. Therefore, both covariance and biochemical analyses support a functional association between residues 77 and 93, which are spatially distant from each other in the mature PR structure. Our data also suggests that these covariance pairs differentially regulate precursor autoprocessing and the mature protease activity.

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Structural topology comparison between mature PR and p6*-PR precursor.The topology map of mature PR (overlaid on a pale orange background) was constructed from information on secondary structures annotated for the single-crystal structure of the mature PR (PDB code 3DKJ). Helices are indicated by cylinders and β-strands by arrowed blocks. Covariant pairs within the mature PR that are previously identified by Wu et al and common to those identified in this study (see Tables 1 and 2) are mapped onto the structural elements as double arrowed lines (upper left). Solid lines connect covariance pairs in close spatial proximity based on the mature PR structure (neighboring), while dashed lines those not in close spatial proximity (non-neighboring). The topology map for the precursor p6*-PR (lower right) is built upon the top 25 (out of 83 with S score > 0.9) covariance pairs identified in this current study with the p6* region colored in pale red. In the lower half, solid lines connect covariant pairs that are in close spatial proximity based on the mature PR structure (neighbor), while dashed arrows indicate those within PR but not in close proximity, or within the p6* domain, and from the p6* to PR domains (non-neighbor). Only pairs unique to this study are shown.
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pone.0123561.g002: Structural topology comparison between mature PR and p6*-PR precursor.The topology map of mature PR (overlaid on a pale orange background) was constructed from information on secondary structures annotated for the single-crystal structure of the mature PR (PDB code 3DKJ). Helices are indicated by cylinders and β-strands by arrowed blocks. Covariant pairs within the mature PR that are previously identified by Wu et al and common to those identified in this study (see Tables 1 and 2) are mapped onto the structural elements as double arrowed lines (upper left). Solid lines connect covariance pairs in close spatial proximity based on the mature PR structure (neighboring), while dashed lines those not in close spatial proximity (non-neighboring). The topology map for the precursor p6*-PR (lower right) is built upon the top 25 (out of 83 with S score > 0.9) covariance pairs identified in this current study with the p6* region colored in pale red. In the lower half, solid lines connect covariant pairs that are in close spatial proximity based on the mature PR structure (neighbor), while dashed arrows indicate those within PR but not in close proximity, or within the p6* domain, and from the p6* to PR domains (non-neighbor). Only pairs unique to this study are shown.

Mentions: Panel A lists the p6*-PR sequence derived from NL4-3 with the p6* sequence in green and PR sequence in black. The mature PR and p6* peptide are numbered separately. The two predicted helices in the p6* region are indicated. Panel B shows the covariance network formed by OMES analysis. Green nodes correspond to p6* residues and yellow nodes correspond to PR residues. Residue 93 and 77 are underlined and highlighted in orange. The edges are color coded per S score values as in Fig 2. Panel C demonstrates locations of V77 (orange) and I93 (red) in the context of a HIV-1 mature PR dimer structure (PDB code 3DJK).


A Functional Interplay between Human Immunodeficiency Virus Type 1 Protease Residues 77 and 93 Involved in Differential Regulation of Precursor Autoprocessing and Mature Protease Activity.

Counts CJ, Ho PS, Donlin MJ, Tavis JE, Chen C - PLoS ONE (2015)

Structural topology comparison between mature PR and p6*-PR precursor.The topology map of mature PR (overlaid on a pale orange background) was constructed from information on secondary structures annotated for the single-crystal structure of the mature PR (PDB code 3DKJ). Helices are indicated by cylinders and β-strands by arrowed blocks. Covariant pairs within the mature PR that are previously identified by Wu et al and common to those identified in this study (see Tables 1 and 2) are mapped onto the structural elements as double arrowed lines (upper left). Solid lines connect covariance pairs in close spatial proximity based on the mature PR structure (neighboring), while dashed lines those not in close spatial proximity (non-neighboring). The topology map for the precursor p6*-PR (lower right) is built upon the top 25 (out of 83 with S score > 0.9) covariance pairs identified in this current study with the p6* region colored in pale red. In the lower half, solid lines connect covariant pairs that are in close spatial proximity based on the mature PR structure (neighbor), while dashed arrows indicate those within PR but not in close proximity, or within the p6* domain, and from the p6* to PR domains (non-neighbor). Only pairs unique to this study are shown.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4404164&req=5

pone.0123561.g002: Structural topology comparison between mature PR and p6*-PR precursor.The topology map of mature PR (overlaid on a pale orange background) was constructed from information on secondary structures annotated for the single-crystal structure of the mature PR (PDB code 3DKJ). Helices are indicated by cylinders and β-strands by arrowed blocks. Covariant pairs within the mature PR that are previously identified by Wu et al and common to those identified in this study (see Tables 1 and 2) are mapped onto the structural elements as double arrowed lines (upper left). Solid lines connect covariance pairs in close spatial proximity based on the mature PR structure (neighboring), while dashed lines those not in close spatial proximity (non-neighboring). The topology map for the precursor p6*-PR (lower right) is built upon the top 25 (out of 83 with S score > 0.9) covariance pairs identified in this current study with the p6* region colored in pale red. In the lower half, solid lines connect covariant pairs that are in close spatial proximity based on the mature PR structure (neighbor), while dashed arrows indicate those within PR but not in close proximity, or within the p6* domain, and from the p6* to PR domains (non-neighbor). Only pairs unique to this study are shown.
Mentions: Panel A lists the p6*-PR sequence derived from NL4-3 with the p6* sequence in green and PR sequence in black. The mature PR and p6* peptide are numbered separately. The two predicted helices in the p6* region are indicated. Panel B shows the covariance network formed by OMES analysis. Green nodes correspond to p6* residues and yellow nodes correspond to PR residues. Residue 93 and 77 are underlined and highlighted in orange. The edges are color coded per S score values as in Fig 2. Panel C demonstrates locations of V77 (orange) and I93 (red) in the context of a HIV-1 mature PR dimer structure (PDB code 3DJK).

Bottom Line: The free mature PR is liberated as a result of precursor autoprocessing upon virion release.Furthermore, the 77I93V covariant enhanced precursor autoprocessing and Gag polyprotein processing but decreased the mature PR activity.Our data also suggests that these covariance pairs differentially regulate precursor autoprocessing and the mature protease activity.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America.

ABSTRACT
HIV-1 protease (PR) is a viral enzyme vital to the production of infectious virions. It is initially synthesized as part of the Gag-Pol polyprotein precursor in the infected cell. The free mature PR is liberated as a result of precursor autoprocessing upon virion release. We previously described a model system to examine autoprocessing in transfected mammalian cells. Here, we report that a covariance analysis of miniprecursor (p6*-PR) sequences derived from drug naïve patients identified a series of amino acid pairs that vary together across independent viral isolates. These covariance pairs were used to build the first topology map of the miniprecursor that suggests high levels of interaction between the p6* peptide and the mature PR. Additionally, several PR-PR covariance pairs are located far from each other (>12 Å Cα to Cα) relative to their positions in the mature PR structure. Biochemical characterization of one such covariance pair (77-93) revealed that each residue shows distinct preference for one of three alkyl amino acids (V, I, and L) and that a polar or charged amino acid at either of these two positions abolishes precursor autoprocessing. The most commonly observed 77V is preferred by the most commonly observed 93I, but the 77I variant is preferred by other 93 variances (L, V, or M) in supporting precursor autoprocessing. Furthermore, the 77I93V covariant enhanced precursor autoprocessing and Gag polyprotein processing but decreased the mature PR activity. Therefore, both covariance and biochemical analyses support a functional association between residues 77 and 93, which are spatially distant from each other in the mature PR structure. Our data also suggests that these covariance pairs differentially regulate precursor autoprocessing and the mature protease activity.

Show MeSH
Related in: MedlinePlus