Comparison of inhibitor binding in HIV‐1 protease and in non‐viral aspartic proteases: the role of the flap

Gustchina, Alla; Weber, Irene T.

doi:10.1016/0014-5793(90)81171-j

Cited by 72 publications

(46 citation statements)

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“…Moreover, the experimentally determined cleavage rates of the cleavable peptides agreed well with the CRM predicted rates on HXB2 and mutated HIV-1 proteases (68% accuracy; RMSEP ¼ 1.01; Figure 1B). Addition of all experimental data to the CRM further increased CRM (Table 3, numbers [4][5][6][7][8][9][10][11][12][13][14][15][16][17][18]. Shown is the predicted versus experimentally determined cleavage rates by HXB2 (red) and mutant HIV-1 proteases, I84V (blue), L90M (magenta), and I84 þ L90M (green).…”

Section: Author Summarymentioning

confidence: 99%

“…Because retroviral proteases are inherently dynamic structures that undergo significant structural changes with binding, we described each structurally aligned amino acid of the 61 retroviral proteases by their principal physicochemical properties (i.e., their z-scales z 1 -z 5 ), rather than using the proteins' static 3-D structures (see Materials and Methods, Figure S1, and Table S2) [15,16]. Similarly, we described the retroviral protease substrates by considering the same principal physicochemical properties of every single amino acid of the octapeptide sequence spanning the P 4 to P 4 9 position (see Materials and Methods for details).…”

Section: Introductionmentioning

confidence: 99%

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A Look inside HIV Resistance through Retroviral Protease Interaction Maps

Kontijevskis¹,

Prūsis²,

Petrovska³

et al. 2005

PLoS Comput Biol

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Retroviruses affect a large number of species, from fish and birds to mammals and humans, with global socioeconomic negative impacts. Here the authors report and experimentally validate a novel approach for the analysis of the molecular networks that are involved in the recognition of substrates by retroviral proteases. Using multivariate analysis of the sequence-based physiochemical descriptions of 61 retroviral proteases comprising wild-type proteases, natural mutants, and drug-resistant forms of proteases from nine different viral species in relation to their ability to cleave 299 substrates, the authors mapped the physicochemical properties and cross-dependencies of the amino acids of the proteases and their substrates, which revealed a complex molecular interaction network of substrate recognition and cleavage. The approach allowed a detailed analysis of the molecular-chemical mechanisms involved in substrate cleavage by retroviral proteases.Citation: Kontijevskis A, Prusis P, Petrovska R, Yahorava S, Mutulis F, et al. (2007) A look inside HIV resistance through retroviral protease interaction maps. PLoS Comput Biol 3(3): e48.

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Section: Author Summarymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A Look inside HIV Resistance through Retroviral Protease Interaction Maps

Kontijevskis¹,

Prūsis²,

Petrovska³

et al. 2005

PLoS Comput Biol

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“…Wat 301, which has been observed in all other inhibitor complexes, makes contacts with the carbonyl oxygens of residues at the P2 and P1' positions, and with the NH groups of residues Ile 50 and Ile 150 on the flaps, thus completely satisfying its hydrogen-bonding capacity. This water molecule possibly plays a crucial role in inducing the fit of the flaps over the inhibitor (Gustchina & Weber, 1990). The ND1 of histidine in the P2 position acts as a hydrogen-bond donor to the main-chain carbonyl oxygen of Gly 48 on the flap.…”

Section: I F O Imentioning

confidence: 99%

Crystal structure of a complex of HIV‐1 protease with a dihydroxyethylene‐containing inhibitor: Comparisons with molecular modeling

Thanki¹,

Rao²,

Foundling³

et al. 1992

Protein Science

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The structure of a crystal complex of recombinant human immunodeficiency virus type 1 (HIV-1) protease with a peptide-mimetic inhibitor containing a dihydroxyethylene isostere insert replacing the scissile bond has been de- The bound inhibitor diastereomer has the R configurations at both of the hydroxyl chiral carbon atoms. One of the diol hydroxyl groups is positioned such that it forms hydrogen bonds with both the active site aspartates, whereas the other interacts with only one of them. Comparison of this X-ray structure with a model-built structure of the inhibitor, published earlier, reveals similar positioning of the backbone atoms and of the side-chain atoms in the P2-P2' region, where the interaction with the protein is strongest. However, the X-ray structure and the model differ considerably in the location of the P3 and P3' end groups, and also in the positioning of the second of the two central hydroxyl groups. Reconstruction of the central portion of the model revealed the source of the hydroxyl discrepancy, which, when corrected, provided a PI-PI' geometry very close to that seen in the X-ray structure.

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“…In the crystal structure of HIV PR with different inhibitors, a conserved water molecule is observed that forms a tetrahedral set of interactions with P, C=O, P,' C=O of the inhibitor, and NH of He50 and Ile50' from the tip of the protease flaps [3].…”

Section: Hydrolysis Of Oligopeptides Representing Other Naturally Occmentioning

confidence: 99%

Activity of Tethered Human Immunodeficiency Virus 1 Protease Containing Mutations in the Flap Region of One Subunit

Tőzsér

Yin

Cheng

et al. 1997

European Journal of Biochemistry

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USA 87, 9660-96641 and its mutants containing amino acid substitutions or deletions or both in only one flap region were expressed in Esclzerichia coli. These mutant enzymes showed various degrees of self-processing and significantly reduced catalytic activity toward oligopeptide substrates compared with the wild type. Kinetic parameters determined for one of the oligopeptide substrates showed a dramatic increase in K,,, and decrease in k,,, values. Unexpectedly, the substrate cleavage was more efficient in low salt concentration for a mutant containing a shortened hydrophilic flap. Assays with oligopeptides representing naturally occurring cleavage sites or oligopeptides containing single amino acid substitutions at the P, and P; substrate positions showed only moderate changes in the substrate specificity of the mutant proteases. Predicted structures for the mutants were constructed by molecular modeling and used to interpret the results of kinetic measurements. In general, the data suggest that the mutated part of the flaps does not have a major role in determining substrate specificity; rather, it provides the hydrophobic environment and hydrogen-bond interactions with the conserved water that are necessary for efficient substrate binding and catalysis.Keywords: human immunodeficiency virus protease; flap mutants ; oligopeptide substrate; substrate specificity; enzyme kinetics.The protease (PR) of human retroviruses is an attractive target for chemotherapy of virus infection and associated diseases, including AIDS [I]. Knowledge of the specificity and mechanism of action of the retroviral PR have been useful in the design of potent inhibitors. The retroviral PR are aspartyl enzymes and are active as dimers of two identical subunits. Comparison of the crystal structures of human immunodeficiency virus 1 (HIV-1) PR with those of HIV-1 PR-inhibitor complexes (for review see [2]) suggested that during binding of the ligand, the two flaps close down on the ligand, providing a hydrophobic environment. The two flaps have an interchain hydrogen-bond connecting their tips. It is not clear whether the flaps contribute to the specificity and catalytic efficiency of the PR. In contrast to the flaps of retroviral PR, the cellular bilobal aspartic proteinases have only one flap, which cannot completely close down on the substrate, and there is no coordinated water molecule as observed in HIV PR-inhibitor structures [3-41.We have tested the effect of mutations in the flap region on the activity and specificity of HIV-1 PR. We used a single-chain tethered-dimer of HIV-1 PR [5]. The crystal structure of this tethered-dimer was recently determined [6] and is nearly identical to the structure of the wild-type two-chain protease. To explore the role of the hydrophobic nature of the amino acid residue at the tip of the flap (Ile50), we introduced a negatively charged (Asp) and a positively charged (His) residue into this position. We introduced mutations only into the flap region of one subunit. The mutation of only one flap was...

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Comparison of inhibitor binding in HIV‐1 protease and in non‐viral aspartic proteases: the role of the flap

Cited by 72 publications

References 20 publications

A Look inside HIV Resistance through Retroviral Protease Interaction Maps

A Look inside HIV Resistance through Retroviral Protease Interaction Maps

Crystal structure of a complex of HIV‐1 protease with a dihydroxyethylene‐containing inhibitor: Comparisons with molecular modeling

Activity of Tethered Human Immunodeficiency Virus 1 Protease Containing Mutations in the Flap Region of One Subunit

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