The Effect of Clade-Specific Sequence Polymorphisms on HIV-1 Protease Activity and Inhibitor Resistance Pathways

Bandaranayake, R.M.; Kolli, Madhavi; King, Nancy M. P.; Nalivaika, E.A.; Héroux, A.; Kakizawa, Junko; Sugiura, Wataru; Schiffer, Celia A.

doi:10.1128/jvi.00505-10

Cited by 34 publications

(41 citation statements)

References 38 publications

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“…Our inhibitor-bound co-crystal structures revealed that the N88D secondary mutation interacts with residue 30 to orient the side chain away from the active site (20) and thereby disrupts the interaction between residue 30 and the inhibitor. This effect is even more pronounced in subtype AE, where N88S pulls D30 out of the active site (21). We also showed that D30 not only is key for inhibitor binding but also is essential for recognition of the p1-p6 cleavage site (8,15,22).…”

Section: H Uman Immunodeficiency Virus Type 1 (Hiv-1) Protease (Pr)mentioning

confidence: 64%

HIV-1 Protease-Substrate Coevolution in Nelfinavir Resistance

Kolli

Özen

KurtYilmaz

et al. 2014

J Virol

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Resistance to various human immunodeficiency virus type 1 (HIV-1) protease inhibitors (PIs) challenges the effectiveness of therapies in treating HIV-1-infected individuals and AIDS patients. The virus accumulates mutations within the protease (PR) that render the PIs less potent. Occasionally, Gag sequences also coevolve with mutations at PR cleavage sites contributing to drug resistance. In this study, we investigated the structural basis of coevolution of the p1-p6 cleavage site with the nelfinavir (NFV) resistance D30N/N88D protease mutations by determining crystal structures of wild-type and NFV-resistant HIV-1 protease in complex with p1-p6 substrate peptide variants with L449F and/or S451N. Alterations of residue 30's interaction with the substrate are compensated by the coevolving L449F and S451N cleavage site mutations. This interdependency in the PR-p1-p6 interactions enhances intermolecular contacts and reinforces the overall fit of the substrate within the substrate envelope, likely enabling coevolution to sustain substrate recognition and cleavage in the presence of PR resistance mutations. IMPORTANCEResistance to human immunodeficiency virus type 1 (HIV-1) protease inhibitors challenges the effectiveness of therapies in treating HIV-1-infected individuals and AIDS patients. Mutations in HIV-1 protease selected under the pressure of protease inhibitors render the inhibitors less potent. Occasionally, Gag sequences also mutate and coevolve with protease, contributing to maintenance of viral fitness and to drug resistance. In this study, we investigated the structural basis of coevolution at the Gag p1-p6 cleavage site with the nelfinavir (NFV) resistance D30N/N88D protease mutations. Our structural analysis reveals the interdependency of protease-substrate interactions and how coevolution may restore substrate recognition and cleavage in the presence of protease drug resistance mutations.

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Section: H Uman Immunodeficiency Virus Type 1 (Hiv-1) Protease (Pr)mentioning

confidence: 64%

HIV-1 Protease-Substrate Coevolution in Nelfinavir Resistance

Kolli

Özen

KurtYilmaz

et al. 2014

J Virol

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“…Only subtle differences in the hydrophobic core are evident between the crystal structures of the subtype B and C-SA proteases. Similarly, the HIV-1 A_E variant, which has polymorphisms in the hydrophobic core, does not display major structural differences in this region relative to the subtype B protease [53]. Analysis of the dynamics of the hydrophobic core is limited because residues in the core are disconnected in the primary structure of the HIV-1 protease.…”

Section: Effect Of Secondary Resistance Mutations On Flap Movementmentioning

confidence: 99%

“…Slow exchange is expected here due to low solvent accessibility and a complex network of interactions around the active-site core. The flap tips (residues at positions [49][50][51][52][53] are the regions of the proteases that display the fastest deuterium incorporation. The flaps are completely solvent-exposed and highly mobile.…”

Section: Dynamics Of the Hiv-1 Proteasesmentioning

confidence: 99%

“…Polymorphic sites of the subtype B protease (PDB ID: 2PC0) [13] and the C-SA protease (PDB ID: 3U71) [37]. The flexible flaps of the protease (residues at positions [46][47][48][49][50][51][52][53][54] are coloured cyan. The fulcrum region (residues at positions 10-23), hinge region (residues at positions 35-42 and 57-61) and cantilever region (residues at positions 62-78) are implicated in flap opening.…”

Section: Introductionmentioning

confidence: 99%

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Amide hydrogen exchange in HIV–1 subtype B and C proteases – insights into reduced drug susceptibility and dimer stability

et al. 2014

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Since its identification, HIV has continued to have a detrimental impact on the lives of millions of people throughout the world. The protease of HIV is a major target in antiviral treatment. The South African HIV–1 subtype C (C–SA) protease displays weaker binding affinity for some clinically approved protease inhibitors in comparison with the HIV–1 subtype B protease. The heavy HIV burden in sub‐Saharan Africa, where subtype C HIV–1 predominates, makes this disparity a topic of great interest. In light of this, the enzyme activity and affinity of protease inhibitors for the subtype B and C–SA proteases were determined. The relative vitality, indicating the selective advantage of polymorphisms, of the C–SA protease relative to the subtype B protease in the presence of ritonavir and darunavir was four‐ and tenfold greater, respectively. Dynamic differences that contribute to the reduced drug susceptibility of the C–SA protease were investigated by performing hydrogen–deuterium exchange/mass spectrometry (HDX/MS) on unbound subtype B and C–SA proteases. The reduced propensity to form the E35–R57 salt bridge, and alterations in the hydrophobic core of the C–SA protease, are proposed to affect the anchoring of the flexible flaps, resulting in an increased proportion of the fully open flap conformation. HDX/MS data suggested that the N–terminus of both proteases is less stable than the C–terminus of the proteases, thus explaining the increased efficacy of dimerization inhibitors targeted toward the C–terminus of HIV proteases. As far as we are aware, this is the first report on assessment of HIV protease dynamics using HDX/MS.

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“…With the formation of a homo-dimer in which each monomer consists of 99 amino residues, the mature HIV-1 protease is produced through processing of the precursor peptide in the viral particle. Polymorphisms are frequently observed, 10,11) and about 500000 sequences have been registered in the Los Alamos HIV database. 12) Polymorphism and/or amino acid mutation have a close relation with the emergence of drug resistance.…”

mentioning

confidence: 99%

A Cluster Analysis on the Structural Diversity of Protein Crystals, Exemplified by Human Immunodeficiency Virus Type 1 Protease

Fudo

Neya

et al. 2014

CHEMICAL & PHARMACEUTICAL BULLETIN

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Information on many protein crystal structures has recently become available due to developments in crystallographic techniques. Even for a single kind of protein, several and sometimes many crystal structures are available. Human immunodeficiency virus type 1 (HIV-1) protease is one of the most extensively studied viral proteins, and about six hundred crystal structures have been determined. In this work, we examined the structural diversity of HIV-1 protease, classifying crystal structures into several groups from the viewpoint of similarity in atom geometry. Using 499 crystal structures downloaded from the Protein Data Bank (PDB), cluster analysis was applied to the whole body of HIV-1 protease and also to a limited number of residues at the binding pocket. As a consequence of clustering with regard to the whole body, 499 crystal structures were separated into 6 groups. It was found that a major factor for this separation is the space group of the crystals and that the space group strongly depends on the agents used in the protein crystallization. Amino acid mutation is a minor factor for separation in clustering. In cluster analysis for a limited number of residues at the binding pocket, crystal structures were not distinctly separated, and no clear factor linked to the separation was clarified. The results suggest that amino acid mutations have little effect on the coordinates of the main-chain atoms of HIV-1 protease. Hence, the changes in drug efficacy or substrate fitness caused by mutations are mainly due to the physicochemical features of amino acid side chains.Key words clustering analysis; crystal structure; amino acid mutation; drug resistance; space group Due to the progress in techniques for protein crystallization and in software for model building, crystal structures of many proteins have been elucidated. The reliability of solved protein structures has also increased.1) The development of a high-energy X-ray source has also been important for advancing crystallographic studies.2) Due to the progress in crystallographic technology, the availability of crystal structures in good quality has enabled us to examine structural differences in proteins in detail. Even for a single kind of protein, an amino acid mutation will cause the difference in its activity. Mutagenesis is one of the best approaches for clarifying the relationship between the protein activity and the mutated amino acid residue. Since protein activity has a close relation with its structure, 3,4) it is of great interest in molecular biology that the influence of amino acid mutation induces the change in protein structure.Apart from artificial mutagenesis, amino acid mutation ceaselessly occurs in the process of evolution. There is a common consensus that the accumulation of amino acid mutations generates a genetic diversity and that the diversity is observed as a difference in protein function in phenotype. 5,6) In general, the mutation rate of viral proteins is much higher than that of protein in eukaryotes. Variants of a virus som...

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The Effect of Clade-Specific Sequence Polymorphisms on HIV-1 Protease Activity and Inhibitor Resistance Pathways

Cited by 34 publications

References 38 publications

HIV-1 Protease-Substrate Coevolution in Nelfinavir Resistance

HIV-1 Protease-Substrate Coevolution in Nelfinavir Resistance

Amide hydrogen exchange in HIV–1 subtype B and C proteases – insights into reduced drug susceptibility and dimer stability

A Cluster Analysis on the Structural Diversity of Protein Crystals, Exemplified by Human Immunodeficiency Virus Type 1 Protease

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