A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase

Hinkley, Trevor; Martins, João; Chappey, Colombe; Haddad, Mojgan; Stawiski, Eric; Whitcomb, Jeannette M.; Petropoulos, Christos J.; Bonhoeffer, Sebastian

doi:10.1038/ng.795

Cited by 175 publications

(243 citation statements)

References 27 publications

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“…Most single mutations did not show strong epistasis when combined, and there was no mean tendency to positive or negative epistasis. Recently, a large-scale analysis of epistasis in the HIV protease described a geographic enrichment of epistasis (27). In the WW data, we found similar evidence for strong epistatic interactions occurring between particular regions.…”

Section: Discussionsupporting

confidence: 75%

A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function

Araya¹,

Fowler

Chen³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

240

264

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The ability of a protein to carry out a given function results from fundamental physicochemical properties that include the protein's structure, mechanism of action, and thermodynamic stability. Traditional approaches to study these properties have typically required the direct measurement of the property of interest, oftentimes a laborious undertaking. Although protein properties can be probed by mutagenesis, this approach has been limited by its low throughput. Recent technological developments have enabled the rapid quantification of a protein's function, such as binding to a ligand, for numerous variants of that protein. Here, we measure the ability of 47,000 variants of a WW domain to bind to a peptide ligand and use these functional measurements to identify stabilizing mutations without directly assaying stability. Our approach is rooted in the well-established concept that protein function is closely related to stability. Protein function is generally reduced by destabilizing mutations, but this decrease can be rescued by stabilizing mutations. Based on this observation, we introduce partner potentiation, a metric that uses this rescue ability to identify stabilizing mutations, and identify 15 candidate stabilizing mutations in the WW domain. We tested six candidates by thermal denaturation and found two highly stabilizing mutations, one more stabilizing than any previously known mutation. Thus, physicochemical properties such as stability are latent within these large-scale protein functional data and can be revealed by systematic analysis. This approach should allow other protein properties to be discovered.deep mutational scanning | epistasis | high-throughput DNA sequencing

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Section: Discussionsupporting

confidence: 75%

A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function

Araya¹,

Fowler

Chen³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

240

264

View full text Add to dashboard Cite

show abstract

“…The correlations induce epistatic effects, a primary or accessory resistance mutation can be either stabilizing or destabilizing depending on the genetic background. Recently epistasis has become a focus for analysis in structural biology and genomics as researchers have begun to successfully link the coevolutionary information in collections of protein sequences with the structural and functional fitness of those proteins (Hinkley et al 2011;Ferguson et al 2013;Mann et al 2014;Figliuzzi et al 2015;Hopf et al 2017;Barton et al 2016b;Butler et al 2016). In the current study, we have used the correlated mutations encoded in a MSA of drug-experienced HIV-1 protease sequences to parametrize a Potts model of sequence statistical energies that can be used as an estimator of stability and relative replicative capacity of individual protease sequences containing drug resistance mutations.…”

Section: Discussionmentioning

confidence: 99%

“…With the increase in available sequence data and the rise in high-throughput fitness measurements (Hinkley et al 2011;Haddox et al 2016;Mavor et al 2016;Wu et al 2016), it should be possible to verify whether the Potts model correctly predicts the trends shown in figure 4 and supplementary figure S6, Supplementary Material online, and the relative fitness cost upon reverting the primary mutation to wildtype for the selected sequences pairs listed in table 1.…”

Section: Figmentioning

confidence: 99%

Inference of epistatic effects leading to entrenchment and drug resistance in HIV-1 protease

Flynn

Haldane

Torbett

et al. 2016

Preprint

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Understanding the complex mutation patterns that give rise to drug resistant viral strains provides a foundation for developing more effective treatment strategies for HIV/AIDS. Multiple sequence alignments of drug-experienced HIV-1 protease sequences contain networks of many pair correlations which can be used to build a (Potts) Hamiltonian model of these mutation patterns. Using this Hamiltonian model, we translate HIV-1 protease sequence covariation data into quantitative predictions for the probability of observing specific mutation patterns which are in agreement with the observed sequence statistics. We find that the statistical energies of the Potts model are correlated with the fitness of individual proteins containing therapy-associated mutations as estimated by in vitro measurements of protein stability and viral infectivity. We show that the penalty for acquiring primary resistance mutations depends on the epistatic interactions with the sequence background. Primary mutations which lead to drug resistance can become highly advantageous (or entrenched) by the complex mutation patterns which arise in response to drug therapy despite being destabilizing in the wildtype background. Anticipating epistatic effects is important for the design of future protease inhibitor therapies.

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“…To impute the fitness of these missing variants, we performed regularized regression on fitness values of observed variants using the following model (Hinkley et al, 2011;Otwinowski and Plotkin, 2014):…”

Section: Imputing the Fitness Of Missing Variantsmentioning

confidence: 99%

Adaptation in protein fitness landscapes is facilitated by indirect paths

Dai

Olson

et al. 2016

Preprint

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The structure of fitness landscapes is critical for understanding adaptive protein evolution. Previous empirical studies on fitness landscapes were confined to either the neighborhood around the wild type sequence, involving mostly single and double mutants, or a combinatorially complete subgraph involving only two amino acids at each site. In reality, the dimensionality of protein sequence space is higher (20 L ) and there may be higher-order interactions among more than two sites. Here we experimentally characterized the fitness landscape of four sites in protein GB1, containing 20 4 = 160,000 variants. We found that while reciprocal sign epistasis blocked many direct paths of adaptation, such evolutionary traps could be circumvented by indirect paths through genotype space involving gain and subsequent loss of mutations. These indirect paths alleviate the constraint on adaptive protein evolution, suggesting that the heretofore neglected dimensions of sequence space may change our views on how proteins evolve.

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A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase

Cited by 175 publications

References 27 publications

A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function

A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function

Inference of epistatic effects leading to entrenchment and drug resistance in HIV-1 protease

Adaptation in protein fitness landscapes is facilitated by indirect paths

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