title: Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease.
abstract: Drug resistance mutations in response to HIV-1 protease inhibitors are selected not only in the drug target but elsewhere in the viral genome, especially at the protease cleavage sites in the precursor protein Gag. To understand the molecular basis of this protease-substrate coevolution, we solved the crystal structures of drug resistant I50V/A71V HIV-1 protease with p1-p6 substrates bearing coevolved mutations. Analyses of the protease-substrate interactions reveal that compensatory coevolved mutations in the substrate do not restore interactions lost due to protease mutations, but instead establish other interactions that are not restricted to the site of mutation. Mutation of a substrate residue has distal effects on other residues' interactions as well, including through the induction of a conformational change in the protease. Additionally, molecular dynamics simulations suggest that restoration of active site dynamics is an additional constraint in the selection of coevolved mutations. Hence, protease-substrate coevolution permits mutational, structural, and dynamic changes via molecular mechanisms that involve distal effects contributing to drug resistance.
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605.
authors.forename: Ayşegül
authors.initials: A
authors.lastname: Özen
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605.
authors.forename: Kuan-Hung
authors.initials: KH
authors.lastname: Lin
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 Nese.KurtYilmaz@umassmed.edu Celia.Schiffer@umassmed.edu.
authors.forename: Nese
authors.identifier: http://orcid.org/0000-0002-5036-676X
authors.initials: N
authors.lastname: Kurt Yilmaz
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 Nese.KurtYilmaz@umassmed.edu Celia.Schiffer@umassmed.edu.
authors.forename: Celia A
authors.initials: CA
authors.lastname: Schiffer
mesh_terms: D019943:Amino Acid Substitution; D018360:Crystallography, X-Ray; D024882:Drug Resistance, Viral / Q000235:genetics*; D019143:Evolution, Molecular; D016333:HIV Protease / Q000235:genetics / Q000378:metabolism*; D015497:HIV-1 / Q000235:genetics / Q000378:metabolism; D006801:Humans; D020125:Mutation, Missense; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000235:genetics / Q000378:metabolism
chemical_list: D054301:gag Gene Products, Human Immunodeficiency Virus; D016333:HIV Protease; C514803:p16 protease, Human immunodeficiency virus 1
keywords: HIV-1 protease; active site dynamics; coevolution; crystallography; drug resistance