University of Massachusetts Medical School Faculty Publications

Title

Optimizing the refinement of merohedrally twinned P61 HIV-1 protease-inhibitor cocrystal structures

UMMS Affiliation

Department of Biochemistry and Molecular Pharmacology; Graduate School of Biomedical Sciences; Schiffer Lab

Publication Date

2020-03-01

Document Type

Article

Disciplines

Amino Acids, Peptides, and Proteins | Biochemistry | Enzymes and Coenzymes | Medicinal-Pharmaceutical Chemistry | Pharmaceutics and Drug Design | Structural Biology | Viruses

Abstract

Twinning is a crystal-growth anomaly in which protein monomers exist in different orientations but are related in a specific way, causing diffraction reflections to overlap. Twinning imposes additional symmetry on the data, often leading to the assignment of a higher symmetry space group. Specifically, in merohedral twinning, reflections from each monomer overlap and require a twin law to model unique structural data from overlapping reflections. Neglecting twinning in the crystallographic analysis of quasi-rotationally symmetric homo-oligomeric protein structures can mask the degree of structural non-identity between monomers. In particular, any deviations from perfect symmetry will be lost if higher than appropriate symmetry is applied during crystallographic analysis. Such cases warrant choosing between the highest symmetry space group possible or determining whether the monomers have distinguishable structural asymmetries and thus require a lower symmetry space group and a twin law. Using hexagonal cocrystals of HIV-1 protease, a C2-symmetric homodimer whose symmetry is broken by bound ligand, it is shown that both assigning a lower symmetry space group and applying a twin law during refinement are critical to achieving a structural model that more accurately fits the electron density. By re-analyzing three recently published HIV-1 protease structures, improvements in nearly every crystallographic metric are demonstrated. Most importantly, a procedure is demonstrated where the inhibitor can be reliably modeled in a single orientation. This protocol may be applicable to many other homo-oligomers in the PDB.

Keywords

HIV-1 protease, homo-oligomers, homodimers, merohedral twinning, twin law

DOI of Published Version

10.1107/S2059798320001989

Source

Lockbaum GJ, Leidner F, Royer WE, Kurt Yilmaz N, Schiffer CA. Optimizing the refinement of merohedrally twinned P61 HIV-1 protease-inhibitor cocrystal structures. Acta Crystallogr D Struct Biol. 2020 Mar 1;76(Pt 3):302-310. doi: 10.1107/S2059798320001989. Epub 2020 Mar 2. PMID: 32133994; PMCID: PMC7057220. Link to article on publisher's site

Related Resources

Link to Article in PubMed

Journal/Book/Conference Title

Acta crystallographica. Section D, Structural biology

PubMed ID

32133994

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