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Tollefson MR, Litman JM, Qi G, O'Connell CE, Wipfler MJ, Marini RJ, Bernabe HV, Tollefson WTA, Braun TA, Casavant TL, Smith RJH, Schnieders MJ. Structural Insights into Hearing Loss Genetics from Polarizable Protein Repacking. Biophys J 2019; 117:602-612. [PMID: 31327459 DOI: 10.1016/j.bpj.2019.06.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/10/2019] [Accepted: 06/25/2019] [Indexed: 12/21/2022] Open
Abstract
Hearing loss is associated with ∼8100 mutations in 152 genes, and within the coding regions of these genes are over 60,000 missense variants. The majority of these variants are classified as "variants of uncertain significance" to reflect our inability to ascribe a phenotypic effect to the observed amino acid change. A promising source of pathogenicity information is biophysical simulation, although input protein structures often contain defects because of limitations in experimental data and/or only distant homology to a template. Here, we combine the polarizable atomic multipole optimized energetics for biomolecular applications force field, many-body optimization theory, and graphical processing unit acceleration to repack all deafness-associated proteins and thereby improve average structure MolProbity score from 2.2 to 1.0. We then used these optimized wild-type models to create over 60,000 structures for missense variants in the Deafness Variation Database, which are being incorporated into the Deafness Variation Database to inform deafness pathogenicity prediction. Finally, this work demonstrates that advanced polarizable atomic multipole force fields are efficient enough to repack the entire human proteome.
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Affiliation(s)
- Mallory R Tollefson
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa; Molecular Otolaryngology & Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Jacob M Litman
- Department of Biochemistry, University of Iowa, Iowa City, Iowa
| | - Guowei Qi
- Department of Biochemistry, University of Iowa, Iowa City, Iowa
| | - Claire E O'Connell
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | - Matthew J Wipfler
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | - Robert J Marini
- Molecular Otolaryngology & Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Hernan V Bernabe
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa; Molecular Otolaryngology & Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | | | - Terry A Braun
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | - Thomas L Casavant
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | - Richard J H Smith
- Molecular Otolaryngology & Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa.
| | - Michael J Schnieders
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa; Department of Biochemistry, University of Iowa, Iowa City, Iowa.
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