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Sharma R, Oak N, Chen W, Gogal R, Kirschner M, Beier F, Schnieders MJ, Spies M, Nichols KE, Wlodarski M. Germline landscape of RPA1, RPA2 and RPA3 variants in pediatric malignancies: identification of RPA1 as a novel cancer predisposition candidate gene. Front Oncol 2023; 13:1229507. [PMID: 37869077 PMCID: PMC10588448 DOI: 10.3389/fonc.2023.1229507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/18/2023] [Indexed: 10/24/2023] Open
Abstract
Replication Protein A (RPA) is single-strand DNA binding protein that plays a key role in the replication and repair of DNA. RPA is a heterotrimer made of 3 subunits - RPA1, RPA2, and RPA3. Germline pathogenic variants affecting RPA1 were recently described in patients with Telomere Biology Disorders (TBD), also known as dyskeratosis congenita or short telomere syndrome. Premature telomere shortening is a hallmark of TBD and results in bone marrow failure and predisposition to hematologic malignancies. Building on the finding that somatic mutations in RPA subunit genes occur in ~1% of cancers, we hypothesized that germline RPA alterations might be enriched in human cancers. Because germline RPA1 mutations are linked to early onset TBD with predisposition to myelodysplastic syndromes, we interrogated pediatric cancer cohorts to define the prevalence and spectrum of rare/novel and putative damaging germline RPA1, RPA2, and RPA3 variants. In this study of 5,993 children with cancer, 75 (1.25%) harbored heterozygous rare (non-cancer population allele frequency (AF) < 0.1%) variants in the RPA heterotrimer genes, of which 51 cases (0.85%) had ultra-rare (AF < 0.005%) or novel variants. Compared with Genome Aggregation Database (gnomAD) non-cancer controls, there was significant enrichment of ultra-rare and novel RPA1, but not RPA2 or RPA3, germline variants in our cohort (adjusted p-value < 0.05). Taken together, these findings suggest that germline putative damaging variants affecting RPA1 are found in excess in children with cancer, warranting further investigation into the functional role of these variants in oncogenesis.
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Affiliation(s)
- Richa Sharma
- Department of Hematology, St. Jude Children´s Research Hospital, Memphis, TN, United States
| | - Ninad Oak
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Rose Gogal
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Martin Kirschner
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Bonn, Germany
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Bonn, Germany
| | - Michael J. Schnieders
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Maria Spies
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Kim E. Nichols
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Marcin Wlodarski
- Department of Hematology, St. Jude Children´s Research Hospital, Memphis, TN, United States
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Boese EA, Drack AV, Roos BR, Alward WLM, Tollefson MR, Schnieders MJ, Scheetz TE, Boldt HC, Stone EM, Fingert JH. GJA3 Genetic Variation and Autosomal Dominant Congenital Cataracts and Glaucoma Following Cataract Surgery. JAMA Ophthalmol 2023; 141:872-879. [PMID: 37589989 PMCID: PMC10436186 DOI: 10.1001/jamaophthalmol.2023.3535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 06/16/2023] [Indexed: 08/18/2023]
Abstract
Importance The p.Asp67Tyr genetic variant in the GJA3 gene is responsible for congenital cataracts in a family with a high incidence of glaucoma following cataract surgery. Objective To describe the clinical features of a family with a strong association between congenital cataracts and glaucoma following cataract surgery secondary to a genetic variant in the GJA3 gene (NM_021954.4:c.199G>T, p.Asp67Tyr). Design, Setting, and Participants This was a retrospective, observational, case series, genetic association study from the University of Iowa spanning 61 years. Examined were the ophthalmic records from 1961 through 2022 of the family members of a 4-generation pedigree with autosomal dominant congenital cataracts. Main Outcomes and Measures Frequency of glaucoma following cataract surgery and postoperative complications among family members with congenital cataract due to the p.Asp67Tyr GJA3 genetic variant. Results Medical records were available from 11 of 12 family members (7 male [63.6%]) with congenital cataract with a mean (SD) follow-up of 30 (21.7) years (range, 0.2-61 years). Eight of 9 patients with congenital cataracts developed glaucoma, and 8 of 8 patients who had cataract surgery at age 2 years or younger developed glaucoma following cataract surgery. The only family member with congenital cataracts who did not develop glaucoma had delayed cataract surgery until 12 and 21 years of age. Five of 11 family members (45.5%) had retinal detachments after cataract extraction and vitrectomy. No patients developed retinal detachments after prophylactic 360-degree endolaser. Conclusions and Relevance The GJA3 genetic variant, p.Asp67Tyr, was identified in a 4-generation congenital cataract pedigree from Iowa. This report suggests that patients with congenital cataract due to some GJA3 genetic variants may be at especially high risk for glaucoma following cataract surgery. Retinal detachments after cataract extraction in the first 2 years of life were also common in this family, and prophylactic retinal endolaser may be indicated at the time of surgery.
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Affiliation(s)
- Erin A. Boese
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City
| | - Arlene V. Drack
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City
| | - Benjamin R. Roos
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City
| | - Wallace L. M. Alward
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City
| | - Mallory R. Tollefson
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City
| | - Michael J. Schnieders
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City
| | - Todd E. Scheetz
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City
| | - H. Culver Boldt
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City
| | - Edwin M. Stone
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City
| | - John H. Fingert
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City
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Tollefson MR, Gogal RA, Weaver AM, Schaefer AM, Marini RJ, Azaiez H, Kolbe DL, Wang D, Weaver AE, Casavant TL, Braun TA, Smith RJH, Schnieders MJ. Assessing variants of uncertain significance implicated in hearing loss using a comprehensive deafness proteome. Hum Genet 2023; 142:819-834. [PMID: 37086329 PMCID: PMC10182131 DOI: 10.1007/s00439-023-02559-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/11/2023] [Indexed: 04/23/2023]
Abstract
Hearing loss is the leading sensory deficit, affecting ~ 5% of the population. It exhibits remarkable heterogeneity across 223 genes with 6328 pathogenic missense variants, making deafness-specific expertise a prerequisite for ascribing phenotypic consequences to genetic variants. Deafness-implicated variants are curated in the Deafness Variation Database (DVD) after classification by a genetic hearing loss expert panel and thorough informatics pipeline. However, seventy percent of the 128,167 missense variants in the DVD are "variants of uncertain significance" (VUS) due to insufficient evidence for classification. Here, we use the deep learning protein prediction algorithm, AlphaFold2, to curate structures for all DVD genes. We refine these structures with global optimization and the AMOEBA force field and use DDGun3D to predict folding free energy differences (∆∆GFold) for all DVD missense variants. We find that 5772 VUSs have a large, destabilizing ∆∆GFold that is consistent with pathogenic variants. When also filtered for CADD scores (> 25.7), we determine 3456 VUSs are likely pathogenic at a probability of 99.0%. Of the 224 genes in the DVD, 166 genes (74%) exhibit one or more missense variants predicted to cause a pathogenic change in protein folding stability. The VUSs prioritized here affect 119 patients (~ 3% of cases) sequenced by the OtoSCOPE targeted panel. Approximately half of these patients previously received an inconclusive report, and reclassification of these VUSs as pathogenic provides a new genetic diagnosis for six patients.
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Affiliation(s)
- Mallory R Tollefson
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, IA, 52242, USA
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Rose A Gogal
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, IA, 52242, USA
| | - A Monique Weaver
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Amanda M Schaefer
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Robert J Marini
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Diana L Kolbe
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Donghong Wang
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Amy E Weaver
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Thomas L Casavant
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, IA, 52242, USA
| | - Terry A Braun
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, IA, 52242, USA
| | - Richard J H Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA.
| | - Michael J Schnieders
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, IA, 52242, USA.
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, IA, 52242, USA.
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Tollefson MR, Gogal RA, Weaver AM, Schaefer AM, Marini RJ, Azaiez H, Kolbe DL, Wang D, Weaver AE, Casavant TL, Braun TA, Smith RJH, Schnieders M. Assessing Variants of Uncertain Significance Implicated in Hearing Loss Using a Comprehensive Deafness Proteome. Res Sq 2023:rs.3.rs-2508462. [PMID: 36778238 PMCID: PMC9915777 DOI: 10.21203/rs.3.rs-2508462/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Hearing loss is the leading sensory deficit, affecting ~ 5% of the population. It exhibits remarkable heterogeneity across 223 genes with 6,328 pathogenic missense variants, making deafness-specific expertise a prerequisite for ascribing phenotypic consequences to genetic variants. Deafness-implicated variants are curated in the Deafness Variation Database (DVD) after classification by a genetic hearing loss expert panel and thorough informatics pipeline. However, seventy percent of the 128,167 missense variants in the DVD are "variants of uncertain significance" (VUS) due to insufficient evidence for classification. Here, we use the deep learning protein prediction algorithm, AlphaFold2, to curate structures for all DVD genes. We refine these structures with global optimization and the AMOEBA force field and use DDGun3D to predict folding free energy differences (∆∆G Fold ) for all DVD missense variants. We find that 5,772 VUSs have a large, destabilizing ∆∆G Fold that is consistent with pathogenic variants. When also filtered for CADD scores (> 25.7), we determine 3,456 VUSs are likely pathogenic at a probability of 99.0%. These VUSs affect 119 patients (~ 3% of cases) sequenced by the OtoSCOPE targeted panel. Approximately half of these patients previously received an inconclusive report, and reclassification of these VUSs as pathogenic provides a new genetic diagnosis for six patients.
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Awotoye W, Mossey PA, Hetmanski JB, Gowans LJJ, Eshete MA, Adeyemo WL, Alade A, Zeng E, Adamson O, Naicker T, Anand D, Adeleke C, Busch T, Li M, Petrin A, Aregbesola BS, Braimah RO, Oginni FO, Oladele AO, Oladayo A, Kayali S, Olotu J, Hassan M, Pape J, Donkor P, Arthur FKN, Obiri-Yeboah S, Sabbah DK, Agbenorku P, Plange-Rhule G, Oti AA, Gogal RA, Beaty TH, Taub M, Marazita ML, Schnieders MJ, Lachke SA, Adeyemo AA, Murray JC, Butali A. Whole-genome sequencing reveals de-novo mutations associated with nonsyndromic cleft lip/palate. Sci Rep 2022; 12:11743. [PMID: 35817949 DOI: 10.1038/s41598-022-15885-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/22/2022] [Indexed: 11/08/2022] Open
Abstract
The majority (85%) of nonsyndromic cleft lip with or without cleft palate (nsCL/P) cases occur sporadically, suggesting a role for de novo mutations (DNMs) in the etiology of nsCL/P. To identify high impact protein-altering DNMs that contribute to the risk of nsCL/P, we conducted whole-genome sequencing (WGS) analyses in 130 African case-parent trios (affected probands and unaffected parents). We identified 162 high confidence protein-altering DNMs some of which are based on available evidence, contribute to the risk of nsCL/P. These include novel protein-truncating DNMs in the ACTL6A, ARHGAP10, MINK1, TMEM5 and TTN genes; as well as missense variants in ACAN, DHRS3, DLX6, EPHB2, FKBP10, KMT2D, RECQL4, SEMA3C, SEMA4D, SHH, TP63, and TULP4. Many of these protein-altering DNMs were predicted to be pathogenic. Analysis using mouse transcriptomics data showed that some of these genes are expressed during the development of primary and secondary palate. Gene-set enrichment analysis of the protein-altering DNMs identified palatal development and neural crest migration among the few processes that were significantly enriched. These processes are directly involved in the etiopathogenesis of clefting. The analysis of the coding sequence in the WGS data provides more evidence of the opportunity for novel findings in the African genome.
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Alimah SN, Sumaryada TI, Nurcholis W, Ambarsari L. Molecular Docking Study of IPBCC.08.610 Glucose Oxidase Mutant for Increasing Gluconic Acid Production. J Kim Sains Apl 2022; 25:169-178. [DOI: 10.14710/jksa.25.5.169-178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Glucose oxidase (GOD) is an oxidoreductase enzyme that catalyzes the oxidation of glucose to gluconolactone and hydrogen peroxide. Then, gluconolactone will be hydrolyzed to gluconic acid. The wide application of gluconic acid in various industries has increased production demand. However, glucose concentrations higher than 40% (w/w) inhibited the conversion of glucose to gluconic acid due to a decrease in the oxygen solubility concentration at pH 6, 30℃, and 1 bar pressure. Therefore, decreasing the value of Km is predicted to reduce saturation and enhance gluconic acid production. This study aimed to analyze the interaction between the IPBCC.08.610 GOD mutant with β-D-Glucose in improving gluconic acid production by decreasing the Km value. Mutations were performed in silico using Chimera and then docked using AutoDock Vina. The mutations resulted in distinct ligand poses in the binding pocket, different -OH conformations of the ligands, and changes in the T554M/D578P mutant’s hydrophobicity index (554 mutated from threonine to methionine, and 578 mutated from aspartate to proline), and decreased ΔG and Km values in the H559D mutant (559 mutated from histidine to aspartate), D578P and T554M/D578P. This decrease might strengthen the ligand-receptor interaction, increasing gluconic acid production. The H559D was the best mutant to increase production based on the ΔG, Km value, and stability due to the addition of hydrogen bonds.
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Hinz BE, Walker SG, Xiong A, Gogal RA, Schnieders MJ, Wallrath LL. In Silico and In Vivo Analysis of Amino Acid Substitutions That Cause Laminopathies. Int J Mol Sci 2021; 22:ijms222011226. [PMID: 34681887 PMCID: PMC8536974 DOI: 10.3390/ijms222011226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 01/08/2023] Open
Abstract
Mutations in the LMNA gene cause diseases called laminopathies. LMNA encodes lamins A and C, intermediate filaments with multiple roles at the nuclear envelope. LMNA mutations are frequently single base changes that cause diverse disease phenotypes affecting muscles, nerves, and fat. Disease-associated amino acid substitutions were mapped in silico onto three-dimensional structures of lamin A/C, revealing no apparent genotype–phenotype connections. In silico analyses revealed that seven of nine predicted partner protein binding pockets in the Ig-like fold domain correspond to sites of disease-associated amino acid substitutions. Different amino acid substitutions at the same position within lamin A/C cause distinct diseases, raising the question of whether the nature of the amino acid replacement or genetic background differences contribute to disease phenotypes. Substitutions at R249 in the rod domain cause muscular dystrophies with varying severity. To address this variability, we modeled R249Q and R249W in Drosophila Lamin C, an orthologue of LMNA. Larval body wall muscles expressing mutant Lamin C caused abnormal nuclear morphology and premature death. When expressed in indirect flight muscles, R249W caused a greater number of adults with wing posturing defects than R249Q, consistent with observations that R249W and R249Q cause distinct muscular dystrophies, with R249W more severe. In this case, the nature of the amino acid replacement appears to dictate muscle disease severity. Together, our findings illustrate the utility of Drosophila for predicting muscle disease severity and pathogenicity of variants of unknown significance.
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Affiliation(s)
- Benjamin E. Hinz
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA; (B.E.H.); (S.G.W.); (A.X.); (M.J.S.)
| | - Sydney G. Walker
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA; (B.E.H.); (S.G.W.); (A.X.); (M.J.S.)
| | - Austin Xiong
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA; (B.E.H.); (S.G.W.); (A.X.); (M.J.S.)
| | - Rose A. Gogal
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA;
| | - Michael J. Schnieders
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA; (B.E.H.); (S.G.W.); (A.X.); (M.J.S.)
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA;
| | - Lori L. Wallrath
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA; (B.E.H.); (S.G.W.); (A.X.); (M.J.S.)
- Correspondence: ; Tel.: +1-319-335-7920
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Michael E, Simonson T. How much can physics do for protein design? Curr Opin Struct Biol 2021; 72:46-54. [PMID: 34461593 DOI: 10.1016/j.sbi.2021.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 01/03/2023]
Abstract
Physics and physical chemistry are an important thread in computational protein design, complementary to knowledge-based tools. They provide molecular mechanics scoring functions that need little or no ad hoc parameter readjustment, methods to thoroughly sample equilibrium ensembles, and different levels of approximation for conformational flexibility. They led recently to the successful redesign of a small protein using a physics-based folded state energy. Adaptive Monte Carlo or molecular dynamics schemes were discovered where protein variants are populated as per their ligand-binding free energy or catalytic efficiency. Molecular dynamics have been used for backbone flexibility. Implicit solvent models have been refined, polarizable force fields applied, and many physical insights obtained.
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Affiliation(s)
- Eleni Michael
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole Polytechnique, 91128, Palaiseau, France
| | - Thomas Simonson
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole Polytechnique, 91128, Palaiseau, France.
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Corrigan RA, Qi G, Thiel AC, Lynn JR, Walker BD, Casavant TL, Lagardere L, Piquemal JP, Ponder JW, Ren P, Schnieders MJ. Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field. J Chem Theory Comput 2021; 17:2323-2341. [PMID: 33769814 DOI: 10.1021/acs.jctc.0c01286] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Computational protein design, ab initio protein/RNA folding, and protein-ligand screening can be too computationally demanding for explicit treatment of solvent. For these applications, implicit solvent offers a compelling alternative, which we describe here for the polarizable atomic multipole AMOEBA force field based on three treatments of continuum electrostatics: numerical solutions to the nonlinear and linearized versions of the Poisson-Boltzmann equation (PBE), the domain-decomposition conductor-like screening model (ddCOSMO) approximation to the PBE, and the analytic generalized Kirkwood (GK) approximation. The continuum electrostatics models are combined with a nonpolar estimator based on novel cavitation and dispersion terms. Electrostatic model parameters are numerically optimized using a least-squares style target function based on a library of 103 small-molecule solvation free energy differences. Mean signed errors for the adaptive Poisson-Boltzmann solver (APBS), ddCOSMO, and GK models are 0.05, 0.00, and 0.00 kcal/mol, respectively, while the mean unsigned errors are 0.70, 0.63, and 0.58 kcal/mol, respectively. Validation of the electrostatic response of the resulting implicit solvents, which are available in the Tinker (or Tinker-HP), OpenMM, and Force Field X software packages, is based on comparisons to explicit solvent simulations for a series of proteins and nucleic acids. Overall, the emergence of performative implicit solvent models for polarizable force fields opens the door to their use for folding and design applications.
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Affiliation(s)
- Rae A Corrigan
- Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, United States
| | - Guowei Qi
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Andrew C Thiel
- Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, United States
| | - Jack R Lynn
- Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, United States
| | - Brandon D Walker
- Department of Biomedical Engineering, University of Texas in Austin, Austin, Texas 78712, United States
| | - Thomas L Casavant
- Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, United States
| | - Louis Lagardere
- Department of Chemistry, Sorbonne Université, F-75005 Paris, France
| | | | - Jay W Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas in Austin, Austin, Texas 78712, United States
| | - Michael J Schnieders
- Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, United States.,Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
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Bi J, Thiel KW, Litman JM, Zhang Y, Devor EJ, Newtson AM, Schnieders MJ, Gonzalez Bosquet J, Leslie KK. Characterization of a TP53 Somatic Variant of Unknown Function From an Ovarian Cancer Patient Using Organoid Culture and Computational Modeling. Clin Obstet Gynecol 2020; 63:109-19. [PMID: 31876640 DOI: 10.1097/GRF.0000000000000516] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In our proof-of-concept study of 1 patient with stage IIIC carcinosarcoma of the ovary, we discovered a rare mutation in the tumor suppressor, TP53, that results in the deletion of N131. Immunofluorescence imaging of the organoid culture revealed hyperstaining of p53 protein. Computational modeling suggests this residue is important for maintaining protein conformation. Drug screening identified the combination of a proteasome inhibitor with a histone deacetylase inhibitor as the most effective treatment. These data provide evidence for the successful culture of a patient tumor and analysis of drug response ex vivo.
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Hagedorn J, Avdic A, Schnieders MJ, Roos BR, Kwon YH, Drack AV, Boese EA, Fingert JH. Nanophthalmos patient with a THR518MET mutation in MYRF, a case report. BMC Ophthalmol 2020; 20:388. [PMID: 33004036 PMCID: PMC7528587 DOI: 10.1186/s12886-020-01659-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/24/2020] [Indexed: 12/13/2022] Open
Abstract
Background Nanophthalmos has a significant genetic background and disease-causing mutations have been recently been reported in the myelin regulatory factor (MYRF) gene. We report clinical features in a patient with nanophthalmos and a Thr518Met MYRF mutation. Case presentation A three-year-old male was discovered to have nanophthalmos after first presenting to the emergency department for a frontal headache, eye pain, emesis, and lethargy. Imaging studies (CT and MRI) were negative except for increased posterior fossa cerebrospinal fluid. Subsequent examinations revealed nanophthalmos (short axial eye lengths 18.1 mm OD and 18.3 mm OS), microcornea, and a large crystalline lens. Peripheral chorioretinal pigment abnormalities were also observed. He experienced episodes of marked ocular hypertension (53 mmHg OD and 60 mmHg) likely due to intermittent angle closure precipitated by nanophthalmos. The ocular hypertension was responsive to topical medicines. Genetic analysis of known nanophthalmos genes MFRP and TMEM98 were negative, while a novel mutation, Thr518Met was detected in MYRF. The Thr518Met mutation was absent from 362 matched normal controls and was extremely rare in a large population database, allele frequency of 0.000024. The Thr518Met mutation altered a highly conserved amino acid in the MYRF protein and three of four algorithms suggested that this mutation is likely pathogenic. Finally, molecular modeling showed that the Thr518Met mutation is damaging to MYRF structure. Together these data suggest that the Thr518Met mutation causes nanophthalmos. Conclusions Nanophthalmos may present at an early age with features of angle closure glaucoma and a Thr518Met mutation in MYRF was detected in a patient with nanophthalmos. Prevalence data, homology data, mutation analysis data, and protein modeling data suggest that this variant is pathogenic and may expand the phenotypic range of syndromic nanophthalmos caused by MYRF mutations to include central nervous system abnormalities (increased posterior fossa cerebrospinal fluid).
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Affiliation(s)
- Joshua Hagedorn
- Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Armin Avdic
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Michael J Schnieders
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Benjamin R Roos
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - Young H Kwon
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - Arlene V Drack
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - Erin A Boese
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - John H Fingert
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA. .,Institute for Vision Research, University of Iowa, Iowa City, IA, USA. .,Medical Education and Research Facility, University of Iowa, 375 Newton Road, Iowa City, IA, 52242, USA.
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