1
|
Himmelreich N, Ramón-Maiques S, Navarrete R, Castejon-Fernandez N, Garbade SF, Martinez A, Desviat LR, Pérez B, Blau N. Significance of utilizing in silico structural analysis and phenotypic data to characterize phenylalanine hydroxylase variants: A PAH landscape. Mol Genet Metab 2024; 142:108514. [PMID: 38905920 DOI: 10.1016/j.ymgme.2024.108514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/23/2024]
Abstract
Phenylketonuria (PKU) is a genetic disorder caused by variations in the phenylalanine hydroxylase (PAH) gene. Among the 3369 reported PAH variants, 33.7% are missense alterations. Unfortunately, 30% of these missense variants are classified as variants of unknown significance (VUS), posing challenges for genetic risk assessment. In our study, we focused on analyzing 836 missense PAH variants following the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines specified by ClinGen PAH Variant Curation Expert Panel (VCEP) criteria. We utilized and compared variant annotator tools like Franklin and Varsome, conducted 3D structural analysis of PAH, and examined active and regulatory site hotspots. In addition, we assessed potential splicing effect of apparent missense variants. By evaluating phenotype data from 22962 PKU patients, our aim was to reassess the pathogenicity of missense variants. Our comprehensive approach successfully reclassified 309 VUSs out of 836 missense variants as likely pathogenic or pathogenic (37%), upgraded 370 likely pathogenic variants to pathogenic, and reclassified one previously considered likely benign variant as likely pathogenic. Phenotypic information was available for 636 missense variants, with 441 undergoing 3D structural analysis and active site hotspot identification for 180 variants. After our analysis, only 6% of missense variants were classified as VUSs, and three of them (c.23A>C/p.Asn8Thr, c.59_60delinsCC/p.Gln20Pro, and c.278A >T/p.Asn93Ile) may be influenced by abnormal splicing. Moreover, a pathogenic variant (c.168G>T/p.Glu56Asp) was identified to have a risk exceeding 98% for modifications of the consensus splice site, with high scores indicating a donor loss of 0.94. The integration of ACMG/AMP guidelines with in silico structural analysis and phenotypic data significantly reduced the number of missense VUSs, providing a strong basis for genetic counseling and emphasizing the importance of metabolic phenotype information in variant curation. This study also sheds light on the current landscape of PAH variants.
Collapse
Affiliation(s)
- Nastassja Himmelreich
- Dietmar-Hopp Metabolic Center and Centre for Pediatrics and Adolescent Medicine, University Children's Hospital, Heidelberg, Germany
| | - Santiago Ramón-Maiques
- Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain; Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-Instituto de Salud Carlos III, Valencia, Spain
| | - Rosa Navarrete
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, CIBERER, IdiPAZ, Universidad Autónoma de Madrid, Madrid, Spain
| | - Natalia Castejon-Fernandez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, CIBERER, IdiPAZ, Universidad Autónoma de Madrid, Madrid, Spain
| | - Sven F Garbade
- Dietmar-Hopp Metabolic Center and Centre for Pediatrics and Adolescent Medicine, University Children's Hospital, Heidelberg, Germany
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Lourdes R Desviat
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, CIBERER, IdiPAZ, Universidad Autónoma de Madrid, Madrid, Spain
| | - Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, CIBERER, IdiPAZ, Universidad Autónoma de Madrid, Madrid, Spain.
| | - Nenad Blau
- Divisions of Metabolism, University Children's Hospital, Zürich, Switzerland.
| |
Collapse
|
2
|
Kadıoğlu Yılmaz B, Bağcı Z. Delays in Newborn Screening for Phenylketonuria from Birth to Diagnosis and Factors Affecting This. CHILDREN (BASEL, SWITZERLAND) 2024; 11:571. [PMID: 38790566 PMCID: PMC11120001 DOI: 10.3390/children11050571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/12/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024]
Abstract
This study aims to evaluate the process of neonatal phenylketonuria (PKU) screening from birth to admission to the pediatric metabolism polyclinic, determining delays in the screening program and the factors influencing them. This study was conducted during 2021-2023. Blood collection dates, results, and probable parameters causing delays in the screening program were recorded. This study included 118 infants. Admission time to the polyclinic was (mean ± SD) 25.2 ± 12.6 days (min-max: 3.4-78.9 days). Admission time was significantly high for refugees, those whose parents were consanguineous, and those who had more heel-prick blood samples taken (p < 0.001, p = 0.005, and p < 0.001, respectively). The first heel-prick blood phenylalanine (phe) level was significantly negatively correlated with the admission time (p < 0.001). Patients' admission time whose first blood phe level < 240 μmol/L was statistically significantly higher than in those with ≥240 μmol/L (p < 0.001). We determined that there were delays in PKU screening from birth to admission to the polyclinic. Being a refugee, the presence of consanguineous marriages, the increase in the number of heel-prick tests, and blood phe levels at a range of 120-240 μmol/L were the factors that played a role in this delay. Taking steps to reduce the impact of these parameters can prevent delays in newborn PKU screening and increase the success of the screening program.
Collapse
Affiliation(s)
- Banu Kadıoğlu Yılmaz
- Department of Pediatric Metabolism, Konya City Hospital, University of Health Sciences, Konya 42020, Türkiye
- Department of Pediatric Nutrition and Metabolism, Faculty of Medicine, Selçuk University, Konya 42250, Türkiye
| | - Zafer Bağcı
- Department of Pediatrics, Konya City Hospital, University of Health Sciences, Konya 42020, Türkiye;
| |
Collapse
|
3
|
Tebieva IS, Mishakova PV, Gabisova YV, Khokhova AV, Kaloeva TG, Marakhonov AV, Shchagina OA, Polyakov AV, Ginter EK, Kutsev SI, Zinchenko RA. Genetic Landscape and Clinical Features of Hyperphenylalaninemia in North Ossetia-Alania: High Frequency of P281L and P211T Genetic Variants in the PAH Gene. Int J Mol Sci 2024; 25:4598. [PMID: 38731816 PMCID: PMC11083185 DOI: 10.3390/ijms25094598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 03/30/2024] [Accepted: 04/05/2024] [Indexed: 05/13/2024] Open
Abstract
This study, conducted in the Republic of North Ossetia-Alania (RNOA), aimed to explore the genetic landscape of hyperphenylalaninemia (HPA) and phenylketonuria (PKU) in the Ossetian population using data from newborn screening (NBS). Through comprehensive molecular genetic analysis of 29 patients with HPA from diverse ethnic backgrounds, two major genetic variants in the PAH gene, P281L and P211T, were identified, constituting 50% of all detected pathogenic alleles in Ossetian patients. Remarkably, these variants exhibited an exceptionally high frequency in the Ossetian population, surpassing global prevalence rates. This study unveiled a notable prevalence of mild forms of HPA (78%), underscoring the importance of genetic counseling for carriers of pathogenic variants in the PAH gene. Moreover, the findings emphasized the necessity for ongoing monitoring of patients with mild forms, as they may lack significant symptoms for diagnosis, potentially impacting offspring. Overall, this research offers valuable insights into the genetic landscape of HPA and PKU in the Ossetian population.
Collapse
Affiliation(s)
- Inna S. Tebieva
- North-Ossetian State Medical Academy, 362003 Vladikavkaz, Russia; (I.S.T.); (T.G.K.)
- Republican Children’s Clinical Hospital, 362003 Vladikavkaz, Russia; (Y.V.G.); (A.V.K.)
| | - Polina V. Mishakova
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (P.V.M.); (A.V.M.); (O.A.S.); (A.V.P.); (E.K.G.); (S.I.K.)
| | - Yulia V. Gabisova
- Republican Children’s Clinical Hospital, 362003 Vladikavkaz, Russia; (Y.V.G.); (A.V.K.)
| | - Alana V. Khokhova
- Republican Children’s Clinical Hospital, 362003 Vladikavkaz, Russia; (Y.V.G.); (A.V.K.)
| | - Tamara G. Kaloeva
- North-Ossetian State Medical Academy, 362003 Vladikavkaz, Russia; (I.S.T.); (T.G.K.)
| | - Andrey V. Marakhonov
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (P.V.M.); (A.V.M.); (O.A.S.); (A.V.P.); (E.K.G.); (S.I.K.)
| | - Olga A. Shchagina
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (P.V.M.); (A.V.M.); (O.A.S.); (A.V.P.); (E.K.G.); (S.I.K.)
| | - Alexander V. Polyakov
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (P.V.M.); (A.V.M.); (O.A.S.); (A.V.P.); (E.K.G.); (S.I.K.)
| | - Evgeny K. Ginter
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (P.V.M.); (A.V.M.); (O.A.S.); (A.V.P.); (E.K.G.); (S.I.K.)
| | - Sergey I. Kutsev
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (P.V.M.); (A.V.M.); (O.A.S.); (A.V.P.); (E.K.G.); (S.I.K.)
| | - Rena A. Zinchenko
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (P.V.M.); (A.V.M.); (O.A.S.); (A.V.P.); (E.K.G.); (S.I.K.)
| |
Collapse
|
4
|
Saygılı S, Koşukcu C, Baştuğ T, Doğan ÖA, Yılmaz EK, Kalyoncu AU, Ağbaş A, Canpolat N, Çalışkan S, Ozaltin F. A novel homozygous missense variant in TBC1D31 in a consanguineous family with congenital anomalies of the kidney and urinary tract (CAKUT). Clin Genet 2023; 104:679-685. [PMID: 37468454 DOI: 10.1111/cge.14406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/28/2023] [Accepted: 07/08/2023] [Indexed: 07/21/2023]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) is the leading cause of chronic kidney disease in the first three decades of life. Until now, more than 180 monogenic causes of isolated or syndromic CAKUT have been described. In addition, copy number variants (CNV) have also been implicated, however, all of these causative factors only explain a small fraction of patients with CAKUT, suggesting that additional yet-to-be-discovered novel genes are present. Herein, we report three siblings (two of them are monozygotic twin) of a consanguineous family with CAKUT. Whole-exome sequencing identified a homozygous variant in TBC1D31. Three dimensional protein modeling as well as molecular dynamics simulations predicted it as pathogenic. We therefore showed for the first time an association between a homozygous TBC1D31 variant with CAKUT in humans, expanding its genetic spectrum.
Collapse
Affiliation(s)
- Seha Saygılı
- Department of Pediatric Nephrology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Türkiye
| | - Can Koşukcu
- Department of Bioinformatics, Hacettepe University Institute of Health Sciences, Ankara, Türkiye
| | - Turgut Baştuğ
- Department of Biophysics, Faculty of Medicine, Hacettepe University, Ankara, Türkiye
| | - Özlem Akgün Doğan
- Department of Pediatric Genetics, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Türkiye
| | - Esra Karabağ Yılmaz
- Department of Pediatric Nephrology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Türkiye
| | - Ayşe Uçar Kalyoncu
- Department of Pediatric Radiology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Türkiye
| | - Ayşe Ağbaş
- Department of Pediatric Nephrology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Türkiye
| | - Nur Canpolat
- Department of Pediatric Nephrology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Türkiye
| | - Salim Çalışkan
- Department of Pediatric Nephrology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Türkiye
| | - Fatih Ozaltin
- Department of Bioinformatics, Hacettepe University Institute of Health Sciences, Ankara, Türkiye
- Department of Pediatric Nephrology, Hacettepe University Faculty of Medicine, Ankara, Türkiye
- Nephrogenetics Laboratory, Department of Pediatric Nephrology, Hacettepe University Faculty of Medicine, Ankara, Türkiye
- Center for Genomics and Rare Diseases, Hacettepe University, Ankara, Türkiye
| |
Collapse
|
5
|
Kurniawan J, Ishida T. Comparing Supervised Learning and Rigorous Approach for Predicting Protein Stability upon Point Mutations in Difficult Targets. J Chem Inf Model 2023; 63:6778-6788. [PMID: 37897811 DOI: 10.1021/acs.jcim.3c00750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2023]
Abstract
Accurate prediction of protein stability upon a point mutation has important applications in drug discovery and personalized medicine. It remains a challenging issue in computational biology. Existing computational prediction methods, which range from mechanistic to supervised learning approaches, have experienced limited progress over the last few decades. This stagnation is largely due to their heavy reliance on both the quantity and quality of the training data. This is evident in recent state-of-the-art methods that continue to yield substantial errors on two challenging blind test sets: frataxin and p53, with average root-mean-square errors exceeding 3 and 1.5 kcal/mol, respectively, which is still above the theoretical 1 kcal/mol prediction barrier. Rigorous approaches, on the other hand, offer greater potential for accuracy without relying on training data but are computationally demanding and require both wild-type and mutant structure information. Although they showed high accuracy for conserving mutations, their performance is still limited for charge-changing mutation cases. This might be due to the lack of an available mutant structure, often represented by a simplified capped peptide. The recent advances in protein structure prediction methods now make it possible to obtain structures comparable to experimental ones, including complete mutant structure information. In this work, we compare the performance of supervised learning-based methods and rigorous approaches for predicting protein stability on point mutations in difficult targets: frataxin and p53. The rigorous alchemical method significantly surpasses state-of-the-art techniques in terms of both the root-mean-squared error and Pearson correlation coefficient in these two challenging blind test sets. Additionally, we propose an improved alchemical method that employs the pmx double-system/single-box approach to accurately predict the folding free energy change upon both conserving and charge-changing mutations. The enhanced protocol can accurately predict both types of mutations, thereby outperforming existing state-of-the-art methods in overall performance.
Collapse
Affiliation(s)
- Jason Kurniawan
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Takashi Ishida
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| |
Collapse
|
6
|
Sarodaya N, Tyagi A, Kim HJ, Colaco JC, Kang JS, Kim WJ, Kim KS, Ramakrishna S. Deubiquitinase USP19 enhances phenylalanine hydroxylase protein stability and its enzymatic activity. Cell Biol Toxicol 2023; 39:2295-2310. [PMID: 35449354 DOI: 10.1007/s10565-022-09719-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/07/2022] [Indexed: 12/13/2022]
Abstract
Phenylalanine hydroxylase (PAH) is the key enzyme in phenylalanine metabolism, deficiency of which is associated with the most common metabolic phenotype of phenylketonuria (PKU) and hyperphenylalaninemia (HPA). A bulk of PKU disease-associated missense mutations in the PAH gene have been studied, and the consequence of each PAH variant vary immensely. Prior research established that PKU-associated variants possess defects in protein folding with reduced cellular stability leading to rapid degradation. However, recent evidence revealed that PAH tetramers exist as a mixture of resting state and activated state whose transition depends upon the phenylalanine concentration and certain PAH variants that fail to modulate the structural equilibrium are associated with PKU disease. Collectively, these findings framed our understanding of the complex genotype-phenotype correlation in PKU. In the current study, we substantiate a link between PAH protein stability and its degradation by the ubiquitin-mediated proteasomal degradation system. Here, we provide an evidence that PAH protein undergoes ubiquitination and proteasomal degradation, which can be reversed by deubiquitinating enzymes (DUBs). We identified USP19 as a novel DUB that regulates PAH protein stability. We found that ectopic expression of USP19 increased PAH protein level, whereas depletion of USP19 promoted PAH protein degradation. Our study indicates that USP19 interacts with PAH and prevents polyubiquitination of PAH subsequently extending the half-life of PAH protein. Finally, the increase in the level of PAH protein by the deubiquitinating activity of USP19 resulted in enhanced metabolic function of PAH. In summary, our study identifies the role of USP19 in regulating PAH protein stability and promotes its metabolic activity. Graphical highlights 1. E3 ligase Cdh1 promotes PAH protein degradation leading to insufficient cellular amount of PAH causing PKU. 2. A balance between E3 ligase and DUB is important to regulate the proteostasis of PAH. 3. USP19 deubiquitinates and stabilizes PAH further protecting it from rapid degradation. 4. USP19 increases the enzymatic activity of PAH, thus maintaining normal Phe levels.
Collapse
Affiliation(s)
- Neha Sarodaya
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
| | - Apoorvi Tyagi
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
| | - Hyun-Jin Kim
- Department of Pharmacology, College of Medicine, Hanyang University, Seoul, South Korea
| | - Jencia Carminha Colaco
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
| | - Ju-Seop Kang
- Department of Pharmacology, College of Medicine, Hanyang University, Seoul, South Korea
| | - Woo Jin Kim
- Department of Internal Medicine and Environmental Health Center, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon, South Korea
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea.
- College of Medicine, Hanyang University, Seoul, South Korea.
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea.
- College of Medicine, Hanyang University, Seoul, South Korea.
| |
Collapse
|
7
|
Abildgaard AB, Nielsen SV, Bernstein I, Stein A, Lindorff-Larsen K, Hartmann-Petersen R. Lynch syndrome, molecular mechanisms and variant classification. Br J Cancer 2023; 128:726-734. [PMID: 36434153 PMCID: PMC9978028 DOI: 10.1038/s41416-022-02059-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/27/2022] Open
Abstract
Patients with the heritable cancer disease, Lynch syndrome, carry germline variants in the MLH1, MSH2, MSH6 and PMS2 genes, encoding the central components of the DNA mismatch repair system. Loss-of-function variants disrupt the DNA mismatch repair system and give rise to a detrimental increase in the cellular mutational burden and cancer development. The treatment prospects for Lynch syndrome rely heavily on early diagnosis; however, accurate diagnosis is inextricably linked to correct clinical interpretation of individual variants. Protein variant classification traditionally relies on cumulative information from occurrence in patients, as well as experimental testing of the individual variants. The complexity of variant classification is due to (1) that variants of unknown significance are rare in the population and phenotypic information on the specific variants is missing, and (2) that individual variant testing is challenging, costly and slow. Here, we summarise recent developments in high-throughput technologies and computational prediction tools for the assessment of variants of unknown significance in Lynch syndrome. These approaches may vastly increase the number of interpretable variants and could also provide important mechanistic insights into the disease. These insights may in turn pave the road towards developing personalised treatment approaches for Lynch syndrome.
Collapse
Affiliation(s)
- Amanda B Abildgaard
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sofie V Nielsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Inge Bernstein
- Department of Surgical Gastroenterology, Aalborg University Hospital, Aalborg, Denmark
- Institute of Clinical Medicine, Aalborg University Hospital, Aalborg University, Aalborg, Denmark
| | - Amelie Stein
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
8
|
Liu HT, Weng CY, Zhou L, Xu HB, Liao ZY, Hong HY, Ye YF, Li SF, Wang YJ, Zheng YG. Coevolving stability and activity of LsCR by a single point mutation and constructing neat substrate bioreaction system. Biotechnol Bioeng 2023; 120:1521-1530. [PMID: 36799475 DOI: 10.1002/bit.28357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/29/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023]
Abstract
Carbonyl reductase (CR)-catalyzed bioreduction in the organic phase and the neat substrate reaction system is a lasting challenge, placing higher requirements on the performance of enzymes. Protein engineering is an effective method to enhance the properties of enzymes for industrial applications. In the present work, a single point mutation E145A on our previously constructed CR mutant LsCRM3 , coevolved thermostability, and activity. Compared with LsCRM3 , the catalytic efficiency kcat /KM of LsCRM3 -E145A (LsCRM4 ) was increased from 6.6 to 21.9 s-1 mM-1 . Moreover, E145A prolonged the half-life t1/2 at 40°C from 4.1 to 117 h, T m ${T}_{m}$ was increased by 5°C, T 50 30 ${T}_{50}^{30}$ was increased by 14.6°C, and Topt was increased by 15°C. Only 1 g/L of lyophilized Escherichia coli cells expressing LsCRM4 completely reduced up to 600 g/L 2-chloro-1-(3,4-difluorophenyl)ethanone (CFPO) within 13 h at 45°C, yielding the corresponding (1S)-2-chloro-1-(3,4-difluorophenyl)ethanol ((S)-CFPL) in 99.5% eeP , with a space-time yield of 1.0 kg/L d, the substrate to catalyst ratios (S/C) of 600 g/g. Compared with LsCRM3 , the substrate loading was increased by 50%, with the S/C increased by 14 times. Compared with LsCRWT , the substrate loading was increased by 6.5 times. In contrast, LsCRM4 completely converted 600 g/L CFPO within 12 h in the neat substrate bioreaction system.
Collapse
Affiliation(s)
- Hua-Tao Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Chun-Yue Weng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Lei Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Hao-Bo Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Zhen-Yu Liao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Han-Yue Hong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Yuan-Fan Ye
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Shu-Fang Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| |
Collapse
|
9
|
Tiemann JKS, Zschach H, Lindorff-Larsen K, Stein A. Interpreting the molecular mechanisms of disease variants in human transmembrane proteins. Biophys J 2023:S0006-3495(22)03941-8. [PMID: 36600598 DOI: 10.1016/j.bpj.2022.12.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/19/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023] Open
Abstract
Next-generation sequencing of human genomes reveals millions of missense variants, some of which may lead to loss of protein function and ultimately disease. Here, we investigate missense variants in membrane proteins-key drivers in cell signaling and recognition. We find enrichment of pathogenic variants in the transmembrane region across 19,000 functionally classified variants in human membrane proteins. To accurately predict variant consequences, one fundamentally needs to understand the underlying molecular processes. A key mechanism underlying pathogenicity in missense variants of soluble proteins has been shown to be loss of stability. Membrane proteins, however, are widely understudied. Here, we interpret variant effects on a larger scale by performing structure-based estimations of changes in thermodynamic stability using a membrane-specific energy function and analyses of sequence conservation during evolution of 15 transmembrane proteins. We find evidence for loss of stability being the cause of pathogenicity in more than half of the pathogenic variants, indicating that this is a driving factor also in membrane-protein-associated diseases. Our findings show how computational tools aid in gaining mechanistic insights into variant consequences for membrane proteins. To enable broader analyses of disease-related and population variants, we include variant mappings for the entire human proteome.
Collapse
Affiliation(s)
- Johanna Katarina Sofie Tiemann
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Henrike Zschach
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Amelie Stein
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
10
|
Phosphorylation of Thr9 Affects the Folding Landscape of the N-Terminal Segment of Human AGT Enhancing Protein Aggregation of Disease-Causing Mutants. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248762. [PMID: 36557898 PMCID: PMC9786777 DOI: 10.3390/molecules27248762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
The mutations G170R and I244T are the most common disease cause in primary hyperoxaluria type I (PH1). These mutations cause the misfolding of the AGT protein in the minor allele AGT-LM that contains the P11L polymorphism, which may affect the folding of the N-terminal segment (NTT-AGT). The NTT-AGT is phosphorylated at T9, although the role of this event in PH1 is unknown. In this work, phosphorylation of T9 was mimicked by introducing the T9E mutation in the NTT-AGT peptide and the full-length protein. The NTT-AGT conformational landscape was studied by circular dichroism, NMR, and statistical mechanical methods. Functional and stability effects on the full-length AGT protein were characterized by spectroscopic methods. The T9E and P11L mutations together reshaped the conformational landscape of the isolated NTT-AGT peptide by stabilizing ordered conformations. In the context of the full-length AGT protein, the T9E mutation had no effect on the overall AGT function or conformation, but enhanced aggregation of the minor allele (LM) protein and synergized with the mutations G170R and I244T. Our findings indicate that phosphorylation of T9 may affect the conformation of the NTT-AGT and synergize with PH1-causing mutations to promote aggregation in a genotype-specific manner. Phosphorylation should be considered a novel regulatory mechanism in PH1 pathogenesis.
Collapse
|
11
|
TMAO to the rescue of pathogenic protein variants. Biochim Biophys Acta Gen Subj 2022; 1866:130214. [PMID: 35902028 DOI: 10.1016/j.bbagen.2022.130214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 07/11/2022] [Accepted: 07/21/2022] [Indexed: 11/22/2022]
Abstract
Trimethylamine N-oxide (TMAO) is a chemical chaperone found in various organisms including humans. Various studies unveiled that it is an excellent protein-stabilizing agent, and induces folding of unstructured proteins. It is also well established that it can counteract the deleterious effects of urea, salt, and hydrostatic pressure on macromolecular integrity. There is also existence of large body of data regarding its ability to restore functional deficiency of various mutant proteins or pathogenic variants by correcting misfolding defects and inhibiting the formation of high-order toxic protein oligomers. Since an important class of human disease called "protein conformational disorders" is due to protein misfolding and/or formation of high-order oligomers, TMAO stands as a promising molecule for the therapeutic intervention of such diseases. The present review has been designed to gather a comprehensive knowledge of the TMAO's effect on the functional restoration of various mutants, identify its shortcomings and explore its potentiality as a lead molecule. Future prospects have also been suitably incorporated.
Collapse
|
12
|
Kampmeyer C, Larsen-Ledet S, Wagnkilde MR, Michelsen M, Iversen HKM, Nielsen SV, Lindemose S, Caregnato A, Ravid T, Stein A, Teilum K, Lindorff-Larsen K, Hartmann-Petersen R. Disease-linked mutations cause exposure of a protein quality control degron. Structure 2022; 30:1245-1253.e5. [PMID: 35700725 DOI: 10.1016/j.str.2022.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/08/2022] [Accepted: 05/18/2022] [Indexed: 10/18/2022]
Abstract
More than half of disease-causing missense variants are thought to lead to protein degradation, but the molecular mechanism of how these variants are recognized by the cell remains enigmatic. Degrons are stretches of amino acids that help mediate recognition by E3 ligases and thus confer protein degradation via the ubiquitin-proteasome system. While degrons that mediate controlled degradation of, for example, signaling components and cell-cycle regulators are well described, so-called protein-quality-control degrons that mediate the degradation of destabilized proteins are poorly understood. Here, we show that disease-linked dihydrofolate reductase (DHFR) missense variants are structurally destabilized and chaperone-dependent proteasome targets. We find two regions in DHFR that act as degrons, and the proteasomal turnover of one of these was dependent on the molecular chaperone Hsp70. Structural analyses by nuclear magnetic resonance (NMR) and hydrogen/deuterium exchange revealed that this degron is buried in wild-type DHFR but becomes transiently exposed in the disease-linked missense variants.
Collapse
Affiliation(s)
- Caroline Kampmeyer
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Sven Larsen-Ledet
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Morten Rose Wagnkilde
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Mathias Michelsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Henriette K M Iversen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Sofie V Nielsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Søren Lindemose
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Alberto Caregnato
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Tommer Ravid
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, 91904 Jerusalem, Israel
| | - Amelie Stein
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
| | - Kaare Teilum
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
| | - Kresten Lindorff-Larsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
| |
Collapse
|
13
|
Katsonis P, Wilhelm K, Williams A, Lichtarge O. Genome interpretation using in silico predictors of variant impact. Hum Genet 2022; 141:1549-1577. [PMID: 35488922 PMCID: PMC9055222 DOI: 10.1007/s00439-022-02457-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 04/17/2022] [Indexed: 02/06/2023]
Abstract
Estimating the effects of variants found in disease driver genes opens the door to personalized therapeutic opportunities. Clinical associations and laboratory experiments can only characterize a tiny fraction of all the available variants, leaving the majority as variants of unknown significance (VUS). In silico methods bridge this gap by providing instant estimates on a large scale, most often based on the numerous genetic differences between species. Despite concerns that these methods may lack reliability in individual subjects, their numerous practical applications over cohorts suggest they are already helpful and have a role to play in genome interpretation when used at the proper scale and context. In this review, we aim to gain insights into the training and validation of these variant effect predicting methods and illustrate representative types of experimental and clinical applications. Objective performance assessments using various datasets that are not yet published indicate the strengths and limitations of each method. These show that cautious use of in silico variant impact predictors is essential for addressing genome interpretation challenges.
Collapse
Affiliation(s)
- Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Kevin Wilhelm
- Graduate School of Biomedical Sciences, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Amanda Williams
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Department of Biochemistry, Human Genetics and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Computational and Integrative Biomedical Research Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| |
Collapse
|
14
|
Høie MH, Cagiada M, Beck Frederiksen AH, Stein A, Lindorff-Larsen K. Predicting and interpreting large-scale mutagenesis data using analyses of protein stability and conservation. Cell Rep 2022; 38:110207. [PMID: 35021073 DOI: 10.1016/j.celrep.2021.110207] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/01/2021] [Accepted: 12/13/2021] [Indexed: 01/23/2023] Open
Abstract
Understanding and predicting the functional consequences of single amino acid changes is central in many areas of protein science. Here, we collect and analyze experimental measurements of effects of >150,000 variants in 29 proteins. We use biophysical calculations to predict changes in stability for each variant and assess them in light of sequence conservation. We find that the sequence analyses give more accurate prediction of variant effects than predictions of stability and that about half of the variants that show loss of function do so due to stability effects. We construct a machine learning model to predict variant effects from protein structure and sequence alignments and show how the two sources of information support one another and enable mechanistic interpretations. Together, our results show how one can leverage large-scale experimental assessments of variant effects to gain deeper and general insights into the mechanisms that cause loss of function.
Collapse
Affiliation(s)
- Magnus Haraldson Høie
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Matteo Cagiada
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Anders Haagen Beck Frederiksen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Amelie Stein
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark.
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark.
| |
Collapse
|
15
|
Characterization of phenylalanine hydroxylase gene variants and analysis of genotype-phenotype correlation in patients with phenylalanine hydroxylase deficiency from Fujian Province, Southeastern China. Mol Biol Rep 2022; 49:10409-10419. [PMID: 36104584 PMCID: PMC9618490 DOI: 10.1007/s11033-022-07579-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 05/06/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND Phenylalanine hydroxylase deficiency (PAHD) is the most prevalent inherited disorder of amino acid metabolism in China. Its complex phenotype includes many variants and genotypes among different populations. METHODS AND RESULTS In this study, we analyzed the phenylalanine hydroxylase gene (PAH) variants in a cohort of 93 PAHD patients from Fujian Province. We also assessed genotype and phenotype correlation in patients with PAHD. A total of 44 different pathogenic variants were identified, including five novel variants. The three most prevalent variants among all patents were c.158G > A, p.(Arg53His) (18.03%), c.721C > T, p.(Arg241Cys) (14.75%), and c.728G > A, p.(Arg243Gln) (7.65%). The frequency of the c.158G > A, p.(Arg53His) variant was highest in patients with mild hyperphenylalaninemia, whereas the frequency of the c.1197A > T, p.(Val399 =) and c.331C > T, p.(Arg111Ter) variants was highest in patients with classic phenylketonuria. The most abundant genotypes observed in PAHD patients were c.[158G > A];[728G > A], c.[158G > A];[442-1G > A], and c.[158G > A];[721C > T]. Comparing allelic phenotype to genotypic phenotype values yielded fairly accurate predictions of phenotype, with an overall consistency rate was 85.71% for PAHD patients. CONCLUSIONS Our study identified a PAH variant spectrum in PAHD patients from Fujian Province, Southeastern China. Quantitative correlation analysis between genotype and phenotype severity is helpful for genetic counseling and management.
Collapse
|
16
|
Makukh HV, Chorna LB, Tyrkus MY, Akopyan HR, Shuvarska VI, Malakhova AY, Poliakova YO. Analysis of the PAH Gene Mutations in the Ukrainian Population: A Report from the West Ukrainian Region. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721050066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
17
|
Nemati H, Yousefi SK, Pourvatan N, Aparviz R, Farzaneh P, Koohpar ZK, Safari F, Asl AS, Ranji N. Mutation analysis of phenylketonuria in the North of Iran. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
18
|
Conde-Giménez M, Sancho J. Unravelling the Complex Denaturant and Thermal-Induced Unfolding Equilibria of Human Phenylalanine Hydroxylase. Int J Mol Sci 2021; 22:ijms22126539. [PMID: 34207146 PMCID: PMC8234983 DOI: 10.3390/ijms22126539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/11/2021] [Accepted: 06/15/2021] [Indexed: 12/27/2022] Open
Abstract
Human phenylalanine hydroxylase (PAH) is a metabolic enzyme involved in the catabolism of L-Phe in liver. Loss of conformational stability and decreased enzymatic activity in PAH variants result in the autosomal recessive disorder phenylketonuria (PKU), characterized by developmental and psychological problems if not treated early. One current therapeutic approach to treat PKU is based on pharmacological chaperones (PCs), small molecules that can displace the folding equilibrium of unstable PAH variants toward the native state, thereby rescuing the physiological function of the enzyme. Understanding the PAH folding equilibrium is essential to develop new PCs for different forms of the disease. We investigate here the urea and the thermal-induced denaturation of full-length PAH and of a truncated form lacking the regulatory and the tetramerization domains. For either protein construction, two distinct transitions are seen in chemical denaturation followed by fluorescence emission, indicating the accumulation of equilibrium unfolding intermediates where the catalytic domains are partly unfolded and dissociated from each other. According to analytical centrifugation, the chemical denaturation intermediates of either construction are not well-defined species but highly polydisperse ensembles of protein aggregates. On the other hand, each protein construction similarly shows two transitions in thermal denaturation measured by fluorescence or differential scanning calorimetry, also indicating the accumulation of equilibrium unfolding intermediates. The similar temperatures of mid denaturation of the two constructions, together with their apparent lack of response to protein concentration, indicate the catalytic domains are unfolded in the full-length PAH thermal intermediate, where they remain associated. That the catalytic domain unfolds in the first thermal transition is relevant for the choice of PCs identified in high throughput screening of chemical libraries using differential scanning fluorimetry.
Collapse
Affiliation(s)
- María Conde-Giménez
- Departamento de Bioquímica y Biología Molecular y Celular, Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50009 Zaragoza, Spain;
| | - Javier Sancho
- Departamento de Bioquímica y Biología Molecular y Celular, Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50009 Zaragoza, Spain;
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
- Correspondence:
| |
Collapse
|
19
|
Gersing SK, Wang Y, Grønbæk-Thygesen M, Kampmeyer C, Clausen L, Willemoës M, Andréasson C, Stein A, Lindorff-Larsen K, Hartmann-Petersen R. Mapping the degradation pathway of a disease-linked aspartoacylase variant. PLoS Genet 2021; 17:e1009539. [PMID: 33914734 PMCID: PMC8084241 DOI: 10.1371/journal.pgen.1009539] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 04/06/2021] [Indexed: 11/19/2022] Open
Abstract
Canavan disease is a severe progressive neurodegenerative disorder that is characterized by swelling and spongy degeneration of brain white matter. The disease is genetically linked to polymorphisms in the aspartoacylase (ASPA) gene, including the substitution C152W. ASPA C152W is associated with greatly reduced protein levels in cells, yet biophysical experiments suggest a wild-type like thermal stability. Here, we use ASPA C152W as a model to investigate the degradation pathway of a disease-causing protein variant. When we expressed ASPA C152W in Saccharomyces cerevisiae, we found a decreased steady state compared to wild-type ASPA as a result of increased proteasomal degradation. However, molecular dynamics simulations of ASPA C152W did not substantially deviate from wild-type ASPA, indicating that the native state is structurally preserved. Instead, we suggest that the C152W substitution interferes with the de novo folding pathway resulting in increased proteasomal degradation before reaching its stable conformation. Systematic mapping of the protein quality control components acting on misfolded and aggregation-prone species of C152W, revealed that the degradation is highly dependent on the molecular chaperone Hsp70, its co-chaperone Hsp110 as well as several quality control E3 ubiquitin-protein ligases, including Ubr1. In addition, the disaggregase Hsp104 facilitated refolding of aggregated ASPA C152W, while Cdc48 mediated degradation of insoluble ASPA protein. In human cells, ASPA C152W displayed increased proteasomal turnover that was similarly dependent on Hsp70 and Hsp110. Our findings underscore the use of yeast to determine the protein quality control components involved in the degradation of human pathogenic variants in order to identify potential therapeutic targets.
Collapse
Affiliation(s)
- Sarah K. Gersing
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yong Wang
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Grønbæk-Thygesen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Caroline Kampmeyer
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lene Clausen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Willemoës
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Amelie Stein
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
20
|
Banford S, McCorvie TJ, Pey AL, Timson DJ. Galactosemia: Towards Pharmacological Chaperones. J Pers Med 2021; 11:jpm11020106. [PMID: 33562227 PMCID: PMC7914515 DOI: 10.3390/jpm11020106] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 02/07/2023] Open
Abstract
Galactosemia is a rare inherited metabolic disease resulting from mutations in the four genes which encode enzymes involved in the metabolism of galactose. The current therapy, the removal of galactose from the diet, is inadequate. Consequently, many patients suffer lifelong physical and cognitive disability. The phenotype varies from almost asymptomatic to life-threatening disability. The fundamental biochemical cause of the disease is a decrease in enzymatic activity due to failure of the affected protein to fold and/or function correctly. Many novel therapies have been proposed for the treatment of galactosemia. Often, these are designed to treat the symptoms and not the fundamental cause. Pharmacological chaperones (PC) (small molecules which correct the folding of misfolded proteins) represent an exciting potential therapy for galactosemia. In theory, they would restore enzyme function, thus preventing downstream pathological consequences. In practice, no PCs have been identified for potential application in galactosemia. Here, we review the biochemical basis of the disease, identify opportunities for the application of PCs and describe how these might be discovered. We will conclude by considering some of the clinical issues which will affect the future use of PCs in the treatment of galactosemia.
Collapse
Affiliation(s)
- Samantha Banford
- South Eastern Health and Social Care Trust, Downpatrick BT30 6RL, UK;
| | - Thomas J. McCorvie
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK;
| | - Angel L. Pey
- Departamento de Química Física, Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain;
| | - David J. Timson
- School of Pharmacy and Biomolecular Sciences, The University of Brighton, Brighton BN2 4GJ, UK
- Correspondence:
| |
Collapse
|
21
|
Burgess NM, Kelso W, Malpas CB, Winton-Brown T, Fazio T, Panetta J, De Jong G, Neath J, Atherton S, Velakoulis D, Walterfang M. The effect of improved dietary control on cognitive and psychiatric functioning in adults with phenylketonuria: the ReDAPT study. Orphanet J Rare Dis 2021; 16:35. [PMID: 33461585 PMCID: PMC7814424 DOI: 10.1186/s13023-020-01668-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/22/2020] [Indexed: 11/16/2022] Open
Abstract
Background Phenylketonuria (PKU) is an autosomal recessive inherited disorder characterised by a deficiency in phenylalanine hydroxylase. Untreated, PKU is associated with a wide range of cognitive and psychiatric sequelae. Contemporary management guidelines recommend lifetime dietary control of phenylalanine (Phe) levels, however many individuals who discontinue dietary control subsequently suffer symptoms of anxiety, depression and disturbances to cognition. We undertook a prospective cohort study of patients with early-treated phenylketonuria who had ceased dietary control to test the hypothesis that resumption of dietary control of PKU is associated with improvements in measures of psychiatric morbidity and cognitive functioning. Methods We re-initiated dietary control for early-treated patients with PKU and monitored cognitive and psychiatric outcomes over a twelve-month period. Assessments included objective cognitive function (measured by cognitive proficiency index (CPI)), anxiety and depression scales. General linear mixed model (GLMM) analyses were performed to assess change in psychometric variables from baseline over twelve months after resumption of dietary control. Results A total of nine patients were recruited. Mean age was 33 years (SD = 8.75), five were female. Mean time off dietary control was 19.1 years (SD = 11.3), and mean baseline phenylalanine (Phe) levels were 1108 µmol/L (SD = 293). GLMM analysis demonstrated a positive relationship between CPI and time on diet (b = 0.56 [95% CI = 0.17, 0.95]). Age, time off diet, Phe levels and depression scores were not associated with cognitive function. There was a negative relationship between time on diet and anxiety (b = − 0.88 95% CI = [− 1.26, − 0.50]) and depression ratings (b = − 0.61, 95% CI = [− 0.95, − 0.26]). Conclusions This study demonstrated improvements in cognitive function, anxiety, and depression ratings associated with resumption of dietary control of PKU. Raw Phe levels were not strongly associated with psychiatric or cognitive scores in this cohort. These findings support the importance of lifelong treatment for PKU in improving the cognitive and psychiatric sequelae of the disease.
Collapse
Affiliation(s)
- Nicholas M Burgess
- Neuropsychiatry Unit, Royal Melbourne Hospital, Level 2, John Cade Building, Melbourne,, 3050, Australia
| | - Wendy Kelso
- Neuropsychiatry Unit, Royal Melbourne Hospital, Level 2, John Cade Building, Melbourne,, 3050, Australia
| | - Charles B Malpas
- Department of Neurology, Royal Melbourne Hospital, Melbourne, Australia.,Clinical Outcomes Research Unit (CORe), Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Melbourne, Australia.,Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Toby Winton-Brown
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Timothy Fazio
- Department of Metabolic Medicine, Royal Melbourne Hospital, Melbourne, Australia.,Melbourne Medical School, Department of Medicine and Radiology, University of Melbourne, Parkville, Australia
| | - Julie Panetta
- Department of Metabolic Medicine, Royal Melbourne Hospital, Melbourne, Australia
| | - Gerard De Jong
- Department of Metabolic Medicine, Royal Melbourne Hospital, Melbourne, Australia
| | - Joanna Neath
- Neuropsychiatry Unit, Royal Melbourne Hospital, Level 2, John Cade Building, Melbourne,, 3050, Australia
| | | | - Dennis Velakoulis
- Neuropsychiatry Unit, Royal Melbourne Hospital, Level 2, John Cade Building, Melbourne,, 3050, Australia.,Melbourne Neuropsychiatry Centre, University of Melbourne and North-Western Mental Health, Melbourne, Australia
| | - Mark Walterfang
- Neuropsychiatry Unit, Royal Melbourne Hospital, Level 2, John Cade Building, Melbourne,, 3050, Australia. .,Melbourne Neuropsychiatry Centre, University of Melbourne and North-Western Mental Health, Melbourne, Australia. .,Florey Institute of Neuroscience and Mental Health, Melbourne, Australia.
| |
Collapse
|
22
|
Hernandez R, Facelli JC. Understanding protein structural changes for oncogenic missense variants. Heliyon 2021; 7:e06013. [PMID: 33553733 PMCID: PMC7846930 DOI: 10.1016/j.heliyon.2021.e06013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/20/2020] [Accepted: 01/15/2021] [Indexed: 12/31/2022] Open
Abstract
Understanding and predicting the changes of protein structure and function upon mutation and their relationship to human health is a critical element to translate the genomic revolution into actionable interventions. Therefore, it is pertinent to explore how mutations result in structural changes leading to pathogenic proteins, but due to the protein structural knowledge gap, experimental approaches are lacking. Protein structure prediction methods, such as I-TASSER, have made it possible to predict the structure of a given amino acid sequence, thus opening a new way to explore protein structure changes upon mutations when experimental information is not available. Using known mutations from the Catalogue of Somatic Mutation in Cancer (COSMIC) and ClinVar databases, we compare predicted structure-derived properties from wild type (WT) and mutated proteins and find differences between the local and global 3D protein structures of the WT and the mutants. The studies in this relatively small sample reveal that the structural changes are quite diverse.
Collapse
Affiliation(s)
- Rolando Hernandez
- Department of Biomedical Informatics and Center for Clinical and Translational Science, The University of Utah, Salt Lake City, Utah, USA
| | - Julio C. Facelli
- Department of Biomedical Informatics and Center for Clinical and Translational Science, The University of Utah, Salt Lake City, Utah, USA
| |
Collapse
|
23
|
Pacheco-García JL, Cano-Muñoz M, Sánchez-Ramos I, Salido E, Pey AL. Naturally-Occurring Rare Mutations Cause Mild to Catastrophic Effects in the Multifunctional and Cancer-Associated NQO1 Protein. J Pers Med 2020; 10:E207. [PMID: 33153185 PMCID: PMC7711955 DOI: 10.3390/jpm10040207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 12/13/2022] Open
Abstract
The functional and pathological implications of the enormous genetic diversity of the human genome are mostly unknown, primarily due to our unability to predict pathogenicity in a high-throughput manner. In this work, we characterized the phenotypic consequences of eight naturally-occurring missense variants on the multifunctional and disease-associated NQO1 protein using biophysical and structural analyses on several protein traits. Mutations found in both exome-sequencing initiatives and in cancer cell lines cause mild to catastrophic effects on NQO1 stability and function. Importantly, some mutations perturb functional features located structurally far from the mutated site. These effects are well rationalized by considering the nature of the mutation, its location in protein structure and the local stability of its environment. Using a set of 22 experimentally characterized mutations in NQO1, we generated experimental scores for pathogenicity that correlate reasonably well with bioinformatic scores derived from a set of commonly used algorithms, although the latter fail to semiquantitatively predict the phenotypic alterations caused by a significant fraction of mutations individually. These results provide insight into the propagation of mutational effects on multifunctional proteins, the implementation of in silico approaches for establishing genotype-phenotype correlations and the molecular determinants underlying loss-of-function in genetic diseases.
Collapse
Affiliation(s)
- Juan Luis Pacheco-García
- Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain; (J.L.P.-G.); (M.C.-M.); (I.S.-R.)
| | - Mario Cano-Muñoz
- Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain; (J.L.P.-G.); (M.C.-M.); (I.S.-R.)
| | - Isabel Sánchez-Ramos
- Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain; (J.L.P.-G.); (M.C.-M.); (I.S.-R.)
| | - Eduardo Salido
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, 38320 Tenerife, Spain;
| | - Angel L. Pey
- Departamento de Química Física y Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| |
Collapse
|
24
|
Pey AL. Towards Accurate Genotype-Phenotype Correlations in the CYP2D6 Gene. J Pers Med 2020; 10:jpm10040158. [PMID: 33049937 PMCID: PMC7711719 DOI: 10.3390/jpm10040158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 10/01/2020] [Indexed: 12/17/2022] Open
Abstract
Establishing accurate and large-scale genotype-phenotype correlations and predictions of individual response to pharmacological treatments are two of the holy grails of Personalized Medicine. These tasks are challenging and require an integrated knowledge of the complex processes that regulate gene expression and, ultimately, protein functionality in vivo, the effects of mutations/polymorphisms and the different sources of interindividual phenotypic variability. A remarkable example of our advances in these challenging tasks is the highly polymorphic CYP2D6 gene, which encodes a cytochrome P450 enzyme involved in the metabolization of many of the most marketed drugs (including SARS-Cov-2 therapies such as hydroxychloroquine). Since the introduction of simple activity scores (AS) over 10 years ago, its ability to establish genotype-phenotype correlations on the drug metabolizing capacity of this enzyme in human population has provided lessons that will help to improve this type of score for this, and likely many other human genes and proteins. Multidisciplinary research emerges as the best approach to incorporate additional concepts to refine and improve such functional/activity scores for the CYP2D6 gene, as well as for many other human genes associated with simple and complex genetic diseases.
Collapse
Affiliation(s)
- Angel L Pey
- Departamento de Química Física, Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| |
Collapse
|
25
|
Investigating the structural impacts of a novel missense variant identified with whole exome sequencing in an Egyptian patient with propionic acidemia. Mol Genet Metab Rep 2020; 25:100645. [PMID: 32995289 PMCID: PMC7502849 DOI: 10.1016/j.ymgmr.2020.100645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/24/2020] [Accepted: 08/24/2020] [Indexed: 12/22/2022] Open
Abstract
Propionic Acidemia (PA) is an inborn error of metabolism caused by variants in the PCCA or PCCB genes, leading to mitochondrial accumulation of propionyl-CoA and its by-products. Here, we report a 2 year-old Egyptian boy with PA who was born to consanguineous parents. Biochemical analysis was performed using tandem mass spectrometry (MS/MS) on the patient's dried blood spots (DBS) followed by urine examination of amino acids using gas chromatography/mass spectrometry (GC/MS). Molecular genetic analysis was carried out using whole-exome sequencing (WES). The PCCA gene sequencing revealed a novel homozygous missense variant affecting the locus (chr13:100962160) of exon 16 of the PCCA gene, resulting in the substitution of the amino acid arginine with proline at site 476 (p.Arg476Pro). Computational analysis revealed that the novel variant might be pathogenic and attributed to decrease the stability and also has an effect on the biotin carboxylase c-terminal domain of the propionyl carboxylase enzyme. The physicochemical properties analysis using NCBI amino acid explorer study revealed restrictions in the side chain and loss of hydrogen bonds due to the variant. On the structural level, the loss of beta-sheet was observed due to the variant proline, which has further led to the loss of surrounding interactions. This loss of beta-sheet and the surrounding interactions might serve the purpose of the structural stability changes. The current study demonstrates that a combination of whole-exome sequencing (WES) and computational analysis are potent tools for validation of diagnosis and classification of disease-causing variants.
Collapse
|
26
|
Sarodaya N, Suresh B, Kim KS, Ramakrishna S. Protein Degradation and the Pathologic Basis of Phenylketonuria and Hereditary Tyrosinemia. Int J Mol Sci 2020; 21:ijms21144996. [PMID: 32679806 PMCID: PMC7404301 DOI: 10.3390/ijms21144996] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022] Open
Abstract
A delicate intracellular balance among protein synthesis, folding, and degradation is essential to maintaining protein homeostasis or proteostasis, and it is challenged by genetic and environmental factors. Molecular chaperones and the ubiquitin proteasome system (UPS) play a vital role in proteostasis for normal cellular function. As part of protein quality control, molecular chaperones recognize misfolded proteins and assist in their refolding. Proteins that are beyond repair or refolding undergo degradation, which is largely mediated by the UPS. The importance of protein quality control is becoming ever clearer, but it can also be a disease-causing mechanism. Diseases such as phenylketonuria (PKU) and hereditary tyrosinemia-I (HT1) are caused due to mutations in PAH and FAH gene, resulting in reduced protein stability, misfolding, accelerated degradation, and deficiency in functional proteins. Misfolded or partially unfolded proteins do not necessarily lose their functional activity completely. Thus, partially functional proteins can be rescued from degradation by molecular chaperones and deubiquitinating enzymes (DUBs). Deubiquitination is an important mechanism of the UPS that can reverse the degradation of a substrate protein by covalently removing its attached ubiquitin molecule. In this review, we discuss the importance of molecular chaperones and DUBs in reducing the severity of PKU and HT1 by stabilizing and rescuing mutant proteins.
Collapse
Affiliation(s)
- Neha Sarodaya
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (B.S.)
| | - Bharathi Suresh
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (B.S.)
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (B.S.)
- College of Medicine, Hanyang University, Seoul 04763, Korea
- Correspondence: (K.-S.K.); or (S.R.)
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (B.S.)
- College of Medicine, Hanyang University, Seoul 04763, Korea
- Correspondence: (K.-S.K.); or (S.R.)
| |
Collapse
|
27
|
Jana K, Mehra R, Dehury B, Blundell TL, Kepp KP. Common mechanism of thermostability in small α- and β-proteins studied by molecular dynamics. Proteins 2020; 88:1233-1250. [PMID: 32368818 DOI: 10.1002/prot.25897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 04/01/2020] [Accepted: 04/29/2020] [Indexed: 12/13/2022]
Abstract
Protein thermostability is important to evolution, diseases, and industrial applications. Proteins use diverse molecular strategies to achieve stability at high temperature, yet reducing the entropy of unfolding seems required. We investigated five small α-proteins and five β-proteins with known, distinct structures and thermostability (Tm ) using multi-seed molecular dynamics simulations at 300, 350, and 400 K. The proteins displayed diverse changes in hydrogen bonding, solvent exposure, and secondary structure with no simple relationship to Tm . Our dynamics were in good agreement with experimental B-factors at 300 K and insensitive to force-field choice. Despite the very distinct structures, the native-state (300 + 350 K) free-energy landscapes (FELs) were significantly broader for the two most thermostable proteins and smallest for the three least stable proteins in both the α- and β-group and with both force fields studied independently (tailed t-test, 95% confidence level). Our results suggest that entropic ensembles stabilize proteins at high temperature due to reduced entropy of unfolding, viz., ΔG = ΔH - TΔS. Supporting this mechanism, the most thermostable proteins were also the least kinetically stable, consistent with broader FELs, typified by villin headpiece and confirmed by specific comparison to a mesophilic ortholog of Thermus thermophilus apo-pyrophosphate phosphohydrolase. We propose that molecular strategies of protein thermostabilization, although diverse, tend to converge toward highest possible entropy in the native state consistent with the functional requirements. We speculate that this tendency may explain why many proteins are not optimally structured and why molten-globule states resemble native proteins so much.
Collapse
Affiliation(s)
| | | | - Budheswar Dehury
- DTU Chemistry, Technical University of Denmark, Lyngby, Denmark.,Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Kasper P Kepp
- DTU Chemistry, Technical University of Denmark, Lyngby, Denmark
| |
Collapse
|
28
|
Tang N, Sandahl TD, Ott P, Kepp KP. Computing the Pathogenicity of Wilson's Disease ATP7B Mutations: Implications for Disease Prevalence. J Chem Inf Model 2019; 59:5230-5243. [PMID: 31751128 DOI: 10.1021/acs.jcim.9b00852] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Genetic variations in the gene encoding the copper-transport protein ATP7B are the primary cause of Wilson's disease. Controversially, clinical prevalence seems much smaller than the prevalence estimated by genetic screening tools, causing fear that many people are undiagnosed, although early diagnosis and treatment is essential. To address this issue, we benchmarked 16 state-of-the-art computational disease-prediction methods against established data of missense ATP7B mutations. Our results show that the quality of the methods varies widely. We show the importance of optimizing the threshold of the methods used to distinguish pathogenic from nonpathogenic mutations against data of clinically confirmed pathogenic and nonpathogenic mutations. We find that most methods use thresholds that predict too many ATP7B mutations to be pathogenic. Thus, our findings explain the current controversy on Wilson's disease prevalence because meta-analysis and text search methods include many computational estimates that lead to higher disease prevalence than clinically observed. As proteins and diseases differ widely, a one-size-fits-all threshold cannot distinguish pathogenic and nonpathogenic mutations efficiently, as shown here. We also show that amino acid changes with small evolutionary substitution probability, mainly due to amino acid volume, are more associated with the disease, implying a pathological effect on the conformational state of the protein, which could affect copper transport or adenosine triphosphate recognition and hydrolysis. These findings may be a first step toward a more quantitative genotype-phenotype relationship of Wilson's disease.
Collapse
Affiliation(s)
- Ning Tang
- DTU Chemistry , Technical University of Denmark , Kemitorvet 206 , 2800 Kongens Lyngby , Denmark
| | - Thomas D Sandahl
- Department of Hepatology and Gastroenterology , Aarhus University Hospital , 8200 Aarhus , Denmark
| | - Peter Ott
- Department of Hepatology and Gastroenterology , Aarhus University Hospital , 8200 Aarhus , Denmark
| | - Kasper P Kepp
- DTU Chemistry , Technical University of Denmark , Kemitorvet 206 , 2800 Kongens Lyngby , Denmark
| |
Collapse
|
29
|
Ansar M, Chung H, Waryah YM, Makrythanasis P, Falconnet E, Rao AR, Guipponi M, Narsani AK, Fingerhut R, Santoni FA, Ranza E, Waryah AM, Bellen HJ, Antonarakis SE. Visual impairment and progressive phthisis bulbi caused by recessive pathogenic variant in MARK3. Hum Mol Genet 2019; 27:2703-2711. [PMID: 29771303 DOI: 10.1093/hmg/ddy180] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 05/02/2018] [Accepted: 05/06/2018] [Indexed: 12/20/2022] Open
Abstract
Developmental eye defects often severely reduce vision. Despite extensive efforts, for a substantial fraction of these cases the molecular causes are unknown. Recessive eye disorders are frequent in consanguineous populations and such large families with multiple affected individuals provide an opportunity to identify recessive causative genes. We studied a Pakistani consanguineous family with three affected individuals with congenital vision loss and progressive eye degeneration. The family was analyzed by exome sequencing of one affected individual and genotyping of all family members. We have identified a non-synonymous homozygous variant (NM_001128918.2: c.1708C > G: p.Arg570Gly) in the MARK3 gene as the likely cause of the phenotype. Given that MARK3 is highly conserved in flies (I: 55%; S: 67%) we knocked down the MARK3 homologue, par-1, in the eye during development. This leads to a significant reduction in eye size, a severe loss of photoreceptors and loss of vision based on electroretinogram (ERG) recordings. Expression of the par-1 p.Arg792Gly mutation (equivalent to the MARK3 variant found in patients) in developing fly eyes also induces loss of eye tissue and reduces the ERG signals. The data in flies and human indicate that the MARK3 variant corresponds to a loss of function. We conclude that the identified mutation in MARK3 establishes a new gene-disease link, since it likely causes structural abnormalities during eye development and visual impairment in humans, and that the function of MARK3/par-1 is evolutionarily conserved in eye development.
Collapse
Affiliation(s)
- Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Hyunglok Chung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Yar M Waryah
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Emilie Falconnet
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Ali Raza Rao
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Michel Guipponi
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Ashok K Narsani
- Institute of Ophthalmology, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Ralph Fingerhut
- Swiss Newborn Screening Laboratory, University Children's Hospital, Zurich, Switzerland
| | - Federico A Santoni
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Emmanuelle Ranza
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Ali M Waryah
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Howard Hughes Medical Institute, Houston, TX, USA
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
| |
Collapse
|
30
|
Abildgaard AB, Stein A, Nielsen SV, Schultz-Knudsen K, Papaleo E, Shrikhande A, Hoffmann ER, Bernstein I, Gerdes AM, Takahashi M, Ishioka C, Lindorff-Larsen K, Hartmann-Petersen R. Computational and cellular studies reveal structural destabilization and degradation of MLH1 variants in Lynch syndrome. eLife 2019; 8:e49138. [PMID: 31697235 PMCID: PMC6837844 DOI: 10.7554/elife.49138] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022] Open
Abstract
Defective mismatch repair leads to increased mutation rates, and germline loss-of-function variants in the repair component MLH1 cause the hereditary cancer predisposition disorder known as Lynch syndrome. Early diagnosis is important, but complicated by many variants being of unknown significance. Here we show that a majority of the disease-linked MLH1 variants we studied are present at reduced cellular levels. We show that destabilized MLH1 variants are targeted for chaperone-assisted proteasomal degradation, resulting also in degradation of co-factors PMS1 and PMS2. In silico saturation mutagenesis and computational predictions of thermodynamic stability of MLH1 missense variants revealed a correlation between structural destabilization, reduced steady-state levels and loss-of-function. Thus, we suggest that loss of stability and cellular degradation is an important mechanism underlying many MLH1 variants in Lynch syndrome. Combined with analyses of conservation, the thermodynamic stability predictions separate disease-linked from benign MLH1 variants, and therefore hold potential for Lynch syndrome diagnostics.
Collapse
Affiliation(s)
- Amanda B Abildgaard
- Department of Biology, The Linderstrøm-Lang Centre for Protein ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Amelie Stein
- Department of Biology, The Linderstrøm-Lang Centre for Protein ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Sofie V Nielsen
- Department of Biology, The Linderstrøm-Lang Centre for Protein ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Katrine Schultz-Knudsen
- Department of Biology, The Linderstrøm-Lang Centre for Protein ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Elena Papaleo
- Department of Biology, The Linderstrøm-Lang Centre for Protein ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Amruta Shrikhande
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular MedicineUniversity of CopenhagenCopenhagenDenmark
| | - Eva R Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular MedicineUniversity of CopenhagenCopenhagenDenmark
| | - Inge Bernstein
- Department of Surgical GastroenterologyAalborg University HospitalAalborgDenmark
| | | | - Masanobu Takahashi
- Department of Medical OncologyTohoku University Hospital, Tohoku UniversitySendaiJapan
| | - Chikashi Ishioka
- Department of Medical OncologyTohoku University Hospital, Tohoku UniversitySendaiJapan
| | - Kresten Lindorff-Larsen
- Department of Biology, The Linderstrøm-Lang Centre for Protein ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Rasmus Hartmann-Petersen
- Department of Biology, The Linderstrøm-Lang Centre for Protein ScienceUniversity of CopenhagenCopenhagenDenmark
| |
Collapse
|
31
|
Stein A, Fowler DM, Hartmann-Petersen R, Lindorff-Larsen K. Biophysical and Mechanistic Models for Disease-Causing Protein Variants. Trends Biochem Sci 2019; 44:575-588. [PMID: 30712981 PMCID: PMC6579676 DOI: 10.1016/j.tibs.2019.01.003] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 12/13/2022]
Abstract
The rapid decrease in DNA sequencing cost is revolutionizing medicine and science. In medicine, genome sequencing has revealed millions of missense variants that change protein sequences, yet we only understand the molecular and phenotypic consequences of a small fraction. Within protein science, high-throughput deep mutational scanning experiments enable us to probe thousands of variants in a single, multiplexed experiment. We review efforts that bring together these topics via experimental and computational approaches to determine the consequences of missense variants in proteins. We focus on the role of changes in protein stability as a driver for disease, and how experiments, biophysical models, and computation are providing a framework for understanding and predicting how changes in protein sequence affect cellular protein stability.
Collapse
Affiliation(s)
- Amelie Stein
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Douglas M Fowler
- Departments of Genome Sciences and Bioengineering, University of Washington, Seattle, WA, USA
| | - Rasmus Hartmann-Petersen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
32
|
Pecimonova M, Kluckova D, Csicsay F, Reblova K, Krahulec J, Procházkova D, Skultety L, Kadasi L, Soltysova A. Structural and Functional Impact of Seven Missense Variants of Phenylalanine Hydroxylase. Genes (Basel) 2019; 10:E459. [PMID: 31208052 PMCID: PMC6628251 DOI: 10.3390/genes10060459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 11/17/2022] Open
Abstract
The molecular genetics of well-characterized inherited diseases, such as phenylketonuria (PKU) and hyperphenylalaninemia (HPA) predominantly caused by mutations in the phenylalanine hydroxylase (PAH) gene, is often complicated by the identification of many novel variants, often with no obvious impact on the associated disorder. To date, more than 1100 PAH variants have been identified of which a substantial portion have unknown clinical significance. In this work, we study the functionality of seven yet uncharacterized PAH missense variants p.Asn167Tyr, p.Thr200Asn, p.Asp229Gly, p.Gly239Ala, p.Phe263Ser, p.Ala342Pro, and p.Ile406Met first identified in the Czech PKU/HPA patients. From all tested variants, three of them, namely p.Asn167Tyr, p.Thr200Asn, and p.Ile406Met, exerted residual enzymatic activity in vitro similar to wild type (WT) PAH, however, when expressed in HepG2 cells, their protein level reached a maximum of 72.1% ± 4.9%, 11.2% ± 4.2%, and 36.6% ± 7.3% compared to WT PAH, respectively. Remaining variants were null with no enzyme activity and decreased protein levels in HepG2 cells. The chaperone-like effect of applied BH4 precursor increased protein level significantly for p.Asn167Tyr, p.Asp229Gly, p.Ala342Pro, and p.Ile406Met. Taken together, our results of functional characterization in combination with in silico prediction suggest that while p.Asn167Tyr, p.Thr200Asn, and p.Ile406Met PAH variants have a mild impact on the protein, p.Asp229Gly, p.Gly239Ala, p.Phe263Ser, and p.Ala342Pro severely affect protein structure and function.
Collapse
Affiliation(s)
- Martina Pecimonova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia.
| | - Daniela Kluckova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia.
| | - Frantisek Csicsay
- Insitute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia.
| | - Kamila Reblova
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic.
| | - Jan Krahulec
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia.
| | - Dagmar Procházkova
- Department of Pediatrics, Medical Faculty of Masaryk University and University Hospital Brno, Černopolní 9, 625 00 Brno, Czech Republic.
| | - Ludovit Skultety
- Insitute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia.
| | - Ludevit Kadasi
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia.
- Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia.
| | - Andrea Soltysova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia.
- Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia.
| |
Collapse
|
33
|
Flydal MI, Alcorlo-Pagés M, Johannessen FG, Martínez-Caballero S, Skjærven L, Fernandez-Leiro R, Martinez A, Hermoso JA. Structure of full-length human phenylalanine hydroxylase in complex with tetrahydrobiopterin. Proc Natl Acad Sci U S A 2019; 116:11229-11234. [PMID: 31118288 PMCID: PMC6561269 DOI: 10.1073/pnas.1902639116] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Phenylalanine hydroxylase (PAH) is a key enzyme in the catabolism of phenylalanine, and mutations in this enzyme cause phenylketonuria (PKU), a genetic disorder that leads to brain damage and mental retardation if untreated. Some patients benefit from supplementation with a synthetic formulation of the cofactor tetrahydrobiopterin (BH4) that partly acts as a pharmacological chaperone. Here we present structures of full-length human PAH (hPAH) both unbound and complexed with BH4 in the precatalytic state. Crystal structures, solved at 3.18-Å resolution, show the interactions between the cofactor and PAH, explaining the negative regulation exerted by BH4 BH4 forms several H-bonds with the N-terminal autoregulatory tail but is far from the catalytic FeII Upon BH4 binding a polar and salt-bridge interaction network links the three PAH domains, explaining the stability conferred by BH4 Importantly, BH4 binding modulates the interaction between subunits, providing information about PAH allostery. Moreover, we also show that the cryo-EM structure of hPAH in absence of BH4 reveals a highly dynamic conformation for the tetramers. Structural analyses of the hPAH:BH4 subunits revealed that the substrate-induced movement of Tyr138 into the active site could be coupled to the displacement of BH4 from the precatalytic toward the active conformation, a molecular mechanism that was supported by site-directed mutagenesis and targeted molecular dynamics simulations. Finally, comparison of the rat and human PAH structures show that hPAH is more dynamic, which is related to amino acid substitutions that enhance the flexibility of hPAH and may increase the susceptibility to PKU-associated mutations.
Collapse
Affiliation(s)
| | - Martín Alcorlo-Pagés
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | | | | | - Lars Skjærven
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Rafael Fernandez-Leiro
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway;
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain;
| |
Collapse
|
34
|
Yan Y, Zhang C, Jin X, Zhang Q, Zheng L, Feng X, Hao S, Gao H, Ma X. Mutation spectrum of PAH gene in phenylketonuria patients in Northwest China: identification of twenty novel variants. Metab Brain Dis 2019; 34:733-745. [PMID: 30747360 DOI: 10.1007/s11011-019-0387-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/20/2019] [Indexed: 10/27/2022]
Abstract
This study was performed to analyze the mutational spectrum of the phenylalanine hydroxylase (PAH) gene in phenylketonuria (PKU) patients in Northwest China, to identify mutational hot spots, and to determine the correlation between variants and clinical phenotypes of PKU. A large cohort of 475 PKU families in Northwest China was enrolled to analyze PAH gene variants using Sanger sequencing, Multiplex ligation-dependent probe amplification (MLPA), and gap-PCR. Bioinformatics software was used to predict the pathogenicity of novel variants and analyze the correlations between PAH gene variants and phenotypes of PKU patients. A total of 895 variants were detected in the 950 alleles of 475 patients with PKU (detection rate: 94.21%), 20 of which were novel variants. Other 108, previously known variants, were also identified, with the three most frequent variants being p.Arg243Gln (14.00%), c.611A > G (5.58%), and p.Tyr356* (4.95%). Seven different large deletion/duplication variants were identified by the MLPA method, including the large deletion c.-4163_-406del3758 with high frequency. A correlation analysis between patient phenotype and gene variant frequency showed that p.Arg53His and p.Gln419Arg were correlated with mild hyperphenylalaninemia (MHP). In conclusion, the mutational spectrum underlying PKU in Northwest China was established for the first time. Functional analysis of 20 novel PAH gene variants enriched the PAH gene mutational spectrum. Correlation analysis between variants frequencies in compound heterozygous patients and phenotype severity is helpful for phenotypic prediction.
Collapse
Affiliation(s)
- Yousheng Yan
- Graduate School of Peking Union Medical College, Beijing, 100730, China
- National Research Institute for Health and Family Planning, No. 12 Dahuisi Road, Beijing, 100081, China
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, 730050, China
| | - Chuan Zhang
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, 730050, China
| | - Xiaohua Jin
- Graduate School of Peking Union Medical College, Beijing, 100730, China
- National Research Institute for Health and Family Planning, No. 12 Dahuisi Road, Beijing, 100081, China
| | - Qinhua Zhang
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, 730050, China
| | - Lei Zheng
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, 730050, China
| | - Xuan Feng
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, 730050, China
| | - Shengju Hao
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, 730050, China
| | - Huafang Gao
- Graduate School of Peking Union Medical College, Beijing, 100730, China.
- National Research Institute for Health and Family Planning, No. 12 Dahuisi Road, Beijing, 100081, China.
| | - Xu Ma
- Graduate School of Peking Union Medical College, Beijing, 100730, China.
- National Research Institute for Health and Family Planning, No. 12 Dahuisi Road, Beijing, 100081, China.
| |
Collapse
|
35
|
In vitro residual activities in 20 variants of phenylalanine hydroxylase and genotype-phenotype correlation in phenylketonuria patients. Gene 2019; 707:239-245. [PMID: 31102715 DOI: 10.1016/j.gene.2019.05.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/12/2019] [Accepted: 05/13/2019] [Indexed: 11/21/2022]
Abstract
Phenylketonuria (PKU), caused by phenylalanine hydroxylase (PAH) gene variants, is a common autosomal inherited metabolic disease. So far, 1111 PAH variants have been revealed. The residual activity of the PAH variants is the key determinant of the metabolic phenotype and BH4 responsiveness in PKU patients. In this study, the spectrum of PAH variants in 1083 Chinese PKU patients was analyzed. Then 20 variants (p.L52F, p.R86P, p.L128P, p.L142P, p.D163N, p.C203G, p.E214G, p.F260L, p.M276T, p.L311R, p.P314A, p.L364F, p.Q375H, p.F382I, p.A395S, p.V412D, p.E108*, p.C203*, p.C284* and p.E353*) were expressed in COS-7 cells. The residual activities and protein expression levels were detected by isotope-dilution liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) and Western blotting, respectively. We compared the results of the phenotypic prediction based on APV and PAH activity respectively, and further explored the relationship between residual activity and phenotype in PKU patients. We reported 9 newly discovered PAH variants for the first time, thereby expanding the spectrum of PAH variants. Among the 20 variants in our assay, 8 variants showed mild impaired residual activities (48-92%) and approximately normal protein expression levels compared to the wild-type PAH. In contrast, 9 variants showed severely impaired residual activities (0-34%) and reduced protein expression. However, three variants (p.L52F, p.F260L and p.P314A) showed impaired residual activities (5%, 32% and 29%), although the proteins were well expressed. We assigned APV scores for 14 variants, in which the results of the phenotypic prediction were consistent for 12/14 (86%) variants based on APV and residual activity respectively, and the residual activity correctly predicted 17/22 (77%) of the patients. Our study helped to further understand the genotype-phenotype correlation in PKU patients.
Collapse
|
36
|
Beaver SK, Mesa-Torres N, Pey AL, Timson DJ. NQO1: A target for the treatment of cancer and neurological diseases, and a model to understand loss of function disease mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:663-676. [PMID: 31091472 DOI: 10.1016/j.bbapap.2019.05.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/07/2019] [Accepted: 05/09/2019] [Indexed: 01/08/2023]
Abstract
NAD(P)H quinone oxidoreductase 1 (NQO1) is a multi-functional protein that catalyses the reduction of quinones (and other molecules), thus playing roles in xenobiotic detoxification and redox balance, and also has roles in stabilising apoptosis regulators such as p53. The structure and enzymology of NQO1 is well-characterised, showing a substituted enzyme mechanism in which NAD(P)H binds first and reduces an FAD cofactor in the active site, assisted by a charge relay system involving Tyr-155 and His-161. Protein dynamics play important role in physio-pathological aspects of this protein. NQO1 is a good target to treat cancer due to its overexpression in cancer cells. A polymorphic form of NQO1 (p.P187S) is associated with increased cancer risk and certain neurological disorders (such as multiple sclerosis and Alzheimer´s disease), possibly due to its roles in the antioxidant defence. p.P187S has greatly reduced FAD affinity and stability, due to destabilization of the flavin binding site and the C-terminal domain, which leading to reduced activity and enhanced degradation. Suppressor mutations partially restore the activity of p.P187S by local stabilization of these regions, and showing long-range allosteric communication within the protein. Consequently, the correction of NQO1 misfolding by pharmacological chaperones is a viable strategy, which may be useful to treat cancer and some neurological conditions, targeting structural spots linked to specific disease-mechanisms. Thus, NQO1 emerges as a good model to investigate loss of function mechanisms in genetic diseases as well as to improve strategies to discriminate between neutral and pathogenic variants in genome-wide sequencing studies.
Collapse
Affiliation(s)
- Sarah K Beaver
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton BN2 4GJ, UK
| | - Noel Mesa-Torres
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071, Spain
| | - Angel L Pey
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071, Spain.
| | - David J Timson
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton BN2 4GJ, UK.
| |
Collapse
|
37
|
Vieira Neto E, Laranjeira F, Quelhas D, Ribeiro I, Seabra A, Mineiro N, Carvalho LM, Lacerda L, Ribeiro MG. Genotype-phenotype correlations and BH 4 estimated responsiveness in patients with phenylketonuria from Rio de Janeiro, Southeast Brazil. Mol Genet Genomic Med 2019; 7:e610. [PMID: 30829006 PMCID: PMC6503030 DOI: 10.1002/mgg3.610] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 01/15/2019] [Accepted: 01/24/2019] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Genetic heterogeneity and compound heterozygosis give rise to a continuous spectrum of phenylalanine hydroxylase deficiency and metabolic phenotypes in phenylketonuria (PKU). The most used parameters for evaluating phenotype in PKU are pretreatment phenylalanine (Phe) levels, tolerance for dietary Phe, and Phe overloading test. Phenotype can vary from a "classic" (severe) form to mild hyperphenylalaninemia, which does not require dietary treatment. A subset of patients is responsive to treatment by the cofactor tetrahydrobiopterin (BH4 ). Genotypes of PKU patients from Rio de Janeiro, Brazil, were compared to predicted and observed phenotypes. Genotype-based estimations of responsiveness to BH4 were also conducted. METHODS Phenotype was defined by pretreatment Phe levels. A standard prediction system based on arbitrary assigned values was employed to measure genotype-phenotype concordance. Patients were also estimated as BH4 -responders according to the responsiveness previously reported for their mutations and genotypes. RESULTS A 48.3% concordance rate between genotype-predicted and observed phenotypes was found. When the predicted phenotypes included those reported at the BIOPKU database, the concordance rate reached 77%. A total of 18 genotypes from 30 patients (29.4%) were estimated as of potential or probable BH4 responsiveness. Inconsistencies were observed in genotypic combinations including the common "moderate" mutations p.R261Q, p.V388M, and p.I65T and the mild mutations p.L48S, p.R68S, and p.L249F. CONCLUSION The high discordance rate between genotype-predicted and observed metabolic phenotypes in this study seems to be due partially to the high frequency of the so-called "moderate" common mutations, p.R261Q, p.V388M, and p.I65T, which are reported to be associated to erratic or more severe than expected metabolic phenotypes. Although our results of BH4 estimated responsiveness must be regarded as tentative, it should be emphasized that genotyping and genotype-phenotype association studies are important in selecting patients to be offered a BH4 overload test, especially in low-resource settings like Brazil.
Collapse
Affiliation(s)
- Eduardo Vieira Neto
- Agência Nacional de Saúde SuplementarGerência de Monitoramento AssistencialRio de JaneiroBrazil
- Serviço de Genética MédicaInstituto de Puericultura e Pediatria Martagão GesteiraUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Francisco Laranjeira
- Centro de Genética Médica Doutor Jacinto MagalhãesUnidade de Bioquímica GenéticaPortoPortugal
| | - Dulce Quelhas
- Centro de Genética Médica Doutor Jacinto MagalhãesUnidade de Bioquímica GenéticaPortoPortugal
- Unidade Multidisciplinar de Investigação BiomédicaUniversidade do PortoPortoPortugal
| | - Isaura Ribeiro
- Centro de Genética Médica Doutor Jacinto MagalhãesUnidade de Bioquímica GenéticaPortoPortugal
- Unidade Multidisciplinar de Investigação BiomédicaUniversidade do PortoPortoPortugal
| | - Alexandre Seabra
- Centro de Genética Médica Doutor Jacinto MagalhãesUnidade de Bioquímica GenéticaPortoPortugal
- Instituto de Ciências Biomédicas Abel SalazarUniversidade do PortoPortoPortugal
| | - Nicole Mineiro
- Centro de Genética Médica Doutor Jacinto MagalhãesUnidade de Bioquímica GenéticaPortoPortugal
| | - Lilian M. Carvalho
- Serviço de MetabologiaInstituto Estadual de Diabetes e Endocrinologia Luiz CapriglioneRio de JaneiroBrazil
| | - Lúcia Lacerda
- Centro de Genética Médica Doutor Jacinto MagalhãesUnidade de Bioquímica GenéticaPortoPortugal
| | - Márcia G. Ribeiro
- Serviço de Genética MédicaInstituto de Puericultura e Pediatria Martagão GesteiraUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
| |
Collapse
|
38
|
Brennecke P, Rasina D, Aubi O, Herzog K, Landskron J, Cautain B, Vicente F, Quintana J, Mestres J, Stechmann B, Ellinger B, Brea J, Kolanowski JL, Pilarski R, Orzaez M, Pineda-Lucena A, Laraia L, Nami F, Zielenkiewicz P, Paruch K, Hansen E, von Kries JP, Neuenschwander M, Specker E, Bartunek P, Simova S, Leśnikowski Z, Krauss S, Lehtiö L, Bilitewski U, Brönstrup M, Taskén K, Jirgensons A, Lickert H, Clausen MH, Andersen JH, Vicent MJ, Genilloud O, Martinez A, Nazaré M, Fecke W, Gribbon P. EU-OPENSCREEN: A Novel Collaborative Approach to Facilitate Chemical Biology. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2019; 24:398-413. [PMID: 30616481 PMCID: PMC6764006 DOI: 10.1177/2472555218816276] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/11/2018] [Accepted: 11/08/2018] [Indexed: 12/27/2022]
Abstract
Compound screening in biological assays and subsequent optimization of hits is indispensable for the development of new molecular research tools and drug candidates. To facilitate such discoveries, the European Research Infrastructure EU-OPENSCREEN was founded recently with the support of its member countries and the European Commission. Its distributed character harnesses complementary knowledge, expertise, and instrumentation in the discipline of chemical biology from 20 European partners, and its open working model ensures that academia and industry can readily access EU-OPENSCREEN's compound collection, equipment, and generated data. To demonstrate the power of this collaborative approach, this perspective article highlights recent projects from EU-OPENSCREEN partner institutions. These studies yielded (1) 2-aminoquinazolin-4(3 H)-ones as potential lead structures for new antimalarial drugs, (2) a novel lipodepsipeptide specifically inducing apoptosis in cells deficient for the pVHL tumor suppressor, (3) small-molecule-based ROCK inhibitors that induce definitive endoderm formation and can potentially be used for regenerative medicine, (4) potential pharmacological chaperones for inborn errors of metabolism and a familiar form of acute myeloid leukemia (AML), and (5) novel tankyrase inhibitors that entered a lead-to-candidate program. Collectively, these findings highlight the benefits of small-molecule screening, the plethora of assay designs, and the close connection between screening and medicinal chemistry within EU-OPENSCREEN.
Collapse
Affiliation(s)
- Philip Brennecke
- EU-OPENSCREEN, Leibniz Research
Institute for Molecular Pharmacology, Berlin, Germany
| | - Dace Rasina
- Organic Synthesis Methodology Group,
Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Oscar Aubi
- Department of Biomedicine, University of
Bergen, Bergen, Norway
| | - Katja Herzog
- EU-OPENSCREEN, Leibniz Research
Institute for Molecular Pharmacology, Berlin, Germany
| | - Johannes Landskron
- Centre for Molecular Medicine
Norway–Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - Bastien Cautain
- Fundación MEDINA, Health Sciences
Technology Park, Granada, Spain
| | | | - Jordi Quintana
- Department of Experimental and Health
Sciences, Universitat Pompeu Fabra, Barcelona, Catalunya, Spain
| | - Jordi Mestres
- Department of Experimental and Health
Sciences, Universitat Pompeu Fabra, Barcelona, Catalunya, Spain
- IMIM Hospital del Mar Medical Research
Institute, Research Program on Biomedical Informatics (GRIB), Barcelona, Spain
| | - Bahne Stechmann
- EU-OPENSCREEN, Leibniz Research
Institute for Molecular Pharmacology, Berlin, Germany
| | - Bernhard Ellinger
- Fraunhofer Institute for Molecular
Biology and Applied Ecology IME, Screening Port, Hamburg, Germany
| | - Jose Brea
- Institute for Research in Molecular
Medicine and Chronic Diseases—BioFarma Research Group, University of Santiago de
Compostela, Santiago de Compostela, Spain
| | - Jacek L. Kolanowski
- Department of Molecular Probes and
Prodrugs, Institute of Bioorganic Chemistry—Polish Academy of Sciences, Poznan,
Poland
| | - Radosław Pilarski
- Department of Molecular Probes and
Prodrugs, Institute of Bioorganic Chemistry—Polish Academy of Sciences, Poznan,
Poland
| | - Mar Orzaez
- Screening Platform, Principe Felipe
Research Center, Valencia, Spain
| | | | - Luca Laraia
- Center for Nanomedicine and
Theranostics, Department of Chemistry, Technical University of Denmark, Lyngby,
Denmark
- Technical University of Denmark,
DK-OPENSCREEN, Lyngby, Denmark
| | - Faranak Nami
- Center for Nanomedicine and
Theranostics, Department of Chemistry, Technical University of Denmark, Lyngby,
Denmark
- Technical University of Denmark,
DK-OPENSCREEN, Lyngby, Denmark
| | - Piotr Zielenkiewicz
- Department of Bioinformatics,
Institute of Biochemistry and Biophysics—Polish Academy of Sciences, Warsaw,
Poland
| | - Kamil Paruch
- Department of Chemistry—CZ-OPENSCREEN,
Masaryk University, Brno, Czech Republic
| | - Espen Hansen
- The Arctic University of Norway,
University of Tromsø, Marbio, Tromsø, Norway
| | - Jens P. von Kries
- Screening Unit, Leibniz Research
Institute for Molecular Pharmacology, Berlin, Germany
| | - Martin Neuenschwander
- Screening Unit, Leibniz Research
Institute for Molecular Pharmacology, Berlin, Germany
| | - Edgar Specker
- Medicinal Chemistry Research Group,
Leibniz Research Institute for Molecular Pharmacology, Berlin, Germany
| | - Petr Bartunek
- Institute of Molecular Genetics of the
ASCR, CZ-OPENSCREEN, Prague, Czech Republic
| | - Sarka Simova
- Institute of Molecular Genetics of the
ASCR, CZ-OPENSCREEN, Prague, Czech Republic
| | - Zbigniew Leśnikowski
- Laboratory of Molecular Virology and
Biological Chemistry, Institute of Medical Biology—Polish Academy of Sciences, Łódź,
Poland
| | - Stefan Krauss
- Department of Immunology and
Transfusion Medicine, Oslo University Hospital, Oslo, Norway
- Hybrid Technology Hub—Centre of
Excellence—Institute of Basic Medical Sciences, University of Oslo, Oslo,
Norway
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular
Medicine—Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Ursula Bilitewski
- Working Group Compound Profiling and
Screening, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Mark Brönstrup
- Department of Chemical Biology,
Helmholtz Centre for Infection Research, Brunswick, Germany
- German Center for Infection Research
(DZIF), partner site Hannover-Brunswick, Brunswick, Germany
| | - Kjetil Taskén
- Centre for Molecular Medicine
Norway–Nordic EMBL Partnership, University of Oslo, Oslo, Norway
- Department of Cancer
Immunology—Institute for Cancer Research, Oslo University Hospital, Oslo,
Norway
- K.G. Jebsen Centre for Cancer
Immunotherapy—Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- K.G. Jebsen Centre for B Cell
Malignancies—Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Aigars Jirgensons
- Organic Synthesis Methodology Group,
Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Heiko Lickert
- Institute of Diabetes and Regeneration
Research, Helmholtz Centre Munich German Research Center for Environmental Health,
Neuherberg, Germany
| | - Mads H. Clausen
- Center for Nanomedicine and
Theranostics, Department of Chemistry, Technical University of Denmark, Lyngby,
Denmark
- Technical University of Denmark,
DK-OPENSCREEN, Lyngby, Denmark
| | | | - Maria J. Vicent
- Screening Platform, Principe Felipe
Research Center, Valencia, Spain
| | - Olga Genilloud
- Fundación MEDINA, Health Sciences
Technology Park, Granada, Spain
| | - Aurora Martinez
- Department of Biomedicine, University of
Bergen, Bergen, Norway
| | - Marc Nazaré
- Medicinal Chemistry Research Group,
Leibniz Research Institute for Molecular Pharmacology, Berlin, Germany
| | | | - Philip Gribbon
- Fraunhofer Institute for Molecular
Biology and Applied Ecology IME, Screening Port, Hamburg, Germany
| |
Collapse
|
39
|
Jung-Kc K, Himmelreich N, Prestegård KS, Shi TJS, Scherer T, Ying M, Jorge-Finnigan A, Thöny B, Blau N, Martinez A. Phenylalanine hydroxylase variants interact with the co-chaperone DNAJC12. Hum Mutat 2019; 40:483-494. [PMID: 30667134 DOI: 10.1002/humu.23712] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/12/2019] [Accepted: 01/19/2019] [Indexed: 12/13/2022]
Abstract
DNAJC12, a type III member of the HSP40/DNAJ family, has been identified as the specific co-chaperone of phenylalanine hydroxylase (PAH) and the other aromatic amino acid hydroxylases. DNAJ proteins work together with molecular chaperones of the HSP70 family to assist in proper folding and maintenance of intracellular stability of their clients. Autosomal recessive mutations in DNAJC12 were found to reduce PAH levels, leading to hyperphenylalaninemia (HPA) in patients without mutations in PAH. In this work, we investigated the interaction of normal wild-type DNAJC12 with mutant PAH in cells expressing several PAH variants associated with HPA in humans, as well as in the Enu1/1 mouse model, homozygous for the V106A-Pah variant, which leads to severe protein instability, accelerated PAH degradation and mild HPA. We found that mutant PAH exhibits increased ubiquitination, instability, and aggregation compared with normal PAH. In mouse liver lysates, we showed that DNAJC12 interacts with monoubiquitin-tagged PAH. This form represented a major fraction of PAH in the Enu1/1 but was also present in liver of wild-type PAH mice. Our results support a role of DNAJC12 in the processing of misfolded ubiquitinated PAH by the ubiquitin-dependent proteasome/autophagy systems and add to the evidence that the DNAJ proteins are important players both for proper folding and degradation of their clients.
Collapse
Affiliation(s)
- Kunwar Jung-Kc
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | | | | | - Tanja Scherer
- Division of Metabolism, University Children's Hospital Zürich, Zürich, Switzerland
| | - Ming Ying
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Beat Thöny
- Division of Metabolism, University Children's Hospital Zürich, Zürich, Switzerland
| | - Nenad Blau
- Dietmar-Hopp-Metabolic Center, University Children's Hospital, Heidelberg, Germany.,Division of Metabolism, University Children's Hospital Zürich, Zürich, Switzerland
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Bergen, Norway
| |
Collapse
|
40
|
Scheller R, Stein A, Nielsen SV, Marin FI, Gerdes AM, Di Marco M, Papaleo E, Lindorff-Larsen K, Hartmann-Petersen R. Toward mechanistic models for genotype-phenotype correlations in phenylketonuria using protein stability calculations. Hum Mutat 2019; 40:444-457. [PMID: 30648773 DOI: 10.1002/humu.23707] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/18/2018] [Accepted: 01/13/2019] [Indexed: 01/22/2023]
Abstract
Phenylketonuria (PKU) is a genetic disorder caused by variants in the gene encoding phenylalanine hydroxylase (PAH), resulting in accumulation of phenylalanine to neurotoxic levels. Here, we analyzed the cellular stability, localization, and interaction with wild-type PAH of 20 selected PKU-linked PAH protein missense variants. Several were present at reduced levels in human cells, and the levels increased in the presence of a proteasome inhibitor, indicating that proteins are proteasome targets. We found that all the tested PAH variants retained their ability to associate with wild-type PAH, and none formed aggregates, suggesting that they are only mildly destabilized in structure. In all cases, PAH variants were stabilized by the cofactor tetrahydrobiopterin (BH4 ), a molecule known to alleviate symptoms in certain PKU patients. Biophysical calculations on all possible single-site missense variants using the full-length structure of PAH revealed a strong correlation between the predicted protein stability and the observed stability in cells. This observation rationalizes previously observed correlations between predicted loss of protein destabilization and disease severity, a correlation that we also observed using new calculations. We thus propose that many disease-linked PAH variants are structurally destabilized, which in turn leads to proteasomal degradation and insufficient amounts of cellular PAH protein.
Collapse
Affiliation(s)
- Rasmus Scheller
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Amelie Stein
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sofie V Nielsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Frederikke I Marin
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark
| | - Miriam Di Marco
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
41
|
Ashe K, Kelso W, Farrand S, Panetta J, Fazio T, De Jong G, Walterfang M. Psychiatric and Cognitive Aspects of Phenylketonuria: The Limitations of Diet and Promise of New Treatments. Front Psychiatry 2019; 10:561. [PMID: 31551819 PMCID: PMC6748028 DOI: 10.3389/fpsyt.2019.00561] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 07/17/2019] [Indexed: 12/30/2022] Open
Abstract
Phenylketonuria (PKU) is a recessive disorder of phenylalanine metabolism due to mutations in the gene for phenylalanine hydroxylase (PAH). Reduced PAH activity results in significant hyperphenylalaninemia, which leads to alterations in cerebral myelin and protein synthesis, as well as reduced levels of serotonin, dopamine, and noradrenaline in the brain. When untreated, brain development is grossly disrupted and significant intellectual impairment and behavioral disturbance occur. The advent of neonatal heel prick screening has allowed for diagnosis at birth, and the institution of a phenylalanine restricted diet. Dietary treatment, particularly when maintained across neurodevelopment and well into adulthood, has resulted in markedly improved outcomes at a cognitive and psychiatric level for individuals with PKU. However, few individuals can maintain full dietary control lifelong, and even with good control, an elevated risk remains of-in particular-mood, anxiety, and attentional disorders across the lifespan. Increasingly, dietary recommendations focus on maintaining continuous dietary treatment lifelong to optimize psychiatric and cognitive outcomes, although the effect of long-term protein restricted diets on brain function remains unknown. While psychiatric illness is very common in adult PKU populations, very little data exist to guide clinicians on optimal treatment. The advent of new treatments that do not require restrictive dietary management, such as the enzyme therapy Pegvaliase, holds the promise of allowing patients a relatively normal diet alongside optimized mental health and cognitive functioning.
Collapse
Affiliation(s)
- Killian Ashe
- Neuropsychiatry Unit, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Wendy Kelso
- Neuropsychiatry Unit, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Sarah Farrand
- Neuropsychiatry Unit, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Julie Panetta
- Statewide Adult Metabolic Service, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Tim Fazio
- Statewide Adult Metabolic Service, Royal Melbourne Hospital, Melbourne, VIC, Australia.,Melbourne Medical School, University of Melbourne, Melbourne, VIC, Australia
| | - Gerard De Jong
- Statewide Adult Metabolic Service, Royal Melbourne Hospital, Melbourne, VIC, Australia.,Melbourne Medical School, University of Melbourne, Melbourne, VIC, Australia
| | - Mark Walterfang
- Neuropsychiatry Unit, Royal Melbourne Hospital, Melbourne, VIC, Australia.,Melbourne Neuropsychiatry Centre, University of Melbourne and North-Western Mental Health, Melbourne, VIC, Australia.,Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC, Australia
| |
Collapse
|
42
|
Fernández-Higuero JÁ, Betancor-Fernández I, Mesa-Torres N, Muga A, Salido E, Pey AL. Structural and functional insights on the roles of molecular chaperones in the mistargeting and aggregation phenotypes associated with primary hyperoxaluria type I. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 114:119-152. [PMID: 30635080 DOI: 10.1016/bs.apcsb.2018.09.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To carry out their biological function in cells, proteins must be folded and targeted to the appropriate subcellular location. These processes are controlled by a vast collection of interacting proteins collectively known as the protein homeostasis network, in which molecular chaperones play a prominent role. Protein homeostasis can be impaired by inherited mutations leading to genetic diseases. In this chapter, we focus on a particular disease, primary hyperoxaluria type 1 (PH1), in which disease-associated mutations exacerbate protein aggregation in the cell and mistarget the peroxisomal alanine:glyoxylate aminotransferase (AGT) protein to mitochondria, in part due to native state destabilization and enhanced interaction with Hsp60, 70 and 90 chaperone systems. After a general introduction of molecular chaperones and PH1, we review our current knowledge on the structural and energetic features of PH1-causing mutants that lead to these particular pathogenic mechanisms. From this perspective, and in the context of the key role of molecular chaperones in PH1 pathogenesis, we present and discuss current and future perspectives for pharmacological treatments for this disease.
Collapse
Affiliation(s)
- José Ángel Fernández-Higuero
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Isabel Betancor-Fernández
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, ITB, University of La Laguna, Tenerife, Spain
| | - Noel Mesa-Torres
- Department of Physical Chemistry, University of Granada, Granada, Spain
| | - Arturo Muga
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Eduardo Salido
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, ITB, University of La Laguna, Tenerife, Spain
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, Granada, Spain.
| |
Collapse
|
43
|
Tao YX, Conn PM. Pharmacoperones as Novel Therapeutics for Diverse Protein Conformational Diseases. Physiol Rev 2018; 98:697-725. [PMID: 29442594 DOI: 10.1152/physrev.00029.2016] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
After synthesis, proteins are folded into their native conformations aided by molecular chaperones. Dysfunction in folding caused by genetic mutations in numerous genes causes protein conformational diseases. Membrane proteins are more prone to misfolding due to their more intricate folding than soluble proteins. Misfolded proteins are detected by the cellular quality control systems, especially in the endoplasmic reticulum, and proteins may be retained there for eventual degradation by the ubiquitin-proteasome system or through autophagy. Some misfolded proteins aggregate, leading to pathologies in numerous neurological diseases. In vitro, modulating mutant protein folding by altering molecular chaperone expression can ameliorate some misfolding. Some small molecules known as chemical chaperones also correct mutant protein misfolding in vitro and in vivo. However, due to their lack of specificity, their potential as therapeutics is limited. Another class of compounds, known as pharmacological chaperones (pharmacoperones), binds with high specificity to misfolded proteins, either as enzyme substrates or receptor ligands, leading to decreased folding energy barriers and correction of the misfolding. Because many of the misfolded proteins are misrouted but do not have defects in function per se, pharmacoperones have promising potential in advancing to the clinic as therapeutics, since correcting routing may ameliorate the underlying mechanism of disease. This review will comprehensively summarize this exciting area of research, surveying the literature from in vitro studies in cell lines to transgenic animal models and clinical trials in several protein misfolding diseases.
Collapse
Affiliation(s)
- Ya-Xiong Tao
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University , Auburn, Alabama ; and Departments of Internal Medicine and Cell Biology, Texas Tech University Health Science Center , Lubbock, Texas
| | - P Michael Conn
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University , Auburn, Alabama ; and Departments of Internal Medicine and Cell Biology, Texas Tech University Health Science Center , Lubbock, Texas
| |
Collapse
|
44
|
Rivera-Barahona A, Navarrete R, García-Rodríguez R, Richard E, Ugarte M, Pérez-Cerda C, Pérez B, Gámez A, Desviat LR. Identification of 34 novel mutations in propionic acidemia: Functional characterization of missense variants and phenotype associations. Mol Genet Metab 2018; 125:266-275. [PMID: 30274917 DOI: 10.1016/j.ymgme.2018.09.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/25/2018] [Accepted: 09/25/2018] [Indexed: 12/28/2022]
Abstract
Propionic acidemia (PA) is caused by mutations in the PCCA and PCCB genes, encoding α and β subunits, respectively, of the mitochondrial enzyme propionyl-CoA carboxylase (PCC). Up to date, >200 pathogenic mutations have been identified, mostly missense defects. Genetic analysis in PA patients referred to the laboratory for the past 15 years identified 20 novel variants in the PCCA gene and 14 in the PCCB gene. 21 missense variants were predicted as probably disease-causing by different bioinformatics algorithms. Structural analysis in the available 3D model of the PCC enzyme indicated potential instability for most of them. Functional analysis in a eukaryotic system confirmed the pathogenic effect for the missense variants and for one amino acid deletion, as they all exhibited reduced or null PCC activity and protein levels compared to wild-type constructs. PCCB variants p.E168del, p.Q58P and p.I460T resulted in medium-high protein levels and no activity. Variants p.R230C and p.C712S in PCCA, and p.G188A, p.R272W and p.H534R in PCCB retained both partial PCC activity and medium-high protein levels. Available patients-derived fibroblasts carriers of some of these mutations were grown at 28 °C or 37 °C and a slight increase in PCC activity or protein could be detected in some cases at the folding-permissive conditions. Examination of available clinical data showed correlation of the results of the functional analysis with disease severity for most mutations, with some notable exceptions, confirming the notion that the final phenotypic outcome in PA is not easily predicted.
Collapse
Affiliation(s)
- Ana Rivera-Barahona
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma, Madrid, Spain; Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, Spain
| | - Rosa Navarrete
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma, Madrid, Spain; Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, Spain
| | - Raquel García-Rodríguez
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma, Madrid, Spain; Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, Spain
| | - Eva Richard
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma, Madrid, Spain; Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, Spain
| | - Magdalena Ugarte
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, Spain
| | - Celia Pérez-Cerda
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, Spain
| | - Belén Pérez
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma, Madrid, Spain; Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, Spain
| | - Alejandra Gámez
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma, Madrid, Spain; Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, Spain
| | - Lourdes R Desviat
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma, Madrid, Spain; Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, Spain.
| |
Collapse
|
45
|
Medina-Carmona E, Betancor-Fernández I, Santos J, Mesa-Torres N, Grottelli S, Batlle C, Naganathan AN, Oppici E, Cellini B, Ventura S, Salido E, Pey AL. Insight into the specificity and severity of pathogenic mechanisms associated with missense mutations through experimental and structural perturbation analyses. Hum Mol Genet 2018; 28:1-15. [DOI: 10.1093/hmg/ddy323] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/09/2018] [Indexed: 12/21/2022] Open
Abstract
Abstract
Most pathogenic missense mutations cause specific molecular phenotypes through protein destabilization. However, how protein destabilization is manifested as a given molecular phenotype is not well understood. We develop here a structural and energetic approach to describe mutational effects on specific traits such as function, regulation, stability, subcellular targeting or aggregation propensity. This approach is tested using large-scale experimental and structural perturbation analyses in over thirty mutations in three different proteins (cancer-associated NQO1, transthyretin related with amyloidosis and AGT linked to primary hyperoxaluria type I) and comprising five very common pathogenic mechanisms (loss-of-function and gain-of-toxic function aggregation, enzyme inactivation, protein mistargeting and accelerated degradation). Our results revealed that the magnitude of destabilizing effects and, particularly, their propagation through the structure to promote disease-associated conformational states largely determine the severity and molecular mechanisms of disease-associated missense mutations. Modulation of the structural perturbation at a mutated site is also shown to cause switches between different molecular phenotypes. When very common disease-associated missense mutations were investigated, we also found that they were not among the most deleterious possible missense mutations at those sites, and required additional contributions from codon bias and effects of CpG sites to explain their high frequency in patients. Our work sheds light on the molecular basis of pathogenic mechanisms and genotype–phenotype relationships, with implications for discriminating between pathogenic and neutral changes within human genome variability from whole genome sequencing studies.
Collapse
Affiliation(s)
- Encarnación Medina-Carmona
- Department of Physical Chemistry, University of Granada, Granada, Spain
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, Perugia
| | - Isabel Betancor-Fernández
- Centre for Biomedical Research on Rare Diseases, Hospital Universitario de Canarias, Tenerife, Spain
| | - Jaime Santos
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Noel Mesa-Torres
- Department of Physical Chemistry, University of Granada, Granada, Spain
| | - Silvia Grottelli
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, Perugia
| | - Cristina Batlle
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IITM), Chennai, India
| | - Elisa Oppici
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada Le Grazie, Verona, Italy
| | - Barbara Cellini
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, Perugia
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Eduardo Salido
- Centre for Biomedical Research on Rare Diseases, Hospital Universitario de Canarias, Tenerife, Spain
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, Granada, Spain
| |
Collapse
|
46
|
Pey AL. Biophysical and functional perturbation analyses at cancer-associated P187 and K240 sites of the multifunctional NADP(H):quinone oxidoreductase 1. Int J Biol Macromol 2018; 118:1912-1923. [PMID: 30009918 DOI: 10.1016/j.ijbiomac.2018.07.051] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 12/14/2022]
Abstract
Once whole-genome sequencing has reached the clinical practice, a main challenge ahead is the high-throughput and accurate prediction of the pathogenicity of genetic variants. However, current prediction tools do not consider explicitly a well-known property of disease-causing mutations: their ability to affect multiple functional sites distant in the protein structure. Here we carried out an extensive biophysical characterization of fourteen mutant variants at two cancer-associated sites of the enzyme NQO1, a paradigm of multi-functional protein. We showed that the magnitude of destabilizing effects, their molecular origins (structural vs. dynamic) and their efficient propagation through the protein structure gradually led to functional perturbations at different sites. Modulation of these structural perturbations also led to switches between molecular phenotypes. Our work supports that experimental and computational perturbation analyses would improve our understanding of the molecular basis of many loss-of-function genetic diseases as well as our ability to accurately predict the pathogenicity of genetic variants in a high-throughput fashion.
Collapse
Affiliation(s)
- Angel L Pey
- Department of Physical Chemistry, University of Granada, Av. Fuentenueva S/N, 18071 Granada, Spain.
| |
Collapse
|
47
|
Scherer T, Allegri G, Sarkissian CN, Ying M, Grisch-Chan HM, Rassi A, Winn SR, Harding CO, Martinez A, Thöny B. Tetrahydrobiopterin treatment reduces brain L-Phe but only partially improves serotonin in hyperphenylalaninemic ENU1/2 mice. J Inherit Metab Dis 2018; 41:709-718. [PMID: 29520738 PMCID: PMC6041158 DOI: 10.1007/s10545-018-0150-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 01/26/2018] [Accepted: 01/30/2018] [Indexed: 12/16/2022]
Abstract
Hyperphenylalaninemia (HPA) caused by hepatic phenylalanine hydroxylase (PAH) deficiency has severe consequences on brain monoamine neurotransmitter metabolism. We have studied monoamine neurotransmitter status and the effect of tetrahydrobiopterin (BH4) treatment in Pahenu1/enu2 (ENU1/2) mice, a model of partial PAH deficiency. These mice exhibit elevated blood L-phenylalanine (L-Phe) concentrations similar to that of mild hyperphenylalaninemia (HPA), but brain levels of L-Phe are still ~5-fold elevated compared to wild-type. We found that brain L-tyrosine, L-tryptophan, BH4 cofactor and catecholamine concentrations, and brain tyrosine hydroxylase (TH) activity were normal in these mice but that brain serotonin, 5-hydroxyindolacetic acid (5HIAA) and 3-methoxy-4-hydroxyphenylglycol (MHPG) content, and brain TH protein, as well as tryptophan hydroxylase type 2 (TPH2) protein levels and activity were reduced in comparison to wild-type mice. Parenteral L-Phe loading conditions did not lead to significant changes in brain neurometabolite concentrations. Remarkably, enteral BH4 treatment, which normalized brain L-Phe levels in ENU1/2 mice, lead to only partial recovery of brain serotonin and 5HIAA concentrations. Furthermore, indirect evidence indicated that the GTP cyclohydrolase I (GTPCH) feedback regulatory protein (GFRP) complex may be a sensor for brain L-Phe elevation to ameliorate the toxic effects of HPA. We conclude that BH4 treatment of HPA toward systemic L-Phe lowering reverses elevated brain L-Phe content but the recovery of TPH2 protein and activity as well as serotonin levels is suboptimal, indicating that patients with mild HPA and mood problems (depression or anxiety) treated with the current diet may benefit from supplementation with BH4 and 5-OH-tryptophan.
Collapse
Affiliation(s)
- Tanja Scherer
- Department of Pediatrics, Divisions of Metabolism and of Clinical Chemistry and Biochemistry, University of Zürich, Zürich, Switzerland
| | - Gabriella Allegri
- Department of Pediatrics, Divisions of Metabolism and of Clinical Chemistry and Biochemistry, University of Zürich, Zürich, Switzerland
| | | | - Ming Ying
- Department of Biomedicine and K.G. Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
| | - Hiu Man Grisch-Chan
- Department of Pediatrics, Divisions of Metabolism and of Clinical Chemistry and Biochemistry, University of Zürich, Zürich, Switzerland
| | - Anahita Rassi
- Department of Pediatrics, Divisions of Metabolism and of Clinical Chemistry and Biochemistry, University of Zürich, Zürich, Switzerland
| | - Shelley R Winn
- Department of Molecular and Medical Genetics, School of Medicine, Oregon Science & Health University, Portland, OR, USA
| | - Cary O Harding
- Department of Molecular and Medical Genetics, School of Medicine, Oregon Science & Health University, Portland, OR, USA
| | - Aurora Martinez
- Department of Biomedicine and K.G. Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Bergen, Norway.
| | - Beat Thöny
- Department of Pediatrics, Divisions of Metabolism and of Clinical Chemistry and Biochemistry, University of Zürich, Zürich, Switzerland.
| |
Collapse
|
48
|
Arbesman J, Ravichandran S, Funchain P, Thompson CL. Melanoma cases demonstrate increased carrier frequency of phenylketonuria/hyperphenylalanemia mutations. Pigment Cell Melanoma Res 2018; 31:529-533. [PMID: 29473999 DOI: 10.1111/pcmr.12695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/09/2018] [Indexed: 11/30/2022]
Abstract
Identifying novel melanoma genetic risk factors informs screening and prevention efforts. Mutations in the phenylalanine hydroxylase gene (the causative gene in phenylketonuria) lead to reduced pigmentation in untreated phenylketonuria patients, and reduced pigmentation is associated with greater melanoma risk. Therefore, we sought to characterize the relationship between phenylketonuria carrier status and melanoma risk. Using National Newborn Screening Reports, we determined the United States phenylketonuria/hyperphenylalanemia carrier frequency in Caucasians to be 1.76%. We examined three publically available melanoma datasets for germline mutations in the phenylalanine hydroxylase gene associated with classic phenylketonuria and/or hyperphenylalanemia. Mutations were identified in 29/814 melanoma patients, with a carrier frequency of 3.56%. There was a twofold enrichment (p-value = 3.4 × 10-5 ) compared to the Caucasian frequency of hyperphenylalanemia/phenylketonuria carriers. These data demonstrate a novel association between phenylalanine hydroxylase carrier status and melanoma risk. Further, functional investigation is warranted to determine the link between phenylalanine hydroxylase mutations and melanomagenesis.
Collapse
Affiliation(s)
- Joshua Arbesman
- Department of Dermatology, Case Western Reserve University, Cleveland, OH, USA
| | | | - Pauline Funchain
- Department of Hematology/Oncology, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Cheryl L Thompson
- Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA
| |
Collapse
|
49
|
Congenital Adrenal Hyperplasia (CAH) due to 21-Hydroxylase Deficiency: A Comprehensive Focus on 233 Pathogenic Variants of CYP21A2 Gene. Mol Diagn Ther 2018; 22:261-280. [DOI: 10.1007/s40291-018-0319-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
50
|
Buß O, Rudat J, Ochsenreither K. FoldX as Protein Engineering Tool: Better Than Random Based Approaches? Comput Struct Biotechnol J 2018; 16:25-33. [PMID: 30275935 PMCID: PMC6158775 DOI: 10.1016/j.csbj.2018.01.002] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/21/2017] [Accepted: 01/20/2018] [Indexed: 02/04/2023] Open
Abstract
Improving protein stability is an important goal for basic research as well as for clinical and industrial applications but no commonly accepted and widely used strategy for efficient engineering is known. Beside random approaches like error prone PCR or physical techniques to stabilize proteins, e.g. by immobilization, in silico approaches are gaining more attention to apply target-oriented mutagenesis. In this review different algorithms for the prediction of beneficial mutation sites to enhance protein stability are summarized and the advantages and disadvantages of FoldX are highlighted. The question whether the prediction of mutation sites by the algorithm FoldX is more accurate than random based approaches is addressed.
Collapse
Affiliation(s)
- Oliver Buß
- Institute of Process Engineering in Life Sciences, Section II: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | | | | |
Collapse
|