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Araujo NA, Bubis J. Analysis of a Novel Peptide That Is Capable of Inhibiting the Enzymatic Activity of the Protein Kinase A Catalytic Subunit-Like Protein from Trypanosoma equiperdum. Protein J 2023; 42:709-727. [PMID: 37713008 DOI: 10.1007/s10930-023-10153-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2023] [Indexed: 09/16/2023]
Abstract
A 26-residue peptide possessing the αN-helix motif of the protein kinase A (PKA) regulatory subunit-like proteins from the Trypanozoom subgenera (VAP26, sequence = VAPYFEKSEDETALILKLLTYNVLFS), was shown to inhibit the enzymatic activity of the Trypanosoma equiperdum PKA catalytic subunit-like protein, in a similar manner that the mammalian heat-stable soluble PKA inhibitor known as PKI. However, VAP26 does not contain the PKI inhibitory sequence. Bioinformatics analyzes of the αN-helix motif from various Trypanozoon PKA regulatory subunit-like proteins suggested that the sequence could form favorable peptide-protein interactions of hydrophobic nature with the PKA catalytic subunit-like protein, which possibly may represent an alternative PKA inhibitory mechanism. The sequence of the αN-helix motif of the Trypanozoon proteins was shown to be highly homologous but significantly divergent from the corresponding αN-helix motifs of their Leishmania and mammalian counterparts. This sequence divergence contrasted with the proposed secondary structure of the αN-helix motif, which appeared conserved in every analyzed regulatory subunit-like protein. In silico mutation experiments at positions I234, L238 and F244 of the αN-helix motif from the Trypanozoon proteins destabilized both the specific motif and the protein. On the contrary, mutations at positions T239 and Y240 stabilized the motif and the protein. These results suggested that the αN-helix motif from the Trypanozoon proteins probably possessed a different evolutionary path than their Leishmania and mammalian counterparts. Moreover, finding stabilizing mutations indicated that new inhibitory peptides may be designed based on the αN-helix motif from the Trypanozoon PKA regulatory subunit-like proteins.
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Affiliation(s)
- Nelson A Araujo
- Escuela de Ciencias Agroalimentarias, Animales y Ambientales, Universidad de O'Higgins, Campus Colchagua, ruta I-90, Km 3, San Fernando, Chile.
| | - José Bubis
- Unidad de Polimorfismo Genético, Genómica y Proteómica, Dirección de Salud, Fundación Instituto de Estudios Avanzados IDEA, Caracas, 1015-A, Venezuela
- Unidad de Señalización Celular y Bioquímica de Parásitos, Dirección de Salud, Fundación Instituto de Estudios Avanzados IDEA, Caracas, 1015-A, Venezuela
- Departamento de Biología Celular, Universidad Simón Bolívar, Apartado 89.000, Caracas, 1081‑A, Venezuela
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2
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Brewer KM, Brewer KK, Richardson NC, Berbari NF. Neuronal cilia in energy homeostasis. Front Cell Dev Biol 2022; 10:1082141. [PMID: 36568981 PMCID: PMC9773564 DOI: 10.3389/fcell.2022.1082141] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/11/2022] [Indexed: 12/13/2022] Open
Abstract
A subset of genetic disorders termed ciliopathies are associated with obesity. The mechanisms behind cilia dysfunction and altered energy homeostasis in these syndromes are complex and likely involve deficits in both development and adult homeostasis. Interestingly, several cilia-associated gene mutations also lead to morbid obesity. While cilia have critical and diverse functions in energy homeostasis, including their roles in centrally mediated food intake and peripheral tissues, many questions remain. Here, we briefly discuss syndromic ciliopathies and monogenic cilia signaling mutations associated with obesity. We then focus on potential ways neuronal cilia regulate energy homeostasis. We discuss the literature around cilia and leptin-melanocortin signaling and changes in ciliary G protein-coupled receptor (GPCR) signaling. We also discuss the different brain regions where cilia are implicated in energy homeostasis and the potential for cilia dysfunction in neural development to contribute to obesity. We close with a short discussion on the challenges and opportunities associated with studies looking at neuronal cilia and energy homeostasis. This review highlights how neuronal cilia-mediated signaling is critical for proper energy homeostasis.
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Affiliation(s)
- Kathryn M. Brewer
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Katlyn K. Brewer
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Nicholas C. Richardson
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Nicolas F. Berbari
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States,Stark Neurosciences Research Institute, Indiana University, Indianapolis, IN, United States,Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, United States,*Correspondence: Nicolas F. Berbari,
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3
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Lee CH, Kang GM, Kim MS. Mechanisms of Weight Control by Primary Cilia. Mol Cells 2022; 45:169-176. [PMID: 35387896 PMCID: PMC9001153 DOI: 10.14348/molcells.2022.2046] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 02/06/2023] Open
Abstract
A primary cilium, a hair-like protrusion of the plasma membrane, is a pivotal organelle for sensing external environmental signals and transducing intracellular signaling. An interesting linkage between cilia and obesity has been revealed by studies of the human genetic ciliopathies Bardet-Biedl syndrome and Alström syndrome, in which obesity is a principal manifestation. Mouse models of cell type-specific cilia dysgenesis have subsequently demonstrated that ciliary defects restricted to specific hypothalamic neurons are sufficient to induce obesity and hyperphagia. A potential mechanism underlying hypothalamic neuron cilia-related obesity is impaired ciliary localization of G protein-coupled receptors involved in the regulation of appetite and energy metabolism. A well-studied example of this is melanocortin 4 receptor (MC4R), mutations in which are the most common cause of human monogenic obesity. In the paraventricular hypothalamus neurons, a blockade of ciliary trafficking of MC4R as well as its downstream ciliary signaling leads to hyperphagia and weight gain. Another potential mechanism is reduced leptin signaling in hypothalamic neurons with defective cilia. Leptin receptors traffic to the periciliary area upon leptin stimulation. Moreover, defects in cilia formation hamper leptin signaling and actions in both developing and differentiated hypothalamic neurons. The list of obesity-linked ciliary proteins is expending and this supports a tight association between cilia and obesity. This article provides a brief review on the mechanism of how ciliary defects in hypothalamic neurons facilitate obesity.
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Affiliation(s)
- Chan Hee Lee
- Department of Biomedical Science, Hallym University, Chuncheon 24252, Korea
| | - Gil Myoung Kang
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Min-Seon Kim
- Division of Endocrinology and Metabolism, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
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4
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Ajadi MB, Soremekun OS, Adewumi AT, Kumalo HM, Soliman MES. Functional Analysis of Single Nucleotide Polymorphism in ZUFSP Protein and Implication in Pathogenesis. Protein J 2021; 40:28-40. [PMID: 33512633 DOI: 10.1007/s10930-021-09962-z] [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] [Accepted: 01/04/2021] [Indexed: 11/25/2022]
Abstract
Researches have revealed that functional non-synonymous Single Nucleotide Polymorphism (nsSNPs) present in the Zinc-finger with UFM1-Specific Peptidase domain protein (ZUFSP) may be involved in genetic instability and carcinogenesis. For the first time, we employed in-silico approach using predictive tools to identify and validate potential nsSNPs that could be pathogenic. Our result revealed that 8 nsSNPs (rs 112738382, rs 140094037, rs 201652589, rs 201847265, rs 202076827, rs 373634906, rs 375114528, rs 772591104) are pathogenic after being subjected to rigorous filtering process. The structural impact of the nsSNPs on ZUFSP structure indicated that the nsSNPs affect the stability of the protein by lowering ZUFSP protein stability. Furthermore, conservation analysis showed that rs 201652589, rs 140094037, rs 201847265, and rs 772591104 were highly conserved. Interestingly, the protein-protein affinity between ZUFSP and Ubiquitin was altered rs 201652589, rs 140094037, rs 201847265, and rs 772591104 had a binding affinity of - 0.46, - 0.83, - 1.62, and - 1.12 kcal/mol respectively. Our study has been able to identify potential nsSNPs that could be used as genetic biomarkers for some diseases arising as a result of aberration in the ZUFSP structure, however, being a predictive study, the identified nsSNPs need to be experimentally investigated.
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Affiliation(s)
- Mary B Ajadi
- Department of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Howard Campus, Durban, 4000, South Africa
- Chemical Pathology Department, Faculty of Basic Medical Sciences, College of Health Sciences, Ladoke Akintola University of Technology, PMB 4400, Osogbo, Nigeria
| | - Opeyemi S Soremekun
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Adeniyi T Adewumi
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Hezekiel M Kumalo
- Department of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Howard Campus, Durban, 4000, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.
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5
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Abduljaleel Z. Structural and Functional Analysis of human lung cancer risk associated hOGG1 variant Ser326Cys in DNA repair gene by molecular dynamics simulation. Noncoding RNA Res 2019; 4:109-119. [PMID: 31891019 PMCID: PMC6926185 DOI: 10.1016/j.ncrna.2019.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/16/2019] [Accepted: 10/16/2019] [Indexed: 12/29/2022] Open
Abstract
Oxidative damaged DNA base lesions are repaired through human 8-oxoguanine DNA glycosylase gene (hOGG1) mediated pathways. A recent report based on the meta-analysis has suggested that the DNA Repair Gene hOGG1 variant Ser326Cys [3p26.2; allele S/C in nucleotide position αHelix2 Ser⇒Cys326] was associated with Lung Cancer risk in Caucasian population will alter the level Zhong et al., 2012. To the best of our knowledge, there has not been any such comprehensive in-silico investigation that validates the functional and structural impact of non-synonymous Lung Cancer Risk Associated Protein Domain (LCRAPD) mutation Ser326Cys (rs1052133) by molecular dynamics (MD) simulation approach following prediction of hOGG1 protein before and after the mutation. Further to the native and mutant protein structures, the amino acid residue and its secondary structure were observed through a solvent accessibility model for protein stability confirmation at the point of mutation. Taken together, this study suggests that the protein functional and structural studies could be a reasonable approach for investigating the impact of nsSNPs in future studies. In addition, 4295 patients samples incorporate with the analysis that genomic data types from cBioPortal. In the result, 4295 cases (91.5%) had alterations in all genes but the frequency of alterations in our targeted hOGG1 gene was shown with and without case alteration in the ratio (Logrank Test P-Value: 0.670) Kaplan-Meier by the number of patients at risk of the survival function.
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Affiliation(s)
- Zainularifeen Abduljaleel
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box: 715, Makkah, 21955, Saudi Arabia.,Science and Technology Unit, Umm Al-Qura University, P.O. Box: 715, Makkah, 21955, Saudi Arabia.,Bircham International University, Av. Sierra, 2, 28691, Villanueva de La Cañada, Madrid, Spain
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6
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Pejaver V, Babbi G, Casadio R, Folkman L, Katsonis P, Kundu K, Lichtarge O, Martelli PL, Miller M, Moult J, Pal LR, Savojardo C, Yin Y, Zhou Y, Radivojac P, Bromberg Y. Assessment of methods for predicting the effects of PTEN and TPMT protein variants. Hum Mutat 2019; 40:1495-1506. [PMID: 31184403 PMCID: PMC6744362 DOI: 10.1002/humu.23838] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/27/2019] [Accepted: 06/06/2019] [Indexed: 01/16/2023]
Abstract
Thermodynamic stability is a fundamental property shared by all proteins. Changes in stability due to mutation are a widespread molecular mechanism in genetic diseases. Methods for the prediction of mutation-induced stability change have typically been developed and evaluated on incomplete and/or biased data sets. As part of the Critical Assessment of Genome Interpretation, we explored the utility of high-throughput variant stability profiling (VSP) assay data as an alternative for the assessment of computational methods and evaluated state-of-the-art predictors against over 7,000 nonsynonymous variants from two proteins. We found that predictions were modestly correlated with actual experimental values. Predictors fared better when evaluated as classifiers of extreme stability effects. While different methods emerging as top performers depending on the metric, it is nontrivial to draw conclusions on their adoption or improvement. Our analyses revealed that only 16% of all variants in VSP assays could be confidently defined as stability-affecting. Furthermore, it is unclear as to what extent VSP abundance scores were reasonable proxies for the stability-related quantities that participating methods were designed to predict. Overall, our observations underscore the need for clearly defined objectives when developing and using both computational and experimental methods in the context of measuring variant impact.
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Affiliation(s)
- Vikas Pejaver
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington
- The eScience Institute, University of Washington, Seattle, Washington
| | - Giulia Babbi
- Department of Pharmacy and Biotechnology, Biocomputing Group, University of Bologna, Bologna, Italy
| | - Rita Casadio
- Department of Pharmacy and Biotechnology, Biocomputing Group, University of Bologna, Bologna, Italy
| | - Lukas Folkman
- School of Information and Communication Technology, Griffith University, Southport, Australia
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Kunal Kundu
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
- Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, Maryland
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, Texas
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas
| | - Pier Luigi Martelli
- Department of Pharmacy and Biotechnology, Biocomputing Group, University of Bologna, Bologna, Italy
| | - Maximilian Miller
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey
| | - John Moult
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland
| | - Lipika R Pal
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
| | - Castrense Savojardo
- Department of Pharmacy and Biotechnology, Biocomputing Group, University of Bologna, Bologna, Italy
| | - Yizhou Yin
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
| | - Yaoqi Zhou
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Southport, Australia
| | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, Massachusetts
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey
- Department of Genetics, Human Genetics Institute, Rutgers University, Piscataway, New Jersey
- Institute for Advanced Study at Technische Universität München (TUM-IAS), Garching/Munich, Germany
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7
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Szymczyk P, Szymańska G, Lipert A, Weremczuk-Jeżyna I, Kochan E. Computer-Aided Saturation Mutagenesis of Arabidopsis thaliana Ent-Copalyl Diphosphate Synthase. Interdiscip Sci 2019; 12:32-43. [PMID: 31309397 PMCID: PMC7007437 DOI: 10.1007/s12539-019-00342-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 07/04/2019] [Accepted: 07/05/2019] [Indexed: 01/12/2023]
Abstract
Ent-copalyl diphosphate synthase controls the biosynthesis of gibberellin plant hormones, which in turn coordinate the expression of numerous enzymes. Some gibberellin-dependent genes encode enzymes coordinating the biosynthesis of tanshinones: diterpene derivatives with broad medical applications. New biotechnological approaches, such as metabolic engineering using naturally occurring or mutated enzymes, have been proposed to meet the growing demand for tanshinones which is currently met by the Chinese medicinal plant Salvia miltiorrhiza Bunge. These mutants may be prepared by directed evolution, saturation mutagenesis or rational enzyme design. In the presented paper, 15,257 non-synonymous variants of Arabidopsis thaliana ent-copalyl diphosphate synthase were obtained using the SNAP2 tool. The obtained forms were screened to isolate variants with potentially improved biological functions. A group of 455 mutants with potentially improved stability was isolated and subjected to further screening on the basis of ligand–substrate affinity, and both secondary structure and active site structure stability. Finally, a group of six single mutants was obtained, which were used to construct double mutants with potentially improved stability and ligand affinity. The potential influence of single mutations on protein stability and ligand affinity was evaluated by double mutant cycle analysis. Finally, the procedure was validated by in silico assessment of the experimentally verified enzyme mutants with reduced enzymatic activity.
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Affiliation(s)
- Piotr Szymczyk
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Medical University of Łódź, 90-151, Lodz, Poland.
| | - Grażyna Szymańska
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Medical University of Łódź, 90-151, Lodz, Poland
| | - Anna Lipert
- Department of Sports Medicine, Medical University of Łódź, 92-213, Lodz, Poland
| | - Izabela Weremczuk-Jeżyna
- Department of Biology and Pharmaceutical Botany, Faculty of Pharmacy, Medical University of Łódź, 90-151, Lodz, Poland
| | - Ewa Kochan
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Medical University of Łódź, 90-151, Lodz, Poland
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8
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Raimondi D, Orlando G, Tabaro F, Lenaerts T, Rooman M, Moreau Y, Vranken WF. Large-scale in-silico statistical mutagenesis analysis sheds light on the deleteriousness landscape of the human proteome. Sci Rep 2018; 8:16980. [PMID: 30451933 PMCID: PMC6242909 DOI: 10.1038/s41598-018-34959-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/26/2018] [Indexed: 12/18/2022] Open
Abstract
Next generation sequencing technologies are providing increasing amounts of sequencing data, paving the way for improvements in clinical genetics and precision medicine. The interpretation of the observed genomic variants in the light of their phenotypic effects is thus emerging as a crucial task to solve in order to advance our understanding of how exomic variants affect proteins and how the proteins' functional changes affect human health. Since the experimental evaluation of the effects of every observed variant is unfeasible, Bioinformatics methods are being developed to address this challenge in-silico, by predicting the impact of millions of variants, thus providing insight into the deleteriousness landscape of entire proteomes. Here we show the feasibility of this approach by using the recently developed DEOGEN2 variant-effect predictor to perform the largest in-silico mutagenesis scan to date. We computed the deleteriousness score of 170 million variants over 15000 human proteins and we analysed the results, investigating how the predicted deleteriousness landscape of the proteins relates to known functionally and structurally relevant protein regions and biophysical properties. Moreover, we qualitatively validated our results by comparing them with two mutagenesis studies targeting two specific proteins, showing the consistency of DEOGEN2 predictions with respect to experimental data.
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Affiliation(s)
- Daniele Raimondi
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, 1050, Brussels, Belgium
- ESAT-STADIUS, KU Leuven, Kasteelpark Arenberg 10, 3001, Leuven, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Gabriele Orlando
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Francesco Tabaro
- Institute of Biosciences and Medical Technology, Arvo Ylpőn katu 34, 33520, Tampere, Finland
| | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, 1050, Brussels, Belgium
- Machine Learning Group, ULB, La Plaine Campus, 1050, Brussels, Belgium
| | - Marianne Rooman
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, 1050, Brussels, Belgium
- Department of BioModeling, BioInformatics & BioProcesses, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - Yves Moreau
- ESAT-STADIUS, KU Leuven, Kasteelpark Arenberg 10, 3001, Leuven, Belgium
- Imec, 3001, Leuven, Belgium
| | - Wim F Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, 1050, Brussels, Belgium.
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
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9
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Liang J, Li L, Jin X, Xu B, Pi L, Liu S, Zhu W, Zhang C, Luan B, Gong L, Zhang C. Pharmacological effect of human melanocortin-2 receptor accessory protein 2 variants on hypothalamic melanocortin receptors. Endocrine 2018; 61:94-104. [PMID: 29704154 DOI: 10.1007/s12020-018-1596-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 04/09/2018] [Indexed: 10/17/2022]
Abstract
PURPOSE Melanocortin-3 receptor (MC3R), melanocortin-4 receptor (MC4R), and a recently identified melanocortin-2 receptor accessory protein 2 (MRAP2), are highly expressed in hypothalamus and coordinately regulate energy homeostasis, but the single cellular transcriptome of melanocortin system remains unknown. Several infrequent MRAP2 variants are reported from severe obese human patients but the mechanisms on how they affect melanocortin signaling are unclear. METHODS First, we performed in silico analysis of mouse hypothalamus RNA sequencing datasets at single-cell resolution from two independent studies. Next, we inspected the three-dimensional conformational alteration of three mutations on MRAP2 protein. Finally, the influence of MRAP2 variants on MC3R and MC4R signaling was analyzed in vitro. RESULTS (1) We confirmed the actual co-expression of Mrap2 with Mc3r and Mc4r, and demonstrated more broad distribution of Mrap2-positive neuronal populations than Mc3r or Mc4r in mouse hypothalamus. (2) Compared with wild-type MRAP2, MRAP2N88Y, and MRAP2R125C showed impaired α-MSH-induced MC4R or MC3R stimulation. (3) MRAP2N88Yexhibited enhanced interaction with MC4R protein and its own. CONCLUSIONS This is the first dedicated description of single-cell transcriptome signature of Mrap2, Mc3r, and Mc4r in the central nerve system and the first evidence describing the unique dimer formation, conformational change, and pharmacological effect of MRAP2 mutations on MC3R signaling.
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MESH Headings
- Adaptor Proteins, Signal Transducing
- Animals
- Carrier Proteins/pharmacology
- Computer Simulation
- Genetic Variation
- Humans
- Hypothalamus/drug effects
- Hypothalamus/metabolism
- Mice
- Mutation/genetics
- Neurons/metabolism
- Nucleic Acid Conformation
- Plasmids
- RNA/genetics
- Receptor, Melanocortin, Type 3/genetics
- Receptor, Melanocortin, Type 3/metabolism
- Receptor, Melanocortin, Type 4/genetics
- Receptor, Melanocortin, Type 4/metabolism
- Receptors, Melanocortin/drug effects
- Signal Transduction/genetics
- alpha-MSH/pharmacology
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Affiliation(s)
- Jinye Liang
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Lei Li
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xuanxuan Jin
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Bingxin Xu
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Linyu Pi
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shangyun Liu
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Wei Zhu
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Cong Zhang
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Bing Luan
- Department of Endocrinology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Lulu Gong
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Chao Zhang
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.
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10
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Nailwal M, Chauhan JB. Computational Analysis of High-Risk SNPs in Human DBY Gene Responsible for Male Infertility: A Functional and Structural Impact. Interdiscip Sci 2018. [PMID: 29520635 DOI: 10.1007/s12539-018-0290-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND DEAD-box helicase 3, Y-linked (DBY) is a candidate gene of the AZF region which is involved in spermatogenesis process. Mutations in the DBY gene may disrupt the spermatogenesis and lead to infertility in men. Identification of functionally neutral mutation from the disease-causing mutation is the biggest challenge in human genetic variation analysis. Owing to the importance of DBY in male infertility, functional analysis was carried out to reveal the association between genetic mutation and phenotypic variation through various in silico approaches. METHODS The present study analyzed the functional consequences of the nsSNPs in human DBY gene using SIFT, PolyPhen 2, PROVEAN, SNAP2, PMut, nsSNPAnalyzer, PhD-SNP and SNPs&GO along with stability analysis through I-Mutant2.0, MuPro and iPTREE-STAB. The conservational analysis of amino acid residues, biophysical properties and conserved domains of the DBY protein was analyzed using various computational tools. The 3D structure of the protein was generated using SPARKS-X and validated using RAMPAGE. RESULTS Out of 1130 SNPs reported in dbSNP, only one nsSNP (G300D) was found to have a functional effect on stability as well as the function of the DBY protein. The results showed the presence of G300 in the putative structure of DBY domain. CONCLUSION To the best of our knowledge, this is the first study to detect pathologically significant nsSNPs (G300D) through a computational approach in the DBY which can be useful for development in potent drug discovery studies.
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Affiliation(s)
- Mili Nailwal
- P.G. Department of Genetics, Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences (ARIBAS), New Vallabh Vidyanagar, Dist-Anand, Gujarat, 388121, India
| | - Jenabhai B Chauhan
- P.G. Department of Genetics, Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences (ARIBAS), New Vallabh Vidyanagar, Dist-Anand, Gujarat, 388121, India.
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11
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Siljee JE, Wang Y, Bernard AA, Ersoy BA, Zhang S, Marley A, Von Zastrow M, Reiter JF, Vaisse C. Subcellular localization of MC4R with ADCY3 at neuronal primary cilia underlies a common pathway for genetic predisposition to obesity. Nat Genet 2018; 50:180-185. [PMID: 29311635 PMCID: PMC5805646 DOI: 10.1038/s41588-017-0020-9] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 11/15/2017] [Indexed: 02/01/2023]
Affiliation(s)
- Jacqueline E Siljee
- Department of Medicine and Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Yi Wang
- Department of Medicine and Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Adelaide A Bernard
- Department of Medicine and Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Baran A Ersoy
- Department of Medicine and Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.,Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Sumei Zhang
- Department of Medicine and Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Aaron Marley
- Department of Psychiatry and Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Mark Von Zastrow
- Department of Psychiatry and Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Christian Vaisse
- Department of Medicine and Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.
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12
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Gallion J, Koire A, Katsonis P, Schoenegge A, Bouvier M, Lichtarge O. Predicting phenotype from genotype: Improving accuracy through more robust experimental and computational modeling. Hum Mutat 2017; 38:569-580. [PMID: 28230923 PMCID: PMC5516182 DOI: 10.1002/humu.23193] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 01/25/2017] [Accepted: 02/04/2017] [Indexed: 11/11/2022]
Abstract
Computational prediction yields efficient and scalable initial assessments of how variants of unknown significance may affect human health. However, when discrepancies between these predictions and direct experimental measurements of functional impact arise, inaccurate computational predictions are frequently assumed as the source. Here, we present a methodological analysis indicating that shortcomings in both computational and biological data can contribute to these disagreements. We demonstrate that incomplete assaying of multifunctional proteins can affect the strength of correlations between prediction and experiments; a variant's full impact on function is better quantified by considering multiple assays that probe an ensemble of protein functions. Additionally, many variants predictions are sensitive to protein alignment construction and can be customized to maximize relevance of predictions to a specific experimental question. We conclude that inconsistencies between computation and experiment can often be attributed to the fact that they do not test identical hypotheses. Aligning the design of the computational input with the design of the experimental output will require cooperation between computational and biological scientists, but will also lead to improved estimations of computational prediction accuracy and a better understanding of the genotype–phenotype relationship.
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Affiliation(s)
- Jonathan Gallion
- Program in Structural and Computational Biology and Molecular BiophysicsBaylor College of MedicineHoustonTexas
| | - Amanda Koire
- Program in Structural and Computational Biology and Molecular BiophysicsBaylor College of MedicineHoustonTexas
| | - Panagiotis Katsonis
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Anne‐Marie Schoenegge
- Department of BiochemistryInstitute for Research in Immunology and CancerUniversité de MontrealQuebecCanada
| | - Michel Bouvier
- Department of BiochemistryInstitute for Research in Immunology and CancerUniversité de MontrealQuebecCanada
| | - Olivier Lichtarge
- Program in Structural and Computational Biology and Molecular BiophysicsBaylor College of MedicineHoustonTexas
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
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13
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Al-Allaf FA, Taher MM, Abduljaleel Z, Bouazzaoui A, Athar M, Bogari NM, Abalkhail HA, Owaidah TM. Molecular Analysis of Factor VIII and Factor IX Genes in Hemophilia Patients: Identification of Novel Mutations and Molecular Dynamics Studies. J Clin Med Res 2017; 9:317-331. [PMID: 28270892 PMCID: PMC5330775 DOI: 10.14740/jocmr2876w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2017] [Indexed: 12/19/2022] Open
Abstract
Background Hemophilias A and B are X-linked bleeding disorders caused by mutations in the factor VIII and factor IX genes, respectively. Our objective was to identify the spectrum of mutations of the factor VIII and factor IX genes in Saudi Arabian population and determine the genotype and phenotype correlations by molecular dynamics (MD) simulation. Methods For genotyping, blood samples from Saudi Arabian patients were collected, and the genomic DNA was amplified, and then sequenced by Sanger method. For molecular simulations, we have used softwares such as CHARMM (Chemistry at Harvard Macromolecular Mechanics; http://www.charmm-gui.org) and GROMACS. In addition, the secondary structure was determined based on the solvent accessibility for the confirmation of the protein stability at the site of mutation. Results Six mutations (three novel and three known) were identified in factor VIII gene, and six mutations (one novel and five known) were identified in factor IX gene. The factor VIII novel mutations identified were c.99G>T, p. (W33C) in exon 1, c.2138 DelA, p. (N713Tfs*9) in eon14, also a novel mutation at splicing acceptor site of exon 23 c.6430 - 1G>A. In factor IX, we found a novel mutation c.855G>C, p. (E285D) in exon 8. These novel mutations were not reported in any factor VIII or factor IX databases previously. The deleterious effects of these novel mutations were confirmed by PolyPhen2 and SIFT programs. Conclusion The protein functional and structural studies and the models built in this work would be appropriate for predicting the effects of deleterious amino acid substitutions causing these genetic disorders. These findings are useful for genetic counseling in the case of consanguineous marriages which is more common in the Saudi Arabia.
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Affiliation(s)
- Faisal A Al-Allaf
- Faculty of Medicine, Department of Medical Genetics, Umm Al-Qura University, Makkah, Kingdom of Saudi Arabia; Molecular Diagnostics Unit, Department of Laboratory Medicine and Blood Bank, King Abdullah Medical City, Makkah, Kingdom of Saudi Arabia; Science and Technology Unit, Umm Al-Qura University, Makkah, Kingdom of Saudi Arabia; These authors contributed equally to this study
| | - Mohiuddin M Taher
- Faculty of Medicine, Department of Medical Genetics, Umm Al-Qura University, Makkah, Kingdom of Saudi Arabia; Science and Technology Unit, Umm Al-Qura University, Makkah, Kingdom of Saudi Arabia; These authors contributed equally to this study
| | - Zainularifeen Abduljaleel
- Faculty of Medicine, Department of Medical Genetics, Umm Al-Qura University, Makkah, Kingdom of Saudi Arabia; Science and Technology Unit, Umm Al-Qura University, Makkah, Kingdom of Saudi Arabia
| | - Abdellatif Bouazzaoui
- Faculty of Medicine, Department of Medical Genetics, Umm Al-Qura University, Makkah, Kingdom of Saudi Arabia; Science and Technology Unit, Umm Al-Qura University, Makkah, Kingdom of Saudi Arabia
| | - Mohammed Athar
- Faculty of Medicine, Department of Medical Genetics, Umm Al-Qura University, Makkah, Kingdom of Saudi Arabia; Science and Technology Unit, Umm Al-Qura University, Makkah, Kingdom of Saudi Arabia
| | - Neda M Bogari
- Faculty of Medicine, Department of Medical Genetics, Umm Al-Qura University, Makkah, Kingdom of Saudi Arabia
| | - Halah A Abalkhail
- Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia
| | - Tarek Ma Owaidah
- Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia
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Thompson MD, Capra V, Clunes MT, Rovati GE, Stankova J, Maj MC, Duffy DL. Cysteinyl Leukotrienes Pathway Genes, Atopic Asthma and Drug Response: From Population Isolates to Large Genome-Wide Association Studies. Front Pharmacol 2016; 7:299. [PMID: 27990118 PMCID: PMC5131607 DOI: 10.3389/fphar.2016.00299] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 08/24/2016] [Indexed: 02/05/2023] Open
Abstract
Genetic variants associated with asthma pathogenesis and altered response to drug therapy are discussed. Many studies implicate polymorphisms in genes encoding the enzymes responsible for leukotriene synthesis and intracellular signaling through activation of seven transmembrane domain receptors, such as the cysteinyl leukotriene 1 (CYSLTR1) and 2 (CYSLTR2) receptors. The leukotrienes are polyunsaturated lipoxygenated eicosatetraenoic acids that exhibit a wide range of pharmacological and physiological actions. Of the three enzymes involved in the formation of the leukotrienes, arachidonate 5 lipoxygenase 5 (ALOX5), leukotriene C4 synthase (LTC4S), and leukotriene hydrolase (LTA4H) are all polymorphic. These polymorphisms often result in variable production of the CysLTs (LTC4, LTD4, and LTE4) and LTB4. Variable number tandem repeat sequences located in the Sp1-binding motif within the promotor region of the ALOX5 gene are associated with leukotriene burden and bronchoconstriction independent of asthma risk. A 444A > C SNP polymorphism in the LTC4S gene, encoding an enzyme required for the formation of a glutathione adduct at the C-6 position of the arachidonic acid backbone, is associated with severe asthma and altered response to the CYSLTR1 receptor antagonist zafirlukast. Genetic variability in the CysLT pathway may contribute additively or synergistically to altered drug responses. The 601 A > G variant of the CYSLTR2 gene, encoding the Met201Val CYSLTR2 receptor variant, is associated with atopic asthma in the general European population, where it is present at a frequency of ∼2.6%. The variant was originally found in the founder population of Tristan da Cunha, a remote island in the South Atlantic, in which the prevalence of atopy is approximately 45% and the prevalence of asthma is 36%. In vitro work showed that the atopy-associated Met201Val variant was inactivating with respect to ligand binding, Ca2+ flux and inositol phosphate generation. In addition, the CYSLTR1 gene, located at Xq13-21.1, has been associated with atopic asthma. The activating Gly300Ser CYSLTR1 variant is discussed. In addition to genetic loci, risk for asthma may be influenced by environmental factors such as smoking. The contribution of CysLT pathway gene sequence variants to atopic asthma is discussed in the context of other genes and environmental influences known to influence asthma.
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Affiliation(s)
- Miles D Thompson
- Biochemical Genetics and Metabolomics Laboratory, Department of Pediatrics, University of California, San Diego, La JollaCA, USA; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ONCanada
| | - Valerie Capra
- Department of Health Sciences, San Paolo Hospital, Università degli Studi di Milano Milano, Italy
| | - Mark T Clunes
- Department of Physiology/Neuroscience, School of Medicine, Saint George's University Saint George's, Grenada
| | - G E Rovati
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano Milano, Italy
| | - Jana Stankova
- Division of Immunology and Allergy, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke QC, Canada
| | - Mary C Maj
- Department of Biochemistry, School of Medicine, Saint George's University Saint George's, Grenada
| | - David L Duffy
- QIMR Berghofer Medical Research Institute, Herston QLD, Australia
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Edrees BM, Athar M, Abduljaleel Z, Al-Allaf FA, Taher MM, Khan W, Bouazzaoui A, Al-Harbi N, Safar R, Al-Edressi H, Alansary K, Anazi A, Altayeb N, Ahmed MA. Functional alterations due to amino acid changes and evolutionary comparative analysis of ARPKD and ADPKD genes. GENOMICS DATA 2016; 10:127-134. [PMID: 27843768 PMCID: PMC5099264 DOI: 10.1016/j.gdata.2016.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/18/2016] [Accepted: 10/30/2016] [Indexed: 12/15/2022]
Abstract
A targeted customized sequencing of genes implicated in autosomal recessive polycystic kidney disease (ARPKD) phenotype was performed to identify candidate variants using the Ion torrent PGM next-generation sequencing. The results identified four potential pathogenic variants in PKHD1 gene [c.4870C > T, p.(Arg1624Trp), c.5725C > T, p.(Arg1909Trp), c.1736C > T, p.(Thr579Met) and c.10628T > G, p.(Leu3543Trp)] among 12 out of 18 samples. However, one variant c.4870C > T, p.(Arg1624Trp) was common among eight patients. Some patient samples also showed few variants in autosomal dominant polycystic kidney disease (ADPKD) disease causing genes PKD1 and PKD2 such as c.12433G > A, p.(Val4145Ile) and c.1445T > G, p.(Phe482Cys), respectively. All causative variants were validated by capillary sequencing and confirmed the presence of a novel homozygous variant c.10628T > G, p.(Leu3543Trp) in a male proband. We have recently published the results of these studies (Edrees et al., 2016). Here we report for the first time the effect of the common mutation p.(Arg1624Trp) found in eight samples on the protein structure and function due to the specific amino acid changes of PKHD1 protein using molecular dynamics simulations. The computational approaches provide tool predict the phenotypic effect of variant on the structure and function of the altered protein. The structural analysis with the common mutation p.(Arg1624Trp) in the native and mutant modeled protein were also studied for solvent accessibility, secondary structure and stabilizing residues to find out the stability of the protein between wild type and mutant forms. Furthermore, comparative genomics and evolutionary analyses of variants observed in PKHD1, PKD1, and PKD2 genes were also performed in some mammalian species including human to understand the complexity of genomes among closely related mammalian species. Taken together, the results revealed that the evolutionary comparative analyses and characterization of PKHD1, PKD1, and PKD2 genes among various related and unrelated mammalian species will provide important insights into their evolutionary process and understanding for further disease characterization and management.
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Affiliation(s)
- Burhan M Edrees
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia; King Fahad Medical City, P.O. Box 59046, Riyadh 11525, Saudi Arabia
| | - Mohammad Athar
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia; Science and Technology Unit, Umm Al Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia
| | - Zainularifeen Abduljaleel
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia; Science and Technology Unit, Umm Al Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia
| | - Faisal A Al-Allaf
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia; Science and Technology Unit, Umm Al Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia; Molecular Diagnostics Unit, Department of Laboratory and Blood Bank, King Abdullah Medical City, Makkah 21955, Saudi Arabia
| | - Mohiuddin M Taher
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia; Science and Technology Unit, Umm Al Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia
| | - Wajahatullah Khan
- Department of Basic Sciences, College of Science and Health Professions, King Saud Bin Abdulaziz University for Health Sciences, P.O. Box 3660, Riyadh 11426, Saudi Arabia
| | - Abdellatif Bouazzaoui
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia; Science and Technology Unit, Umm Al Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia
| | - Naffaa Al-Harbi
- Department of Pediatric, King Faisal Specialist Hospital and Research Centre, P.O. Box 40047, Jeddah 21499, Saudi Arabia
| | - Ramzia Safar
- Madinah Maternity and Children's Hospital, P.O. Box 5073, Madinah 42318, Saudi Arabia
| | - Howaida Al-Edressi
- Madinah Maternity and Children's Hospital, P.O. Box 5073, Madinah 42318, Saudi Arabia
| | - Khawala Alansary
- King Fahad Medical City, P.O. Box 59046, Riyadh 11525, Saudi Arabia
| | - Abulkareem Anazi
- King Fahad Medical City, P.O. Box 59046, Riyadh 11525, Saudi Arabia
| | - Naji Altayeb
- King Fahad Medical City, P.O. Box 59046, Riyadh 11525, Saudi Arabia
| | - Muawia A Ahmed
- King Salman Armed Forces Hospital, P.O. box 100, Tabuk, Saudi Arabia
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Basharat Z, Messaoudi A, Ruba S, Yasmin A. NQO1 rs1800566 polymorph is more prone to NOx induced lung injury: Endorsing deleterious functionality through informatics approach. Gene 2016; 591:14-20. [DOI: 10.1016/j.gene.2016.06.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 06/12/2016] [Accepted: 06/23/2016] [Indexed: 02/06/2023]
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18
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Abitbol M, Legrand R, Tiret L. A missense mutation inmelanocortin 1 receptoris associated with the red coat colour in donkeys. Anim Genet 2014; 45:878-80. [DOI: 10.1111/age.12207] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2014] [Indexed: 11/30/2022]
Affiliation(s)
- M. Abitbol
- Université Paris-Est Créteil; Ecole Nationale Vétérinaire d'Alfort; Maisons-Alfort France
- UMR955 INRA-ENVA de Génétique Fonctionnelle et Médicale; Institut National de la Recherche Agronomique; Maisons-Alfort France
| | - R. Legrand
- Université Paris-Est Créteil; Ecole Nationale Vétérinaire d'Alfort; Maisons-Alfort France
- UMR955 INRA-ENVA de Génétique Fonctionnelle et Médicale; Institut National de la Recherche Agronomique; Maisons-Alfort France
| | - L. Tiret
- Université Paris-Est Créteil; Ecole Nationale Vétérinaire d'Alfort; Maisons-Alfort France
- UMR955 INRA-ENVA de Génétique Fonctionnelle et Médicale; Institut National de la Recherche Agronomique; Maisons-Alfort France
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Yachdav G, Kloppmann E, Kajan L, Hecht M, Goldberg T, Hamp T, Hönigschmid P, Schafferhans A, Roos M, Bernhofer M, Richter L, Ashkenazy H, Punta M, Schlessinger A, Bromberg Y, Schneider R, Vriend G, Sander C, Ben-Tal N, Rost B. PredictProtein--an open resource for online prediction of protein structural and functional features. Nucleic Acids Res 2014; 42:W337-43. [PMID: 24799431 PMCID: PMC4086098 DOI: 10.1093/nar/gku366] [Citation(s) in RCA: 435] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
PredictProtein is a meta-service for sequence analysis that has been predicting
structural and functional features of proteins since 1992. Queried with a
protein sequence it returns: multiple sequence alignments, predicted aspects of
structure (secondary structure, solvent accessibility, transmembrane helices
(TMSEG) and strands, coiled-coil regions, disulfide bonds and disordered
regions) and function. The service incorporates analysis methods for the
identification of functional regions (ConSurf), homology-based inference of Gene
Ontology terms (metastudent), comprehensive subcellular localization prediction
(LocTree3), protein–protein binding sites (ISIS2),
protein–polynucleotide binding sites (SomeNA) and predictions of the
effect of point mutations (non-synonymous SNPs) on protein function (SNAP2). Our
goal has always been to develop a system optimized to meet the demands of
experimentalists not highly experienced in bioinformatics. To this end, the
PredictProtein results are presented as both text and a series of intuitive,
interactive and visually appealing figures. The web server and sources are
available at http://ppopen.rostlab.org.
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Affiliation(s)
- Guy Yachdav
- Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany Biosof LLC, New York, NY 10001, USA TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), TUM (Technische Universität München), Garching/Munich 85748, Germany
| | - Edda Kloppmann
- Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany New York Consortium on Membrane Protein Structure (NYCOMPS), Columbia University, New York, NY 10032, USA
| | - Laszlo Kajan
- Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany
| | - Maximilian Hecht
- Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), TUM (Technische Universität München), Garching/Munich 85748, Germany
| | - Tatyana Goldberg
- Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), TUM (Technische Universität München), Garching/Munich 85748, Germany
| | - Tobias Hamp
- Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany
| | - Peter Hönigschmid
- Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising 85354, Germany
| | - Andrea Schafferhans
- Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany
| | - Manfred Roos
- Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany
| | - Michael Bernhofer
- Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany
| | - Lothar Richter
- Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany
| | - Haim Ashkenazy
- The Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Marco Punta
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK Institute for Food and Plant Sciences WZW-Weihenstephan, Alte Akademie 8, Freising 85350, Germany
| | - Avner Schlessinger
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Yana Bromberg
- Biosof LLC, New York, NY 10001, USA Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Reinhard Schneider
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Gerrit Vriend
- Luxembourg University & Luxembourg Centre for Systems Biomedicine, 4362 Belval, Luxembourg
| | - Chris Sander
- CMBI, NCMLS, Radboudumc Nijmegen Medical Centre, 6525 GA Nijmegen, The Netherlands
| | - Nir Ben-Tal
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, 10065 NY, USA
| | - Burkhard Rost
- Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany Biosof LLC, New York, NY 10001, USA New York Consortium on Membrane Protein Structure (NYCOMPS), Columbia University, New York, NY 10032, USA The Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel Department of Biochemistry and Molecular Biophysics & New York Consortium on Membrane Protein Structure (NYCOMPS), Columbia University, New York, NY 10032, USA Institute for Advanced Study (TUM-IAS), Garching/Munich 85748, Germany
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Abduljaleel Z, Al-Allaf FA, Khan W, Athar M, Shahzad N, Taher MM, Elrobh M, Alanazi MS, El-Huneidi W. Evidence of trem2 variant associated with triple risk of Alzheimer's disease. PLoS One 2014; 9:e92648. [PMID: 24663666 PMCID: PMC3963925 DOI: 10.1371/journal.pone.0092648] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 02/25/2014] [Indexed: 12/27/2022] Open
Abstract
Alzheimer's disease is one of the main causes of dementia among elderly individuals and leads to the neurodegeneration of different areas of the brain, resulting in memory impairments and loss of cognitive functions. Recently, a rare variant that is associated with 3-fold higher risk of Alzheimer's disease onset has been found. The rare variant discovered is a missense mutation in the loop region of exon 2 of Trem2 (rs75932628-T, Arg47His). The aim of this study was to investigate the evidence for potential structural and functional significance of Trem2 gene variant (Arg47His) through molecular dynamics simulations. Our results showed the alteration caused due to the variant in TREM2 protein has significant effect on the ligand binding affinity as well as structural configuration. Based on molecular dynamics (MD) simulation under salvation, the results confirmed that native form of the variant (Arg47His) might be responsible for improved compactness, hence thereby improved protein folding. Protein simulation was carried out at different temperatures. At 300K, the deviation of the theoretical model of TREM2 protein increased from 2.0 Å at 10 ns. In contrast, the deviation of the Arg47His mutation was maintained at 1.2 Å until the end of the simulation (t = 10 ns), which indicated that Arg47His had reached its folded state. The mutant residue was a highly conserved region and was similar to "immunoglobulin V-set" and "immunoglobulin-like folds". Taken together, the result from this study provides a biophysical insight on how the studied variant could contribute to the genetic susceptibility to Alzheimer's disease.
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Affiliation(s)
- Zainularifeen Abduljaleel
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
- Genome Research Chair Unit, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
- * E-mail:
| | - Faisal A. Al-Allaf
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Wajahatullah Khan
- Department of Basic Sciences, College of Science and Health Professions, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Mohammad Athar
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Naiyer Shahzad
- Department of Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mohiuddin M. Taher
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mohamed Elrobh
- Genome Research Chair Unit, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed S. Alanazi
- Genome Research Chair Unit, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Waseem El-Huneidi
- Department of Basic Sciences, College of Science and Health Professions, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
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21
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Klein A, Riazanov A, Hindle MM, Baker CJO. Benchmarking infrastructure for mutation text mining. J Biomed Semantics 2014; 5:11. [PMID: 24568600 PMCID: PMC3939821 DOI: 10.1186/2041-1480-5-11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 02/05/2014] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Experimental research on the automatic extraction of information about mutations from texts is greatly hindered by the lack of consensus evaluation infrastructure for the testing and benchmarking of mutation text mining systems. RESULTS We propose a community-oriented annotation and benchmarking infrastructure to support development, testing, benchmarking, and comparison of mutation text mining systems. The design is based on semantic standards, where RDF is used to represent annotations, an OWL ontology provides an extensible schema for the data and SPARQL is used to compute various performance metrics, so that in many cases no programming is needed to analyze results from a text mining system. While large benchmark corpora for biological entity and relation extraction are focused mostly on genes, proteins, diseases, and species, our benchmarking infrastructure fills the gap for mutation information. The core infrastructure comprises (1) an ontology for modelling annotations, (2) SPARQL queries for computing performance metrics, and (3) a sizeable collection of manually curated documents, that can support mutation grounding and mutation impact extraction experiments. CONCLUSION We have developed the principal infrastructure for the benchmarking of mutation text mining tasks. The use of RDF and OWL as the representation for corpora ensures extensibility. The infrastructure is suitable for out-of-the-box use in several important scenarios and is ready, in its current state, for initial community adoption.
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Affiliation(s)
- Artjom Klein
- Computer Science And Applied Statistics Department, University of New Brunswick, Saint John, Canada
| | | | - Matthew M Hindle
- Synthetic and Systems Biology, Edinburgh University, Edinburgh, UK
| | - Christopher JO Baker
- Computer Science And Applied Statistics Department, University of New Brunswick, Saint John, Canada
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22
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Yachdav G, Hecht M, Pasmanik-Chor M, Yeheskel A, Rost B. HeatMapViewer: interactive display of 2D data in biology. F1000Res 2014; 3:48. [PMID: 24860644 PMCID: PMC4023661 DOI: 10.12688/f1000research.3-48.v1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/31/2014] [Indexed: 11/20/2022] Open
Abstract
Summary: The HeatMapViewer is a BioJS component that lays-out and renders two-dimensional (2D) plots or heat maps that are ideally suited to visualize matrix formatted data in biology such as for the display of microarray experiments or the outcome of mutational studies and the study of SNP-like sequence variants. It can be easily integrated into documents and provides a powerful, interactive way to visualize heat maps in web applications. The software uses a scalable graphics technology that adapts the visualization component to any required resolution, a useful feature for a presentation with many different data-points. The component can be applied to present various biological data types. Here, we present two such cases – showing gene expression data and visualizing mutability landscape analysis. Availability:https://github.com/biojs/biojs;
http://dx.doi.org/10.5281/zenodo.7706.
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Affiliation(s)
- Guy Yachdav
- TUM, Department of Informatics, Bioinformatics & Computational Biology, 5748 Garching/ Munich, Germany ; TUM Graduate School of Information Science in Health (GSISH), 85748 Garching/Munich, Germany ; Biosof LLC, New York, NY, 10001, USA
| | - Maximilian Hecht
- TUM, Department of Informatics, Bioinformatics & Computational Biology, 5748 Garching/ Munich, Germany ; TUM Graduate School of Information Science in Health (GSISH), 85748 Garching/Munich, Germany
| | - Metsada Pasmanik-Chor
- Bioinformatics Unit, G.S.W. Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Adva Yeheskel
- Bioinformatics Unit, G.S.W. Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Burkhard Rost
- TUM, Department of Informatics, Bioinformatics & Computational Biology, 5748 Garching/ Munich, Germany ; TUM Graduate School of Information Science in Health (GSISH), 85748 Garching/Munich, Germany ; Biosof LLC, New York, NY, 10001, USA
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23
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Thompson MD, Cole DEC, Capra V, Siminovitch KA, Rovati GE, Burnham WM, Rana BK. Pharmacogenetics of the G protein-coupled receptors. Methods Mol Biol 2014; 1175:189-242. [PMID: 25150871 DOI: 10.1007/978-1-4939-0956-8_9] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Pharmacogenetics investigates the influence of genetic variants on physiological phenotypes related to drug response and disease, while pharmacogenomics takes a genome-wide approach to advancing this knowledge. Both play an important role in identifying responders and nonresponders to medication, avoiding adverse drug reactions, and optimizing drug dose for the individual. G protein-coupled receptors (GPCRs) are the primary target of therapeutic drugs and have been the focus of these studies. With the advance of genomic technologies, there has been a substantial increase in the inventory of naturally occurring rare and common GPCR variants. These variants include single-nucleotide polymorphisms and insertion or deletions that have potential to alter GPCR expression of function. In vivo and in vitro studies have determined functional roles for many GPCR variants, but genetic association studies that define the physiological impact of the majority of these common variants are still limited. Despite the breadth of pharmacogenetic data available, GPCR variants have not been included in drug labeling and are only occasionally considered in optimizing clinical use of GPCR-targeted agents. In this chapter, pharmacogenetic and genomic studies on GPCR variants are reviewed with respect to a subset of GPCR systems, including the adrenergic, calcium sensing, cysteinyl leukotriene, cannabinoid CB1 and CB2 receptors, and the de-orphanized receptors such as GPR55. The nature of the disruption to receptor function is discussed with respect to regulation of gene expression, expression on the cell surface (affected by receptor trafficking, dimerization, desensitization/downregulation), or perturbation of receptor function (altered ligand binding, G protein coupling, constitutive activity). The large body of experimental data generated on structure and function relationships and receptor-ligand interactions are being harnessed for the in silico functional prediction of naturally occurring GPCR variants. We provide information on online resources dedicated to GPCRs and present applications of publically available computational tools for pharmacogenetic studies of GPCRs. As the breadth of GPCR pharmacogenomic data becomes clearer, the opportunity for routine assessment of GPCR variants to predict disease risk, drug response, and potential adverse drug effects will become possible.
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Affiliation(s)
- Miles D Thompson
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, Canada, M5S 1A8,
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24
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Hecht M, Bromberg Y, Rost B. News from the protein mutability landscape. J Mol Biol 2013; 425:3937-48. [PMID: 23896297 DOI: 10.1016/j.jmb.2013.07.028] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 07/08/2013] [Accepted: 07/19/2013] [Indexed: 12/16/2022]
Abstract
Some mutations of protein residues matter more than others, and these are often conserved evolutionarily. The explosion of deep sequencing and genotyping increasingly requires the distinction between effect and neutral variants. The simplest approach predicts all mutations of conserved residues to have an effect; however, this works poorly, at best. Many computational tools that are optimized to predict the impact of point mutations provide more detail. Here, we expand the perspective from the view of single variants to the level of sketching the entire mutability landscape. This landscape is defined by the impact of substituting every residue at each position in a protein by each of the 19 non-native amino acids. We review some of the powerful conclusions about protein function, stability and their robustness to mutation that can be drawn from such an analysis. Large-scale experimental and computational mutagenesis experiments are increasingly furthering our understanding of protein function and of the genotype-phenotype associations. We also discuss how these can be used to improve predictions of protein function and pathogenicity of missense variants.
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Affiliation(s)
- Maximilian Hecht
- Department of Bioinformatics and Computational Biology I12, Technische Universität München, Boltzmannstrasse 3, 85748 Garching, Germany.
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25
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Evidence of colorectal cancer risk associated variant Lys25Ser in the proximity of human bone morphogenetic protein 2. Gene 2013; 522:75-83. [DOI: 10.1016/j.gene.2013.03.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 03/08/2013] [Indexed: 11/18/2022]
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26
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Ersoy BA, Pardo L, Zhang S, Thompson DA, Millhauser G, Govaerts C, Vaisse C. Mechanism of N-terminal modulation of activity at the melanocortin-4 receptor GPCR. Nat Chem Biol 2012; 8:725-30. [PMID: 22729149 PMCID: PMC3657613 DOI: 10.1038/nchembio.1008] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 05/14/2012] [Indexed: 01/29/2023]
Abstract
Most of our understanding of G protein-coupled receptor (GPCR) activation has been focused on the direct interaction between diffusible ligands and their seven-transmembrane domains. However, a number of these receptors depend on their extracellular N-terminal domain for ligand recognition and activation. To dissect the molecular interactions underlying both modes of activation at a single receptor, we used the unique properties of the melanocortin-4 receptor (MC4R), a GPCR that shows constitutive activity maintained by its N-terminal domain and is physiologically activated by the peptide α-melanocyte stimulating hormone (αMSH). We find that activation by the N-terminal domain and αMSH relies on different key residues in the transmembrane region. We also demonstrate that agouti-related protein, a physiological antagonist of MC4R, acts as an inverse agonist by inhibiting N terminus-mediated activation, leading to the speculation that a number of constitutively active orphan GPCRs could have physiological inverse agonists as sole regulators.
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Affiliation(s)
- Baran A Ersoy
- Department of Medicine, University of California–San Francisco, San Francisco, California, USA
- The Diabetes Center, University of California–San Francisco, San Francisco, California, USA
| | - Leonardo Pardo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sumei Zhang
- Department of Medicine, University of California–San Francisco, San Francisco, California, USA
- The Diabetes Center, University of California–San Francisco, San Francisco, California, USA
| | - Darren A Thompson
- Department of Chemistry and Biochemistry, University of California–Santa Cruz, Santa Cruz, California, USA
| | - Glenn Millhauser
- Department of Chemistry and Biochemistry, University of California–Santa Cruz, Santa Cruz, California, USA
| | - Cedric Govaerts
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, Brussels, Belgium
| | - Christian Vaisse
- Department of Medicine, University of California–San Francisco, San Francisco, California, USA
- The Diabetes Center, University of California–San Francisco, San Francisco, California, USA
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27
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Schaefer C, Bromberg Y, Achten D, Rost B. Disease-related mutations predicted to impact protein function. BMC Genomics 2012; 13 Suppl 4:S11. [PMID: 22759649 PMCID: PMC3394413 DOI: 10.1186/1471-2164-13-s4-s11] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background Non-synonymous single nucleotide polymorphisms (nsSNPs) alter the protein sequence and can cause disease. The impact has been described by reliable experiments for relatively few mutations. Here, we study predictions for functional impact of disease-annotated mutations from OMIM, PMD and Swiss-Prot and of variants not linked to disease. Results Most disease-causing mutations were predicted to impact protein function. More surprisingly, the raw predictions scores for disease-causing mutations were higher than the scores for the function-altering data set originally used for developing the prediction method (here SNAP). We might expect that diseases are caused by change-of-function mutations. However, it is surprising how well prediction methods developed for different purposes identify this link. Conversely, our predictions suggest that the set of nsSNPs not currently linked to diseases contains very few strong disease associations to be discovered. Conclusions Firstly, annotations of disease-causing nsSNPs are on average so reliable that they can be used as proxies for functional impact. Secondly, disease-causing nsSNPs can be identified very well by methods that predict the impact of mutations on protein function. This implies that the existing prediction methods provide a very good means of choosing a set of suspect SNPs relevant for disease.
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Affiliation(s)
- Christian Schaefer
- Bioinformatics-i12, Informatics, Technical University Munich, Boltzmannstrasse 3, Garching/Munich, Germany.
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28
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Hao DC, Feng Y, Xiao R, Xiao PG. Non-neutral nonsynonymous single nucleotide polymorphisms in human ABC transporters: the first comparison of six prediction methods. Pharmacol Rep 2012; 63:924-34. [PMID: 22001980 DOI: 10.1016/s1734-1140(11)70608-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 02/07/2011] [Indexed: 11/28/2022]
Abstract
Nonsynonymous single nucleotide polymorphisms (nsSNPs) in coding regions that can lead to amino acid changes may cause alteration of protein function and account for susceptibility to disease and altered drug/xenobiotic response. Abundant nsSNPs have been found in genes coding for human ATP-binding cassette (ABC) transporters, but there is little known about the relationship between the genotype and phenotype of nsSNPs in these membrane proteins. In addition, it is unknown which prediction method is better suited for the prediction of non-neutral nsSNPs of ABC transporters. We have identified 2,172 validated nsSNPs in 49 human ABC transporter genes from the Ensembl genome database and the NCBI SNP database. Using six different algorithms, 41 to 52% of nsSNPs in ABC transporter genes were predicted to have functional impacts on protein function. Predictions largely agreed with the available experimental annotations. Overall, 78.5% of non-neutral nsSNPs were predicted correctly as damaging by SNAP, which together with SIFT and PolyPhen, was superior to the prediction methods Pmut, PhD-SNP, and Panther. This study also identified any amino acids that were likely to be functionally critical but have not yet been studied experimentally. There was significant concordance between the predicted results of SIFT and PolyPhen. Evolutionarily non-neutral (destabilizing) amino acid substitutions are predicted to be the basis for the pathogenic alteration of ABC transporter activity that is associated with disease susceptibility and altered drug/xenobiotic response.
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Affiliation(s)
- Da Cheng Hao
- Laboratory of Biotechnology, College of Environment, Dalian Jiaotong University, Dalian 116028, China.
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29
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Fanelli F, De Benedetti PG. Update 1 of: computational modeling approaches to structure-function analysis of G protein-coupled receptors. Chem Rev 2011; 111:PR438-535. [PMID: 22165845 DOI: 10.1021/cr100437t] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Francesca Fanelli
- Dulbecco Telethon Institute, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena, Italy.
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Davoli R, Braglia S, Valastro V, Annaratone C, Comella M, Zambonelli P, Nisi I, Gallo M, Buttazzoni L, Russo V. Analysis of MC4R polymorphism in Italian Large White and Italian Duroc pigs: association with carcass traits. Meat Sci 2011; 90:887-92. [PMID: 22197097 DOI: 10.1016/j.meatsci.2011.11.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 10/28/2011] [Accepted: 11/08/2011] [Indexed: 11/18/2022]
Abstract
The melanocortin-4 receptor (MC4R) gene codes for a G protein transmembrane receptor playing an important role in energy homeostasis control. In pig a single nucleotide polymorphism c.1426G>A has been identified and associated to average daily gain, feed intake and fatness traits but a lack of agreement on the effects of the gene on carcass traits in different breeds comes out from many studies. In the present study the c.1426G>A polymorphism is analysed in two Italian pig breeds, Large White and Duroc to study the association of the MC4R gene with some carcass traits. The results show that the c.1426G>A polymorphism affects daily gain, feed conversion ratio and ham weight in both breeds, lean cuts in the Italian Duroc and backfat thickness in the Italian Large White. The presence of MC4R mRNA transcript in different porcine tissues was analysed.
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Affiliation(s)
- R Davoli
- Department of Agri-food Protection and Valorisation (DIPROVAL), Faculty of Agriculture, University of Bologna, Reggio Emilia, Italy.
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31
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Protein disorder--a breakthrough invention of evolution? Curr Opin Struct Biol 2011; 21:412-8. [PMID: 21514145 DOI: 10.1016/j.sbi.2011.03.014] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 03/29/2011] [Accepted: 03/29/2011] [Indexed: 11/21/2022]
Abstract
As an operational definition, we refer to regions in proteins that do not adopt regular three-dimensional structures in isolation, as disordered regions. An antipode to disorder would be 'well-structured' rather than 'ordered'. Here, we argue for the following three hypotheses. Firstly, it is more useful to picture disorder as a distinct phenomenon in structural biology than as an extreme example of protein flexibility. Secondly, there are many very different flavors of protein disorder, nevertheless, it seems advantageous to portray the universe of all possible proteins in terms of two main types: well-structured, disordered. There might be a third type 'other' but we have so far no positive evidence for this. Thirdly, nature uses protein disorder as a tool to adapt to different environments. Protein disorder is evolutionarily conserved and this maintenance of disorder is highly nontrivial. Increasingly integrating protein disorder into the toolbox of a living cell was a crucial step in the evolution from simple bacteria to complex eukaryotes. We need new advanced computational methods to study this new milestone in the advance of protein biology.
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van den Berg L, van Beekum O, Heutink P, Felius BA, van de Heijning MPM, Strijbis S, van Spaendonk R, Piancatelli D, Garner KM, El Aouad R, Sistermans E, Adan RAH, Delemarre-van de Waal HA. Melanocortin-4 receptor gene mutations in a Dutch cohort of obese children. Obesity (Silver Spring) 2011; 19:604-11. [PMID: 20966905 DOI: 10.1038/oby.2010.259] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The most common monogenic form of obesity is caused by mutations in the gene encoding the melanocortin-4 receptor (MC4R). We have screened the MC4R coding sequence in 291 patients of a Dutch outpatient pediatric obesity clinic. We analyzed the minimal promoter region of the gene in a random subgroup of 217 children. Our aims were (i) to determine the frequency of MC4R mutations in a cohort of Dutch clinically obese children and (ii) to search for mutations in the promoter of the gene. Eleven MC4R coding variants were detected. Five children had mutations that have been shown to affect receptor function by other research groups (p.Y35X, p.I251fs, p.G231S). These children did not have earlier onset of obesity or higher BMI-SDS than the remainder of the cohort. One child had a novel nonsynonymous coding mutation (p.L304F). This variant showed a markedly decreased cell surface expression in in vitro experiments and is thus expected to be pathogenic. We detected 12 variants in the MC4R flanking regions. Five of these were not previously described (c.-1101C>T, c.-705A>T, c.-461A>G, c.-312T>C, c.-213A>G). We investigated these mutations by family studies and a bioinformatic approach. We conclude that rare heterozygous mutations in the coding sequence of MC4R account for some severe obesity cases in the Dutch population. These patients are difficult to recognize in a clinical setting. We generated a list of all MC4R variants that were described in the literature so far, which can aid the interpretation of mutations found in a diagnostic setting.
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Affiliation(s)
- Linda van den Berg
- Department of Paediatrics, Leiden University Medical Center, Leiden, The Netherlands.
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Xiang Z, Proneth B, Dirain ML, Litherland SA, Haskell-Luevano C. Pharmacological characterization of 30 human melanocortin-4 receptor polymorphisms with the endogenous proopiomelanocortin-derived agonists, synthetic agonists, and the endogenous agouti-related protein antagonist. Biochemistry 2010; 49:4583-600. [PMID: 20462274 DOI: 10.1021/bi100068u] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The melanocortin-4 receptor (MC4R) is a G-protein-coupled receptor (GPCR) that is expressed in the central nervous system and has a role in regulating feeding behavior, obesity, energy homeostasis, male erectile response, and blood pressure. Since the report of the MC4R knockout mouse in 1997, the field has been searching for links between this genetic biomarker and human obesity and type 2 diabetes. More then 80 single nucleotide polymorphisms (SNPs) have been identified from human patients, both obese and nonobese controls. Many significant studies have been performed examining the pharmacological characteristics of these hMC4R SNPs in attempts to identify a molecular defects/insights that might link a genetic factor to the obese phenotype observed in patients possessing these mutations. Our laboratory has previously reported the pharmacological characterization of 40 of these polymorphic hMC4 receptors with multiple endogenous and synthetic ligands. The goal of the current study is to perform a similar comprehensive side-by-side characterization of 30 additional human hMC4R with single nucleotide polymorphisms using multiple endogenous agonists [alpha-, beta-, and gamma(2)-melanocyte stimulating hormones (MSH) and adrenocorticotropin (ACTH)], the antagonist agouti-related protein hAGRP(87-132), and synthetic agonists [NDP-MSH, MTII, and the tetrapeptide Ac-His-dPhe-Arg-Trp-NH(2) (JRH887-9)]. These in vitro data, in some cases, provide a putative molecular link between dysfunctional hMC4R's and human obesity. These 30 hMC4R SNPs include R7H, R18H, R18L, S36Y, P48S, V50M, F51L, E61K, I69T, D90N, S94R, G98R, I121T, A154D, Y157S, W174C, G181D, F202L, A219 V, I226T, G231S, G238D, N240S, C271R, S295P, P299L, E308K, I317V, L325F, and 750DelGA. All but the N240S hMC4R were identified in obese patients. Additionally, we have characterized a double I102T/V103I hMC4R. In addition to the pharmacological characterization, the hMC4R variants were evaluated for cell surface expression by flow cytometry. The F51L, I69T, and A219V hMC4Rs possessed full agonist activity and significantly decreased endogenous agonist ligand potency. At the E61K, D90N, Y157S, and C271R hMC4Rs, all agonist ligands examined were only partially efficacious in generating a maximal signaling response (partial agonists) and possessed significantly decreased endogenous agonist ligand potency. Only the A219V, G238D, and S295P hMC4Rs possessed significantly decreased AGRP(87-132) antagonist potency. These data provide new information for use in GPCR computational development as well as insights into MC4R structure ad function.
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Affiliation(s)
- Zhimin Xiang
- Department of Pharmacodynamics, University of Florida, Gainesville, Florida 32610, USA
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Abstract
The melanocortin-4 receptor (MC4R) was cloned in 1993 by degenerate PCR; however, its function was unknown. Subsequent studies suggest that the MC4R might be involved in regulating energy homeostasis. This hypothesis was confirmed in 1997 by a series of seminal studies in mice. In 1998, human genetic studies demonstrated that mutations in the MC4R gene can cause monogenic obesity. We now know that mutations in the MC4R are the most common monogenic form of obesity, with more than 150 distinct mutations reported thus far. This review will summarize the studies on the MC4R, from its cloning and tissue distribution to its physiological roles in regulating energy homeostasis, cachexia, cardiovascular function, glucose and lipid homeostasis, reproduction and sexual function, drug abuse, pain perception, brain inflammation, and anxiety. I will then review the studies on the pharmacology of the receptor, including ligand binding and receptor activation, signaling pathways, as well as its regulation. Finally, the pathophysiology of the MC4R in obesity pathogenesis will be reviewed. Functional studies of the mutant MC4Rs and the therapeutic implications, including small molecules in correcting binding and signaling defect, and their potential as pharmacological chaperones in rescuing intracellularly retained mutants, will be highlighted.
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Affiliation(s)
- Ya-Xiong Tao
- Department of Anatomy, Physiology, and Pharmacology, Auburn University, Alabama 36849-5519, USA.
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Sester M, Koebernick K, Owen D, Ao M, Bromberg Y, May E, Stock E, Andrews L, Groh V, Spies T, Steinle A, Menz B, Burgert HG. Conserved amino acids within the adenovirus 2 E3/19K protein differentially affect downregulation of MHC class I and MICA/B proteins. THE JOURNAL OF IMMUNOLOGY 2009; 184:255-67. [PMID: 19949079 DOI: 10.4049/jimmunol.0902343] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Successful establishment and persistence of adenovirus (Ad) infections are facilitated by immunosubversive functions encoded in the early transcription unit 3 (E3). The E3/19K protein has a dual role, preventing cell surface transport of MHC class I/HLA class I (MHC-I/HLA-I) Ags and the MHC-I-like molecules (MHC-I chain-related chain A and B [MICA/B]), thereby inhibiting both recognition by CD8 T cells and NK cells. Although some crucial functional elements in E3/19K have been identified, a systematic analysis of the functional importance of individual amino acids is missing. We now have substituted alanine for each of 21 aas in the luminal domain of Ad2 E3/19K conserved among Ads and investigated the effects on HLA-I downregulation by coimmunoprecipitation, pulse-chase analysis, and/or flow cytometry. Potential structural alterations were monitored using conformation-dependent E3/19K-specific mAbs. The results revealed that only a small number of mutations abrogated HLA-I complex formation (e.g., substitutions W52, M87, and W96). Mutants M87 and W96 were particularly interesting as they exhibited only minimal structural changes suggesting that these amino acids make direct contacts with HLA-I. The considerable number of substitutions with little functional defects implied that E3/19K may have additional cellular target molecules. Indeed, when assessing MICA/B cell-surface expression we found that mutation of T14 and M82 selectively compromised MICA/B downregulation with essentially no effect on HLA-I modulation. In general, downregulation of HLA-I was more severely affected than that of MICA/B; for example, substitutions W52, M87, and W96 essentially abrogated HLA-I modulation while largely retaining the ability to sequester MICA/B. Thus, distinct conserved amino acids seem preferentially important for a particular functional activity of E3/19K.
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Affiliation(s)
- Martina Sester
- Department of Biological Sciences, University of Warwick, Coventry, United Kingdom
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