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Primetis E, Chavlis S, Pavlidis P. Evolutionary models of amino acid substitutions based on the tertiary structure of their neighborhoods. Proteins 2021; 89:1565-1576. [PMID: 34278605 DOI: 10.1002/prot.26178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 05/27/2021] [Accepted: 07/11/2021] [Indexed: 11/10/2022]
Abstract
Intra-protein residual vicinities depend on the involved amino acids. Energetically favorable vicinities (or interactions) have been preserved during evolution, while unfavorable vicinities have been eliminated. We describe, statistically, the interactions between amino acids using resolved protein structures. Based on the frequency of amino acid interactions, we have devised an amino acid substitution model that implements the following idea: amino acids that have similar neighbors in the protein tertiary structure can replace each other, while substitution is more difficult between amino acids that prefer different spatial neighbors. Using known tertiary structures for α-helical membrane (HM) proteins, we build evolutionary substitution matrices. We constructed maximum likelihood phylogenies using our amino acid substitution matrices and compared them to widely-used methods. Our results suggest that amino acid substitutions are associated with the spatial neighborhoods of amino acid residuals, providing, therefore, insights into the amino acid substitution process.
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Affiliation(s)
- Elias Primetis
- Department of Biology, University of Crete, Heraklion, Greece.,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Hellas, Heraklion, Greece
| | - Spyridon Chavlis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Hellas, Heraklion, Greece
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology, Hellas, Heraklion, Greece
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Vilariño-Güell C, Zimprich A, Martinelli-Boneschi F, Herculano B, Wang Z, Matesanz F, Urcelay E, Vandenbroeck K, Leyva L, Gris D, Massaad C, Quandt JA, Traboulsee AL, Encarnacion M, Bernales CQ, Follett J, Yee IM, Criscuoli MG, Deutschländer A, Reinthaler EM, Zrzavy T, Mascia E, Zauli A, Esposito F, Alcina A, Izquierdo G, Espino-Paisán L, Mena J, Antigüedad A, Urbaneja-Romero P, Ortega-Pinazo J, Song W, Sadovnick AD. Exome sequencing in multiple sclerosis families identifies 12 candidate genes and nominates biological pathways for the genesis of disease. PLoS Genet 2019; 15:e1008180. [PMID: 31170158 PMCID: PMC6553700 DOI: 10.1371/journal.pgen.1008180] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 05/07/2019] [Indexed: 12/12/2022] Open
Abstract
Multiple sclerosis (MS) is an inflammatory disease of the central nervous system characterized by myelin loss and neuronal dysfunction. Although the majority of patients do not present familial aggregation, Mendelian forms have been described. We performed whole-exome sequencing analysis in 132 patients from 34 multi-incident families, which nominated likely pathogenic variants for MS in 12 genes of the innate immune system that regulate the transcription and activation of inflammatory mediators. Rare missense or nonsense variants were identified in genes of the fibrinolysis and complement pathways (PLAU, MASP1, C2), inflammasome assembly (NLRP12), Wnt signaling (UBR2, CTNNA3, NFATC2, RNF213), nuclear receptor complexes (NCOA3), and cation channels and exchangers (KCNG4, SLC24A6, SLC8B1). These genes suggest a disruption of interconnected immunological and pro-inflammatory pathways as the initial event in the pathophysiology of familial MS, and provide the molecular and biological rationale for the chronic inflammation, demyelination and neurodegeneration observed in MS patients.
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Affiliation(s)
| | | | - Filippo Martinelli-Boneschi
- Laboratory of Human Genetics of Neurological Disorders, CNS Inflammatory Unit, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- MS Unit and Department of Neurology, IRCCS Policlinico San Donato, Milan, Italy
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Bruno Herculano
- Townsend Family Laboratories, Department of Psychiatry, University of British Columbia, Vancouver, Canada
| | - Zhe Wang
- Townsend Family Laboratories, Department of Psychiatry, University of British Columbia, Vancouver, Canada
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of the Capital Medical University, Beijing, China
| | - Fuencisla Matesanz
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina López Neyra (IPBLN), CSIC, Granada, Spain
| | - Elena Urcelay
- Immunology Dept, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
- Red Española de Esclerosis Múltiple REEM, Madrid, Spain
| | - Koen Vandenbroeck
- Achucarro Basque Center for Neuroscience, Universidad del País Vasco (UPV/EHU), Leioa, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Laura Leyva
- Red Española de Esclerosis Múltiple REEM, Madrid, Spain
- Instituto de Investigación Biomédica de Málaga-IBIMA, Unidad de Gestion Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Denis Gris
- Division of Immunology, Department of Pediatrics, CR-CHUS, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Canada
| | - Charbel Massaad
- Toxicology, Pharmacology and Cell Signalisation—UMR-S 1124 Université Paris Descartes, Paris, France
| | - Jacqueline A. Quandt
- Department of Pathology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Anthony L. Traboulsee
- Division of Neurology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Mary Encarnacion
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Cecily Q. Bernales
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Jordan Follett
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Irene M. Yee
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Maria G. Criscuoli
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Angela Deutschländer
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, United States of America
- Department of Clinical Genomics, Mayo Clinic Florida, Jacksonville, FL, United States of America
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, United States of America
| | - Eva M. Reinthaler
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Tobias Zrzavy
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Elisabetta Mascia
- Laboratory of Human Genetics of Neurological Disorders, CNS Inflammatory Unit, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Zauli
- Laboratory of Human Genetics of Neurological Disorders, CNS Inflammatory Unit, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federica Esposito
- Laboratory of Human Genetics of Neurological Disorders, CNS Inflammatory Unit, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Antonio Alcina
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina López Neyra (IPBLN), CSIC, Granada, Spain
| | | | - Laura Espino-Paisán
- Immunology Dept, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
- Red Española de Esclerosis Múltiple REEM, Madrid, Spain
| | - Jorge Mena
- Achucarro Basque Center for Neuroscience, Universidad del País Vasco (UPV/EHU), Leioa, Spain
| | - Alfredo Antigüedad
- Neurology Department, Hospital Universitario de Cruces, S/N, Baracaldo, Spain
| | - Patricia Urbaneja-Romero
- Red Española de Esclerosis Múltiple REEM, Madrid, Spain
- Instituto de Investigación Biomédica de Málaga-IBIMA, Unidad de Gestion Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Jesús Ortega-Pinazo
- Instituto de Investigación Biomédica de Málaga-IBIMA, Unidad de Gestion Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Weihong Song
- Townsend Family Laboratories, Department of Psychiatry, University of British Columbia, Vancouver, Canada
| | - A. Dessa Sadovnick
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- Division of Neurology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
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Saidijam M, Azizpour S, Patching SG. Amino acid composition analysis of human secondary transport proteins and implications for reliable membrane topology prediction. J Biomol Struct Dyn 2016; 35:929-949. [PMID: 27159787 DOI: 10.1080/07391102.2016.1167622] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Secondary transporters in humans are a large group of proteins that transport a wide range of ions, metals, organic and inorganic solutes involved in energy transduction, control of membrane potential and osmotic balance, metabolic processes and in the absorption or efflux of drugs and xenobiotics. They are also emerging as important targets for development of new drugs and as target sites for drug delivery to specific organs or tissues. We have performed amino acid composition (AAC) and phylogenetic analyses and membrane topology predictions for 336 human secondary transport proteins and used the results to confirm protein classification and to look for trends and correlations with structural domains and specific substrates and/or function. Some proteins showed statistically high contents of individual amino acids or of groups of amino acids with similar physicochemical properties. One recurring trend was a correlation between high contents of charged and/or polar residues with misleading results in predictions of membrane topology, which was especially prevalent in Mitochondrial Carrier family proteins. We demonstrate how charged or polar residues located in the middle of transmembrane helices can interfere with their identification by membrane topology tools resulting in missed helices in the prediction. Comparison of AAC in the human proteins with that in 235 secondary transport proteins from Escherichia coli revealed similar overall trends along with differences in average contents for some individual amino acids and groups of similar amino acids that are presumed to result from a greater number of functions and complexity in the higher organism.
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Affiliation(s)
- Massoud Saidijam
- a Department of Molecular Medicine and Genetics, Research Centre for Molecular Medicine, School of Medicine , Hamadan University of Medical Sciences , Hamadan , Iran
| | - Sonia Azizpour
- a Department of Molecular Medicine and Genetics, Research Centre for Molecular Medicine, School of Medicine , Hamadan University of Medical Sciences , Hamadan , Iran
| | - Simon G Patching
- b School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , UK
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Meshorer E, Toiber D, Zurel D, Sahly I, Dori A, Cagnano E, Schreiber L, Grisaru D, Tronche F, Soreq H. Combinatorial Complexity of 5′ Alternative Acetylcholinesterase Transcripts and Protein Products. J Biol Chem 2004; 279:29740-51. [PMID: 15123727 DOI: 10.1074/jbc.m402752200] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
To explore the scope and significance of alternate promoter usage and its putative inter-relationship to alternative splicing, we searched expression sequence tags for the 5' region of acetylcholinesterase (ACHE) genes. Three and five novel first exons were identified in human and mouse ACHE genes, respectively. Reverse transcription-PCR and in situ hybridization validated most of the predicted transcripts, and sequence analyses of the corresponding genomic DNA regions suggest evolutionarily conserved promoters for each of the novel exons identified. Distinct tissue specificity and stress-related expression patterns of these exons predict combinatorial complexity with known 3' alternative AChE mRNA transcripts. Unexpectedly one of the 5' exons encodes an extended N terminus in-frame with the known AChE sequence, extending the increased complexity to the protein level. The resultant membrane variant(s), designated N-AChE, is developmentally regulated in human brain neurons and blood mononuclear cells. Alternative promoter usage combined with alternative splicing may thus lead to stress-dependent combinatorial complexity of AChE mRNA transcripts and their protein products.
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Affiliation(s)
- Eran Meshorer
- Department of Biological Chemistry and the Israel Center of Neuronal Computation, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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