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Garzon M, Mainali S. Deep structure of DNA for genomic analysis. Hum Mol Genet 2021; 31:576-586. [PMID: 34508577 DOI: 10.1093/hmg/ddab272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 01/09/2023] Open
Abstract
Recent advances in next generation sequencing, deep networks and other bioinformatic tools have enabled us to mine huge amount of genomic information about living organisms in the post-microarray era. However, these tools do not explicitly factor in the role of the underlying DNA biochemistry (particularly, DNA hybridization) essential to life processes. Here, we focus more precisely on the role that DNA hybridization plays in determining properties of biological organisms at the macro-level. We illustrate its role with solutions to challenging problems in human disease. These solutions are made possible by novel structural properties of DNA hybridization landscapes revealed by a metric model of oligonucleotides of a common length that makes them reminiscent of some planets in our solar system, particularly earth and saturn. They allow a judicious selection of so-called noncrosshybridizing (nxh) bases that offer substantial reduction of DNA sequences of arbitrary length into a few informative features. The quality assessment of the information extracted by them is high because of their very low Shannon Entropy, i.e. they minimize the degree of uncertainty in hybridization that makes results on standard microarrays irreproducible. For example, SNP classification (pathogenic/nonpathogenic) and pathogen identification can be solved with high sensitivity (~77%/100%) and specificity (~92%/100%, respectively) for combined taxa on a sample of over 264 fully coding sequences in whole bacterial genomes and fungal mitochondrial genomes using machine learning (ML) models. These methods can be applied to several other interesting research questions that could be addressed with similar genomic analyses.
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Affiliation(s)
- Max Garzon
- The University of Memphis, Computer Science, Memphis, TN 38152, USA
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Carbonara K, Andonovski M, Coorssen JR. Proteomes Are of Proteoforms: Embracing the Complexity. Proteomes 2021; 9:38. [PMID: 34564541 PMCID: PMC8482110 DOI: 10.3390/proteomes9030038] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/24/2021] [Accepted: 08/29/2021] [Indexed: 12/17/2022] Open
Abstract
Proteomes are complex-much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess the myriad of proteoforms that arise at any point before, after, and between translation and transcription (e.g., isoforms, splice variants, and post-translational modifications [PTM]), as well as newly defined species. There are numerous analytical methods currently used to address proteome depth and here we critically evaluate these in terms of the current 'state-of-the-field'. We thus discuss both pros and cons of available approaches and where improvements or refinements are needed to quantitatively characterize proteomes. To enable a next-generation approach, we suggest that advances lie in transdisciplinarity via integration of current proteomic methods to yield a unified discipline that capitalizes on the strongest qualities of each. Such a necessary (if not revolutionary) shift cannot be accomplished by a continued primary focus on proteo-genomics/-transcriptomics. We must embrace the complexity. Yes, these are the hard questions, and this will not be easy…but where is the fun in easy?
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Affiliation(s)
| | | | - Jens R. Coorssen
- Faculties of Applied Health Sciences and Mathematics & Science, Departments of Health Sciences and Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada; (K.C.); (M.A.)
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Abstract
Protein function can be allosterically regulated by changes in structure or dynamics. PDZ domains are classic examples for studies of allostery in single protein domains. However, PDZ domains are often found in multidomain proteins; in particular, PDZ3 is located in a supramodule containing three domains. The allosteric network in PDZ3 has never been studied in the presence of the adjacent domains. Here we map the allosteric network for a PDZ3:ligand complex, both in isolation and in the context of a supramodule. We demonstrate that the allosteric network is highly dependent on this supertertiary structure, with broad implications for studies of allostery in single domains. The notion that protein function is allosterically regulated by structural or dynamic changes in proteins has been extensively investigated in several protein domains in isolation. In particular, PDZ domains have represented a paradigm for these studies, despite providing conflicting results. Furthermore, it is still unknown how the association between protein domains in supramodules, consitituting so-called supertertiary structures, affects allosteric networks. Here, we experimentally mapped the allosteric network in a PDZ:ligand complex, both in isolation and in the context of a supramodular structure, and show that allosteric networks in a PDZ domain are highly dependent on the supertertiary structure in which they are present. This striking sensitivity of allosteric networks to the presence of adjacent protein domains is likely a common property of supertertiary structures in proteins. Our findings have general implications for prediction of allosteric networks from primary and tertiary structures and for quantitative descriptions of allostery.
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Pollet H, Cloos AS, Stommen A, Vanderroost J, Conrard L, Paquot A, Ghodsi M, Carquin M, Léonard C, Guthmann M, Lingurski M, Vermylen C, Killian T, Gatto L, Rider M, Pyr dit Ruys S, Vertommen D, Vikkula M, Brouillard P, Van Der Smissen P, Muccioli GG, Tyteca D. Aberrant Membrane Composition and Biophysical Properties Impair Erythrocyte Morphology and Functionality in Elliptocytosis. Biomolecules 2020; 10:biom10081120. [PMID: 32751168 PMCID: PMC7465299 DOI: 10.3390/biom10081120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 12/17/2022] Open
Abstract
Red blood cell (RBC) deformability is altered in inherited RBC disorders but the mechanism behind this is poorly understood. Here, we explored the molecular, biophysical, morphological, and functional consequences of α-spectrin mutations in a patient with hereditary elliptocytosis (pEl) almost exclusively expressing the Pro260 variant of SPTA1 and her mother (pElm), heterozygous for this mutation. At the molecular level, the pEI RBC proteome was globally preserved but spectrin density at cell edges was increased. Decreased phosphatidylserine vs. increased lysophosphatidylserine species, and enhanced lipid peroxidation, methemoglobin, and plasma acid sphingomyelinase (aSMase) activity were observed. At the biophysical level, although membrane transversal asymmetry was preserved, curvature at RBC edges and rigidity were increased. Lipid domains were altered for membrane:cytoskeleton anchorage, cholesterol content and response to Ca2+ exchange stimulation. At the morphological and functional levels, pEl RBCs exhibited reduced size and circularity, increased fragility and impaired membrane Ca2+ exchanges. The contribution of increased membrane curvature to the pEl phenotype was shown by mechanistic experiments in healthy RBCs upon lysophosphatidylserine membrane insertion. The role of lipid domain defects was proved by cholesterol depletion and aSMase inhibition in pEl. The data indicate that aberrant membrane content and biophysical properties alter pEl RBC morphology and functionality.
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Affiliation(s)
- Hélène Pollet
- CELL Unit & PICT Imaging Platform, de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (H.P.); (A.-S.C.); (A.S.); (J.V.); (L.C.); (M.G.); (M.C.); (C.L.); (M.G.); (M.L.); (P.V.D.S.)
| | - Anne-Sophie Cloos
- CELL Unit & PICT Imaging Platform, de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (H.P.); (A.-S.C.); (A.S.); (J.V.); (L.C.); (M.G.); (M.C.); (C.L.); (M.G.); (M.L.); (P.V.D.S.)
| | - Amaury Stommen
- CELL Unit & PICT Imaging Platform, de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (H.P.); (A.-S.C.); (A.S.); (J.V.); (L.C.); (M.G.); (M.C.); (C.L.); (M.G.); (M.L.); (P.V.D.S.)
| | - Juliette Vanderroost
- CELL Unit & PICT Imaging Platform, de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (H.P.); (A.-S.C.); (A.S.); (J.V.); (L.C.); (M.G.); (M.C.); (C.L.); (M.G.); (M.L.); (P.V.D.S.)
| | - Louise Conrard
- CELL Unit & PICT Imaging Platform, de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (H.P.); (A.-S.C.); (A.S.); (J.V.); (L.C.); (M.G.); (M.C.); (C.L.); (M.G.); (M.L.); (P.V.D.S.)
| | - Adrien Paquot
- Bioanalysis and Pharmacology of Bioactive Lipids Research Group, Louvain Drug Research Institute, UCLouvain, 1200 Brussels, Belgium; (A.P.); (G.G.M.)
| | - Marine Ghodsi
- CELL Unit & PICT Imaging Platform, de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (H.P.); (A.-S.C.); (A.S.); (J.V.); (L.C.); (M.G.); (M.C.); (C.L.); (M.G.); (M.L.); (P.V.D.S.)
| | - Mélanie Carquin
- CELL Unit & PICT Imaging Platform, de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (H.P.); (A.-S.C.); (A.S.); (J.V.); (L.C.); (M.G.); (M.C.); (C.L.); (M.G.); (M.L.); (P.V.D.S.)
| | - Catherine Léonard
- CELL Unit & PICT Imaging Platform, de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (H.P.); (A.-S.C.); (A.S.); (J.V.); (L.C.); (M.G.); (M.C.); (C.L.); (M.G.); (M.L.); (P.V.D.S.)
| | - Manuel Guthmann
- CELL Unit & PICT Imaging Platform, de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (H.P.); (A.-S.C.); (A.S.); (J.V.); (L.C.); (M.G.); (M.C.); (C.L.); (M.G.); (M.L.); (P.V.D.S.)
| | - Maxime Lingurski
- CELL Unit & PICT Imaging Platform, de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (H.P.); (A.-S.C.); (A.S.); (J.V.); (L.C.); (M.G.); (M.C.); (C.L.); (M.G.); (M.L.); (P.V.D.S.)
| | - Christiane Vermylen
- PEDI Unit, Institut de Recherche Expérimentale et Clinique & Saint-Luc Hospital, UCLouvain, 1200 Brussels, Belgium;
| | - Theodore Killian
- Computational Biology and Bioinformatics Unit, de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (T.K.); (L.G.)
| | - Laurent Gatto
- Computational Biology and Bioinformatics Unit, de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (T.K.); (L.G.)
| | - Mark Rider
- PHOS Unit & MASSPROT Proteomics Platform, de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (M.R.); (S.P.d.R.); (D.V.)
| | - Sébastien Pyr dit Ruys
- PHOS Unit & MASSPROT Proteomics Platform, de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (M.R.); (S.P.d.R.); (D.V.)
| | - Didier Vertommen
- PHOS Unit & MASSPROT Proteomics Platform, de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (M.R.); (S.P.d.R.); (D.V.)
| | - Miikka Vikkula
- Human Molecular Genetics, de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (M.V.); (P.B.)
- Walloon Excellence in Life Sciences and Biotechnology (WELBIO), de Duve Institute, UCLouvain, 1200 Brussels, Belgium
| | - Pascal Brouillard
- Human Molecular Genetics, de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (M.V.); (P.B.)
| | - Patrick Van Der Smissen
- CELL Unit & PICT Imaging Platform, de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (H.P.); (A.-S.C.); (A.S.); (J.V.); (L.C.); (M.G.); (M.C.); (C.L.); (M.G.); (M.L.); (P.V.D.S.)
| | - Giulio G. Muccioli
- Bioanalysis and Pharmacology of Bioactive Lipids Research Group, Louvain Drug Research Institute, UCLouvain, 1200 Brussels, Belgium; (A.P.); (G.G.M.)
| | - Donatienne Tyteca
- CELL Unit & PICT Imaging Platform, de Duve Institute, UCLouvain, 1200 Brussels, Belgium; (H.P.); (A.-S.C.); (A.S.); (J.V.); (L.C.); (M.G.); (M.C.); (C.L.); (M.G.); (M.L.); (P.V.D.S.)
- Correspondence:
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Fleming JR, Rigden DJ, Mayans O. The importance of chain context in assessing small nucleotide variants in titin: in silico case study of the I10-I11 tandem and its arrhythmic right ventricular cardiomyopathy linked position T2580. J Biomol Struct Dyn 2020; 39:3480-3490. [PMID: 32396765 DOI: 10.1080/07391102.2020.1768148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Non-synonymous small nucleotide variations (nsSNVs) in the giant muscle protein, titin, have key roles in the development of several myopathologies. Although there is considerable motive to screen at-risk individuals for nsSNVs, to identify patients in early disease stages while therapeutic intervention is still possible, the clinical significance of most titin variations remains unclear. Therefore, there is a growing need to establish methods to classify nsSNVs in a simple, economic and rapid manner. Due to its strong correlation to arrhythmogenic right ventricular cardiomyopathy (ARVC), one particular mutation in titin-T2580I, located in the I10 immunoglobulin domain-has received considerable attention. Here, we use the I10-I11 tandem as a case study to explore the possible benefits of considering the titin chain context-i.e. domain interfaces-in the assessment of titin nsSNVs. Specifically, we investigate which exchanges mimic the conformational molecular phenotype of the T2580I mutation at the I10-I11 domain interface. Then, we computed a residue stability landscape for domains alone and in tandem to define a Domain Interface Score (DIS) which identifies several hotspot residues. Our findings suggest that the T2580 position is highly sensitive to exchange and that any variant found in this position should be considered with care. Furthermore, we conclude that the consideration of the higher order structure of the titin chain is important to gain accurate insights into the vulnerability of positions in linker regions and that titin nsSNV prediction benefits from a contextual analysis. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- J R Fleming
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - D J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - O Mayans
- Department of Biology, University of Konstanz, Konstanz, Germany
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Srivastava A, Singh J, Singh Yadav SP, Arya P, Kalim F, Rose P, Ashish, Kundu B. The Gelsolin Pathogenic D187N Mutant Exhibits Altered Conformational Stability and Forms Amyloidogenic Oligomers. Biochemistry 2018; 57:2359-2372. [DOI: 10.1021/acs.biochem.8b00039] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Ankit Srivastava
- Kusuma School of Biological Sciences, IIT Delhi, New Delhi 110016, India
| | - Jasdeep Singh
- Kusuma School of Biological Sciences, IIT Delhi, New Delhi 110016, India
| | | | - Prabha Arya
- Kusuma School of Biological Sciences, IIT Delhi, New Delhi 110016, India
| | - Fouzia Kalim
- Kusuma School of Biological Sciences, IIT Delhi, New Delhi 110016, India
| | - Pooja Rose
- Kusuma School of Biological Sciences, IIT Delhi, New Delhi 110016, India
| | - Ashish
- CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Bishwajit Kundu
- Kusuma School of Biological Sciences, IIT Delhi, New Delhi 110016, India
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Braselmann E, Chaney JL, Clark PL. Folding the proteome. Trends Biochem Sci 2013; 38:337-44. [PMID: 23764454 DOI: 10.1016/j.tibs.2013.05.001] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 05/01/2013] [Accepted: 05/02/2013] [Indexed: 02/07/2023]
Abstract
Protein folding is an essential prerequisite for protein function and hence cell function. Kinetic and thermodynamic studies of small proteins that refold reversibly were essential for developing our current understanding of the fundamentals of protein folding mechanisms. However, we still lack sufficient understanding to accurately predict protein structures from sequences, or the effects of disease-causing mutations. To date, model proteins selected for folding studies represent only a small fraction of the complexity of the proteome and are unlikely to exhibit the breadth of folding mechanisms used in vivo. We are in urgent need of new methods - both theoretical and experimental - that can quantify the folding behavior of a truly broad set of proteins under in vivo conditions. Such a shift in focus will provide a more comprehensive framework from which to understand the connections between protein folding, the molecular basis of disease, and cell function and evolution.
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Affiliation(s)
- Esther Braselmann
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
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