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Mittal A, Chauhan A. Aspects of Biological Replication and Evolution Independent of the Central Dogma: Insights from Protein-Free Vesicular Transformations and Protein-Mediated Membrane Remodeling. J Membr Biol 2022; 255:185-209. [PMID: 35333977 PMCID: PMC8951669 DOI: 10.1007/s00232-022-00230-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/06/2022] [Indexed: 11/21/2022]
Abstract
Biological membrane remodeling is central to living systems. In spite of serving as “containers” of whole-living systems and functioning as dynamic compartments within living systems, biological membranes still find a “blue collar” treatment compared to the “white collar” nucleic acids and proteins in biology. This may be attributable to the fact that scientific literature on biological membrane remodeling is only 50 years old compared to ~ 150 years of literature on proteins and a little less than 100 years on nucleic acids. However, recently, evidence for symbiotic origins of eukaryotic cells from data only on biological membranes was reported. This, coupled with appreciation of reproducible amphiphilic self-assemblies in aqueous environments (mimicking replication), has already initiated discussions on origins of life beyond nucleic acids and proteins. This work presents a comprehensive compilation and meta-analyses of data on self-assembly and vesicular transformations in biological membranes—starting from model membranes to establishment of Influenza Hemagglutinin-mediated membrane fusion as a prototypical remodeling system to a thorough comparison between enveloped mammalian viruses and cellular vesicles. We show that viral membrane fusion proteins, in addition to obeying “stoichiometry-driven protein folding”, have tighter compositional constraints on their amino acid occurrences than general-structured proteins, regardless of type/class. From the perspective of vesicular assemblies and biological membrane remodeling (with and without proteins) we find that cellular vesicles are quite different from viruses. Finally, we propose that in addition to pre-existing thermodynamic frameworks, kinetic considerations in de novo formation of metastable membrane structures with available “third-party” constituents (including proteins) were not only crucial for origins of life but also continue to offer morphological replication and/or functional mechanisms in modern life forms, independent of the central dogma.
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Affiliation(s)
- Aditya Mittal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi (IIT Delhi), Hauz Khas, New Delhi, 110016, India. .,Supercomputing Facility for Bioinformatics and Computational Biology (SCFBio), IIT Delhi, Hauz Khas, New Delhi, 110016, India.
| | - Akanksha Chauhan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi (IIT Delhi), Hauz Khas, New Delhi, 110016, India
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2
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Freitas AA. Investigating the role of Simpson's paradox in the analysis of top-ranked features in high-dimensional bioinformatics datasets. Brief Bioinform 2021; 21:421-428. [PMID: 30629111 DOI: 10.1093/bib/bby126] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/16/2018] [Accepted: 12/04/2018] [Indexed: 01/05/2023] Open
Abstract
An important problem in bioinformatics consists of identifying the most important features (or predictors), among a large number of features in a given classification dataset. This problem is often addressed by using a machine learning-based feature ranking method to identify a small set of top-ranked predictors (i.e. the most relevant features for classification). The large number of studies in this area has, however, an important limitation: they ignore the possibility that the top-ranked predictors occur in an instance of Simpson's paradox, where the positive or negative association between a predictor and a class variable reverses sign upon conditional on each of the values of a third (confounder) variable. In this work, we review and investigate the role of Simpson's paradox in the analysis of top-ranked predictors in high-dimensional bioinformatics datasets, in order to avoid the potential danger of misinterpreting an association between a predictor and the class variable. We perform computational experiments using four well-known feature ranking methods from the machine learning field and five high-dimensional datasets of ageing-related genes, where the predictors are Gene Ontology terms. The results show that occurrences of Simpson's paradox involving top-ranked predictors are much more common for one of the feature ranking methods.
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Burdukiewicz M, Sidorczuk K, Rafacz D, Pietluch F, Bąkała M, Słowik J, Gagat P. CancerGram: An Effective Classifier for Differentiating Anticancer from Antimicrobial Peptides. Pharmaceutics 2020; 12:pharmaceutics12111045. [PMID: 33142753 PMCID: PMC7692641 DOI: 10.3390/pharmaceutics12111045] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 01/10/2023] Open
Abstract
Antimicrobial peptides (AMPs) constitute a diverse group of bioactive molecules that provide multicellular organisms with protection against microorganisms, and microorganisms with weaponry for competition. Some AMPs can target cancer cells; thus, they are called anticancer peptides (ACPs). Due to their small size, positive charge, hydrophobicity and amphipathicity, AMPs and ACPs interact with negatively charged components of biological membranes. AMPs preferentially permeabilize microbial membranes, but ACPs additionally target mitochondrial and plasma membranes of cancer cells. The preference towards mitochondrial membranes is explained by their membrane potential, membrane composition resulting from α-proteobacterial origin and the fact that mitochondrial targeting signals could have evolved from AMPs. Taking into account the therapeutic potential of ACPs and millions of deaths due to cancer annually, it is of vital importance to find new cationic peptides that selectively destroy cancer cells. Therefore, to reduce the costs of experimental research, we have created a robust computational tool, CancerGram, that uses n-grams and random forests for predicting ACPs. Compared to other ACP classifiers, CancerGram is the first three-class model that effectively classifies peptides into: ACPs, AMPs and non-ACPs/non-AMPs, with AU1U amounting to 0.89 and a Kappa statistic of 0.65. CancerGram is available as a web server and R package on GitHub.
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Affiliation(s)
- Michał Burdukiewicz
- Faculty of Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, 01968 Senftenberg, Germany;
- Why R? Foundation, 03-214 Warsaw, Poland;
| | - Katarzyna Sidorczuk
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 50-383 Wrocław, Poland; (K.S.); (F.P.)
| | - Dominik Rafacz
- Why R? Foundation, 03-214 Warsaw, Poland;
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland; (M.B.); (J.S.)
| | - Filip Pietluch
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 50-383 Wrocław, Poland; (K.S.); (F.P.)
| | - Mateusz Bąkała
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland; (M.B.); (J.S.)
| | - Jadwiga Słowik
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland; (M.B.); (J.S.)
| | - Przemysław Gagat
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 50-383 Wrocław, Poland; (K.S.); (F.P.)
- Correspondence:
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Mittal A, Changani AM, Taparia S, Goel D, Parihar A, Singh I. Structural disorder originates beyond narrow stoichiometric margins of amino acids in naturally occurring folded proteins. J Biomol Struct Dyn 2020; 39:2364-2375. [PMID: 32238088 DOI: 10.1080/07391102.2020.1751299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Rigorous analyses of Euclidean distances between non-peptide bonded residues in structures of several thousand naturally occurring folded proteins yielded a surprising "margin of life" for percentage occurrence of individual amino acids in naturally occurring folded proteins. On one hand, the concept of "margin of life", referring to lower than expected variances in average stoichiometric occurrences of individual amino acids in folded proteins, remains unchallenged since its discovery a decade ago. On the other hand, within this past decade there has been a strong emergence of a gradual paradigm shift in biology, from sequence-structure-function in proteins to sequence-disorder-function, fuelled by discoveries on functional implications of intrinsically disordered proteins (primary sequences that do not form stable structures). Thus the applicability of "margin of life" to peptide-bonded residues in all known natural proteins, adopting stable structures vis-à-vis intrinsically disordered needs to be explored. Therefore in this work, we analyze compositions of the complete naturally occurring primary sequence space (over 560000 sequences) after dividing it into mutually exclusive subsets of structured and intrinsically disordered proteins along with a subset without any structural information. While finding that occurrence of different peptides (up to pentapeptides) is a direct consequence of the relative occurrences of their constituting residues in folded proteins, we report that structural disorder in natural proteins originates beyond the narrow stoichiometric margins of amino acids found in structured proteins.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aditya Mittal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi (IIT Delhi), New Delhi, India.,Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi (IIT Delhi), New Delhi, India
| | | | - Sakshi Taparia
- Department of Mathematics (Bachelors program in Mathematics & Computing), Indian Institute of Technology Delhi (IIT Delhi), New Delhi, India
| | - Deepanshu Goel
- Department of Biochemical Engineering and Biotechnology (Bachelors program), Indian Institute of Technology Delhi (IIT Delhi), New Delhi, India
| | - Animesh Parihar
- Department of Biochemical Engineering and Biotechnology (Bachelors program), Indian Institute of Technology Delhi (IIT Delhi), New Delhi, India
| | - Ishan Singh
- Department of Computer Science & Engineering (Bachelors program Computer Science), Indian Institute of Technology Delhi (IIT Delhi), New Delhi, India
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Prokaryotic and Mitochondrial Lipids: A Survey of Evolutionary Origins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019. [PMID: 31502197 DOI: 10.1007/978-3-030-21162-2_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Mitochondria and bacteria share a myriad of properties since it is believed that the powerhouses of the eukaryotic cell have evolved from a prokaryotic origin. Ribosomal RNA sequences, DNA architecture and metabolism are strikingly similar in these two entities. Proteins and nucleic acids have been a hallmark for comparison between mitochondria and prokaryotes. In this chapter, similarities (and differences) between mitochondrial and prokaryotic membranes are addressed with a focus on structure-function relationship of different lipid classes. In order to be suitable for the theme of the book, a special emphasis is reserved to the effects of bioactive sphingolipids, mainly ceramide, on mitochondrial membranes and their roles in initiating programmed cell death.
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Singh S, Ponnappan N, Verma A, Mittal A. Osmotic tolerance of avian erythrocytes to complete hemolysis in solute free water. Sci Rep 2019; 9:7976. [PMID: 31138851 PMCID: PMC6538707 DOI: 10.1038/s41598-019-44487-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 05/17/2019] [Indexed: 01/17/2023] Open
Abstract
Osmotic behavior of erythrocytes is not only important clinically, but is also significant in understanding of material transport across biological membranes. It is most commonly studied through fragiligrams – plots of the degree of hemolysis as a function of extracellular osmolarity. A fundamental assumption in experimental and theoretical studies on osmolarity driven transport of water across the plasma membranes of all cells is the sigmoidal nature of their osmotic behavior. Sigmoidal data is mathematically monotonic showing either a decreasing only or an increasing only trend, but not both, within certain thresholds; beyond these thresholds the data is asymptotic or flat. Fragiligrams of erythrocytes are usually sigmoidal, with maximal hemolysis in plain solute-free water and often up to a certain extracellular hypotonic environment. In this work, we report a new discovery of non-monotonic osmotic behavior of avian erythrocytes. In contrast to the expected monotonic fragiligrams obtained for mammalian erythrocytes, fragiligrams of avian erythrocytes show non-monotonic curves. Maximal hemolysis of avian erythrocytes was not observed at the most hypotonic conditions – instead, maximal hemolysis was observed at mild hypotonic conditions. Hemolysis of avian erythrocytes first increases then decreases with increasing extracellular osmolarity. We also report that the non-monotonic fragiligrams of chicken erythrocytes are converted to the expected monotonic sigmoids subsequent to controlled extracellular trypsinization. While possibly having profound evolutionary implications for vertebrates, the findings reported in this work have a direct impact on understanding of avian physiology. Our results also compel revisiting of experimental and theoretical models for understanding material transport across biological membranes under different osmotic conditions.
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Affiliation(s)
- Snigdha Singh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi (IIT Delhi), Hauz Khas, New Delhi, 110016, India
| | - Nisha Ponnappan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi (IIT Delhi), Hauz Khas, New Delhi, 110016, India
| | - Anand Verma
- National Institute of Pathology - Indian Council of Medical Research (ICMR), New Delhi, 110029, India.,Green trace consulting Pvt Ltd, Delhi, 110096, India
| | - Aditya Mittal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi (IIT Delhi), Hauz Khas, New Delhi, 110016, India.
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Occurrence of tocopheryl fatty acid esters in vegetables and their non-digestibility by artificial digestion juices. Sci Rep 2018; 8:7657. [PMID: 29769635 PMCID: PMC5955885 DOI: 10.1038/s41598-018-25997-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/02/2018] [Indexed: 01/22/2023] Open
Abstract
Tocopheryl fatty acid esters (TFAE) consist of tocopherols esterified to fatty acids, but only little is known about this substance class. In this study, twelve vegetable groups were screened on TFAE and contents of (free) tocopherols and TFAE were determined in red bell pepper, red chili pepper, cucumber and walnut (n = 5, respectively). Intact TFAE were separated by solid phase extraction from free tocopherols and analyzed by GC/MS. Highest TFAE values were determined in chili pepper (4.0–16 mg/100 g fresh weight, FW) and walnut (4.1–12 mg/100 g FW), followed by bell pepper (1.3–1.5 mg/100 g FW) and cucumber (0.06–0.2 mg/100 g FW). Contribution of TFAE to the total tocopherol content ranged from 7–84%. Neither the treatment with artificial digestion juices nor exposure to sunlight showed degradation of TFAE. This substance class might represent a hitherto overlooked storage form for free tocopherols in plants as they occur to be more stable. But as the ester bond in medium chain TFAE seems not to be fissile in the human body, they might not contribute in the same way as free tocopherols to the vitamin E activity of vegetables and might have to be determined separately.
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Abstract
Biological membranes, comprised of proteins anchored by their trans-membrane domains (TMDs) creating a semi-permeable phase with lipid constituents, serve as 'checkposts' for not only intracellular trafficking in eukaryotic cells but also for material transactions of all living cells with external environments. Hydropathy (or hydrophobicity) plots of 'bitopic' proteins (i.e. having single alpha-helical TMDs) are routinely utilized in biochemistry texts for predicting their TMDs. The number of amino acids (i.e. TMD length) embedded as alpha-helices may serve as indicators of thickness of biological membranes in which they reside under assumptions that are universally applied for fixing window sizes for identifying TMDs using hydropathy plots. In this work we explore variations in thickness of different eukaryotic biological membranes (reflected by TMD lengths of their resident proteins) over evolutionary time scales. Rigorous in silico analyses of over 23,000 non-redundant membrane proteins residing in different subcellular locations from over 200 genomes of fungi, plants, non-mammalian vertebrates and mammals, reveal that differences in plasma membrane and organellar TMD lengths have decreased over time (scales) of eukaryotic cellular evolution. While earlier work has indicated decreasing differences in TMD lengths with increasing 'perceived' organismal complexity, this work is the first report on TMD length variations as a function of evolutionary time of eukaryotic cellular systems. We report that differences in TMD lengths of bitopic proteins residing in plasma membranes and other intra-cellular locations have decreased with evolutionary time, suggesting better/more avenues of intracellular trafficking in the emergence of eukaryotic organisms.
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Affiliation(s)
- Aditya Mittal
- a Kusuma School of Biological Sciences, Indian Institute of Technology Delhi , Hauz Khas, New Delhi 110016 , India
| | - Snigdha Singh
- a Kusuma School of Biological Sciences, Indian Institute of Technology Delhi , Hauz Khas, New Delhi 110016 , India
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Singh S, Mittal A. Transmembrane Domain Lengths Serve as Signatures of Organismal Complexity and Viral Transport Mechanisms. Sci Rep 2016; 6:22352. [PMID: 26925972 PMCID: PMC4772119 DOI: 10.1038/srep22352] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/12/2016] [Indexed: 12/24/2022] Open
Abstract
It is known that membrane proteins are important in various secretory pathways, with
a possible role of their transmembrane domains (TMDs) as sorting determinant
factors. One key aspect of TMDs associated with various
“checkposts” (i.e. organelles) of intracellular trafficking
is their length. To explore possible linkages in organisms with varying
“complexity” and differences in TMD lengths of membrane
proteins associated with different organelles (such as Endoplasmic Reticulum, Golgi,
Endosomes, Nucleus, Plasma Membrane), we analyzed ~70000 membrane
protein sequences in over 300 genomes of fungi, plants, non-mammalian vertebrates
and mammals. We report that as we move from simpler to complex organisms, variation
in organellar TMD lengths decreases, especially compared to their respective plasma
membranes, with increasing organismal complexity. This suggests an evolutionary
pressure in modulating length of TMDs of membrane proteins with increasing
complexity of communication between sub-cellular compartments. We also report
functional applications of our findings by discovering remarkable distinctions in
TMD lengths of membrane proteins associated with different intracellular transport
pathways. Finally, we show that TMD lengths extracted from viral proteins can serve
as somewhat weak indicators of viral replication sites in plant cells but very
strong indicators of different entry pathways employed by animal viruses.
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Affiliation(s)
- Snigdha Singh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Aditya Mittal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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Jiamsakul A, Kerr SJ, Chandrasekaran E, Huelgas A, Taecharoenkul S, Teeraananchai S, Wan G, Ly PS, Kiertiburanakul S, Law M. The occurrence of Simpson's paradox if site-level effect was ignored in the TREAT Asia HIV Observational Database. J Clin Epidemiol 2016; 76:183-92. [PMID: 26854260 DOI: 10.1016/j.jclinepi.2016.01.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 01/20/2016] [Accepted: 01/29/2016] [Indexed: 12/22/2022]
Abstract
OBJECTIVES In multisite human immunodeficiency virus (HIV) observational cohorts, clustering of observations often occurs within sites. Ignoring clustering may lead to "Simpson's paradox" (SP) where the trend observed in the aggregated data is reversed when the groups are separated. This study aimed to investigate the SP in an Asian HIV cohort and the effects of site-level adjustment through various Cox regression models. STUDY DESIGN AND SETTING Survival time from combination antiretroviral therapy (cART) initiation was analyzed using four Cox models: (1) no site adjustment; (2) site as a fixed effect; (3) stratification through site; and (4) shared frailty on site. RESULTS A total of 6,454 patients were included from 23 sites in Asia. SP was evident in the year of cART initiation variable. Model (1) shows the hazard ratio (HR) for years 2010-2014 was higher than the HR for 2006-2009, compared to 2003-2005 (HR = 0.68 vs. 0.61). Models (2)-(4) consistently implied greater improvement in survival for those who initiated in 2010-2014 than 2006-2009 contrasting findings from model (1). The effects of other significant covariates on survival were similar across four models. CONCLUSIONS Ignoring site can lead to SP causing reversal of treatment effects. Greater emphasis should be made to include site in survival models when possible.
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Affiliation(s)
| | - Stephen J Kerr
- HIV-NAT, The Thai Red Cross AIDS Research Centre, Bangkok, Thailand; Department of Global Health, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | | | | | | | | | - Gang Wan
- Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Penh Sun Ly
- National Center for HIV/AIDS, Dermatology & STDs, Phnom Penh, Cambodia
| | | | - Matthew Law
- The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
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