1
|
Arshad M, Noor N, Iqbal Z, Jaleel H. In silico analysis of missense SNPs in TNFR1a and their possible therapeutic or pathogenic role in immune diseases. Hum Immunol 2023; 84:609-617. [PMID: 37748952 DOI: 10.1016/j.humimm.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 09/27/2023]
Abstract
Tumor necrosis factor alpha (TNFa) is an inflammatory cytokine that is involved in the pathogenesis of various inflammatory disorders including rheumatoid arthritis. TNF-alpha receptor I (TNFR1a) is one of the receptors TNFa binds with for its activation. Any variation in this receptor might affect the role of TNFa in successive events. Amino acid residue substitutions might happen in TNFR1a through non-synonymous single nucleotide polymorphisms (nsSNPs) which may alter the functioning of TNFa, hence, identifying any such substitutions is of paramount significance. In this study, six nsSNPs at five different evolutionary conserved regions are predicted to be detrimental to the structure and/or function of TNFR1a by using numerous computational tools. Their 3D models are also proposed in this study. Besides, they were found to reduce the stability and affect the molecular mechanisms of this protein. Two contrasting possibilities might happen because of these substitutions. One, they might reduce the production of TNFa which is overexpressed in inflammatory diseases, hence can play therapeutic role in such diseases. Second, they might possibly hinder the apoptosis to occur which can effectuate the uncontrolled division of cells, hence can be pathogenic in diseases like cancer. Further investigations on these nsSNPs using animal models and at cellular level will open doors to understand the underlying mechanisms behind various diseases.
Collapse
Affiliation(s)
- Maria Arshad
- Department of Biochemistry and Molecular Biology, University of Iceland, Reykjavik, Iceland.
| | - Nabeel Noor
- Shalamar Medical & Dental College, Lahore, Pakistan
| | - Zunair Iqbal
- Shalamar Medical & Dental College, Lahore, Pakistan
| | - Hadiqa Jaleel
- Department of Research & Innovation, Shalamar Institute of Health Sciences, Lahore, Pakistan
| |
Collapse
|
2
|
Ruan B, He Y, Chen Y, Choi EJ, Chen Y, Motabar D, Solomon T, Simmerman R, Kauffman T, Gallagher DT, Orban J, Bryan PN. Design and characterization of a protein fold switching network. Nat Commun 2023; 14:431. [PMID: 36702827 PMCID: PMC9879998 DOI: 10.1038/s41467-023-36065-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/13/2023] [Indexed: 01/27/2023] Open
Abstract
To better understand how amino acid sequence encodes protein structure, we engineered mutational pathways that connect three common folds (3α, β-grasp, and α/β-plait). The structures of proteins at high sequence-identity intersections in the pathways (nodes) were determined using NMR spectroscopy and analyzed for stability and function. To generate nodes, the amino acid sequence encoding a smaller fold is embedded in the structure of an ~50% larger fold and a new sequence compatible with two sets of native interactions is designed. This generates protein pairs with a 3α or β-grasp fold in the smaller form but an α/β-plait fold in the larger form. Further, embedding smaller antagonistic folds creates critical states in the larger folds such that single amino acid substitutions can switch both their fold and function. The results help explain the underlying ambiguity in the protein folding code and show that new protein structures can evolve via abrupt fold switching.
Collapse
Affiliation(s)
- Biao Ruan
- Potomac Affinity Proteins, 11305 Dunleith Pl, North Potomac, MD, 20878, USA
| | - Yanan He
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
| | - Yingwei Chen
- Potomac Affinity Proteins, 11305 Dunleith Pl, North Potomac, MD, 20878, USA
| | - Eun Jung Choi
- Potomac Affinity Proteins, 11305 Dunleith Pl, North Potomac, MD, 20878, USA
| | - Yihong Chen
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
| | - Dana Motabar
- Potomac Affinity Proteins, 11305 Dunleith Pl, North Potomac, MD, 20878, USA
- Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Tsega Solomon
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Richard Simmerman
- Potomac Affinity Proteins, 11305 Dunleith Pl, North Potomac, MD, 20878, USA
| | - Thomas Kauffman
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - D Travis Gallagher
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
- National Institute of Standards and Technology and the University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
| | - John Orban
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA.
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA.
| | - Philip N Bryan
- Potomac Affinity Proteins, 11305 Dunleith Pl, North Potomac, MD, 20878, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA.
| |
Collapse
|