1
|
Bashir A, Li S, Ye Y, Zheng Q, Rajani K, Bashir F, Shah NN, Yang D, Xue M, Wang H, Zheng C. The SARS-CoV-2 spike protein contains a furin cleavage site located in a short loop between antiparallel β-strands. Int J Biol Macromol 2024:136020. [PMID: 39368587 DOI: 10.1016/j.ijbiomac.2024.136020] [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: 03/30/2024] [Revised: 08/22/2024] [Accepted: 09/23/2024] [Indexed: 10/07/2024]
Abstract
The furin cleavage site (FCS) of the SARS-CoV-2 spike protein, which connects the S1/S2 junction, is essential for facilitating fusion with host cells. The wild-type (Wt) SARS-CoV-2 spike protein, PDB ID: 6yvb, lacks a sequence of amino acid residues, including the FCS that links the S1/S2 junction. For the first time, we demonstrated that a stretch of 14 amino acid residues (677QTNSPRRARSVASQ689) forms an antiparallel β-sheet and contains the PRRAR sequence in the FCS within a short loop. Upon comparing the loop content of the S1/S2 junction with that of Wt SARS-CoV-2 containing PRRAR in the FCS, we observed a decrease in antiparallel β-sheet content and an increase in loop content in the B.1.1.7 variant with HRRAR in the FCS. This short loop within an antiparallel β-sheet can serve as a docking site for various proteases, including TMPRSS2 and α1AT. We conducted a 300-ns simulation of the SARS-CoV-2 receptor binding domain (RBD) using several antibacterial and antiviral ligands commonly used to treat various infections. Our findings indicate that the receptor binding domain (RBD) comprising the receptor binding motif (RBM) utilizes β6 and a significant portion of the loop to bind with ligands, suggesting its potential for treating SARS-CoV-2 infections.
Collapse
Affiliation(s)
- Arif Bashir
- Department of Clinical Biochemistry & Biotechnology, Government College for Women, Nawa-Kadal, Srinagar 190002, India
| | - Shun Li
- Department of Immunology, School of Basic Medical Sciences, Chengdu Medical College, Chengdu, Sichuan, China
| | - Yu Ye
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Qingcong Zheng
- Department of Spinal Surgery, the First Affiliated Hospital of Fujian Medical University, Fuzhou 350004, China
| | - K Rajani
- Department of Biotechnology, Indian Institute of Technology, Chennai 600036, India
| | - Fahim Bashir
- Department of Environmental Science, University of Kashmir, 190006, India
| | - Naveed Nazir Shah
- Department of Chest Medicine, Government Medical College, Srinagar, Jammu and Kashmir 190001, India
| | - Debin Yang
- Department of Pediatrics, Children's Affiliated Hospital of Zhengzhou University, Zhengzhou 450018, China
| | - Mengzhou Xue
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450014, China.
| | - Huiqing Wang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, China.
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.
| |
Collapse
|
2
|
Mróz J, Pelc M, Mitusińska K, Chorostowska-Wynimko J, Jezela-Stanek A. Computational Tools to Assist in Analyzing Effects of the SERPINA1 Gene Variation on Alpha-1 Antitrypsin (AAT). Genes (Basel) 2024; 15:340. [PMID: 38540399 PMCID: PMC10970068 DOI: 10.3390/genes15030340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 06/14/2024] Open
Abstract
In the rapidly advancing field of bioinformatics, the development and application of computational tools to predict the effects of single nucleotide variants (SNVs) are shedding light on the molecular mechanisms underlying disorders. Also, they hold promise for guiding therapeutic interventions and personalized medicine strategies in the future. A comprehensive understanding of the impact of SNVs in the SERPINA1 gene on alpha-1 antitrypsin (AAT) protein structure and function requires integrating bioinformatic approaches. Here, we provide a guide for clinicians to navigate through the field of computational analyses which can be applied to describe a novel genetic variant. Predicting the clinical significance of SERPINA1 variation allows clinicians to tailor treatment options for individuals with alpha-1 antitrypsin deficiency (AATD) and related conditions, ultimately improving the patient's outcome and quality of life. This paper explores the various bioinformatic methodologies and cutting-edge approaches dedicated to the assessment of molecular variants of genes and their product proteins using SERPINA1 and AAT as an example.
Collapse
Affiliation(s)
- Jakub Mróz
- Tunneling Group, Biotechnology Center, Silesian University of Technology, Krzywoustego St. 8, 44-100 Gliwice, Poland;
| | - Magdalena Pelc
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, 26 Plocka St., 01-138 Warsaw, Poland; (M.P.); (J.C.-W.)
| | - Karolina Mitusińska
- Tunneling Group, Biotechnology Center, Silesian University of Technology, Krzywoustego St. 8, 44-100 Gliwice, Poland;
| | - Joanna Chorostowska-Wynimko
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, 26 Plocka St., 01-138 Warsaw, Poland; (M.P.); (J.C.-W.)
| | - Aleksandra Jezela-Stanek
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, 26 Plocka St., 01-138 Warsaw, Poland; (M.P.); (J.C.-W.)
| |
Collapse
|
3
|
Das NR, Chaudhury KN, Pal D. Improved NMR-data-compliant protein structure modeling captures context-dependent variations and expands the scope of functional inference. Proteins 2023; 91:412-435. [PMID: 36287124 DOI: 10.1002/prot.26439] [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: 05/10/2022] [Revised: 09/12/2022] [Accepted: 10/20/2022] [Indexed: 11/13/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy can reveal conformational states of a protein in physiological conditions. However, sparsely available NMR data for a protein with large degrees of freedom can introduce structural artifacts in the built models. Currently used state-of-the-art methods deriving protein structure and conformation from NMR deploy molecular dynamics (MD) coupled with simulated annealing for building models. We provide an alternate graph-based modeling approach, where we first build substructures from NMR-derived distance-geometry constraints combined in one shot to form the core structure. The remaining molecule with inadequate data is modeled using a hybrid approach respecting the observed distance-geometry constraints. One-shot structure building is rarely undertaken for large and sparse data systems, but our data-driven bottom-up approach makes this uniquely feasible by suitable partitioning of the problem. A detailed comparison of select models with state-of-art methods reveals differences in the secondary structure regions wherein the correctness of our models is confirmed by NMR data. Benchmarking of 106 protein-folds covering 38-282 length structures shows minimal experimental-constraint violations while conforming to other structure quality parameters such as the proper folding, steric clash, and torsion angle violation based on Ramachandran plot criteria. Comparative MD studies using select protein models from a state-of-art method and ours under identical experimental parameters reveal distinct conformational dynamics that could be attributed to protein structure-function. Our work is thus useful in building enhanced NMR-evidence-based models that encapsulate the contextual secondary and tertiary structure variations present during the experimentation and expand the scope of functional inference.
Collapse
Affiliation(s)
- Niladri R Das
- IISc Mathematics Initiative, Indian Institute of Science, Bangalore, India.,Department of Electrical Engineering, Indian Institute of Science, Bangalore, India
| | - Kunal N Chaudhury
- Department of Electrical Engineering, Indian Institute of Science, Bangalore, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
| |
Collapse
|
4
|
Hernández-Pérez JM, González Carracedo MA, García AC, Pérez JAP. Molecular characterization of PI * S hangzhou , a SERPINA1 allele from continental China encoding a defective alpha-1-antitrypsin. Front Pediatr 2022; 10:985892. [PMID: 36186645 PMCID: PMC9518693 DOI: 10.3389/fped.2022.985892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/23/2022] [Indexed: 12/02/2022] Open
Abstract
Alpha-1-antitrypsin deficiency (AATD) is a heritable condition that predisposes to respiratory and hepatic complications. Screenings in East Asia human populations for the AATD alleles most commonly found among Caucasians have yielded poor outcomes. Serum alpha-1-antitrypsin (AAT) levels, AAT phenotypes, and sequences of SERPINA1 gene were examined in a Chinese child with a moderate deficit of serum AAT, who had suffered several episodes of liver disease, as well as in his first-order relatives. Results allowed the identification of PI * S hangzhou , a novel SERPINA1 defective allele, which has been characterized by a L276R substitution, found in a SERPINA1-M3 genetic background. Moreover, potential effects of PI * S hangzhou mutation over the AAT structure were studied by 3D homology modeling. The presence of an arginine residue at position 276 could destabilize the tertiary structure of AAT, since it occurs at a highly conserved hydrophobic cavity in the protein surface, and very close to two positively-charged lysine residues. Attending to the frequency of R276 variant reported in databases for individuals of East Asian ancestry, the PI * S hangzhou allele may explain the global prevalence of the PiS phenotype observed in China.
Collapse
Affiliation(s)
| | - Mario A González Carracedo
- Genetics Laboratory, Institute of Tropical Diseases and Public Health of the Canary Islands (IUETSPC), University of La Laguna, San Cristóbal de La Laguna, Spain
| | | | - José A Pérez Pérez
- Genetics Laboratory, Institute of Tropical Diseases and Public Health of the Canary Islands (IUETSPC), University of La Laguna, San Cristóbal de La Laguna, Spain
| |
Collapse
|