1
|
Sarmah S, Hazarika U, Das SM, Quraishi S, Bhatta A, Belwal VK, Jha AN, Singha Roy A. Deciphering the interactions of phytochemicals with ovalbumin, the major food allergen from egg white: spectroscopic and computational studies. LUMINESCENCE 2022; 37:2105-2122. [PMID: 36271635 DOI: 10.1002/bio.4401] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 12/14/2022]
Abstract
Ovalbumin (OVA), the major component of egg white, has been used as a model carrier protein to study the interaction of four bioactive phytochemicals 6-hydroxyflavone, chrysin, naringin, and naringenin. A static quenching mechanism was primarily associated with the complexation of the flavonoids with OVA. Hydrophobic forces play a major part in the stability of the complexes. The structural changes within the protein in response to flavonoid binding revealed a decrease in OVA's α-helical content. The hypothesized binding site for flavonoids in OVA overlaps with one or more immunoglobulin E-binding epitopes that may have some effect in the immunoglobulin E response pathway. The flavonoids remain in the same binding site throughout the simulation time and impart protein stability by forming different noncovalent interactions. This study presents comprehensive information about the interaction of the flavonoids with OVA and the associated structural variations after the binding, which might help researchers better comprehend similar medication pharmacodynamics and provide critical information for future therapeutic development.
Collapse
Affiliation(s)
- Sharat Sarmah
- Department of Chemistry, National Institute of Technology, Shillong, Meghalaya, India
| | - Upasana Hazarika
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
| | - Sony Moni Das
- Department of Chemistry, National Institute of Technology, Shillong, Meghalaya, India
| | - Sana Quraishi
- Department of Chemistry, National Institute of Technology, Shillong, Meghalaya, India
| | - Anindita Bhatta
- Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, Shillong, India
| | - Vinay Kumar Belwal
- Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Anupam Nath Jha
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
| | - Atanu Singha Roy
- Department of Chemistry, National Institute of Technology, Shillong, Meghalaya, India
| |
Collapse
|
2
|
Indari O, Kumar Singh A, Tiwari D, Chandra Jha H, Nath Jha A. Deciphering antiviral efficacy of malaria box compounds against malaria exacerbating viral pathogens- Epstein Barr Virus and SARS-CoV-2, an in silico study. MEDICINE IN DRUG DISCOVERY 2022; 16:100146. [DOI: 10.1016/j.medidd.2022.100146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 08/18/2022] [Accepted: 09/04/2022] [Indexed: 11/10/2022] Open
|
3
|
Chakraborty J. In-silico structural analysis of Pseudomonas syringae effector HopZ3 reveals ligand binding activity and virulence function. JOURNAL OF PLANT RESEARCH 2021; 134:599-611. [PMID: 33730245 DOI: 10.1007/s10265-021-01274-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
Bacterial acetyltransferase effectors belonging to the Yersinia outer protein J (YopJ) group inhibit multiple immune signaling pathways in human and plants. The present study determines in-silico acetyl-coenzyme A (AcCoA) binding and Arabidopsis immune regulator RPM1-interacting protein4 (RIN4) peptide interactions to YopJ effector hypersensitivity and pathogenesis-dependent outer proteinZ3 (HopZ3) from Pseudomonas syringae. Phylogenetic analysis revealed that HopZ3 was clustered by acetyltransferase effectors from plant bacterial pathogens. Structural juxtaposition shows HopZ3 comprises topology matched closer with HopZ1a than PopP2 effectors, respectively. AcCoA binds HopZ3 at two sites i.e., substrate binding pocket and catalytic site. AcCoA interactions to substrate binding pocket was transient and dissipated upon in-silico mutation of Ser 279 residue whereas, attachment to catalytic site was found to be stable in the presence of inositol hexaphosphate (IP6) as a co-factor. Interface atoms used for measuring hydrogen bond distances, bound or accessible surface area, and root-mean-square fluctuation (RMSF) values, suggests that the HopZ3 complex stabilizes after binding to AcCoA ligand and RIN4 peptide. The few non-conserved polymorphic residues that have been displayed on HopZ3 surface presumably confer intracellular recognitions within hosts. Collectively, homology modeling and interactive docking experiments were used to substantiate Arabidopsis immune 'guardee' interactions to HopZ3.
Collapse
|
4
|
Exploring the interaction of bioactive kaempferol with serum albumin, lysozyme and hemoglobin: A biophysical investigation using multi-spectroscopic, docking and molecular dynamics simulation studies. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2020; 205:111825. [DOI: 10.1016/j.jphotobiol.2020.111825] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 02/05/2020] [Accepted: 02/17/2020] [Indexed: 01/08/2023]
|
5
|
Das S, Sarmah S, Hazarika Z, Rohman MA, Sarkhel P, Jha AN, Singha Roy A. Targeting the heme protein hemoglobin by (−)-epigallocatechin gallate and the study of polyphenol–protein association using multi-spectroscopic and computational methods. Phys Chem Chem Phys 2020; 22:2212-2228. [DOI: 10.1039/c9cp05301h] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
(−)-Epigallocatechin gallate binds to BHb and exhibits anti-glycating as well as antioxidant behaviors towards glycation and photo-oxidation of BHb.
Collapse
Affiliation(s)
- Sourav Das
- Department of Chemistry
- National Institute of Technology Meghalaya
- Shillong-793003
- India
| | - Sharat Sarmah
- Department of Chemistry
- National Institute of Technology Meghalaya
- Shillong-793003
- India
| | - Zaved Hazarika
- Department of Molecular Biology and Biotechnology
- Tezpur University
- Tezpur 784028
- India
| | - Mostofa Ataur Rohman
- Centre for Advanced Studies
- Department of Chemistry
- North-Eastern Hill University
- Shillong 793022
- India
| | - Pallavi Sarkhel
- Department of Chemistry
- Birla Institute of Technology Mesra
- Jharkhand 835215
- India
| | - Anupam Nath Jha
- Department of Molecular Biology and Biotechnology
- Tezpur University
- Tezpur 784028
- India
| | - Atanu Singha Roy
- Department of Chemistry
- National Institute of Technology Meghalaya
- Shillong-793003
- India
| |
Collapse
|
6
|
Ahmad S, Gromiha MM, Raghava GPS, Schönbach C, Ranganathan S. APBioNet's annual International Conference on Bioinformatics (InCoB) returns to India in 2018. BMC Genomics 2019; 19:266. [PMID: 30999857 PMCID: PMC7402400 DOI: 10.1186/s12864-019-5582-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
InCoB, one of the largest annual bioinformatics conferences in the Asia-Pacific region since its launch in 2002, returned to New Delhi, India after 12 years, with a conference attendance of 314 delegates. The 2018 conference had sessions on Big Data and Algorithms, Next Generation Sequencing and Omics Science, Structure, Function and Interactions, Disease and Drug Discovery and Plant and Agricultural Bioinformatics. The conference also featured an industry track as well as panel discussions on Women in Bioinformatics and Democratization vs. Quality control in academic publishing. Asia Pacific Bioinformatics Interaction & Networking Society (APbians) was launched as an APBionet Special Interest Group. Of the 52 oral presentations made, 22 were accepted in supplemental issues of BMC Bioinformatics, BMC Genomics or BMC Medical Genomics and are briefly reviewed here. Next year’s InCoB will be held in Jakarta, Indonesia from September 10–12, 2019.
Collapse
Affiliation(s)
- Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110 067, India
| | - Michael M Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamilnadu, 600 036, India
| | - Gajendra P S Raghava
- Centre for Computational Biology, Indraprastha Institute of Information Technology, Okhla Industrial Estate, Phase III, New Delhi, 110020, India
| | - Christian Schönbach
- Department of Biology, School of Science and Technology, Nazarbayev University, Astana, Kazakhstan.,International Research Center for Medical Sciences, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia. .,Transformational Bioinformatics, Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Sydney, Australia.
| |
Collapse
|
7
|
Bora N, Nath Jha A. An integrative approach using systems biology, mutational analysis with molecular dynamics simulation to challenge the functionality of a target protein. Chem Biol Drug Des 2019; 93:1050-1060. [PMID: 30891955 DOI: 10.1111/cbdd.13502] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 01/08/2019] [Accepted: 01/31/2019] [Indexed: 01/05/2023]
Abstract
Visceral leishmaniasis affects millions of people worldwide in areas where Leishmania donovani is endemic. The protozoan species serves a greater threat as it has gradually evolved drug resistance whereby requiring newer approaches to treat the infection. State-of-art techniques are mostly directed toward finding better targets extracted from the available proteome data. In light of recent computational advancements, we ascertain and validate one such target, adenylosuccinate lyase (ADSL) by implementation of in-silico methods which led to the identification of critical amino acid residues that affects its functional attributes. Our target selection was based on comprehensive topological analysis of a knowledge-based protein-protein interaction network. Subsequently, mutations were incorporated and the dynamic behavior of mutated and native proteins was traced using MD simulations for a total time span of 600 ns. Comparative analysis of the native and mutated structures exhibited perceptible changes in the ligand-bound catalytic region with respect to time. The unfavorable changes in the orientations of specific catalytic residues, His118 and His196, induced by generated mutations reduce the enzyme specificity. In summary, this integrative approach is able to select a target against pathogen, identify crucial residues, and challenge its functionality through the selected mutations.
Collapse
Affiliation(s)
- Nikita Bora
- Computational Biophysics Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | - Anupam Nath Jha
- Computational Biophysics Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| |
Collapse
|