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Dhar R, Bowman AM, Hatungimana B, Sg Slusky J. Evolutionary Engineering a Larger Porin Using a Loop-to-Hairpin Mechanism. J Mol Biol 2023; 435:168292. [PMID: 37769963 PMCID: PMC11215794 DOI: 10.1016/j.jmb.2023.168292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/03/2023]
Abstract
In protein evolution, diversification is generally driven by genetic duplication. The hallmarks of this mechanism are visible in the repeating topology of various proteins. In outer membrane β-barrels, duplication is visible with β-hairpins as the repeating unit of the barrel. In contrast to the overall use of duplication in diversification, a computational study hypothesized evolutionary mechanisms other than hairpin duplications leading to increases in the number of strands in outer membrane β-barrels. Specifically, the topology of some 16- and 18-stranded β-barrels appear to have evolved through a loop to β-hairpin transition. Here we test this novel evolutionary mechanism by creating a chimeric protein from an 18-stranded β-barrel and an evolutionarily related 16-stranded β-barrel. The chimeric combination of the two was created by replacing loop L3 of the 16-stranded barrel with the sequentially matched transmembrane β-hairpin region of the 18-stranded barrel. We find the resulting chimeric protein is stable and has characteristics of increased strand number. This study provides the first experimental evidence supporting the evolution through a loop to β-hairpin transition.
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Affiliation(s)
- Rik Dhar
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA. https://twitter.com/Rik_Skywalker
| | - Alexander M Bowman
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA
| | - Brunojoel Hatungimana
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA
| | - Joanna Sg Slusky
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA; Computational Biology Program, The University of Kansas, Lawrence, KS 66047, USA.
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2
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Dhar R, Bowman AM, Hatungimana B, Slusky JS. Evolutionary engineering a larger porin using a loop-to-hairpin mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544993. [PMID: 37398247 PMCID: PMC10312768 DOI: 10.1101/2023.06.14.544993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
In protein evolution, diversification is generally driven by genetic duplication. The hallmarks of this mechanism are visible in the repeating topology of various proteins. In outer membrane β-barrels, duplication is visible with β-hairpins as the repeating unit of the barrel. In contrast to the overall use of duplication in diversification, a computational study hypothesized evolutionary mechanisms other than hairpin duplications leading to increases in the number of strands in outer membrane β-barrels. Specifically, the topology of some 16- and 18-stranded β-barrels appear to have evolved through a loop to β-hairpin transition. Here we test this novel evolutionary mechanism by creating a chimeric protein from an 18-stranded β-barrel and an evolutionarily related 16-stranded β-barrel. The chimeric combination of the two was created by replacing loop L3 of the 16-stranded barrel with the sequentially matched transmembrane β-hairpin region of the 18-stranded barrel. We find the resulting chimeric protein is stable and has characteristics of increased strand number. This study provides the first experimental evidence supporting the evolution through a loop to β-hairpin transition. Highlights We find evidence supporting a novel diversification mechanism in membrane β-barrelsThe mechanism is the conversion of an extracellular loop to transmembrane β-hairpinA chimeric protein modeling this mechanism folds stably in the membraneThe chimera has more β-structure and a larger pore, consistent with a loop-to-hairpin transition.
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Affiliation(s)
- Rik Dhar
- Department of Molecular Biosciences, The University of Kansas, Lawrence KS 66045
| | - Alexander M Bowman
- Department of Molecular Biosciences, The University of Kansas, Lawrence KS 66045
| | | | - Joanna Sg Slusky
- Department of Molecular Biosciences, The University of Kansas, Lawrence KS 66045
- Computational Biology Program, The University of Kansas, Lawrence KS 66047
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3
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George A, Ravi R, Tiwari PB, Srivastava SR, Jain V, Mahalakshmi R. Engineering a Hyperstable Yersinia pestis Outer Membrane Protein Ail Using Thermodynamic Design. J Am Chem Soc 2022; 144:1545-1555. [DOI: 10.1021/jacs.1c05964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anjana George
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal - 462066, India
| | - Roshika Ravi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal - 462066, India
| | - Pankaj Bharat Tiwari
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal - 462066, India
| | - Shashank Ranjan Srivastava
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal - 462066, India
| | - Vikas Jain
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal - 462066, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal - 462066, India
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Lee J, Song WJ. Folding of Circularly Permuted and Split Outer Membrane Protein F via Electrostatic Interactions with Terminal Residues. Biochemistry 2021; 60:1787-1796. [PMID: 34060805 DOI: 10.1021/acs.biochem.1c00195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Membrane proteins are essential targets in drug design, biosensing, and catalysis. In this study, we explored the folding of engineered outer membrane protein F (OmpF), an abundant and functional β-barrel protein expressed in Gram-negative bacteria. We carried out circular permutation, splitting and self-complementation, and point mutation. The folding efficiency and kinetic analyses demonstrated that the N- and C-terminal residues of OmpF played critical roles in folding via electrostatic interactions with lipid headgroups. Our results indicate that native porins without charged terminal residues may be tightly downregulated to retain the integrity of the outer membrane, and this modification may facilitate the insertion and folding of modified membrane proteins under in vitro and in vivo conditions for various applications.
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Affiliation(s)
- Jaewon Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Woon Ju Song
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
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5
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Outer membrane protein evolution. Curr Opin Struct Biol 2021; 68:122-128. [PMID: 33493965 DOI: 10.1016/j.sbi.2021.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/16/2020] [Accepted: 01/02/2021] [Indexed: 01/31/2023]
Abstract
Outer membrane proteins have remarkably homogeneous structure. They are all up down β-barrels. Up down barrels themselves are composed of repeated sets of β-hairpins. The consistency of the usage of the β-hairpin throughout the outer membrane milieu allows for interrogation of the evolution of these repetitive structures. Here we describe recent investigations of outer membrane protein evolution and how evolutionary precepts have been used for novel outer membrane protein design.
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6
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Puentes PR, Henao MC, Torres CE, Gómez SC, Gómez LA, Burgos JC, Arbeláez P, Osma JF, Muñoz-Camargo C, Reyes LH, Cruz JC. Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches. Antibiotics (Basel) 2020; 9:E854. [PMID: 33265897 PMCID: PMC7759991 DOI: 10.3390/antibiotics9120854] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
One of the challenges of modern biotechnology is to find new routes to mitigate the resistance to conventional antibiotics. Antimicrobial peptides (AMPs) are an alternative type of biomolecules, naturally present in a wide variety of organisms, with the capacity to overcome the current microorganism resistance threat. Here, we reviewed our recent efforts to develop a new library of non-rationally produced AMPs that relies on bacterial genome inherent diversity and compared it with rationally designed libraries. Our approach is based on a four-stage workflow process that incorporates the interplay of recent developments in four major emerging technologies: artificial intelligence, molecular dynamics, surface-display in microorganisms, and microfluidics. Implementing this framework is challenging because to obtain reliable results, the in silico algorithms to search for candidate AMPs need to overcome issues of the state-of-the-art approaches that limit the possibilities for multi-space data distribution analyses in extremely large databases. We expect to tackle this challenge by using a recently developed classification algorithm based on deep learning models that rely on convolutional layers and gated recurrent units. This will be complemented by carefully tailored molecular dynamics simulations to elucidate specific interactions with lipid bilayers. Candidate AMPs will be recombinantly-expressed on the surface of microorganisms for further screening via different droplet-based microfluidic-based strategies to identify AMPs with the desired lytic abilities. We believe that the proposed approach opens opportunities for searching and screening bioactive peptides for other applications.
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Affiliation(s)
- Paola Ruiz Puentes
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogota DC 111711, Colombia; (P.R.P.); (P.A.)
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - María C. Henao
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogota DC 111711, Colombia;
| | - Carlos E. Torres
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Saúl C. Gómez
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Laura A. Gómez
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Juan C. Burgos
- Chemical Engineering Program, Universidad de Cartagena, Cartagena 130015, Colombia;
| | - Pablo Arbeláez
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogota DC 111711, Colombia; (P.R.P.); (P.A.)
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Johann F. Osma
- Department of Electrical and Electronic Engineering, Universidad de los Andes, Bogota DC 111711, Colombia;
| | - Carolina Muñoz-Camargo
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Luis H. Reyes
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogota DC 111711, Colombia;
| | - Juan C. Cruz
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide 5005, Australia
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7
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Horne JE, Brockwell DJ, Radford SE. Role of the lipid bilayer in outer membrane protein folding in Gram-negative bacteria. J Biol Chem 2020; 295:10340-10367. [PMID: 32499369 PMCID: PMC7383365 DOI: 10.1074/jbc.rev120.011473] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/03/2020] [Indexed: 01/09/2023] Open
Abstract
β-Barrel outer membrane proteins (OMPs) represent the major proteinaceous component of the outer membrane (OM) of Gram-negative bacteria. These proteins perform key roles in cell structure and morphology, nutrient acquisition, colonization and invasion, and protection against external toxic threats such as antibiotics. To become functional, OMPs must fold and insert into a crowded and asymmetric OM that lacks much freely accessible lipid. This feat is accomplished in the absence of an external energy source and is thought to be driven by the high thermodynamic stability of folded OMPs in the OM. With such a stable fold, the challenge that bacteria face in assembling OMPs into the OM is how to overcome the initial energy barrier of membrane insertion. In this review, we highlight the roles of the lipid environment and the OM in modulating the OMP-folding landscape and discuss the factors that guide folding in vitro and in vivo We particularly focus on the composition, architecture, and physical properties of the OM and how an understanding of the folding properties of OMPs in vitro can help explain the challenges they encounter during folding in vivo Current models of OMP biogenesis in the cellular environment are still in flux, but the stakes for improving the accuracy of these models are high. OMP folding is an essential process in all Gram-negative bacteria, and considering the looming crisis of widespread microbial drug resistance it is an attractive target. To bring down this vital OMP-supported barrier to antibiotics, we must first understand how bacterial cells build it.
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Affiliation(s)
- Jim E Horne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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Calabrese AN, Schiffrin B, Watson M, Karamanos TK, Walko M, Humes JR, Horne JE, White P, Wilson AJ, Kalli AC, Tuma R, Ashcroft AE, Brockwell DJ, Radford SE. Inter-domain dynamics in the chaperone SurA and multi-site binding to its outer membrane protein clients. Nat Commun 2020; 11:2155. [PMID: 32358557 PMCID: PMC7195389 DOI: 10.1038/s41467-020-15702-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 03/18/2020] [Indexed: 01/11/2023] Open
Abstract
The periplasmic chaperone SurA plays a key role in outer membrane protein (OMP) biogenesis. E. coli SurA comprises a core domain and two peptidylprolyl isomerase domains (P1 and P2), but its mechanisms of client binding and chaperone function have remained unclear. Here, we use chemical cross-linking, hydrogen-deuterium exchange mass spectrometry, single-molecule FRET and molecular dynamics simulations to map the client binding site(s) on SurA and interrogate the role of conformational dynamics in OMP recognition. We demonstrate that SurA samples an array of conformations in solution in which P2 primarily lies closer to the core/P1 domains than suggested in the SurA crystal structure. OMP binding sites are located primarily in the core domain, and OMP binding results in conformational changes between the core/P1 domains. Together, the results suggest that unfolded OMP substrates bind in a cradle formed between the SurA domains, with structural flexibility between domains assisting OMP recognition, binding and release.
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Affiliation(s)
- Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Bob Schiffrin
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Matthew Watson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Martin Walko
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Julia R Humes
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Jim E Horne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Paul White
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Antreas C Kalli
- Astbury Centre for Structural Molecular Biology and School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Alison E Ashcroft
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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Iyer BR, Gupta S, Noordeen H, Ravi R, Pawar MD, George A, Mahalakshmi R. Molecular Switch between Structural Compaction and Thermodynamic Stability by the Xxx-Pro Interface in Transmembrane β-Barrels. Biochemistry 2020; 59:303-314. [PMID: 31777252 DOI: 10.1021/acs.biochem.9b00731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transmembrane β-barrel scaffolds found in outer membrane proteins are formed and stabilized by a defined pattern of interstrand intraprotein H-bonds, in hydrophobic lipid bilayers. Introducing the conformationally constrained proline in β-barrels can cause significant destabilization of these structural regions that require H-bonding, with proline additionally acting as a secondary structure breaker. Membrane protein β-barrels are therefore expected to show poor tolerance to the presence of a transmembrane proline. Here, we assign a thermodynamic measure for the extent to which a single proline can be tolerated at the C-terminal interface of the model transmembrane β-barrel PagP. We find that proline drastically destabilizes PagP by 7.0 kcal mol-1 with respect to wild-type PagP (F161 → P161). Interestingly, strategic modulation of the preceding residue can modify the measured energetics. Placing a hydrophobic or bulky side chain as the preceding residue increases the thermodynamic stability by ≤8.0 kcal mol-1. While polar substituents at the preceding residue decrease the PagP stability, these residues demonstrate stronger tertiary packing interactions in the barrel and retain the catalytic activity of native PagP. This biophysical interplay between enhanced thermodynamic stability and attaining a structurally compact functional β-barrel scaffold highlights the detrimental effect caused by proline incorporation. Our findings also reveal alternative mechanisms that protein sequences can employ to salvage the structural integrity of transmembrane protein structures.
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Affiliation(s)
- Bharat Ramasubramanian Iyer
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Swadha Gupta
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Henna Noordeen
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Roshika Ravi
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Meera Daulatrao Pawar
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Anjana George
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
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