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Bera S, Kar RK, Mondal S, Pahan K, Bhunia A. Correction to "Structural Elucidation of the Cell-Penetrating Penetratin Peptide in Model Membranes at the Atomic Level: Probing Hydrophobic Interactions in the Blood-Brain Barrier". Biochemistry 2024; 63:1234. [PMID: 38598682 DOI: 10.1021/acs.biochem.4c00118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
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2
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Kar RK. An idea to explore: Cultivating the art of proposal writing among graduate students. Biochem Mol Biol Educ 2024; 52:369-372. [PMID: 38409737 DOI: 10.1002/bmb.21822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 12/20/2023] [Accepted: 02/11/2024] [Indexed: 02/28/2024]
Abstract
Proposal writing is an essential requirement for making progress in academics. Learning this skill necessitates support from a mentor to cultivate effective habits. It entails effective strategies from graduate students, such as literature reading and using online tools. Additionally, they must develop an understanding of resource accountability, system thinking, and considering deadlines as a driving force. Good practices for effective proposal writing also involve planning to summarize the work done in the field. Moreover, it requires ideal mentor support by providing timely assistance, helping students overcome impostor syndrome, sharing successful proposals, and creating a cooperative environment.
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Affiliation(s)
- Rajiv K Kar
- Jyoti and Bhupat Mehta School of Health Sciences and Technology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
- Center for Nanotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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3
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Barik S, Panda AK, Biswas VK, Das S, Chakraborty A, Beura S, Modak R, Raghav SK, Kar RK, Biswas A. Lysine acetylation of Hsp16.3: Effect on its structure, chaperone function and influence towards the growth of Mycobacterium tuberculosis. Int J Biol Macromol 2024; 268:131763. [PMID: 38657928 DOI: 10.1016/j.ijbiomac.2024.131763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/09/2024] [Accepted: 04/20/2024] [Indexed: 04/26/2024]
Abstract
Hsp16.3 plays a vital role in the slow growth of Mycobacterium tuberculosis via its chaperone function. Many secretory proteins, including Hsp16.3 undergo acetylation in vivo. Seven lysine (K) residues (K64, K78, K85, K114, K119, K132 and K136) in Hsp16.3 are acetylated inside pathogen. However, how lysine acetylation affects its structure, chaperone function and pathogen's growth is still elusive. We examined these aspects by executing in vitro chemical acetylation (acetic anhydride modification) and by utilizing a lysine acetylation mimic mutant (K64Q/K78Q/K85Q/K114Q/K119Q/K132Q/K136Q). Far- and near-UV CD measurements revealed that the chemically acetylated proteins(s) and acetylation mimic mutant has altered secondary and tertiary structure than unacetylated/wild-type protein. The chemical modification and acetylation mimic mutation also disrupted the oligomeric assembly, increased surface hydrophobicity and reduced stability of Hsp16.3, as revealed by GF-HPLC, 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid binding and urea denaturation experiments, respectively. These structural changes collectively led to an enhancement in chaperone function (aggregation and thermal inactivation prevention ability) of Hsp16.3. Moreover, when the H37Rv strain expressed the acetylation mimic mutant protein, its growth was slower in comparison to the strain expressing the wild-type/unacetylated Hsp16.3. Altogether, these findings indicated that lysine acetylation improves the chaperone function of Hsp16.3 which may influence pathogen's growth in host environment.
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Affiliation(s)
- Subhashree Barik
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Alok Kumar Panda
- Environmental Science Laboratory, School of Applied Sciences, Kalinga Institute of Industrial Technology, Deemed to be University, Bhubaneswar, Odisha 751024, India
| | - Viplov Kumar Biswas
- Immunogenomics and Systems Biology Laboratory, Institute of Life Sciences (ILS), Bhubaneswar, Odisha 751023, India; School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, Odisha, India
| | - Sheetal Das
- Jyoti and Bhupat Mehta School of Health Sciences and Technology, Center for Nanotechnology, Indian Institute of Technology Guwahati, Assam, India
| | - Ayon Chakraborty
- University Institute of Biotechnology, University Centre for Research & Development, Chandigarh University, Mohali, India
| | - Shibangini Beura
- Infection and Epigenetics Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, Odisha, India
| | - Rahul Modak
- Infection and Epigenetics Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, Odisha, India
| | - Sunil Kumar Raghav
- Immunogenomics and Systems Biology Laboratory, Institute of Life Sciences (ILS), Bhubaneswar, Odisha 751023, India
| | - Rajiv K Kar
- Jyoti and Bhupat Mehta School of Health Sciences and Technology, Center for Nanotechnology, Indian Institute of Technology Guwahati, Assam, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India.
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Panda R, Panda PK, Krishnamoorthy J, Kar RK. Network analysis of chromophore binding site in LOV domain. Comput Biol Med 2023; 161:106996. [PMID: 37201443 DOI: 10.1016/j.compbiomed.2023.106996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/16/2023] [Accepted: 05/01/2023] [Indexed: 05/20/2023]
Abstract
Photoreceptor proteins are versatile toolbox for developing biosensors for optogenetic applications. These molecular tools get activated upon illumination of blue light, which in turn offers a non-invasive method for gaining high spatiotemporal resolution and precise control of cellular signal transduction. The Light-Oxygen-Voltage (LOV) domain family of proteins is a well-recognized system for constructing optogenetic devices. Translation of these proteins into efficient cellular sensors is possible by tuning their photochemistry lifetime. However, the bottleneck is the need for more understanding of the relationship between the protein environment and photocycle kinetics. Significantly, the effect of the local environment also modulates the electronic structure of chromophore, which perturbs the electrostatic and hydrophobic interaction within the binding site. This work highlights the critical factors hidden in the protein networks, linking with their experimental photocycle kinetics. It presents an opportunity to quantitatively examine the alternation in chromophore's equilibrium geometry and identify details which have substantial implications in designing synthetic LOV constructs with desirable photocycle efficiency.
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Affiliation(s)
- Rishab Panda
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Punjab, India
| | - Pritam K Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20, Uppsala, Sweden; Division of Immunology and Chronic Disease, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Rajiv K Kar
- Jyoti and Bhupat Mehta School of Health Sciences and Technology, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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González-Viegas M, Kar RK, Miller AF, Mroginski MA. Non-covalent interactions that tune the reactivities of the flavins in bifurcating electron transferring flavoprotein. J Biol Chem 2023:104762. [PMID: 37119850 DOI: 10.1016/j.jbc.2023.104762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 05/01/2023] Open
Abstract
Bifurcating electron transferring flavoproteins (Bf-ETFs) tune chemically identical flavins to two contrasting roles. To understand how, we used hybrid quantum mechanical molecular mechanical calculations to characterize non-covalent interactions applied to each flavin by the protein. Our computations replicated the differences between the reactivities of the flavins: the electron transferring flavin (ETflavin) was calculated to stabilize anionic semiquinone (ASQ) as needed to execute its single-electron transfers, whereas the Bf flavin (Bfflavin) was found to disfavor the ASQ state more than does free flavin and to be less susceptible to reduction. The stability of ETflavin ASQ was attributed in part to H-bond donation to the flavin O2 from a nearby His side chain, via comparison of models employing different tautomers of His. This H-bond between O2 and the ET site was uniquely strong in the ASQ state, whereas reduction of ETflavin to the anionic hydroquinone (AHQ) was associated with side chain reorientation, backbone displacement and reorganization of its H-bond network including a Tyr from the other domain and subunit of the ETF. The Bf site was less responsive overall, but formation of the Bfflavin AHQ allowed a nearby Arg side chain to adopt an alternative rotamer that can H-bond to the Bfflavin O4. This would stabilize the anionic Bfflavin and rationalize effects of mutation at this position. Thus, our computations provide insights on states and conformations that have not been possible to characterize experimentally, offering explanations for observed residue conservation and raising possibilities that can now be tested.
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Affiliation(s)
- María González-Viegas
- Department of Chemistry, Technische Universität - Berlin, Berlin, Germany; Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Rajiv K Kar
- Department of Chemistry, Technische Universität - Berlin, Berlin, Germany
| | - Anne-Frances Miller
- Department of Chemistry, Technische Universität - Berlin, Berlin, Germany; Department of Chemistry, University of Kentucky, Lexington KY, U.S.A..
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6
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Kar RK. Benefits of hybrid QM/MM over traditional classical mechanics in pharmaceutical systems. Drug Discov Today 2023; 28:103374. [PMID: 36174967 DOI: 10.1016/j.drudis.2022.103374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/27/2022] [Accepted: 09/22/2022] [Indexed: 02/02/2023]
Abstract
Hybrid quantum mechanics/molecular mechanics (QM/MM) is one of the most reliable approaches for accurately modeling and studying the complex pharmaceutical discovery system. Classical mechanics has significantly accelerated the drug discovery process in the past decade. However, the current challenge is the large pool of false positives, which require extensive validation. Hybrid QM/MM is an effective solution for accurately studying ligand binding, structural mechanisms, free energy evaluation, and spectroscopic characterization. This article highlights the methodological details relevant to cost-effective hybrid QM/MM methods. This approach, combined with traditional pharmacoinformatics methods, could be a reliable strategy to balance the cost and accuracy of the calculations.
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Affiliation(s)
- Rajiv K Kar
- Jyoti and Bhupat Mehta School of Health Sciences and Technology, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India.
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7
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Asido M, Kar RK, Kriebel CN, Braun M, Glaubitz C, Schapiro I, Wachtveitl J. Transient near-UV absorption of the light-driven sodium pump Krokinobacter eikastus rhodopsin 2: a spectroscopic marker for retinal configuration. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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8
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Abstract
Flavins are central to countless enzymes but display different reactivities depending on their environments. This is understood to reflect modulation of the flavin electronic structure. To understand changes in orbital natures, energies, and correlation over the ring system, we begin by comparing seven flavin variants differing at C8, exploiting their different electronic spectra to validate quantum chemical calculations. Ground state calculations replicate a Hammett trend and reveal the significance of the flavin π-system. Comparison of higher-level theories establishes CC2 and ACD(2) as methods of choice for characterization of electronic transitions. Charge transfer character and electron correlation prove responsive to the identity of the substituent at C8. Indeed, bond length alternation analysis demonstrates extensive conjugation and delocalization from the C8 position throughout the ring system. Moreover, we succeed in replicating a particularly challenging UV/Vis spectrum by implementing hybrid QM/MM in explicit solvents. Our calculations reveal that the presence of nonbonding lone pairs correlates with the change in the UV/Vis spectrum observed when the 8-methyl is replaced by NH2, OH, or SH. Thus, our computations offer routes to understanding the spectra of flavins with different modifications. This is a first step toward understanding how the same is accomplished by different binding environments.
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Affiliation(s)
- Rajiv K Kar
- Faculty II-Mathematics and Natural Sciences, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Sam Chasen
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Maria-Andrea Mroginski
- Faculty II-Mathematics and Natural Sciences, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Anne-Frances Miller
- Faculty II-Mathematics and Natural Sciences, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany.,Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
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Tulsiyan K, Jena S, González-Viegas M, Kar RK, Biswal HS. Structural Dynamics of RNA in the Presence of Choline Amino Acid Based Ionic Liquid: A Spectroscopic and Computational Outlook. ACS Cent Sci 2021; 7:1688-1697. [PMID: 34729412 PMCID: PMC8554839 DOI: 10.1021/acscentsci.1c00768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Indexed: 05/03/2023]
Abstract
Ribonucleic acid (RNA) is exceedingly sensitive to degradation compared to DNA. The current protocol for storage of purified RNA requires freezing conditions below -20 °C. Recent advancements in biological chemistry have identified amino acid-based ionic liquids as suitable preservation media for RNA, even in the presence of degrading enzymes. However, the mechanistic insight into the interaction between ILs and RNA is unclear. To the best of our knowledge, no attempts are made so far to provide a molecular view. This work aims to establish a detailed understanding of how ILs enable structural stability to RNA sourced from Torula yeast. Herein, we manifest the hypothesis of multimodal binding of IL and its minimal perturbation to the macromolecular structure, with several spectroscopic techniques such as time-resolved fluorescence and fluorescence correlation spectroscopy (FCS) aided with molecular dynamics at microsecond time scales. Relevant structural and thermodynamic details from biophysical experiments confirm that even long-term RNA preservation with ILs is a possible alternative devoid of any structural deformation. These results establish a unifying mechanism of how ILs are maintaining conformational integrity and thermal stability. The atomistic insights are transferable for their potential applications in drug delivery and biomaterials by considering the advantages of having maximum structural retention and minimum toxicity.
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Affiliation(s)
- Kiran
Devi Tulsiyan
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, District, Khurda, 752050, Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Subhrakant Jena
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, District, Khurda, 752050, Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - María González-Viegas
- Institut
für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, 10115 Berlin, Germany
| | - Rajiv K. Kar
- Faculty
II-Mathematics and Natural Sciences, Technische
Universität Berlin, Sekr. PC 14, Strasse des 17, Juni 135, D-10623 Berlin, Germany
| | - Himansu S. Biswal
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, District, Khurda, 752050, Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
- . Phone: +91-674-2494 185/186
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10
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Sakib Hossain DM, Panda AK, Manna A, Mohanty S, Bhattacharjee P, Bhattacharyya S, Saha T, Chakraborty S, Kar RK, Das T, Chatterjee S, Sa G. Retraction Notice to: FoxP3 Acts as a Cotranscription Factor with STAT3 in Tumor-Induced Regulatory T Cells. Immunity 2021; 54:2167. [PMID: 34525341 DOI: 10.1016/j.immuni.2021.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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Chakraborty I, Kar RK, Sarkar D, Kumar S, Maiti NC, Mandal AK, Bhunia A. Solvent Relaxation NMR: A Tool for Real-Time Monitoring Water Dynamics in Protein Aggregation Landscape. ACS Chem Neurosci 2021; 12:2903-2916. [PMID: 34292711 DOI: 10.1021/acschemneuro.1c00262] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Solvent dynamics strongly induce the fibrillation of an amyloidogenic system. Probing the solvation mechanism is crucial as it enables us to predict different proteins' functionalities, such as the aggregation propensity, structural flexibility, and toxicity. This work shows that a straightforward NMR method in conjunction with phenomenological models gives a global and qualitative picture of water dynamics at different concentrations and temperatures. Here, we study amyloid system Aβ40 and its fragment AV20 (A21-V40) and G37L (mutation at Gly37 → Leu of AV20), having different aggregation and toxic properties. The independent validation of this method is elucidated using all-atom classical MD simulation. These two state-of-the-art techniques are pivotal in linking the effect of solvent environment in the near hydration-shell to their aggregation nature. The time-dependent modulation in solvent dynamics probed with the NMR solvent relaxation method can be further adopted to gain insight into amyloidogenesis and link with their toxicity profiles.
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Affiliation(s)
| | - Rajiv K. Kar
- Faculty II-Mathematics and Natural Sciences, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Dibakar Sarkar
- Department of Biophysics, Bose Institute, Kolkata 700054, India
| | - Sourav Kumar
- Department of Biophysics, Bose Institute, Kolkata 700054, India
| | - Nakul C. Maiti
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Atin Kumar Mandal
- Division of Molecular Medicine, Bose Institute, Kolkata 700054, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata 700054, India
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12
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Choudhury S, Jena S, Sahoo DK, Shekh S, Kar RK, Dhakad A, Gowd KH, Biswal HS. Gram-Scale Synthesis of 1,8-Naphthyridines in Water: The Friedlander Reaction Revisited. ACS Omega 2021; 6:19304-19313. [PMID: 34337267 PMCID: PMC8320145 DOI: 10.1021/acsomega.1c02798] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
The products of the Friedlander reaction, i.e., 1,8-naphthyridines, have far-reaching impacts in materials science, chemical biology, and medicine. The reported synthetic methodologies elegantly orchestrate the diverse synthetic routes of naphthyridines but require harsh reaction conditions, organic solvents, and expensive metal catalysts. Here, we introduce gram-scale synthesis of 1,8-naphthyridines in water using an inexpensive and biocompatible ionic liquid (IL) as a catalyst. This is the first-ever report on the synthesis of naphthyridines in water. This is a one-step reaction, and the product separation is relatively easy. The choline hydroxide (ChOH) is used as a metal-free, nontoxic, and water-soluble catalyst. In comparison to other catalysts reported in the literature, ChOH has the advantage of forming an additional hydrogen bond with the reactants, which is the vital step for the reaction to happen in water. Density functional theory (DFT) and noncovalent interaction (NCI) plot index analysis provide the plausible reaction mechanism for the catalytic cycle and confirm that hydrogen bonds with the IL catalyst are pivotal to facilitate the reaction. Molecular docking and molecular dynamics (MD) simulations are also performed to demonstrate the potentialities of the newly synthesized products as drugs. Through MD simulations, it was established that the tetrahydropyrido derivative of naphthyridine (10j) binds to the active sites of the ts3 human serotonin transporter (hSERT) (PDB ID: 6AWO) without perturbing the secondary structure, suggesting that 10j can be a potential preclinical drug candidate for hSERT inhibition and depression treatment.
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Affiliation(s)
- Shubhranshu
Shekhar Choudhury
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni,
Khurda, 752050 Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Subhrakant Jena
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni,
Khurda, 752050 Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Dipak Kumar Sahoo
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni,
Khurda, 752050 Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Shamasoddin Shekh
- Department
of Chemistry, Central University of Karnataka, Kalaburagi 585367, Karnataka, India
| | - Rajiv K. Kar
- Fritz
Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ambuj Dhakad
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni,
Khurda, 752050 Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Konkallu Hanumae Gowd
- Department
of Chemistry, Central University of Karnataka, Kalaburagi 585367, Karnataka, India
| | - Himansu S. Biswal
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni,
Khurda, 752050 Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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13
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Asido M, Kar RK, Kriebel CN, Braun M, Glaubitz C, Schapiro I, Wachtveitl J. Transient Near-UV Absorption of the Light-Driven Sodium Pump Krokinobacter eikastus Rhodopsin 2: A Spectroscopic Marker for Retinal Configuration. J Phys Chem Lett 2021; 12:6284-6291. [PMID: 34213348 DOI: 10.1021/acs.jpclett.1c01436] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We report a transient signature in the near-UV absorption of Krokinobacter eikastus rhodopsin 2 (KR2), which spans from the femtosecond up to the millisecond time scale. The signature rises with the all-trans to 13-cis isomerization of retinal and decays with the reisomerization to all-trans in the late photocycle, making it a promising marker band for retinal configuration. Hybrid quantum mechanics/molecular mechanics simulations show that the near-UV absorption signal corresponds to an S0 → S3 and/or an S0 → S5 transition, which is present in all photointermediates. These transitions exhibit a negligible spectral shift by the altering protein environment, in contrast to the main absorption band. This is rationalized by the extension of the transition densities that omits the Schiff base nitrogen. Further characterization and first steps into possible optogenetic applications were performed with near-UV quenching experiments of an induced photostationary state, yielding an ultrafast regeneration of the parent state of KR2.
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Affiliation(s)
- Marvin Asido
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany
| | - Rajiv K Kar
- Fritz Haber Center for Molecular Dynamics Research at the Institute of Chemistry, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Clara Nassrin Kriebel
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt am Main, Germany
| | - Markus Braun
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt am Main, Germany
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research at the Institute of Chemistry, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany
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14
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Kar RK. Computational Resources for Bioscience Education. Appl Biochem Biotechnol 2021; 193:3418-3424. [PMID: 34101113 PMCID: PMC8184869 DOI: 10.1007/s12010-021-03601-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/28/2021] [Indexed: 11/29/2022]
Abstract
With the ongoing laboratory restrictions, it is often challenging for bioscience students to make satisfactory progress in their projects. A long-standing practice in multi-disciplinary research is to use computational and theoretical method to corroborate with experiment findings. In line with the lack of opportunity to access laboratory instruments, the pandemic situation is a win-win scenario for scholars to focus on computational methods. This communication outline some of the standalone tools and webservers that bioscience students can successfully learn and adopt to obtain in-depth insights into biochemistry, biophysics, biotechnology, and bioengineering research work.
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Affiliation(s)
- Rajiv K Kar
- Faculty II-Mathematics and Natural Sciences, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623, Berlin, Germany.
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15
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Jena S, Tulsiyan KD, Kar RK, Kisan HK, Biswal HS. Doubling Förster Resonance Energy Transfer Efficiency in Proteins with Extrinsic Thioamide Probes: Implications for Thiomodified Nucleobases. Chemistry 2021; 27:4373-4383. [PMID: 33210381 DOI: 10.1002/chem.202004627] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Indexed: 12/29/2022]
Abstract
Designing a potential protein-ligand pair is pivotal, not only to track the protein structure dynamics, but also to assist in an atomistic understanding of drug delivery. Herein, the potential of a small model thioamide probe being used to study albumin proteins is reported. By monitoring the Förster resonance energy transfer (FRET) dynamics with the help of fluorescence spectroscopic techniques, a twofold enhancement in the FRET efficiency of 2-thiopyridone (2TPY), relative to that of its amide analogue, is observed. Molecular dynamics simulations depict the relative position of the free energy minimum to be quite stable in the case of 2TPY through noncovalent interactions with sulfur, which help to enhance the FRET efficiency. Finally, its application is shown by pairing thiouracils with protein. It is found that the site-selective sulfur atom substitution approach and noncovalent interactions with sulfur can substantially enhance the FRET efficiency, which could be a potential avenue to explore in the design of FRET probes to study the structure and dynamics of biomolecules.
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Affiliation(s)
- Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Jatni, Khurda, Bhubaneswar, 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Jatni, Khurda, Bhubaneswar, 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Rajiv K Kar
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Hemanta K Kisan
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel.,Department of Chemistry, Utkal University, 751004, Bhubaneswar, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Jatni, Khurda, Bhubaneswar, 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
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16
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Mroginski MA, Adam S, Amoyal GS, Barnoy A, Bondar AN, Borin VA, Church JR, Domratcheva T, Ensing B, Fanelli F, Ferré N, Filiba O, Pedraza-González L, González R, González-Espinoza CE, Kar RK, Kemmler L, Kim SS, Kongsted J, Krylov AI, Lahav Y, Lazaratos M, NasserEddin Q, Navizet I, Nemukhin A, Olivucci M, Olsen JMH, Pérez de Alba Ortíz A, Pieri E, Rao AG, Rhee YM, Ricardi N, Sen S, Solov'yov IA, De Vico L, Wesolowski TA, Wiebeler C, Yang X, Schapiro I. Frontiers in Multiscale Modeling of Photoreceptor Proteins. Photochem Photobiol 2021; 97:243-269. [PMID: 33369749 DOI: 10.1111/php.13372] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/01/2020] [Indexed: 02/06/2023]
Abstract
This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.
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Affiliation(s)
| | - Suliman Adam
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gil S Amoyal
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Avishai Barnoy
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Veniamin A Borin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jonathan R Church
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tatiana Domratcheva
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Department Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Bernd Ensing
- Van 't Hoff Institute for Molecular Science and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Amsterdam, The Netherlands
| | - Francesca Fanelli
- Department of Life Sciences, Center for Neuroscience and Neurotechnology, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
| | | | - Ofer Filiba
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Laura Pedraza-González
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy
| | - Ronald González
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | | | - Rajiv K Kar
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lukas Kemmler
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Seung Soo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Yigal Lahav
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.,MIGAL - Galilee Research Institute, S. Industrial Zone, Kiryat Shmona, Israel
| | - Michalis Lazaratos
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Qays NasserEddin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isabelle Navizet
- MSME, Univ Gustave Eiffel, CNRS UMR 8208, Univ Paris Est Creteil, Marne-la-Vallée, France
| | - Alexander Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy.,Chemistry Department, Bowling Green State University, Bowling Green, OH, USA
| | - Jógvan Magnus Haugaard Olsen
- Department of Chemistry, Aarhus University, Aarhus, Denmark.,Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Alberto Pérez de Alba Ortíz
- Van 't Hoff Institute for Molecular Science and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Amsterdam, The Netherlands
| | - Elisa Pieri
- Aix-Marseille Univ, CNRS, ICR, Marseille, France
| | - Aditya G Rao
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Niccolò Ricardi
- Département de Chimie Physique, Université de Genève, Genève, Switzerland
| | - Saumik Sen
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Luca De Vico
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy
| | | | - Christian Wiebeler
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Xuchun Yang
- Chemistry Department, Bowling Green State University, Bowling Green, OH, USA
| | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
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17
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Sokolovski SG, Zherebtsov EA, Kar RK, Golonka D, Stabel R, Chichkov NB, Gorodetsky A, Schapiro I, Möglich A, Rafailov EU. Two-photon conversion of a bacterial phytochrome. Biophys J 2021; 120:964-974. [PMID: 33545103 DOI: 10.1016/j.bpj.2021.01.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/20/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
In nature, sensory photoreceptors underlie diverse spatiotemporally precise and generally reversible biological responses to light. Photoreceptors also serve as genetically encoded agents in optogenetics to control by light organismal state and behavior. Phytochromes represent a superfamily of photoreceptors that transition between states absorbing red light (Pr) and far-red light (Pfr), thus expanding the spectral range of optogenetics to the near-infrared range. Although light of these colors exhibits superior penetration of soft tissue, the transmission through bone and skull is poor. To overcome this fundamental challenge, we explore the activation of a bacterial phytochrome by a femtosecond laser emitting in the 1 μm wavelength range. Quantum chemical calculations predict that bacterial phytochromes possess substantial two-photon absorption cross sections. In line with this notion, we demonstrate that the photoreversible Pr ↔ Pfr conversion is driven by two-photon absorption at wavelengths between 1170 and 1450 nm. The Pfr yield was highest for wavelengths between 1170 and 1280 nm and rapidly plummeted beyond 1300 nm. By combining two-photon activation with bacterial phytochromes, we lay the foundation for enhanced spatial resolution in optogenetics and unprecedented penetration through bone, skull, and soft tissue.
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Affiliation(s)
- Serge G Sokolovski
- Optoelectronics and Biomedical Photonics Group, AIPT, Aston University, Birmingham, United Kingdom
| | - Evgeny A Zherebtsov
- Optoelectronics and Measurement Techniques, University of Oulu, Oulu, Finland; Cell Physiology and Pathology Laboratory, Orel State University, Orel, Russia
| | - Rajiv K Kar
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Golonka
- Photobiochemistry, University of Bayreuth, Bayreuth, Germany
| | - Robert Stabel
- Photobiochemistry, University of Bayreuth, Bayreuth, Germany
| | - Nikolai B Chichkov
- Optoelectronics and Biomedical Photonics Group, AIPT, Aston University, Birmingham, United Kingdom
| | - Andrei Gorodetsky
- ITMO University, St. Petersburg, Russia; Department of Chemistry, Imperial College London, London, United Kingdom; School of Physics and Astronomy, University of Birmingham, Birmingham, United Kingdom
| | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Andreas Möglich
- Photobiochemistry, University of Bayreuth, Bayreuth, Germany.
| | - Edik U Rafailov
- Optoelectronics and Biomedical Photonics Group, AIPT, Aston University, Birmingham, United Kingdom.
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18
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Ratha BN, Kar RK, Brender JR, Pariary R, Sahoo B, Kalita S, Bhunia A. High-resolution structure of a partially folded insulin aggregation intermediate. Proteins 2020; 88:1648-1659. [PMID: 32683793 DOI: 10.1002/prot.25983] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 06/11/2020] [Accepted: 07/12/2020] [Indexed: 01/01/2023]
Abstract
Insulin has long been served as a model for protein aggregation, both due to the importance of aggregation in the manufacture of insulin and because the structural biology of insulin has been extensively characterized. Despite intensive study, details about the initial triggers for aggregation have remained elusive at the molecular level. We show here that at acidic pH, the aggregation of insulin is likely initiated by a partially folded monomeric intermediate. High-resolution structures of the partially folded intermediate show that it is coarsely similar to the initial monomeric structure but differs in subtle details-the A chain helices on the receptor interface are more disordered and the B chain helix is displaced from the C-terminal A chain helix when compared to the stable monomer. The result of these movements is the creation of a hydrophobic cavity in the center of the protein that may serve as nucleation site for oligomer formation. Knowledge of this transition may aid in the engineering of insulin variants that retain the favorable pharamacokinetic properties of monomeric insulin but are more resistant to aggregation.
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Affiliation(s)
- Bhisma N Ratha
- Department of Biophysics, Bose Institute, Kolkata, India
| | - Rajiv K Kar
- Department of Biophysics, Bose Institute, Kolkata, India
| | - Jeffrey R Brender
- Radiation Biology Branch, National Institutes of Health, Bethesda, Maryland, USA
| | - Ranit Pariary
- Department of Biophysics, Bose Institute, Kolkata, India
| | | | - Sujan Kalita
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata, India
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19
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Anwar S, Shamsi A, Kar RK, Queen A, Islam A, Ahmad F, Hassan MI. Structural and biochemical investigation of MARK4 inhibitory potential of cholic acid: Towards therapeutic implications in neurodegenerative diseases. Int J Biol Macromol 2020; 161:596-604. [PMID: 32535203 DOI: 10.1016/j.ijbiomac.2020.06.078] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 02/06/2023]
Abstract
Microtubule affinity regulating kinase (MARK4) is considered as a potential drug target for diabetes, cancer, and neurodegenerative diseases. Since the role of MARK4 in the phosphorylation of tau protein and subsequently Alzheimer's disease has been established, therefore, we have investigated the binding affinity and MARK4 inhibitory potential of cholic acid (CHA) using both computational and spectroscopic methods. Molecular docking suggested a strong binding of CHA to the functionally important residues of MARK4. We further performed 500 ns molecular dynamics simulation which suggested the MARK4-CHA system was quite stable throughout the simulation trajectory. CHA potential binds to the MARK4 with a binding constant (K) of 107 M-1 at 288 K. Further, MARK4 activity was inhibited by CHA with an IC50 = 5.5 μM. Further insights into the thermodynamic parameters suggested that MARK4-CHA complex formation is driven by both electrostatic and van der Waals interactions. Overall study provides a rationale to use CHA in the drug development via MARK4 inhibition, towards possible therapeutic implications in neurodegenerative diseases.
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Affiliation(s)
- Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Rajiv K Kar
- Fritz Haber Center for Molecular Dynamic Research, Hebrew University of Jerusalem, Israel
| | - Aarfa Queen
- Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India..
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20
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Ratha BN, Kar RK, Bednarikova Z, Gazova Z, Kotler SA, Raha S, De S, Maiti NC, Bhunia A. Molecular Details of a Salt Bridge and Its Role in Insulin Fibrillation by NMR and Raman Spectroscopic Analysis. J Phys Chem B 2020; 124:1125-1136. [PMID: 31958230 DOI: 10.1021/acs.jpcb.9b10349] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Insulin, a simple polypeptide hormone with huge biological importance, has long been known to self-assemble in vitro and form amyloid-like fibrillar aggregates. Utilizing high-resolution NMR, Raman spectroscopy, and computational analysis, we demonstrate that the fluctuation of the carboxyl terminal (C-ter) residues of the insulin B-chain plays a key role in the growth phase of insulin aggregation. By comparing the insulin sourced from bovine, human, and the modified glargine (GI), we observed reduced aggregation propensity in the GI variant, resulting from two additional Arg residues at its C-ter. NMR analysis showed atomic contacts and residue-specific interactions, particularly the salt bridge and H-bond formed among the C-ter residues Arg31B, Lys29B, and Glu4A. These inter-residue interactions were reflected in strong nuclear Overhauser effects among Arg31BδH-Glu4AδH and Lys29BδHs-Glu4AδH in GI, as well as the associated downfield chemical shift of several A-chain amino terminal (N-ter) residues. The two additional Arg residues of GI, Arg31B and Arg32B, enhanced the stability of the GI native structure by strengthening the Arg31B, Lys29B, and Glu4A salt bridge, thus reducing extensive thermal distortion and fluctuation of the terminal residues. The high stability of the salt bridge retards tertiary collapse, a crucial biochemical event for oligomerization and subsequent fibril formation. Circular dichroism and Raman spectroscopic measurement also suggest slow structural distortion in the early phase of the aggregation of GI because of the restricted mobility of the C-ter residues as explained by NMR. In addition, the structural and dynamic parameters derived from molecular dynamics simulations of insulin variants highlight the role of residue-specific contacts in aggregation and amyloid-like fibril formation.
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Affiliation(s)
- Bhisma N Ratha
- Department of Biophysics , Bose Institute , P-1/12 CIT Scheme VII (M) , Kolkata 700054 , India
| | - Rajiv K Kar
- Department of Biophysics , Bose Institute , P-1/12 CIT Scheme VII (M) , Kolkata 700054 , India
| | - Zuzana Bednarikova
- Department of Biophysics , Institute of Experimental Physics Slovak Academy of Sciences , Kosice 040 01 , Slovakia
| | - Zuzana Gazova
- Department of Biophysics , Institute of Experimental Physics Slovak Academy of Sciences , Kosice 040 01 , Slovakia
| | - Samuel A Kotler
- National Center for Advancing Translational Sciences , National Institutes of Health , Rockville , Maryland 20850 , United States
| | - Sreyan Raha
- Department of Physics , Bose Institute , 93/1 APC Road , Kolkata 700009 , India
| | - Soumya De
- School of Bioscience , IIT Kharagpur , Kharagpur 721302 , India
| | - Nakul C Maiti
- Division Structural Biology and Bioinformatics , CSIR-Indian Institute of Chemical Biology , Kolkata 700032 , India
| | - Anirban Bhunia
- Department of Biophysics , Bose Institute , P-1/12 CIT Scheme VII (M) , Kolkata 700054 , India
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21
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Anwar S, Kar RK, Haque MA, Dahiya R, Gupta P, Islam A, Ahmad F, Hassan MI. Effect of pH on the structure and function of pyruvate dehydrogenase kinase 3: Combined spectroscopic and MD simulation studies. Int J Biol Macromol 2020; 147:768-777. [PMID: 31982536 DOI: 10.1016/j.ijbiomac.2020.01.218] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 12/22/2022]
Abstract
Pyruvate dehydrogenase kinase-3 (PDK3) plays important role in the glucose metabolism and is associated with cancer progression, and thus being considered as an attractive target for cancer therapy. In this study, we employed spectroscopic techniques to study the structural and conformational changes in the PDK3 at varying pH conditions ranging from pH 2.0 to 12.0. UV/Vis, fluorescence and circular dichroism spectroscopic measurements revealed that PDK3 maintains its native-like structure (both secondary and tertiary) in the alkaline conditions (pH 7.0-12.0). However, a significant loss in the structure was observed under acidic conditions (pH 2.0-6.0). The propensity of aggregate formation at pH 4.0 was estimated by thioflavin T fluorescence measurements. To further complement structural data, kinase activity assay was performed, and maximum activity of PDK3 was observed at pH 7.0-8.0 range; whereas, its activity was lost under acidic pH. To further see conformational changes at atomistic level we have performed all-atom molecular dynamics at different pH conditions for 150 ns. A well defined correlation was observed between experimental and computational studies. This work highlights the significance of structural dependence of pH for wide implications in protein-protein interaction, biological function and drug design procedures.
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Affiliation(s)
- Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Rajiv K Kar
- Fritz Haber Center for Molecular Dynamic Research, Hebrew University of Jerusalem, Israel
| | - Md Anzarul Haque
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Rashmi Dahiya
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Preeti Gupta
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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22
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Ding Y, Kiryutin AS, Yurkovskaya AV, Sosnovsky DV, Sagdeev RZ, Bannister S, Kottke T, Kar RK, Schapiro I, Ivanov KL, Matysik J. Nuclear spin-hyperpolarization generated in a flavoprotein under illumination: experimental field-dependence and theoretical level crossing analysis. Sci Rep 2019; 9:18436. [PMID: 31804538 PMCID: PMC6895156 DOI: 10.1038/s41598-019-54671-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 11/15/2019] [Indexed: 11/25/2022] Open
Abstract
The solid-state photo-chemically induced dynamic nuclear polarization (photo-CIDNP) effect generates non-equilibrium nuclear spin polarization in frozen electron-transfer proteins upon illumination and radical-pair formation. The effect can be observed in various natural photosynthetic reaction center proteins using magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy, and in a flavin-binding light-oxygen-voltage (LOV) domain of the blue-light receptor phototropin. In the latter system, a functionally instrumental cysteine has been mutated to interrupt the natural cysteine-involving photochemistry allowing for an electron transfer from a more distant tryptophan to the excited flavin mononucleotide chromophore. We explored the solid-state photo-CIDNP effect and its mechanisms in phototropin-LOV1-C57S from the green alga Chlamydomonas reinhardtii by using field-cycling solution NMR. We observed the 13C and, to our knowledge, for the first time, 15N photo-CIDNP signals from phototropin-LOV1-C57S. Additionally, the 1H photo-CIDNP signals of residual water in the deuterated buffer of the protein were detected. The relative strengths of the photo-CIDNP effect from the three types of nuclei, 1H, 13C and 15N were measured in dependence of the magnetic field, showing their maximum polarizations at different magnetic fields. Theoretical level crossing analysis demonstrates that anisotropic mechanisms play the dominant role at high magnetic fields.
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Affiliation(s)
- Yonghong Ding
- Institut für Analytische Chemie, Universität Leipzig, Linnéstr. 3, 04103, Leipzig, Germany
| | - Alexey S Kiryutin
- International Tomography Center, Siberian Branch of Russian Academy of Sciences, Institutskaya, 3а, Novosibirsk, 630090, Russia
- Novosibirsk State University, Pirogova 1, Novosibirsk, 630090, Russia
| | - Alexandra V Yurkovskaya
- International Tomography Center, Siberian Branch of Russian Academy of Sciences, Institutskaya, 3а, Novosibirsk, 630090, Russia
- Novosibirsk State University, Pirogova 1, Novosibirsk, 630090, Russia
| | - Denis V Sosnovsky
- International Tomography Center, Siberian Branch of Russian Academy of Sciences, Institutskaya, 3а, Novosibirsk, 630090, Russia
- Novosibirsk State University, Pirogova 1, Novosibirsk, 630090, Russia
| | - Renad Z Sagdeev
- International Tomography Center, Siberian Branch of Russian Academy of Sciences, Institutskaya, 3а, Novosibirsk, 630090, Russia
- Novosibirsk State University, Pirogova 1, Novosibirsk, 630090, Russia
| | - Saskia Bannister
- Physical and Biophysical Chemistry, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Rajiv K Kar
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Konstantin L Ivanov
- International Tomography Center, Siberian Branch of Russian Academy of Sciences, Institutskaya, 3а, Novosibirsk, 630090, Russia
- Novosibirsk State University, Pirogova 1, Novosibirsk, 630090, Russia
| | - Jörg Matysik
- Institut für Analytische Chemie, Universität Leipzig, Linnéstr. 3, 04103, Leipzig, Germany.
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23
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Ratha BN, Kar RK, Kalita S, Kalita S, Raha S, Singha A, Garai K, Mandal B, Bhunia A. Sequence specificity of amylin-insulin interaction: a fragment-based insulin fibrillation inhibition study. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2019; 1867:405-415. [DOI: 10.1016/j.bbapap.2019.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/03/2019] [Accepted: 01/13/2019] [Indexed: 01/10/2023]
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24
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Kar RK, Brender JR, Ghosh A, Bhunia A. Nonproductive Binding Modes as a Prominent Feature of Aβ 40 Fiber Elongation: Insights from Molecular Dynamics Simulation. J Chem Inf Model 2018; 58:1576-1586. [PMID: 30047732 DOI: 10.1021/acs.jcim.8b00169] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The formation of amyloid fibers has been implicated in a number of neurodegenerative diseases. The growth of amyloid fibers is strongly thermodynamically favorable, but kinetic traps exist where the incoming monomer binds in an incompatible conformation that blocks further elongation. Unfortunately, this process is difficult to follow experimentally at the atomic level. It is also too complex to simulate in full detail and to date has been explored either through coarse-grained simulations, which may miss many important interactions, or full atomic simulations, in which the incoming peptide is constrained to be near the ideal fiber geometry. Here we use an alternate approach starting from a docked complex in which the monomer is from an experimental NMR structure of one of the major conformations in the unbound ensemble, a largely unstructured peptide with the central hydrophobic region in a 310 helix. A 1000 ns full atomic simulation in explicit solvent shows the formation of a metastable intermediate by sequential, concerted movements of both the fiber and the monomer. A Markov state model shows that the unfolded monomer is trapped at the end of the fiber in a set of interconverting antiparallel β-hairpin conformations. The simulation here may serve as a model for the binding of other non-β-sheet conformations to amyloid fibers.
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Affiliation(s)
- Rajiv K Kar
- Department of Biophysics , Bose Institute , P-1/12 CIT Scheme VII (M) , Kolkata 700054 , India
| | - Jeffrey R Brender
- Radiation Biology Branch , National Institutes of Health , Bethesda , Maryland 20814 , United States
| | - Anirban Ghosh
- Department of Biophysics , Bose Institute , P-1/12 CIT Scheme VII (M) , Kolkata 700054 , India
| | - Anirban Bhunia
- Department of Biophysics , Bose Institute , P-1/12 CIT Scheme VII (M) , Kolkata 700054 , India
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Mukherjee S, Kar RK, Nanga RPR, Mroue KH, Ramamoorthy A, Bhunia A. Accelerated molecular dynamics simulation analysis of MSI-594 in a lipid bilayer. Phys Chem Chem Phys 2018; 19:19289-19299. [PMID: 28702543 DOI: 10.1039/c7cp01941f] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multidrug resistance against the existing antibiotics is one of the most challenging threats across the globe. Antimicrobial peptides (AMPs), in this regard, are considered to be one of the effective alternatives that can overcome bacterial resistance. MSI-594, a 24-residue linear alpha-helical cationic AMP, has been shown to function via the carpet mechanism to disrupt bacterial membrane systems. To better understand the role of lipid composition in the function of MSI-594, in the present study, eight different model membrane systems have been studied using accelerated molecular dynamics (aMD) simulations. The simulated results are helpful in discriminating the particular effects of cationic MSI-594 against zwitterionic POPC, anionic POPG and POPS, and neutral POPE lipid moieties. Additionally, the effects of various heterogeneous POPC/POPG (7 : 3), POPC/POPS (7 : 3), and POPG/POPE (1 : 3 and 3 : 1) bilayer systems on the dynamic interaction of MSI-594 have also been investigated. The effect on the lipid bilayer due to the interaction with the peptide is characterized by lipid acyl-chain order, membrane thickness, and acyl-chain dynamics. Our simulation results show that the lipid composition affects the membrane interaction of MSI-594, suggesting that membrane selectivity is crucial to its mechanism of action. The results reported in this study are helpful to obtain accurate atomistic-level information governing MSI-594 and its membrane disruptive antimicrobial mechanism of action, and to design next generation potent antimicrobial peptides.
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Affiliation(s)
- Shruti Mukherjee
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700 054, India.
| | - Rajiv K Kar
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700 054, India.
| | - Ravi Prakash Reddy Nanga
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA. and Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kamal H Mroue
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700 054, India.
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26
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Datta A, Yadav V, Ghosh A, Choi J, Bhattacharyya D, Kar RK, Ilyas H, Dutta A, An E, Mukhopadhyay J, Lee D, Sanyal K, Ramamoorthy A, Bhunia A. Mode of Action of a Designed Antimicrobial Peptide: High Potency against Cryptococcus neoformans. Biophys J 2017; 111:1724-1737. [PMID: 27760359 DOI: 10.1016/j.bpj.2016.08.032] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 08/11/2016] [Accepted: 08/29/2016] [Indexed: 12/11/2022] Open
Abstract
There is a significant need for developing compounds that kill Cryptococcus neoformans, the fungal pathogen that causes meningoencephalitis in immunocompromised individuals. Here, we report the mode of action of a designed antifungal peptide, VG16KRKP (VARGWKRKCPLFGKGG) against C. neoformans. It is shown that VG16KRKP kills fungal cells mainly through membrane compromise leading to efflux of ions and cell metabolites. Intracellular localization, inhibition of in vitro transcription, and DNA binding suggest a secondary mode of action for the peptide, hinting at possible intracellular targets. Atomistic structure of the peptide determined by NMR experiments on live C. neoformans cells reveals an amphipathic arrangement stabilized by hydrophobic interactions among A2, W5, and F12, a conventional folding pattern also known to play a major role in peptide-mediated Gram-negative bacterial killing, revealing the importance of this motif. These structural details in the context of live cell provide valuable insights into the design of potent peptides for effective treatment of human and plant fungal infections.
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Affiliation(s)
- Aritreyee Datta
- Department of Biophysics, P-1/12 CIT Scheme VII (M), Kolkata, India
| | - Vikas Yadav
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Anirban Ghosh
- Department of Biophysics, P-1/12 CIT Scheme VII (M), Kolkata, India
| | - Jaesun Choi
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul, Korea
| | | | - Rajiv K Kar
- Department of Biophysics, P-1/12 CIT Scheme VII (M), Kolkata, India
| | - Humaira Ilyas
- Department of Biophysics, P-1/12 CIT Scheme VII (M), Kolkata, India
| | | | - Eunseol An
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul, Korea
| | | | - Dongkuk Lee
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul, Korea
| | - Kaustuv Sanyal
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | | | - Anirban Bhunia
- Department of Biophysics, P-1/12 CIT Scheme VII (M), Kolkata, India.
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27
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Roy A, Dutta A, Roy D, Ganguly P, Ghosh R, Kar RK, Bhunia A, Mukhopadhyay J, Chaudhuri S. Deciphering the role of the AT-rich interaction domain and the HMG-box domain of ARID-HMG proteins of Arabidopsis thaliana. Plant Mol Biol 2016; 92:371-88. [PMID: 27503561 DOI: 10.1007/s11103-016-0519-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 07/28/2016] [Indexed: 05/22/2023]
Abstract
ARID-HMG DNA-binding proteins represent a novel group of HMG-box containing protein family where the AT-rich interaction domain (ARID) is fused with the HMG-box domain in a single polypeptide chain. ARID-HMG proteins are highly plant specific with homologs found both in flowering plants as well as in moss such as Physcomitrella. The expression of these proteins is ubiquitous in plant tissues and primarily localises in the cell nucleus. HMGB proteins are involved in several nuclear processes, but the role of ARID-HMG proteins in plants remains poorly explored. Here, we performed DNA-protein interaction studies with Arabidopsis ARID-HMG protein HMGB11 (At1g55650) to understand the functionality of this protein and its individual domains. DNA binding assays revealed that AtHMGB11 can bind double-stranded DNA with a weaker affinity (Kd = 475 ± 17.9 nM) compared to Arabidopsis HMGB1 protein (Kd = 39.8 ± 2.68 nM). AtHMGB11 also prefers AT-rich DNA as a substrate and shows structural bias for supercoiled DNA. Molecular docking of the DNA-AtHMGB11 complex indicated that the protein interacts with the DNA major groove, mainly through its ARID domain and the junction region connecting the ARID and the HMG-box domain. Also, predicted by the docking model, mutation of Lys(85) from the ARID domain and Arg(199) & Lys(202) from the junction region affects the DNA binding affinity of AtHMGB11. In addition, AtHMGB11 and its truncated form containing the HMG-box domain can not only promote DNA mini-circle formation but are also capable of inducing negative supercoils into relaxed plasmid DNA suggesting the involvement of this protein in several nuclear events. Overall, the study signifies that both the ARID and the HMG-box domain contribute to the optimal functioning of ARID-HMG protein in vivo.
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Affiliation(s)
- Adrita Roy
- Division of Plant Biology, Bose Institute, Kolkata, 700054, India
| | - Arkajyoti Dutta
- Department of Chemistry, Bose Institute, Kolkata, 700054, India
| | - Dipan Roy
- Division of Plant Biology, Bose Institute, Kolkata, 700054, India
| | - Payel Ganguly
- Division of Plant Biology, Bose Institute, Kolkata, 700054, India
| | - Ritesh Ghosh
- School of Biotechnology, Yeungnam University, Gyeongsan, 712-749, South Korea
| | - Rajiv K Kar
- Department of Biophysics, Bose Institute, Kolkata, 700054, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata, 700054, India
| | | | - Shubho Chaudhuri
- Division of Plant Biology, Bose Institute, Kolkata, 700054, India.
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28
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Roy A, Dutta A, Roy D, Ganguly P, Ghosh R, Kar RK, Bhunia A, Mukhopadhyay J, Chaudhuri S. Erratum to: Deciphering the role of the AT-rich interaction domain and the HMG-box domain of ARID-HMG proteins of Arabidopsis thaliana. Plant Mol Biol 2016; 92:389-390. [PMID: 27596368 DOI: 10.1007/s11103-016-0534-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Adrita Roy
- Division of Plant Biology, Bose Institute, Kolkata, 700054, India
| | - Arkajyoti Dutta
- Department of Chemistry, Bose Institute, Kolkata, 700054, India
| | - Dipan Roy
- Division of Plant Biology, Bose Institute, Kolkata, 700054, India
| | - Payel Ganguly
- Division of Plant Biology, Bose Institute, Kolkata, 700054, India
| | - Ritesh Ghosh
- School of Biotechnology, Yeungnam University, Gyeongsan, 712-749, South Korea
| | - Rajiv K Kar
- Department of Biophysics, Bose Institute, Kolkata, 700054, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata, 700054, India
| | | | - Shubho Chaudhuri
- Division of Plant Biology, Bose Institute, Kolkata, 700054, India.
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Bera S, Kar RK, Mondal S, Pahan K, Bhunia A. Structural Elucidation of the Cell-Penetrating Penetratin Peptide in Model Membranes at the Atomic Level: Probing Hydrophobic Interactions in the Blood-Brain Barrier. Biochemistry 2016; 55:4982-96. [PMID: 27532224 PMCID: PMC5014585 DOI: 10.1021/acs.biochem.6b00518] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cell-penetrating peptides (CPPs) have shown promise in nonpermeable therapeutic drug delivery, because of their ability to transport a variety of cargo molecules across the cell membranes and their noncytotoxicity. Drosophila antennapedia homeodomain-derived CPP penetratin (RQIKIWFQNRRMKWKK), being rich in positively charged residues, has been increasingly used as a potential drug carrier for various purposes. Penetratin can breach the tight endothelial network known as the blood-brain barrier (BBB), permitting treatment of several neurodegenerative maladies, including Alzheimer's disease, Parkinson's disease, and Huntington's disease. However, a detailed structural understanding of penetratin and its mechanism of action is lacking. This study defines structural features of the penetratin-derived peptide, DK17 (DRQIKIWFQNRRMKWKK), in several model membranes and describes a membrane-induced conformational transition of the DK17 peptide in these environments. A series of biophysical experiments, including high-resolution nuclear magnetic resonance spectroscopy, provides the three-dimensional structure of DK17 in different membranes mimicking the BBB or total brain lipid extract. Molecular dynamics simulations support the experimental results showing preferential binding of DK17 to particular lipids at atomic resolution. The peptide conserves the structure of the subdomain spanning residues Ile6-Arg11, despite considerable conformational variation in different membrane models. In vivo data suggest that the wild type, not a mutated sequence, enters the central nervous system. Together, these data highlight important structural and functional attributes of DK17 that could be utilized in drug delivery for neurodegenerative disorders.
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Affiliation(s)
- Swapna Bera
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII(M), Kolkata 700054, India
| | - Rajiv K Kar
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII(M), Kolkata 700054, India
| | - Susanta Mondal
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Kalipada Pahan
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
- Division of Research and Development, Jesse Brown Veterans Affairs Medical Center, 820 South Damen Avenue, Chicago, IL, USA
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII(M), Kolkata 700054, India
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Dikhit MR, Purkait B, Singh R, Sahoo BR, Kumar A, Kar RK, Ansari MY, Saini S, Abhishek K, Sahoo GC, Das S, Das P. Activity of a novel sulfonamide compound 2-nitro-N-(pyridin-2-ylmethyl)benzenesulfonamide against Leishmania donovani. Drug Des Devel Ther 2016; 10:1753-61. [PMID: 27307706 PMCID: PMC4887065 DOI: 10.2147/dddt.s96650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
New treatments for visceral leishmaniasis, caused by Leishmania donovani, are needed to overcome sustained toxicity, cost, and drug resistance. The aim of this study was to evaluate the therapeutic effects of 2-nitro-N-(pyridin-2-ylmethyl)benzenesulfonamide (2NB) against promastigote and amastigote forms of L. donovani and examine its effect in combination with amphotericin B (AmB) against AmB-resistant clinical isolates. Effects were assessed against extracellular promastigotes in vitro and intracellular amastigotes in L. donovani-infected macrophages. Levels of inducible nitric oxide and Th1 and Th2 cytokines were measured in infected 2NB-treated macrophages, and levels of reactive oxygen species and NO were measured in 2NB-treated macrophages. 2NB was active against promastigotes and intracellular amastigotes with 50% inhibitory concentration values of 38.5±1.5 µg/mL and 86.4±2.4 µg/mL, respectively. 2NB was not toxic to macrophages. Parasite titer was reduced by >85% in infected versus uninfected macrophages at a 2NB concentration of 120 µg/mL. The parasiticidal activity was associated with increased levels of Th1 cytokines, NO, and reactive oxygen species. Finally, 2NB increased the efficacy of AmB against AmB-resistant L. donovani. These results demonstrate 2NB to be an antileishmanial agent, opening up a new avenue for the development of alternative chemotherapies against visceral leishmaniasis.
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Affiliation(s)
- Manas R Dikhit
- Department of Molecular Parasitology and Biomedical Informatics, Rajendra Memorial Research Institute of Medical Sciences, Indian Council of Medical Research, Agamkuan, Patna, Bihar, India
| | - Bidyut Purkait
- Department of Molecular Parasitology and Biomedical Informatics, Rajendra Memorial Research Institute of Medical Sciences, Indian Council of Medical Research, Agamkuan, Patna, Bihar, India
| | - Ruby Singh
- Department of Molecular Parasitology and Biomedical Informatics, Rajendra Memorial Research Institute of Medical Sciences, Indian Council of Medical Research, Agamkuan, Patna, Bihar, India
| | - Bikash Ranjan Sahoo
- Laboratory of Molecular Biophysics, Institute for Protein Research, Osaka University, Japan
| | - Ashish Kumar
- Department of Molecular Parasitology and Biomedical Informatics, Rajendra Memorial Research Institute of Medical Sciences, Indian Council of Medical Research, Agamkuan, Patna, Bihar, India
| | - Rajiv K Kar
- Biomolecular Nuclear Magnetic Resonance and Drug Design Laboratory, Department of Biophysics, Bose Institute, Kolkata, West Bengal, India
| | - Md Yousuf Ansari
- Department of Molecular Parasitology and Biomedical Informatics, Rajendra Memorial Research Institute of Medical Sciences, Indian Council of Medical Research, Agamkuan, Patna, Bihar, India; Department of Pharmacoinformatics, Hajipur, India
| | - Savita Saini
- Department of Molecular Parasitology and Biomedical Informatics, Rajendra Memorial Research Institute of Medical Sciences, Indian Council of Medical Research, Agamkuan, Patna, Bihar, India; Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, India
| | - Kumar Abhishek
- Department of Molecular Parasitology and Biomedical Informatics, Rajendra Memorial Research Institute of Medical Sciences, Indian Council of Medical Research, Agamkuan, Patna, Bihar, India
| | - Ganesh C Sahoo
- Department of Molecular Parasitology and Biomedical Informatics, Rajendra Memorial Research Institute of Medical Sciences, Indian Council of Medical Research, Agamkuan, Patna, Bihar, India
| | - Sushmita Das
- Department of Microbiology, All India Institute of Medical Sciences, Patna, Bihar, India
| | - Pradeep Das
- Department of Molecular Parasitology and Biomedical Informatics, Rajendra Memorial Research Institute of Medical Sciences, Indian Council of Medical Research, Agamkuan, Patna, Bihar, India
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Kar RK, Gazova Z, Bednarikova Z, Mroue KH, Ghosh A, Zhang R, Ulicna K, Siebert HC, Nifantiev NE, Bhunia A. Evidence for Inhibition of Lysozyme Amyloid Fibrillization by Peptide Fragments from Human Lysozyme: A Combined Spectroscopy, Microscopy, and Docking Study. Biomacromolecules 2016; 17:1998-2009. [DOI: 10.1021/acs.biomac.6b00165] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rajiv K. Kar
- Department
of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Zuzana Gazova
- Department
of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
- Department
of Medical and Clinical Biochemistry Faculty of Medicine, Safarik University, Trieda SNP 1, 040 11 Kosice, Slovakia
| | - Zuzana Bednarikova
- Department
of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
- Department
of Biochemistry, Institute of Chemistry, Faculty of Science, Safarik University, Srobarova 2, 041 54 Kosice, Slovakia
| | - Kamal H. Mroue
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Anirban Ghosh
- Department
of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Ruiyan Zhang
- RI-B-NT Research
Institute
of Bioinformatics and Nanotechnology, Franziusallee 177, 24148 Kiel, Germany
| | - Katarina Ulicna
- Department
of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
- Institute
of Biology and Ecology, Faculty of Science, Safarik University, Srobarova 2, 041 54 Kosice, Slovakia
| | - Hans-Christian Siebert
- RI-B-NT Research
Institute
of Bioinformatics and Nanotechnology, Franziusallee 177, 24148 Kiel, Germany
| | - Nikolay E. Nifantiev
- N.
D. Zellinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - Anirban Bhunia
- Department
of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
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32
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Kar RK, Mroue KH, Kumar D, Tejo BA, Bhunia A. Structure and Dynamics of Antifreeze Protein–Model Membrane Interactions: A Combined Spectroscopic and Molecular Dynamics Study. J Phys Chem B 2016; 120:902-14. [DOI: 10.1021/acs.jpcb.5b11164] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rajiv K. Kar
- Department
of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700 054, India
| | - Kamal H. Mroue
- Biophysics
and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Dinesh Kumar
- Center
of Biomedical Magnetic Resonance, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Lucknow 226014, India
| | - Bimo A. Tejo
- Department
of Biotechnology, Surya University, Tangerang 15810, Indonesia
| | - Anirban Bhunia
- Department
of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700 054, India
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Bera S, Korshavn KJ, Kar RK, Lim MH, Ramamoorthy A, Bhunia A. Biophysical insights into the membrane interaction of the core amyloid-forming Aβ40fragment K16–K28 and its role in the pathogenesis of Alzheimer's disease. Phys Chem Chem Phys 2016; 18:16890-901. [DOI: 10.1039/c6cp02023b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Role of central hydrophobic region of Aβ40 in membrane interaction.
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Affiliation(s)
- Swapna Bera
- Department of Biophysics
- Bose Institute
- Kolkata 700 054
- India
| | | | - Rajiv K. Kar
- Department of Biophysics
- Bose Institute
- Kolkata 700 054
- India
| | - Mi Hee Lim
- Department of Chemistry
- Ulsan National Institute of Science and Technology (UNIST)
- Ulsan
- Republic of Korea
| | | | - Anirban Bhunia
- Department of Biophysics
- Bose Institute
- Kolkata 700 054
- India
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Kar RK, Bhunia A. Biophysical and biochemical aspects of antifreeze proteins: Using computational tools to extract atomistic information. Progress in Biophysics and Molecular Biology 2015; 119:194-204. [DOI: 10.1016/j.pbiomolbio.2015.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/04/2015] [Indexed: 01/09/2023]
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Affiliation(s)
- Rajiv K. Kar
- Department
of Biophysics, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, India
| | - Anirban Bhunia
- Department
of Biophysics, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, India
- Biophysics
and Department of Chemistry, University of Michigan, 930 N. University
Avenue, Ann Arbor, Michigan 48109, United States
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Ghosh A, Ratha BN, Gayen N, Mroue KH, Kar RK, Mandal AK, Bhunia A. Biophysical Characterization of Essential Phosphorylation at the Flexible C-Terminal Region of C-Raf with 14-3-3ζ Protein. PLoS One 2015; 10:e0135976. [PMID: 26295714 PMCID: PMC4546627 DOI: 10.1371/journal.pone.0135976] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 07/28/2015] [Indexed: 02/07/2023] Open
Abstract
Phosphorylation at the C-terminal flexible region of the C-Raf protein plays an important role in regulating its biological activity. Auto-phosphorylation at serine 621 (S621) in this region maintains C-Raf stability and activity. This phosphorylation mediates the interaction between C-Raf and scaffold protein 14-3-3ζ to activate the downstream MEK kinase pathway. In this study, we have defined the interaction of C-terminal peptide sequence of C-Raf with 14-3-3ζ protein and determined the possible structural adaptation of this region. Biophysical elucidation of the interaction was carried out using phosphopeptide (residue number 615–630) in the presence of 14-3-3ζ protein. Using isothermal titration calorimetry (ITC), a high binding affinity with micro-molar range was found to exist between the peptide and 14-3-3ζ protein, whereas the non-phosphorylated peptide did not show any appreciable binding affinity. Further interaction details were investigated using several biophysical techniques such as circular dichroism (CD), fluorescence, and nuclear magnetic resonance (NMR) spectroscopy, in addition to molecular modeling. This study provides the molecular basis for C-Raf C-terminal-derived phosphopeptide interaction with 14-3-3ζ protein as well as structural insights responsible for phosphorylated S621-mediated 14-3-3ζ binding at an atomic resolution.
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Affiliation(s)
- Anirban Ghosh
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata, 700 054, India
| | - Bhisma Narayan Ratha
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata, 700 054, India
| | - Nilanjan Gayen
- Department of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata, 700 054, India
| | - Kamal H. Mroue
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109–1055, United States of America
| | - Rajiv K. Kar
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata, 700 054, India
| | - Atin K. Mandal
- Department of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata, 700 054, India
- * E-mail: (AKM); (AB)
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata, 700 054, India
- * E-mail: (AKM); (AB)
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Ghosh S, Jana J, Kar RK, Chatterjee S, Dasgupta D. Plant alkaloid chelerythrine induced aggregation of human telomere sequence--a unique mode of association between a small molecule and a quadruplex. Biochemistry 2015; 54:974-86. [PMID: 25566806 DOI: 10.1021/bi501117x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Small molecules that interact with G-quadruplex structures formed by the human telomeric region and stabilize them have the potential to evolve as anticancer therapeutic agents. Herein we report the interaction of a putative anticancer agent from a plant source, chelerythrine, with the human telomeric DNA sequence. It has telomerase inhibitory potential as demonstrated from telomerase repeat amplification assay in cancer cell line extract. We have attributed this to the quadruplex binding potential of the molecule and characterized the molecular details of the interaction by means of optical spectroscopy such as absorbance and circular dichroism and calorimetric techniques such as isothermal titration calorimetry and differential scanning calorimetry. The results show that chelerythrine binds with micromolar dissociation constant and 2:1 binding stoichiometry to the human telomeric DNA sequence. Chelerythrine association stabilizes the G-quadruplex. Nuclear magnetic resonance spectroscopy ((1)H and (31)P) shows that chelerythrine binds to both G-quartet and phosphate backbone of the quadruplex leading to quadruplex aggregation. Molecular dynamics simulation studies support the above inferences and provide further insight into the mechanism of ligand binding. The specificity toward quartet binding for chelerythrine is higher compared to that of groove binding. MM-PBSA calculation mines out the energy penalty for quartet binding to be -4.7 kcal/mol, whereas that of the groove binding is -1.7 kcal/mol. We propose that the first chelerythrine molecule binds to the quartet followed by a second molecule which binds to the groove. This second molecule might bring about aggregation of the quadruplex structure which is evident from the results of nuclear magnetic resonance.
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Affiliation(s)
- Saptaparni Ghosh
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics , Block-AF, Sector-I, Bidhannagar, Kolkata-700064, India
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Saha T, Kar RK, Sa G. Structural and sequential context of p53: A review of experimental and theoretical evidence. Prog Biophys Mol Biol 2014; 117:250-263. [PMID: 25550083 DOI: 10.1016/j.pbiomolbio.2014.12.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/14/2014] [Accepted: 12/16/2014] [Indexed: 12/18/2022]
Abstract
Approximately 27 million people are suffering from cancer that contains either an inactivating missense mutation of TP53 gene or partially abrogated p53 signaling pathway. Concerted action of folded and intrinsically disordered domains accounts for multi-faceted role of p53. The intricacy of dynamic p53 structure is believed to shed light on its cellular activity for developing new cancer therapies. In this review, insights into structural details of p53, diverse single point mutations affecting its core domain, thermodynamic understanding and therapeutic strategies for pharmacological rescue of p53 function has been illustrated. An effort has been made here to bridge the structural and sequential evidence of p53 from experimental to computational studies. First, we focused on the individual domains and the crucial protein-protein or DNA-protein contacts that determine conformation and dynamic behavior of p53. Next, the oncogenic mutations associated with cancer and its contribution to thermodynamic fluctuation has been discussed. Thus the emerging anti-cancer strategies include targeting of destabilized cancer mutants with selective inhibition of its negative regulators. Recent advances in development of small molecule inhibitors and peptides exploiting p53-MDM2 interaction has been included. In a nutshell, this review attempts to describe structural biology of p53 which provide new openings for structure-guided rescue.
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Affiliation(s)
- Taniya Saha
- Division of Molecular Medicine, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, India
| | - Rajiv K Kar
- Division of Biophysics, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, India
| | - Gaurisankar Sa
- Division of Molecular Medicine, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, India.
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Sudheendra US, Dhople V, Datta A, Kar RK, Shelburne CE, Bhunia A, Ramamoorthy A. Membrane disruptive antimicrobial activities of human β-defensin-3 analogs. Eur J Med Chem 2014; 91:91-9. [PMID: 25112689 DOI: 10.1016/j.ejmech.2014.08.021] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 08/05/2014] [Accepted: 08/06/2014] [Indexed: 01/26/2023]
Abstract
Human beta defensin-3 (HβD-3) is a host-defense protein exhibiting antibacterial activity towards both Gram-negative and Gram-positive bacteria. There is considerable interest in the function of this protein due to its increased salt tolerance and activity against Gram-positive Staphylococcus aureus. In this study, analogs of HβD-3 devoid of N and C terminal regions are investigated to determine the influence of specific structural motif on antimicrobial activity and selectivity between Gram-positive and Gram-negative bacteria. Circular dichroism, fluorescence and solid-state NMR experiments have been used to investigate the conformation and mode of action of HβD3 analogs with various model membranes to mimic bacterial inner and outer membranes and also mammalian membranes. Our studies specifically focused on determining four major characteristics: (i) interaction of HβD3 analogs with phospholipid vesicles composed of zwitterionic PC or anionic PE:PG vesicles and LPS; (ii) conformation of HβD3-peptide analogs in the presence of PC or PE:PG vesicles; (iii) ability of HβD3 analogs to permeate phospholipid vesicles composed of PC or PE:PG; and (iv) activities on bacteria cells and erythrocytes. Our results infer that the linear peptide L25P and its cyclic form C25P are more active than L21P and C21P analogs. However, they are less active than the parent peptide, thus pointing towards the importance of the N terminal domain in its biological activity. The variation in the activities of L21P/C21P and L25P/C25P also suggest the importance of the positively charged residues at the C terminus in providing selectivity particularly to Gram-negative bacteria.
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Affiliation(s)
- U S Sudheendra
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Vishnu Dhople
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Aritreyee Datta
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Rajiv K Kar
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Charles E Shelburne
- Department of Biologic and Materials Sciences, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India.
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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Abstract
Regulation of stomatal aperture is crucial in terrestrial plants for controlling water loss and gaseous exchange with environment. While much is known of signaling for stomatal opening induced by blue light and the role of hormones, little is known about the regulation of stomatal closing in darkness. The present study was aimed to verify their role in stomatal regulation in darkness. Epidermal peelings from the leaves of Commelina benghalensis were incubated in a defined medium in darkness for 1 h followed by a 1 h incubation in different test solutions [H2O2, propyl gallate, ethrel (ethylene), AgNO3, sodium orthovanadate, tetraethyl ammonium chloride, CaCl2, LaCl3, separately and in combination] before stomatal apertures were measured under the microscope. In the dark stomata remained closed under treatments with ethylene and propyl gallate but opened widely in the presence of H2O2 and AgNO3. The opening effect was largely unaffected by supplementing the treatment with Na-vanadate (PM H+ ATPase inhibitor) and tetraethyl ammonium chloride (K(+)-channel inhibitor) except that opening was significantly inhibited by the latter in presence of H2O2. On the other hand, H2O2 could not override the closing effect of ethylene at any concentrations while a marginal opening of stomata was found when Ag NO3 treatment was given together with propyl gallate. CaCl2 treatment opened stomata in the darkness while LaCl3 maintained stomata closed. A combination of LaCl3 and propyl gallate strongly promoted stomatal opening. A probable action of ethylene in closing stomata of Commelina benghalensis in dark has been proposed.
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Affiliation(s)
- R K Kar
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Visva-Bharati University, Santiniketan-731 235, West Bengal, India
| | - N Parvin
- Department of Botany, Biology-1, Biocentre, Ludwig Maximillians, University of Munich, 82152 Martinsried, Germany
| | - D Laha
- Centre for Plant Molecular Biology, Eberhard Karls, University of Tuebingen, Auf der Morgenstelle 1, 72076 Tuebingen, Germany
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Hossain DMS, Panda AK, Manna A, Mohanty S, Bhattacharjee P, Bhattacharyya S, Saha T, Chakraborty S, Kar RK, Das T, Chatterjee S, Sa G. FoxP3 acts as a cotranscription factor with STAT3 in tumor-induced regulatory T cells. Immunity 2013; 39:1057-69. [PMID: 24315995 DOI: 10.1016/j.immuni.2013.11.005] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 11/12/2013] [Indexed: 01/10/2023]
Abstract
FoxP3, a lineage-specification factor, executes its multiple activities mostly through transcriptional regulation of target genes. We identified an interleukin-10 (IL-10)-producing FoxP3(+) T regulatory cell population that contributes to IL-10-dependent type 2 cytokine bias in breast-cancer patients. Although genetic ablation of FOXP3 inhibited IL10 transcription, genome-wide analysis ruled out its role as a transcription factor for IL10. In-depth analysis revealed that histone acetyl transterase-1, in association with FoxP3, modified the IL10 promoter epigenetically, making a space for docking STAT3-FoxP3 complexes. A predictive docking module with target-receptor specificity, along with exon-deletion and site-directed mutagenesis studies, showed that STAT3 binds through its N-terminal floppy domain to the exon 2 β sheet region of FoxP3 to form STAT3-FoxP3 complexes. Such cotranscriptional activity of FoxP3 extended to other STAT3-target genes that lack FoxP3-binding sites. These results suggest a function of FoxP3, where, failing to achieve direct promoter occupancy, FoxP3 promotes transcription in association with the locus-specific transcription factor STAT3.
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Affiliation(s)
- Dewan Md Sakib Hossain
- Division of Molecular Medicine, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, India
| | - Abir K Panda
- Division of Molecular Medicine, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, India
| | - Argha Manna
- Division of Molecular Medicine, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, India
| | - Suchismita Mohanty
- Division of Molecular Medicine, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, India
| | - Pushpak Bhattacharjee
- Division of Molecular Medicine, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, India
| | - Sankar Bhattacharyya
- Division of Molecular Medicine, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, India
| | - Taniya Saha
- Division of Molecular Medicine, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, India
| | - Sreeparna Chakraborty
- Division of Molecular Medicine, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, India
| | - Rajiv K Kar
- Department of Biophysics, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, India
| | - Tanya Das
- Division of Molecular Medicine, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, India
| | - Gaurisankar Sa
- Division of Molecular Medicine, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, India.
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Banerjee V, Kar RK, Datta A, Parthasarathi K, Chatterjee S, Das KP, Bhunia A. Use of a small peptide fragment as an inhibitor of insulin fibrillation process: a study by high and low resolution spectroscopy. PLoS One 2013; 8:e72318. [PMID: 24009675 PMCID: PMC3756998 DOI: 10.1371/journal.pone.0072318] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 07/10/2013] [Indexed: 01/13/2023] Open
Abstract
A non-toxic, nine residue peptide, NIVNVSLVK is shown to interfere with insulin fibrillation by various biophysical methods. Insulin undergoes conformational changes under certain stress conditions leading to amyloid fibrils. Fibrillation of insulin poses a problem in its long-term storage, reducing its efficacy in treating type II diabetes. The dissociation of insulin oligomer to monomer is the key step for the onset of fibrillation. The time course of insulin fibrillation at 62°C using Thioflavin T fluorescence shows an increase in the lag time from 120 min without peptide to 236 min with peptide. Transmission electron micrographs show branched insulin fibrils in its absence and less inter-fibril association in its presence. Upon incubation at 62°C and pH 2.6, insulin lost some α-helical structure as seen by Fourier transformed infra-red spectroscopy (FT-IR), but if the peptide is added, secondary structure is almost fully maintained for 3 h, though lost partially at 4 h. FT-IR spectroscopy also shows that insulin forms the cross beta structure indicative of fibrils beyond 2 h, but in the presence of the peptide, α-helix retention is seen till 4 h. Both size exclusion chromatography and dynamic light scattering show that insulin primarily exists as trimer, whose conversion to a monomer is resisted by the peptide. Saturation transfer difference nuclear magnetic resonance confirms that the hydrophobic residues in the peptide are in close contact with an insulin hydrophobic groove. Molecular dynamics simulations in conjunction with principal component analyses reveal how the peptide interrupts insulin fibrillation. In vitro hemolytic activity of the peptide showed insignificant cytotoxicity against HT1080 cells. The insulin aggregation is probed due to the inter play of two key residues, Phe(B24) and Tyr(B26) monitored from molecular dynamics simulations studies. Further new peptide based leads may be developed from this nine residue peptide.
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Affiliation(s)
| | - Rajiv K. Kar
- Biomolecular NMR and Drug Design Laboratory, Department of Biophysics, Bose Institute, Kolkata, India
| | - Aritreyee Datta
- Biomolecular NMR and Drug Design Laboratory, Department of Biophysics, Bose Institute, Kolkata, India
| | | | - Subhrangsu Chatterjee
- Biomolecular NMR and Drug Design Laboratory, Department of Biophysics, Bose Institute, Kolkata, India
| | - Kali P. Das
- Department of Chemistry, Bose Institute, Kolkata, India
| | - Anirban Bhunia
- Biomolecular NMR and Drug Design Laboratory, Department of Biophysics, Bose Institute, Kolkata, India
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Kar RK, Suryadevara P, Sahoo BR, Sahoo GC, Dikhit MR, Das P. Exploring novel KDR inhibitors based on pharmaco-informatics methodology. SAR QSAR Environ Res 2013; 24:215-234. [PMID: 23437769 DOI: 10.1080/1062936x.2013.765912] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Kinase-insert domain-containing receptor (KDR) is one of the important mediators of Vascular endothelial growth factor (VEGF) function in endothelial cells. Inhibition of KDR can be therapeutically advantageous for treatment of a number of diseases. The present study focuses on exploring novel KDR inhibitors by means of pharmaco-informatics methodologies. Three-dimensional quantitative structure-activity relationship (3D-QSAR) analysis by atom-based pharmacophore mapping over a set of 85 molecules provides a proposition regarding the molecular fingerprint that can be optimized for designing more active inhibitors. The model was statistically validated with Q(2) = 0.865 for training and r(2) = 0.789, Pearson-r = 0.903 for test set molecules; r(2)(0.925) by external validation suggests model robustness and indicates it as a strong query for screening any compound library. Virtual screening shows the importance of active site and hinge region residue for interaction with KDR inhibitors. Remarkably the retrieved hits contain a urea backbone, implicating urea derivatives as promising candidate for designing KDR inhibitors. The hydrophobicity of active site, which has until now been overlooked, has been raised into the picture by this study. This can impact on KDR drug development. The study thus quantifies crucial structural requirements necessary for a favourable interaction with the receptor binding site while the cooperative pattern provides important structural clues to chemists for framing potent medicinal agents in future.
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Affiliation(s)
- R K Kar
- Biomedical Informatics Centre, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
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Shah SHH, Kar RK, Asmawi AA, Rahman MBA, Murad AMA, Mahadi NM, Basri M, Rahman RNZA, Salleh AB, Chatterjee S, Tejo BA, Bhunia A. Solution structures, dynamics, and ice growth inhibitory activity of peptide fragments derived from an antarctic yeast protein. PLoS One 2012; 7:e49788. [PMID: 23209600 PMCID: PMC3509122 DOI: 10.1371/journal.pone.0049788] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 10/12/2012] [Indexed: 12/04/2022] Open
Abstract
Exotic functions of antifreeze proteins (AFP) and antifreeze glycopeptides (AFGP) have recently been attracted with much interest to develop them as commercial products. AFPs and AFGPs inhibit ice crystal growth by lowering the water freezing point without changing the water melting point. Our group isolated the Antarctic yeast Glaciozyma antarctica that expresses antifreeze protein to assist it in its survival mechanism at sub-zero temperatures. The protein is unique and novel, indicated by its low sequence homology compared to those of other AFPs. We explore the structure-function relationship of G. antarctica AFP using various approaches ranging from protein structure prediction, peptide design and antifreeze activity assays, nuclear magnetic resonance (NMR) studies and molecular dynamics simulation. The predicted secondary structure of G. antarctica AFP shows several α-helices, assumed to be responsible for its antifreeze activity. We designed several peptide fragments derived from the amino acid sequences of α-helical regions of the parent AFP and they also showed substantial antifreeze activities, below that of the original AFP. The relationship between peptide structure and activity was explored by NMR spectroscopy and molecular dynamics simulation. NMR results show that the antifreeze activity of the peptides correlates with their helicity and geometrical straightforwardness. Furthermore, molecular dynamics simulation also suggests that the activity of the designed peptides can be explained in terms of the structural rigidity/flexibility, i.e., the most active peptide demonstrates higher structural stability, lower flexibility than that of the other peptides with lower activities, and of lower rigidity. This report represents the first detailed report of downsizing a yeast AFP into its peptide fragments with measurable antifreeze activities.
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Affiliation(s)
- Syed Hussinien H. Shah
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Rajiv K. Kar
- Department of Biophysics, Bose Institute, Kolkata, West Bengal, India
| | - Azren A. Asmawi
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | | | | | - Nor M. Mahadi
- Malaysia Genome Institute, UKM Bangi, Selangor, Malaysia
| | - Mahiran Basri
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha A. Rahman
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Abu B. Salleh
- Malaysia Genome Institute, UKM Bangi, Selangor, Malaysia
| | | | - Bimo A. Tejo
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata, West Bengal, India
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Abstract
Light treatment markedly accelerated chlorophyll loss in Hydrilla (Hydrilla verticillata [L.f.] Royle) over dark treatment whereas such acceleration could not be observed in spinach (Spinacia oleracea L.) leaf segments. Spermine, a polyamine, retarded the loss of chlorophyll in the dark but markedly accelerated this loss in the light during senescence of Hydrilla leaves. However, such effect of spermine in the dark was not so pronounced in spinach. The loss of protein was slower in the light than in the dark in both the species. Spermine arrested the loss of protein (as in spinach) or even raised the protein level over initial (as in Hydrilla). Loss of both soluble and insoluble protein was slower in light than in darkness. Spermine treatment, either in light or darkness, markedly accelerated the loss of soluble protein but raised the level of insoluble protein over initial in both the species. The pattern of change in alpha-amino nitrogen in either species could be correlated well with that of protein level. In Hydrilla, light increased the soluble protein fraction over initial and this rise was prevented by cycloheximide and not by chloramphenicol. Also, spermine augmented the protease activity (both acid and neutral) while light retarded the rise in protease activity during senescence of either species. Although spermine treatment reduced the leaching of alpha-amino nitrogen and electrolytes in Hydrilla, it augmented the same in spinach.
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Affiliation(s)
- R K Kar
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Burdwan University, Burdwan 713104, India
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