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Meher K, Paithankar H, Hosur RV, Lopus M. Antiproliferative efficacy and mechanism of action of garlic phytochemicals-functionalized gold nanoparticles in triple-negative breast cancer cells. Biomed Mater 2024; 19:035039. [PMID: 38682577 DOI: 10.1088/1748-605x/ad3ff9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/17/2024] [Indexed: 05/01/2024]
Abstract
Fabrication of gold nanoparticles (GNPs) with phytochemicals is an emerging green nanotechnology approach with therapeutic implications. Garlic, known for its culinary and medicinal properties, has been extensively investigated for its anticancer properties. Here, we report a method to substantially enhance the antiproliferative potency of garlic by functionalizing its phytochemicals to GNPs and demonstrate a possible mechanism of action of these nanoparticles in the triple-negative breast cancer cell line, MDA-MB-231. Garlic gold nanoparticles (As-GNPs) were synthesized using garlic extract (As-EX) and gold chloride and characterized using a variety of spectroscopy techniques, and transmission electron microscopy (TEM). Compared to As-EX, which has a negligible effect on the viability of the cells, As-GNPs inhibited cell viability with an IC50of 0.310 ± 0.04 mg ml-1and strongly inhibited the clonogenic and migratory propensities of these cells. As indicated by TEM, the As-GNPs entered the cells via endocytosis and dispersed in the cellular milieu. Since tubulin, the protein involved in cell division, is a verified target for several antiproliferative drugs, we next examined whether the As-GNPs interact with this protein. The As-GNPs showed concentration-dependent binding to purified tubulin, slightly but consistently perturbing its secondary helical integritywithout grossly damaging the tertiary structure of the protein or the net polymer mass of the microtubules, as indicated by a tryptophan-quenching assay, far UV-circular dichroism spectroscopy, anilinonaphthalene sulfonate-binding assay, and polymer mass analysis, respectively. In cells, As-GNPs killed the cancer cells without cell cycle arrest, as evidenced by flow cytometry.
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Affiliation(s)
- Kimaya Meher
- School of Biological Sciences, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Mumbai 400098, India
| | - Harshad Paithankar
- School of Chemical Sciences, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Mumbai 400098, India
| | - Ramakrishna V Hosur
- School of Chemical Sciences, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Mumbai 400098, India
| | - Manu Lopus
- School of Biological Sciences, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Mumbai 400098, India
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Shukla S, Bhattacharya A, Sehrawat P, Agarwal P, Shobhawat R, Malik N, Duraisamy K, Rangan NS, Hosur RV, Kumar A. Disorder in CENP-A Cse4 tail-chaperone interaction facilitates binding with Ame1/Okp1 at the kinetochore. Structure 2024:S0969-2126(24)00084-4. [PMID: 38565139 DOI: 10.1016/j.str.2024.03.002] [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: 02/06/2023] [Revised: 11/16/2023] [Accepted: 03/06/2024] [Indexed: 04/04/2024]
Abstract
The centromere is epigenetically marked by a histone H3 variant-CENP-A. The budding yeast CENP-A called Cse4, consists of an unusually long N-terminus that is known to be involved in kinetochore assembly. Its disordered chaperone, Scm3 is responsible for the centromeric deposition of Cse4 as well as in the maintenance of a segregation-competent kinetochore. In this study, we show that the Cse4 N-terminus is intrinsically disordered and interacts with Scm3 at multiple sites, and the complex does not gain any substantial structure. Additionally, the complex forms a synergistic association with an essential inner kinetochore component (Ctf19-Mcm21-Okp1-Ame1), and a model has been suggested to this effect. Thus, our study provides mechanistic insights into the Cse4 N-terminus-chaperone interaction and also illustrates how intrinsically disordered proteins mediate assembly of complex multiprotein networks, in general.
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Affiliation(s)
- Shivangi Shukla
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | | | - Parveen Sehrawat
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Prakhar Agarwal
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Rahul Shobhawat
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Nikita Malik
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Kalaiyarasi Duraisamy
- Centre for Advanced Protein Studies, Syngene International Limited, Bangalore, India
| | | | - Ramakrishna V Hosur
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Ashutosh Kumar
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India.
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Upadhyay M, Hosur RV, Jha A, Bharti K, Mali PS, Jha AK, Mishra B, Kumar A. Myricetin encapsulated chitosan nanoformulation for management of type 2 diabetes: Preparation, optimization, characterization and in vivo activity. Biomater Adv 2023; 153:213542. [PMID: 37418933 DOI: 10.1016/j.bioadv.2023.213542] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/09/2023]
Abstract
Type 2 diabetes mellitus (T2DM) is a serious and alarming disease attracting widespread attention. It is not a single metabolic disease; over time, it leads to serious disorders, namely, diabetic nephropathy, neuropathy, retinopathy and several cardiovascular, hepatocellular complications. The increase in T2DM cases in recent times has attracted significant attention. Currently, the medications available have side effects, and injectables are painful, causing trauma to the patients. Therefore, it is imperative to come up with oral delivery. In this background we report here a nanoformulation carrying natural small molecule Myricetin (MYR) encapsulated within Chitosan nanoparticles (CHT-NPs). MYR-CHT-NPs were prepared by ionic gelation method and evaluated using different characterization techniques. The in vitro release of MYR from CHT NPs in different physiological media showed pH dependence. in vivo pharmacodynamic study followed by oral administration in Albino Wistar rats showed better glycaemic control than existing drug. Further, the optimized nanoparticles also exhibited controlled increase in weight as compared to Metformin. The biochemistry profile of rats treated with nanoformulation reduced the levels of several pathological biomarkers, indicating additional benefits of MYR. Histopathological images exhibited no toxicity or changes in the major organs section in contrast to normal control, suggesting safe oral administration of the encapsulated MYR. Thus, we conclude that MYR-CHT-NPs represent an attractive delivery vehicle in improving the blood glucose level with controlled weight and have the potential to be safely administered orally for the management of T2DM.
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Affiliation(s)
- Mansi Upadhyay
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Ramakrishna V Hosur
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Abhishek Jha
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (BHU) Varanasi, 221005, India
| | - Kanchan Bharti
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (BHU) Varanasi, 221005, India
| | - Pramod S Mali
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Akash Kumar Jha
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Brahmeshwar Mishra
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (BHU) Varanasi, 221005, India
| | - Ashutosh Kumar
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India.
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Bera A, Singh S, D'Souza JS, Hosur RV, Mishra P. Effect of UV Stress on the Structure and Function of Pro-apoptotic Bid and Anti-apoptotic Bcl-xl proteins. Chembiochem 2023; 24:e202200682. [PMID: 36597005 DOI: 10.1002/cbic.202200682] [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: 11/20/2022] [Revised: 12/31/2022] [Accepted: 01/02/2023] [Indexed: 01/05/2023]
Abstract
Ultraviolet C (UV-C) radiation induces apoptosis in mammalian cells via the mitochondrion-mediated pathway. The Bcl-2 family of proteins are the regulators of the mitochondrial pathway of apoptosis and appears responsive to UV-C radiation. It is unknown how the structure and, effectively, the function of these proteins are directly impacted by UV-C exposure. Here, we present the effect of UV-C irradiation on the structure and function of pro-apoptotic Bid-FL and anti-apoptotic Bcl-xlΔC proteins. Using a variety of biophysical tools, we show that, following UV-C irradiation, the structures of Bcl-xlΔC and Bid-FL are irreversibly altered. Bcl-xLΔC is found to be more sensitive to UV stress than Bid-FL Interestingly, UV-C exposure shows dramatic chemical shift perturbations in consequence of dramatic structural perturbations (α-helix to β-sheet) in the BH3- binding region, a crucial segment of Bcl-xlΔC. Furter it has been shown that UV-exposed Bcl-xlΔC has reduced efficacy of its interactions with pro-apoptotic tBid.
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Affiliation(s)
- Akash Bera
- Department of Biophysics, University of Mumbai Santacruz (E) Kalina, Mumbai, 400101, India
| | - Suraj Singh
- Department of Biophysics, University of Mumbai Santacruz (E) Kalina, Mumbai, 400101, India
| | - Jacinta S D'Souza
- Department of Biology, UM-DAE Centre for Excellence in Basic Sciences Santacruz (E) Kalina, Mumbai, 400101, India
| | - Ramakrishna V Hosur
- Department of Biology, UM-DAE Centre for Excellence in Basic Sciences Santacruz (E) Kalina, Mumbai, 400101, India
| | - Pushpa Mishra
- Department of Biophysics, University of Mumbai Santacruz (E) Kalina, Mumbai, 400101, India
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Bopardikar M, Koti Ainavarapu SR, Hosur RV. Pyrogallol, Corilagin and Chebulagic acid target the "fuzzy coat" of alpha-synuclein to inhibit the fibrillization of the protein. RSC Adv 2022; 12:35770-35777. [PMID: 36545068 PMCID: PMC9749937 DOI: 10.1039/d2ra04358k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/13/2022] [Indexed: 12/15/2022] Open
Abstract
The accumulation of the intrinsically disordered protein alpha-synuclein (αSyn) in the form of insoluble fibrillar aggregates in the central nervous system is linked to a variety of neurodegenerative disorders such as Parkinson's disease, Lewy body dementia, and multiple system atrophy. Here we show that Pyrogallol, Corilagin and Chebulagic acid, compounds containing a different number of catechol rings, are independently capable of delaying and reducing the extent of αSyn fibrillization. The efficiency of inhibition was found to correlate with the number of catechol rings. Further, our NMR studies reveal that these compounds interact with the N-terminal region of αSyn which is unstructured even in the fibrillar form of the protein and is known as the "fuzzy coat" of fibrils. Thus, Corilagin and Chebulagic acid target the fuzzy coat of αSyn and not the amyloid core which is a common target for the inhibition of protein fibrillization. Our results indicate that the N-terminus also plays a key role in the fibrillization of αSyn.
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Affiliation(s)
- Mandar Bopardikar
- Department of Chemical Sciences, Tata Institute of Fundamental ResearchHomi Bhabha Road, ColabaMumbai 400005India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental ResearchHomi Bhabha Road, ColabaMumbai 400005India
| | - Ramakrishna V. Hosur
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Kalina CampusSantacruzMumbai 400098India
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Mohana Rao Kakita V, Hosur RV. Mahalanobis distance correlation: A novel approach for quantitating changes in multidimensional NMR spectra in biological applications. J Magn Reson 2022; 337:107165. [PMID: 35202919 DOI: 10.1016/j.jmr.2022.107165] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/29/2022] [Accepted: 02/06/2022] [Indexed: 06/14/2023]
Abstract
We present here a novel protocol for quantitating changes in the NMR spectra, which is based on Mahalanobis statistics. In a two dimensional NMR spectrum, the various peaks are taken to represent a distribution, and the two chemical shifts along the orthogonal axes and the peak intensities constitute three observables. All these observables vary in a correlated manner. Taking account of these, the Mahalanobis distance (MD) reflects the distance of any chosen peak from the centre of the distribution. For quantitating changes in a particular spectrum (say A) with N peaks (altered protein NMR spectrum) with respect to a reference spectrum (say B) with M peaks (original protein NMR spectrum), a composite spectrum with N + M peaks is generated. A one-to-one correspondence between N MD values considering all the N peaks in A and the same N peaks in the composite spectrum (A + B) is calculated. The MD distance of corresponding peaks in two different distributions can be correlated to assess the changes in the spectra during the course of a biological phenomenon, or as a result of biomolecular interactions. We have demonstrated these ideas, first, using the 1H-15N HSQC spectrum of Ubiquitin, and then application of these has been demonstrated for monitoring progression of fibrillation of the protein α-Synuclein, in absence and presence of safranal, a known inhibitor of fibrillation of the protein. The method is in general applicable to multidimensional NMR spectra, does not require extensive data collection, and allows quantitative assessment of spectral changes via a single parameter. We believe that the method will have wide ranging applications to monitor many biological phenomena, and will also be useful in an industrial environment for mass comparison of molecules in a rapid manner.
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Affiliation(s)
- Veera Mohana Rao Kakita
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Kalina, Mumbai, Maharashtra 400098, India.
| | - Ramakrishna V Hosur
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Kalina, Mumbai, Maharashtra 400098, India; Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, Maharashtra 400076, India.
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Rachineni K, Rao Kakita VM, Awasthi NP, Shirke VS, Hosur RV, Chandra Shukla S. Identifying type of sugar adulterants in honey: Combined application of NMR spectroscopy and supervised machine learning classification. Curr Res Food Sci 2022; 5:272-277. [PMID: 35141528 PMCID: PMC8816647 DOI: 10.1016/j.crfs.2022.01.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 12/25/2021] [Accepted: 01/09/2022] [Indexed: 02/01/2023] Open
Abstract
Nuclear magnetic resonance (NMR) is a powerful analytical tool which can be used for authenticating honey, at chemical constituent levels by enabling identification and quantification of the spectral patterns. However, it is still challenging, as it may be a person-centric analysis or a time-consuming process to analyze many honey samples in a limited time. Hence, automating the NMR spectral analysis of honey with the supervised machine learning models accelerates the analysis process and especially food chemistry researcher or food industry with non-NMR experts would benefit immensely from such advancements. Here, we have successfully demonstrated this technology by considering three major sugar adulterants, i.e., brown rice syrup, corn syrup, and jaggery syrup, in honey at varying concentrations. The necessary supervised machine learning classification analysis is performed by using logistic regression, deep learning-based neural network, and light gradient boosting machines schemes. NMR helps to identify the fingerprints of honey chemical constituents. Combined NMR and ML tools can determine the type of adulteration in honey. Supervised classification schemes, Logistic regression, DNN, and LGBM are utilized. Corn, brown rice, and jaggery adulterations are discriminated in honey.
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Affiliation(s)
- Kavitha Rachineni
- Export Inspection Agency – Mumbai, E-3, Industrial Area (MIDC), Andheri East, Mumbai, 400 093, India
- Corresponding author.
| | - Veera Mohana Rao Kakita
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santacruz, Mumbai, 400 098, India
| | - Neeraj Praphulla Awasthi
- Export Inspection Agency – Mumbai, E-3, Industrial Area (MIDC), Andheri East, Mumbai, 400 093, India
| | - Vrushali Siddesh Shirke
- Export Inspection Agency – Mumbai, E-3, Industrial Area (MIDC), Andheri East, Mumbai, 400 093, India
| | - Ramakrishna V. Hosur
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santacruz, Mumbai, 400 098, India
| | - Satish Chandra Shukla
- Export Inspection Agency- Chennai (Head Office), 6th Floor CMDA Tower-II, No: 1 Gandhi Irwin Road, Egmore, Chennai, 600008, India
- Corresponding author.
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Choudhary S, Lopus M, Hosur RV. Targeting disorders in unstructured and structured proteins in various diseases. Biophys Chem 2021; 281:106742. [PMID: 34922214 DOI: 10.1016/j.bpc.2021.106742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 06/29/2021] [Revised: 12/05/2021] [Accepted: 12/09/2021] [Indexed: 12/31/2022]
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs) are proteins and protein segments that usually do not acquire well-defined folded structures even under physiological conditions. They are abundantly present and challenge the "one sequence-one structure-one function" theory due to a lack of stable secondary and/or tertiary structure. Due to conformational flexibility, IDPs/IDPRs can bind with multiple interacting partners with high-specificity and low-affinity and perform essential biological functions associated with signalling, recognition and regulation. Mis-functioning and mis-regulation of IDPs and IDPRs causes disorder in disordered proteins and disordered protein segments which results in numerous human diseases, such as cancer, Parkinson's disease (PD), Alzheimer's disease (AD), diabetes, metabolic disorders, systemic disorders and so on. Due to the strong connection of IDPs/IDPRs with human diseases they are considered potentential targets for drug therapy. Since they disobey the "one sequence-one structure-one function" concept, IDPs/IDPRs are complex systems for drug targeting. This review summarises various protein disorder diseases and different methods for therapeutic targeting of disordered proteins/segments. Targeting IDPs/IDPRs for diseases will open up a new era of rational drug design and drug discovery.
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Affiliation(s)
- Sinjan Choudhary
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidhyanagri Campus, Kalina, Mumbai 400098, India.
| | - Manu Lopus
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidhyanagri Campus, Kalina, Mumbai 400098, India.
| | - Ramakrishna V Hosur
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidhyanagri Campus, Kalina, Mumbai 400098, India.
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Patel S, Hosur RV. Replica exchange molecular dynamics simulations reveal self-association sites in M-crystallin caused by mutations provide insights of cataract. Sci Rep 2021; 11:23270. [PMID: 34857812 PMCID: PMC8639718 DOI: 10.1038/s41598-021-02728-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/09/2021] [Indexed: 11/09/2022] Open
Abstract
Crystallins are ubiquitous, however, prevalence is seen in eye lens. Eye lens crystallins are long-lived and structural intactness is required for maintaining lens transparency and protein solubility. Mutations in crystallins often lead to cataract. In this study, we performed mutations at specific sites of M-crystallin, a close homologue of eye lens crystallin and studied by using replica exchange molecular dynamics simulation with generalized Born implicit solvent model. Mutations were made on the Ca2+ binding residues (K34D and S77D) and in the hydrophobic core (W45R) which is known to cause congenital cataract in homologous γD-crystallin. The chosen mutations caused large motion of the N-terminal Greek key, concomitantly broke the interlocking Greek keys interactions and perturbed the compact core resulting in several folded and partially unfolded states. Partially unfolded states exposed large hydrophobic patches that could act as precursors for self-aggregation. Accumulation of such aggregates is the potential cause of cataract in homologous eye lens crystallins.
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Affiliation(s)
- Sunita Patel
- UM-DAE Centre for Excellence in Basic Sciences, Mumbai University Campus, Vidyanagari, Mumbai, 400098, India.
| | - Ramakrishna V. Hosur
- grid.452882.1UM-DAE Centre for Excellence in Basic Sciences, Mumbai University Campus, Vidyanagari, Mumbai, 400098 India
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Singh S, Barnes CA, D'Souza JS, Hosur RV, Mishra P. Curcumin, a potential initiator of apoptosis via direct interactions with Bcl-xL and Bid. Proteins 2021; 90:455-464. [PMID: 34528298 DOI: 10.1002/prot.26238] [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: 02/26/2021] [Revised: 08/18/2021] [Accepted: 09/07/2021] [Indexed: 11/07/2022]
Abstract
Apoptosis is a naturally occurring process during the growth and development of multicellular organisms and is increasingly active during times of cellular stress such as in response to intracellular DNA damage when removal of the host cell is paramount to prevent cancer. Unfortunately, once formed, cancer cells become impervious to apoptosis, creating a desperate need to identify an approach to induce apoptosis in these cells. An attractive option is to focus efforts on developing and locating compounds which activate apoptosis using natural compounds. Curcumin is a natural component in turmeric and is well-known for its pharmacological effects in preventing and combating many ailments and has been shown to decrease the rapid proliferation of a wide variety of tumor cells. However, to date, the apoptotic intermediates and interactions through which curcumin exerts its cytotoxic effects are unknown. Motivated by reports linking the intracellular modulation of the concentrations of Bid and Bcl-xL, following curcumin administration to cancer cells, we set out to probe for potential intermolecular interactions of these proteins with curcumin. Using several biophysical techniques, most notably, fluorescence, circular dichroism and nuclear magnetic resonance spectroscopy, we reveal binding interactions of curcumin with both Bcl-xLΔC and full-length Bid (Bid-FL) and prove that this binding is hydrophobically driven and localized to well-known functional regions of each protein. Specifically, our NMR studies show that while Bid-FL interacts with curcumin through its hydrophobic and pore forming helices (α6-α7), Bcl-xLΔC interacts with curcumin via its BH3 binding pocket (α2-α3-α4-α5), a critical region for mediating apoptosis.
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Affiliation(s)
- Suraj Singh
- Department of Biophysics, University of Mumbai, Santacruz (E), Mumbai, India
| | - C Ashley Barnes
- NIDDK, National Institute of Health, Bethesda, Maryland, USA
| | - Jacinta S D'Souza
- UM-DAE Centre for Excellence in Basic Sciences, Mumbai University Campus, Santacruz (E), Mumbai, India
| | - Ramakrishna V Hosur
- UM-DAE Centre for Excellence in Basic Sciences, Mumbai University Campus, Santacruz (E), Mumbai, India
| | - Pushpa Mishra
- Department of Biophysics, University of Mumbai, Santacruz (E), Mumbai, India
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Arthanari H, Chary KVR, Szyperski T, Ramanathan KV, Hosur RV, Suryaprakash N, Raghothama S, Jagannathan NR, Norton RS, Prabhakaran EN, Kondaish P, Mukherjee SP, Adiga SK, Vadrevu R, Bhunia A, Joseph D. Hanudatta S. Atreya (1974-2020). Magn Reson Chem 2021; 59:201-212. [PMID: 33565121 DOI: 10.1002/mrc.5130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/01/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Kandala V R Chary
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Thomas Szyperski
- Department of Chemistry, State University of New York at Buffalo and Northeast Structural Genomics Consortium, Buffalo, NY, USA
| | | | - Ramakrishna V Hosur
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | | | | | - Naranamangalam R Jagannathan
- Department of Radiology, Chettinad Academy of Research and Education, Kelambakkam, India
- Department of Radiology, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
- Department of Electrical Engineering, IIT Madras, Chennai, India
| | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Erode N Prabhakaran
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, India
| | - Paturu Kondaish
- Department of Molecular Reproduction, Development and Genetics Indian Institute of Science, Bangalore, India
| | | | - Satish Kumar Adiga
- Department of Clinical Embryology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - RamaKrishna Vadrevu
- Department of Biological Sciences, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Hyderabad, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata, India
| | - David Joseph
- NMR Research Centre, Indian Institute of Science, Bangalore, India
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Nirmala JG, Rachineni K, Choudhary S, Hosur RV, Lopus M. Triphala polyphenols-functionalized gold nanoparticles impair cancer cell survival through induction of tubulin dysfunction. J Drug Deliv Sci Technol 2021. [DOI: 10.1016/j.jddst.2020.102167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Rao Kakita VM, Hosur RV. All-in-one NMR spectroscopy of small organic molecules: complete chemical shift assignment from a single NMR experiment. RSC Adv 2020; 10:21174-21179. [PMID: 35518727 PMCID: PMC9054363 DOI: 10.1039/d0ra03417g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/29/2020] [Indexed: 11/21/2022] Open
Abstract
A new class of NOAH NMR experiments (NOAH-AST and NOAH-ASTPS), with the abbreviations, A: 1,1-ADEQUATE, S: sensitivity improved version of multiplicity-edited (ME)-HSQC, T: TOCSY, and TPS: pure shift TOCSY, are reported to obtain complete chemical shift assignments of small organic molecules from a single NMR experiment. While NOAH-AST provides 13C–13C, 1H–13C, and 1H–1H connectivities for molecules with well resolved chemical shifts, NOAH-ASTPS experiments discern 1H–1H connectivities even in complex organic molecules such as steroids at ultra-high resolution. These methods are very flexible and allow to record data through non-uniform-sampling, which reduces the experimental time to a great extent. In order to make these methods friendly to non-NMR experts (especially organic chemists and natural product scientists), python scripts have been developed and they help researchers in using these methods. All-in-one NOAH-AST/NOAH-ASTPS provides complete chemical shift information (13C–13C/1H–13C/1H–1H) of small organic molecules from a single NMR experiment.![]()
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Bhattacharya A, Shukla VK, Hosur RV, Kumar A. Backbone and side-chain resonance assignments of centromeric protein Scm3 from Saccharomyces cerevisiae. Biomol NMR Assign 2019; 13:267-273. [PMID: 30937734 DOI: 10.1007/s12104-019-09889-8] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/08/2019] [Indexed: 06/09/2023]
Abstract
The centromeric chromatin plays an essential role in regulating the attachment of microtubules and controlling the segregation of sister chromatids during mitosis. In budding yeast, the evolutionary conserved histone variant, Cse4 is a vital component of the multiprotein kinetochore complex and is recruited to the centromere through its chaperone, Suppressor of chromosome mis-segregation (Scm3). Scm3 is an inner kinetochore protein crucial for the formation of a functional inner kinetochore. Scm3 has been known to play an active role in the assembly of the centromeric nucleosome and its deletion has been found to have deleterious effects on the cells leading to chromosome segregation defects. However, structural details of monomeric full length Scm3 have remained elusive so far. Here, we report the backbone and side-chain resonance assignments of centromeric protein, Scm3. 1H, 13C and 15N chemical shifts of Scm3 have been obtained by various 2D and 3D heteronuclear NMR experiments at pH 7.4 and 283 K.
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Affiliation(s)
- Anusri Bhattacharya
- UM-DAE-Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Mumbai, 400098, India
| | - Vaibhav Kumar Shukla
- UM-DAE-Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Mumbai, 400098, India
| | - Ramakrishna V Hosur
- UM-DAE-Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Mumbai, 400098, India.
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
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15
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Kakita VMR, Rachineni K, Hosur RV. Ultraclean Pure Shift NMR Spectroscopy with Adiabatic Composite Refocusing Pulses: Application to Metabolite Samples. ChemistrySelect 2019. [DOI: 10.1002/slct.201902238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Veera Mohana Rao Kakita
- UM-DAE-Centre for Excellence in Basic SciencesUniversity of MumbaiKalina Campus, Santacruz 400 098 Mumbai India
| | - Kavitha Rachineni
- Department of Biosciences and BioengineeringIndian Institute of Technology Bombay, Powai 400076 Mumbai India
| | - Ramakrishna V Hosur
- UM-DAE-Centre for Excellence in Basic SciencesUniversity of MumbaiKalina Campus, Santacruz 400 098 Mumbai India
- Department of Biosciences and BioengineeringIndian Institute of Technology Bombay, Powai 400076 Mumbai India
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16
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Save SS, Rachineni K, Hosur RV, Choudhary S. Natural compound safranal driven inhibition and dis-aggregation of α-synuclein fibrils. Int J Biol Macromol 2019; 141:585-595. [PMID: 31505208 DOI: 10.1016/j.ijbiomac.2019.09.053] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/25/2019] [Accepted: 09/06/2019] [Indexed: 10/26/2022]
Abstract
Self-assembly of α-synuclein (α-Syn) is linked with a variety of neurodegenerative diseases collectively called as α-synucleiopathies. Therefore, discovering suitable inhibitors for this self-association process of α-Syn is a subject of intense research. In this background, we have demonstrated here that the natural compound, Safranal, delays/inhibits α-Syn fibrillation/aggregation, and we have also characterized its mode of action. The α-Syn fibrillation/aggregation kinetics studies in combination with TEM studies demonstrated that Safranal effectively inhibits α-Syn fibrillation/aggregation. NMR studies revealed that Safranal binds with α-Syn and stabilizes the monomeric protein. ANS fluorescence and CD measurements indicated that Safranal binds to the hydrophobic residues of the protein and causes delay in the formation of β-sheet rich structures which are crucial for the fibrillation to occur. The results obtained from fluorescence quenching, NMR and ANS binding assays, when analysed taking into consideration the molecular structure of Safranal provide valuable insights into the mechanism of inhibition of α-Syn fibrillation/aggregation. We infer that inhibition of α-Syn fibrillation/aggregation is primarily driven by hydrophobic interactions between Safranal and the protein. Further, Safranal is also seen to dis-aggregates pre-formed α-Syn fibrils. These findings implicate that Safranal could become a potent therapeutic intervention in Parkinson's disease and other protein aggregation related disorders.
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Affiliation(s)
- Shreyada S Save
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidhyanagri Campus, Kalina, Mumbai 400098, India
| | - Kavitha Rachineni
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidhyanagri Campus, Kalina, Mumbai 400098, India
| | - Ramakrishna V Hosur
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidhyanagri Campus, Kalina, Mumbai 400098, India
| | - Sinjan Choudhary
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidhyanagri Campus, Kalina, Mumbai 400098, India.
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17
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Rao Kakita VM, Joshi MV, Hosur RV. G-SERF Editing in Two-Dimensional Pure-Shift Total Correlation Spectroscopy: Scalar Coupling Measurements for a Group of Spins in Organic Molecules. Chemphyschem 2019; 20:1559-1566. [PMID: 30997947 DOI: 10.1002/cphc.201900174] [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: 02/21/2019] [Revised: 04/13/2019] [Indexed: 11/10/2022]
Abstract
A novel G-SERF-PSYCHE-TOCSY (gradient encoded selective refocusing in pure shift yielded by chirp excitation version of total correlation spectroscopy) NMR pulse scheme has been proposed, which produces TOCSY chemical shift correlations, on one hand, and scalar coupling values for the spins scalarly coupled to irradiated resonances, by showing them as doublets along the indirect dimension, on the other. Therefore, recording such an experiment, for a group of spins with overlapping chemical shifts, in organic molecules can adequately provide scalar coupling information in a G-SERF manner along the indirect dimensions, and they can be assigned to particular spin pairs. Such COSY chemical shift correlations (which appear as doublets for the scalarly coupled spins) can be readily discriminated from the TOCSY peaks (which do not show such splitting) in the G-SERF-PSYCHE-TOCSY spectrum.
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Affiliation(s)
- Veera Mohana Rao Kakita
- UM-DAE-Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santacruz, Mumbai, 400 098, India
| | - Mamata V Joshi
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), 1-Homi Bhabha Road, Colaba, Mumbai, 400 005, India
| | - Ramakrishna V Hosur
- UM-DAE-Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santacruz, Mumbai, 400 098, India.,Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
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18
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Patel S, Krishnan B, Hosur RV, Chary KVR. Mechanistic Insights from Replica Exchange Molecular Dynamics Simulations into Mutation Induced Disordered-to-Ordered Transition in Hahellin, a βγ-Crystallin. J Phys Chem B 2019; 123:5086-5098. [DOI: 10.1021/acs.jpcb.9b03845] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sunita Patel
- UM-DAE Centre for Excellence in Basic Sciences, Mumbai University Campus, Mumbai 400098, India
- Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Bal Krishnan
- Indian Institute of Science Education and Research, Berhampur, 760010, India
| | - Ramakrishna V. Hosur
- UM-DAE Centre for Excellence in Basic Sciences, Mumbai University Campus, Mumbai 400098, India
- Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Kandala V. R. Chary
- Tata Institute of Fundamental Research, Hyderabad 500107, India
- Tata Institute of Fundamental Research, Mumbai 400005, India
- Indian Institute of Science Education and Research, Berhampur, 760010, India
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19
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Bopardikar M, Bhattacharya A, Rao Kakita VM, Rachineni K, Borde LC, Choudhary S, Koti Ainavarapu SR, Hosur RV. Triphala inhibits alpha-synuclein fibrillization and their interaction study by NMR provides insights into the self-association of the protein. RSC Adv 2019; 9:28470-28477. [PMID: 35529629 PMCID: PMC9071048 DOI: 10.1039/c9ra05551g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/31/2019] [Indexed: 11/21/2022] Open
Abstract
The process of assembly and accumulation of the intrinsically disordered protein (IDP), alpha-synuclein (αSyn) into amyloid fibrils is a pathogenic process leading to several neurodegenerative disorders such as Parkinson's disease, multiple system atrophy and others. Although several molecules are known to inhibit αSyn fibrillization, the mechanism of inhibition is just beginning to emerge. Here, we report the inhibition of fibrillization of αSyn by Triphala, a herbal preparation in the traditional Indian medical system of Ayurveda. Triphala was found to be a rich source of polyphenols which are known to act as amyloid inhibitors. ThT fluorescence and TEM studies showed that Triphala inhibited the fibrillization of αSyn. However, it was observed that Triphala does not disaggregate preformed αSyn fibrils. Further, native-PAGE showed that Triphala reduces the propensity of αSyn to oligomerize during the lag phase of fibrillization. Our NMR results showed that certain stretches of residues in the N-terminal and NAC regions of αSyn play an anchor role in the self-association process of the protein, thereby providing mechanistic insights into the early events during αSyn fibrillization. Triphala inhibits αSyn self-association by interacting with anchoring regions which are responsible for αSyn oligomerization.![]()
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Affiliation(s)
- Mandar Bopardikar
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai 400005
- India
| | - Anusri Bhattacharya
- UM-DAE Centre for Excellence in Basic Sciences
- University of Mumbai
- Kalina Campus
- Mumbai 400098
- India
| | - Veera Mohana Rao Kakita
- UM-DAE Centre for Excellence in Basic Sciences
- University of Mumbai
- Kalina Campus
- Mumbai 400098
- India
| | - Kavitha Rachineni
- UM-DAE Centre for Excellence in Basic Sciences
- University of Mumbai
- Kalina Campus
- Mumbai 400098
- India
| | - Lalit C. Borde
- Department of Biological Sciences
- Tata Institute of Fundamental Research
- Mumbai 400005
- India
| | - Sinjan Choudhary
- UM-DAE Centre for Excellence in Basic Sciences
- University of Mumbai
- Kalina Campus
- Mumbai 400098
- India
| | | | - Ramakrishna V. Hosur
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai 400005
- India
- UM-DAE Centre for Excellence in Basic Sciences
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20
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Kakita VMR, Rachineni K, Bopardikar M, Hosur RV. NMR supersequences with real-time homonuclear broadband decoupling: Sequential acquisition of protein and small molecule spectra in a single experiment. J Magn Reson 2018; 297:108-112. [PMID: 30384129 DOI: 10.1016/j.jmr.2018.10.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/08/2018] [Accepted: 10/21/2018] [Indexed: 06/08/2023]
Abstract
NOAH (NMR byOrderedAcquisition using 1H-detection) type of pure shift NMR pulse scheme has been designed for the efficient utilization of magnetization that presents in a spin-system under consideration. The proposed strategy, PROSMASH-HSQC2 (PROtein-HSQC and SMAll molecule-HSQC Signals with Homodecoupling) uses the real-time BIRD pure shift NMR strategy and two HSQC spectra (13C-HSQC for small molecules and 15N-HSQC for 15N-isotopic labelled proteins) can be recorded in a single NMR experiment. Thus, this method permits precise determination of drug-protein interactions at atomic levels by monitoring the chemical shift perturbations, and will have potential applications in drug discovery programs.
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Affiliation(s)
- Veera Mohana Rao Kakita
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santacruz, Mumbai 400 098, India
| | - Kavitha Rachineni
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santacruz, Mumbai 400 098, India
| | - Mandar Bopardikar
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), 1-Homi Bhabha Road, Colaba, Mumbai 400 005, India
| | - Ramakrishna V Hosur
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santacruz, Mumbai 400 098, India; Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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21
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Kakita VMR, Hosur RV. Real-time J-upscaling in two-dimensional pure shift diagonal NMR: Simultaneous resolution enhancement in chemical shifts and scalar couplings. J Magn Reson 2018; 296:176-180. [PMID: 30286413 DOI: 10.1016/j.jmr.2018.09.012] [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] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 06/08/2023]
Abstract
A two-dimensional real-time J-upscaled pure shift diagonal pulse scheme, JS-PSYCHE-DIAG has been developed. This method enhances the resolution in scalar coupling multiplets by real-time J-upscaling during the direct acquisition, and these J-upscaled multiplets resolve on the diagonal at the respective pure shift positions, which results in resolution enhancement in chemical shifts. Thus, both chemical shifts and scalar couplings get better resolved simultaneously in the same NMR experiment. The efficacy of the present method has been demonstrated, (i) on hesperidin for resolving the J-upscaled multiplets belonging to diastereomers and (ii) on a natural product, strychnine, to measure small scalar couplings including the long range values.
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Affiliation(s)
- Veera Mohana Rao Kakita
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santacruz, Mumbai 400 098, India
| | - Ramakrishna V Hosur
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santacruz, Mumbai 400 098, India.
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22
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Kakita VMR, Rachineni K, Hosur RV. Fast and simultaneous determination of 1 H- 1 H and 1 H- 19 F scalar couplings in complex spin systems: Application of PSYCHE homonuclear broadband decoupling. Magn Reson Chem 2018; 56:1043-1046. [PMID: 28731512 DOI: 10.1002/mrc.4635] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 07/13/2017] [Accepted: 07/17/2017] [Indexed: 06/07/2023]
Abstract
The present manuscript focuses on fast and simultaneous determination of 1 H-1 H and 1 H-19 F scalar couplings in fluorinated complex steroid molecules. Incorporation of broadband PSYCHE homonuclear decoupling in the indirect dimension of zero-quantum filtered diagonal experiments (F1-PSYCHE-DIAG) suppresses 1 H-1 H scalar couplings; however, it retains 1 H-19 F scalar couplings (along F1 dimension) for the 19 F coupled protons while preserving the pure-shift nature for 1 H resonances uncoupled to 19 F. In such cases, along the direct dimensions, 1 H-1 H scalar coupling multiplets deconvolute and they appear as duplicated multiplets for the 19 F coupled protons, which facilitates unambiguous discrimination of 19 F coupled 1 H chemical sites from the others. Further, as an added advantage, data acquisition has been accelerated by invoking the known ideas of spectral aliasing in the F1-PSYCHE-DIAG scheme and experiments demand only ~10 min of spectrometer times.
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Affiliation(s)
- Veera Mohana Rao Kakita
- UM-DAE-Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santa Cruz, Mumbai, 400 098, India
| | - Kavitha Rachineni
- UM-DAE-Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santa Cruz, Mumbai, 400 098, India
| | - Ramakrishna V Hosur
- UM-DAE-Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santa Cruz, Mumbai, 400 098, India
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), 1-Homi Bhabha Road, Colaba, Mumbai, 400 005, India
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23
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Rachineni K, Kakita VMR, Hosur RV. Multiple homonuclear band-selective decoupling NMR: Fast and unambiguous determination of diastereomeric excess. Magn Reson Chem 2018; 56:1037-1042. [PMID: 28730621 DOI: 10.1002/mrc.4634] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 07/13/2017] [Accepted: 07/14/2017] [Indexed: 06/07/2023]
Abstract
Discrimination and quantification of chiral stereoisomers have been studied by different analytical methods, and NMR has emerged as a powerful one with the advancements in pure-shift NMR methods. In the present manuscript, an al-F1F2-MHOBS-DIAG NMR method for the quantification of diastereomeric excess ratio (dr) has been proposed and demonstrated, using hesperidin and naringin mixtures. This method enables simultaneous quantification of dr at multiple resonances, in a single experiment, and it takes only 10 min to record. The present method uses spectral aliasing and thus demands only very few indirect dwell increments. Further, the measured dr values are very reliable, because we consider several spins for the quantification.
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Affiliation(s)
- Kavitha Rachineni
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santa Cruz, Mumbai, 400 098, India
| | - Veera Mohana Rao Kakita
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santa Cruz, Mumbai, 400 098, India
| | - Ramakrishna V Hosur
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santa Cruz, Mumbai, 400 098, India
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), 1-Homi Bhabha Road, Colaba, Mumbai, 400 005, India
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Kakita VMR, Kupče Ē, Bharatam J, Hosur RV. Rapid elucidation of chemical shift correlations in complex NMR spectra of organic molecules: Two-dimensional Hadamard pure shift NMR spectroscopy. J Magn Reson 2018; 293:77-81. [PMID: 29908413 DOI: 10.1016/j.jmr.2018.06.006] [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] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/02/2018] [Accepted: 06/07/2018] [Indexed: 06/08/2023]
Abstract
Novel two dimensional Hadamard encoding/decoding based pure shift NMR acquisition techniques (TOCSY and HSQC) have been developed, which provide chemical shift information at ultra high resolution in very short spectrometer times. The efficacy of these methods for rapid assignment of chemical shifts in complex NMR spectra of organic molecules/natural products has been demonstrated. This would be of great help for rapid analysis of samples during separation of complex mixtures.
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Affiliation(s)
- Veera Mohana Rao Kakita
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santacruz, Mumbai 400 098, India
| | - Ēriks Kupče
- Bruker (UK) Ltd., Banner Lane, Coventry CV4 9GH, UK
| | - Jagadeesh Bharatam
- Centre for NMR and Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Ramakrishna V Hosur
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santacruz, Mumbai 400 098, India; Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), 1-Homi Bhabha Road, Colaba, Mumbai 400 005, India.
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25
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Kshirsagar R, Khan K, Joshi MV, Hosur RV, Muniyappa K. Probing the Potential Role of Non-B DNA Structures at Yeast Meiosis-Specific DNA Double-Strand Breaks. Biophys J 2017; 112:2056-2074. [PMID: 28538144 DOI: 10.1016/j.bpj.2017.04.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 04/13/2017] [Accepted: 04/19/2017] [Indexed: 12/29/2022] Open
Abstract
A plethora of evidence suggests that different types of DNA quadruplexes are widely present in the genome of all organisms. The existence of a growing number of proteins that selectively bind and/or process these structures underscores their biological relevance. Moreover, G-quadruplex DNA has been implicated in the alignment of four sister chromatids by forming parallel guanine quadruplexes during meiosis; however, the underlying mechanism is not well defined. Here we show that a G/C-rich motif associated with a meiosis-specific DNA double-strand break (DSB) in Saccharomyces cerevisiae folds into G-quadruplex, and the C-rich sequence complementary to the G-rich sequence forms an i-motif. The presence of G-quadruplex or i-motif structures upstream of the green fluorescent protein-coding sequence markedly reduces the levels of gfp mRNA expression in S. cerevisiae cells, with a concomitant decrease in green fluorescent protein abundance, and blocks primer extension by DNA polymerase, thereby demonstrating the functional significance of these structures. Surprisingly, although S. cerevisiae Hop1, a component of synaptonemal complex axial/lateral elements, exhibits strong affinity to G-quadruplex DNA, it displays a much weaker affinity for the i-motif structure. However, the Hop1 C-terminal but not the N-terminal domain possesses strong i-motif binding activity, implying that the C-terminal domain has a distinct substrate specificity. Additionally, we found that Hop1 promotes intermolecular pairing between G/C-rich DNA segments associated with a meiosis-specific DSB site. Our results support the idea that the G/C-rich motifs associated with meiosis-specific DSBs fold into intramolecular G-quadruplex and i-motif structures, both in vitro and in vivo, thus revealing an important link between non-B form DNA structures and Hop1 in meiotic chromosome synapsis and recombination.
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Affiliation(s)
- Rucha Kshirsagar
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Krishnendu Khan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Mamata V Joshi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Ramakrishna V Hosur
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.
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Shukla VK, Singh JS, Vispute N, Ahmad B, Kumar A, Hosur RV. Unfolding of CPR3 Gets Initiated at the Active Site and Proceeds via Two Intermediates. Biophys J 2017; 112:605-619. [PMID: 28256221 DOI: 10.1016/j.bpj.2016.12.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/01/2016] [Accepted: 12/13/2016] [Indexed: 12/29/2022] Open
Abstract
Cyclophilin catalyzes the ubiquitous process "peptidyl-prolyl cis-trans isomerization," which plays a key role in protein folding, regulation, and function. Here, we present a detailed characterization of the unfolding of yeast mitochondrial cyclophilin (CPR3) induced by urea. It is seen that CPR3 unfolding is reversible and proceeds via two intermediates, I1 and I2. The I1 state has native-like secondary structure and shows strong anilino-8-naphthalenesulphonate binding due to increased exposure of the solvent-accessible cluster of non-polar groups. Thus, it has some features of a molten globule. The I2 state is more unfolded, but it retains some residual secondary structure, and shows weak anilino-8-naphthalenesulphonate binding. Chemical shift perturbation analysis by 1H-15N heteronuclear single quantum coherence spectra reveals disruption of the tertiary contacts among the regions close to the active site in the first step of unfolding, i.e., the N-I1 transition. Both of the intermediates, I1 and I2, showed a propensity to self-associate under stirring conditions, but their kinetic profiles are different; the native protein did not show any such tendency under the same conditions. All these observations could have significant implications for the function of the protein.
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Affiliation(s)
- Vaibhav Kumar Shukla
- UM-DAE-Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Mumbai, India
| | - Jai Shankar Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Neha Vispute
- UM-DAE-Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Mumbai, India
| | - Basir Ahmad
- UM-DAE-Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Mumbai, India
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, India.
| | - Ramakrishna V Hosur
- UM-DAE-Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Mumbai, India; Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India.
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Kakita VMR, Hosur RV. Hadamard Homonuclear Broadband Decoupled TOCSY NMR: Improved Efficacy in Detecting Long-range Chemical Shift Correlations. Chemphyschem 2016; 17:4037-4042. [DOI: 10.1002/cphc.201600769] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/30/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Veera Mohana Rao Kakita
- UM-DAE-Centre for Excellence in Basic Sciences; University of Mumbai; Kalina Campus, Santa Cruz Mumbai 400 098 India
| | - Ramakrishna V. Hosur
- UM-DAE-Centre for Excellence in Basic Sciences; University of Mumbai; Kalina Campus, Santa Cruz Mumbai 400 098 India
- Department of Chemical Sciences; Tata Institute of Fundamental Research (TIFR); 1-Homi Bhabha Road, Colaba Mumbai 400 005 India
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28
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Kakita VMR, Hosur RV. Non-Uniform-Sampling Ultrahigh Resolution TOCSY NMR: Analysis of Complex Mixtures at Microgram Levels. Chemphyschem 2016; 17:2304-8. [DOI: 10.1002/cphc.201600255] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Veera M. R. Kakita
- UM-DAE Centre for Excellence in Basic Sciences; Mumbai University Campus, Kalina, Santa Cruz Mumbai 400 098 India
| | - Ramakrishna V. Hosur
- UM-DAE Centre for Excellence in Basic Sciences; Mumbai University Campus, Kalina, Santa Cruz Mumbai 400 098 India
- Department of Chemical Sciences; Tata Institute of Fundamental Research (TIFR); 1-Homi Bhabha Road, Colaba Mumbai 400 005 India
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Shukla VK, Singh JS, Trivedi D, Hosur RV, Kumar A. NMR assignments of mitochondrial cyclophilin Cpr3 from Saccharomyces cerevisiae. Biomol NMR Assign 2016; 10:203-206. [PMID: 26897529 DOI: 10.1007/s12104-016-9667-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 02/05/2016] [Indexed: 06/05/2023]
Abstract
Cyclophilins regulate protein folding, transport and signalling through catalysis of proline isomerization, and are ubiquitously expressed in both prokaryotes and eukaryotes. Cpr3 is the yeast mitochondrial cyclophilin and it is structurally and biophysically uncharacterized so far. Yeast cyclophilin gene cpr3 is essential for the lactate metabolism. Here, we report (1)H, (13)C, and (15)N chemical shift assignments of Cpr3 protein determined by various 2D and 3D heteronuclear NMR experiments at pH 6.5, and temperature 298 K.
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Affiliation(s)
- Vaibhav Kumar Shukla
- UM-DAE-Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Mumbai, 400098, India
| | - Jai Shankar Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, 400076, India
| | - Dipesh Trivedi
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, 400076, India
| | - Ramakrishna V Hosur
- UM-DAE-Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Mumbai, 400098, India.
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, 400076, India.
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Mukherjee D, Mishra P, Joshi M, Thakur PK, Hosur RV, Jarori GK. EWGWS insert in Plasmodium falciparum ookinete surface enolase is involved in binding of PWWP containing peptides: Implications to mosquito midgut invasion by the parasite. Insect Biochem Mol Biol 2016; 68:13-22. [PMID: 26592350 DOI: 10.1016/j.ibmb.2015.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/12/2015] [Accepted: 11/16/2015] [Indexed: 06/05/2023]
Abstract
There are multiple stages in the life cycle of Plasmodium that invade host cells. Molecular machinery involved is such host-pathogen interactions constitute excellent drug targets and/or vaccine candidates. A screen using a phage display library has previously demonstrated presence of enolase on the surface of the Plasmodium ookinete. Phage-displayed peptides that bound to the ookinete contained a conserved motif (PWWP) in their sequence. Here, direct binding of these peptides with recombinant Plasmodium falciparum enolase (rPfeno) was investigated. These peptides showed specific binding to rPfeno, but failed to bind to other enolases. Plasmodium spp enolases are distinct in having an insert of five amino acids ((104)EWGWS(108)) that is not found in host enolases. The possibility of this insert being the recognition motif for the PWWP containing peptides was examined, (i) by comparing the binding of the peptides with rPfeno and a deletion variant Δ-rPfeno lacking (104)EWGWS(108), (ii) by measuring the changes in proton chemical shifts of PWWP peptides on binding to different enolases and (iii) by inter-molecular docking experiment to locate the peptide binding site. Results from these studies showed that the pentapeptide insert of Pfeno indeed constitutes the binding site for the PWWP domain containing peptide ligands. Search for sequences homologous to phage displayed peptides among peritrophic matrix proteins resulted in identification of perlecan, laminin, peritrophin and spacran. The possibility of these PWWP domain-containing proteins in the peritrophic matrix of insect gut to interact with ookinete cell surface enolase and facilitate the invasion of mosquito midgut epithelium is discussed.
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Affiliation(s)
- Debanjan Mukherjee
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Pushpa Mishra
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Mamata Joshi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Prasoon Kumar Thakur
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisbon, 1649- 028 Lisbon, Portugal
| | - R V Hosur
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Gotam K Jarori
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India.
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31
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Mishra P, Sharma S, Hosur RV. 152 Molten globule behavior of apicomplexan protein P2 from Plasmodium falciparumand Toxoplasma gondii. J Biomol Struct Dyn 2015. [DOI: 10.1080/07391102.2015.1032785] [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: 10/23/2022]
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32
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Mishra P, Choudhary S, Hosur RV. Ribosomal Protein P2 from apicomplexan parasite Toxoplasma gondii is intrinsically a molten globule. Biophys Chem 2015; 200-201:27-33. [DOI: 10.1016/j.bpc.2015.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/20/2015] [Accepted: 03/22/2015] [Indexed: 11/30/2022]
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Mishra P, Choudhary S, Mukherjee S, Sengupta D, Sharma S, Hosur RV. Molten globule nature of Plasmodium falciparum P2 homo-tetramer. Biochem Biophys Rep 2015; 1:97-107. [PMID: 29124138 PMCID: PMC5668626 DOI: 10.1016/j.bbrep.2015.03.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 03/20/2015] [Accepted: 03/23/2015] [Indexed: 11/24/2022] Open
Abstract
The P2 protein in Plasmodium falciparum has a high tendency to oligomerize, which seems to drive many of its non-ribosomal functions. During nuclear division of the parasite inside RBC, P2 translocates to the RBC surface as a tetramer. From a systematic study using variety of biophysical techniques, NMR spectral characteristics and relaxation dispersion measurements under different conditions of pH and/or urea concentrations, we deduce that (i) PfP2, an almost entirely helical protein, forms a molten globule monomer at low pH, (ii) at physiological pH, and at micro-molar concentrations, PfP2 is a stable tetramer wherein two dimmers associate sideways with close packing of helices at the interface, and (iii) the molten globule characteristic of the monomer is preserved in the tetramer. This dynamism in the structure of PfP2 may have functional implications since it is known that different kinds of oligomers are transiently formed in the parasite. Plasmodium falciparum P2 (PfP2) is a molten globule. PfP2 is a monomer at pH 2 and a tetramer at physiological pH. The step-wise assembly of the tetramer has been elucidated. A model structure for the PfP2-tetramer has been derived.
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Affiliation(s)
- Pushpa Mishra
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, Maharashtra, India
| | - Sinjan Choudhary
- UM-DAE Centre for Excellence in Basic Sciences, Mumbai University Campus, Mumbai 400098, Maharashtra, India
| | - Sujoy Mukherjee
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Kolkata 700032, West Bengal, India
| | - Disha Sengupta
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, Maharashtra, India
| | - Shobhona Sharma
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, Maharashtra, India
| | - Ramakrishna V Hosur
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, Maharashtra, India.,UM-DAE Centre for Excellence in Basic Sciences, Mumbai University Campus, Mumbai 400098, Maharashtra, India
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Reddy JG, Kumar D, Hosur RV. Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins. Magn Reson Chem 2015; 53:79-87. [PMID: 25178811 DOI: 10.1002/mrc.4135] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 07/29/2014] [Accepted: 08/04/2014] [Indexed: 06/03/2023]
Abstract
Protein NMR spectroscopy has expanded dramatically over the last decade into a powerful tool for the study of their structure, dynamics, and interactions. The primary requirement for all such investigations is sequence-specific resonance assignment. The demand now is to obtain this information as rapidly as possible and in all types of protein systems, stable/unstable, soluble/insoluble, small/big, structured/unstructured, and so on. In this context, we introduce here two reduced dimensionality experiments – (3,2)D-hNCOcanH and (3,2)D-hNcoCAnH – which enhance the previously described 2D NMR-based assignment methods quite significantly. Both the experiments can be recorded in just about 2-3 h each and hence would be of immense value for high-throughput structural proteomics and drug discovery research. The applicability of the method has been demonstrated using alpha-helical bovine apo calbindin-D9k P43M mutant (75 aa) protein. Automated assignment of this data using AUTOBA has been presented, which enhances the utility of these experiments. The backbone resonance assignments so derived are utilized to estimate secondary structures and the backbone fold using Web-based algorithms. Taken together, we believe that the method and the protocol proposed here can be used for routine high-throughput structural studies of proteins.
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Affiliation(s)
- Jithender G Reddy
- Department of Chemical Sciences, Tata Institute of Fundamental Research, 1-Homi Bhabha Road, Colaba, Mumbai, 400005, India
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35
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Reddy JG, Hosur RV. A reduced dimensionality NMR pulse sequence and an efficient protocol for unambiguous assignment in intrinsically disordered proteins. J Biomol NMR 2014; 59:199-210. [PMID: 24854885 DOI: 10.1007/s10858-014-9839-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 05/08/2014] [Indexed: 05/21/2023]
Abstract
Resonance assignment in intrinsically disordered proteins poses a great challenge because of poor chemical shift dispersion in most of the nuclei that are commonly monitored. Reduced dimensionality (RD) experiments where more than one nuclei are co-evolved simultaneously along one of the time axes of a multi-dimensional NMR experiment help to resolve this problem partially, and one can conceive of different combinations of nuclei for co-evolution depending upon the magnetization transfer pathways and the desired information content in the spectrum. Here, we present a RD experiment, (4,3)D-hNCOCAnH, which uses a combination of CO and CA chemical shifts along one of the axes of the 3-dimensional spectrum, to improve spectral dispersion on one hand, and provide information on four backbone atoms of every residue-HN, N, CA and CO chemical shifts-from a single experiment, on the other. The experiment provides multiple unidirectional sequential (i → i - 1) amide (1)H correlations along different planes of the spectrum enabling easy assignment of most nuclei along the protein backbone. Occasional ambiguities that may arise due to degeneracy of amide proton chemical shifts are proposed to be resolved using the HNN experiment described previously (Panchal et al. in J Biomol NMR 20:135-147, 2001). Applications of the experiment and the assignment protocol have been demonstrated using intrinsically disordered α-synuclein (140 aa) protein.
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Affiliation(s)
- Jithender G Reddy
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), 1, Homi Bhabha Road, Colaba, 400005, Mumbai, India
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36
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Borana MS, Mishra P, Pissurlenkar RR, Hosur RV, Ahmad B. Curcumin and kaempferol prevent lysozyme fibril formation by modulating aggregation kinetic parameters. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2014; 1844:670-80. [DOI: 10.1016/j.bbapap.2014.01.009] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 01/01/2014] [Accepted: 01/14/2014] [Indexed: 10/25/2022]
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Reddy JG, Hosur RV. Complete backbone and DENQ side chain NMR assignments in proteins from a single experiment: implications to structure-function studies. J Struct Funct Genomics 2014; 15:25-32. [PMID: 24535112 DOI: 10.1007/s10969-014-9175-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 02/10/2014] [Indexed: 06/03/2023]
Abstract
Resonance assignment is the first and the most crucial step in all nuclear magnetic resonance (NMR) investigations on structure-function relationships in biological macromolecules. Often, the assignment exercise has to be repeated several times when specific interactions with ligands, substrates etc., have to be elucidated for understanding the functional mechanisms. While the protein backbone serves to provide a scaffold, the side chains interact directly with the ligands. Such investigations will be greatly facilitated, if there are rapid methods for obtaining exhaustive information with minimum of NMR experimentation. In this context, we present here a pulse sequence which exploits the recently introduced technique of parallel detection of multiple nuclei, e.g. (1)H and (13)C, and results in two 3D-data sets simultaneously. These yield complete backbone resonance assignment ((1)H(N), (15)N, (13)CO, (1)Hα/(13)Cα, and (1)Hβ/(13)Cβ chemical shifts) and side chain assignment of D, E, N and Q residues. Such an exhaustive assignment has the potential of yielding accurate 3D structures using one or more of several algorithms which calculate structures of the molecules very reliably on the basis of NMR chemical shifts alone. The side chain assignments of D, E, N, and Q will be extremely valuable for interaction studies with different ligands; D and E side chains are known to be involved in majority of catalytic activities. Utility of this experiment has been demonstrated with Ca(2+) bound M-crystallin, which contains largely D, E, N and Q residues at the metal binding sites.
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Affiliation(s)
- Jithender G Reddy
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, 400 005, India
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38
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Abstract
We present here an NMR pulse sequence with 5 independent incrementable time delays within the frame of a 3-dimensional experiment, by incorporating polarization sharing and dual receiver concepts. This has been applied to directly record 3D-HA(CA)NH and 3D-HACACO spectra of proteins simultaneously using parallel detection of (1)H and (13)C nuclei. While both the experiments display intra-residue backbone correlations, the 3D-HA(CA)NH provides also sequential 'i - 1 → i' correlation along the (1)Hα dimension. Both the spectra contain special peak patterns at glycine locations which serve as check points during the sequential assignment process. The 3D-HACACO spectrum contains, in addition, information on prolines and side chains of residues having H-C-CO network (i.e., (1)Hβ, (13)Cβ and (13)COγ of Asp and Asn, and (1)Hγ, (13)Cγ and (13)COδ of Glu and Gln), which are generally absent in most conventional proton detected experiments.
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Affiliation(s)
- Jithender G Reddy
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
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39
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Affiliation(s)
- Pushpa Mishra
- a Department of Chemical Sciences , Tata Institute of Fundamental Research , Mumbai , India
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40
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Reddy JG, Hosur RV. Reduced Dimensionality (4,3)D-HN(C)NH for Rapid Assignment of 1HN–15N HSQC Peaks in Proteins: An Analytical Tool for Protein Folding, Proteomics, and Drug Discovery Programs. Anal Chem 2012; 84:10404-10. [DOI: 10.1021/ac302656k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Jithender G. Reddy
- Department of Chemical
Sciences, Tata Institute of Fundamental Research, 1-Homi Bhabha Road, Colaba, Mumbai−400005,
India
| | - Ramakrishna V. Hosur
- Department of Chemical
Sciences, Tata Institute of Fundamental Research, 1-Homi Bhabha Road, Colaba, Mumbai−400005,
India
- UM-DAE
Centre for
Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santa Cruz, Mumbai−400098,
India
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41
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Kumar D, Gautam A, Hosur RV. A unified NMR strategy for high-throughput determination of backbone fold of small proteins. ACTA ACUST UNITED AC 2012; 13:201-12. [DOI: 10.1007/s10969-012-9144-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 09/18/2012] [Indexed: 11/30/2022]
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42
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Chakraborty S, Susmitha AL, Hosur RV. Selective lighting up of segments around Gly, Ala and Ser/Thr in proteins. Magn Reson Chem 2012; 50:587-91. [PMID: 22806716 DOI: 10.1002/mrc.3843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 06/12/2012] [Accepted: 06/14/2012] [Indexed: 05/23/2023]
Abstract
Direct detection of (13) C nucleus can be used as a valuable alternative where (1) H detection poses a challenge due to relaxation effects, chemical exchange and poor chemical shift dispersion. In this context, we have designed a suite of 2D (13) C(α) -detected hNCA experiments that provide sequential correlations of (13) C(α) with (15) N on one hand and efficient spectroscopic labeling of certain groups of residues, namely, Gly, Ala, Ser and Thr, on the other. These residues act as checkpoints in the sequential walk, which in turn offer new possibilities of backbone assignment of small proteins from a set of 2D experiments, thereby providing great economy in terms of spectrometer time. The direct identification of peptide segments around Gly, Ala, Ser and Thr residues along a protein chain will be highly valuable for deriving important information on sites of ligand binding, phosphorylation, inhibitor/substrate binding, understanding protein folding pathways, comprehending local conformational dynamics etc. without having to obtain complete sequence-specific assignments, which can be time consuming and at times formidable, especially in large proteins. We have illustratively demonstrated the multifaceted applications of these variants of 2D experiments on ubiquitin and M-crystallin. We foresee that these 2D hNCA experiments will provide economic and efficient strategies for studying the structure and function of proteins.
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Affiliation(s)
- Swagata Chakraborty
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, 400 005, India
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43
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Rout MK, Reddy JG, Phillips M, Hosur RV. Single point mutation induced alterations in the equilibrium structural transitions on the folding landscape of HIV-1 protease. J Biomol Struct Dyn 2012; 31:684-93. [PMID: 22909351 DOI: 10.1080/07391102.2012.707459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Equilibrium folding-unfolding transitions are hard to study in HIV-1 protease (PR) because of its autolytic properties. Further, the protease exhibits many tolerant point mutations some of which also impart drug resistance to the protein. It is conceivable that the mutations affect protein's function by altering its folding characteristics; these would clearly depend on the nature of the mutations themselves. In this background, we report here NMR studies on the effects of D25 N mutation, which removes one negative charge from the protein at the active site, on the equilibrium folding behaviour of PR starting from its acetic acid denatured state. It is observed that in PRD25N two slowly exchanging conformations are present at the N-terminal. One of them is similar to that of PR. Though the conformational and dynamics preferences of PR and PRD25N are fairly similar in 9 M acetic acid, they seem to undergo different folding transitions when acetic acid concentration is reduced. The differences are seen in the active site, in the flap, and in the hinge of the flap regions. The present study suggests that such differences, though different in detail, would occur for other mutations as well, and also for different initial denatured states. These would have significant regulatory implications for the efficacy of protease function.
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Affiliation(s)
- Manoj Kumar Rout
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, 400005, India
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44
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Chakraborty S, Hosur RV. Intrinsic vs environment driven equilibrium folding transitions in GTPase effector domain of dynamin: NMR insights. Protein Pept Lett 2012; 19:1297-301. [PMID: 22670673 DOI: 10.2174/092986612803521693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 05/09/2012] [Accepted: 05/09/2012] [Indexed: 11/22/2022]
Abstract
Relative importance of the intrinsic properties of the polypeptide chain vis-a-vis the environmental influences, in driving the folding of a protein, has been a subject of extensive debate and investigation. Folding/misfolding lead to self association in many systems, which have biological functional significance. We compare here, the NMR derived equilibrium folding transitions driven under different environmental conditions in the GTPase Effector Domain of dynamin, which self-associates into megadalton size species. We conclude that though hierarchy of folding and association of GED is substantially influenced by the solvents, these properties, to a good extent are also driven by intrinsic properties of the polypeptide chain, and the regions that form secondary structures, the types of secondary structures formed in those regions, and finally the regions that participate in the self-association are the same, indicating near neighbor interactions would have a telling effect on the final outcome of the folding process. These observations would open a new reliable frontier for elucidating the multiple folding trajectories and consequent self-association, by simulations in vacuum, for this protein.
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Affiliation(s)
- Swagata Chakraborty
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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45
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Kumar D, Borkar A, Hosur RV. Facile backbone (1H, 15N, 13Ca, and 13C') assignment of 13C/15N-labeled proteins using orthogonal projection planes of HNN and HN(C)N experiments and its automation. Magn Reson Chem 2012; 50:357-363. [PMID: 22508472 DOI: 10.1002/mrc.3801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Revised: 01/22/2012] [Accepted: 01/27/2012] [Indexed: 05/31/2023]
Abstract
Recently, we introduced an efficient high-throughput protocol for backbone assignment of small folded proteins based on two-dimensional (2D) projections of HN(C)N suite of experiments and its automation [Borkar et al., J. Biomol. NMR 2011, 50(3), 285-297]. This strategy provides complete sequence-specific assignment of backbone ((1)H, (15)N, (13)C(α), and (13)C') resonances in less than a day; thus, it has great implications for high-throughput structural proteomics. However, in cases when such small folded protein exhibits substantial amide (1)H shift degeneracy (typically seen in alpha-helical proteins), the strategy may fail or lead to ambiguities. Another limitation is with respect to the identification of checkpoints from the variants of 2D-hncNH spectrum. For example, a protein with many GG, GA, AA, SS, TS, TT, and TS types of dipeptide stretches along its sequence, thus the identification of NH cross-peak corresponding to second G, A, S, or T becomes difficult. In this backdrop, we present here two improvements to enhance the utility of the proposed high-throughput AUTOmatic Backbone Assignment protocol: (i) use of 2D-hNnH spectrum and its variants that display additional (1)H-(15)N correlations and thus help to resolve ambiguities arising because of amide (1)H shift degeneracy and (ii) optimization of the τ(CN) delay in the 2D-hncNH experiment that, when properly adjusted, is observed to help remove ambiguities in the identification of the checkpoints. These improvements have also been incorporated in the automation program AUTOmatic Backbone Assignment. Finally, the performance of the strategy and the automation has been demonstrated using the chicken SH3 domain protein.
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Affiliation(s)
- Dinesh Kumar
- Centre of Biomedical Magnetic Resonance, SGPGIMS Campus, Raibareli Road-226014, Lucknow, 400005, India.
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46
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Borkar A, Rout MK, Hosur RV. Denaturation of HIV-1 Protease (PR) Monomer by Acetic Acid: Mechanistic and Trajectory Insights from Molecular Dynamics Simulations and NMR. J Biomol Struct Dyn 2012; 29:893-903. [DOI: 10.1080/073911012010525025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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47
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Rout MK, Mishra P, Atreya HS, Hosur RV. Reduced dimensionality 3D HNCAN for unambiguous HN, CA and N assignment in proteins. J Magn Reson 2012; 216:161-168. [PMID: 22370721 DOI: 10.1016/j.jmr.2012.01.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 01/16/2012] [Accepted: 01/28/2012] [Indexed: 05/31/2023]
Abstract
We present here an improvisation of HNN (Panchal, Bhavesh et al., 2001) called RD 3D HNCAN for backbone (HN, CA and (15)N) assignment in both folded and unfolded proteins. This is a reduced dimensionality experiment which employs CA chemical shifts to improve dispersion. Distinct positive and negative peak patterns of various triplet segments along the polypeptide chain observed in HNN are retained and these provide start and check points for the sequential walk. Because of co-incrementing of CA and (15)N, peaks along one of the dimensions appear at sums and differences of the CA and (15)N chemical shifts. This changes the backbone assignment protocol slightly and we present this in explicit detail. The performance of the experiment has been demonstrated using Ubiquitin and Plasmodium falciparum P2 proteins. The experiment is particularly valuable when two neighboring amino acid residues have nearly identical backbone (15)N chemical shifts.
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Affiliation(s)
- Manoj Kumar Rout
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400 005, India
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48
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Chakraborty S, Pratihar S, Hosur RV. NMR derived model of GTPase effector domain (GED) self association: relevance to dynamin assembly. PLoS One 2012; 7:e30109. [PMID: 22253896 PMCID: PMC3257262 DOI: 10.1371/journal.pone.0030109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/16/2011] [Accepted: 12/09/2011] [Indexed: 11/18/2022] Open
Abstract
Self-association of dynamin to form spiral structures around lipidic vesicles during endocytosis is largely mediated by its 'coiled coil' GTPase Effector Domain (GED), which, in vitro, self-associates into huge helical assemblies. Residue-level structural characterizations of these assemblies and understanding the process of association have remained a challenge. It is also impossible to get folded monomers in the solution phase. In this context, we have developed here a strategy to probe the self-association of GED by first dissociating the assembly using Dimethyl Sulfoxide (DMSO) and then systematically monitoring the refolding into helix and concomitant re-association using NMR spectroscopy, as DMSO concentration is progressively reduced. The short segment, Arg109 - Met116, acts as the nucleation site for helix formation and self-association. Hydrophobic and complementary charge interactions on the surfaces drive self-association, as the helices elongate in both the directions resulting in an antiparallel stack. A small N-terminal segment remains floppy in the assembly. Following these and other published results on inter-domain interactions, we have proposed a plausible mode of dynamin self assembly.
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Affiliation(s)
- Swagata Chakraborty
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Supriya Pratihar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Ramakrishna V. Hosur
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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Chakraborty S, Krishna Mohan P, Hosur RV. Residual structure and dynamics in DMSO-d6 denatured Dynein Light Chain protein. Biochimie 2012; 94:231-41. [DOI: 10.1016/j.biochi.2011.10.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 10/25/2011] [Indexed: 10/15/2022]
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Chakraborty S, Paul S, Hosur RV. Simultaneous acquisition of 13Cα-15N and 1H-15N-15N sequential correlations in proteins: application of dual receivers in 3D HNN. J Biomol NMR 2012; 52:5-10. [PMID: 22203187 DOI: 10.1007/s10858-011-9596-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Accepted: 12/08/2011] [Indexed: 05/31/2023]
Abstract
We describe here, adaptation of the HNN pulse sequence for multiple nuclei detection using two independent receivers by utilizing the detectable (13)C(α) transverse magnetization which was otherwise dephased out in the conventional HNN experiment. It enables acquisition of 2D (13)C(α)-(15)N sequential correlations along with the standard 3D (15)N-(15)N-(1)H correlations, which provides directionality to sequential walk in HNN, on one hand, and enhances the speed of backbone assignment, on the other. We foresee that the implementation of dual direct detection opens up new avenues for a wide variety of modifications that would further enhance the value and applications of the experiment, and enable derivation of hitherto impossible information.
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Affiliation(s)
- Swagata Chakraborty
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, 400005, India
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