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Singh Y, Sarkar D, Duari S, G S, Indra Guru PK, M V H, Singh D, Bhardwaj S, Kalia J. Dissecting the contributions of membrane affinity and bivalency of the spider venom protein DkTx to its sustained mode of TRPV1 activation. J Biol Chem 2023; 299:104903. [PMID: 37302551 PMCID: PMC10404664 DOI: 10.1016/j.jbc.2023.104903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/03/2023] [Accepted: 06/05/2023] [Indexed: 06/13/2023] Open
Abstract
The spider venom protein, double-knot toxin (DkTx), partitions into the cellular membrane and binds bivalently to the pain-sensing ion channel, TRPV1, triggering long-lasting channel activation. In contrast, its monovalent single knots membrane partition poorly and invoke rapidly reversible TRPV1 activation. To discern the contributions of the bivalency and membrane affinity of DkTx to its sustained mode of action, here, we developed diverse toxin variants including those containing truncated linkers between individual knots, precluding bivalent binding. Additionally, by appending the single-knot domains to the Kv2.1 channel-targeting toxin, SGTx, we created monovalent double-knot proteins that demonstrated higher membrane affinity and more sustained TRPV1 activation than the single-knots. We also produced hyper-membrane affinity-possessing tetra-knot proteins, (DkTx)2 and DkTx-(SGTx)2, that demonstrated longer-lasting TRPV1 activation than DkTx, establishing the central role of the membrane affinity of DkTx in endowing it with its sustained TRPV1 activation properties. These results suggest that high membrane affinity-possessing TRPV1 agonists can potentially serve as long-acting analgesics.
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Affiliation(s)
- Yashaswi Singh
- Department of Biology, Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
| | - Debayan Sarkar
- Department of Biology, Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
| | - Subhadeep Duari
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
| | - Shashaank G
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
| | - Pawas Kumar Indra Guru
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
| | - Hrishikesh M V
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
| | - Dheerendra Singh
- Department of Biology, Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, India
| | - Sahil Bhardwaj
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
| | - Jeet Kalia
- Department of Biology, Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India; Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, India; Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India.
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2
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Kurbanov M, Kirsch ZJ, Krishna J, Dutta R, Vachet RW, Thayumanavan S. Multisite Labeling of Proteins Using the Ligand-Directed Reactivity of Triggerable Michael Acceptors. Bioconjug Chem 2023; 34:1130-1138. [PMID: 37220065 PMCID: PMC10363337 DOI: 10.1021/acs.bioconjchem.3c00155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Targeted modification of endogenous proteins without genetic manipulation of protein expression machinery has a range of applications from chemical biology to drug discovery. Despite being demonstrated to be effective in various applications, target-specific protein labeling using ligand-directed strategies is limited by stringent amino acid selectivity. Here, we present highly reactive ligand-directed triggerable Michael acceptors (LD-TMAcs) that feature rapid protein labeling. Unlike previous approaches, the unique reactivity of LD-TMAcs enables multiple modifications on a single target protein, effectively mapping the ligand binding site. This capability is attributed to the tunable reactivity of TMAcs that enable the labeling of several amino acid functionalities via a binding-induced increase in local concentration while remaining fully dormant in the absence of protein binding. We demonstrate the target selectivity of these molecules in cell lysates using carbonic anhydrase as the model protein. Furthermore, we demonstrate the utility of this method by selectively labeling membrane-bound carbonic anhydrase XII in live cells. We envision that the unique features of LD-TMAcs will find use in target identification, investigation of binding/allosteric sites, and studying membrane proteins.
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Affiliation(s)
- Myrat Kurbanov
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Zachary J Kirsch
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Jithu Krishna
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Ranit Dutta
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Richard W Vachet
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Center for Bioactive Delivery, Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - S Thayumanavan
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Center for Bioactive Delivery, Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Department of Biomedical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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3
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Reddy MM, Bhandari P, Hati KC, Sandanaraj BS. Rational Design of Self-Assembling Artificial Proteins Utilizing a Micelle-Assisted Protein Labeling Technology (MAPLabTech): Testing the Scope. Chembiochem 2022; 23:e202100607. [PMID: 35181981 DOI: 10.1002/cbic.202100607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/03/2022] [Indexed: 11/07/2022]
Abstract
Self-assembling artificial proteins (SAPs) have gained enormous interest in recent years due to their applications in different fields. Synthesis of well-defined monodisperse SAPs is accomplished predominantly through genetic methods. However, the last decade has witnessed the use of a few chemical technologies for this purpose. In particular, micelle-assisted protein labeling technology (MAPLabTech) has made huge progress in this area. The first generation MAPLabTech focused on site-specific labeling of the active-site residue of serine proteases to make SAPs. Further, this methodology was exploited for labeling of N-terminal residue of a globular protein to make functional SAPs. In this study, we describe the synthesis of novel SAPs by developing a chemical method for site-specific labeling of a surface-exposed cysteine residue of globular proteins. In addition, we disclose the synthesis of redox-sensitive SAPs and their systematic self-assembly and disassembly studies using size-exclusion chromatography. Altogether these studies further expand the scope of MAPLabTech in different fields such as vaccine design, targeted drug delivery, diagnostic imaging, biomaterials, and tissue engineering.
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Affiliation(s)
- Mullapudi Mohan Reddy
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, India
| | - Pavankumar Bhandari
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, India
| | - Kshitish Chandra Hati
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, India
| | - Britto S Sandanaraj
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, India
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
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4
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Reddy MM, Bathla P, Sandanaraj BS. A Universal Chemical Method for Rational Design of Protein-Based Nanoreactors*. Chembiochem 2021; 22:3042-3048. [PMID: 34339092 DOI: 10.1002/cbic.202100315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/30/2021] [Indexed: 12/28/2022]
Abstract
Self-assembly of a monomeric protease to form a multi-subunit protein complex "proteasome" enables targeted protein degradation in living cells. Naturally occurring proteasomes serve as an inspiration and blueprint for the design of artificial protein-based nanoreactors. Here we disclose a general chemical strategy for the design of proteasome-like nanoreactors. Micelle-assisted protein labeling (MAPLab) technology along with the N-terminal bioconjugation strategy is utilized for the synthesis of a well-defined monodisperse self-assembling semi-synthetic protease. The designed protein is programmed to self-assemble into a proteasome-like nanostructure which preserves the functional properties of native protease.
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Affiliation(s)
- Mullapudi Mohan Reddy
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, India
| | - Punita Bathla
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Britto S Sandanaraj
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, India.,Department of Biology, Indian Institute of Science Education and Research, Pune, India
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5
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Bhandari PJ, Sandanaraj BS. Rational Design of Programmable Monodisperse Semi-Synthetic Protein Nanomaterials Containing Engineered Disulfide Functionality*. Chembiochem 2021; 22:2966-2972. [PMID: 34265138 DOI: 10.1002/cbic.202100288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/15/2021] [Indexed: 12/28/2022]
Abstract
The reversible nature of disulfide functionality has been exploited to design intelligent materials such as nanocapsules, micelles, vesicles, inorganic nanoparticles, peptide and nucleic acid nanodevices. Herein, we report a new chemical methodology for the construction redox-sensitive protein assemblies using monodisperse facially amphiphilic protein-dendron bioconjugates. The disulfide functionality is strategically placed between the dendron and protein domains. The custom designed bioconjugates self-assembled into nanoscopic objects of a defined size dictated by the nature of dendron domain. The stimuli-responsive behavior of the protein assemblies is demonstrated using a suitable redox trigger.
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Affiliation(s)
| | - Britto S Sandanaraj
- Department of Chemistry, Indian Institute of Science Education and Research -, Pune, India.,Department of Biology, Indian Institute of Science Education and Research -, Pune, India
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6
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Bhandari PJ, Reddy MM, Rao KJ, Sandanaraj BS. Rapid Chemical Synthesis of Self-Assembling Semi-Synthetic Proteins. J Org Chem 2021; 86:8576-8589. [PMID: 34133144 DOI: 10.1021/acs.joc.1c00195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The design of well-defined monodispersed self-assembling semi-synthetic proteins is emerging as a promising research avenue. These proteins hold great potential to be used as scaffolds for various protein nanotechnology applications. Currently, there are very few chemical methods reported; however, they suffer from elaborate multistep organic synthesis. Herein, we report a new chemical methodology for the rapid synthesis of a diverse set of semi-synthetic protein families, which include protein amphiphiles, facially amphiphilic protein-dendron conjugates, and pH-sensitive protein-dendron conjugates. This chemical method holds great potential to access a wide variety of semi-synthetic proteins in a short time.
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Affiliation(s)
| | - Mullapudi Mohan Reddy
- Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, India
| | | | - Britto S Sandanaraj
- Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, India
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
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7
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Bhandari PJ, Sandanaraj BS. Programmed and Sequential Disassembly of Multi-responsive Supramolecular Protein Nanoassemblies: A Detailed Mechanistic Investigation. Chembiochem 2020; 22:876-887. [PMID: 33073455 DOI: 10.1002/cbic.202000581] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/18/2020] [Indexed: 12/19/2022]
Abstract
The rational design of a multi-responsive protein-based supramolecular system that can predictably respond to more than one stimulus remains an essential but highly challenging goal in biomolecular engineering. Herein, we report a novel chemical method for the construction of multi-responsive supramolecular nanoassemblies using custom-designed facially amphiphilic monodisperse protein-dendron bioconjugates. The macromolecular synthons contain a globular hydrophilic protein domain site-specifically conjugated to photo-responsive hydrophobic benzyl-ether dendrons of different generations through oligo(ethylene glycol) linkers of defined length. The size of the protein nanoassemblies can be systematically tuned by choosing an appropriate dendron or linker of defined length. Exposure of protein nanoassemblies to light results in partial rather than complete disassembly of the complex. The newly formed protein nanoparticle no longer responds to light but could be disassembled into constitutive monomers under acidic conditions or by further treatment with a small molecule. More interestingly, the distribution ratio of the assembled versus disassembled states of protein nanoassemblies after photochemical reaction does not depend on dendron generation, the nature of the linker functionality or the identity of the protein, but is heavily influenced by the linker length. In sum, this work discloses a new chemical method for the rational design of a monodisperse multi-responsive protein-based supramolecular system with exquisite control over the disassembly process.
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Affiliation(s)
- Pavankumar Janardhan Bhandari
- Department of Chemistry, Indian Institute of Science Education and Research, 100 Homi Bhabha Road, Pune, 411008, India
| | - Britto S Sandanaraj
- Department of Chemistry, Indian Institute of Science Education and Research, 100 Homi Bhabha Road, Pune, 411008, India.,Department of Biology, Indian Institute of Science Education and Research, 100 Homi Bhabha Road, Pune, 411008, India
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8
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Chakraborty S, Khamrui R, Ghosh S. Redox responsive activity regulation in exceptionally stable supramolecular assembly and co-assembly of a protein. Chem Sci 2020; 12:1101-1108. [PMID: 34163877 PMCID: PMC8179030 DOI: 10.1039/d0sc05312k] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/14/2020] [Indexed: 11/23/2022] Open
Abstract
Supramolecular assembly of biomolecules/macromolecules stems from the desire to mimic complex biological structures and functions of living organisms. While DNA nanotechnology is already in an advanced stage, protein assembly is still in its infancy as it is a significantly difficult task due to their large molecular weight, conformational complexity and structural instability towards variation in temperature, pH or ionic strength. This article reports highly stable redox-responsive supramolecular assembly of a protein Bovine serum albumin (BSA) which is functionalized with a supramolecular structure directing unit (SSDU). The SSDU consists of a benzamide functionalized naphthalene-diimide (NDI) chromophore which is attached with the protein by a bio-reducible disulfide linker. The SSDU attached protein (NDI-BSA) exhibits spontaneous supramolecular assembly in water by off-set π-stacking among the NDI chromophores, leading to the formation of spherical nanoparticles (diameter: 150-200 nm). The same SSDU when connected with a small hydrophilic wedge (NDI-1) instead of the large globular protein, exhibits a different π-stacking mode with relatively less longitudinal displacement which results in a fibrillar network and hydrogelation. Supramolecular co-assembly of NDI-BSA and NDI-1 (3 : 7) produces similar π-stacking and an entangled 1D morphology. Both the spherical assembly of NDI-BSA or the fibrillar co-assembly of NDI-BSA + NDI-1 (3 : 7) provide sufficient thermal stability to the protein as its thermal denaturation could be completely surpassed while the secondary structure remained intact. However, the esterase like activity of the protein reduced significantly as a result of such supramolecular assembly indicating limited access by the substrate to the active site of the enzyme located in the confined environment. In the presence of glutathione (GSH), a biologically important tri-peptide, due to the cleavage of the disulfide bond, the protein became free and was released, resulting in fully regaining its enzymatic activity. Such supramolecular assembly provided excellent protection to the protein against enzymatic hydrolysis as the relative hydrolysis was estimated to be <30% for the co-assembled protein with respect to the free protein under identical conditions. Similar to bioactivity, the enzymatic hydrolysis also became prominent after GSH-treatment, confirming that the lack of hydrolysis in the supramolecularly assembled state is indeed related to the confinement of the protein in the nanostructure assembly.
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Affiliation(s)
- Saptarshi Chakraborty
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science 2A and 2B Raja S. C. Mullick Road Kolkata India-700032
| | - Rajesh Khamrui
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science 2A and 2B Raja S. C. Mullick Road Kolkata India-700032
| | - Suhrit Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science 2A and 2B Raja S. C. Mullick Road Kolkata India-700032
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9
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Mathur Y, Sreyas S, Datar PM, Sathian MB, Hazra AB. CobT and BzaC catalyze the regiospecific activation and methylation of the 5-hydroxybenzimidazole lower ligand in anaerobic cobamide biosynthesis. J Biol Chem 2020; 295:10522-10534. [PMID: 32503839 PMCID: PMC7397103 DOI: 10.1074/jbc.ra120.014197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/01/2020] [Indexed: 11/06/2022] Open
Abstract
Vitamin B12 and other cobamides are essential cofactors required by many organisms and are synthesized by a subset of prokaryotes via distinct aerobic and anaerobic routes. The anaerobic biosynthesis of 5,6-dimethylbenzimidazole (DMB), the lower ligand of vitamin B12, involves five reactions catalyzed by the bza operon gene products, namely the hydroxybenzimidazole synthase BzaAB/BzaF, phosphoribosyltransferase CobT, and three methyltransferases, BzaC, BzaD, and BzaE, that conduct three distinct methylation steps. Of these, the methyltransferases that contribute to benzimidazole lower ligand diversity in cobamides remain to be characterized, and the precise role of the bza operon protein CobT is unclear. In this study, we used the bza operon from the anaerobic bacterium Moorella thermoacetica (comprising bzaA-bzaB-cobT-bzaC) to examine the role of CobT and investigate the activity of the first methyltransferase, BzaC. We studied the phosphoribosylation catalyzed by MtCobT and found that it regiospecifically activates 5-hydroxybenzimidazole (5-OHBza) to form the 5-OHBza-ribotide (5-OHBza-RP) isomer as the sole product. Next, we characterized the domains of MtBzaC and reconstituted its methyltransferase activity with the predicted substrate 5-OHBza and with two alternative substrates, the MtCobT product 5-OHBza-RP and its riboside derivative 5-OHBza-R. Unexpectedly, we found that 5-OHBza-R is the most favored MtBzaC substrate. Our results collectively explain the long-standing observation that the attachment of the lower ligand in anaerobic cobamide biosynthesis is regiospecific. In conclusion, we validate MtBzaC as a SAM:hydroxybenzimidazole-riboside methyltransferase (HBIR-OMT). Finally, we propose a new pathway for the synthesis and activation of the benzimidazolyl lower ligand in anaerobic cobamide biosynthesis.
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Affiliation(s)
- Yamini Mathur
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Sheryl Sreyas
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, India
| | - Prathamesh M Datar
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, India
| | - Manjima B Sathian
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, India
| | - Amrita B Hazra
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, India
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Sandanaraj BS, Bhandari PJ, Reddy MM, Lohote AB, Sahoo B. Design, Synthesis, and Self‐Assembly Studies of a Suite of Monodisperse, Facially Amphiphilic, Protein–Dendron Conjugates. Chembiochem 2019; 21:408-416. [DOI: 10.1002/cbic.201900341] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Britto S. Sandanaraj
- Departments of Chemistry & BiologyIndian Institute of Science Education and Research (IISER) Pune 411 008 India
| | | | - Mullapudi Mohan Reddy
- Departments of Chemistry & BiologyIndian Institute of Science Education and Research (IISER) Pune 411 008 India
| | - Akshay Bhagwan Lohote
- Departments of Chemistry & BiologyIndian Institute of Science Education and Research (IISER) Pune 411 008 India
| | - Bankanidhi Sahoo
- Tata Institute of Fundamental Research Hyderabad (TIFR Hyd) Hyderabad 500019 India
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11
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Sandanaraj BS, Reddy MM, Rao KJ, Bhandari PJ. Rational Design of Semi‐Synthetic Protein Complexes with the Defined Oligomeric State. ChemistrySelect 2019. [DOI: 10.1002/slct.201901317] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Britto S Sandanaraj
- Department of ChemistryIndian Institute of Science Education and Research (IISER), Pune 411 008 India
| | - Mullapudi Mohan Reddy
- Department of ChemistryIndian Institute of Science Education and Research (IISER), Pune 411 008 India
| | - Kasuladevu Jagannadha Rao
- Department of ChemistryIndian Institute of Science Education and Research (IISER), Pune 411 008 India
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