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Goswami S, Manna B, Chattopadhyay K, Ghosh A, Datta S. Role of Conformational Change and Glucose Binding Sites in the Enhanced Glucose Tolerance of Agrobacterium tumefaciens 5A GH1 β-Glucosidase Mutants. J Phys Chem B 2021; 125:9402-9416. [PMID: 34384214 DOI: 10.1021/acs.jpcb.1c02150] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
β-Glucosidases are often inhibited by their reaction product glucose and a barrier to the efficient lignocellulosic biomass hydrolysis to glucose. We had previously reported the mutants, C174V, and H229S, with a nearly 2-fold increased glucose tolerance over the wild type (WT), H0HC94, encoded in Agrobacterium tumefaciens 5A (apparent Ki,Glc = 686 mM). We report our steady-state and time-resolved intrinsic fluorescence spectroscopy, circular dichroism, and isothermal titration calorimetry (ITC) studies to further understand increased glucose tolerance. Changes in the mutants' emission intensity and the differential change in quenching rate in the absence and presence of glucose reflect changes in protein conformation by glucose. Time-resolved lifetime and anisotropy measurements further indicated the microenvironment differences across solvent-exposed tryptophan residues and a higher hydrodynamic radius due to glucose binding, respectively. ITC measurements confirmed the increase of glucose binding sites in the mutants. The experiment results were supported by molecular dynamics simulations, which revealed significant variations in the glucose-protein hydrogen-bonding profiles. Protein structure network analysis of the simulated structures further indicates the mutants' conformation change than the WT. Computational studies also indicated additional glucose binding sites in mutants. Our results indicate the role of glucose binding in modulating the enzyme response to glucose.
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Affiliation(s)
- Shubhasish Goswami
- Protein Engineering Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Bharat Manna
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Krishnananda Chattopadhyay
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mallick Road, Kolkata 700032, India
| | - Amit Ghosh
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India.,P. K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Supratim Datta
- Protein Engineering Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India.,Center for the Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India.,Center for the Climate and Environmental Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
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Di Nardo G, Di Venere A, Zhang C, Nicolai E, Castrignanò S, Di Paola L, Gilardi G, Mei G. Polymorphism on human aromatase affects protein dynamics and substrate binding: spectroscopic evidence. Biol Direct 2021; 16:8. [PMID: 33902660 PMCID: PMC8073906 DOI: 10.1186/s13062-021-00292-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 04/08/2021] [Indexed: 01/07/2023] Open
Abstract
Human aromatase is a member of the cytochrome P450 superfamily, involved in steroid hormones biosynthesis. In particular, it converts androgen into estrogens being therefore responsible for the correct sex steroids balance. Due to its capacity in producing estrogens it has also been considered as a promising target for breast cancer therapy. Two single-nucleotide polymorphisms (R264C and R264H) have been shown to alter aromatase activity and they have been associated to an increased or decreased risk for estrogen-dependent pathologies. Here, the effect of these mutations on the protein dynamics is investigated by UV/FTIR and time resolved fluorescence spectroscopy. H/D exchange rates were measured by FTIR for the three proteins in the ligand-free, substrate- and inhibitor-bound forms and the data indicate that the wild-type enzyme undergoes a conformational change leading to a more compact tertiary structure upon substrate or inhibitor binding. Indeed, the H/D exchange rates are decreased when a ligand is present. In the variants, the exchange rates in the ligand-free and -bound forms are similar, indicating that a structural change is lacking, despite the single amino acid substitution is located in the peripheral shell of the protein molecule. Moreover, the fluorescence lifetimes data show that the quenching effect on tryptophan-224 observed upon ligand binding in the wild-type, is absent in both variants. Since this residue is located in the catalytic pocket, these findings suggest that substrate entrance and/or retention in the active site is partially compromised in both mutants. A contact network analysis demonstrates that the protein structure is organized in two main clusters, whose connectivity is altered by ligand binding, especially in correspondence of helix-G, where the amino acid substitutions occur. Our findings demonstrate that SNPs resulting in mutations on aromatase surface modify the protein flexibility that is required for substrate binding and catalysis. The cluster analysis provides a rationale for such effect, suggesting helix G as a possible target for aromatase inhibition.
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Affiliation(s)
- Giovanna Di Nardo
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123, Turin, Italy
| | - Almerinda Di Venere
- Dipartimento di Medicina Sperimentale, Università di Roma Tor Vergata, Via Montpellier 1, 00133, Rome, Italy
| | - Chao Zhang
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123, Turin, Italy
| | - Eleonora Nicolai
- Dipartimento di Medicina Sperimentale, Università di Roma Tor Vergata, Via Montpellier 1, 00133, Rome, Italy
| | - Silvia Castrignanò
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123, Turin, Italy
| | - Luisa Di Paola
- Dipartimento di Ingegneria, Unità di Fondamenti Chimico-Fisici dell'Ingegneria Chimica, Università Campus Bio-Medico di Roma, via Álvaro del Portillo 21, 00128, Rome, Italy
| | - Gianfranco Gilardi
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123, Turin, Italy.
| | - Giampiero Mei
- Dipartimento di Medicina Sperimentale, Università di Roma Tor Vergata, Via Montpellier 1, 00133, Rome, Italy.
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Pedersen JN, Sørensen HV, Otzen DE. Stabilizing vitamin D3 using the molten globule state of α-lactalbumin. J Dairy Sci 2018; 101:1817-1826. [DOI: 10.3168/jds.2017-13818] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/17/2017] [Indexed: 11/19/2022]
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Singh MI, Jain V. Identification and Characterization of an Inside-Out Folding Intermediate of T4 Phage Sliding Clamp. Biophys J 2017; 113:1738-1749. [PMID: 29045868 DOI: 10.1016/j.bpj.2017.08.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/15/2017] [Accepted: 08/28/2017] [Indexed: 10/18/2022] Open
Abstract
Protein folding process involves formation of transiently occurring intermediates that are difficult to isolate and characterize. It is both necessary and interesting to characterize the structural conformations adopted by these intermediates, also called molten globules (MG), to understand protein folding. Here, we investigated the equilibrium (un)folding intermediate state of T4 phage gene product 45 (gp45, also known as DNA polymerase processivity factor or sliding clamp) obtained during chemical denaturation. We show that gp45 undergoes substantial conformational rearrangement during unfolding and forms an expanded dry-MG. By monitoring the fluorescence of tryptophans that were strategically introduced at various sites, we demonstrate that the urea-treated molecule has its surface residues flip inside the core, and closely placed residues move farther. We were also able to isolate and purify the MG form of gp45 in native condition (i.e., nondenaturing buffer, at physiological pH and temperature); characteristics of this purified molecule substantially match with urea-treated wild-type gp45. To the best of our knowledge, this is one of the few reports that demonstrate the isolation and purification of a protein folding intermediate in native condition. We believe that our work not only allows us to dissect the process of protein folding, but will also help in the designing of folding inhibitors against sliding clamps to treat a wide variety of diseases from bacterial infection to cancer, due to the vast presence of clamps in all the domains of life.
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Affiliation(s)
- Manika Indrajit Singh
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, India
| | - Vikas Jain
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, India.
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Ithychanda SS, Dou K, Robertson SP, Qin J. Structural and thermodynamic basis of a frontometaphyseal dysplasia mutation in filamin A. J Biol Chem 2017; 292:8390-8400. [PMID: 28348077 DOI: 10.1074/jbc.m117.776740] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/10/2017] [Indexed: 01/12/2023] Open
Abstract
Filamin-mediated linkages between transmembrane receptors (TR) and the actin cytoskeleton are crucial for regulating many cytoskeleton-dependent cellular processes such as cell shape change and migration. A major TR binding site in the immunoglobulin repeat 21 (Ig21) of filamin is masked by the adjacent repeat Ig20, resulting in autoinhibition. The TR binding to this site triggers the relief of Ig20 and protein kinase A (PKA)-mediated phosphorylation of Ser-2152, thereby dynamically regulating the TR-actin linkages. A P2204L mutation in Ig20 reportedly cause frontometaphyseal dysplasia, a skeletal disorder with unknown pathogenesis. We show here that the P2204L mutation impairs a hydrophobic core of Ig20, generating a conformationally fluctuating molten globule-like state. Consequently, unlike in WT filamin, where PKA-mediated Ser-2152 phosphorylation is ligand-dependent, the P2204L mutant is readily accessible to PKA, promoting ligand-independent phosphorylation on Ser-2152. Strong TR peptide ligands from platelet GP1bα and G-protein-coupled receptor MAS effectively bound Ig21 by displacing Ig20 from autoinhibited WT filamin, but surprisingly, the capacity of these ligands to bind the P2204L mutant was much reduced despite the mutation-induced destabilization of the Ig20 structure that supposedly weakens the autoinhibition. Thermodynamic analysis indicated that compared with WT filamin, the conformationally fluctuating state of the Ig20 mutant makes Ig21 enthalpically favorable to bind ligand but with substantial entropic penalty, resulting in total higher free energy and reduced ligand affinity. Overall, our results reveal an unusual structural and thermodynamic basis for the P2204L-induced dysfunction of filamin and frontometaphyseal dysplasia disease.
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Affiliation(s)
- Sujay S Ithychanda
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
| | - Kevin Dou
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
| | | | - Jun Qin
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195.
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Mensch C, Barron LD, Johannessen C. Ramachandran mapping of peptide conformation using a large database of computed Raman and Raman optical activity spectra. Phys Chem Chem Phys 2016; 18:31757-31768. [DOI: 10.1039/c6cp05862k] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A novel ROA database is reported that assigns peptide structures in detail by pattern recognition of the experimental spectrum.
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Affiliation(s)
- Carl Mensch
- Department of Chemistry
- University of Antwerp
- Antwerp
- Belgium
- Department of Inorganic and Physical Chemistry
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