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Mukherjee P, Mukhopadhyay TK, Mukherjee M, Roy P, Ghosh R, Sardar PS, Ghosh S. Triplet state spectroscopy reveals involvement of the buried tryptophan residue 310 in Glyceraldehyde-3-phosphate dehydrogenase (GAPD) in the interaction with acrylamide. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 307:123622. [PMID: 37956485 DOI: 10.1016/j.saa.2023.123622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/31/2023] [Accepted: 11/04/2023] [Indexed: 11/15/2023]
Abstract
Using conventional steady state and time resolved fluorescence study of the interaction between a multi-tryptophan protein and a quencher, it is difficult, if not impossible to identify the particular tryptophan residue/residues involved in the interaction. In this work we have exemplified the above contention using a multi-tryptophan protein, Glyceraldehyde-3-phosphate dehydrogenase (GAPD) from rabbit muscle having three tryptophan (Trp) residues at positions 84, 193 and 310 and a neutral quencher acrylamide in Tris buffer of pH 7.5. From the steady state and time resolved fluorescence quenching (at 298 K) with acrylamide Ksv, K and kq for the system have been calculated. Low temperature phosphorescence (LTP) spectra at 77 K of GAPD in suitable cryosolvent is known to exhibit two (0,0) bands corresponding to two tryptophan residues 193 and 310. Using the LTP study of free GAPD and GAPD - acrylamide it is possible to identify that the buried Trp 310 residue is specifically involved in the interaction with acrylamide. This is possible without doing any site-directed mutagenesis of GAPD which contains Trp residues at 84, 193 and 310. Tyrosine 320 is also specifically quenched. The results have been corroborated using the molecular docking studies. Molecular Dynamics simulation supports our contention of the involvement of Trp 310 and also shows that the other nearest residues of acrylamide are Val175 and Val232.
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Affiliation(s)
| | - Titas Kumar Mukhopadhyay
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Manini Mukherjee
- Chemical Division, State Unit: Karnataka and Goa, Geological Survey of India, Bangalore 560111, India
| | - Pritam Roy
- Molecular Bacteriology, Katholieke Universiteit Leuven, Belgium
| | - Rina Ghosh
- Department of Chemistry, St. Xavier's College, Kolkata 700016, India
| | - Pinki Saha Sardar
- Department of Chemistry, The Bhawanipur Education Society College, Kolkata 700020, India
| | - Sanjib Ghosh
- Department of Chemistry, Adamas University, Barasat, West Bengal, India.
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Paul S, Sepay N, Sarkar S, Roy P, Dasgupta S, Saha Sardar P, Majhi A. Interaction of serum albumins with fluorescent ligand 4-azido coumarin: spectroscopic analysis and molecular docking studies. NEW J CHEM 2017. [DOI: 10.1039/c7nj02335a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The investigation of the binding of 4-AC to biomolecular systems using photophysical techniques and molecular docking studies.
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Affiliation(s)
- Sandip Paul
- Department of Chemistry
- Presidency University
- Kolkata 700 073
- India
| | - Nasim Sepay
- Department of Chemistry
- Presidency University
- Kolkata 700 073
- India
| | - Shrabana Sarkar
- Department of Chemistry
- Presidency University
- Kolkata 700 073
- India
| | - Pritam Roy
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur
- India
| | - Swagata Dasgupta
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur
- India
| | - Pinki Saha Sardar
- The Department of Chemistry
- The Bhawanipur Education Society College
- Kolkata 700020
- India
| | - Anjoy Majhi
- Department of Chemistry
- Presidency University
- Kolkata 700 073
- India
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Mukherjee M, Ghosh R, Chattopadhyay K, Ghosh S. pH-induced structural change of a multi-tryptophan protein MPT63 with immunoglobulin-like fold: identification of perturbed tryptophan residue/residues. J Biomol Struct Dyn 2015; 33:2145-60. [DOI: 10.1080/07391102.2014.992043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Manini Mukherjee
- Department of Chemistry, Presidency University , Kolkata 700 073, India
| | - Ranendu Ghosh
- Department of Chemical and Biomolecular Engineering, University of Delaware , Newark, DE, USA
| | - Krishnananda Chattopadhyay
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology , Kolkata 700 032, India
| | - Sanjib Ghosh
- Department of Chemistry, Presidency University , Kolkata 700 073, India
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Ghorai SK, Tripathy DR, Dasgupta S, Ghosh S. Location and binding mechanism of an ESIPT probe 3-hydroxy-2-naphthoic acid in unsaturated fatty acid bound serum albumins. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 131:1-15. [DOI: 10.1016/j.jphotobiol.2013.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/08/2013] [Accepted: 12/06/2013] [Indexed: 10/25/2022]
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Mukherjee M, Saha Sardar P, Ghorai SK, Samanta SK, Roy AS, Dasgupta S, Ghosh S. A comparative study of interaction of tetracycline with several proteins using time resolved anisotropy, phosphorescence, docking and FRET. PLoS One 2013; 8:e60940. [PMID: 23593355 PMCID: PMC3623961 DOI: 10.1371/journal.pone.0060940] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 03/04/2013] [Indexed: 11/18/2022] Open
Abstract
A comparative study of the interaction of an antibiotic Tetracycline hydrochloride (TC) with two albumins, Human serum albumin (HSA) and Bovine serum albumin (BSA) along with Escherichia Coli Alkaline Phosphatase (AP) has been presented exploiting the enhanced emission and anisotropy of the bound drug. The association constant at 298 K is found to be two orders of magnitude lower in BSA/HSA compared to that in AP with number of binding site being one in each case. Fluorescence resonance energy transfer (FRET) and molecular docking studies have been employed for the systems containing HSA and BSA to find out the particular tryptophan (Trp) residue and the other residues in the proteins involved in the binding process. Rotational correlation time (θc) of the bound TC obtained from time resolved anisotropy of TC in all the protein-TC complexes has been compared to understand the binding mechanism. Low temperature (77 K) phosphorescence (LTP) spectra of Trp residues in the free proteins (HSA/BSA) and in the complexes of HSA/BSA have been used to specify the role of Trp residues in FRET and in the binding process. The results have been compared with those obtained for the complex of AP with TC. The photophysical behaviour (viz., emission maximum, quantum yield, lifetime and θc) of TC in various protic and aprotic polar solvents has been determined to address the nature of the microenvironment of TC in the protein-drug complexes.
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Affiliation(s)
| | | | | | | | - Atanu Singha Roy
- Department of Chemistry, Indian Institute of Technology, Kharagpur, India
| | - Swagata Dasgupta
- Department of Chemistry, Indian Institute of Technology, Kharagpur, India
| | - Sanjib Ghosh
- Department of Chemistry, Presidency University, Kolkata, India
- * E-mail:
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Ghosh R, Mukherjee M, Chattopadhyay K, Ghosh S. Unusual Optical Resolution of All Four Tryptophan Residues in MPT63 Protein by Phosphorescence Spectroscopy: Assignment and Significance. J Phys Chem B 2012; 116:12489-500. [DOI: 10.1021/jp307526f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ranendu Ghosh
- Structural Biology & Bio-Informatics Division, Indian Institute of Chemical Biology, Kolkata-700 032, India
| | - Manini Mukherjee
- Department of Chemistry, Presidency University, Kolkata 700 073, India
| | - Krishnananda Chattopadhyay
- Structural Biology & Bio-Informatics Division, Indian Institute of Chemical Biology, Kolkata-700 032, India
| | - Sanjib Ghosh
- Department of Chemistry, Presidency University, Kolkata 700 073, India
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Kerwin BA, Aoki KH, Gonelli M, Strambini GB. Differentiation of the local structure around tryptophan 51 and 64 in recombinant human erythropoietin by tryptophan phosphorescence. Photochem Photobiol 2008; 84:1172-81. [PMID: 18331401 DOI: 10.1111/j.1751-1097.2008.00307.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recombinant human erythropoietin is a 4-helix bundle, glycosylated cytokine containing three tryptophan residues at positions 51, 64 and 88 whose phosphorescence emission may represent a sensitive probe of the structure at multiple sites near or at the protein surface. This report characterizes the phosphorescence properties (spectral energy, thermal spectral relaxation and phosphorescence lifetime), from low temperature glasses to ambient temperature, of the native protein plus that of three single point mutation analogs where each Trp was replaced by Phe. The structural information inferred from the phosphorescence parameters was essentially in good agreement with the structure of the Escherichia coli-produced nonglycosylated protein determined by nuclear magnetic resonance (Cheetham et al., Nat Struct Biol [1998] 5:861). The results showed that the fluorescence and phosphorescence spectra of the native protein were entirely due to independent contributions of Trp51 and Trp64 and that Trp88 was quenched under all conditions. The phosphorescence emissions of Trp51 and Trp64 were differentiated by their unique spectra at 77 K with Trp64 exhibiting an unusually blueshifted spectrum likely due to the attractive interaction of Arg110 and Lys116 with the ground state dipole of Trp64. In the native protein the room temperature phosphorescence lifetime of Trp64 was relatively short with a time of 1.62 ms whereas the lifetime of Trp51 was five-fold longer. Characterization of the single point mutation analogs showed that each lifetime was composed of multiple components revealing the presence of multiple stable conformations of the protein at these surface sites.
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Affiliation(s)
- Bruce A Kerwin
- Department of Pharmaceutics, Amgen, Inc., Thousand Oaks, CA, USA.
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Nishimura G, Pack CG, Tamura M. Phosphorescence decay time measurements using intensity correlation spectroscopy. Exp Mol Pathol 2007; 82:175-83. [PMID: 17346700 DOI: 10.1016/j.yexmp.2007.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2006] [Revised: 01/12/2007] [Accepted: 01/17/2007] [Indexed: 10/23/2022]
Abstract
In this paper, we report on phosphorescence measurements for oxygen dynamics in cells by means of a correlation method, which is an expansion of the fluorescence correlation spectroscopy. The intensity correlation function of the emission excited by a pulsed light source was measured. With changing the pulse timing, both the fluorescence correlation function and the decay time of phosphorescence could be analyzed. This method was applied for the analysis of the oxygen dynamics in HeLa cells stained by Pd(II)-porphine. The decay function consisted of two exponential components, which might be attributed to free and protein-bound forms of Pd(II)-porphine in the cell, respectively. The relative change of the oxygen concentration under normal and uncoupled respiration conditions was also measured. The simplicity of this method is a great advantage in the biological applications. Although the current system we used was limited in the temporal resolution, the method is in principle applicable to faster decay time measurements down to the nano-second range of the fluorescence decay times.
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Affiliation(s)
- Goro Nishimura
- Biophysics Laboratory, Research Institute for Electronic Science, Hokkaido University, N12W6, Sapporo 060-0812, Japan.
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