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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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5
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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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6
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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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Löwenich D, Kleinermanns K. Porphyrin Fluorescence Dominates UV Photoemission of Folded Cytochrome c. Photochem Photobiol 2007; 83:1308-12. [DOI: 10.1111/j.1751-1097.2007.00145.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Varga A, Flachner B, Gráczer E, Osváth S, Szilágyi AN, Vas M. Correlation between conformational stability of the ternary enzyme-substrate complex and domain closure of 3-phosphoglycerate kinase. FEBS J 2005; 272:1867-85. [PMID: 15819882 DOI: 10.1111/j.1742-4658.2005.04618.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
3-phosphoglycerate kinase (PGK) is a typical two-domain hinge-bending enzyme with a well-structured interdomain region. The mechanism of domain-domain interaction and its regulation by substrate binding is not yet fully understood. Here the existence of strong cooperativity between the two domains was demonstrated by following heat transitions of pig muscle and yeast PGKs using differential scanning microcalorimetry and fluorimetry. Two mutants of yeast PGK containing a single tryptophan fluorophore either in the N- or in the C-terminal domain were also studied. The coincidence of the calorimetric and fluorimetric heat transitions in all cases indicated simultaneous, highly cooperative unfolding of the two domains. This cooperativity is preserved in the presence of substrates: 3-phosphoglycerate bound to the N domain or the nucleotide (MgADP, MgATP) bound to the C domain increased the structural stability of the whole molecule. A structural explanation of domain-domain interaction is suggested by analysis of the atomic contacts in 12 different PGK crystal structures. Well-defined backbone and side-chain H bonds, and hydrophobic and electrostatic interactions between side chains of conserved residues are proposed to be responsible for domain-domain communication. Upon binding of each substrate newly formed molecular contacts are identified that firstly explain the order of the increased heat stability in the various binary complexes, and secondly describe the possible route of transmission of the substrate-induced conformational effects from one domain to the other. The largest stability is characteristic of the native ternary complex and is abolished in the case of a chemically modified inactive form of PGK, the domain closure of which was previously shown to be prevented [Sinev MA, Razgulyaev OI, Vas M, Timchenko AA & Ptitsyn OB (1989) Eur J Biochem180, 61-66]. Thus, conformational stability correlates with domain closure that requires simultaneous binding of both substrates.
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Affiliation(s)
- Andrea Varga
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary
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9
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Gershenson A, Gafni A, Steel D. Comparison of the Time-resolved Absorption and Phosphorescence from the Tryptophan Triplet State in Proteins in Solution. Photochem Photobiol 1998. [DOI: 10.1111/j.1751-1097.1998.tb05216.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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May A, Vas M, Harlos K, Blake C. 2.0 A resolution structure of a ternary complex of pig muscle phosphoglycerate kinase containing 3-phospho-D-glycerate and the nucleotide Mn adenylylimidodiphosphate. Proteins 1996; 24:292-303. [PMID: 8778776 DOI: 10.1002/(sici)1097-0134(199603)24:3<292::aid-prot2>3.0.co;2-j] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The crystal structure of a ternary complex of pig muscle phosphoglycerate kinase (PGK) containing 3-phosphoglycerate (3-PG) and manganese adenylylimidodiphosphate (Mn AMP-PNP) has been determined and refined at 2.0 A resolution. The complex differs from the true substrate ternary complex only in the presence of an imido- rather than an oxylink between beta- and gamma-phosphates of the bound nucleotide. The 3-PG is bound in a similar manner to that observed in binary complexes. The nucleotide is bound in a similar manner to Mg ADP except that the metal ion is coordinated by all three alpha-, beta-, and gamma-phosphates, but not by the protein. The gamma-phosphate, which is transferred in the reaction, is not bound by the protein. One further characteristic of the ternary complex is that Arg-38 moves to a position where its guanidinium group makes a triple interaction with the N-terminal domain, the C-terminal domain, and the 1-carboxyl group of the bound 3-PG. Although a hinge-bending conformation change is seen in the ternary complex, it is no larger than that observed in the 3-PG binary complex. To reduce that distance between two bound substrates to a value consistent with the direct in-line transfer known to occur in PGK, we modeled the closure of a pronounced cleft in the protein structure situated between the bound substrates. This closure suggested a mechanism of catalysis that involves the "capture" of the gamma-phosphate by Arg-38 and the N-terminus of helix-14, which has a conserved Gly-Gly-Gly phosphate binding motif. We propose that nucleophilic attack by the 1-carboxyl group of the 3-PG on the gamma-phosphorus follows the capture of the gamma-phosphate, leading to a pentacoordinate transition state that may be stabilized by hydrogen bonds donated by the NH groups in the N-terminus of helix 14 and the guanidinium group of Arg-38. During the course of the reaction the metal ion is proposed to migrate to a position coordinating the alpha- and beta-phosphates and the carboxyl group of Asp-374. The mechanism is consistent with the structural information from binary and ternary substrate complexes and much solution data, and gives a major catalytic role to Arg-38, as indicated by site-directed mutagenesis.
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Affiliation(s)
- A May
- Laboratory of Molecular Biophysics, University of Oxford, United Kingdom
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11
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Cioni P, Gabellieri E, Gonnelli M, Strambini GB. Heterogeneity of protein conformation in solution from the lifetime of tryptophan phosphorescence. Biophys Chem 1994; 52:25-34. [PMID: 17020825 DOI: 10.1016/0301-4622(94)00039-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/1993] [Accepted: 02/27/1994] [Indexed: 11/27/2022]
Abstract
The decay of Trp phosphorescence of proteins in fluid solutions was shown to provide a sensitive tool for probing the conformational homogeneity of these macromolecules in the millisecond to second time scale. Upon examination of 15 single Trp emitting proteins multiexponential decays were observed in 12 cases, a demonstration that the presence of slowly interconverting conformers in solution is more the norm rather than an exception. The amplitude of preexponential terms, from which the conformer equilibrium is derived, was found to be a sensitive function of solvent composition (buffer, pH, ionic strength and glycerol cosolvent), temperature, and complex formation with substrates and cofactors. In many cases, raising the temperature, a point is reached at which the decay becomes practically monoexponential, meaning that conformer interconversion rates have become commensurate with the triplet lifetime. Estimation of activation free energy barriers to interconversion shows that the large values of DeltaG* are rather similar among polypeptides and that the protein substates involved are sufficiently long-lived to display individual binding/catalytic properties.
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Affiliation(s)
- P Cioni
- Istituto di Biofisica, CNR, Via S. Lorenzo 26, 56127 Pisa, Italy
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12
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Schlyer BD, Schauerte JA, Steel DG, Gafni A. Time-resolved room temperature protein phosphorescence: nonexponential decay from single emitting tryptophans. Biophys J 1994; 67:1192-202. [PMID: 7811933 PMCID: PMC1225475 DOI: 10.1016/s0006-3495(94)80588-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The single room temperature phosphorescent (RTP) residue of horse liver alcohol dehydrogenase (LADH). Trp-314, and of alkaline phosphatase (AP), Trp-109, show nonexponential phosphorescence decays when the data are collected to a high degree of precision. Using the maximum entropy method (MEM) for the analysis of these decays, it is shown that AP phosphorescence decay is dominated by a single Gaussian distribution, whereas for LADH the data reveal two amplitude packets. The lifetime-normalized width of the MEM distribution for both proteins is larger than that obtained for model monoexponential chromophores (e.g., terbium in water and pyrene in cyclohexane). Experiments show that the nonexponential decay is fundamental; i.e., an intrinsic property of the pure protein. Because phosphorescence reports on the state of the emitting chromophore, such nonexponential behavior could be caused by the presence of excited state reactions. However, it is also well known that the phosphorescence lifetime of a tryptophan residue is strongly dependent on the local flexibility around the indole moiety. Hence, the nonexponential phosphorescence decay may also be caused by the presence of at least two states of different local rigidity (in the vicinity of the phosphorescing tryptophan) corresponding to different ground state conformers. The observation that in the chemically homogeneous LADH sample the phosphorescence decay kinetics depends on the excitation wavelength further supports this latter interpretation. This dependence is caused by the wavelength-selective excitation of Trp-314 in a subensemble of LADH molecules with differing hydrophobic and rigid environments. With this interpretation, the data show that interconversion of these states occurs on a time scale long compared with the phosphorescence decay (0.1-1.0 s). Further experiments reveal that with increasing temperature the distributed phosphorescence decay rates for both AP and LADH broaden, thus indicating that either 1) the number of conformational states populated at higher temperature increases or 2) the temperature differentially affects individual conformer states. The nature of the observed heterogeneous triplet state kinetics and their relationship to aspects of protein dynamics are discussed.
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Affiliation(s)
- B D Schlyer
- Institute of Gerontology, University of Michigan, Ann Arbor 48109
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Kwon OS, Blazquez M, Churchich JE. Luminescence spectroscopy of pyridoxic acid and pyridoxic acid bound to proteins. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 219:807-12. [PMID: 8112332 DOI: 10.1111/j.1432-1033.1994.tb18561.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Luminescence techniques, i.e. fluorescence and phosphorescence, have been employed to study pyridoxic acid bound to proteins through a stable amide linkage. Proteins tagged with 4-pyridoxic acid display the following fluorescence properties: (a) emission and excitation spectra centered at around 430 and 320 nm, respectively; (b) fluorescence quantum yields of 0.3-0.4 and (c) average decay times covering the range 8-9.6 ns. The fluorescence properties of the probe have been used to study the dynamics of the protein in the nanosecond time scale. In the absence of molecular oxygen, free and bound 4-pyridoxic acid exhibit long-lived emission at room temperature. The long-lived emission is red-shifted when compared to fluorescence and decays with average life times ranging over 2.2-0.6 ms depending on the nature of the protein. The fluorophore pyridoxic acid covalently linked to proteins is suitable to study the dynamics of proteins, i.e. fast and slow motions of the macromolecule in the nanosecond and millisecond time scales, respectively.
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Affiliation(s)
- O S Kwon
- Department of Biochemistry, University of Tennessee, Knoxville 37996-0840
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Mersol JV, Steel DG, Gafni A. Detection of intermediate protein conformations by room temperature tryptophan phosphorescence spectroscopy during denaturation of Escherichia coli alkaline phosphatase. Biophys Chem 1993; 48:281-91. [PMID: 8298060 DOI: 10.1016/0301-4622(93)85015-a] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The reversible denaturation of Escherichia coli alkaline phosphatase (AP) was followed by monitoring changes in enzymatic activity as well as by measurements of the time-resolved room temperature phosphorescence from Trp 109. It is well known that the denaturants, ethylene diamine tetraacetic acid (EDTA), acid and guanidine hydrochloride (GdnHCl) inactive AP by different mechanisms as reflected by differences in the time dependence of inactivation. However, further information about structural changes that result during inactivation is obtained by measurement of the phosphorescence intensity and radiative decay rate. Time-resolved tryptophan phosphorescence is exquisitely sensitive to changes in the local environment of the emitting residue, unlike the steady state phosphorescence intensity which is a composite of both the lifetime and concentration of the emitting protein species. The results show that while inactivation in EDTA proceeds by loss of the zinc ion as expected, denaturation in acid or GdnHCl produces a heterogeneous population of AP molecules, detected by a distribution analysis of the phosphorescence lifetime, which may reflect multiple pathways to the final unfolded state. Time-resolved phosphorescence also demonstrates the existence of an enzymatically active but structurally less rigid intermediate state during unfolding. As the rigidity decreases, the susceptibility to further denaturation decreases at lower pH but increases with GdnHCl concentration. The experiments provide new insight into the mechanism of denaturation of AP and demonstrate the sensitivity of time-resolved room temperature phosphorescence to the structural details of intermediate states produced during unfolding of proteins.
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Affiliation(s)
- J V Mersol
- Department of Physics, Institute of Gerontology, University of Michigan, Ann Arbor 48109-2007
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