1
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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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2
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Seckfort D, Lynch GC, Pettitt BM. The lac repressor hinge helix in context: The effect of the DNA binding domain and symmetry. Biochim Biophys Acta Gen Subj 2020; 1864:129538. [PMID: 31958546 DOI: 10.1016/j.bbagen.2020.129538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 01/04/2023]
Abstract
The Lac system of genes has been an important model system in understanding gene regulation. When the dimer lac repressor protein binds to the correct DNA sequence, the hinge region of the protein goes through a disorder to order transition. The hinge region is disordered when binding to nonoperator sequences. This region of the protein must pay a conformational entropic penalty to order when it is bound to operator DNA. Structural studies show that this region is flexible. Previous simulations showed that this region is disordered when free in solution without the DNA binding domain present. Our simulations corroborate that this region is extremely flexible in solution, but we find that the presence of the DNA binding domain proximal to the hinge helix and salt make the ordered conformation more favorable even without DNA present.
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Affiliation(s)
- Danielle Seckfort
- Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston 77030, TX, USA; Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston 77555, TX, USA
| | - Gillian C Lynch
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston 77555, TX, USA
| | - B Montgomery Pettitt
- Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston 77030, TX, USA; Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston 77555, TX, USA.
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3
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Seckfort D, Montgomery Pettitt B. Price of disorder in the lac repressor hinge helix. Biopolymers 2018; 110:e23239. [PMID: 30485404 DOI: 10.1002/bip.23239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/12/2018] [Accepted: 10/04/2018] [Indexed: 12/26/2022]
Abstract
The Lac system of genes has been pivotal in understanding gene regulation. When the lac repressor protein binds to the correct DNA sequence, the hinge region of the protein goes through a disorder to order transition. The structure of this region of the protein is well understood when it is in this bound conformation, but less so when it is not. Structural studies show that this region is flexible. Our simulations show this region is extremely flexible in solution; however, a high concentration of salt can help kinetically trap the hinge helix. Thermodynamically, disorder is more favorable without the DNA present.
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Affiliation(s)
- Danielle Seckfort
- Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas
| | - B Montgomery Pettitt
- Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas.,Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas
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4
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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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5
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Sousa FL, Parente DJ, Hessman JA, Chazelle A, Teichmann SA, Swint-Kruse L. Data on publications, structural analyses, and queries used to build and utilize the AlloRep database. Data Brief 2016; 8:948-57. [PMID: 27508249 PMCID: PMC4961497 DOI: 10.1016/j.dib.2016.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/22/2016] [Accepted: 07/04/2016] [Indexed: 01/08/2023] Open
Abstract
The AlloRep database (www.AlloRep.org) (Sousa et al., 2016) [1] compiles extensive sequence, mutagenesis, and structural information for the LacI/GalR family of transcription regulators. Sequence alignments are presented for >3000 proteins in 45 paralog subfamilies and as a subsampled alignment of the whole family. Phenotypic and biochemical data on almost 6000 mutants have been compiled from an exhaustive search of the literature; citations for these data are included herein. These data include information about oligomerization state, stability, DNA binding and allosteric regulation. Protein structural data for 65 proteins are presented as easily-accessible, residue-contact networks. Finally, this article includes example queries to enable the use of the AlloRep database. See the related article, “AlloRep: a repository of sequence, structural and mutagenesis data for the LacI/GalR transcription regulators” (Sousa et al., 2016) [1].
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Affiliation(s)
- Filipa L Sousa
- Institute of Molecular Evolution, Heinrich-Heine Universität Düsseldorf, Universitätstrasse 1, 40225 Düsseldorf, Germany
| | - Daniel J Parente
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jacob A Hessman
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Allen Chazelle
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Sarah A Teichmann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Liskin Swint-Kruse
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160, USA
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6
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Parente DJ, Ray JCJ, Swint-Kruse L. Amino acid positions subject to multiple coevolutionary constraints can be robustly identified by their eigenvector network centrality scores. Proteins 2015; 83:2293-306. [PMID: 26503808 DOI: 10.1002/prot.24948] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 09/21/2015] [Accepted: 10/14/2015] [Indexed: 12/21/2022]
Abstract
As proteins evolve, amino acid positions key to protein structure or function are subject to mutational constraints. These positions can be detected by analyzing sequence families for amino acid conservation or for coevolution between pairs of positions. Coevolutionary scores are usually rank-ordered and thresholded to reveal the top pairwise scores, but they also can be treated as weighted networks. Here, we used network analyses to bypass a major complication of coevolution studies: For a given sequence alignment, alternative algorithms usually identify different, top pairwise scores. We reconciled results from five commonly-used, mathematically divergent algorithms (ELSC, McBASC, OMES, SCA, and ZNMI), using the LacI/GalR and 1,6-bisphosphate aldolase protein families as models. Calculations used unthresholded coevolution scores from which column-specific properties such as sequence entropy and random noise were subtracted; "central" positions were identified by calculating various network centrality scores. When compared among algorithms, network centrality methods, particularly eigenvector centrality, showed markedly better agreement than comparisons of the top pairwise scores. Positions with large centrality scores occurred at key structural locations and/or were functionally sensitive to mutations. Further, the top central positions often differed from those with top pairwise coevolution scores: instead of a few strong scores, central positions often had multiple, moderate scores. We conclude that eigenvector centrality calculations reveal a robust evolutionary pattern of constraints-detectable by divergent algorithms--that occur at key protein locations. Finally, we discuss the fact that multiple patterns coexist in evolutionary data that, together, give rise to emergent protein functions.
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Affiliation(s)
- Daniel J Parente
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160
| | - J Christian J Ray
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, 66047
| | - Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160
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7
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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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8
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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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9
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Ghosh G, Mandal DK. Novel unfolding sequence of banana lectin: Folded, unfolded and natively unfolded-like monomeric states in guanidine hydrochloride. Biochimie 2013; 99:138-45. [PMID: 24316282 DOI: 10.1016/j.biochi.2013.11.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 11/23/2013] [Indexed: 11/16/2022]
Abstract
The sequence of unfolding events of dimeric banana lectin (Banlec), as induced by guanidine hydrochloride (GdnHCl), has been investigated by size-exclusion HPLC, fluorescence, far-UV CD, low temperature phosphorescence and selective chemical modification. 8-Anilino-1-naphthalenesulfonate (ANS) binding indicates a structured unfolding intermediate which has been characterized as dissociated monomer by size-exclusion chromatography. Interestingly, the unfolding elution pattern reveals two distinct unfolded states. One is a usual random coil. The other represents a novel species having elution behavior and structural compactness (Stokes radius) similar to dissociated monomer but showing no regular secondary structure as determined by far-UV CD, thus resembling a natively unfolded state. N-Bromosuccinimide (NBS) oxidation shows that single tryptophan residue remains unmodified in dissociated monomer intermediate while the same is oxidized in natively unfolded-like species. Such difference in tryptophan environment in these species is supported by acrylamide quenching studies, and phosphorescence results at 77 K which show a blue-shift of (0,0) band from 414.8 nm to 409.2 nm. The present results reveal subtlety of structural characteristics of unfolded states of Banlec in GdnHCl, which provide important insight in protein unfolding reaction.
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Affiliation(s)
- Goutam Ghosh
- Department of Chemistry, Presidency University, 86/1 College Street, Kolkata 700 073, India
| | - Dipak K Mandal
- Department of Chemistry, Presidency University, 86/1 College Street, Kolkata 700 073, India.
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10
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Mandal P, Molla AR, Mandal DK. Denaturation of bovine spleen galectin-1 in guanidine hydrochloride and fluoroalcohols: structural characterization and implications for protein folding. J Biochem 2013; 154:531-40. [DOI: 10.1093/jb/mvt084] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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11
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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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12
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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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13
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Ghosh G, Mandal DK. Differing structural characteristics of molten globule intermediate of peanut lectin in urea and guanidine-HCl. Int J Biol Macromol 2012; 51:188-95. [DOI: 10.1016/j.ijbiomac.2012.05.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 05/07/2012] [Accepted: 05/07/2012] [Indexed: 10/28/2022]
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14
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Mandal P, Mandal DK. Localization and environment of tryptophans in different structural states of concanavalin A. J Fluoresc 2011; 21:2123-32. [PMID: 21748239 DOI: 10.1007/s10895-011-0913-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 07/04/2011] [Indexed: 10/18/2022]
Abstract
We have investigated the localization and environment of tryptophan residues in different quaternary and conformational states (tetrameric, dimeric, monomeric and unfolded) of metallized and demetallized concanavalin A (ConA) by selective chemical modification, fluorescence, and phosphorescence. ConA has four tryptophan residues (Trp 40, Trp 88, Trp 109 and Trp 182) per subunit. The pattern of oxidation by N-bromosuccinimide (NBS) shows that NBS modifies, in dimer, only Trp 182 which remains inaccessible in tetramer, two (Trp 88 along with Trp 182) in monomer, all four in unfolded form in presence of EDTA, and three (possibly Trp 40 along with Trp 88 and Trp 182) in unfolded form from native or remetallized ConA. Utilizing wavelength-selective fluorescence approach, we have observed a red edge excitation shift (REES) of 6-8 nm for tetramer and dimer. A more pronounced REES (11 nm) is observed for oxidized monomer compared to REES (3 nm) for unoxidized species. Acrylamide quenching shows the Stern-Volmer constant (K(SV)) for dimer, monomer, unfolded ConA and unfolded apo-ConA being 3.8, 5.2, 12.8, 14.0 M(-1), respectively. Phosphorescence studies at 77 K give more structured spectra, with two (0,0) bands at 406.2 (weak) and 413.2 nm for tetramer. However, a single (0,0) band appears at 413.2 for dimer and 412.6 nm for monomer, while the (0,0) band of the oxidized monomer is red shifted to 414.4 nm. These results may provide important insight into subtlety of organization and environment of tryptophans in the context of folding and structural studies of oligomeric proteins including lectins.
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Affiliation(s)
- Pritha Mandal
- Department of Chemistry & Biochemistry, Presidency University, Kolkata 700 073, India
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15
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Sen D, Mandal DK. Pea lectin unfolding reveals a unique molten globule fragment chain. Biochimie 2011; 93:409-17. [DOI: 10.1016/j.biochi.2010.10.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 10/19/2010] [Indexed: 10/18/2022]
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16
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Molla AR, Maity SS, Ghosh S, Mandal DK. Organization and dynamics of tryptophan residues in tetrameric and monomeric soybean agglutinin: studies by steady-state and time-resolved fluorescence, phosphorescence and chemical modification. Biochimie 2009; 91:857-67. [PMID: 19383525 DOI: 10.1016/j.biochi.2009.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Accepted: 04/11/2009] [Indexed: 10/20/2022]
Abstract
We have investigated the organization and dynamics of tryptophan residues in tetrameric, monomeric and unfolded states of soybean agglutinin (SBA) by selective chemical modification, steady-state and time-resolved fluorescence, and phosphorescence. Oxidation with N-bromosuccinimide (NBS) modifies two tryptophans (Trp 60 and Trp 132) in tetramer, four (Trp 8, Trp 203 and previous two) in monomer, and all six (Trp 8, Trp 60, Trp 132, Trp 154, Trp 203 and Trp 226) in unfolded state. Utilizing wavelength-selective fluorescence approach, we have observed a red-edge excitation shift (REES) of 10 and 5 nm for tetramer and monomer, respectively. A more pronounced REES (21 nm) is observed after NBS oxidation. These results are supported by fluorescence anisotropy experiments. Acrylamide quenching shows the Stern-Volmer constant (K(SV)) for tetramer, monomer and unfolded SBA being 2.2, 5.0 and 14.6 M(-1), respectively. Time-resolved fluorescence studies exhibit biexponential decay with the mean lifetime increasing along tetramer (1.0 ns) to monomer (1.9 ns) to unfolded (3.6 ns). Phosphorescence studies at 77 K give more structured spectra, with two (0,0) bands at 408.6 (weak) and 413.2 nm for tetramer. However, a single (0,0) band appears at 411.8 and 407.2 nm for monomer and unfolded SBA, respectively. The exposure of hydrophobic surface in SBA monomer has been examined by 8-anilino-1-naphthalenesulfonate (ANS) binding, which shows approximately 20-fold increase in ANS fluorescence compared to that for tetramer. The mean lifetime of ANS also shows a large increase (12.0 ns) upon binding to monomer. These results may provide important insight into the role of tryptophans in the folding and association of SBA, and oligomeric proteins in general.
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Affiliation(s)
- Anisur R Molla
- Department of Chemistry & Biochemistry, Presidency College, 86/1 College Street, Kolkata 700 073, West Bengal, India
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17
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Sardar PS, Samanta S, Maity SS, Dasgupta S, Ghosh S. Energy Transfer Photophysics from Serum Albumins to Sequestered 3-Hydroxy-2-Naphthoic Acid, an Excited State Intramolecular Proton-Transfer Probe. J Phys Chem B 2008; 112:3451-61. [DOI: 10.1021/jp074598+] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Sardar PS, Maity SS, Ghosh S, Chatterjee J, Maiti TK, Dasgupta S. Characterization of the Tryptophan Residues of Human Placental Ribonuclease Inhibitor and Its Complex with Bovine Pancreatic Ribonuclease A by Steady-State and Time-Resolved Emission Spectroscopy. J Phys Chem B 2006; 110:21349-56. [PMID: 17048964 DOI: 10.1021/jp064832g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human placental ribonuclease inhibitor (hRI) containing six tryptophan (Trp) residues located at positions 19, 261, 263, 318, 375, and 438 and its complex with RNase A have been studied using steady-state and time-resolved fluorescence (298 K) as well as low-temperature phosphorescence (77 K). Two Trp residues in wild-type hRI and also in the protein-protein complex with RNase A are resolved optically. The accessible surface area values of Trp residues in the wild-type hRI and its complex and consideration of inter-Trp energy transfer in the wild-type hRI reveal that one of the Trp residues is Trp19, which is located in a hydrophobic buried region. The other Trp residue is tentatively assigned as Trp375 based on experimental results on wild-type hRI and its complex. This residue in the wild-type hRI is more or less solvent exposed. Both the Trp residues are perturbed slightly on complex formation. Trp19 moves slightly toward a more hydrophobic region, and the environment of Trp375 becomes less solvent exposed. The complex formation also results in a more heterogeneous environment for both the optically resolved Trp residues.
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19
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Ghosh S, Misra A, Ozarowski A, Maki AH. Low-Temperature Study of Photoinduced Energy Transfer from Tryptophan Residues of Escherichia coli Alkaline Phosphatase to Bound Terbium. J Phys Chem B 2003. [DOI: 10.1021/jp030522b] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sanjib Ghosh
- Department of Chemistry, Presidency College, 86/1 College Street, Calcutta 700073, India, and the Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616
| | - Ajay Misra
- Department of Chemistry, Presidency College, 86/1 College Street, Calcutta 700073, India, and the Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616
| | - Andrzej Ozarowski
- Department of Chemistry, Presidency College, 86/1 College Street, Calcutta 700073, India, and the Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616
| | - August H. Maki
- Department of Chemistry, Presidency College, 86/1 College Street, Calcutta 700073, India, and the Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616
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Li S, Rosen BP, Borges-Walmsley MI, Walmsley AR. Evidence for cooperativity between the four binding sites of dimeric ArsD, an As(III)-responsive transcriptional regulator. J Biol Chem 2002; 277:25992-6002. [PMID: 11980902 DOI: 10.1074/jbc.m201619200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ArsD is a trans-acting repressor of the arsRDABC operon that confers resistance to arsenicals and antimonials in Escherichia coli. It possesses two-pairs of vicinal cysteine residues, Cys(12)-Cys(13) and Cys(112)-Cys(113), that potentially form separate binding sites for the metalloids that trigger dissociation of ArsD from the operon. However, as a homodimer it has four vicinal cysteine pairs. Titration of the steady-state fluorescence of ArsD with metalloids revealed positive cooperativity, with a Hill coefficient of 2, between these sites. Disruption of the Cys(112)-Cys(113) site by mutagenesis of arsD, but not the Cys(12)-Cys(13) site, largely abolished this cooperativity, indicative of interactions between adjacent Cys(112)-Cys(113) sites within the dimer. The kinetics of metalloid binding were determined by stopped flow spectroscopy; the rate increased in a sigmoidal manner, with a Hill coefficient of 4, indicating that the pre-steady-state measurements reported cooperativity between all four sites of the dimer rather than just the intermolecular interactions reported by the steady-state measurements. The kinetics of Sb(III) displacement by As(III) revealed that the metalloid-binding sites behave differentially, with the rapid exchange of As(III) for Sb(III) at one site retarding the release of Sb(III) from the other sites. We propose a model involving the sequential binding and release of metalloids by the four binding sites of dimeric ArsD, with only one site releasing free metalloids.
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Affiliation(s)
- Song Li
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan 48201, USA
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Ozarowski A, Misra A, Ghosh S, Maki AH. Spin−Lattice Relaxation of the Tryptophan Triplet State Varies with Its Protein Environment. J Phys Chem B 2002. [DOI: 10.1021/jp014272f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrzej Ozarowski
- Department of Chemistry, University of California, Davis, Davis, California 95616
| | - Ajay Misra
- Department of Chemistry, University of California, Davis, Davis, California 95616
| | - Sanjib Ghosh
- Department of Chemistry, University of California, Davis, Davis, California 95616
| | - August H. Maki
- Department of Chemistry, University of California, Davis, Davis, California 95616
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Misra A, Ozarowski A, Casas-Finet JR, Maki AH. Effect of nucleic acid binding on the triplet state properties of tetrapeptides containing tryptophan and 6-methyltryptophan: a study by phosphorescence and ODMR spectroscopy. Biochemistry 2000; 39:13772-80. [PMID: 11076516 DOI: 10.1021/bi0015663] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Complexes of four peptides [KWGK, KGWK, K(6MeW)GK, KG(6MeW)K] with the nucleic acids [poly(A), poly(C), poly(U), poly(I), and rG(8)] have been investigated by phosphorescence and optically detected magnetic resonance (ODMR) spectroscopy. The intrinsic spectroscopic probes used in these studies are tryptophan (W) and 6-methyltryptophan (6MeW). Binding to the nucleic acids results in a red-shift of the phosphorescence 0,0-band (delta E(0,0)) of the aromatic residue as well as a reduction of its zero-field splitting parameter (delta D). Results are compared with earlier studies of the HIV-1 nucleocapsid protein, NCp7, that contains a single tryptophan residue (Trp37) within a retroviral zinc finger sequence. Binding of poly(A) or poly(U) to the tetrapeptides induces larger delta E(0,0) and delta D than when bound to NCp7, indicating stronger stacking interactions. Poly(I), on the other hand, produces larger shifts in Trp37 of NCp7. Binding of rG(8) produces sequence-dependent effects in the peptides. When bound to NCp7, but in contrast with tetrapeptide binding, nucleic acids produce large changes in triplet state kinetics consistent with enhanced spin-orbit coupling. These results are discussed in terms of three limiting types of tryptophan-base interaction: intercalation, aromatic stacking, and edge-on interaction. These should have differing effects on the properties of the triplet state.
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Affiliation(s)
- A Misra
- Department of Chemistry, University of California, Davis, California 95616, USA
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Medek A, Hajduk PJ, Mack J, Fesik SW. The Use of Differential Chemical Shifts for Determining the Binding Site Location and Orientation of Protein-Bound Ligands. J Am Chem Soc 2000. [DOI: 10.1021/ja993921m] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ales Medek
- Pharmaceutical Discovery Division Abbott Laboratories, Abbott Park, Illinois 60064
| | - Philip J. Hajduk
- Pharmaceutical Discovery Division Abbott Laboratories, Abbott Park, Illinois 60064
| | - Jamey Mack
- Pharmaceutical Discovery Division Abbott Laboratories, Abbott Park, Illinois 60064
| | - Stephen W. Fesik
- Pharmaceutical Discovery Division Abbott Laboratories, Abbott Park, Illinois 60064
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