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Mariam J, Krishnamoorthy G, Anand R. Use of 6‐Methylisoxanthopterin, a Fluorescent Guanine Analog, to Probe Fob1‐Mediated Dynamics at the Stalling Fork Barrier DNA Sequences. Chem Asian J 2019; 14:4760-4766. [DOI: 10.1002/asia.201901061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/19/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Jessy Mariam
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 Maharashtra India
| | | | - Ruchi Anand
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 Maharashtra India
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2
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Serag MF, Aikeremu A, Tsukamoto R, Piwoński H, Abadi M, Kaji N, Dwyer JR, Baba Y, Habuchi S. Geometry-Based Self-Assembly of Histone-DNA Nanostructures at Single-Nucleotide Resolution. ACS NANO 2019; 13:8155-8168. [PMID: 31244030 DOI: 10.1021/acsnano.9b03259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Histones are basic protein monomers capable of interacting with DNA, providing the mechanism of DNA compaction inside the cell nucleus. The well-ordered assembly process of histone and DNA is a potential candidate as the approach for building DNA-protein nanostructures. Here, utilizing the sequence-independent histone-DNA interaction, we present an approach to self-assemble histones and single-stranded DNA (ssDNA) to form well-defined histone-DNA (sHD) nanoparticles and their multidimensional cross-linked complexes (cHD). By using various molecular biology and microscopy techniques, we elucidate the structure of these complexes, and we show that they are formed at carefully controlled conditions of temperature, ionic strength, concentration, and incubation time. We also demonstrate using a set of ssDNA molecular rulers and a geometric accommodation model that the assembly of sHD and cHD particles proceeds with precise geometry so that the number of ssDNA in these particles can be programmed by the length of ssDNA. We further show that the formation of cHD amplifies the effect of the length of ssDNA on the self-assembly, allowing for distinguishing ssDNA of different lengths at single nucleotide resolution. We envision that our geometry-directed approach of self-assembling histone-DNA nanostructures and the fundamental insights can serve as a structural platform to advance building precisely ordered DNA-protein nanostructures.
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Affiliation(s)
- Maged F Serag
- Biological and Environmental Science and Engineering Division , King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
- Department of Biomolecular Engineering, Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
- ImPACT Research Center for Advanced Nanobiodevices , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
| | - Aimaiti Aikeremu
- Biological and Environmental Science and Engineering Division , King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
| | - Ryoko Tsukamoto
- Department of Biomolecular Engineering, Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
- ImPACT Research Center for Advanced Nanobiodevices , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
| | - Hubert Piwoński
- Biological and Environmental Science and Engineering Division , King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
| | - Maram Abadi
- Biological and Environmental Science and Engineering Division , King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
| | - Noritada Kaji
- Department of Applied Chemistry, Graduate School of Engineering , Kyushu University , 744 Motooka , Nishi-ku, Fukuoka 819-0395 , Japan
- JST, PRESTO , 4-1-8 Honcho , Kawaguchi , Saitama 332-0012 , Japan
| | - Jason R Dwyer
- Department of Chemistry , University of Rhode Island , 140 Flagg Road , Kingston , Rhode Island 02881 , United States
| | - Yoshinobu Baba
- Department of Biomolecular Engineering, Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
- ImPACT Research Center for Advanced Nanobiodevices , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
- National Institute of Advanced Industrial Science and Technology (AIST) , Takamatsu 761-0395 , Japan
- School of Pharmacy , Kaohsiung Medical University , Kaohsiung 807 , Taiwan , R.O.C
| | - Satoshi Habuchi
- Biological and Environmental Science and Engineering Division , King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
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Biswas A, Mariam J, Kombrabail M, Narayan S, Krishnamoorthy G, Anand R. Site-Specific Fluorescence Dynamics To Probe Polar Arrest by Fob1 in Replication Fork Barrier Sequences. ACS OMEGA 2017; 2:7389-7399. [PMID: 30023550 PMCID: PMC6045349 DOI: 10.1021/acsomega.7b01117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/12/2017] [Indexed: 06/08/2023]
Abstract
Fob1 protein plays an important role in aging and maintains genomic stability by avoiding clashes between the replication and transcription machinery. It facilitates polar arrest by binding to replication fork barrier (RFB) sites, present within the nontranscribed spacer region of the ribosomal DNA. Here, we investigate the mechanism of unidirectional arrest by creating multiple prosthetic forks within the RFB, with fluorescent adenine analogue 2-aminopurine incorporated site-specifically in both the "permissible" and "nonpermissible" directions. The motional dynamics of the RFB-Fob1 complexes analyzed by fluorescence lifetime and fluorescence anisotropy decay kinetics shows that Fob1 adopts a clamp-lock model of arrest and causes stronger perturbation with the bases in the double-stranded region of the nonpermissible-directed forks over those of the permissible directed ones, thereby creating a polar barrier. Corroborative thermal melting studies reveal a skewed distribution of GC content within the RFB sequence that potentially assists in Fob1-mediated arrest.
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Affiliation(s)
- Anwesha Biswas
- Department
of Chemistry, Indian Institute of Technology
Bombay, Mumbai, Maharashtra 400076, India
| | - Jessy Mariam
- Department
of Chemistry, Indian Institute of Technology
Bombay, Mumbai, Maharashtra 400076, India
| | - Mamta Kombrabail
- Department
of Chemical Sciences, Tata Institute of
Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Satya Narayan
- Department
of Chemical Sciences, Tata Institute of
Fundamental Research, Mumbai, Maharashtra 400005, India
| | - G. Krishnamoorthy
- Department
of Chemistry, Indian Institute of Technology
Bombay, Mumbai, Maharashtra 400076, India
- Department
of Chemical Sciences, Tata Institute of
Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Ruchi Anand
- Department
of Chemistry, Indian Institute of Technology
Bombay, Mumbai, Maharashtra 400076, India
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4
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Voltz K, Léonard J, Touceda PT, Conyard J, Chaker Z, Dejaegere A, Godet J, Mély Y, Haacke S, Stote RH. Quantitative sampling of conformational heterogeneity of a DNA hairpin using molecular dynamics simulations and ultrafast fluorescence spectroscopy. Nucleic Acids Res 2016; 44:3408-19. [PMID: 26896800 PMCID: PMC4838372 DOI: 10.1093/nar/gkw077] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/29/2016] [Indexed: 01/22/2023] Open
Abstract
Molecular dynamics (MD) simulations and time resolved fluorescence (TRF) spectroscopy were combined to quantitatively describe the conformational landscape of the DNA primary binding sequence (PBS) of the HIV-1 genome, a short hairpin targeted by retroviral nucleocapsid proteins implicated in the viral reverse transcription. Three 2-aminopurine (2AP) labeled PBS constructs were studied. For each variant, the complete distribution of fluorescence lifetimes covering 5 orders of magnitude in timescale was measured and the populations of conformers experimentally observed to undergo static quenching were quantified. A binary quantification permitted the comparison of populations from experimental lifetime amplitudes to populations of aromatically stacked 2AP conformers obtained from simulation. Both populations agreed well, supporting the general assumption that quenching of 2AP fluorescence results from pi-stacking interactions with neighboring nucleobases and demonstrating the success of the proposed methodology for the combined analysis of TRF and MD data. Cluster analysis of the latter further identified predominant conformations that were consistent with the fluorescence decay times and amplitudes, providing a structure-based rationalization for the wide range of fluorescence lifetimes. Finally, the simulations provided evidence of local structural perturbations induced by 2AP. The approach presented is a general tool to investigate fine structural heterogeneity in nucleic acid and nucleoprotein assemblies.
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Affiliation(s)
- Karine Voltz
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964, Centre National de Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - Jérémie Léonard
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, CNRS UMR 7504, Université de Strasbourg, Strasbourg, France
| | - Patricia Tourón Touceda
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, CNRS UMR 7504, Université de Strasbourg, Strasbourg, France
| | - Jamie Conyard
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, CNRS UMR 7504, Université de Strasbourg, Strasbourg, France
| | - Ziyad Chaker
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, CNRS UMR 7504, Université de Strasbourg, Strasbourg, France
| | - Annick Dejaegere
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964, Centre National de Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - Julien Godet
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch Cedex, France
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch Cedex, France
| | - Stefan Haacke
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, CNRS UMR 7504, Université de Strasbourg, Strasbourg, France
| | - Roland H Stote
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964, Centre National de Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, 67404 Illkirch, France
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Biswas A, Narayan S, Kallianpur MV, Krishnamoorthy G, Anand R. Mode of DNA binding with γ-butyrolactone receptor protein CprB from Streptomyces coelicolor revealed by site-specific fluorescence dynamics. Biochim Biophys Acta Gen Subj 2015; 1850:2283-92. [PMID: 26278022 DOI: 10.1016/j.bbagen.2015.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/16/2015] [Accepted: 08/12/2015] [Indexed: 11/27/2022]
Abstract
BACKGROUND The γ-butyrolactone (GBL) binding transcription factors in Streptomyces species are known for their involvement in quorum sensing where they control the expression of various genes initiating secondary metabolic pathways. The structurally characterized member of this family CprB from Streptomyces coelicolor had earlier been demonstrated to bind a multitude of sequences containing a specific binding signature. Though structural breakthrough has been obtained for its complex with a consensus DNA sequence there is, however a dearth of information regarding the overall and site specific dynamics of protein-DNA interaction. METHODS To delineate the effect of CprB on the bound DNA, changes in motional dynamics of the fluorescent probe 2-aminopurine were monitored at three conserved base positions (5th, 12th and 23rd) for two DNA sequences: the consensus and the biologically relevant cognate element, on complex formation. RESULTS The changes in lifetime and generalized order parameter revealed a similarity in the binding pattern of the protein to both sequences with greater dynamic restriction at the end positions, 5th and 23rd, as compared to the middle 12th position. Also differences within this pattern demonstrated the influence of even small changes in sequence on protein interactions. CONCLUSIONS Here the study of motional dynamics was instrumental in establishing a structural footprint for the cognate DNA sequence and explaining the dynamics for the consensus DNA from structural correspondence. GENERAL SIGNIFICANCE Motional dynamics can be a powerful tool to efficiently study the mode of DNA binding to proteins that interact differentially with a plethora of DNA sequences, even in the absence of structural breakthrough.
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Affiliation(s)
- Anwesha Biswas
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Satya Narayan
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Mamata V Kallianpur
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - G Krishnamoorthy
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India.
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India.
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6
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2-aminopurine as a fluorescent probe of DNA conformation and the DNA–enzyme interface. Q Rev Biophys 2015; 48:244-79. [DOI: 10.1017/s0033583514000158] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AbstractNearly 50 years since its potential as a fluorescent base analogue was first recognized, 2-aminopurine (2AP) continues to be the most widely used fluorescent probe of DNA structure and the perturbation of that structure by interaction with enzymes and other molecules. In this review, we begin by considering the origin of the dramatic and intriguing difference in photophysical properties between 2AP and its structural isomer, adenine; although 2AP differs from the natural base only in the position of the exocyclic amine group, its fluorescence intensity is one thousand times greater. We then discuss the mechanism of interbase quenching of 2AP fluorescence in DNA, which is the basis of its use as a conformational probe but remains imperfectly understood. There are hundreds of examples in the literature of the use of changes in the fluorescence intensity of 2AP as the basis of assays of conformational change; however, in this review we will consider in detail only a few intensity-based studies. Our primary aim is to highlight the use of time-resolved fluorescence measurements, and the interpretation of fluorescence decay parameters, to explore the structure and dynamics of DNA. We discuss the salient features of the fluorescence decay of 2AP when incorporated in DNA and review the use of decay measurements in studying duplexes, single strands and other structures. We survey the use of 2AP as a probe of DNA-enzyme interaction and enzyme-induced distortion, focusing particularly on its use to study base flipping and the enhanced mechanistic insights that can be gained by a detailed analysis of the decay parameters, rather than merely monitoring changes in fluorescence intensity. Finally we reflect on the merits and shortcomings of 2AP and the prospects for its wider adoption as a fluorescence-decay-based probe.
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Narayan S, Kombrabail MH, Das S, Singh H, Chary KVR, Rao BJ, Krishnamoorthy G. Site-specific fluorescence dynamics in an RNA 'thermometer' reveals the role of ribosome binding in its temperature-sensitive switch function. Nucleic Acids Res 2014; 43:493-503. [PMID: 25477380 PMCID: PMC4288164 DOI: 10.1093/nar/gku1264] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
RNA thermometers control the translation of several heat shock and virulence genes by their temperature-sensitive structural transitions. Changes in the structure and dynamics of MiniROSE RNA, which regulates translation in the temperature range of 20–45°C, were studied by site specifically replacing seven adenine residues with the fluorescent analog, 2-aminopurine (2-AP), one at a time. Dynamic fluorescence observables of 2-AP-labeled RNAs were compared in their free versus ribosome-bound states for the first time. Noticeably, position dependence of fluorescence observables, which was prominent at 20°C, was persistent even at 45ºC, suggesting the persistence of structural integrity up to 45ºC. Interestingly, position-dependent dispersion of fluorescence lifetime and quenching constant at 45°C was ablated in ribosome-bound state, when compared to those at 20°C, underscoring loss of structural integrity at 45°C, in ribosome-bound RNA. Significant increase in the value of mean lifetime for 2-AP corresponding to Shine–Dalgarno sequences, when the temperature was raised from 20 to 45°C, to values seen in the presence of urea at 45°C was a strong indicator of melting of the 3D structure of MiniROSE RNA at 45°C, only when it was ribosome bound. Taken all together, we propose a model where we invoke that ribosome binding of the RNA thermometer critically regulates temperature sensing functions in MiniROSE RNA.
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Affiliation(s)
- Satya Narayan
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Mamta H Kombrabail
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Sudipta Das
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500075, India
| | - Himanshu Singh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Kandala V R Chary
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Basuthkar J Rao
- Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India
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Das R, Duportail G, Ghose A, Richert L, Klymchenko A, Chakraborty S, Yesylevskyy S, Mely Y. Tuning excited-state proton transfer dynamics of a 3-hydroxychromone dye in supramolecular complexes via host–guest steric compatibility. Phys Chem Chem Phys 2014; 16:776-84. [DOI: 10.1039/c3cp52597j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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9
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Singh TS, Rao BJ, Krishnamoorthy G. GTP binding leads to narrowing of the conformer population while preserving the structure of the RNA aptamer: a site-specific time-resolved fluorescence dynamics study. Biochemistry 2012; 51:9260-9. [PMID: 23110669 DOI: 10.1021/bi301110u] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, we employed a combination of steady-state and time-resolved fluorescence spectroscopy and studied the site-specific dynamics in a GTP aptamer using 2-aminopurine as a fluorescent probe. We compared the dynamics of the GTP-bound aptamer with that of the free aptamer as well as when it is denatured. GTP binding leads to an overall compaction of structure in the aptamer. The general pattern of fluorescence lifetimes and correlation times scanned across several locations in the aptamer does not seem to change following GTP binding. However, a remarkable narrowing of the lifetime distribution of the aptamer ensues following its compaction by GTP binding. Interestingly, such a "conformational narrowing" is evident from the lifetime readouts of the nucleotide belonging to the stem as well as the "bulge" part of the aptamer, independent of whether it is directly interacting with GTP. Taken together, these results underscore the importance of an overall intrinsic structure associated with the free aptamer that is further modulated following GTP binding. This work provides strong support for the "conformational selection" hypothesis of ligand binding.
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Affiliation(s)
- T Sanjoy Singh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400 005, India
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10
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Das R, Duportail G, Richert L, Klymchenko A, Mély Y. Sensing micelle hydration by proton-transfer dynamics of a 3-hydroxychromone dye: role of the surfactant headgroup and chain length. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:7147-7159. [PMID: 22515420 DOI: 10.1021/la300103a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The dynamics of the excited-state intramolecular proton-transfer (ESIPT) reaction of 2-(2'-furyl)-3-hydroxychromone (FHC) was studied in micelles by time-resolved fluorescence. The proton-transfer dynamics of FHC was found to be sensitive to the hydration and charge of the micelles, demonstrated through a decrease of the ESIPT rate constant (k(PT)) in the sequence cationic → nonionic → anionic micelles. A remarkably slow ESIPT with a time constant (τ(PT)) of ~100 ps was observed in the anionic sodium dodecyl sulfate and sodium tetradecyl sulfate micelles, whereas it was quite fast (τ(PT) ≈ 15 ps) in the cationic cetyltrimethylammonium bromide and tetradecyltrimethylammonium bromide micelles. In the nonionic micelles of Brij-78, Brij-58, Tween-80, and Tween-20, ESIPT occurred with time constants (τ(PT) ≈ 35-65 ps) intermediate between those of the cationic and anionic micelles. The slower ESIPT dynamics in the anionic micelles than the cationic micelles is attributed to a relatively stronger hydration of the negatively charged headgroups of the former than the positively charged headgroups of the latter, which significantly weakens the intramolecular hydrogen bond of FHC in the Stern layer of the anionic micelles compared to the latter. In addition, electrostatic attraction between the positively charged -N(CH(3))(3)(+) headgroups and the negatively charged 4-carbonyl moiety of FHC effectively screens the intramolecular hydrogen bond from the perturbation of water molecules in the micelle-water interface of the cationic micelles, whereas in the anionic micelles, this screening of the intramolecular hydrogen bond is much less efficient due to an electrostatic repulsion between its negatively charged -OSO(3)(-) headgroups and the 4-carbonyl moiety. As for the nonionic micelles, a moderate level of hydration, and the absence of any charged headgroups, causes an ESIPT dynamics faster than that of the anionic but slower than that of the cationic micelles. Furthermore, the ESIPT rate decreased with a decrease of the hydrophobic chain length of the surfactants due to the stronger hydration of the micelles of shorter chain surfactants than those of longer chain surfactants, arising from a less compact packing of the former surfactants compared to the latter surfactants.
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Affiliation(s)
- Ranjan Das
- Department of Chemistry, West Bengal State University, Barasat, Kolkata 700126, India
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11
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Role of active site rigidity in activity: MD simulation and fluorescence study on a lipase mutant. PLoS One 2012; 7:e35188. [PMID: 22514720 PMCID: PMC3325981 DOI: 10.1371/journal.pone.0035188] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 03/09/2012] [Indexed: 11/19/2022] Open
Abstract
Relationship between stability and activity of enzymes is maintained by underlying conformational flexibility. In thermophilic enzymes, a decrease in flexibility causes low enzyme activity while in less stable proteins such as mesophiles and psychrophiles, an increase in flexibility is associated with enhanced enzyme activity. Recently, we identified a mutant of a lipase whose stability and activity were enhanced simultaneously. In this work, we probed the conformational dynamics of the mutant and the wild type lipase, particularly flexibility of their active site using molecular dynamic simulations and time-resolved fluorescence techniques. In contrast to the earlier observations, our data show that active site of the mutant is more rigid than wild type enzyme. Further investigation suggests that this lipase needs minimal reorganization/flexibility of active site residues during its catalytic cycle. Molecular dynamic simulations suggest that catalytically competent active site geometry of the mutant is relatively more preserved than wild type lipase, which might have led to its higher enzyme activity. Our study implies that widely accepted positive correlation between conformation flexibility and enzyme activity need not be stringent and draws attention to the possibility that high enzyme activity can still be accomplished in a rigid active site and stable protein structures. This finding has a significant implication towards better understanding of involvement of dynamic motions in enzyme catalysis and enzyme engineering through mutations in active site.
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12
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Bhattacharya M, Mukhopadhyay S. Structural and Dynamical Insights into the Molten-Globule Form of Ovalbumin. J Phys Chem B 2011; 116:520-31. [DOI: 10.1021/jp208416d] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mily Bhattacharya
- Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali 140306, India
| | - Samrat Mukhopadhyay
- Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali 140306, India
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