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Pospíšil P, Cwiklik L, Sýkora J, Hof M, Greetham GM, Towrie M, Vlček A. Solvent-Dependent Excited-State Evolution of Prodan Dyes. J Phys Chem B 2021; 125:13858-13867. [PMID: 34914398 DOI: 10.1021/acs.jpcb.1c09030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Excited-state character and dynamics of two 6-(dimethylamino)-2-acylnaphthalene dyes (Prodan and Badan-SCH2CH2OH) were studied by picosecond time-resolved IR spectroscopy (TRIR) in solvents of different polarity and relaxation times: hexane, CD3OD, and glycerol-d8. In all these solvents, near-UV excitation initially produced the same S1(ππ*) excited state characterized by a broad TRIR signal. A very fast decay (3, ∼100 ps) followed in hexane, whereas conversion to a distinct IR spectrum with a ν(C═O) band downshifted by 76 cm-1 occurred in polar/H-bonding solvents, slowing down on going from CD3OD (1, 23 ps) to glycerol-d8 (5.5, 51, 330 ps). The final relaxed excited state was assigned as planar Me2N → C═O intramolecular charge transfer S1(ICT) by comparing experimental and TDDFT-calculated spectra. TRIR conversion kinetics are comparable to those of early stages of multiexponential fluorescence decay and dynamic fluorescence red-shift. This work presents a strong evidence that Prodan-type dyes undergo solvation-driven charge separation in their S1 state, which is responsible for the dynamic fluorescence Stokes shift observed in polar/H-bonding solvents. The time evolution of the optically prepared S1(ππ*) state to the S1(ICT) final state reflects environment relaxation and solvation dynamics. This finding rationalizes the widespread use of Prodan-type dyes as probes of environment dynamics and polarity.
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Affiliation(s)
- Petr Pospíšil
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, CZ-18223 Prague, Czech Republic
| | - Lukasz Cwiklik
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, CZ-18223 Prague, Czech Republic
| | - Jan Sýkora
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, CZ-18223 Prague, Czech Republic
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, CZ-18223 Prague, Czech Republic
| | - Gregory M Greetham
- Central Laser Facility, Research Complex at Harwell, STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Michael Towrie
- Central Laser Facility, Research Complex at Harwell, STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Antonín Vlček
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, CZ-18223 Prague, Czech Republic.,Department of Chemistry, Queen Mary University of London, E1 4NS London, United Kingdom
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Scollo F, Evci H, Amaro M, Jurkiewicz P, Sykora J, Hof M. What Does Time-Dependent Fluorescence Shift (TDFS) in Biomembranes (and Proteins) Report on? Front Chem 2021; 9:738350. [PMID: 34778202 PMCID: PMC8586494 DOI: 10.3389/fchem.2021.738350] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/21/2021] [Indexed: 11/17/2022] Open
Abstract
The organization of biomolecules and bioassemblies is highly governed by the nature and extent of their interactions with water. These interactions are of high intricacy and a broad range of methods based on various principles have been introduced to characterize them. As these methods view the hydration phenomena differently (e.g., in terms of time and length scales), a detailed insight in each particular technique is to promote the overall understanding of the stunning “hydration world.” In this prospective mini-review we therefore critically examine time-dependent fluorescence shift (TDFS)—an experimental method with a high potential for studying the hydration in the biological systems. We demonstrate that TDFS is very useful especially for phospholipid bilayers for mapping the interfacial region formed by the hydrated lipid headgroups. TDFS, when properly applied, reports on the degree of hydration and mobility of the hydrated phospholipid segments in the close vicinity of the fluorophore embedded in the bilayer. Here, the interpretation of the recorded TDFS parameters are thoroughly discussed, also in the context of the findings obtained by other experimental techniques addressing the hydration phenomena (e.g., molecular dynamics simulations, NMR spectroscopy, scattering techniques, etc.). The differences in the interpretations of TDFS outputs between phospholipid biomembranes and proteins are also addressed. Additionally, prerequisites for the successful TDFS application are presented (i.e., the proper choice of fluorescence dye for TDFS studies, and TDFS instrumentation). Finally, the effects of ions and oxidized phospholipids on the bilayer organization and headgroup packing viewed from TDFS perspective are presented as application examples.
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Affiliation(s)
- Federica Scollo
- J. Heyrovský Institute of Physical Chemistry of the CAS, Prague, Czechia
| | - Hüseyin Evci
- J. Heyrovský Institute of Physical Chemistry of the CAS, Prague, Czechia
| | - Mariana Amaro
- J. Heyrovský Institute of Physical Chemistry of the CAS, Prague, Czechia
| | - Piotr Jurkiewicz
- J. Heyrovský Institute of Physical Chemistry of the CAS, Prague, Czechia
| | - Jan Sykora
- J. Heyrovský Institute of Physical Chemistry of the CAS, Prague, Czechia
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry of the CAS, Prague, Czechia
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Photophysical Properties of BADAN Revealed in the Study of GGBP Structural Transitions. Int J Mol Sci 2021; 22:ijms222011113. [PMID: 34681772 PMCID: PMC8540541 DOI: 10.3390/ijms222011113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/06/2021] [Accepted: 10/09/2021] [Indexed: 01/14/2023] Open
Abstract
The fluorescent dye BADAN (6-bromoacetyl-2-dimetylaminonaphtalene) is widely used in various fields of life sciences, however, the photophysical properties of BADAN are not fully understood. The study of the spectral properties of BADAN attached to a number of mutant forms of GGBP, as well as changes in its spectral characteristics during structural changes in proteins, allowed to shed light on the photophysical properties of BADAN. It was shown that spectral properties of BADAN are determined by at least one non-fluorescent and two fluorescent isomers with overlapping absorbing bands. It was found that BADAN fluorescence is determined by the unsolvated "PICT" (planar intramolecular charge transfer state) and solvated "TICT" (twisted intramolecular charge transfer state) excited states. While "TICT" state can be formed both as a result of the "PICT" state solvation and as a result of light absorption by the solvated ground state of the dye. BADAN fluorescence linked to GGBP/H152C apoform is quenched by Trp 183, but this effect is inhibited by glucose intercalation. New details of the changes in the spectral characteristics of BADAN during the unfolding of the protein apo and holoforms have been obtained.
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Puff N, Staneva G, Angelova MI, Seigneuret M. Improved Characterization of Raft-Mimicking Phase-Separation Phenomena in Lipid Bilayers Using Laurdan Fluorescence with Log-Normal Multipeak Analysis. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:4347-4356. [PMID: 32233510 DOI: 10.1021/acs.langmuir.0c00412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The study of biomimetic model membrane systems undergoing liquid-ordered (Lo)-liquid-disordered (Ld) phase separation using spectroscopic methods has played an important role in understanding the properties of lipid rafts in plasma membranes. In particular, the membrane-associated fluorescence probe Laurdan has proved to be a very efficient reporter of Lo-Ld phase separation in lipid bilayers using the general polarization (GP) parameter. A limitation of the GP approach is that it monitors only global average packing so that the contribution of each phase remains undetermined. The decomposition of Laurdan emission spectra has been proposed as an additional approach to overcoming this limitation. Here, further developments of this method for the study of Lo-Ld phase separation are described here for Laurdan in sphingomyelin-phosphatidylcholine-cholesterol large unilamellar vesicles. Lipid compositions corresponding to homogeneous Lo or Ld phases as well as undergoing thermally induced Lo-Ld phase separation were investigated. In addition, the occurrence of phase separation was checked by the fluorescence imaging of giant unilamellar vesicles. Decomposition into three log-normal components is used to show that an intermediate energy component is specifically associated with the occurrence of the Lo phase, with a small contribution from this component occurring above the phase-separation temperature being attributable to phase fluctuations. The ratio RX of the relative area of this intermediate-energy peak to that of the low-energy peak is shown to provide a straightforward index of Lo-Ld phase separation as a function of temperature, which is occasionally more sensitive than GP. It is also shown that RX can be used in conjunction with GP to gain further insight into Lo-Ld, the phase-separation processes. This latter feature is illustrated by the influence of the alcohol butanol on the Lo-Ld phase separation in sphingomyelin-phosphatidylcholine-cholesterol bilayers by showing that the effect of the alcohol occurs specifically at the onset of the phase separation, indicating a line tension mechanism. It is proposed that the three components of log-normal decomposition approaching Laurdan emission spectra provide a useful improvement for characterizing Lo-Ld phase-separation phenomena.
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Affiliation(s)
- Nicolas Puff
- Sorbonne Université, Faculté des Sciences et Ingénierie, UFR 925 Physique, Paris F-75005, France
- Université Paris Diderot - Paris 7, Université de Paris, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, Paris F-75013, France
| | - Galya Staneva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Miglena I Angelova
- Sorbonne Université, Faculté des Sciences et Ingénierie, UFR 925 Physique, Paris F-75005, France
- Université Paris Diderot - Paris 7, Université de Paris, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, Paris F-75013, France
| | - Michel Seigneuret
- Université Paris Diderot - Paris 7, Université de Paris, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, Paris F-75013, France
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Srivastava A, Karmakar S, Debnath A. Quantification of spatio-temporal scales of dynamical heterogeneity of water near lipid membranes above supercooling. SOFT MATTER 2019; 15:9805-9815. [PMID: 31746927 DOI: 10.1039/c9sm01725a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A hydrated 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) lipid membrane is investigated using an all atom molecular dynamics simulation at 308 K to determine the physical sources of universal slow relaxations of hydration layers and length-scale of the spatially heterogeneous dynamics. Continuously residing interface water (IW) molecules hydrogen bonded to different moieties of lipid heads in the membrane are identified. The non-Gaussian parameters of all classes of IW molecules show a cross-over from cage vibration to translational diffusion. A significant non-Gaussianity is observed for the IW molecules exhibiting large length correlations in translational van Hove functions. Two time-scales for the ballistic motions and hopping transitions are obtained from the self intermediate scattering functions of the IW molecules with an additional long relaxation, which disappears for bulk water. The long relaxation time-scales for the IW molecules obtained from the self intermediate scattering functions are in good accordance with the hydrogen bond relaxation time-scales irrespective of the nature of the chemical confinement and the confinement lifetime. Employing a block analysis approach, the length-scale of dynamical heterogeneities is captured from a transition from non-Gaussianity to Gaussianity in van Hove correlation functions of the IW molecules. The heterogeneity length-scale is comparable to the wave-length of the small and weak undulations of the membrane calculated by Fourier transforms of lipid tilts. This opens up a new avenue towards a possible correlation between heterogeneity length-scale and membrane curvature more significant for rippled membranes. Thus, our analyses provide a measure towards the spatio-temporal scale of dynamical heterogeneity of confined water near membranes.
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Affiliation(s)
- Abhinav Srivastava
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, India.
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6
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Fischermeier E, Pospíšil P, Sayed A, Hof M, Solioz M, Fahmy K. Dipolar Relaxation Dynamics at the Active Site of an ATPase Regulated by Membrane Lateral Pressure. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201611582] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Elisabeth Fischermeier
- Helmholtz-Zentrum Dresden-Rossendorf Institute of Resource Ecology Bautzner Landstrasse 400 01328 Dresden Germany
- Technische Universität Dresden Biotechnology Center Tatzberg 47-49, 01307 Dresden Germany
- Nationales Zentrum für Tumorerkrankungen Heidelberg Im Neuenheimer Feld 460 69120 Heidelberg Germany
| | - Petr Pospíšil
- J. Heyrovský Inst. Physical Chemistry of the A.S.C.R. v.v.i. Prague Czech Republic
| | - Ahmed Sayed
- Helmholtz-Zentrum Dresden-Rossendorf Institute of Resource Ecology Bautzner Landstrasse 400 01328 Dresden Germany
- Technische Universität Dresden Biotechnology Center Tatzberg 47-49, 01307 Dresden Germany
- Institute for Experimental Physics I Universität Leipzig Linnéstrasse 5 04103 Leipzig Germany
| | - Martin Hof
- J. Heyrovský Inst. Physical Chemistry of the A.S.C.R. v.v.i. Prague Czech Republic
| | - Marc Solioz
- University of Bern Dept. of Clinical Pharmacology Murtenstrasse 35 3008 Bern Switzerland
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden-Rossendorf Institute of Resource Ecology Bautzner Landstrasse 400 01328 Dresden Germany
- Technische Universität Dresden Biotechnology Center Tatzberg 47-49, 01307 Dresden Germany
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7
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Fischermeier E, Pospíšil P, Sayed A, Hof M, Solioz M, Fahmy K. Dipolar Relaxation Dynamics at the Active Site of an ATPase Regulated by Membrane Lateral Pressure. Angew Chem Int Ed Engl 2016; 56:1269-1272. [DOI: 10.1002/anie.201611582] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Elisabeth Fischermeier
- Helmholtz-Zentrum Dresden-Rossendorf Institute of Resource Ecology Bautzner Landstrasse 400 01328 Dresden Germany
- Technische Universität Dresden Biotechnology Center Tatzberg 47-49, 01307 Dresden Germany
- Nationales Zentrum für Tumorerkrankungen Heidelberg Im Neuenheimer Feld 460 69120 Heidelberg Germany
| | - Petr Pospíšil
- J. Heyrovský Inst. Physical Chemistry of the A.S.C.R. v.v.i. Prague Czech Republic
| | - Ahmed Sayed
- Helmholtz-Zentrum Dresden-Rossendorf Institute of Resource Ecology Bautzner Landstrasse 400 01328 Dresden Germany
- Technische Universität Dresden Biotechnology Center Tatzberg 47-49, 01307 Dresden Germany
- Institute for Experimental Physics I Universität Leipzig Linnéstrasse 5 04103 Leipzig Germany
| | - Martin Hof
- J. Heyrovský Inst. Physical Chemistry of the A.S.C.R. v.v.i. Prague Czech Republic
| | - Marc Solioz
- University of Bern Dept. of Clinical Pharmacology Murtenstrasse 35 3008 Bern Switzerland
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden-Rossendorf Institute of Resource Ecology Bautzner Landstrasse 400 01328 Dresden Germany
- Technische Universität Dresden Biotechnology Center Tatzberg 47-49, 01307 Dresden Germany
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8
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Fonin A, Kuznetsova I, Turoverov K. Spectral properties of BADAN in solutions with different polarities. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.01.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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9
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Reverse micelles as a tool for probing solvent modulation of protein dynamics: Reverse micelle encapsulated hemoglobin. Chem Phys 2013; 430:88-97. [PMID: 24039330 DOI: 10.1016/j.chemphys.2013.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Hydration waters impact protein dynamics. Dissecting the interplay between hydration waters and dynamics requires a protein that manifests a broad range of dynamics. Proteins in reverse micelles (RMs) have promise as tools to achieve this objective because the water content can be manipulated. Hemoglobin is an appropriate tool with which to probe hydration effects. We describe both a protocol for hemoglobin encapsulation in reverse micelles and a facile method using PEG and cosolvents to manipulate water content. Hydration properties are probed using the water-sensitive fluorescence from Hb bound pyranine and covalently attached Badan. Protein dynamics are probed through ligand recombination traces derived from photodissociated carbonmonoxy hemoglobin on a log scale that exposes the potential role of both α and β solvent fluctuations in modulating protein dynamics. The results open the possibility of probing hydration level phenomena in this system using a combination of NMR and optical probes.
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10
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Amaro M, Brezovský J, Kováčová S, Maier L, Chaloupková R, Sýkora J, Paruch K, Damborský J, Hof M. Are Time-Dependent Fluorescence Shifts at the Tunnel Mouth of Haloalkane Dehalogenase Enzymes Dependent on the Choice of the Chromophore? J Phys Chem B 2013; 117:7898-906. [DOI: 10.1021/jp403708c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mariana Amaro
- J. Heyrovsky Institute of Physical
Chemistry of the ASCR, v. v. i., Academy of Sciences of the Czech Republic, Dolejskova 3, 182 23 Praha, Czech
Republic
| | - Jan Brezovský
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Silvia Kováčová
- International Centre for Clinical
Research, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
- Department of Chemistry, Faculty
of Science, Masaryk University, Kamenice
5/A8, 625 00 Brno, Czech Republic
| | - Lukáš Maier
- International Centre for Clinical
Research, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
- Department of Chemistry, Faculty
of Science, Masaryk University, Kamenice
5/A8, 625 00 Brno, Czech Republic
| | - Radka Chaloupková
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Jan Sýkora
- J. Heyrovsky Institute of Physical
Chemistry of the ASCR, v. v. i., Academy of Sciences of the Czech Republic, Dolejskova 3, 182 23 Praha, Czech
Republic
| | - Kamil Paruch
- International Centre for Clinical
Research, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
- Department of Chemistry, Faculty
of Science, Masaryk University, Kamenice
5/A8, 625 00 Brno, Czech Republic
| | - Jiří Damborský
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Centre for Clinical
Research, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Martin Hof
- J. Heyrovsky Institute of Physical
Chemistry of the ASCR, v. v. i., Academy of Sciences of the Czech Republic, Dolejskova 3, 182 23 Praha, Czech
Republic
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11
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Krepkiy D, Gawrisch K, Swartz KJ. Structural interactions between lipids, water and S1-S4 voltage-sensing domains. J Mol Biol 2012; 423:632-47. [PMID: 22858867 PMCID: PMC3616881 DOI: 10.1016/j.jmb.2012.07.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 07/17/2012] [Accepted: 07/20/2012] [Indexed: 10/28/2022]
Abstract
Membrane proteins serve crucial signaling and transport functions, yet relatively little is known about their structures in membrane environments or how lipids interact with these proteins. For voltage-activated ion channels, X-ray structures suggest that the mobile voltage-sensing S4 helix would be exposed to the membrane, and functional studies reveal that lipid modification can profoundly alter channel activity. Here, we use solid-state NMR to investigate structural interactions of lipids and water with S1-S4 voltage-sensing domains and to explore whether lipids influence the structure of the protein. Our results demonstrate that S1-S4 domains exhibit extensive interactions with lipids and that these domains are heavily hydrated when embedded in a membrane. We also find evidence for preferential interactions of anionic lipids with S1-S4 domains and that these interactions have lifetimes on the timescale of ≤ 10(-3)s. Arg residues within S1-S4 domains are well hydrated and are positioned in close proximity to lipids, exhibiting local interactions with both lipid headgroups and acyl chains. Comparative studies with a positively charged lipid lacking a phosphodiester group reveal that this lipid modification has only modest effects on the structure and hydration of S1-S4 domains. Taken together, our results demonstrate that Arg residues in S1-S4 voltage-sensing domains reside in close proximity to the hydrophobic interior of the membrane yet are well hydrated, a requirement for carrying charge and driving protein motions in response to changes in membrane voltage.
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Affiliation(s)
- Dmitriy Krepkiy
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892 USA
| | - Klaus Gawrisch
- Laboratory of Membrane Biochemistry and Biophysics, National Institute of Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892 USA
| | - Kenton J. Swartz
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892 USA
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12
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Wong WT, Chan KC, So PK, Yap HK, Chung WH, Leung YC, Wong KY, Zhao Y. Increased structural flexibility at the active site of a fluorophore-conjugated beta-lactamase distinctively impacts its binding toward diverse cephalosporin antibiotics. J Biol Chem 2011; 286:31771-80. [PMID: 21705325 DOI: 10.1074/jbc.m110.198895] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Ω-loop at the active site of β-lactamases exerts significant impact on the kinetics and substrate profile of these enzymes by forming part of the substrate binding site and posing as steric hindrance toward bulky substrates. Mutating certain residues on the Ω-loop has been a general strategy for molecular evolution of β-lactamases to expand their hydrolytic activity toward extended-spectrum antibiotics through a mechanism believed to involve enhanced structural flexibility of the Ω-loop. Yet no structural information is available that demonstrates such flexibility or its relation to substrate profile and enzyme kinetics. Here we report an engineered β-lactamase that contains an environment-sensitive fluorophore conjugated near its active site to probe the structural dynamics of the Ω-loop and to detect the binding of diverse substrates. Our results show that this engineered β-lactamase has improved binding kinetics and positive fluorescence signal toward oxyimino-cephalosporins, but shows little such effect to non-oxyimino-cephalosporins. Structural studies reveal that the Ω-loop adopts a less stabilized structure, and readily undergoes conformational change to accommodate the binding of bulky oxyimino-cephalosporins while no such change is observed for non-oxyimino-cephalosporins. Mutational studies further confirm that this substrate-induced structural change is directly responsible for the positive fluorescence signal specific to oxyimino-cephalosporins. Our data provide mechanistic evidence to support the long-standing model that the evolutionary strategy of mutating the Ω-loop leads to increased structural flexibility of this region, which in turn facilitates the binding of extended spectrum β-lactam antibiotics. The oxyimino-cephalosporin-specific fluorescence profile of our engineered β-lactamase also demonstrates the possibility of designing substrate-selective biosensing systems.
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Affiliation(s)
- Wai-Ting Wong
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
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Fluorescence Probing in Structurally Anisotropic Materials. ADVANCED FLUORESCENCE REPORTERS IN CHEMISTRY AND BIOLOGY III 2011. [DOI: 10.1007/978-3-642-18035-4_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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14
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van Oort B, Eremeeva EV, Koehorst RBM, Laptenok SP, van Amerongen H, van Berkel WJH, Malikova NP, Markova SV, Vysotski ES, Visser AJWG, Lee J. Picosecond fluorescence relaxation spectroscopy of the calcium-discharged photoproteins aequorin and obelin. Biochemistry 2009; 48:10486-91. [PMID: 19810751 DOI: 10.1021/bi901436m] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Addition of calcium ions to the Ca(2+)-regulated photoproteins, such as aequorin and obelin, produces a blue bioluminescence originating from a fluorescence transition of the protein-bound product, coelenteramide. The kinetics of several transient fluorescent species of the bound coelenteramide is resolved after picosecond-laser excitation and streak camera detection. The initially formed spectral distributions at picosecond-times are broad, evidently comprised of two contributions, one at higher energy (approximately 25,000 cm(-1)) assigned as from the Ca(2+)-discharged photoprotein-bound coelenteramide in its neutral state. This component decays much more rapidly (t(1/2) approximately 2 ps) in the case of the Ca(2+)-discharged obelin than aequorin (t(1/2) approximately 30 ps). The second component at lower energy shows several intermediates in the 150-500 ps times, with a final species having spectral maxima 19 400 cm(-1), bound to Ca(2+)-discharged obelin, and 21 300 cm(-1), bound to Ca(2+)-discharged aequorin, and both have a fluorescence decay lifetime of 4 ns. It is proposed that the rapid kinetics of these fluorescence transients on the picosecond time scale, correspond to times for relaxation of the protein structural environment of the binding cavity.
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Affiliation(s)
- Bart van Oort
- Laboratory of Biophysics, Wageningen University, The Netherlands
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15
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Viruses: incredible nanomachines. New advances with filamentous phages. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:541-50. [PMID: 19680644 PMCID: PMC2841255 DOI: 10.1007/s00249-009-0523-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 07/06/2009] [Accepted: 07/09/2009] [Indexed: 12/11/2022]
Abstract
During recent decades, bacteriophages have been at the cutting edge of new developments in molecular biology, biophysics, and, more recently, bionanotechnology. In particular filamentous viruses, for example bacteriophage M13, have a virion architecture that enables precision building of ordered and defect-free two and three-dimensional structures on a nanometre scale. This could not have been possible without detailed knowledge of coat protein structure and dynamics during the virus reproduction cycle. The results of the spectroscopic studies conducted in our group compellingly demonstrate a critical role of membrane embedment of the protein both during infectious entry of the virus into the host cell and during assembly of the new virion in the host membrane. The protein is effectively embedded in the membrane by a strong C-terminal interfacial anchor, which together with a simple tilt mechanism and a subtle structural adjustment of the extreme end of its N terminus provides favourable thermodynamical association of the protein in the lipid bilayer. This basic physicochemical rule cannot be violated and any new bionanotechnology that will emerge from bacteriophage M13 should take this into account.
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