The Experts below are selected from a list of 1866 Experts worldwide ranked by ideXlab platform
Dafydd D Jones - One of the best experts on this subject based on the ideXlab platform.
-
molecular basis for functional switching of gfp by two disparate non native post translational modifications of a Phenyl Azide reaction handle
Chemical Science, 2016Co-Authors: Andrew M Hartley, Samuel C Reddington, Pierre J Rizkallah, Harley L Worthy, Dafydd D JonesAbstract:Through the genetic incorporation of a single Phenyl Azide group into superfolder GFP (sfGFP) at residue 148 we provide a molecular description of how this highly versatile chemical handle can be used to positively switch protein function in vitro and in vivo via either photochemistry or bioconjugation. Replacement of H148 with p-azido-L-Phenylalanine (azF) blue shifts the major excitation peak ∼90 nm by disrupting the H-bond and proton transfer network that defines the chromophore charged state. Bioorthogonal click modification with a simple dibenzylcyclooctyne or UV irradiation shifts the neutral-anionic chromophore equilibrium, switching fluorescence to the optimal ∼490 nm excitation. Click modification also improved quantum yield over both the unmodified and original protein. Crystal structures of both the click modified and photochemically converted forms show that functional switching is due to local conformational changes that optimise the interaction networks surrounding the chromophore. Crystal structure and mass spectrometry studies of the irradiated protein suggest that the Phenyl Azide converts to a dehydroazepine and/or an azepinone. Thus, protein embedded Phenyl Azides can be used beyond simple photocrosslinkers and passive conjugation handles, and mimic many natural post-translational modifications: modulation though changes in interaction networks.
-
genetically encoded Phenyl Azide photochemistry drives positive and negative functional modulation of a red fluorescent protein
RSC Advances, 2015Co-Authors: Samuel C Reddington, Pierre J Rizkallah, Peter Duncan Watson, Sarunas Driezis, Andrew M Hartley, Dafydd D JonesAbstract:The photochemical properties of Phenyl Azide have been exploited to modulate the function of a red autofluorescent protein, mCherry. Using genetic code reprogramming, Phenyl Azide chemistry has been introduced at functionally strategic positions in mCherry leading to deactivation, activation or enhancement upon UV irradiation.
-
genetically encoding Phenyl Azide chemistry new uses and ideas for classical biochemistry
Biochemical Society Transactions, 2013Co-Authors: Samuel C Reddington, Pierre J Rizkallah, Peter Duncan Watson, Eric Michael Tippmann, Dafydd D JonesAbstract:Introducing new physicochemical properties into proteins through genetically encoded Uaa (unnatural amino acid) incorporation can lead to the generation of proteins with novel properties not normally accessible with the 20 natural amino acids. Phenyl Azide chemistry represents one such useful addition to the protein repertoire. Classically used in biochemistry as a non-specific photochemical protein cross-linker, genetically encoding Phenyl Azide chemistry at selected residues provides more powerful routes to post-translationally modify protein function in situ. The two main routes are modulation by light (optogenetics) and site-specific bio-orthogonal modification (bioconjugation) via Click chemistry. In the present article, we discuss both approaches and their influence on protein function.
-
different photochemical events of a genetically encoded Phenyl Azide define and modulate gfp fluorescence
Angewandte Chemie, 2013Co-Authors: Samuel C Reddington, Pierre J Rizkallah, Peter Duncan Watson, Rachel Pearson, Eric Michael Tippmann, Dafydd D JonesAbstract:Expanding the genetic code opens new avenues to modulate protein function in real time. By genetically incorporating photoreactive Phenyl Azide, the fluorescent properties of green fluorescent protein (GFP) can be modulated by light. Depending on the residue in GFP programmed to incorporate the Phenyl Azide, different effects on function and photochemical pathways are observed.
Kendall N. Houk - One of the best experts on this subject based on the ideXlab platform.
-
Reactivity and regioselectivity in 1,3-dipolar cycloadditions of Azides to strained alkynes and alkenes: a computational study.
Journal of the American Chemical Society, 2009Co-Authors: Franziska Schoenebeck, Daniel H. Ess, Gavin O. Jones, Kendall N. HoukAbstract:The transition states and activation barriers of the 1,3-dipolar cycloadditions of Azides with cycloalkynes and cycloalkenes were explored using B3LYP density functional theory (DFT) and spin component scaled SCS-MP2 methods. A survey of benzyl Azide cycloadditions to substituted cyclooctynes (OMe, Cl, F, CN) showed that fluorine substitution has the most dramatic effect on reactivity. Azide cycloadditions to 3-substituted cyclooctynes prefer 1,5-addition regiochemistry in the gas phase, but CPCM solvation abolishes the regioselectivity preference, in accord with experiments in solution. The activation energies for Phenyl Azide addition to cycloalkynes decrease considerably as the ring size is decreased (cyclononyne ΔG⧧ = 29.2 kcal/mol, cyclohexyne ΔG⧧ = 14.1 kcal/mol). The origin of this trend is explained by the distortion/interaction model. Cycloalkynes are predicted to be significantly more reactive dipolarophiles than cycloalkenes. The activation barriers for the cycloadditions of Phenyl Azide and pi...
-
Transition states of strain-promoted metal-free click chemistry: 1,3-dipolar cycloadditions of Phenyl Azide and cyclooctynes.
Organic letters, 2008Co-Authors: Daniel H. Ess, Gavin O. Jones, Kendall N. HoukAbstract:Density functional theory (B3LYP) calculations on the transition states for the Huisgen 1,3-dipolar cycloadditions of Phenyl Azide with acetylene, cyclooctyne, and difluorocyclooctyne are reported. The low activation energy of the cyclooctyne “strain-promoted” cycloaddition (ΔE⧧ = 8.0) compared to the strain-free acetylene cycloaddition (ΔE⧧ = 16.2) is due to decreased distortion energy (ΔEd⧧) of cyclooctyne (ΔΔEd⧧ = 4.6) and Phenyl Azide (ΔΔEd⧧ = 4.5) to achieve that cycloaddition transition state. Electronegative fluorine substituents on cyclooctyne further increase the rate of cycloaddition by increasing interaction energies.
Samuel C Reddington - One of the best experts on this subject based on the ideXlab platform.
-
molecular basis for functional switching of gfp by two disparate non native post translational modifications of a Phenyl Azide reaction handle
Chemical Science, 2016Co-Authors: Andrew M Hartley, Samuel C Reddington, Pierre J Rizkallah, Harley L Worthy, Dafydd D JonesAbstract:Through the genetic incorporation of a single Phenyl Azide group into superfolder GFP (sfGFP) at residue 148 we provide a molecular description of how this highly versatile chemical handle can be used to positively switch protein function in vitro and in vivo via either photochemistry or bioconjugation. Replacement of H148 with p-azido-L-Phenylalanine (azF) blue shifts the major excitation peak ∼90 nm by disrupting the H-bond and proton transfer network that defines the chromophore charged state. Bioorthogonal click modification with a simple dibenzylcyclooctyne or UV irradiation shifts the neutral-anionic chromophore equilibrium, switching fluorescence to the optimal ∼490 nm excitation. Click modification also improved quantum yield over both the unmodified and original protein. Crystal structures of both the click modified and photochemically converted forms show that functional switching is due to local conformational changes that optimise the interaction networks surrounding the chromophore. Crystal structure and mass spectrometry studies of the irradiated protein suggest that the Phenyl Azide converts to a dehydroazepine and/or an azepinone. Thus, protein embedded Phenyl Azides can be used beyond simple photocrosslinkers and passive conjugation handles, and mimic many natural post-translational modifications: modulation though changes in interaction networks.
-
genetically encoded Phenyl Azide photochemistry drives positive and negative functional modulation of a red fluorescent protein
RSC Advances, 2015Co-Authors: Samuel C Reddington, Pierre J Rizkallah, Peter Duncan Watson, Sarunas Driezis, Andrew M Hartley, Dafydd D JonesAbstract:The photochemical properties of Phenyl Azide have been exploited to modulate the function of a red autofluorescent protein, mCherry. Using genetic code reprogramming, Phenyl Azide chemistry has been introduced at functionally strategic positions in mCherry leading to deactivation, activation or enhancement upon UV irradiation.
-
genetically encoding Phenyl Azide chemistry new uses and ideas for classical biochemistry
Biochemical Society Transactions, 2013Co-Authors: Samuel C Reddington, Pierre J Rizkallah, Peter Duncan Watson, Eric Michael Tippmann, Dafydd D JonesAbstract:Introducing new physicochemical properties into proteins through genetically encoded Uaa (unnatural amino acid) incorporation can lead to the generation of proteins with novel properties not normally accessible with the 20 natural amino acids. Phenyl Azide chemistry represents one such useful addition to the protein repertoire. Classically used in biochemistry as a non-specific photochemical protein cross-linker, genetically encoding Phenyl Azide chemistry at selected residues provides more powerful routes to post-translationally modify protein function in situ. The two main routes are modulation by light (optogenetics) and site-specific bio-orthogonal modification (bioconjugation) via Click chemistry. In the present article, we discuss both approaches and their influence on protein function.
-
different photochemical events of a genetically encoded Phenyl Azide define and modulate gfp fluorescence
Angewandte Chemie, 2013Co-Authors: Samuel C Reddington, Pierre J Rizkallah, Peter Duncan Watson, Rachel Pearson, Eric Michael Tippmann, Dafydd D JonesAbstract:Expanding the genetic code opens new avenues to modulate protein function in real time. By genetically incorporating photoreactive Phenyl Azide, the fluorescent properties of green fluorescent protein (GFP) can be modulated by light. Depending on the residue in GFP programmed to incorporate the Phenyl Azide, different effects on function and photochemical pathways are observed.
Darran Dafydd Jones - One of the best experts on this subject based on the ideXlab platform.
-
site specific protein photochemical covalent attachment to carbon nanotube side walls and its electronic impact on single molecule function
Bioconjugate Chemistry, 2020Co-Authors: Suzanne Thomas, Harley L Worthy, Adam Beachey, Emyr J. Macdonald, Martin Elliott, Oliver K. Castell, David Jamieson, Rebecca Gwyther, Benjamin James Bowen, Darran Dafydd JonesAbstract:Functional integration of proteins with carbon-based nanomaterials such as nanotubes holds great promise in emerging electronic and optoelectronic applications. Control over protein attachment poses a major challenge for consistent and useful device fabrication, especially when utilizing single/few molecule properties. Here, we exploit genetically encoded Phenyl Azide photochemistry to define the direct covalent attachment of four different proteins, including the fluorescent protein GFP and a β-lactamase binding protein (BBP), to carbon nanotube side walls. AFM showed that on attachment BBP could still recognize and bind additional protein components. Single molecule fluorescence revealed that on attachment to SWCNTs function was retained and there was feedback to GFP in terms of fluorescence intensity and improved resistance to photobleaching; GFP is fluorescent for much longer on attachment. The site of attachment proved important in terms of electronic impact on GFP function, with the attachment site ...
Harley L Worthy - One of the best experts on this subject based on the ideXlab platform.
-
site specific protein photochemical covalent attachment to carbon nanotube side walls and its electronic impact on single molecule function
Bioconjugate Chemistry, 2020Co-Authors: Suzanne Thomas, Harley L Worthy, Adam Beachey, Emyr J. Macdonald, Martin Elliott, Oliver K. Castell, David Jamieson, Rebecca Gwyther, Benjamin James Bowen, Darran Dafydd JonesAbstract:Functional integration of proteins with carbon-based nanomaterials such as nanotubes holds great promise in emerging electronic and optoelectronic applications. Control over protein attachment poses a major challenge for consistent and useful device fabrication, especially when utilizing single/few molecule properties. Here, we exploit genetically encoded Phenyl Azide photochemistry to define the direct covalent attachment of four different proteins, including the fluorescent protein GFP and a β-lactamase binding protein (BBP), to carbon nanotube side walls. AFM showed that on attachment BBP could still recognize and bind additional protein components. Single molecule fluorescence revealed that on attachment to SWCNTs function was retained and there was feedback to GFP in terms of fluorescence intensity and improved resistance to photobleaching; GFP is fluorescent for much longer on attachment. The site of attachment proved important in terms of electronic impact on GFP function, with the attachment site ...
-
molecular basis for functional switching of gfp by two disparate non native post translational modifications of a Phenyl Azide reaction handle
Chemical Science, 2016Co-Authors: Andrew M Hartley, Samuel C Reddington, Pierre J Rizkallah, Harley L Worthy, Dafydd D JonesAbstract:Through the genetic incorporation of a single Phenyl Azide group into superfolder GFP (sfGFP) at residue 148 we provide a molecular description of how this highly versatile chemical handle can be used to positively switch protein function in vitro and in vivo via either photochemistry or bioconjugation. Replacement of H148 with p-azido-L-Phenylalanine (azF) blue shifts the major excitation peak ∼90 nm by disrupting the H-bond and proton transfer network that defines the chromophore charged state. Bioorthogonal click modification with a simple dibenzylcyclooctyne or UV irradiation shifts the neutral-anionic chromophore equilibrium, switching fluorescence to the optimal ∼490 nm excitation. Click modification also improved quantum yield over both the unmodified and original protein. Crystal structures of both the click modified and photochemically converted forms show that functional switching is due to local conformational changes that optimise the interaction networks surrounding the chromophore. Crystal structure and mass spectrometry studies of the irradiated protein suggest that the Phenyl Azide converts to a dehydroazepine and/or an azepinone. Thus, protein embedded Phenyl Azides can be used beyond simple photocrosslinkers and passive conjugation handles, and mimic many natural post-translational modifications: modulation though changes in interaction networks.