Cis−Trans Isomerization of Organic Molecules and Biomolecules:  Implications and Applications

Dugave, Christophe; Demange, Luc

doi:10.1021/cr0104375

Cited by 920 publications

(672 citation statements)

References 714 publications

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“…CypA is an archetypal and extensively studied enzyme belonging to the family of peptidyl prolyl isomerases (PPIases), speeding the cis-trans isomerization of peptidyl prolyl ω-bond in its protein substrates by more than 10 5 times (30)(31)(32)(33)(34). In five independent microsecond-long simulations, we monitored the dynamics in wild-type CypA, V29L variant of CypA, CypA bound to a substrate analogue in the trans, transition state, and cis configurations.…”

mentioning

confidence: 99%

Dynamical network of residue–residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation

Doshi

Holliday

Eisenmesser

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

152

186

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Detailed understanding of how conformational dynamics orchestrates function in allosteric regulation of recognition and catalysis remains ambiguous. Here, we simulate CypA using multiple-microsecond-long atomistic molecular dynamics in explicit solvent and carry out NMR experiments. We analyze a large amount of time-dependent multidimensional data with a coarse-grained approach and map key dynamical features within individual macrostates by defining dynamics in terms of residue-residue contacts. The effects of substrate binding are observed to be largely sensed at a location over 15 Å from the active site, implying its importance in allostery. Using NMR experiments, we confirm that a dynamic cluster of residues in this distal region is directly coupled to the active site. Furthermore, the dynamical network of interresidue contacts is found to be coupled and temporally dispersed, ranging over 4 to 5 orders of magnitude. Finally, using network centrality measures we demonstrate the changes in the communication network, connectivity, and influence of CypA residues upon substrate binding, mutation, and during catalysis. We identify key residues that potentially act as a bottleneck in the communication flow through the distinct regions in CypA and, therefore, as targets for future mutational studies. Mapping these dynamical features and the coupling of dynamics to function has crucial ramifications in understanding allosteric regulation in enzymes and proteins, in general.allostery | enzyme dynamics | residue-residue contacts | Cyclophilin A | molecular dynamics

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mentioning

confidence: 99%

Dynamical network of residue–residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation

Doshi

Holliday

Eisenmesser

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

152

186

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“…Basing on these determinations curves of progression of the reaction were found ( Figure 2) showing quite symmetric increase in molar ratio of isomer E in the reaction mixture with simultaneous decrease of the share of isomer Z. These progression curves were analyzed by applying standard kinetic equations, 21 which unequivocally indicated that the studied reaction is of the first order, with k1 value of (12.43 ± 0.27)×10 Preparative conversion of substituted Z ΔPhe into E ΔPhe, 22 as well as such isomerization of this dehydroamino acid in several peptides has been described previously. 23,24 However, these papers, dedicated to the photochemical reactions of slightly different aromatic dehydroamino acids, state that this process is not so simple and is accompanied by variable photochemical cyclizations.…”

Section: Resultsmentioning

confidence: 99%

Kinetics of photochemical isomerization of TFA-Gly-ZΔPhe into TFA-Gly-EΔPhe

Makowski¹,

Jewgiński²,

Hurek³

et al. 2017

Arkivoc

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The kinetics of photoisomerization of trifluoroacetyl-(Z)-dehydrophenylalanylglycine into trifluoroacetyl-(E)-dehydrophenylalanylglycine was studied in the hope that light-induced reaction could be useful as a means of preparation of the E-dehydropeptides. The obtained results indicate that if this reaction carried out under irradiation with light of wavelength 360 nm it is practically irreversible and gave nearly quantitatively pure Eisomer Significantly, expected cyclic side-products were not observed in the reaction mixture, thus proving the preparative potential of the elaborated procedure.

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“…[19] Recently, these derivatives have also found numerous new applications ranging from optical waveguides [20] and data storage devices [21] to lightswitchable receptors [22] , and it is likely that new applications and discoveries will be made as the chemistries and structures are further refined. [23] In contrast, very few examples of the synthesis or utilization of (N-phenyl-N'- [1,3,5]triazinyl)diazenes [24,25] , and even less of bis- [1,3,5]triazinyl diazenes [26,27] , can be found in the literature.…”

Section: Introductionmentioning

confidence: 99%

Preparation and characterization of bis‐[1,3,5]triazinyl diazenes and their utilization as flame retardants in polypropylene films

Tirri

Aubert

Pawelec

et al. 2014

J of Applied Polymer Sci

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A series of bis- [1,3,5]triazinyl diazenes and two metal complexes thereof were synthesized and tested as new flame retardants in polypropylene films. It was observed that electron withdrawing triazinyl ring substituents (i.e. Cl and phenyl moieties) improved the thermal stability of diazene compounds, whereas electron donating groups (i.e. methoxy, dimethylamino and ethylthio moieties) had a destabilizing effect. TGA, DTA/DSC, NMR and ATR-FTIR were used for the characterization. Quantum mechanical modeling (Gaussian 09) was also utilized to facilitate the interpretation of the NMR data. Bis-(4,6-dichloro-[1,3,5]triazin-2-yl)-diazene 1 and bis-(4,6-dimethoxy-[1,3,5]triazin-2-yl)-diazene 2 were found to be effective flame retardants in polypropylene films and DIN4102-1 B2 classification was reached already at a loading of 0.5 wt%. Interestingly, the copper complex of 2 showed even higher fire retardant activity than its precursor 2, whereas the corresponding zinc complex exhibited lower flame retardant efficacy than its precursor.

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Cis−Trans Isomerization of Organic Molecules and Biomolecules: Implications and Applications

Cited by 920 publications

References 714 publications

Dynamical network of residue–residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation

Dynamical network of residue–residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation

Kinetics of photochemical isomerization of TFA-Gly-ZΔPhe into TFA-Gly-EΔPhe

Preparation and characterization of bis‐[1,3,5]triazinyl diazenes and their utilization as flame retardants in polypropylene films

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