Exploring the capabilities of TDDFT calculations to explain the induced chirality upon a binding process: A simple case, 3-carboxycoumarin

Varlan, Aurica; Hillebrand, Mihaela

doi:10.1016/j.molstruc.2012.11.060

Cited by 13 publications

(5 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As an example of the simplest case, we present the 1 : 1 interaction of 3-carboxy-coumarin with BSA. 56 Gradually increasing the protein concentration, ICD spectra of 3-carboxy-coumarin were recorded in the range of its absorption bands, reflecting a conformational change occurring upon binding, due to the steric restriction imposed by the protein site. The experimental ICD spectrum presents three bands located at 319 (+), 290 (+) and below 280 (À) nm.…”

Section: Applications Of the Methodsmentioning

confidence: 99%

Theoretical ECD calculations – a useful tool for estimating the conformational change of a ligand in the binding pocket of proteins

Ionescu

Matei

Tablet

et al. 2013

Phys. Chem. Chem. Phys.

Self Cite

View full text Add to dashboard Cite

The correlation of experimentally induced circular dichroism (ICD) spectra recorded from (a)chiral ligands during their binding to proteins with simulated electronic circular dichroism (ECD) spectra via time-dependent density functional theory calculations was used for obtaining structural information on the ligands in the protein binding sites. A three step procedure is reported, involving the optimization of the most relevant conformers of the different ligand species presumed to be present in the system, the calculation of their ECD spectra and the comparison of the theoretical spectra with the experimental ones. This approach was exemplified for several model systems that can yield ICD signals through steric hindrance of a degree of freedom in the protein pocket. The method was found to be suitable to identify the bound form(s) for flexible molecular systems in which several species can coexist in solution. The effect of several functional/basis set combinations was tested, aiming to establish which one gives the most reliable results.

show abstract

Section: Applications Of the Methodsmentioning

confidence: 99%

Theoretical ECD calculations – a useful tool for estimating the conformational change of a ligand in the binding pocket of proteins

Ionescu

Matei

Tablet

et al. 2013

Phys. Chem. Chem. Phys.

Self Cite

View full text Add to dashboard Cite

show abstract

“…The protein structure (PDB ID: 4F5S) [48] was obtained from the RSCB Protein Data Bank [49]. The geometry of the SA anion was optimized by DFT/B3LYP/6-311G++ level of theory using the Gaussian 03 software [50], as previously described [51]. The molecular docking was performed using the Autodock Vina 1.1.2 software [52].…”

Section: Molecular Dockingmentioning

confidence: 99%

Impact of Sinapic Acid on Bovine Serum Albumin Thermal Stability

Precupas,

Popa

2024

IJMS

View full text Add to dashboard Cite

The thermal stability of bovine serum albumin (BSA) in Tris buffer, as well as the effect of sinapic acid (SA) on protein conformation were investigated via calorimetric (differential scanning microcalorimetry—μDSC), spectroscopic (dynamic light scattering—DLS; circular dichroism—CD), and molecular docking approaches. μDSC data revealed both the denaturation (endotherm) and aggregation (exotherm) of the protein, demonstrating the dual effect of SA on protein thermal stability. With an increase in ligand concentration, (i) protein denaturation shifts to a higher temperature (indicating native form stabilization), while (ii) the aggregation process shifts to a lower temperature (indicating enhanced reactivity of the denatured form). The stabilization effect of SA on the native structure of the protein was supported by CD results. High temperature (338 K) incubation induced protein unfolding and aggregation, and increasing the concentration of SA altered the size distribution of the protein population, as DLS measurements demonstrated. Complementary information offered by molecular docking allowed for the assessment of the ligand binding within the Sudlow’s site I of the protein. The deeper insight into the SA–BSA interaction offered by the present study may serve in the clarification of ligand pharmacokinetics and pharmacodynamics, thus opening paths for future research and therapeutic applications.

show abstract

“…The crystal structure of laccase (PDB ID:1GYC) was obtained from the RCSB Protein Databank [35]. The structures of ABTS and methyl red were optimized using density functional theory with B3LYP functional and 6-31G* basis set by Gaussian03 software [36], as previously reported for other ligands [37,38]. AutoDock tools [39] were used to convert ABTS, methyl red and enzyme structures to pdbqt format [40].…”

Section: Molecular Dockingmentioning

confidence: 99%

The Immobilization of Laccase on Mixed Polymeric Microspheres for Methyl Red Decomposition

et al. 2022

View full text Add to dashboard Cite

Means of eliminating water pollutants or transforming them into less hazardous compounds by green catalysis are desired. The current work was developed with the goal of discovering supports suited for laccase (Lc) immobilization. The effect of the chitosan (CS) molecular weight (Mw) or the polyacrylic acid (PAA) addition was evaluated in microsphere formulation and enzyme immobilization by ESEM, rheology, operational stability, and kinetics. As a practical application, the synthesized products were tested in the methyl red (MR) decomposition and the product identification was performed by high-resolution mass spectrometry. Depending on the required properties, the laccase activity profile (pH, temperature, storage, and Michaelis–Menten parameters) and rheological strength can be modulated by varying the molecular mass of CS or by adding PAA in the support formulation. The immobilized products having the best features regarding MR degradation and recycling abilities were the medium Mw CS microspheres and the system with low Mw CS complexed by PAA, respectively. The degradation mechanism of the dye was proposed accordingly with the identified products by mass spectroscopy. The findings emphasize the potential of the proposed immobilization products to be exploited as viable biocatalysts for dye-contaminated water.

show abstract

Exploring the capabilities of TDDFT calculations to explain the induced chirality upon a binding process: A simple case, 3-carboxycoumarin

Cited by 13 publications

References 38 publications

Theoretical ECD calculations – a useful tool for estimating the conformational change of a ligand in the binding pocket of proteins

Theoretical ECD calculations – a useful tool for estimating the conformational change of a ligand in the binding pocket of proteins

Impact of Sinapic Acid on Bovine Serum Albumin Thermal Stability

The Immobilization of Laccase on Mixed Polymeric Microspheres for Methyl Red Decomposition

Contact Info

Product

Resources

About