Interaction of Lysozyme with Dyes

Subramanian, M.; Sheshadri, B.S.; Venkatappa, M. P.

doi:10.1093/oxfordjournals.jbchem.a134819

Cited by 12 publications

(6 citation statements)

References 2 publications

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“…As shown in Figure a, the addition of individual protein may induce the fluorescence recovery of quenched triple-color QD-BPB complexes, suggesting the stronger binding affinity of protein-BPB complex than that of QD-BPB complex. In each fluorescence channel, the recovered fluorescence intensity varies from the protein to the protein depending on both their hydrophobicity and the total number of positively charged residues. , Moreover, each protein generates a distinct triple-channel pattern (3 channels ×10 proteins ×6 replicates) which may function as a fingerprint for differentiation. The fluorescence response patterns (Figure a, see Table S3) are subjected to a linear discriminant analysis (LDA), with the first two factors being plotted and visualized.…”

Section: Resultsmentioning

confidence: 99%

Multicolor Quantum Dot-Based Chemical Nose for Rapid and Array-Free Differentiation of Multiple Proteins

Zhang

Tang

et al. 2016

Anal. Chem.

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Nanomaterial-based differential sensors (e.g., chemical nose) have shown great potential for identification of multiple proteins because of their modulatable recognition and transduction capability but with the limitation of array separation, single-channel read-out, and long incubation time. Here, we develop a multicolor quantum dot (QD)-based multichannel sensing platform for rapid identification of multiple proteins in an array-free format within 1 min. A protein-binding dye of bromophenol blue (BPB) is explored as an efficient reversible quencher of QDs, and the mixture of BPB with multicolor QDs may generate the quenched QD-BPB complexes. The addition of proteins will disrupt the QD-BPB complexes as a result of the competitive protein-BPB binding, inducing the separation of BPB from the QDs and the generation of distinct fluorescence patterns. The multicolor patterns may be collected at a single-wavelength excitation and differentiated by a linear discriminant analysis (LDA). This multichannel sensing platform allows for the discrimination of ten proteins and seven cell lines with the fastest response rate reported to date, holding great promise for rapid and high-throughput medical diagnostics.

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Section: Resultsmentioning

confidence: 99%

Multicolor Quantum Dot-Based Chemical Nose for Rapid and Array-Free Differentiation of Multiple Proteins

Zhang

Tang

et al. 2016

Anal. Chem.

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“…The other method is the use of the concept of Wyman's binding potential . On the assumption that there exists only two protein species (one is the bare protein and the other is the fully loaded protein with ligands), the apparent Gibbs free energy of binding was evaluated, − on the further assumption that there exists the predominant species that binds average-bound-number ligands. Although this approach is expected to provide a rough estimation of the Gibbs free energy of binding in the limit of high ligand concentration for a highly cooperative system, it is difficult for us to picture the real nature of the cooperativity from this information because the above two assumptions contradict each other.…”

Section: Introductionmentioning

confidence: 99%

Cooperative Ligand Binding to Globular Protein: A Statistical Mechanical Theory Based on a Simple Geometrical Model and Its Application to Lysozyme Systems

Murakami

1999

Langmuir

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A simple geometrical model for statistical mechanical analysis of cooperative binding of monoionic ligands to globular proteins was developed. It is assumed that the ligand has the charged group, which is able to bind the oppositely charged residues on protein surface by electrostatic interactions, and the hydrophobic region, which causes cooperativity by the interactions between bound ligands. The bound ligand together with the side chain of the ionic residue is assumed to be mobile over the protein surface within the tangential half sphere with the center at the β-carbon of the side chain and the radius of the effective ligand length. The potential around a bound ligand was approximated by the cylindrical square-well potential with an exclusion core along the center line. The shape of protein was assumed to be spherical. The distance between charged residues on the protein surface was taken from crystallographic data. Grand partition function was calculated as the sum of the terms of all possible bound states. In each term, the electrostatic free energy was taken into account as the Debye−Huckel type electrostatic potential energy for the distribution of isolated charges, and the partition function due to hydrophobic and/or stacking interactions was calculated as the product of pairwise interactions. The model was applied to the binding of an anionic azo dye or anionic surfactants to hen egg white lysozyme at several experimental conditions. The calculated binding isotherms well-reproduced the experimental data. The values of the model parameters estimated were consistent with the ligand size and the magnitude of hydrophobic interaction. Other detailed information such as species fraction, variance, and bound fraction of each site was obtained. The results show the wide applicability of the present model theory.

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“…The binding of BPB to lysozyme has also been characterized in solution by different techniques (Krishnamoorthy & Prabhananda, 1982a;Madhusudan & Vijayan, 1992;Yue, Niu et al, 2008;Subramanian et al, 1984). Fluorescence-quenching experiments suggest that BPB binds to a single site in lysozyme placed 3.6 Å from Trp62, with a dissociation constant of 3.62 Â 10 À4 M at 25 C (experiments conducted in sodium acetate at pH 6.0; Yue, Niu et al, 2008).…”

Section: Discussionmentioning

confidence: 99%

Lysozyme crystals dyed with bromophenol blue: where has the dye gone?

Plaza-Garrido

Salinas-Garcia

Alba-Elena

et al. 2020

Acta Cryst Sect D Struct Biol

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Protein crystals can easily be coloured by adding dyes to their mother liquor, but most structures of these protein–dye complexes remain unsolved. Here, structures of lysozyme in complex with bromophenol blue obtained by soaking orthorhombic and tetragonal crystals in a saturated solution of the dye at different pH values from 5.0 to 7.5 are reported. Two different binding sites can be found in the lysozyme–bromophenol blue crystals: binding site I is located near the amino- and carboxyl-termini, while binding site II is located adjacent to helices α1 (residues 4–15) and α3 (residues 88–100). In the orthorhombic crystals soaked at pH 7.0, binding of the dye takes place in both sites without significant changes in the unit cell. However, soaking tetragonal crystals with bromophenol blue results in two different complexes. Crystals soaked at pH 5.5 (HEWL-T1) show a single dye molecule bound to site II, and the crystals belong to space group P43212 without significant changes in the unit cell (a = b = 78.50, c = 37.34 Å). On the other hand, crystals soaked at pH 6.5 in the presence of imidazole (HEWL-T2) show up to eight molecules of the dye bound to site II, and display changes in space group (P212121) and unit cell (a = 38.00, b = 76.65, c = 84.86 Å). In all of the structures, the dye molecules are placed at the surface of the protein near to positively charged residues accessible through the main solvent channels of the crystal. Differences in the arrangement of the dye molecules at the surface of the protein suggest that the binding is not specific and is mainly driven by electrostatic interactions.

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Interaction of Lysozyme with Dyes

Cited by 12 publications

References 2 publications

Multicolor Quantum Dot-Based Chemical Nose for Rapid and Array-Free Differentiation of Multiple Proteins

Multicolor Quantum Dot-Based Chemical Nose for Rapid and Array-Free Differentiation of Multiple Proteins

Cooperative Ligand Binding to Globular Protein: A Statistical Mechanical Theory Based on a Simple Geometrical Model and Its Application to Lysozyme Systems

Lysozyme crystals dyed with bromophenol blue: where has the dye gone?

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