Exploring the interaction of bioactive kaempferol with serum albumin, lysozyme and hemoglobin: A biophysical investigation using multi-spectroscopic, docking and molecular dynamics simulation studies

Das, Sourav; Hazarika, Zaved; Sarmah, Sharat; Baruah, Kakali; Rohman, Mostofa Ataur; Paul, Debojit; Jha, Anupam Nath; Roy, Atanu Singha

doi:10.1016/j.jphotobiol.2020.111825

Cited by 75 publications

(35 citation statements)

References 82 publications

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“…In addition, lysozyme is clinically available to promote the repair of injured tissues, to correct the degree of immune activation, and to reduce the acute inflammatory reaction, especially in burn wound infection and herpes treatment [4]. Lysozyme has a globular fold divided into two domains, whose native conformation displays four α-helix structures and a three-strand antiparallel β-sheet [5] which consist of 129 amino acid residues, including six Trp residues, three of which (Trp 62, Trp 63, and Trp 108) locate in the active pocket of the helices domain of lysozyme [6]. erefore, it is very meaningful to research the change of helices domain structure which is closely associated with the activity of lysozyme.…”

Section: Introductionmentioning

confidence: 99%

The Effect of Luteolin and Luteoloside on the Secondary Structure of Lysozyme

Cui

et al. 2021

Journal of Food Quality

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The changes of lysozyme conformation in the absence and presence of luteolin and luteoloside were investigated by spectral analysis including fluorescence, UV, CD, Raman, and ATR-FTIR, and the biological activity of lysozyme was investigated by lysozyme assay kit. The results showed that the microenvironment hydrophobicity of lysozyme increased and peptide extension decreased with the addition of luteolin or luteoloside. The α-helix of lysozyme might be influenced by luteolin or luteoloside, and its relative content had a significant difference after adding luteolin or luteoloside by the ATR-FTIR method, which was reconfirmed by CD and Raman spectra. The lysozyme activity changed obviously after adding luteolin or luteoloside. All of the conclusions above indicated the active site of lysozyme in the α-helix might be influenced by luteolin and luteoloside.

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Section: Introductionmentioning

confidence: 99%

The Effect of Luteolin and Luteoloside on the Secondary Structure of Lysozyme

Cui

et al. 2021

Journal of Food Quality

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“…They investigated the protein folding mechanism of villin with explicit solvation [42]. Apart from proteins, the technique has been extended to study other relevant biomolecules [43,44] and protein-nanoparticle interactions [45][46][47][48][49]. Simulation of any system revolves around lot of factors.…”

Section: Molecular Dynamics: the Computational Microscopementioning

confidence: 99%

Role of Force Fields in Protein Function Prediction

Hazarika¹,

Rajkhowa²,

Jha³

2021

Homology Molecular Modeling - Perspectives and Applications

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The world today, although, has developed an elaborate health system to fortify against known and unknown diseases, it continues to be challenged by new as well as emerging, and re-emerging infectious disease threats with severity and probable fluctuations. These threats also have varying costs for morbidity and mortality, as well as for a complex set of socioeconomic outcomes. Some of these diseases are often caused by pathogens which use humans as host. In such cases, it becomes paramount responsibility to dig out the source of pathogen survival to stop their population growth. Sequencing genomes has been finessed so much in the 21st century that complete genomes of any pathogen can be sequenced in a matter of days following which; different potential drug targets are needed to be identified. Structure modeling of the selected sequences is an initial step in structure-based drug design (SBDD). Dynamical study of predicted models provides a stable target structure. Results of these in-silico techniques greatly depend on force field (FF) parameters used. Thus, in this chapter, we intend to discuss the role of FF parameters used in protein structure prediction and molecular dynamics simulation to provide a brief overview on this area.

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“…For interactions, MD simulations can be used to explore conformational responses upon binding, such as the induction of secondary structure, stabilization or release of loops as well as determining intermolecular contacts between ligand and target protein [173][174][175][176]. Another advantage of molecular dynamics simulation is the possibility of modeling the systems at different temperatures to access how the solvent affects the internal motion of proteins and predict the interaction mechanism [177][178][179][180].…”

Section: Molecular Dynamics By Computer Simulationmentioning

confidence: 99%

1H, 13C, and 15N resonance assignments of CW domain of the N-methyltransferase ASHH2 free and bound to the mono-, di- and tri-methylated histone H3 tail peptides

et al. 2018

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The ASHH2 CW domain is responsible for recognizing the methylation state at lysine 4 of histone 3 N-terminal tails and implicated in the recruitment of the ASHH2 methyltransferase enzyme correctly to the histones. The ASHH2 CW domain binds H3 lysine motifs that can be either mono-, di-, or tri-methylated [ARTK(meX)QTAR, where X denotes the number of methylations], but binds strongest to monomethylated instances (K values reported in the range of 1 µm to 500 nM). Hoppmann et al. published the uncomplexed NMR structure of an ASHH2 CW domain in 2011. Here we document the assignment of a shortened ASHH2 CW construct, CW42, with similar binding affinity and better expression yields than the one used to solve the uncomplexed structure. We also perform H-N HSQC-monitored titrations that document at which protein-peptide ratios the complex is saturated. Backbone resonance assignments are presented for this shortened ASHH2 CW domain alone and bound to an H3 histone tail mimicking peptide monomethylated on lysine 4 (ARTK(me1)QTAR). Likewise, the assignment was also performed for the protein in complex with the dimethylated (ARTK(me2)QTAR) and trimethylated (ARTK(me3)QTAR) peptide. Overall, these two latter situations displayed a similar perturbation of shifts as the mono-methylated instance. In the case of the monomethylated histone tail mimic, side-chain assignment of CW42 in this complex was performed and reported in addition to backbone assignment, in preparation of a future solution structure determination and dynamics characterization of the CW42-ARTK(me1)QTAR complex.

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Exploring the interaction of bioactive kaempferol with serum albumin, lysozyme and hemoglobin: A biophysical investigation using multi-spectroscopic, docking and molecular dynamics simulation studies

Cited by 75 publications

References 82 publications

The Effect of Luteolin and Luteoloside on the Secondary Structure of Lysozyme

The Effect of Luteolin and Luteoloside on the Secondary Structure of Lysozyme

Role of Force Fields in Protein Function Prediction

1H, 13C, and 15N resonance assignments of CW domain of the N-methyltransferase ASHH2 free and bound to the mono-, di- and tri-methylated histone H3 tail peptides

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