A Spectroscopic and Molecular Simulation Approach toward the Binding Affinity between Lysozyme and Phenazinium Dyes: An Effect on Protein Conformation.
A comparative study of binding interaction between Safranin O (SO) and Neutral Red (NR) with lysozyme (Lyz) has been reported using several spectroscopic methods along with computational approaches. Steady-state fluorescence measurements revealed static quenching as the major quenching mechanism in Lyz-SO and Lyz-NR interaction, which is further supported by time-resolved fluorescence and UV-vis measurements. Additionally, binding and thermodynamic parameters of these interactions are calculated from temperature dependent fluorescence data. Moreover, conformational changes of protein upon binding with SO and NR are provided by synchronous and circular dichroism (CD) measurements. Molecular docking study provided the exact binding location of SO and NR in lysozyme. Along with this study, molecular dynamics simulation is carried out to measure the stability of Lyz, Lyz-SO, and Lyz-NR complex. The present study revealed the strong binding affinity of dyes with lysozyme, and this study would be helpful toward medical and environmental science.
Department of Chemistry, National Institute of Technology (NIT) , Rourkela, Odisha, India.
Sabera
S
Millan
Department of Chemistry, National Institute of Technology (NIT) , Rourkela, Odisha, India.
Lakkoji
L
Satish
Department of Bioinformatics, Central University of South Bihar , Patna, India.
Krishnendu
K
Bera
Department of Chemistry, National Institute of Technology (NIT) , Rourkela, Odisha, India.
B
B
Susrisweta
Department of Bioinformatics, Central University of South Bihar , Patna, India.
Durg Vijay
DV
Singh
Department of Chemistry, National Institute of Technology (NIT) , Rourkela, Odisha, India.
Harekrushna
0000-0003-2655-1196
H
Sahoo
D000818:Animals; D001665:Binding Sites; D002645:Chickens; D002942:Circular Dichroism; D005456:Fluorescent Dyes / Q000737:chemistry / Q000378:metabolism*; D006860:Hydrogen Bonding; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D009113:Muramidase / Q000737:chemistry / Q000378:metabolism*; D009499:Neutral Red / Q000737:chemistry / Q000378:metabolism*; D010619:Phenazines / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation / Q000187:drug effects; D013050:Spectrometry, Fluorescence; D013816:Thermodynamics
D005456:Fluorescent Dyes; D010619:Phenazines; D009499:Neutral Red; C421864:hen egg lysozyme; D009113:Muramidase; C009195:safranine T