Binding characteristics of staphylococcal protein A and streptococcal protein G for fragment crystallizable portion of human immunoglobulin G

Lee, Hae Gon; Kang, Sangmo; Lee, Joon Sang

doi:10.1016/j.csbj.2021.05.048

Cited by 24 publications

(7 citation statements)

References 70 publications

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“…For this analysis, molecular docking studies are used extensively [58] , [59] . Before starting the discussion, it is essential to know that the terms binding energy and binding affinity are in inverse relation with each other, and better ligand-protein complex results from more negative binding energy [60] . The binding affinity is the strength of the binding interaction between the ligand and receptor, and the binding energy describes the binding strength of the ligand in the binding pocket of the receptor.…”

Section: Resultsmentioning

confidence: 99%

Exploring the inhibitory potential of novel piperidine-derivatives against main protease (Mpro) of SARS-CoV-2: A hybrid approach consisting of molecular docking, MD simulations and MMPBSA analysis

Rafique

Muhammad

Iqbal

et al. 2023

Journal of Molecular Liquids

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Section: Resultsmentioning

confidence: 99%

Exploring the inhibitory potential of novel piperidine-derivatives against main protease (Mpro) of SARS-CoV-2: A hybrid approach consisting of molecular docking, MD simulations and MMPBSA analysis

Rafique

Muhammad

Iqbal

et al. 2023

Journal of Molecular Liquids

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“…A truncated octahedral TIP3P [ 38 ] water box with 10 Å was employed to solvate the protein–ligand complex. Two rounds of minimizations were performed, including the steepest descent and conjugate gradient algorithms [ 39 , 40 , 41 ]. Then, both systems were heated up from 0 to 300 K within 1 ns of MD simulations under the canonical ensemble, using the position restraints of 10 kcal/(mol∙Å 2 ) on the solute atoms.…”

Section: Methodsmentioning

confidence: 99%

Mechanistic Insights into the Mechanism of Inhibitor Selectivity toward the Dark Kinase STK17B against Its High Homology STK17A

Liu

Zhang

et al. 2022

Molecules

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As a member of the death-associated protein kinase (DAPK) family, STK17B plays an important role in the regulation of cellular apoptosis and has been considered as a promising drug target for hepatocellular carcinoma. However, the highly conserved ATP-binding site of protein kinases represents a challenge to design selective inhibitors for a specific DAPK isoform. In this study, molecular docking, multiple large-scale molecular dynamics (MD) simulations, and binding free energy calculations were performed to decipher the molecular mechanism of the binding selectivity of PKIS43 toward STK17B against its high homology STK17A. MD simulations revealed that STK17A underwent a significant conformational arrangement of the activation loop compared to STK17B. The binding free energy predictions suggested that the driving force to control the binding selectivity of PKIS43 was derived from the difference in the protein–ligand electrostatic interactions. Furthermore, the per-residue free energy decomposition unveiled that the energy contribution from Arg41 at the phosphate-binding loop of STK17B was the determinant factor responsible for the binding specificity of PKIS43. This study may provide useful information for the rational design of novel and potent selective inhibitors toward STK17B.

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“…The binding energy and the equilibrium dissociation constant (K D ) were calculated by the YASARA software, version 19.5.23. The most stable conformation of the receptor was determined based on the ligand with the lowest binding energy, indicated by the most negative value [29]. The tighter the ligand-protein binding, or the greater the affinity between them, the smaller the dissociation constant [30].…”

Section: Molecular Docking (Zdock)mentioning

confidence: 99%

Mechanism Analysis of Antimicrobial Peptide NoPv1 Related to Potato Late Blight through a Computer-Aided Study

Zhou,

Wen,

2024

IJMS

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Phytophthora infestans (Mont.) de Bary, the oomycotic pathogen responsible for potato late blight, is the most devastating disease of potato production. The primary pesticides used to control oomycosis are phenyl amide fungicides, which cause environmental pollution and toxic residues harmful to both human and animal health. To address this, an antimicrobial peptide, NoPv1, has been screened to target Plasmopara viticola cellulose synthase 2 (PvCesA2) to inhibit the growth of Phytophthora infestans (P. infestans). In this study, we employed AlphaFold2 to predict the three-dimensional structure of PvCesA2 along with NoPv peptides. Subsequently, utilizing computational methods, we dissected the interaction mechanism between PvCesA2 and these peptides. Based on this analysis, we performed a saturation mutation of NoPv1 and successfully obtained the double mutants DP1 and DP2 with a higher affinity for PvCesA2. Meanwhile, dynamics simulations revealed that both DP1 and DP2 utilize a mechanism akin to the barrel-stave model for penetrating the cell membrane. Furthermore, the predicted results showed that the antimicrobial activity of DP1 was superior to that of NoPv1 without being toxic to human cells. These findings may offer insights for advancing the development of eco-friendly pesticides targeting various oomycete diseases, including late blight.

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Binding characteristics of staphylococcal protein A and streptococcal protein G for fragment crystallizable portion of human immunoglobulin G

Abstract: Graphical abstract

Cited by 24 publications

References 70 publications

Exploring the inhibitory potential of novel piperidine-derivatives against main protease (Mpro) of SARS-CoV-2: A hybrid approach consisting of molecular docking, MD simulations and MMPBSA analysis

Exploring the inhibitory potential of novel piperidine-derivatives against main protease (Mpro) of SARS-CoV-2: A hybrid approach consisting of molecular docking, MD simulations and MMPBSA analysis

Mechanistic Insights into the Mechanism of Inhibitor Selectivity toward the Dark Kinase STK17B against Its High Homology STK17A

Mechanism Analysis of Antimicrobial Peptide NoPv1 Related to Potato Late Blight through a Computer-Aided Study

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