Molecular dynamics simulations and analysis for bioinformatics undergraduate students

Justino, Gonçalo C.; Nascimento, Catarina P.; Justino, Marta C.

doi:10.1002/bmb.21512

Cited by 25 publications

(6 citation statements)

References 47 publications

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“…The rather small amplitude of the gyration radius (Rg, Figure 5 A) indicates that the protein size remains stable during the simulation time [ 16 , 35 ], during which the fluctuation of Rg for α-LA at 368 K was slightly more severe with a standard deviation of 0.01 nm. In addition, the larger the Rg, the greater the expansion of the system.…”

Section: Resultsmentioning

confidence: 99%

Investigation of the Structure and Allergic Potential of Whey Protein by Both Heating Sterilization and Simulation with Molecular Dynamics

Zhang

et al. 2022

Foods

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As the main allergens in milk, whey proteins are heat-sensitive proteins and are widespread in dairy products and items in which milk proteins are involved as food additives. The present work sought to investigate the effect of heating sterilization on the allergenicity of α-lactalbumin (α-LA) and β-lactoglobulin (β-LG), the main composite and allergen in whey protein isolate (WPI), by combining molecular dynamics with experimental techniques for detecting the spatial structure and IgE binding capacity. The structure of WPI was basically destroyed at heat sterilization conditions of 95 °C for 5 min and 65 °C for 30 min by SDS-PAGE analysis and spectroscopic analysis. In addition, α-lactalbumin (α-LA) may be more sensitive to temperature, resulting in exposure to allergic epitopes and increasing the allergic potential, while the binding capacity of β-lactoglobulin (β-LG) to IgE was reduced under 65 °C for 30 min. By the radius of gyration (Rg) and root-mean-square deviation (RMSD) plots calculated in molecular dynamics simulations, α-LA was less structurally stable at 368 K, while β-LG remained stable at higher temperatures, indicating that α-LA was more thermally sensitive. In addition, we observed that the regions significantly affected by temperatures were associated with the capacity of allergic epitopes (α-LA 80–101 and β-LG 82–93, 105–121) to bind IgE through root-mean-standard fluctuation (RMSF) plots, which may influence the two major allergens. We inferred that these regions are susceptible to structural changes after sterilization, thus affecting the allergenicity of allergens.

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Section: Resultsmentioning

confidence: 99%

Investigation of the Structure and Allergic Potential of Whey Protein by Both Heating Sterilization and Simulation with Molecular Dynamics

Zhang

et al. 2022

Foods

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“…GROMACS utilities were used for the analysis of the MD simulations [83] . The root mean square deviation (RMSD) of atom position for ligand and protein was calculated by fitting protein backbone atom with the gmx_rms subprogram [84] .…”

Section: Methodsmentioning

confidence: 99%

“…GROMACS utilities were used for the analysis of the MD simulations. [83] The root mean square deviation (RMSD) of atom position for ligand and protein was calculated by fitting protein backbone atom with the gmx_rms subprogram. [84] Similarly, root mean square fluctuations (RMSF) based on the protein C-alpha atoms were calculated using gmx_rmsf.…”

Section: Trajectory Analysismentioning

confidence: 99%

Combined in vitro/in silico approaches, molecular dynamics simulations and safety assessment of the multifunctional properties of thymol and carvacrol: A comparative insight

Akermi,

Smaoui,

Chaari

et al. 2024

Chemistry & Biodiversity

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Bioactive compounds derived from medicinal plants have acquired immense attentiveness in drug discovery and development. The present study investigated in vitro and predicted in silico the antibacterial, antifungal, and antiviral properties of thymol and carvacrol, and assessed their safety. The performed microbiological assays against Pseudomonas aeruginosa, Escherichia coli, Salmonella enterica Typhimurium revealed that the minimal inhibitory concentration values ranged from (0.078 to 0.312 mg/mL) and the minimal fungicidal concentration against Candida albicans was 0.625 mg/mL. Molecular docking simulations, stipulated that these compounds could inhibit bacterial replication and transcription functions by targeting DNA and RNA polymerases receptors with docking scores varying between (‐5.1 to ‐6.9 kcal/mol). Studied hydroxylated monoterpenes could hinder C. albicans growth by impeding lanosterol 14α‐demethylase enzyme and showed a (ΔG = ‐6.2 and ‐6.3 kcal/mol). Computational studies revealed that thymol and carvacrol could target the SARS‐Cov‐2 spike protein of the Omicron variant RBD domain. Molecular dynamics simulations disclosed that these compounds have a stable dynamic behavior over 100 ns as compared to remdesivir. Chemo‐computational toxicity prediction using Protox II webserver indicated that thymol and carvacrol could be safely and effectively used as drug candidates to tackle bacterial, fungal, and viral infections as compared to chemical medication.

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“…For example, undergraduate students assigned to solve the crystal structure of a small protein from its electron density map were very successful even without knowledge of the protein sequence, modeling ambiguous residues using chemical knowledge to identify local interactions, and in some cases producing a better result than the original structure (35). Other activities have focused on the use of molecular dynamics tools to teach structure visualization, ligand interactions (36), and noncovalent interresidue interactions (37).…”

Section: Scientific and Pedagogical Backgroundmentioning

confidence: 99%

Active Learning Module for Protein Structure Analysis Using Novel Enzymes

et al. 2022

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A major challenge for science educators is teaching foundational concepts while introducing their students to current research. Here we describe an active learning module developed to teach protein structure fundamentals while supporting ongoing research in enzyme discovery. It can be readily implemented in both entry-level and upper-division college biochemistry or biophysics courses. Preactivity lectures introduced fundamentals of protein secondary structure and provided context for the research projects, and a homework assignment familiarized students with 3-dimensional visualization of biomolecules with UCSF Chimera, a free protein structure viewer. The activity is an online survey in which students compare structure elements in papain, a well-characterized cysteine protease from Carica papaya, to novel homologous proteases identified from the genomes of an extremophilic microbe (Halanaerobium praevalens) and 2 carnivorous plants (Drosera capensis and Cephalotus follicularis). Students were then able to identify, with varying levels of accuracy, a number of structural features in cysteine proteases that could expedite the identification of novel or biochemically interesting cysteine proteases for experimental validation in a university laboratory. Student responses to a postactivity survey were largely positive and constructive, describing points in the activity that could be improved and indicating that the activity was an engaging way to learn about protein structure.

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Molecular dynamics simulations and analysis for bioinformatics undergraduate students

Cited by 25 publications

References 47 publications

Investigation of the Structure and Allergic Potential of Whey Protein by Both Heating Sterilization and Simulation with Molecular Dynamics

Investigation of the Structure and Allergic Potential of Whey Protein by Both Heating Sterilization and Simulation with Molecular Dynamics

Combined in vitro/in silico approaches, molecular dynamics simulations and safety assessment of the multifunctional properties of thymol and carvacrol: A comparative insight

Active Learning Module for Protein Structure Analysis Using Novel Enzymes

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