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The Inducible System: Antigens
Published in Julius P. Kreier, Infection, Resistance, and Immunity, 2022
The hold that the antibody has on the antigen is made possible by various types of close contacts. Atoms brought into proximity may be held together by a collection of weak forces: ionic bonds, hydrogen bonds, hydrophobic interactions, and van der Waals forces (produced by the localized induction of partial charges). These weak forces sum up over the surface of the contact. The greater the number and closeness of these contacts, the greater the total binding force. The empirical and mathematically expressed measure of the strength of the total force is called affinity. The affinity of an antibody for a given antigen is an important measure used in the study of the workings of the immune system.
Preliminary Phytochemical Screening and Identification of Bioactive Compounds from Banana Inflorescence and to Find the Interactions on Molecular Docking for PCOS
Published in Parimelazhagan Thangaraj, Phytomedicine, 2020
M. C. Kamaraj, Suman Thamburaj, R. Akshaya, V. Bhanu Deepthi
The X-ray crystallographic structures of the protein 3RUK were retrieved from the RCSB database with PDB ID 3RUK. Computational analysis was done to compute the ligand protein binding affinity of the compound. Docking calculations were carried out using DockingServer (Bikadi and Hazai 2009). The MMFF94 force field was used for the energy minimization of the ligand using DockingServer (Halgren 1996). Gasteiger partial charges were added to the ligand atoms. The non-polar hydrogen atoms were merged and the rotatable bonds were defined. The docking calculations were carried out on a rennin-angiotensin II protein model. The essential hydrogen atoms, Kollman united atom type charges, and salvation parameters were added with the aid of AutoDock tools. Affinity (grid) maps of 20 × 20 × 20 Å grid points and 0.375 Å spacing were generated using the AutoGrid program (Morris et al. 1998). AutoDock parameters set and distance—dependent dielectric functions were used in the calculation of the van der Waals and the electrostatic terms, respectively. Docking simulations were performed using the Lamarckian genetic algorithm and the Solis and Wets local search method (Solis and Wets 1981). The initial position, orientation, and torsions of the ligand molecules were set randomly. Each docking experiment was derived from ten different runs that were set to terminate after a maximum of 250,000 energy evaluations. The population size was set to 150. During the search, a translational step of 0.2 Å and quaternion and torsion steps of 5 were applied (Kuldeep and Satpal 2013).
Translation
Published in Paul Pumpens, Single-Stranded RNA Phages, 2020
Finally, Poudel et al. (2017) approached the MS2 coat-operator interaction by using large-scale ab initio computation centered on critical aspects of the consensus protein-RNA interactions recognition motif. The density functional theory (DFT) calculations were carried out on two nucleoprotein complexes, a wild type and a mutated type corresponding to the Protein Data Bank entries 1ZDH (Valegård et al. 1997) and 5MSF (Rowsell et al. 1998). The calculated partial charge distribution of residues and the strength of hydrogen bonding between them made it possible to locate the exact binding sites with strongest hydrogen bondings identified to be Lys43-A-4, Arg49-C-13, Tyr85-C-5, and Lys61-C-5, due to the change in the sequence of the mutated RNA. Because of computational limitations, these calculations were restricted to a single subunit of an asymmetrical unit of the virus, including the MS2 coat monomer and operator. Remarkably, this appeared to be the largest ab initio quantum computation performed on a complex biomolecular system to date (Poudel et al. 2017). Figure 16.8 presents the final outline of the interactions.
A computational method for predicting the aggregation propensity of IgG1 and IgG4(P) mAbs in common storage buffers
Published in mAbs, 2022
James T. Heads, Sebastian Kelm, Kerry Tyson, Alastair D. G. Lawson
We used discrete charge rather than partial charge to simplify the charge scoring system. The pH values chosen for analysis (pH 7.4 and pH 5.0) are sufficiently described by discrete charge due to the dominant contribution of charged side chains at these pH values, and their prominent involvement in protein–protein self-interactions. The amino acids with electrically charged side chains used for our calculations were arginine, lysine, histidine, aspartic acid, and glutamic acid. Basic residues were binned into two groups, residues with positively charged side chains at pH 7.4 (lysine and arginine) and residues with positively charged side chains at pH 5.0 (histidine, lysine and arginine). Residues with negatively charged side chains at pH 7.4 and pH 5.0 included aspartic acid and glutamic acid. Net charge was determined by subtracting the number of negatively charged residues from the number of positively charged residues, at a given pH. The predictions are based on typical storage buffer salt concentrations (50 mM −150 mM), substantial deviations from these salt concentrations would compromise the accuracy of the prediction due to salt shielding effects.24
Repurposing levocetirizine hydrochloride loaded into cationic ceramide/phospholipid composite (CCPCs) for management of alopecia: central composite design optimization, in- silico and in-vivo studies
Published in Drug Delivery, 2022
Rofida Albash, Rania Moataz El-Dahmy, Mohammed I. A. Hamed, Khaled M. Darwish, Abdulrahman M. Alahdal, Amira B. Kassem, Abdurrahman M. Fahmy
The docking protocol proceeded through a validated comprehensive workflow described within our previous study (Albash et al., 2021a). Briefly, the isomeric molecular structure of LVC and the optimum CCPCs additives; PC, ceramide III, phytantriol DDAB, and HA were constructed and energy minimized (gradient RMS 1 × 10−5 Kcal/mol.A2 at Amber10:EHT forcefield) via the MOE software (CCG, Montreal, Canada). Docking of the drug as well as the optimum CCPCs additives sequentially proceeded on the PC target molecule through the triangular-matcher approach and London/dG ranking scoring system. The ten top-scored binding modes were subsequentially refined via energy minimization within the target interface before being restored using the Generalized Born-solvation_VI/Weighted-Surface Area/dG forcefield. The latter scoring relied on van der Waals hydrophobic, Coulomb’s electrostatic potentials, electrostatic solvation potentials, loaded partial charges, and exposure-weighted surface area (Vilar et al., 2008). The predicted ligand/target complex was selected based on favored docking energies (high negative-valued Kcal/mol) in addition to obtaining relevant/strong intermolecular binding contacts (polar/hydrophobic) between the investigated molecules. Optimum hydrogen bonding was set at 3.0 Å bond length and 20° bond angle thresholds, while ≤ 5 Å was assigned for the hydrophobic contacts (de Souza et al., 2019; Albuquerque et al., 2020).
Prediction of novel inhibitors for Crotalus adamanteus
l -amino acid oxidase by repurposing FDA-approved drugs: a virtual screening and molecular dynamics simulation investigation
Published in Drug and Chemical Toxicology, 2021
Mostafa Khedrinia, Hassan Aryapour, Manijeh Mianabadi
Docking is an automatic computer algorithm that determines how compounds bind to the active site of the target protein (Mech 2014). For this purpose, after confirming the validity of the modeled protein, it was used for the docking process. Docking process was performed using Autodock Vina and UCSF Chimera (Pettersen et al.2004, Chen et al.2015, Koebel et al.2016). To search grid box, we used Chimera options, so the grid size was set to 16 × 16 × 16 XYZ and centered at 60 56 63. Then, hydrogen atoms were added to the modeled structure and the partial charges were assigned using the AMBER force field (Jakalian et al.2002). Then, the 2D structure of FDA-approved drugs was obtained from the DrugBank database and converted to 3D form. The first set of small molecules contained 1836 structures but after filtering, applied molecular weight between 100 and 2000 g/mol, the data-set size reached to 1760 compounds. At the end of docking, for analysis of the protein–ligand complexes, we considered several factors such as binding energy, hydrogen bonds, and the orientation of the poses within the binding site.