Molecular geometry describes the overall shape of a molecule in terms of how the atoms inside it are arranged. Examples of simple structures are linear molecules like carbon dioxide (0=C=0) and tetrahedral molecules like methane, which consists of a carbon atom with four hydrogen atoms surroundin...
Models, MolecularCytochrome-c PeroxidaseElectron Transportmyo-Inositol-1-phosphate synthase (EC 5.5.1.4.) from rat testes, an NAD(+)-containing enzyme that converts D-glucose 6-phosphate to IL-myo-inositol-1-phosphate was immobilized together with its cofactor and bovine serum albumin by cross...
To verify the functional relevance of those residues involved in the substrate binding of SLC19A1, we mutated them individually and tested their effects on the transport activity in HEK293F cells (Fig.2g; Supplementary Fig.S1b). Substitutions of Glu123, Arg133, Tyr281, and Arg373 with alanin...
belongs to the β-branch of class A GPCRs and displays constitutive activity10(50% activity independent of the endogenous ligand ghrelin). The ghrelin receptor exerts a wide range of physiological functions, including appetite regulation, alcohol consumption, adipocyte metabolism, and glucose homeostasis...
(Fig.3). The QM/MM models that were built using the density functional theory on LPMO belonging to the AA9 family fromThermoascus aurantiacusshed light on the geometry and coordination chemistry of the reactive oxygen with Cu(II) atom. The results indicated that the formation of the complex ...
Schulten [61] performed molecular simulations of systems including DOM, water, and the xenobiotic pentachlorophenol (a pesticide), atrazine (a herbicide), and DDT (an insecticide). Geometry optimization calculations were performed to analyze energetics and hydrogen bonds. It was found that van der ...
Apart from this, there are several other methods like random walk algorithms (e.g., CONFGEN), MD simulations (MOE), distance geometry based (RDKIT), and knowledge-based (CORINA) algorithms for efficient conformational sampling of small molecules (Labute, 2010; Riniker & Landrum, 2015; Watts ...
geometry changes and theab initiocalculations point to an Lb-like excited state for the monomer. FC fits of emission spectra of the binary water cluster and quantum chemical calculations show that the emission of the water cluster also takes place from an Lb-like excited state structure. However...
Borrok MJ, Kiessling LL, Forest KT: Conformational changes of glucose/galactose-binding protein illuminated by open, unliganded, and ultra-high-resolution ligand-bound structures. Protein Sci 2007, 16(6):1032–1041. 10.1110/ps.062707807 Article PubMed Central CAS PubMed Google Scholar Bagaria A...
Second, compared to the S327A mutant, the asparagine replacement of a histidine residue in H443N was expected to cause fewer perturbations to the triad geometry and thus to ligand binding due to the similar volume and solubility between these two residues. To facilitate the expression of both ...