low energy conformations
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The spatial structure of ACTH-(6-9)-PGP molecule has been investigated using theoretical conformational analysis method. Amino acid sequence of the N-terminal pentapeptide fragment of His-Phe-Arg-Trp-Pro of this molecule conforms to the fragment 6-9 of ACTH hormone. Calculations of conformational states of this molecule are carried out regarding nonvalent, electrostatic and torsional interactions and the energy of hydrogen bonds. The spatial structure of the His-Phe-Arg-Trp-Pro-Gly-Pro molecule was estimated on the low–energy conformations of the N-terminal tetrapeptide fragment His-Phe-Arg-Trp and C-terminal tripeptide fragment Pro-Gly-Pro of this molecule. It is shown that the spatial structure of heptapeptide molecule can be presented by 11 low-energy forms of the main chain. The low–energy conformations of this molecule, the values of dihedral angles of the backbone and side chains of the amino acid residues were founded and the energies of intra- and inter-residual interactions were determined.

Carbohydrate-based oxepines are valuable intermediates for the synthesis of septanose carbohydrates. Here we report the characterization of the preferred conformations of D-glucose and D-mannose based oxepines 1 and 2 using...

: The appropriate selection of initial receptor structure has been the "cornerstone" or foundation of successful structure-based virtual screening (SBVS), and plagued the structure-based design with a significantly practical problem to determine the major physiological states or important transition states of receptors (e.g. proteins with multiple low-energy conformations and ligand-dependent conformational dynamics). It is well known that current SBVS methods lack capacity to capture and characterize the intrinsic receptor flexibility with ideal cost-effectiveness. In recent years, cryoelectron microscopy (cryo-EM) has been routinely applied in the determination of biomolecular assemblies within physiological state. In this work, we review the roles of cryo-EM and ensemble docking methods to present the intrinsically dynamic behavior of biomacromolecules, as well as the ever-improving estimation of ligand binding affinities and receptor-ligand thermodynamics. Finally, we also provide an attitude for the further researches on the modeling receptor dynamics.

A key challenge in conformer sampling is finding low-energy conformations using a small number of energy evaluations. By extracting patterns of correlated torsions, we improve the efficiency of Bayesian Optimization in finding optimal conformations.

Abstract Discovering the low-energy conformations of a molecule is of great interest to computational chemists, with applications in in silico materials design and drug discovery. In this paper, we propose a variable neighbourhood search heuristic for the conformational search problem. Using the structure of a molecule, neighbourhoods are chosen to allow for the efficient use of a binary quadratic optimizer for conformational search. The method is flexible with respect to the choice of molecular force field and the number of discretization levels in the search space, and can be further generalized to take advantage of higher-order binary polynomial optimizers. It is well-suited for the use of devices such as quantum annealers. After carefully defining neighbourhoods, the method easily adapts to the size and topology of these devices, allowing for seamless scaling alongside their future improvements.

Cryo-EM is a powerful method for determining protein structures. But it requires computational assistance. Physics-based computations have the power to give low-free-energy structures and ensembles of populations, but have been computationally limited to only small soluble proteins. Here, we introduce CryoFold. By integrating data of varying sparsity from electron density maps of 3–5 Å resolution with coarse-grained physical knowledge of secondary and tertiary interactions, CryoFold determines ensembles of protein structures directly from sequence. We give six examples showing its broad capabilities, over proteins ranging from 72 to 2000 residues, including membrane and multi-domain proteins, and including results from two EMDB competitions. The ensembles CryoFold predicts starting from the density data of a single known protein conformation encompass multiple low-energy conformations, all of which are experimentally validated and biologically relevant.

Through reducing the system InCl3-Li-DTBB(cat.) in THF at room temperature and in the absence of any additives or anti-caking ligand, we have synthesized indium nanoparticles (InNPs) of about 4 nm. The catalyst was employed in the allylation of carbonyl compounds, giving excellent yields of the corresponding homoallylic alcohols. We have established that the reaction products come from a γ-coupling via a six members cyclic transition state, type Zimmerman–Traxler. Relative to the selectivity, the allylation with crotyl bromide of ortho substituted benzaldehydes (e.g., o-NO2, o-OMe, o-Cl, o-CF3) showed syn selectivity. With the aim to improve the mentioned selectivity, we synthetized o-iPrO-benzaldehyde, and evaluated the reaction with crotyl bromide and InNPs. The homoallylic alcohol 1-(2-isopropoxyphenyl)-2-methylbut-3-en-1-ol was obtained almost quantitatively after 1h as a mixture of the syn- and anti- isomers. The relationship observed by 1H-RMN was 75:25, but we did not know if the syn-isomer was the dominant because the product has not been reported in the scientific literature. Based on this, and in order to determinate which 1H-NMR signals correspond to each isomer, we started computational theoretical and NMR studies. The initial conformational analysis was performed using the semiempirical PM3 method, then we work with the B3LYP functional, applying the 6-31+G* basis set and the solvent effect (chloroform) was evaluated with the PCM model as implemented in Gaussian09. So, we found thirteen low-energy conformations for the syn-diastereomer and six low-energy conformations for the anti-diastereomer. On the other hand, we have carried out NMR experiments such as 1H, 13C, HSQC, to assign the signals of each diastereomer; and experiments such as NOESY, selective NOE, JRes, homo- and hetero-nuclear J-coupled and J-decoupling, to be able to measure coupling constants and establish the structure of each diastereomer.

γ-amino butyric acid aminotransferase (GABA-AT) is a pyridoxal phosphate (PLP) dependent enzyme that catalyses thedegradation of γ-amino butyric acid (GABA). γ-amino butyric acid aminotransferase (GABA-AT) inhibitors are used to treat epilepsy.Objective: The aim of this study was to search anthraquinone scaffolds as novel GABA-AT inhibitors using virtual screening based approach.Materials and Methods: AutoDock Tools® 1.4.6 and MGL Tools® 1.5.4 software were used to find out binding score, inhibition constant andconformational poses of the ligands inside the active site. AutoDock uses interaction maps to generate ensemble of low energy conformations andAMBER force field to estimate the free energy of binding of a ligand to its target. Result and Discussion: Estimated binding energies of topscoring molecules (derivatives of the natural product anthraquinone) were found quite low (e-53M) as compared to that of vigabtrin (-5.5Kcal/mol). Conclusion: These theoretical findings suggesting, the utility of virtual screening as a computational tool as well as significance ofanthraquinone scaffolds as potential GABA-AT in-activators.