Centre for Integrative Biology, IGBMC, CNRS-INSERM-UdS, 1 rue Laurent Fries, BP 10142, 67404 Illkirch, France ; Département de Physique, Faculté des Sciences et des Technologies, Université de Lorraine, 54506 Vandoeuvre-lès-Nancy, France.
Published: August 2015
AI Article Synopsis
Article Abstract
Improvements in structural biology methods, in particular crystallography and cryo-electron microscopy, have created an increased demand for the refinement of atomic models against low-resolution experimental data. One way to compensate for the lack of high-resolution experimental data is to use information about model geometry that can be utilized in refinement in the form of stereochemical restraints or constraints. Here, the definition and calculation of the restraints that can be imposed on planar atomic groups, in particular the angle between such groups, are described. Detailed derivations of the restraint targets and their gradients are provided so that they can be readily implemented in other contexts. Practical implementations of the restraints, and of associated data structures, in the () are presented.
Despite the remarkable resistance of the nucleic acid phosphodiester backbone to degradation affording genetic stability, the P-O bond must be broken during DNA repair and RNA metabolism, among many other critical cellular processes. Nucleases are powerful enzymes that can enhance the uncatalyzed rate of phosphodiester bond cleavage by up to ∼10-fold. Despite the most well accepted hydrolysis mechanism involving two metals (M to activate a water nucleophile and M to stabilize the leaving group), experimental evidence suggests that some nucleases can use a single metal to facilitate the chemical step, a controversial concept in the literature.
Chitosan is a nontoxic biopolymer with many potential biomedical and material applications due to its biodegradability, biocompatibility, and antimicrobial properties. Here, fully atomistic molecular dynamics simulations and enhanced sampling methods have been used to study the adsorption mechanism of chitosan oligomers on a silica surface from an aqueous solution. The free energy of adsorption of chitosan on a silica surface was calculated to be 0.
Department of Spine Surgery and Musculoskeletal Tumor, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University Wuhan 430071 China
Replacement of a carbonyl group with fluorinated bioisostere (, CF[double bond, length as m-dash]C) has been adopted as a key tactical strategy in drug design and development, which typically improves potency and modulates lipophilicity while maintaining biological activity. Consequently, new -difluoroalkenation reactions have undoubtedly accelerated this shift, and conceptually innovative practices would be of great benefit to medicinal chemists. Here we describe an expeditous protocol for the direct assembly of furan-substituted -difluoroalkenes PFTB-promoted cross-coupling of ene-yne-ketones and difluorocarbene.
Noncovalent interactions (NCI) play a central role in numerous physical, chemical, and biological phenomena. An accurate description of NCI is the key to success for any theoretical study in such areas. Although quantum mechanics (QM) methods such as dispersion-corrected density functional theory are sufficiently accurate, their applications are practical only for <300 atoms and <100 ps of simulation time.
Carboncones and fullerenes are exemplary π-conjugated carbon nanomaterials with unsaturated, positively curved surfaces, enabling the attachment of atoms or functional groups to enhance their physicochemical properties. However, predicting and understanding the addition patterns in functionalized carboncones and fullerenes are extremely challenging due to the formidable complexity of the regioselectivity exhibited in the adducts. Existing predictive models fall short in systems where the carbon molecular framework undergoes severe distortion upon high degrees of addition.
