Hundreds Of Crystal Structures Research Articles

The Stibium Bond or the Antimony-Centered Pnictogen Bond: The Covalently Bound Antimony Atom in Molecular Entities in Crystal Lattices as a Pnictogen Bond Donor.

A stibium bond, i.e., a non-covalent interaction formed by covalently or coordinately bound antimony, occurs in chemical systems when there is evidence of a net attractive interaction between the electrophilic region associated with an antimony atom and a nucleophile in another, or the same molecular entity. This is a pnictogen bond and are likely formed by the elements of the pnictogen family, Group 15, of the periodic table, and is an inter- or intra-molecular non-covalent interaction. This overview describes a set of illustrative crystal systems that were stabilized (at least partially) by means of stibium bonds, together with other non-covalent interactions (such as hydrogen bonds and halogen bonds), retrieved from either the Cambridge Structure Database (CSD) or the Inorganic Crystal Structure Database (ICSD). We demonstrate that these databases contain hundreds of crystal structures of various dimensions in which covalently or coordinately bound antimony atoms in molecular entities feature positive sites that productively interact with various Lewis bases containing O, N, F, Cl, Br, and I atoms in the same or different molecular entities, leading to the formation of stibium bonds, and hence, being partially responsible for the stability of the crystals. The geometric features, pro-molecular charge density isosurface topologies, and extrema of the molecular electrostatic potential model were collectively examined in some instances to illustrate the presence of Sb-centered pnictogen bonding in the representative crystal systems considered.

Exploring the conformational space of a receptor for drug design: An ERα case study

Protein flexibility is challenging for both experimentalists and modellers, especially in the field of drug design. Estrogen Receptor alpha (ERα) is an extensively studied Nuclear Receptor (NR) and a well-known therapeutic target with an important role in development and physiology. It is also a frequent off-target in standard toxicity tests for endocrine disruption. Here, we aim to evaluate the degree to which the conformational space and macromolecular flexibility of this well-characterized drug target can be described. Our approach exploits hundreds of crystallographic structures by means of molecular dynamics simulations and of virtual screening. The analysis of hundreds of crystal structures confirms the presence of two main conformational states, known as ’agonist’ and ’antagonist’, that mainly differ by the orientation of the C-terminal helix H12 which serves to close the binding pocket. ERα also shows some loop flexibility, as well as variable side-chain orientations in its active site. We scrutinized the extent to which standard molecular dynamics simulations or crystallographic refinement as ensemble recapitulate most of the variability features seen by the array of available crystal structures. In parallel, we investigated on the kind and extent of flexibility that are required to achieve convincing docking for all high-affinity ERα ligands present in BindingDB. Using either only one conformation with a few side-chains set flexible, or static structure ensembles in parallel during docking led to good quality and similar pose predictions. These results suggest that the several hundreds of crystal structures already known can properly describe the whole conformational universe of ERα′s ligand binding domain. This opens the road for better drug design and affinity computation.

Conformation-dependent restraints for polynucleotides: the sugar moiety.

Stereochemical restraints are commonly used to aid the refinement of macromolecular structures obtained by experimental methods at lower resolution. The standard restraint library for nucleic acids has not been updated for over two decades and needs revision. In this paper, geometrical restraints for nucleic acids sugars are derived using information from high-resolution crystal structures in the Cambridge Structural Database. In contrast to the existing restraints, this work shows that different parts of the sugar moiety form groups of covalent geometry dependent on various chemical and conformational factors, such as the type of ribose or the attached nucleobase, and ring puckering or rotamers of the glycosidic (χ) or side-chain (γ) torsion angles. Moreover, the geometry of the glycosidic link and the endocyclic ribose bond angles are functionally dependent on χ and sugar pucker amplitude (τm), respectively. The proposed restraints have been positively validated against data from the Nucleic Acid Database, compared with an ultrahigh-resolution Z-DNA structure in the Protein Data Bank, and tested by re-refining hundreds of crystal structures in the Protein Data Bank. The conformation-dependent sugar restraints presented in this work are publicly available in REFMAC, PHENIX and SHELXL format through a dedicated RestraintLib web server with an API function.

Noncovalent Interactions in Succinic and Maleic Anhydride Derivatives

Herein, we present a study of the short contacts that several heterocycles of the same family, namely, succinic and maleic anhydrides, maleimide, and succinimide establish in their condensed phases. DFT calculations on model systems in the gas phase have allowed us to calibrate the strength of such interactions, obtaining associated energies up to 2 kcal/mol. We have performed MEP and EDA analysis to unveil their nature, which is mainly electrostatic with some London dispersion contribution. Furthermore, the origin of the interaction is the existence of a charge depletion region (a π-hole) in the inner part of the rings. This hole interacts with a Lewis base in a precise topological way, with the contacts showing a high directionality as revealed by the analysis of hundreds of crystal structures. We believe that the description for the first time of these interactions, along with their abundance, can assist their use as a tool in crystal design.

Solution Conformation of the Unbound HIV-1 Protease Derived from Residual Dipolar Couplings Measured at Ambient and High-Pressure Conditions

The flexibility of the glycine-rich flaps are known to be essential for the catalytic activity of the HIV-1 Protease but their exact conformations at the different stages of the enzymatic pathway remain yet to be determined. While hundreds of crystal structures of protease-inhibitor complexes have been solved, only a dozen of unbound protease structures have been reported to date. These structures reveal a large heterogeneity of flap conformations, ranging from closed, to semi-open and wide-open conformations. We used here NMR spectroscopy to determine the flap orientation of the unbound protease in solution. The conformation of the flaps was determined by comparing the measured residual dipolar couplings to reference crystal structures representing the closed, semi-open and wide-open states. The data clearly indicate that the apo protease adopts a closed conformation in solution, similar to an inhibitor-bound state. We also compared the effect of high-pressure on the flap conformations of an apo and inhibitor-bound protease by measuring backbone residual dipolar couplings up to 1 kbar. A rigid-body motion model was derived to characterize the pressure-induced conformational changes of the flaps. While a minimal rearrangement of the flaps was observed in the case of the inhibitor-protease complex, we observed a significant pressure-induced rotation of the flaps in the case of the apo protease. These results highlight the intrinsic conformational flexibility of the unbound protease and offer a new perspective to understand the mechanism of ligand and inhibitor binding.

Conformation of inhibitor-free HIV-1 protease derived from NMR spectroscopy in a weakly oriented solution.

Flexibility of the glycine-rich flaps is known to be essential for catalytic activity of the HIV-1 protease, but their exact conformations at the different stages of the enzymatic pathway remain subject to much debate. Although hundreds of crystal structures of protease-inhibitor complexes have been solved, only about a dozen inhibitor-free protease structures have been reported. These latter structures reveal a large diversity of flap conformations, ranging from closed to semi-open to wide open. To evaluate the average structure in solution, we measured residual dipolar couplings (RDCs) and compared these to values calculated for crystal structures representative of the closed, semi-open, and wide-open states. The RDC data clearly indicate that the inhibitor-free protease, on average, adopts a closed conformation in solution that is very similar to the inhibitor-bound state. By contrast, a highly drug-resistant protease mutant, PR20, adopts the wide-open flap conformation.

Zinc Coordination Spheres in Protein Structures

Zinc metalloproteins are one of the most abundant and structurally diverse proteins in nature. In these proteins, the Zn(II) ion possesses a multifunctional role as it stabilizes the fold of small zinc fingers, catalyzes essential reactions in enzymes of all six classes, or assists in the formation of biological oligomers. Previously, a number of database surveys have been conducted on zinc proteins to gain broader insights into their rich coordination chemistry. However, many of these surveys suffer from severe flaws and misinterpretations or are otherwise limited. To provide a more comprehensive, up-to-date picture on zinc coordination environments in proteins, zinc containing protein structures deposited in the Protein Data Bank (PDB) were analyzed in detail. A statistical analysis in terms of zinc coordinating amino acids, metal-to-ligand bond lengths, coordination number, and structural classification was performed, revealing coordination spheres from classical tetrahedral cysteine/histidine binding sites to more complex binuclear sites with carboxylated lysine residues. According to the results, coordination spheres of hundreds of crystal structures in the PDB could be misinterpreted due to symmetry-related molecules or missing electron densities for ligands. The analysis also revealed increasing average metal-to-ligand bond length as a function of crystallographic resolution, which should be taken into account when interrogating metal ion binding sites. Moreover, one-third of the zinc ions present in crystal structures are artifacts, merely aiding crystal formation and packing with no biological significance. Our analysis provides solid evidence that a minimal stable zinc coordination sphere is made up by four ligands and adopts a tetrahedral coordination geometry.

The power of vanadate in crystallographic investigations of phosphoryl transfer enzymes

The formation of transition state mimics of phosphoryl transfer reactions with the metal oxoanion vanadate is a powerful technique in macromolecular crystallography. The tendency of vanadate to form pentacovalent complexes exhibiting trigonal bipyramidal geometry makes this compound a close approximation of the transition state for such reactions. In many cases, vanadate complexes provide the most accurate visualization of the transition state that can be reasonably achieved. A survey of the Protein Data Bank reveals that a relatively small number of structures (39, representing 23 unique proteins) include vanadate, yet these structures represent four of the six E.C. categories of enzymes, and were obtained in crystals with pH values ranging from 5.0 to 7.8. Vanadate has additional advantages over other compounds such as aluminum fluoride, beryllium fluoride and nitrate used for visualization of transition state mimics in that vanadate readily forms covalent bonds with a variety of ligands and has produced a wider variety of transition state mimics. Given the hundreds of crystal structures that have been solved for phosphoryl transfer enzymes, it is surprising that vanadate has not been used more frequently for visualization of transition state analogs. We propose that an opportunity exists for vanadate to become a more commonly utilized component of the macromolecular crystallographer's toolbox.

Past and Present Crystallographic Work at the NBS/NIST Reactor.

Neutron diffraction at NBS/NIST started soon after the NBS reactor became operational in the summer of 1969. Since that time, literally hundreds of crystal structures have been determined and refined using single crystal and powder neutron diffraction data, collected with a variety of instruments. This work has been usually done in collaboration with other NBS/NIST divisions and/or universities and industrial laboratories. In parallel with the technical developments and the experimental work, also theoretical aspects of crystal geometry have been clarified, and significant improvements in the techniques of profile refinements have been made. It is therefore understandable that a comprehensive description of all the crystallographic studies carried out up to the present is impossible under the constraints of space and time imposed by a review of this type, and, in the following sections, we will limit ourselves to give, only a brief account of the topics which, in our opinion, represent the highlights of the work carried out at the reactor.

ChemInform Abstract: Angular Preferences of Intermolecular Forces Around Halogen Centers: Preferred Directions of Approach of Electrophiles and Nucleophiles Around the Carbon‐Halogen Bond.

AbstractFor the understanding of special interactions the authors analyze the environment around halogen centers in hundreds of crystal structures.