Multiple Crystal Structures Research Articles

Active Site Mapping of an Aspartic Protease by Multiple Fragment Crystal Structures: Versatile Warheads To Address a Catalytic Dyad.

Crystallography is frequently used as follow-up method to validate hits identified by biophysical screening cascades. The capacity of crystallography to directly screen fragment libraries is often underestimated, due to its supposed low-throughput and need for high-quality crystals. We applied crystallographic fragment screening to map the protein-binding site of the aspartic protease endothiapepsin by individual soaking experiments. Here, we report on 41 fragments binding to the catalytic dyad and adjacent specificity pockets. The analysis identifies already known warheads but also reveals hydrazide, pyrazole, or carboxylic acid fragments as novel functional groups binding to the dyad. A remarkable swapping of the S1 and S1' pocket between structurally related fragments is explained by either steric demand, required displacement of a well-bound water molecule, or changes of trigonal-planar to tetrahedral geometry of an oxygen functional group in a side chain. Some warheads simultaneously occupying both S1 and S1' are promising starting points for fragment-growing strategies.

Long-Lived Five-Coordinate Platinum(IV) Intermediates: Regiospecific C–C Coupling

Three different phosphine derivatives of doubly cyclometalated diphenypyridine complexes of Pt(II), 1, were reacted with methyl iodide to give octahedral Pt(IV) complexes, 2, as two isomers. Treatment of either isomer of complexes 2 with AgBF4, to abstract iodide, gave long-lived five-coordinate complexes 3, which could be trapped as pyridine adducts. Complexes 3 underwent a C–C coupling reaction, at a rate that depended on phosphine size, to give a methyl group attached to the original diphenylpyridine. Recylometalation was then performed, and the cycle of reactions was repeated to give a diphenylpyridine doubly methylated on only one phenyl, with complete regiospecificity. NMR was used to demonstrate the geometry of all complexes in solution, with multiple X-ray crystal structures confirming these assignments.

Natural and non-natural amino-acid side-chain substitutions: affinity and diffraction studies of meditope-Fab complexes.

Herein, multiple crystal structures of meditope peptide derivatives incorporating natural and unnatural amino acids bound to the cetuximab Fab domain are presented. The affinity of each derivative was determined by surface plasmon resonance and correlated to the atomic structure. Overall, it was observed that the hydrophobic residues in the meditope peptide, Phe3, Leu5 and Leu10, could accommodate a number of moderate substitutions, but these invariably reduced the overall affinity and half-life of the interaction. In one case, the substitution of Phe3 by histidine led to a change in the rotamer conformation, in which the imidazole ring flipped to a solvent-exposed position. Based on this observation, Phe3 was substituted by diphenylalanine and it was found that the phenyl rings in this variant mimic the superposition of the Phe3 and His3 structures, producing a moderate increase, of 1.4-fold, in the half-life of the complex. In addition, it was observed that substitution of Leu5 by tyrosine and glutamate strongly reduced the affinity, whereas the substitution of Leu5 by diphenylalanine moderately reduced the half-life (by approximately fivefold). Finally, it was observed that substitution of Arg8 and Arg9 by citrulline dramatically reduced the overall affinity, presumably owing to lost electrostatic interactions. Taken together, these studies provide insight into the meditope-cetuximab interaction at the atomic level.

Structure and Dynamics of Extracellular Loops in Human Aquaporin-1 from Solid-State NMR and Molecular Dynamics.

Multiple moderate-resolution crystal structures of human aquaporin-1 have provided a foundation for understanding the molecular mechanism of selective water translocation in human cells. To gain insight into the interfacial structure and dynamics of human aquaporin-1 in a lipid environment, we performed nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics simulations. Using magic angle spinning solid-state NMR, we report a near complete resonance assignment of the human aquaporin-1. Chemical shift analysis of the secondary structure identified pronounced deviations from crystallographic structures in extracellular loops A and C, including the cis Y37-P38 bond in loop A, as well as ordering and immobilization of loop C. Site-specific H/D exchange measurements identify a number of protected nitrogen-bearing side chains and backbone amide groups, involved in stabilizing the loops. A combination of molecular dynamics simulations with NMR-derived restraints and filtering based on solvent accessibility allowed for the determination of a structural model of extracellular loops largely consistent with NMR results. The simulations reveal loop stabilizing interactions that alter the extracellular surface of human AQP1, with possible implications for water transport regulation through the channel. Modulation of water permeation may occur as a result of rearrangement of side chains from loop C in the extracellular vestibule of hAQP1, affecting the aromatic arginine selectivity filter.

Cold Sintering: A Paradigm Shift for Processing and Integration of Ceramics

AbstractThis paper describes a sintering technique for ceramics and ceramic‐based composites, using water as a transient solvent to effect densification (i.e. sintering) at temperatures between room temperature and 200 °C. To emphasize the incredible reduction in sintering temperature relative to conventional thermal sintering this new approach is named the “Cold Sintering Process” (CSP). Basically CSP uses a transient aqueous environment to effect densification by a mediated dissolution–precipitation process. CSP of NaCl, alkali molybdates and V2O5 with small concentrations of water are described in detail, but the process is extended and demonstrated for a diverse range of chemistries (oxides, carbonates, bromides, fluorides, chlorides and phosphates), multiple crystal structures, and multimaterial applications. Furthermore, the properties of selected CSP samples are demonstrated to be essentially equivalent as samples made by conventional thermal sintering.

Cold Sintering: A Paradigm Shift for Processing and Integration of Ceramics.

This paper describes a sintering technique for ceramics and ceramic-based composites, using water as a transient solvent to effect densification (i.e. sintering) at temperatures between room temperature and 200 °C. To emphasize the incredible reduction in sintering temperature relative to conventional thermal sintering this new approach is named the "Cold Sintering Process" (CSP). Basically CSP uses a transient aqueous environment to effect densification by a mediated dissolution-precipitation process. CSP of NaCl, alkali molybdates and V2 O5 with small concentrations of water are described in detail, but the process is extended and demonstrated for a diverse range of chemistries (oxides, carbonates, bromides, fluorides, chlorides and phosphates), multiple crystal structures, and multimaterial applications. Furthermore, the properties of selected CSP samples are demonstrated to be essentially equivalent as samples made by conventional thermal sintering.

Effect of detergent binding on cytochrome P450 2B4 structure as analyzed by X-ray crystallography and deuterium-exchange mass spectrometry

Multiple crystal structures of CYP2B4 have demonstrated the binding of the detergent 5-cyclohexyl-1-pentyl-β-D-maltoside (CYMAL-5) in a peripheral pocket located adjacent to the active site. To explore the consequences of detergent binding, X-ray crystal structures of the peripheral pocket mutant CYP2B4 F202W were solved in the presence of hexaethylene glycol monooctyl ether (C8E6) and CYMAL-5. The structure in the presence of CYMAL-5 illustrated a closed conformation indistinguishable from the previously solved wild-type. In contrast, the F202W structure in the presence of C8E6 revealed a detergent molecule that coordinated the heme-iron and extended to the protein surface through the substrate access channel 2f. Despite the overall structural similarity of these detergent complexes, remarkable differences were observed in the A, A′, and H helices, the F-G cassette, the C-D and β4 loop region. Hydrogen-deuterium exchange mass spectrometry (DXMS) was employed to probe these differences and to test the effect of detergents in solution. The presence of either detergent increased the H/D exchange rate across the plastic regions, and the results obtained by DXMS in solution were consistent in general with the relevant structural snapshots. The study provides insight into effect of detergent binding and the interpretation of associated conformational dynamics of CYP2B4.

Cyclization strategies of meditopes: affinity and diffraction studies of meditope-Fab complexes.

Recently, a unique binding site for a cyclic 12-residue peptide was discovered within a cavity formed by the light and heavy chains of the cetuximab Fab domain. In order to better understand the interactions that drive this unique complex, a number of variants including the residues within the meditope peptide and the antibody, as well as the cyclization region of the meditope peptide, were created. Here, multiple crystal structures of meditope peptides incorporating different cyclization strategies bound to the central cavity of the cetuximab Fab domain are presented. The affinity of each cyclic derivative for the Fab was determined by surface plasmon resonance and correlated to structural differences. Overall, it was observed that the disulfide bond used to cyclize the peptide favorably packs against a hydrophobic `pocket' and that amidation and acetylation of the original disulfide meditope increased the overall affinity ∼2.3-fold. Conversely, replacing the terminal cysteines with serines and thus creating a linear peptide reduced the affinity over 50-fold, with much of this difference being reflected in a decrease in the on-rate. Other cyclization methods, including the formation of a lactam, reduced the affinity but not to the extent of the linear peptide. Collectively, the structural and kinetic data presented here indicate that small perturbations introduced by different cyclization strategies can significantly affect the affinity of the meditope-Fab complex.

PTCLab: free and open-source software for calculating phase transformation crystallography

PTCLab(Phase Transformation Crystallography Lab) is free and open-source software to calculate the crystallographic features formed during a phase transformation, such as orientation relationship, interface orientation, interfacial structureetc. This program covers the crystallographic theories for both martensitic and diffusional transformation and allows users to represent the results in stereographic projection. The crystallographic models treated inPTCLabinclude the classical phenomenological theory of martensite crystallography (PTMC), the double shear version of PTMC, the invariant line model, O-lattice theory, the O-line model, the recently developed three-dimensional near coincidence site method, the edge-to-edge matching model and variant selection analysis. In addition, a number of basic crystallographic calculations for single or multiple crystal structures can be performed with the calculation pad. High-quality composite stereographic projection and electron diffraction patterns can be also obtained by the present application.PTCLabis written in Python, runnable cross platform, and is distributed at https://sourceforge.net/projects/tclab/.

Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles.

Ensemble docking can be a successful virtual screening technique that addresses the innate conformational heterogeneity of macromolecular drug targets. Yet, lacking a method to identify a subset of conformational states that effectively segregates active and inactive small molecules, ensemble docking may result in the recommendation of a large number of false positives. Here, three knowledge-based methods that construct structural ensembles for virtual screening are presented. Each method selects ensembles by optimizing an objective function calculated using the receiver operating characteristic (ROC) curve: either the area under the ROC curve (AUC) or a ROC enrichment factor (EF). As the number of receptor conformations, N, becomes large, the methods differ in their asymptotic scaling. Given a set of small molecules with known activities and a collection of target conformations, the most resource intense method is guaranteed to find the optimal ensemble but scales as O(2N). A recursive approximation to the optimal solution scales as O(N2), and a more severe approximation leads to a faster method that scales linearly, O(N). The techniques are generally applicable to any system, and we demonstrate their effectiveness on the androgen nuclear hormone receptor (AR), cyclin-dependent kinase 2 (CDK2), and the peroxisome proliferator-activated receptor δ (PPAR-δ) drug targets. Conformations that consisted of a crystal structure and molecular dynamics simulation cluster centroids were used to form AR and CDK2 ensembles. Multiple available crystal structures were used to form PPAR-δ ensembles. For each target, we show that the three methods perform similarly to one another on both the training and test sets.

Characterization and small-molecule stabilization of the multisite tandem binding between 14-3-3 and the R domain of CFTR

Cystic fibrosis is a fatal genetic disease, most frequently caused by the retention of the CFTR (cystic fibrosis transmembrane conductance regulator) mutant protein in the endoplasmic reticulum (ER). The binding of the 14-3-3 protein to the CFTR regulatory (R) domain has been found to enhance CFTR trafficking to the plasma membrane. To define the mechanism of action of this protein-protein interaction, we have examined the interaction in vitro. The disordered multiphosphorylated R domain contains nine different 14-3-3 binding motifs. Furthermore, the 14-3-3 protein forms a dimer containing two amphipathic grooves that can potentially bind these phosphorylated motifs. This results in a number of possible binding mechanisms between these two proteins. Using multiple biochemical assays and crystal structures, we show that the interaction between them is governed by two binding sites: The key binding site of CFTR (pS768) occupies one groove of the 14-3-3 dimer, and a weaker, secondary binding site occupies the other binding groove. We show that fusicoccin-A, a natural-product tool compound used in studies of 14-3-3 biology, can stabilize the interaction between 14-3-3 and CFTR by selectively interacting with a secondary binding motif of CFTR (pS753). The stabilization of this interaction stimulates the trafficking of mutant CFTR to the plasma membrane. This definition of the druggability of the 14-3-3-CFTR interface might offer an approach for cystic fibrosis therapeutics.

Structural semiconductor-to-semimetal phase transition in two-dimensional materials induced by electrostatic gating.

Dynamic control of conductivity and optical properties via atomic structure changes is of technological importance in information storage. Energy consumption considerations provide a driving force towards employing thin materials in devices. Monolayer transition metal dichalcogenides are nearly atomically thin materials that can exist in multiple crystal structures, each with distinct electrical properties. By developing new density functional-based methods, we discover that electrostatic gating device configurations have the potential to drive structural semiconductor-to-semimetal phase transitions in some monolayer transition metal dichalcogenides. Here we show that the semiconductor-to-semimetal phase transition in monolayer MoTe2 can be driven by a gate voltage of several volts with appropriate choice of dielectric. We find that the transition gate voltage can be reduced arbitrarily by alloying, for example, for MoxW1−xTe2 monolayers. Our findings identify a new physical mechanism, not existing in bulk materials, to dynamically control structural phase transitions in two-dimensional materials, enabling potential applications in phase-change electronic devices.

Preserving Both Anion and Cation Sublattice Features during a Nanocrystal Cation-Exchange Reaction: Synthesis of Metastable Wurtzite-Type CoS and MnS.

The ability to selectively synthesize one particular polymorph in a solid-state system having multiple crystal structures with the same composition is important for accessing desired properties. Solution-mediated reactions, including anion and cation exchange, that chemically transform colloidal nanoparticles with pre-programmed structural features into targeted products have emerged as a powerful platform for predictably accessing metastable polymorphs. While nanocrystal ion-exchange reactions that retain anion sublattice features are well known, analogous reactions that preserve cation sublattice features are much less common, and guidelines for predictably targeting such sublattice features are not well established. Here, we report that both anion and cation sublattice features--hexagonal close-packed anions and tetrahedrally coordinated cations--can be preserved during cation exchange of roxbyite-type Cu2-xS nanocrystals to selectively produce wurtzite-type CoS and MnS. These polymorphs, which are metastable in bulk systems, form relative to other accessible structures having cubic close-packed anions and/or octahedrally coordinated cations. To facilitate these transformations, the scope of existing nanocrystal cation-exchange reactions was expanded to include 3d transition metal systems that previously have not been investigated in depth.

Discovery of Novel ROCK1 Inhibitors via Integrated Virtual Screening Strategy and Bioassays.

Rho-associated kinases (ROCKs) have been regarded as promising drug targets for the treatment of cardiovascular diseases, nervous system diseases and cancers. In this study, a novel integrated virtual screening protocol by combining molecular docking and pharmacophore mapping based on multiple ROCK1 crystal structures was utilized to screen the ChemBridge database for discovering potential inhibitors of ROCK1. Among the 38 tested compounds, seven of them exhibited significant inhibitory activities of ROCK1 (IC50 < 10 μM) and the most potent one (compound TS-f22) with the novel scaffold of 4-Phenyl-1H-pyrrolo [2,3-b] pyridine had an IC50 of 480 nM. Then, the structure-activity relationships of 41 analogues of TS-f22 were examined. Two potent inhibitors were proven effective in inhibiting the phosphorylation of the downstream target in the ROCK signaling pathway in vitro and protecting atorvastatin-induced cerebral hemorrhage in vivo. The high hit rate (28.95%) suggested that the integrated virtual screening strategy was quite reliable and could be used as a powerful tool for identifying promising active compounds for targets of interest.

Molecular biology: DNA repair without flipping out.

Time-resolved molecular snapshots of the bacterial enzyme AlkD reveal an unprecedented mechanism for the recognition and removal of damaged bases in DNA, with implications for cell biology and cancer therapy. See Letter p.254 Not all DNA damage manifests as breaks; for example, ultraviolet light and drugs can modify DNA bases, and these lesions also need to be repaired. Many repair enzymes recognize lesions by 'flipping' bases into a pocket to interrogate whether or not it is damaged. Brandt Eichman and colleagues have now solved multiple crystal structures of the DNA glycosylase AlkD from Bacillus cereus, bound to DNA sequences containing various modified bases. They find, surprisingly, that neither recognition nor catalysis involves base flipping. Instead, AlkD scans the phosphodeoxyribose backbone for increased cationic charge imparted by the alkylated base, and then uses the positive charge to facilitate cleavage of the glycosidic bond. These findings explain AlkD's specificity for cationic lesions.

Protein Flexibility in Docking-Based Virtual Screening: Discovery of Novel Lymphoid-Specific Tyrosine Phosphatase Inhibitors Using Multiple Crystal Structures.

Incorporating protein flexibility is a major challenge for docking-based virtual screening. With an increasing number of available crystal structures, ensemble docking with multiple protein structures is an efficient approach to deal with protein flexibility. Herein, we report the successful application of a docking-based virtual screen using multiple crystal structures to discover novel inhibitors of lymphoid-specific tyrosine phosphatase (LYP), a potential drug target for autoimmune diseases. The appropriate use of multiple protein structures allowed a better enrichment than a single structure in the recovery of known inhibitors. Subsequently, an optimal ensemble of LYP structures was selected and used in docking-based virtual screening. Eight novel LYP inhibitors (IC50 ranging from 7.95 to 56.6 μM) were identified among 23 hit compounds. Further studies demonstrated that the most active compound B15 possessed some selectivity over other protein phosphatases and could effectively up-regulate TCR (T cell receptor)-mediated signaling in Jurkat T cells. These novel hits not only provided good starting points for the development of therapeutic agents useful in autoimmune diseases but also demonstrated the advantages of choosing an appropriate ensemble of protein structures in docking-based virtual screening over using a single protein conformation.

A user-friendly web portal for analyzing conformational changes in structures of Mycobacterium tuberculosis

Initiation of the Tuberculosis Structural Consortium has resulted in the expansion of the Mycobacterium tuberculosis (MTB) protein structural database. Currently, 969 experimentally solved structures are available for 354 MTB proteins. This includes multiple crystal structures for a given protein under different functional conditions, such as the presence of different ligands or mutations. In depth analysis of the multiple structures reveal that subtle differences exist in conformations of a given protein under varied conditions. Therefore, it is immensely important to understand the conformational differences between the multiple structures of a given protein in order to select the most suitable structure for molecular docking and structure-based drug designing. Here, we introduce a web portal ( http://bmi.icmr.org.in/mtbsd/torsion.php ) that we developed to provide comparative data on the ensemble of available structures of MTB proteins, such as Cα root means square deviation (RMSD), sequence identity, presence of mutations and torsion angles. Additionally, torsion angles were used to perform principal component analysis (PCA) to identify the conformational differences between the structures. Additionally, we present a few case studies to demonstrate this database. Graphical Abstract Conformational changes seen in the structures of the enoyl-ACP reductase protein encoded by the Mycobacterial gene inhA.

Database optimization for empirical interatomic potential models

Weighted least squares fitting to a database of quantum mechanical calculations can determine the optimal parameters of empirical potential models. While algorithms exist to provide optimal potential parameters for a given fitting database of structures with corresponding energy-related predictions and to estimate prediction errors using Bayesian sampling, defining an optimal fitting database based on potential predictions remains elusive. A testing set of structures and energy-related predictions provides an empirical measure of potential transferability. Here, we propose an objective function for fitting databases based on testing set errors. The objective function allows the optimization of the weights in a fitting database, the assessment of the adding or removing of structures in the fitting database, or the comparison of two different fitting databases. To showcase this technique, we consider an example Lennard-Jones potential for Ti, where modeling multiple complicated crystal structures is difficult for a radial pair potential. The algorithm finds different optimal fitting databases, depending on the objective function of potential prediction error for a testing set.

A Dominant Factor for Structural Classification of Protein Crystals.

With the increasing number of solved protein crystal structures, much information on protein shape and atom geometry has become available. It is of great interest to know the structural diversity for a single kind of protein. Our preliminary study suggested that multiple crystal structures of a single kind of protein can be classified into several groups from the viewpoint of structural similarity. In order to broadly examine this finding, cluster analysis was applied to the crystal structures of hemoglobin (Hb), myoglobin (Mb), human serum albumin (HSA), hen egg-white lysozyme (HEWL), and human immunodeficiency virus type 1 protease (HIV-1 PR), downloaded from the Protein Data Bank (PDB). As a result of classification by cluster analysis, 146 crystal structures of Hb were separated into five groups. The crystal structures of Mb (n = 284), HEWL (n = 336), HSA (n = 63), and HIV-1 PR (n = 488) were separated into six, five, three, and six groups, respectively. It was found that a major factor causing these structural separations is the space group of crystals and that crystallizing agents have an influence on the crystal structures. Amino acid mutation is a minor factor for the separation because no obvious point mutation making a specific cluster group was observed for the five kinds of proteins. In the classification of Hb and Mb, the species of protein source such as humans, rabbits, and mice is another significant factor. When the difference in amino sequence is large among species, the species of protein source is the primary factor causing cluster separation in the classification of crystal structures.

Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP.

The SZMAP method computes binding free energies and the corresponding thermodynamic components for water molecules in the binding site of a protein structure [ SZMAP, 1.0.0 ; OpenEye Scientific Software Inc. : Santa Fe, NM, USA , 2011 ]. In this work, the ability of SZMAP to predict water structure and thermodynamic stability is examined for the X-ray crystal structures of a series of protein-ligand complexes. SZMAP results correlate with higher-level replica exchange thermodynamic integration double decoupling calculations of the absolute free energy of bound waters in the test set complexes. In addition, SZMAP calculations show good agreement with experimental data in terms of water conservation (across multiple crystal structures) and B-factors over a subset of the test set. In particular, the SZMAP neutral entropy difference term calculated at crystallographic water positions within each of the complex structures correlates well with whether that crystallographic water is conserved or displaceable. Furthermore, the calculated entropy of the water probe relative to the continuum shows a significant degree of correlation with the B-factors associated with the oxygen atoms of the water molecules. Taken together, these results indicate that SZMAP is capable of quantitatively predicting water positions and their energetics and is potentially a useful tool for determining which waters to attempt to displace, maintain, or build in through water-mediated interactions when evolving a lead series during a drug discovery program.