Showing papers by "George M. Sheldrick published in 2014"

Ion permeation in K + channels occurs by direct Coulomb knock-on

Abstract: Potassium channels selectively conduct K(+) ions across cellular membranes with extraordinary efficiency. Their selectivity filter exhibits four binding sites with approximately equal electron density in crystal structures with high K(+) concentrations, previously thought to reflect a superposition of alternating ion- and water-occupied states. Consequently, cotranslocation of ions with water has become a widely accepted ion conduction mechanism for potassium channels. By analyzing more than 1300 permeation events from molecular dynamics simulations at physiological voltages, we observed instead that permeation occurs via ion-ion contacts between neighboring K(+) ions. Coulomb repulsion between adjacent ions is found to be the key to high-efficiency K(+) conduction. Crystallographic data are consistent with directly neighboring K(+) ions in the selectivity filter, and our model offers an intuitive explanation for the high throughput rates of K(+) channels.

Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server

Abstract: Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server

Refinement of macromolecular structures against neutron data with SHELXL2013.

Abstract: Some of the improvements in SHELX2013 make SHELXL convenient to use for refinement of macromolecular structures against neutron data without the support of X-ray data. The new NEUT instruction adjusts the behaviour of the SFAC instruction as well as the default bond lengths of the AFIX instructions. This work presents a protocol on how to use SHELXL for refinement of protein structures against neutron data. It includes restraints extending the Engh & Huber [Acta Cryst. (1991), A47, 392–400] restraints to H atoms and discusses several of the features of SHELXL that make the program particularly useful for the investigation of H atoms with neutron diffraction. SHELXL2013 is already adequate for the refinement of small molecules against neutron data, but there is still room for improvement, like the introduction of chain IDs for the refinement of macromolecular structures.

A Catalyst with Two‐Coordinate Nickel: Theoretical and Catalytic Studies

Abstract: The bisadduct (cAAC)2NiIICl2 [1; cAAC = cyclic (alkyl)(amino)carbene] was directly synthesized by treating cAAC with NiCl2. Compound 1 was reduced to (cAAC)2Ni0 (2) by using lithium diisopropylamide or KC8. Crystals of 2 were stable under an inert gas for several months and decomposed upon heating above 165 °C. On the basis of the calculated natural bond orbital charge values of the nickel atom in 2, the oxidation state of nickel was determined to be between NiI and Ni0 (+0.34). Theoretical calculations suggested a closed-shell singlet electronic configuration of 2 with little biradical character. Ab initio multiconfigurational C(R)ASSCF/CASPT2 calculations predicted a closed-shell singlet electronic configuration (Ni0), whereas excited spin states possessed NiI character with unpaired electrons on neighboring carbon atoms. The catalytic activity of complex 2 was investigated for the homocoupling of various unactivated aryl chlorides/fluorides. The biaryls were obtained in good yields at moderate temperature. Theoretical studies showed that an intermediate containing NiIII was more favored than one with NiIV.

On the temperature dependence of H-Uiso in the riding hydrogen model

Abstract: The temperature dependence of H-Uiso in N-acetyl-l-4-hydroxyproline monohydrate is investigated. Imposing a constant temperature-independent multiplier of 1.2 or 1.5 for the riding hydrogen model is found to be inaccurate, and severely underestimates H-Uiso below 100 K. Neutron diffraction data at temperatures of 9, 150, 200 and 250 K provide benchmark results for this study. X-ray diffraction data to high resolution, collected at temperatures of 9, 30, 50, 75, 100, 150, 200 and 250 K (synchrotron and home source), reproduce neutron results only when evaluated by aspherical-atom refinement models, since these take into account bonding and lone-pair electron density; both invariom and Hirshfeld-atom refinement models enable a more precise determination of the magnitude of H-atom displacements than independent-atom model refinements. Experimental efforts are complemented by computing displacement parameters following the TLS+ONIOM approach. A satisfactory agreement between all approaches is found.

Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA.

Abstract: Mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities, is caused by an inherited deficiency of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). More than 100 mutations in the SGSH gene have been found to reduce or eliminate its enzymatic activity. However, the molecular understanding of the effect of these mutations has been confined by a lack of structural data for this enzyme. Here, the crystal structure of glycosylated SGSH is presented at 2 A resolution. Despite the low sequence identity between this unique N-sulfatase and the group of O-sulfatases, they share a similar overall fold and active-site architecture, including a catalytic formylglycine, a divalent metal-binding site and a sulfate-binding site. However, a highly conserved lysine in O-sulfatases is replaced in SGSH by an arginine (Arg282) that is positioned to bind the N-linked sulfate substrate. The structure also provides insight into the diverse effects of pathogenic mutations on SGSH function in mucopolysaccharidosis type IIIA and convincing evidence for the molecular consequences of many missense mutations. Further, the molecular characterization of SGSH mutations will lay the groundwork for the development of structure-based drug design for this devastating neurodegenerative disorder.

Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries.

Abstract: Protein–DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein–DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite the fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein–DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein–DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. Whereas for typical proteins main-chain α-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures.

Corrigendum: Exploiting tertiary structure through local folds for crystallographic phasing

Abstract: Corrigendum: Exploiting tertiary structure through local folds for crystallographic phasing

Structure of Hormaomycin, a Naturally Occurring Cyclic Octadepsipeptide, in the Crystal

Abstract: The structure of hormaomycin has been determined in two crystals grown under different conditions, i. e. in the absence and in the presence of magnesium chloride. In both crystals, the macrocyclic hexadepsipeptide assumes a rather flat conformation, and the dipeptide side chain resides in the same equatorial plane. This is a significant difference in comparison with the compact bent conformation of hormaomycin in solution, as previously determined by an extensive NMR study

Molecular architecture with carbohydrate functionalized β-peptides adopting 314-helical conformation.

Abstract: Carbohydrate recognition is essential in cellular interactions and biological processes It is characterized by structural diversity, multivalency and cooperative effects To evaluate carbohydrate interaction and recognition, the structurally defined attachment of sugar units to a rigid template is highly desired β-Peptide helices offer conformationally stable templates for the linear presentation of sugar units in defined distances The synthesis and β-peptide incorporation of sugar-β-amino acids are described providing the saccharide units as amino acid side chain The respective sugar-β-amino acids are accessible by Michael addition of ammonia to sugar units derivatized as α,β-unsaturated esters Three sugar units were incorporated in β-peptide oligomers varying the sugar (glucose, galactose, xylose) and sugar protecting groups The influence of sugar units and the configuration of sugar-β-amino acids on β-peptide secondary structure were investigated by CD spectroscopy

Triostin A Derived Cyclopeptide as Architectural Template for the Alignment of Four Recognition Units

Abstract: The DNA bisintercalator triostin A is structurally based on a disulfide-bridged depsipeptide scaffold that provides preorganization of two quinoxaline units in 10.5 A distance. Triostin A analogues are synthesized with nucleobase recognition units replacing the quinoxalines and containing two additional recognition units in between. Thus, four nucleobase recognition units are organized on a rigid template, well suited for DNA double strand interactions. The new tetra-nucleobase binders are synthesized as aza-TANDEM derivatives lacking the N-methylation of triostin A and based on a cyclopeptide backbone. Synthesis of two tetra-nucleobase aza-TANDEM derivatives is established, DNA interaction analyzed by microscale thermophoresis, cytotoxic activity studied and a nucleobase sequence dependent self-aggregation investigated by mass spectrometry.