Generalized crystallography

X-ray crystal structure analysis can now be seen as a special kind of microscopy which is being extended to the recognition and examination of many kinds of ordered structure more general than crystals and which leads to their synthesis or construction by various methods. Electron microscopy and many other techniques now combine to give a coherent science of structure at the scale range of Ångstroms to microns, atoms to assemblies visible to the eye, which should continue to be called crystallography although it overlaps with nanotechnology, molecular biology, and solid state physics. Most generally, a crystal is a structure the description of which is much smaller than the structure itself and this view leads to the consideration of structures as carriers of information and on to wider concerns with growth, form, morphogenesis, and life itself

Probing the effects of steric bulk on the solution-phase behaviour and redox chemistry of cobalt-diimine complexes

Cobalt-diimine complexes are important structural and redox-active elements in supramolecular assemblies. However, functionalisation of the diimine ligand adjacent to the N-donor atoms can affect dramatically the types of Co-diimine complexes that can form and their redox activity. Herein, we compare the solution phase and redox chemistry of Co(II) complexes with 1,10-phenanthroline, 5,5′-dimethyl-2,2′-bipyridine and 2,9-dimethyl-1,10-phenanthroline (neocuproine). In acetonitrile solutions containing Co(NO3)2 and neocuproine, the dominant species is the mono-diimine complex [Co(neocuproine)(NO3)(CH3CN)2]+. This complex cannot be oxidised, either electrochemically nor with iodine. We rationalise this behaviour by considering the steric constraints placed upon the metal centre by the bulky methyl substituents on the neocuproine ligand. Furthermore, from solutions of [Co(neocuproine)(NO3)(CH3CN)2]+, crystals of formula [Co(neocuproine)2(NO3)]+·[Co(neocuproine)(NO3)3]− can be obtained. We believe that this work will guide the development of Co-diimine supramolecular assemblies by highlighting the extent to which substituents close to the N-donor atoms affect which species form in solution, and their likely redox activity

Crystal structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine

ClpX is a AAA+ machine that uses the energy of ATP binding and hydrolysis to unfold native proteins and translocate unfolded polypeptides into the ClpP peptidase. The crystal structures presented here reveal striking asymmetry in ring hexamers of nucleotide-free and nucleotide-bound ClpX. Asymmetry arises from large changes in rotation between the large and small AAA+ domains of individual subunits. These differences prevent nucleotide binding to two subunits, generate a staggered arrangement of ClpX subunits and pore loops around the hexameric ring, and provide a mechanism for coupling conformational changes caused by ATP binding or hydrolysis in one subunit to flexing motions of the entire ring. Our structures explain numerous solution studies of ClpX function, predict mechanisms for pore elasticity during translocation of irregular polypeptides, and suggest how repetitive conformational changes might be coupled to mechanical work during the ATPase cycle of ClpX and related molecular machines.National Institutes of Health (U.S.) (Grant number AI-15706

Diffraction Patterns of Layered Close-packed Structures from Hidden Markov Models

We recently derived analytical expressions for the pairwise (auto)correlation functions (CFs) between modular layers (MLs) in close-packed structures (CPSs) for the wide class of stacking processes describable as hidden Markov models (HMMs) [Riechers \etal, (2014), Acta Crystallogr.~A, XX 000-000]. We now use these results to calculate diffraction patterns (DPs) directly from HMMs, discovering that the relationship between the HMMs and DPs is both simple and fundamental in nature. We show that in the limit of large crystals, the DP is a function of parameters that specify the HMM. We give three elementary but important examples that demonstrate this result, deriving expressions for the DP of CPSs stacked (i) independently, (ii) as infinite-Markov-order randomly faulted 2H and 3C stacking structures over the entire range of growth and deformation faulting probabilities, and (iii) as a HMM that models Shockley-Frank stacking faults in 6H-SiC. While applied here to planar faulting in CPSs, extending the methods and results to planar disorder in other layered materials is straightforward. In this way, we effectively solve the broad problem of calculating a DP---either analytically or numerically---for any stacking structure---ordered or disordered---where the stacking process can be expressed as a HMM.Comment: 18 pages, 6 figures, 3 tables; http://csc.ucdavis.edu/~cmg/compmech/pubs/dplcps.ht

Restricting shuttling in bis(imidazolium)…pillar[5]arene rotaxanes using metal coordination

Metal coordination to a series of bis(imidazolium)…pillar[5]arene [2]rotaxanes through the formation of metal-carbene bonds facilitates a new strategy to restrict the shuttling motion in [2]rotaxanes. Whereas the pillar[5]arene macrocycle rapidly shuttles along the full length of the bis(imidazolium) rod for the parent [2]rotaxane, Ag(I) coordination to the imidazolium groups through the formation of N-heterocyclic carbenes leads to restricted motion, effectively confining the shuttling motion of the [2]rotaxane. The Ag(I) coordinated [2]rotaxanes can be reacted further, either removing the Agcarbene species to recreate the parent [2]rotaxane, or reaction with more bulky Pd(II) species to further restrict the shuttling motion through steric inhibition

Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins

<p>Abstract</p> <p>Background</p> <p>Phosphorylation of proteins plays a crucial role in the regulation and activation of metabolic and signaling pathways and constitutes an important target for pharmaceutical intervention. Central to the phosphorylation process is the recognition of specific target sites by protein kinases followed by the covalent attachment of phosphate groups to the amino acids serine, threonine, or tyrosine. The experimental identification as well as computational prediction of phosphorylation sites (P-sites) has proved to be a challenging problem. Computational methods have focused primarily on extracting predictive features from the local, one-dimensional sequence information surrounding phosphorylation sites.</p> <p>Results</p> <p>We characterized the spatial context of phosphorylation sites and assessed its usability for improved phosphorylation site predictions. We identified 750 non-redundant, experimentally verified sites with three-dimensional (3D) structural information available in the protein data bank (PDB) and grouped them according to their respective kinase family. We studied the spatial distribution of amino acids around phosphorserines, phosphothreonines, and phosphotyrosines to extract signature 3D-profiles. Characteristic spatial distributions of amino acid residue types around phosphorylation sites were indeed discernable, especially when kinase-family-specific target sites were analyzed. To test the added value of using spatial information for the computational prediction of phosphorylation sites, Support Vector Machines were applied using both sequence as well as structural information. When compared to sequence-only based prediction methods, a small but consistent performance improvement was obtained when the prediction was informed by 3D-context information.</p> <p>Conclusion</p> <p>While local one-dimensional amino acid sequence information was observed to harbor most of the discriminatory power, spatial context information was identified as relevant for the recognition of kinases and their cognate target sites and can be used for an improved prediction of phosphorylation sites. A web-based service (Phos3D) implementing the developed structure-based P-site prediction method has been made available at <url>http://phos3d.mpimp-golm.mpg.de</url>.</p

Acid/base-triggered switching of circularly polarized luminescence and electronic circular dichroism in organic and organometallic helicenes.

Electronic circular dichroism and circularly polarized luminescence acid/base switching activity has been demonstrated in helicene-bipyridine proligand 1 a and in its “rollover” cycloplatinated derivative 2 a. Whereas proligand 1 a displays a strong bathochromic shift (>160 nm) of the nonpolarized and circularly polarized luminescence upon protonation, complex 2 a displays slightly stronger emission. This strikingly different behavior between singlet emission in the organic helicene and triplet emission in the organometallic derivative has been rationalized by using quantum-chemical calculations. The very large bathochromic shift of the emission observed upon protonation of azahelicene-bipyridine 1 a has been attributed to the decrease in aromaticity (promoting a charge-transfer-type transition rather than a π–π* transition) as well as an increase in the HOMO–LUMO character of the transition and stabilization of the LUMO level upon protonation