BODIL: a molecular modeling environment for structure-function analysis and drug design

BODIL is a molecular modeling environment geared to help the user to quickly identify key features of proteins critical to molecular recognition, especially (1) in drug discovery applications, and (2) to understand the structural basis for function. The program incorporates state-of-the-art graphics, sequence and structural alignment methods, among other capabilities needed in modern structure–function–drug target research. BODIL has a flexible design that allows on-the-fly incorporation of new modules, has intelligent memory management, and fast multi-view graphics. A beta version of BODIL and an accompanying tutorial are available at http://www.abo.fi/fak/mnf/bkf/research/johnson/bodil.html     

Weak $$A_\infty $$ Weights and Weak Reverse Hölder Property in a Space of Homogeneous Type

In the Euclidean setting, the Fujii–Wilson-type \(A_\infty \) weights satisfy a reverse Hölder inequality (RHI), but in spaces of homogeneous type the best-known result has been that \(A_\infty \) weights satisfy only a weak reverse Hölder inequality. In this paper, we complement the results of Hytönen, Pérez and Rela and show that there exist both \(A_\infty \) weights that do not satisfy an RHI and a genuinely weaker weight class that still satisfies a weak RHI. We also show that all the weights that satisfy a weak RHI have a self-improving property, but the self-improving property of the strong reverse Hölder weights fails in a general space of homogeneous type. We prove most of these purely non-dyadic results using convenient dyadic systems and techniques.     

Quantitative weighted estimates for rough homogeneous singular integrals

We consider homogeneous singular kernels, whose angular part is bounded, but need not have any continuity. For the norm of the corresponding singular integral operators on the weighted space L ²(w), we obtain a bound that is quadratic in A ₂ constant \({\left[ w \right]_{{A_2}}}\). We do not know if this is sharp, but it is the best known quantitative result for this class of operators. The proof relies on a classical decomposition of these operators into smooth pieces, for which we use a quantitative elaboration of Lacey's dyadic decomposition of Dini-continuous operators: the dependence of constants on the Dini norm of the kernels is crucial to control the summability of the series expansion of the rough operator. We conclude with applications and conjectures related to weighted bounds for powers of the Beurling transform.     

Modular Architecture of Protein Binding Units for Designing Properties of Cellulose Nanomaterials

Molecular biomimetic models suggest that proteins in the soft matrix of nanocomposites have a multimodular architecture. Engineered proteins were used together with nanofibrillated cellulose (NFC) to show how this type of architecture leads to function. The proteins consist of two cellulose‐binding modules (CBM) separated by 12‐, 24‐, or 48‐mer linkers. Engineering the linkers has a considerable effects on the interaction between protein and NFC in both wet colloidal state and a dry film. The protein optionally incorporates a multimerizing hydrophobin (HFB) domain connected by another linker. The modular structure explains effects in the hydrated gel state, as well as the deformation of composite materials through stress distribution and crosslinking. Based on this work, strategies can be suggested for tuning the mechanical properties of materials through the coupling of protein modules and their interlinking architectures.     

Computer-assisted identification of multitrace electrophoretic patterns in differential display experiments

Modern multicapillary devices allow researchers to address increasingly complex biological questions involving comparisons of gene expression patterns across electrophoretic samples under various experimental conditions. As labor-intensive visual evaluation of the electrophoretic results is often the bottleneck of large-scale differential display (DD) studies, one way to further streamline this process is to focus only on a highly compressed list of the most potential patterns that are likely to provide reliable findings. To enable the identification of such candidate patterns, we present a computer-assisted method for objective ranking of multitrace peak patterns in DD experiments. The fundamental component of the multitrace pattern ranking method (MRANK) is the multiple alignment algorithm that allows for discovery of patterns involving sets of peak complexes from various electrophoretic samples. A score value is attached to each detected pattern which characterizes how accurately the pattern resembles the desired pattern query, freely defined by the researcher. The ranked pattern list produced by MRANK is validated against visual evaluation in terms of detecting and ranking a group of relevant patterns in a DD analysis of T-helper cell differentiation. We demonstrate high enrichment of the desired patterns on top of the score-ranked list (e.g., 90% of the visually selected patterns are discovered by looking through the first 3% of patterns in the ranked list of all patterns). The results suggest that a substantial amount of manual labor can be saved without compromising the accuracy of the findings by prioritizing the patterns according to MRANK output in the visual confirmation phase.     

Electron ionization mass spectra of aryl- and benzyl-substituted 2,3-dihydroimidazo[1,2-a]pyrimidine-5,7(1H,6H)-diones

The electron ionization mass spectra of the 1-phenyl-, 1-benzyl- and 6-benzyl-1-phenyl-2,3-dihydroimidazo[1,2-a]pyrimidine-5,7(1H,6H)-dione derivatives were recorded at 70 eV to find out the effects of substituents on their fragmentations. Fragmentation pathways were studied using B/E and B(2)/E scans. Some fragmentations involved the loss of C(3)HO(2) or carbon suboxide. The possibility of keto-enol tautomerism was also studied. For comparison selected compounds were studied using (1)H and (13)C NMR spectroscopy to reveal the presence of possible tautomerism. Some ions including [M-OH](+) and [M-HCO](+) and NMR results indicate that the enol form is predominant both in the gas and in the liquid phase.     

Self-organized nanostructures of poly(4-vinylpyridine), polyaniline and polyamides due to metal complexation

Comb-shaped supramolecules are constructed using flexible polymers and semi-rigid conjugated undoped or doped conjugated polymers upon complexing Zinc dodecyl benzene sulphonate, Zn(DBS)₂. Selforganized nanostructures are formed in the bulk due to competing attractive interactions (coordination or water mediated hydrogen bonding) and repulsive polar/nonpolar interactions, showing characteristic long periods of ca. 30 Å.     

Benzenedisulfonic Acid as an ALD/MLD Building Block for Crystalline Metal-Organic Thin Films**

Two new atomic/molecular layer deposition processes for depositing crystalline metal-organic thin films, built from 1,4-benzenedisulfonate (BDS) as the organic linker and Cu or Li as the metal node, are reported. The processes yield in-situ crystalline but hydrated Cu-BDS and Li-BDS films; in the former case, the crystal structure is of a previously known metal-organic-framework-like structure, while in the latter case not known from previous studies. Both hydrated materials can be readily dried to obtain the crystalline unhydrated phases. The stability and the ionic conductivity of the unhydrated Li-BDS films were characterized to assess their applicability as a thin film solid polymer Li-ion conductor.