GIS: a comprehensive source for protein structure similarities

A web service for analysis of protein structures that are sequentially or non-sequentially similar was generated. Recently, the non-sequential structure alignment algorithm GANGSTA+ was introduced. GANGSTA+ can detect non-sequential structural analogs for proteins stated to possess novel folds. Since GANGSTA+ ignores the polypeptide chain connectivity of secondary structure elements (i.e. α-helices and β-strands), it is able to detect structural similarities also between proteins whose sequences were reshuffled during evolution. GANGSTA+ was applied in an all-against-all comparison on the ASTRAL40 database (SCOP version 1.75), which consists of >10 000 protein domains yielding about 55 × 106 possible protein structure alignments. Here, we provide the resulting protein structure alignments as a public web-based service, named GANGSTA+ Internet Services (GIS). We also allow to browse the ASTRAL40 database of protein structures with GANGSTA+ relative to an externally given protein structure using different constraints to select specific results. GIS allows us to analyze protein structure families according to the SCOP classification scheme. Additionally, users can upload their own protein structures for pairwise protein structure comparison, alignment against all protein structures of the ASTRAL40 database (SCOP version 1.75) or symmetry analysis. GIS is publicly available at http://agknapp.chemie.fu-berlin.de/gplus

An Anti-Human ICAM-1 Antibody Inhibits Rhinovirus-Induced Exacerbations of Lung Inflammation

Human rhinoviruses (HRV) cause the majority of common colds and acute exacerbations of asthma and chronic obstructive pulmonary disease (COPD). Effective therapies are urgently needed, but no licensed treatments or vaccines currently exist. Of the 100 identified serotypes, ∼90% bind domain 1 of human intercellular adhesion molecule-1 (ICAM-1) as their cellular receptor, making this an attractive target for development of therapies; however, ICAM-1 domain 1 is also required for host defence and regulation of cell trafficking, principally via its major ligand LFA-1. Using a mouse anti-human ICAM-1 antibody (14C11) that specifically binds domain 1 of human ICAM-1, we show that 14C11 administered topically or systemically prevented entry of two major groups of rhinoviruses, HRV16 and HRV14, and reduced cellular inflammation, pro-inflammatory cytokine induction and virus load in vivo. 14C11 also reduced cellular inflammation and Th2 cytokine/chemokine production in a model of major group HRV-induced asthma exacerbation. Interestingly, 14C11 did not prevent cell adhesion via human ICAM-1/LFA-1 interactions in vitro, suggesting the epitope targeted by 14C11 was specific for viral entry. Thus a human ICAM-1 domain-1-specific antibody can prevent major group HRV entry and induction of airway inflammation in vivo

Industrially scalable and cost-effective Mn2+ doped ZnxCd1−xS/ZnS nanocrystals with 70% photoluminescence quantum yield, as efficient down-shifting materials in photovoltaics

We present colloidally stable and highly luminescent ZnxCd1−xS:Mn/ZnS core–shell nanocrystals (NCs) synthesized via a simple non-injection one-pot, two-step synthetic route, which can be easily upscaled. A systematic variation of the reaction component, parameters and thickness of the ZnS shell yielded doped nanocrystals with a very high photoluminescence quantum yield (Φpl) of 70%, which is the highest value yet reported for these Mn-doped sulfide-semiconductor NCs. These materials can be synthesized with high reproducibility in large quantities of the same high quality, i.e., the same Φpl using accordingly optimized reaction conditions. The application of these zero-reabsorption high quality NCs in the light conversion layers, deposited on top of a commercial monocrystalline silicon (mono-Si) solar cell, led to a significant enhancement of the external quantum efficiency (EQE) of this device in the ultraviolet spectral region between 300 and 400 nm up to ca. 12%. EQE enhancement is reflected by an increase in the power conversion efficiency (PCE) by nearly 0.5 percentage points and approached the theoretical limit (0.6%) expected from down-shifting for this Si solar cell. The resulting PCE may result in a BoM (bill of materials) cost reduction of app. 3% for mono-Si photovoltaic modules. Such small but distinct improvements are expected to pave the road for an industrial application of doped semiconductor NCs as cost-effective light converters for silicon photovoltaic (PV) and other optoelectronic applications

Superimposé: a 3D structural superposition server

The Superimposé webserver performs structural similarity searches with a preference towards 3D structure-based methods. Similarities can be detected between small molecules (e.g. drugs), parts of large structures (e.g. binding sites of proteins) and entire proteins. For this purpose, a number of algorithms were implemented and various databases are provided. Superimposé assists the user regarding the selection of a suitable combination of algorithm and database. After the computation on our server infrastructure, a visual assessment of the results is provided. The structure-based in silico screening for similar drug-like compounds enables the detection of scaffold-hoppers with putatively similar effects. The possibility to find similar binding sites can be of special interest in the functional analysis of proteins. The search for structurally similar proteins allows the detection of similar folds with different backbone topology. The Superimposé server is available at: http://bioinformatics.charite.de/superimpose

TS-AMIR: a topology string alignment method for intensive rapid protein structure comparison

<p>Abstract</p> <p>Background</p> <p>In structural biology, similarity analysis of protein structure is a crucial step in studying the relationship between proteins. Despite the considerable number of techniques that have been explored within the past two decades, the development of new alternative methods is still an active research area due to the need for high performance tools.</p> <p>Results</p> <p>In this paper, we present TS-AMIR, a Topology String Alignment Method for Intensive Rapid comparison of protein structures. The proposed method works in two stages: In the first stage, the method generates a topology string based on the geometric details of secondary structure elements, and then, utilizes an n-gram modelling technique over entropy concept to capture similarities in these strings. This initial correspondence map between secondary structure elements is submitted to the second stage in order to obtain the alignment at the residue level. Applying the Kabsch method, a heuristic step-by-step algorithm is adopted in the second stage to align the residues, resulting in an optimal rotation matrix and minimized RMSD. The performance of the method was assessed in different information retrieval tests and the results were compared with those of CE and TM-align, representing two geometrical tools, and YAKUSA, 3D-BLAST and SARST as three representatives of linear encoding schemes. It is shown that the method obtains a high running speed similar to that of the linear encoding schemes. In addition, the method runs about 800 and 7200 times faster than TM-align and CE respectively, while maintaining a competitive accuracy with TM-align and CE.</p> <p>Conclusions</p> <p>The experimental results demonstrate that linear encoding techniques are capable of reaching the same high degree of accuracy as that achieved by geometrical methods, while generally running hundreds of times faster than conventional programs.</p

Resonant X ray photoelectron spectroscopy identification of atomic contributions to valence states

Valence electronic structure is crucial for understanding and predicting reactivity. Valence non resonant Xray photoelectron spectroscopy NRXPS provides a direct method for probing the overall valence electronic structure. However, it is often difficult to separate the varying contributions to NRXPS; for example, contributions of solutes in solvents or functional groups in complex molecules. In this work we show that valence resonant X ray photoelectron spectroscopy RXPS is a vital tool for obtaining atomic contributions to valence states. We combine RXPS with NRXPS and density functional theory calculations to demonstrate the validity of using RXPS to identify atomic contributions for a range of solutes both neutral and ionic and solvents both molecular solvents and ionic liquids . Furthermore, the one electron picture of RXPS holds for all of the closed shell molecules ions studied, although the situation for an open shell metal complex is more complicated. Factors needed to obtain a strong RXPS signal are investigated in order to predict the types of systems RXPS will work best for; a balance of element electronegativity and bonding type is found to be important. Additionally, the dependence of RXPS spectra on both varying solvation environment and varying local covalent bonding is probed. We find that RXPS is a promising fingerprint method for identifying species in solution, due to the spectral shape having a strong dependence on local covalency but a weak dependence on solvation environmen

Tableau-based protein substructure search using quadratic programming

<p>Abstract</p> <p>Background</p> <p>Searching for proteins that contain similar substructures is an important task in structural biology. The exact solution of most formulations of this problem, including a recently published method based on tableaux, is too slow for practical use in scanning a large database.</p> <p>Results</p> <p>We developed an improved method for detecting substructural similarities in proteins using tableaux. Tableaux are compared efficiently by solving the quadratic program (QP) corresponding to the quadratic integer program (QIP) formulation of the extraction of maximally-similar tableaux. We compare the accuracy of the method in classifying protein folds with some existing techniques.</p> <p>Conclusion</p> <p>We find that including constraints based on the separation of secondary structure elements increases the accuracy of protein structure search using maximally-similar subtableau extraction, to a level where it has comparable or superior accuracy to existing techniques. We demonstrate that our implementation is able to search a structural database in a matter of hours on a standard PC.</p