Context-based identification of protein-protein interfaces and "hot-spot" residues

Reliable determination of protein-protein interaction sites is of critical importance for structure-based design of small molecules modulating protein function through macromolecular interfaces. We present an alignment-free computational method for prediction of protein-protein interface residues. The method ("iPred") is based on a knowledge-based scoring function adapted from the field of protein folding and small molecule docking. Based on a training set of 394 hetero-dimeric proteins iPred achieves sustained accuracy on an external unbound test set. Prediction robustness was assessed from more than 1500 diverse complexes containing homo- and hetero-dimers. The technique does not rely on sequence conservation, so that rapid interface identification is possible even for proteins for which homologs are unknown or lack conserved residue patterns in interface region. Functional "hot-spot" residues are enriched among the predicted interface residues, rendering the method predestined for macromolecular binding site identification and drug design studies aiming at modulating protein-protein interaction that might influence protein function. For a comparative structural model of peptidase HtrA from Helicobacter pylori, we performed mutation studies for predicted hot-spot residues, which were confirmed as functionally relevant for HtrA activity or oligomerization.     

Assay Related Target Similarity (ARTS) - chemogenomics approach for quantitative comparison of biological targets

Computer-based chemogenomics approaches compare macromolecular drug targets based on their amino acid sequences or derived properties, by similarity of their ligands, or according to ligand-target interaction models. Here we present ARTS (Assay Related Target Similarity) as a quantitative index that estimates target similarity directly from measured affinities of a set of probe compounds. This approach reduces the risk of deducing artificial target relationships from mutually inactive compounds. ARTS implements a scoring scheme that matches intertarget similarity based on dose-response measurements. While all experimentally derived target similarities have a tendency to be data set-dependent, we demonstrate that ARTS depends less on the used data set than the commonly used Pearson correlation or Tanimoto index.     

Rotational spectrum of trans-trans diethyl ether in the ground and three excited vibrational states

We report the results of a comprehensive reinvestigation of the rotational spectrum of diethyl ether based on broadband millimetre-wave spectra recently recorded at The Ohio State University and in Warsaw, covering the frequency region 108-366 GHz. The data set for the ground vibrational state of trans-trans diethyl ether has been extended to over 2000 lines and improved spectroscopic constants have been determined. Rotational spectra in the first excited vibrational states of the three lowest vibrational modes of trans-trans-diethyl ether, ν₂₀, ν₃₉, and ν₁₂ have been assigned. The v₂₀ = 1 and v₃₉ = 1 states are near 100 cm⁻¹ in vibrational term value and are coupled by a strong c-axis Coriolis interaction, which gives rise to many spectacular manifestations in the rotational spectrum. All of these effects have been successfully fitted for a dataset comprising over 3000 transitions, leading to precise determination of the energy difference between these states, (ΔE/hc)=10.400222(5) cm⁻¹. A newly developed software package for assignment and analysis of broadband spectra is described and made available.     

Linearformen in Logarithmen von U-Zahlen und Transzendenz von Potenzen II

Ohne Zusammenfassung     

Spectroscopy among the stars

The space between the stars is not void, but filled with interstellar matter, mainly composed of dust and gas, which gather in large interstellar clouds. In our Galaxy these interstellar clouds are distributed along a thin, but extended layer which basically traces out the spiral distribution of matter: the stars, the gas, and the dust component. Up to the present time more than 100 different molecules have been identified in interstellar molecular clouds. The majority of the interstellar molecules constitute carbon containing organic substances. During the past years, overwhelming evidence has been gathered, mainly through spectroscopic observations, that interstellar molecular clouds provide the birthplaces for stars. In fact detailed high spectral and spatial resolution spectroscopic measurements reveal physical and chemical processes of the intricate star formation process.     

The millimeter wave rotational spectrum of N-cyanomethanimine,CH2NCN

The rotational spectrum of the short-lived species N-cyanomethanimine, CH₂NCN, has been measured in the frequency range 100–250 GHz. The observed transitions allow the determination of the rotational and centrifugal distortion constants and the nitrogen quadrupole coupling constants for both nitrogen nuclei. The N-cyanomethanimine spectrum was measured directly in the products of the pyrolysis of trimethylenetetrazole. The rotational constants obtained are A = 63 372.995(11) MHz, B = 5 449.347 90(28) MHz, and C = 5 009.559 86(29) MHz; the quadrupole coupling constants are χ_aa = 2.057(39) MHz and χ_bb ? χ_cc = ?7.205(21) MHz for the imine nitrogen, and χ_aa = ?3.264(33) MHz and χ_bb ? χ_cc = ?1.630(18) MHz for the cyano-group nitrogen. The accurate constants obtained allow the calculation of the line position and hyperfine structure of any rotational transition appropriate for a radioastronomical search.     

Ionic Interactions in a Polarizable Dipolar Hard-Sphere Solvent

Potentials of mean forces of ions in infinitely diluted solutions are calculated by means of a general virial expansion for systems with short and long range interactions. The screened potentials are calculated by the MSA-approximation for the chain sum in the mixture model.     

The rotational a-type sepctra of 15N-labeled diazirine,H2CN2

The rotational a-type spectra of isotopically enriched diazirine isotopomers, H₂¹²C¹⁴N¹⁵N and H₂¹²C¹⁵N₂, have been recorded in the region between 8 and 300 GHZ; the latter isotopomer has been observed for the first time. Using Watson's A-reduced Hamiltonian, the rotational constants and the quartic and some sextic centrifugal distortion constants have been determined for the ground vibrational states.