Accuracy of bound peptide structures determined by exchange transferred nuclear Overhauser data: A simulation study

The exchange-transferred NOE method to determine the three-dimensional structure of peptides bound to proteins, or other macromolecular systems, is becoming increasingly important in drug design efforts and for large or multicomponent assemblies, such as membrane receptors, where structural analysis of the full system is intractable. The exchange-transferred nuclear Overhauser effect spectroscopy (etNOESY) method allows the determination of the bound-state conformation of the peptide from the intra-molecular NOE interactions between ligand protons. Because only ligand–ligand NOEs are generally observable, the etNOESY method is restricted to fewer NOEs per residue than direct protein structure determination. In addition, the averaging of relaxation rates between free and bound states affects the measured cross-peak intensities, and possibly the accuracy of distance estimates. Accordingly, the study reported here was conducted to examine the conditions required to define a reliable structure. The program CORONA was used to simulate etNOE data using a rate-matrix including magnetic relaxation and exchange rates for two peptide–protein complexes derived from the reference complex of cAMP-dependent protein kinase ligated with a 24-residue inhibitor peptide. The results indicate that reasonably accurate peptide structures can be determined with relatively few NOE interactions when the interactions occur between non-neighboring residues. The reliability of the structural result is suggested from the pattern of NOE interactions. A structure with an accuracy of approximately 1.3 Å rms difference for the main-chain atoms can be obtained when etNOE interactions between non-neighboring residues occur over the length of the peptide. The global precision is higher (approximately 0.9 Å rms difference) but is not correlated to global accuracy. A local definition of precision along the backbone appears to be a good indicator of the local accuracy.     

Markov chain Monte Carlo fitting of single-channel data from inositol trisphosphate receptors

In many cell types, the inositol trisphosphate receptor (IPR) is one of the important components that control intracellular calcium dynamics, and an understanding of this receptor (which is also a calcium channel) is necessary for an understanding of calcium oscillations and waves. Recent advances in experimental techniques now allow for the measurement of single-channel activity of the IPR in conditions similar to its native environment, and these data can be used to determine the rate constants in Markov models of the IPR. We illustrate a parameter estimation method based on Markov chain Monte Carlo, which can be used to fit directly to single-channel data, and determining, as an intrinsic part of the fit, the times at which the IPR is opening and closing. We show, using simulated data, the most complex Markov model that can be unambiguously determined from steady-state data and show that non-steady-state data is required to determine more complex models.     

Nachweis des Teleomorph Mycosphaerella graminicola (Fuckel) Schroeter (Anamorph: Septoria tritici Rob. apud Desm.) in der Bundesrepublik Deutschland

Evidence of the teleomorph Mycosphaerella graminicola (Fuckel) Schroeter. (anamorph: Septoria tritici Rob. apud Desm.) in the Federal Republic of Germany Due to the fullfillment of certain biological requirements, the dominant occurrence of Septoria tritici is restricted mainly to the milder climate of maritime regions. However, following mild winters in continental climatic zones, an increased and yield damaging appearance, which is additionally influenced by early sowing dates, can be observed. Previous proofs of the teleomorph Mycosphaerella graminicola (Fuckel) Schroeter were found in Australia, Brazil, Great Britain, Chile and the USA., With the first proof of teleomorph in Bavaria and herewith the complete life cycle, the optimum mechanism for an early and widespread primary infection of young wheat plants has been confirmed.