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GTP regulates the microtubule nucleation activity of γ-tubulin

Abstract

Not specified

Authors: Linda Gombos, Annett Neuner, Mykhaylo Berynskyy, Luca L. Fava, Rebecca C. Wade, Carsten Sachse, Elmar Schiebel

Date Published: 1st Nov 2013

Publication Type: Journal

Challenges for an enzymatic reaction kinetics database.

Abstract (Expand)

The scientific literature contains a tremendous amount of kinetic data describing the dynamic behaviour of biochemical reactions over time. These data are needed for computational modelling to create … models of biochemical reaction networks and to obtain a better understanding of the processes in living cells. To extract the knowledge from the literature, biocurators are required to understand a paper and interpret the data. For modellers, as well as experimentalists, this process is very time consuming because the information is distributed across the publication and, in most cases, is insufficiently structured and often described without standard terminology. In recent years, biological databases for different data types have been developed. The advantages of these databases lie in their unified structure, searchability and the potential for augmented analysis by software, which supports the modelling process. We have developed the SABIO-RK database for biochemical reaction kinetics. In the present review, we describe the challenges for database developers and curators, beginning with an analysis of relevant publications up to the export of database information in a standardized format. The aim of the present review is to draw the experimentalist's attention to the problem (from a data integration point of view) of incompletely and imprecisely written publications. We describe how to lower the barrier to curators and improve this situation. At the same time, we are aware that curating experimental data takes time. There is a community concerned with making the task of publishing data with the proper structure and annotation to ontologies much easier. In this respect, we highlight some useful initiatives and tools.

Authors: U. Wittig, M. Rey, R. Kania, M. Bittkowski, L. Shi, M. Golebiewski, A. Weidemann, W. Muller, I. Rojas

Date Published: 30th Oct 2013

Publication Type: Journal

Origin and Scope of Long-Range Stabilizing Interactions and Associated SOMO–HOMO Conversion in Distonic Radical Anions

Abstract (Expand)

High-level quantum-chemical methods have been used to study the scope and physical origin of the significant long-range stabilizing interactions between nonmutually conjugated anion and radical moieties … in SOMO–HOMO converted distonic radical anions. In such species, deprotonation of the acid fragment can stabilize the remote radical by tens of kilojoules, or, analogously, formation of a stable radical (by abstraction or homolytic cleavage reactions) increases the acidity of a remote acid by several pKa units. This stabilization can be broadly classified as a new type of polar effect that originates in Coloumbic interactions but, in contrast to standard polar effects, persists in radicals with no charge-separated (i.e., dipole) resonance contributors, is nondirectional, and hence of extremely broad scope. The stabilization upon deprotonation is largest when a highly delocalized radical is combined with an initially less stable anion (i.e., the conjugate base of a weaker acid), and is negligible for highly localized radicals and/or stable anions. The effect is largest in the gas phase and low-polarity solvents but is quenched in water, where the anion is sufficiently stabilized. These simple rules can be employed to design various switchable compounds able to reversibly release radicals in response to pH for use in, for example, organic synthesis or nitroxide-mediated polymerization. Moreover, given its wide chemical scope, this effect is likely to influence the protonation state of many biological substrates under radical attack and may contribute to enzyme catalysis.

Authors: Ganna Gryn’ova, Michelle L. Coote

Date Published: 3rd Oct 2013

Publication Type: Journal

Organism-Adapted Specificity of the Allosteric Regulation of Pyruvate Kinase in Lactic Acid Bacteria

Abstract

Not specified

Authors: Nadine Veith, Anna Feldman-Salit, Vlad Cojocaru, Stefan Henrich, Ursula Kummer, Rebecca C. Wade

Date Published: 25th Jul 2013

Publication Type: Journal

Regulation of the Activity of Lactate Dehydrogenases from Four Lactic Acid Bacteria

Abstract

Not specified

Authors: Anna Feldman-Salit, Silvio Hering, Hanan L. Messiha, Nadine Veith, Vlad Cojocaru, Antje Sieg, Hans V. Westerhoff, Bernd Kreikemeyer, Rebecca C. Wade, Tomas Fiedler

Date Published: 19th Jul 2013

Publication Type: Journal

Brownian dynamics simulation of protein diffusion in crowded environments

Abstract

Not specified

Authors: Paolo Mereghetti, Rebecca C. Wade

Date Published: 18th Jul 2013

Publication Type: Proceedings

Dynamic enzyme docking to the ribosome coordinates N-terminal processing with polypeptide folding

Abstract

Not specified

Authors: Arzu Sandikci, Felix Gloge, Michael Martinez, Matthias P Mayer, Rebecca Wade, Bernd Bukau, Günter Kramer

Date Published: 1st Jul 2013

Publication Type: Journal

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