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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. [ABSTRACT FROM AUTHOR]

Two divergent modelling methodologies have been adopted to increase our understanding of metabolism and its regulation. Constraint-based modelling highlights the optimal path through a stoichiometric network within certain physicochemical constraints. Such an approach requires minimal biological data to make quantitative inferences about network behaviour; however, constraint-based modelling is unable to give an insight into cellular substrate concentrations. In contrast, kinetic modelling aims to characterize fully the mechanics of each enzymatic reaction. This approach suffers because parameterizing mechanistic models is both costly and time-consuming. In this paper, we outline a method for developing a kinetic model for a metabolic network, based solely on the knowledge of reaction stoichiometries. Fluxes through the system, estimated by flux balance analysis, are allowed to vary dynamically according to linlog kinetics. Elasticities are estimated from stoichiometric considerations. When compared to a popular branched model of yeast glycolysis, we observe an excellent agreement between the real and approximate models, despite the absence of (and indeed the requirement for) experimental data for kinetic constants. Moreover, using this particular methodology affords us analytical forms for steady state determination, stability analyses and studies of dynamical behaviour. [ABSTRACT FROM AUTHOR]

Presents an abstracts of research papers related to biochemistry. "Cocrystals of Photosystem I With Its Soluble Natural Electron Acceptor Ferredoxin at 4 A Resolution," by R. Fromme, and H. Yu; "Breaking Biological Symmetry in Membrane Proteins:How PsaC Evolved to Orient Asymmetrically on the Photosystem I Core," by J. H. Golbeck and M. Antonkine; "The Primary Light Energy Conversion in Bacterial Reaction Centers:Coupling Electron Transfer and Nuclear Motions," by V. A. Shuvalov.

Presents an abstracts of research papers related to biochemistry. "Mechanism of the Multiprotein RNA Polymerase II," by P. Cramer; "Regulation of Transcription by RNA Polymerase II by the Multi-functional Ccr4-Not Complex," by H. M. Timmers and K. W. Mulder; "Functionally Distinct ADA2-containing Histone Acetylase Complexes in Drosophila," by I. M. Boros and T. Pankotai.

Presents an abstracts of research papers related to biochemistry. "Reference Measurement Procedures and External Quality Assessment Schemes," by H. Reinauer and . Kaiser; "International Standardization of Protein Measurement," by C. C. Heuck; "The HUPO Brain Proteome Project," by H. E. Meyer.

Presents an abstracts of research papers related to biochemistry. "Protein interactions in cell signaling and polarity," by T. Pawson; "Regulation and Function of the Proto-oncogene Protein Kinase B/Akt," by B. A. Hemmings; "Casein Kinase 2 Interacts With and Regulates Subcellular Localization of S6K," by G. Panasyuk, V. Filonenko and I. Gout; "Knockdown of BChE by Sequence-specific siRNAs Changes PKCb- and JNK Expression," by E. Bodur and P. G. Layer.

Presents an abstracts of research papers related to biochemistry. "Hemolysis of Human Red Blood Cells by Riboflavin-Cu(II) System:Enhancement by Azide," by I. Ali and I. Naseem; "Effects of Nat5 Aminotermional Acetyltransferase Inhibition on HeLa Cells," by A. Ametzazurra and E. Larrea; "Plants As Alternative Systems for Recombinant Protein Production:Medicago Truncatula As an Emerging Production System," by R. Abranches and S. Marcel.

Presents an abstracts of research papers related to biochemistry. "Aquaporin Water Channels:From Atomic Structure to Clinical Medicine," by P. Agre; "The Cardiac Glycoside Binding Site of the Na,K-ATPase Plays a Role in Blood Pressure Regulation," by J. Lingrel, I. Dostanic and J, Neumann; "TRP Channels, Mediators of Sensory Signaling," by C. Montell.

Presents an abstracts of research papers related to biochemistry. "Tricking Cancer Cells to Die," by A. Levitzki; "IkB Kinases in Innate Immunity and Cancer," by M. Karin; "Structure-based Discovery of Non-peptidic Small Molecule Inhibitors of Caspase-3," by J. Sakai and A. Yoshimori; "Receptor Tyrosine Kinase Inhibition in Cancer Therapy:From Monospecific to Multi-targeted Drugs," by A. Ullrich.

Presents abstracts of research papers related to biochemistry. "Sox9 Controls Both Chondrocyte Differentiation and Proliferation," by B. de Crombrugghe, A. Haruhiko and A. Yuko; "The Role of Chondrocyte-matrix Attachment Complexes in Skeletal Development," by A. Aszodi, C. Noclae and A. Raducanu; "The Extracellular Matrix 1 Gene Is Essential for Early Mouse Development," by S. Sercu, J. Liekens and L. Umans.

Presents an abstracts of research papers related to biochemistry. "Stress and Misfolded Proteins:Modulators of Neurodegenerative Diseases and Longevity," by R. I. Morimoto, J. Morley, H. Brignull, S. Garcia, K. Richter and C. Kaiser; "Chaperone Machines of the Cytosol," by B. Bukau; "The Substrate Spectrum of the Eucaryotic Chaperonin TRIC/CCT Revelead by Genomic Approaches," by J. Frydman.

This is a series of papers (three reviews and five regular papers) focused on Mitochondria from authors contributing to two FEBS courses on Mitochondria held in 2012. These papers focus on: (i) mitochondrial biogenesis (regulation by phosphorylation, import of SOD1 and Mia40, mitophagy and tRNA variants) or (ii) mitochondrial pathology (ischaemia, obesity and Parkinson's disease). [ABSTRACT FROM AUTHOR]