AmyPro: a database of proteins with validated amyloidogenic regions

Soluble functional proteins may transform into insoluble amyloid fibrils that deposit in a variety of tissues. Amyloid formation is a hallmark of age-related degenerative disorders. Perhaps surprisingly, amyloid fibrils can also be beneficial and are frequently exploited for diverse functional roles in organisms. Here we introduce AmyPro, an open-access database providing a comprehensive, carefully curated collection of validated amyloid fibril-forming proteins from all kingdoms of life classified into broad functional categories (http://amypro.net). In particular, AmyPro provides the boundaries of experimentally validated amyloidogenic sequence regions, short descriptions of the functional relevance of the proteins and their amyloid state, a list of the experimental techniques applied to study the amyloid state, important structural/functional/variation/mutation data transferred from UniProt, a list of relevant PDB structures categorized according to protein states, database cross-references and literature references. AmyPro greatly improves on similar currently available resources by incorporating both prions and functional amyloids in addition to pathogenic amyloids, and allows users to screen their sequences against the entire collection of validated amyloidogenic sequence fragments. By enabling further elucidation of the sequential determinants of amyloid fibril formation, we hope AmyPro will enhance the development of new methods for the precise prediction of amyloidogenic regions within proteins

Real-time modelling of indoor particulate matter concentration in poultry houses using broiler activity and ventilation rate

Measuring particulate matter concentration in poultry houses remains as a difficult task, primarily because aerosol analysers are expensive, require specialist knowledge to operate and are labour intensive to maintain. However, it is well known that high concentrations of particulate matter causes health and welfare problems with livestock, farm workers and people living in the vicinity of the farm premises. In this work, a data-based mechanistic model is developed to relate broiler activity and ventilation rate with indoor particulate matter concentration. For six complete growing cycles, in a U.K. commercial poultry farm, broiler activity was monitored using a camera-based flock monitoring system (eYeNamic®) and ventilation rate was measured. Indoor particulate matter concentration was continuously monitored by measuring size-segregated mass fraction concentrations with the aerosol analyser DustTrakTM. A discrete-time multi-input single-output time-invariant parameters Transfer Function model was developed to determine the particulate dynamics within each day of the growing cycle in the poultry house using broiler activity and ventilation rate as inputs. This model monitored indoor particulate matter concentration with an average accuracy of RT2=(51±26)%. A dynamic linear regression modelling with time-variant parameters improved average accuracy with RT2=(97.7±1.3)%. It forecasted one sample-ahead the indoor particulate matter concentration level, using a time window of 14 samples, with a mean relative prediction error, MRPE=(4.6±3.2)%. Thus, dynamic modelling with time-variant parameters has the potential to be part of a control system to manage in real-time indoor particulate matter concentration in broiler houses.status: publishe

Orbital Kondo behavior from dynamical structural defects

The interaction between an atom moving in a model double-well potential and the conduction electrons is treated using renormalization group methods in next-to-leading logarithmic order. A large number of excited states is taken into account and the Kondo temperature $T_K$ is computed as a function of barrier parameters. We find that for special parameters $T_K$ can be close to $1 {\rm K}$ and it can be of the same order of magnitude as the renormalized splitting $\Delta$. However, in the perturbative regime we always find that T_K \alt \Delta with a T_K \alt 1 {\rm K} [Aleiner {\em et al.}, Phys. Rev. Lett. {\bf 86}, 2629 (2001)]. We also find that $\Delta$ remains unrenormalized at energies above the Debye frequency, $\omega_{\rm Debye}$.Comment: 9 pages, 9 figures, RevTe

E-MSD: improving data deposition and structure quality

The Macromolecular Structure Database (MSD) () [H. Boutselakis, D. Dimitropoulos, J. Fillon, A. Golovin, K. Henrick, A. Hussain, J. Ionides, M. John, P. A. Keller, E. Krissinel et al. (2003) E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. Nucleic Acids Res., 31, 458–462.] group is one of the three partners in the worldwide Protein DataBank (wwPDB), the consortium entrusted with the collation, maintenance and distribution of the global repository of macromolecular structure data [H. Berman, K. Henrick and H. Nakamura (2003) Announcing the worldwide Protein Data Bank. Nature Struct. Biol., 10, 980.]. Since its inception, the MSD group has worked with partners around the world to improve the quality of PDB data, through a clean up programme that addresses inconsistencies and inaccuracies in the legacy archive. The improvements in data quality in the legacy archive have been achieved largely through the creation of a unified data archive, in the form of a relational database that stores all of the data in the wwPDB. The three partners are working towards improving the tools and methods for the deposition of new data by the community at large. The implementation of the MSD database, together with the parallel development of improved tools and methodologies for data harvesting, validation and archival, has lead to significant improvements in the quality of data that enters the archive. Through this and related projects in the NMR and EM realms the MSD continues to improve the quality of publicly available structural data

Structure of human Fe–S assembly subcomplex reveals unexpected cysteine desulfurase architecture and acyl-ACP–ISD11 interactions

In eukaryotes, sulfur is mobilized for incorporation into multiple biosynthetic pathways by a cysteine desulfurase complex that consists of a catalytic subunit (NFS1), LYR protein (ISD11), and acyl carrier protein (ACP). This NFS1-ISD11-ACP (SDA) complex forms the core of the iron-sulfur (Fe-S) assembly complex and associates with assembly proteins ISCU2, frataxin (FXN), and ferredoxin to synthesize Fe-S clusters. Here we present crystallographic and electron microscopic structures of the SDA complex coupled to enzyme kinetic and cell-based studies to provide structure-function properties of a mitochondrial cysteine desulfurase. Unlike prokaryotic cysteine desulfurases, the SDA structure adopts an unexpected architecture in which a pair of ISD11 subunits form the dimeric core of the SDA complex, which clarifies the critical role of ISD11 in eukaryotic assemblies. The different quaternary structure results in an incompletely formed substrate channel and solvent-exposed pyridoxal 5'-phosphate cofactor and provides a rationale for the allosteric activator function of FXN in eukaryotic systems. The structure also reveals the 4'-phosphopantetheine-conjugated acyl-group of ACP occupies the hydrophobic core of ISD11, explaining the basis of ACP stabilization. The unexpected architecture for the SDA complex provides a framework for understanding interactions with acceptor proteins for sulfur-containing biosynthetic pathways, elucidating mechanistic details of eukaryotic F e-S cluster biosynthesis, and clarifying how defects in Fe-S cluster assembly lead to diseases such as Friedreich's ataxia. Moreover, our results support a lock-and-key model in which LYR proteins associate with acyl-ACP as a mechanism for fatty acid biosynthesis to coordinate the expression, Fe-S cofactor maturation, and activity of the respiratory complexes. Keywords: LYR; ACP; iron-sulfur cluster; PLP; frataxi

Estimation of interdomain flexibility of N-terminus of factor H using residual dipolar couplings

Characterization of segmental flexibility is needed to understand the biological mechanisms of the very large category of functionally diverse proteins, exemplified by the regulators of complement activation, that consist of numerous compact modules or domains linked by short, potentially flexible, sequences of amino acid residues. The use of NMR-derived residual dipolar couplings (RDCs), in magnetically aligned media, to evaluate interdomain motion is established but only for two-domain proteins. We focused on the three N-terminal domains (called CCPs or SCRs) of the important complement regulator, human factor H (i.e. FH1-3). These domains cooperate to facilitate cleavage of the key complement activation-specific protein fragment, C3b, forming iC3b that no longer participates in the complement cascade. We refined a three-dimensional solution structure of recombinant FH1-3 based on nuclear Overhauser effects and RDCs. We then employed a rudimentary series of RDC datasets, collected in media containing magnetically aligned bicelles (disk-like particles formed from phospholipids) under three different conditions, to estimate interdomain motions. This circumvents a requirement of previous approaches for technically difficult collection of five independent RDC datasets. More than 80% of conformers of this predominantly extended three-domain molecule exhibit flexions of < 40 °. Such segmental flexibility (together with the local dynamics of the hypervariable loop within domain 3), could facilitate recognition of C3b via initial anchoring and eventual reorganization of modules to the conformation captured in the previously solved crystal structure of a C3b:FH1-4 complex