Resolving environmental drivers of microbial community structure in Antarctic soils

Antarctic soils are extremely cold, dry, and oligotrophic, yet harbour surprisingly high bacterial diversity. The severity of environmental conditions has constrained the development of multi-trophic communities, and species richness and distribution is thought to be driven primarily by abiotic factors. Sites in northern and southern Victoria Land were sampled for bacterial community structure and soil physicochemical properties in conjunction with the US and New Zealand Latitudinal Gradient Project. Bacterial community structure was determined using a high-resolution molecular fingerprinting method for 80 soil samples from Taylor Valley and Cape Hallett sites which are separated by five degrees of latitude and have distinct soil chemistry. Taylor Valley is part of the McMurdo Dry Valleys, while Cape Hallett is the site of a penguin rookery and contains ornithogenic soils. The influence of soil moisture, pH, conductivity, ammonia, nitrate, total nitrogen and organic carbon on community structure was revealed using Spearman rank correlation, Mantel test, and principal components analysis. High spatial variability was detected in bacterial communities and community structure was correlated with soil moisture and pH. Both unique and shared bacterial community members were detected at Taylor Valley and Cape Hallett despite the considerable distance between the sites

TOPDB: topology data bank of transmembrane proteins

The Topology Data Bank of Transmembrane Proteins (TOPDB) is the most complete and comprehensive collection of transmembrane protein datasets containing experimentally derived topology information currently available. It contains information gathered from the literature and from public databases available on the internet for more than a thousand transmembrane proteins. TOPDB collects details of various experiments that were carried out to learn about the topology of particular transmembrane proteins. In addition to experimental data from the literature, an extensive collection of structural data was also compiled from PDB and from PDBTM. Because topology information is often incomplete, for each protein in the database the most probable topology that is consistent with the collected experimental constraints was also calculated using the HMMTOP transmembrane topology prediction algorithm. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases. The web interface of TOPDB includes tools for searching, relational querying and data browsing as well as for visualization. TOPDB is designed to bridge the gap between the number of transmembrane proteins available in sequence databases and the publicly accessible topology information of experimentally or computationally studied transmembrane proteins. TOPDB is available at http://topdb.enzim.hu

Convex Constraint Decomposition of Circular Dichroism Curves of Proteins

A new algorithm, called convex analysis, has been developed to deduce the chiral contribution of the common secondary structures directly from experimental circular dichroism (CD) curves of a large number of proteins. The analysis is based on CD data reported by Yang et aU Test runs were performed on sets of artificial protein spectra created by the Monte Carlo technique using poly-u-Iysine based component spectra. Application of the decomposition algorithm for the created sets of spectra resulted in component spectra [B (2, i)] and weights [C (i, k)] with excellent Pearson correlation coefficients (r).2 The algori thm, independent of X-ray data, revealed that the CD spectrum of a given protein is composed of at least four independent sources of chirality. Three of the computed component curves show remarkable resemblance to the CD spectra of known protein secondary structures. This approach yields a significant improvement compared to the eigenvector analysis of Hennessey and Johnson." The new method is a useful tool not only in analyzing CD spectra but also in treating other decomposition problems where an additivity constraint is valid

TMFunction: database for functional residues in membrane proteins

We have developed the database TMFunction, which is a collection of more than 2900 experimentally observed functional residues in membrane proteins. Each entry includes the numerical values for the parameters IC50 (measure of the effectiveness of a compound in inhibiting biological function), Vmax (maximal velocity of transport), relative activity of mutants with respect to wild-type protein, binding affinity, dissociation constant, etc., which are important for understanding the sequence–structure–function relationship of membrane proteins. In addition, we have provided information about name and source of the protein, Uniprot and Protein Data Bank codes, mutational and literature information. Furthermore, TMFunction is linked to related databases and other resources. We have set up a web interface with different search and display options so that users have the ability to get the data in several ways. TMFunction is freely available at http://tmbeta-genome.cbrc.jp/TMFunction/

TOPDOM: database of domains and motifs with conservative location in transmembrane proteins

Summary: The TOPDOM database is a collection of domains and sequence motifs located consistently on the same side of the membrane in α-helical transmembrane proteins. The database was created by scanning well-annotated transmembrane protein sequences in the UniProt database by specific domain or motif detecting algorithms. The identified domains or motifs were added to the database if they were uniformly annotated on the same side of the membrane of the various proteins in the UniProt database. The information about the location of the collected domains and motifs can be incorporated into constrained topology prediction algorithms, like HMMTOP, increasing the prediction accuracy

Role of the N-terminal transmembrane domain in the endo-lysosomal targeting and function of the human ABCB6 protein.

ABCB6 is a homodimeric ATP-binding cassette (ABC) transporter present in the plasma membrane and in intracellular organelles. The intracellular localization of ABCB6 has been a matter of debate, as it has been suggested to reside in the mitochondria and the endo-lysosomal system. Using a variety of imaging modalities including confocal and electron microscopy we confirm the endo-lysosomal localization of ABCB6 and show that the protein is internalized from the plasma membrane through endocytosis, to be distributed to multivesicular bodies and lysosomes. In addition to the canonical nucleotide binding (NBD) and transmembrane domains (TMD), ABCB6 contains a unique N-terminal transmembrane domain (TMD0), which does not show sequence homology to known proteins. We investigated the functional role of these domains through the molecular dissection of ABCB6. We find that the folding, dimerization, membrane insertion and ATP binding/hydrolysis of the core ABCB6 complex devoid of TMD0 is preserved. However, in contrast to the full-length transporter, the core ABCB6 construct is retained at the plasma membrane, and does not appear in Rab5-positive endosomes. TMD0 is directly targeted to the lysosomes, without a passage to the plasma membrane. Collectively, our results reveal that TMD0 represents an independently folding unit, which is dispensable for catalysis, but has a crucial role in the lysosomal targeting of ABCB6