Biomedical subjects

Christian Zwieb

Publications and source records attributed to Christian Zwieb.

5 recordsLinked to original sources

PubMed2003

tmRDB (tmRNA database).

Maintained at the University of Texas Health Science Center at Tyler, Texas, the tmRNA database (tmRDB) is accessible at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html with mirror sites located at Auburn University, Auburn, Alabama (http://www.ag.auburn.edu/mirror/tmRDB/) and the Bioinformatics Research Center, Aarhus, Denmark (http://www.bioinf.au.dk/tmRDB/). The tmRDB collects and distributes information relevant to the study of tmRNA. In trans-translation, this molecule combines properties of tRNA and mRNA and binds several proteins to form the tmRNP. Related RNPs are likely to be functional in all bacteria. In this release of tmRDB, 186 new entries from 10 bacterial groups for a total of 274 tmRNA sequences have been added. Lists of the tmRNAs and the corresponding tmRNA-encoded tag-peptides are presented in alphabetical and phylogenetic order. The tmRNA sequences are aligned manually, assisted by computational tools, to determine base pairs supported by comparative sequence analysis. The tmRNA alignment, available in a variety of formats, provides the basis for the secondary and tertiary structure of each tmRNA molecule. Three-dimensional models of the tmRNAs and their associated proteins in PDB format give evidence for the recent progress that has been made in the understanding of tmRNP structure and function.

Bacteria↗

PubMed2003

SRPDB: Signal Recognition Particle Database.

The Signal Recognition Particle Database (SRPDB) at http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html and http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html assists in the better understanding of the structure and function of the signal recognition particle (SRP), a ribonucleoprotein complex that recognizes signal sequences as they emerge from the ribosome. SRPDB provides alphabetically and phylogenetically ordered lists of SRP RNA and SRP protein sequences. The SRP RNA alignment emphasizes base pairs supported by comparative sequence analysis to derive accurate SRP RNA secondary structures for each species. This release includes a total of 181 SRP RNA sequences, 7 protein SRP9, 11 SRP14, 31 SRP19, 113 SRP54 (Ffh), 9 SRP68 and 12 SRP72 sequences. There are 44 new sequences of the SRP receptor alpha subunit and its FtsY homolog (a total of 99 entries). Additional data are provided for polypeptides with established or potential roles in SRP-mediated protein targeting, such as the beta subunit of SRP receptor, Flhf, Hbsu and cpSRP43. Also available are motifs for the identification of new SRP RNA sequences, 2D representations, three-dimensional models in PDB format, and links to the high-resolution structures of several SRP components. New to this version of SRPDB is the introduction of a relational database system and a SRP RNA prediction server (SRP-Scan) which allows the identification of SRP RNAs within genome sequences and also generates secondary structure diagrams.

Amino Acid Sequence↗

PubMed2002

Reconstitution of the signal recognition particle of the halophilic archaeon Haloferax volcanii.

The signal recognition particle (SRP) is a ribonucleoprotein complex involved in the recognition and targeting of nascent extracytoplasmic proteins in all three domains of life. In Archaea, SRP contains 7S RNA like its eukaryal counterpart, yet only includes two of the six protein subunits found in the eukaryal complex. To further our understanding of the archaeal SRP, 7S RNA, SRP19 and SRP54 of the halophilic archaeon Haloferax volcanii have been expressed and purified, and used to reconstitute the ternary SRP complex. The availability of SRP components from a haloarchaeon offers insight into the structure, assembly and function of this ribonucleoprotein complex at saturating salt conditions. While the amino acid sequences of H.volcanii SRP19 and SRP54 are modified presumably as an adaptation to their saline surroundings, the interactions between these halophilic SRP components and SRP RNA appear conserved, with the possibility of a few exceptions. Indeed, the H.volcanii SRP can assemble in the absence of high salt. As reported with other archaeal SRPs, the limited binding of H.volcanii SRP54 to SRP RNA is enhanced in the presence of SRP19. Finally, immunolocalization reveals that H.volcanii SRP54 is found in the cytosolic fraction, where it is associated with the ribosomal fraction of the cell.

Amino Acid Sequence↗

PubMed2002

Systematic site-directed mutagenesis of human protein SRP54: interactions with signal recognition particle RNA and modes of signal peptide recognition.

The amino acid residues of human protein SRP54 which are required for binding to SRP RNA were identified by generating 40 nonoverlapping tri-alanine alterations within its methionine-rich M-domain (SRP54M). The mutant polypeptides were expressed in Escherichia coli, and their ability to bind to human and Methanococcus jannaschii SRP RNA were determined in vitro. Residues at positions 379-387, 394-396, 400-405, and 409-411 of human SRP54 were within the predicted RNA binding site, and their alteration abolished the binding activities of the mutant polypeptides as expected. Changes at positions 418-423 had intermediate effects. Polypeptides containing mutations of 328-TLR-330 were inactive although these residues were far away from the presumed RNA binding site in the crystal structure of the free protein. Using the structures of the E. coli Ffh/4.5S core and of the human SRP54m dimer as templates, a molecular model of the complex between human SRP RNA helix 8 and a single SRP54M molecule was constructed in which Leucine 329 was positioned in closer proximity to the RNA binding domain. This representation was supported by studies of the SRP54m monomer/dimer ratio using gel filtration. The results were consistent with a change in the shape of the signal peptide binding groove upon binding of SRP54 to SRP RNA. We propose that the SRP RNA and a small region centered at a bulky nonpolar amino acid residue at position 329 of protein SRP54 play a critical role in the SRP-dependent binding and release of signal peptides.

Amino Acid Sequence↗

PubMed2002

Solution structure of protein SRP19 of Archaeoglobus fulgidus signal recognition particle.

Protein SRP19 is an essential RNA-binding component of the signal recognition particle (SRP) in Archaea and Eucarya. A three-dimensional solution structure of the 104 residue SRP19 from the hyperthermophilic archaeon Archaeoglobus fulgidus, designated as Af19, was determined by NMR spectroscopy. Af19 contains three beta-strands, two alpha-helical regions, arranged in a betaalphabetabetaalpha topology, a 3(10) helix, and a disordered C-terminal tail. This fold is similar to the betaalphabetabetaalphabeta RNP motif present in numerous other RNA-binding proteins, which engage their cognate RNAs using conserved sequence motifs present within beta-strands 1 and 3. Mutagenesis studies of human SRP19, however, reveal the major contact sites with SRP RNA reside within loops 1, 3, and 4. These contacts were verified by the crystal structure of human SRP19 complexed to SRP RNA helix 6 reported subsequent to the submission of the manuscript. The crystal structure also reveals that, unlike canonical RNP motifs, SRP19 does not engage specific RNA bases through conserved sequence motifs present within beta-strands 1 and 3. Instead, SRP19 uses residues both within and flanking beta-strand 1 to stabilize the complex through direct and indirect contacts to the phosphate backbone of the tetraloop, leaving the bases of the tetraloop exposed. This, coupled with the fact that SRP19 appears relatively rigid and undergoes only minor changes in structure upon RNA binding, may underlie the molecular basis by which SRP19 functions to initiate SRP assembly.

Amino Acid Sequence↗