1,555 research outputs found
Recent improvements to the PROSITE database
The PROSITE database consists of a large collection of biologically meaningful signatures that are described as patterns or profiles. Each signature is linked to documentation that provides useful biological information on the protein family, domain or functional site identified by the signature. The PROSITE web page has been redesigned and several tools have been implemented to help the user discover new conserved regions in their own proteins and to visualize domain arrangements. We also introduced the facility to search PDB with a PROSITE entry or a user's pattern and visualize matched positions on 3D structures. The latest version of PROSITE (release 18.17 of November 30, 2003) contains 1676 entries. The database is accessible at http://www.expasy.org/prosit
Molecular mechanisms of the non-coenzyme action of thiamin in brain. Biochemical, structural and pathway analysis
Thiamin (vitamin B1) is a pharmacological agent boosting central metabolism through the action of the coenzyme thiamin diphosphate (ThDP). However, positive effects, including improved cognition,
of high thiamin doses in neurodegeneration may be observed without increased ThDP or ThDPdependent enzymes in brain. Here, we determine protein partners and metabolic pathways where
thiamin acts beyond its coenzyme role. Malate dehydrogenase, glutamate dehydrogenase and pyridoxal kinase were identified as abundant proteins binding to thiamin- or thiazolium-modified
sorbents. Kinetic studies, supported by structural analysis, revealed allosteric regulation of these proteins by thiamin and/or its derivatives. Thiamin triphosphate and adenylated thiamin triphosphate
activate glutamate dehydrogenase. Thiamin and ThDP regulate malate dehydrogenase isoforms and pyridoxal kinase. Thiamin regulation of enzymes related to malate-aspartate shuttle may impact
on malate/citrate exchange, responsible for exporting acetyl residues from mitochondria. Indeed, bioinformatic analyses found an association between thiamin- and thiazolium-binding proteins
and the term acetylation. Our interdisciplinary study shows that thiamin is not only a coenzyme for acetyl-CoA production, but also an allosteric regulator of acetyl-CoA metabolism including
regulatory acetylation of proteins and acetylcholine biosynthesis. Moreover, thiamin action in neurodegeneration may also involve neurodegeneration-related 14-3-3, DJ-1 and β-amyloid precursor
proteins identified among the thiamin- and/or thiazolium-binding proteins
A Molecular Biology Database Digest
Computational Biology or Bioinformatics has been defined as the application of mathematical
and Computer Science methods to solving problems in Molecular Biology that require large scale
data, computation, and analysis [18]. As expected, Molecular Biology databases play an essential
role in Computational Biology research and development. This paper introduces into current
Molecular Biology databases, stressing data modeling, data acquisition, data retrieval, and the
integration of Molecular Biology data from different sources. This paper is primarily intended
for an audience of computer scientists with a limited background in Biology
Lipoproteins of Mycobacterium tuberculosis : an abundant and functionally diverse class of cell envelope components
Mycobacterium tuberculosis remains the predominant bacterial scourge of mankind. Understanding of its biology and pathogenicity has been greatly advanced by the determination of whole genome sequences for this organism. Bacterial lipoproteins are a functionally diverse class of membrane-anchored proteins. The signal peptides of these proteins direct their export and post-translational lipid modification. These signal peptides are amenable to bioinformatic analysis, allowing the lipoproteins encoded in whole genomes to be catalogued. This review applies bioinformatic methods to the identification and functional characterisation of the lipoproteins encoded in the M. tuberculosis genomes. Ninety nine putative lipoproteins were identified and so this family of proteins represents ca. 2.5% of the M. tuberculosis predicted proteome. Thus, lipoproteins represent an important class of cell envelope proteins that may contribute to the virulence of this major pathogen
Tomato EF-Tsmt, a functional mitochondrial translation elongation factor from higher plants
Ethylene-induced ripening in tomato (Lycopersicon esculentum) resulted in the accumulation of a transcript
designated LeEF-Tsmt that encodes a protein with significant homology to bacterial Ts translational elongation
factor (EF-Ts). Transient expression in tobacco and sunflower protoplasts of full-length and truncated LeEF-Tsmt-
GFP fusion constructs and confocal microscopy observations clearly demonstrated the targeting of LeEF-Tsmt
to mitochondria and not to chloroplasts and the requirement for a signal peptide for the proper sorting of the
protein. Escherichia coli recombinant LeEF-Tsmt co-eluted from Ni-NTA resins with a protein corresponding to
the molecular weight of the elongation factor EF-Tu of E. coli, indicating an interaction with bacterial EF-Tu.
Increasing the GDP concentration in the extraction buffer reduced the amount of EF-Tu in the purified LeEF-Tsmt
fraction. The purified LeEF-Tsmt stimulated the poly(U)-directed polymerization of phenylalanine 10-fold in the
presence of EF-Tu. Furthermore, LeEF-Tsmt was capable of catalysing the nucleotide exchange reaction with E.
coli EF-Tu. Altogether, these data demonstrate that LeEF-Tsmt encodes a functional mitochondrial EF-Ts. LeEFTsmt
represents the first mitochondrial elongation factor to be isolated and functionally characterized in higher
plants
A structural study for the optimisation of functional motifs encoded in protein sequences
BACKGROUND: A large number of PROSITE patterns select false positives and/or miss known true positives. It is possible that – at least in some cases – the weak specificity and/or sensitivity of a pattern is due to the fact that one, or maybe more, functional and/or structural key residues are not represented in the pattern. Multiple sequence alignments are commonly used to build functional sequence patterns. If residues structurally conserved in proteins sharing a function cannot be aligned in a multiple sequence alignment, they are likely to be missed in a standard pattern construction procedure. RESULTS: Here we present a new procedure aimed at improving the sensitivity and/ or specificity of poorly-performing patterns. The procedure can be summarised as follows: 1. residues structurally conserved in different proteins, that are true positives for a pattern, are identified by means of a computational technique and by visual inspection. 2. the sequence positions of the structurally conserved residues falling outside the pattern are used to build extended sequence patterns. 3. the extended patterns are optimised on the SWISS-PROT database for their sensitivity and specificity. The method was applied to eight PROSITE patterns. Whenever structurally conserved residues are found in the surface region close to the pattern (seven out of eight cases), the addition of information inferred from structural analysis is shown to improve pattern selectivity and in some cases selectivity and sensitivity as well. In some of the cases considered the procedure allowed the identification of functionally interesting residues, whose biological role is also discussed. CONCLUSION: Our method can be applied to any type of functional motif or pattern (not only PROSITE ones) which is not able to select all and only the true positive hits and for which at least two true positive structures are available. The computational technique for the identification of structurally conserved residues is already available on request and will be soon accessible on our web server. The procedure is intended for the use of pattern database curators and of scientists interested in a specific protein family for which no specific or selective patterns are yet available
"Multiple Sequence Alignment Using External Sources Of Information"
Multiple sequence alignment is an alignment of three or more protein
or nucleic acid sequences. The alignment area has always been of much
interest for researchers, this is due to that fact that many scientifi c researchs
depend in their workflow on sequence alignments. Thus, having an alignment
of high quality is of high importance. Much work has been done and is
still carried in this field to help improving the quality of alignments. Many
approaches have been developed so far for performing pairwise and multiple
sequence alignments, yet, most of those approaches rely basically on the
sequences to be aligned as their only input. Recently, some approaches began
to incorporate additional sources of information in the alignment process, the
sources of external data can come from user knowledge or online databases.
This data, when integrated in the workflow of the alignment programs, may
add new constraints to the produced alignment and improve its quality
by making it biologically more meaningful. In this thesis, I will introduce
new approaches for multiple sequence alignment which use the alignment
software DIALIGN along with external information from databases, where
useful information is extracted and then integrated in the alignment process.
By testing those approaches on benchmark databases, I will show that
using additional data during alignment produced better results than using
DIALIGN alone without any external input other than the sequences to be
aligned
- …