Biomedical subjects

Merridee A Wouters

Publications and source records attributed to Merridee A Wouters.

9 recordsLinked to original sources

PubMed2006

Mechanism of allosteric regulation of transglutaminase 2 by GTP.

Allosteric regulation is a fundamental mechanism of biological control. Here, we investigated the allosteric mechanism by which GTP inhibits cross-linking activity of transglutaminase 2 (TG2), a multifunctional protein, with postulated roles in receptor signaling, extracellular matrix assembly, and apoptosis. Our findings indicate that at least two components are involved in functionally coupling the allosteric site and active center of TG2, namely (i) GTP binding to mask a conformationally destabilizing switch residue, Arg-579, and to facilitate interdomain interactions that promote adoption of a compact, catalytically inactive conformation and (ii) stabilization of the inactive conformation by an uncommon H bond between a cysteine (Cys-277, an active center residue) and a tyrosine (Tyr-516, a residue located on a loop of the beta-barrel 1 domain that harbors the GTP-binding site). Although not essential for GTP-mediated inhibition of cross-linking, this H bond enhances the rate of formation of the inactive conformer.

Allosteric Regulation↗

PubMed2006

Analysis of protein sequence and interaction data for candidate disease gene prediction.

Linkage analysis is a successful procedure to associate diseases with specific genomic regions. These regions are often large, containing hundreds of genes, which make experimental methods employed to identify the disease gene arduous and expensive. We present two methods to prioritize candidates for further experimental study: Common Pathway Scanning (CPS) and Common Module Profiling (CMP). CPS is based on the assumption that common phenotypes are associated with dysfunction in proteins that participate in the same complex or pathway. CPS applies network data derived from protein-protein interaction (PPI) and pathway databases to identify relationships between genes. CMP identifies likely candidates using a domain-dependent sequence similarity approach, based on the hypothesis that disruption of genes of similar function will lead to the same phenotype. Both algorithms use two forms of input data: known disease genes or multiple disease loci. When using known disease genes as input, our combined methods have a sensitivity of 0.52 and a specificity of 0.97 and reduce the candidate list by 13-fold. Using multiple loci, our methods successfully identify disease genes for all benchmark diseases with a sensitivity of 0.84 and a specificity of 0.63. Our combined approach prioritizes good candidates and will accelerate the disease gene discovery process.

Algorithms↗

PubMed2006

High torsional energy disulfides: relationship between cross-strand disulfides and right-handed staples.

Redox-active disulfides are capable of being oxidized and reduced under physiological conditions. The enzymatic role of redox-active disulfides in thiol-disulfide reductases is well-known, but redox-active disulfides are also present in non-enzymatic protein structures where they may act as switches of protein function. Here, we examine disulfides linking adjacent beta-strands (cross-strand disulfides), which have been reported to be redox-active. Our previous work has established that these cross-strand disulfides have high torsional energies, a quantity likely to be related to the ease with which the disulfide is reduced. We examine the relationship between conformations of disulfides and their location in protein secondary structures. By identifying the overlap between cross-strand disulfides and various conformations, we wish to address whether the high torsional energy of a cross-strand disulfide is sufficient to confer redox activity or whether other factors, such as the presence of the cross-strand disulfide in a strained beta-sheet, are required.

Computational Biology↗

PubMed2005

Comparison of sequence and structure-based datasets for nonredundant structural data mining.

Structural data mining studies attempt to deduce general principles of protein structure from solved structures deposited in the protein data bank (PDB). The entire database is unsuitable for such studies because it is not representative of the ensemble of protein folds. Given that novel folds continue to be unearthed, some folds are currently unrepresented in the PDB while other folds are overrepresented. Overrepresentation can easily be avoided by filtering the dataset. PDB_SELECT is a well-used representative subset of the PDB that has been deduced by sequence comparison. Specifically, structures with sequences that exhibit a pairwise sequence identity above a threshold value are weeded from the dataset. Although length criteria for pairwise alignments have a structural basis, this automated method of pruning is essentially sequence-based and runs into problems in the twilight zone, possibly resulting in some folds being overrepresented. The value-added structure databases SCOP and CATH are also a potential source of a nonredundant dataset. Here we compare the sequence-derived dataset PDB_SELECT with the structural databases SCOP (Structural Classification Of Proteins) and CATH (Class-Architecture-Topology-Homology). We show that some folds remain overrepresented in the PDB_SELECT dataset while other folds are not represented at all. However, SCOP and CATH also have their own problems such as the labor-intensiveness of the update process and the problem of determining whether all folds are equally or sufficiently distant. We discuss areas where further work is required.

Amino Acid Sequence↗

PubMed2005

Evolution of distinct EGF domains with specific functions.

EGF domains are extracellular protein modules cross-linked by three intradomain disulfides. Past studies suggest the existence of two types of EGF domain with three-disulfides, human EGF-like (hEGF) domains and complement C1r-like (cEGF) domains, but to date no functional information has been related to the two different types, and they are not differentiated in sequence or structure databases. We have developed new sequence patterns based on the different C-termini to search specifically for the two types of EGF domains in sequence databases. The exhibited sensitivity and specificity of the new pattern-based method represents a significant advancement over the currently available sequence detection techniques. We re-annotated EGF sequences in the latest release of Swiss-Prot looking for functional relationships that might correlate with EGF type. We show that important post-translational modifications of three-disulfide EGFs, including unusual forms of glycosylation and post-translational proteolytic processing, are dependent on EGF subtype. For example, EGF domains that are shed from the cell surface and mediate intercellular signaling are all hEGFs, as are all human EGF receptor family ligands. Additional experimental data suggest that functional specialization has accompanied subtype divergence. Based on our structural analysis of EGF domains with three-disulfide bonds and comparison to laminin and integrin-like EGF domains with an additional inter-domain disulfide, we propose that these hEGF and cEGF domains may have arisen from a four-disulfide ancestor by selective loss of different cysteine residues.

Amino Acid Sequence↗

PubMed2004

Mutated MESP2 causes spondylocostal dysostosis in humans.

Spondylocostal dysostosis (SCD) is a term given to a heterogeneous group of disorders characterized by abnormal vertebral segmentation (AVS). We have previously identified mutations in the Delta-like 3 (DLL3) gene as a major cause of autosomal recessive spondylocostal dysostosis. DLL3 encodes a ligand for the Notch receptor and, when mutated, defective somitogenesis occurs resulting in a consistent and distinctive pattern of AVS affecting the entire spine. From our study cohort of cases of AVS, we have identified individuals and families with abnormal segmentation of the entire spine but no mutations in DLL3, and, in some of these, linkage to the DLL3 locus at 19q13.1 has been excluded. Within this group, the radiological phenotype differs mildly from that of DLL3 mutation-positive SCD and is variable, suggesting further heterogeneity. Using a genomewide scanning strategy in one consanguineous family with two affected children, we demonstrated linkage to 15q21.3-15q26.1 and furthermore identified a 4-bp duplication mutation in the human MESP2 gene that codes for a basic helix-loop-helix transcription factor. No MESP2 mutations were found in a further 7 patients with related radiological phenotypes in whom abnormal segmentation affected all vertebrae, nor in a further 12 patients with diverse phenotypes.

Basic Helix-Loop-Helix Proteins↗

PubMed2004

Cross-strand disulphides in cell entry proteins: poised to act.

Cross-strand disulphides (CSDs) are unusual bonds that link adjacent strands in the same beta-sheet. Their peculiarity relates to the high potential energy stored in these bonds, both as torsional energy in the highly strained disulphide linkage and as deformation energy stored in the sheet itself. CSDs are relatively rare in protein structures but are conspicuous by their presence in proteins that are involved in cell entry. The finding that entry of botulinum neurotoxin and HIV into mammalian cells involves cleavage of CSDs suggests that the activity of other cell entry proteins may likewise involve cleavage of these bonds. We examine emerging evidence of the involvement of these unusual disulphides in cell entry events.

Bacterial Proteins↗

PubMed2003

Evolutionary specialization of a tryptophan indole group for transition-state stabilization by eukaryotic transglutaminases.

Covalent posttranslational protein modifications by eukaryotic transglutaminases proceed by a kinetic pathway of acylation and deacylation. Ammonia is released as the acylenzyme is formed, whereas the cross-linked product is released later in the deacylation step. Superposition of the active sites of transglutaminase type 2 (TG2) and the structurally related cysteine protease, papain, indicates that in the formation of tetrahedral intermediates, the backbone nitrogen of the catalytic Cys-277 and the N1 nitrogen of Trp-241 of TG2 could contribute to transition-state stabilization. The importance of this Trp-241 side chain was demonstrated by examining the kinetics of dansylcadaverine incorporation into a model peptide. Although substitution of the Trp-241 side chain with Ala or Gly had only a small effect on the Michaelis constant Km (1.5-fold increase), it caused a >300-fold lowering of the catalytic rate constant kcat. The wild-type and mutant TG2-catalyzed release of ammonia showed kinetics similar to the kinetics for the formation of cross-linked product, indicating that transition-state stabilization in the acylation step was rate-limiting. In papain, a Gln residue is at the position of TG2-Trp-241. The conservation of Trp-241 in all eukaryotic transglutaminases and the finding that W241Q-TG2 had a much lower kcat than wild-type enzyme suggest evolutionary specialization in the use of the indole group. This notion is further supported by the observation that transition-state-stabilizing side chains of Tyr and His that operate in some serine and metalloproteases only partially substituted for Trp.

Acylation↗

PubMed2003

A despecialization step underlying evolution of a family of serine proteases.

In the trypsin superfamily of serine proteases, non-trypsin-like primary specificities have arisen in only two monophyletic descendent subbranches. We have recreated an ancestor to one of these subbranches (granzyme) using phylogenetic inference, gene synthesis, and protein expression. This ancestor has two unusual properties. First, it has broad primary specificity encompassing the entire repertoire of novel primary specificities found in its descendents. Second, unlike extant members that have narrow primary specificities, the ancestor exhibits tolerance to mutational changes in primary specificity-conferring residues-that is, structural plasticity. Molecular modeling and mutagenesis studies indicate that these unusual properties are due to a particularly wide substrate binding pocket. These two crucial properties of the ancestor not only distinguish it from its extant descendents but also from the trypsin-like proteases that preceded it. This indicates that a despecialization step, characterized by broad specificity and structural plasticity, underlies evolution of new primary specificities in this protease superfamily.

Amino Acid Sequence↗