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Mathew E Sowa

Publications and source records attributed to Mathew E Sowa.

10 recordsLinked to original sources
PubMed2006

From loops to chains: unraveling the mysteries of polyubiquitin chain specificity and processivity.

Regulated protein degradation via polyubiquitination controls almost every aspect of eukaryotic cellular biology; however, the precise mechanism by which specifically linked polyubiquitin chains are formed on target proteins as well as how the processivity of chain elongation is achieved remains a mystery. Recent work using the yeast ubiquitin ligase SCF(Cdc4) and the ubiquitin conjugating enzyme, Cdc34, has helped to answer these questions by identifying the determinants of lysine-48 specific ubiquitin chain polymerization.

Models, Molecular↗
PubMed2004

Computational and biochemical identification of a nuclear pore complex binding site on the nuclear transport carrier NTF2.

Nuclear transport carriers interact with proteins of the nuclear pore complex (NPC) to transport their cargo across the nuclear envelope. One such carrier is nuclear transport factor 2 (NTF2), whose import cargo is the small GTPase Ran. A domain highly homologous to the small NTF2 protein (14kDa) is also found in a number of additional proteins, which together make up the NTF2 domain containing superfamily of proteins. Using structural, computational and biochemical analysis we have identified a functional site that is present throughout this superfamily, and our results indicate that this site functions as an NPC binding site in NTF2. Previously we showed that a D23A mutant of NTF2 exhibits increased affinity for the NPC. The mechanism of this mutation, however, was unknown as this region of NTF2 had not been implicated in binding to NPC proteins. Here we show that the D23A mutation in NTF2 does not result in gross structural changes affecting other known NPC binding sites. Instead, the D23 residue is located in an evolutionarily important region in the NTF2 domain containing superfamily, that in NTF2, is involved in binding to the NPC.

Active Transport, Cell Nucleus↗
PubMed2003

The structure of ClpB: a molecular chaperone that rescues proteins from an aggregated state.

Molecular chaperones assist protein folding by facilitating their "forward" folding and preventing aggregation. However, once aggregates have formed, these chaperones cannot facilitate protein disaggregation. Bacterial ClpB and its eukaryotic homolog Hsp104 are essential proteins of the heat-shock response, which have the remarkable capacity to rescue stress-damaged proteins from an aggregated state. We have determined the structure of Thermus thermophilus ClpB (TClpB) using a combination of X-ray crystallography and cryo-electron microscopy (cryo-EM). Our single-particle reconstruction shows that TClpB forms a two-tiered hexameric ring. The ClpB/Hsp104-linker consists of an 85 A long and mobile coiled coil that is located on the outside of the hexamer. Our mutagenesis and biochemical data show that both the relative position and motion of this coiled coil are critical for chaperone function. Taken together, we propose a mechanism by which an ATP-driven conformational change is coupled to a large coiled-coil motion, which is indispensable for protein disaggregation.

Adenosine Triphosphate↗
PubMed2003

An accurate, sensitive, and scalable method to identify functional sites in protein structures.

Functional sites determine the activity and interactions of proteins and as such constitute the targets of most drugs. However, the exponential growth of sequence and structure data far exceeds the ability of experimental techniques to identify their locations and key amino acids. To fill this gap we developed a computational Evolutionary Trace method that ranks the evolutionary importance of amino acids in protein sequences. Studies show that the best-ranked residues form fewer and larger structural clusters than expected by chance and overlap with functional sites, but until now the significance of this overlap has remained qualitative. Here, we use 86 diverse protein structures, including 20 determined by the structural genomics initiative, to show that this overlap is a recurrent and statistically significant feature. An automated ET correctly identifies seven of ten functional sites by the least favorable statistical measure, and nine of ten by the most favorable one. These results quantitatively demonstrate that a large fraction of functional sites in the proteome may be accurately identified from sequence and structure. This should help focus structure-function studies, rational drug design, protein engineering, and functional annotation to the relevant regions of a protein.

Amino Acid Motifs↗
PubMed2003

Acceleration of key reactions as a strategy to elucidate the rate-limiting chemistry underlying phototransduction inactivation.

PURPOSE: A reconstituted system was used to establish a strategy to determine the rate-limiting chemistry responsible for recovery of the dim-flash response in rod photoreceptors. METHODS: A general approach for identifying the rate-limiting step in a series of reactions is to evaluate the consequences of accelerating each step separately, while monitoring the rate of formation of the end product of the series. This strategy was applied to the reactions involved in quenching phototransduction in bovine rod outer segment (bROS) homogenates. The decay of photoactivated rhodopsin (R*) and inactivation of transducin by guanosine triphosphate (GTP) hydrolysis are the leading candidates for limiting the rate of phototransduction turn-off. These reactions were accelerated separately and together by adding hydroxylamine and/or the regulator of G-protein signaling-9 catalytic domain (RGS9d) while monitoring phosphodiesterase (PDE) activity triggered by a pulse of light in bROS homogenates. RESULTS: PDE activity in bROS homogenates triggered by a flash of light returned to its dark value with a rate constant of 0.087 +/- 0.002 seconds in this system. The rate of PDE recovery increased to 0.11 +/- 0.004 seconds when R* decay was accelerated with 10 to 50 mM hydroxylamine, suggesting that R* inactivation limits the rate of phototransduction turn-off under these conditions. Adding both hydroxylamine and RGS9d, a factor that accelerates transducin inactivation, increased the rate of PDE decay even further. RGS9d had no effect on PDE recovery kinetics unless quenching of R* was also accelerated. CONCLUSIONS: Under in vitro conditions in bROS homogenates, the quenching of R* normally limits the rate of phototransduction shut-off. If R* decay is accelerated, inactivation of transducin by GTP hydrolysis becomes rate limiting. This study offers a general approach that could be used to investigate the rate-limiting chemistry of phototransduction turn-off in vivo.

3',5'-Cyclic-GMP Phosphodiesterases↗
PubMed2002

Structural clusters of evolutionary trace residues are statistically significant and common in proteins.

Given the massive increase in the number of new sequences and structures, a critical problem is how to integrate these raw data into meaningful biological information. One approach, the Evolutionary Trace, or ET, uses phylogenetic information to rank the residues in a protein sequence by evolutionary importance and then maps those ranked at the top onto a representative structure. If these residues form structural clusters, they can identify functional surfaces such as those involved in molecular recognition. Now that a number of examples have shown that ET can identify binding sites and focus mutational studies on their relevant functional determinants, we ask whether the method can be improved so as to be applicable on a large scale. To address this question, we introduce a new treatment of gaps resulting from insertions and deletions, which streamlines the selection of sequences used as input. We also introduce objective statistics to assess the significance of the total number of clusters and of the size of the largest one. As a result of the novel treatment of gaps, ET performance improves measurably. We find evolutionarily privileged clusters that are significant at the 5% level in 45 out of 46 (98%) proteins drawn from a variety of structural classes and biological functions. In 37 of the 38 proteins for which a protein-ligand complex is available, the dominant cluster contacts the ligand. We conclude that spatial clustering of evolutionarily important residues is a general phenomenon, consistent with the cooperative nature of residues that determine structure and function. In practice, these results suggest that ET can be applied on a large scale to identify functional sites in a significant fraction of the structures in the protein databank (PDB). This approach to combining raw sequences and structure to obtain detailed insights into the molecular basis of function should prove valuable in the context of the Structural Genomics Initiative.

Binding Sites↗
PubMed2002

Evolutionary predictions of binding surfaces and interactions.

Rapid progress in structural biology and whole-genome sequencing technology means that, for many protein families, structural and evolutionary information are readily available. Recent developments demonstrate how this information can be integrated to identify canonical determinants of protein structure and function. Among these determinants, those residues that are on protein surfaces are especially likely to form binding sites and are the logical choice for further mutational analysis and drug targeting.

Binding Sites↗
PubMed2002

Characterization of retinal guanylate cyclase-activating protein 3 (GCAP3) from zebrafish to man.

Calmodulin-like neuronal Ca2+-binding proteins (NCBPs) are expressed primarily in neurons and contain a combination of four functional and nonfunctional EF-hand Ca2+-binding motifs. The guanylate cyclase-activating proteins 1-3 (GCAP1-3), the best characterized subgroup of NCBPs, function in the regulation of transmembrane guanylate cyclases 1-2 (GC1-2). The pairing of GCAPs and GCs in vivo depends on cell expression. Therefore, we investigated the expression of these genes in retina using in situ hybridization and immunocytochemistry. Our results demonstrate that GCAP1, GCAP2, GC1 and GC2 are expressed in human rod and cone photoreceptors, while GCAP3 is expressed exclusively in cones. As a consequence of extensive modification, the GCAP3 gene is not expressed in mouse retina. However, this lack of evolutionary conservation appears to be restricted to only some species as we cloned all three GCAPs from teleost (zebrafish) retina and localized them to rod cells, short single cones (GCAP1-2), and all subtypes of cones (GCAP3). Furthermore, sequence comparisons and evolutionary trace analysis coupled with functional testing of the different GCAPs allowed us to identify the key conserved residues that are critical for GCAP structure and function, and to define class-specific residues for the NCBP subfamilies.

Animals↗
PubMedDate not supplied

The ClpB/Hsp104 molecular chaperone-a protein disaggregating machine.

ClpB and Hsp104 (ClpB/Hsp104) are essential proteins of the heat-shock response and belong to the class 1 family of Clp/Hsp100 AAA+ ATPases. Members of this family form large ring structures and contain two AAA+ modules, which consist of a RecA-like nucleotide-binding domain (NBD) and an alpha-helical domain. Furthermore, ClpB/Hsp104 has a longer middle region, the ClpB/Hsp104-linker, which is essential for chaperone activity. Unlike other Clp/Hsp100 proteins, however, ClpB/Hsp104 neither associates with a cellular protease nor directs the degradation of its substrate proteins. Rather, ClpB/Hsp104 is a bona fide molecular chaperone, which has the remarkable ability to rescue proteins from an aggregated state. The full recovery of these proteins requires the assistance of the cognate DnaK/Hsp70 chaperone system. The mechanism of this "bi-chaperone" network, however, remains elusive. Here we review the current understanding of the structure-function relationship of the ClpB/Hsp104 molecular chaperone and its role in protein disaggregation.

Heat-Shock Proteins↗