Biomedical subjects

K O Wrzeszczynski

Publications and source records attributed to K O Wrzeszczynski.

3 recordsLinked to original sources

PubMed2004

Annotating proteins from endoplasmic reticulum and Golgi apparatus in eukaryotic proteomes.

The sub-cellular localization of a native protein constitutes one coarse-grained aspect of its function. Transport between compartments is often regulated through short sequence motifs. Here, we analyzed experimentally characterized endoplasmic reticulum (ER)/ Golgi retrieval motifs and investigated the accuracy of homology-transfer. Only the C-terminal ER retrieval motifs KDEL, HDEL and AIAKE were sufficiently specific. However, even unspecific motifs may help, provided we know the probability for localization given the motif. We provided such estimates. We also rigorously estimated the accuracy and coverage for inferring ER and Golgi localization through homology-transfer by sequence similarity. In entire proteomes, we could thereby annotate 3304 ER (3182 membrane) and 1853 Golgi (759 membrane) proteins. We identified another putative 5157 globular and 3941 membrane ER or Golgi proteins. Each experimental annotation yielded, on average, one to three high-accuracy and five to six low-accuracy homology-transfers in the six proteomes. These numbers will increase with each new experimental annotation.

Amino Acid Motifs↗

PubMed2003

Automatic prediction of protein function.

Most methods annotating protein function utilise sequence homology to proteins of experimentally known function. Such a homology-based annotation transfer is problematic and limited in scope. Therefore, computational biologists have begun to develop ab initio methods that predict aspects of function, including subcellular localization, post-translational modifications, functional type and protein-protein interactions. For the first two cases, the most accurate approaches rely on identifying short signalling motifs, while the most general methods utilise tools of artificial intelligence. An outstanding new method predicts classes of cellular function directly from sequence. Similarly, promising methods have been developed predicting protein-protein interaction partners at acceptable levels of accuracy for some pairs in entire proteomes. No matter how difficult the task, successes over the last few years have clearly paved the way for ab initio prediction of protein function.

Computational Biology↗

PubMed1994

Activation of bovine liver glutamate dehydrogenase by covalent reaction of adenosine 5'-O-[S-(4-bromo-2,3-dioxobutyl)thiophosphate] with arginine-459 at an ADP regulatory site.

Bovine liver glutamate dehydrogenase is an allosteric enzyme which is activated by ADP. The affinity label adenosine 5'-O-[S-(4-bromo-2,3-dioxobutyl)thiophosphate] (AMPSBDB), a new ADP analog featuring a reactive group at a position equivalent to that of the pyrophosphate, reacts with this glutamate dehydrogenase to yield enzyme containing about 0.9 mol/mol of enzyme subunit. The reaction results in a time-dependent irreversible activation of the enzyme. Glutamate dehydrogenase (8.9 microM subunit) modified with 10-60 microM AMPSBDB is about 3.2-fold more active than native enzyme. The modified enzyme is still inhibited by GTP and by high concentrations of NADH, but is no longer activated by ADP. The addition to the reaction mixture of (a) NADH or alpha-ketoglutarate; (b) GTP + NADH; or (c) alpha-ketoglutarate + NADH has little effect on the functional changes produced by AMPSBDB; whereas, the reaction is prevented by ADP. Purification of labeled peptide from proteolytic and chemical digests of [2-3H]AMPSBDB-modified enzyme leads to identification of Arg459 as the target amino acid. We conclude that AMPSBDB functions as an ADP mimic covalently bound to Arg459 within the ADP activator site of the allosteric bovine liver glutamate dehydrogenase.

Adenosine Diphosphate↗