Biology subjects

Kalman, Z. E.

Publications and source records attributed to Kalman, Z. E..

3 recordsLinked to original sources

bioRxiv2021

PSINDB: A comprehensive database of postsynaptic protein-protein interactions

The postsynaptic region is the receiving part of the synapse comprising thousands of proteins forming an elaborate and dynamically changing network indispensable for the molecular mechanisms behind fundamental phenomena such as learning and memory. Despite the growing amount of information about individual protein-protein interactions in this network, these data are mostly scattered in the literature or are stored in generic databases that are not designed to display aspects which are fundamental to understanding postsynaptic functions. To overcome these limitations we collected postsynaptic protein-protein interactions (PPIs) together with a high amount of detailed structural and biological information and launched a freely available resource, the Postsynaptic Interaction Database (PSINDB) to make these data and annotations accessible. PSINDB includes tens of thousands of binding regions together with structural features mediating and regulating the formation of PPIs, annotated with detailed experimental information about each interaction. PSINDB is expected to be useful for numerous aspects of molecular neurobiology research, from experiment design to network and systems biology-based modeling and analysis of changes in the protein network upon various stimuli. PSINDB is available at http://psindb.itk.ppke.hu/.

bioinformatics↗

bioRxiv2021

A preliminary study on the cistrome of human postsynaptic density from an evolutionary and network-based perspective

The postsynaptic density (PSD) is a neuronal organelle that consists of thousands of protein complexes, having a role in signal transduction. The emergence of the complexes is dependent on the presence of proteins provided by gene expression. In this research we used Chip-seq data supported by protein level information. We developed a pipeline using data from five neuronal transcription factors, which reduces the false-positive hits of identified binding sites. In addition we found correlation between co-regulation and protein complex formation. The developed method paves the way for a future for large scale analysis utilizing a more comprehensive set of transcription factors.

bioinformatics↗

bioRxiv2020

Distribution of disease-causing germline mutations in coiled-coils suggests essential role of their N-terminal region

Next-generation sequencing resulted in the identification of a huge number of naturally occurring variations in human proteins. The correct interpretation of the functional effects of these variations necessitates the understanding of how they modulate protein structure. Coiled-coils are -helical structures responsible for a diverse range of functions, but most importantly, they facilitate the structural organization of macromolecular scaffolds via oligomerization. In this study, we analyzed a comprehensive set of disease-associated germline mutations in coiled-coil structures. Our results highlight the essential role of residues near the N-terminal part of coiled-coil regions, possibly critical for superhelix assembly and folding in some cases. We also show that coiled-coils of different oligomerization states exhibit characteristically distinct patterns of disease-causing mutations. Our study provides structural and functional explanations on how disease emerges through the mutation of these structural motifs.

bioinformatics↗