Posts Tagged ‘protein interaction’

Visualizing Unfolded Protein Movement Within the Cell

 :: Posted by American Biotechnologist on 12-10-2014

In an interesting study, Professor Martin Gruebele from the University of Illinois, led a team that developed a way to watch how unfolded proteins move through a cell using a fluorescent microscope and three-dimensional diffusion modeling.

While it had been widely considered that, due to their large size, unfolded proteins move slower through cells than their folded counterparts, the current study found that interactions between unfolded proteins and chaperones play a large part in controlling the velocity of protein movement throughout the cell. In general, unfolded protein binds to chaperones which help facilitate their movement throughout the cell. When the ratio of unfolded proteins to chaperones becomes too high, the unfolded protein gets stuck in a cellular traffic jam which retards their movement throughout the cell.

In addition, unfolded proteins also bind to other non-chaperone proteins which, in effect, disrupt their flow within the cell.

The team plans to use a specialized microscope to study other proteins and how unfolding affects their diffusion, to see if the properties they observed are universal or if each protein has its own response.

Citation: Guo M, Gelman H, Gruebele M (2014) Coupled Protein Diffusion and Folding in the Cell. PLoS ONE 9(12): e113040. doi:10.1371/journal.pone.0113040

Making Sense of Biological Pathways

 :: Posted by American Biotechnologist on 10-11-2010

Over the last several years, the amount of information regarding protein–protein interactions has grown exponentially. In order to accommodate all of that information, hundreds of databases have been created which reside in numerous places throughout the internet. While the existence of disparate databases has been helpful in memorializing the hard work of protein scientists, finding and subsequently mining those databases has become akin to navigating a complicated maze of information.

Thanks to the hard work of Thomas Klingström and Dariusz Plewczynski a valuable tool has been created to help reduce the time necessary to gain a broad overview of protein-protein-interaction-databases. Recently published in Briefings in Bioinformatics, the Pathguide contains information about 325 biological pathway related resources and molecular interaction related resources. These include links to databases on protein-protein interactions, metabolic and signaling pathways, Transcription Factors / Gene Regulatory Networks, Protein-Compound Interactions, Genetic Interaction Networks, Protein Sequences and Pathway Diagrams.

In addition to the hyperlinked list of databases, Klingström and Plewczynski created a network diagram showing the links among many databases in Pathguide with with linkouts to database details and to the database itself. The network diagram is organized by database name and category and has a legend that includes Interactions, Pathways, Predictive interactions, Metamining, Exchange format language, Unifying efforts, and a few uncategorized databases.

You can checkout the pathguide at