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Light-activated protein interaction with high spatial subcellular confinement.

ABSTRACT: Methods to acutely manipulate protein interactions at the subcellular level are powerful tools in cell biology. Several blue-light-dependent optical dimerization tools have been developed. In these systems one protein component of the dimer (the bait) is directed to a specific subcellular location, while the other component (the prey) is fused to the protein of interest. Upon illumination, binding of the prey to the bait results in its subcellular redistribution. Here, we compared and quantified the extent of light-dependent dimer occurrence in small, subcellular volumes controlled by three such tools: Cry2/CIB1, iLID, and Magnets. We show that both the location of the photoreceptor protein(s) in the dimer pair and its (their) switch-off kinetics determine the subcellular volume where dimer formation occurs and the amount of protein recruited in the illuminated volume. Efficient spatial confinement of dimer to the area of illumination is achieved when the photosensitive component of the dimerization pair is tethered to the membrane of intracellular compartments and when on and off kinetics are extremely fast, as achieved with iLID or Magnets. Magnets and the iLID variants with the fastest switch-off kinetics induce and maintain protein dimerization in the smallest volume, although this comes at the expense of the total amount of dimer. These findings highlight the distinct features of different optical dimerization systems and will be useful guides in the choice of tools for specific applications.

SUBMITTER: Benedetti L

PROVIDER: S-EPMC5877946 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundMany biological processes are mediated by dynamic interactions between and among proteins. In order to interact, two proteins must co-occur spatially and temporally. As protein-protein interactions (PPIs) and subcellular location (SCL) are discovered via separate empirical approaches, PPI and SCL annotations are independent and might complement each other in helping us to understand the role of individual proteins in cellular networks. We expect reliable PPI annotations to show that proteins interacting in vivo are co-located in the same cellular compartment. Our goal here is to evaluate the potential of using PPI annotation in determining SCL of proteins in human, mouse, fly and yeast, and to identify and quantify the factors that contribute to this complementarity.ResultsUsing publicly available data, we evaluate the hypothesis that interacting proteins must be co-located within the same subcellular compartment. Based on a large, manually curated PPI dataset, we demonstrate that a substantial proportion of interacting proteins are in fact co-located. We develop an approach to predict the SCL of a protein based on the SCL of its interaction partners, given sufficient confidence in the interaction itself. The frequency of false positive PPIs can be reduced by use of six lines of supporting evidence, three based on type of recorded evidence (empirical approach, multiplicity of databases, and multiplicity of literature citations) and three based on type of biological evidence (inferred biological process, domain-domain interactions, and orthology relationships), with biological evidence more-effective than recorded evidence. Our approach performs better than four existing prediction methods in identifying the SCL of membrane proteins, and as well as or better for soluble proteins.ConclusionUnderstanding cellular systems requires knowledge of the SCL of interacting proteins. We show how PPI data can be used more effectively to yield reliable SCL predictions for both soluble and membrane proteins. Scope exists for further improvement in our understanding of cellular function through consideration of the biological context of molecular interactions.

Project description:BackgroundDiabetes mellitus characterized by hyperglycemia as a result of insufficient production of or reduced sensitivity to insulin poses a growing threat to the health of people. It is a heterogeneous disorder with multiple etiologies consisting of type 1 diabetes, type 2 diabetes, gestational diabetes and so on. Diabetes-associated protein/gene prediction is a key step to understand the cellular mechanisms related to diabetes mellitus. Compared with experimental methods, computational predictions of candidate proteins/genes are cheaper and more effortless. Protein-protein interaction (PPI) data produced by the high-throughput technology have been used to prioritize candidate disease genes/proteins. However, the false interactions in the PPI data seriously hurt computational methods performance. In order to address that particular question, new methods are developed to identify candidate disease genes/proteins via integrating biological data from other sources.ResultsIn this study, a new framework called PDMG is proposed to predict candidate disease genes/proteins. First, the weighted networks are building in terms of the combination of the subcellular localization information and PPI data. To form the weighted networks, the importance of each compartment is evaluated based on the number of interacted proteins in this compartment. This is because the very different roles played by different compartments in cell activities. Besides, some compartments are more important than others. Based on the evaluated compartments, the interactions between proteins are scored and the weighted PPI networks are constructed. Second, the known disease genes are extracted from OMIM database as the seed genes to expand disease-specific networks based on the weighted networks. Third, the weighted values between a protein and its neighbors in the disease-related networks are added together and the sum is as the score of the protein. Last but not least, the proteins are ranked based on descending order of their scores. The candidate proteins in the top are considered to be associated with the diseases and are potential disease-related proteins. Various types of data, such as type 2 diabetes-associated genes, subcellular localizations and protein interactions, are used to test PDMG method.ConclusionsThe results show that the proteins/genes functionally exerting a direct influence over diabetes are consistently placed at the head of the queue. PDMG expands and ranks 445 candidate proteins from the seed set including original 27 type 2 diabetes proteins. Out of the top 27 proteins, 14 proteins are the real type 2 diabetes proteins. The literature extracted from the PubMed database has proved that, out of 13 novel proteins, 8 proteins are associated with diabetes.

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Light-activated protein interaction with high spatial subcellular confinement.

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