The goal of systems biology is to gain a more complete understanding of biological systems by viewing all of their components and the interactions between them simultaneously. Until recently, the most complete global view of a biological system was through the use of gene expression or proteinprotein interaction data. With the increasing number of high-throughput technologies for measuring geno...

Chi, C. 2010. Post-synaptic Density Disc Large Zo-1 (PDZ) Domains. From Folding and Binding to Drug Targeting. Acta Universitatis Upsaliensis. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 573. 42 pp. Uppsala. Understanding how proteins fold and bind is interesting since these processes are central to most biological activity. Protein folding and protein-...

Protein-protein interactions, which result in either transient or long-lived complexes, play a central role in the processes happening in the cells. Perturbations in those interaction networks can lead to disease. Understanding the mechanisms of proteinprotein binding is inherently difficult due to the range of potential interactions, the molecular rearrangement associated with binding, and the...

The increasing availability of biological networks (proteinprotein interaction graphs, metabolic and transcriptional networks, etc.) is offering new opportunities to analyze their topological properties and possibly gain new insights in their design principles. Here we concentrate on the problem of de novo identification of the building modules of networks, which we refer to as network modules....

Karlsson, A. 2017. Characterization and Engineering of Protein-Protein Interactions Involving PDZ Domains. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 1292. 39 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-554-9798-9. The work presented in this thesis has contributed with knowledge to several aspects of proteinprotein interaction involving PD...

Åberg, E. 2018. Evolution of Interactions Involving Intrinsically Disordered Proteins. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 1424. 44 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-513-0226-3. This thesis describes the evolution of intrinsically disordered proteins and their interaction partners. The work presented is a combination of ph...

The enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase mediates cholesterol biosynthesis by converting HMG-CoA to mevalonic acid. Although the focus has been on its effects on cholesterol, because mevalonic acid is also required for isoprenoid synthesis, it may also affect other important biological processes. Isoprenoids are converted by transferases to farnesyl and geranylgerany...

The signal-transduction network of a mammalian cell integrates internal and external cues to initiate adaptive responses. Among the cell-surface receptors are the G protein–coupled receptors (GPCRs), which have remarkable signal-integrating capabilities. Binding of extracellular signals stabilizes intracellular-domain conformations that selectively activate intracellular proteins. Hereby, multi...

A novel breadth-first based structural clustering method for graphs is proposed. Clustering is an important task for analyzing complex networks such as biological networks, World Wide Web and social networks. The clusters are of various shapes such as cliques and stars, for example, in ProteinProtein Interactive(PPI) networks. Traditional algorithms may detect clique-shaped clusters, but they f...