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Proteomic and computational methods in systems modeling of cellular signaling
R Kleppe1, E Kjarland, F Selheim
1Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway. rune.kleppe@biomed.uib.no
Current Pharmaceutical Biotechnology
|June 23, 2006
Summary
Understanding cellular signaling requires dynamic, quantitative data. Integrating computational modeling with high-throughput methods offers powerful predictive models for healthy and diseased states.
Area of Science:
- Cellular Biology
- Systems Biology
- Computational Biology
Background:
- Cellular signaling is fundamental to cell behavior and disease.
- High-throughput omics methods provide static, qualitative data on molecular networks.
- Dynamic, quantitative data is crucial for understanding complex cellular processes.
Purpose of the Study:
- To review methodologies for in silico modeling of cellular pathways.
- To discuss methods for acquiring large-scale quantitative biological data.
- To explore the integration of modeling and data for predictive biological insights.
Main Methods:
- In silico modeling approaches for cellular pathways.
- High-throughput quantitative and temporal data acquisition techniques.
- Bioinformatics and computational analysis of large-scale biological data.
Main Results:
- Existing omics methods offer limited qualitative and static information.
- Emerging high-throughput methods provide quantitative and temporal data.
- In silico models reveal underlying properties of dynamic cellular features.
Conclusions:
- Integrating computational modeling with quantitative data generates powerful predictive models.
- These models enhance understanding of systems properties in health and disease.
- Predictive models can guide the development of effective pharmacological interventions.
Related Concept Videos
01:33Proteomics
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
01:23Overview of Cell Signaling
Despite the protective membrane that separates a cell from the environment, cells need the ability to detect and respond to environmental changes. Additionally, cells often need to communicate with one another. Unicellular and multicellular organisms use a variety of cell signaling mechanisms to communicate with the environment.
Cells respond to many types of information, often through receptor proteins positioned on the membrane. For example, skin cells respond to and transmit touch...
Cells respond to many types of information, often through receptor proteins positioned on the membrane. For example, skin cells respond to and transmit touch...
01:23Overview of Cell Signaling
Despite the protective membrane that separates a cell from the environment, cells need the ability to detect and respond to environmental changes. Additionally, cells often need to communicate with one another. Unicellular and multicellular organisms use a variety of cell signaling mechanisms to communicate with the environment.
Cells respond to many types of information, often through receptor proteins positioned on the membrane. For example, skin cells respond to and transmit touch...
Cells respond to many types of information, often through receptor proteins positioned on the membrane. For example, skin cells respond to and transmit touch...
01:19Interactions Between Signaling Pathways
Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...