3: Details of Protein Structure
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- 3.1: Introduction
- Proteins are the workhorses of cells, responsible for just about all aspects of life (look at oxytocin in the cartoon)! They are comprised of one or more polypeptides. In this chapter, we look at the different levels of protein structure…, in fact what it takes to be a functional protein.
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- 3.3: Changes in Protein Shape Can Cause Disease
- While the conformation of a protein determines its biological function, an allosteric change (change in shape) can moderate or disrupt its function. Under normal circumstances, cells use changes in protein shape to regulate metabolism. Such allosteric regulation is well documented in familiar biochemical pathways such as glycolysis and is discussed in more detail elsewhere. Less well understood is how (or why) is why conformational change in some proteins cells has devastating effects.
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- 3.4: Quaternary Structure
- Quaternary structure describes a protein composed of two or more polypeptides. Like tertiary structure, multimeric polypeptide are formed by the same kinds of non-covalent interactions and may be stabilized disulfide bonds. Specifically, a dimer contains two, a trimer three, a tetramer four polypeptides… and so on.
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- 3.5: Some Proteins are Chemically Modified and Others Require Prosthetic Groups to be Biologically Active
- Many polypeptides are modified after translation, for instance by phosphorylation or glycosylation (addition of one or more phosphates or sugars respectively to specific amino acids in the chain). These modifications account for and enhance the molecular and functional diversity of proteins within and across species.
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- 3.6: Protein Domains, Motifs, and Folds in Protein Structure
- These two and many other proteins have this domain, allowing them to bind a molecule of phosphatidyl-inositol triphosphate that is generated as part of a common cell-signaling pathway. The implication of this common domain is that a cell can have signaling pathways that allowing it to respond to different signals that lead to the same response, albeit under different conditions and probably at different times. Proteins are typically described as consisting of several distinct sub-structures, dis
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- 3.7: Proteins, Genes and Evolution- How Many Proteins are We?
- If evolution did not have to select totally new proteins for each new cellular function, then how many genes does it take to make an organism? The number of genes in an organism that encode proteins may be far fewer than the number of proteins they actually make. Current estimates suggest that it takes just 25,000 genes make and operate a human and all its proteins (check out Pertea and Salzberg at Estimating the number of genes in the human genome).
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- 3.8: View 3D Animated Images of Proteins in the NCBI Database
- We can’t see them with our own eyes, but viewed by X-Ray diffraction, proteins exhibit exquisite diversity. You can get an X-Ray eye’s view of protein structures at National Center for Biological Information’s Cn3D database. Here’s how to access three- dimensional animated images of proteins from the database:
Thumbnail: An enzyme binding site that would normally bind substrate can alternatively bind a competitive inhibitor, preventing substrate access. Dihydrofolate reductase is inhibited by methotrexate which prevents binding of its substrate, folic acid. Binding site in blue, inhibitor in green, and substrate in black (PDB: 4QI9). (CC BY 4.0; Thomas Shafee ).