Proteins

The course covers the three-dimensional nature of proteins, protein assembly, protein domains, protein families and structural evolution, dynamic proteins, catalytic proteins, and studying protein function. Students will learn about the peptide bond, protein structures, chaperones, protein modification, protein families, protein dynamics, catalytic mechanisms, and protein analysis methods. The teaching method includes lectures, readings, and practical examples. This course is intended for individuals interested in biochemistry, molecular biology, or protein science.

• Introduction
• Learning outcomes
• 1 The three-dimensional nature of proteins
• 1 The three-dimensional nature of proteins
• 1.1 Introduction
• 1.2 The peptide bond and primary structure of proteins
• 1.3 Protein secondary structure
• 1.3.1 Helices
• 1.3.2 β pleated sheets
• 1.3.3 Reverse turns and loops
• 1.3.4 Coil conformations
• 1.4 Protein tertiary structure
• 1.4.1 Motifs and supersecondary structures
• 1.4.2 Protein fold
• 1.4.3 Protein domains
• 1.4.4 Covalent cross-linkages stabilise protein structure
• 1.5 Quaternary structure
• 1.6 Fibrous proteins
• 1.7 Summary of Section 1
• 2 Assembling a functioning protein
• 2 Assembling a functioning protein
• 2.1 Introduction
• 2.2 Chaperones help polypeptides to fold
• 2.3 Some proteins require small-molecule cofactors
• 2.4 The covalent modification of proteins
• 2.4.1 Glycosylation
• 2.4.2 Lipid-linked proteins and lipoproteins
• 2.5 Summary of Section 2
• 3 Protein domains
• 3 Protein domains
• 3.1 Introduction
• 3.2 Structural domains
• 3.3 Binding domains in intracellular signalling proteins
• 3.4 The functional domains of Src
• 3.5 Summary of Section 3
• 4 Protein families and structural evolution
• 4 Protein families and structural evolution
• 4.1 Introduction
• 4.2 Amino acid sequence homologies and why they occur
• 4.3 Conserved protein domains
• 4.4 Predicting conformation from sequence
• 4.5 Summary of Section 4
• 5 Dynamic proteins
• 5 Dynamic proteins
• 5.1 Introduction
• 5.2 All proteins bind other molecules
• 5.3 Regulating protein conformation and activity
• 5.3.1 Allosteric regulation
• 5.3.2 Cooperative binding
• 5.3.3 Phosphorylation of proteins as a means of regulating activity
• 5.3.4 G proteins
• 5.4 Protein–protein interactions
• 5.5 Summary of Section 5
• 6 Catalytic proteins
• 6 Catalytic proteins
• 6.1 Introduction
• 6.2 Catalytic mechanisms
• 6.2.1 Redistribution of electrons in the substrate
• 6.3 Lysozyme
• 6.4 Carboxypeptidase A
• 6.5 Multienzyme complexes
• 6.6 Summary of Section 6
• 7 Studying protein function
• 7 Studying protein function
• 7.1 Introduction
• 7.2 Site-directed mutagenesis
• 7.3 Studying protein–protein interactions
• 7.3.1 Physical methods for demonstrating an interaction between proteins
• 7.3.1 Library-based methods for demonstrating an interaction between proteins
• 7.4 Proteomics
• 7.5 Summary of Section 7
• Conclusion
• References
• Acknowledgements