4: Proteins- Structure and Folding
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- 4.2: Levels of Protein Structure
- Proteins are the workhorses of the cell. Virtually everything that goes on inside of cells happens as a result of the actions of proteins. Among other things, protein enzymes catalyze the vast majority of cellular reactions, mediate signaling, give structure both to cells and to multicellular organisms, and exert control over the expression of genes. Life, as we know it, would not exist if there were no proteins. The versatility of proteins arises because of their varied structures.
- 4.3: Secondary Structure
- Secondary structures are those repetitive structures involving H bond between amide H and carbonyl O in- the main chain. These include alpha helices, beta strands (sheets) and reverse turns.
- 4.4: Protein folding
- To think about how proteins fold, we have to think dynamically. Luckily we have the tools of molecular dynamics (MD) at our fingertips which helps us imagine how these processes take place and concomitantly how to probe protein folding experimentally. View the following two MD simulations and compare the spontaenously formation of a micelle and the folding of a protein before we delve into the complex topic of protein folding and stability.
- 4.6: Protein function, domains and cooperativity
- tertiary, and quaternary) of protein structure and discussed example proteins/motifs exhibiting them. In this section, we will examine from a functional perspective a few proteins/domains whose function relies on secondary, tertiary, or quaternary structure.
- 4.7: The Three-Dimensional Structure of Proteins
- 4.7.1: Main Chain Conformations
- 4.7.2: Secondary Structure and Loops
- 4.7.3: Tertiary, Quaternary, and Symmetrical Structures
- 4.7.4: Secondary Structural Motifs and Domains
- 4.7.5: Protein with Alpha, Alpha-Beta, Beta and Little Secondary Structure
- 4.7.6: Intrinsically Disordered Proteins
- 4.7.7: Fibrillar Proteins
- 4.7.8: Protein Folding and Unfolding (Denaturation) - Dynamics
- 4.7.9: Protein Stability - Thermodynamics
- 4.7.10: Protein Aggregates - Amyloids, Prions and Intracellular Granules
- 4.7.11: Biomolecular Visualization - Conceptions and Misconceptions
- 4.7.12: Laboratory Determination of the Thermodynamic Parameters for Protein Denaturation
- 4.7.13: Predicting Structure and Function of Biomolecules Through Natural Language Processing Tools
- 4.7.14: Predicting Structure from Sequence and Sequence from Structure/Function (New 10/24)
- 4.7.15: Chapter 4 Questions