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4: Protein structure and function

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    • 4.1: From Amino Acids to Peptides
    • 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.
    • 4.5: 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.
    • 4.6: Protein Aggregation
      We have seen that protein aggregates complicate the lives of people who study protein folding in vitro and who try to express human proteins in prokaryotes like E. Coli in vivo. Instead of viewing these aggregates as junk, some now study them avidly. It turns out that these aggregates are not as non-specific as earlier believed. In addition, an understanding of how and when they form will give us clues into the etiology and treatment of some of the most debilitating and feared diseases.
    • 4.7: Prions and Disease
      The problem in the transmissible spongiform encephalopathies (TSE's) is that amyloid-like protein aggregates form which appear to be neurotoxic. The protein found in the plaques has the same primary sequence as the PrPc but a different secondary and presumably tertiary structure. The protein found in the plaques, called the PrPsc (the scrapie form of the the normal protein) is insoluble in aqueuous solution, protease resistant.

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