Protein folds and IV structure

Published on April 19, 2020 Reviewed on November 27, 2022   19 min

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Greetings. Welcome to this Principles of Biochemistry lecture series. My name is Jerry Feigenson. I am a professor in the Department of Molecular Biology and Genetics at Cornell University in the USA. In the fourth lecture, you saw characteristics of protein structure. You saw alpha helices, beta sheets, turns, collagen. These can be partly described by their values of angles Phi and Psi. These secondary structures, as well as less well-defined loops, can pack together into the stable protein fold, of which there are about 1,400 folds known. Proteins can be classified by the important characteristics of fold, super family and family.
In this fifth lecture, you will learn that multiple folds can occur in a single polypeptide chain and you will see that more than one polypeptide chain can come together in what is called quaternary structure. That quaternary structure can be very stable or else transient to transmit a signal. The transient quaternary structure is used to create signals that appear, then disappear.
Multiple folds can occur within a single polypeptide chain. On this slide, I will show you two examples. First, let's look at pyruvate kinase. Pyruvate kinase has three different folds. Why does it need three different folds? Pyruvate kinase binds pyruvate, it binds ATP, and it is regulated. Now let's take a look at pyruvate kinase. Here's one fold. It is formed from amino acids 116-223, forms a cap over the catalytic site. Just below this fold, there's a fold shown in green. This is the kinase domain. It has amino acids one through 115 and amino acids 224-387. And at the bottom of this picture of pyruvate kinase, we see a third fold. This is from amino acids 388-530. This is the regulatory domain. All large proteins, and we'll call pyruvate kinase a large protein. All large proteins have more than one fold. Often a fold is a continuous sequence of amino acids, and you see that with folds at the top, 116-223, that's a continuous run of amino acids. And the fold at the bottom, 388-530, that's a continuous run-up amino acids, but the fold in middle the kinase domain, that is non-continuous amino acids interrupted by another fold. Let's take a look at another protein of HIV reverse transcriptase. It has four different folds. Why does it need four different kinds of folds? It has a complex job to do. Copies viral RNA, synthesizes DNA and it degrades DNA. What else can we say about these multiple folds in a single polypeptide chain. Well, first of all, if we consider all life forms from simple life forms to the most complex, all 1,400 types of individual protein folds are found in all life forms, most simple to most complex. Let me say one more thing about these. The entire path of a single polypeptide chain, including all the folds, we call that the tertiary structure and then if we think about all life forms and the different folds we'll notice a pattern of evolution. And that is the more complex life forms have proteins that have combinations of folds to make new protein capabilities and complexities. We find that repeated folds can occur within a single polypeptide chain.