Atypical Ramachandran Plots - Online Tutor, Practice Problems & Exam Prep

Glycine and proline exhibit atypical Ramachandran plots due to their unique R groups. Glycine, with the smallest R group, allows for permissible bond angles across all quadrants, minimizing steric hindrance. In contrast, proline's bulky cyclic R group restricts phi and psi bond angles primarily to one quadrant, limiting its conformational flexibility. Understanding these differences is crucial for grasping protein structure and function, as they influence the secondary and tertiary structures of proteins.

Atypical Ramachandran Plots

So now that we know the basics of a Ramachandran plot, we're going to talk about atypical Ramachandran plots. It turns out that there are 2 amino acids with atypical Ramachandran plots, and those are glycine and proline. By atypical, we really mean that they have very unique Ramachandran plots. The other 18 amino acids all have Ramachandran plots that are very similar and look like the ones that we saw in our previous lesson. However, glycine and proline have really unique Ramachandran plots that stand out from all the other 18. We'll first talk about glycine's Ramachandran plot and then we'll discuss proline's Ramachandran plot in a different video.

Glycine's Ramachandran plot is atypical because glycine has a very small R group. In fact, it's the smallest R group of them all, and its R group is so small that it does not significantly limit the phi and psi bond rotations encountered by glycine's R group. Recall that glycine's three-letter code is GLY, and its one-letter code is G. Again, glycine's R group is the smallest, which allows for significantly more flexibility. Recall from our previous lesson that the white regions in a Ramachandran plot represent non-permissible angles, and they're non-permissible due to steric hindrance. In our previous Ramachandran plot, if you remember, the right side of the Ramachandran plot was predominantly non-permissible, mostly white except for tiny regions. But with glycine's Ramachandran plot, notice that it has permissible bond angles in pretty much every single quadrant: the left quadrant, upper left, bottom left, upper right, and bottom right. Glycine's Ramachandran plot can take on permissible bond angles in virtually every single quadrant, which is very unique.

Glycine is the only amino acid that has this ability due to its very small R group that encounters very little steric hindrance. This is a key feature of glycine, and we will be able to refer back to this in some of our different topics later throughout our course. It's important to keep in mind that glycine's R group gives it this special feature of adapting different bond angles that other amino acids can't take on, and it can fit into small spaces that other amino acids can't fit into.

This concludes our lesson on the atypical Ramachandran plot of glycine. We'll get some practice, and then we'll talk about the atypical Ramachandran plot of proline. I'll see you guys in those videos.

Why does Gly have a uniquely interesting Ramachandran plot in comparison to the other α-amino acids?

• A. Its small R-group restricts the φ and ψ bond rotations via noncovalent interactions.
• B. Glycine's R-group forms strong hydrogen bonds that greatly frees its bond rotations.
• C. Gly's R-group avoids steric hindrance & expands regions of energetically permissible φ and ψ bond angles.
• D. b and c.

Atypical Ramachandran Plots

So now that we've talked about glycine's unique Ramachandran plot, let's talk about proline's Ramachandran plot which is also unique. Proline's Ramachandran plot is unique because proline has a bulky cyclic R group, and its bulky cyclic R group really does greatly restrict or limit the phi and psi bond rotations. In our example below, we'll be able to fill in the R group of proline, recall some of its abbreviations, and we'll talk about proline's Ramachandran plot. Recall that Proline's three-letter code is just "pro," and its one-letter code is just "P." Just like "P," proline's R group really does resemble the loop of a "P." Just like a "P" has a backbone, so does proline. Proline has this amino acid backbone. Then just like proline, the "P" has a loop just like this. Proline's R group really does look like the loop of a flipped "P." That can help remind you of its structure. Also, you can think of the proline pentagon. So, they both start with "P," and that can help remind you that its R group is going to form like a pentagon type shape. It's going to have these points here that need to be connected. These points are all going to be methylene groups or CH₂ groups. It's just going to be CH₂, CH₂, CH₂, and then it connects back to the nitrogen. Again, because it connects back to the nitrogen here, the amino group of proline has one less hydrogen than all other amino acids. Something important to keep in mind as we move forward. Notice that glycine's R group is really bulky and cyclic, and there's a lot of steric hindrance encountered there, and that ends up restricting both the phi and the psi bond angles that we see here. In glycine's Ramachandran plot, on the x-axis, we have the phi bond angles and on the side of the Ramachandran plot, we have the psi bond angles. There's really only one region that has permissible bond angles in it. Remember that the darker the region is, the more permissible it is. The light regions represent less permissible. There is a little bit that of permissibility that extends into the bottom left quadrant here, but there's not much at all and there's definitely no dark shaded regions in the bottom left, and that's something that's very different from all the other amino acids, because the all the other amino acids really have dark shaded regions down in this quadrant as well, but that's lacking in Ramachandran plot. You'll also notice that there's nothing, there are no permissible regions on the right half of the Ramachandran plot. This is really, really restricted and it's something that's very unique and interesting to keep in mind. Hopefully, by comparing glycine's Ramachandran plot to Proline's Ramachandran plot, you'll get a better understanding of what a Ramachandran plot is really trying to show you. Again, with glycine's Ramachandran plot, its R group is so small that it does not limit phi and psi bond angles. By not restricting those phi and psi bond angles, it takes on regions in all 4 quadrants. That's glycine. But with proline, on the other hand, it's pretty much the complete opposite. Its bulky cyclic R group restricts those phi and psi bond angles really to just one quadrant in the upper left. And, there is a little bit in the bottom left, but not a lot and no dark regions. So again, hopefully this helped your understanding of Ramachandran plots and I'll see you guys in the practice video.

The Ramachandran plot of Leu most likely resembles which of the following plots?

• A.
• B.
• C.

Here’s what students ask on this topic:

What makes glycine's Ramachandran plot unique?

Glycine's Ramachandran plot is unique because glycine has the smallest R group among all amino acids, which is just a hydrogen atom. This minimal steric hindrance allows glycine to adopt permissible bond angles in all four quadrants of the Ramachandran plot. Unlike other amino acids, which have restricted regions due to their larger R groups, glycine's plot shows permissible angles across a wide range, making it highly flexible in protein structures. This flexibility allows glycine to fit into tight spaces within proteins, influencing their secondary and tertiary structures.

Why does proline have an atypical Ramachandran plot?

Proline has an atypical Ramachandran plot due to its bulky cyclic R group, which forms a ring structure that connects back to the nitrogen in the amino group. This cyclic structure significantly restricts the phi (φ) and psi (ψ) bond angles, limiting permissible bond angles primarily to one quadrant in the Ramachandran plot. The restricted conformational flexibility of proline influences the protein's secondary structure, often introducing kinks or turns in polypeptide chains. This unique property makes proline crucial in the formation of specific protein structures, such as collagen helices.

How do glycine and proline influence protein structure differently?

Glycine and proline influence protein structure differently due to their unique R groups. Glycine, with its small R group, allows for a wide range of bond angles, making it highly flexible and able to fit into tight spaces within proteins. This flexibility is crucial for the formation of loops and turns in protein structures. In contrast, proline's bulky cyclic R group restricts its bond angles, limiting its conformational flexibility. Proline often introduces kinks or turns in polypeptide chains, which can disrupt regular secondary structures like alpha-helices and beta-sheets. These distinct properties make both amino acids essential for specific structural roles in proteins.

What are the implications of glycine's flexibility in protein structures?

Glycine's flexibility in protein structures has several important implications. Its ability to adopt a wide range of bond angles allows it to fit into tight spaces and accommodate various conformations. This flexibility is crucial for the formation of loops, turns, and other irregular structures in proteins. Glycine is often found in regions where the polypeptide chain needs to make sharp bends or in the active sites of enzymes where conformational changes are necessary for function. Its unique properties also make it essential in the formation of collagen helices and other specialized protein structures.

Why is understanding atypical Ramachandran plots important in biochemistry?

Understanding atypical Ramachandran plots is important in biochemistry because they provide insights into the conformational flexibility and structural roles of specific amino acids like glycine and proline. These plots help predict the permissible bond angles and steric constraints of amino acids, which are crucial for understanding protein folding, stability, and function. Knowledge of atypical Ramachandran plots aids in the design of peptides and proteins with desired structural properties and can inform the study of protein misfolding diseases. Overall, they are essential tools for elucidating the relationship between amino acid sequences and protein structures.