Learn to simulate a glycan using GLYCAM-Web. Then, learn how to visualize the simulated glycan in 3D.
Optionally, see the Alternate Protocols section to learn three other ways to simulate a glycan at GLYCAM-Web.
This Scenario will use the glycan below as its example system. You are welcome to try using a different glycan.
This glycan is found in mucins and certain variations of it are relevant to cancer.
Here’s what Essentials of Glycobiology (Ch. 9) has to say about it. In the text below, the T-antigen is DGalpb1-3DGalpNAca, which is also known as the Core 1 O-glycan.
"In many serum glycoproteins and mucins, the T antigen is substituted by sialic acid at C-3 of galactose and at C-6 of N-acetylgalactosamine. These substitutions add a negative charge to the O-GalNAc glycan. They also prevent other modifications of core 1. The cell surfaces of many leukemia and tumor cells contain large numbers of sialylated core 1 O-GalNAc glycans. On rare occasions, core 1 remains unsubstituted, leaving the T antigen exposed, for example, in cancer and inflammatory bowel disease. In these cases, it is likely that there is an abnormality in either the sialylation of core 1 or further extension and branching of core 1."
Unlike peptide and DNA sequences, glycans generally do not form stable secondary structures. Also, they form branches in ways that peptides and DNA generally do not. Luckily, many of their structural preferences are established, and it is relatively easy to have a computer generate a realistic model.
GLYCAM-Web builds your glycan up from templates containing reasonable monosaccharide geometries. It connects them to each other using known preferences for linkage geometries.
All the protocols in this Scenario – the main one and all the alternates – introduce parts of the Oligosaccharide Modeling Services (OMS) at GLYCAM-Web.
You will need to be able to completely specify the chemical makeup of your glycan. In general, if you have the sequence for your glycan, you have all the information you need. If in doubt, expand the inset below to learn more.
If you don’t have a specific glycan in mind, no problem! You can just follow along with the example implementation.
(a) In black type: a fully specified sequence of a disaccharide with derivatives. In gray are indicated its components, numbered as follows for convenience in this figure:
(b, c, d) The same sequence represented using (b) a chemical scheme, (c) 3D sticks, and (d) GLYCAM-Web’s variant of SNFG notation.
The website uses a carbohydrate nomenclature called GLYCAM Condensed Notation. People who are familiar with other nomenclatures for glycan sequences usually find it pretty easy to learn.
Want to learn more about carbohydrate structure in general? Check out the references in the box!
This Scenario requires very little of you. Exactly how little depends on what you would like to do:
You will need complete information about the chemical makeup of your glycan. See above, in Background, if you need help with that.
The simplest thing to do will be to follow the example used herein. However, the Carbohydrate Builder will keep you from building something invalid. So, feel free to just click around and see what happens. For an even simpler interface, see the 3D Structure Libraries section in Alternate Protocols.
These instructions are for the version of the Carbohydrate uilder which builds from left to right.
The example sequence for this scenario is:
Here, we will use the Carbohydrate Builder‘s point-and-click interface to set the chemical sequence for the oligosaccharide. (Link will open in a new window). Afterwards, check out the Alternate Protocols section, below, for other ways to set the sequence.
Build up a linear sequence starting from any monosaccharide at a non-reducing end and going all the way to the reducing end. We will call this the main chain.
The main chain we will use for our example comprises the bold-faced, black portions in the sequence:
Note that all except the portion in brackets is part of the main chain.
When you first open the Carbohydrate Builder, this is what you will see:
When you first arrive at the Carbohydrate Builder, this is what you will see. Note the portions of the page that are active: Isomer, and Monosaccharide. If you want to ensure the isomer (D or L) for your monosaccharide, then choose it in the Isomer box, Otherwise, just choose a monosaccharide, and the builder will choose the most common isomer for you.
Now, click on Neu5Ac. At this point, the dialog will change and the Configuration buttons will become active. Note that you could also have clicked D before clicking Neu5Ac.
The Linkage buttons will only become enabled for positions that make sense for the current context.
If you have just selected a ketose as your monosaccharide, the Linkage box will look like this. Note that it already knows that your linkage will be 2-x.
Choose 2-3 as the linkage. At this point, the Isomer and Monosaccharide boxes become active again. Finish building the main chain. After you have built the sequence as far as the reducing-end GalpNAc, note that the Aglycon box is active and choose to terminate with an -OH.
This box shows the available reducing-end terminations. Clicking one of these signals the termination of the main chain in the glycan sequence.
At this point, you have finished the main chain. Now you will add the other Neup5Ac as a branch off of the GalpNAc. Your Sequence box should look very similar to the one below.
Once you have terminated your main chain with an aglycon, the Sequence box gives you a number of options. If your glycan is complete, merely click Done. Alternately, you can Add a Branch or Add a Derivative.
If you want to learn about adding derivatives (such as sulfate or methyl groups), see Alternate Protocols.
Click on Add Branch. Notice the change in the Sequence box:
After you have clicked Add Branch, the CB will need to know where it will go. Note the Branch Options portion of the dialog. The monosaccharides that are able to receive a new branch are highlighted. Choose the monosaccharide where your branch will terminate.
Click on the GalpNAc. Now, in the sequence, just in front of the GalpNAc, you will see a new set of square brackets:
When you have chosen a location for your branch, the dialog places a set of square brackets where the new branch will go. As you build the branch, its sequence will show inside these brackets.
Here is a reminder of the sequence. Shown in bold are the parts not yet added:
Build the DNeup5Aca2-6 portion. When you have chosen the ‘2-6’, the Finish Branch option will become active:
If the Finish Branch button is not available, it is likely that you are trying to connect the branch at an already occupied location. Try a different linkage option.
Click on Finish Branch and then on Done.
After clicking Done, you will proceed to the Options page. Note that the molecule shown is not minimized yet. You aren’t required to set any additional options, but they are available. This Scenario assumes that you do not make changes. To learn more about the available options, see Additional Information – Descriptions of Available Options, below.
This image shows all possible options. At the top, the sequence for your molecule is shown. If you are happy with that and wish to accept the website defaults, you may simply click Generate Selected Structures. You may also need to deselect structures if more than 64 structures would be built. The page will not allow progress if zero, or more than 64 structures would be built with the current selection. Here, only 12 would be generated.
After clicking Generate Selected Structures. you will be taken to a page where you can visualize and/or download structure files for your glycan.
As shown in the image, once the build for any given glycan is complete, a “Visualize” button will become active. Clicking the button will open a frame in which a 3D, interactive representation of your glycan will be visible.
From the same page, you can download structure files for your glycan.
Most people will just want a PDB file for their glycan. If that is all you want, clicking the “Download” button will get you the single PDB file.
If you want any other file type, you must download all files for the glycan. If multiple structures are present, then you can choose to download all files for one or more of the structures. To learn more about the types of files in the download, please see the Annotated Output – Files available for download section.
This section contains additional comments about the output.
Info about that
Here is a post explaining how to use VMD to view glycans in PDB files.
a description of all the available files
How to find publication-worthy information about your structure’s generation.
How to cite the builder.
Additional information that might be useful to some.
This section explains the different options available to you after you complete a glycan sequence.
info about rotamers – what they are and how we generate them.
About setting glycosidic angles using the Angles dialog.
How this works
How the minimization happens
Choose this method if
All the arguments for the Carbohydrate Builder apply here, too, except that your glycan is a glycosaminoglycan (GAG).