load=1crnAminoacids
Structure
There are hundreds of amino acids, mainly found in soils and microorganisms, although only 20 of them can participate in the genetic code for translation into proteins.
In order to start observing some of these amino acids, download the structure of Glycine from a file saved on your hard drive as “gly.png” or by File, Get Mol (and typing gly afterwards). Note the amino and carboxylate groups in the CPK stain. Identify the structure of the amino acid:
In order to start observing some of these amino acids, download the structure of Glycine from a file saved on your hard drive as “gly.png” or by File, Get Mol (and typing gly afterwards). Note the amino and carboxylate groups in the CPK stain. Identify the structure of the amino acid:
What is the side chain of Gly?
And the carbon skeleton?
Note that glycine has a formal color code (CPK, Corey, Pauling, Koltun) for carbon (gray), nitrogen (blue), phosphorus or sulfur (yellow), and hydrogen (white). Several polymeric structures, however, are loaded without the presence of the hydrogen atom. For example, load the structure of the plant protein crambine, but this time using the Jmol* Console (File,Console):
Note that the hydrogen atoms are not displayed in the structure. To make them appear, you need to configure Jmol through the Console window:
set pdbAddHydrogensThe message pdbAddHydrogens = true should appear. You will now be able to view the hydrogen atoms of crambine by loading it again.
For longer command sequences, you can use the Jmol* Editor instead of the Console. The Editor allows you to insert commands line by line, with explanatory comments for each one. To do this, simply click on Editor in the Console itself. Once the window is open, you can compose a sequence of commands or paste a previously created one.
As an example, the following code snippet loads the amino acid Glutamate, calculates its partial charge, and renders it in rods showing the values of the charges. To “run” it, simply copy and paste into the open Editor:
As an example, the following code snippet loads the amino acid Glutamate, calculates its partial charge, and renders it in rods showing the values of the charges. To “run” it, simply copy and paste into the open Editor:
# Script for observations of the amino acid Glutamate:
load $glu # micromolecule loading (note that the equal sign refers to macromolecules with PDB attributes, and not to micromolecules - $; and also note that an amino acid can be loaded by typing its 3-letter abbreviation)
calculate partialcharge # partial charge
wireframe only # exclusive rendering of rods
label %P
# labeling of partial charges on atomsAs already mentioned, it is not necessary to have Jmol installed or the Jmol directory and its executable in Java on your computer. The program can be accessed through applets found on several websites, such as:
The links below lead to some websites that allow remote access to JSmol:
St. Olaf College - Jmol & JSmol (direct applet for JSmol) - interface with some commands in buttons.
St. Olaf College 2 - more elaborate interface, with several examples, buttons and commands by hyperlink.
IZA-SC - Comissão de Estruturas de Valencia (ES) - very simplified interface.
To “run” the previous script, for example,
Go to the St. Olaf College - Jmol & JSmol) website;
Start the Console (bottom left corner of the screen);
Copy the script above and paste it into the Console.
Alternatively, instead of copying/pasting a piece of code, Jmol makes it possible to load the script, as long as it is previously saved with the spt attribute (for script). In fact, the script can be saved in any simple text editor, keeping this spt attribute.
The image below illustrates the result of the script for glutamate.
To export images created in Jmol, simply follow the Menu, or the command below typed in the Console of the standalone program or through the JSmol link:
write glutamato_cargas.jpg # png and pdf attributes are also possibleJSmol - An Applet for Displaying Jmol in Internet Browsers
Among the advantages of using Jmol to view molecular models is the aforementioned possibility of using the program over the Internet, without the need for local installation (PC). This flexibility is guaranteed by the help of an applet developed in HTML5, JSmol, which compiles Jmol using JavaScript, instead of JAVA. This way there is no need for Jmol or JAVA to be locally installed.
To facilitate the study of molecular models in this material, these subsequent chapters will include a link called JSmol to access a new display tab integrated into the applet, showing a water molecule and the Console for scripting, as follows:
Alternatively, molecular models will also be made available as a JSmol applet on the same content page when convenient, such as the glutamate molecule:
This way, simply right-click on any area of the open “JSmol” window and select any item from the Menu or use the Console, in the same way as for the standalone program installed locally on the PC.
Other amino acid structures can list the various groups (nonpolar aliphatic and aromatic, as well as neutral, basic and acidic polar groups), as follows:
Other amino acids can be loaded online in File, Get Mol in the installed application, or through the Console, in this case:
load $amino acid name or its 3-letter abbreviationThere are several websites for studying biomolecules with the help of JSmol, including amino acids. For example, the Interactive Molecules Section developed by the Department of Veterinary Clinical Pathology at UFRGS.
Metabolic Derivatives
Using the local or internet Jmol window (JSmol), load the file gaba from the Menu or Console (load $gaba) and position it so that it looks similar to what was presented in the Jmol session containing the Glu model; do you see similarities? It is a metabolic derivative of the amino acid, of utmost importance in neurological control, called \(\gamma\)-aminobutyric acid, GABA, a neurodepressant of the nervous system.
Now load the amino acid Pro. Where is the amino group of the carbon skeleton? By rotating the structure, you can see that this group belongs to the side chain, being inserted in a pyrrolidine ring.
If you use the arrows to recover the previous partial charge command, you will also see that it is an amino acid with a side chain close to neutrality, thus being classified as neutral polar in some books.
Other Examples (structure and derivatives)
Now load His. Note that, like Pro, His also has a ring, but this is only in the side chain (imidazole ring). To see it better, change the background:
background lightyellowIn principle, you would risk saying that this is a negatively charged amino acid, based on the values presented. However, these values refer to the atom, in this case O and N. On the contrary, while O does not participate in the side chain, but rather in the carbon skeleton, negatively charged N acts as a nucleophile, attracting H and forming an amine. This amine can exhibit a neutral or positive charge, depending on the pH in which it is inserted, and according to its pKa value, in this case, 6.0. Thus, at an acidic pH, His is strongly protonated in N, characterizing the amino acid as basic (positive). At physiological pH, however, its content is distributed in neutral and basic forms. As a whole, it is characterized as a basic amino acid.
Histidine has a derived metabolite that is very important in the homeostasis of inflammation. Load histamine and compare it to its precursor.
Now load Trp. It also has a ring, indole, which is strongly aromatic (see the double bonds) and which gives this characteristic to the amino acid. Trp has a well-known metabolic derivative, serotonin. Serotonin is therefore a metabolic derivative of an amino acid, a chemical mediator of body relaxation, therefore linked to the administration of so-called serotonergics against anxiety.
Now load Cys. Note that there is a sulfur atom in its side chain. Click on the yellow sphere and see what appears in the Console. The first two numbers refer to the number of the atom in the structure, and the last three to its XYZ spatial coordinates of the atom. The thiol group of the Cys side chain gives it a strongly reactive character, capable of forming covalent bonds or bonds of similar magnitude with halogens (iodoacetate, for example), another thiol group (forming disulfides in proteins) and even gold (used in nanomaterials research and surface functionalization). Cys has a side chain pKa value of 8.3, although in proteins it can range from 5 to 10.
For another metabolic derivative, load Phe. Note that it can also be classified as an aromatic amino acid (benzene). Also see Tyr and note the difference with Phe. It is no coincidence that Phe is a precursor of Tyr in metabolism, the former being an essential amino acid (it needs to be ingested) for mammals, and Tyr is not. Also as an aromatic, the phenolic ring of Tyr has a pKa, although far from the physiological one, with a value of 10.4. There are several important metabolic derivatives of Tyr, one of which is the main thyroid hormone, thyroxine.
To view it, load thyroxine and view its structure. Click on the purple sphere and see that it is an iodine atom in the Console. Since there are four iodine atoms, the structure is also called tetraiodothyronine (or T4 in clinical jargon).
Well, that’s it for now. This chapter is not intended to cover the characteristics of all 20 protein amino acids, which would be somewhat boring, but rather to allow familiarization with the subject, as well as with the use of Jmol itself. Therefore, it is suggested that the student download and study, with the help of a textbook or the internet, the other amino acid structures, evaluate their characteristics and reactivity of the side chains, as well as important metabolic derivatives.