Jmol molecular viewing
Last update on the 14th of February, 2017Molecular viewing is used to present molecules in visual way to extract significant data about its structure and functionality. J(S)mol is among other computer programs used for this purpose. The work below is a training one with goal to graphically study protein structures, hydrogen bonds and obtain some skills necessary for using J(S)mol.
Viewing
Mercuric reductase of Pseudomonas aeruginosa (PDB ID: 1ZK7) is presented in the JSmol applet below. The protein is relatively close to this protein in terms of functionality. All representations are listed in a script, which starts when the applet is loaded. To see next representation press "Resume" button, to start the script again press "Start script" button.
The script file is available for download at this link.
Hydrogen bonds
Hydrogen bonds provide and support protein secondary structure. The two most common structual elements are alpha helixes and beta sheets. It is important to know such attributes of particular hydrogen bond as its length and N-O-C angle. These attributes of several bonds in the mercuric reductase are shown in table 1. The values are obtained with Jmol measurement instruments.
| # | Atom names | Bond length, Å | N-O-C angle, ° |
|---|---|---|---|
| Alpha helixes | |||
| 1 | N(84LEU)-O(80ASP) | 3.15 | 154.6 |
| 2 | N(85LEU)-O(81ARG) | 2.75 | 153 |
| 3 | N(86ALA)-O(82SER) | 3.01 | 148.6 |
| 4 | N(87GLN)-O(83LYS) | 3.12 | 149.8 |
| Beta strands | |||
| 5 | N(371ASP)-O(397ILE) | 3.22 | 141.9 |
| 6 | N(397ILE)-O(371ASP) | 2.99 | 164.2 |
| 7 | N(373ARG)-O(395LEU) | 3.17 | 153.1 |
| 8 | N(395LEU)-O(373ARG) | 2.97 | 165.7 |
The values are quite various but overall the bond length is close to 3Å, that fits theoretical predictions. As it is clearly seen, length values of alpha helix are more variable and chaotic than the ones of beta strands. This could be explained by the assumption that alpha helix is a more variable structure than beta sheet in terms of backbone dihedral angles of aminoacid residues because of special "architecture" of each structure.
Another important obseration is about periodicity of hydrogen bonds and atoms connected by them. In alpha helixes hydrogen bonds connect O and N of nth and (n+4)th residues, respectively, whereas in beta sheets such pairs are N(x)-O(y), O(x)-N(y), N(x+2)-O(y-2), O(x+2)-N(y-2), e.t.c. In the first case the explanation is that geometrical properties of helix are conserved while in the second case the explanation is that trans-disposition of carbonyl groups across peptide bond periodicaly changes orientation of carbonyl and imino groups from inside to outside according to shared space of two strands. This feature provides the ability of beta strands to form beta sheets.
The table provides average value of N-O-C angle as 150 degrees. This fact may be explained by the assumption that the protein surrounding affects elements so that the best angle is about 150 degrees. The values related to helixes are less variable than the ones related to strands, although the second set are clearly periodical. This observation strengthens previous explanations and assumptions.