3.1.1 Ковалентные связи

Disulfide bond is the type of covalent bonds which connects sulfur atoms (S-S) in two cysteine amino acids. Disulfide bridges in proteins are formed between thiol groups (-SH) of cysteine residues as a result of oxidative folding. The angle between planes where both sulfur atoms are in is approximately 90°. Another sulfur containing amino acid, methionine are not able to form disulfide bridges. We found 3 molecules of cysteine in ABCB10 protein, but they don't form disulfide bridges because of a big distance

Команда "rectrict Cys" позволила нам убедиться в отсутствии данного типа связей.

Peptide bond — bond which links amino acids in protein. Pairing between C-N and carboxyl group C=O makes peptide bond 10% shorter that it should be. The bond becomes double binding, and resonant structures appear. Since it is difficult to rotate two forms of peptide bond emerge (cys- and trans isomers). Cis conformation is energetically don't have advantageous. Therefore, almost all peptide groups in proteins are in trans conformation^[2] In ABCB10 protein peptide bonds were measured. The average length of bonds is 1.35 Å.

Результаты измерений представлены в следующей таблице:

3.1.2 Hydrogen bonds

Водородная связь — тип взаимодействия электростатической и частично ковалентной природы. Связь формируется при наличии атома электроатрицательного элемента и связанного с другим электроотрицательным элементом атома водорода, находящимися на достаточно близком расстоянии. Результатры измерений представлены в таблице:

3.1.3 Salt bridges

Iogenic groups (residues of glutamic, aspartic acids; histidine, lysine and arginine) participate in ionic interactions, forming the so-called salt bridges. Negatively charged carboxyl groups of the Asp and Glu radicals and positively charged groups of the Lys, Arg, or His acids are involved in the interactions. These interactions are possible both inside the protein and between different molecules.

There are several approaches to finding salt bridges. You can that manually, to do that you’ll have to isolate the polar residues of amino acids and color them in accordance with the charge. And then visually look for those amino acid residues that most likely can form an ionic bond. You can make a different approach and use the calculator of protein interactions, ionic ones in particular.

We used both ways, but for the sake of fidelity we decided to focus on the second, which we used PIC: Protein Interactions Calculator for. According to machine calculations, there are 25 salt bridges in the protein totally.

Two of them were examined in detail: one between [GLU] 356 and [ARG] 357, the second between [LYS] 650 and [ASP] 593. You can see the result in the Image 2 and Image 3 respectively.

3.1.4 Hydrophobic interactions

Stacking interactions

Stacking interactions are non-covalent interactions between organic compounds containing aromatic systems. They are most widely represented in DNA, where they increase the stability of the molecular structure, but are also found in proteins.

In proteins, this effect can be realized with aromatic amino acids - Phe, Tyr, Trp. The so-called T-stacking is characterized by the following features: hydrogen atoms with a partial positive charge of one aromatic system are directed to the center of the other aromatic system perpendicular to the plane of the latte^[3].

The search for stacking interactions in the protein was carried out with the help of the Protein Interactions Calculator^[4]. Calculator output:

Graphical images of some of the found interactions are shown on the figures. By analyzing the angles between amino acid residues, we can suppose that these are T-stackings (angle ≈90 °)