MALTOPORIN MALTOTRIOSE COMPLEX

Introduction

Maltoporin is a membrane protein, which allows GRAM-negative bacteria, such as Escherichia coli to transport maltose and maltodextrins across its outer membrane. It is indispensable for the transport of long oligosaccharides, since they cannot pass through nonspecific porins.[1] Three beta-barrels form the channel of the protein.(Pic. 1) The sugars are guided into and through the channel construction by hydrophobic interactions with the “greasy slide”- a hydrophobic path composed of aromatic residues and located at the channel lining.[1,2] The protein is also known as LamB, as it is misused by a bacterial virus phage Lambda to recognise bacteria.

Ligands

Pic. 1 Protein structure colored by chains

Protein-protein contacts

Hydrophobic interactions play two important roles in a maltoporin molecule: firstly, hydrophobic lining of the channel, as was previously mentioned, allows oligosaccharides to passively enter the cell; secondly, hydrophobic cores of the protein form its quaternary structure. It is from this angle that we have considered the hydrophobic core located between the A and B subunits and formed around a tryptophane residue (TRP101:A). The applet shows the residue and the atoms surrounding it within the distance of 7 angstrom, but no closer than 1 angstrom. As can be seen from the applet, within the distance of 3 angstrom there are only atoms, covalently bound to the residue (only 5 atoms), within the distance of 4 angstrom there are 30. From this it can be deduced that the average interatomic distance is about 3.5 angstrom.

Disulphide bridges
Disulfide bridges are the only example of covalent bonds that stabilize the tertiary structure of the protein. The bond is formed between two cysteine residues. In the molecule there are three disulphide bridges, one in each subunit. The bridge from the subunit A can be seen in the picture below (CYS022:A– CYS038:A). The measured torsion angle is 102.9°, whereas the length of the bond is 2.03 angstrom.

This type of interactions is electrostatic in its nature. Salt bridges are formed in proteins between the charged parts of a molecule, such as carboxyl group, which is negatively charged at medium and high pH values, and amine group, which is positively charged at the same pH values. Such bonds can be formed with any angles and at a relatively big distance, however they participate in forming the protein structure only if it is under 5 angstrom. The lengths of some of these electrostatic interactions in a malporin molecule can be found in a table below. Salt bridges also help the protein form its tertiary and quaternary structure. The interaction between c and 043GLU:B, 082ARG:B and 073ASP:C can be seen in the picture (Pic. 4).

The salt bridges between the positively and negatively charged residues, whose ionized radicals were orientated in a certain way relative to one another, were found manually. It should also be noted that the distance was measured between the functional groups, whose charges are distributed equally between the atoms, so listing the names of atoms, between which the distance was actually measured, is rather pointless.

Pic.4 Salt bridges

Ligand-protein interactions

Magnesium ion forms 6 bonds with the protein (for one of the resonance states their median length is 2. 54 angstrom): it interacts with each of the two oxygen atoms of the radicals from the three aspartic acids. (Table 1) Those bonds have already been shown in the protein structure, which was downloaded from PDB. However, we could have predicted their existance without looking at the lines connecting the atoms in the picture. It is well known that the distance between the atoms range between 1 and 4 angstroms [6]. By executing “restrict(4, 422:C)” in Jmol, where 4 is the longest possible distance and 422:C – magnesium ion, we can find all atoms that fall into the 4 angstrom distance of the magnesium atom. What would be left is three aspartic acid residues – positively charged magnisium ion is held in place by the negatively charged carboxyl groups.

Hydrogen bonds between the maltotriose molecules and th protein can be seen not by executing “calculate hbonds”, but on the PDB website, by clicking on «Ligand interaction» in a «Small Molecules» block.

Hydrogen bonds were measured by executing “measure” in Jmol. The median length value is indeed very close to that of the ideal 3.04 angstrem[7]. It should be noted that it would also be possible to find the bonds with a “within” command. For example, if the upper limit of the length of a hydrogen bond were taken as 3.5 angstrem, the result of the “select within(3.5, 431:A)” execution, where 431:A is glucose, would look like this:

Pic.5. The result of the select within(3.5, 431:A) execution

We can see the same atoms that form hydrogen bonds according to PDB (see applet).