An atlas of contacts of a Mycobacterium smegmatis transcription initiation complex

The complex that we have taken to explore is common for Mycobacterium tuberculosis.
This organism is not used as a model in the majority of mechanistic studies on bacterial transcription initiation. However, it is a causative agent of tuberculosis, that is why the full picture of transcription process is needed to draw up a better treatment.
The discussed complex consists of 7 subunits (chains) and a great number of ligands as Zn and Mg ions, sulfate ion and ethane-1,2-diol. More detailed information about the ligands is arranged in the table 'Description of the low molecular weight ligands of the complex'.

RbpA and Card are two main factors of transcription in this complex:

• RbpA comprises four structural elements. One end of this factor interacts with RNAP (RNA polymerase) while other structural elements are associated with DNA phosphate backbone. The factor interaction may modulate transcription initiation, such a role is not evident solely from examination of the structure.
  
• CarD's main function appears to be to stabilize RNA polymerase open promoter complex. It also binds with minor groove of DNA, TRP residue is involved in this interaction^[2].
  

Resent studies shows that CarD and RbpA likely function together, this contributes to higher activation of transcription. While observing factors separately lower activation is detected^[3].

We used Jmol program several times while doing this task. It provides all necessary measurements and visualizations.

The methods of searching were different for each case:

• We select the amount of atoms that are placed within 3Å from ligand for detecting covalent bonds. After that we create the visualization of the ligand and amino acids' residues containing the selected atoms.
• We study positively and negatively charged amino acids' residues that are placed not far from each other to detect salt bridges (two groups are defined, the first one with Glu and Asp in it and Arg, His, Lys for the second group). The same method is used for detecting bonds between negatively charged sulfate ion ligand and nearby positively charged residues.
• The hydrogen bonds were found with the help of installed command of Jmol - 'hbond'.
• We examine the residues of aromatic amino acids (Trp, Tyr and His) for detecting stacking interactions. The residues that are close to each other and are focused in the same way (one aromatic ring above the other) draw our attention. The same method for finding interactions between residues and nitrogenous bases.
• We select all hydrophobic residues of both chains and then highlight those being within 5Å from each other to show the hydrophobic interactions between different chains.

General information on the complex, hydrophobic interaction between the two chains of the protein, salt bridge between sulfate ion and [ARG]457 and stacking between [TRP]287 and the minor groove of DNA were studied by Anastasia Yudina.
Information of ligands, biomolecular identifiers UniProt, salt bridge between [ARG]144 and [GLU]27, hydrogen bonds of the alpha-chain, hydrogen bonds of the beta-bundles, stacking between [TYR]134 and [TYR]241, covalent bond between [ASP]537, Mg and [ASP]539 and hydrogen bond between [THR]1230 and [EDO]2009 were studied by Ekaterina Guseva.
The report page (text editing, page design and scripts), a brief review of the search of contacts, studies of covalent bonds between [CYS]75, 78, 62, 60 and Zn, salt bridge between [ARG]79, [LYS]74, 76 and DNA backing were made by Andrey Buyan.