IISc research develops computational models of bacteria cell walls

The team of researchers established an ‘Atomic model’ using computer simulation

NT Correspondent

Bengaluru: In two research studies that were conducted by researchers from the Indian Institute of Science (IISC) and Unilever, computational models of bacteria cell walls were developed. These walls can fasten the screening of antimicrobial molecules which can attach diseasecausing bacteria, researchers informed. Bacterial cells are enveloped by a cell membrane, which is surrounded by a cell wall.

Bacteria like Escherichia coli (E Coli) are known to be gram-negative which is that their cell walls contain a layer of peptide sugar complexes, known as peptidoglycans, and another coating called the outer lipid membrane, they informed, adding that , Staphylococcus aureus, is gram-positive and has several layers of peptidoglycans.

Antimicrobials are designed to kill the bacteria by either disrupting the cell walls' membrane, destabilizing the present peptidoglycan layer or, the technique of trans locating through cell wall layers and disrupting the cell membrane which is present inside.

A former Ph.D. student at the Department of Chemical Engineering (CE), IISC said, “Cell envelope, which is a large part of the process, is overlooked as the interaction between antimicrobial molecules and cellular barriers are not well grasped.”

The team of researchers established an ‘Atomic model” using computer simulation which recreates the structure of the cell wall and breaks it down to individual atomic levels. Parameters such as sizes of sugar, chains of the peptidoglycans, the orientation of peptides, and distribution of the void size were incorporated.

Ganapathy Ayappa, Professor at CE said, “The peptidoglycan structure is semi-permeable as nutrients and protein required by the bacteria have to pass through the structure. The voids enable a smooth passage for antimicrobials”.Research associate at CE Rakesh Vaiwala said that they are the first group to produce a comprehensive molecular model of the cell wall of S aureus. Researchers tested the effectiveness of the model with the help of the supercomputing facility available with known samples.

They further elaborated by saying that Melittin, a short peptide, shows higher binding efficiency to the E Coli cell wall in comparison to gram-positive S aureus. It was also found that Melittin interacts with peptides which are known as trans peptidation in peptidoglycan biosynthesis, which can disrupt cell wall integrity.

Thymol, a naturally occurring small molecule is present in the cell wall of S aureus.The team used the model to draw comparatives out of the movement of different surfactant molecules through the layer of E Coli, in which the peptidoglycan resides.

The team was able to show a link between the length and tail, alongside the antimicrobial efficacy of surfactants. It was also observed that the shorterchain surfactants killed bacteria at a higher rate than longer-chained surfactants.Jaydeep Kumar Basu, Professor in the Department of Physics collaborated with the team to formulate vesicles composed of E Coli extraction and observed their interaction with Surfactant under the microscope.

Ganapathy Ayappa also shared that the computational models downsize the search for potential antimicrobials in a smaller subset of molecules for testing.