HT4 L1: Allosteric pathways

HT4: Visualization

L1 (Lecture): Visualizing allosteric pathways in oligomeric enzymes


Zoran Štefanić
Division of Physical Chemistry
Ruđer Bošković Institute
E-mail: [email protected]

Visualizing molecular structures and their interactions is essential for understanding their function. A number of computer programs that serve this purpose have become indispensable tools in this niche. Programs such as Pymol, Chimera, and Coot, to mention perhaps the most known examples, all have their devoted followers based on their strengths and shortcomings. However, as the daily tasks of a scientist are ever more complex and interdisciplinary, the need for tighter integration of visualization programs with other programming tools becomes a must.

The lecture will be based on the results of the project ALOKOMP1 and the role of visualization in the project. The project tries to understand the nature of allosteric communication in a class of oligomeric enzymes called purine nucleoside phosphorylases2, by combining the data from static molecular structures stored in PDB with data coming from MD simulations on those structures, unified in a form of a relational database. This database is well suited for identifying hidden connections (pathways) between different enzyme regions, which is the basis of allostery. The approach relies heavily on using programmatic methods and visualization of the underlying data relationships to cope with the complexity and the amount of data contained in the database. This way we will try to raise the awareness of prospective users of these emerging programming environments. A use case of integrating a visual environment with the relational data stored in the background will show how humans can deal with large amounts of data if it is suitably transformed and presented. Also, libraries for 2D visualization such as D3.js will also be employed in conjunction with relational and networked data.

Figure 1. Examples of visualizations used in the Alokomp project. Visualizing large amounts of data in stored in the relational form can be a daunting task. Nevertheless, finding the appropriate visual form may be the crucial step in finding the answers.


1, financed by Croatian Science Foundation (project grant IP-2019-04-6764)

2 Marta Narczyk, Marta Ilona Wojtyś, Ivana Leščić Ašler, Biserka Žinić, Marija Luić, Elżbieta Katarzyna Jagusztyn-Krynicka, Zoran Štefanić & Agnieszka Bzowska (2022) Interactions of 2,6-substituted purines with purine nucleoside phosphorylase from Helicobacter pylori in solution and in the crystal, and the effects of these compounds on cell cultures of this bacterium, Journal of Enzyme Inhibition and Medicinal Chemistry, 37:1, 1083-1097, DOI: 10.1080/14756366.2022.2061965