DC Science Series #1 - Pablo Porragas Paseiro (DC9)
Welcome to the SYNSENSO DC Science Series. In this series of blog posts, we talk about the scientific projects we are working on as Doctoral Candidates in the SYNSENSO network and share what we are discovering through our research. Enjoy!
Hello!
My name is Pablo Porragas Paseiro, DC#9 within the SYNSENSO network. I grew up in the USA but have spent the past five years living in various European countries. My interest in science has taken me to fascinating places, where I’ve had the chance to explore its diversity and complexity. During my time in Boulder, Colorado, USA, I studied Integrative Physiology and Public Health. There, I was inspired by the tangible impact directed science can have on a global scale, from personalised medicine to tracking infectious diseases.
These interests led me to Uppsala University in Sweden, where I pursued a Master’s degree in Infection Biology. I learned about the diverse infectious agents that remain significant challenges worldwide and the vital work scientists are doing to create a better future. My Master’s thesis focused on characterising intestinal bacteria to determine the antibiotic resistance profiles of microbes colonising the intestinal tract.
After completing my studies, I joined SYNSENSO and Dynamic Biosensors under the supervision of Dr Ralf Strasser, diving into the world of synthetic biology. Here, I explore innovative approaches to address key challenges in science. My project focuses on using the biochip technologies at Dynamic Biosensors to design new methods for studying binding interactions. This includes employing DNA origami nanostructures to investigate conformational changes and synthesising RNA aptamers for analysis on the chip surface. These adaptable techniques can tackle a wide array of scientific questions in fields such as cancer and infectious disease research. I am excited to continue expanding my knowledge in synthetic biology and contributing to the discoveries that drive scientific progress.
Please read on for a detailed explanation of one area of my project.
Introduction
Protein function is intrinsically linked to its three-dimensional structure. These structures include the arrangement of side chains to form catalytic pockets in enzymes or the complementary determining regions in antibodies. Many proteins fulfil their functions through complex conformational changes triggered by ligand binding or interactions with signalling molecules (e.g., nucleoside triphosphates, hormones) [1]. Consequently, many small molecule and peptide-based drugs act by (de)stabilising specific protein conformational states.
Drug discovery efforts can significantly benefit from an automated biosensor platform capable of detecting conformational changes upon ligand binding while measuring kinetic and equilibrium dissociation constants. Here, we introduce a new molecular biosensor design integrated with our current switchSENSE® technology, enabling relative protein size analysis and detection of conformational changes in large protein complexes under physiological conditions.
Results and Discussion
Our biosensor platform leverages the electrical actuation of DNA-based nanolevers tethered to an electrode surface. By applying alternating potentials to the electrode, the nanolever’s oscillating motion is controlled. The angular velocity of the nanolever is determined by its hydrodynamic friction within the solvent [2]. As a result, relative shape changes in a protein attached to the distal end of the nanolever can be inferred from variations in angular velocity.
To analyse large protein complexes under physiological conditions, we use a long, rigid, and slender DNA origami nanolever with a high negative charge density. This design enables us to distinguish differences in the conformational states of various proteins [3] (Figure 1).
Figure 1: Electrical actuation of DNA origami nanolevers for measuring protein and other biomolecule conformational changes.
Conclusion
Having demonstrated the ability to discern small differences in protein conformational states, we will now expand our library of protein and biomolecule conformational changes induced by small molecule and peptide-based ligands.
References
[1] Grant BJ, Gorfe AA, McCammon JA., Curr Opin Struct Biol., 2010, doi: 10.1016/j.sbi.2009.12.004.
[2] Langer A, Kaiser W, Svejda M, et. al., J. Am. Chem. Soc., 2014, doi: 10.1021/jp410640z
[3] Kroener F, Heerwig A, Kaiser W, et. al., J. Am. Chem. Soc., 2017, doi: 10.1021/jacs.7b10862
Text by Pablo Porragas Paseiro, DC 9 (Cell-free synthesis of RNA aptamers on a biochip). To find out more about Pablo, visit his profile.