Studies on receptor-ligand molecular recognition - a retrospective on my doctoral and postdoctoral work

  • Event Date: 2024-06-19
  • Complex Systems
  • Speaker: Dr. Zoltan Palmai(Généthon, Évry-Courcouronnes)  /  Host:
    Place: Online

Title: Studies on receptor-ligand molecular recognition - a retrospective on my doctoral and postdoctoral work
Speaker:Dr. Zoltan Palmai(Généthon, Évry-Courcouronnes)
Time:2024/06/19 (Wed.) 16:00
Meeting link:

The main goals of my research have been to analyze and understand the structural, dynamic and energetic background of the molecular recognition between receptors and their ligands for different bio macromolecule systems such as proteins and lipid molecules using various computational modeling techniques in collaboration with experimentalist colleagues.
I examined the effect of ligand binding on the dynamics of multi-domain proteins – a kinase(PGK) (Semmelweis University, Hungary) and an ion channel (NMDAR) (Ecole Normale Superieure Cachan, France) using MD simulations. Both proteins are important targets for potential drug candidates either in the domain of cancer (PGK) or neurodegenerative (NMDAR) therapy. Therefore, the molecular details of the effect of ligand binding on dynamics are of utmost interest to design efficient drugs. Interestingly, in both cases the ligand bound complexes showed reduced flexibility and more directional fluctuations compared to the apo forms. We determined important key residues characterizing the directions of the motions, also allosteric signaling pathways connecting the binding sites and the key residues. For PGK, we elucidated the important dynamic conditions for efficient phosphorylation needed for the activation of anticancer and antiviral drugs. For NMDAR, we proposed a mechanistic dynamic model of the ligand-dependent gating mechanism – a synchronic, balance-spring-type screwing of the transmembrane domain – which is an important step towards designing channel blocker inhibitor drugs.
In a subsequent study (Ecole Polytechnique, France), I used computational protein design to suggest mutations in an aminoacyl tRNA synthetase (aaRS), TyrRS that could increase its D-Tyr binding further, relative to L-Tyr. D-amino acids have been suggested to be useful for the treatment of cancer, since they increase the half-life of anticancer peptide drugs when incorporated in their backbone. D-amino acids might be introduced into proteins using engineered aaRSs. We tested the effects of mutations by probing the aminoacyl-adenylation reaction through pyrophosphate exchange experiments. We also performed alchemical free energy simulations to obtain L-Tyr/D-Tyr binding free energy differences. We found two mutants active towards D-Tyr; one of these had an inverted stereospecificity, with a large preference for D-Tyr.
Subsequently I engaged in an interdisciplinary study (Nagoya University, Japan) to understand the molecular recognition between a transporter, SWEET and its ligands, sucrose and gibberellin (GA). SWEET plays an important role in the allocation of sucrose in plants. Some SWEETs were shown to also mediate transport of the plant growth regulator gibberellin. The close physiological relationship between sucrose and GA raised the questions of whether there is a functional connection and whether one or both of the substrates are physiologically relevant. To dissect these two activities, I predicted binding interactions that might be selective for sucrose or GA using molecular docking and MD simulation. Transport assays confirmed these predictions. In transport assays, one of the mutants had 7x higher relative GA activity, and another mutant only transported sucrose. The impaired pollen viability and germination in the double mutant was complemented by the sucrose- but not by the GA-selective mutant, indicating that sucrose is the physiologically relevant substrate and that GA transport capacity is dispensable in the context of male fertility. These findings are also relevant in the context of the role of SWEETs in pathogen susceptibility.
Lastly, I investigated the molecular recognition between lipid micelles as receptors and monomeric lipid molecules as ligands in the framework of studying the origin of life, i.e. the so-called Lipid World hypothesis (Weizmann Institute of Science, Israel). Mixed lipid micelles were proposed to facilitate life through their documented growth dynamics and catalytic properties. Our previous research predicted that micellar self-reproduction involves catalyzed accretion of lipid molecules by the residing lipids, leading to compositional homeostasis. We employed MD simulations to examine the self-assembly of variegated lipid clusters, allowing us to measure entry and exit rates of monomeric lipids into pre-micelles with different compositions and sizes. We observed considerable rate-modifications that depend on the assembly composition and scrutinized the underlying mechanisms as well as the energy contributions. We described the measured potential for compositional homeostasis in our simulated mixed micelles affirming the basis for micellar self-reproduction, with implications for the study of the origin of life.