Understanding the Molecular Mechanisms of Cancer-Related Processes
A key focus of our research is to unravel the molecular mechanisms underlying disease-related cellular processes at an atomic level. We concentrate on two fundamental biological pathways: the molecular switch regulating cell growth and the enzymatic mechanisms of small GTPases—both of which have critical implications for oncology.
Approximately 20% of all cancers are linked to malfunctioning Ras proteins, which act as molecular switches controlling cell proliferation. Mutations in Ras can disrupt its normal regulatory function, leading to uncontrolled cell growth and tumor development. In collaboration with Caroline Kamerlin (Georgia Tech) and the Center for Protein Diagnostics (Ruhr University Bochum), we investigate the atomic-level effects of oncogenic Ras mutations and their role in cancer progression. Insights from our studies contribute to improving molecular oncology diagnostics and therapeutic strategies.
Enzymatic Catalysis of GTP Hydrolysis in Small GTPases
Small GTPases, such as Ras, regulate numerous cellular processes through GDP-to-GTP exchange, functioning as molecular switches. These proteins are turned “on” by GTP binding and switched “off” by GTP hydrolysis. The hydrolysis reaction is vital for controlling growth signals in living cells. Oncogenic mutations in Ras disrupt this reaction, preventing proper downregulation of growth signals, which in turn contributes to cancer development.
Our research aims to decipher the detailed reaction mechanisms of GTP hydrolysis catalyzed by Ras. To achieve this, we have developed a workflow that integrates biomolecular simulations, time-resolved Fourier-transformed infrared (FTIR) spectroscopy, and X-ray crystallographic structural analysis. This approach enables us to resolve the catalytic process at an unprecedented spatiotemporal resolution and understand how Ras accelerates GTP hydrolysis by several orders of magnitude compared to its spontaneous rate in water.
Using molecular mechanics (MM), quantum mechanics (QM), and hybrid QM/MM simulations, we gain detailed insights into the structure, dynamics, and charge distribution of the Ras active site. Our findings show that Ras and its associated GTPase-activating proteins (GAPs) induce conformational changes that lower the activation energy required for hydrolysis. Specifically, Ras rotates the γ-phosphate relative to the β-phosphate into an energetically unfavorable conformation, and GAP binding further alters the alignment of the phosphate groups. Additionally, a protein-induced charge shift at the γ-phosphate optimizes conditions for nucleophilic attack, facilitating efficient hydrolysis. These findings exemplify the power of combining vibrational spectroscopy with biomolecular simulations to uncover protein catalysis mechanisms at atomic detail.
Structural Insights into Ras Function and Membrane Clustering
In collaboration with the Chinese Academy of Sciences-Max Planck Gesellschaft Partner Institute for Computational Biology (CAS MPG PICB) in Shanghai, we have resolved the detailed structure and protein environment of GTP during a transient intermediate state. Furthermore, our research has demonstrated that Ras clustering at cellular membranes is driven by dimerization. This discovery, derived from a combination of molecular dynamics simulations, attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy, and F?rster Resonance Energy Transfer (FRET) experiments, provides new insights into Ras organization and function in the cellular membrane environment.
By integrating advanced computational and experimental approaches, our research enhances the understanding of disease-related molecular mechanisms and contributes to the development of targeted cancer therapies.