Our Research


Overview

Proteins are the primary effectors of cells. They are highly organized in a variety of assemblies, forming the basis of well-regulated pathways and networks to precisely execute a plethora of cellular processes. Alternations of proteins expression, and their interaction networks are linked to many physiological and pathological conditions. Our main interest is to develop and apply mass spectrometry-based approaches to understand the spatial organization and dynamic regulation of protein complexes in space and time during cellular processes such as signaling and differentiation.


Developing high-throughput proteome-wide XL-MS strategy (methodological)

 

To comprehensively understand the protein interactome, our group has developed a novel XL-MS method to characterize the structures and interactions of various protein complexes in a high-throughput manner. This approach allows us to handle highly complex samples and simultaneously investigate stable and dynamic protein assemblies by capturing their residue-residue connectivities in vivo. In the future, we aim to unveil the full potential of this technique by designing novel cross-linkers, implementing creative approaches for cross-link enrichment, developing a cutting-edge data analysis pipeline, and applying state-of-the-art MS technology. We integrate expertise from synthetic chemistry, analytical chemistry, mass spectrometry and informatics, aiming to reach unprecedented analytical depth, complexity and precision in interactome profiling. 

XL-MS workflow and its applications


Establishing the structural interactomes of organelles and synapses (biological)

Organelles are specialized compartments within the cell, in which proteins are selectively imported to work cooperatively to conduct a variety of cellular functions. Although many organelles were discovered decades ago and found to play essential roles for the cell, questions regarding to which extent protein complexes cooperate within and between organelles remain completely elusive. One of the major obstacles in characterizing organellar interactomes is that these proteins are often membrane-embedded/associated, generally highly organized in the three-dimensional space, and thus recalcitrant to purification by standard procedures. Therefore, in many cases, only the most stable ‘core’ complexes can be studied by classical structural biology approaches.

To overcome these limitations, our group studies the structural interactome of proteins in their organellular environment using our newly developed cross-linking mass spectrometry approach. We focus on two organelles, the endoplasmic reticulum and mitochondria, the functions of which are linked to a wide variety of physiological/pathological conditions. A comprehensive map of the structural interactomes of these organelles will provide crucial insights into the interaction patterns, the binding interfaces, and the three-dimensional organization of protein complexes and supercomplexes. Functional studies are also performed to further characterize newly discovered protein interactions and networks.

In addition, we are interested in exploring synaptic protein interaction networks with subcompartmental specificity, defining interactomes of the presynaptic active zone, synaptic vesicles (SVs), endosomes and the postsynaptic density (PSD). Since different compartments contribute to the precision of neuronal signaling and to synaptic plasticity, these studies are instrumental for understanding synaptic function, its adaptations to different types of stimuli and, ultimately, the molecular basis of memory and learning.

In both biological avenues, we combine the structural interatomic information with complementary approaches from structural biology, molecular biology, cell biology, neuroscience and informatics, to gain a more detailed understanding of how protein assemblies are arranged and co-operated in different biological scenarios.

A) Image is adapted from EMBO J. 2016 Dec 15;35(24):2634-2657 with permission. B) Cross-link mapping on 80S ribosome provides novel insights of SERBP1 localization  (Nat Methods. 2015 Dec;12(12):1179-84). C) Nuclear interactome profiled by XL-MS.

A) Image is adapted from EMBO J. 2016 Dec 15;35(24):2634-2657 with permission. B) Cross-link mapping on 80S ribosome provides novel insights of SERBP1 localization

(Nat Methods. 2015 Dec;12(12):1179-84). C) Nuclear interactome profiled by XL-MS.