Overview and Purposes

Integrative Structure Determination

collecting data from diverse sources at different levels of resolution,

translating data into spatial restraints

sampling by satisfaction of all the restraints to computationally generate an ensemble of structures

analyzing of the ensemble of solutions.

Integrative structure determination approaches (http://salilab.org/imp) help address this need by providing powerful tools for determining structures and dynamics of proteins and complexes.

Nuclear Pore Complex

The Nuclear Pore Complex (NPC) is a large macromolecular assembly of ~50 MDa and is the sole mediator of macromolecular transport between the nucleus and the cytoplasm

By integrating diverse structural data (including the 3,077 chemical cross-links, a Cryo-electron tomography map, 147 SAXS profiles of 18 Nups, and quantitative mass spectrometry data), I determined a sub-nanometer precision structure for the entire 552-protein yeast NPC, mapping the NPC's functional elements in unprecedented detail (Nature, 2018).

Nup82 Complex

combination of 1,131 chemical cross-links, EM 2D images, and SAXS data

Nup84 complex

integration of 286 chemical cross-links together with other information sources such as EM, X-ray crystallography, etc.

Nup 133

19 SAXS profiles and 23 negative-stain EM class average, as well as the X-ray crystal structures

SEA complex

The TORC1 pathway controls eukaryotic cell growth and cellular responses to a variety of signals (e.g. nutrients, hormones, and stresses).

The SEA complex is situated at the vacuole membrane in yeast and implicated in the cellular response to different stresses via its regulation of the TORC1 pathway.

Integrative structural modeling with

Affinity purification : 23 interactions between proteins and domains

188 Chemical cross-links

SEA complex emerges as a modulator that can coordinate both structural and enzymatic activities necessary for the effective functioning of the TORC1 pathway

SAXS experiments and applications to the integrative structure modeling

SAXS (Small Angle X-ray Scattering) provides information about the shapes and sizes of proteins and assemblies in solution.

For the past decade, by performing SAXS, I contributed to determining structures and dynamics of numerous systems, which vary in size and complexity from small proteins (e.g. prion , λ-repressor, ubiquitin, SH3 domain, and amelogenin) to large macromolecular assemblies including spindle pole body (manuscript in preparation) and the NPC.

To enlarge the depth and scope of the research, I utilized other techniques, such as EM, KITA, fluorescence and circular dichroism.

In particular, one sample system for which I collected a large amount of SAXS data is the NPC.

I have collected SAXS profiles for 147 discrete NPC components during my postdoctoral training (manuscript in preparation). Consequently, these SAXS profiles are typically combined with other sources of data and information, such as X-ray crystal structures and EM images, for the integrative structure modeling.

Furthermore, I have also contributed in a major way to the development of computational methods for the integration of SAXS (as well as FRET) data into the Integrative Modeling Platform (IMP), publishing 7 articles on this subject.

Future goals & Perspective

  • Integrate into one comprehensive picture of the structure, dynamics, and function of biomolecules
  • Provide key insights into development of new diagnostic and therapeutic tools
  • Perform sutiable structurally-informative experiemtns and develop computational methods to integrate diverse emerging sources of experimental data ranging from biophysical to genomic.