Identification of Molecular Structure in Biomolecular Condensates

Liquid-liquid phase separation (LLPS) is a key mechanism for the formation of biomolecular condensates, including typical membrane-free organelles (nucleoli, nuclear speckles and stress granules), as well as heterochromatin, super-enhancers, centrosomes and precursors. They have multiple roles in cells, including cellular signaling, RNA metabolism, stress adaptation, transcription and the organization of neuronal synapses in the brain. Their assembly and composition are tightly controlled by the cell and their dysregulation has been associated with cancer, neurodegenerative diseases and aging. Understanding the molecular mechanisms of cohesive function requires an understanding of the structure of their components. Current knowledge suggests that multivalent interactions mediating LLPS are mediated by folded structural domains connected by disordered junctions or by favorable interaction residues or motifs within intrinsically disordered regions (IDRs).

Fig. 1. (Super-)molecular structural properties that define dense phases. (Peran I, et al., 2020)

Customized Services

A full understanding of the molecular function of biomolecular condensates requires a comprehensive understanding of the structural features of phase separation-mediated interactions and the supramolecular structure within the dense phase. We expect to utilize a combination of solution- and solid-state-NMR spectroscopy, scattering and single-molecule fluorescence techniques, and molecular simulations to help our clients understand the structural features of condensates at the molecular level.

Based on our understanding of LLPS-mediated molecular mechanisms and molecular structures within liquid dense phases, CD BioSciences provides comprehensive services for the characterization of molecular structures of biomolecular condensates.

• Analysis of Protein Primary and Secondary Structure in Biomolecular Condensates
  Membraneless organelle components containing intrinsically disordered low-complexity structural domains are enriched for proteins and assembled into amyloid-like protofibrils with crossed β-structures. We analyze the LLPS process using a solid-state-NMR spectroscopic approach for structural characterization of the protofibrils. In addition, we provide a solution-NMR spectroscopy method to analyze the structure of low-complexity domains in the dense phase.
• Analysis of Protein Tertiary Structure in Biomolecular Condensates
  Folded structural domain repeats in phase-separated proteins interact with linear motif repeats in the binding mate through multivalent interactions. We can help you identify the high-resolution structure of individual complexes. In addition, we can visually anticipate specific properties that affect the supramolecular structure within the dense phase, such as linkage length and sequence.
• Analysis of DNA Structure in Biomolecular Condensates
  Structural features of DNA can facilitate phase separation and influence the properties of the resulting biomolecular condensates. We can help you characterize specific DNA sequences and local structures, providing information on local flexibility of DNA, flexibility of DNA, 3D features of the genome and DNA modifications in LLPS.
• Analysis of RNA Structure in Biomolecular Condensates
  RNA is an important component of biomolecular condensates and facilitates phase separation through RNA/RNA and protein/RNA interactions. We develop cutting-edge techniques to determine the structure of dense-phase RNA and the supramolecular structure formed.

Our Methods for Analyzing the Structure of Biomolecular Condensates

• X-ray diffraction.
• Cryo-electron microscopy and tomography.
• Scattering methods.
• Single molecule fluorescence spectroscopy.

Working closely with international biophysicists and structural biologists, we are committed to quantifying whole-phase behavior, material properties, and the atomic and supramolecular structure of dense phases. We use a multi-pronged approach that includes characterization of structure and dynamics at multiple length and time scales. Identifying all members of a biomolecular condensate helps gain a deeper understanding of the internal structure and dynamics that give the condensate its function and offers new opportunities for discovery and innovation. If you have any special requirements for our services, please feel free to contact us. We are looking forward to working together with your attractive projects.