Phase Transition Biophysical Services of Biocondensates

Many functions of eukaryotic cells are confined to compartments that are not separated by membranes. At the linear size of the biological mesoscale, compartments are often tens or even hundreds of different macromolecules filling each individual compartment and interacting within it, thus conferring varying degrees of internal order on the compartment. The physicochemical drivers of compartment biogenesis, maintenance, and decomposition, as well as their ability to concentrate macromolecules in the absence of an encapsulating membrane, have attracted considerable interest. However, how building blocks interact to produce mesoscale structures that lack strong internal order is less well understood and more difficult to model. Phase transition physics provides a conceptual framework and a mathematical toolkit to describe the assembly, maintenance, and solubilization of biomolecular condensates. Several analytical frameworks have been used to describe the phase behavior of biomolecular condensates, including the Flory-Huggins theory, Huggins theory, etc.

Fig. 1. Hierarchy of compartment assembly. (Musacchio A, 2022)

Customized Services

Focusing on the identification, characterization, and visualization of discrete and highly specific interactions of biomolecular condensates, our molecular biologists successfully develop a variety of quantitative and qualitative models for understanding intracellular phase transitions to help you analyze the mutual assembly and interactions between the building blocks of compartments. Here, we construct simple and powerful sticker-spacer models to map the sequence and structure of biomolecular condensates to the driving forces required for higher-order assembly.

Based on our strong expertise in liquid-liquid phase separation biophysics, CD BioSciences offers specialized phase transition biophysical services for condensates.

• Identification of Stickers and Spacers
  Extensive use of the sticker-spacer framework for analyzing the role of phase separation in membrane-free compartment biogenesis requires identification of stickers and spacers, with the following two main strategies:

Ⅰ. Identify individual residue types or short motifs in mutant sequences and determine their impact on the driving force of phase separation.

Ⅱ. Combine NMR spectroscopy and Monte Carlo simulation methods to identify aromatic residues and demonstrate their ability to form cohesive interactions by their ability to compress chains in a manner dependent on the number of aromatic residues.

• Determine the Strength of Sticker Interactions
  To help customers implement sticker and spacer models in simulations or through analytical theory, the strength of sticker interactions needs to be determined. Where the interaction strength of paired aromatic-aromatic interactions is extracted from the overall dimension of the set of variants that titrate the number of aromatic residues. Smaller interaction strengths were obtained by analyzing sticker-spacer and spacer-spacer interactions.

• Inspection of PTM in the Context of Sticker and Spacer Models
  PTM modifications alter the charge and hydrophobicity, thereby changing the molecular interactions in which proteins can participate, promoting or inhibiting LLPS driving forces, and modulating the material properties of the condensate. We provide examination of PTM in the context of the sticker-spacer model to help interpret and predict the effects of PTM.

Applications of Sticker-Spacer Models

• Provide a convenient framework to understand the driving forces of biomolecular condensate assembly.
• Quantitatively predict the phase behavior of variants.
• Quantify the effects of increasing and decreasing stickers.
• Predict the effect of changing sticker strength and pattern.
• Help understand the effect of spacer solventization.
• Help understand the effect of PTM on the phase behavior of condensates.
• Provide a mechanistic understanding of disease mutations.

Our sticker-spacer models provide a conceptual understanding of the drivers of phase separation of biomolecular condensates and which elements of the sequence are most important to their phase behavior. This model promises in the future to improve your ability to predict phase behavior from sequences alone, improve your understanding of biomolecular cohesion formation, and provide a strong physical basis for understanding a large number of biological processes. 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.