Seminars

Abstract

Protein folding research has been dominated by the assumption that thermodynamics determines protein structure and function. And that when the folding process is compromised in vivo the proteostasis machinery — chaperones, deaggregases, the proteasome — work to restore proteins to their soluble, functional form or degrade them to maintain the cellular pool of proteins in a quasi-equilibrium state. During the past decade, however, more and more proteins have been identified for which altering only their speed of synthesis alters their structure and function, the efficiency of the down-stream processes they take part in, and cellular phenotype. Indeed, evidence has emerged that evolutionary selection pressures have encoded translation-rate information into mRNA molecules to coordinate diverse co-translational processes. Thus, non-equilibrium physics can play a fundamental role in influencing nascent protein behavior, mRNA sequence evolution, and disease. In this talk I will discuss my lab's efforts to understand and model this phenomenon through the development application of theoretical tools from the physical sciences including coarse-grained simulations, chemical kinetics and statistical mechanics.

Abstract

Biological macromolecules function in dense, crowded cellular environments. Early studies of crowding effects have emphasized volume exclusion effects, but it is becoming clear that frequent non-specific interactions between proteins, nucleic acids, and metabolites may be the more important factor in modulating the structure and dynamics of biomolecules. Computer simulation studies at different scales of a series of models ranging from concentrated homogeneous protein solutions to models of bacterial cytoplasms are presented to explore the effects of non-specific quinary protein-protein interactions on protein stability and dynamics. One focus is on the formation of transient clusters that determine diffusive properties and lead to liquid-liquid phase transitions. The computational results are related to existing experimental data and the challenges and opportunities to expand the current studies to whole-cell modeling in molecular detail are discussed.

Abstract

Carcinoma-associated fibroblasts (CAFs) can be detected during early stages of cancer development in tumor stroma. CAFs are often associated with high-grade malignancies of poor prognosis in breast cancer and other squamous cell carcinomas by secreting cytokines promoting cancer cells to replicate, metastasize and resist apoptosis. Understanding the mechanisms by which normal stroma-dwelling cells transform to CAFs might inspire strategies to suppress CAF induction and improve prognosis. Normal fibroblasts (NFs) in stroma can be induced to CAFs by exosomes containing microRNA and cytokines, which are secreted by cancer cells. However, it is not clear how these CAF-inducing factors secreted by cancer cells can reach stromal NFs on the other side of the basement membrane (BM) in vivo: At the early stages of breast cancer, cancer cells do not exhibit high expression of metalloproteases (MMPs) to digest extracellular matrix (ECM), which imposes a diffusion barrier for CAF-inducing factors to reach stroma. Microscopically, the diffusion barrier is formed by the laminin/fibronectin fibrils in the BM and collagen fibrils in the stroma. Moreover, at early stages cancer cells are not yet metastatic and cannot migrate into the proximity of stromal NFs. Despite the lack of physical proximity and low MMP secretion, we observed a series of force-dependent events initiated by cancer cells which might enable CAF induction. First, cancer cells use the strong forces to mechanically remodel the ECM fibril organization in the tumor microenvironment to enhance the diffusion of CAF-inducing factors. Second, cancer cells exert the forces to directly activate mechanosignaling pathways in the stromal fibroblasts to induce CAF phenotypes. In particular, we observed that the diffusion rate of CAF-inducing factors correlates with the degree of ECM fibril alignment, and is important in CAF induction. We found that it is early-stage breast cancer cells which align the ECM fibrils so that the diffusion rate is increased. Furthermore, we observed that ECM remodeling was associated with long-range (>1000 μm) mechanical forces collectively generated by epithelial spheroids. Overall, we conclude that cancer cells of epithelial origin can facilitate CAF induction, through long-range mechanical forces, by decreasing diffusion barrier across BM.