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Articles 1 - 7 of 7
Full-Text Articles in Biophysics
Microtubule Self-Organization With Active And Passive Crosslinkers, Prashali Chauhan
Microtubule Self-Organization With Active And Passive Crosslinkers, Prashali Chauhan
Dissertations - ALL
Humans have always been trying to unravel principles that guide how things around us function, all the way from galactic ovements to basic building blocks of matter. The physical and chemical properties of ‘biological’ systems govern processes all the way from molecular interactions of proteins to the form and function of individual living organisms. In this work, I focus on the proteins which help give shape and structure to the smallest building block of life, the cell and associated mechanisms of building fundamental cellular architectures, like the mitotic spindle. Mitosis takes place by microtubules aligning themselves in anti-parallel fashion with …
Vimentin Inside And Outside The Cell: From Cell Spreading To Nuclear Mechanics To Covid-19, Maxx Swoger
Vimentin Inside And Outside The Cell: From Cell Spreading To Nuclear Mechanics To Covid-19, Maxx Swoger
Dissertations - ALL
Cells are constantly subjected to both external forces encountered from the extracellular environment and internal stresses generated by the cell necessary to migrate and undergo healthy cellular function. Central to the ability of cells to both generate and mediate forces is the cell cytoskeleton, which forms the muscles and bones for cells. There are three main components of the cell cytoskeleton: microtubules, actin, and intermediate filaments. The role of actin and microtubules in cell function, particularly force generation and mediation have been well studied; however, the role of intermediate filaments is less understood. Intermediate filaments represent a broad and diverse …
Wdr5 Network Analysis Using Ensemble Approaches, Ali Imran
Wdr5 Network Analysis Using Ensemble Approaches, Ali Imran
Dissertations - ALL
Understanding the properties of protein-protein interactions (PPIs) is necessary to deconvolute the processes inside living organisms. As such, research in this regard has significant implications for gaining insight into cancers and other diseases. Once understood, drugs can be designed to target these diseases. In these chapters we focus on the network of interactions of WD40 repeat protein 5 (WDR5), a known hub protein. Several of its interactions are significant for regulation of histone methylation and consequently epigenetic regulation. These interacting partners include the SET1 family of proteins and retinoblastoma binding protein-5 (RbBP5). In this work we used multiple ensemble measurement …
Self-Organization Of Microtubule And Associated Protein Map65, Sumon Sahu
Self-Organization Of Microtubule And Associated Protein Map65, Sumon Sahu
Dissertations - ALL
One of the most fascinating micron-scale structures in the biological world is the cell cytoskele- ton, with numerous components of different sizes, shapes, and geometries working together. How the local interactions of these macromolecules and polymers in nano-scale help self- organize into this higher-order micron-scale structure remains an open question in the field of biophysics. In this thesis, via a minimal two-protein in vitro system containing cytoskeletal fiber microtubule and associated protein MAP65, I try to address self-organization through passive entropic force mechanisms. I use techniques like protein purification, light microscopy, and image analysis to quantify my results. First, I …
The Phase Behavior Of Ubqln Proteins And Implications For Protein Quality Control, Yiran Yang
The Phase Behavior Of Ubqln Proteins And Implications For Protein Quality Control, Yiran Yang
Dissertations - ALL
The ubiquitin-proteasome system (UPS) and autophagy are essential pathways for maintaining protein quality control (PQC) in cells. Misfolded proteins and large aggregates are cleared by UPS and autophagy signaled by ubiquitin (Ub) or polyubiquitin (polyUb) chains. Shuttle proteins facilitate cargo transporting by interacting with both ubiquitin and degradation machineries. Previously, our lab discovered that the shuttle protein Ubiquilin-2 (UBQLN2) is recruited to stress granules in cells and undergoes liquid-liquid phase separation (LLPS) in vitro. LLPS is a biophysical process by which proteins separate themselves from the surrounding aqueous solution by forming protein-rich droplets. The overarching goals of this work are …
Direct Single Molecule Imaging Of Enhanced Diffusion For Enzymes And Enzyme-Conjugated Dna Origami, Mengqi Xu
Direct Single Molecule Imaging Of Enhanced Diffusion For Enzymes And Enzyme-Conjugated Dna Origami, Mengqi Xu
Dissertations - ALL
Enzymes have been shown to diffuse faster in the presence of their substrates. Recently, we revealed new insights into this process of enhanced diffusion using single-particle tracking (SPT) with total internal reflection fluorescence (TIRF) microscopy. We found that the mobility of individual enzymes was enhanced three-fold in the presence of the substrate, and the motion remained Brownian. We showed that the relative increase in diffusion is independent of the total enzyme concentrations; and the oligomerization state of enzymes did not change during the catalytic turnover. These experiments ruled out the possibility that the enhanced enzyme diffusion was caused by the …
Characterizing Multivalent Interactions Between Folded Protein Domains And Intrinsically Disordered Regions Or Peptide Substrates, Tongyin Zheng
Characterizing Multivalent Interactions Between Folded Protein Domains And Intrinsically Disordered Regions Or Peptide Substrates, Tongyin Zheng
Dissertations - ALL
Protein-protein interactions (PPIs) play central roles in most biological processes. Studying PPIs is a fundamental step in understanding the molecular basis of cellular processes such as cell-cell contact, enzyme activity, and transient assembly of signaling complexes or cellular structures. In this work, we employed a combination of biophysical and biochemical methods to characterize PPIs, with a focus on interactions between structured domains and intrinsically disordered regions or peptide substrates.The subject of Chapter two is prolyl isomerase Ess1, which is an essential enzyme found in Saccharomyces cerevisiae. Ess1 regulates the transcription and co-transcriptional RNA processing by catalyzing the isomerization of serine-proline …