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Biochemistry, Biophysics, and Structural Biology Commons

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Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Tertiary Alphabet For The Observable Protein Structural Universe, Craig\ O. Mackenzie, Jianfu Zhou, Gevorg Grigoryan Nov 2016

Tertiary Alphabet For The Observable Protein Structural Universe, Craig\ O. Mackenzie, Jianfu Zhou, Gevorg Grigoryan

Open Dartmouth: Faculty Open Access Scholarship

Here, we systematically decompose the known protein structural universe into its basic elements, which we dub tertiary structural motifs (TERMs). A TERM is a compact backbone fragment that captures the secondary, tertiary, and quaternary environments around a given residue, comprising one or more disjoint segments (three on average). We seek the set of universal TERMs that capture all structure in the Protein Data Bank (PDB), finding remarkable degeneracy. Only ∼600 TERMs are sufficient to describe 50% of the PDB at sub-Angstrom resolution. However, more rare geometries also exist, and the overall structural coverage grows logarithmically with the number of TERMs ...


Dissection Of Molecular Assembly Dynamics By Tracking Orientation And Position Of Single Molecules In Live Cells, Shalin B. Mehta, Molly Mcquilken, Patrick J. La Riviere, Patricia Occhipinti, Amitabh Verma, Rudolf Oldenbourg, Amy Gladfelter, Tomomi Tani Sep 2016

Dissection Of Molecular Assembly Dynamics By Tracking Orientation And Position Of Single Molecules In Live Cells, Shalin B. Mehta, Molly Mcquilken, Patrick J. La Riviere, Patricia Occhipinti, Amitabh Verma, Rudolf Oldenbourg, Amy Gladfelter, Tomomi Tani

Open Dartmouth: Faculty Open Access Scholarship

Regulation of order, such as orientation and conformation, drives the function of most molecular assemblies in living cells but remains difficult to measure accurately through space and time. We built an instantaneous fluorescence polarization microscope, which simultaneously images position and orientation of fluorophores in living cells with single-molecule sensitivity and a time resolution of 100 ms. We developed image acquisition and analysis methods to track single particles that interact with higher-order assemblies of molecules. We tracked the fluctuations in position and orientation of molecules from the level of an ensemble of fluorophores down to single fluorophores. We tested our system ...


Septin Assemblies Form By Diffusion-Driven Annealing On Membranes, Andrew A. Bridges, Huaiying Zhang, Shalin B. Mehta, Patricia Occhipinti, Tomomi Tani, Amy S. Gladfelter Feb 2014

Septin Assemblies Form By Diffusion-Driven Annealing On Membranes, Andrew A. Bridges, Huaiying Zhang, Shalin B. Mehta, Patricia Occhipinti, Tomomi Tani, Amy S. Gladfelter

Open Dartmouth: Faculty Open Access Scholarship

Septins assemble into filaments and higher-order structures that act as scaffolds for diverse cell functions including cytokinesis, cell polarity, and membrane remodeling. Despite their conserved role in cell organization, little is known about how septin filaments elongate and are knitted together into higher-order assemblies. Using fluorescence correlation spectroscopy, we determined that cytosolic septins are in small complexes, suggesting that septin filaments are not formed in the cytosol. When the plasma membrane of live cells is monitored by total internal reflection fluorescence microscopy, we see that septin complexes of variable size diffuse in two dimensions. Diffusing septin complexes collide and make ...