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Other Biochemistry, Biophysics, and Structural Biology Commons™
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- Protein dynamics (2)
- Auxin (1)
- Bioinformatics (1)
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- Comparative Genomics (1)
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- Computational biophysics (1)
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- Protein evolution (1)
- Shoot Apical Meristem (1)
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Articles 1 - 4 of 4
Full-Text Articles in Other Biochemistry, Biophysics, and Structural Biology
Erecta Family Genes Regulate The Shoot Apical Meristem And Organ Formation, Daniel A. Degennaro
Erecta Family Genes Regulate The Shoot Apical Meristem And Organ Formation, Daniel A. Degennaro
Doctoral Dissertations
Plants are sessile and must adjust their organ growth to their environments. A reservoir of stem cells in the shoot apical meristem (SAM) supplies cells for differentiation into organs. The SAM must balance organ production with stem cell maintenance. The ERECTA family (ERfs) encodes the leucine-rich repeat receptor-like kinases ERECTA (ER), ERECTA-LIKE 1 (ERL1), and ERL2. ERf signaling regulates organ initiation and stem cell maintenance. Results presented in this work include the following:
1) WUSCHEL (WUS) and CLAVATA3 (CLV3) make up a negative feedback loop to maintain SAM size. WUS and CLV3 expression localization is critical for …
Computer Simulations Of Biological Systems: From Protein Dynamics To Drug Discovery, Rupesh Agarwal
Computer Simulations Of Biological Systems: From Protein Dynamics To Drug Discovery, Rupesh Agarwal
Doctoral Dissertations
Computational biophysics methods such as molecular dynamics (MD) simulations are often used in combination with experimental techniques like neutron scattering, NMR, and FTIR to explore protein conformational landscapes. With the improvements in experimental techniques, there is also a need to continually optimize the MD forcefield parameters to make precise predictions that match experimental results. To complement many of these experiments, an accurate model of deuteration is frequently required, but has been elusive. In our work, we developed a novel method to capture isotope effects in classical MD simulations by re-parameterization of the bonded terms of the CHARMM forcefield using quantum …
Complex Non-Equilibrium Structural Dynamics In Globular Proteins, Xiaohu Hu
Complex Non-Equilibrium Structural Dynamics In Globular Proteins, Xiaohu Hu
Doctoral Dissertations
Internal structural motions in proteins are essential to their functions. In this present dissertation, we present the results from an extensive set of molecular dynamics simulations of three very different globular proteins and demonstrate that the structural fluctuations observed are highly complex, manifesting in non-ergodic and self-similar subdiffusive dynamics with non-exponential relaxation behavior. The characteristic time of the motion observed at a given timescale is dependent on the length of the observation time, indicating an aging effect. By comparing the simulation results to the existing single-molecule fluorescence spectroscopic data on other globular proteins, we found the characteristic relaxation time for …
Comparative Genomics Of Microbial Chemoreceptor Sequence, Structure, And Function, Aaron Daniel Fleetwood
Comparative Genomics Of Microbial Chemoreceptor Sequence, Structure, And Function, Aaron Daniel Fleetwood
Doctoral Dissertations
Microbial chemotaxis receptors (chemoreceptors) are complex proteins that sense the external environment and signal for flagella-mediated motility, serving as the GPS of the cell. In order to sense a myriad of physicochemical signals and adapt to diverse environmental niches, sensory regions of chemoreceptors are frenetically duplicated, mutated, or lost. Conversely, the chemoreceptor signaling region is a highly conserved protein domain. Extreme conservation of this domain is necessary because it determines very specific helical secondary, tertiary, and quaternary structures of the protein while simultaneously choreographing a network of interactions with the adaptor protein CheW and the histidine kinase CheA. This dichotomous …