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Full-Text Articles in Physics
Supertertiary Structural Dynamics Modulate Function In Postsynaptic Density Protein 95, George L. Hamilton Iii
Supertertiary Structural Dynamics Modulate Function In Postsynaptic Density Protein 95, George L. Hamilton Iii
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Proteins, RNA, and DNA serve as the primary sub-cellular machinery that give rise to the necessary functions of life. The long-standing paradigm has been that the structures of biomolecules, or the arrangement of the subunits that make up a biomolecule, determine biological function. However, biomolecules are not static objects. Instead, they often undergo structural rearrangements that are crucial to enabling and regulating their functions. In my thesis I present several studies of the interplay between the structures, dynamics, and functions of biomolecules that combine experimental fluorescence spectroscopy and computational methods to probe these systems at the single-molecule level. In particular, …
Biophysical Interaction Between Nanoparticles And Biomolecules, Slaven Radic
Biophysical Interaction Between Nanoparticles And Biomolecules, Slaven Radic
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In the last two decades nanotechnology market has undergone remarkable growth. Breakthroughs in nanomaterial synthesis increased diverse nanomaterials production and subsequently their application. Owing to its large surface to volume ratio and remarkable physical properties not seen in the bulk materials, nanoparticles are finding emerging use in industry and medicine. Hence, it is expectable that at some point these nanomaterials will end up released into the environment and interact with bio systems. The purpose of this dissertation is to elicit implications of nanomaterial transformation once it gets inside biological milieu.
Delphi Web Server: A Comprehensive Online Suite For Electrostatic Calculations Of Biological Macromolecules And Their Complexes., Subhra Sarkar, Shawn Witham, Jie Zhang, Maxim Zhenirovskyy, Walter Rocchia
Delphi Web Server: A Comprehensive Online Suite For Electrostatic Calculations Of Biological Macromolecules And Their Complexes., Subhra Sarkar, Shawn Witham, Jie Zhang, Maxim Zhenirovskyy, Walter Rocchia
Publications
Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output …