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Articles 1 - 8 of 8
Full-Text Articles in Biological and Chemical 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
All Dissertations
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, …
Protein Conformational Entropy Is Not Slaved To Water, Bryan S Marques, Matthew A Stetz, Christine Jorge, Kathleen G Valentine, A Joshua Wand, Nathaniel V Nucci
Protein Conformational Entropy Is Not Slaved To Water, Bryan S Marques, Matthew A Stetz, Christine Jorge, Kathleen G Valentine, A Joshua Wand, Nathaniel V Nucci
College of Science & Mathematics Departmental Research
Conformational entropy can be an important element of the thermodynamics of protein functions such as the binding of ligands. The observed role for conformational entropy in modulating molecular recognition by proteins is in opposition to an often-invoked theory for the interaction of protein molecules with solvent water. The "solvent slaving" model predicts that protein motion is strongly coupled to various aspects of water such as bulk solvent viscosity and local hydration shell dynamics. Changes in conformational entropy are manifested in alterations of fast internal side chain motion that is detectable by NMR relaxation. We show here that the fast-internal side …
Information Content, Charge Transport Properties, And Computational Capacities Of Proteins, Joseph Murphy Brisendine Jr.
Information Content, Charge Transport Properties, And Computational Capacities Of Proteins, Joseph Murphy Brisendine Jr.
Dissertations, Theses, and Capstone Projects
This thesis is the beginning of an attempt to build a coherent theory of the properties of proteins based in information theory and the duality of information theory and nonequilibrium thermodynamics. Throughout, we will adopt the viewpoint that information can act as a thermodynamic potential, which is necessary to understand how biological processes are both enabled and constrained by the laws of thermodynamics. Understanding information as a form of thermodynamic potential also clarifies the description of proteins and other biological macromolecules as “molecular machines”: meso-scale structures with emergent causal powers which perform work on their environments by irreversibly dissipating energy …
A Lego® Brewster Angle Microscope For Quantitative Monolayer Film Analysis, Nicholas Benz
A Lego® Brewster Angle Microscope For Quantitative Monolayer Film Analysis, Nicholas Benz
Physics
In order to study single-molecule thick films and their phase behavior we built a Brewster Angle Microscope (BAM). BAM’s are inherently expensive due to their accuracy and precision. We built a fully functional BAM using Lego® Mindstorm® kits for the fraction of the price of a commercial BAM. And by utilizing the 10µm patented Lego® tolerance, comparable accuracy was attained. The BAM was mounted to a Langmuir-trough and will be used for laboratory experiments for optics and physical chemistry along with research on lung surfactant and on liquid crystals.
Biophysical Interaction Between Nanoparticles And Biomolecules, Slaven Radic
Biophysical Interaction Between Nanoparticles And Biomolecules, Slaven Radic
All Dissertations
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 …
Continued Development Of An Empirical Function For Predicting And Rationalizing Protein–Protein Binding Affinities, Joseph Audie
Continued Development Of An Empirical Function For Predicting And Rationalizing Protein–Protein Binding Affinities, Joseph Audie
Chemistry & Physics Faculty Publications
Here we summarize recent work on the continued development of our fast and simple empirical equation for predicting and structurally rationalizing protein–protein and protein–peptide binding affinities. Our empirical expression consists of six regression-weighted physical descriptors and derives from two key simplifying assumptions: (1) the assumption of rigid-body association and (2) the assumption that all contributions not explicitly considered in the equation make a net contribution to binding of ≈0 kcal. Within the strict framework of rigid-body association, we tested relative binding affinity predictions using our empirical equation against the corresponding experimental binding free energy data for 197 interface alanine mutants. …
A Novel Empirical Free Energy Function That Explains And Predicts Protein–Protein Binding Affinities, Joseph Audie, Suzanne Scarlata
A Novel Empirical Free Energy Function That Explains And Predicts Protein–Protein Binding Affinities, Joseph Audie, Suzanne Scarlata
Chemistry & Physics Faculty Publications
A free energy function can be defined as a mathematical expression that relates macroscopic free energy changes to microscopic or molecular properties. Free energy functions can be used to explain and predict the affinity of a ligand for a protein and to score and discriminate between native and non-native binding modes. However, there is a natural tension between developing a function fast enough to solve the scoring problem but rigorous enough to explain and predict binding affinities. Here, we present a novel, physics-based free energy function that is computationally inexpensive, yet explanatory and predictive. The function results from a derivation …