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Mechanism Of Fiber Assembly: Treatment Of Aβ Peptide Aggregation With A Coarse-Grained United-Residue Force Field, Ana Rojas, Adam Liwo, Dana Browne, Harold A. Scheraga
Mechanism Of Fiber Assembly: Treatment Of Aβ Peptide Aggregation With A Coarse-Grained United-Residue Force Field, Ana Rojas, Adam Liwo, Dana Browne, Harold A. Scheraga
Faculty Publications
The growth mechanism of β-amyloid (Aβ) peptide fibrils was studied by a physics-based coarse-grained united-residue model and molecular dynamics (MD) simulations. To identify the mechanism of monomer addition to an Aβ1-40 fibril, we placed an unstructured monomer at a distance of 20 Å from a fibril template and allowed it to interact freely with the latter. The monomer was not biased towards fibril conformation by either the force field or the MD algorithm. With the use of a coarse-grained model with replica-exchange molecular dynamics, a longer timescale was accessible, making it possible to observe how the monomers probe different binding …
Molecular Dynamics Simulations Suggest That Rna Three-Way Junctions Can Act As Flexible Rna Structural Elements In The Ribosome, Neocles B. Leontis, Ivana Beššová, Kamila Réblová, Jiří Šponer
Molecular Dynamics Simulations Suggest That Rna Three-Way Junctions Can Act As Flexible Rna Structural Elements In The Ribosome, Neocles B. Leontis, Ivana Beššová, Kamila Réblová, Jiří Šponer
Chemistry Faculty Publications
We present extensive explicit solvent molecular dynamics analysis of three RNA three-way junctions (3WJs) from the large ribosomal subunit: the 3WJ formed by Helices 90-92 (H90-H92) of 23S rRNA; the 3WJ formed by H42-H44 organizing the GTPase associated center (GAC) of 23S rRNA; and the 3WJ of 5S rRNA. H92 near the peptidyl transferase center binds the 3'-CCA end of amino-acylated tRNA. The GAC binds protein factors and stimulates GTP hydrolysis driving protein synthesis. The 5S rRNA binds the central protuberance and A-site finger (ASF) involved in bridges with the 30S subunit. The simulations reveal that all three 3WJs possess …
Applications Of Molecular Dynamics Techniques And Spectroscopic Theories To Aqueous Interfaces, Anthony Green
Applications Of Molecular Dynamics Techniques And Spectroscopic Theories To Aqueous Interfaces, Anthony Green
USF Tampa Graduate Theses and Dissertations
The primary goal of spectroscopy is to obtain molecularly detailed information about the system under study. Sum frequency generation (SFG) vibrational spectroscopy is a nonlinear optical technique that is highly interface specific, and is therefore a powerful tool for understanding interfacial structure and dynamics. SFG is a second order, electronically nonresonant, polarization experiment and is consequently dipole forbidden in isotropic media such as a bulk liquid. Interfaces, however, serve to break the symmetry and produce a signal. Theoretical approximations to vibrational spectra of O-H stretching at aqueous interfaces are constructed using time correlation function (TCF) and instantaneous normal mode (INM) …
A Study Of Grain Rotations And Void Nucleation In Aluminum Triple Junctions Using Molecular Dynamics And Crystal Plasticity, Matthew William Priddy
A Study Of Grain Rotations And Void Nucleation In Aluminum Triple Junctions Using Molecular Dynamics And Crystal Plasticity, Matthew William Priddy
Theses and Dissertations
This study focuses on molecular dynamics (MD) simulations, coupled with a discrete mathematical framework, and crystal plasticity (CP) simulations to investigate micro void nucleation and the plastic spin. The origin and historical use of the plastic spin are discussed with particular attention to quantifying the plastic spin at the atomistic scale. Two types of MD simulations are employed: (a) aluminum single crystals undergoing simple shear and (b) aluminum triple junctions (TJ) with varying grain orientations and textures undergoing uniaxial tension. The high-angle grain boundary simulations nucleate micro voids at or around the TJ and the determinant of the deformation gradient …
Event-Driven Molecular Dynamics Simulations Of Protein Mixtures, Marek Cyran
Event-Driven Molecular Dynamics Simulations Of Protein Mixtures, Marek Cyran
Theses
The structure of liquids is central to their thermodynamic properties and is described in a probabilistic manner. The structure is a consequence of the forces between the molecules and may be investigated with the use of many techniques. One of these techniques is the use of computer simulation, and in particular the techniques are called Monte Carlo Statistical Thermodynamic simulation, and Molecular Dynamics. In this thesis we construct a program that is capable of carrying out Event-Driven Molecular Dynamics simulation of mixtures of particles that have stepwise constant pair potential energies. We have implemented our simulation for the case of …
Intrinsic Contact Geometry Of Protein Dynamics, Yosi Shibberu, Allen Holder, David Cooper
Intrinsic Contact Geometry Of Protein Dynamics, Yosi Shibberu, Allen Holder, David Cooper
Mathematical Sciences Technical Reports (MSTR)
We introduce a new measure for comparing protein structures that is especially applicable to analysis of molecular dynamics simulation results. The new measure generalizes the widely used root-mean-squared-deviation (RMSD) measure from three dimensional to n-dimensional Euclidean space, where n equals the number of atoms in the protein molecule. The new measure shows that despite significant fluctuations in the three dimensional geometry of the estrogen receptor protein, the protein's intrinsic contact geometry is remarkably stable over nanosecond time scales. The new measure also identifies significant structural changes missed by RMSD for a residue that plays a key biological role in …
The Mechanism Of Mitochondrial Folate Transport By The Mitochondrial Folate Transporter, Scott Alan Lawrence
The Mechanism Of Mitochondrial Folate Transport By The Mitochondrial Folate Transporter, Scott Alan Lawrence
Theses and Dissertations
The mitochondrial folate transport protein (MFT) functions to transport folates into the mitochondrial matrix. The MFT is a member of a mitochondrial carrier family (MCF) of proteins that have a high degree of sequence and structural similarities, yet they transport vastly different substrates at high specificities. In this dissertation research, the folate-specific transport mechanism of the MFT was explored using experimental and computational techniques. MFT residues that differed from MCF consensus residues in conserved PxD/ExxK/R motifs and at a predicted substrate-binding site common to all MCF proteins were investigated. Site-directed mutagenesis of these anomalous residues in the MFT revealed that …
An Analysis Of Prominent Water Models By Molecular Dynamics Simulations, Quentin Ramon Johnson
An Analysis Of Prominent Water Models By Molecular Dynamics Simulations, Quentin Ramon Johnson
Chemistry Theses
Water is the most common solvent for most biological reactions, therefore it is vital that we fully understand water and all its properties. The complex hydrogen bonding network that water forms can influence protein-protein and protein-substrate interactions and can slow protein conformational shifts. Here, I examine an important property of water known as energetic roughness. The network of interactions between individual water molecules affect the energy landscape of proteins by altering the underlying energetic roughness. I have attributed this roughness to the making and breaking of hydrogen bonds as the network of hydrogen bonds constantly adopts new conformations. Through a …
Conformational Dynamics Of Single Pre-Mrna Molecules During In Vitro Splicing, J. Abelson, M. Blanco, M. A. Ditzler, F. Fuller, P. Aravamudhan, M. Wood, T. Villa, D. E. Ryan, J. A. Pleiss, Corina Maeder, C. Guthrie
Conformational Dynamics Of Single Pre-Mrna Molecules During In Vitro Splicing, J. Abelson, M. Blanco, M. A. Ditzler, F. Fuller, P. Aravamudhan, M. Wood, T. Villa, D. E. Ryan, J. A. Pleiss, Corina Maeder, C. Guthrie
Chemistry Faculty Research
The spliceosome is a complex small nuclear RNA (snRNA)-protein machine that removes introns from pre-mRNAs via two successive phosphoryl transfer reactions. The chemical steps are isoenergetic, yet splicing requires at least eight RNA-dependent ATPases responsible for substantial conformational rearrangements. To comprehensively monitor pre-mRNA conformational dynamics, we developed a strategy for single-molecule FRET (smFRET) that uses a small, efficiently spliced yeast pre-mRNA, Ubc4, in which donor and acceptor fluorophores are placed in the exons adjacent to the 5′ and 3′ splice sites. During splicing in vitro, we observed a multitude of generally reversible time-and ATP-dependent conformational transitions of individual pre-mRNAs. The …
The Wrinkling Of Thin Elastic Sheets: Application To Cell Mechanics, Hamid Mohammadi
The Wrinkling Of Thin Elastic Sheets: Application To Cell Mechanics, Hamid Mohammadi
Digitized Theses
The wrinkling of thin sheets has been of great interest in various fields ranging from mechanics to biology. Despite significant progress in understanding the morphology and the dynamics of wrinkling patterns under static boundary conditions, little is known about how wrinkles behave when they are extremely driven. When in contact with an adhering particle, elastic sheets possess competing mechanically stable, wrinkled geometries if their thickness is below a critical value. In this thesis, molecular dynamics simulations are used to show that adhering particles moving laterally over a wrinkled elastic sheet induce instability transition of the wrinkles. These dynamics produce a …
Development Of Atomistic Potentials For Silicate Materials And Coarse-Grained Simulation Of Self-Assembly At Surfaces, Brian Barnes
Development Of Atomistic Potentials For Silicate Materials And Coarse-Grained Simulation Of Self-Assembly At Surfaces, Brian Barnes
All Theses and Dissertations (ETDs)
This thesis is composed of two parts. The first is a study of evolutionary strategies for parametrization of empirical potentials, and their application in development of a charge-transfer potential for silica. An evolutionary strategy was meta-optimized for use in empirical potential parametrization, and a new charge-transfer empirical model was developed for use with isobaric-isothermal ensemble molecular dynamics simulations. The second is a study of thermodynamics and self-assembly in a particular class of athermal two-dimensional lattice models. The effects of shape on self-assembly and thermodynamics for polyominoes and tetrominoes were examined. Many interesting results were observed, including complex clustering, non-ideal mixing, …
An Examination Of Oxysterol Effects On Membrane Bilayers Using Molecular Dynamics Simulations, Brett Olsen
An Examination Of Oxysterol Effects On Membrane Bilayers Using Molecular Dynamics Simulations, Brett Olsen
All Theses and Dissertations (ETDs)
My thesis work focuses on understanding the role of biological membranes in cellular processes. I am particularly interested in how small molecules perturb membrane structure and regulate membrane function. Membranes are primarily responsible for segregating different compartments of biological cells from each other. However, they have other roles as well, including influencing signal transduction in the cell, both through associated membrane proteins and directly through alterations in membrane organization. In order to understand how small molecules change membranes, I use molecular dynamics simulations of small simplified membranes to examine, at an atomic-level detail, how the addition of small molecules to …
A Study Of The Elongation Of Fibrils Of The Alzheimer's Amyloid Beta Protein With A Coarse-Grained Force Field, Ana Rojas
LSU Doctoral Dissertations
Alzheimer’s disease (AD) is a brain disorder named after the German psychiatrist Alois Alzheimer, who first described the disease in 1906. AD is a form of dementia, characterized by impairment of memory and other intellectual abilities, caused by the loss of neurons and synapses (the structures that permit communication between neurons) in certain regions of the brain. Although the mechanism by which neurons are affected is not yet well understood, research points to a small protein, the beta-amyloid peptide (Abeta), as the first suspect. Ab chains are present in the brains of healthy individuals, but in AD patients, they associate …