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Molecular Mechanisms Underlying Enhanced Hemichannel Function Of A Cataract-Associated Cx50 Mutant, Jun-Jie Tong, Umair Khan, Bassam George Haddad, Peter J. Minogue, Eric C. Beyer, Vivian M. Berthoud, Steve L. Reichow, Lisa Ebihra
Molecular Mechanisms Underlying Enhanced Hemichannel Function Of A Cataract-Associated Cx50 Mutant, Jun-Jie Tong, Umair Khan, Bassam George Haddad, Peter J. Minogue, Eric C. Beyer, Vivian M. Berthoud, Steve L. Reichow, Lisa Ebihra
Chemistry Faculty Publications and Presentations
Connexin-50 (Cx50) is among the most frequently mutated genes associated with congenital cataracts. Although most of these disease-linked variants cause loss of function because of misfolding or aberrant trafficking, others directly alter channel properties. The mechanistic bases for such functional defects are mostly unknown. We investigated the functional and structural properties of a cataract-linked mutant, Cx50T39R (T39R), in the Xenopus oocyte system. T39R exhibited greatly enhanced hemichannel currents with altered voltage-gating properties compared to Cx50 and induced cell death. Coexpression of mutant T39R with wild-type Cx50 (to mimic the heterozygous state) resulted in hemichannel currents whose properties were indistinguishable from …
Mechanisms Of Connexin-46 And -50 Intercellular Channel Function And Stability By Molecular Dynamics Simulations, Bassam George Haddad
Mechanisms Of Connexin-46 And -50 Intercellular Channel Function And Stability By Molecular Dynamics Simulations, Bassam George Haddad
Dissertations and Theses
Gap junctions make up a class of intercellular channels that characteristically connect the cytoplasm of directly apposed cells through large assemblies, or plaques, constituted by a multitude of intercellular channels. Gap junction mediated intercellular communication is critical for a variety of physiological functions, from coordinating electrical impulses in the heart and brain to maintaining homeostasis in most tissues. There are 21 isoforms of connexins, the constituent subunit of the gap junction, expressed in a tissue dependent manner. Gap junctions formed from different isoforms exhibit distinct biophysical properties, such as gating kinetics and sensitivity, as well as unique permeability and selectivity …
Functional Role Of The N-Terminal Domain In Connexin 46/50 By In Silico Mutagenesis And Molecular Dynamics Simulation, Umair Khan
University Honors Theses
Connexins form intercellular channels known as gap junctions that facilitate diverse physiological roles, from long-range electrical and chemical coupling to nutrient exchange. Recent structural studies on Cx46 and Cx50 have defined a novel and stable open state and implicated the amino-terminal (NT) domain as a major contributor to functional differences between connexin isoforms. This thesis presents two studies which use molecular dynamics simulations with these new structures to provide mechanistic insight into the function and behavior of the NTH in Cx46 and Cx50. In the first, residues in the NTH that differ between Cx46 and Cx50 are swapped between the …
Entropy Production And Volume Contraction In Thermostated Hamiltonian Dynamics, John D. Ramshaw
Entropy Production And Volume Contraction In Thermostated Hamiltonian Dynamics, John D. Ramshaw
Physics Faculty Publications and Presentations
Patra et al. [Int. J. Bifurcat. Chaos 26, 1650089 (2016)] recently showed that the time-averaged rates of entropy production and phase-space volume contraction are equal for several different molecular dynamics methods used to simulate nonequilibrium steady states in Hamiltonian systems with thermostated temperature gradients. This equality is a plausible statistical analog of the second law of thermodynamics. Here we show that those two rates are identically equal in a wide class of methods in which the thermostat variables z are determined by ordinary differential equations of motion (i.e., methods of the Nosé-Hoover or integral feedback control type). This …
Group I Intron Internal Guide Sequence Binding Strength As A Component Of Ribozyme Network Formation, Elizabeth Satterwhite, Jessica Anne Mellor Yeates, Niles Lehman
Group I Intron Internal Guide Sequence Binding Strength As A Component Of Ribozyme Network Formation, Elizabeth Satterwhite, Jessica Anne Mellor Yeates, Niles Lehman
Chemistry Faculty Publications and Presentations
Origins-of-life research requires searching for a plausible transition from simple chemicals to larger macromolecules that can both hold information and catalyze their own production. We have previously shown that some group I intron ribozymes possess the ability to help synthesize other ribozyme genotypes by recombination reactions in small networks in an autocatalytic fashion. By simplifying these recombination reactions, using fluorescent anisotropy, we quantified the thermodynamic binding strength between two nucleotides of two group I intron RNA fragments for all 16 possible genotype combinations. We provide evidence that the binding strength (KD) between the 3-nucleotide internal guide sequence …
Ribozyme/Duplex Binding Interactions As A Thermodynamic Basis For Chemical Game Theory, Elizabeth Satterwhite
Ribozyme/Duplex Binding Interactions As A Thermodynamic Basis For Chemical Game Theory, Elizabeth Satterwhite
University Honors Theses
Origins of life research requires searching for a plausible transition from simple chemicals to larger macromolecules that can both hold information and catalyze their own production. It has been shown that some classes of RNA molecules possess the ability to help other RNA molecules form by recombination reactions in an auto-catalytic fashion.1 By simplifying these recombination reactions, the thermodynamic binding strength between two nucleotides of two molecules can be quantified for all 16 possible genotype combinations. The purpose of this research is to provide evidence that the thermodynamic binding strength between the tag and internal guide sequence (IGS) is …
Allosteric Mechanism Of Water Channel Gating By Ca2+–Calmodulin, Steve Reichow, Daniel M. Clemens, J. Alfredo Freites, Karin L. Németh-Cahalan, Matthias Heyden, Douglas J. Tobias, James E. Hall, Tamir Gonen
Allosteric Mechanism Of Water Channel Gating By Ca2+–Calmodulin, Steve Reichow, Daniel M. Clemens, J. Alfredo Freites, Karin L. Németh-Cahalan, Matthias Heyden, Douglas J. Tobias, James E. Hall, Tamir Gonen
Chemistry Faculty Publications and Presentations
Calmodulin (CaM) is a universal regulatory protein that communicates the presence of calcium to its molecular targets and correspondingly modulates their function. This key signaling protein is important for controlling the activity of hundreds of membrane channels and transporters. However, our understanding of the structural mechanisms driving CaM regulation of full-length membrane proteins has remained elusive. In this study, we determined the pseudo-atomic structure of full-length mammalian aquaporin-0 (AQP0, Bos Taurus) in complex with CaM using electron microscopy to understand how this signaling protein modulates water channel function. Molecular dynamics and functional mutation studies reveal how CaM binding inhibits AQP0 …
Erratum: "Environmental Swap Energy And Role Of Configurational Entropy In Transfer Of Small Molecules From Water Into Alkanes", Pavel Smejtek, Robert Campbell Word
Erratum: "Environmental Swap Energy And Role Of Configurational Entropy In Transfer Of Small Molecules From Water Into Alkanes", Pavel Smejtek, Robert Campbell Word
Physics Faculty Publications and Presentations
Presents correction to an article related to configurational entropy in transfer of small molecules from water into alkanes, published in the 2005 issue of "The Journal Chemical Physics" and is available online at: http://archives.pdx.edu/ds/psu/8364
Environmental Swap Energy And Role Of Configurational Entropy In Transfer Of Small Molecules From Water Into Alkanes, Pavel Smejtek, Robert Campbell Word
Environmental Swap Energy And Role Of Configurational Entropy In Transfer Of Small Molecules From Water Into Alkanes, Pavel Smejtek, Robert Campbell Word
Physics Faculty Publications and Presentations
We studied the effect of segmented solvent molecules on the free energy of transfer of small molecules from water into alkanes (hexane, heptane, octane, decane, dodecane, tetradecane, and hexadecane). For these alkanes we measured partition coefficients of benzene, 3-methylindole (3MI), 2,3,4,6-tetrachlorophenol (TeCP), and 2,4,6-tribromophenol (TriBP) at 3, 11, 20, 3, and 47 °C. For 3MI, TeCP, and TriBP the dependence of free energy of transfer on length of alkane chains was found to be very different from that for benzene. In contrast to benzene, the energy of transfer for 3MI, TeCP, and TriBP was independent of the number of carbons …
Decay Of Molecules At Spherical Surfaces: Nonlocal Effects, P.T. Leung
Decay Of Molecules At Spherical Surfaces: Nonlocal Effects, P.T. Leung
Physics Faculty Publications and Presentations
The decay rates for molecules in the vicinity of a metallic sphere are investigated in a phenomenological approach for very close molecule-surface distances d. The Fuchs-Claro model [Phys. Rev. B 35, 3722 (1987)] is adopted to describe the polarizability of the sphere with the nonlocal dielectric response being accounted for within the hydrodynamic description. The results show significant differences when compared with those obtained previously within a local description for dlsim50 Aring, with extra resonances observed in the high-frequency regime, a phenomenon similar to that noted previously by Ruppin (1982), in his calculation of the extinction cross section for such …
Energy-Transfer Theory For The Classical Decay Rates Of Molecules At Rough Metallic Surfaces, P.T. Leung, Thomas F. George
Energy-Transfer Theory For The Classical Decay Rates Of Molecules At Rough Metallic Surfaces, P.T. Leung, Thomas F. George
Physics Faculty Publications and Presentations
The problem of the decay rates for molecules at rough metallic surfaces is considered, where the classical electromagnetic energy-transfer theory of Chance, Prock, and Silbey for a flat surface is generalized to the case of a rough boundary. A dynamical theory is constructed through the combination of the Sommerfeld antenna theory and the integral equation formalism of Maxwell's equations at rough boundaries established mainly by Maradudin, Mills, and Agarwal. Perturbative solutions are obtained and numerical results are given with reference to a shallow sinusoidal grating surface. The results, when compared with those obtained previously from the application of the image …
An Approximate Variational Method For Improved Thermodynamics Of Molecular Fluids, M. S. Shaw, J. D. Johnson, John D. Ramshaw
An Approximate Variational Method For Improved Thermodynamics Of Molecular Fluids, M. S. Shaw, J. D. Johnson, John D. Ramshaw
Physics Faculty Publications and Presentations
For a certain class of thermodynamic perturbation theories, a generalization of the Gibbs-Bogoliubov inequality holds through second order of perturbation theory and for a subset of terms the inequality is true to infinite order. Using this approximate variational principle, a perturbation theory is chosen for which the Helmholtz free energy of the reference system is minimized under the constraint that the first order term is identically zero. We apply these ideas to the determination of effective spherical potentials that accurately reproduce the thermodynamics of nonspherical molecular potentials. For a diatomic-Lennard-Jones (DLJ) potential with l ∕σ = 0.793, the resulting spherical …
Brownian Motion In A Flowing Fluid, John D. Ramshaw
Brownian Motion In A Flowing Fluid, John D. Ramshaw
Physics Faculty Publications and Presentations
A phenomenological theory is developed for Brownian motion in a flowing incompressible fluid. The Brownian particles are regarded as an ideal gas subject to a position- and time-dependent force field that represents interactions with the host fluid. This approach immediately leads to deterministic partial differential equations of motion for the Brownian particles. These equations are then examined in the limit of large friction, in which they imply an expression for the diffusional mass flux of Brownian particles. This expression is a sum of terms representing concentration, forced, thermal, and pressure diffusion. Comparisons are made with earlier work, and with the …