Conformations of Isolated Macromolecules in Solution and on the Surface

This dissertation studies different aspects of conformational properties of polymers. Two specific topics include (i) the deviations of single macromolecule conformations in the q-solution from the classical description, and (ii) conformations, order and flow of molecular brushes on solid surfaces. In solution we studied the deviations of single macromolecule conformations at the q-conditions from the predictions of classical theories. The previously unknown long range correlations in the conformations of linear polymers in a q-solvent were found using analytical calculations and molecular dynamics simulations. Long range power law decay of the bond vector correlation function hcosfi ¡« s.3/2 dominate the standard exponential decay hcosfi = e.s/lp , where f is the angle between the two bonds, s is their separation along the chain contour and lp is the persistence length. These long-range correlations lead to significant deviations of polymer size from ideal with mean square end-to-end distance hR2i.b2N ¡« ¡ÌN, where N is the number of Kuhn segments of size b. These findings are explained by a fine interplay of polymer connectivity and the non-zero range of monomer interactions. Moreover, this effect is not specific for dilute q-solutions and exists in semidilute solutions and melts of polymers. Our theory is in good agreement with the experimental data on Flory characteristic ratio, as well as with results of computer simulations. On surfaces, brush-like macromolecules were visualized by the atomic force microscopy (AFM). In order to quantitatively analyze conformations of visualized molecules we developed the corresponding algorithms and software. This software enables detection of the molecular contour, measurement of molecule size, area, orientational and nematic order parameters, etc. In addition, the automated procedure of molecular detection reduced the time and improved the quality of analysis of image series. Using our method we have studied the molecular weight and polydispersity of linear and multi-arm molecular brushes, the spontaneous curvature of grafted molecules, which is caused by competition of conformational entropy of side chains and elasticity of backbone, behavior of brushes in a matrix of linear polymer, the effect of structure of multi-armed brushes on their 2d orientational order, the dynamics and conformational transitions of individual molecules in the precursor layer of spreading droplet, the spontaneous scission of grafted molecules with long side-chains

Discrete Molecular Dynamics: An Efficient And Versatile Simulation Method For Fine Protein Characterization

Until now it has been impractical to observe protein folding in silico for proteins larger than 50 residues. Limitations of both force field accuracy and computational efficiency make the folding problem very challenging. Here we employ discrete molecular dynamics (DMD) simulations with an all-atom force field to fold fast-folding proteins. We extend the DMD force field by introducing long-range electrostatic interactions to model salt-bridges and a sequence-dependent semi-empirical potential accounting for natural tendencies of certain amino acid sequences to form specific secondary structures. We enhance the computational performance by parallelizing the DMD algorithm. Using a small number of commodity computers, we achieve sampling quality and folding accuracy comparable to the explicit-solvent simulations performed on high-end hardware. We demonstrate that DMD can be used to observe equilibrium folding of villin headpiece and WW domain, study two-state folding kinetics and sample near-native states in ab initio folding of proteins of ~100 residues

Hybrid Dynamics Simulation Engine for Metalloproteins

Quality computational description of metalloproteins is a great challenge due to the vast span of time- and lengthscales characteristic of their existence. We present an efficient new method that allows for robust characterization of metalloproteins. It combines quantum mechanical (QM) description of the metal-containing active site, and extensive dynamics of the protein captured by discrete molecular dynamics (DMD) (QM/DMD). DMD samples the entire protein, including the backbone, and most of the active site, except for the immediate coordination region of the metal. QM operates on the part of the protein of electronic and chemical significance, which may include tens to hundreds of atoms. The breathing quantum-classical boundary provides a continuous mutual feedback between the two machineries. We test QM/DMD using the Fe-containing electron transporter protein, rubredoxin, and its three mutants as a model. QM/DMD can provide a reliable balanced description of metalloproteins’ structure, dynamics, and electronic structure in a reasonable amount of time. As an illustration of QM/DMD capabilities, we then predict the structure of the Ca2+ form of the enzyme catechol O-methyl transferase, which, unlike the native Mg2+ form, is catalytically inactive. The Mg2+ site is ochtahedral, but the Ca2+ is 7-coordinate and features the misalignment of the reacting parts of the system. The change is facilitated by the backbone adjustment. QM/DMD is ideal and fast for providing this level of structural insight

Light Regulation of Protein Dimerization and Kinase Activity in Living Cells Using Photocaged Rapamycin and Engineered FKBP

We developed a new system for light-induced protein dimerization in living cells using a novel photocaged analog of rapamycin (pRap) together with an engineered rapamycin binding domain (iFKBP). Using focal adhesion kinase as a target, we demonstrated successful light-mediated regulation of protein interaction and localization in living cells. Modification of this approach enabled light-triggered activation of a protein kinase and initiation of kinase-induced phenotypic changes in vivo

Article pubs.acs.org/JPCB Discrete Molecular Dynamics: An Efficient And Versatile Simulation Method For Fine Protein Characterization

*S Supporting Information ABSTRACT: Until now it has been impractical to observe protein folding in silico for proteins larger than 50 residues. Limitations of both force field accuracy and computational efficiency make the folding problem very challenging. Here we employ discrete molecular dynamics (DMD) simulations with an all-atom force field to fold fast-folding proteins. We extend the DMD force field by introducing long-range electrostatic interactions to model salt-bridges and a sequence-dependent semiempirical potential accounting for natural tendencies of certain amino acid sequences to form specific secondary structures. We enhance the computational performance by parallelizing the DMD algorithm. Using a small number of commodity computers, we achieve sampling quality and folding accuracy comparable to the explicit-solvent simulations performed on high-end hardware. We demonstrate that DMD can be used to observe equilibrium folding of villin headpiece and WW domain, study two-state folding kinetics, and sample near-native states in ab initio folding of proteins of ∼100 residues

Hybrid Dynamics Simulation Engine for Metalloproteins

ABSTRACT Quality computational description of metalloproteins is a great challenge due to the vast span of time- and lengthscales characteristic of their existence. We present an efficient new method that allows for robust characterization of metalloproteins. It combines quantum mechanical (QM) description of the metal-containing active site, and extensive dynamics of the protein captured by discrete molecular dynamics (DMD) (QM/DMD). DMD samples the entire protein, including the backbone, and most of the active site, except for the immediate coordination region of the metal. QM operates on the part of the protein of electronic and chemical significance, which may include tens to hundreds of atoms. The breathing quantum-classical boundary provides a continuous mutual feedback between the two machineries. We test QM/DMD using the Fe-containing electron transporter protein, rubredoxin, and its three mutants as a model. QM/DMD can provide a reliable balanced description of metalloproteins ’ structure, dynamics, and electronic structure in a reasonable amount of time. As an illustration of QM/DMD capabilities, we then predict the structure of the Ca 2þ form of the enzyme catechol O-methyl transferase, which, unlike the native Mg 2þ form, is catalytically inactive. The Mg 2þ site is ochtahedral, but the Ca 2þ is 7-coordinate and features the misalignment of the reacting parts of the system. The change is facilitated by the backbone adjustment. QM/DMD is ideal and fast for providing this level of structural insight

Pore Dynamics and Conductance of RyR1 Transmembrane Domain

AbstractRyanodine receptors (RyR) are calcium release channels, playing a major role in the regulation of muscular contraction. Mutations in skeletal muscle RyR (RyR1) are associated with congenital diseases such as malignant hyperthermia and central core disease (CCD). The absence of high-resolution structures of RyR1 has limited our understanding of channel function and disease mechanisms at the molecular level. Previously, we have reported a hypothetical structure of the RyR1 pore-forming region, obtained by homology modeling and supported by mutational scans, electrophysiological measurements, and cryo-electron microscopy. Here, we utilize the expanded model encompassing six transmembrane helices to calculate the RyR1 pore region conductance, to analyze its structural stability, and to hypothesize the mechanism of the Ile4897 CCD-associated mutation. The calculated conductance of the wild-type RyR1 suggests that the proposed pore structure can sustain ion currents measured in single-channel experiments. We observe a stable pore structure on timescales of 0.2 μs, with multiple cations occupying the selectivity filter and cytosolic vestibule, but not the inner chamber. We further suggest that stability of the selectivity filter critically depends on the interactions between the I4897 residue and several hydrophobic residues of the neighboring subunit. Loss of these interactions in the case of polar substitution I4897T results in destabilization of the selectivity filter, a possible cause of the CCD-specific reduced Ca2+ conductance

Multiarm molecular brushes: Effect of the number of arms on the molecular weight polydispersity and surface ordering

Individual molecules of multiarm starlike molecular brushes were visualized by atomic force microscopy. In the studied series of brushes, the number of arms varied from one for a linear chain to four, while the length of the side chains was kept approximately constant. Molecular visualization provided a unique opportunity for independent size characterization of the brush arms separately from that of the entire molecule. In agreement with the Schulz-Flory theory for chain coupling, the polydispersity of the total length was significantly lower than that of the arm length. The variation in polydispersity had an effect on molecular ordering. Lateral compression of the starlike brushes caused a transition from an extended dendritic-like conformation to a compact disklike conformation. In contrast to one-, two-, and three-arm brushes, the four-arm molecules with a lower polydispersity index of 1.04 demonstrated local hexagonal order.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Descripción del desempeño reproductivo de cerdas puras y cruzadas en la Escuela Agrícola Panamericana

32 P.La Granja Porcina Educativa de la Escuela Agrícola Panamericana maneja tres razas puras y cruces, se realizó un análisis creando grupos contemporáneos por años desde el 2000 hasta el 2012, analizando nueve variables reproductivas, raza por raza y también por paridad. Además se realizaron correlaciones entre las variables: Lechones nacidos totales – peso promedio del lechón al nacimiento, lechones destetados – peso promedio al destete, longitud de lactancia – peso promedio del lechón al destete, largo de longitud – periodo abierto. Todos los datos obtenidos fueron generados por el programa Pigchamp®. Para cada variable reproductiva se crearon dos cuadros, uno por genética y otro por paridad. Las correlaciones se hicieron tomando las medias anuales de cada variable. El principal problema observado en la granja porcina es la alta mortalidad predestete (14%). Además la tasa de concepción no es la adecuada (72%), encontrándose muy por debajo de lo recomendado (84%). Las variables tuvieron mejor eficiencia en las cerdas cruzadas, lo cual nos indica que una correcta recombinación genética, potencializa el rendimiento del cerdo.1. Índice de cuadro, figuras y anexos 2. Introducción 3. Materiales y métodos 4. Resultados y discusión 5. Conclusiones 6. Recomendaciones 7. Literatura citada 8. Anexos