Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: the myoglobin case.

PubMed

Papaleo, Elena; Mereghetti, Paolo; Fantucci, Piercarlo; Grandori, Rita; De Gioia, Luca

2009-01-01

Several molecular dynamics (MD) simulations were used to sample conformations in the neighborhood of the native structure of holo-myoglobin (holo-Mb), collecting trajectories spanning 0.22 micros at 300 K. Principal component (PCA) and free-energy landscape (FEL) analyses, integrated by cluster analysis, which was performed considering the position and structures of the individual helices of the globin fold, were carried out. The coherence between the different structural clusters and the basins of the FEL, together with the convergence of parameters derived by PCA indicates that an accurate description of the Mb conformational space around the native state was achieved by multiple MD trajectories spanning at least 0.14 micros. The integration of FEL, PCA, and structural clustering was shown to be a very useful approach to gain an overall view of the conformational landscape accessible to a protein and to identify representative protein substates. This method could be also used to investigate the conformational and dynamical properties of Mb apo-, mutant, or delete versions, in which greater conformational variability is expected and, therefore identification of representative substates from the simulations is relevant to disclose structure-function relationship.

Two-dimensional vibrational spectroscopy of the amide I band of crystalline acetanilide: Fermi resonance, conformational substates, or vibrational self-trapping?

NASA Astrophysics Data System (ADS)

Edler, J.; Hamm, P.

2003-08-01

Two-dimensional infrared (2D-IR) spectroscopy is applied to investigate acetanilide, a molecular crystal consisting of quasi-one-dimensional hydrogen bonded peptide units. The amide-I band exhibits a double peak structure, which has been attributed to different mechanisms including vibrational self-trapping, a Fermi resonance, or the existence of two conformational substates. The 2D-IR spectrum of crystalline acetanilide is compared with that of two different molecular systems: (i) benzoylchloride, which exhibits a strong symmetric Fermi resonance and (ii) N-methylacetamide dissolved in methanol which occurs in two spectroscopically distinguishable conformations. Both 2D-IR spectra differ significantly from that of crystalline acetanilide, proving that these two alternative mechanisms cannot account for the anomalous spectroscopy of crystalline acetanilide. On the other hand, vibrational self-trapping of the amide-I band can naturally explain the 2D-IR response.

Conformational flexibility of arginine-82 as source for the heterogeneous and pH-dependent kinetics of the primary proton transfer step in the bacteriorhodopsin photocycle: An electrostatic model

NASA Astrophysics Data System (ADS)

Scharnagl, Christina; Fischer, Sighart F.

1996-11-01

We use equilibrium thermodynamic concepts to relate protein conformational and protonation substates and their pH-dependent population to kinetic schemes for the rise of the M intermediate in the photocycle of bacteriorhodopsin. Conformational flexibility of arginine R82 is described by a two-state model. The analysis accounts for the electrostatic coupling between its orientation and hydrogen ion titration and presents a structural basis for the linkage between the protonation states of the primary proton acceptor, aspartate D85, and the extracellular release group, glutamate E204. We find that the charge state of D85 is a significant determinant for the orientation of R82. The molecular model predicts the following: the primary proton transfer to D85 can be described by a kinetic scheme with two heterogeneous substates. They control the event with different activation parameters due to the reorientation of R82 away from the chromophore binding site. Their population depends on the external pH and the proton exchange equilibrium between the membrane buried residues and the bulk aqueous solvent. Proton transfer in the physiologic pH range is strongly activated and followed by the reorientation of R82 which shifts the equilibrium toward complete transfer. In the alkaline pH region a different mechanism operates, which involves the increased population of a substate with already reoriented R82 as a consequence of the deprotonation of E204, leading to accelerated proton transfer. Assuming full proton exchange equilibrium with the bulk water on the millisecond time scale leads to an increased population of substates which are non-productive for proton transfer.

Fast, clash-free RNA conformational morphing using molecular junctions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heliou, Amelie; Budday, Dominik; Fonseca, Rasmus

Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. As a result, despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groupsmore » of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Furthermore, our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation.« less

Fast, clash-free RNA conformational morphing using molecular junctions

DOE PAGES

Heliou, Amelie; Budday, Dominik; Fonseca, Rasmus; ...

2017-03-13

Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. As a result, despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groupsmore » of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Furthermore, our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation.« less

Free energy landscape of the Michaelis complex of lactate dehydrogenase: A network analysis of atomistic simulations

NASA Astrophysics Data System (ADS)

Pan, Xiaoliang; Schwartz, Steven

2015-03-01

It has long been recognized that the structure of a protein is a hierarchy of conformations interconverting on multiple time scales. However, the conformational heterogeneity is rarely considered in the context of enzymatic catalysis in which the reactant is usually represented by a single conformation of the enzyme/substrate complex. Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of two forms of the cofactor nicotinamide adenine dinucleotide (NADH and NAD+). Recent experimental results suggest that multiple substates exist within the Michaelis complex of LDH, and they are catalytic competent at different reaction rates. In this study, millisecond-scale all-atom molecular dynamics simulations were performed on LDH to explore the free energy landscape of the Michaelis complex, and network analysis was used to characterize the distribution of the conformations. Our results provide a detailed view of the kinetic network the Michaelis complex and the structures of the substates at atomistic scale. It also shed some light on understanding the complete picture of the catalytic mechanism of LDH.

Free energy surface of the Michaelis complex of lactate dehydrogenase: a network analysis of microsecond simulations.

PubMed

Pan, Xiaoliang; Schwartz, Steven D

2015-04-30

It has long been recognized that the structure of a protein creates a hierarchy of conformations interconverting on multiple time scales. The conformational heterogeneity of the Michaelis complex is of particular interest in the context of enzymatic catalysis in which the reactant is usually represented by a single conformation of the enzyme/substrate complex. Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of two forms of the cofactor nicotinamide adenine dinucleotide (NADH and NAD(+)). Recent experimental results suggest that multiple substates exist within the Michaelis complex of LDH, and they show a strong variance in their propensity toward the on-enzyme chemical step. In this study, microsecond-scale all-atom molecular dynamics simulations were performed on LDH to explore the free energy landscape of the Michaelis complex, and network analysis was used to characterize the distribution of the conformations. Our results provide a detailed view of the kinetic network of the Michaelis complex and the structures of the substates at atomistic scales. They also shed light on the complete picture of the catalytic mechanism of LDH.

Mapping Conformational Dynamics of Proteins Using Torsional Dynamics Simulations

PubMed Central

Gangupomu, Vamshi K.; Wagner, Jeffrey R.; Park, In-Hee; Jain, Abhinandan; Vaidehi, Nagarajan

2013-01-01

All-atom molecular dynamics simulations are widely used to study the flexibility of protein conformations. However, enhanced sampling techniques are required for simulating protein dynamics that occur on the millisecond timescale. In this work, we show that torsional molecular dynamics simulations enhance protein conformational sampling by performing conformational search in the low-frequency torsional degrees of freedom. In this article, we use our recently developed torsional-dynamics method called Generalized Newton-Euler Inverse Mass Operator (GNEIMO) to study the conformational dynamics of four proteins. We investigate the use of the GNEIMO method in simulations of the conformationally flexible proteins fasciculin and calmodulin, as well as the less flexible crambin and bovine pancreatic trypsin inhibitor. For the latter two proteins, the GNEIMO simulations with an implicit-solvent model reproduced the average protein structural fluctuations and sample conformations similar to those from Cartesian simulations with explicit solvent. The application of GNEIMO with replica exchange to the study of fasciculin conformational dynamics produced sampling of two of this protein’s experimentally established conformational substates. Conformational transition of calmodulin from the Ca2+-bound to the Ca2+-free conformation occurred readily with GNEIMO simulations. Moreover, the GNEIMO method generated an ensemble of conformations that satisfy about half of both short- and long-range interresidue distances obtained from NMR structures of holo to apo transitions in calmodulin. Although unconstrained all-atom Cartesian simulations have failed to sample transitions between the substates of fasciculin and calmodulin, GNEIMO simulations show the transitions in both systems. The relatively short simulation times required to capture these long-timescale conformational dynamics indicate that GNEIMO is a promising molecular-dynamics technique for studying domain motion in proteins. PMID:23663843

Mapping conformational dynamics of proteins using torsional dynamics simulations.

PubMed

Gangupomu, Vamshi K; Wagner, Jeffrey R; Park, In-Hee; Jain, Abhinandan; Vaidehi, Nagarajan

2013-05-07

All-atom molecular dynamics simulations are widely used to study the flexibility of protein conformations. However, enhanced sampling techniques are required for simulating protein dynamics that occur on the millisecond timescale. In this work, we show that torsional molecular dynamics simulations enhance protein conformational sampling by performing conformational search in the low-frequency torsional degrees of freedom. In this article, we use our recently developed torsional-dynamics method called Generalized Newton-Euler Inverse Mass Operator (GNEIMO) to study the conformational dynamics of four proteins. We investigate the use of the GNEIMO method in simulations of the conformationally flexible proteins fasciculin and calmodulin, as well as the less flexible crambin and bovine pancreatic trypsin inhibitor. For the latter two proteins, the GNEIMO simulations with an implicit-solvent model reproduced the average protein structural fluctuations and sample conformations similar to those from Cartesian simulations with explicit solvent. The application of GNEIMO with replica exchange to the study of fasciculin conformational dynamics produced sampling of two of this protein's experimentally established conformational substates. Conformational transition of calmodulin from the Ca(2+)-bound to the Ca(2+)-free conformation occurred readily with GNEIMO simulations. Moreover, the GNEIMO method generated an ensemble of conformations that satisfy about half of both short- and long-range interresidue distances obtained from NMR structures of holo to apo transitions in calmodulin. Although unconstrained all-atom Cartesian simulations have failed to sample transitions between the substates of fasciculin and calmodulin, GNEIMO simulations show the transitions in both systems. The relatively short simulation times required to capture these long-timescale conformational dynamics indicate that GNEIMO is a promising molecular-dynamics technique for studying domain motion in proteins. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Thermal and Denaturation Studies of the Time-Resolved Fluorescence Decay of Human Superoxide Dismutase

NASA Astrophysics Data System (ADS)

Silva, Norberto De Jesus

Previous studies have shown that time-resolved fluorescence decay of various single tryptophan proteins is best described by a distribution of fluorescence lifetimes rather than one or two lifetimes. The thermal dependence of the lifetime distributions is consistent with the hypothesis that proteins fluctuate between a hierarchy of many conformational substates. With this scenario as a theoretical framework, the correlations between protein dynamic and structure are investigated by studying the time-resolved fluorescence and anisotropy decay of the single tryptophan (Trp) residue of human superoxide dismutase (HSOD) over a wide range of temperatures and at different denaturant concentrations. First, it is demonstrated that the center of the lifetime distribution can characterize the average deactivation environment of the excited Trp-protein system. A qualitative model is introduced to explain the time-resolved fluorescence decay of HSOD in 80% glycerol over a wide range of temperatures. The dynamical model features isoenergetic conformational substates separated by a hierarchy of energy barriers. The HSOD system is also investigated as a function of denaturant concentration in aqueous solution. As a function of guanidine hydrochloride (GdHCl), the width of the fluorescence lifetime distribution of HSOD displays a maximum which is not coincident with the fully denatured form of HSOD at 6.5M GdHCl. Furthermore, the width for the fully denatured form of HSOD is greater than that of the native form. This is consistent with the scenario that more conformational substates are being created upon denaturation of HSOD. HSOD is a dimeric protein and it was observed that the width of the lifetime distribution of HSOD at intermediate GdHCl concentrations increased with decreasing protein concentration. In addition, the secondary structure of HSOD at intermediate GdHCl concentration does not change with protein concentration. These results suggest that HSOD display structural microheterogeneity which is consistent with the hypothesis of conformational substates. Further analysis show that, during denaturation, the monomeric form of HSOD is an intermediate which displays native-like secondary structure and fluctuating tertiary structure; i.e., the monomeric form of HSOD is a molten globule.

Energy landscape of LeuT from molecular simulations

NASA Astrophysics Data System (ADS)

Gur, Mert; Zomot, Elia; Cheng, Mary Hongying; Bahar, Ivet

2015-12-01

The bacterial sodium-coupled leucine transporter (LeuT) has been broadly used as a structural model for understanding the structure-dynamics-function of mammalian neurotransmitter transporters as well as other solute carriers that share the same fold (LeuT fold), as the first member of the family crystallographically resolved in multiple states: outward-facing open, outward-facing occluded, and inward-facing open. Yet, a complete picture of the energy landscape of (sub)states visited along the LeuT transport cycle has been elusive. In an attempt to visualize the conformational spectrum of LeuT, we performed extensive simulations of LeuT dimer dynamics in the presence of substrate (Ala or Leu) and co-transported Na+ ions, in explicit membrane and water. We used both conventional molecular dynamics (MD) simulations (with Anton supercomputing machine) and a recently introduced method, collective MD, that takes advantage of collective modes of motions predicted by the anisotropic network model. Free energy landscapes constructed based on ˜40 μs trajectories reveal multiple substates occluded to the extracellular (EC) and/or intracellular (IC) media, varying in the levels of exposure of LeuT to EC or IC vestibules. The IC-facing transmembrane (TM) helical segment TM1a shows an opening, albeit to a smaller extent and in a slightly different direction than that observed in the inward-facing open crystal structure. The study provides insights into the spectrum of conformational substates and paths accessible to LeuT and highlights the differences between Ala- and Leu-bound substates.

Energy landscape of LeuT from molecular simulations.

PubMed

Gur, Mert; Zomot, Elia; Cheng, Mary Hongying; Bahar, Ivet

2015-12-28

The bacterial sodium-coupled leucine transporter (LeuT) has been broadly used as a structural model for understanding the structure-dynamics-function of mammalian neurotransmitter transporters as well as other solute carriers that share the same fold (LeuT fold), as the first member of the family crystallographically resolved in multiple states: outward-facing open, outward-facing occluded, and inward-facing open. Yet, a complete picture of the energy landscape of (sub)states visited along the LeuT transport cycle has been elusive. In an attempt to visualize the conformational spectrum of LeuT, we performed extensive simulations of LeuT dimer dynamics in the presence of substrate (Ala or Leu) and co-transported Na(+) ions, in explicit membrane and water. We used both conventional molecular dynamics (MD) simulations (with Anton supercomputing machine) and a recently introduced method, collective MD, that takes advantage of collective modes of motions predicted by the anisotropic network model. Free energy landscapes constructed based on ∼40 μs trajectories reveal multiple substates occluded to the extracellular (EC) and/or intracellular (IC) media, varying in the levels of exposure of LeuT to EC or IC vestibules. The IC-facing transmembrane (TM) helical segment TM1a shows an opening, albeit to a smaller extent and in a slightly different direction than that observed in the inward-facing open crystal structure. The study provides insights into the spectrum of conformational substates and paths accessible to LeuT and highlights the differences between Ala- and Leu-bound substates.

Energy landscape of LeuT from molecular simulations

PubMed Central

Gur, Mert; Zomot, Elia; Cheng, Mary Hongying; Bahar, Ivet

2015-01-01

The bacterial sodium-coupled leucine transporter (LeuT) has been broadly used as a structural model for understanding the structure-dynamics-function of mammalian neurotransmitter transporters as well as other solute carriers that share the same fold (LeuT fold), as the first member of the family crystallographically resolved in multiple states: outward-facing open, outward-facing occluded, and inward-facing open. Yet, a complete picture of the energy landscape of (sub)states visited along the LeuT transport cycle has been elusive. In an attempt to visualize the conformational spectrum of LeuT, we performed extensive simulations of LeuT dimer dynamics in the presence of substrate (Ala or Leu) and co-transported Na+ ions, in explicit membrane and water. We used both conventional molecular dynamics (MD) simulations (with Anton supercomputing machine) and a recently introduced method, collective MD, that takes advantage of collective modes of motions predicted by the anisotropic network model. Free energy landscapes constructed based on ∼40 μs trajectories reveal multiple substates occluded to the extracellular (EC) and/or intracellular (IC) media, varying in the levels of exposure of LeuT to EC or IC vestibules. The IC-facing transmembrane (TM) helical segment TM1a shows an opening, albeit to a smaller extent and in a slightly different direction than that observed in the inward-facing open crystal structure. The study provides insights into the spectrum of conformational substates and paths accessible to LeuT and highlights the differences between Ala- and Leu-bound substates. PMID:26723619

Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations

PubMed Central

Budday, Dominik; Leyendecker, Sigrid; van den Bedem, Henry

2015-01-01

Proteins operate and interact with partners by dynamically exchanging between functional substates of a conformational ensemble on a rugged free energy landscape. Understanding how these substates are linked by coordinated, collective motions requires exploring a high-dimensional space, which remains a tremendous challenge. While molecular dynamics simulations can provide atomically detailed insight into the dynamics, computational demands to adequately sample conformational ensembles of large biomolecules and their complexes often require tremendous resources. Kinematic models can provide high-level insights into conformational ensembles and molecular rigidity beyond the reach of molecular dynamics by reducing the dimensionality of the search space. Here, we model a protein as a kinematic linkage and present a new geometric method to characterize molecular rigidity from the constraint manifold Q and its tangent space Q at the current configuration q. In contrast to methods based on combinatorial constraint counting, our method is valid for both generic and non-generic, e.g., singular configurations. Importantly, our geometric approach provides an explicit basis for collective motions along floppy modes, resulting in an efficient procedure to probe conformational space. An atomically detailed structural characterization of coordinated, collective motions would allow us to engineer or allosterically modulate biomolecules by selectively stabilizing conformations that enhance or inhibit function with broad implications for human health. PMID:26213417

Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations

NASA Astrophysics Data System (ADS)

Budday, Dominik; Leyendecker, Sigrid; van den Bedem, Henry

2015-10-01

Proteins operate and interact with partners by dynamically exchanging between functional substates of a conformational ensemble on a rugged free energy landscape. Understanding how these substates are linked by coordinated, collective motions requires exploring a high-dimensional space, which remains a tremendous challenge. While molecular dynamics simulations can provide atomically detailed insight into the dynamics, computational demands to adequately sample conformational ensembles of large biomolecules and their complexes often require tremendous resources. Kinematic models can provide high-level insights into conformational ensembles and molecular rigidity beyond the reach of molecular dynamics by reducing the dimensionality of the search space. Here, we model a protein as a kinematic linkage and present a new geometric method to characterize molecular rigidity from the constraint manifold Q and its tangent space Tq Q at the current configuration q. In contrast to methods based on combinatorial constraint counting, our method is valid for both generic and non-generic, e.g., singular configurations. Importantly, our geometric approach provides an explicit basis for collective motions along floppy modes, resulting in an efficient procedure to probe conformational space. An atomically detailed structural characterization of coordinated, collective motions would allow us to engineer or allosterically modulate biomolecules by selectively stabilizing conformations that enhance or inhibit function with broad implications for human health.

Conformational fluctuations in a green fluorescent protein-like Akane family protein: a high-pressure fluorescence study at 0.1-700 MPa

NASA Astrophysics Data System (ADS)

Maeno, Akihiro; Kato, Yuko; Jimbo, Mitsuru; Amada, Kei; Mita, Hajime; Akasaka, Kazuyuki

2017-04-01

We have investigated conformational fluctuations in a new green fluorescent protein(GFP)-like protein rb-Akane found in a red-brown-colored octocoral, Scleronephthya gracillima (Kuekenthal)), with high pressure fluorescence spectroscopy at 0.1-700 MPa. Besides the green fluorescence at 510 nm, two red fluorescence peaks are observed at 590 and 629 nm, the relative intensity of which varies reversibly with pressure. The phenomenon is interpreted as representing the cis-trans isomerization of the chromophore accompanied by the conformational transition between two sub-states of the red fluorescence form of rb-Akane. The two sub-states are separated only marginally in free energy (ΔG0 = 1.9 ± 0.4 kJ mol-1), but significantly in partial molar volume (ΔV0 = -19.8 ± 1.4 ml mol-1) at 0.1 MPa (pH 7.5, 25°C). Above 500 MPa, the fluorescence at λmax 629 nm undergoes another reversible change with pressure, showing the onset of unfolding.

How main-chains of proteins explore the free-energy landscape in native states.

PubMed

Senet, Patrick; Maisuradze, Gia G; Foulie, Colette; Delarue, Patrice; Scheraga, Harold A

2008-12-16

Understanding how a single native protein diffuses on its free-energy landscape is essential to understand protein kinetics and function. The dynamics of a protein is complex, with multiple relaxation times reflecting a hierarchical free-energy landscape. Using all-atom molecular dynamics simulations of an alpha/beta protein (crambin) and a beta-sheet polypeptide (BS2) in their "native" states, we demonstrate that the mean-square displacement of dihedral angles, defined by 4 successive C(alpha) atoms, increases as a power law of time, t(alpha), with an exponent alpha between 0.08 and 0.39 (alpha = 1 corresponds to Brownian diffusion), at 300 K. Residues with low exponents are located mainly in well-defined secondary elements and adopt 1 conformational substate. Residues with high exponents are found in loops/turns and chain ends and exist in multiple conformational substates, i.e., they move on multiple-minima free-energy profiles.

How main-chains of proteins explore the free-energy landscape in native states

PubMed Central

Senet, Patrick; Maisuradze, Gia G.; Foulie, Colette; Delarue, Patrice; Scheraga, Harold A.

2008-01-01

Understanding how a single native protein diffuses on its free-energy landscape is essential to understand protein kinetics and function. The dynamics of a protein is complex, with multiple relaxation times reflecting a hierarchical free-energy landscape. Using all-atom molecular dynamics simulations of an α/β protein (crambin) and a β-sheet polypeptide (BS2) in their “native” states, we demonstrate that the mean-square displacement of dihedral angles, defined by 4 successive Cα atoms, increases as a power law of time, tα, with an exponent α between 0.08 and 0.39 (α = 1 corresponds to Brownian diffusion), at 300 K. Residues with low exponents are located mainly in well-defined secondary elements and adopt 1 conformational substate. Residues with high exponents are found in loops/turns and chain ends and exist in multiple conformational substates, i.e., they move on multiple-minima free-energy profiles. PMID:19073932

Structural characterization of Burkholderia pseudomallei adenylate kinase (Adk): Profound asymmetry in the crystal structure of the 'open' state

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buchko, G.W.; Robinson, H.; Abendroth, J.

2010-04-16

In all organisms adenylate kinases (Adks) play a vital role in cellular energy metabolism and nucleic acid synthesis. Due to differences in catalytic properties between the Adks found in prokaryotes and in the cytoplasm of eukaryotes, there is interest in targeting this enzyme for new drug therapies against infectious bacterial agents. Here we report the 2.1 {angstrom} resolution crystal structure for the 220-residue Adk from Burkholderia pseudomallei (BpAdk), the etiological agent responsible for the infectious disease melioidosis. The general structure of apo BpAdk is similar to other Adk structures, composed of a CORE subdomain with peripheral ATP-binding (ATP{sub bd}) andmore » LID subdomains. The two molecules in the asymmetric unit have significantly different conformations, with a backbone RMSD of 1.46 {angstrom}. These two BpAdk conformations may represent 'open' Adk sub-states along the preferential pathway to the 'closed' substrate-bound state.« less

Impact of mutations on the allosteric conformational equilibrium

PubMed Central

Weinkam, Patrick; Chen, Yao Chi; Pons, Jaume; Sali, Andrej

2012-01-01

Allostery in a protein involves effector binding at an allosteric site that changes the structure and/or dynamics at a distant, functional site. In addition to the chemical equilibrium of ligand binding, allostery involves a conformational equilibrium between one protein substate that binds the effector and a second substate that less strongly binds the effector. We run molecular dynamics simulations using simple, smooth energy landscapes to sample specific ligand-induced conformational transitions, as defined by the effector-bound and unbound protein structures. These simulations can be performed using our web server: http://salilab.org/allosmod/. We then develop a set of features to analyze the simulations and capture the relevant thermodynamic properties of the allosteric conformational equilibrium. These features are based on molecular mechanics energy functions, stereochemical effects, and structural/dynamic coupling between sites. Using a machine-learning algorithm on a dataset of 10 proteins and 179 mutations, we predict both the magnitude and sign of the allosteric conformational equilibrium shift by the mutation; the impact of a large identifiable fraction of the mutations can be predicted with an average unsigned error of 1 kBT. With similar accuracy, we predict the mutation effects for an 11th protein that was omitted from the initial training and testing of the machine-learning algorithm. We also assess which calculated thermodynamic properties contribute most to the accuracy of the prediction. PMID:23228330

Functional Sub-states by High-pressure Macromolecular Crystallography.

PubMed

Dhaussy, Anne-Claire; Girard, Eric

2015-01-01

At the molecular level, high-pressure perturbation is of particular interest for biological studies as it allows trapping conformational substates. Moreover, within the context of high-pressure adaptation of deep-sea organisms, it allows to decipher the molecular determinants of piezophily. To provide an accurate description of structural changes produced by pressure in a macromolecular system, developments have been made to adapt macromolecular crystallography to high-pressure studies. The present chapter is an overview of results obtained so far using high-pressure macromolecular techniques, from nucleic acids to virus capsid through monomeric as well as multimeric proteins.

Phosphorylation of rat brain purified mitochondrial Voltage-Dependent Anion Channel by c-Jun N-terminal kinase-3 modifies open-channel noise.

PubMed

Gupta, Rajeev

2017-09-02

The drift kinetic energy of ionic flow through single ion channels cause vibrations of the pore walls which are observed as open-state current fluctuations (open-channel noise) during single-channel recordings. Vibration of the pore wall leads to transitions among different conformational sub-states of the channel protein in the open-state. Open-channel noise analysis can provide important information about the different conformational sub-state transitions and how biochemical modifications of ion channels would affect their transport properties. It has been shown that c-Jun N-terminal kinase-3 (JNK3) becomes activated by phosphorylation in various neurodegenerative diseases and phosphorylates outer mitochondrion associated proteins leading to neuronal apoptosis. In our earlier work, JNK3 has been reported to phosphorylate purified rat brain mitochondrial voltage-dependent anion channel (VDAC) in vitro and modify its conductance and opening probability. In this article we have compared the open-state noise profile of the native and the JNK3 phosphorylated VDAC using Power Spectral Density vs frequency plots. Power spectral density analysis of open-state noise indicated power law with average slope value α ≈1 for native VDAC at both positive and negative voltage whereas average α value < 0.5 for JNK3 phosphorylated VDAC at both positive and negative voltage. It is proposed that 1/f 1 power law in native VDAC open-state noise arises due to coupling of ionic transport and conformational sub-states transitions in open-state and this coupling is perturbed as a result of channel phosphorylation. Copyright © 2017 Elsevier Inc. All rights reserved.

QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin

PubMed Central

Savol, Andrej J.; Burger, Virginia M.; Agarwal, Pratul K.; Ramanathan, Arvind; Chennubhotla, Chakra S.

2011-01-01

Motivation: Molecular dynamics (MD) simulations have dramatically improved the atomistic understanding of protein motions, energetics and function. These growing datasets have necessitated a corresponding emphasis on trajectory analysis methods for characterizing simulation data, particularly since functional protein motions and transitions are often rare and/or intricate events. Observing that such events give rise to long-tailed spatial distributions, we recently developed a higher-order statistics based dimensionality reduction method, called quasi-anharmonic analysis (QAA), for identifying biophysically-relevant reaction coordinates and substates within MD simulations. Further characterization of conformation space should consider the temporal dynamics specific to each identified substate. Results: Our model uses hierarchical clustering to learn energetically coherent substates and dynamic modes of motion from a 0.5 μs ubiqutin simulation. Autoregressive (AR) modeling within and between states enables a compact and generative description of the conformational landscape as it relates to functional transitions between binding poses. Lacking a predictive component, QAA is extended here within a general AR model appreciative of the trajectory's temporal dependencies and the specific, local dynamics accessible to a protein within identified energy wells. These metastable states and their transition rates are extracted within a QAA-derived subspace using hierarchical Markov clustering to provide parameter sets for the second-order AR model. We show the learned model can be extrapolated to synthesize trajectories of arbitrary length. Contact: ramanathana@ornl.gov; chakracs@pitt.edu PMID:21685101

Molecular dynamics simulation of nitric oxide in myoglobin

USGS Publications Warehouse

Lee, Myung Won; Meuwly, Markus

2012-01-01

The infrared (IR) spectroscopy and ligand migration of photodissociated nitric oxide (NO) in and around the active sites in myoglobin (Mb) are investigated. A distributed multipolar model for open-shell systems is developed and used, which allows one to realistically describe the charge distribution around the diatomic probe molecule. The IR spectra were computed from the trajectories for two conformational substates at various temperatures. The lines are narrow (width of 3–7 cm–1 at 20–100 K), in agreement with the experimental observations where they have widths of 4–5 cm–1 at 4 K. It is found that within one conformational substate (B or C) the splitting of the spectrum can be correctly described compared with recent experiments. Similar to photodissociated CO in Mb, additional substates exist for NO in Mb, which are separated by barriers below 1 kcal/mol. Contrary to full quantum mechanical calculations, however, the force field and mixed QM/MM simulations do not correctly describe the relative shifts between the B- and C-states relative to gas-phase NO. Free energy simulations establish that NO preferably localizes in the distal site and the barrier for migration to the neighboring Xe4 pocket is ΔGB→C = 1.7–2.0 kcal/mol. The reverse barrier is ΔGB←C = 0.7 kcal/mol, which agrees well with the experimental value of 0.7 kcal/mol, estimated from kinetic data.

Geometries and Electronic Structures of Cyanide Adducts of the Non-Heme Iron Active Site of Superoxide Reductases: Vibrational and ENDOR Studies†

PubMed Central

Clay, Michael D.; Yang, Tran-Chin; Jenney, Francis E.; Kung, Irene Y.; Cosper, Christopher A.; Krishnan, Rangan; Kurtz, Donald M.; Adams, Michael W.W.; Hoffman, Brian M.; Johnson, Michael K.

2008-01-01

We have added cyanide to oxidized 1Fe and 2Fe superoxide reductase (SOR) as a surrogate for the putative ferric-(hydro)peroxo intermediate in the reaction of the enzymes with superoxide, and have used vibrational and ENDOR spectroscopies to study the properties of the active-site paramagnetic iron center. Addition of cyanide changes the active-site iron center in oxidized SOR from rhombic high-spin ferric (S = 5/2) to axial-like low-spin ferric (S = 1/2). Low-temperature resonance Raman and ENDOR data show that the bound cyanide adopts three distinct conformations in Fe(III)-CN SOR. On the basis of 13CN, C15N, and 13C15N isotope shifts of the Fe–CN stretching/Fe–C–N bending modes, resonance Raman studies of 1Fe-SOR indicate one near-linear conformation (Fe–C–N angle ∼175°) and two distinct bent conformations (Fe–C–N angles < 140°). FTIR studies of 1Fe-SOR at ambient temperatures reveals three bound C–N stretching frequencies in the oxidized (ferric) state and one in the reduced (ferrous) state indicating that the conformational heterogeneity in cyanide binding is a characteristic of the ferric state and is not caused by freezing-in of conformational substates at low temperature. 13C-ENDOR spectra for the 13CN-bound ferric active sites in both 1Fe- and 2Fe-SORs also show three well-resolved Fe–C–N conformations. Analysis of the 13C hyperfine tensors for the three substates of the 2Fe-SOR within a simple heuristic model for the Fe-C bonding gives values for the Fe–C–N angles in the three substates of ca. 123° (C3), 133° (C2), taking a reference value from vibrational studies of 175° (C1 species). Resonance Raman and ENDOR studies of SOR variants, in which the conserved glutamate and lysine residues in a flexible loop above the substrate binding pocket have been individually replaced by alanine, indicate that the side chains of these two residues are not involved in direct interaction with bound cyanide. The implications of these results for understanding the mechanism of SOR are discussed. PMID:16401073

Phosphorylation of an intrinsically disordered segment in Ets1 shifts conformational sampling toward binding-competent substates.

PubMed

Bui, Jennifer M; Gsponer, Jörg

2014-08-05

Functions of many proteins are affected by posttranslational modifications of intrinsically disordered (ID) regions, yet little is known about the underlying molecular mechanisms. By combining molecular dynamics simulations and protein docking, we demonstrate that the addition of phosphates to an ID segment adjacent to the PNT domain of Ets1 directs conformational sampling toward substates that are most compatible with high-affinity binding of the TAZ1 domain of its coactivator CBP. The phosphate charges disrupt salt bridges and thereby open a hydrophobic cleft and expose hydrophobic residues at the ID N terminus. The structure of the PNT-TAZ1 complex that we determined shows that PNT binds to TAZ1 via these hydrophobic regions in a similar manner to how it interacts with other partners. Our calculations reveal a dual effect of phosphorylation in that it changes the dynamics of PNT so that it becomes more compatible for TAZ1 binding and increases complementarity with this binding partner. Copyright © 2014 Elsevier Ltd. All rights reserved.

Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach.

PubMed

Curuksu, Jeremy; Zacharias, Martin

2009-03-14

Although molecular dynamics (MD) simulations have been applied frequently to study flexible molecules, the sampling of conformational states separated by barriers is limited due to currently possible simulation time scales. Replica-exchange (Rex)MD simulations that allow for exchanges between simulations performed at different temperatures (T-RexMD) can achieve improved conformational sampling. However, in the case of T-RexMD the computational demand grows rapidly with system size. A Hamiltonian RexMD method that specifically enhances coupled dihedral angle transitions has been developed. The method employs added biasing potentials as replica parameters that destabilize available dihedral substates and was applied to study coupled dihedral transitions in nucleic acid molecules. The biasing potentials can be either fixed at the beginning of the simulation or optimized during an equilibration phase. The method was extensively tested and compared to conventional MD simulations and T-RexMD simulations on an adenine dinucleotide system and on a DNA abasic site. The biasing potential RexMD method showed improved sampling of conformational substates compared to conventional MD simulations similar to T-RexMD simulations but at a fraction of the computational demand. It is well suited to study systematically the fine structure and dynamics of large nucleic acids under realistic conditions including explicit solvent and ions and can be easily extended to other types of molecules.

Proline cis-trans isomerization in staphylococcal nuclease: multi-substrate free energy perturbation calculations.

PubMed Central

Hodel, A.; Rice, L. M.; Simonson, T.; Fox, R. O.; Brünger, A. T.

1995-01-01

Staphylococcal nuclease A exists in two folded forms that differ in the isomerization state of the Lys 116-Pro 117 peptide bond. The dominant form (90% occupancy) adopts a cis peptide bond, which is observed in the crystal structure. NMR studies show that the relatively small difference in free energy between the cis and trans forms (delta Gcis-->trans approximately 1.2 kcal/mol) results from large and nearly compensating differences in enthalpy and entropy (delta Hcis-->trans approximately delta TScis-->trans approximately 10 kcal/mol). There is evidence from X-ray crystal structures that the structural differences between the cis and the trans forms of nuclease are confined to the conformation of residues 112-117, a solvated protein loop. Here, we obtain a thermodynamic and structural description of the conformational equilibrium of this protein loop through an exhaustive conformational search that identified several substates followed by free energy simulations between the substrates. By partitioning the search into conformational substates, we overcame the multiple minima problem in this particular case and obtained precise and reproducible free energy values. The protein and water environment was implicitly modeled by appropriately chosen nonbonded terms between the explicitly treated loop and the rest of the protein. These simulations correctly predicted a small free energy difference between the cis and trans forms composed of larger, compensating differences in enthalpy and entropy. The structural predictions of these simulations were qualitatively consistent with known X-ray structures of nuclease variants and yield a model of the unknown minor trans conformation. PMID:7613463

Role of conformational dynamics in the evolution of novel enzyme function.

PubMed

Maria-Solano, Miguel A; Serrano-Hervás, Eila; Romero-Rivera, Adrian; Iglesias-Fernández, Javier; Osuna, Sílvia

2018-05-21

The free energy landscape concept that describes enzymes as an ensemble of differently populated conformational sub-states in dynamic equilibrium is key for evaluating enzyme activity, enantioselectivity, and specificity. Mutations introduced in the enzyme sequence can alter the populations of the pre-existing conformational states, thus strongly modifying the enzyme ability to accommodate alternative substrates, revert its enantiopreferences, and even increase the activity for some residual promiscuous reactions. In this feature article, we present an overview of the current experimental and computational strategies to explore the conformational free energy landscape of enzymes. We provide a series of recent publications that highlight the key role of conformational dynamics for the enzyme evolution towards new functions and substrates, and provide some perspectives on how conformational dynamism should be considered in future computational enzyme design protocols.

Conformational Transition Pathways in Signaling and Enzyme Catalysis Explored by Computational Methods

NASA Astrophysics Data System (ADS)

Pachov, Dimitar V.

Biomolecules are dynamic in nature and visit a number of states while performing their biological function. However, understanding how they interconvert between functional substates is a challenging task. In this thesis, we employ enhanced computational strategies to reveal in atomistic resolution transition states and molecular mechanism along conformational pathways of the signaling protein Nitrogen Regulatory Protein C (NtrC) and the enzyme Adenylate Kinase (Adk). Targeted Molecular Dynamics (TMD) simulations and NMR experiments have previously found the active/inactive interconversion of NtrC is stabilized by non-native transient contacts. To find where along the conformational pathway they lie and probe the existence of multiple intermediates, a beyond 8mus-extensive mapping of the conformational landscape was performed by a multitude of straightforward MD simulations relaxed from the biased TMD pathway. A number of metastable states stabilized by local interactions was found to underline the conformational pathway of NtrC. Two spontaneous transitions of the last stage of the active-to-inactive conversion were identified and used in path sampling procedures to generate an ensemble of truly dynamic reactive pathways. The transition state ensemble (TSE) and mechanistic descriptors of this transition were revealed in atomic detail and verified by committor analysis. By analyzing how pressure affects the dynamics and function of two homologous Adk proteins - the P.Profundum Adk surviving at 700atm pressure in the deep sea, and the E. coli Adk that lives at ambient pressures - we indirectly obtained atomic information about the TSE of the large-amplitude rate-limiting conformational opening of the Adk lids. Guided by NMR experiments showing significantly decreased activation volumes of the piezophile compared to its mesophilic counterpart, TMD simulations revealed the formation of an extended hydrogen-bonded water network in the transition state of the piezophile that can explain the experimentally measured activation volume differences. The transition state of the conformational change was proposed to lie close to the closed state. Additionally, a number of descriptors were used to characterize the free energy landscape of the mesophile. It was found that the features of landscape are highly sensitive to the binding of different ligands, their protonation states and the presence of magnesium.

Automated identification of functional dynamic networks from X-ray crystallography

PubMed Central

van den Bedem, Henry; Bhabha, Gira; Yang, Kun; Wright, Peter E.; Fraser, James S.

2013-01-01

Protein function often depends on the exchange between conformational substates. Allosteric ligand binding or distal mutations can stabilize specific active site conformations and consequently alter protein function. In addition to comparing independently determined X-ray crystal structures, alternative conformations observed at low levels of electron density have the potential to provide mechanistic insights into conformational dynamics. Here, we report a new multi-conformer contact network algorithm (CONTACT) that identifies networks of conformationally heterogeneous residues directly from high-resolution X-ray crystallography data. Contact networks in Escherichia coli dihydrofolate reductase (ecDHFR) predict the long-range pattern of NMR chemical shift perturbations of an allosteric mutation. A comparison of contact networks in wild type and mutant ecDHFR suggests how mutations that alter optimized networks of coordinated motions can impair catalytic function. Thus, CONTACT-guided mutagenesis will allow the structure-dynamics-function relationship to be exploited in protein engineering and design. PMID:23913260

Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR

PubMed Central

Fenwick, R. Bryn; van den Bedem, Henry; Fraser, James S.; Wright, Peter E.

2014-01-01

Detailed descriptions of atomic coordinates and motions are required for an understanding of protein dynamics and their relation to molecular recognition, catalytic function, and allostery. Historically, NMR relaxation measurements have played a dominant role in the determination of the amplitudes and timescales (picosecond–nanosecond) of bond vector fluctuations, whereas high-resolution X-ray diffraction experiments can reveal the presence of and provide atomic coordinates for multiple, weakly populated substates in the protein conformational ensemble. Here we report a hybrid NMR and X-ray crystallography analysis that provides a more complete dynamic picture and a more quantitative description of the timescale and amplitude of fluctuations in atomic coordinates than is obtainable from the individual methods alone. Order parameters (S2) were calculated from single-conformer and multiconformer models fitted to room temperature and cryogenic X-ray diffraction data for dihydrofolate reductase. Backbone and side-chain order parameters derived from NMR relaxation experiments are in excellent agreement with those calculated from the room-temperature single-conformer and multiconformer models, showing that the picosecond timescale motions observed in solution occur also in the crystalline state. These motions are quenched in the crystal at cryogenic temperatures. The combination of NMR and X-ray crystallography in iterative refinement promises to provide an atomic resolution description of the alternate conformational substates that are sampled through picosecond to nanosecond timescale fluctuations of the protein structure. The method also provides insights into the structural heterogeneity of nonmethyl side chains, aromatic residues, and ligands, which are less commonly analyzed by NMR relaxation measurements. PMID:24474795

Influence of electric field on the amyloid-β(29-42) peptides embedded in a membrane bilayer

NASA Astrophysics Data System (ADS)

Lu, Yan; Shi, Xiao-Feng; Salsbury, Freddie R.; Derreumaux, Philippe

2018-01-01

Alzheimer's disease is linked to various types of aggregates of amyloid-β (Aβ) peptide and their interactions with protein receptors and neuronal cell membranes. Little is known on the impact of the electric field on membrane-embedded Aβ. Here we use atomistic molecular dynamics simulations to study the effects of a constant electric field on the conformations of Aβ29-42 dimer inside a membrane, where the electric field has a strength of 20 mV/nm which exists across the membrane of a human neuron. Starting from α-helix peptides, the transmembrane electric field (TMEF) accelerates the conversion from the Gly-out substate to the Gly-side and Gly-in substates. Starting from β-sheet peptides, TMEF induces changes of the kink and tilt angles at Gly33 and Gly37. Overall, in the simulations totaling 10 μs, TMEF establishes new ground states for the dimer, similar to induced-fit in ligand binding. Our findings indicate that TMEF can stabilize rare conformations of amyloid peptides, and this could influence the cleavage of the amyloid precursor protein and the formation of β-sheet oligomers in membrane bilayers.

Relaxation Dynamics in Heme Proteins.

NASA Astrophysics Data System (ADS)

Scholl, Reinhard Wilhelm

A protein molecule possesses many conformational substates that are likely arranged in a hierarchy consisting of a number of tiers. A hierarchical organization of conformational substates is expected to give rise to a multitude of nonequilibrium relaxation phenomena. If the temperature is lowered, transitions between substates of higher tiers are frozen out, and relaxation processes characteristic of lower tiers will dominate the observational time scale. This thesis addresses the following questions: (i) What is the energy landscape of a protein? How does the landscape depend on the environment such as pH and viscosity, and how can it be connected to specific structural parts? (ii) What relaxation phenomena can be observed in a protein? Which are protein specific, and which occur in other proteins? How does the environment influence relaxations? (iii) What functional form best describes relaxation functions? (iv) Can we connect the motions to specific structural parts of the protein molecule, and are these motions important for the function of the protein?. To this purpose, relaxation processes after a pressure change are studied in carbonmonoxy (CO) heme proteins (myoglobin-CO, substrate-bound and substrate-free cytochrome P450cam-CO, chloroperoxidase-CO, horseradish peroxidase -CO) between 150 K and 250 K using FTIR spectroscopy to monitor the CO bound to the heme iron. Two types of p -relaxation experiments are performed: p-release (200 to ~eq40 MPa) and p-jump (~eq40 to 200 MPa) experiments. Most of the relaxations fall into one of three groups and are characterized by (i) nonexponential time dependence and non-Arrhenius temperature dependence (FIM1( nu), FIM1(Gamma)); (ii) exponential time dependence and non-Arrhenius temperature dependence (FIM0(A_{i}to A_{j})); exponential time dependence and Arrhenius temperature dependence (FIMX( nu)). The influence of pH is studied in myoglobin-CO and shown to have a strong influence on the substate population of the highest tier, tier 0, but not on the relaxation rates. Two different viscosities in myoglobin-CO are compared. The dependence of relaxations on the thermodynamic history of a sample is shown. For substrate-free P450cam-CO, relaxations after a p-jump are observed far above the glass transition of the protein-solvent system.

Gauche Ethyl Alcohol: Laboratory Assignments and Interstellar Identification

NASA Technical Reports Server (NTRS)

Pearson, J. C.; Sastry, K. V. L. N.; Herbst, Eric; DeLucia, Frank C.

1997-01-01

Ethyl alcohol (ethanol) is known to possess a pair of closely spaced excited torsional substates (gauche+, gauche-) at an energy of approximately 57 K above the ground (trans) torsional substate. We report an extended analysis of some gauche - gauche+ Q-branch ((Delta)J = 0) transitions with a three-substate fixed frame axis method (FFAM) Hamiltonian. Our approach accounts for complex trans-gauche interactions for the first time. In addition, we are able to obtain intensities for perturbed rotational transitions, and to determine the trans to gauche+ separation to be 1185399.1 MHz. A complete ground state rotational-torsional partition function accounting for the previously neglected gauche substates is presented. Based on our analysis, a total of 14 U lines obtained towards Orion KL can now be assigned to gauche substates of ethanol. Analysis of these lines yields a rotational temperature of 223 K and a total (trans + gauche) column density of 7.0 x 10(exp 15)/sq cm. The column density is in reasonable agreement with the recent value of 2-3 x 10(exp 15)/sq cm based on observations of trans-ethanol by Ohishi et al., although there is some disparity in the rotational temperatures. Eight additional U lines in the literature are assigned to transitions of gauche ethanol.

Characterizing RNA ensembles from NMR data with kinematic models

PubMed Central

Fonseca, Rasmus; Pachov, Dimitar V.; Bernauer, Julie; van den Bedem, Henry

2014-01-01

Functional mechanisms of biomolecules often manifest themselves precisely in transient conformational substates. Researchers have long sought to structurally characterize dynamic processes in non-coding RNA, combining experimental data with computer algorithms. However, adequate exploration of conformational space for these highly dynamic molecules, starting from static crystal structures, remains challenging. Here, we report a new conformational sampling procedure, KGSrna, which can efficiently probe the native ensemble of RNA molecules in solution. We found that KGSrna ensembles accurately represent the conformational landscapes of 3D RNA encoded by NMR proton chemical shifts. KGSrna resolves motionally averaged NMR data into structural contributions; when coupled with residual dipolar coupling data, a KGSrna ensemble revealed a previously uncharacterized transient excited state of the HIV-1 trans-activation response element stem–loop. Ensemble-based interpretations of averaged data can aid in formulating and testing dynamic, motion-based hypotheses of functional mechanisms in RNAs with broad implications for RNA engineering and therapeutic intervention. PMID:25114056

The role of protein dynamics in the evolution of new enzyme function.

PubMed

Campbell, Eleanor; Kaltenbach, Miriam; Correy, Galen J; Carr, Paul D; Porebski, Benjamin T; Livingstone, Emma K; Afriat-Jurnou, Livnat; Buckle, Ashley M; Weik, Martin; Hollfelder, Florian; Tokuriki, Nobuhiko; Jackson, Colin J

2016-11-01

Enzymes must be ordered to allow the stabilization of transition states by their active sites, yet dynamic enough to adopt alternative conformations suited to other steps in their catalytic cycles. The biophysical principles that determine how specific protein dynamics evolve and how remote mutations affect catalytic activity are poorly understood. Here we examine a 'molecular fossil record' that was recently obtained during the laboratory evolution of a phosphotriesterase from Pseudomonas diminuta to an arylesterase. Analysis of the structures and dynamics of nine protein variants along this trajectory, and three rationally designed variants, reveals cycles of structural destabilization and repair, evolutionary pressure to 'freeze out' unproductive motions and sampling of distinct conformations with specific catalytic properties in bi-functional intermediates. This work establishes that changes to the conformational landscapes of proteins are an essential aspect of molecular evolution and that change in function can be achieved through enrichment of preexisting conformational sub-states.

13C ENDOR Spectroscopy of Lipoxygenase-Substrate Complexes Reveals the Structural Basis for C-H Activation by Tunneling.

PubMed

Horitani, Masaki; Offenbacher, Adam R; Carr, Cody A Marcus; Yu, Tao; Hoeke, Veronika; Cutsail, George E; Hammes-Schiffer, Sharon; Klinman, Judith P; Hoffman, Brian M

2017-02-08

In enzymatic C-H activation by hydrogen tunneling, reduced barrier width is important for efficient hydrogen wave function overlap during catalysis. For native enzymes displaying nonadiabatic tunneling, the dominant reactive hydrogen donor-acceptor distance (DAD) is typically ca. 2.7 Å, considerably shorter than normal van der Waals distances. Without a ground state substrate-bound structure for the prototypical nonadiabatic tunneling system, soybean lipoxygenase (SLO), it has remained unclear whether the requisite close tunneling distance occurs through an unusual ground state active site arrangement or by thermally sampling conformational substates. Herein, we introduce Mn 2+ as a spin-probe surrogate for the SLO Fe ion; X-ray diffraction shows Mn-SLO is structurally faithful to the native enzyme. 13 C ENDOR then reveals the locations of 13 C10 and reactive 13 C11 of linoleic acid relative to the metal; 1 H ENDOR and molecular dynamics simulations of the fully solvated SLO model using ENDOR-derived restraints give additional metrical information. The resulting three-dimensional representation of the SLO active site ground state contains a reactive (a) conformer with hydrogen DAD of ∼3.1 Å, approximately van der Waals contact, plus an inactive (b) conformer with even longer DAD, establishing that stochastic conformational sampling is required to achieve reactive tunneling geometries. Tunneling-impaired SLO variants show increased DADs and variations in substrate positioning and rigidity, confirming previous kinetic and theoretical predictions of such behavior. Overall, this investigation highlights the (i) predictive power of nonadiabatic quantum treatments of proton-coupled electron transfer in SLO and (ii) sensitivity of ENDOR probes to test, detect, and corroborate kinetically predicted trends in active site reactivity and to reveal unexpected features of active site architecture.

Crystal structure of acetanilide at 15 and 295 K by neutron diffraction. Lack of evidence for proton transfer along the N-H...O hydrogen bond

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, S.W.; Eckert, J.; Barthes, M.

1995-11-02

The crystal structure of acetanilide C{sub 8}H{sub 9}NO, M{sub r} = 135.17, orthorhombic, space group Pbca, Z=8, has been determined from neutron diffraction data at 15 and 295 K. The crystal data obtained are presented. This new investigation of the structure of acetanilide has been undertaken in order to assess a recent suggestion that confirmational substates in the amide proton position may be responsible for the vibrational anomalies. We found no evidence for multiple conformations or transfer along the N-H...O hydrogen bond of the amide proton at either temperature. However the intramolecular O...H6 distance from O to the nearest phenylmore » ring proton is unusually short and the amide proton has relatively close contacts with one of the phenyl and one of the methyl protons, which may well affect the vibrational parameters of the respective molecular groups. 44 refs., 6 figs., 5 tabs.« less

Atomistic details of the disordered states of KID and pKID. Implications in coupled binding and folding.

PubMed

Ganguly, Debabani; Chen, Jianhan

2009-04-15

Intrinsically disordered proteins (IDPs) are a newly recognized class of functional proteins for which a lack of stable tertiary fold is required for function. Because of the heterogeneous and dynamical nature, molecular modeling is necessary to provide the missing details of disordered states of IDP that are crucial for understanding their functions. In particular, generalized Born (GB) implicit solvent, combined with replica exchange (REX), might offer an optimal balance between accuracy and efficiency for modeling IDPs. We carried out extensive REX simulations in an optimized GB force field to characterize the disordered states of a regulatory IDP, KID domain of transcription factor CREB, and its phosphorylated form, pKID. The results revealed that both KID and pKID, though highly disordered on the tertiary level, are compact and mainly occupy a small number of helical substates. Interestingly, although phosphorylation of KID Ser133 leads only to marginal changes in average helicities on the ensemble level, underlying conformational substates differ significantly. In particular, pSer133 appears to restrict the accessible conformational space of the loop region and thus reduces the entropic cost of KID folding upon binding to the KIX domain of CREB-binding protein. Such an expanded role of phosphorylation in the KID:KIX recognition was not previously recognized because of a lack of substantial conformational changes on the ensemble level and inaccessibility of the structural details from experiments. The results also suggest that an implicit solvent-based modeling framework, despite various existing limitations, might be feasible for accurate atomistic simulation of small IDPs in general.

ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution

PubMed Central

Kurkcuoglu, Zeynep; Bahar, Ivet; Doruker, Pemra

2016-01-01

Accurate sampling of conformational space and, in particular, the transitions between functional substates has been a challenge in molecular dynamic (MD) simulations of large biomolecular systems. We developed an Elastic Network Model (ENM)-based computational method, ClustENM, for sampling large conformational changes of biomolecules with various sizes and oligomerization states. ClustENM is an iterative method that combines ENM with energy minimization and clustering steps. It is an unbiased technique, which requires only an initial structure as input, and no information about the target conformation. To test the performance of ClustENM, we applied it to six biomolecular systems: adenylate kinase (AK), calmodulin, p38 MAP kinase, HIV-1 reverse transcriptase (RT), triosephosphate isomerase (TIM), and the 70S ribosomal complex. The generated ensembles of conformers determined at atomic resolution show good agreement with experimental data (979 structures resolved by X-ray and/or NMR) and encompass the subspaces covered in independent MD simulations for TIM, p38, and RT. ClustENM emerges as a computationally efficient tool for characterizing the conformational space of large systems at atomic detail, in addition to generating a representative ensemble of conformers that can be advantageously used in simulating substrate/ligand-binding events. PMID:27494296

Quasithermodynamic Contributions to the Fluctuations of a Protein Nanopore

PubMed Central

2015-01-01

Proteins undergo thermally activated conformational fluctuations among two or more substates, but a quantitative inquiry on their kinetics is persistently challenged by numerous factors, including the complexity and dynamics of various interactions, along with the inability to detect functional substates within a resolvable time scale. Here, we analyzed in detail the current fluctuations of a monomeric β-barrel protein nanopore of known high-resolution X-ray crystal structure. We demonstrated that targeted perturbations of the protein nanopore system, in the form of loop-deletion mutagenesis, accompanying alterations of electrostatic interactions between long extracellular loops, produced modest changes of the differential activation free energies calculated at 25 °C, ΔΔG⧧, in the range near the thermal energy but substantial and correlated modifications of the differential activation enthalpies, ΔΔH⧧, and entropies, ΔΔS⧧. This finding indicates that the local conformational reorganizations of the packing and flexibility of the fluctuating loops lining the central constriction of this protein nanopore were supplemented by changes in the single-channel kinetics. These changes were reflected in the enthalpy–entropy reconversions of the interactions between the loop partners with a compensating temperature, TC, of ∼300 K, and an activation free energy constant of ∼41 kJ/mol. We also determined that temperature has a much greater effect on the energetics of the equilibrium gating fluctuations of a protein nanopore than other environmental parameters, such as the ionic strength of the aqueous phase as well as the applied transmembrane potential, likely due to ample changes in the solvation activation enthalpies. There is no fundamental limitation for applying this approach to other complex, multistate membrane protein systems. Therefore, this methodology has major implications in the area of membrane protein design and dynamics, primarily by revealing a better quantitative assessment on the equilibrium transitions among multiple well-defined and functionally distinct substates of protein channels and pores. PMID:25479108

Effects of ligand binding on the conformation and internal dynamics in specific regions of porcine pancreatic phospholipase A2 with tryptophan as a probe: a study combining time-resolved fluorescence spectroscopy and site-directed mutagenesis (same as p. 100)

NASA Astrophysics Data System (ADS)

Kuipers, Oscar; Vincent, Michel; Brochon, Jean-Claude; Verheij, Bert; de Haas, Gerard; Gallay, Jacques

1990-05-01

Exploration of the effect of ligand-protein interactions on conformational substates and internal dynamics in different regions of phospholipase A2 from porcine pancreas (PLA2), was performed by combining site-directed mutagenesis and time-resolved fluorescence measurements. The single tryptophan residue (Trp-3) in the wild type protein was replaced by a phenylalanine residue, whereafter Trp was substituted either for leucine-31 ,located in the calcium binding loop, or for phenylalanine-94, located at the "back side" of the enzyme, in a-helix E (Dijkstra et al., J. Mol. Biol., 147, 97-123, 1981). Analyses by the Maximum Entropy Method (MIEM) of the total fluorescence intensity decays, provide in each case a distribution of separate lifetime classes, which can be interpreted as reflecting the existence of discrete conformational substates in slow exchange with respect to the time-scale of the decay kinetics. The fluorescence decay of the W94 mutant is dominated by an extremely short excited state lifetime of ~60 ps, probably arising from the presence of two proximate disulfide bridges. Time-resolved fluorescence anisotropy studies show that the Trp residue near the NH2 terminus (Trp-3) undergoes a more limited rotational motion than the Trp-3 1 located in the calcium binding loop. The widest angular rotation is observed at position 94, in a-helix E. Calcium binding displays the strongest influence on the lifetime distribution of Trp-31: a major local conformation corresponding to a lifetime class with a barycenter value of ~5.5 ns and contributing to ~50% of the decay is selected. The conformations giving rise to the short lifetimes ((tau)1 and (tau)2 lifetime classes) become less important. The contribution of the third lifetime class (c3) stays at a constant value of 30%. In the presence of calcium, the amplitude of motion is wider than without the ion. There is virtually no effect of calcium binding on the lifetime distribution of the Trp residue at the 3 or the 94 position. Binding of the monomeric substrate analog n-dodecylphosphocholine (C12PN) in the presence of calcium hardly affects neither the Trp-3 excited state population distribution, nor its rotational dynamics. The binding of C12PN monomers to the W31 mutant further increases the contribution of the t4lifetime class at the expense of c2. A more restricted rotation of the Trp-31 residue is also induced. The binding of the micellar substrate analog n-hexadecylphosphocholine (C16PN) in the presence of calcium is very efficient in modifying the lifetime distribution of Trp-3. Essentially, one major broad lifetime population (centered at ~2.6 ns) is revealed by MEM analysis of the total intensity decay. The internal motion is slowed down and the angle of rotation is much smaller in this conformation. Neither the excited state lifetime distribution of Trp-31 nor its dynamics are affected by micelle binding relative to monomer binding. In conclusion, by placing a single Tip-residue at strategic positions along the peptide chain of PLA2, relevant to the binding of biological ligands, an excellent model system for the study of selective perturbations of conformational substates and internal dynamics is provided.

Effects of ligand binding on the conformation and internal dynamics in specific regions of porcine pancreatic phospholipase A2 with tryptophan as a probe: a study combinging time-resolved fluorescence spectroscopy and site-directed mutagenesis (same as p. 628)

NASA Astrophysics Data System (ADS)

Kuipers, Oscar; Vincent, Michel; Brochon, Jean-Claude; Verheij, Bert; de Haas, Gerard; Gallay, Jacques

1990-05-01

Exploration of the effect of ligand-protein interactions on conformational substates and internal dynamics in different regions of phospholipase A2 from porcine pancreas (PLA2), was performed by combining site-directed mutagenesis and time-resolved fluorescence measurements. The single tryptophan residue (Trp-3) in the wild type protein was replaced by a phenylalanine residue, whereafter Tip was substituted either for leucine-3 1 ,located in the calcium binding ioop, or for phenylalanine-94, located at the "back side" of the enzyme, in a-helix E (Dijkstra et al., J. Mol. Biol., 147, 97-123, 1981). Analyses by the Maximum Entropy Method (MEM) of the total fluorescence intensity decays, provide in each case a distribution of separate lifetime classes, which can be interpreted as reflecting the existence of discrete conformational substates in slow exchange with respect to the time-scale of the decay kinetics. The fluorescence decay of the W94 mutant is. dominated by an extremely short excited state lifetime of ~60 ps, probably arising from the presence of two proximate disulfide bridges. Time-resolved fluorescence anisotropy studies show that the Trp residue near the NH2 terminus (Trp-3) undergoes a more limited rotational motion than the Trp-3 1 located in the calcium binding loop. The widest angular rotation is observed at position 94, in a-helix E. Calcium binding displays the strongest influence on the lifetime distribution of Trp-3 1: a major local conformation corresponding to a lifetime class with a barycenter value of -5.5 ns and contributing to ~50% of the decay is selected. The conformations giving rise to the short lifetimes (τ1 and τ2 lifetime classes) become less important. The contribution of the third lifetime class (c3) stays at a constant value of 30%. In the presence of calcium, the amplitude of motion is wider than without the ion. There is virtually no effect of calcium binding on the lifetime distribution of the Trp residue at the 3 or the 94 position. Binding of the monomeric substrate analog n-dodecylphosphocholine (C12PN) in the presence of calcium hardly affects neither the Trp-3 excited state population distribution, nor its rotational dynamics. The binding of C12PN monomers to the W31 mutant further increases the contribution of the τ4 lifetime class at the expense of c2. A more restricted rotation of the Trp-3 1 residue is also induced. The binding of the micellar substrate analog n-hexadecylphosphocholine (C16PN) in the presence of calcium is very efficient in modifying the lifetime distribution of Trp-3. Essentially, one major broad lifetime population (centered at ~2.6 ns) is revealed by MEM analysis of the total intensity decay. The internal motion is slowed down and the angle of rotation is much smaller in this conformation. Neither the excited state lifetime distribution of Trp-31 nor its dynamics are affected by micelle binding relative to monomer binding. In conclusion, by placing a single Tip-residue at strategic positions along the peptide chain of PLA2, relevant to the binding of biological ligands, an excellent model system for the study of selective perturbations of conformational substates and internal dynamics is provided.

Hypothesized diprotomeric enzyme complex supported by stochastic modelling of palytoxin-induced Na/K pump channels

PubMed Central

Vilallonga, Gabriel D.; de Almeida, Antônio-Carlos G.; Ribeiro, Kelison T.; Campos, Sergio V. A.

2018-01-01

The sodium–potassium pump (Na+/K+ pump) is crucial for cell physiology. Despite great advances in the understanding of this ionic pumping system, its mechanism is not completely understood. We propose the use of a statistical model checker to investigate palytoxin (PTX)-induced Na+/K+ pump channels. We modelled a system of reactions representing transitions between the conformational substates of the channel with parameters, concentrations of the substates and reaction rates extracted from simulations reported in the literature, based on electrophysiological recordings in a whole-cell configuration. The model was implemented using the UPPAAL-SMC platform. Comparing simulations and probabilistic queries from stochastic system semantics with experimental data, it was possible to propose additional reactions to reproduce the single-channel dynamic. The probabilistic analyses and simulations suggest that the PTX-induced Na+/K+ pump channel functions as a diprotomeric complex in which protein–protein interactions increase the affinity of the Na+/K+ pump for PTX. PMID:29657808

Structure-Function Perturbation and Dissociation of Tetrameric Urate Oxidase by High Hydrostatic Pressure

PubMed Central

Girard, Eric; Marchal, Stéphane; Perez, Javier; Finet, Stéphanie; Kahn, Richard; Fourme, Roger; Marassio, Guillaume; Dhaussy, Anne-Claire; Prangé, Thierry; Giffard, Marion; Dulin, Fabienne; Bonneté, Françoise; Lange, Reinhard; Abraini, Jacques H.; Mezouar, Mohamed; Colloc'h, Nathalie

2010-01-01

Abstract Structure-function relationships in the tetrameric enzyme urate oxidase were investigated using pressure perturbation. As the active sites are located at the interfaces between monomers, enzyme activity is directly related to the integrity of the tetramer. The effect of hydrostatic pressure on the enzyme was investigated by x-ray crystallography, small-angle x-ray scattering, and fluorescence spectroscopy. Enzymatic activity was also measured under pressure and after decompression. A global model, consistent with all measurements, discloses structural and functional details of the pressure-induced dissociation of the tetramer. Before dissociating, the pressurized protein adopts a conformational substate characterized by an expansion of its substrate binding pocket at the expense of a large neighboring hydrophobic cavity. This substate should be adopted by the enzyme during its catalytic mechanism, where the active site has to accommodate larger intermediates and product. The approach, combining several high-pressure techniques, offers a new (to our knowledge) means of exploring structural and functional properties of transient states relevant to protein mechanisms. PMID:20483346

Digital combined instrument transformer for automated electric power supply control systems of mining companies

NASA Astrophysics Data System (ADS)

Topolsky, D. V.; Gonenko, T. V.; Khatsevskiy, V. F.

2017-10-01

The present paper discusses ways to solve the problem of enhancing operating efficiency of automated electric power supply control systems of mining companies. According to the authors, one of the ways to solve this problem is intellectualization of the electric power supply control system equipment. To enhance efficiency of electric power supply control and electricity metering, it is proposed to use specially designed digital combined instrument current and voltage transformers. This equipment conforms to IEC 61850 international standard and is adapted for integration into the digital substation structure. Tests were performed to check conformity of an experimental prototype of the digital combined instrument current and voltage transformer with IEC 61850 standard. The test results have shown that the considered equipment meets the requirements of the standard.

Integrative, Dynamic Structural Biology at Atomic Resolution—It’s About Time

PubMed Central

van den Bedem, Henry; Fraser, James S.

2015-01-01

Biomolecules adopt a dynamic ensemble of conformations, each with the potential to interact with binding partners or perform the chemical reactions required for a multitude of cellular functions. Recent advances in X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, and other techniques are helping us realize the dream of seeing—in atomic detail—how different parts of biomolecules exchange between functional sub-states using concerted motions. Integrative structural biology has advanced our understanding of the formation of large macromolecular complexes and how their components interact in assemblies by leveraging data from many low-resolution methods. Here, we review the growing opportunities for integrative, dynamic structural biology at the atomic scale, contending there is increasing synergistic potential between X-ray crystallography, NMR, and computer simulations to reveal a structural basis for protein conformational dynamics at high resolution. PMID:25825836

Impaired protein conformational landscapes as revealed in anomalous Arrhenius prefactors.

PubMed

Nagel, Zachary D; Dong, Ming; Bahnson, Brian J; Klinman, Judith P

2011-06-28

A growing body of data supports a role for protein motion in enzyme catalysis. In particular, the ability of enzymes to sample catalytically relevant conformational substates has been invoked to model kinetic and spectroscopic data. However, direct experimental links between rapidly interconverting conformations and the chemical steps of catalysis remain rare. We report here on the kinetic analysis and characterization of the hydride transfer step catalyzed by a series of mutant thermophilic alcohol dehydrogenases (ht-ADH), presenting evidence for Arrhenius prefactor values that become enormously elevated above an expected value of approximately 10(13) s(-1) when the enzyme operates below its optimal temperature range. Restoration of normal Arrhenius behavior in the ht-ADH reaction occurs at elevated temperatures. A simple model, in which reduced temperature alters the ability of the ht-ADH variants to sample the catalytically relevant region of conformational space, can reproduce the available data. These findings indicate an impaired landscape that has been generated by the combined condition of reduced temperature and mutation at a single, active-site hydrophobic side chain. The broader implication is that optimal enzyme function requires the maintenance of a relatively smooth landscape that minimizes low energy traps.

Impaired protein conformational landscapes as revealed in anomalous Arrhenius prefactors

PubMed Central

Nagel, Zachary D.; Dong, Ming; Bahnson, Brian J.; Klinman, Judith P.

2011-01-01

A growing body of data supports a role for protein motion in enzyme catalysis. In particular, the ability of enzymes to sample catalytically relevant conformational substates has been invoked to model kinetic and spectroscopic data. However, direct experimental links between rapidly interconverting conformations and the chemical steps of catalysis remain rare. We report here on the kinetic analysis and characterization of the hydride transfer step catalyzed by a series of mutant thermophilic alcohol dehydrogenases (ht-ADH), presenting evidence for Arrhenius prefactor values that become enormously elevated above an expected value of approximately 1013 s-1 when the enzyme operates below its optimal temperature range. Restoration of normal Arrhenius behavior in the ht-ADH reaction occurs at elevated temperatures. A simple model, in which reduced temperature alters the ability of the ht-ADH variants to sample the catalytically relevant region of conformational space, can reproduce the available data. These findings indicate an impaired landscape that has been generated by the combined condition of reduced temperature and mutation at a single, active-site hydrophobic side chain. The broader implication is that optimal enzyme function requires the maintenance of a relatively smooth landscape that minimizes low energy traps. PMID:21670258

Ground potential rise characteristics of urban step-down substations fed by power cables - A practical example

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sobral, S.T.; Barbosa, J.O.; Numes, J.V.C.

1988-10-01

This paper shows some special ground potential rise characteristics of substations fed by power cables. These characteristics were detected during the study of the interconnected ground system of 14 step-down urban substations fed by the 138 kV underground cable network serving the South Zone of Rio de Janeiro city in Brazil. As this type of system is very common in large cities, the subject can be of general interest for the industry. It was verified that when a fault occurs at a ''cable substation'' (a substation fed exclusively by power cables), almost no ground potential effects were detected at themore » faulted substation or at the other ''cable substations'' of the 138 kV network. However, high values of ground potential occurred at the ''transition substations'' (substations in which the power cables are connected to overhead 138 kV transmission lines, with steel groundwires). That ground potential was enough to produce shocks and equipment damage in certain ''transition substations''. It was verified that this problem has no relation with potential transfer. The paper shows also that the utilization of overhead lines with ACSR groundwires on the initial spans closer to the ''transition substation'' would be enough to avoid the problem. Even if the ACSR conductor is used only at the initial section of one of the lines, a reduction of the problem would be obtained. The paper shows also that the utilization of ACSR ground-wires near the ''transition substations'' contributes to reduce the amount of the copper necessary to control step, touch and mess potentials in these substations. Additional mitigation procedures are also examined in the paper.« less

Couplings between hierarchical conformational dynamics from multi-time correlation functions and two-dimensional lifetime spectra: Application to adenylate kinase

NASA Astrophysics Data System (ADS)

Ono, Junichi; Takada, Shoji; Saito, Shinji

2015-06-01

An analytical method based on a three-time correlation function and the corresponding two-dimensional (2D) lifetime spectrum is developed to elucidate the time-dependent couplings between the multi-timescale (i.e., hierarchical) conformational dynamics in heterogeneous systems such as proteins. In analogy with 2D NMR, IR, electronic, and fluorescence spectroscopies, the waiting-time dependence of the off-diagonal peaks in the 2D lifetime spectra can provide a quantitative description of the dynamical correlations between the conformational motions with different lifetimes. The present method is applied to intrinsic conformational changes of substrate-free adenylate kinase (AKE) using long-time coarse-grained molecular dynamics simulations. It is found that the hierarchical conformational dynamics arise from the intra-domain structural transitions among conformational substates of AKE by analyzing the one-time correlation functions and one-dimensional lifetime spectra for the donor-acceptor distances corresponding to single-molecule Förster resonance energy transfer experiments with the use of the principal component analysis. In addition, the complicated waiting-time dependence of the off-diagonal peaks in the 2D lifetime spectra for the donor-acceptor distances is attributed to the fact that the time evolution of the couplings between the conformational dynamics depends upon both the spatial and temporal characters of the system. The present method is expected to shed light on the biological relationship among the structure, dynamics, and function.

Hierarchical sampling for metastable conformers determines biomolecular recognition: the case of malectin and diglucosylated N-glycan interactions.

PubMed

Mamidi, Ashalatha Sreshty; Surolia, Avadhesha

2015-01-01

Structural information over the entire course of binding interactions based on the analyses of energy landscapes is described, which provides a framework to understand the events involved during biomolecular recognition. Conformational dynamics of malectin's exquisite selectivity for diglucosylated N-glycan (Dig-N-glycan), a highly flexible oligosaccharide comprising of numerous dihedral torsion angles, are described as an example. For this purpose, a novel approach based on hierarchical sampling for acquiring metastable molecular conformations constituting low-energy minima for understanding the structural features involved in a biologic recognition is proposed. For this purpose, four variants of principal component analysis were employed recursively in both Cartesian space and dihedral angles space that are characterized by free energy landscapes to select the most stable conformational substates. Subsequently, k-means clustering algorithm was implemented for geometric separation of the major native state to acquire a final ensemble of metastable conformers. A comparison of malectin complexes was then performed to characterize their conformational properties. Analyses of stereochemical metrics and other concerted binding events revealed surface complementarity, cooperative and bidentate hydrogen bonds, water-mediated hydrogen bonds, carbohydrate-aromatic interactions including CH-π and stacking interactions involved in this recognition. Additionally, a striking structural transition from loop to β-strands in malectin CRD upon specific binding to Dig-N-glycan is observed. The interplay of the above-mentioned binding events in malectin and Dig-N-glycan supports an extended conformational selection model as the underlying binding mechanism.

The allosteric switching mechanism in bacteriophage MS2

NASA Astrophysics Data System (ADS)

Perkett, Matthew R.; Mirijanian, Dina T.; Hagan, Michael F.

2016-07-01

We use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopts different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we use all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We discuss changes in molecular interactions responsible for this shift. We then identify networks of amino acids with correlated motions to reveal the mechanism by which effects of TR binding span the protein. We find that TR binding strongly affects residues located at the 5-fold and quasi-sixfold interfaces in the assembled capsid, suggesting a mechanism by which the TR binding could direct formation of the native capsid geometry. The analysis predicts amino acids whose substitution by mutagenesis could alter populations of the conformational substates or their transition rates.

Mixture models for protein structure ensembles.

PubMed

Hirsch, Michael; Habeck, Michael

2008-10-01

Protein structure ensembles provide important insight into the dynamics and function of a protein and contain information that is not captured with a single static structure. However, it is not clear a priori to what extent the variability within an ensemble is caused by internal structural changes. Additional variability results from overall translations and rotations of the molecule. And most experimental data do not provide information to relate the structures to a common reference frame. To report meaningful values of intrinsic dynamics, structural precision, conformational entropy, etc., it is therefore important to disentangle local from global conformational heterogeneity. We consider the task of disentangling local from global heterogeneity as an inference problem. We use probabilistic methods to infer from the protein ensemble missing information on reference frames and stable conformational sub-states. To this end, we model a protein ensemble as a mixture of Gaussian probability distributions of either entire conformations or structural segments. We learn these models from a protein ensemble using the expectation-maximization algorithm. Our first model can be used to find multiple conformers in a structure ensemble. The second model partitions the protein chain into locally stable structural segments or core elements and less structured regions typically found in loops. Both models are simple to implement and contain only a single free parameter: the number of conformers or structural segments. Our models can be used to analyse experimental ensembles, molecular dynamics trajectories and conformational change in proteins. The Python source code for protein ensemble analysis is available from the authors upon request.

The allosteric switching mechanism in bacteriophage MS2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perkett, Matthew R.; Mirijanian, Dina T.; Hagan, Michael F., E-mail: hagan@brandeis.edu

2016-07-21

We use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopts different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we usemore » all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We discuss changes in molecular interactions responsible for this shift. We then identify networks of amino acids with correlated motions to reveal the mechanism by which effects of TR binding span the protein. We find that TR binding strongly affects residues located at the 5-fold and quasi-sixfold interfaces in the assembled capsid, suggesting a mechanism by which the TR binding could direct formation of the native capsid geometry. The analysis predicts amino acids whose substitution by mutagenesis could alter populations of the conformational substates or their transition rates.« less

Couplings between hierarchical conformational dynamics from multi-time correlation functions and two-dimensional lifetime spectra: Application to adenylate kinase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ono, Junichi; Takada, Shoji; Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502

2015-06-07

An analytical method based on a three-time correlation function and the corresponding two-dimensional (2D) lifetime spectrum is developed to elucidate the time-dependent couplings between the multi-timescale (i.e., hierarchical) conformational dynamics in heterogeneous systems such as proteins. In analogy with 2D NMR, IR, electronic, and fluorescence spectroscopies, the waiting-time dependence of the off-diagonal peaks in the 2D lifetime spectra can provide a quantitative description of the dynamical correlations between the conformational motions with different lifetimes. The present method is applied to intrinsic conformational changes of substrate-free adenylate kinase (AKE) using long-time coarse-grained molecular dynamics simulations. It is found that the hierarchicalmore » conformational dynamics arise from the intra-domain structural transitions among conformational substates of AKE by analyzing the one-time correlation functions and one-dimensional lifetime spectra for the donor-acceptor distances corresponding to single-molecule Förster resonance energy transfer experiments with the use of the principal component analysis. In addition, the complicated waiting-time dependence of the off-diagonal peaks in the 2D lifetime spectra for the donor-acceptor distances is attributed to the fact that the time evolution of the couplings between the conformational dynamics depends upon both the spatial and temporal characters of the system. The present method is expected to shed light on the biological relationship among the structure, dynamics, and function.« less

The allosteric switching mechanism in bacteriophage MS2

PubMed Central

Perkett, Matthew R.; Mirijanian, Dina T.

2016-01-01

We use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopts different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we use all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We discuss changes in molecular interactions responsible for this shift. We then identify networks of amino acids with correlated motions to reveal the mechanism by which effects of TR binding span the protein. We find that TR binding strongly affects residues located at the 5-fold and quasi-sixfold interfaces in the assembled capsid, suggesting a mechanism by which the TR binding could direct formation of the native capsid geometry. The analysis predicts amino acids whose substitution by mutagenesis could alter populations of the conformational substates or their transition rates. PMID:27448905

77 FR 58828 - Northern Indiana Public Service Company; Notice of Petition for Declaratory Order

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-24

... kV transmission line from the Reynolds substation to the Greentown substation and (2) substation upgrades at Reynolds substation, including a 765 kV/345kV transformer, a Multi-Value Project approved under...

Dynamic neutron scattering from conformational dynamics. I. Theory and Markov models

NASA Astrophysics Data System (ADS)

Lindner, Benjamin; Yi, Zheng; Prinz, Jan-Hendrik; Smith, Jeremy C.; Noé, Frank

2013-11-01

The dynamics of complex molecules can be directly probed by inelastic neutron scattering experiments. However, many of the underlying dynamical processes may exist on similar timescales, which makes it difficult to assign processes seen experimentally to specific structural rearrangements. Here, we show how Markov models can be used to connect structural changes observed in molecular dynamics simulation directly to the relaxation processes probed by scattering experiments. For this, a conformational dynamics theory of dynamical neutron and X-ray scattering is developed, following our previous approach for computing dynamical fingerprints of time-correlation functions [F. Noé, S. Doose, I. Daidone, M. Löllmann, J. Chodera, M. Sauer, and J. Smith, Proc. Natl. Acad. Sci. U.S.A. 108, 4822 (2011)]. Markov modeling is used to approximate the relaxation processes and timescales of the molecule via the eigenvectors and eigenvalues of a transition matrix between conformational substates. This procedure allows the establishment of a complete set of exponential decay functions and a full decomposition into the individual contributions, i.e., the contribution of every atom and dynamical process to each experimental relaxation process.

40 CFR 35.1615 - Substate agreements.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 1 2014-07-01 2014-07-01 false Substate agreements. 35.1615 Section 35... STATE AND LOCAL ASSISTANCE Cooperative Agreements for Protecting and Restoring Publicly Owned Freshwater Lakes § 35.1615 Substate agreements. States may make financial assistance available to substate agencies...

40 CFR 35.1615 - Substate agreements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 1 2010-07-01 2010-07-01 false Substate agreements. 35.1615 Section 35... STATE AND LOCAL ASSISTANCE Cooperative Agreements for Protecting and Restoring Publicly Owned Freshwater Lakes § 35.1615 Substate agreements. States may make financial assistance available to substate agencies...

Fault Current Distribution and Pole Earth Potential Rise (EPR) Under Substation Fault

NASA Astrophysics Data System (ADS)

Nnassereddine, M.; Rizk, J.; Hellany, A.; Nagrial, M.

2013-09-01

New high-voltage (HV) substations are fed by transmission lines. The position of these lines necessitates earthing design to ensure safety compliance of the system. Conductive structures such as steel or concrete poles are widely used in HV transmission mains. The earth potential rise (EPR) generated by a fault at the substation could result in an unsafe condition. This article discusses EPR based on substation fault. The pole EPR assessment under substation fault is assessed with and without mutual impedance consideration. Split factor determination with and without the mutual impedance of the line is also discussed. Furthermore, a simplified formula to compute the pole grid current under substation fault is included. Also, it includes the introduction of the n factor which determines the number of poles that required earthing assessments under substation fault. A case study is shown.

Using Immersive Virtual Reality for Electrical Substation Training

ERIC Educational Resources Information Center

Tanaka, Eduardo H.; Paludo, Juliana A.; Cordeiro, Carlúcio S.; Domingues, Leonardo R.; Gadbem, Edgar V.; Euflausino, Adriana

2015-01-01

Usually, distribution electricians are called upon to solve technical problems found in electrical substations. In this project, we apply problem-based learning to a training program for electricians, with the help of a virtual reality environment that simulates a real substation. Using this virtual substation, users may safely practice maneuvers…

Dynamic Simulation on the Installation Process of HGIS in Transformer Substation

NASA Astrophysics Data System (ADS)

Lin, Tao; Li, Shaohua; Wang, Hu; Che, Deyong; Qi, Guangcai; Yao, Jianfeng; Zhang, Qingzhe

The technological requirements of Hypid Gas Insulated Switchgear (HGIS) installation in transformer substation is high and the control points of quality is excessive. Most of the engineers and technicians in the construction enterprises are not familiar with equipments of HGIS. In order to solve these problem, equipments of HGIS is modeled on the computer by SolidWorks software. Installation process of civil foundation and closed-type equipments is optimized dynamically with virtual assemble technology. Announcements and application work are composited into animation file. Skills of modeling and simulation is tidied classify as well. The result of the visual dynamic simulation can instruct the actual construction process of HGIS to a certain degree and can promote reasonable construction planning and management. It can also improve the method and quality of staff training for electric power construction enterprises.

High resolution approach to the native state ensemble kinetics and thermodynamics.

PubMed

Wu, Sangwook; Zhuravlev, Pavel I; Papoian, Garegin A

2008-12-15

Many biologically interesting functions such as allosteric switching or protein-ligand binding are determined by the kinetics and mechanisms of transitions between various conformational substates of the native basin of globular proteins. To advance our understanding of these processes, we constructed a two-dimensional free energy surface (FES) of the native basin of a small globular protein, Trp-cage. The corresponding order parameters were defined using two native substructures of Trp-cage. These calculations were based on extensive explicit water all-atom molecular dynamics simulations. Using the obtained two-dimensional FES, we studied the transition kinetics between two Trp-cage conformations, finding that switching process shows a borderline behavior between diffusive and weakly-activated dynamics. The transition is well-characterized kinetically as a biexponential process. We also introduced a new one-dimensional reaction coordinate for the conformational transition, finding reasonable qualitative agreement with the two-dimensional kinetics results. We investigated the distribution of all the 38 native nuclear magnetic resonance structures on the obtained FES, analyzing interactions that stabilize specific low-energy conformations. Finally, we constructed a FES for the same system but with simple dielectric model of water instead of explicit water, finding that the results were surprisingly similar in a small region centered on the native conformations. The dissimilarities between the explicit and implicit model on the larger-scale point to the important role of water in mediating interactions between amino acid residues.

Substation alarm multiplexing system (SAMS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

ElBadaly, H.; Gaughan, J.; Ward, G.

1996-03-01

This paper describes an on going R&D project to develop, design, install, and assess the field performance of an advanced substation alarm system. SAMS provides a highly fault-tolerant system for the reporting of equipment alarms. SAMS separates and identifies each of the multiple alarm contacts, transmits an alarm condition over existing substation two-wire system, and displays the alarm source, and its associated technical information, on a touch-screen monitor inside the substation control room, and a remote central location and on a hand held terminal which may be carried anywhere within the substation. SAMS is currently installed at the Sherman Creekmore » substation in the Bronx for the purpose of a three month field evaluation.« less

Study on Noise Prediction Model and Control Schemes for Substation

PubMed Central

Gao, Yang; Liu, Songtao

2014-01-01

With the government's emphasis on environmental issues of power transmission and transformation project, noise pollution has become a prominent problem now. The noise from the working transformer, reactor, and other electrical equipment in the substation will bring negative effect to the ambient environment. This paper focuses on using acoustic software for the simulation and calculation method to control substation noise. According to the characteristics of the substation noise and the techniques of noise reduction, a substation's acoustic field model was established with the SoundPLAN software to predict the scope of substation noise. On this basis, 4 reasonable noise control schemes were advanced to provide some helpful references for noise control during the new substation's design and construction process. And the feasibility and application effect of these control schemes can be verified by using the method of simulation modeling. The simulation results show that the substation always has the problem of excessive noise at boundary under the conventional measures. The excess noise can be efficiently reduced by taking the corresponding noise reduction methods. PMID:24672356

Deep learning based state recognition of substation switches

NASA Astrophysics Data System (ADS)

Wang, Jin

2018-06-01

Different from the traditional method which recognize the state of substation switches based on the running rules of electrical power system, this work proposes a novel convolutional neuron network-based state recognition approach of substation switches. Inspired by the theory of transfer learning, we first establish a convolutional neuron network model trained on the large-scale image set ILSVRC2012, then the restricted Boltzmann machine is employed to replace the full connected layer of the convolutional neuron network and trained on our small image dataset of 110kV substation switches to get a stronger model. Experiments conducted on our image dataset of 110kV substation switches show that, the proposed approach can be applicable to the substation to reduce the running cost and implement the real unattended operation.

Driving Calmodulin Protein towards Conformational Shift by Changing Ionization States of Select Residues

NASA Astrophysics Data System (ADS)

Negi, Sunita; Rana Atilgan, Ali; Atilgan, Canan

2012-12-01

Proteins are complex systems made up of many conformational sub-states which are mainly determined by the folded structure. External factors such as solvent type, temperature, pH and ionic strength play a very important role in the conformations sampled by proteins. Here we study the conformational multiplicity of calmodulin (CaM) which is a protein that plays an important role in calcium signaling pathways in the eukaryotic cells. CaM can bind to a variety of other proteins or small organic compounds, and mediates different physiological processes by activating various enzymes. Binding of calcium ions and proteins or small organic molecules to CaM induces large conformational changes that are distinct to each interacting partner. In particular, we discuss the effect of pH variation on the conformations of CaM. By using the pKa values of the charged residues as a basis to assign protonation states, the conformational changes induced in CaM by reducing the pH are studied by molecular dynamics simulations. Our current view suggests that at high pH, barrier crossing to the compact form is prevented by repulsive electrostatic interactions between the two lobes. At reduced pH, not only is barrier crossing facilitated by protonation of residues, but also conformations which are on average more compact are attained. The latter are in accordance with the fluorescence resonance energy transfer experiment results of other workers. The key events leading to the conformational change from the open to the compact conformation are (i) formation of a salt bridge between the N-lobe and the linker, stabilizing their relative motions, (ii) bending of the C-lobe towards the N-lobe, leading to a lowering of the interaction energy between the two-lobes, (iii) formation of a hydrophobic patch between the two lobes, further stabilizing the bent conformation by reducing the entropic cost of the compact form, (iv) sharing of a Ca+2 ion between the two lobes.

Project FOOTPRINT: Substation modeling and simulations for E1 pulses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, Scott D.; Larson, D. J.; Kirkendall, B. A.

This report includes a presentation with an: Introduction to CW coupling; Introduction to single-pulse coupling; Description of E1 waveforms; Structures in a substation yard --articulated (as part of the substation's defined electrical functionality)--unarticulated (not as part of the substation's defined electrical functionality); Coupling --electrical coupling (capacitive coupling) --magnetic coupling (inductive coupling); Connectivity to long-line transmission lines; Control infrastructure; Summary; and References.

View of EPA Farm power substation, facing westsouthwest Nevada ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

View of EPA Farm power substation, facing west-southwest - Nevada Test Site, Environmental Protection Agency Farm, Power Substation, Area 15, Yucca Flat, 10-2 Road near Circle Road, Mercury, Nye County, NV

Resilient Core Networks for Energy Distribution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuntze, Nicolai; Rudolph, Carsten; Leivesley, Sally

2014-07-28

Abstract—Substations and their control are crucial for the availability of electricity in today’s energy distribution. Ad- vanced energy grids with Distributed Energy Resources require higher complexity in substations, distributed functionality and communication between devices inside substations and between substations. Also, substations include more and more intelligent devices and ICT based systems. All these devices are connected to other systems by different types of communication links or are situated in uncontrolled environments. Therefore, the risk of ICT based attacks on energy grids is growing. Consequently, security measures to counter these risks need to be an intrinsic part of energy grids. Thismore » paper introduces the concept of a Resilient Core Network to interconnected substations. This core network provides essen- tial security features, enables fast detection of attacks and allows for a distributed and autonomous mitigation of ICT based risks.« less

Cherry-picking functionally relevant substates from long md trajectories using a stratified sampling approach.

PubMed

Chandramouli, Balasubramanian; Mancini, Giordano

2016-01-01

Classical Molecular Dynamics (MD) simulations can provide insights at the nanoscopic scale into protein dynamics. Currently, simulations of large proteins and complexes can be routinely carried out in the ns-μs time regime. Clustering of MD trajectories is often performed to identify selective conformations and to compare simulation and experimental data coming from different sources on closely related systems. However, clustering techniques are usually applied without a careful validation of results and benchmark studies involving the application of different algorithms to MD data often deal with relatively small peptides instead of average or large proteins; finally clustering is often applied as a means to analyze refined data and also as a way to simplify further analysis of trajectories. Herein, we propose a strategy to classify MD data while carefully benchmarking the performance of clustering algorithms and internal validation criteria for such methods. We demonstrate the method on two showcase systems with different features, and compare the classification of trajectories in real and PCA space. We posit that the prototype procedure adopted here could be highly fruitful in clustering large trajectories of multiple systems or that resulting especially from enhanced sampling techniques like replica exchange simulations. Copyright: © 2016 by Fabrizio Serra editore, Pisa · Roma.

Workers' exposure to electric fields during the task 'maintenance of an operating device of circuit breaker from a service platform' at 110-kV substations.

PubMed

Korpinen, Leena; Pääkkönen, Rauno

2018-02-26

The objective of the study was to investigate occupational exposure to electric fields during the task 'maintenance of an operating device of circuit breaker from a service platform' at 110-kV substations. The aim was also to compare the results to Directive 2013/35/EU. At 16 substations, 255 electric field measurements were performed. The highest mean value of the electric fields was 9.6 kV⋅m -1 . At 63% of substations the maximum values were over 10.0 kV⋅m -1 , and at 31% of the substations the 75th percentiles were over 10.0 kV⋅m -1 , which is the low action level (AL) according to Directive 2013/35/EU. All measured values were below the high AL (20.0 kV⋅m -1 ). In the future, it is important to take into account that the measurements were only taken at Finnish 110-kV substations; therefore, it is not possible to generalize these results to other countries and different types of substations.

Maternal residential proximity to sources of extremely low frequency electromagnetic fields and adverse birth outcomes in a UK cohort.

PubMed

de Vocht, Frank; Hannam, Kimberly; Baker, Philip; Agius, Raymond

2014-04-01

Studies have suggested that exposure to extremely low frequency electromagnetic fields (ELF-EMF) may be associated with increased risk of adverse birth outcomes. This study tested the hypothesis that close proximity to residential ELF-EMF sources is associated with a reduction in birth weight and increased the risk of low birthweight (LBW), small for gestational age (SGA) and spontaneous preterm birth (SPTB). Closest residential proximity to high voltage cables, overhead power lines, substations or towers during pregnancy was calculated for 140356 singleton live births between 2004 and 2008 in Northwest England. Associations between proximity and risk for LBW, SGA and SPTB were calculated, as well as associations with birth weight directly. Associations were adjusted for maternal age, ethnicity, parity and for part of the population additionally for maternal smoking during pregnancy. Reduced average birth weight of 212 g (95% confidence interval (CI): -395 to -29 g) was found for close proximity to a source, and was largest for female births (-251 g (95% CI: -487 to -15 g)). No statistically significant increased risks for any clinical birth outcomes with residential proximity of 50 m or less were observed. Living close (50 m or less) to a residential ELF-EMF source during pregnancy is associated with suboptimal growth in utero, with stronger effects in female than in males. However, only a few pregnant women live this close to high voltage cables, overhead power lines, substations or towers, likely limiting its public health impact. © 2014 Wiley Periodicals, Inc.

Spectral methods for study of the G-protein-coupled receptor rhodopsin. II. Magnetic resonance methods

NASA Astrophysics Data System (ADS)

Struts, A. V.; Barmasov, A. V.; Brown, M. F.

2016-02-01

This article continues our review of spectroscopic studies of G-protein-coupled receptors. Magnetic resonance methods including electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) provide specific structural and dynamical data for the protein in conjunction with optical methods (vibrational, electronic spectroscopy) as discussed in the accompanying article. An additional advantage is the opportunity to explore the receptor proteins in the natural membrane lipid environment. Solid-state 2H and 13C NMR methods yield information about both the local structure and dynamics of the cofactor bound to the protein and its light-induced changes. Complementary site-directed spin-labeling studies monitor the structural alterations over larger distances and correspondingly longer time scales. A multiscale reaction mechanism describes how local changes of the retinal cofactor unlock the receptor to initiate large-scale conformational changes of rhodopsin. Activation of the G-protein-coupled receptor involves an ensemble of conformational substates within the rhodopsin manifold that characterize the dynamically active receptor.

Conformational heterogeneity of the calmodulin binding interface

NASA Astrophysics Data System (ADS)

Shukla, Diwakar; Peck, Ariana; Pande, Vijay S.

2016-04-01

Calmodulin (CaM) is a ubiquitous Ca2+ sensor and a crucial signalling hub in many pathways aberrantly activated in disease. However, the mechanistic basis of its ability to bind diverse signalling molecules including G-protein-coupled receptors, ion channels and kinases remains poorly understood. Here we harness the high resolution of molecular dynamics simulations and the analytical power of Markov state models to dissect the molecular underpinnings of CaM binding diversity. Our computational model indicates that in the absence of Ca2+, sub-states in the folded ensemble of CaM's C-terminal domain present chemically and sterically distinct topologies that may facilitate conformational selection. Furthermore, we find that local unfolding is off-pathway for the exchange process relevant for peptide binding, in contrast to prior hypotheses that unfolding might account for binding diversity. Finally, our model predicts a novel binding interface that is well-populated in the Ca2+-bound regime and, thus, a candidate for pharmacological intervention.

Nearly reversible conformational change of amyloid fibrils as revealed by pH-jump experiments.

PubMed

Yamaguchi, Kei-ichi; Kamatari, Yuji O; Fukuoka, Mayuko; Miyaji, Reiji; Kuwata, Kazuo

2013-10-01

pH-jump induced conformational transitions between substates of preformed amyloid fibrils made by a fragmented peptide of helix 2 (H2 peptide) of MoPrP were detected, and their kinetics were analyzed using a novel pH-jump apparatus specially designed for observing amyloids. Previously, we reported that H2 peptide formed ordered fibrils with a minimum at 207 nm on CD spectra at pH 2.9 (named pH 2.9 fibrils), but formed aggregate-like fibrils with a minimum at 220 nm at pH 7.5 (named pH 7.5 fibrils). When pH-jump from 2.9 to 7.5 was performed, the CD spectrum changed instantly, but the finally observed ellipticities were clearly distinct from those of pH 7.5 fibrils. Thus, the finally observed state is termed 'pH 7.5-like fibrils'. However, pH 7.5-like fibrils reverted to the conformation very similar to that of the pH 2.9 fibrils when the pH of the solution was restored to 2.9. Then, we examined the kinetics of the nearly reversible conformational changes between pH 2.9 fibrils and pH 7.5-like fibrils using ANS fluorescence stopped-flow, and we observed relatively fast phases (0.7-18 s(-1)). In contrast, the conversion between pH 7.5-like fibrils and pH 7.5 fibrils never occurred (<0.2 day(-1)). Thus, H2 fibrils can be switched readily between distinct conformations separated by a low energy barrier, while a large energy barrier clearly separated the different conformations. These conformational varieties of amyloid fibrils may explain the physical basis of the diversity in prion.

Nullspace Sampling with Holonomic Constraints Reveals Molecular Mechanisms of Protein Gαs.

PubMed

Pachov, Dimitar V; van den Bedem, Henry

2015-07-01

Proteins perform their function or interact with partners by exchanging between conformational substates on a wide range of spatiotemporal scales. Structurally characterizing these exchanges is challenging, both experimentally and computationally. Large, diffusional motions are often on timescales that are difficult to access with molecular dynamics simulations, especially for large proteins and their complexes. The low frequency modes of normal mode analysis (NMA) report on molecular fluctuations associated with biological activity. However, NMA is limited to a second order expansion about a minimum of the potential energy function, which limits opportunities to observe diffusional motions. By contrast, kino-geometric conformational sampling (KGS) permits large perturbations while maintaining the exact geometry of explicit conformational constraints, such as hydrogen bonds. Here, we extend KGS and show that a conformational ensemble of the α subunit Gαs of heterotrimeric stimulatory protein Gs exhibits structural features implicated in its activation pathway. Activation of protein Gs by G protein-coupled receptors (GPCRs) is associated with GDP release and large conformational changes of its α-helical domain. Our method reveals a coupled α-helical domain opening motion while, simultaneously, Gαs helix α5 samples an activated conformation. These motions are moderated in the activated state. The motion centers on a dynamic hub near the nucleotide-binding site of Gαs, and radiates to helix α4. We find that comparative NMA-based ensembles underestimate the amplitudes of the motion. Additionally, the ensembles fall short in predicting the accepted direction of the full activation pathway. Taken together, our findings suggest that nullspace sampling with explicit, holonomic constraints yields ensembles that illuminate molecular mechanisms involved in GDP release and protein Gs activation, and further establish conformational coupling between key structural elements of Gαs.

Nullspace Sampling with Holonomic Constraints Reveals Molecular Mechanisms of Protein Gαs

PubMed Central

Pachov, Dimitar V.; van den Bedem, Henry

2015-01-01

Proteins perform their function or interact with partners by exchanging between conformational substates on a wide range of spatiotemporal scales. Structurally characterizing these exchanges is challenging, both experimentally and computationally. Large, diffusional motions are often on timescales that are difficult to access with molecular dynamics simulations, especially for large proteins and their complexes. The low frequency modes of normal mode analysis (NMA) report on molecular fluctuations associated with biological activity. However, NMA is limited to a second order expansion about a minimum of the potential energy function, which limits opportunities to observe diffusional motions. By contrast, kino-geometric conformational sampling (KGS) permits large perturbations while maintaining the exact geometry of explicit conformational constraints, such as hydrogen bonds. Here, we extend KGS and show that a conformational ensemble of the α subunit Gαs of heterotrimeric stimulatory protein Gs exhibits structural features implicated in its activation pathway. Activation of protein Gs by G protein-coupled receptors (GPCRs) is associated with GDP release and large conformational changes of its α-helical domain. Our method reveals a coupled α-helical domain opening motion while, simultaneously, Gαs helix α5 samples an activated conformation. These motions are moderated in the activated state. The motion centers on a dynamic hub near the nucleotide-binding site of Gαs, and radiates to helix α4. We find that comparative NMA-based ensembles underestimate the amplitudes of the motion. Additionally, the ensembles fall short in predicting the accepted direction of the full activation pathway. Taken together, our findings suggest that nullspace sampling with explicit, holonomic constraints yields ensembles that illuminate molecular mechanisms involved in GDP release and protein Gs activation, and further establish conformational coupling between key structural elements of Gαs. PMID:26218073

Energetic and spatial parameters for gating of the bacterial large conductance mechanosensitive channel, MscL

NASA Technical Reports Server (NTRS)

Sukharev, S. I.; Sigurdson, W. J.; Kung, C.; Sachs, F.

1999-01-01

MscL is multimeric protein that forms a large conductance mechanosensitive channel in the inner membrane of Escherichia coli. Since MscL is gated by tension transmitted through the lipid bilayer, we have been able to measure its gating parameters as a function of absolute tension. Using purified MscL reconstituted in liposomes, we recorded single channel currents and varied the pressure gradient (P) to vary the tension (T). The tension was calculated from P and the radius of curvature was obtained using video microscopy of the patch. The probability of being open (Po) has a steep sigmoidal dependence on T, with a midpoint (T1/2) of 11.8 dyn/cm. The maximal slope sensitivity of Po/Pc was 0.63 dyn/cm per e-fold. Assuming a Boltzmann distribution, the energy difference between the closed and fully open states in the unstressed membrane was DeltaE = 18.6 kBT. If the mechanosensitivity arises from tension acting on a change of in-plane area (DeltaA), the free energy, TDeltaA, would correspond to DeltaA = 6.5 nm2. MscL is not a binary channel, but has four conducting states and a closed state. Most transition rates are independent of tension, but the rate-limiting step to opening is the transition between the closed state and the lowest conductance substate. This transition thus involves the greatest DeltaA. When summed over all transitions, the in-plane area change from closed to fully open was 6 nm2, agreeing with the value obtained in the two-state analysis. Assuming a cylindrical channel, the dimensions of the (fully open) pore were comparable to DeltaA. Thus, the tension dependence of channel gating is primarily one of increasing the external channel area to accommodate the pore of the smallest conducting state. The higher conducting states appear to involve conformational changes internal to the channel that don't involve changes in area.

AUTOMATED UTILITY SERVICE AREA ASSESSMENT UNDER EMERGENCY CONDITIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

G. TOOLE; S. LINGER

2001-01-01

All electric utilities serve power to their customers through a variety of functional levels, notably substations. The majority of these components consist of distribution substations operating at lower voltages while a small fraction are transmission substations. There is an associated geographical area that encompasses customers who are served, defined as the service area. Analysis of substation service areas is greatly complicated by several factors: distribution networks are often highly interconnected which allows a multitude of possible switching operations; also, utilities dynamically alter the network topology in order to respond to emergency events. As a result, the service area for amore » substation can change radically. A utility will generally attempt to minimize the number of customers outaged by switching effected loads to alternate substations. In this manner, all or a portion of a disabled substation's load may be served by one or more adjacent substations. This paper describes a suite of analytical tools developed at Los Alamos National Laboratory (LANL), which address the problem of determining how a utility might respond to such emergency events. The estimated outage areas derived using the tools are overlaid onto other geographical and electrical layers in a geographic information system (GIS) software application. The effects of a power outage on a population, other infrastructures, or other physical features, can be inferred by the proximity of these features to the estimated outage area.« less

Structural assessment of highway "N" power substation under earthquake loads.

DOT National Transportation Integrated Search

2009-10-01

In this study, the Highway N Substation was analyzed with a finite element model (FEM) for its vulnerability. The rigid bus and electric switch components were characterized with full scale shake table tests. Each component of the substation wa...

Substation Reactive Power Regulation Strategy

NASA Astrophysics Data System (ADS)

Zhang, Junfeng; Zhang, Chunwang; Ma, Daqing

2018-01-01

With the increasing requirements on the power supply quality and reliability of distribution network, voltage and reactive power regulation of substations has become one of the indispensable ways to ensure voltage quality and reactive power balance and to improve the economy and reliability of distribution network. Therefore, it is a general concern of the current power workers and operators that what kind of flexible and effective control method should be used to adjust the on-load tap-changer (OLTC) transformer and shunt compensation capacitor in a substation to achieve reactive power balance in situ, improve voltage pass rate, increase power factor and reduce active power loss. In this paper, based on the traditional nine-zone diagram and combining with the characteristics of substation, a fuzzy variable-center nine-zone diagram control method is proposed and used to make a comprehensive regulation of substation voltage and reactive power. Through the calculation and simulation of the example, this method is proved to have satisfactorily reconciled the contradiction between reactive power and voltage in real-time control and achieved the basic goal of real-time control of the substation, providing a reference value to the practical application of the substation real-time control method.

17. Photocopy of photograph showing excavation of South Bank Substation ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

17. Photocopy of photograph showing excavation of South Bank Substation site, 15 May 1939 (from the BPA Photo Archives, Portland, Oregon, Negative No. 345), LOOKING WEST - Bonneville Power Administration South Bank Substation, I-84, South of Bonneville Dam Powerhouse, Bonneville, Multnomah County, OR

20 CFR 631.82 - Substate allocation.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 20 Employees' Benefits 3 2010-04-01 2010-04-01 false Substate allocation. 631.82 Section 631.82 Employees' Benefits EMPLOYMENT AND TRAINING ADMINISTRATION, DEPARTMENT OF LABOR PROGRAMS UNDER TITLE III OF THE JOB TRAINING PARTNERSHIP ACT Disaster Relief Employment Assistance § 631.82 Substate allocation...

An application of data mining in district heating substations for improving energy performance

NASA Astrophysics Data System (ADS)

Xue, Puning; Zhou, Zhigang; Chen, Xin; Liu, Jing

2017-11-01

Automatic meter reading system is capable of collecting and storing a huge number of district heating (DH) data. However, the data obtained are rarely fully utilized. Data mining is a promising technology to discover potential interesting knowledge from vast data. This paper applies data mining methods to analyse the massive data for improving energy performance of DH substation. The technical approach contains three steps: data selection, cluster analysis and association rule mining (ARM). Two-heating-season data of a substation are used for case study. Cluster analysis identifies six distinct heating patterns based on the primary heat of the substation. ARM reveals that secondary pressure difference and secondary flow rate have a strong correlation. Using the discovered rules, a fault occurring in remote flow meter installed at secondary network is detected accurately. The application demonstrates that data mining techniques can effectively extrapolate potential useful knowledge to better understand substation operation strategies and improve substation energy performance.

Application of service oriented architecture for sensors and actuators in district heating substations.

PubMed

Gustafsson, Jonas; Kyusakov, Rumen; Mäkitaavola, Henrik; Delsing, Jerker

2014-08-21

Hardwired sensor installations using proprietary protocols found in today's district heating substations limit the potential usability of the sensors in and around the substations. If sensor resources can be shared and re-used in a variety of applications, the cost of sensors and installation can be reduced, and their functionality and operability can be increased. In this paper, we present a new concept of district heating substation control and monitoring, where a service oriented architecture (SOA) is deployed in a wireless sensor network (WSN), which is integrated with the substation. IP-networking is exclusively used from sensor to server; hence, no middleware is needed for Internet integration. Further, by enabling thousands of sensors with SOA capabilities, a System of Systems approach can be applied. The results of this paper show that it is possible to utilize SOA solutions with heavily resource-constrained embedded devices in contexts where the real-time constrains are limited, such as in a district heating substation.

Application of Service Oriented Architecture for Sensors and Actuators in District Heating Substations

PubMed Central

Gustafsson, Jonas; Kyusakov, Rumen; Mäkitaavola, Henrik; Delsing, Jerker

2014-01-01

Hardwired sensor installations using proprietary protocols found in today's district heating substations limit the potential usability of the sensors in and around the substations. If sensor resources can be shared and re-used in a variety of applications, the cost of sensors and installation can be reduced, and their functionality and operability can be increased. In this paper, we present a new concept of district heating substation control and monitoring, where a service oriented architecture (SOA) is deployed in a wireless sensor network (WSN), which is integrated with the substation. IP-networking is exclusively used from sensor to server; hence, no middleware is needed for Internet integration. Further, by enabling thousands of sensors with SOA capabilities, a System of Systems approach can be applied. The results of this paper show that it is possible to utilize SOA solutions with heavily resource-constrained embedded devices in contexts where the real-time constrains are limited, such as in a district heating substation. PMID:25196165

30 CFR 77.811 - Movement of portable substations and transformers.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Movement of portable substations and transformers. 77.811 Section 77.811 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF... and transformers. Portable substations and transformers shall be deenergized before they are moved...

30 CFR 77.811 - Movement of portable substations and transformers.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Movement of portable substations and transformers. 77.811 Section 77.811 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF... and transformers. Portable substations and transformers shall be deenergized before they are moved...

30 CFR 77.811 - Movement of portable substations and transformers.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Movement of portable substations and transformers. 77.811 Section 77.811 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF... and transformers. Portable substations and transformers shall be deenergized before they are moved...

30 CFR 77.811 - Movement of portable substations and transformers.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Movement of portable substations and transformers. 77.811 Section 77.811 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF... and transformers. Portable substations and transformers shall be deenergized before they are moved...

30 CFR 77.811 - Movement of portable substations and transformers.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Movement of portable substations and transformers. 77.811 Section 77.811 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF... and transformers. Portable substations and transformers shall be deenergized before they are moved...

Research on Vibration Test in Urban Indoor Substation

NASA Astrophysics Data System (ADS)

Ma, Yuchao; Mo, Juan; Xu, Jin; Fan, Baozhen

2018-01-01

The problem of vibration and noise of urban indoor substations has becoming more and more socially concerned.The urban indoor substation of 110kV and its conjoined buildings were taken as the research object and the vibration tests of the transformer and each floor slab were respectively carried out.The sound vibration characteristics and sound transmission rules of the urban indoor substation were obtained through the time-frequency analysis and coherence analysis of the test data. The vibration spectrum of transformer body was mainly 100Hz together with its multiplying factors and the vibration characteristics of the floor slab were basically the same as those of the transformer body. it is crucial to control the vibration and noise transmission in the equipment floor of the urban indoor substation.

Conformational Fluctuations in G-Protein-Coupled Receptors

NASA Astrophysics Data System (ADS)

Brown, Michael F.

2014-03-01

G-protein-coupled receptors (GPCRs) comprise almost 50% of pharmaceutical drug targets, where rhodopsin is an important prototype and occurs naturally in a lipid membrane. Rhodopsin photoactivation entails 11-cis to all-trans isomerization of the retinal cofactor, yielding an equilibrium between inactive Meta-I and active Meta-II states. Two important questions are: (1) Is rhodopsin is a simple two-state switch? Or (2) does isomerization of retinal unlock an activated conformational ensemble? For an ensemble-based activation mechanism (EAM) a role for conformational fluctuations is clearly indicated. Solid-state NMR data together with theoretical molecular dynamics (MD) simulations detect increased local mobility of retinal after light activation. Resultant changes in local dynamics of the cofactor initiate large-scale fluctuations of transmembrane helices that expose recognition sites for the signal-transducing G-protein. Time-resolved FTIR studies and electronic spectroscopy further show the conformational ensemble is strongly biased by the membrane lipid composition, as well as pH and osmotic pressure. A new flexible surface model (FSM) describes how the curvature stress field of the membrane governs the energetics of active rhodopsin, due to the spontaneous monolayer curvature of the lipids. Furthermore, influences of osmotic pressure dictate that a large number of bulk water molecules are implicated in rhodopsin activation. Around 60 bulk water molecules activate rhodopsin, which is much larger than the number of structural waters seen in X-ray crystallography, or inferred from studies of bulk hydrostatic pressure. Conformational selection and promoting vibrational motions of rhodopsin lead to activation of the G-protein (transducin). Our biophysical data give a paradigm shift in understanding GPCR activation. The new view is: dynamics and conformational fluctuations involve an ensemble of substates that activate the cognate G-protein in the amplified visual response.

20. Photocopy of photograph showing the completed South Bank Substation, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

20. Photocopy of photograph showing the completed South Bank Substation, 4 November 1939 (from the BPA Photo Archives, Negative No. 6556), LOOKING NORTHWEST WITH THE BONNEVILLE DAM POWERHOUSE AND TRANSMISSION TOWERS IN BACKGROUND - Bonneville Power Administration South Bank Substation, I-84, South of Bonneville Dam Powerhouse, Bonneville, Multnomah County, OR

Research on the Best Root Span of 500kV Substation Frame Based on Finite Element

NASA Astrophysics Data System (ADS)

Chen, Hao; Fang, Qing; Chen, Haoyuan

2018-01-01

A-shaped and steel tube structures have been widely applied when designing 500kV substation frame in China. While, compared with steel tube, angle steels have an advantage of easy-transporting, especially in oversea projects. However, researches on substation frame with angle steel were not enough. In order to find out the best root span of 500kV substation frame under similar engineering conditions, using the overseas project substation frame as an example, the substation frames with different root span have been detailed calculated, to find the best root span according to the cost of it. When the height of column is about 30m, the root suggestion value is 6.1m×3.1m. And then, the buckling analysis of the overall structure has been carried out by ANSYS, to find out that the weak part of the structure is in the middle of it. The structural adjustment is carried out for the weak part, including adjusting the web members and the chord members, to obtain a higher bearing capacity of the structure.

Energies and 2'-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations.

PubMed

Mládek, Arnošt; Banáš, Pavel; Jurečka, Petr; Otyepka, Michal; Zgarbová, Marie; Šponer, Jiří

2014-01-14

Sugar-phosphate backbone is an electronically complex molecular segment imparting RNA molecules high flexibility and architectonic heterogeneity necessary for their biological functions. The structural variability of RNA molecules is amplified by the presence of the 2'-hydroxyl group, capable of forming multitude of intra- and intermolecular interactions. Bioinformatics studies based on X-ray structure database revealed that RNA backbone samples at least 46 substates known as rotameric families. The present study provides a comprehensive analysis of RNA backbone conformational preferences and 2'-hydroxyl group orientations. First, we create a benchmark database of estimated CCSD(T)/CBS relative energies of all rotameric families and test performance of dispersion-corrected DFT-D3 methods and molecular mechanics in vacuum and in continuum solvent. The performance of the DFT-D3 methods is in general quite satisfactory. The B-LYP-D3 method provides the best trade-off between accuracy and computational demands. B3-LYP-D3 slightly outperforms the new PW6B95-D3 and MPW1B95-D3 and is the second most accurate density functional of the study. The best agreement with CCSD(T)/CBS is provided by DSD-B-LYP-D3 double-hybrid functional, although its large-scale applications may be limited by high computational costs. Molecular mechanics does not reproduce the fine energy differences between the RNA backbone substates. We also demonstrate that the differences in the magnitude of the hyperconjugation effect do not correlate with the energy ranking of the backbone conformations. Further, we investigated the 2'-hydroxyl group orientation preferences. For all families, we conducted a QM and MM hydroxyl group rigid scan in gas phase and solvent. We then carried out set of explicit solvent MD simulations of folded RNAs and analyze 2'-hydroxyl group orientations of different backbone families in MD. The solvent energy profiles determined primarily by the sugar pucker match well with the distribution data derived from the simulations. The QM and MM energy profiles predict the same 2'-hydroxyl group orientation preferences. Finally, we demonstrate that the high energy of unfavorable and rarely sampled 2'-hydroxyl group orientations can be attributed to clashes between occupied orbitals.

Hydrology Analysis and Modelling for Klang River Basin Flood Hazard Map

NASA Astrophysics Data System (ADS)

Sidek, L. M.; Rostam, N. E.; Hidayah, B.; Roseli, ZA; Majid, W. H. A. W. A.; Zahari, N. Z.; Salleh, S. H. M.; Ahmad, R. D. R.; Ahmad, M. N.

2016-03-01

Flooding, a common environmental hazard worldwide has in recent times, increased as a result of climate change and urbanization with the effects felt more in developing countries. As a result, the explosive of flooding to Tenaga Nasional Berhad (TNB) substation is increased rapidly due to existing substations are located in flood prone area. By understanding the impact of flood to their substation, TNB has provided the non-structure mitigation with the integration of Flood Hazard Map with their substation. Hydrology analysis is the important part in providing runoff as the input for the hydraulic part.

76 FR 45609 - Notice of Availability of the Draft Environmental Impact Statement for the Gateway West 230/500...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-29

... Johnston Power Plant at Glenrock, Wyoming, to the proposed Hemingway Substation near Melba, Idaho. The... Johnston Power Plant at Glenrock, Wyoming, and the planned Aeolus Substation near Hanna, Wyoming. Segment... Anticline Substation near the Jim Bridger Power Plant, located approximately 30 miles east of Rock Springs...

Effects of Catalytic Action and Ligand Binding on Conformational Ensembles of Adenylate Kinase.

PubMed

Onuk, Emre; Badger, John; Wang, Yu Jing; Bardhan, Jaydeep; Chishti, Yasmin; Akcakaya, Murat; Brooks, Dana H; Erdogmus, Deniz; Minh, David D L; Makowski, Lee

2017-08-29

Crystal structures of adenylate kinase (AdK) from Escherichia coli capture two states: an "open" conformation (apo) obtained in the absence of ligands and a "closed" conformation in which ligands are bound. Other AdK crystal structures suggest intermediate conformations that may lie on the transition pathway between these two states. To characterize the transition from open to closed states in solution, X-ray solution scattering data were collected from AdK in the apo form and with progressively increasing concentrations of five different ligands. Scattering data from apo AdK are consistent with scattering predicted from the crystal structure of AdK in the open conformation. In contrast, data from AdK samples saturated with Ap5A do not agree with that calculated from AdK in the closed conformation. Using cluster analysis of available structures, we selected representative structures in five conformational states: open, partially open, intermediate, partially closed, and closed. We used these structures to estimate the relative abundances of these states for each experimental condition. X-ray solution scattering data obtained from AdK with AMP are dominated by scattering from AdK in the open conformation. For AdK in the presence of high concentrations of ATP and ADP, the conformational ensemble shifts to a mixture of partially open and closed states. Even when AdK is saturated with Ap5A, a significant proportion of AdK remains in a partially open conformation. These results are consistent with an induced-fit model in which the transition of AdK from an open state to a closed state is initiated by ATP binding.

Analysis of the 35 KV substation secondary system

NASA Astrophysics Data System (ADS)

Zhao, Yong; Jiang, Jianguo; Jiang, Chunlei; Ren, Shuang; Liu, Songbin

2017-04-01

This paper analyzes the status of the two system of some 35KV users' substation in Daqing oil field, the deficiencies of the two system of the existing 35KV substation are found out. And put forward the opinion of acceptance in the future work. I hope it can able to work in the future on the protection of professional help.

Shielding of substations against direct lightning strokes by shield wires

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chowdhuri, P.

1994-01-01

A new analysis for shielding outdoor substations against direct lightning strokes by shield wires is proposed. The basic assumption of this proposed method is that any lightning stroke which penetrates the shields will cause damage. The second assumption is that a certain level of risk of failure must be accepted, such as one or two failures per 100 years. The proposed method, using electrogeometric model, was applied to design shield wires for two outdoor substations: (1) 161-kV/69-kV station, and (2) 500-kV/161-kV station. The results of the proposed method were also compared with the shielding data of two other substations.

IET. Exclusion guard house (TAN621) and unit substation (TAN622). Elevations ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

IET. Exclusion guard house (TAN-621) and unit substation (TAN-622). Elevations and floor plan. Also show concrete pad for substation. Ralph M. Parsons 902-4-ANP-621-622-A&S 411. Date: February 1954. Approved by INEEL Classification Office for public release. INEEL index code no. 035-0621-60-693-106968 - Idaho National Engineering Laboratory, Test Area North, Scoville, Butte County, ID

Simulation study on the lightning overvoltage invasion control transformer intelligent substation

NASA Astrophysics Data System (ADS)

Xi, Chuyan; Hao, Jie; Zhang, Ying

2018-04-01

By simulating lightning on substation line of one intelligent substation, research the influence of different lightning points on lightning invasion wave overvoltage, and the necessity of arrester for the main transformer. The results show, in a certain lightning protection measures, the installation of arrester nearby the main transformer can effectively reduce the overvoltage value of bus and the main transformer [1].

Shift in the equilibrium between on and off states of the allosteric switch in Ras-GppNHp affected by small molecules and bulk solvent composition.

PubMed

Holzapfel, Genevieve; Buhrman, Greg; Mattos, Carla

2012-08-07

Ras GTPase cycles between its active GTP-bound form promoted by GEFs and its inactive GDP-bound form promoted by GAPs to affect the control of various cellular functions. It is becoming increasingly apparent that subtle regulation of the GTP-bound active state may occur through promotion of substates mediated by an allosteric switch mechanism that induces a disorder to order transition in switch II upon ligand binding at an allosteric site. We show with high-resolution structures that calcium acetate and either dithioerythritol (DTE) or dithiothreitol (DTT) soaked into H-Ras-GppNHp crystals in the presence of a moderate amount of poly(ethylene glycol) (PEG) can selectively shift the equilibrium to the "on" state, where the active site appears to be poised for catalysis (calcium acetate), or to what we call the "ordered off" state, which is associated with an anticatalytic conformation (DTE or DTT). We also show that the equilibrium is reversible in our crystals and dependent on the nature of the small molecule present. Calcium acetate binding in the allosteric site stabilizes the conformation observed in the H-Ras-GppNHp/NOR1A complex, and PEG, DTE, and DTT stabilize the anticatalytic conformation observed in the complex between the Ras homologue Ran and Importin-β. The small molecules are therefore selecting biologically relevant conformations in the crystal that are sampled by the disordered switch II in the uncomplexed GTP-bound form of H-Ras. In the presence of a large amount of PEG, the ordered off conformation predominates, whereas in solution, in the absence of PEG, switch regions appear to remain disordered in what we call the off state, unable to bind DTE.

Shift in the Equilibrium between On and Off States of the Allosteric Switch in Ras-GppNHp Affected by Small Molecules and Bulk Solvent Composition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holzapfel, Genevieve; Buhrman, Greg; Mattos, Carla

2012-08-31

Ras GTPase cycles between its active GTP-bound form promoted by GEFs and its inactive GDP-bound form promoted by GAPs to affect the control of various cellular functions. It is becoming increasingly apparent that subtle regulation of the GTP-bound active state may occur through promotion of substates mediated by an allosteric switch mechanism that induces a disorder to order transition in switch II upon ligand binding at an allosteric site. We show with high-resolution structures that calcium acetate and either dithioerythritol (DTE) or dithiothreitol (DTT) soaked into H-Ras-GppNHp crystals in the presence of a moderate amount of poly(ethylene glycol) (PEG) canmore » selectively shift the equilibrium to the 'on' state, where the active site appears to be poised for catalysis (calcium acetate), or to what we call the 'ordered off' state, which is associated with an anticatalytic conformation (DTE or DTT). We also show that the equilibrium is reversible in our crystals and dependent on the nature of the small molecule present. Calcium acetate binding in the allosteric site stabilizes the conformation observed in the H-Ras-GppNHp/NOR1A complex, and PEG, DTE, and DTT stabilize the anticatalytic conformation observed in the complex between the Ras homologue Ran and Importin-{beta}. The small molecules are therefore selecting biologically relevant conformations in the crystal that are sampled by the disordered switch II in the uncomplexed GTP-bound form of H-Ras. In the presence of a large amount of PEG, the ordered off conformation predominates, whereas in solution, in the absence of PEG, switch regions appear to remain disordered in what we call the off state, unable to bind DTE.« less

An expansion plan for the 60 Hz power distribution system at KSC: LC-39 substations load allocation plan

NASA Technical Reports Server (NTRS)

Kalu, Alex

1990-01-01

The increasing load density in the LC-39 area of Kennedy Space Center (KSC) can be met by either modifying the existing substation and increasing its capacity or by planning an additional new substation. Evidence that the later approach is more economical, enhances the system reliability, and would produce more satisfactory performance indices is provided. Network theory is the basis for the optimal location determination of the proposed substation. A load reallocation plan which minimizes investment cost and power losses and meets other desirable system features is drafted. The report should be useful to the system designer and can be a useful guideline for future facility planners.

Experimental adoption of RCM in EDF substations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heroin, G.; Aupied, J.; Sanchis, G.

1996-08-01

EDF, after testing Reliability Centered Maintenance (RCM) on systems used in nuclear power plants, has now successfully extended RCM to all of its nuclear power plants. In the light of this experience, EDF has committed itself to a pilot study on a line bay of a 400 kV substation in 1992. The RCM method as applied benefited from EDF`s policy of maintenance, introduced five years ago on all substations, which has enhanced prospects of reliability. The original feature in the selection of maintenance tasks was that it brought into play two criteria for failure assessment - frequency and seriousness -more » and two criteria for maintenance task selection - efficiency and facility. The final outcome of RCM as applied to substation maintenance is to categorize maintenance tasks into: (1) essential maintenance tasks, (2) optional tasks, depending on the type and location of the substation, as well as on factors relating to local management of maintenance policy, and (3) unnecessary tasks.« less

[Offshore substation workers' exposure to harmful factors - Actions minimizing risk of hazards].

PubMed

Piotrowski, Paweł Janusz; Robak, Sylwester; Polewaczyk, Mateusz Maksymilian; Raczkowski, Robert

2016-01-01

The current development of electric power industry in Poland, especially in the field of renewable energy sources, including wind power, brings about the need to introduce legislation on new work environment. The development of occupational safety and health (OSH) regulations that must be met by new workplaces, such as offshore substations becomes necessary in view of the construction of modern offshore wind power plants - offshore wind farms. Staying on offshore substation is associated with an increased exposure to harmful health factors: physical, chemical, biological and psychophysical. The main sources of health risks on offshore substations are: temperature, electromagnetic field, noise from operating wind turbines, direct and alternating current, chemicals, Legionella bacteria and social isolation of people. The aim of this article is to draw attention to the problem of offshore substation workers' exposure to harmful factors and to present methods of preventing and reducing the risk-related adverse health effects. In this paper, there are identified and described risks occurring on offshore substations (fire, explosion, lightning, accidents at work). Some examples of the means and the methods for reducing the negative impact of exposure on the human health are presented and discussed. The article also highlights the need to develop appropriate laws and health and safety regulations concerning the new working environment at the offshore substations. The review of researches and international standards shows that some of them can be introduced into the Polish labor market. This work is available in Open Access model and licensed under a CC BY-NC 3.0 PL license.

Touch and step potential analysis at 23.9kV to 4.16kV & 13.8kV to 4.16kV distribution substations with pad-mounted transformers, floating grounds, and other exposed ungrounded metal bodies using WinIGS

NASA Astrophysics Data System (ADS)

Guzman, David G.

An electrical substation is composed of various subsystems that allow for the effective and safe operation of the power grid. One of the subsystems integrating a conventional substation is defined as the ground grid system. This system allows for the effective operation of the power grid and all the electrical equipment connected to it by providing a ground potential reference, commonly known as the system ground. In addition, the ground grid system provides safety to the workers and the public transiting inside or living nearby a substation by reducing the step and touch potential (or voltage) levels present during a system fault. In today's utility industry practices there is an increasing trend for using pad-mounted electrical equipment for substation applications in an effort to construct new or upgrade existing electrical facilities inside limited property spaces. This thesis work presents an analysis for the effects of touch and step voltages at existing distribution substations where 23.9kV to 4.16kV & 13.8kV to 4.16kV pad-mounted transformers and other pad-mounted switchgear was installed to replace the traditional station class equipment. Moreover, this study will expose modeling techniques employed to define and determine the effects of floating grounds and other exposed metal bodies inside or surrounding these substations using WinIGS; this is in an effort to determine any risks of electric shock associated with this type of installations. The results presented in this work are intended to verify the requirements for the ground grid analysis and design for 4.16kV distribution substations with pad-mounted equipment in order to prevent dangerous step and touch voltage levels appearing at these sites during system faults; and ultimately prevent exposing individuals to the risk of an electric shock.

Dynamic conformational switching in the chemokine ligand is essential for G-protein-coupled receptor activation

PubMed Central

Joseph, Prem Raj B.; Sawant, Kirti V.; Isley, Angela; Pedroza, Mesias; Garofalo, Roberto P.; Richardson, Ricardo M.; Rajarathnam, Krishna

2014-01-01

Chemokines mediate diverse functions from organogenesis to mobilizing leucocytes, and are unusual agonists for class-A GPCRs (G-protein-coupled receptors) because of their large size and multi-domain structure. The current model for receptor activation, which involves interactions between chemokine N-loop and receptor N-terminal residues (Site-I) and between chemokine N-terminal and receptor extracellular loop/transmembrane residues (Site-II), fails to describe differences in ligand/receptor selectivity and the activation of multiple signalling pathways. In the present study, we show in neutrophil-activating chemokine CXCL8 that the highly conserved GP (glycine-proline) motif located distal to both N-terminal and N-loop residues couples Site-I and Site-II interactions. Mutations in the GP motif caused various differences from native-like function to complete loss of activity that could not be correlated with the specific mutation, receptor affinity or subtype, or a specific signalling pathway. NMR studies indicated that the GP motif does not influence Site-I interactions, but molecular dynamics simulations suggested that this motif dictates substates of the CXCL8 conformational ensemble. We conclude that the GP motif enables diverse receptor functions by controlling cross-talk between Site-I and Site-II, and further propose that the repertoire of chemokine functions is best described by a conformational ensemble model in which a network of long-range coupled indirect interactions mediate receptor activity. PMID:24032673

Design of a laser navigation system for the inspection robot used in substation

NASA Astrophysics Data System (ADS)

Zhu, Jing; Sun, Yanhe; Sun, Deli

2017-01-01

Aimed at the deficiency of the magnetic guide and RFID parking system used by substation inspection robot now, a laser navigation system is designed, and the system structure, the method of map building and positioning are all introduced. The system performance is tested in a 500kV substation, and the result show that the repetitive precision of navigation system is precise enough to help the robot fulfill inspection tasks.

An improved method for predicting the lightning performance of high and extra-high-voltage substation shielding

NASA Astrophysics Data System (ADS)

Vinh, T.

1980-08-01

There is a need for better and more effective lightning protection for transmission and switching substations. In the past, a number of empirical methods were utilized to design systems to protect substations and transmission lines from direct lightning strokes. The need exists for convenient analytical lightning models adequate for engineering usage. In this study, analytical lightning models were developed along with a method for improved analysis of the physical properties of lightning through their use. This method of analysis is based upon the most recent statistical field data. The result is an improved method for predicting the occurrence of sheilding failure and for designing more effective protection for high and extra high voltage substations from direct strokes.

Characteristic Analysis of DC Electric Railway Systems with Superconducting Power Cables Connecting Power Substations

NASA Astrophysics Data System (ADS)

Ohsaki, H.; Matsushita, N.; Koseki, T.; Tomita, M.

2014-05-01

The application of superconducting power cables to DC electric railway systems has been studied. It could leads to an effective use of regenerative brake, improved energy efficiency, effective load sharing among the substations, etc. In this study, an electric circuit model of a DC feeding system is built and numerical simulation is carried out using MATLAB-Simulink software. A modified electric circuit model with an AC power grid connection taken into account is also created to simulate the influence of the grid connection. The analyses have proved that a certain amount of energy can be conserved by introducing superconducting cables, and that electric load distribution and concentration among the substations depend on the substation output voltage distribution.

Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer

PubMed Central

Dršata, Tomáš; Pérez, Alberto; Orozco, Modesto; Morozov, Alexandre V.; Šponer, Jiřĺ; Lankaš, Filip

2013-01-01

The Dickerson–Drew dodecamer (DD) d-[CGCGAATTCGCG]2 is a prototypic B-DNA molecule whose sequence-specific structure and dynamics have been investigated by many experimental and computational studies. Here, we present an analysis of DD properties based on extensive atomistic molecular dynamics (MD) simulations using different ionic conditions and water models. The 0.6–2.4-µs-long MD trajectories are compared to modern crystallographic and NMR data. In the simulations, the duplex ends can adopt an alternative base-pairing, which influences the oligomer structure. A clear relationship between the BI/BII backbone substates and the basepair step conformation has been identified, extending previous findings and exposing an interesting structural polymorphism in the helix. For a given end pairing, distributions of the basepair step coordinates can be decomposed into Gaussian-like components associated with the BI/BII backbone states. The nonlocal stiffness matrices for a rigid-base mechanical model of DD are reported for the first time, suggesting salient stiffness features of the central A-tract. The Riemann distance and Kullback–Leibler divergence are used for stiffness matrix comparison. The basic structural parameters converge very well within 300 ns, convergence of the BI/BII populations and stiffness matrices is less sharp. Our work presents new findings about the DD structural dynamics, mechanical properties, and the coupling between basepair and backbone configurations, including their statistical reliability. The results may also be useful for optimizing future force fields for DNA. PMID:23976886

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

PubMed Central

Zgarbová, Marie; Luque, F. Javier; Šponer, Jiří; Cheatham, Thomas E.; Otyepka, Michal; Jurečka, Petr

2013-01-01

We present a refinement of the backbone torsion parameters ε and ζ of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as εζOL1, were derived from quantum-mechanical calculations with inclusion of conformation-dependent solvation effects according to the recently reported methodology (J. Chem. Theory Comput. 2012, 7(9), 2886-2902). The performance of the refined parameters was analyzed by means of extended molecular dynamics (MD) simulations for several representative systems. The results showed that the εζOL1 refinement improves the backbone description of B-DNA double helices and G-DNA stem. In B-DNA simulations, we observed an average increase of the helical twist and narrowing of the major groove, thus achieving better agreement with X-ray and solution NMR data. The balance between populations of BI and BII backbone substates was shifted towards the BII state, in better agreement with ensemble-refined solution experimental results. Furthermore, the refined parameters decreased the backbone RMS deviations in B-DNA MD simulations. In the antiparallel guanine quadruplex (G-DNA) the εζOL1 modification improved the description of non-canonical α/γ backbone substates, which were shown to be coupled to the ε/ζ torsion potential. Thus, the refinement is suggested as a possible alternative to the current ε/ζ torsion potential, which may enable more accurate modeling of nucleic acids. However, long-term testing is recommended before its routine application in DNA simulations. PMID:24058302

Stabilization of Helivcal Order in the Thick Filaments by Blebbistatin: Further Evidence of Coexisting Multiple Conformations of Myosin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, S.; White, H; Offer, G

2009-01-01

The degree of helical order of the thick filament of mammalian skeletal muscle is highly dependent on temperature and the nature of the ligand. Previously, we showed that there was a close correlation between the conformation of the myosin heads on the surface of the thick filaments and the extent of their helical order. Helical order required the heads to be in the closed conformation. In addition, we showed that, with the same ligand bound at the active site, three conformations of myosin coexisted in equilibrium. Hitherto, however, there was no detectable helical order as measured by x-ray diffraction undermore » the temperatures studied for myosin with MgADP and the nucleotide-free myosin, raising the possibility that the concept of multiple conformations has limited validity. In this study, blebbistatin was used to stabilize the closed conformation of myosin. The degree of helical order is substantially improved with MgATP at low temperature or with MgADP or in the absence of nucleotide. The thermodynamic parameters of the disorder?order transition and the characteristics of the ordered array were not significantly altered by binding blebbistatin. The simplest explanation is that the binding of blebbistatin increases the proportion of myosin in the closed conformation from being negligible to substantial. These results provide further evidence for the coexistence of multiple conformations of myosin under a wide range of conditions and for the closed conformation being directly coupled to helical order.« less

The Millimeter- and Submillimeter-Wave Spectrum of Gauche-Ethyl Alcohol

NASA Technical Reports Server (NTRS)

Pearson, J. C.; Sastry, K. V. L. N.; Herbst, Eric; DeLucia, Frank C.

1996-01-01

We report an investigation of the rotational-torsional spectrum of the gauche rotational isomers of ethyl alcohol in the 51-505 GHz frequency region. Over a thousand transitions between rotational levels in the gauche substates of the ground OH torsional state have been measured and assigned. These transitions involve rotational quantum numbers J and K(sub a) up to 30 and 15, respectively, and are of two types: alpha-type transitions between levels in either the gauche+ or the gauche-substate, and c-type transitions between rotational levels in the different substates. The majority of these transitions have been fit satisfactorily using a two-state Hamiltonian based on the Fixed Framework Axis Method (FFAM). The rotation, distortion, and interaction constants have been determined along with the energy difference between the two gauche substates. The derived constants can be used to predict many more transitions accurately for astronomical purposes. The J and K(sub a) region where the two-state analysis can be used has been determined. The basis for a three-state analysis including the trans substate is presented and the applicability of the FFAM approach is discussed.

Modulation of the Conformational Dynamics of Apo-Adenylate Kinase through a π-Cation Interaction.

PubMed

Halder, Ritaban; Manna, Rabindra Nath; Chakraborty, Sandipan; Jana, Biman

2017-06-15

Large-scale conformational transition from open to closed state of adenylate kinase (ADK) is essential for its catalytic cycle. Apo-ADK undergoes conformational transition in a way that closely resembles an open-to-closed conformational transition. Here, equilibrium simulations, free-energy simulations, and quantum mechanics/molecular mechanics (QM/MM) calculations in combination with several bioinformatics approaches have been used to explore the molecular origin of this conformational transition in apo-ADK. In addition to its conventional open state, Escherichia coli apo-ADK adopts conformations that resemble a closed-like intermediate, the "half-open-half-closed" (HOHC) state, and a π-cation interaction can account for the stability of this HOHC state. Energetics and the electronic properties of this π-cation interaction have been explored using QM/MM calculations. Upon rescinding the π-cation interaction, the conformational landscape of the apo-ADK changes completely. The apo-ADK population is shifted completely toward the open state. This π-cation interaction is highly conserved in bacterial ADK; the cationic guanidinium moiety of a conserved ARG interacts with the delocalized π-electron cloud of either PHE or TYR. Interestingly, this study demonstrates the modulation of a principal protein dynamics by a conserved specific π-cation interaction across different organisms.

On the Roles of Substrate Binding and Hinge Unfolding in Conformational Changes of Adenylate Kinase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brokaw, Jason B.; Chu, Jhih-wei

2010-11-17

We characterized the conformational change of adenylate kinase (AK) between open and closed forms by conducting five all-atom molecular-dynamics simulations, each of 100 ns duration. Different initial structures and substrate binding configurations were used to probe the pathways of AK conformational change in explicit solvent, and no bias potential was applied. A complete closed-to-open and a partial open-to-closed transition were observed, demonstrating the direct impact of substrate-mediated interactions on shifting protein conformation. The sampled configurations suggest two possible pathways for connecting the open and closed structures of AK, affirming the prediction made based on available x-ray structures and earlier worksmore » of coarse-grained modeling. The trajectories of the all-atom molecular-dynamics simulations revealed the complexity of protein dynamics and the coupling between different domains during conformational change. Calculations of solvent density and density fluctuations surrounding AK did not show prominent variation during the transition between closed and open forms. Finally, we characterized the effects of local unfolding of an important hinge near Pro177 on the closed-to-open transition of AK and identified a novel mechanism by which hinge unfolding modulates protein conformational change. The local unfolding of Pro177 hinge induces alternative tertiary contacts that stabilize the closed structure and prevent the opening transition.« less

29 CFR 1926.957 - Construction in energized substations.

Code of Federal Regulations, 2014 CFR

2014-07-01

..., DEPARTMENT OF LABOR (CONTINUED) SAFETY AND HEALTH REGULATIONS FOR CONSTRUCTION Power Transmission and Distribution § 1926.957 Construction in energized substations. (a) Work near energized equipment facilities. (1...

29 CFR 1926.957 - Construction in energized substations.

Code of Federal Regulations, 2013 CFR

2013-07-01

..., DEPARTMENT OF LABOR (CONTINUED) SAFETY AND HEALTH REGULATIONS FOR CONSTRUCTION Power Transmission and Distribution § 1926.957 Construction in energized substations. (a) Work near energized equipment facilities. (1...

29 CFR 1926.957 - Construction in energized substations.

Code of Federal Regulations, 2012 CFR

2012-07-01

..., DEPARTMENT OF LABOR (CONTINUED) SAFETY AND HEALTH REGULATIONS FOR CONSTRUCTION Power Transmission and Distribution § 1926.957 Construction in energized substations. (a) Work near energized equipment facilities. (1...

Supplement Analysis for the Transmission System Vegetation Management Program FEIS (DOE/EIS-0285/SA-101) Spokane Region

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rosales, Michael A.

2002-09-13

Vegetation Management for Substations and Non-Electric Facilities. BPA proposes to manage vegetation inside and around electrical substations and associated facilities. Vegetation management within the substation shall include the bare ground management of all graveled areas. These areas shall primarily be maintained with the use of herbicides. The management of vegetation outside the substation and associated facilities shall include: 1) bare ground management of perimeter roads and parking areas; 2) mechanical and/or spot herbicidal control of some broadleaves and noxious weeds; 3) mowing, fertilizing, and broadleaf control of landscaped lawn areas; 4) weed control in ornamental shrub areas; and 5) areasmore » requiring only mechanical control to manage unwanted/danger trees, grasses, and shrubs.« less

Supplement Analysis for the Transmission System Vegetation Management Program FEIS (DOE/EIS-0285/SA-64)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hutchinson, Ken

2002-04-26

Vegetation Management for Substations and Non-Electric Facilities in the Walla Walla Region. BPA proposes to manage vegetation inside and around electrical substations and associated facilities. Vegetation management within the substation shall include the bare ground management of all graveled areas. These areas shall primarily be maintained with the use of herbicides. The management of vegetation outside the substation and associated facilities shall include: 1) bare ground management of perimeter roads and parking areas; 2) mechanical and/or spot herbicidal control of some broadleaves and noxious weeds; 3) mowing, fertilizing, and broadleaf control of landscaped lawn areas; 4) weed control in ornamentalmore » shrub areas; and 4) areas requiring only mechanical control to manage unwanted/danger trees, grasses, and shrubs.« less

IEC 61850: Technology Standards and Cyber-Security Threats

DOE Office of Scientific and Technical Information (OSTI.GOV)

Youssef, Tarek A; El Hariri, mohamed; Bugay, Nicole

Substations constitute a fundamental part in providing reliable electricity to consumers. For a substation to maintain electricity reliability and its own real-time operability, communication between its components is inevitable. Before the emergence of IEC 61850, inter-substation communication was established via expensive copper wires with limited capabilities. IEC 61850 is the standard set by the International Electrotechnical Commission (IEC) Technical Committee Number 57 Working Group 10 and IEEE for Ethernet (IEEE 802.3)-based communication in electrical substations. Like many power grid systems standards, IEC 61850 was set without extensive consideration for critical security measures. This paper discusses IEC 61850 technology standards andmore » applications thoroughly and points out major security vulnerabilities it introduces in the context of current cyber-physical smart grid systems.« less

Relating conformation to function in integrin α5β1.

PubMed

Su, Yang; Xia, Wei; Li, Jing; Walz, Thomas; Humphries, Martin J; Vestweber, Dietmar; Cabañas, Carlos; Lu, Chafen; Springer, Timothy A

2016-07-05

Whether β1 integrin ectodomains visit conformational states similarly to β2 and β3 integrins has not been characterized. Furthermore, despite a wealth of activating and inhibitory antibodies to β1 integrins, the conformational states that these antibodies stabilize, and the relation of these conformations to function, remain incompletely characterized. Using negative-stain electron microscopy, we show that the integrin α5β1 ectodomain adopts extended-closed and extended-open conformations as well as a bent conformation. Antibodies SNAKA51, 8E3, N29, and 9EG7 bind to different domains in the α5 or β1 legs, activate, and stabilize extended ectodomain conformations. Antibodies 12G10 and HUTS-4 bind to the β1 βI domain and hybrid domains, respectively, activate, and stabilize the open headpiece conformation. Antibody TS2/16 binds a similar epitope as 12G10, activates, and appears to stabilize an open βI domain conformation without requiring extension or hybrid domain swing-out. mAb13 and SG/19 bind to the βI domain and βI-hybrid domain interface, respectively, inhibit, and stabilize the closed conformation of the headpiece. The effects of the antibodies on cell adhesion to fibronectin substrates suggest that the extended-open conformation of α5β1 is adhesive and that the extended-closed and bent-closed conformations are nonadhesive. The functional effects and binding sites of antibodies and fibronectin were consistent with their ability in binding to α5β1 on cell surfaces to cross-enhance or inhibit one another by competitive or noncompetitive (allosteric) mechanisms.

Transition-State Ensembles Navigate the Pathways of Enzyme Catalysis.

PubMed

Mickert, Matthias J; Gorris, Hans H

2018-06-07

Transition-state theory (TST) provides an important framework for analyzing and explaining the reaction rates of enzymes. TST, however, needs to account for protein dynamic effects and heterogeneities in enzyme catalysis. We have analyzed the reaction rates of β-galactosidase and β-glucuronidase at the single molecule level by using large arrays of femtoliter-sized chambers. Heterogeneities in individual reaction rates yield information on the intrinsic distribution of the free energy of activation (Δ G ‡ ) in an enzyme ensemble. The broader distribution of Δ G ‡ in β-galactosidase compared to β-glucuronidase is attributed to β-galactosidase's multiple catalytic functions as a hydrolase and a transglycosylase. Based on the catalytic mechanism of β-galactosidase, we show that transition-state ensembles do not only contribute to enzyme catalysis but can also channel the catalytic pathway to the formation of different products. We conclude that β-galactosidase is an example of natural evolution, where a new catalytic pathway branches off from an established enzyme function. The functional division of work between enzymatic substates explains why the conformational space represented by the enzyme ensemble is larger than the conformational space that can be sampled by any given enzyme molecule during catalysis.

Concerted Interconversion between Ionic Lock Substates of the β2 Adrenergic Receptor Revealed by Microsecond Timescale Molecular Dynamics

PubMed Central

Romo, Tod D.; Grossfield, Alan; Pitman, Michael C.

2010-01-01

Abstract The recently solved crystallographic structures for the A2A adenosine receptor and the β1 and β2 adrenergic receptors have shown important differences between members of the class-A G-protein-coupled receptors and their archetypal model, rhodopsin, such as the apparent breaking of the ionic lock that stabilizes the inactive structure. Here, we characterize a 1.02 μs all-atom simulation of an apo-β2 adrenergic receptor that is missing the third intracellular loop to better understand the inactive structure. Although we find that the structure is remarkably rigid, there is a rapid influx of water into the core of the protein, as well as a slight expansion of the molecule relative to the crystal structure. In contrast to the x-ray crystal structures, the ionic lock rapidly reforms, although we see an activation-precursor-like event wherein the ionic lock opens for ∼200 ns, accompanied by movements in the transmembrane helices associated with activation. When the lock reforms, we see the structure return to its inactive conformation. We also find that the ionic lock exists in three states: closed (or locked), semi-open with a bridging water molecule, and open. The interconversion of these states involves the concerted motion of the entire protein. We characterize these states and the concerted motion underlying their interconversion. These findings may help elucidate the connection between key local events and the associated global structural changes during activation. PMID:20074514

30 CFR 56.4130 - Electric substations and liquid storage facilities.

Code of Federal Regulations, 2010 CFR

2010-07-01

... LABOR METAL AND NONMETAL MINE SAFETY AND HEALTH SAFETY AND HEALTH STANDARDS-SURFACE METAL AND NONMETAL MINES Fire Prevention and Control Prohibitions/precautions/housekeeping § 56.4130 Electric substations...

20. Zoo Substation. Philadelphia, Philadelphia Co., PA. Sec. 1101, MP ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

20. Zoo Substation. Philadelphia, Philadelphia Co., PA. Sec. 1101, MP 87.25. - Northeast Railroad Corridor, Amtrak route between Delaware-Pennsylvania & Pennsylvania-New Jersey state lines, Philadelphia, Philadelphia County, PA

Structural architecture of prothrombin in solution revealed by single molecule spectroscopy

DOE PAGES

Pozzi, Nicola; Bystranowska, Dominika; Zuo, Xiaobing; ...

2016-07-19

The coagulation factor prothrombin has a complex spatial organization of its modular assembly that comprises the N-terminal Gla domain, kringle-1, kringle-2, and the C-terminal protease domain connected by three intervening linkers. Here we use single molecule Förster resonance energy transfer to access the conformational landscape of prothrombin in solution and uncover structural features of functional significance that extend recent x-ray crystallographic analysis. Prothrombin exists in equilibrium between two alternative conformations, open and closed. The closed conformation predominates (70%) and features an unanticipated intramolecular collapse of Tyr 93 in kringle-1 onto Trp 547 in the protease domain that obliterates access tomore » the active site and protects the zymogen from autoproteolytic conversion to thrombin. The open conformation (30%) is more susceptible to chymotrypsin digestion and autoactivation, and features a shape consistent with recent x-ray crystal structures. Small angle x-ray scattering measurements of prothrombin wild type stabilized 70% in the closed conformation and of the mutant Y93A stabilized 80% in the open conformation directly document two envelopes that differ 50 Å in length. These findings reveal important new details on the conformational plasticity of prothrombin in solution and the drastic structural difference between its alternative conformations. Prothrombin uses the intramolecular collapse of kringle-1 onto the active site in the closed form to prevent autoactivation. As a result, the open-closed equilibrium also defines a new structural framework for the mechanism of activation of prothrombin by prothrombinase.« less

Giant K-doubling and in-plane/out-of-plane mixing in the asymmetric methyl-bending bands of CH3SH

NASA Astrophysics Data System (ADS)

Guislain, B. G.; Reid, E. M.; Lees, R. M.; Xu, Li-Hong; Twagirayezu, S.; Perry, D. S.; Thapaliya, B. P.; Dawadi, M. B.; Billinghurst, B. E.

2017-05-01

In analyzing high-resolution spectra of the methyl-deformation bands of methyl mercaptan recorded at the Canadian Light Source synchrotron, we have encountered interesting interactions between certain levels of the ν4 in-plane asymmetric CH3-bending mode and its ν10 out-of-plane bending partner below. The origin of the K = 0A ν4 substate is just 0.2 cm-1 higher than that of the K = 2A ν10 substate, while the K = 0E ν4 origin is only 0.035 cm-1 below the K = 2E ν10 origin. These very close accidental near-degeneracies lead to substantial perturbations in the spectrum. For the former, the A+/A- asymmetry K-doublet coupling rules are such that the A- component of the 2A ν10 doublet interacts and mixes strongly with the 0A+ ν4 levels whereas the 2A+ component is unaffected. The 2A- levels are pushed rapidly downwards by the coupling creating an extremely large apparent K = 2A asymmetry splitting. We call this "giant K-doubling" by analogy with a comparable phenomenon seen for methanol. The 0A+ ν4 state, in turn, is perturbed upward and passes through the descending K = 1A+ ν4 state between J = 22 and 23, leading to distinct local perturbations near the level-crossing. The 0E ν4 and 2E ν10 coupling produces a correspondingly strong repulsion and mixing between those two substates, and gives rise to a forbidden K = 0 ← 3E intermode sub-band in the spectrum via intensity borrowing.

Giant K-doubling and in-plane/out-of-plane mixing in the asymmetric methyl-bending bands of CH 3SH

DOE PAGES

Guislain, B. G.; Reid, E. M.; Lees, R. M.; ...

2017-03-02

In analyzing high-resolution spectra of the methyl-deformation bands of methyl mercaptan recorded at the Canadian Light Source synchrotron, we have encountered interesting interactions between certain levels of the ν 4 in-plane asymmetric CH 3-bending mode and its ν 10 out-of-plane bending partner below. The origin of the K = 0A ν 4 substate is just 0.2 cm -1 higher than that of the K = 2A ν 10 substate, while the K = 0E ν 4 origin is only 0.035 cm -1 below the K = 2E ν 10 origin. These very close accidental near-degeneracies lead to substantial perturbations inmore » the spectrum. For the former, the A +/A - asymmetry K-doublet coupling rules are such that the A - component of the 2A ν 10 doublet interacts and mixes strongly with the 0A + ν 4 levels whereas the 2A + component is unaffected. The 2A - levels are pushed rapidly downwards by the coupling creating an extremely large apparent K = 2A asymmetry splitting. We call this “giant K-doubling” by analogy with a comparable phenomenon seen for methanol. The 0A + ν 4 state, in turn, is perturbed upward and passes through the descending K = 1A + ν 4 state between J = 22 and 23, leading to distinct local perturbations near the level-crossing. The 0E ν 4 and 2E ν 10 coupling produces a correspondingly strong repulsion and mixing between those two substates, and gives rise to a forbidden K = 0 ← 3E intermode sub-band in the spectrum via intensity borrowing.« less

Giant K-doubling and in-plane/out-of-plane mixing in the asymmetric methyl-bending bands of CH 3SH

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guislain, B. G.; Reid, E. M.; Lees, R. M.

In analyzing high-resolution spectra of the methyl-deformation bands of methyl mercaptan recorded at the Canadian Light Source synchrotron, we have encountered interesting interactions between certain levels of the ν 4 in-plane asymmetric CH 3-bending mode and its ν 10 out-of-plane bending partner below. The origin of the K = 0A ν 4 substate is just 0.2 cm -1 higher than that of the K = 2A ν 10 substate, while the K = 0E ν 4 origin is only 0.035 cm -1 below the K = 2E ν 10 origin. These very close accidental near-degeneracies lead to substantial perturbations inmore » the spectrum. For the former, the A +/A - asymmetry K-doublet coupling rules are such that the A - component of the 2A ν 10 doublet interacts and mixes strongly with the 0A + ν 4 levels whereas the 2A + component is unaffected. The 2A - levels are pushed rapidly downwards by the coupling creating an extremely large apparent K = 2A asymmetry splitting. We call this “giant K-doubling” by analogy with a comparable phenomenon seen for methanol. The 0A + ν 4 state, in turn, is perturbed upward and passes through the descending K = 1A + ν 4 state between J = 22 and 23, leading to distinct local perturbations near the level-crossing. The 0E ν 4 and 2E ν 10 coupling produces a correspondingly strong repulsion and mixing between those two substates, and gives rise to a forbidden K = 0 ← 3E intermode sub-band in the spectrum via intensity borrowing.« less

Analysis of Cytochrome P450 CYP119 Ligand-dependent Conformational Dynamics by Two-dimensional NMR and X-ray Crystallography*

PubMed Central

Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie; Lampe, Jed N.; Nishida, Clinton R.; de Montellano, Paul R. Ortiz

2015-01-01

Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. We used two-dimensional 1H,15N HSQC chemical shift perturbation mapping of 15N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop with various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. The results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states. PMID:25670859

Conformer-specific hydrogen atom tunnelling in trifluoromethylhydroxycarbene

NASA Astrophysics Data System (ADS)

Mardyukov, Artur; Quanz, Henrik; Schreiner, Peter R.

2017-01-01

Conformational control of organic reactions is at the heart of the biomolecular sciences. To achieve a particular reactivity, one of many conformers may be selected, for instance, by a (bio)catalyst, as the geometrically most suited and appropriately reactive species. The equilibration of energetically close-lying conformers is typically assumed to be facile and less energetically taxing than the reaction under consideration itself: this is termed the 'Curtin-Hammett principle'. Here, we show that the trans conformer of trifluoromethylhydroxycarbene preferentially rearranges through a facile quantum-mechanical hydrogen tunnelling pathway, while its cis conformer is entirely unreactive. Hence, this presents the first example of a conformer-specific hydrogen tunnelling reaction. The Curtin-Hammett principle is not applicable, due to the high barrier between the two conformers.

Energy storage and alternatives to improve train voltage on a mass transit system

NASA Astrophysics Data System (ADS)

Gordon, S. P.; Rorke, W. S.

1995-04-01

The wide separation of substations in the Bay Area Rapid Transit system's transbay tunnel contributes to voltage sag when power demand is high. In the future, expansions to the system will exacerbate this problem by increasing traffic density. Typically, this situation is remedied through the installation of additional substations to increase the system's power capacity. We have evaluated the efficacy of several alternatives to this approach - specifically, installation of an 8 megajoule energy storage system, modification of the existing substations, or reduction of the resistance of the running rails or the third rail. To support this analysis, we have developed a simple model of the traction power system in the tunnel. We have concluded that the storage system does not have sufficient capacity to deal with the expected voltage sags; in this application, the alternatives present more effective solutions. We have also investigated the potential impact of these system upgrades on expected future capital outlays by BART for traction power infrastructure additions. We have found that rail or substation upgrades may reduce the need for additional substations. These upgrades may also be effective on other parts of the BART system and on other traction power systems.

Structural communication between the chromophore-binding pocket and the N-terminal extension in plant phytochrome phyB.

PubMed

Velázquez Escobar, Francisco; Buhrke, David; Fernandez Lopez, Maria; Shenkutie, Sintayehu Manaye; von Horsten, Silke; Essen, Lars-Oliver; Hughes, Jon; Hildebrandt, Peter

2017-05-01

The N-terminal extension (NTE) of plant phytochromes has been suggested to play a functional role in signaling photoinduced structural changes. Here, we use resonance Raman spectroscopy to study the effect of the NTE on the chromophore structure of B-type phytochromes from two evolutionarily distant plants. NTE deletion seems to have no effect on the chromophore in the inactive Pr state, but alters the torsion of the C-D ring methine bridge and the surrounding hydrogen bonding network in the physiologically active Pfr state. These changes are accompanied by a shift of the conformational equilibrium between two Pfr substates, which might affect the thermal isomerization rate of the C-D double bond and, thus, account for the effect of the NTE on the dark reversion kinetics. © 2017 Federation of European Biochemical Societies.

46. MISSISSIPPI BASIN MODEL AT CLINTON SUBSTATION. DETAIL OF INFLOW ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

46. MISSISSIPPI BASIN MODEL AT CLINTON SUBSTATION. DETAIL OF INFLOW CONTROLLER WITH ORIGINAL CAPACITOR BANK. - Waterways Experiment Station, Hydraulics Laboratory, Halls Ferry Road, 2 miles south of I-20, Vicksburg, Warren County, MS

125. TRANSFORMER SUBSTATIONS ON NORTH SIDE OF TRANSFORMER ROOM (112), ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

125. TRANSFORMER SUBSTATIONS ON NORTH SIDE OF TRANSFORMER ROOM (112), FACING SOUTH - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 West, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field

NASA Astrophysics Data System (ADS)

Unan, Hulya; Yildirim, Ahmet; Tekpinar, Mustafa

2015-07-01

Adenylate kinase is a widely used test case for many conformational transition studies. It performs a large conformational transition between closed and open conformations while performing its catalytic function. To understand conformational transition mechanism and impact of force field choice on E. Coli adenylate kinase, we performed all-atom explicit solvent classical molecular dynamics simulations starting from the closed conformation with four commonly used force fields, namely, Amber99, Charmm27, Gromos53a6, Opls-aa. We carried out 40 simulations, each one 200 ns. We analyzed completely 12 of them that show full conformational transition from the closed state to the open one. Our study shows that different force fields can have a bias toward different transition pathways. Transition time scales, frequency of conformational transitions, order of domain motions and free energy landscapes of each force field may also vary. In general, Amber99 and Charmm27 behave similarly while Gromos53a6 results have a resemblance to the Opls-aa force field results.

Structures of closed and open conformations of dimeric human ATM

PubMed Central

Baretić, Domagoj; Pollard, Hannah K.; Fisher, David I.; Johnson, Christopher M.; Santhanam, Balaji; Truman, Caroline M.; Kouba, Tomas; Fersht, Alan R.; Phillips, Christopher; Williams, Roger L.

2017-01-01

ATM (ataxia-telangiectasia mutated) is a phosphatidylinositol 3-kinase–related protein kinase (PIKK) best known for its role in DNA damage response. ATM also functions in oxidative stress response, insulin signaling, and neurogenesis. Our electron cryomicroscopy (cryo-EM) suggests that human ATM is in a dynamic equilibrium between closed and open dimers. In the closed state, the PIKK regulatory domain blocks the peptide substrate–binding site, suggesting that this conformation may represent an inactive or basally active enzyme. The active site is held in this closed conformation by interaction with a long helical hairpin in the TRD3 (tetratricopeptide repeats domain 3) domain of the symmetry-related molecule. The open dimer has two protomers with only a limited contact interface, and it lacks the intermolecular interactions that block the peptide-binding site in the closed dimer. This suggests that the open conformation may be more active. The ATM structure shows the detailed topology of the regulator-interacting N-terminal helical solenoid. The ATM conformational dynamics shown by the structures represent an important step in understanding the enzyme regulation. PMID:28508083

On issue of reconstruction at central distribution substation by example of one of plants of Chelyabinsk region

NASA Astrophysics Data System (ADS)

Brylina, O. G.; Semenova, K. D.; Shashkin, V. YU

2018-03-01

The article considers the issues of increasing the reliability and economy of the distribution substation. The result is found due to the reconstruction of the central distribution substation and one of the plants of Chelyabinsk region. The reasons for the reconstruction are explained. A comparison of oil and vacuum circuit breakers is made. The advantages of vacuum circuit breakers are shown. Alternative replacement of cables is offered. The basic technical characteristics of the cable brands are shown. The results of reconstruction are proved.

170. Credit SHS. Northern California Power Company substation, Bully Hill ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

170. Credit SHS. Northern California Power Company substation, Bully Hill Mine area. Note lack of vegetation, caused by nearby copper smelting works. - Battle Creek Hydroelectric System, Battle Creek & Tributaries, Red Bluff, Tehama County, CA

NY32649 ELECTRICAL SUBSTATION (BUILDING 2675) AND EDUCATION CENTER (BUILDING 2670) ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

NY-326-49 ELECTRICAL SUBSTATION (BUILDING 2675) AND EDUCATION CENTER (BUILDING 2670) AT NORTH END OF ARIZONA AVENUE. VIEW TO NORTHEAST. - Plattsburgh Air Force Base, U.S. Route 9, Plattsburgh, Clinton County, NY

The dynamics of camphor in the cytochrome P450 CYP101D2

PubMed Central

Vohra, Shabana; Musgaard, Maria; Bell, Stephen G; Wong, Luet-Lok; Zhou, Weihong; Biggin, Philip C

2013-01-01

The recent crystal structures of CYP101D2, a cytochrome P450 protein from the oligotrophic bacterium Novosphingobium aromaticivorans DSM12444 revealed that both the native (substrate-free) and camphor-soaked forms have open conformations. Furthermore, two other potential camphor-binding sites were also identified from electron densities in the camphor-soaked structure, one being located in the access channel and the other in a cavity on the surface near the F-helix side of the F-G loop termed the substrate recognition site. These latter sites may be key intermediate positions on the pathway for substrate access to or product egress from the active site. Here, we show via the use of unbiased atomistic molecular dynamics simulations that despite the open conformation of the native and camphor-bound crystal structures, the underlying dynamics of CYP101D2 appear to be very similar to other CYP proteins. Simulations of the native structure demonstrated that the protein is capable of sampling many different conformational substates. At the same time, simulations with the camphor positioned at various locations within the access channel or recognition site show that movement towards the active site or towards bulk solvent can readily occur on a short timescale, thus confirming many previously reported in silico studies using steered molecular dynamics. The simulations also demonstrate how the fluctuations of an aromatic gate appear to control access to the active site. Finally, comparison of camphor-bound simulations with the native simulations suggests that the fluctuations can be of similar level and thus are more representative of the conformational selection model rather than induced fit. PMID:23832606

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hermeston, Mark W.

BPA proposes total vegetation management (bareground) in the electrical substations, and, noxious weed management and maintenance of landscaping within the property boundaries of the listed facilities. These facilities are all located within the Covington District of the Snohomish Region. BPA proposes to manage vegetation inside and around electrical substations and associated facilities. Vegetation management within the substations will include bareground management by herbicides of all areas within the fenced perimeter of the facility including a bareground zone of up to 3 meters (10 feet) outside of the fenced area. The management of vegetation outside the substation and associated facilities willmore » include: 1) bare ground management of perimeter roads and parking areas; 2) control of noxious weeds throughout property boundaries; 3) mowing, fertilizing, and weed control of landscaped lawn and mulched areas; 4) weed control in ornamental shrub areas; and 5) areas requiring only mechanical control to manage unwanted/danger trees, grasses, and shrubs.« less

Residential exposure from extremely low frequency electromagnetic field (ELF EMF) radiation

NASA Astrophysics Data System (ADS)

Parthasarathy, Shamesh Raj; Tukimin, Roha

2018-01-01

ELF EMF radiation have received considerable attention as a potential threat to the safety and health of people living in the vicinity of high voltage transmission lines, electric distribution substations, power stations and even in close proximity to electronics and electrical household appliances. The paper highlights the study on the ELF EMF safety assessment performed at residences comprising of an owner-occupied house, a completed vacant house and an under construction condominium. The objectives of this study were to determine the ELF EMF radiation exposure level from the high voltage transmission line, electric distribution substation, power station and electrical household appliances in the residences, and to assess the potential exposure received by the occupants at the assessed locations. The results were logged in the electric and magnetic field strength with the units of volt per meter (V/m) and miliGauss (mG) respectively. The instrument setup and measurement protocols during the assessment were adopted from standard measurement method and procedures stipulated under the Institute of Electrical and Electronics Engineers (IEEE) Standard. The results were compared with the standards recommended in the International Commission on Non-Ionizing Radiation Protection (ICNIRP) guidelines.

Structural Architecture of Prothrombin in Solution Revealed by Single Molecule Spectroscopy.

PubMed

Pozzi, Nicola; Bystranowska, Dominika; Zuo, Xiaobing; Di Cera, Enrico

2016-08-26

The coagulation factor prothrombin has a complex spatial organization of its modular assembly that comprises the N-terminal Gla domain, kringle-1, kringle-2, and the C-terminal protease domain connected by three intervening linkers. Here we use single molecule Förster resonance energy transfer to access the conformational landscape of prothrombin in solution and uncover structural features of functional significance that extend recent x-ray crystallographic analysis. Prothrombin exists in equilibrium between two alternative conformations, open and closed. The closed conformation predominates (70%) and features an unanticipated intramolecular collapse of Tyr(93) in kringle-1 onto Trp(547) in the protease domain that obliterates access to the active site and protects the zymogen from autoproteolytic conversion to thrombin. The open conformation (30%) is more susceptible to chymotrypsin digestion and autoactivation, and features a shape consistent with recent x-ray crystal structures. Small angle x-ray scattering measurements of prothrombin wild type stabilized 70% in the closed conformation and of the mutant Y93A stabilized 80% in the open conformation directly document two envelopes that differ 50 Å in length. These findings reveal important new details on the conformational plasticity of prothrombin in solution and the drastic structural difference between its alternative conformations. Prothrombin uses the intramolecular collapse of kringle-1 onto the active site in the closed form to prevent autoactivation. The open-closed equilibrium also defines a new structural framework for the mechanism of activation of prothrombin by prothrombinase. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Rates and equilibrium constants of the ligand-induced conformational transition of an HCN ion channel protein domain determined by DEER spectroscopy.

PubMed

Collauto, Alberto; DeBerg, Hannah A; Kaufmann, Royi; Zagotta, William N; Stoll, Stefan; Goldfarb, Daniella

2017-06-14

Ligand binding can induce significant conformational changes in proteins. The mechanism of this process couples equilibria associated with the ligand binding event and the conformational change. Here we show that by combining the application of W-band double electron-electron resonance (DEER) spectroscopy with microfluidic rapid freeze quench (μRFQ) it is possible to resolve these processes and obtain both equilibrium constants and reaction rates. We studied the conformational transition of the nitroxide labeled, isolated carboxy-terminal cyclic-nucleotide binding domain (CNBD) of the HCN2 ion channel upon binding of the ligand 3',5'-cyclic adenosine monophosphate (cAMP). Using model-based global analysis, the time-resolved data of the μRFQ DEER experiments directly provide fractional populations of the open and closed conformations as a function of time. We modeled the ligand-induced conformational change in the protein using a four-state model: apo/open (AO), apo/closed (AC), bound/open (BO), bound/closed (BC). These species interconvert according to AC + L ⇌ AO + L ⇌ BO ⇌ BC. By analyzing the concentration dependence of the relative contributions of the closed and open conformations at equilibrium, we estimated the equilibrium constants for the two conformational equilibria and the open-state ligand dissociation constant. Analysis of the time-resolved μRFQ DEER data gave estimates for the intrinsic rates of ligand binding and unbinding as well as the rates of the conformational change. This demonstrates that DEER can quantitatively resolve both the thermodynamics and the kinetics of ligand binding and the associated conformational change.

Analysis of cytochrome P450 CYP119 ligand-dependent conformational dynamics by two-dimensional NMR and X-ray crystallography.

PubMed

Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie; Lampe, Jed N; Nishida, Clinton R; de Montellano, Paul R Ortiz

2015-04-17

Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. We used two-dimensional (1)H,(15)N HSQC chemical shift perturbation mapping of (15)N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop with various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. The results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Analysis of Cytochrome P450 CYP119 Ligand-dependent Conformational Dynamics by Two-dimensional NMR and X-ray Crystallography

DOE PAGES

Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie; ...

2015-02-10

Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. In this paper, we used two-dimensional 1H,15N HSQC chemical shift perturbation mapping of 15N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop withmore » various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. Finally, the results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states.« less

Analysis of Cytochrome P450 CYP119 Ligand-dependent Conformational Dynamics by Two-dimensional NMR and X-ray Crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie

Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. In this paper, we used two-dimensional 1H,15N HSQC chemical shift perturbation mapping of 15N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop withmore » various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. Finally, the results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states.« less

78 FR 9687 - Prineville Energy Storage, LLC; Notice of Preliminary Permit Application Accepted for Filing and...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-11

... PDCI to the Ponderosa substation, or (ii) the Bonneville Power Administration (BPA) existing transmission line corridor and then running parallel to the BPA line to the Ponderosa substation; and (9...

POWERHOUSES, SOUTH ELEVATIONS SHOWING OIL HOUSE, FILER SUBSTATION, AND DRAFT ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

POWERHOUSES, SOUTH ELEVATIONS SHOWING OIL HOUSE, FILER SUBSTATION, AND DRAFT TUBE OUTLET (TAILRACE), VERTICAL VIEW; FACING WEST - Shoshone Falls Hydroelectric Project, Canyon Road, North Bank of Snake River below Shoshone Falls, Tipperary Corner, Jerome County, ID

Conformational heterogeneity in closed and open states of the KcsA potassium channel in lipid bicelles

PubMed Central

Kim, Dorothy M.; Dikiy, Igor; Upadhyay, Vikrant; Posson, David J.

2016-01-01

The process of ion channel gating—opening and closing—involves local and global structural changes in the channel in response to external stimuli. Conformational changes depend on the energetic landscape that underlies the transition between closed and open states, which plays a key role in ion channel gating. For the prokaryotic, pH-gated potassium channel KcsA, closed and open states have been extensively studied using structural and functional methods, but the dynamics within each of these functional states as well as the transition between them is not as well understood. In this study, we used solution nuclear magnetic resonance (NMR) spectroscopy to investigate the conformational transitions within specific functional states of KcsA. We incorporated KcsA channels into lipid bicelles and stabilized them into a closed state by using either phosphatidylcholine lipids, known to favor the closed channel, or mutations designed to trap the channel shut by disulfide cross-linking. A distinct state, consistent with an open channel, was uncovered by the addition of cardiolipin lipids. Using selective amino acid labeling at locations within the channel that are known to move during gating, we observed at least two different slowly interconverting conformational states for both closed and open channels. The pH dependence of these conformations and the predictable disruptions to this dependence observed in mutant channels with altered pH sensing highlight the importance of conformational heterogeneity for KcsA gating. PMID:27432996

Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li+, Na+, K+ and Rb+ via Water-Mediated Hydrogen Bonding

PubMed Central

Savelyev, Alexey; MacKerell, Alexander D.

2015-01-01

Recently, we reported the differential impact of the monovalent cations Li+, Na+, K+ and Rb+ on DNA conformational properties. These were identified from variations in the calculated solution-state X-ray DNA spectra as a function of the ion type in the solvation buffer in MD simulations using our recently developed polarizable force field based on the classical Drude oscillator. Changes in the DNA structure were found to mainly involve variations in the minor groove width. Because minor groove dimensions vary significantly in protein-DNA complexes and have been shown to play a critical role in both specific and nonspecific DNA readout, understanding the origins of the observed differential DNA modulation by the first-group monovalent ions is of great biological importance. In the present study we show that the primary microscopic mechanism for the phenomenon is the formation of the water-mediated hydrogen bonds between solvated cations located inside the minor groove and simultaneously to two DNA strands, a process whose intensity and impact on DNA structure depends on both the type of the ion and DNA sequence. Additionally, it is shown that formation of such ion-DNA hydrogen bond complexes appreciably modulates the conformation of the backbone by increasing the population of the BII substate. Notably, the differential impact of the ions on DNA conformational behavior is only predicted by the Drude polarizable model for DNA, with virtually no effect observed from MD simulations utilizing the additive CHARMM36 model. Analysis of dipole moments of the water shows the Drude SWM4 model to possess high sensitivity to changes in the local environment, which indicates the important role of electronic polarization in the salt-dependent conformational properties. This also suggests that inclusion of polarization effects is required to model even relatively simple biological systems such as DNA in various ionic solutions. PMID:26575937

8. VIEW EASTNORTHEAST OF TRANSFORMER BAYS AND SUBSTATION; BUILDING 8 ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

8. VIEW EAST-NORTHEAST OF TRANSFORMER BAYS AND SUB-STATION; BUILDING 8 IS AT EXTREME LEFT CENTER; BUILD-ING 50 IS VISIBLE AT LEFT CENTER BEHIND BUILDING 8 - Scovill Brass Works, 59 Mill Street, Waterbury, New Haven County, CT

Study on the system-level test method of digital metering in smart substation

NASA Astrophysics Data System (ADS)

Zhang, Xiang; Yang, Min; Hu, Juan; Li, Fuchao; Luo, Ruixi; Li, Jinsong; Ai, Bing

2017-03-01

Nowadays, the test methods of digital metering system in smart substation are used to test and evaluate the performance of a single device, but these methods can only effectively guarantee the accuracy and reliability of the measurement results of a digital metering device in a single run, it does not completely reflect the performance when each device constitutes a complete system. This paper introduced the shortages of the existing test methods. A system-level test method of digital metering in smart substation was proposed, and the feasibility of the method was proved by the actual test.

Advanced Micro Grid Energy Management Coupled with Integrated Volt/VAR Control for Improved Energy Efficiency, Energy Security, and Power Quality at DoD Installations

DTIC Science & Technology

2016-10-28

constraints and wire routing issues. • Outside sites have more space, but require outdoor rated equipment (NEMA outdoor rated.. ) and more maintenance...sustainable power, in many different types, sizes and capacities, as follows: • Cogen Plant #1 B1579: 7.2MW gas-fired turbine at Substation “AA...Cogen Plant #2 B1991: (2) 4.6MW gas-fired turbines at “Gillespie” Substation • 300kW fuel cell at Substation “AA” • PPA: 1.015MW solar photovoltaic

Pilot Non-Conformance to Alerting System Commands During Closely Spaced Parallel Approaches

NASA Technical Reports Server (NTRS)

Pritchett, Amy R.; Hansman, R. John

1997-01-01

Pilot non-conformance to alerting system commands has been noted in general and to a TCAS-like collision avoidance system in a previous experiment. This paper details two experiments studying collision avoidance during closely-spaced parallel approaches in instrument meteorological conditions (IMC), and specifically examining possible causal factors of, and design solutions to, pilot non-conformance.

Parallel pathways and free-energy landscapes for enzymatic hydride transfer probed by hydrostatic pressure.

PubMed

Pudney, Christopher R; McGrory, Tom; Lafite, Pierre; Pang, Jiayun; Hay, Sam; Leys, David; Sutcliffe, Michael J; Scrutton, Nigel S

2009-05-25

Mutation of an active-site residue in morphinone reductase leads to a conformationally rich landscape that enhances the rate of hydride transfer from NADH to FMN at standard pressure (1 bar). Increasing the pressure causes interconversion between different conformational substates in the mutant enzyme. While high pressure reduces the donor-acceptor distance in the wild-type enzyme, increased conformational freedom "dampens" its effect in the mutant.We show that hydride transfer from NADH to FMN catalysed by the N189A mutant of morphinone reductase occurs along parallel "chemical" pathways in a conformationally rich free-energy landscape. We have developed experimental kinetic and spectroscopic tools by using hydrostatic pressure to explore this free-energy landscape. The crystal structure of the N189A mutant enzyme in complex with the unreactive coenzyme analogue NADH(4) indicates that the nicotinamide moiety of the analogue is conformationally less restrained than the corresponding structure of the wild-type NADH(4) complex. This increased degree of conformational freedom in the N189A enzyme gives rise to the concept of multiple reactive configurations (MRCs), and we show that the relative population of these states across the free-energy landscape can be perturbed experimentally as a function of pressure. Specifically, the amplitudes of individual kinetic phases that were observed in stopped-flow studies of the hydride transfer reaction are sensitive to pressure; this indicates that pressure drives an altered distribution across the energy landscape. We show by absorbance spectroscopy that the loss of charge-transfer character of the enzyme-coenzyme complex is attributed to the altered population of MRCs on the landscape. The existence of a conformationally rich landscape in the N189A mutant is supported by molecular dynamics simulations at low and high pressure. The work provides firm experimental and computational support for the existence of parallel pathways arising from multiple conformational states of the enzyme-coenzyme complex. Hydrostatic pressure is a powerful and general probe of multidimensional energy landscapes that can be used to analyse experimentally parallel pathways for enzyme-catalysed reactions. We suggest that this is especially the case following directed mutation of a protein, which can lead to increased population of reactant states that are essentially inaccessible in the free-energy landscape of wild-type enzyme.

Charge neutralization in the active site of the catalytic trimer of aspartate transcarbamoylase promotes diverse structural changes.

PubMed

Endrizzi, James A; Beernink, Peter T

2017-11-01

A classical model for allosteric regulation of enzyme activity posits an equilibrium between inactive and active conformations. An alternative view is that allosteric activation is achieved by increasing the potential for conformational changes that are essential for catalysis. In the present study, substitution of a basic residue in the active site of the catalytic (C) trimer of aspartate transcarbamoylase with a non-polar residue results in large interdomain hinge changes in the three chains of the trimer. One conformation is more open than the chains in both the wild-type C trimer and the catalytic chains in the holoenzyme, the second is closed similar to the bisubstrate-analog bound conformation and the third hinge angle is intermediate to the other two. The active-site 240s loop conformation is very different between the most open and closed chains, and is disordered in the third chain, as in the holoenzyme. We hypothesize that binding of anionic substrates may promote similar structural changes. Further, the ability of the three catalytic chains in the trimer to access the open and closed active-site conformations simultaneously suggests a cyclic catalytic mechanism, in which at least one of the chains is in an open conformation suitable for substrate binding whereas another chain is closed for catalytic turnover. Based on the many conformations observed for the chains in the isolated catalytic trimer to date, we propose that allosteric activation of the holoenzyme occurs by release of quaternary constraint into an ensemble of active-site conformations. © 2017 The Protein Society.

47. MISSISSIPPI BASIN MODEL AT CLINTON SUBSTATION. VIEW OF STAGE ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

47. MISSISSIPPI BASIN MODEL AT CLINTON SUBSTATION. VIEW OF STAGE TRANSMITTER AT ALTON, ILLINOIS MODEL SECTION, AND LOCK AND DAM (OLD #26) SIMULATOR. - Waterways Experiment Station, Hydraulics Laboratory, Halls Ferry Road, 2 miles south of I-20, Vicksburg, Warren County, MS

7. VIEW OF THE MODERN SUBSTATION (FOREGROUND), WITH THE OLD ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

7. VIEW OF THE MODERN SUBSTATION (FOREGROUND), WITH THE OLD SWITCHING BUILDING IN THE BACKGROUND, LOOKING SOUTHWEST. - Washington Water Power Company Post Falls Power Plant, Middle Channel Powerhouse & Dam, West of intersection of Spokane & Fourth Streets, Post Falls, Kootenai County, ID

Harmonic Characteristics of Rectifier Substations and Their Impact on Audio Frequency Track Circuits

DOT National Transportation Integrated Search

1982-05-01

This report describes the basic operation of substation rectifier equipment and the modes of possible interference with audio frequency track circuits used for train detection, cab signalling, and vehicle speed control. It also includes methods of es...

7 CFR 1710.252 - Construction work plans-power supply borrowers.

Code of Federal Regulations, 2012 CFR

2012-01-01

... operating systems of supporting power pools and to connect with adjacent power suppliers; (4) Improvements..., new substations and substation improvements and replacements, and Systems Control and Data Acquisition... include studies of load flows, voltage regulation, and stability characteristics to demonstrate system...

7 CFR 1710.252 - Construction work plans-power supply borrowers.

Code of Federal Regulations, 2014 CFR

2014-01-01

... operating systems of supporting power pools and to connect with adjacent power suppliers; (4) Improvements..., new substations and substation improvements and replacements, and Systems Control and Data Acquisition... include studies of load flows, voltage regulation, and stability characteristics to demonstrate system...

7 CFR 1710.252 - Construction work plans-power supply borrowers.

Code of Federal Regulations, 2011 CFR

2011-01-01

... operating systems of supporting power pools and to connect with adjacent power suppliers; (4) Improvements..., new substations and substation improvements and replacements, and Systems Control and Data Acquisition... include studies of load flows, voltage regulation, and stability characteristics to demonstrate system...

7 CFR 1710.252 - Construction work plans-power supply borrowers.

Code of Federal Regulations, 2010 CFR

2010-01-01

... operating systems of supporting power pools and to connect with adjacent power suppliers; (4) Improvements..., new substations and substation improvements and replacements, and Systems Control and Data Acquisition... include studies of load flows, voltage regulation, and stability characteristics to demonstrate system...

7 CFR 1710.252 - Construction work plans-power supply borrowers.

Code of Federal Regulations, 2013 CFR

2013-01-01

... operating systems of supporting power pools and to connect with adjacent power suppliers; (4) Improvements..., new substations and substation improvements and replacements, and Systems Control and Data Acquisition... include studies of load flows, voltage regulation, and stability characteristics to demonstrate system...

78 FR 50026 - Basin Electric Power Cooperative, Inc.: Notice of Intent To Prepare a Supplemental Draft...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-16

... transmission lines, 5 new substations, modifications to 4 existing substations, maintenance access roads... address the construction, operation, and maintenance of Basin Electric's proposed Project. The Project includes construction, operation and maintenance of approximately 275 [[Page 50027

Kennedy Space Center, Space Shuttle Processing, and International Space Station Program Overview

NASA Technical Reports Server (NTRS)

Higginbotham, Scott Alan

2011-01-01

Topics include: International Space Station assembly sequence; Electrical power substation; Thermal control substation; Guidance, navigation and control; Command data and handling; Robotics; Human and robotic integration; Additional modes of re-supply; NASA and International partner control centers; Space Shuttle ground operations.

A Fuzzy-Based Control Method for Smoothing Power Fluctuations in Substations along High-Speed Railways

NASA Astrophysics Data System (ADS)

Sugio, Tetsuya; Yamamoto, Masayoshi; Funabiki, Shigeyuki

The use of an SMES (Superconducting Magnetic Energy Storage) for smoothing power fluctuations in a railway substation has been discussed. This paper proposes a smoothing control method based on fuzzy reasoning for reducing the SMES capacity at substations along high-speed railways. The proposed smoothing control method comprises three countermeasures for reduction of the SMES capacity. The first countermeasure involves modification of rule 1 for smoothing out the fluctuating electric power to its average value. The other countermeasures involve the modification of the central value of the stored energy control in the SMES and revision of the membership function in rule 2 for reduction of the SMES capacity. The SMES capacity in the proposed smoothing control method is reduced by 49.5% when compared to that in the nonrevised control method. It is confirmed by computer simulations that the proposed control method is suitable for smoothing out power fluctuations in substations along high-speed railways and for reducing the SMES capacity.

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

PubMed Central

Lavery, Richard; Zakrzewska, Krystyna; Beveridge, David; Bishop, Thomas C.; Case, David A.; Cheatham, Thomas; Dixit, Surjit; Jayaram, B.; Lankas, Filip; Laughton, Charles; Maddocks, John H.; Michon, Alexis; Osman, Roman; Orozco, Modesto; Perez, Alberto; Singh, Tanya; Spackova, Nada; Sponer, Jiri

2010-01-01

It is well recognized that base sequence exerts a significant influence on the properties of DNA and plays a significant role in protein–DNA interactions vital for cellular processes. Understanding and predicting base sequence effects requires an extensive structural and dynamic dataset which is currently unavailable from experiment. A consortium of laboratories was consequently formed to obtain this information using molecular simulations. This article describes results providing information not only on all 10 unique base pair steps, but also on all possible nearest-neighbor effects on these steps. These results are derived from simulations of 50–100 ns on 39 different DNA oligomers in explicit solvent and using a physiological salt concentration. We demonstrate that the simulations are converged in terms of helical and backbone parameters. The results show that nearest-neighbor effects on base pair steps are very significant, implying that dinucleotide models are insufficient for predicting sequence-dependent behavior. Flanking base sequences can notably lead to base pair step parameters in dynamic equilibrium between two conformational sub-states. Although this study only provides limited data on next-nearest-neighbor effects, we suggest that such effects should be analyzed before attempting to predict the sequence-dependent behavior of DNA. PMID:19850719

Exploration of the Energy Landscape of Acetylcholinesterase by Molecular Dynamics Simulation.

NASA Astrophysics Data System (ADS)

McCammon, J. Andrew

2002-03-01

Proteins have rough energy landscapes. Often more states than just the ground state are occupied and have biological functions. It is essential to study these conformational substates and the dynamical transitions among them. Acetylcholinesterase (AChE) is an important enzyme that has biological functions including the termination of synaptic transmission signals. X-ray structures show that it has an active site that is accessible only via a long and narrow channel from its surface. Therefore the fact that acetylcholine and larger ligands can reach the active site is believed to reflect the protein's structural fluctuation. We carried out long molecular dynamics simulations to investigate the dynamics of AChE and its relation to biological function, and compared our results with experiments. The results reveal several "doors" that open intermittantly between the active site and the surface. Instead of having simple exponential decay correlation functions, the time series of these channels reveal complex, fractal gating between conformations. We also compared the AChE dynamics data with those from an AchE-fasciculin complex. (Fasciculin is a small protein that is a natural inhibitor of AChE.) The results show remarkable effects of the protein-protein interaction, including allosteric and dynamical inhibition by fasciculin besides direct steric blocking. More information and images can be found at http://mccammon.ucsd.edu

Tracking G-protein-coupled receptor activation using genetically encoded infrared probes.

PubMed

Ye, Shixin; Zaitseva, Ekaterina; Caltabiano, Gianluigi; Schertler, Gebhard F X; Sakmar, Thomas P; Deupi, Xavier; Vogel, Reiner

2010-04-29

Rhodopsin is a prototypical heptahelical family A G-protein-coupled receptor (GPCR) responsible for dim-light vision. Light isomerizes rhodopsin's retinal chromophore and triggers concerted movements of transmembrane helices, including an outward tilting of helix 6 (H6) and a smaller movement of H5, to create a site for G-protein binding and activation. However, the precise temporal sequence and mechanism underlying these helix rearrangements is unclear. We used site-directed non-natural amino acid mutagenesis to engineer rhodopsin with p-azido-l-phenylalanine residues incorporated at selected sites, and monitored the azido vibrational signatures using infrared spectroscopy as rhodopsin proceeded along its activation pathway. Here we report significant changes in electrostatic environments of the azido probes even in the inactive photoproduct Meta I, well before the active receptor state was formed. These early changes suggest a significant rotation of H6 and movement of the cytoplasmic part of H5 away from H3. Subsequently, a large outward tilt of H6 leads to opening of the cytoplasmic surface to form the active receptor photoproduct Meta II. Thus, our results reveal early conformational changes that precede larger rigid-body helix movements, and provide a basis to interpret recent GPCR crystal structures and to understand conformational sub-states observed during the activation of other GPCRs.

Flexibility of the Cu,Zn superoxide dismutase structure investigated at 0.57 GPa.

PubMed

Ascone, Isabella; Savino, Carmelinda; Kahn, Richard; Fourme, Roger

2010-06-01

The 2 A resolution crystal structure of bovine erythrocyte Cu,Zn superoxide dismutase (CuZnSOD) has been determined by X-ray diffraction at high pressure (0.57 GPa) and room temperature. At 0.57 GPa the secondary, tertiary and quaternary structures are similar to other previously determined bovine erythrocyte CuZnSOD structures. Nevertheless, pressure has a localized impact on the atomic coordinates of C(alpha) atoms and on side chains. The compression of the crystal and of the protein backbone is anisotropic. This anisotropy is discussed, taking into account intermolecular contacts and protein conformation. Pressure perturbation highlights the more flexible zones in the protein such as the electrostatic loop. At 0.57 GPa, a global shift of the dimetallic sites in both subunits and changes in the oxidation state of Cu were observed. The flexibility of the electrostatic loop may be useful for the interaction of different metal carriers in the copper-uptake process, whereas the flexibility of the metal sites involved in the activity of the protein could contribute to explaining the ubiquitous character of CuZnSODs, which are found in organisms living in very different conditions, including the deep-sea environment. This work illustrates the potential of combining X-ray crystallography with high pressure to promote and stabilize higher energy conformational substates.

42. MISSISSIPPI BASIN MODEL AT CLINTON SUBSTATION. DETAIL OF 200 ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

42. MISSISSIPPI BASIN MODEL AT CLINTON SUBSTATION. DETAIL OF 200 GALLON PER MINUTE INFLOW CONTROLLER WITH NEW PROGRAMMER, LOCATED ALONG THE NATCHEZ SECTION OF THE MODEL. - Waterways Experiment Station, Hydraulics Laboratory, Halls Ferry Road, 2 miles south of I-20, Vicksburg, Warren County, MS

Public magnetic field exposure based on internal current density for electric low voltage systems.

PubMed

Keikko, Tommi; Seesvuori, Reino; Hyvönen, Martti; Valkealahti, Seppo

2009-04-01

A measurement concept utilizing a new magnetic field exposure metering system has been developed for indoor substations where voltage is transformed from a medium voltage of 10 or 20 kV to a low voltage of 400 V. The new metering system follows the guidelines published by the International Commission on Non-Ionizing Radiation Protection. It can be used to measure magnetic field values, total harmonic distortion of the magnetic field, magnetic field exposure ratios for public and workers, load current values, and total harmonic distortion of the load current. This paper demonstrates how exposure to non-sinusoidal magnetic fields and magnetic flux density exposure values can be compared directly with limit values for internal current densities in a human body. Further, we present how the magnetic field and magnetic field exposure behaves in the vicinity of magnetic field sources within the indoor substation and in the neighborhood. Measured magnetic fields around the substation components have been used to develop a measurement concept by which long-term measurements in the substations were performed. Long-term measurements revealed interesting and partly unexpected dependencies between the measured quantities, which have been further analyzed. The principle of this paper is to substitute a demanding exposure measurement with measurements of the basic quantities like the 50 Hz fundamental magnetic field component, which can be estimated based on the load currents for certain classes of substation lay-out.

X-ray crystallographic and MD simulation studies on the mechanism of interfacial activation of a family I.3 lipase with two lids.

PubMed

Angkawidjaja, Clement; Matsumura, Hiroyoshi; Koga, Yuichi; Takano, Kazufumi; Kanaya, Shigenori

2010-07-02

The interfacial activation mechanism of family I.3 lipase from Pseudomonas sp. MIS38 (PML), which has two alpha-helical lids (lid1 and lid2), was investigated using a combination of X-ray crystallography and molecular dynamics (MD) simulation. The crystal structure of PML in an open conformation was determined at 2.1 A resolution in the presence of Ca(2+) and Triton X-100. Comparison of this structure with that in the closed conformation indicates that both lids greatly change their positions and lid1 is anchored by the calcium ion (Ca1) in the open conformation. This structure was not seriously changed even when the protein was dialyzed extensively against the Ca(2+)-free buffer containing Triton X-100 before crystallization, indicating that the open conformation is fairly stable unless a micellar substance is removed. The crystal structure of the PML derivative, in which the active site serine residue (Ser207) is diethylphosphorylated by soaking the crystal of PML in the open conformation in a solution containing diethyl p-nitrophenyl phosphate, was also determined. This structure greatly resembles that in the open conformation, indicating that PML structure in the open conformation represents that in the active form. MD simulation of PML in the open conformation in the absence of micelles showed that lid2 closes first, while lid1 maintains its open conformation. Likewise, MD simulation of PML in the closed conformation in the absence of Ca(2+) and in the presence of octane or trilaurin micelles showed that lid1 opens, while lid2 remains closed. These results suggest that Ca1 functions as a hook for stabilization of a fully opened conformation of lid1 and for initiation of subsequent opening of lid2. Copyright 2010 Elsevier Ltd. All rights reserved.

Pyruvate Dehydrogenase Kinase-4 Structures Reveal a Metastable Open Conformation Fostering Robust Core-free Basal Activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wynn, R. Max; Kato, Masato; Chuang, Jacinta L.

2008-10-21

Human pyruvate dehydrogenase complex (PDC) is down-regulated by pyruvate dehydrogenase kinase (PDK) isoforms 1-4. PDK4 is overexpressed in skeletal muscle in type 2 diabetes, resulting in impaired glucose utilization. Here we show that human PDK4 has robust core-free basal activity, which is considerably higher than activity levels of other PDK isoforms stimulated by the PDC core. PDK4 binds the L3 lipoyl domain, but its activity is not significantly stimulated by any individual lipoyl domains or the core of PDC. The 2.0-{angstrom} crystal structures of the PDK4 dimer with bound ADP reveal an open conformation with a wider active-site cleft, comparedmore » with that in the closed conformation epitomized by the PDK2-ADP structure. The open conformation in PDK4 shows partially ordered C-terminal cross-tails, in which the conserved DW (Asp{sup 394}-Trp{sup 395}) motif from one subunit anchors to the N-terminal domain of the other subunit. The open conformation fosters a reduced binding affinity for ADP, facilitating the efficient removal of product inhibition by this nucleotide. Alteration or deletion of the DW-motif disrupts the C-terminal cross-tail anchor, resulting in the closed conformation and the nearly complete inactivation of PDK4. Fluorescence quenching and enzyme activity data suggest that compounds AZD7545 and dichloroacetate lock PDK4 in the open and the closed conformational states, respectively. We propose that PDK4 with bound ADP exists in equilibrium between the open and the closed conformations. The favored metastable open conformation is responsible for the robust basal activity of PDK4 in the absence of the PDC core.« less

Pyruvate dehydrogenase kinase-4 structures reveal a metastable open conformation fostering robust core-free basal activity.

PubMed

Wynn, R Max; Kato, Masato; Chuang, Jacinta L; Tso, Shih-Chia; Li, Jun; Chuang, David T

2008-09-12

Human pyruvate dehydrogenase complex (PDC) is down-regulated by pyruvate dehydrogenase kinase (PDK) isoforms 1-4. PDK4 is overexpressed in skeletal muscle in type 2 diabetes, resulting in impaired glucose utilization. Here we show that human PDK4 has robust core-free basal activity, which is considerably higher than activity levels of other PDK isoforms stimulated by the PDC core. PDK4 binds the L3 lipoyl domain, but its activity is not significantly stimulated by any individual lipoyl domains or the core of PDC. The 2.0-A crystal structures of the PDK4 dimer with bound ADP reveal an open conformation with a wider active-site cleft, compared with that in the closed conformation epitomized by the PDK2-ADP structure. The open conformation in PDK4 shows partially ordered C-terminal cross-tails, in which the conserved DW (Asp(394)-Trp(395)) motif from one subunit anchors to the N-terminal domain of the other subunit. The open conformation fosters a reduced binding affinity for ADP, facilitating the efficient removal of product inhibition by this nucleotide. Alteration or deletion of the DW-motif disrupts the C-terminal cross-tail anchor, resulting in the closed conformation and the nearly complete inactivation of PDK4. Fluorescence quenching and enzyme activity data suggest that compounds AZD7545 and dichloroacetate lock PDK4 in the open and the closed conformational states, respectively. We propose that PDK4 with bound ADP exists in equilibrium between the open and the closed conformations. The favored metastable open conformation is responsible for the robust basal activity of PDK4 in the absence of the PDC core.

43. MISSISSIPPI BASIN MODEL AT CLINTON SUBSTATION. DETAIL OF 200 ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

43. MISSISSIPPI BASIN MODEL AT CLINTON SUBSTATION. DETAIL OF 200 GALLON PER MINUTE INFLOW CONTROLLER WITH NEW PROGRAMMER, LOCATED ALONG THE NATCHEZ SECTION OF THE MODEL. NOTE CONTROL BUILDING AT LEFT. - Waterways Experiment Station, Hydraulics Laboratory, Halls Ferry Road, 2 miles south of I-20, Vicksburg, Warren County, MS

18. Photocopy of photograph showing foundation framing of South Bank ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

18. Photocopy of photograph showing foundation framing of South Bank Substation, 11 June 1939 (from the BPA Photo Archives, Negative No. 347), LOOKING NORTH WITH THE BONNEVILLE DAM POWERHOUSE IN BACKGROUND - Bonneville Power Administration South Bank Substation, I-84, South of Bonneville Dam Powerhouse, Bonneville, Multnomah County, OR

123. ARAI Substation (ARA726) plan, elevation, security fence details, and ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

123. ARA-I Substation (ARA-726) plan, elevation, security fence details, and sections. Norman Engineering Company 961-area/SF-726-E-1. Date: January 1959. Ineel index code no. 068-0726-10-613-102778. - Idaho National Engineering Laboratory, Army Reactors Experimental Area, Scoville, Butte County, ID

30 CFR 56.4130 - Electric substations and liquid storage facilities.

Code of Federal Regulations, 2011 CFR

2011-07-01

...) Unburied, flammable or combustible liquid storage tanks. (3) Any group of containers used for storage of more than 60 gallons of flammable or combustible liquids. (b) The area within the 25-foot perimeter... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Electric substations and liquid storage...

30 CFR 56.4130 - Electric substations and liquid storage facilities.

Code of Federal Regulations, 2014 CFR

2014-07-01

...) Unburied, flammable or combustible liquid storage tanks. (3) Any group of containers used for storage of more than 60 gallons of flammable or combustible liquids. (b) The area within the 25-foot perimeter... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Electric substations and liquid storage...

30 CFR 56.4130 - Electric substations and liquid storage facilities.

Code of Federal Regulations, 2012 CFR

2012-07-01

...) Unburied, flammable or combustible liquid storage tanks. (3) Any group of containers used for storage of more than 60 gallons of flammable or combustible liquids. (b) The area within the 25-foot perimeter... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Electric substations and liquid storage...

30 CFR 56.4130 - Electric substations and liquid storage facilities.

Code of Federal Regulations, 2013 CFR

2013-07-01

...) Unburied, flammable or combustible liquid storage tanks. (3) Any group of containers used for storage of more than 60 gallons of flammable or combustible liquids. (b) The area within the 25-foot perimeter... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Electric substations and liquid storage...

40 CFR 256.60 - Requirements for public participation in State and substate plans.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 24 2010-07-01 2010-07-01 false Requirements for public participation in State and substate plans. 256.60 Section 256.60 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) SOLID WASTES GUIDELINES FOR DEVELOPMENT AND IMPLEMENTATION OF STATE SOLID WASTE...

Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates

PubMed Central

Tuszynski, Jack A.; Gallo, Diego; Morbiducci, Umberto; Danani, Andrea

2016-01-01

The Josephin Domain (JD), i.e. the N-terminal domain of Ataxin 3 (At3) protein, is an interesting example of competition between physiological function and aggregation risk. In fact, the fibrillogenesis of Ataxin 3, responsible for the spinocerebbellar ataxia 3, is strictly related to the JD thermodynamic stability. Whereas recent NMR studies have demonstrated that different JD conformations exist, the likelihood of JD achievable conformational states in solution is still an open issue. Marked differences in the available NMR models are located in the hairpin region, supporting the idea that JD has a flexible hairpin in dynamic equilibrium between open and closed states. In this work we have carried out an investigation on the JD conformational arrangement by means of both classical molecular dynamics (MD) and Metadynamics employing essential coordinates as collective variables. We provide a representation of the free energy landscape characterizing the transition pathway from a JD open-like structure to a closed-like conformation. Findings of our in silico study strongly point to the closed-like conformation as the most likely for a Josephin Domain in water. PMID:26745628

Drastic changes in conformational dynamics of the antiterminator M2-1 regulate transcription efficiency in Pneumovirinae

PubMed Central

Leyrat, Cedric; Renner, Max; Harlos, Karl; Huiskonen, Juha T; Grimes, Jonathan M

2014-01-01

The M2-1 protein of human metapneumovirus (HMPV) is a zinc-binding transcription antiterminator which is highly conserved among pneumoviruses. We report the structure of tetrameric HMPV M2-1. Each protomer features a N-terminal zinc finger domain and an α-helical tetramerization motif forming a rigid unit, followed by a flexible linker and an α-helical core domain. The tetramer is asymmetric, three of the protomers exhibiting a closed conformation, and one an open conformation. Molecular dynamics simulations and SAXS demonstrate a dynamic equilibrium between open and closed conformations in solution. Structures of adenosine monophosphate- and DNA- bound M2-1 establish the role of the zinc finger domain in base-specific recognition of RNA. Binding to ‘gene end’ RNA sequences stabilized the closed conformation of M2-1 leading to a drastic shift in the conformational landscape of M2-1. We propose a model for recognition of gene end signals and discuss the implications of these findings for transcriptional regulation in pneumoviruses. DOI: http://dx.doi.org/10.7554/eLife.02674.001 PMID:24842877

Integrability conditions for Killing-Yano tensors and conformal Killing-Yano tensors

NASA Astrophysics Data System (ADS)

Batista, Carlos

2015-01-01

The integrability conditions for the existence of a conformal Killing-Yano tensor of arbitrary order are worked out in all dimensions and expressed in terms of the Weyl tensor. As a consequence, the integrability conditions for the existence of a Killing-Yano tensor are also obtained. By means of such conditions, it is shown that in certain Einstein spaces one can use a conformal Killing-Yano tensor of order p to generate a Killing-Yano tensor of order (p -1 ) . Finally, it is proved that in maximally symmetric spaces the covariant derivative of a Killing-Yano tensor is a closed conformal Killing-Yano tensor and that every conformal Killing-Yano tensor is uniquely decomposed as the sum of a Killing-Yano tensor and a closed conformal Killing-Yano tensor.

Conformational Changes in Orotidine 5-Monophosphate Decarboxylase: "Remote" Residues That Stabilize the Active Conformation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wood, B.; Amyes, T; Fedorov, A

2010-01-01

The structural factors responsible for the extraordinary rate enhancement ({approx}10{sup 17}) of the reaction catalyzed by orotidine 5{prime}-monophosphate decarboxylase (OMPDC) have not been defined. Catalysis requires a conformational change that closes an active site loop and 'clamps' the orotate base proximal to hydrogen-bonded networks that destabilize the substrate and stabilize the intermediate. In the OMPDC from Methanobacter thermoautotrophicus, a 'remote' structurally conserved cluster of hydrophobic residues that includes Val 182 in the active site loop is assembled in the closed, catalytically active conformation. Substitution of these residues with Ala decreases k{sub cat}/K{sub m} with a minimal effect on k{sub cat},more » providing evidence that the cluster stabilizes the closed conformation. The intrinsic binding energies of the 5{prime}-phosphate group of orotidine 5{prime}-monophosphate for the mutant enzymes are similar to that for the wild type, supporting this conclusion.« less

19. Photocopy of photograph showing framing of concrete walls of ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

19. Photocopy of photograph showing framing of concrete walls of South Bank Substation, 18 July 1939 (from the BPA Photo Archives, Negative No. 365), LOOKING NORTHWEST WITH THE BONNEVILLE DAM POWERHOUSE IN BACKGROUND - Bonneville Power Administration South Bank Substation, I-84, South of Bonneville Dam Powerhouse, Bonneville, Multnomah County, OR

30 CFR 57.4130 - Surface electric substations and liquid storage facilities.

Code of Federal Regulations, 2013 CFR

2013-07-01

... liquid storage tanks. (3) Any group of containers used for storage of more than 60 gallons of flammable... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Surface electric substations and liquid storage facilities. 57.4130 Section 57.4130 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF...

30 CFR 57.4130 - Surface electric substations and liquid storage facilities.

Code of Federal Regulations, 2012 CFR

2012-07-01

... liquid storage tanks. (3) Any group of containers used for storage of more than 60 gallons of flammable... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Surface electric substations and liquid storage facilities. 57.4130 Section 57.4130 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF...

30 CFR 57.4130 - Surface electric substations and liquid storage facilities.

Code of Federal Regulations, 2011 CFR

2011-07-01

... liquid storage tanks. (3) Any group of containers used for storage of more than 60 gallons of flammable... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Surface electric substations and liquid storage facilities. 57.4130 Section 57.4130 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF...

30 CFR 57.4130 - Surface electric substations and liquid storage facilities.

Code of Federal Regulations, 2014 CFR

2014-07-01

... liquid storage tanks. (3) Any group of containers used for storage of more than 60 gallons of flammable... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Surface electric substations and liquid storage facilities. 57.4130 Section 57.4130 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF...

75 FR 7470 - Pine Prairie Energy Center, LLC; Notice of Application

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-19

... electric motor drive compressor units instead of the four 4,700 hp natural gas-fueled units previously authorized; (2) construct and operate a new electrical substation at the Pine Prairie Gas Handling Facility and approximately 1,200 feet of aerial electric power lines between the new substation and the...

40 CFR 256.60 - Requirements for public participation in State and substate plans.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 25 2014-07-01 2014-07-01 false Requirements for public participation in State and substate plans. 256.60 Section 256.60 Protection of Environment ENVIRONMENTAL PROTECTION... shall: (1) Publicize information in news media having broad audiences in the geographic area; (2) Place...

40 CFR 256.60 - Requirements for public participation in State and substate plans.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 26 2013-07-01 2013-07-01 false Requirements for public participation in State and substate plans. 256.60 Section 256.60 Protection of Environment ENVIRONMENTAL PROTECTION... shall: (1) Publicize information in news media having broad audiences in the geographic area; (2) Place...

40 CFR 256.60 - Requirements for public participation in State and substate plans.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 26 2012-07-01 2011-07-01 true Requirements for public participation in State and substate plans. 256.60 Section 256.60 Protection of Environment ENVIRONMENTAL PROTECTION... shall: (1) Publicize information in news media having broad audiences in the geographic area; (2) Place...

40 CFR 256.60 - Requirements for public participation in State and substate plans.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 25 2011-07-01 2011-07-01 false Requirements for public participation in State and substate plans. 256.60 Section 256.60 Protection of Environment ENVIRONMENTAL PROTECTION... shall: (1) Publicize information in news media having broad audiences in the geographic area; (2) Place...

Identification and Single-Cell Functional Characterization of an Endodermally Biased Pluripotent Substate in Human Embryonic Stem Cells.

PubMed

Allison, Thomas F; Smith, Andrew J H; Anastassiadis, Konstantinos; Sloane-Stanley, Jackie; Biga, Veronica; Stavish, Dylan; Hackland, James; Sabri, Shan; Langerman, Justin; Jones, Mark; Plath, Kathrin; Coca, Daniel; Barbaric, Ivana; Gokhale, Paul; Andrews, Peter W

2018-05-09

Human embryonic stem cells (hESCs) display substantial heterogeneity in gene expression, implying the existence of discrete substates within the stem cell compartment. To determine whether these substates impact fate decisions of hESCs we used a GFP reporter line to investigate the properties of fractions of putative undifferentiated cells defined by their differential expression of the endoderm transcription factor, GATA6, together with the hESC surface marker, SSEA3. By single-cell cloning, we confirmed that substates characterized by expression of GATA6 and SSEA3 include pluripotent stem cells capable of long-term self-renewal. When clonal stem cell colonies were formed from GATA6-positive and GATA6-negative cells, more of those derived from GATA6-positive cells contained spontaneously differentiated endoderm cells than similar colonies derived from the GATA6-negative cells. We characterized these discrete cellular states using single-cell transcriptomic analysis, identifying a potential role for SOX17 in the establishment of the endoderm-biased stem cell state. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Molecular Simulation Uncovers the Conformational Space of the λ Cro Dimer in Solution

PubMed Central

Ahlstrom, Logan S.; Miyashita, Osamu

2011-01-01

The significant variation among solved structures of the λ Cro dimer suggests its flexibility. However, contacts in the crystal lattice could have stabilized a conformation which is unrepresentative of its dominant solution form. Here we report on the conformational space of the Cro dimer in solution using replica exchange molecular dynamics in explicit solvent. The simulated ensemble shows remarkable correlation with available x-ray structures. Network analysis and a free energy surface reveal the predominance of closed and semi-open dimers, with a modest barrier separating these two states. The fully open conformation lies higher in free energy, indicating that it requires stabilization by DNA or crystal contacts. Most NMR models are found to be unstable conformations in solution. Intersubunit salt bridging between Arg4 and Glu53 during simulation stabilizes closed conformations. Because a semi-open state is among the low-energy conformations sampled in simulation, we propose that Cro-DNA binding may not entail a large conformational change relative to the dominant dimer forms in solution. PMID:22098751

Binding mechanism and dynamic conformational change of C subunit of PKA with different pathways

PubMed Central

Chu, Wen-Ting; Chu, Xiakun; Wang, Jin

2017-01-01

The catalytic subunit of PKA (PKAc) exhibits three major conformational states (open, intermediate, and closed) during the biocatalysis process. Both ATP and substrate/inhibitor can effectively induce the conformational changes of PKAc from open to closed states. Aiming to explore the mechanism of this allosteric regulation, we developed a coarse-grained model and analyzed the dynamics of conformational changes of PKAc during binding by performing molecular dynamics simulations for apo PKAc, binary PKAc (PKAc with ATP, PKAc with PKI), and ternary PKAc (PKAc with ATP and PKI). Our results suggest a mixed binding mechanism of induced fit and conformational selection, with the induced fit dominant. The ligands can drive the movements of Gly-rich loop as well as some regions distal to the active site in PKAc and stabilize them at complex state. In addition, there are two parallel pathways (pathway with PKAc-ATP as an intermediate and pathway PKAc-PKI as an intermediate) during the transition from open to closed states. By molecular dynamics simulations and rate constant analyses, we find that the pathway through PKAc-ATP intermediate is the main binding route from open to closed state because of the fact that the bound PKI will hamper ATP from successful binding and significantly increase the barrier for the second binding subprocess. These findings will provide fundamental insights of the mechanisms of PKAc conformational change upon binding. PMID:28855336

Binding mechanism and dynamic conformational change of C subunit of PKA with different pathways.

PubMed

Chu, Wen-Ting; Chu, Xiakun; Wang, Jin

2017-09-19

The catalytic subunit of PKA (PKAc) exhibits three major conformational states (open, intermediate, and closed) during the biocatalysis process. Both ATP and substrate/inhibitor can effectively induce the conformational changes of PKAc from open to closed states. Aiming to explore the mechanism of this allosteric regulation, we developed a coarse-grained model and analyzed the dynamics of conformational changes of PKAc during binding by performing molecular dynamics simulations for apo PKAc, binary PKAc (PKAc with ATP, PKAc with PKI), and ternary PKAc (PKAc with ATP and PKI). Our results suggest a mixed binding mechanism of induced fit and conformational selection, with the induced fit dominant. The ligands can drive the movements of Gly-rich loop as well as some regions distal to the active site in PKAc and stabilize them at complex state. In addition, there are two parallel pathways (pathway with PKAc-ATP as an intermediate and pathway PKAc-PKI as an intermediate) during the transition from open to closed states. By molecular dynamics simulations and rate constant analyses, we find that the pathway through PKAc-ATP intermediate is the main binding route from open to closed state because of the fact that the bound PKI will hamper ATP from successful binding and significantly increase the barrier for the second binding subprocess. These findings will provide fundamental insights of the mechanisms of PKAc conformational change upon binding.

Ligand induced change of β2 adrenergic receptor from active to inactive conformation and its implication for the closed/open state of the water channel: insight from molecular dynamics simulation, free energy calculation and Markov state model analysis.

PubMed

Bai, Qifeng; Pérez-Sánchez, Horacio; Zhang, Yang; Shao, Yonghua; Shi, Danfeng; Liu, Huanxiang; Yao, Xiaojun

2014-08-14

The reported crystal structures of β2 adrenergic receptor (β2AR) reveal that the open and closed states of the water channel are correlated with the inactive and active conformations of β2AR. However, more details about the process by which the water channel states are affected by the active to inactive conformational change of β2AR remain illusive. In this work, molecular dynamics simulations are performed to study the dynamical inactive and active conformational change of β2AR induced by inverse agonist ICI 118,551. Markov state model analysis and free energy calculation are employed to explore the open and close states of the water channel. The simulation results show that inverse agonist ICI 118,551 can induce water channel opening during the conformational transition of β2AR. Markov state model (MSM) analysis proves that the energy contour can be divided into seven states. States S1, S2 and S5, which represent the active conformation of β2AR, show that the water channel is in the closed state, while states S4 and S6, which correspond to the intermediate state conformation of β2AR, indicate the water channel opens gradually. State S7, which represents the inactive structure of β2AR, corresponds to the full open state of the water channel. The opening mechanism of the water channel is involved in the ligand-induced conformational change of β2AR. These results can provide useful information for understanding the opening mechanism of the water channel and will be useful for the rational design of potent inverse agonists of β2AR.

Molecular dynamics simulations of transitions for ECD epidermal growth factor receptors show key differences between human and drosophila forms of the receptors.

PubMed

Perilla, Juan R; Leahy, Daniel J; Woolf, Thomas B

2013-07-01

Recent X-ray structural work on the Drosophila epidermal growth factor receptor (EFGR) has suggested an asymmetric dimer that rationalizes binding affinity measurements that go back decades (Alvarado et al., Cell 2010;142:568-579; Dawson et al., Structure 2007;15:942-954; Lemmon et al., Embo J 1997;16:281-294; Mattoon et al., Proc Natl Acad Sci USA 2004;101:923-928; Mayawala et al., Febs Lett 2005;579:3043-3047; Ozcan et al., Proc Natl Acad Sci USA 2006;103:5735-5740). This type of asymmetric structure has not been seen for the human EGF receptor family and it may or may not be important for function in that realm. We hypothesize that conformational changes in the Drosophila system have been optimized for the transition, whereas the barrier for the same transition is much higher in the human forms. To address our hypothesis we perform dynamic importance sampling (DIMS) (Perilla et al., J Comput Chem 2010;32:196-209) for barrier crossing transitions in both Drosophila and human EFGRs. For each set of transitions, we work from the hypothesis, based on results from the AdK system, that salt-bridge pairs making and breaking connections are central to the conformational change. To evaluate the effectiveness of the salt-bridges as drivers for the conformational change, we use the effective transfer entropy based on stable state MD calculations (Kamberaj and Der Vaart, Biophys J 2009;97:1747-1755) to define a reduced subset of degrees of freedom that seem to be important for driving the transition (Perilla and Woolf, J Chem Phys 2012;136:164101). Our results suggest that salt-bridge making and breaking is not the dominant factor in driving the symmetric to asymmetric transition, but that instead it is a result of more concerted and correlated functional motions within a subset of the dimer structures. Furthermore, the analysis suggests that the set of residues involved in the transitions from the Drosophila relative to the human forms differs and that this difference in substate distributions relates to why the asymmetric form may be more common to Drosophila than to the human forms. We close with a discussion about the residues that may be changed in the human and the Drosophila forms to potentially shift the kinetics of the symmetric to asymmetric transition. Copyright © 2013 Wiley Periodicals, Inc.

77 FR 73651 - Cascade Energy Storage, LLC; Notice of Preliminary Permit Application Accepted for Filing and...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-11

... City Light's existing 230-kV transmission line, or (ii) Bonneville Power Administration's (BPA) existing Custer-Monroe 500-kV line, or (iii) BPA existing Murray substation, or (iv) a new 4.5-mile- long... and then to the BPA Murray substation; and (9) appurtenant facilities. The estimated annual generation...

Supplement Analysis for the Transmission System Vegetation Management Program FEIS (DOE/EIS-0285/SA-74)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Howington, John

2002-07-01

Vegetation Management for five Substations in the Malin District. BPA proposes total vegetation management (bare ground) in the electrical substations, and, noxious weed management and maintenance of landscaping within the property boundaries of the listed facilities. These facilities are all located within the Malin District of the Redmond Region.

Supplement Analysis for the Transmission System Vegetation Management Program FEIS (DOE/EIS-0285/SA-82)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Howington, John

2002-08-13

Vegetation Management for twenty-four Substations in the Burley District. BPA proposes total vegetation management (bare ground) in the electrical substations, and, noxious weed management and maintenance of landscaping within the property boundaries of the listed facilities. These facilities are all located within the Burley District of the Idaho Falls Region.

Supplement Analysis for the Transmission System Vegetation Management Program FEIS (DOE/EIS-0285/SA-78)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Howington, John

2002-07-01

Vegetation Management for ten Substations in the Redmond District. BPA proposes total vegetation management (bare ground) in the electrical substations, and, noxious weed management and maintenance of landscaping within the property boundaries of the listed facilities. These facilities are all located within the Redmond District of the Redmond Region.

Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins

PubMed Central

Kurkcuoglu, Zeynep; Doruker, Pemra

2016-01-01

Incorporating receptor flexibility in small ligand-protein docking still poses a challenge for proteins undergoing large conformational changes. In the absence of bound structures, sampling conformers that are accessible by apo state may facilitate docking and drug design studies. For this aim, we developed an unbiased conformational search algorithm, by integrating global modes from elastic network model, clustering and energy minimization with implicit solvation. Our dataset consists of five diverse proteins with apo to complex RMSDs 4.7–15 Å. Applying this iterative algorithm on apo structures, conformers close to the bound-state (RMSD 1.4–3.8 Å), as well as the intermediate states were generated. Dockings to a sequence of conformers consisting of a closed structure and its “parents” up to the apo were performed to compare binding poses on different states of the receptor. For two periplasmic binding proteins and biotin carboxylase that exhibit hinge-type closure of two dynamics domains, the best pose was obtained for the conformer closest to the bound structure (ligand RMSDs 1.5–2 Å). In contrast, the best pose for adenylate kinase corresponded to an intermediate state with partially closed LID domain and open NMP domain, in line with recent studies (ligand RMSD 2.9 Å). The docking of a helical peptide to calmodulin was the most challenging case due to the complexity of its 15 Å transition, for which a two-stage procedure was necessary. The technique was first applied on the extended calmodulin to generate intermediate conformers; then peptide docking and a second generation stage on the complex were performed, which in turn yielded a final peptide RMSD of 2.9 Å. Our algorithm is effective in producing conformational states based on the apo state. This study underlines the importance of such intermediate states for ligand docking to proteins undergoing large transitions. PMID:27348230

Conformational change of adenosine deaminase during ligand-exchange in a crystal.

PubMed

Kinoshita, Takayoshi; Tada, Toshiji; Nakanishi, Isao

2008-08-15

Adenosine deaminase (ADA) perpetuates chronic inflammation by degrading extracellular adenosine which is toxic for lymphocytes. ADA has two distinct conformations: open form and closed form. From the crystal structures with various ligands, the non-nucleoside type inhibitors bind to the active site occupying the critical water-binding-position and sustain the open form of apo-ADA. In contrast, substrate mimics do not occupy the critical position, and induce the large conformational change to the closed form. However, it is difficult to predict the binding of (+)-erythro-9-(2-hydroxy-3-nonyl)adenine (EHNA), as it possesses characteristic parts of both the substrate and the non-nucleoside inhibitors. The crystal structure shows that EHNA binds to the open form through a novel recognition of the adenine base accompanying conformational change from the closed form of the PR-ADA complex in crystalline state.

A new test procedure to evaluate the performance of substations for collective heating systems

NASA Astrophysics Data System (ADS)

Baetens, Robin; Verhaert, Ivan

2017-11-01

The overall heat demand of a single dwelling, existing out of space heating and domestic hot water production, decreases due to higher insulation rates. Because of this, investing in efficient and renewable heat generation becomes less interesting. Therefore, to incorporate renewables or residual heat on a larger scale, district heating or collective heating systems grow in importance. Within this set-up, the substation is responsible for the interaction between local demand for comfort and overall energy performance of the collective heating system. Many different configurations of substations exist, which influence both local comfort and central system performance. Next to that, also hybrids exist with additional local energy input. To evaluate performance of such substations, a new experimental-based test procedure is developed in order to evaluate these different aspects, characterized by the two roles a substation has, namely as heat generator and as heat consumer. The advantage of this approach is that an objective comparison between individual and central systems regarding performance on delivering local comfort can be executed experimentally. The lab set-up consists out of three different subsystems, namely the central system, the domestic hot water consumption and the local space heating. The central system can work with different temperature regimes and control strategies, as these aspects have proven to have the largest influence on actual performance. The domestic hot water system is able to generate similar tap profiles according to eco-design regulation for domestic hot water generation. The space heating system is able to demand a modular heat load.

Closed Conformal Killing-Yano Tensor and Uniqueness of Generalized Kerr-NUT-de Sitter Spacetime

NASA Astrophysics Data System (ADS)

Houri, Tsuyoshi

We classify all spacetimes with a rank-2 closed conformal Killing-Yano tensor. They give a generalization of Kerr-NUT-de Sitter spacetime. The Einstein condition is explicitly solved. The Kerr-NUT-de Sitter spacetime is obtained as a spacetime with a non-degenerate CKY tensor.

Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex

PubMed Central

Llácer, Jose L.; Hussain, Tanweer; Marler, Laura; Aitken, Colin Echeverría; Thakur, Anil; Lorsch, Jon R.; Hinnebusch, Alan G.; Ramakrishnan, V.

2015-01-01

Summary Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and eIF5. The PIC, in an open conformation, attaches to the 5′ end of the mRNA and scans to locate the start codon, whereupon it closes to arrest scanning. We present single particle cryo-electron microscopy (cryo-EM) reconstructions of 48S PICs from yeast in these open and closed states, at 6.0 Å and 4.9 Å, respectively. These reconstructions show eIF2β as well as a configuration of eIF3 that appears to encircle the 40S, occupying part of the subunit interface. Comparison of the complexes reveals a large conformational change in the 40S head from an open mRNA latch conformation to a closed one that constricts the mRNA entry channel and narrows the P site to enclose tRNAi, thus elucidating key events in start codon recognition. PMID:26212456

Parallel cascade selection molecular dynamics (PaCS-MD) to generate conformational transition pathway

NASA Astrophysics Data System (ADS)

Harada, Ryuhei; Kitao, Akio

2013-07-01

Parallel Cascade Selection Molecular Dynamics (PaCS-MD) is proposed as a molecular simulation method to generate conformational transition pathway under the condition that a set of "reactant" and "product" structures is known a priori. In PaCS-MD, the cycle of short multiple independent molecular dynamics simulations and selection of the structures close to the product structure for the next cycle are repeated until the simulated structures move sufficiently close to the product. Folding of 10-residue mini-protein chignolin from the extended to native structures and open-close conformational transition of T4 lysozyme were investigated by PaCS-MD. In both cases, tens of cycles of 100-ps MD were sufficient to reach the product structures, indicating the efficient generation of conformational transition pathway in PaCS-MD with a series of conventional MD without additional external biases. Using the snapshots along the pathway as the initial coordinates, free energy landscapes were calculated by the combination with multiple independent umbrella samplings to statistically elucidate the conformational transition pathways.

View west of load dispatch model board; section covers substations ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

View west of load dispatch model board; section covers substations from edgerly (right) to thorndale and west yard (left). Instruments at bottom of center board section formerly monitored energy usage and were replaced by a computerized monitoring system. - Thirtieth Street Station, Load Dispatch Center, Thirtieth & Market Streets, Railroad Station, Amtrak (formerly Pennsylvania Railroad Station), Philadelphia, Philadelphia County, PA

16. EXTERIOR NORTH END OF TULE RIVER POWERHOUSE SHOWING POWERHOUSE ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

16. EXTERIOR NORTH END OF TULE RIVER POWERHOUSE SHOWING POWERHOUSE AT PHOTO CENTER, SUBSTATION AT PHOTO RIGHT FOREGROUND, OFFICE BEHIND SUBSTATION AT RIGHT OF POWERHOUSE, AND MACHINE SHOP AT LEFT OF POWERHOUSE. THIS PHOTOGRAPH DUPLICATES HISTORIC VIEW SHOWN IN PHOTO CA-216-17. VIEW TO SOUTHEAST. - Tule River Hydroelectric Project, Water Conveyance System, Middle Fork Tule River, Springville, Tulare County, CA

Procedures and criteria for increasing the earthquake resistance level of electrical substations and special installations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Couch, R.W.; Deacon, R.J.

1973-09-30

This report defines a procedure and provides basic information needed to determine the modifications required to make electrical substations and special installations of the Bonneville Power Administration (BPA) more resistant to strong earthquake ground motion. It also provides a procedure for developing an effective plan for establishing the sequence, or priority, of providing the required modifications.

78 FR 70546 - Erie Boulevard Hydropower, L.P.; Notice of Application Accepted for Filing, Soliciting Motions To...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-26

... (kV) generator leads extending about 25 feet to an adjacent electrical substation containing a 2.4/4.8-kV, 600-kilovolt-amperes, step-up transformer bank. A transmission line owned and operated by... with the electrical grid at the substation. At the time the Commission issued the original license for...

Supplement Analysis for the Transmission System Vegetation Management Program FEIS (DOE/EIS-0285/SA-96) - Snohomish District Substations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hermeston, Mark W.

2002-07-19

Proposed Action: Vegetation Management for facilities located in the Snohomish District. BPA proposes total vegetation management (bareground) in the electrical substations, and, noxious weed management and maintenance of landscaping within the property boundaries of the listed facilities. These facilities are all located within the Snohomish District of the Snohomish Region.

Peptide Modulation of Class I Major Histocompatibility Complex Protein Molecular Flexibility and the Implications for Immune Recognition*

PubMed Central

Hawse, William F.; Gloor, Brian E.; Ayres, Cory M.; Kho, Kevin; Nuter, Elizabeth; Baker, Brian M.

2013-01-01

T cells use the αβ T cell receptor (TCR) to recognize antigenic peptides presented by class I major histocompatibility complex proteins (pMHCs) on the surfaces of antigen-presenting cells. Flexibility in both TCRs and peptides plays an important role in antigen recognition and discrimination. Less clear is the role of flexibility in the MHC protein; although recent observations have indicated that mobility in the MHC can impact TCR recognition in a peptide-dependent fashion, the extent of this behavior is unknown. Here, using hydrogen/deuterium exchange, fluorescence anisotropy, and structural analyses, we show that the flexibility of the peptide binding groove of the class I MHC protein HLA-A*0201 varies significantly with different peptides. The variations extend throughout the binding groove, impacting regions contacted by TCRs as well as other activating and inhibitory receptors of the immune system. Our results are consistent with statistical mechanical models of protein structure and dynamics, in which the binding of different peptides alters the populations and exchange kinetics of substates in the MHC conformational ensemble. Altered MHC flexibility will influence receptor engagement, impacting conformational adaptations, entropic penalties associated with receptor recognition, and the populations of binding-competent states. Our results highlight a previously unrecognized aspect of the “altered self” mechanism of immune recognition and have implications for specificity, cross-reactivity, and antigenicity in cellular immunity. PMID:23836912

Conformational transitions in DNA polymerase I revealed by single-molecule FRET

PubMed Central

Santoso, Yusdi; Joyce, Catherine M.; Potapova, Olga; Le Reste, Ludovic; Hohlbein, Johannes; Torella, Joseph P.; Grindley, Nigel D. F.; Kapanidis, Achillefs N.

2010-01-01

The remarkable fidelity of most DNA polymerases depends on a series of early steps in the reaction pathway which allow the selection of the correct nucleotide substrate, while excluding all incorrect ones, before the enzyme is committed to the chemical step of nucleotide incorporation. The conformational transitions that are involved in these early steps are detectable with a variety of fluorescence assays and include the fingers-closing transition that has been characterized in structural studies. Using DNA polymerase I (Klenow fragment) labeled with both donor and acceptor fluorophores, we have employed single-molecule fluorescence resonance energy transfer to study the polymerase conformational transitions that precede nucleotide addition. Our experiments clearly distinguish the open and closed conformations that predominate in Pol-DNA and Pol-DNA-dNTP complexes, respectively. By contrast, the unliganded polymerase shows a broad distribution of FRET values, indicating a high degree of conformational flexibility in the protein in the absence of its substrates; such flexibility was not anticipated on the basis of the available crystallographic structures. Real-time observation of conformational dynamics showed that most of the unliganded polymerase molecules sample the open and closed conformations in the millisecond timescale. Ternary complexes formed in the presence of mismatched dNTPs or complementary ribonucleotides show unique FRET species, which we suggest are relevant to kinetic checkpoints that discriminate against these incorrect substrates. PMID:20080740

Independent Power Generation in a Modern Electrical Substation Based on Thermoelectric Technology

NASA Astrophysics Data System (ADS)

Li, Z. M.; Zhao, Y. Q.; Liu, W.; Wei, B.; Qiu, M.; Lai, X. K.

2017-05-01

Because of many types of electrical equipment with high power in substations, the potentiality of energy conservation is quite large. From this viewpoint, thermoelectric materials may be chosen to produce electrical energy using the waste heat produced in substations. Hence, a thermoelectric generation system which can recycle the waste heat from electric transformers was proposed to improve the energy efficiency and reduce the burden of the oil cooling system. An experimental prototype was fabricated to perform the experiment and to verify the feasibility. The experimental results showed that the output power could achieve 16 W from waste heat of 900 W, and that the power conversion efficiency was approximately 1.8%. Therefore, power generation is feasible by using the waste heat from the transformers based on thermoelectric technology.

The arrestin-1 finger loop interacts with two distinct conformations of active rhodopsin.

PubMed

Elgeti, Matthias; Kazmin, Roman; Rose, Alexander S; Szczepek, Michal; Hildebrand, Peter W; Bartl, Franz J; Scheerer, Patrick; Hofmann, Klaus Peter

2018-03-23

Signaling of the prototypical G protein-coupled receptor (GPCR) rhodopsin through its cognate G protein transducin (G t ) is quenched when arrestin binds to the activated receptor. Although the overall architecture of the rhodopsin/arrestin complex is known, many questions regarding its specificity remain unresolved. Here, using FTIR difference spectroscopy and a dual pH/peptide titration assay, we show that rhodopsin maintains certain flexibility upon binding the "finger loop" of visual arrestin (prepared as synthetic peptide ArrFL-1). We found that two distinct complexes can be stabilized depending on the protonation state of E3.49 in the conserved (D)ERY motif. Both complexes exhibit different interaction modes and affinities of ArrFL-1 binding. The plasticity of the receptor within the rhodopsin/ArrFL-1 complex stands in contrast to the complex with the C terminus of the G t α-subunit (GαCT), which stabilizes only one specific substate out of the conformational ensemble. However, G t α-subunit binding and both ArrFL-1-binding modes involve a direct interaction to conserved R3.50, as determined by site-directed mutagenesis. Our findings highlight the importance of receptor conformational flexibility and cytoplasmic proton uptake for modulation of rhodopsin signaling and thereby extend the picture provided by crystal structures of the rhodopsin/arrestin and rhodopsin/ArrFL-1 complexes. Furthermore, the two binding modes of ArrFL-1 identified here involve motifs of conserved amino acids, which indicates that our results may have elucidated a common modulation mechanism of class A GPCR-G protein/-arrestin signaling. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Modulation of calmodulin plasticity by the effect of macromolecular crowding.

PubMed

Homouz, Dirar; Sanabria, Hugo; Waxham, M Neal; Cheung, Margaret S

2009-09-04

In vitro biochemical reactions are most often studied in dilute solution, a poor mimic of the intracellular space of eukaryotic cells, which are crowded with mobile and immobile macromolecules. Such crowded conditions exert volume exclusion and other entropic forces that have the potential to impact chemical equilibria and reaction rates. In this article, we used the well-characterized and ubiquitous molecule calmodulin (CaM) and a combination of theoretical and experimental approaches to address how crowding impacts CaM's conformational plasticity. CaM is a dumbbell-shaped molecule that contains four EF hands (two in the N-lobe and two in the C-lobe) that each could bind Ca(2+), leading to stabilization of certain substates that favor interactions with other target proteins. Using coarse-grained molecular simulations, we explored the distribution of CaM conformations in the presence of crowding agents. These predictions, in which crowding effects enhance the population of compact structures, were then confirmed in experimental measurements using fluorescence resonance energy transfer techniques of donor- and acceptor-labeled CaM under normal and crowded conditions. Using protein reconstruction methods, we further explored the folding-energy landscape and examined the structural characteristics of CaM at free-energy basins. We discovered that crowding stabilizes several different compact conformations, which reflects the inherent plasticity in CaM's structure. From these results, we suggest that the EF hands in the C-lobe are flexible and can be thought of as a switch, while those in the N-lobe are stiff, analogous to a rheostat. New combinatorial signaling properties may arise from the product of the differential plasticity of the two distinct lobes of CaM in the presence of crowding. We discuss the implications of these results for modulating CaM's ability to bind Ca(2+) and target proteins.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wurzburg, Beth A.; Kim, Beomkyu; Tarchevskaya, Svetlana S.

IgE antibodies interact with the high affinity IgE Fc receptor, FcϵRI, and activate inflammatory pathways associated with the allergic response. The IgE-Fc region, comprising the C-terminal domains of the IgE heavy chain, binds FcϵRI and can adopt different conformations ranging from a closed form incompatible with receptor binding to an open, receptor-bound state. A number of intermediate states are also observed in different IgE-Fc crystal forms. To further explore this apparent IgE-Fc conformational flexibility and to potentially trap a closed, inactive state, we generated a series of disulfide bond mutants. Here we describe the structure and biochemical properties of anmore » IgE-Fc mutant that is trapped in the closed, non-receptor binding state via an engineered disulfide at residue 335 (Cys-335). Reduction of the disulfide at Cys-335 restores the ability of IgE-Fc to bind to its high affinity receptor, FcϵRIα. The structure of the Cys-335 mutant shows that its conformation is within the range of previously observed, closed form IgE-Fc structures and that it retains the hydrophobic pocket found in the hinge region of the closed conformation. Locking the IgE-Fc into the closed state with the Cys-335 mutation does not affect binding of two other IgE-Fc ligands, omalizumab and DARPin E2_79, demonstrating selective blocking of the high affinity receptor binding.« less

Crossing symmetry in alpha space

NASA Astrophysics Data System (ADS)

Hogervorst, Matthijs; van Rees, Balt C.

2017-11-01

We initiate the study of the conformal bootstrap using Sturm-Liouville theory, specializing to four-point functions in one-dimensional CFTs. We do so by decomposing conformal correlators using a basis of eigenfunctions of the Casimir which are labeled by a complex number α. This leads to a systematic method for computing conformal block decompositions. Analyzing bootstrap equations in alpha space turns crossing symmetry into an eigenvalue problem for an integral operator K. The operator K is closely related to the Wilson transform, and some of its eigenfunctions can be found in closed form.

Quantifying side-chain conformational variations in protein structure

PubMed Central

Miao, Zhichao; Cao, Yang

2016-01-01

Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs. PMID:27845406

Quantifying side-chain conformational variations in protein structure

NASA Astrophysics Data System (ADS)

Miao, Zhichao; Cao, Yang

2016-11-01

Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs.

Quantifying side-chain conformational variations in protein structure.

PubMed

Miao, Zhichao; Cao, Yang

2016-11-15

Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs.

Molecular conformation of the full-length tumor suppressor NF2/Merlin—a small angle neutron scattering study

PubMed Central

Khajeh, Jahan Ali; Ju, Jeong Ho; Atchiba, Moussoubaou; Allaire, Marc; Stanley, Christopher; Heller, William T.; Callaway, David J.E.; Bu, Zimei

2014-01-01

Summary The tumor suppressor protein Merlin inhibits cell proliferation upon establishing cell-cell contacts. Because Merlin has high sequence similarity to the Ezrin-Radixin-Moesin (ERM) family of proteins, the structural model of ERM protein autoinhibition and cycling between closed/resting and open/active conformational states is often employed to explain Merlin function. However, recent biochemical studies suggest alternative molecular models of Merlin function. Here, we have determined the low resolution molecular structure and binding activity of Merlin and a Merlin(S518D) mutant that mimics the inactivating phosphorylation at S518 using small angle neutron scattering (SANS) and binding experiments. SANS shows that in solution both Merlin and Merlin(S518D) adopt a closed conformation, but binding experiments indicate that a significant fraction of either Merlin or Merlin(S518D) is capable of binding to the target protein NHERF1. Upon binding to the phosphatidylinositol 4,5-bisphosphate lipid, the wild-type Merlin adopts a more open conformation than in solution, but Merlin(S518D) remains in a closed conformation. This study supports a rheostat model of Merlin in NHERF1 binding, and contributes to resolve a controversy about the molecular conformation and binding activity of Merlin. PMID:24882693

78 FR 62348 - Erie Boulevard Hydropower L.P.; Notice of Application Tendered for Filing With the Commission and...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-18

... 100 feet; and (7) 2.4-kilovolt (kV) generator leads extending about 25 feet to an adjacent electrical substation containing a 2.4/4.8-kV, 600-kilovolt-amperes, step-up transformer bank. A transmission line owned... project interconnects with the electrical grid at the substation. At the time the Commission issued the...

Service Building No. 620. Detail of north elevation and entrance ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Service Building No. 620. Detail of north elevation and entrance to substation & windowns in top of elevator shafts no. 2 & stair no. 1 & section thru substation (dry dock associates, June 12, 1941). In files of Cushman & Wakefield, building 501, Philadelphia Naval Business Center. - Naval Base Philadelphia-Philadelphia Naval Shipyard, Service Building, Dry Docks No. 4 & 5, League Island, Philadelphia, Philadelphia County, PA

Design of a two-level power system linear state estimator

NASA Astrophysics Data System (ADS)

Yang, Tao

The availability of synchro-phasor data has raised the possibility of a linear state estimator if the inputs are only complex currents and voltages and if there are enough such measurements to meet observability and redundancy requirements. Moreover, the new digital substations can perform some of the computation at the substation itself resulting in a more accurate two-level state estimator. The objective of this research is to develop a two-level linear state estimator processing synchro-phasor data and estimating the states at both the substation level and the control center level. Both the mathematical algorithms that are different from those in the present state estimation procedure and the layered architecture of databases, communications and application programs that are required to support this two-level linear state estimator are described in this dissertation. Besides, as the availability of phasor measurements at substations will increase gradually, this research also describes how the state estimator can be enhanced to handle both the traditional state estimator and the proposed linear state estimator simultaneously. This provides a way to immediately utilize the benefits in those parts of the system where such phasor measurements become available and provides a pathway to transition to the smart grid of the future. The design procedure of the two-level state estimator is applied to two study systems. The first study system is the IEEE-14 bus system. The second one is the 179 bus Western Electricity Coordinating Council (WECC) system. The static database for the substations is constructed from the power flow data of these systems and the real-time measurement database is produced by a power system dynamic simulating tool (TSAT). Time-skew problems that may be caused by communication delays are also considered and simulated. We used the Network Simulator (NS) tool to simulate a simple communication system and analyse its time delay performance. These time delays were too small to affect the results especially since the measurement data is time-stamped and the state estimator for these small systems could be run with subseconf frequency. Keywords: State Estimation, Synchro-Phasor Measurement, Distributed System, Energy Control Center, Substation, Time-skew

Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.

PubMed

Burusco, Kepa K; Bruce, Neil J; Alibay, Irfan; Bryce, Richard A

2015-10-26

Free energy simulations are an established computational tool in modelling chemical change in the condensed phase. However, sampling of kinetically distinct substates remains a challenge to these approaches. As a route to addressing this, we link the methods of thermodynamic integration (TI) and swarm-enhanced sampling molecular dynamics (sesMD), where simulation replicas interact cooperatively to aid transitions over energy barriers. We illustrate the approach by using alchemical alkane transformations in solution, comparing them with the multiple independent trajectory TI (IT-TI) method. Free energy changes for transitions computed by using IT-TI grew increasingly inaccurate as the intramolecular barrier was heightened. By contrast, swarm-enhanced sampling TI (sesTI) calculations showed clear improvements in sampling efficiency, leading to more accurate computed free energy differences, even in the case of the highest barrier height. The sesTI approach, therefore, has potential in addressing chemical change in systems where conformations exist in slow exchange. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop.

PubMed

Borkar, Aditi N; Vallurupalli, Pramodh; Camilloni, Carlo; Kay, Lewis E; Vendruscolo, Michele

2017-01-25

RNA molecules in solution tend to undergo structural fluctuations of relatively large amplitude and to populate a range of different conformations some of which with low populations. It is still very challenging, however, to characterise the structures of these low populated states and to understand their functional roles. In the present study, we address this problem by using NMR residual dipolar couplings (RDCs) as structural restraints in replica-averaged metadynamics (RAM) simulations. By applying this approach to a 14-mer RNA hairpin containing the prototypical UUCG tetraloop motif, we show that it is possible to construct the free energy landscape of this RNA molecule. This free energy landscapes reveals the surprisingly rich dynamics of the UUCG tetraloop and identifies the multiple substates that exist in equilibrium owing to thermal fluctuations. The approach that we present is general and can be applied to the study of the free energy landscapes of other RNA or RNA-protein systems.

Structural Basis for Catalytic Activation of a Serine Recombinase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keenholtz, Ross A.; Rowland, Sally-J.; Boocock, Martin R.

2014-10-02

Sin resolvase is a site-specific serine recombinase that is normally controlled by a complex regulatory mechanism. A single mutation, Q115R, allows the enzyme to bypass the entire regulatory apparatus, such that no accessory proteins or DNA sites are required. Here, we present a 1.86 {angstrom} crystal structure of the Sin Q115R catalytic domain, in a tetrameric arrangement stabilized by an interaction between Arg115 residues on neighboring subunits. The subunits have undergone significant conformational changes from the inactive dimeric state previously reported. The structure provides a new high-resolution view of a serine recombinase active site that is apparently fully assembled, suggestingmore » roles for the conserved active site residues. The structure also suggests how the dimer-tetramer transition is coupled to assembly of the active site. The tetramer is captured in a different rotational substate than that seen in previous hyperactive serine recombinase structures, and unbroken crossover site DNA can be readily modeled into its active sites.« less

Ligand binding turns moth pheromone-binding protein into a pH sensor: effect on the Antheraea polyphemus PBP1 conformation.

PubMed

Katre, Uma V; Mazumder, Suman; Prusti, Rabi K; Mohanty, Smita

2009-11-13

In moths, pheromone-binding proteins (PBPs) are responsible for the transport of the hydrophobic pheromones to the membrane-bound receptors across the aqueous sensillar lymph. We report here that recombinant Antheraea polyphemus PBP1 (ApolPBP1) picks up hydrophobic molecule(s) endogenous to the Escherichia coli expression host that keeps the protein in the "open" (bound) conformation at high pH but switches to the "closed" (free) conformation at low pH. This finding has bearing on the solution structures of undelipidated lepidopteran moth PBPs determined thus far. Picking up a hydrophobic molecule from the host expression system could be a common feature for lipid-binding proteins. Thus, delipidation is critical for bacterially expressed lipid-binding proteins. We have shown for the first time that the delipidated ApolPBP1 exists primarily in the closed form at all pH levels. Thus, current views on the pH-induced conformational switch of PBPs hold true only for the ligand-bound open conformation of the protein. Binding of various ligands to delipidated ApolPBP1 studied by solution NMR revealed that the protein in the closed conformation switches to the open conformation only at or above pH 6.0 with a protein to ligand stoichiometry of approximately 1:1. Mutation of His(70) and His(95) to alanine drives the equilibrium toward the open conformation even at low pH for the ligand-bound protein by eliminating the histidine-dependent pH-induced conformational switch. Thus, the delipidated double mutant can bind ligand even at low pH in contrast to the wild type protein as revealed by fluorescence competitive displacement assay using 1-aminoanthracene and solution NMR.

Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case

PubMed Central

Li, Dechang; Liu, Ming S.; Ji, Baohua

2015-01-01

Conformational transition describes the essential dynamics and mechanism of enzymes in pursuing their various functions. The fundamental and practical challenge to researchers is to quantitatively describe the roles of large-scale dynamic transitions for regulating the catalytic processes. In this study, we tackled this challenge by exploring the pathways and free energy landscape of conformational changes in adenylate kinase (AdK), a key ubiquitous enzyme for cellular energy homeostasis. Using explicit long-timescale (up to microseconds) molecular dynamics and bias-exchange metadynamics simulations, we determined at the atomistic level the intermediate conformational states and mapped the transition pathways of AdK in the presence and absence of ligands. There is clearly chronological operation of the functional domains of AdK. Specifically in the ligand-free AdK, there is no significant energy barrier in the free energy landscape separating the open and closed states. Instead there are multiple intermediate conformational states, which facilitate the rapid transitions of AdK. In the ligand-bound AdK, the closed conformation is energetically most favored with a large energy barrier to open it up, and the conformational population prefers to shift to the closed form coupled with transitions. The results suggest a perspective for a hybrid of conformational selection and induced fit operations of ligand binding to AdK. These observations, depicted in the most comprehensive and quantitative way to date, to our knowledge, emphasize the underlying intrinsic dynamics of AdK and reveal the sophisticated conformational transitions of AdK in fulfilling its enzymatic functions. The developed methodology can also apply to other proteins and biomolecular systems. PMID:26244746

Hazard zoning around electric substations of petrochemical industries by stimulation of extremely low-frequency magnetic fields.

PubMed

Hosseini, Monireh; Monazzam, Mohammad Reza; Farhang Matin, Laleh; Khosroabadi, Hossein

2015-05-01

Electromagnetic fields in recent years have been discussed as one of the occupational hazards at workplaces. Hence, control and assessment of these physical factors is very important to protect and promote the health of employees. The present study was conducted to determine hazard zones based on assessment of extremely low-frequency magnetic fields at electric substations of a petrochemical complex in southern Iran, using the single-axis HI-3604 device. In measurement of electromagnetic fields by the single-axis HI-3604 device, the sensor screen should be oriented in a way to be perpendicular to the field lines. Therefore, in places where power lines are located in different directions, it is required to keep the device towards three axes of x, y, and z. For further precision, the measurements should be repeated along each of the three axes. In this research, magnetic field was measured, for the first time, in three axes of x, y, and z whose resultant value was considered as the value of magnetic field. Measurements were done based on IEEE std 644-1994. Further, the spatial changes of the magnetic field surrounding electric substations were stimulated using MATLAB software. The obtained results indicated that the maximum magnetic flux density was 49.90 μT recorded from boiler substation, while the minimum magnetic flux density of 0.02 μT was measured at the control room of the complex. As the stimulation results suggest, the spaces around incoming panels, transformers, and cables were recognized as hazardous zones of indoor electric substations. Considering the health effects of chronic exposure to magnetic fields, it would be possible to minimize exposure to these contaminants at workplaces by identification of risky zones and observation of protective considerations.

The spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase β

PubMed Central

Koag, Myong-Chul; Nam, Kwangho; Lee, Seongmin

2014-01-01

To provide molecular-level insights into the spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase β (polβ), we report four crystal structures of polβ complexed with dG•dTTP and dA•dCTP mismatches in the presence of Mg2+ or Mn2+. The Mg2+-bound ground-state structures show that the dA•dCTP-Mg2+ complex adopts an ‘intermediate’ protein conformation while the dG•dTTP-Mg2+ complex adopts an open protein conformation. The Mn2+-bound ‘pre-chemistry-state’ structures show that the dA•dCTP-Mn2+ complex is structurally very similar to the dA•dCTP-Mg2+ complex, whereas the dG•dTTP-Mn2+ complex undergoes a large-scale conformational change to adopt a Watson–Crick-like dG•dTTP base pair and a closed protein conformation. These structural differences, together with our molecular dynamics simulation studies, suggest that polβ increases replication fidelity via a two-stage mismatch discrimination mechanism, where one is in the ground state and the other in the closed conformation state. In the closed conformation state, polβ appears to allow only a Watson–Crick-like conformation for purine•pyrimidine base pairs, thereby discriminating the mismatched base pairs based on their ability to form the Watson–Crick-like conformation. Overall, the present studies provide new insights into the spontaneous replication error and the replication fidelity mechanisms of polβ. PMID:25200079

Analysis of the Isolated SecA DEAD Motor Suggests a Mechanism for Chemical-Mechanical Coupling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nithianantham, Stanley; Shilton, Brian H

The preprotein cross-linking domain and C-terminal domains of Escherichia coli SecA were removed to create a minimal DEAD motor, SecA-DM. SecA-DM hydrolyzes ATP and has the same affinity for ADP as full-length SecA. The crystal structure of SecA-DM in complex with ADP was solved and shows the DEAD motor in a closed conformation. Comparison with the structure of the E. coli DEAD motor in an open conformation (Protein Data Bank ID 2FSI) indicates main-chain conformational changes in two critical sequences corresponding to Motif III and Motif V of the DEAD helicase family. The structures that the Motif III and Motifmore » V sequences adopt in the DEAD motor open conformation are incompatible with the closed conformation. Therefore, when the DEAD motor makes the transition from open to closed, Motif III and Motif V are forced to change their conformations, which likely functions to regulate passage through the transition state for ATP hydrolysis. The transition state for ATP hydrolysis for the SecA DEAD motor was modeled based on the conformation of the Vasa helicase in complex with adenylyl imidodiphosphate and RNA (Protein Data Bank ID 2DB3). A mechanism for chemical-mechanical coupling emerges, where passage through the transition state for ATP hydrolysis is hindered by the conformational changes required in Motif III and Motif V, and may be promoted by binding interactions with the preprotein substrate and/or other translocase domains and subunits.« less

Analysis of the Isolated SecA DEAD Motor Suggests a Mechanism for Chemical-Mechanical Coupling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nithianantham, Stanley; Shilton, Brian H

2011-09-28

The preprotein cross-linking domain and C-terminal domains of Escherichia coli SecA were removed to create a minimal DEAD motor, SecA-DM. SecA-DM hydrolyzes ATP and has the same affinity for ADP as full-length SecA. The crystal structure of SecA-DM in complex with ADP was solved and shows the DEAD motor in a closed conformation. Comparison with the structure of the E. coli DEAD motor in an open conformation (Protein Data Bank ID 2FSI) indicates main-chain conformational changes in two critical sequences corresponding to Motif III and Motif V of the DEAD helicase family. The structures that the Motif III and Motifmore » V sequences adopt in the DEAD motor open conformation are incompatible with the closed conformation. Therefore, when the DEAD motor makes the transition from open to closed, Motif III and Motif V are forced to change their conformations, which likely functions to regulate passage through the transition state for ATP hydrolysis. The transition state for ATP hydrolysis for the SecA DEAD motor was modeled based on the conformation of the Vasa helicase in complex with adenylyl imidodiphosphate and RNA (Protein Data Bank ID 2DB3). A mechanism for chemical-mechanical coupling emerges, where passage through the transition state for ATP hydrolysis is hindered by the conformational changes required in Motif III and Motif V, and may be promoted by binding interactions with the preprotein substrate and/or other translocase domains and subunits.« less

Conformal Nets II: Conformal Blocks

NASA Astrophysics Data System (ADS)

Bartels, Arthur; Douglas, Christopher L.; Henriques, André

2017-08-01

Conformal nets provide a mathematical formalism for conformal field theory. Associated to a conformal net with finite index, we give a construction of the `bundle of conformal blocks', a representation of the mapping class groupoid of closed topological surfaces into the category of finite-dimensional projective Hilbert spaces. We also construct infinite-dimensional spaces of conformal blocks for topological surfaces with smooth boundary. We prove that the conformal blocks satisfy a factorization formula for gluing surfaces along circles, and an analogous formula for gluing surfaces along intervals. We use this interval factorization property to give a new proof of the modularity of the category of representations of a conformal net.

Conformational states of the full-length glucagon receptor

PubMed Central

Yang, Linlin; Yang, Dehua; de Graaf, Chris; Moeller, Arne; West, Graham M.; Dharmarajan, Venkatasubramanian; Wang, Chong; Siu, Fai Y.; Song, Gaojie; Reedtz-Runge, Steffen; Pascal, Bruce D.; Wu, Beili; Potter, Clinton S.; Zhou, Hu; Griffin, Patrick R.; Carragher, Bridget; Yang, Huaiyu; Wang, Ming-Wei; Stevens, Raymond C.; Jiang, Hualiang

2015-01-01

Class B G protein-coupled receptors are composed of an extracellular domain (ECD) and a seven-transmembrane (7TM) domain, and their signalling is regulated by peptide hormones. Using a hybrid structural biology approach together with the ECD and 7TM domain crystal structures of the glucagon receptor (GCGR), we examine the relationship between full-length receptor conformation and peptide ligand binding. Molecular dynamics (MD) and disulfide crosslinking studies suggest that apo-GCGR can adopt both an open and closed conformation associated with extensive contacts between the ECD and 7TM domain. The electron microscopy (EM) map of the full-length GCGR shows how a monoclonal antibody stabilizes the ECD and 7TM domain in an elongated conformation. Hydrogen/deuterium exchange (HDX) studies and MD simulations indicate that an open conformation is also stabilized by peptide ligand binding. The combined studies reveal the open/closed states of GCGR and suggest that glucagon binds to GCGR by a conformational selection mechanism. PMID:26227798

Inter and intra substation communications: Requirements and solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adamiak, M.; Patterson, R.; Melcher, J.

1995-10-01

As the substation communication world searches for the ``Promised LAN,`` it would be helpful to have a roadmap to give direction to the search. Many are the expectations of a LAN flowing with data and able to connect with any Intelligent Electronic Device (IED) that was ever made. Such expectations must be tempered with the cost and complexity of achieving them. This paper presents an outline of the communication requirements of the myriad of IED`s in existence in the substation today as well as the expectations of what second generation microprocessor based devices might be able to do. Requirements willmore » focus on language issues, system capabilities, performance requirements, external interfaces, environmental, and quality issues. Some attention will also be given to the architecture of a solution and some guidelines as to how this structure might be built.« less

Autonomous navigation method for substation inspection robot based on travelling deviation

NASA Astrophysics Data System (ADS)

Yang, Guoqing; Xu, Wei; Li, Jian; Fu, Chongguang; Zhou, Hao; Zhang, Chuanyou; Shao, Guangting

2017-06-01

A new method of edge detection is proposed in substation environment, which can realize the autonomous navigation of the substation inspection robot. First of all, the road image and information are obtained by using an image acquisition device. Secondly, the noise in the region of interest which is selected in the road image, is removed with the digital image processing algorithm, the road edge is extracted by Canny operator, and the road boundaries are extracted by Hough transform. Finally, the distance between the robot and the left and the right boundaries is calculated, and the travelling distance is obtained. The robot's walking route is controlled according to the travel deviation and the preset threshold. Experimental results show that the proposed method can detect the road area in real time, and the algorithm has high accuracy and stable performance.

Energy Saving in DC Electric Railways by Battery Substation

NASA Astrophysics Data System (ADS)

Sugimoto, Takeshi

New rolling vehicles used in dc electric railways are of the regenerative type. At less busy time a part of regenerative power is not used for powering vehicles, and canceled by changed air brake. Recently, significant attention has been paid to the development of secondary batteries for hybrid and electric motorcars. The use of this battery enables reduction in electric power consumption. Because we can charge excess regenerative power and use for powering vehicles after. Before the fact we compared the actual and simulated effective coefficient of regenerative energy, we confirmed the suitability of the simulation model. In this simulation, we studied the energy-saving effect of the battery substations and determined the battery capacity at which maximum power saving is achieved. We found that the power consumption could be reduced remarkably by using a 15-20kWh battery substation.

Concerted Dynamic Motions of an FABP4 Model and Its Ligands Revealed by Microsecond Molecular Dynamics Simulations

PubMed Central

2015-01-01

In this work, we investigate the dynamic motions of fatty acid binding protein 4 (FABP4) in the absence and presence of a ligand by explicitly solvated all-atom molecular dynamics simulations. The dynamics of one ligand-free FABP4 and four ligand-bound FABP4s is compared via multiple 1.2 μs simulations. In our simulations, the protein interconverts between the open and closed states. Ligand-free FABP4 prefers the closed state, whereas ligand binding induces a conformational transition to the open state. Coupled with opening and closing of FABP4, the ligand adopts distinct binding modes, which are identified and compared with crystal structures. The concerted dynamics of protein and ligand suggests that there may exist multiple FABP4–ligand binding conformations. Thus, this work provides details about how ligand binding affects the conformational preference of FABP4 and how ligand binding is coupled with a conformational change of FABP4 at an atomic level. PMID:25231537

Concerted dynamic motions of an FABP4 model and its ligands revealed by microsecond molecular dynamics simulations.

PubMed

Li, Yan; Li, Xiang; Dong, Zigang

2014-10-14

In this work, we investigate the dynamic motions of fatty acid binding protein 4 (FABP4) in the absence and presence of a ligand by explicitly solvated all-atom molecular dynamics simulations. The dynamics of one ligand-free FABP4 and four ligand-bound FABP4s is compared via multiple 1.2 μs simulations. In our simulations, the protein interconverts between the open and closed states. Ligand-free FABP4 prefers the closed state, whereas ligand binding induces a conformational transition to the open state. Coupled with opening and closing of FABP4, the ligand adopts distinct binding modes, which are identified and compared with crystal structures. The concerted dynamics of protein and ligand suggests that there may exist multiple FABP4-ligand binding conformations. Thus, this work provides details about how ligand binding affects the conformational preference of FABP4 and how ligand binding is coupled with a conformational change of FABP4 at an atomic level.

Trapping a 96° domain rotation in two distinct conformations by engineered disulfide bridges

PubMed Central

Schultz-Heienbrok, Robert; Maier, Timm; Sträter, Norbert

2004-01-01

Engineering disulfide bridges is a common technique to lock a protein movement in a defined conformational state. We have designed two double mutants of Escherichia coli 5′-nucleotidase to trap the enzyme in both an open (S228C, P513C) and a closed (P90C, L424C) conformation by the formation of disulfide bridges. The mutant proteins have been expressed, purified, and crystallized, to structurally characterize the designed variants. The S228C, P513C is a double mutant crystallized in two different crystal forms with three independent conformers, which differ from each other by a rotation of up to 12° of the C-terminal domain with respect to the N-terminal domain. This finding, as well as an analysis of the domain motion in the crystal, indicates that the enzyme still exhibits considerable residual domain flexibility. In the double mutant that was designed to trap the enzyme in the closed conformation, the structure analysis reveals an unexpected intermediate conformation along the 96° rotation trajectory between the open and closed enzyme forms. A comparison of the five independent conformers analyzed in this study shows that the domain movement of the variant enzymes is characterized by a sliding movement of the residues of the domain interface along the interface, which is in contrast to a classical closure motion where the residues of the domain interface move perpendicular to the interface. PMID:15215524

Aluminum and its effect in the equilibrium between folded/unfolded conformation of NADH.

PubMed

Formoso, Elena; Mujika, Jon I; Grabowski, Slawomir J; Lopez, Xabier

2015-11-01

Nicotinamide adenine dinucleotide (NADH) is one of the most abundant cofactor employed by proteins and enzymes. The molecule is formed by two nucleotides that can lead to two main conformations: folded/closed and unfolded/open. Experimentally, it has been determined that the closed form is about 2 kcal/mol more stable than the open formed. Computationally, a correct description of the NADH unfolding process is challenging due to different reasons: 1) The unfolding process shows a very low energy difference between the two conformations 2) The molecule can form a high number of internal hydrogen bond interactions 3) Subtle effects such as dispersion may be important. In order to tackle all these effects, we have employed a number of different state of the art computational techniques, including: a) well-tempered metadynamics, b) geometry optimizations, and c) Quantum Theory of Atoms in Molecules (QTAIM) calculations, to investigate the conformational change of NADH in solution and interacting with aluminum. All the results indicate that aluminum indeed favors the closed conformation of NADH, due mainly to the formation of a more rigid structure through key hydrogen bond interactions. Copyright © 2015 Elsevier Inc. All rights reserved.

Illuminating the Mechanistic Roles of Enzyme Conformational Dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hanson, Jeffrey A.; Dunderstadt, Karl; Watkins, Lucas P.

2007-11-13

Many enzymes mold their structures to enclose substrates in their active sites such that conformational remodeling may be required during each catalytic cycle. In adenylate kinase (AK), this involves a large-amplitude rearrangement of the enzyme’s lid domain. Using our method of high-resolution single-molecule FRET, we directly followed AK’s domain movements on its catalytic time scale. To quantitatively measure the enzyme’s entire conformational distribution, we have applied maximum entropy-based methods to remove photon-counting noise from single-molecule data. This analysis shows unambiguously that AK is capable of dynamically sampling two distinct states, which correlate well with those observed by x-ray crystallography. Unexpectedly,more » the equilibrium favors the closed, active-site-forming configurations even in the absence of substrates. Our experiments further showed that interaction with substrates, rather than locking the enzyme into a compact state, restricts the spatial extent of conformational fluctuations and shifts the enzyme’s conformational equilibrium toward the closed form by increasing the closing rate of the lid. Integrating these microscopic dynamics into macroscopic kinetics allows us to model lid opening-coupled product release as the enzyme’s rate-limiting step.« less

USSR and Eastern Europe Scientific Abstracts, Cybernetics, Computers and Automation Technology, Number 31

DTIC Science & Technology

1978-02-09

incorporation of subsystems and tasks into systems are specified by state and industrial- sector standards. However, such rigid requirements interfere...construction of the step-down substation, without which the new sector is inoperable. The question of who will build the substation is still unresolved... economico -mathematical evaluation). Among such applications, program decks completed by the "Soyuzsistemprom" are those for data integra- tion and

New model of inverting substation for DC traction with regenerative braking system

NASA Astrophysics Data System (ADS)

Omar, Abdul Malek Saidina; Samat, Ahmad Asri Abd; Isa, Siti Sarah Mat; Shamsuddin, Sarah Addyani; Jamaludin, Nur Fadhilah; Khyasudeen, Muhammad Farris

2017-08-01

This paper presents a power electronic devices application focus on modeling, analysis, and control of switching power converter in the inverting DC substation with regenerative braking system which is used to recycle the surplus regenerative power by feed it back to the main AC grid. The main objective of this research is to improve the switching power electronic converter of the railway inverting substation and optimize the maximum kinetic energy recovery together with minimum power losses from the railway braking system. Assess performance including efficiency and robustness will be evaluated in order to get the best solution for the design configuration. Research methodology included mathematical calculation, simulation, and detail analysis on modeling of switching power converter on inverting substation. The design stage separates to four main areas include rectification mode, regenerative mode, control inverter mode and filtering mode. The simulation result has shown that the regenerative inverter has a capability to accept a maximum recovery power on the regeneration mode. Total energy recovery has increase and power losses have decreases because inverter abilities to transfer the surplus energy back to the main AC supply. An Inverter controller with PWM Generator and PI Voltage Regulator has been designed to control voltage magnitude and frequency of the DC traction system.

A comparative study of electric load curve changes in an urban low-voltage substation in Spain during the economic crisis (2008-2013).

PubMed

Lara-Santillán, Pedro M; Mendoza-Villena, Montserrat; Fernández-Jiménez, L Alfredo; Mañana-Canteli, Mario

2014-01-01

This paper presents a comparative study of the electricity consumption (EC) in an urban low-voltage substation before and during the economic crisis (2008-2013). This low-voltage substation supplies electric power to near 400 users. The EC was measured for an 11-year period (2002-2012) with a sampling time of 1 minute. The study described in the paper consists of detecting the changes produced in the load curves of this substation along the time due to changes in the behaviour of consumers. The EC was compared using representative curves per time period (precrisis and crisis). These representative curves were obtained after a computational process, which was based on a search for days with similar curves to the curve of a determined (base) date. This similitude was assessed by the proximity on the calendar, day of the week, daylight time, and outdoor temperature. The last selection parameter was the error between the nearest neighbour curves and the base date curve. The obtained representative curves were linearized to determine changes in their structure (maximum and minimum consumption values, duration of the daily time slot, etc.). The results primarily indicate an increase in the EC in the night slot during the summer months in the crisis period.

Draft Supplement to the Environmental Statement Fiscal Year 1976 Proposed Program : Facilty Location Evaluation for Franklin-Badger Canyon 230-kV Line and Badger Canyon Substation Study Area 74-6B.

DOE Office of Scientific and Technical Information (OSTI.GOV)

United States. Bonneville Power Administration.

1974-10-22

Proposed is the construction of a 15-mile, 230-kV double-circuit transmission line from Franklin Substation near Pasco, Washington, to a proposed new Badger Canyon Substation to be constructed 5 miles west of Kennewick, Washington. Depending on the final route location chosen, approximately 15 miles of 230-kV double circuit transmission line requiring 5.6 miles of new and 9.4 miles of existing right-of-way would be needed as well as approximately 2500 feet of new access road. Land use affected includes crossing Sacajawea State Park and passig through irrigated cropland and grassland on existing right-of-way, and depending on the alternative route chosen, could crossmore » land proposed for residential development and a proposed interstate highway. An additional 10 to 11 acres of potential cropland would be required for the proposed substation. Disturbance to wildlife during construction would occur and habitat associated with the above land uses would be eliminated. Some erosion and sedimentation would occur. Visual impacts would affect Sacajawea State Park, a proposed highway, and potential residential development land. Noise and other disturbances to residents will occur, primarily during construction.« less

Toward elucidating the heat activation mechanism of the TRPV1 channel gating by molecular dynamics simulation

PubMed Central

Wen, Han; Qin, Feng; Zheng, Wenjun

2016-01-01

As a key cellular sensor, the TRPV1 cation channel undergoes a gating transition from a closed state to an open state in response to various physical and chemical stimuli including noxious heat. Despite years of study, the heat activation mechanism of TRPV1 gating remains enigmatic at the molecular level. Toward elucidating the structural and energetic basis of TRPV1 gating, we have performed molecular dynamics (MD) simulations (with cumulative simulation time of 3 μs), starting from the high-resolution closed and open structures of TRPV1 solved by cryo-electron microscopy. In the closed-state simulations at 30°C, we observed a stably closed channel constricted at the lower gate (near residue I679), while the upper gate (near residues G643 and M644) is dynamic and undergoes flickery opening/closing. In the open-state simulations at 60°C, we found higher conformational variation consistent with a large entropy increase required for the heat activation, and both the lower and upper gates are dynamic with transient opening/closing. Through ensemble-based structural analyses of the closed state vs. the open state, we revealed pronounced closed-to-open conformational changes involving the membrane proximal domain (MPD) linker, the outer pore, and the TRP helix, which are accompanied by breaking/forming of a network of closed/open-state specific hydrogen bonds. By comparing the closed-state simulations at 30°C and 60°C, we observed heat-activated conformational changes in the MPD linker, the outer pore, and the TRP helix that resemble the closed-to-open conformational changes, along with partial formation of the open-state specific hydrogen bonds. Some of the residues involved in the above key hydrogen bonds were validated by previous mutational studies. Taken together, our MD simulations have offered rich structural and dynamic details beyond the static structures of TRPV1, and promising targets for future mutagenesis and functional studies of the TRPV1 channel. PMID:27699868

Models of Voltage-Dependent Conformational Changes in NaChBac Channels

PubMed Central

Shafrir, Yinon; Durell, Stewart R.; Guy, H. Robert

2008-01-01

Models of the transmembrane region of the NaChBac channel were developed in two open/inactivated and several closed conformations. Homology models of NaChBac were developed using crystal structures of Kv1.2 and a Kv1.2/2.1 chimera as templates for open conformations, and MlotiK and KcsA channels as templates for closed conformations. Multiple molecular-dynamic simulations were performed to refine and evaluate these models. A striking difference between the S4 structures of the Kv1.2-like open models and MlotiK-like closed models is the secondary structure. In the open model, the first part of S4 forms an α-helix, and the last part forms a 310 helix, whereas in the closed model, the first part of S4 forms a 310 helix, and the last part forms an α-helix. A conformational change that involves this type of transition in secondary structure should be voltage-dependent. However, this transition alone is not sufficient to account for the large gating charge movement reported for NaChBac channels and for experimental results in other voltage-gated channels. To increase the magnitude of the motion of S4, we developed another model of an open/inactivated conformation, in which S4 is displaced farther outward, and a number of closed models in which S4 is displaced farther inward. A helical screw motion for the α-helical part of S4 and a simple axial translation for the 310 portion were used to develop models of these additional conformations. In our models, four positively charged residues of S4 moved outwardly during activation, across a transition barrier formed by highly conserved hydrophobic residues on S1, S2, and S3. The S4 movement was coupled to an opening of the activation gate formed by S6 through interactions with the segment linking S4 to S5. Consistencies of our models with experimental studies of NaChBac and Kv channels are discussed. PMID:18641074

X-ray Crystal Structure of Aristolochene Synthase from Aspergillus terreus and Evolution of Templates for the Cyclization of Farnesyl Diphosphate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shishova,E.; Di Costanzo, L.; Cane, D.

2007-01-01

Aristolochene synthase from Aspergillus terreus catalyzes the cyclization of the universal sesquiterpene precursor, farnesyl diphosphate, to form the bicyclic hydrocarbon aristolochene. The 2.2 {angstrom} resolution X-ray crystal structure of aristolochene synthase reveals a tetrameric quaternary structure in which each subunit adopts the {alpha}-helical class I terpene synthase fold with the active site in the 'open', solvent-exposed conformation. Intriguingly, the 2.15 {angstrom} resolution crystal structure of the complex with Mg{sup 2+}{sub 3}-pyrophosphate reveals ligand binding only to tetramer subunit D, which is stabilized in the 'closed' conformation required for catalysis. Tetramer assembly may hinder conformational changes required for the transition frommore » the inactive open conformation to the active closed conformation, thereby accounting for the attenuation of catalytic activity with an increase in enzyme concentration. In both conformations, but especially in the closed conformation, the active site contour is highly complementary in shape to that of aristolochene, and a catalytic function is proposed for the pyrophosphate anion based on its orientation with regard to the presumed binding mode of aristolochene. A similar active site contour is conserved in aristolochene synthase from Penicillium roqueforti despite the substantial divergent evolution of these two enzymes, while strikingly different active site contours are found in the sesquiterpene cyclases 5-epi-aristolochene synthase and trichodiene synthase. Thus, the terpenoid cyclase active site plays a critical role as a template in binding the flexible polyisoprenoid substrate in the proper conformation for catalysis. Across the greater family of terpenoid cyclases, this template is highly evolvable within a conserved {alpha}-helical fold for the synthesis of terpene natural products of diverse structure and stereochemistry.« less

Kinematic analysis and simulation of a substation inspection robot guided by magnetic sensor

NASA Astrophysics Data System (ADS)

Xiao, Peng; Luan, Yiqing; Wang, Haipeng; Li, Li; Li, Jianxiang

2017-01-01

In order to improve the performance of the magnetic navigation system used by substation inspection robot, the kinematic characteristics is analyzed based on a simplified magnetic guiding system model, and then the simulation process is executed to verify the reasonability of the whole analysis procedure. Finally, some suggestions are extracted out, which will be helpful to guide the design of the inspection robot system in the future.

20 CFR 645.210 - What is meant by the terms “entity” and “project” in the statutory phrase “an entity that...

Code of Federal Regulations, 2012 CFR

2012-04-01

... a project”, means: (a) For WtW substate formula funds: (1) “Entity” means the PIC, local board (or... to § 645.400 of this part) which administers the WtW substate formula funds in a local area(s). This... formula funds allotted to the entity described in section (a)(1) of this paragraph. (b) For WtW Governors...

20 CFR 645.210 - What is meant by the terms “entity” and “project” in the statutory phrase “an entity that...

Code of Federal Regulations, 2014 CFR

2014-04-01

... a project”, means: (a) For WtW substate formula funds: (1) “Entity” means the PIC, local board (or... to § 645.400 of this part) which administers the WtW substate formula funds in a local area(s). This... formula funds allotted to the entity described in section (a)(1) of this paragraph. (b) For WtW Governors...

Supplemental Environmental Assessment: Lighthouse Substation Cape Canaveral Air Force Station Florida

DTIC Science & Technology

2007-10-01

associated with transmission lines is generally due to either corona or “spark gap” discharges. When the electric field at the surface of a conductor... corona , will be initiated from the conductor into the Chapter 3: Affected Environment Supplemental Environmental Assessment – Lighthouse Substation at...Cape Canaveral Air Force Station 24 surrounding air. The intensity of the corona increases with the voltage of the line and is dependent on the

Two-way communication and analysis program on LANDSAT

NASA Technical Reports Server (NTRS)

1983-01-01

Community workshops, field visits, telephone surveys, and other research reveals that professionals at the substate level are interested in and open to consideration of LANDSAT as a planning and resource management tool, but are at the same time skeptical about some of the inherent problems with LANDSAT such as cost, resolution, frequency of coverage, and data continuity. The principal requirements for increasing the utilization of LANDSAT by potential substate users were identified and documented. Without a committment from the Federal Government for increased substrate utilization and the availability of trained professionals to meet the needs of a largely new user community, substrate activity is likely to remain at a minimum. Well conceived and well executed demonstration projects could play a critical role is shaping the technology's ability to be more sensitive to substate user needs and interests as well as validating the effectiveness of this data to a skeptical audience.

Design of online monitoring and forecasting system for electrical equipment temperature of prefabricated substation based on WSN

NASA Astrophysics Data System (ADS)

Qi, Weiran; Miao, Hongxia; Miao, Xuejiao; Xiao, Xuanxuan; Yan, Kuo

2016-10-01

In order to ensure the safe and stable operation of the prefabricated substations, temperature sensing subsystem, temperature remote monitoring and management subsystem, forecast subsystem are designed in the paper. Wireless temperature sensing subsystem which consists of temperature sensor and MCU sends the electrical equipment temperature to the remote monitoring center by wireless sensor network. Remote monitoring center can realize the remote monitoring and prediction by monitoring and management subsystem and forecast subsystem. Real-time monitoring of power equipment temperature, history inquiry database, user management, password settings, etc., were achieved by monitoring and management subsystem. In temperature forecast subsystem, firstly, the chaos of the temperature data was verified and phase space is reconstructed. Then Support Vector Machine - Particle Swarm Optimization (SVM-PSO) was used to predict the temperature of the power equipment in prefabricated substations. The simulation results found that compared with the traditional methods SVM-PSO has higher prediction accuracy.

Tracking problem solving by multivariate pattern analysis and Hidden Markov Model algorithms.

PubMed

Anderson, John R

2012-03-01

Multivariate pattern analysis can be combined with Hidden Markov Model algorithms to track the second-by-second thinking as people solve complex problems. Two applications of this methodology are illustrated with a data set taken from children as they interacted with an intelligent tutoring system for algebra. The first "mind reading" application involves using fMRI activity to track what students are doing as they solve a sequence of algebra problems. The methodology achieves considerable accuracy at determining both what problem-solving step the students are taking and whether they are performing that step correctly. The second "model discovery" application involves using statistical model evaluation to determine how many substates are involved in performing a step of algebraic problem solving. This research indicates that different steps involve different numbers of substates and these substates are associated with different fluency in algebra problem solving. Copyright © 2011 Elsevier Ltd. All rights reserved.

Non-polynomial closed string field theory: loops and conformal maps

NASA Astrophysics Data System (ADS)

Hua, Long; Kaku, Michio

1990-11-01

Recently, we proposed the complete classical action for the non-polynomial closed string field theory, which succesfully reproduced all closed string tree amplitudes. (The action was simultaneously proposed by the Kyoto group). In this paper, we analyze the structure of the theory. We (a) compute the explicit conformal map for all g-loop, p-puncture diagrams, (b) compute all one-loop, two-puncture maps in terms of hyper-elliptic functions, and (c) analyze their modular structure. We analyze, but do not resolve, the question of modular invariance.

Associations between Family Communication Patterns, Sibling Closeness, and Adoptive Status

PubMed Central

Samek, Diana R.; Rueter, Martha A.

2011-01-01

Previous research has demonstrated the protective effect of family and sibling closeness on child adjustment, but fewer studies have investigated how closeness is promoted within families. Guided by Family Communication Patterns Theory, we tested the association between family communication and sibling emotional and behavioral closeness, and whether adoptive status moderated this relationship. Participating families included 616 adoptive and non-adoptive families with two adolescent children. Hypotheses were tested using structural equation modeling. Sibling closeness was highest in families that emphasized both conversation and conformity and lowest in families that emphasized only conversation or neither conversation nor conformity. Emotional and behavioral closeness were differentially associated with adoption status, sibling age, and sibling gender. Few moderating effects of adoption status were found. Post hoc analyses showed moderating effects of sibling gender composition. PMID:21984844

Associations between Family Communication Patterns, Sibling Closeness, and Adoptive Status.

PubMed

Samek, Diana R; Rueter, Martha A

2011-10-01

Previous research has demonstrated the protective effect of family and sibling closeness on child adjustment, but fewer studies have investigated how closeness is promoted within families. Guided by Family Communication Patterns Theory, we tested the association between family communication and sibling emotional and behavioral closeness, and whether adoptive status moderated this relationship. Participating families included 616 adoptive and non-adoptive families with two adolescent children. Hypotheses were tested using structural equation modeling. Sibling closeness was highest in families that emphasized both conversation and conformity and lowest in families that emphasized only conversation or neither conversation nor conformity. Emotional and behavioral closeness were differentially associated with adoption status, sibling age, and sibling gender. Few moderating effects of adoption status were found. Post hoc analyses showed moderating effects of sibling gender composition.

Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open ↔ Closed Transitions

PubMed Central

Beckstein, Oliver; Denning, Elizabeth J.; Perilla, Juan R.; Woolf, Thomas B.

2009-01-01

Adenylate kinase (AdK), a phosphotransferase enzyme, plays an important role in cellular energy homeostasis. It undergoes a large conformational change between an open and a closed state, even in the absence of substrate. We investigate the apo-AdK transition at the atomic level both with free energy calculations and our new dynamic importance sampling (DIMS) molecular dynamics (MD) method. DIMS is shown to sample biologically relevant conformations as verified by comparing an ensemble of hundreds of DIMS transitions to AdK crystal structure intermediates. The simulations reveal in atomic detail how hinge regions partially and intermittently unfold during the transition. Conserved salt bridges are seen to have important structural and dynamic roles; in particular four ionic bonds are identified that open in a sequential, zipper-like fashion and thus dominate the free energy landscape of the transition. Transitions between the closed and open conformations only have to overcome moderate free energy barriers. Unexpectedly, the closed and open state encompass broad free energy basins that contain conformations differing in domain hinge motions by up to 40°. The significance of these extended states is discussed in relation to recent experimental FRET measurements. Taken together, these results demonstrate how a small number of cooperative key interactions can shape the overall dynamics of an enzyme and suggest an “all-or-nothing” mechanism for the opening and closing of AdK. Our efficient DIMS-MD computer simulation approach can provide a detailed picture of a functionally important macromolecular transition and thus help to interpret and suggest experiments to probe the conformational landscape of dynamic proteins such as AdK. PMID:19751742

Voltage-dependent conformational changes in connexin channels.

PubMed

Bargiello, Thaddeus A; Tang, Qingxiu; Oh, Seunghoon; Kwon, Taekyung

2012-08-01

Channels formed by connexins display two distinct types of voltage-dependent gating, termed V(j)- or fast-gating and loop- or slow-gating. Recent studies, using metal bridge formation and chemical cross-linking have identified a region within the channel pore that contributes to the formation of the loop-gate permeability barrier. The conformational changes are remarkably large, reducing the channel pore diameter from 15 to 20Å to less than 4Å. Surprisingly, the largest conformational change occurs in the most stable region of the channel pore, the 3(10) or parahelix formed by amino acids in the 42-51 segment. The data provide a set of positional constraints that can be used to model the structure of the loop-gate closed state. Less is known about the conformation of the V(j)-gate closed state. There appear to be two different mechanisms; one in which conformational changes in channel structure are linked to a voltage sensor contained in the N-terminus of Cx26 and Cx32 and a second in which the C-terminus of Cx43 and Cx40 may act either as a gating particle to block the channel pore or alternatively to stabilize the closed state. The later mechanism utilizes the same domains as implicated in effecting pH gating of Cx43 channels. It is unclear if the two V(j)-gating mechanisms are related or if they represent different gating mechanisms that operate separately in different subsets of connexin channels. A model of the V(j)-closed state of Cx26 hemichannel that is based on the X-ray structure of Cx26 and electron crystallographic structures of a Cx26 mutation suggests that the permeability barrier for V(j)-gating is formed exclusively by the N-terminus, but recent information suggests that this conformation may not represent a voltage-closed state. Closed state models are considered from a thermodynamic perspective based on information from the 3.5Å Cx26 crystal structure and molecular dynamics (MD) simulations. The applications of computational and experimental methods to define the path of allosteric molecular transitions that link the open and closed states are discussed. This article is part of a Special Issue entitled: The Communicating junctions, composition, structure and characteristics. Copyright © 2011 Elsevier B.V. All rights reserved.

Interactions within the yeast t-SNARE Sso1p that control SNARE complex assembly.

PubMed

Munson, M; Chen, X; Cocina, A E; Schultz, S M; Hughson, F M

2000-10-01

In the eukaryotic secretory and endocytic pathways, transport vesicles shuttle cargo among intracellular organelles and to and from the plasma membrane. Cargo delivery entails fusion of the transport vesicle with its target, a process thought to be mediated by membrane bridging SNARE protein complexes. Temporal and spatial control of intracellular trafficking depends in part on regulating the assembly of these complexes. In vitro, SNARE assembly is inhibited by the closed conformation adopted by the syntaxin family of SNAREs. To visualize this closed conformation directly, the X-ray crystal structure of a yeast syntaxin, Sso1p, has been determined and refined to 2.1 A resolution. Mutants designed to destabilize the closed conformation exhibit accelerated rates of SNARE assembly. Our results provide insight into the mechanism of SNARE assembly and its intramolecular and intermolecular regulation.

Understanding the kinetic mechanism of RNA single base pair formation

PubMed Central

Xu, Xiaojun; Yu, Tao; Chen, Shi-Jie

2016-01-01

RNA functions are intrinsically tied to folding kinetics. The most elementary step in RNA folding is the closing and opening of a base pair. Understanding this elementary rate process is the basis for RNA folding kinetics studies. Previous studies mostly focused on the unfolding of base pairs. Here, based on a hybrid approach, we investigate the folding process at level of single base pairing/stacking. The study, which integrates molecular dynamics simulation, kinetic Monte Carlo simulation, and master equation methods, uncovers two alternative dominant pathways: Starting from the unfolded state, the nucleotide backbone first folds to the native conformation, followed by subsequent adjustment of the base conformation. During the base conformational rearrangement, the backbone either retains the native conformation or switches to nonnative conformations in order to lower the kinetic barrier for base rearrangement. The method enables quantification of kinetic partitioning among the different pathways. Moreover, the simulation reveals several intriguing ion binding/dissociation signatures for the conformational changes. Our approach may be useful for developing a base pair opening/closing rate model. PMID:26699466

The gating cycle of a K+ channel at atomic resolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cuello, Luis G.; Cortes, D. Marien; Perozo, Eduardo

C-type inactivation in potassium channels helps fine-tune long-term channel activity through conformational changes at the selectivity filter. Here, through the use of cross-linked constitutively open constructs, we determined the structures of KcsA’s mutants that stabilize the selectivity filter in its conductive (E71A, at 2.25 Å) and deep C-type inactivated (Y82A at 2.4 Å) conformations. These structural snapshots represent KcsA’s transient open-conductive (O/O) and the stable open deep C-type inactivated states (O/I), respectively. The present structures provide an unprecedented view of the selectivity filter backbone in its collapsed deep C-type inactivated conformation, highlighting the close interactions with structural waters and themore » local allosteric interactions that couple activation and inactivation gating. Together with the structures associated with the closed-inactivated state (C/I) and in the well-known closed conductive state (C/O), this work recapitulates, at atomic resolution, the key conformational changes of a potassium channel pore domain as it progresses along its gating cycle.« less

Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes

PubMed Central

Duchi, Diego; Gryte, Kristofer; Robb, Nicole C; Morichaud, Zakia; Sheppard, Carol; Wigneshweraraj, Sivaramesh

2018-01-01

Abstract Transcription initiation is a major step in gene regulation for all organisms. In bacteria, the promoter DNA is first recognized by RNA polymerase (RNAP) to yield an initial closed complex. This complex subsequently undergoes conformational changes resulting in DNA strand separation to form a transcription bubble and an RNAP-promoter open complex; however, the series and sequence of conformational changes, and the factors that influence them are unclear. To address the conformational landscape and transitions in transcription initiation, we applied single-molecule Förster resonance energy transfer (smFRET) on immobilized Escherichia coli transcription open complexes. Our results revealed the existence of two stable states within RNAP–DNA complexes in which the promoter DNA appears to adopt closed and partially open conformations, and we observed large-scale transitions in which the transcription bubble fluctuated between open and closed states; these transitions, which occur roughly on the 0.1 s timescale, are distinct from the millisecond-timescale dynamics previously observed within diffusing open complexes. Mutational studies indicated that the σ70 region 3.2 of the RNAP significantly affected the bubble dynamics. Our results have implications for many steps of transcription initiation, and support a bend-load-open model for the sequence of transitions leading to bubble opening during open complex formation. PMID:29177430

Mapping Polymerization and Allostery of Hemoglobin S Using Point Mutations

PubMed Central

Weinkam, Patrick; Sali, Andrej

2014-01-01

Hemoglobin is a complex system that undergoes conformational changes in response to oxygen, allosteric effectors, mutations, and environmental changes. Here, we study allostery and polymerization of hemoglobin and its variants by application of two previously described methods: (i) AllosMod for simulating allostery dynamics given two allosterically related input structures and (ii) a machine-learning method for dynamics- and structure-based prediction of the mutation impact on allostery (Weinkam et al. J. Mol. Biol. 2013), now applicable to systems with multiple coupled binding sites such as hemoglobin. First, we predict the relative stabilities of substates and microstates of hemoglobin, which are determined primarily by entropy within our model. Next, we predict the impact of 866 annotated mutations on hemoglobin’s oxygen binding equilibrium. We then discuss a subset of 30 mutations that occur in the presence of the sickle cell mutation and whose effects on polymerization have been measured. Seven of these HbS mutations occur in three predicted druggable binding pockets that might be exploited to directly inhibit polymerization; one of these binding pockets is not apparent in the crystal structure but only in structures generated by AllosMod. For the 30 mutations, we predict that mutation-induced conformational changes within a single tetramer tend not to significantly impact polymerization; instead, these mutations more likely impact polymerization by directly perturbing a polymerization interface. Finally, our analysis of allostery allows us to hypothesize why hemoglobin evolved to have multiple subunits and a persistent low frequency sickle cell mutation. PMID:23957820

The power grid monitoring promotion of Liaoning December 14th accident

NASA Astrophysics Data System (ADS)

Zhou, Zhi; Gao, Ziji; He, Xiaoyang; Li, Tie; Jin, Xiaoming; Wang, Mingkai; Qu, Zhi; Sun, Chenguang

2018-02-01

This paper introduces the main responsibilities of power grid monitoring and the accident of Liaoning Power Grid 500kV Xujia transformer substation at December 14th, 2016. This paper analyzes the problems exposed in this accident from the aspects of abnormal information judgment, fault information collection, auxiliary video monitoring, online monitoring of substation equipment, puts forward the corresponding improvement methods and summarizes the methods of improving the professional level of power grid equipment monitoring.

A Comparative Study of Electric Load Curve Changes in an Urban Low-Voltage Substation in Spain during the Economic Crisis (2008–2013)

PubMed Central

Lara-Santillán, Pedro M.; Mendoza-Villena, Montserrat; Fernández-Jiménez, L. Alfredo; Mañana-Canteli, Mario

2014-01-01

This paper presents a comparative study of the electricity consumption (EC) in an urban low-voltage substation before and during the economic crisis (2008–2013). This low-voltage substation supplies electric power to near 400 users. The EC was measured for an 11-year period (2002–2012) with a sampling time of 1 minute. The study described in the paper consists of detecting the changes produced in the load curves of this substation along the time due to changes in the behaviour of consumers. The EC was compared using representative curves per time period (precrisis and crisis). These representative curves were obtained after a computational process, which was based on a search for days with similar curves to the curve of a determined (base) date. This similitude was assessed by the proximity on the calendar, day of the week, daylight time, and outdoor temperature. The last selection parameter was the error between the nearest neighbour curves and the base date curve. The obtained representative curves were linearized to determine changes in their structure (maximum and minimum consumption values, duration of the daily time slot, etc.). The results primarily indicate an increase in the EC in the night slot during the summer months in the crisis period. PMID:24895677

National Maglev initiative: California line electric utility power system requirements

NASA Technical Reports Server (NTRS)

Save, Phil

1994-01-01

The electrical utility power system requirements were determined for a Maglev line from San Diego to San Francisco and Sacramento with a maximum capacity of 12,000 passengers an hour in each direction at a speed of 300 miles per hour, or one train every 30 seconds in each direction. Basically the Maglev line requires one 50-MVA substation every 12.5 miles. The need for new power lines to serve these substations and their voltage levels are based not only on equipment loading criteria but also on limitations due to voltage flicker and harmonics created by the Maglev system. The resulting power system requirements and their costs depend mostly on the geographical area, urban or suburban with 'strong' power systems, or mountains and rural areas with 'weak' power systems. A reliability evaluation indicated that emergency power sources, such as a 10-MW battery at each substation, were not justified if sufficient redundancy is provided in the design of the substations and the power lines serving them. With a cost of $5.6 M per mile, the power system requirements, including the 12-kV DC cables and the inverters along the Maglev line, were found to be the second largest cost component of the Maglev system, after the cost of the guideway system ($9.1 M per mile), out of a total cost of $23 M per mile.

The Millimeter-Wave Spectrum of Methacrolein. Torsion-Rotation Effects in the Excited States

NASA Astrophysics Data System (ADS)

Zakharenko, Olena; Motiyenko, R. A.; Aviles Moreno, Juan-Ramon; Huet, T. R.

2015-06-01

Last year we reported the analysis of the rotational spectrum of s-trans conformer of methacrolein CH2=C(CH3)CHO in the ground vibrational state. In this talk we report the study of its low lying excited vibrational states. The study is based on room-temperature absorption spectra of methacrolein recorded in the frequency range 150 - 465 GHz using the spectrometer in Lille. The new results include assignment of the first excited torsional state (131 cm-1), and the joint analysis of the vt = 0 and vt = 1 states, that allowed us to improve the model in the frame of Rho-Axis-Method (RAM) Hamiltonian and to remove some strong correlations between parameters. Also we assigned the first excited vibrational state of the skeletal torsion mode (170 cm-1). The inverse sequence of A and E tunneling substates as well as anomalous A-E splittings observed for the rotational lines of vsk = 1 state clearly indicate a coupling between methyl torsion and skeletal torsion. However we were able to fit within experimental accuracy the rotational lines of vsk = 1 state using the RAM Hamiltonian. Because of the inversion of the A and E tunneling substates the rotational lines of the vsk = 1 states were assumed to belong to a virtual first excited torsional state. Finally, we assigned several low-Ka rotational transitions of the excited vibrational states above 200 cm-1 but their analysis is complicated by different rotation-vibration interactions. In particular there is an evidence of the Fermi-type resonance between the second excited torsional state and the first excited state of the in-plane skeletal bending mode (265 cm-1). Support from the French Laboratoire d'Excellence CaPPA (Chemical and Physical Properties of the Atmosphere) through contract ANR-10-LABX-0005 of the Programme d'Investissements d'Avenir is acknowledged. Zakharenko O. et al., 69th ISMS, 2014, TI01

Performance of bulk oil circuit breaker (BOCB) influenced by its parameters (Case study at the substation of Bogor Baru)

NASA Astrophysics Data System (ADS)

Goeritno, Arief; Rasiman, Syofyan

2017-06-01

Performance examination of the bulk oil circuit breaker that is influenced by its parameters at the Substation of Bogor Baru (the State Electricity Company = PLN) has been done. It is found that (1) dielectric strength of oil still qualifies as an insulating and cooling medium, because the average value of the measurement result is still above the minimum value allowed, where the minimum limit of 80 kV/2.5 cm or 32 kV/cm; (2) the simultaneity of the CB's contacts is still eligible, so that the BOCB can still be operated, because the difference of time between the highest and lowest values when the BOCB's contacts are opened/closed are less than (Δt<) 10 milliseconds (if meeting the PLN standards as recommended by Alsthom); and (3) the parameter of resistance according to the standards, where (i) the resistance of insulation has a value far above the allowed threshold, while the minimum standards are above 2,000 Mn (if meeting the ANSI standards) or on the value of 2,000 MΩ (if meeting PLN standards), (ii) the resistance of contacts has a value far above the allowed threshold, while the minimum standards are below 350 µΩ (if meeting ANSI standards) or on the value of 200 µΩ (if meeting PLN standards). The resistance of grounding is equal to the maximum limit specified, while the maximum standard is on the value of 0.5 Ω (if meeting PLN standard).

Modelling GIC Flow in New Zealand's Electrical Transmission Grid

NASA Astrophysics Data System (ADS)

Divett, T.; Thomson, A. W. P.; Ingham, M.; Rodger, C. J.; Beggan, C.; Kelly, G.

2016-12-01

Transformers in Transpower New Zealand Ltd's electrical grid have been impacted by geomagnetically induced currents (GIC) during geomagnetic storms, for example in November 2001. In this study we have developed an initial model of the South Island's power grid to advance understanding of the impact of GIC on New Zealand's (NZ) grid. NZ's latitude and island setting mean that modelling approaches successfully used in the UK in the past can be used. Vasseur and Weidelt's thin sheet model is applied to model the electric field as a function of magnetic field and conductance. However the 4 km deep ocean near NZ's coast compared to the UK's relatively shallow continental shelf waters restricts the range of frequency and spatial grid that can be used due to assumptions in the thin sheet model. Some early consequences of these restrictions will be discussed. Lines carrying 220kV, 110kV and 66kV make up NZ's electrical transmission grid with multiple earthing nodes at each substation. Transpower have measured DC earth currents at 17 nodes in NZ's South Island grid for 15 years, including observations at multiple transformers for some substations. Different transformers at the same substation can experience quite different GIC during space weather events. Therefore we have initially modelled each transformer in some substations separately to compare directly with measured currents.Ultimately this study aims to develop a validated modelling tool that will be used to strengthen NZ's grid against the risks of space weather. Further, mitigation tactics which could be used to reduce the threat to the electrical grid will be evaluated. In particular we will focus at the transformer level where the risk lies, and not at the substation level as has been commonly done to date. As we will validate our model against the extensive Transpower observations, this will be a valuable confirmation of the approaches used by the wider international community.

Toward elucidating the heat activation mechanism of the TRPV1 channel gating by molecular dynamics simulation.

PubMed

Wen, Han; Qin, Feng; Zheng, Wenjun

2016-12-01

As a key cellular sensor, the TRPV1 cation channel undergoes a gating transition from a closed state to an open state in response to various physical and chemical stimuli including noxious heat. Despite years of study, the heat activation mechanism of TRPV1 gating remains enigmatic at the molecular level. Toward elucidating the structural and energetic basis of TRPV1 gating, we have performed molecular dynamics (MD) simulations (with cumulative simulation time of 3 μs), starting from the high-resolution closed and open structures of TRPV1 solved by cryo-electron microscopy. In the closed-state simulations at 30°C, we observed a stably closed channel constricted at the lower gate (near residue I679), while the upper gate (near residues G643 and M644) is dynamic and undergoes flickery opening/closing. In the open-state simulations at 60°C, we found higher conformational variation consistent with a large entropy increase required for the heat activation, and both the lower and upper gates are dynamic with transient opening/closing. Through ensemble-based structural analyses of the closed state versus the open state, we revealed pronounced closed-to-open conformational changes involving the membrane proximal domain (MPD) linker, the outer pore, and the TRP helix, which are accompanied by breaking/forming of a network of closed/open-state specific hydrogen bonds. By comparing the closed-state simulations at 30°C and 60°C, we observed heat-activated conformational changes in the MPD linker, the outer pore, and the TRP helix that resemble the closed-to-open conformational changes, along with partial formation of the open-state specific hydrogen bonds. Some of the residues involved in the above key hydrogen bonds were validated by previous mutational studies. Taken together, our MD simulations have offered rich structural and dynamic details beyond the static structures of TRPV1, and promising targets for future mutagenesis and functional studies of the TRPV1 channel. Proteins 2016; 84:1938-1949. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

The research of full automatic oil filtering control technology of high voltage insulating oil

NASA Astrophysics Data System (ADS)

Gong, Gangjun; Zhang, Tong; Yan, Guozeng; Zhang, Han; Chen, Zhimin; Su, Chang

2017-09-01

In this paper, the design scheme of automatic oil filter control system for transformer oil in UHV substation is summarized. The scheme specifically includes the typical double tank filter connection control method of the transformer oil of the UHV substation, which distinguishes the single port and the double port connection structure of the oil tank. Finally, the design scheme of the temperature sensor and respirator is given in detail, and the detailed evaluation and application scenarios are given for reference.

Replacement of Ser108 in Plasmodium falciparum enolase results in weak Mg(II) binding: role of a parasite-specific pentapeptide insert in stabilizing the active conformation of the enzyme.

PubMed

Dutta, Sneha; Mukherjee, Debanjan; Jarori, Gotam K

2015-06-01

A distinct structural feature of Plasmodium falciparum enolase (Pfeno) is the presence of a five amino acid insert -104EWGWS108- that is not found in host enolases. Its conservation among apicomplexan enolases has raised the possibility of its involvement in some important physiological function(s). Deletion of this sequence is known to lower k(cat)/K(m), increase K(a) for Mg(II) and convert dimer into monomers (Vora HK, Shaik FR, Pal-Bhowmick I, Mout R & Jarori GK (2009) Arch Biochem Biophys 485, 128-138). These authors also raised the possibility of the formation of an H-bond between Ser108 and Leu49 that could stabilize the apo-Pfeno in an active closed conformation that has high affinity for Mg(II). Here, we examined the effect of replacement of Ser108 with Gly/Ala/Thr on enzyme activity, Mg(II) binding affinity, conformational states and oligomeric structure and compared it with native recombinant Pfeno. The results obtained support the view that Ser108 is likely to be involved in the formation of certain crucial H-bonds with Leu49. The presence of these interactions can stabilize apo-Pfeno in an active closed conformation similar to that of Mg(II) bound yeast enolase. As predicted, S108G/A-Pfeno variants (where Ser108-Leu49 H-bonds are likely to be disrupted) were found to exist in an open conformation and had low affinity for Mg(II). They also required Mg(II) induced conformational changes to acquire the active closed conformational state essential for catalysis. The possible physiological relevance of apo-Pfeno being in such an active state is discussed. © 2015 FEBS.

The effect of tensile stress on the conformational free energy landscape of disulfide bonds.

PubMed

Anjukandi, Padmesh; Dopieralski, Przemyslaw; Ribas-Arino, Jordi; Marx, Dominik

2014-01-01

Disulfide bridges are no longer considered to merely stabilize protein structure, but are increasingly recognized to play a functional role in many regulatory biomolecular processes. Recent studies have uncovered that the redox activity of native disulfides depends on their C-C-S-S dihedrals, χ2 and χ'2. Moreover, the interplay of chemical reactivity and mechanical stress of disulfide switches has been recently elucidated using force-clamp spectroscopy and computer simulation. The χ2 and χ'2 angles have been found to change from conformations that are open to nucleophilic attack to sterically hindered, so-called closed states upon exerting tensile stress. In view of the growing evidence of the importance of C-C-S-S dihedrals in tuning the reactivity of disulfides, here we present a systematic study of the conformational diversity of disulfides as a function of tensile stress. With the help of force-clamp metadynamics simulations, we show that tensile stress brings about a large stabilization of the closed conformers, thereby giving rise to drastic changes in the conformational free energy landscape of disulfides. Statistical analysis shows that native TDi, DO and interchain Ig protein disulfides prefer open conformations, whereas the intrachain disulfide bridges in Ig proteins favor closed conformations. Correlating mechanical stress with the distance between the two a-carbons of the disulfide moiety reveals that the strain of intrachain Ig protein disulfides corresponds to a mechanical activation of about 100 pN. Such mechanical activation leads to a severalfold increase of the rate of the elementary redox S(N)2 reaction step. All these findings constitute a step forward towards achieving a full understanding of functional disulfides.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wurzburg, Beth A; Jardetzky, Theodore S; Stanford)

The structure of immunoglobulin E (IgE)-Fc 3-4 has been solved in three new crystal forms, providing 13 snapshots of the Fc conformation and revealing a diverse range of open-closed motions among subunit chains and dimers. A more detailed analysis of the open-to-closed motion of IgE-Fc 3-4 was possible with so many structures, and the new structures allow a more thorough examination of the flexibility of IgE-Fc and its implications for receptor binding. The existence of a hydrophobic pocket at the elbow region of the Fc appears to be conformation dependent and suggests a means of regulating the IgE-Fc conformation (andmore » potentially receptor binding) with small molecules.« less

The Structure of a High Fidelity DNA Polymerase Bound to a Mismatched Nucleotide Reveals an “Ajar” Intermediate Conformation in the Nucleotide Selection Mechanism*

PubMed Central

Wu, Eugene Y.; Beese, Lorena S.

2011-01-01

To achieve accurate DNA synthesis, DNA polymerases must rapidly sample and discriminate against incorrect nucleotides. Here we report the crystal structure of a high fidelity DNA polymerase I bound to DNA primer-template caught in the act of binding a mismatched (dG:dTTP) nucleoside triphosphate. The polymerase adopts a conformation in between the previously established “open” and “closed” states. In this “ajar” conformation, the template base has moved into the insertion site but misaligns an incorrect nucleotide relative to the primer terminus. The displacement of a conserved active site tyrosine in the insertion site by the template base is accommodated by a distinctive kink in the polymerase O helix, resulting in a partially open ternary complex. We suggest that the ajar conformation allows the template to probe incoming nucleotides for complementarity before closure of the enzyme around the substrate. Based on solution fluorescence, kinetics, and crystallographic analyses of wild-type and mutant polymerases reported here, we present a three-state reaction pathway in which nucleotides either pass through this intermediate conformation to the closed conformation and catalysis or are misaligned within the intermediate, leading to destabilization of the closed conformation. PMID:21454515

Image acquisition device of inspection robot based on adaptive rotation regulation of polarizer

NASA Astrophysics Data System (ADS)

Dong, Maoqi; Wang, Xingguang; Liang, Tao; Yang, Guoqing; Zhang, Chuangyou; Gao, Faqin

2017-12-01

An image processing device of inspection robot with adaptive polarization adjustment is proposed, that the device includes the inspection robot body, the image collecting mechanism, the polarizer and the polarizer automatic actuating device. Where, the image acquisition mechanism is arranged at the front of the inspection robot body for collecting equipment image data in the substation. Polarizer is fixed on the automatic actuating device of polarizer, and installed in front of the image acquisition mechanism, and that the optical axis of the camera vertically goes through the polarizer and the polarizer rotates with the optical axis of the visible camera as the central axis. The simulation results show that the system solves the fuzzy problems of the equipment that are caused by glare, reflection of light and shadow, and the robot can observe details of the running status of electrical equipment. And the full coverage of the substation equipment inspection robot observation target is achieved, which ensures the safe operation of the substation equipment.

A Novel Wide-Area Backup Protection Based on Fault Component Current Distribution and Improved Evidence Theory

PubMed Central

Zhang, Zhe; Kong, Xiangping; Yin, Xianggen; Yang, Zengli; Wang, Lijun

2014-01-01

In order to solve the problems of the existing wide-area backup protection (WABP) algorithms, the paper proposes a novel WABP algorithm based on the distribution characteristics of fault component current and improved Dempster/Shafer (D-S) evidence theory. When a fault occurs, slave substations transmit to master station the amplitudes of fault component currents of transmission lines which are the closest to fault element. Then master substation identifies suspicious faulty lines according to the distribution characteristics of fault component current. After that, the master substation will identify the actual faulty line with improved D-S evidence theory based on the action states of traditional protections and direction components of these suspicious faulty lines. The simulation examples based on IEEE 10-generator-39-bus system show that the proposed WABP algorithm has an excellent performance. The algorithm has low requirement of sampling synchronization, small wide-area communication flow, and high fault tolerance. PMID:25050399

A Study on Effect of Concrete Foundations on Resistance and Surface Potentials of Gas Insulated Substation Grounding Systems

NASA Astrophysics Data System (ADS)

Rao, Mandava Mohana

2017-10-01

Ground resistance of high voltage substations must be as low as possible for safe grounding of their equipment both during normal and fault conditions. However, in gas insulated substations (GIS), even though resistance is low, it does not ensure the step and touch potentials of the grounding system within permissible levels. In the present study, an analytical model has been developed to calculate ground resistance, step and touch potentials of a grounding system used for GIS. Different models have been proposed for the evaluation of number of grounding rods to be inserted in to the ground. The effect of concrete foundations on above performance parameters has been analyzed by considering various fault currents, soil/earth resistivities and number of grounding rods. Finally, design optimization of GIS grounding system has been reported for fault currents in the order of 63 kA located in earth resistivity of 100Ω-m and above.

On-rail solution for autonomous inspections in electrical substations

NASA Astrophysics Data System (ADS)

Silva, Bruno P. A.; Ferreira, Rafael A. M.; Gomes, Selson C.; Calado, Flavio A. R.; Andrade, Roberto M.; Porto, Matheus P.

2018-05-01

This work presents an alternative solution for autonomous inspections in electrical substations. The autonomous system is a robot that moves on rails, collects infrared and visible images of selected targets, also processes the data and predicts the components lifetime. The robot moves on rails to overcome difficulties found in not paved substations commonly encountered in Brazil. We take advantage of using rails to convey the data by them, minimizing the electromagnetic interference, and at the same time transmitting electrical energy to feed the autonomous system. As part of the quality control process, we compared thermographic inspections made by the robot with inspections made by a trained thermographer using a scientific camera Flir® SC660. The results have shown that the robot achieved satisfactory results, identifying components and measuring temperature accurately. The embodied routine considers the weather changes along the day, providing a standard result of the components thermal response, also gives the uncertainty of temperature measurement, contributing to the quality in the decision making process.

The Effects of Temperature on Political Violence: Global Evidence at the Subnational Level

PubMed Central

Bollfrass, Alexander; Shaver, Andrew

2015-01-01

A number of studies have demonstrated an empirical relationship between higher ambient temperatures and substate violence, which have been extrapolated to make predictions about the security implications of climate change. This literature rests on the untested assumption that the mechanism behind the temperature-conflict link is that disruption of agricultural production provokes local violence. Using a subnational-level dataset, this paper demonstrates that the relationship: (1) obtains globally, (2) exists at the substate level — provinces that experience positive temperature deviations see increased conflict; and (3) occurs even in regions without significant agricultural production. Diminished local farm output resulting from elevated temperatures is unlikely to account for the entire increase in substate violence. The findings encourage future research to identify additional mechanisms, including the possibility that a substantial portion of the variation is brought about by the well-documented direct effects of temperature on individuals' propensity for violence or through macroeconomic mechanisms such as food price shocks. PMID:25992616

Hiding Critical Targets in Smart Grid Networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bao, Wei; Li, Qinghua

With the integration of advanced communication technologies, the power grid is expected to greatly enhance efficiency and reliability of future power systems. However, since most electrical devices in power grid substations are connected via communication networks, cyber security of these communication networks becomes a critical issue. Real-World incidents such as Stuxnet have shown the feasibility of compromising a device in the power grid network to further launch more sophisticated attacks. To deal with security attacks of this spirit, this paper aims to hide critical targets from compromised internal nodes and hence protect them from further attacks launched by those compromisedmore » nodes. In particular, we consider substation networks and propose to add carefully-controlled dummy traffic to a substation network to make critical target nodes indistinguishable from other nodes in network traffic patterns. This paper describes the design and evaluation of such a scheme. Evaluations show that the scheme can effectively protect critical nodes with acceptable communication cost.« less

Grizzly Substation Fiber Optics : Environmental Assessment.

DOE Office of Scientific and Technical Information (OSTI.GOV)

United States. Bonneville Power Administration.

1998-02-01

This notice announces BPA`s decision to construct, operate, and maintain the Grizzly Substation Fiber Optic Project (Project). This Project is part of a continuing effort by BPA to complete a regionwide upgrade of its existing telecommunications system. The US Forest Service and BPA jointly prepared the Grizzly Substation Fiber Optic Project Environmental Assessment (EA) (DOE/EA-1241) evaluating the potential environmental impacts of the Proposed Action, the Underground Installation Alternative, and the No Action Alternative. Based on the analysis in the EA, the US Forest Service and BPA have determined that the Proposed Action is not a major Federal action significantly affectingmore » the quality of the human environment, within the meaning of the National Environmental Policy Act (NEPA) of 1969. Therefore, the preparation of an Environmental Impact Statement (EIS) is not required and BPA is issuing this FONSI. The US Forest Service has separately issued a FONSI and Decision Notice authorizing BPA to construct, operate, and maintain the Project within the Crooked River National Grassland (Grassland).« less

A health examination of railway high-voltage substation workers exposed to ELF electromagnetic fields.

PubMed

Baroncelli, P; Battisti, S; Checcucci, A; Comba, P; Grandolfo, M; Serio, A; Vecchia, P

1986-01-01

This is a cross-sectional survey on the health conditions of railways workers active in 258 interconnection and conversion substations all over Italy. Measurements performed in both kinds of substations operating at 220 kV have shown that maximum levels of the electric field strength and of the magnetic flux density at 50 Hz are of the order of 5 kV/m and 15 microT, respectively. Three subject groups, differently exposed (1, 10, 20 h/week), and an unexposed control group, for a total number of 627 workers, constitute the population at study. All subjects underwent a general medical examination, laboratory investigations, and a series of selected examinations relative to three systems (nervous, cardiovascular, and haematopoietic) considered at higher risk. No differences have been found between the exposed and the control groups. It is concluded that workers exposed to ELF electromagnetic fields of moderate strength do not show the presence of clear effects on their state of health.

Enhanced conformational sampling technique provides an energy landscape view of large-scale protein conformational transitions.

PubMed

Shao, Qiang

2016-10-26

Large-scale conformational changes in proteins are important for their functions. Tracking the conformational change in real time at the level of a single protein molecule, however, remains a great challenge. In this article, we present a novel in silico approach with the combination of normal mode analysis and integrated-tempering-sampling molecular simulation (NMA-ITS) to give quantitative data for exploring the conformational transition pathway in multi-dimensional energy landscapes starting only from the knowledge of the two endpoint structures of the protein. The open-to-closed transitions of three proteins, including nCaM, AdK, and HIV-1 PR, were investigated using NMA-ITS simulations. The three proteins have varied structural flexibilities and domain communications in their respective conformational changes. The transition state structure in the conformational change of nCaM and the associated free-energy barrier are in agreement with those measured in a standard explicit-solvent REMD simulation. The experimentally measured transition intermediate structures of the intrinsically flexible AdK are captured by the conformational transition pathway measured here. The dominant transition pathways between the closed and fully open states of HIV-1 PR are very similar to those observed in recent REMD simulations. Finally, the evaluated relaxation times of the conformational transitions of three proteins are roughly at the same level as reported experimental data. Therefore, the NMA-ITS method is applicable for a variety of cases, providing both qualitative and quantitative insights into the conformational changes associated with the real functions of proteins.

Combining theoretical and experimental data to decipher CFTR 3D structures and functions.

PubMed

Hoffmann, Brice; Elbahnsi, Ahmad; Lehn, Pierre; Décout, Jean-Luc; Pietrucci, Fabio; Mornon, Jean-Paul; Callebaut, Isabelle

2018-05-19

Cryo-electron microscopy (cryo-EM) has recently provided invaluable experimental data about the full-length cystic fibrosis transmembrane conductance regulator (CFTR) 3D structure. However, this experimental information deals with inactive states of the channel, either in an apo, quiescent conformation, in which nucleotide-binding domains (NBDs) are widely separated or in an ATP-bound, yet closed conformation. Here, we show that 3D structure models of the open and closed forms of the channel, now further supported by metadynamics simulations and by comparison with the cryo-EM data, could be used to gain some insights into critical features of the conformational transition toward active CFTR forms. These critical elements lie within membrane-spanning domains but also within NBD1 and the N-terminal extension, in which conformational plasticity is predicted to occur to help the interaction with filamin, one of the CFTR cellular partners.

Pyrazole amino acids: hydrogen bonding directed conformations of 3-amino-1H-pyrazole-5-carboxylic acid residue.

PubMed

Kusakiewicz-Dawid, Anna; Porada, Monika; Ochędzan-Siodłak, Wioletta; Broda, Małgorzata A; Bujak, Maciej; Siodłak, Dawid

2017-09-01

A series of model compounds containing 3-amino-1H-pyrazole-5-carboxylic acid residue with N-terminal amide/urethane and C-terminal amide/hydrazide/ester groups were investigated by using NMR, Fourier transform infrared, and single-crystal X-ray diffraction methods, additionally supported by theoretical calculations. The studies demonstrate that the most preferred is the extended conformation with torsion angles ϕ and ψ close to ±180°. The studied 1H-pyrazole with N-terminal amide/urethane and C-terminal amide/hydrazide groups solely adopts this energetically favored conformation confirming rigidity of that structural motif. However, when the C-terminal ester group is present, the second conformation with torsion angles ϕ and ψ close to ±180° and 0°, respectively, is accessible. The conformational equilibrium is observed in NMR and Fourier transform infrared studies in solution in polar environment as well as in the crystal structures of other related compounds. The observed conformational preferences are clearly related to the presence of intramolecular interactions formed within the studied residue. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

Structural Changes Fundamental to Gating of the Cystic Fibrosis Transmembrane Conductance Regulator Anion Channel Pore.

PubMed

Linsdell, Paul

2017-01-01

Cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an epithelial cell anion channel. Potentiator drugs used in the treatment of cystic fibrosis act on the channel to increase overall channel function, by increasing the stability of its open state and/or decreasing the stability of its closed state. The structure of the channel in either the open state or the closed state is not currently known. However, changes in the conformation of the protein as it transitions between these two states have been studied using functional investigation and molecular modeling techniques. This review summarizes our current understanding of the architecture of the transmembrane channel pore that controls the movement of chloride and other small anions, both in the open state and in the closed state. Evidence for different kinds of changes in the conformation of the pore as it transitions between open and closed states is described, as well as the mechanisms by which these conformational changes might be controlled to regulate normal channel gating. The ways that key conformational changes might be targeted by small compounds to influence overall CFTR activity are also discussed. Understanding the changes in pore structure that might be manipulated by such small compounds is key to the development of novel therapeutic strategies for the treatment of cystic fibrosis.

Electrochemical control of a DNA Holliday Junction nanoswitch by Mg2+ ions.

PubMed

Ferapontova, E E; Mountford, C P; Crain, J; Buck, A H; Dickinson, P; Beattie, J S; Ghazal, P; Terry, J G; Walton, A J; Mount, A R

2008-11-15

The molecular conformation of a synthetic branched, 4-way DNA Holliday junction (HJ) was electrochemically switched between the open and closed (stacked) conformers. Switching was achieved by electrochemically induced quantitative release of Mg(2+) ions from the oxidised poly(N-methylpyrrole) film (PPy), which contained polyacrylate as an immobile counter anion and Mg(2+) ions as charge compensating mobile cations. This increase in the Mg(2+) concentration screened the electrostatic repulsion between the widely separated arms in the open HJ configuration, inducing switching to the closed conformation. Upon electrochemical reduction of PPy, entrapment of Mg(2+) ions back into the PPy film induced the reverse HJ switching from the closed to open state. The conformational transition was monitored using fluorescence resonance energy transfer (FRET) between donor and acceptor dyes each located at the terminus of one of the arms. The demonstrated electrochemical control of the conformation of the used probe-target HJ complex, previously reported as a highly sequence specific nanodevice for detecting of unlabelled target [Buck, A.H., Campbell, C.J., Dickinson, P., Mountford, C.P., Stoquert, H.C., Terry, J.G., Evans, S.A.G., Keane, L., Su, T.J., Mount, A.R., Walton, A.J., Beattie, J.S., Crain, J., Ghazal, P., 2007. Anal. Chem., 79, 4724-4728], allows the development of electronically addressable DNA nanodevices and label-free gene detection assays.

Assessment of the risk of failure of high voltage substations due to environmental conditions and pollution on insulators.

PubMed

Castillo Sierra, Rafael; Oviedo-Trespalacios, Oscar; Candelo, John E; Soto, Jose D

2015-07-01

Pollution on electrical insulators is one of the greatest causes of failure of substations subjected to high levels of salinity and environmental pollution. Considering leakage current as the main indicator of pollution on insulators, this paper focuses on establishing the effect of the environmental conditions on the risk of failure due to pollution on insulators and determining the significant change in the magnitude of the pollution on the insulators during dry and humid periods. Hierarchical segmentation analysis was used to establish the effect of environmental conditions on the risk of failure due to pollution on insulators. The Kruskal-Wallis test was utilized to determine the significant changes in the magnitude of the pollution due to climate periods. An important result was the discovery that leakage current was more common on insulators during dry periods than humid ones. There was also a higher risk of failure due to pollution during dry periods. During the humid period, various temperatures and wind directions produced a small change in the risk of failure. As a technical result, operators of electrical substations can now identify the cause of an increase in risk of failure due to pollution in the area. The research provides a contribution towards the behaviour of the leakage current under conditions similar to those of the Colombian Caribbean coast and how they affect the risk of failure of the substation due to pollution.

Comparison of electric field exposure monitoring instrumentation. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bracken, T.D.

1985-06-01

Electric field exposure monitoring instrumentation was compared and evaluated during three days of tests performed in 60-Hz electric fields. A conducting vest exposure meter and a small electric field exposure meter (EFEM) located in a shirt pocket, arm band or hard hat were compared in a series of static and dynamic tests. In some tests, the devices were worn simultaneously without interference to provide separate measures of identical exposure. Tests with stationary subjects wearing the instruments were used to measure the effects of grounding, and to establish the meter response in a standard posture for each subject. Dynamic occupational exposuremore » simulations were used to compare accumulated measurements of exposure between instruments and to compare measurements with predicted exposures. The simulations were based on analysis of the work-related behavior of substation electricians and operators. Electrician's tasks at ground level and in a bucket truck were simulated near an energized test line. A simulated substation inspection was performed in a 230 kV substation. The exposure measurements demonstrated an overall consistency between the meters. The vest demonstrated less intersubject variability and less detailed exposure characterization. Measurements with the shirt pocket EFEM were below those made with the vest and with the EFEM in other locations. Insulation provided by shoe soles appeared to be the largest factor in reducing measured exposures during the substation inspection below those predicted from the unperturbed field. Improvements in meter design and additional measurements are suggested. 11 refs., 20 figs., 28 tabs.« less

Applications of NMR and computational methodologies to study protein dynamics.

PubMed

Narayanan, Chitra; Bafna, Khushboo; Roux, Louise D; Agarwal, Pratul K; Doucet, Nicolas

2017-08-15

Overwhelming evidence now illustrates the defining role of atomic-scale protein flexibility in biological events such as allostery, cell signaling, and enzyme catalysis. Over the years, spin relaxation nuclear magnetic resonance (NMR) has provided significant insights on the structural motions occurring on multiple time frames over the course of a protein life span. The present review article aims to illustrate to the broader community how this technique continues to shape many areas of protein science and engineering, in addition to being an indispensable tool for studying atomic-scale motions and functional characterization. Continuing developments in underlying NMR technology alongside software and hardware developments for complementary computational approaches now enable methodologies to routinely provide spatial directionality and structural representations traditionally harder to achieve solely using NMR spectroscopy. In addition to its well-established role in structural elucidation, we present recent examples that illustrate the combined power of selective isotope labeling, relaxation dispersion experiments, chemical shift analyses, and computational approaches for the characterization of conformational sub-states in proteins and enzymes. Copyright © 2017 Elsevier Inc. All rights reserved.

Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase

PubMed Central

Mukherjee, Shayantani; Warshel, Arieh

2011-01-01

Understanding the nature of energy transduction in life processes requires a quantitative description of the energetics of the conversion of ATP to ADP by ATPases. Previous attempts to do so have provided an interesting insight but could not account for the rotary mechanism by a nonphenomenological structure/energy description. In particular it has been very challenging to account for the observations of the 80° and 40° rotational substates, without any prior information about such states in the simulation procedure. Here we use a coarse-grained model of F1-ATPase and generate, without the adjustment of phenomenological parameters, a structure-based free energy landscape that reproduces the energetics of the mechanochemical process. It is found that the landscape along the relevant rotary path is determined by the electrostatic free energy and not by steric effects. Furthermore, the generated surface and the corresponding Langevin dynamics simulations identify a hidden conformational barrier that provides a new fundamental interpretation of the catalytic dwell and illuminate the nature of the energy conversion process. PMID:22143769

Computational Study on the Inhibitor Binding Mode and Allosteric Regulation Mechanism in Hepatitis C Virus NS3/4A Protein

PubMed Central

Xue, Weiwei; Yang, Ying; Wang, Xiaoting; Liu, Huanxiang; Yao, Xiaojun

2014-01-01

HCV NS3/4A protein is an attractive therapeutic target responsible for harboring serine protease and RNA helicase activities during the viral replication. Small molecules binding at the interface between the protease and helicase domains can stabilize the closed conformation of the protein and thus block the catalytic function of HCV NS3/4A protein via an allosteric regulation mechanism. But the detailed mechanism remains elusive. Here, we aimed to provide some insight into the inhibitor binding mode and allosteric regulation mechanism of HCV NS3/4A protein by using computational methods. Four simulation systems were investigated. They include: apo state of HCV NS3/4A protein, HCV NS3/4A protein in complex with an allosteric inhibitor and the truncated form of the above two systems. The molecular dynamics simulation results indicate HCV NS3/4A protein in complex with the allosteric inhibitor 4VA adopts a closed conformation (inactive state), while the truncated apo protein adopts an open conformation (active state). Further residue interaction network analysis suggests the communication of the domain-domain interface play an important role in the transition from closed to open conformation of HCV NS3/4A protein. However, the inhibitor stabilizes the closed conformation through interaction with several key residues from both the protease and helicase domains, including His57, Asp79, Asp81, Asp168, Met485, Cys525 and Asp527, which blocks the information communication between the functional domains interface. Finally, a dynamic model about the allosteric regulation and conformational changes of HCV NS3/4A protein was proposed and could provide fundamental insights into the allosteric mechanism of HCV NS3/4A protein function regulation and design of new potent inhibitors. PMID:24586263

Syntaxin1a variants lacking an N-peptide or bearing the LE mutation bind to Munc18a in a closed conformation

DOE PAGES

Colbert, Karen N.; Hattendorf, Douglas A.; Weiss, Thomas M.; ...

2013-07-15

In neurons, soluble N-ethylmaleimide–sensitive factor attachment receptor (SNARE) proteins drive the fusion of synaptic vesicles to the plasma membrane through the formation of a four-helix SNARE complex. Members of the Sec1/Munc18 protein family regulate membrane fusion through interactions with the syntaxin family of SNARE proteins. The neuronal protein Munc18a interacts with a closed conformation of the SNARE protein syntaxin1a (Syx1a) and with an assembled SNARE complex containing Syx1a in an open conformation. The N-peptide of Syx1a (amino acids 1–24) has been implicated in the transition of Munc18a-bound Syx1a to Munc18a-bound SNARE complex, but the underlying mechanism is not understood. Inmore » addition, we report the X-ray crystal structures of Munc18a bound to Syx1a with and without its native N-peptide (Syx1aΔN), along with small-angle X-ray scattering (SAXS) data for Munc18a bound to Syx1a, Syx1aΔN, and Syx1a L165A/E166A (LE), a mutation thought to render Syx1a in a constitutively open conformation. We show that all three complexes adopt the same global structure, in which Munc18a binds a closed conformation of Syx1a. We also identify a possible structural connection between the Syx1a N-peptide and SNARE domain that might be important for the transition of closed-to-open Syx1a in SNARE complex assembly. Although the role of the N-peptide in Munc18a-mediated SNARE complex assembly remains unclear, our results demonstrate that the N-peptide and LE mutation have no effect on the global conformation of the Munc18a–Syx1a complex.« less

Structure-Based Design of a Soluble Prefusion-Closed HIV-1 Env Trimer with Reduced CD4 Affinity and Improved Immunogenicity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chuang, Gwo-Yu; Geng, Hui; Pancera, Marie

ABSTRACT The HIV-1 envelope (Env) trimer is a target for vaccine design as well as a conformational machine that facilitates virus entry by transitioning between prefusion-closed, CD4-bound, and coreceptor-bound conformations by transitioning into a postfusion state. Vaccine designers have sought to restrict the conformation of the HIV-1 Env trimer to its prefusion-closed state as this state is recognized by most broadly neutralizing, but not nonneutralizing, antibodies. We previously identified a disulfide bond, I201C-A433C (DS), which stabilizes Env in the vaccine-desired prefusion-closed state. When placed into the context of BG505 SOSIP.664, a soluble Env trimer mimic developed by Sanders, Moore, andmore » colleagues, the engineered DS-SOSIP trimer showed reduced conformational triggering by CD4. Here, we further stabilize DS-SOSIP through a combination of structure-based design and 96-well-based expression and antigenic assessment. From 103 designs, we identified one, named DS-SOSIP.4mut, with four additional mutations at the interface of potentially mobile domains of the prefusion-closed structure. We also determined the crystal structures of DS-SOSIP.4mut at 4.1-Å resolution and of an additional DS-SOSIP.6mut variant at 4.3-Å resolution, and these confirmed the formation of engineered disulfide bonds. Notably, DS-SOSIP.4mut elicited a higher ratio of tier 2 autologous titers versus tier 1 V3-sensitive titers than BG505 SOSIP.664. DS-SOSIP.4mut also showed reduced recognition of CD4 and increased thermostability. The improved antigenicity, thermostability, and immunogenicity of DS-SOSIP.4mut suggest utility as an immunogen or a serologic probe; moreover, the specific four alterations identified here, M154, M300, M302, and L320 (4mut), can also be transferred to other HIV-1 Env trimers of interest to improve their properties. IMPORTANCEOne approach to elicit broadly neutralizing antibodies against HIV-1 is to stabilize the structurally flexible HIV-1 envelope (Env) trimer in a conformation that displays predominantly broadly neutralizing epitopes and few to no nonneutralizing epitopes. The prefusion-closed conformation of HIV-1 Env has been identified as one such preferred conformation, and a current leading vaccine candidate is the BG505 DS-SOSIP variant, comprising two disulfides and an Ile-to-Pro mutation of Env from strain BG505. Here, we introduced additional mutations to further stabilize BG505 DS-SOSIP in the vaccine-preferred prefusion-closed conformation. In guinea pigs, our best mutant, DS-SOSIP.4mut, elicited a significantly higher ratio of autologous versus V3-directed neutralizing antibody responses than the SOSIP-stabilized form. We also observed an improvement in thermostability and a reduction in CD4 affinity. With improved antigenicity, stability, and immunogenicity, DS-SOSIP.4mut-stabilized trimers may have utility as HIV-1 immunogens or in other antigen-specific contexts, such as with B-cell probes.« less

Pilot Non-Conformance to Alerting System Commands

NASA Technical Reports Server (NTRS)

Pritchett, Amy R.; Hansman, R. John

1997-01-01

Instances of pilot non-conformance to alerting system commands have been identified in previous studies. Pilot non-conformance changes the final behavior of the system, and therefore may reduce actual performance from that anticipated. A simulator study has examined pilot non-conformance, using the task of collision avoidance during closely spaced parallel approaches as a case study. Consonance between the display and the alerting system was found to significantly improve subject agreement with automatic alerts. Based on these results, a more general discussion of the factors involved in pilot conformance is given, and design guidelines for alerting systems are given.

Structure of a thermophilic F1-ATPase inhibited by an ε-subunit: deeper insight into the ε-inhibition mechanism.

PubMed

Shirakihara, Yasuo; Shiratori, Aya; Tanikawa, Hiromi; Nakasako, Masayoshi; Yoshida, Masasuke; Suzuki, Toshiharu

2015-08-01

F1-ATPase (F1) is the catalytic sector in F(o)F1-ATP synthase that is responsible for ATP production in living cells. In catalysis, its three catalytic β-subunits undergo nucleotide occupancy-dependent and concerted open-close conformational changes that are accompanied by rotation of the γ-subunit. Bacterial and chloroplast F1 are inhibited by their own ε-subunit. In the ε-inhibited Escherichia coli F1 structure, the ε-subunit stabilizes the overall conformation (half-closed, closed, open) of the β-subunits by inserting its C-terminal helix into the α3β3 cavity. The structure of ε-inhibited thermophilic F1 is similar to that of E. coli F1, showing a similar conformation of the ε-subunit, but the thermophilic ε-subunit stabilizes another unique overall conformation (open, closed, open) of the β-subunits. The ε-C-terminal helix 2 and hook are conserved between the two structures in interactions with target residues and in their positions. Rest of the ε-C-terminal domains are in quite different conformations and positions, and have different modes of interaction with targets. This region is thought to serve ε-inhibition differently. For inhibition, the ε-subunit contacts the second catches of some of the β- and α-subunits, the N- and C-terminal helices, and some of the Rossmann fold segments. Those contacts, as a whole, lead to positioning of those β- and α- second catches in ε-inhibition-specific positions, and prevent rotation of the γ-subunit. Some of the structural features are observed even in IF1 inhibition in mitochondrial F1. © 2015 FEBS.

Time-Resolved Small-Angle X-ray Scattering Reveals Millisecond Transitions of a DNA Origami Switch.

PubMed

Bruetzel, Linda K; Walker, Philipp U; Gerling, Thomas; Dietz, Hendrik; Lipfert, Jan

2018-04-11

Self-assembled DNA structures enable creation of specific shapes at the nanometer-micrometer scale with molecular resolution. The construction of functional DNA assemblies will likely require dynamic structures that can undergo controllable conformational changes. DNA devices based on shape complementary stacking interactions have been demonstrated to undergo reversible conformational changes triggered by changes in ionic environment or temperature. An experimentally unexplored aspect is how quickly conformational transitions of large synthetic DNA origami structures can actually occur. Here, we use time-resolved small-angle X-ray scattering to monitor large-scale conformational transitions of a two-state DNA origami switch in free solution. We show that the DNA device switches from its open to its closed conformation upon addition of MgCl 2 in milliseconds, which is close to the theoretical diffusive speed limit. In contrast, measurements of the dimerization of DNA origami bricks reveal much slower and concentration-dependent assembly kinetics. DNA brick dimerization occurs on a time scale of minutes to hours suggesting that the kinetics depend on local concentration and molecular alignment.

The relative isoperimetric inequality on a conformally parabolic manifold with boundary

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kesel'man, Vladimir M

2011-07-31

For an arbitrary noncompact n-dimensional Riemannian manifold with a boundary of conformally parabolic type it is proved that there exists a conformal change of metric such that a relative isoperimetric inequality of the same form as in the closed n-dimensional Euclidean half-space holds on the manifold with the new metric. This isoperimetric inequality is asymptotically sharp. Bibliography: 6 titles.

High-precision multi-node clock network distribution.

PubMed

Chen, Xing; Cui, Yifan; Lu, Xing; Ci, Cheng; Zhang, Xuesong; Liu, Bo; Wu, Hong; Tang, Tingsong; Shi, Kebin; Zhang, Zhigang

2017-10-01

A high precision multi-node clock network for multiple users was built following the precise frequency transmission and time synchronization of 120 km fiber. The network topology adopts a simple star-shaped network structure. The clock signal of a hydrogen maser (synchronized with UTC) was recovered from a 120 km telecommunication fiber link and then was distributed to 4 sub-stations. The fractional frequency instability of all substations is in the level of 10 -15 in a second and the clock offset instability is in sub-ps in root-mean-square average.

Structural studies of Saccharomyces cerevesiae mitochondrial NADP-dependent isocitrate dehydrogenase in different enzymatic states reveal substantial conformational changes during the catalytic reaction.

PubMed

Peng, Yingjie; Zhong, Chen; Huang, Wei; Ding, Jianping

2008-09-01

Isocitrate dehydrogenases (IDHs) catalyze oxidative decarboxylation of isocitrate (ICT) into alpha-ketoglutarate (AKG). We report here the crystal structures of Saccharomyces cerevesiae mitochondrial NADP-IDH Idp1p in binary complexes with coenzyme NADP, or substrate ICT, or product AKG, and in a quaternary complex with NADPH, AKG, and Ca(2+), which represent different enzymatic states during the catalytic reaction. Analyses of these structures identify key residues involved in the binding of these ligands. Comparisons among these structures and with the previously reported structures of other NADP-IDHs reveal that eukaryotic NADP-IDHs undergo substantial conformational changes during the catalytic reaction. Binding or release of the ligands can cause significant conformational changes of the structural elements composing the active site, leading to rotation of the large domain relative to the small and clasp domains along two hinge regions (residues 118-124 and residues 284-287) while maintaining the integrity of its secondary structural elements, and thus, formation of at least three distinct overall conformations. Specifically, the enzyme adopts an open conformation when bound to NADP, a quasi-closed conformation when bound to ICT or AKG, and a fully closed conformation when bound to NADP, ICT, and Ca(2+) in the pseudo-Michaelis complex or with NADPH, AKG, and Ca(2+) in the product state. The conformational changes of eukaryotic NADP-IDHs are quite different from those of Escherichia coli NADP-IDH, for which significant conformational changes are observed only between two forms of the apo enzyme, suggesting that the catalytic mechanism of eukaryotic NADP-IDHs is more complex than that of EcIDH, and involves more fine-tuned conformational changes.

Structural studies of Saccharomyces cerevesiae mitochondrial NADP-dependent isocitrate dehydrogenase in different enzymatic states reveal substantial conformational changes during the catalytic reaction

PubMed Central

Peng, Yingjie; Zhong, Chen; Huang, Wei; Ding, Jianping

2008-01-01

Isocitrate dehydrogenases (IDHs) catalyze oxidative decarboxylation of isocitrate (ICT) into α-ketoglutarate (AKG). We report here the crystal structures of Saccharomyces cerevesiae mitochondrial NADP-IDH Idp1p in binary complexes with coenzyme NADP, or substrate ICT, or product AKG, and in a quaternary complex with NADPH, AKG, and Ca2+, which represent different enzymatic states during the catalytic reaction. Analyses of these structures identify key residues involved in the binding of these ligands. Comparisons among these structures and with the previously reported structures of other NADP-IDHs reveal that eukaryotic NADP-IDHs undergo substantial conformational changes during the catalytic reaction. Binding or release of the ligands can cause significant conformational changes of the structural elements composing the active site, leading to rotation of the large domain relative to the small and clasp domains along two hinge regions (residues 118–124 and residues 284–287) while maintaining the integrity of its secondary structural elements, and thus, formation of at least three distinct overall conformations. Specifically, the enzyme adopts an open conformation when bound to NADP, a quasi-closed conformation when bound to ICT or AKG, and a fully closed conformation when bound to NADP, ICT, and Ca2+ in the pseudo-Michaelis complex or with NADPH, AKG, and Ca2+ in the product state. The conformational changes of eukaryotic NADP-IDHs are quite different from those of Escherichia coli NADP-IDH, for which significant conformational changes are observed only between two forms of the apo enzyme, suggesting that the catalytic mechanism of eukaryotic NADP-IDHs is more complex than that of EcIDH, and involves more fine-tuned conformational changes. PMID:18552125

Energetics of subdomain movements and fluorescence probe solvation environment change in ATP-bound myosin.

PubMed

Harris, Michael J; Woo, Hyung-June

2008-11-01

Energetics of conformational changes experienced by an ATP-bound myosin head detached from actin was studied by all-atom explicit water umbrella sampling simulations. The statistics of coupling between large scale domain movements and smaller scale structural features were examined, including the closing of the ATP binding pocket, and a number of key hydrogen bond formations shown to play roles in structural and biochemical studies. The statistics for the ATP binding pocket open/close transition show an evolution of the relative stability from the open state in the early stages of the recovery stroke to the stable closed state after the stroke. The change in solvation environment of the fluorescence probe Trp507 (scallop numbering; 501 in Dictyostelium discoideum) indicates that the probe faithfully reflects the closing of the binding pocket as previously shown in experimental studies, while being directly coupled to roughly the early half of the overall large scale conformational change of the converter domain rotation. The free energy change of this solvation environment change, in particular, is -1.3 kcal/mol, in close agreement with experimental estimates. In addition, our results provide direct molecular level data allowing for interpretations of the fluorescence experiments of myosin conformational change in terms of the de-solvation of Trp side chain.

The crystal structure of the D-alanine-D-alanine ligase from Acinetobacter baumannii suggests a flexible conformational change in the central domain before nucleotide binding.

PubMed

Huynh, Kim-Hung; Hong, Myoung-ki; Lee, Clarice; Tran, Huyen-Thi; Lee, Sang Hee; Ahn, Yeh-Jin; Cha, Sun-Shin; Kang, Lin-Woo

2015-11-01

Acinetobacter baumannii, which is emerging as a multidrug-resistant nosocomial pathogen, causes a number of diseases, including pneumonia, bacteremia, meningitis, and skin infections. With ATP hydrolysis, the D-alanine-D-alanine ligase (DDL) catalyzes the synthesis of D-alanyl-D-alanine, which is an essential component of bacterial peptidoglycan. In this study, we determined the crystal structure of DDL from A. baumannii (AbDDL) at a resolution of 2.2 Å. The asymmetric unit contained six protomers of AbDDL. Five protomers had a closed conformation in the central domain, while one protomer had an open conformation in the central domain. The central domain with an open conformation did not interact with crystallographic symmetry-related protomers and the conformational change of the central domain was not due to crystal packing. The central domain of AbDDL can have an ensemble of the open and closed conformations before the binding of substrate ATP. The conformational change of the central domain is important for the catalytic activity and the detail information will be useful for the development of inhibitors against AbDDL and putative antibacterial agents against A. baumannii. The AbDDL structure was compared with that of other DDLs that were in complex with potent inhibitors and the catalytic activity of AbDDL was confirmed using enzyme kinetics assays.

Identification of Rare Lewis Oligosaccharide Conformers in Aqueous Solution Using Enhanced Sampling Molecular Dynamics.

PubMed

Alibay, Irfan; Burusco, Kepa K; Bruce, Neil J; Bryce, Richard A

2018-03-08

Determining the conformations accessible to carbohydrate ligands in aqueous solution is important for understanding their biological action. In this work, we evaluate the conformational free-energy surfaces of Lewis oligosaccharides in explicit aqueous solvent using a multidimensional variant of the swarm-enhanced sampling molecular dynamics (msesMD) method; we compare with multi-microsecond unbiased MD simulations, umbrella sampling, and accelerated MD approaches. For the sialyl Lewis A tetrasaccharide, msesMD simulations in aqueous solution predict conformer landscapes in general agreement with the other biased methods and with triplicate unbiased 10 μs trajectories; these simulations find a predominance of closed conformer and a range of low-occupancy open forms. The msesMD simulations also suggest closed-to-open transitions in the tetrasaccharide are facilitated by changes in ring puckering of its GlcNAc residue away from the 4 C 1 form, in line with previous work. For sialyl Lewis X tetrasaccharide, msesMD simulations predict a minor population of an open form in solution corresponding to a rare lectin-bound pose observed crystallographically. Overall, from comparison with biased MD calculations, we find that triplicate 10 μs unbiased MD simulations may not be enough to fully sample glycan conformations in aqueous solution. However, the computational efficiency and intuitive approach of the msesMD method suggest potential for its application in glycomics as a tool for analysis of oligosaccharide conformation.

Development of Simulated Disturbing Source for Isolation Switch

NASA Astrophysics Data System (ADS)

Cheng, Lin; Liu, Xiang; Deng, Xiaoping; Pan, Zhezhe; Zhou, Hang; Zhu, Yong

2018-01-01

In order to simulate the substation in the actual scene of the harsh electromagnetic environment, and then research on electromagnetic compatibility testing of electronic instrument transformer, On the basis of the original isolation switch as a harassment source of the electronic instrument transformer electromagnetic compatibility test system, an isolated switch simulation source system was developed, to promote the standardization of the original test. In this paper, the circuit breaker is used to control the opening and closing of the gap arc to simulate the operating of isolating switch, and the isolation switch simulation harassment source system is designed accordingly. Comparison with the actual test results of the isolating switch, it is proved that the system can meet the test requirements, and the simulation harassment source system has good stability and high reliability.

A mass weighted chemical elastic network model elucidates closed form domain motions in proteins

PubMed Central

Kim, Min Hyeok; Seo, Sangjae; Jeong, Jay Il; Kim, Bum Joon; Liu, Wing Kam; Lim, Byeong Soo; Choi, Jae Boong; Kim, Moon Ki

2013-01-01

An elastic network model (ENM), usually Cα coarse-grained one, has been widely used to study protein dynamics as an alternative to classical molecular dynamics simulation. This simple approach dramatically saves the computational cost, but sometimes fails to describe a feasible conformational change due to unrealistically excessive spring connections. To overcome this limitation, we propose a mass-weighted chemical elastic network model (MWCENM) in which the total mass of each residue is assumed to be concentrated on the representative alpha carbon atom and various stiffness values are precisely assigned according to the types of chemical interactions. We test MWCENM on several well-known proteins of which both closed and open conformations are available as well as three α-helix rich proteins. Their normal mode analysis reveals that MWCENM not only generates more plausible conformational changes, especially for closed forms of proteins, but also preserves protein secondary structures thus distinguishing MWCENM from traditional ENMs. In addition, MWCENM also reduces computational burden by using a more sparse stiffness matrix. PMID:23456820

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Jiusheng; van den Bedem, Henry; Brunger, Axel T.

Calmodulin (CaM) is the primary calcium signaling protein in eukaryotes and has been extensively studied using various biophysical techniques. Prior crystal structures have noted the presence of ambiguous electron density in both hydrophobic binding pockets of Ca 2+-CaM, but no assignment of these features has been made. In addition, Ca 2+-CaM samples many conformational substates in the crystal and accurately modeling the full range of this functionally important disorder is challenging. In order to characterize these features in a minimally biased manner, a 1.0 Å resolution single-wavelength anomalous diffraction data set was measured for selenomethionine-substituted Ca 2+-CaM. Density-modified electron-density mapsmore » enabled the accurate assignment of Ca 2+-CaM main-chain and side-chain disorder. These experimental maps also substantiate complex disorder models that were automatically built using low-contour features of model-phased electron density. Furthermore, experimental electron-density maps reveal that 2-methyl-2,4-pentanediol (MPD) is present in the C-terminal domain, mediates a lattice contact between N-terminal domains and may occupy the N-terminal binding pocket. The majority of the crystal structures of target-free Ca 2+-CaM have been derived from crystals grown using MPD as a precipitant, and thus MPD is likely to be bound in functionally critical regions of Ca 2+-CaM in most of these structures. The adventitious binding of MPD helps to explain differences between the Ca 2+-CaM crystal and solution structures and is likely to favor more open conformations of the EF-hands in the crystal.« less

Förster-type energy transfer as a probe for changes in local fluctuations of the protein matrix.

PubMed

Somogyi, B; Matkó, J; Papp, S; Hevessy, J; Welch, G R; Damjanovich, S

1984-07-17

Much evidence, on both theoretical and experimental sides, indicates the importance of local fluctuations (in energy levels, conformational substates, etc.) of the macromolecular matrix in the biological activity of proteins. We describe here a novel application of the Förster-type energy-transfer process capable of monitoring changes both in local fluctuations and in conformational states of macromolecules. A new energy-transfer parameter, f, is defined as an average transfer efficiency, [E], normalized by the actual average quantum efficiency of the donor fluorescence, [phi D]. A simple oscillator model (for a one donor-one acceptor system) is presented to show the sensitivity of this parameter to changes in amplitudes of local fluctuations. The different modes of averaging (static, dynamic, and intermediate cases) occurring for a given value of the average transfer rate, [kt], and the experimental requirements as well as limitations of the method are also discussed. The experimental tests were performed on the ribonuclease T1-pyridoxamine 5'-phosphate conjugate (a one donor-one acceptor system) by studying the change of the f parameter with temperature, an environmental parameter expectedly perturbing local fluctuations of proteins. The parameter f increased with increasing temperature as expected on the basis of the oscillator model, suggesting that it really reflects changes of fluctuation amplitudes (significant changes in the orientation factor, k2, as well as in the spectral properties of the fluorophores can be excluded by anisotropy measurements and spectral investigations). Possibilities of the general applicability of the method are also discussed.

Characterizing Peptide β-HAIRPIN Loops via Cold Ion Spectroscopy of Model Compounds

NASA Astrophysics Data System (ADS)

Lawler, John T.; DeBlase, Andrew F.; Harrilal, Christopher P.; Fischer, Joshua L.; McLuckey, Scott A.; Zwier, Timothy S.

2017-06-01

The introduction of non-native D-amino acids into peptides is known to reduce conformational entropy in peptides. D-proline has been shown to promote the formation of β-hairpin loops when paired with Gly, providing a framework for building these loops with different lengths of anti-parallel beta-sheet. This study seeks to characterize and compare the conformational preferences of a model protonated pentapeptide containing DPG, [YAP^{D}GA+H]^{+}, with its L-Pro counterpart via conformation specific cold ion spectroscopy as a foundation for future consideration of larger beta-hairpin models. The UV spectrum of YAP^{D}GA of the Tyr chromophore is beautifully sharp, but contains a complicated set of transitions that could arise from the presence of more than one conformer. To assess this possibility, we recorded non-conformation specific IR "gain" spectra in the hydride stretch region. The IR spectrum so obtained displays a set of five strong IR transitions that bear a close resemblance to those found in one of the conformers of its close analog, [YAP^{D}AA+H]^{+}, signaling that a single conformer dominates the population. Two transitions at 3392 and 3464 cm-1 are slightly shifted versions of the C10 and C14 hydrogen bonds found in one of the conformers of [YAP^{D}AA+H]^{+}, and are characteristic of formation of a β-hairpin loop. Notably, in [YAP^{D}GA+H]^{+}, there is at most a minor second conformer with a free carboxylic acid OH, appearing weakly in the IR "gain" spectrum. As expected, the UV spectrum of YAP^{L}GA is more congested, which suggests the presence of multiple conformers. Further investigation into this peptide will reveal the conformational preferences of the L-pro containing molecule. Preliminary data affirms that D-proline containing peptides show reduced conformational states when compared to their natural counterparts.

Discrimination between closed and open forms of lipases using electrophoretic techniques.

PubMed

Miled, N; Riviere, M; Cavalier, J F; Buono, G; Berti, L; Verger, R

2005-03-15

The enhanced catalytic activity of lipases is often associated with structural changes. The three-dimensional (3D) structures showed that the covalently inhibited lipases exist under their open conformations, in contrast to their native closed forms. We studied the inhibition of various lipases--human and dog gastric lipases, human pancreatic lipase, and Humicola lanuginosa lipase--by the octyl-undecyl phosphonate inhibitor, and we measured the subsequent modifications of their respective electrophoretic mobility. Furthermore, the experimental values of the isoelectric points found for the native (closed) and inhibited (open) lipases are in agreement with theoretical calculations based on the electrostatic potential. We concluded that there is a significant difference in the isoelectric points between the closed (native) and open (inhibited) conformations of the four lipases investigated. Thus, analysis of the electrophoretic pattern is proposed as an easy experimental tool to differentiate between a closed and an open form of a given lipase.

Mutation that blocks ATP binding creates a pseudokinase stabilizing the scaffolding function of kinase suppressor of Ras, CRAF and BRAF.

PubMed

Hu, Jiancheng; Yu, Haiyang; Kornev, Alexandr P; Zhao, Jianping; Filbert, Erin L; Taylor, Susan S; Shaw, Andrey S

2011-04-12

Because mutations in RAS and BRAF represent the most common mutations found in human tumors, identification of inhibitors has been a major goal. Surprisingly, new oncogenic BRAF specific inhibitors inhibit cells transformed with mutated BRAF but paradoxically stimulate the growth of cells transformed with RAS. Here, we show that the mechanism for activation is via drug-induced dimer formation between CRAF and kinase suppressor of Ras (KSR)1. To understand the function of KSR1, we generated a KSR1 mutant that cannot bind ATP but stabilizes the closed, active conformation of KSR1. Molecular modeling suggested that the mutant stabilizes the two hydrophobic spines critical for the closed active conformation. We, therefore, could use the mutant to discriminate between the scaffold versus kinase functions of KSR1. The KSR1 mutant bound constitutively to RAF and mitogen-activated protein kinase kinase (MEK) but could not reconstitute activity suggesting that the catalytic activity of KSR1 is required for its function. Analogous mutations in BRAF and CRAF allowed us to test the generality of the model. The mutation induced changes consistent with the active, closed conformation of both kinases and confirmed that BRAF functions distinctly from CRAF in the MAP kinase pathway. Not only does this work suggest that KSR1 may function as a kinase, we anticipate that the mutation that we generated may be broadly applicable to stabilize the closed conformation of other kinases many of which may also form dimers.

A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations.

PubMed

Ferrada, Evandro; Vergara, Ismael A; Melo, Francisco

2007-01-01

The correct discrimination between native and near-native protein conformations is essential for achieving accurate computer-based protein structure prediction. However, this has proven to be a difficult task, since currently available physical energy functions, empirical potentials and statistical scoring functions are still limited in achieving this goal consistently. In this work, we assess and compare the ability of different full atom knowledge-based potentials to discriminate between native protein structures and near-native protein conformations generated by comparative modeling. Using a benchmark of 152 near-native protein models and their corresponding native structures that encompass several different folds, we demonstrate that the incorporation of close non-bonded pairwise atom terms improves the discriminating power of the empirical potentials. Since the direct and unbiased derivation of close non-bonded terms from current experimental data is not possible, we obtained and used those terms from the corresponding pseudo-energy functions of a non-local knowledge-based potential. It is shown that this methodology significantly improves the discrimination between native and near-native protein conformations, suggesting that a proper description of close non-bonded terms is important to achieve a more complete and accurate description of native protein conformations. Some external knowledge-based energy functions that are widely used in model assessment performed poorly, indicating that the benchmark of models and the specific discrimination task tested in this work constitutes a difficult challenge.

Substrate Binding Drives Active-Site Closing of Human Blood Group B Galactosyltransferase as Revealed by Hot-Spot Labeling and NMR Spectroscopy Experiments.

PubMed

Weissbach, Sophie; Flügge, Friedemann; Peters, Thomas

2018-05-04

Crystallography has shown that human blood group A (GTA) and B (GTB) glycosyltransferases undergo transitions between "open", "semiclosed", and "closed" conformations upon substrate binding. However, the timescales of the corresponding conformational reorientations are unknown. Crystal structures show that the Trp and Met residues are located at "conformational hot spots" of the enzymes. Therefore, we utilized 15 N side-chain labeling of Trp residues and 13 C-methyl labeling of Met residues to study substrate-induced conformational transitions of GTB. Chemical-shift perturbations (CSPs) of Met and Trp residues in direct contact with substrate ligands reflect binding kinetics, whereas the CSPs of Met and Trp residues at remote sites reflect conformational changes of the enzyme upon substrate binding. Acceptor binding is fast on the chemical-shift timescale with rather small CSPs in the range of less than approximately 20 Hz. Donor binding matches the intermediate exchange regime to yield an estimate for exchange rate constants of approximately 200-300 Hz. Donor or acceptor binding to GTB saturated with acceptor or donor substrate, respectively, is slow (<10 Hz), as are coupled protein motions, reflecting mutual allosteric control of donor and acceptor binding. Remote CSPs suggest that substrate binding drives the enzyme into the closed state required for catalysis. These findings should contribute to better understanding of the mechanism of glycosyl transfer of GTA and GTB. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Leukaemia and residence near electricity transmission equipment: a case-control study.

PubMed Central

Coleman, M. P.; Bell, C. M.; Taylor, H. L.; Primic-Zakelj, M.

1989-01-01

A population-based case-control study of leukaemia and residential proximity to electricity supply equipment has been carried out in south-east England. A total of 771 leukaemias was studied, matched for age, sex, year of diagnosis and district of residence to 1,432 controls registered with a solid tumour excluding lymphoma; 231 general population controls aged 18 and over from one part of the study area were also used. The potential for residential exposure to power frequency magnetic fields from power-lines and transformer substations was assessed indirectly from the distance, type and loading of the equipment near each subject's residence. Only 0.6% of subjects lived within 100 m of an overhead power-line, and the risk of leukaemia relative to cancer controls for residence within 100 m was 1.45 (95% confidence interval (CI) 0.54-3.88); within 50 m the relative risk was 2.0 but with a wider confidence interval (95% CI 0.4-9.0). Over 40% of subjects lived within 100 m of a substation, for which the relative risk of leukaemia was 0.99. Residence within 25 m carried a risk of 1.3 (95% CI 0.8-2.0). Weighted exposure indices incorporating measures of the current load carried by the substations did not materially alter these risks estimates. For persons aged less than 18 the relative risk of leukaemia from residence within 50 m of a substation was higher than in adults (PR = 1.5, 95% CI 0.7-3.4). PMID:2486298

Electrical distribution studies for the 200 Area tank farms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fisler, J.B.

1994-08-26

This is an engineering study providing reliability numbers for various design configurations as well as computer analyses (Captor/Dapper) of the existing distribution system to the 480V side of the unit substations. The objective of the study was to assure the adequacy of the existing electrical system components from the connection at the high voltage supply point through the transformation and distribution equipment to the point where it is reduced to its useful voltage level. It also was to evaluate the reasonableness of proposed solutions of identified deficiencies and recommendations of possible alternate solutions. The electrical utilities are normally considered themore » most vital of the utility systems on a site because all other utility systems depend on electrical power. The system accepts electric power from the external sources, reduces it to a lower voltage, and distributes it to end-use points throughout the site. By classic definition, all utility systems extend to a point 5 feet from the facility perimeter. An exception is made to this definition for the electric utilities at this site. The electrical Utility System ends at the low voltage section of the unit substation, which reduces the voltage from 13.8 kV to 2,400, 480, 277/480 or 120/208 volts. These transformers are located at various distances from existing facilities. The adequacy of the distribution system which transports the power from the main substation to the individual area substations and other load centers is evaluated and factored into the impact of the future load forecast.« less

LIM domain protein TES changes its conformational states in different cellular compartments.

PubMed

Zhong, Yingli; Zhu, Jiaolian; Wang, Yan; Zhou, Jianlin; Ren, Kaiqun; Ding, Xiaofeng; Zhang, Jian

2009-01-01

The human TESTIN (TES) is a putative tumor suppressor and localizes to the cytoplasm as a component of focal adhesions and cell contacts. TES contains a PET domain in the NH(2)-terminus and three tandem LIM domains in the COOH-terminus. It has been hypothesized that interactions between two termini of TES might lead to a "closed" conformational state of the protein. Here, we provide evidence for different conformational states of TES. We confirmed that the NH(2)-terminus of TES can interact with its third LIM domain in the COOH-terminus by GST pull-down assays. In addition, antisera against the full-length or two truncations of TES were prepared to examine the relationship between the conformation and cellular distribution of the protein. We found that these antisera recognize different regions of TES and showed that TES is co-localised with the marker protein B23 in nucleolus, in addition to its localization in endoplasmic reticulum (ER). Furthermore, our co-immunoprecipitation (co-IP) analysis of TES and B23 demonstrated their co-existence in the same complex. Taken together, our results suggest that TES has different conformational states in different cellular compartments, and a "closed" conformational state of TES may be involved in nucleolar localization.

Toward an Enhanced Sampling Molecular Dynamics Method for Studying Ligand-Induced Conformational Changes in Proteins.

PubMed

Andersen, Ole Juul; Grouleff, Julie; Needham, Perri; Walker, Ross C; Jensen, Frank

2015-11-19

Current enhanced sampling molecular dynamics methods for studying large conformational changes in proteins suffer from certain limitations. These include, among others, the need for user defined collective variables, the prerequisite of both start and end point structures of the conformational change, and the need for a priori knowledge of the amount by which to boost specific parts of the potential. In this paper, a framework is proposed for a molecular dynamics method for studying ligand-induced conformational changes, in which the nonbonded interactions between the ligand and the protein are used to calculate a biasing force. The method requires only a single input structure, and does not entail the use of collective variables. We provide a proof-of-concept for accelerating conformational changes in three simple test molecules, as well as promising results for two proteins known to undergo domain closure upon ligand binding. For the ribose-binding protein, backbone root-mean-square deviations as low as 0.75 Å compared to the crystal structure of the closed conformation are obtained within 50 ns simulations, whereas no domain closures are observed in unbiased simulations. A skewed closed structure is obtained for the glutamine-binding protein at high bias values, indicating that specific protein-ligand interactions might suppress important protein-protein interactions.

Noise kernels of stochastic gravity in conformally-flat spacetimes

NASA Astrophysics Data System (ADS)

Cho, H. T.; Hu, B. L.

2015-03-01

The central object in the theory of semiclassical stochastic gravity is the noise kernel, which is the symmetric two point correlation function of the stress-energy tensor. Using the corresponding Wightman functions in Minkowski, Einstein and open Einstein spaces, we construct the noise kernels of a conformally coupled scalar field in these spacetimes. From them we show that the noise kernels in conformally-flat spacetimes, including the Friedmann-Robertson-Walker universes, can be obtained in closed analytic forms by using a combination of conformal and coordinate transformations.

Casper to Dave Johnston 230-kV Transmission Line Project: Environmental assessment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1986-01-01

Western proposes to reconstruct the existing Casper-Glendo North 115-kV Transmission Line to 230-kV between a point 1.1 miles northeast of the Pacific Power and Light (Pacific) Casper Substation and the Dave Johnston (DJ) Powerplant near Glenrock, Wyoming. As part of the proposed action, Western proposes to remove the portion of the existing Casper-Glendo South 115-kV Transmission Line between Western's Casper Substation and the intersection with the Casper-Glendo North Transmission Line, about 15 miles east of Casper. The removed portion of the Casper-Glendo North Transmission Line would be rebuilt on steel, single-shaft, structures. The section between the point northeast of themore » Pacific Substation and the intersection with the Casper-Glendo South Transmission Line would be double circuit (230-kV/115-kV). At the intersection of the north and south lines, the new 115-kV section would be tied to the remaining portion of the Casper-Glendo South Line to complete the 115-kV Casper-Glendo circuit. 52 refs.,12 figs., 14 tabs.« less

Historical precedence and technical requirements of biological weapons use : a threat assessment.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Estes, Daniel P.; Vogel, Kathleen Margaret; Gaudioso, Jennifer Marie

2004-05-01

The threat from biological weapons is assessed through both a comparative historical analysis of the patterns of biological weapons use and an assessment of the technological hurdles to proliferation and use that must be overcome. The history of biological weapons is studied to learn how agents have been acquired and what types of states and substate actors have used agents. Substate actors have generally been more willing than states to use pathogens and toxins and they have focused on those agents that are more readily available. There has been an increasing trend of bioterrorism incidents over the past century, butmore » states and substate actors have struggled with one or more of the necessary technological steps. These steps include acquisition of a suitable agent, production of an appropriate quantity and form, and effective deployment. The technological hurdles associated with the steps present a real barrier to producing a high consequence event. However, the ever increasing technological sophistication of society continually lowers the barriers, resulting in a low but increasing probability of a high consequence bioterrorism event.« less

Intercomparison of magnetic field measurements near MV/LV transformer substations: methodological planning and results.

PubMed

Violanti, S; Fraschetta, M; Adda, S; Caputo, E

2009-12-01

Within the framework of Environmental Agencies system's activities, coordinated by ISPRA (superior institute for environmental protection and research), a comparison among measurements was designed and accomplished, in order to go into depth on the matter of measurement problems and to evaluate magnetic field at power frequencies. These measurements have been taken near medium voltage /low voltage transformer substation. This project was developed with the contribution of several experts who belong to different Regional Agencies. In three of these regions, substations having specific international standard characteristics were chosen; then a measurement and data analysis protocol was arranged. Data analysis showed a good level of coherence among results obtained by different laboratories. However, a range of problems emerged, either during the protocol predisposition and definition of the data analysis procedure or during the execution of measures and data reprocessing, because of the spatial and temporal variability of magnetic field. These problems represent elements of particular interest in determining a correct measurement methodology, whose purpose is the comparison with limits of exposure, attention values and quality targets.

DReAM: Demand Response Architecture for Multi-level District Heating and Cooling Networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhattacharya, Saptarshi; Chandan, Vikas; Arya, Vijay

In this paper, we exploit the inherent hierarchy of heat exchangers in District Heating and Cooling (DHC) networks and propose DReAM, a novel Demand Response (DR) architecture for Multi-level DHC networks. DReAM serves to economize system operation while still respecting comfort requirements of individual consumers. Contrary to many present day DR schemes that work on a consumer level granularity, DReAM works at a level of hierarchy above buildings, i.e. substations that supply heat to a group of buildings. This improves the overall DR scalability and reduce the computational complexity. In the first step of the proposed approach, mathematical models ofmore » individual substations and their downstream networks are abstracted into appropriately constructed low-complexity structural forms. In the second step, this abstracted information is employed by the utility to perform DR optimization that determines the optimal heat inflow to individual substations rather than buildings, in order to achieve the targeted objectives across the network. We validate the proposed DReAM framework through experimental results under different scenarios on a test network.« less

5,10-Methylene-5,6,7,8-tetrahydrofolate conformational transitions upon binding to thymidylate synthase: molecular mechanics and continuum solvent studies

NASA Astrophysics Data System (ADS)

Jarmuła, Adam; Cieplak, Piotr; Montfort, William R.

2005-02-01

We applied the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approach to evaluate relative stability of the extended (flat) and C-shaped (bent) solution conformational forms of the 5,10-methylene-5,6,7,8-tetrahydrofolate (mTHF) molecule in aqueous solution. Calculations indicated that both forms have similar free energies in aqueous solution but detailed energy components are different. The bent solution form has lower intramolecular electrostatic and van der Waals interaction energies. The flat form has more favorable solvation free energy and lower contribution from the bond, angle and torsion angle molecular mechanical internal energies. We exploit these results and combine them with known crystallographic data to provide a model for the progressive binding of the mTHF molecule, a natural cofactor of thymidylate synthase (TS), to the complex forming in the TS-catalyzed reaction. We propose that at the time of initial weak binding in the open enzyme the cofactor molecule remains in a close balance between the flat and bent solution conformations, with neither form clearly favored. Later, thymidylate synthase undergoes conformational change leading to the closure of the active site and the mTHF molecule is withdrawn from the solvent. That effect shifts the thermodynamic equilibrium of the mTHF molecule toward the bent solution form. At the same time, burying the cofactor molecule in the closed active site produces numerous contacts between mTHF and protein that render change in the shape of the mTHF molecule. As a result, the bent solution conformer is converted to more strained L-shaped bent enzyme conformer of the mTHF molecule. The strain in the bent enzyme conformation allows for the tight binding of the cofactor molecule to the productive ternary complex that forms in the closed active site, and facilitates the protonation of the imidazolidine N10 atom, which promotes further reaction.

Conformation-driven quantum interference effects mediated by through-space conjugation in self-assembled monolayers

NASA Astrophysics Data System (ADS)

Carlotti, Marco; Kovalchuk, Andrii; Wächter, Tobias; Qiu, Xinkai; Zharnikov, Michael; Chiechi, Ryan C.

2016-12-01

Tunnelling currents through tunnelling junctions comprising molecules with cross-conjugation are markedly lower than for their linearly conjugated analogues. This effect has been shown experimentally and theoretically to arise from destructive quantum interference, which is understood to be an intrinsic, electronic property of molecules. Here we show experimental evidence of conformation-driven interference effects by examining through-space conjugation in which π-conjugated fragments are arranged face-on or edge-on in sufficiently close proximity to interact through space. Observing these effects in the latter requires trapping molecules in a non-equilibrium conformation closely resembling the X-ray crystal structure, which we accomplish using self-assembled monolayers to construct bottom-up, large-area tunnelling junctions. In contrast, interference effects are completely absent in zero-bias simulations on the equilibrium, gas-phase conformation, establishing through-space conjugation as both of fundamental interest and as a potential tool for tuning tunnelling charge-transport in large-area, solid-state molecular-electronic devices.

Mechanistic insight into the functional transition of the enzyme guanylate kinase induced by a single mutation

PubMed Central

Zhang, Yuebin; Niu, Huiyan; Li, Yan; Chu, Huiying; Shen, Hujun; Zhang, Dinglin; Li, Guohui

2015-01-01

Dramatic functional changes of enzyme usually require scores of alterations in amino acid sequence. However, in the case of guanylate kinase (GK), the functional novelty is induced by a single (S→P) mutation, leading to the functional transition of the enzyme from a phosphoryl transfer kinase into a phosphorprotein interaction domain. Here, by using molecular dynamic (MD) and metadynamics simulations, we provide a comprehensive description of the conformational transitions of the enzyme after mutating serine to proline. Our results suggest that the serine plays a crucial role in maintaining the closed conformation of wild-type GK and the GMP recognition. On the contrary, the S→P mutant exhibits a stable open conformation and loses the ability of ligand binding, which explains its functional transition from the GK enzyme to the GK domain. Furthermore, the free energy profiles (FEPs) obtained by metadymanics clearly demonstrate that the open-closed conformational transition in WT GK is positive correlated with the process of GMP binding, indicating the GMP-induced closing motion of GK enzyme, which is not observed in the mutant. In addition, the FEPs show that the S→P mutation can also leads to the mis-recognition of GMP, explaining the vanishing of catalytic activity of the mutant. PMID:25672880

Crystal structure analysis, covalent docking, and molecular dynamics calculations reveal a conformational switch in PhaZ7 PHB depolymerase.

PubMed

Kellici, Tahsin F; Mavromoustakos, Thomas; Jendrossek, Dieter; Papageorgiou, Anastassios C

2017-07-01

An open and a closed conformation of a surface loop in PhaZ7 extracellular poly(3-hydroxybutyrate) depolymerase were identified in two high-resolution crystal structures of a PhaZ7 Y105E mutant. Molecular dynamics (MD) simulations revealed high root mean square fluctuations (RMSF) of the 281-295 loop, in particular at residue Asp289 (RMSF 7.62 Å). Covalent docking between a 3-hydroxybutyric acid trimer and the catalytic residue Ser136 showed that the binding energy of the substrate is significantly more favorable in the open loop conformation compared to that in the closed loop conformation. MD simulations with the substrate covalently bound depicted 1 Å RMSF higher values for the residues 281-295 in comparison to the apo (substrate-free) form. In addition, the presence of the substrate in the active site enhanced the ability of the loop to adopt a closed form. Taken together, the analysis suggests that the flexible loop 281-295 of PhaZ7 depolymerase can act as a lid domain to control substrate access to the active site of the enzyme. Proteins 2017; 85:1351-1361. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Mechanistic insight into the functional transition of the enzyme guanylate kinase induced by a single mutation.

PubMed

Zhang, Yuebin; Niu, Huiyan; Li, Yan; Chu, Huiying; Shen, Hujun; Zhang, Dinglin; Li, Guohui

2015-02-12

Dramatic functional changes of enzyme usually require scores of alterations in amino acid sequence. However, in the case of guanylate kinase (GK), the functional novelty is induced by a single (S→P) mutation, leading to the functional transition of the enzyme from a phosphoryl transfer kinase into a phosphorprotein interaction domain. Here, by using molecular dynamic (MD) and metadynamics simulations, we provide a comprehensive description of the conformational transitions of the enzyme after mutating serine to proline. Our results suggest that the serine plays a crucial role in maintaining the closed conformation of wild-type GK and the GMP recognition. On the contrary, the S→P mutant exhibits a stable open conformation and loses the ability of ligand binding, which explains its functional transition from the GK enzyme to the GK domain. Furthermore, the free energy profiles (FEPs) obtained by metadymanics clearly demonstrate that the open-closed conformational transition in WT GK is positive correlated with the process of GMP binding, indicating the GMP-induced closing motion of GK enzyme, which is not observed in the mutant. In addition, the FEPs show that the S→P mutation can also leads to the mis-recognition of GMP, explaining the vanishing of catalytic activity of the mutant.

The results of systems tests of the 500 kV busbar controllable shunting reactor in the Tavricheskaya substation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gusev, S. I.; Karpov, V. N.; Kiselev, A. N.

2009-09-15

The results of systems tests of the 500 kV busbar magnetization-controllable shunting reactor (CSR), set up in the Tavricheskaya substation, including measurements of the quality of the electric power, the harmonic composition of the network currents of the reactor for different values of the reactive power consumed, the determination of the regulating characteristics of the reactor, the speed of response of the shunting reactor in the current and voltage stabilization modes, and also the operation of the reactor under dynamic conditions for different perturbations, are presented. The results obtained are analyzed.

Underlying thermodynamics of pH-dependent allostery.

PubMed

Di Russo, Natali V; Martí, Marcelo A; Roitberg, Adrian E

2014-11-13

Understanding the effects of coupling protein protonation and conformational states is critical to the development of drugs targeting pH sensors and to the rational engineering of pH switches. In this work, we address this issue by performing a comprehensive study of the pH-regulated switch from the closed to the open conformation in nitrophorin 4 (NP4) that determines its pH-dependent activity. Our calculations show that D30 is the only amino acid that has two significantly different pKas in the open and closed conformations, confirming its critical role in regulating pH-dependent behavior. In addition, we describe the free-energy landscape of the conformational change as a function of pH, obtaining accurate estimations of free-energy barriers and equilibrium constants using different methods. The underlying thermodynamic model of the switch workings suggests the possibility of tuning the observed pKa only through the conformational equilibria, keeping the same conformation-specific pKas, as evidenced by the proposed K125L mutant. Moreover, coupling between the protonation and conformational equilibria results in efficient regulation and pH-sensing around physiological pH values only for some combinations of protonation and conformational equilibrium constants, placing constraints on their possible values and leaving a narrow space for protein molecular evolution. The calculations and analysis presented here are of general applicability and provide a guide as to how more complex systems can be studied, offering insight into how pH-regulated allostery works of great value for designing drugs that target pH sensors and for rational engineering of pH switches beyond the common histidine trigger.

Cinetica de oxidacion de polimeros conductores: poli-3,4- etilendioxitiofeno

NASA Astrophysics Data System (ADS)

Caballero Romero, Maria

Films of poly-3,4-ethylenedioxythiophene (PEDOT) perchlorate used as electrodes in liquid electrolytes incorporate anions and solvent during oxidation for charge and osmotic balance: the film swells. During reduction the film shrinks, closes its structure trapping counterions getting then rising conformational packed states by expulsion of counterions and solvent. Here by potential step from the same reduced initial state to the same oxidized final state the rate coefficient, the activation energy and reaction orders related to the counterion concentration in solution and to the concentration of active centers in the polymer film, were attained following the usual methodology used for chemical and electrochemical kinetics. Now the full methodology was repeated using different reduced-shrunk or reduced-conformational compacted initial states every time. Those initial states were attained by reduction of the oxidized film at rising cathodic potentials for the same reduction time each. Rising reduced and conformational compacted states give slower subsequent oxidation rates by potential step to the same anodic potential every time. The activation energy, the reaction coefficient and reaction orders change for rising conformational compacted initial states. Decreasing rate constants and increasing activation energies are obtained for the PEDOT oxidation from increasing conformational compacted initial states. The experimental activation energy presents two linear ranges as a function of the initial reduced-compacted state. Using as initial states for the oxidation open structures attained by reduction at low cathodic potentials, activation energies attained were constant: namely the chemical activation energy. Using as initial states for the oxidation deeper reduced, closed and packed conformational structures, the activation energy includes two components: the constant chemical energy plus the conformational energy required to relax the conformational structure generating free volume which allows the entrance of the balancing counterions required for the reaction. The conformational energy increases linearly as a function of the reduction-compaction potential. The kinetic magnitudes include conformational and structural information. The Chemical Kinetics becomes Structural (or conformational) Chemical Kinetics.

Transverse conformal Killing forms on Kähler foliations

NASA Astrophysics Data System (ADS)

Jung, Seoung Dal

2015-04-01

On a closed, connected Riemannian manifold with a Kähler foliation of codimension q = 2 m, any transverse Killing r(≥ 2) -form is parallel (Jung and Jung, 2012). In this paper, we study transverse conformal Killing forms on Kähler foliations. In fact, if the foliation is minimal, then for any transverse conformal Killing r-form ϕ(2 ≤ r ≤ q - 2), Jϕ is parallel. Here J is defined in Section 4.

New open conformation of SMYD3 implicates conformational selection and allostery

PubMed Central

Spellmon, Nicholas; Sun, Xiaonan; Xue, Wen; Holcomb, Joshua; Chakravarthy, Srinivas; Shang, Weifeng; Edwards, Brian; Sirinupong, Nualpun; Li, Chunying; Yang, Zhe

2016-01-01

SMYD3 plays a key role in cancer cell viability, adhesion, migration and invasion. SMYD3 promotes formation of inducible regulatory T cells and is involved in reducing autoimmunity. However, the nearly “closed” substrate-binding site and poor in vitro H3K4 methyltransferase activity have obscured further understanding of this oncogenically related protein. Here we reveal that SMYD3 can adopt an “open” conformation using molecular dynamics simulation and small-angle X-ray scattering. This ligand-binding-capable open state is related to the crystal structure-like closed state by a striking clamshell-like inter-lobe dynamics. The two states are characterized by many distinct structural and dynamical differences and the conformational transition pathway is mediated by a reversible twisting motion of the C-terminal domain (CTD). The spontaneous transition from the closed to open states suggests two possible, mutually non-exclusive models for SMYD3 functional regulation and the conformational selection mechanism and allostery may regulate the catalytic or ligand binding competence of SMYD3. This study provides an immediate clue to the puzzling role of SMYD3 in epigenetic gene regulation. PMID:28050603

49 CFR 178.39 - Specification 3BN seamless nickel cylinders.

Code of Federal Regulations, 2013 CFR

2013-10-01

... manufactured using equipment and processes adequate to ensure that each cylinder produced conforms to the.... A reasonably smooth and uniform surface finish is required. Cylinders closed in by spinning process... plugs, etc.) for those openings. Threads conforming to the following are required on openings: (1...

49 CFR 178.39 - Specification 3BN seamless nickel cylinders.

Code of Federal Regulations, 2014 CFR

2014-10-01

... manufactured using equipment and processes adequate to ensure that each cylinder produced conforms to the.... A reasonably smooth and uniform surface finish is required. Cylinders closed in by spinning process... plugs, etc.) for those openings. Threads conforming to the following are required on openings: (1...

49 CFR 178.39 - Specification 3BN seamless nickel cylinders.

Code of Federal Regulations, 2012 CFR

2012-10-01

... manufactured using equipment and processes adequate to ensure that each cylinder produced conforms to the.... A reasonably smooth and uniform surface finish is required. Cylinders closed in by spinning process... plugs, etc.) for those openings. Threads conforming to the following are required on openings: (1...

49 CFR 178.346-4 - Outlets.

Code of Federal Regulations, 2010 CFR

2010-10-01

... must conform to § 178.345-11 and this section. (b) External self-closing stop-valves are not authorized as an alternative to internal self-closing stop-valves on loading/unloading outlets. [Amdt. 178-89...

Ligand Selectivity Mechanism and Conformational Changes in Guanine Riboswitch by Molecular Dynamics Simulations and Free Energy Calculations.

PubMed

Hu, Guodong; Ma, Aijing; Wang, Jihua

2017-04-24

Riboswitches regulate gene expression through direct and specific interactions with small metabolite molecules. Binding of a ligand to its RNA target is high selectivity and affinity and induces conformational changes of the RNA's secondary and tertiary structure. The structural difference of two purine riboswitches aptamers is caused by only one single mutation, where cytosine 74 in the guanine riboswitch is corresponding to a uracil 74 in adenine riboswitch. Here we employed molecular dynamics (MD) simulation, molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and thermodynamic integration computational methodologies to evaluate the energetic and conformational changes of ligands binding to purine riboswitches. The snapshots used in MM-PBSA calculation were extracted from ten 50 ns MD simulation trajectories for each complex. These free energy results are in consistent with the experimental data and rationalize the selectivity of the riboswitches for different ligands. In particular, it is found that the loss in binding free energy upon mutation is mainly electrostatic in guanine (GUA) and riboswitch complex. Furthermore, new hydrogen bonds are found in mutated complexes. To reveal the conformational properties of guanine riboswitch, we performed a total of 6 μs MD simulations in both the presence and the absence of the ligand GUA. The MD simulations suggest that the conformation of guanine riboswitch depends on the distance of two groups in the binding pocket of ligand. The conformation is in a close conformation when U51-A52 is close to C74-U75.

Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase

PubMed Central

2012-01-01

Background During elongation, multi-subunit RNA polymerases (RNAPs) cycle between phosphodiester bond formation and nucleic acid translocation. In the conformation associated with catalysis, the mobile “trigger loop” of the catalytic subunit closes on the nucleoside triphosphate (NTP) substrate. Closing of the trigger loop is expected to exclude water from the active site, and dehydration may contribute to catalysis and fidelity. In the absence of a NTP substrate in the active site, the trigger loop opens, which may enable translocation. Another notable structural element of the RNAP catalytic center is the “bridge helix” that separates the active site from downstream DNA. The bridge helix may participate in translocation by bending against the RNA/DNA hybrid to induce RNAP forward movement and to vacate the active site for the next NTP loading. The transition between catalytic and translocation conformations of RNAP is not evident from static crystallographic snapshots in which macromolecular motions may be restrained by crystal packing. Results All atom molecular dynamics simulations of Thermus thermophilus (Tt) RNAP reveal flexible hinges, located within the two helices at the base of the trigger loop, and two glycine hinges clustered near the N-terminal end of the bridge helix. As simulation progresses, these hinges adopt distinct conformations in the closed and open trigger loop structures. A number of residues (described as “switch” residues) trade atomic contacts (ion pairs or hydrogen bonds) in response to changes in hinge orientation. In vivo phenotypes and in vitro activities rendered by mutations in the hinge and switch residues in Saccharomyces cerevisiae (Sc) RNAP II support the importance of conformational changes predicted from simulations in catalysis and translocation. During simulation, the elongation complex with an open trigger loop spontaneously translocates forward relative to the elongation complex with a closed trigger loop. Conclusions Switching between catalytic and translocating RNAP forms involves closing and opening of the trigger loop and long-range conformational changes in the atomic contacts of amino acid side chains, some located at a considerable distance from the trigger loop and active site. Trigger loop closing appears to support chemistry and the fidelity of RNA synthesis. Trigger loop opening and limited bridge helix bending appears to promote forward nucleic acid translocation. PMID:22676913

Post-Translational Phosphorylation of Serine 74 of Human Deoxycytidine Kinase Favors the Enzyme Adopting the Open Conformation Making It Competent for Nucleoside Binding and Release

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hazra, Saugata; Szewczak, Andrzej; Ort, Stephan

2012-03-26

Deoxycytidine kinase (dCK) uses either ATP or UTP as a phosphoryl donor to catalyze the phosphorylation of nucleoside acceptors. The kinetic properties of human dCK are modulated in vivo by phosphorylation of serine 74. This residue is a part of the insert region and is distant from the active site. Replacing the serine with a glutamic acid (S74E variant) can mimic phosphorylation of Ser74. To understand how phosphorylation affects the catalytic properties of dCK, we examined the S74E variant of dCK both structurally and kinetically. We observe that the presence of a glutamic acid at position 74 favors the adoptionmore » by the enzyme of the open conformation. Glu74 stabilizes the open conformation by directly interacting with the indole side chain of Trp58, a residue that is in the proximity of the base of the nucleoside substrate. The open dCK conformation is competent for the binding of nucleoside but not for phosphoryl transfer. In contrast, the closed conformation is competent for phosphoryl transfer but not for product release. Thus, dCK must make the transition between the open and closed states during the catalytic cycle. We propose a reaction scheme for dCK that incorporates the transition between the open and closed states, and this serves to rationalize the observed kinetic differences between wild-type dCK and the S74E variant.« less

ESTIMATING RISK TO CALIFORNIA ENERGY INFRASTRUCTURE FROM PROJECTED CLIMATE CHANGE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sathaye, Jayant; Dale, Larry; Larsen, Peter

2011-06-22

This report outlines the results of a study of the impact of climate change on the energy infrastructure of California and the San Francisco Bay region, including impacts on power plant generation; transmission line and substation capacity during heat spells; wildfires near transmission lines; sea level encroachment upon power plants, substations, and natural gas facilities; and peak electrical demand. Some end-of-century impacts were projected:Expected warming will decrease gas-fired generator efficiency. The maximum statewide coincident loss is projected at 10.3 gigawatts (with current power plant infrastructure and population), an increase of 6.2 percent over current temperature-induced losses. By the end ofmore » the century, electricity demand for almost all summer days is expected to exceed the current ninetieth percentile per-capita peak load. As much as 21 percent growth is expected in ninetieth percentile peak demand (per-capita, exclusive of population growth). When generator losses are included in the demand, the ninetieth percentile peaks may increase up to 25 percent. As the climate warms, California's peak supply capacity will need to grow faster than the population.Substation capacity is projected to decrease an average of 2.7 percent. A 5C (9F) air temperature increase (the average increase predicted for hot days in August) will diminish the capacity of a fully-loaded transmission line by an average of 7.5 percent.The potential exposure of transmission lines to wildfire is expected to increase with time. We have identified some lines whose probability of exposure to fire are expected to increase by as much as 40 percent. Up to 25 coastal power plants and 86 substations are at risk of flooding (or partial flooding) due to sea level rise.« less

Cocaine use in the past year is associated with altitude of residence.

PubMed

Fiedler, Kristen K; Kim, Namkug; Kondo, Douglas G; Renshaw, Perry F

2012-06-01

Recently, increased rates of suicide in US counties at higher altitudes have been noted. Because of the documented association between cocaine use and suicide, we hypothesized that there would be a correlation between incidence of cocaine use and altitude of residence. Cocaine use data were obtained from the Substate Substance Abuse Estimates from the 1999-2001 National Surveys on Drug Use and Health. Data related to the percentages of people 12 years or older who used cocaine in the past year. Average elevation for US counties was calculated using the Shuttle Radar Topography Mission elevation data set, and subject region elevation was calculated by averaging the weighted elevations of each region's relevant counties. The correlation between elevation of a substate region and incidence of cocaine use in that region was calculated using Pearson correlation coefficients. A significant correlation exists between mean altitude of a substate region and incidence of cocaine use in that region (r = 0.34; P < 0.0001). Regression analysis controlling for age, sex, race, education level, income, unemployment, and population density was performed. Altitude remained a significant factor (P = 0.007), whereas male sex (P = 0.008) and possessing less than a college education (P < 0.0001) were also significant predictors of self-reported cocaine use in the past year. It is important to note that cocaine use was assessed in isolation of other drugs of abuse, an additional confounding variable. This study demonstrates a significant correlation between altitude of substate region of residence and incidence of cocaine use. It is possible that stress response due to hypoxia is responsible; however, this requires further investigation. However, because other substance use was not assessed, specificity of this association is unknown. In addition, this correlation may help explain the increased rate of suicide in areas of higher elevation.

The importance of substate surveillance in detection of geographic oral health inequalities in a small state.

PubMed

Anderson, Ludmila; Martin, Nancy R; Flynn, Regina T; Knight, Susan

2012-01-01

Considering that 42% of children and adolescents and 91% of dentate adults experience dental caries, oral disease is a public health problem. Although the population's oral health is improving, certain subgroups remain at increased risk for dental disease. To assess the oral health status at the substate level and explore the possibility of geographic oral health inequalities in New Hampshire while building upon existing surveillance data sets. We used the Third Grade Oral Health and NH Behavioral Risk Factor Surveillance System surveys. We ensured the availability of substate level data and compared county/region specific estimates. New Hampshire. Adults and third-grade students in public schools. The prevalence of dental caries, untreated caries, and dental sealants among children; and the insurance status, utilization of dental services, and edentulism among adults. Of the 10 counties, the northernmost Coos County had consistently worse outcomes when compared with other counties. Only 64% of adult Coos County residents reported a dental visit in the past year; of these, 66% reported dental cleaning. Among adults 65 years and older, 29% were edentulous. In comparison with the state overall, these estimates were 76%, 77%, and 19%, respectively. Coos County third-grade students had the highest prevalence of dental caries experience (64% compared with 44% in New Hampshire) and untreated caries (31% compared with 12%), and only 24% had dental sealants (state prevalence is 60%). Overall oral health status in our state is favorable and comparable with the nation, yet significant geographic inequalities exist among children and adults. The oral health status of disparate groups can be improved using tailored interventions such as community water fluoridation or expansion of school-based dental sealant programs. Surveillance at the substate level is an essential part of the planning, targeting, and progress monitoring.

Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal A Novel Type IA Topoisomerase-DNA Conformational Intermediate

PubMed Central

Changela, Anita; DiGate, Russell J.; Mondragón, Alfonso

2007-01-01

Summary E. coli DNA topoisomerase III belongs to the type IA family of DNA topoisomerases, which transiently cleave single-stranded DNA (ssDNA) via a 5′ phosphotyrosine intermediate. We have solved crystal structures of wild-type E. coli topoisomerase III bound to an 8-base ssDNA molecule in three different pH environments. The structures reveal the enzyme in three distinct conformational states while bound to DNA. One conformation resembles the one observed previously with a DNA-bound, catalytically inactive mutant of topoisomerase III where DNA binding realigns catalytic residues to form a functional active site. Another conformation represents a novel intermediate in which DNA is bound along the ssDNA-binding groove but does not enter the active site, which remains in a catalytically inactive, closed state. A third conformation shows an intermediate state where the enzyme is still in a closed state, but the ssDNA is starting to invade the active site. For the first time, the active site region in the presence of both the catalytic tyrosine and ssDNA substrate is revealed for a type IA DNA topoisomerase, although there is no evidence of ssDNA cleavage. Comparative analysis of the various conformational states suggests a sequence of domain movements undertaken by the enzyme upon substrate binding. PMID:17331537

Commuting symmetry operators of the Dirac equation, Killing-Yano and Schouten-Nijenhuis brackets

NASA Astrophysics Data System (ADS)

Cariglia, Marco; Krtouš, Pavel; Kubizňák, David

2011-07-01

In this paper we derive the most general first-order symmetry operator commuting with the Dirac operator in all dimensions and signatures. Such an operator splits into Clifford even and Clifford odd parts which are given in terms of odd Killing-Yano and even closed conformal Killing-Yano inhomogeneous forms, respectively. We study commutators of these symmetry operators and give necessary and sufficient conditions under which they remain of the first-order. In this specific setting we can introduce a Killing-Yano bracket, a bilinear operation acting on odd Killing-Yano and even closed conformal Killing-Yano forms, and demonstrate that it is closely related to the Schouten-Nijenhuis bracket. An important nontrivial example of vanishing Killing-Yano brackets is given by Dirac symmetry operators generated from the principal conformal Killing-Yano tensor [hep-th/0612029]. We show that among these operators one can find a complete subset of mutually commuting operators. These operators underlie separability of the Dirac equation in Kerr-NUT-(A)dS spacetimes in all dimensions [arXiv:0711.0078].

Pilot Non-Conformance to Alerting System Commands During Closely Spaced Parallel Approaches

NASA Technical Reports Server (NTRS)

Pritchett, Amy Ruth; Hansman, R. John; Corker, Kevin (Technical Monitor)

1997-01-01

Cockpit alerting systems monitor potentially hazardous situations, both inside and outside the aircraft. When a hazard is projected to occur, the alerting system displays alerts and/or command decisions to the pilot. However, pilots have been observed to not conform to alerting system commands by delaying their response or by not following the automatic commands exactly. This non-conformance to the automatic alerting system can reduce its benefit. Therefore, a need exists to understand the causes and effects of pilot non-conformance in order to develop automatic alerting systems whose commands the pilots are more likely to follow. These considerations were examined through flight simulator evaluations of the collision avoidance task during closely spaced parallel approaches. This task provided a useful case-study because the effects of non-conformance can be significant, given the time-critical nature of the task. A preliminary evaluation of alerting systems identified non-conformance in over 40% of the cases and a corresponding drop in collision avoidance performance. A follow-on experiment found subjects' alerting and maneuver selection criteria were consistent with different strategies than those used by automatic systems, indicating the pilot may potentially disagree with the alerting system if the pilot attempts to verify automatic alerts and commanded avoidance maneuvers. A final experiment found supporting automatic alerts with the explicit display of its underlying criteria resulted in more consistent subject reactions. In light of these experimental results, a general discussion of pilot non-conformance is provided. Contributing factors in pilot non-conformance include a lack of confidence in the automatic system and mismatches between the alerting system's commands and the pilots' own decisions based on the information available to them. The effects of non-conformance on system performance are discussed. Possible methods of reconciling mismatches are given, and design considerations for alerting systems which alleviate the problem of non-conformance are provided.

Conformational effects on circular dichroism in the photoelectron angular distribution.

PubMed

Di Tommaso, Devis; Stener, Mauro; Fronzoni, Giovanna; Decleva, Piero

2006-04-10

The B-spline density-functional method has been applied to the conformers of the (1R, 2R)-1,2-dibromo-1,2-dichloro-1,2-difluoroethane molecule. The cross section, asymmetry, and dichroic parameters relative to core and valence orbitals, which do not change their nature along the conformational curve, have been systematically studied. While the cross section and the asymmetry parameter are weakly affected, the dichroic parameter appears to be rather sensitive to the particular conformer of the molecule, suggesting that this dynamical property could be a useful tool for conformational analysis. The computational method has also been applied to methyl rotation in methyloxirane. Unexpected and dramatic sensitivity of the dichroic-parameter profile to the methyl rotation, both in the core and valence states, has been found. Boltzmann averaging over the conformers reproduces quite closely the profiles previously obtained for the minimum-energy conformation, which is in good agreement with the experimental results.

Citrate synthase proteins in extremophilic organisms: Studies within a structure-based model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Różycki, Bartosz, E-mail: rozycki@ifpan.edu.pl; Cieplak, Marek

2014-12-21

We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the closed and two in the open conformations. Even though the proteins belong to the same fold, the model distinguishes the properties of these proteins in a way which is consistent with experiments. For instance, the thermophilic proteins are more stable thermodynamically than their mesophilic and cryophilic homologues, which we observe both in the magnitude of thermal fluctuations near the native state and in the kineticsmore » of thermal unfolding. The level of stability correlates with the average coordination number for amino acid contacts and with the degree of structural compactness. The pattern of positional fluctuations along the sequence in the closed conformation is different than in the open conformation, including within the active site. The modes of correlated and anticorrelated movements of pairs of amino acids forming the active site are very different in the open and closed conformations. Taken together, our results show that the precise location of amino acid contacts in the native structure appears to be a critical element in explaining the similarities and differences in the thermodynamic properties, local flexibility, and collective motions of the different forms of the enzyme.« less

Characterization of archaeal group II chaperonin-ADP-metal fluoride complexes: implications that group II chaperonins operate as a "two-stroke engine".

PubMed

Iizuka, Ryo; Yoshida, Takao; Ishii, Noriyuki; Zako, Tamotsu; Takahashi, Kazunobu; Maki, Kosuke; Inobe, Tomonao; Kuwajima, Kunihiro; Yohda, Masafumi

2005-12-02

Group II chaperonins, found in Archaea and in the eukaryotic cytosol, act independently of a cofactor corresponding to GroES of group I chaperonins. Instead, the helical protrusion at the tip of the apical domain forms a built-in lid of the central cavity. Although many studies on the lid's conformation have been carried out, the conformation in each step of the ATPase cycle remains obscure. To clarify this issue, we examined the effects of ADP-aluminum fluoride (AlFx) and ADP-beryllium fluoride (BeFx) complexes on alpha-chaperonin from the hyperthermophilic archaeum, Thermococcus sp. strain KS-1. Biochemical assays, electron microscopic observations, and small angle x-ray scattering measurements demonstrate that alpha-chaperonin incubated with ADP and BeFx exists in an asymmetric conformation; one ring is open, and the other is closed. The result indicates that alpha-chaperonin also shares the inherent functional asymmetry of bacterial and eukaryotic cytosolic chaperonins. Most interestingly, addition of ADP and BeFx induced alpha-chaperonin to encapsulate unfolded proteins in the closed ring but did not trigger their folding. Moreover, alpha-chaperonin incubated with ATP and AlFx or BeFx adopted a symmetric closed conformation, and its functional turnover was inhibited. These forms are supposed to be intermediates during the reaction cycle of group II chaperonins.

Citrate synthase proteins in extremophilic organisms: Studies within a structure-based model

NASA Astrophysics Data System (ADS)

RóŻycki, Bartosz; Cieplak, Marek

2014-12-01

We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the closed and two in the open conformations. Even though the proteins belong to the same fold, the model distinguishes the properties of these proteins in a way which is consistent with experiments. For instance, the thermophilic proteins are more stable thermodynamically than their mesophilic and cryophilic homologues, which we observe both in the magnitude of thermal fluctuations near the native state and in the kinetics of thermal unfolding. The level of stability correlates with the average coordination number for amino acid contacts and with the degree of structural compactness. The pattern of positional fluctuations along the sequence in the closed conformation is different than in the open conformation, including within the active site. The modes of correlated and anticorrelated movements of pairs of amino acids forming the active site are very different in the open and closed conformations. Taken together, our results show that the precise location of amino acid contacts in the native structure appears to be a critical element in explaining the similarities and differences in the thermodynamic properties, local flexibility, and collective motions of the different forms of the enzyme.

Effects of protonation state of Asp181 and position of active site water molecules on the conformation of PTP1B.

PubMed

Ozcan, Ahmet; Olmez, Elif Ozkirimli; Alakent, Burak

2013-05-01

In protein tyrosine phosphatase 1B (PTP1B), the flexible WPD loop adopts a closed conformation (WPDclosed ) in the active state of PTP1B, bringing the catalytic Asp181 close to the active site pocket, while WPD loop is in an open conformation (WPDopen ) in the inactive state. Previous studies showed that Asp181 may be protonated at physiological pH, and ordered water molecules exist in the active site. In the current study, molecular dynamics simulations are employed at different Asp181 protonation states and initial positions of active site water molecules, and compared with the existing crystallographic data of PTP1B. In WPDclosed conformation, the active site is found to maintain its conformation only in the protonated state of Asp181 in both free and liganded states, while Asp181 is likely to be deprotonated in WPDopen conformation. When the active site water molecule network that is a part of the free WPDclosed crystal structure is disrupted, intermediate WPD loop conformations, similar to that in the PTPRR crystal structure, are sampled in the MD simulations. In liganded PTP1B, one active site water molecule is found to be important for facilitating the orientation of Cys215 and the phosphate ion, thus may play a role in the reaction. In conclusion, conformational stability of WPD loop, and possibly catalytic activity of PTP1B, is significantly affected by the protonation state of Asp181 and position of active site water molecules, showing that these aspects should be taken into consideration both in MD simulations and inhibitor design. Copyright © 2013 Wiley Periodicals, Inc.

A quantum leap into the IED age

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patterson, R.C.

1996-11-01

The integration of pattern recognition, artificial intelligence and advanced communication technologies in utility substation IED`s (Intelligent Electronic Devices) has opened the door to practical and cost effective automation of power distribution systems. A major driver for the application of these new technologies has been the research directed toward the detection of high-impedance faults. The commercial products which embody these complex detection functions have already expanded to include most of the protection, control, and monitoring required at a utility substation. These new Super-IED`s enable major utility initiatives, such as power quality management, improved public safety, operation and maintenance productivity, and powermore » system automation.« less

Doubly Fed Induction Generator in an Offshore Wind Power Plant Operated at Rated V/Hz: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Muljadi, E.; Singh, M.; Gevorgian, V.

2012-06-01

This paper introduces the concept of constant Volt/Hz operation of offshore wind power plants. The deployment of offshore WPPs requires power transmission from the plant to the load center inland. Since this power transmission requires submarine cables, there is a need to use High-Voltage Direct Current transmission, which is economical for transmission distances longer than 50 kilometers. In the concept presented here, the onshore substation is operated at 60 Hz synced with the grid, and the offshore substation is operated at variable frequency and voltage, thus allowing the WPP to be operated at constant Volt/Hz.

Analysis of the 60-Hz power system at KSC: The Orsino substation

NASA Technical Reports Server (NTRS)

Kalu, Alex O.

1989-01-01

An analysis of the Orsino Substation, a component (50 percent) of the 60-Hertz electric power system at the Kennedy Space Center, is presented. Presented here are separate single-line diagrams of the sixteen feeder circuits to permit easy access to information on the individual feeders for future planning. The load condition of each feeder and load break switch are presented and a heuristic reliability analysis of the system is performed. Information is given about the system fashion useful for decision making purposes. The beauty of it is in the simplified manner by which information about the system can be obtained.

Study on the Transient Process of 500kV Substations Secondary Equipment

NASA Astrophysics Data System (ADS)

Li, Hongbo; Li, Pei; Zhang, Yanyan; Niu, Lin; Gao, Nannan; Si, Tailong; Guo, Jiadong; Xu, Min-min; Li, Guofeng; Guo, Liangfeng

2017-05-01

By analyzing on the reason of the lightning accident occur in the substation, the way of lightning incoming surge invading the secondary system is summarized. The interference source acts on the secondary system through various coupling paths. It mainly consists of four ways: the conductance coupling mode, the Capacitive Coupling Mode, the inductive coupling mode, The Radiation Interference Model. Then simulated the way with the program-ATP. At last, from the three aspects of low-voltage power supply system, the impact potential distribution of grounding grid, the secondary system and the computer system. The lightning protection measures is put forward.

An Economic Analysis and Approach for Health Care Preparedness in a Substate Region.

PubMed

Stryckman, Benoit; Grace, Thomas L; Schwarz, Peter; Marcozzi, David

2015-08-01

To demonstrate the application of economics to health care preparedness by estimating the financial return on investment in a substate regional emergency response team and to develop a financial model aimed at sustaining community-level disaster readiness. Economic evaluation methods were applied to the experience of a regional Pennsylvania response capability. A cost-benefit analysis was performed by using information on funding of the response team and 17 real-world events the team responded to between 2008 and 2013. By use of the results of the cost-benefit analysis as well as information on the response team's catchment area, a risk-based insurance-like membership model was built. The cost-benefit analysis showed a positive return after 6 years of investment in the regional emergency response team. Financial modeling allowed for the calculation of premiums for 2 types of providers within the emergency response team's catchment area: hospitals and long-term care facilities. The analysis indicated that preparedness activities have a positive return on their investment in this substate region. By applying economic principles, communities can estimate their return on investment to make better business decisions in an effort to increase the sustainability of emergency preparedness programs at the regional level.

Progress of gas-insulated transformers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Togawa, Y.; Ikeda, M.; Toda, K.

The world`s first transformer was manufactured at Ganz in Hungary in 1885. Two years later in 1887 patents applications were made for about oil immersed transformers in the US. Since then, oil immersed types have predominated for medium- and large-capacity transformers, which are now giving way to gas insulated transformers in some areas. Behind such trends are plans to construct substations inside buildings or underground, because of the difficulty in acquiring land for substations in large cities where power demand is concentrated. Requirements are protection against accidents, compactness and overall economy. Total gas insulated substations combining GIS units and gasmore » insulated transformers these needs. Demand for gas insulated transformers has been increasing rapidly, particularly in Japan and Hong Kong. First, relatively small-capacity models below 20--30 MVA were put into practical use and today 275 kV, 300 MVa models are in use and 500kV, 1,500 MVA models are coming into use. Engineering is progressing very rapidly in these areas. This paper describes the design techniques and important maintenance techniques for the latest gas insulated transformers from 5,000 kVA to 300 MVA.« less

IEA Wind Task 26: Offshore Wind Farm Baseline Documentation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smart, Gavin; Smith, Aaron; Warner, Ethan

This document has been produced to provide the definition and rationale for the Baseline Offshore Wind Farm established within IEA Wind Task 26--Cost of Wind Energy. The Baseline has been developed to provide a common starting point for country comparisons and sensitivity analysis on key offshore wind cost and value drivers. The baseline project reflects an approximate average of the characteristics of projects installed between 2012 and 2014, with the project life assumed to be 20 years. The baseline wind farm is located 40 kilometres (km) from construction and operations and maintenance (O&M) ports and from export cable landfall. Themore » wind farm consists of 100 4-megawatt (MW) wind turbines mounted on monopile foundations in an average water depth of 25 metres (m), connected by 33-kilovolt (kV) inter-array cables. The arrays are connected to a single offshore substation (33kV/220kV) mounted on a jacket foundation, with the substation connected via a single 220kV export cable to an onshore substation, 10km from landfall. The wind farm employs a port-based O&M strategy using crew-transfer vessels.« less

Occupational exposure to electric and magnetic fields during work tasks at 110 kV substations in the Tampere region.

PubMed

Korpinen, Leena H; Pääkkönen, Rauno J

2010-04-01

The occupational exposure to electric and magnetic fields during various work tasks at seven 110 kV substations in Finland's Tampere region was studied. The aim was to investigate if the action values (10 kV/m for the E-field and 500 microT for the B-field) of the EU Directive 2004/40/EC were exceeded. Electric and magnetic fields were measured during the following work tasks: (1) walking or operating devices on the ground; (2) working from a service platform; (3) working around the power transformer on the ground or using a ladder; and (4) changing a bulb from a man hoist. In work task 2 "working from a service platform" the measured electric field (maximum value 16.6 kV/m) exceeded 10 kV/m in three cases. In the future it is important to study if the limit value (10 mA/m(2)) of Directive 2004/40/EC is exceeded at 110 kV substations. The occupational 500 microT action value of the magnetic flux density field (B-field) was not exceeded in any working situation.

Torsion-rotation-vibration effects in the ground and first excited states of methacrolein, a major atmospheric oxidation product of isoprene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zakharenko, O.; Motiyenko, R. A.; Aviles Moreno, J.-R.

Methacrolein is a major oxidation product of isoprene emitted in the troposphere. New spectroscopy information is provided with the aim to allow unambiguous identification of this complex molecule, characterized by a large amplitude motion associated with the methyl top. State-of-the-art millimeter-wave spectroscopy experiments coupled to quantum chemical calculations have been performed. For the most stable s-trans conformer of atmospheric interest, the torsional and rotational structures have been characterized for the ground state, the first excited methyl torsional state (ν{sub 27}), and the first excited skeletal torsional state (ν{sub 26}). The inverse sequence of A and E tunneling sub-states as wellmore » as anomalous A-E splittings observed for the rotational lines of v{sub 26} = 1 state clearly indicates a coupling between methyl torsion and skeletal torsion. A comprehensive set of molecular parameters has been obtained. The far infrared spectrum of Durig et al. [Spectrochim. Acta, Part A 42, 89–103 (1986)] was reproduced, and a Fermi interaction between ν{sub 25} and 2ν{sub 27} was evidenced.« less

Improved activity of α-chymotrypsin on silica particles - A high-pressure stopped-flow study.

PubMed

Schuabb, Vitor; Winter, Roland; Czeslik, Claus

2016-11-01

Pressure is well known to affect the catalytic rate of enzymes dissolved in solution. To better understand enzyme kinetics at aqueous-solid interfaces, we have carried out a high-pressure stopped-flow activity study of α-chymotrypsin (α-CT) that is adsorbed on silica particles and, for comparison, dissolved in solution. The enzyme reaction was modulated using pressures up to 2000bar and recorded using the high-pressure stopped-flow technique. The results indicate an 8-fold enhancement of the turnover number upon α-CT adsorption and a further increase of the catalytic rate in the pressure range up to 1000bar. From the pressure dependence of the catalytic rate, apparent activation volumes have been determined. In the adsorbed state of α-CT, a pronounced change of the activation volume is found with increasing pressure. Furthermore, owing to suppression of its autolysis, a significantly longer storage time of α-CT can be achieved when the enzyme is adsorbed on silica particles. The results obtained are discussed in terms of a surface-induced selection of conformational substates of the enzyme-substrate complex. Copyright © 2016 Elsevier B.V. All rights reserved.

Slow Domain Motions of an Oligomeric Protein from Deep-Sea Hyperthermophile probed by Neutron Spin Echo

NASA Astrophysics Data System (ADS)

Bhowmik, Debsindhu; Shrestha, Utsab; Dhindsa, Gurpreet; Sharp, Melissa; Stingaciu, Laura R.; Chu, Xiang-Qiang; Xiang-Qiang Chu Team

Deep-sea microorganisms have the ability to survive under extreme conditions, such as high pressure and high temperature. In this work, we used the combination of the neutron spin-echo (NSE) and the small angle neutron scattering (SANS) techniques to study the inter-domain motions of the inorganic pyrophosphate (IPPase) enzyme derived from thermostable microorganisms Thermococcus thioreducens. The IPPase has hexameric quaternary structure with molecular mass of approx. 120kDa (each subunit of 20kDa), which is a large oligomeric structure. The understanding of its slow inter-domain motions can be the key to explain how they are able to perform catalytic activity at higher temperature compared to mesophilic enzymes, thus leading to adapt to extreme environment present at the seabed. The NSE can probe these slow motions directly in the time domain up to several tens of nanoseconds at the nanometers length scales, while the corresponding structural change can be explored by the SANS. Our results provide a better picture of the local flexibility and conformational substates unique to these types of proteins, which will help us better understandthe relation between protein dynamics and their biological activities

How and How Much Molecular Conformation Affects Electronic Circular Dichroism: The Case of 1,1-Diarylcarbinols.

PubMed

Padula, Daniele; Pescitelli, Gennaro

2018-01-09

Chiroptical spectra such as electronic circular dichroism (ECD) are said to be much more sensitive to conformation than their non-chiroptical counterparts, however, it is difficult to demonstrate such a common notion in a clear-cut way. We run DFT and TDDFT calculations on two closely related 1,1-diarylmethanols which show mirror-image ECD spectra for the same absolute configuration. We demonstrate that the main reason for the different chiroptical response of the two compounds lies in different conformational ensembles, caused by a single hydrogen-to-methyl substitution. We conclude that two compounds, having the same configuration but different conformation, may exhibit mirror-image ECD signals, stressing the importance and impact of conformational factors on ECD spectra.

Conformational dynamics of a G-protein α subunit is tightly regulated by nucleotide binding.

PubMed

Goricanec, David; Stehle, Ralf; Egloff, Pascal; Grigoriu, Simina; Plückthun, Andreas; Wagner, Gerhard; Hagn, Franz

2016-06-28

Heterotrimeric G proteins play a pivotal role in the signal-transduction pathways initiated by G-protein-coupled receptor (GPCR) activation. Agonist-receptor binding causes GDP-to-GTP exchange and dissociation of the Gα subunit from the heterotrimeric G protein, leading to downstream signaling. Here, we studied the internal mobility of a G-protein α subunit in its apo and nucleotide-bound forms and characterized their dynamical features at multiple time scales using solution NMR, small-angle X-ray scattering, and molecular dynamics simulations. We find that binding of GTP analogs leads to a rigid and closed arrangement of the Gα subdomain, whereas the apo and GDP-bound forms are considerably more open and dynamic. Furthermore, we were able to detect two conformational states of the Gα Ras domain in slow exchange whose populations are regulated by binding to nucleotides and a GPCR. One of these conformational states, the open state, binds to the GPCR; the second conformation, the closed state, shows no interaction with the receptor. Binding to the GPCR stabilizes the open state. This study provides an in-depth analysis of the conformational landscape and the switching function of a G-protein α subunit and the influence of a GPCR in that landscape.

Conformational dynamics of a G-protein α subunit is tightly regulated by nucleotide binding

PubMed Central

Goricanec, David; Stehle, Ralf; Egloff, Pascal; Grigoriu, Simina; Wagner, Gerhard; Hagn, Franz

2016-01-01

Heterotrimeric G proteins play a pivotal role in the signal-transduction pathways initiated by G-protein–coupled receptor (GPCR) activation. Agonist–receptor binding causes GDP-to-GTP exchange and dissociation of the Gα subunit from the heterotrimeric G protein, leading to downstream signaling. Here, we studied the internal mobility of a G-protein α subunit in its apo and nucleotide-bound forms and characterized their dynamical features at multiple time scales using solution NMR, small-angle X-ray scattering, and molecular dynamics simulations. We find that binding of GTP analogs leads to a rigid and closed arrangement of the Gα subdomain, whereas the apo and GDP-bound forms are considerably more open and dynamic. Furthermore, we were able to detect two conformational states of the Gα Ras domain in slow exchange whose populations are regulated by binding to nucleotides and a GPCR. One of these conformational states, the open state, binds to the GPCR; the second conformation, the closed state, shows no interaction with the receptor. Binding to the GPCR stabilizes the open state. This study provides an in-depth analysis of the conformational landscape and the switching function of a G-protein α subunit and the influence of a GPCR in that landscape. PMID:27298341

DOE Office of Scientific and Technical Information (OSTI.GOV)

Changela, Anita; DiGate, Russell J.; Mondragon, Alfonso

Escherichia coli DNA topoisomerase III belongs to the type IA family of DNA topoisomerases, which transiently cleave single-stranded DNA (ssDNA) via a 5{prime} phosphotyrosine intermediate. We have solved crystal structures of wild-type E. coli topoisomerase III bound to an eight-base ssDNA molecule in three different pH environments. The structures reveal the enzyme in three distinct conformational states while bound to DNA. One conformation resembles the one observed previously with a DNA-bound, catalytically inactive mutant of topoisomerase III where DNA binding realigns catalytic residues to form a functional active site. Another conformation represents a novel intermediate in which DNA is boundmore » along the ssDNA-binding groove but does not enter the active site, which remains in a catalytically inactive, closed state. A third conformation shows an intermediate state where the enzyme is still in a closed state, but the ssDNA is starting to invade the active site. For the first time, the active site region in the presence of both the catalytic tyrosine and ssDNA substrate is revealed for a type IA DNA topoisomerase, although there is no evidence of ssDNA cleavage. Comparative analysis of the various conformational states suggests a sequence of domain movements undertaken by the enzyme upon substrate binding.« less

Structure of the Biliverdin Cofactor in the Pfr State of Bathy and Prototypical Phytochromes*

PubMed Central

Salewski, Johannes; Escobar, Francisco Velazquez; Kaminski, Steve; von Stetten, David; Keidel, Anke; Rippers, Yvonne; Michael, Norbert; Scheerer, Patrick; Piwowarski, Patrick; Bartl, Franz; Frankenberg-Dinkel, Nicole; Ringsdorf, Simone; Gärtner, Wolfgang; Lamparter, Tilman; Mroginski, Maria Andrea; Hildebrandt, Peter

2013-01-01

Phytochromes act as photoswitches between the red- and far-red absorbing parent states of phytochromes (Pr and Pfr). Plant phytochromes display an additional thermal conversion route from the physiologically active Pfr to Pr. The same reaction pattern is found in prototypical biliverdin-binding bacteriophytochromes in contrast to the reverse thermal transformation in bathy bacteriophytochromes. However, the molecular origin of the different thermal stabilities of the Pfr states in prototypical and bathy bacteriophytochromes is not known. We analyzed the structures of the chromophore binding pockets in the Pfr states of various bathy and prototypical biliverdin-binding phytochromes using a combined spectroscopic-theoretical approach. For the Pfr state of the bathy phytochrome from Pseudomonas aeruginosa, the very good agreement between calculated and experimental Raman spectra of the biliverdin cofactor is in line with important conclusions of previous crystallographic analyses, particularly the ZZEssa configuration of the chromophore and its mode of covalent attachment to the protein. The highly homogeneous chromophore conformation seems to be a unique property of the Pfr states of bathy phytochromes. This is in sharp contrast to the Pfr states of prototypical phytochromes that display conformational equilibria between two sub-states exhibiting small structural differences at the terminal methine bridges A-B and C-D. These differences may mainly root in the interactions of the cofactor with the highly conserved Asp-194 that occur via its carboxylate function in bathy phytochromes. The weaker interactions via the carbonyl function in prototypical phytochromes may lead to a higher structural flexibility of the chromophore pocket opening a reaction channel for the thermal (ZZE → ZZZ) Pfr to Pr back-conversion. PMID:23603902

Transition paths of Met-enkephalin from Markov state modeling of a molecular dynamics trajectory.

PubMed

Banerjee, Rahul; Cukier, Robert I

2014-03-20

Conformational states and their interconversion pathways of the zwitterionic form of the pentapeptide Met-enkephalin (MetEnk) are identified. An explicit solvent molecular dynamics (MD) trajectory is used to construct a Markov state model (MSM) based on dihedral space clustering of the trajectory, and transition path theory (TPT) is applied to identify pathways between open and closed conformers. In the MD trajectory, only four of the eight backbone dihedrals exhibit bistable behavior. Defining a conformer as the string XXXX with X = "+" or "-" denoting, respectively, positive or negative values of a given dihedral angle and obtaining the populations of these conformers shows that only four conformers are highly populated, implying a strong correlation among these dihedrals. Clustering in dihedral space to construct the MSM finds the same four bistable dihedral angles. These state populations are very similar to those found directly from the MD trajectory. TPT is used to obtain pathways, parametrized by committor values, in dihedral state space that are followed in transitioning from closed to open states. Pathway costs are estimated by introducing a kinetics-based procedure that orders pathways from least (shortest) to greater cost paths. The least costly pathways in dihedral space are found to only involve the same XXXX set of dihedral angles, and the conformers accessed in the closed to open transition pathways are identified. For these major pathways, a correlation between reaction path progress (committors) and the end-to-end distance is identified. A dihedral space principal component analysis of the MD trajectory shows that the first three modes capture most of the overall fluctuation, and pick out the same four dihedrals having essentially all the weight in those modes. A MSM based on root-mean-square backbone clustering was also carried out, with good agreement found with dihedral clustering for the static information, but with results that differ significantly for the pathway analysis.

Antibacterial properties of (2,3)-alpha- and (2,3)-beta-methylene analogs of penicillin G.

PubMed Central

Christenson, J G; Pruess, D L; Talbot, M K; Keith, D D

1988-01-01

The penam nucleus can assume two conformations; these are designated open and closed. The synthetic (2,3)-alpha- and (2,3)-beta-methylenepenams can be regarded as analogs of the open and closed conformations, respectively. It has been shown that the beta-methylenepenams are essentially inactive, suggesting that the closed conformation of penams is also inactive. In this study, we investigated a series of beta-lactams, all of which contained phenylacetamido side chains: penicillin G, the (2,3)-alpha- and (2,3)-beta-methylenepenams, and the 3-acetoxymethyl- and 3-methylcephalosporins. The alpha-methylenepenam and penicillin G were the most active compounds, while the beta-methylene isomer was only poorly active. Results with permeability mutants suggested that the alpha-methylene compound penetrated the outer membrane somewhat more readily than penicillin G did. The intrinsic potency of the alpha-methylenepenam appeared to be similar to that of penicillin G, on the basis of their affinities for penicillin-binding proteins and their abilities to inhibit peptidoglycan synthesis in ether-permeabilized Escherichia coli, while the beta-methylene analog had very poor intrinsic potency. The alpha-methylene analog was about 10-fold more efficient (Vmax/Km) than penicillin G as a substrate for the cephalosporinases from Enterobacter cloacae and Proteus vulgaris, but it was about 40-fold less efficient with penicillinase from Staphylococcus aureus. These results strongly support the hypothesis that the active conformation of penams is the open conformation and suggest that the position in space of the carboxyl group relative to the beta-lactam carbonyl is an important determinant of cephalosporinlike character, as distinct from penicillinlike character. Images PMID:3190190

Lid dynamics of porcine pancreatic lipase in non-aqueous solvents.

PubMed

Haque, Neshatul; Prabhu, N Prakash

2016-10-01

Understanding the dynamics of enzymes in organic solvents has wider implications on their industrial applications. Pancreatic lipases, which show activity in their lid open-state, demonstrate enhanced activity in organic solvents at higher temperatures. However, the lid dynamics of pancreatic lipases in non-aqueous environment is yet to be clearly understood. Dynamics of porcine pancreatic lipase (PPL) in open and closed conformations was followed in ethanol, toluene, and octanol using molecular simulation methods. In silico double mutant D250V and E254L of PPL (PPLmut-Cl) was created and its lid opening dynamics in water and in octanol was analyzed. PPL showed increase in solvent accessible surface area and decrease in packing density as the polarity of the surrounded solvent decreased. Breaking the interactions between D250-Y115, and D250-E254 in PPLmut-Cl directed the lid to attain open-state conformation. Major energy barriers during the lid movement in water and in octanol were identified. Also, the trajectories of lid movement were found to be different in these solvents. Only the double mutant at higher temperature showed lid opening movement suggesting the essential role of the three residues in holding the lid in closed conformation. The lid opening dynamics was faster in octanol than water suggesting that non-polar solvents favor open conformation of the lid. This study identifies important interactions between the lid and the residues in domain 1 which possibly keeps the lid in closed conformation. Also, it explains the rearrangements of residue-residue interactions during lid opening movement in water and in octanol. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular Dynamics Simulation of the Allosteric Regulation of eIF4A Protein from the Open to Closed State, Induced by ATP and RNA Substrates

PubMed Central

Meng, Hongqing; Li, Chaoqun; Wang, Yan; Chen, Guangju

2014-01-01

Background Eukaryotic initiation factor 4A (eIF4A) plays a key role in the process of protein translation initiation by facilitating the melting of the 5′ proximal secondary structure of eukaryotic mRNA for ribosomal subunit attachment. It was experimentally postulated that the closed conformation of the eIF4A protein bound by the ATP and RNA substrates is coupled to RNA duplex unwinding to promote protein translation initiation, rather than an open conformation in the absence of ATP and RNA substrates. However, the allosteric process of eIF4A from the open to closed state induced by the ATP and RNA substrates are not yet fully understood. Methodology In the present work, we constructed a series of diplex and ternary models of the eIF4A protein bound by the ATP and RNA substrates to carry out molecular dynamics simulations, free energy calculations and conformation analysis and explore the allosteric properties of eIF4A. Results The results showed that the eIF4A protein completes the conformational transition from the open to closed state via two allosteric processes of ATP binding followed by RNA and vice versa. Based on cooperative allosteric network analysis, the ATP binding to the eIF4A protein mainly caused the relative rotation of two domains, while the RNA binding caused the proximity of two domains via the migration of RNA bases in the presence of ATP. The cooperative binding of ATP and RNA for the eIF4A protein plays a key role in the allosteric transition. PMID:24465900

Grid generation using classical techniques

NASA Technical Reports Server (NTRS)

Moretti, G.

1980-01-01

A brief historical review of conformal mapping and its applications to problems in fluid mechanics and electromagnetism is presented. The use of conformal mapping as a grid generator is described. The philosophy of the 'closed form' approach and its application to a Neumann problem is discussed. Karman-Trefftz mappings and grids for ablated, three dimensional bodies are also discussed.

Run-Curve Design for Energy Saving Operation in a Modern DC-Electrification

NASA Astrophysics Data System (ADS)

Koseki, Takafumi; Noda, Takashi

Mechanical brakes are often used by electric trains. These brakes have a few problems like response speed, coefficient of friction, maintenance cost and so on. As a result, methods for actively using regenerative brakes are required. In this paper, we propose the useful pure electric braking, which would involve ordinary brakes by only regenerative brakes without any mechanical brakes at high speed. Benefits of our proposal include a DC-electrification system with regenerative substations that can return powers to the commercial power system and a train that can use the full regenerative braking force. We furthermore evaluate the effects on running time and energies saved by regenerative substations in the proposed method.

A survey of industry practices regarding shielding of substations against direct lightning strokes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mousa, A.M.; Wehling, R.J.

1993-01-01

A survey of industry practices regarding shielding of substations against direct lightning strokes is presented and analyzed. The survey is based on responses from 114 companies including consultants and utilities both from within and from outside North America. The survey identifies the shielding design methods in use, the factors affecting the selection of a shielding method, the shielding design criteria and the governing factors, the performance of the different shielding methods and miscellaneous related aspects. The survey revealed a large number (35) of shielding failure incidents; 34 of which occurred in systems designed using either the fixed shielding angle methodmore » or Wagner's 1942 method.« less

Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA

PubMed Central

Linder, Tobias; de Groot, Bert L.; Stary-Weinzinger, Anna

2013-01-01

The bacterial potassium channel KcsA, which has been crystallized in several conformations, offers an ideal model to investigate activation gating of ion channels. In this study, essential dynamics simulations are applied to obtain insights into the transition pathways and the energy profile of KcsA pore gating. In agreement with previous hypotheses, our simulations reveal a two phasic activation gating process. In the first phase, local structural rearrangements in TM2 are observed leading to an intermediate channel conformation, followed by large structural rearrangements leading to full opening of KcsA. Conformational changes of a highly conserved phenylalanine, F114, at the bundle crossing region are crucial for the transition from a closed to an intermediate state. 3.9 µs umbrella sampling calculations reveal that there are two well-defined energy barriers dividing closed, intermediate, and open channel states. In agreement with mutational studies, the closed state was found to be energetically more favorable compared to the open state. Further, the simulations provide new insights into the dynamical coupling effects of F103 between the activation gate and the selectivity filter. Investigations on individual subunits support cooperativity of subunits during activation gating. PMID:23658510

Electrostatic Interactions at the Dimer Interface Stabilize the E. coli β Sliding Clamp.

PubMed

Purohit, Anirban; England, Jennifer K; Douma, Lauren G; Tondnevis, Farzaneh; Bloom, Linda B; Levitus, Marcia

2017-08-22

Sliding clamps are ring-shaped oligomeric proteins that encircle DNA and associate with DNA polymerases for processive DNA replication. The dimeric Escherichia coli β-clamp is closed in solution but must adopt an open conformation to be assembled onto DNA by a clamp loader. To determine what factors contribute to the stability of the dimer interfaces in the closed conformation and how clamp dynamics contribute to formation of the open conformation, we identified conditions that destabilized the dimer and measured the effects of these conditions on clamp dynamics. We characterized the role of electrostatic interactions in stabilizing the β-clamp interface. Increasing salt concentration results in decreased dimer stability and faster subunit dissociation kinetics. The equilibrium dissociation constant of the dimeric clamp varies with salt concentration as predicted by simple charge-screening models, indicating that charged amino acids contribute to the remarkable stability of the interface at physiological salt concentrations. Mutation of a charged residue at the interface (Arg-103) weakens the interface significantly, whereas effects are negligible when a hydrophilic (Ser-109) or a hydrophobic (Ile-305) amino acid is mutated instead. It has been suggested that clamp opening by the clamp loader takes advantage of spontaneous opening-closing fluctuations at the clamp's interface, but our time-resolved fluorescence and fluorescence correlation experiments rule out conformational fluctuations that lead to a significant fraction of open states. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Microsecond molecular dynamics simulations provide insight into the ATP-competitive inhibitor-induced allosteric protection of Akt kinase phosphorylation.

PubMed

Mou, Linkai; Cui, Tongwei; Liu, Weiguang; Zhang, Hong; Cai, Zhanxiu; Lu, Shaoyong; Gao, Guojun

2017-05-01

Akt is a serine/threonine protein kinase, a critical mediator of growth factor-induced survival in key cellular pathways. Allosteric signaling between protein intramolecular domains requires long-range communication mediated by hotspot residues, often triggered by ligand binding. Here, based on extensive 3 μs explicit solvent molecular dynamics (MD) simulations of Akt1 kinase domain in the unbound (apo) and ATP-competitive inhibitor, GDC-0068-bound states, we propose a molecular mechanism for allosteric regulation of Akt1 kinase phosphorylation by GDC-0068 binding to the ATP-binding site. MD simulations revealed that the apo Akt1 is flexible with two disengaged N- and C-lobes, equilibrated between the open and closed conformations. GDC-0068 occupancy of the ATP-binding site shifts the conformational equilibrium of Akt1 from the open conformation toward the closed conformation and stabilizes the closed state. This effect enables allosteric signal propagation from the GDC-0068 to the phosphorylated T308 (pT308) in the activation loop and restrains phosphatase access to pT308, thereby protecting the pT308 in the GDC-0068-bound Akt1. Importantly, functional hotspots involved in the allosteric communication from the GDC-0068 to the pT308 are identified. Our analysis of GDC-0068-induced allosteric protection of Akt kinase phosphorylation yields important new insights into the molecular mechanism of allosteric regulation of Akt kinase activity. © 2016 John Wiley & Sons A/S.

Kinetic Dissection of the Pre-existing Conformational Equilibrium in the Trypsin Fold*

PubMed Central

Vogt, Austin D.; Chakraborty, Pradipta; Di Cera, Enrico

2015-01-01

Structural biology has recently documented the conformational plasticity of the trypsin fold for both the protease and zymogen in terms of a pre-existing equilibrium between closed (E*) and open (E) forms of the active site region. How such plasticity is manifested in solution and affects ligand recognition by the protease and zymogen is poorly understood in quantitative terms. Here we dissect the E*-E equilibrium with stopped-flow kinetics in the presence of excess ligand or macromolecule. Using the clotting protease thrombin and its zymogen precursor prethrombin-2 as relevant models we resolve the relative distribution of the E* and E forms and the underlying kinetic rates for their interconversion. In the case of thrombin, the E* and E forms are distributed in a 1:4 ratio and interconvert on a time scale of 45 ms. In the case of prethrombin-2, the equilibrium is shifted strongly (10:1 ratio) in favor of the closed E* form and unfolds over a faster time scale of 4.5 ms. The distribution of E* and E forms observed for thrombin and prethrombin-2 indicates that zymogen activation is linked to a significant shift in the pre-existing equilibrium between closed and open conformations that facilitates ligand binding to the active site. These findings broaden our mechanistic understanding of how conformational transitions control ligand recognition by thrombin and its zymogen precursor prethrombin-2 and have direct relevance to other members of the trypsin fold. PMID:26216877

Cross-protection in Neisseria meningitidis serogroups Y and W polysaccharides: A comparative conformational analysis.

PubMed

Kuttel, Michelle M; Timol, Zaheer; Ravenscroft, Neil

2017-06-29

The capsular polysaccharide is the main virulence factor in meningococcus. The capsular polysaccharides for meningococcal serogroups Y and W are almost identical polymers of hexose-sialic acid, suggesting the possibility of cross-protection between group Y and W vaccines. However, early studies indicated that they elicit different levels of cross-protection. Here we explore the conformations of the meningococcal Y and W polysaccharides with molecular dynamics simulations of three repeating unit oligosaccharide strands. We find differences in Y and W antigen conformation: the Y polysaccharide has a single dominant conformation, whereas W exhibits a family of conformations including the Y conformation. This result is supported by our NMR NOESY analysis, which indicates key close contacts for W that are not present in Y. These conformational differences provide an explanation for the different levels of cross-protection measured for the Y and W monovalent vaccines and the high group W responses observed in HibMenCY-TT vaccinees. Copyright © 2017 Elsevier Ltd. All rights reserved.

Modeling Conformational Transitions and Energetics of Ligand Binding with the Glutamate Receptor Ligand Binding Domain

NASA Astrophysics Data System (ADS)

Kurnikova, Maria

2009-03-01

Understanding of protein motion and energetics of conformational transitions is crucial to understanding protein function. The glutamate receptor ligand binding domain (GluR2 S1S2) is a two lobe protein, which binds ligand at the interface of two lobes and undergoes conformational transition. The cleft closure conformational transition of S1S2 has been implicated in gating of the ion channel formed by the transmembrane domain of the receptor. In this study we present a composite multi-faceted theoretical analysis of the detailed mechanism of this conformational transition based on rigid cluster decomposition of the protein structure [1] and identifying hydrogen bonds that are responsible for stabilizing the closed conformation [2]. Free energy of the protein reorganization upon ligand binding was calculated using combined Thermodynamic Integration (TI) and Umbrella Sampling (US) simulations [3]. Ligand -- protein interactions in the binding cleft were analyzed using Molecular Dynamics, continuum electrostatics and QM/MM models [4]. All model calculations compare well with corresponding experimental measurements. [4pt] [1] Protein Flexibility using Constraints from Molecular Dynamics Simulations T. Mamonova, B. Hespenheide, R. Straub, M. F. Thorpe, M. G. Kurnikova , Phys. Biol., 2, S137 (2005)[0pt] [2] Theoretical Study of the Glutamate Receptor Ligand Binding Domain Flexibility and Conformational Reorganization T. Mamonova, K. Speranskiy, and M. Kurnikova , Prot.: Struct., Func., Bioinf., 73,656 (2008)[0pt] [3] Energetics of the cleft closing transition and glutamate binding in the Glutamate Receptor ligand Binding Domain T. Mamonova, M. Yonkunas, and M. Kurnikova Biochemistry 47, 11077 (2008)[0pt] [4] On the Binding Determinants of the Glutamate Agonist with the Glutamate Receptor Ligand Binding Domain K. Speranskiy and M. Kurnikova Biochemistry 44, 11208 (2005)

SU-F-T-635: Lung SBRT: Dosimetric and Treatment Time Comparison of Volumetric-Modulated Arc Therapy and Three-Dimensional Conformal Radiotherapy in Clinically Treated Cases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, J; Xu, Z; Baker, J

Purpose: To compare three-dimensional conformal radiotherapy (3D CRT) and volumetric-modulated arc therapy (VMAT) in lung stereotactic body radiation therapy (SBRT) Methods: A retrospective study of clinically treated lung SBRT cases treated between 2010 and 2015 at our hospital was performed. All treatment modalities were included in this evaluation (VMAT, 3D CRT, static IMRT, and dynamic conformal arc therapy). However, the majority of treatment modalities were either VMAT or 3D CRT. Treatment times of patients and dosimetric plan quality metrics were compared. Treatment times were calculated based on the time the therapist opened and closed the patient’s treatment plan. This treatmentmore » time closely approximates the utilization time of the treatment room. The dosimetric plan quality metrics evaluated include ICRU conformity index, the volume of 105% prescribed dose outside PTV, the ratio of volume of 50% prescribed dose to the volume of PTV, the percentage of maximum dose at 2 cm away from PTV to the prescribed dose, and the V20 (percentage of lung volume receiving 20 Gy or more). Results: Treatment time comparisons show that on average VMAT has shorter treatment times than 3D CRT. Dose conformity, defined by the ICRU conformity index, and high dose spillage, defined by the volume of 105% dose outside the PTV, is reduced when using VMAT compared to 3D CRT. V20 and intermediate dose spillage/fall-off metrics of VMAT and 3D are not significantly different. Conclusion: Clinically treated lung SBRT cases indicate VMAT is superior to 3D with regard to shorter treatment times, plan dose conformity, and plan high dose spillage.« less

A 735 kV shunt reactors automatic switching system for Hydro-Quebec network

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bernard, S.; Trudel, G.; Scott, G.

1996-11-01

In recent years, Hydro-Quebec has undertaken a major program to upgrade the reliability of its transmission system. Much efforts have been directed toward increasing the system`s capacity to withstand extreme contingencies, usually caused by multiple incidents or the successive tripping of transmission lines. In order to counter such events, Hydro-Quebec has adopted a defensive scheme. Based entirely on automatic action, this scheme will mainly rely on: a 735 kV shunt reactor switching system (called MAIS); a generation rejection and/or remote load-shedding system (called RPTC); an underfrequency load-shedding system. The MAIS system, which is the subject of this paper, will bemore » implemented in 22 substations and is required to control voltage on the system after a severe event. Each MAIS system, acting locally, is entirely independent and will close or trip shunt reactors in response to local conditions.« less

Long range dynamic effects of point-mutations trap a response regulator in an active conformation

PubMed Central

Bobay, Benjamin G.; Thompson, Richele J.; Hoch, James A.; Cavanagh, John

2010-01-01

When a point-mutation in a protein elicits a functional change, it is most common to assign this change to local structural perturbations. Here we show that point-mutations, distant from an essential highly dynamic kinase recognition loop in the response regulator Spo0F, lock this loop in an active conformation. This ‘conformational trapping’ results in functionally hyperactive Spo0F. Consequently, point-mutations are seen to affect functionally critical motions both close to and far from the mutational site. PMID:20828564

Projective mappings and dimensions of vector spaces of three types of Killing-Yano tensors on pseudo Riemannian manifolds of constant curvature

NASA Astrophysics Data System (ADS)

Mikeš, Josef; Stepanov, Sergey; Hinterleitner, Irena

2012-07-01

In our paper we have determined the dimension of the space of conformal Killing-Yano tensors and the dimensions of its two subspaces of closed conformal Killing-Yano and Killing-Yano tensors on pseudo Riemannian manifolds of constant curvature. This result is a generalization of well known results on sharp upper bounds of the dimensions of the vector spaces of conformal Killing-Yano, Killing-Yano and concircular vector fields on pseudo Riemannian manifolds of constant curvature.

Symmetric factorization of the conformation tensor in viscoelastic fluid models

NASA Astrophysics Data System (ADS)

Thomases, Becca; Balci, Nusret; Renardy, Michael; Doering, Charles

2010-11-01

The positive definite symmetric polymer conformation tensor possesses a unique symmetric square root that satisfies a closed evolution equation in the Oldroyd-B and FENE-P models of viscoelastic fluid flow. When expressed in terms of the velocity field and the symmetric square root of the conformation tensor, these models' equations of motion formally constitute an evolution in a Hilbert space with a total energy functional that defines a norm. Moreover, this formulation is easily implemented in direct numerical simulations resulting in significant practical advantages in terms of both accuracy and stability.

NMR and X-ray studies of isomeric 22,23-dihydroxy stigmastanes

NASA Astrophysics Data System (ADS)

Khripach, Vladimir A.; Zhabinskii, Vladimir N.; Ivanova, Galina V.; Fando, Galina P.; Tsavlovskii, Dmitrii V.; Khripach, Natalya B.; Lyakhov, Alexander S.; Misharin, Alexander Yu.

2010-06-01

A comparative conformational study of steroidal side chain of (22 R,23 R)- and (22 S,23 S)-dihydroxy stigmastane derivatives was performed using single crystal X-ray diffraction and NMR spectroscopy. The preferred conformation in solution was shown to be close to that in the crystal. (22 R,23 R)-Isomers typical for natural plant steroid hormones brassinosteroids adopt a conformation in which both hydroxyl groups are pointed toward unhindered α-side of the steroidal plane and can thus participate in biochemical processes. Unnatural (22 S,23 S)-counterparts exhibit a conformation with the two hydroxyl groups oriented in the opposite direction and sterically hindered by 21-methyl group and terminal side chain fragment.

Development of Protection and Control Unit for Distribution Substation

NASA Astrophysics Data System (ADS)

Iguchi, Fumiaki; Hayashi, Hideyuki; Takeuchi, Motohiro; Kido, Mitsuyasu; Kobayashi, Takashi; Yanaoka, Atsushi

The Recently, electronics and IT technologies have been rapidly innovated and have been introduced to power system protection & control system to achieve high reliability, maintainability and more functionality. Concerning the distribution substation application, digital relays have been applied for more than 10 years. Because of a number of electronic devices used for it, product cost becomes higher. Also, products installed during the past high-growth period will be at the end of lifetime and will be replaced. Therefore, replacing market is expected to grow and the reduction of cost is demanded. Considering above mentioned background, second generation digital protection and control unit as a successor is designed to have following concepts. Functional integration based on advanced digital technologies, Ethernet LAN based indoor communication network, cost reduction and downsizing. Pondering above concepts, integration of protection and control function is adopted in contrary to the functional segregation applied to the previous system in order to achieve one-unit concept. Also the adoption of Ethernet LAN for inter-unit communication is objective. This report shows the development of second-generation digital relay for distribution substation, which is equipped with control function and Ethernet LAN by reducing the size of auxiliary transformer unit and the same size as previous product is realized.

Measurement and Modeling of Personal Exposure to the Electric and Magnetic Fields in the Vicinity of High Voltage Power Lines.

PubMed

Tourab, Wafa; Babouri, Abdesselam

2016-06-01

This work presents an experimental and modeling study of the electromagnetic environment in the vicinity of a high voltage substation located in eastern Algeria (Annaba city) specified with a very high population density. The effects of electromagnetic fields emanating from the coupled multi-lines high voltage power systems (MLHV) on the health of the workers and people living in proximity of substations has been analyzed. Experimental Measurements for the Multi-lines power system proposed have been conducted in the free space under the high voltage lines. Field's intensities were measured using a referenced and calibrated electromagnetic field meter PMM8053B for the levels 0 m, 1 m, 1.5 m and 1.8 m witch present the sensitive's parts as organs and major functions (head, heart, pelvis and feet) of the human body. The measurement results were validated by numerical simulation using the finite element method and these results are compared with the limit values of the international standards. We project to set own national standards for exposure to electromagnetic fields, in order to achieve a regional database that will be at the disposal of partners concerned to ensure safety of people and mainly workers inside high voltage electrical substations.

Heterogeneous Wireless Networks for Smart Grid Distribution Systems: Advantages and Limitations.

PubMed

Khalifa, Tarek; Abdrabou, Atef; Shaban, Khaled; Gaouda, A M

2018-05-11

Supporting a conventional power grid with advanced communication capabilities is a cornerstone to transferring it to a smart grid. A reliable communication infrastructure with a high throughput can lay the foundation towards the ultimate objective of a fully automated power grid with self-healing capabilities. In order to realize this objective, the communication infrastructure of a power distribution network needs to be extended to cover all substations including medium/low voltage ones. This shall enable information exchange among substations for a variety of system automation purposes with a low latency that suits time critical applications. This paper proposes the integration of two heterogeneous wireless technologies (such as WiFi and cellular 3G/4G) to provide reliable and fast communication among primary and secondary distribution substations. This integration allows the transmission of different data packets (not packet replicas) over two radio interfaces, making these interfaces act like a one data pipe. Thus, the paper investigates the applicability and effectiveness of employing heterogeneous wireless networks (HWNs) in achieving the desired reliability and timeliness requirements of future smart grids. We study the performance of HWNs in a realistic scenario under different data transfer loads and packet loss ratios. Our findings reveal that HWNs can be a viable data transfer option for smart grids.

Heterogeneous Wireless Networks for Smart Grid Distribution Systems: Advantages and Limitations

PubMed Central

Khalifa, Tarek; Abdrabou, Atef; Gaouda, A. M.

2018-01-01

Supporting a conventional power grid with advanced communication capabilities is a cornerstone to transferring it to a smart grid. A reliable communication infrastructure with a high throughput can lay the foundation towards the ultimate objective of a fully automated power grid with self-healing capabilities. In order to realize this objective, the communication infrastructure of a power distribution network needs to be extended to cover all substations including medium/low voltage ones. This shall enable information exchange among substations for a variety of system automation purposes with a low latency that suits time critical applications. This paper proposes the integration of two heterogeneous wireless technologies (such as WiFi and cellular 3G/4G) to provide reliable and fast communication among primary and secondary distribution substations. This integration allows the transmission of different data packets (not packet replicas) over two radio interfaces, making these interfaces act like a one data pipe. Thus, the paper investigates the applicability and effectiveness of employing heterogeneous wireless networks (HWNs) in achieving the desired reliability and timeliness requirements of future smart grids. We study the performance of HWNs in a realistic scenario under different data transfer loads and packet loss ratios. Our findings reveal that HWNs can be a viable data transfer option for smart grids. PMID:29751633

Draft Supplement to the Environmental Statement Fiscal Year 1975 Proposed Program : Facility Location Evaluation for San Juan Island Service : Decatur Land Line and East Lopez Island Substation Study Area 74-7.

DOE Office of Scientific and Technical Information (OSTI.GOV)

United States. Bonneville Power Administration.

1974-03-08

Proposed construction of a 1.7-mile 34.5-kV double-circuit transmission line crossing Decatur Island from east to west. The new line would replace 0.7 of a mile of an existing BPA 24.5-kV line and would then parallel and existing 24.5-kV line for a distance of 1.0 mile. The proposal also requires the construction of a new substation to be located on the eastern side of Lopez Island, Washington. The additional easement required for the proposed transmission line would remove about 1.1 acres of forestland from timber production diverting it to nonforest uses compatable with the transmission line right-of-way. Depending upon the actualmore » site location the Lopez Island Substation could remove from 1 to 3.2 acres of forestland and 2 acres of pastureland from production. Disturbance of game in the immediate vicintiy of the transmission facilities will occur during construction, as will some soil erosion primarily during and immediately after construction, siltation in nearby streams, disturbance of nearby residents from noise and dust during construction, and some degradation of AM reception immediately adjacent to the right-of-way. 7 figs.« less

How maltose influences structural changes to bind to maltose-binding protein: results from umbrella sampling simulation.

PubMed

Mascarenhas, Nahren Manuel; Kästner, Johannes

2013-02-01

A well-studied periplasmic-binding protein involved in the abstraction of maltose is maltose-binding protein (MBP), which undergoes a ligand-induced conformational transition from an open (ligand-free) to a closed (ligand-bound) state. Umbrella sampling simulations have been us to estimate the free energy of binding of maltose to MBP and to trace the potential of mean force of the unbinding event using the center-of-mass distance between the protein and ligand as the reaction coordinate. The free energy thus obtained compares nicely with the experimentally measured value justifying our theoretical basis. Measurement of the domain angle (N-terminal-domain - hinge - C-terminal-domain) along the unbinding pathway established the existence of three different states. Starting from a closed state, the protein shifts to an open conformation during the initial unbinding event of the ligand then resides in a semi-open conformation and later resides predominantly in an open-state. These transitions along the ligand unbinding pathway have been captured in greater depth using principal component analysis. It is proposed that in mixed-model, both conformational selection and an induced-fit mechanism combine to the ligand recognition process in MBP. Copyright © 2012 Wiley Periodicals, Inc.

Interaction of dihydrofolate reductase with methotrexate: Ensemble and single-molecule kinetics

NASA Astrophysics Data System (ADS)

Rajagopalan, P. T. Ravi; Zhang, Zhiquan; McCourt, Lynn; Dwyer, Mary; Benkovic, Stephen J.; Hammes, Gordon G.

2002-10-01

The thermodynamics and kinetics of the interaction of dihydrofolate reductase (DHFR) with methotrexate have been studied by using fluorescence, stopped-flow, and single-molecule methods. DHFR was modified to permit the covalent addition of a fluorescent molecule, Alexa 488, and a biotin at the N terminus of the molecule. The fluorescent molecule was placed on a protein loop that closes over methotrexate when binding occurs, thus causing a quenching of the fluorescence. The biotin was used to attach the enzyme in an active form to a glass surface for single-molecule studies. The equilibrium dissociation constant for the binding of methotrexate to the enzyme is 9.5 nM. The stopped-flow studies revealed that methotrexate binds to two different conformations of the enzyme, and the association and dissociation rate constants were determined. The single-molecule investigation revealed a conformational change in the enzyme-methotrexate complex that was not observed in the stopped-flow studies. The ensemble averaged rate constants for this conformation change in both directions is about 2-4 s1 and is attributed to the opening and closing of the enzyme loop over the bound methotrexate. Thus the mechanism of methotrexate binding to DHFR involves multiple steps and protein conformational changes.

Proposed Columbia Wind Farm No. 1 : Final Environmental Impact Statement, Joint NEPA/SEPA.

DOE Office of Scientific and Technical Information (OSTI.GOV)

United States. Bonneville Power Administration; Klickitat County

1995-09-01

CARES proposes to construct and operate the 25 megawatt Columbia Wind Farm No. 1 (Project) in the Columbia Hills area of Klickitat County, Washington known as Juniper Point. Wind is not a constant resource and based on the site wind measurement data, it is estimated that the Project would generate approximately 7 average annual MWs of electricity. BPA proposes to purchase the electricity generated by the Project. CARES would execute a contractual agreement with a wind developer, to install approximately 91 wind turbines and associated facilities to generate electricity. The Project`s construction and operation would include: install concrete pier foundationsmore » for each wind turbine; install 91 model AWT-26 wind turbines using 43 m high guyed tubular towers on the pier foundations; construct a new 115/24-kv substation; construct a 149 m{sup 2} steel operations and maintenance building; install 25 pad mount transformers along the turbine access roads; install 4.0 km of underground 24 kv power collection lines to collect power from individual turbines to the end of turbine strings; install 1.2 km of underground communication and transmission lines from each turbine to a pad mount transformer; install 5.6 km of 24 kv wood pole transmission lines to deliver electricity from the pad mount transformers to the Project substation; install 3.2 km of 115 kv wood pole transmission lines to deliver electricity from the Project substation to the Public Utility District No. 1 of Klickitat County(PUD)115 kv Goldendale line; interconnect with the BPA transmission system through the Goldendale line and Goldendale substation owned by the PUD; reconstruct, upgrade, and maintain 8.0 km of existing roads; construct and maintain 6.4 km of new graveled roads along the turbine strings and to individual turbines; and install meteorological towers guyed with rebar anchors on the Project site.« less

Leap-dynamics: efficient sampling of conformational space of proteins and peptides in solution.

PubMed

Kleinjung, J; Bayley, P; Fraternali, F

2000-03-31

A molecular simulation scheme, called Leap-dynamics, that provides efficient sampling of protein conformational space in solution is presented. The scheme is a combined approach using a fast sampling method, imposing conformational 'leaps' to force the system over energy barriers, and molecular dynamics (MD) for refinement. The presence of solvent is approximated by a potential of mean force depending on the solvent accessible surface area. The method has been successfully applied to N-acetyl-L-alanine-N-methylamide (alanine dipeptide), sampling experimentally observed conformations inaccessible to MD alone under the chosen conditions. The method predicts correctly the increased partial flexibility of the mutant Y35G compared to native bovine pancreatic trypsin inhibitor. In particular, the improvement over MD consists of the detection of conformational flexibility that corresponds closely to slow motions identified by nuclear magnetic resonance techniques.

Laser probes of the potential energy landscapes and conformational isomerization dynamics of flexible biomolecules

NASA Astrophysics Data System (ADS)

Dian, Brian; Clarkson, Jasper; Zwier, Timothy

2003-03-01

Using a combination of 2-color resonant two-photon ionization (R2PI), laser-induced fluorescence excitation (LIF), resonant ion-dip infrared spectroscopy (RIDIRS), fluorescence-dip infrared spectroscopy (FDIRS), and UV-UV hole-burning spectroscopy, the conformational preferences of a series of flexible biomolecules, including melatonin, N-acetyl-tryptophan methyl amide (NATMA), and their close analogs, have been determined in a molecular beam. These molecules are sufficiently complex to have hundreds of conformational minima, yet small enough that their potential energy landscapes can be explored in some detail. Once the conformational preferences of the molecules are established, these molecules are then studied using infrared-ultraviolet hole-filling and IR-induced population transfer spectroscopy. These methods utilize selective infrared excitation of single conformations of the molecule in the early portions of a gas-phase expansion, followed by collisional re-cooling of the excited population into its conformational minima for subsequent conformation-specific detection. Efficient isomerization is induced by the infrared excitation that redistributes population between the same conformations that have population in the absence of infrared excitation. Examples will be given in which the quantum yields for transfer of the population into the various conformational minima depend both on which conformation is excited and on which hydride stretch vibration is excited within a given conformation; that is, they are both conformation-selective and mode-selective.

Supplement Analysis for the Transmission System Vegetation Management Program FEIS (DOE/EIS-0285/SA-137- Chemawa-Salem 1&2)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sherer, Brett M.

Vegetation Management for the Chemawa-Salem #1 115 kV and #2 230 kV transmission lines from Chemawa Substation to Salem Substation. BPA proposes to remove unwanted vegetation along the right-of-way, access roads, switch platforms, and around tower structures of the subject transmission line corridor that may impede the operation and maintenance of the identified transmission lines. BPA plans to conduct vegetation control with the goal of removing tall growing vegetation that is currently or will soon be a hazard to the transmission line. BPA’s overall goal is to have lowgrowing plant communities along the rights-of-way to control the development of potentiallymore » threatening vegetation.« less

Supplement Analysis for the Transmission System Vegetation Management Program FEIS (DOE/EIS-0285/SA-141- Salem Albany #2)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barndt, Shawn L.

Vegetation Management for the Salem Albany #2 115 kV transmission line from Salem Substation to Albany Substation. BPA proposes to remove unwanted vegetation along the right-of-way, access roads, switch platforms, microwave beam paths, and around tower structures of the subject transmission line corridor that may impede the operation and maintenance of the identified transmission lines. BPA plans to conduct vegetation control with the goal of removing tall growing vegetation that is currently or will soon be a hazard to the transmission line. BPA’s overall goal is to have low-growing plant communities along the rights-of-way to control the development of potentiallymore » threatening vegetation.« less

Type B investigation of electrical fault in 351 Substation, December 4, 1994

DOE Office of Scientific and Technical Information (OSTI.GOV)

Debban, H.L.; Shearer, C.A.; Boger, R.M.

1995-02-01

On December 4, 1994, at 2132:10 hours, an electrical failure of a cable-tapping splice resulted in a fire in the 300 Area of the DOE Hanford Site. The fire occurred in the yard of Substation 351 in electrical Vault R122V, where the cable-tapping splice was located. The fire incinerated all cables passing to and through the vault causing them to fail. The failure of the cables resulted in a power outage to twenty customers in the 300 Area. The vault was electrically isolated, and power was restored to the electrical distribution system at 2311 hours. This report contains the accidentmore » scenario, accident analysis, direct cause and root and contributing causes.« less

Abundant closed form solutions of the conformable time fractional Sawada-Kotera-Ito equation using (G‧ / G) -expansion method

NASA Astrophysics Data System (ADS)

Al-Shawba, Altaf Abdulkarem; Gepreel, K. A.; Abdullah, F. A.; Azmi, A.

2018-06-01

In current study, we use the (G‧ / G) -expansion method to construct the closed form solutions of the seventh order time fractional Sawada-Kotera-Ito (TFSKI) equation based on conformable fractional derivative. As a result, trigonometric, hyperbolic and rational functions solutions with arbitrary constants are obtained. When the arbitrary constants are taken some special values, the periodic and soliton solutions are obtained from the travelling wave solutions. The obtained solutions are new and not found elsewhere. The effect of the fractional order on some of these solutions are represented graphically to illustrate the behavior of the exact solutions when the parameter take some special choose.

Quantum theory of the structure and bonding in proteins. Part 11. A simplified method and its application to the α-amino-isobutyric acid residue

NASA Astrophysics Data System (ADS)

Peters, David; Peters, Jane

Information about the preferred conformation of the α-amino-isobutyric acid residue (α-AIB) is obtained without explicit computation of its wave function. The conformation of lowest energy of this residue is close to the usual helical conformation and so the residue may occur at the 2 position of a type I or I' bend or in either position of a type III or III' bend. The available experimental information refers to a β bend formed from α-AIB-PRO and then the theory and experiment agree that the only possibility is a type III bend. It is predicted that a β sheet structure may be formed at rather higher energy and in the planar and not the pleated form. There is no apparent reason why this residue should not form an α helix. The simplified method used here is closely related to the partitioned potential energy methods which are widely used in this subject.

Evidence for an intermediate conformational state of LacY.

PubMed

Jiang, Xiaoxu; Guan, Lan; Zhou, Yonggang; Hong, Wen-Xu; Zhang, Qinghai; Kaback, H Ronald

2012-03-20

LacY mutant Cys154 → Gly exhibits a periplasmic-closed crystal structure identical to the WT, but is periplasmic-open in the membrane. The mutant hardly catalyzes transport, but binds galactosides from either side of the membrane with the same affinity and is resistant to site-directed proteolysis relative to the pseudo-WT. Site-directed alkylation was also applied to 11 single-Cys mutants in Cys154 → Gly LacY in right-side-out membrane vesicles or after solubilization and purification in dodecyl-β-D-maltopyranoside (DDM). Unlike the pseudo-WT, Cys replacements on the periplasmic side of the Cys154 → Gly mutant label rapidly in the membrane without sugar, but labeling decreases markedly after the mutant proteins are purified. Thus, Cys154 → Gly LacY likely favors a higher-energy intermediate periplasmic-open conformation in situ, but collapses to a lower-energy periplasmic-closed conformation in DDM after purification. Notably, branched-chain or neopentyl glycol maltoside detergents stabilize Cys154 → Gly LacY in the membrane-embedded form.

Large interdomain rearrangement triggered by suppression of micro- to millisecond dynamics in bacterial Enzyme I

NASA Astrophysics Data System (ADS)

Venditti, Vincenzo; Tugarinov, Vitali; Schwieters, Charles D.; Grishaev, Alexander; Clore, G. Marius

2015-01-01

Enzyme I (EI), the first component of the bacterial phosphotransfer signal transduction system, undergoes one of the largest substrate-induced interdomain rearrangements documented to date. Here we characterize the perturbations generated by two small molecules, the natural substrate phosphoenolpyruvate and the inhibitor α-ketoglutarate, on the structure and dynamics of EI using NMR, small-angle X-ray scattering and biochemical techniques. The results indicate unambiguously that the open-to-closed conformational switch of EI is triggered by complete suppression of micro- to millisecond dynamics within the C-terminal domain of EI. Indeed, we show that a ligand-induced transition from a dynamic to a more rigid conformational state of the C-terminal domain stabilizes the interface between the N- and C-terminal domains observed in the structure of the closed state, thereby promoting the resulting conformational switch and autophosphorylation of EI. The mechanisms described here may be common to several other multidomain proteins and allosteric systems.

Chapter 5. Hidden Symmetry and Exact Solutions in Einstein Gravity

NASA Astrophysics Data System (ADS)

Yasui, Y.; Houri, T.

Conformal Killing-Yano tensors are introduced as ageneralization of Killing vectors. They describe symmetries of higher-dimensional rotating black holes. In particular, a rank-2 closed conformal Killing-Yano tensor generates the tower of both hidden symmetries and isometries. We review a classification of higher-dimensional spacetimes admitting such a tensor, and present exact solutions to the Einstein equations for these spacetimes.

Computational Studies on Sirtuins from Trypanosoma cruzi: Structures, Conformations and Interactions with Phytochemicals

PubMed Central

Sacconnay, Lionel; Angleviel, Melissa; Randazzo, Giuseppe Marco; Marçal Ferreira Queiroz, Marcos; Ferreira Queiroz, Emerson; Wolfender, Jean-Luc; Carrupt, Pierre-Alain; Nurisso, Alessandra

2014-01-01

Background The silent-information regulator 2 proteins, otherwise called sirtuins, are currently considered as emerging anti-parasitic targets. Nicotinamide, a pan-sirtuin inhibitor, is known to cause kinetoplast alterations and the arrested growth of T. cruzi, the protozoan responsible for Chagas disease. These observations suggested that sirtuins from this parasite (TcSir2rp1 and TcSir2rp3) could play an important role in the regulation of the parasitic cell cycle. Thus, their inhibition could be exploited for the development of novel anti-trypanosomal compounds. Methods Homology modeling was used to determine the three-dimensional features of the sirtuin TcSir2rp1 from T. cruzi. The apo-form of human SIRT2 and the same structure solved in complex with its co-substrate NAD+ allowed the modeling of TcSir2rp1 in the open and closed conformational states. Molecular docking studies were then carried out. A library composed of fifty natural and diverse compounds that are known to be active against this parasite, was established based on the literature and virtually screened against TcSir2rp1 and TcSir2rp3, which was previously modeled by our group. Results In this study, two conformational states of TcSir2rp1 were described for the first time. The molecular docking results of compounds capable of binding sirtuins proved to be meaningful when the closed conformation of the protein was taken into account for calculations. This specific conformation was then used for the virtual screening of antritrypanosomal phytochemicals against TcSir2rp1 and TcSir2rp3. The calculations identified a limited number of scaffolds extracted from Vismia orientalis, Cussonia zimmermannii, Amomum aculeatum and Anacardium occidentale that potentially interact with both proteins. Conclusions The study provided reliable models for future structure-based drug design projects concerning sirtuins from T. cruzi. Molecular docking studies highlighted not only the advantages of performing in silico interaction studies on their closed conformations but they also suggested the potential mechanism of action of four phytochemicals known for their anti-trypanosomal activity in vitro. PMID:24551254

Mechanism of the αβ Conformational Change in F1-ATPase after ATP Hydrolysis: Free-Energy Simulations

PubMed Central

Ito, Yuko; Ikeguchi, Mitsunori

2015-01-01

One of the motive forces for F1-ATPase rotation is the conformational change of the catalytically active β subunit due to closing and opening motions caused by ATP binding and hydrolysis, respectively. The closing motion is accomplished in two steps: the hydrogen-bond network around ATP changes and then the entire structure changes via B-helix sliding, as shown in our previous study. Here, we investigated the opening motion induced by ATP hydrolysis using all-atom free-energy simulations, combining the nudged elastic band method and umbrella sampling molecular-dynamics simulations. Because hydrolysis requires residues in the α subunit, the simulations were performed with the αβ dimer. The results indicate that the large-scale opening motion is also achieved by the B-helix sliding (in the reverse direction). However, the sliding mechanism is different from that of ATP binding because sliding is triggered by separation of the hydrolysis products ADP and Pi. We also addressed several important issues: 1), the timing of the product Pi release; 2), the unresolved half-closed β structure; and 3), the ADP release mechanism. These issues are fundamental for motor function; thus, the rotational mechanism of the entire F1-ATPase is also elucidated through this αβ study. During the conformational change, conserved residues among the ATPase proteins play important roles, suggesting that the obtained mechanism may be shared with other ATPase proteins. When combined with our previous studies, these results provide a comprehensive view of the β-subunit conformational change that drives the ATPase. PMID:25564855

Identifying initiation and elongation inhibitors of dengue virus RNA polymerase in a high-throughput lead-finding campaign.

PubMed

Smith, Thomas M; Lim, Siew Pheng; Yue, Kimberley; Busby, Scott A; Arora, Rishi; Seh, Cheah Chen; Wright, S Kirk; Nutiu, Razvan; Niyomrattanakit, Pornwaratt; Wan, Kah Fei; Beer, David; Shi, Pei-Yong; Benson, Timothy E

2015-01-01

Dengue virus (DENV) is the most significant mosquito-borne viral pathogen in the world and is the cause of dengue fever. The DENV RNA-dependent RNA polymerase (RdRp) is conserved among the four viral serotypes and is an attractive target for antiviral drug development. During initiation of viral RNA synthesis, the polymerase switches from a "closed" to "open" conformation to accommodate the viral RNA template. Inhibitors that lock the "closed" or block the "open" conformation would prevent viral RNA synthesis. Herein, we describe a screening campaign that employed two biochemical assays to identify inhibitors of RdRp initiation and elongation. Using a DENV subgenomic RNA template that promotes RdRp de novo initiation, the first assay measures cytosine nucleotide analogue (Atto-CTP) incorporation. Liberated Atto fluorophore allows for quantification of RdRp activity via fluorescence. The second assay uses the same RNA template but is label free and directly detects RdRp-mediated liberation of pyrophosphates of native ribonucleotides via liquid chromatography-mass spectrometry. The ability of inhibitors to bind and stabilize a "closed" conformation of the DENV RdRp was further assessed in a differential scanning fluorimetry assay. Last, active compounds were evaluated in a renilla luciferase-based DENV replicon cell-based assay to monitor cellular efficacy. All assays described herein are medium to high throughput, are robust and reproducible, and allow identification of inhibitors of the open and closed forms of DENV RNA polymerase. © 2014 Society for Laboratory Automation and Screening.

Improved Modeling of Open Waveguide Aperture Radiators for use in Conformal Antenna Arrays

NASA Astrophysics Data System (ADS)

Nelson, Gregory James

Open waveguide apertures have been used as radiating elements in conformal arrays. Individual radiating element model patterns are used in constructing overall array models. The existing models for these aperture radiating elements may not accurately predict the array pattern for TEM waves which are not on boresight for each radiating element. In particular, surrounding structures can affect the far field patterns of these apertures, which ultimately affects the overall array pattern. New models of open waveguide apertures are developed here with the goal of accounting for the surrounding structure effects on the aperture far field patterns such that the new models make accurate pattern predictions. These aperture patterns (both E plane and H plane) are measured in an anechoic chamber and the manner in which they deviate from existing model patterns are studied. Using these measurements as a basis, existing models for both E and H planes are updated with new factors and terms which allow the prediction of far field open waveguide aperture patterns with improved accuracy. These new and improved individual radiator models are then used to predict overall conformal array patterns. Arrays of open waveguide apertures are constructed and measured in a similar fashion to the individual aperture measurements. These measured array patterns are compared with the newly modeled array patterns to verify the improved accuracy of the new models as compared with the performance of existing models in making array far field pattern predictions. The array pattern lobe characteristics are then studied for predicting fully circularly conformal arrays of varying radii. The lobe metrics that are tracked are angular location and magnitude as the radii of the conformal arrays are varied. A constructed, measured array that is close to conforming to a circular surface is compared with a fully circularly conformal modeled array pattern prediction, with the predicted lobe angular locations and magnitudes tracked, plotted and tabulated. The close match between the patterns of the measured array and the modeled circularly conformal array verifies the validity of the modeled circularly conformal array pattern predictions.

Residue-Specific Side-Chain Polymorphisms via Particle Belief Propagation.

PubMed

Ghoraie, Laleh Soltan; Burkowski, Forbes; Li, Shuai Cheng; Zhu, Mu

2014-01-01

Protein side chains populate diverse conformational ensembles in crystals. Despite much evidence that there is widespread conformational polymorphism in protein side chains, most of the X-ray crystallography data are modeled by single conformations in the Protein Data Bank. The ability to extract or to predict these conformational polymorphisms is of crucial importance, as it facilitates deeper understanding of protein dynamics and functionality. In this paper, we describe a computational strategy capable of predicting side-chain polymorphisms. Our approach extends a particular class of algorithms for side-chain prediction by modeling the side-chain dihedral angles more appropriately as continuous rather than discrete variables. Employing a new inferential technique known as particle belief propagation, we predict residue-specific distributions that encode information about side-chain polymorphisms. Our predicted polymorphisms are in relatively close agreement with results from a state-of-the-art approach based on X-ray crystallography data, which characterizes the conformational polymorphisms of side chains using electron density information, and has successfully discovered previously unmodeled conformations.

Probing the Conformational Landscape of Polyether Building Blocks in Supersonic Jets

NASA Astrophysics Data System (ADS)

Bocklitz, Sebastian; Hewett, Daniel M.; Zwier, Timothy S.; Suhm, Martin A.

2016-06-01

Polyethylene oxides (Polyethylene glycoles) and their phenoxy-capped analogs represent a prominent class of important polymers that are highly used as precursor molecules in supramolecular reactions. After a detailed study on the simplest representative (1,2-dimethoxyethane) [1], we present results on oligoethylene oxides with increasing chain lengths obtained by spontaneous Raman scattering in a supersonic jet. Through variation of stagnation pressure, carrier gas, nozzle distance and temperature we gain information on the conformational landscape as well as the mutual interconversion of low energy conformers. The obtained results are compared to state-of-the-art quantum chemical calculations. Additionally, we present UV as well as IR-UV and UV-UV double resonance studies on 1-methoxy-2-phenoxyethane in a supersonic jet. These complementary techniques allow for conformationally selective electronic and vibrational spectra in a closely related conformational landscape. [1] S. Bocklitz, M. A. Suhm, Constraining the Conformational Landscape of a Polyether Building Block by Raman Jet Spectroscopy, Z. Phys. Chem. 2015, 229, 1625-1648.

Cyclo-biphenalenyl Biradicaloid Molecular Materials: Conformation, Tautomerization, Magnetism, and Thermochromism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Jingsong; Meunier, Vincent; Tian, Yong-Hui

2010-01-01

Phenalenyl and its derivatives have recently attracted a great deal of interest as a result of a two-electron multicenter (2e/mc) - bonding between two -stacked phenalenyl units. The 2e/mc bonded -dimers are close in energy to the -dimers of phenalenyl and therefore fickle properties may emerge from bond fluctuation, yielding smart -functional materials. Here, we examine the valence tautomerization of two cyclo-biphenalenyl biradicaloid molecular materials with chair and boat conformations by spin-restricted (R) and unrestricted (U) DFT using the M06 and B3LYP functionals. We found that the chair conformation involves a 2e/4c - bonded structure, whereas the boat conformation involvesmore » a 2e/12c - bonded structure on their potential energy surfaces. The global minimum for the chair conformation is the -bonded structure, whereas it is the - bonded structure for the boat conformation. The chair conformation exhibits a stepwise [3,3]-sigmatropic rearrangement, and calculations predict a negligible paramagnetic susceptibility near room temperature. In comparison, the paramagnetism of the boat conformation should be observable by SQUID and ESR. According to the energy differences of the respective - and -dimers of the two conformations and the UV-vis calculations, the color of the chair conformation is expected to become darker, whereas that of the boat conformation should become lighter with increasing temperature.« less

Conformational Flexibility of Human Casein Kinase Catalytic Subunit Explored by Metadynamics

PubMed Central

Gouron, Aurélie; Milet, Anne; Jamet, Helene

2014-01-01

Casein kinase CK2 is an essential enzyme in higher organisms, catalyzing the transfer of the γ phosphate from ATP to serine and threonine residues on protein substrates. In a number of animal tumors, CK2 activity has been shown to escape normal cellular control, making it a potential target for cancer therapy. Several crystal structures of human CK2 have been published with different conformations for the CK2α catalytic subunit. This variability reflects a high flexibility for two regions of CK2α: the interdomain hinge region, and the glycine-rich loop (p-loop). Here, we present a computational study simulating the equilibrium between three conformations involving these regions. Simulations were performed using well-tempered metadynamics combined with a path collective variables approach. This provides a reference pathway describing the conformational changes being studied, based on analysis of free energy surfaces. The free energies of the three conformations were found to be close and the paths proposed had low activation barriers. Our results indicate that these conformations can exist in water. This information should be useful when designing inhibitors specific to one conformation. PMID:24606937

A computational study of the open and closed forms of the N-lobe human serum transferrin apoprotein.

PubMed

Rinaldo, David; Field, Martin J

2003-12-01

Human serum transferrin tightly binds ferric ions in the blood stream but is able to release them in cells by a process involving receptor-mediated endocytosis and decrease in pH. Iron binding and release are accompanied by a large conformation change. In this study, we investigate theoretically the open and closed forms of the N-lobe human serum transferrin apoprotein by performing pKa calculations and molecular dynamics and free-energy simulations. In agreement with the hypothesis based on the x-ray crystal structures, our calculations show that there is a shift in the pKa values of the lysines forming the dilysine trigger when the conformation changes. We argue, however, that simple electrostatic repulsion between the lysines is not sufficient to trigger domain opening and, instead, propose an alternative explanation for the dilysine-trigger effect. Analysis of the molecular dynamics and free-energy results indicate that the open form is more mobile than the closed form and is much more stable at pH 5.3, in large part due to entropic effects. Despite a lower free energy, the dynamics simulation of the open form shows that it is flexible enough to sample conformations that are consistent with iron binding.

Atropisomerism about aryl-Csp(3) bonds: the electronic and steric influence of ortho-substituents on conformational exchange in cannabidiol and linderatin derivatives.

PubMed

Berber, Hatice; Lameiras, Pedro; Denhez, Clément; Antheaume, Cyril; Clayden, Jonathan

2014-07-03

Terpenylation reactions of substituted phenols were used to prepare cannabidiol and linderatin derivatives, and their structure and conformational behavior in solution were investigated by NMR and, for some representative examples, by DFT. VT-NMR spectra and DFT calculations were used to determine the activation energies of the conformational change arising from restricted rotation about the aryl-Csp(3) bond that lead to two unequally populated rotameric epimers. The NBO calculation was applied to explain the electronic stabilization of one conformer over another by donor-acceptor charge transfer interactions. Conformational control arises from a combination of stereoelectronic and steric effects between substituents in close contact with each other on the two rings of the endocyclic epoxide atropisomers. This study represents the first exploration of the stereoelectronic origins of atropisomerism around C(sp(2))-C(sp(3)) single bonds through theoretical calculations.

Precise structural analysis of α-helical polypeptide by quantum-chemical calculation related to reciprocal side-chain combination of two L-phenylalanine residues

NASA Astrophysics Data System (ADS)

Niimura, Subaru; Kurosu, Hiromichi; Shoji, Akira

2010-04-01

To clarify the positive role of side-chain conformation in the stability of protein secondary structure (main-chain conformation), we successfully calculated the optimization structure of a series of well-defined α-helical octadecapeptides composed of two L-phenylalanine (Phe) and 16 L-alanine (Ala) residues, based on the molecular orbital calculation with density functional theory (DFT/B3LYP/6-31G(d)). From the total energy calculation and the precise secondary structural analysis, we found that the conformational stability of the α-helix is closely related to the reciprocal side-chain combinations (such as positional relation and side-chain conformation) of two Phe residues in this system. Furthermore, we demonstrated that the 1H, 13C, 15N and 17O isotropic chemical shifts of each Phe residue depend on the respective side-chain conformations of the Phe residue.

30 CFR 75.340 - Underground electrical installations.

Code of Federal Regulations, 2012 CFR

2012-07-01

... electrical installations. (a) Underground transformer stations, battery charging stations, substations... with transformers that are either dry-type or contain nonflammable liquid, if they are located at or...

30 CFR 75.340 - Underground electrical installations.

Code of Federal Regulations, 2014 CFR

2014-07-01

... electrical installations. (a) Underground transformer stations, battery charging stations, substations... with transformers that are either dry-type or contain nonflammable liquid, if they are located at or...

30 CFR 75.340 - Underground electrical installations.

Code of Federal Regulations, 2013 CFR

2013-07-01

... electrical installations. (a) Underground transformer stations, battery charging stations, substations... with transformers that are either dry-type or contain nonflammable liquid, if they are located at or...

30 CFR 75.340 - Underground electrical installations.

Code of Federal Regulations, 2011 CFR

2011-07-01

... electrical installations. (a) Underground transformer stations, battery charging stations, substations... with transformers that are either dry-type or contain nonflammable liquid, if they are located at or...

30 CFR 75.340 - Underground electrical installations.

Code of Federal Regulations, 2010 CFR

2010-07-01

... electrical installations. (a) Underground transformer stations, battery charging stations, substations... with transformers that are either dry-type or contain nonflammable liquid, if they are located at or...

36 CFR 292.21 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-07-01

.../forest/grazing uses may also consist of uses related to and in furtherance of the protection of... transmission line systems, substations, commercial radio transmitters, relays or repeater stations, antennas...

36 CFR 292.21 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

.../forest/grazing uses may also consist of uses related to and in furtherance of the protection of... transmission line systems, substations, commercial radio transmitters, relays or repeater stations, antennas...

Understanding nucleotide-regulated FtsZ filament dynamics and the monomer assembly switch with large-scale atomistic simulations.

PubMed

Ramírez-Aportela, Erney; López-Blanco, José Ramón; Andreu, José Manuel; Chacón, Pablo

2014-11-04

Bacterial cytoskeletal protein FtsZ assembles in a head-to-tail manner, forming dynamic filaments that are essential for cell division. Here, we study their dynamics using unbiased atomistic molecular simulations from representative filament crystal structures. In agreement with experimental data, we find different filament curvatures that are supported by a nucleotide-regulated hinge motion between consecutive FtsZ monomers. Whereas GTP-FtsZ filaments bend and twist in a preferred orientation, thereby burying the nucleotide, the differently curved GDP-FtsZ filaments exhibit a heterogeneous distribution of open and closed interfaces between monomers. We identify a coordinated Mg(2+) ion as the key structural element in closing the nucleotide site and stabilizing GTP filaments, whereas the loss of the contacts with loop T7 from the next monomer in GDP filaments leads to open interfaces that are more prone to depolymerization. We monitored the FtsZ monomer assembly switch, which involves opening/closing of the cleft between the C-terminal domain and the H7 helix, and observed the relaxation of isolated and filament minus-end monomers into the closed-cleft inactive conformation. This result validates the proposed switch between the low-affinity monomeric closed-cleft conformation and the active open-cleft FtsZ conformation within filaments. Finally, we observed how the antibiotic PC190723 suppresses the disassembly switch and allosterically induces closure of the intermonomer interfaces, thus stabilizing the filament. Our studies provide detailed structural and dynamic insights into modulation of both the intrinsic curvature of the FtsZ filaments and the molecular switch coupled to the high-affinity end-wise association of FtsZ monomers.

Submillimeterwave Spectroscopy of Highly Astrophysical Interest Molecule: Hydroxyacetonitrile

NASA Astrophysics Data System (ADS)

Margules, L.; Motiyenko, R. A.; Guillemin, J.-C.

2013-06-01

Hydroxyacetonitrile is a simple derivative of methanol. This molecule has a strong astrophysical interest. In astrophysical environment, the formation of hydroxyacetonitrile (HOCH_2CN), has been shown to compete with aminomethanol (NH_2CH_2OH), a glycine precursor, through the Strecker synthesis, in addition its photochemistry leads to the formation of formylcyanide (CHOCN), ketenimine (CH_2CNH), formaldehyde (CH_2O), hydrogen cyanide (HCN), carbon monoxyde (CO). Its detection in the ISM will provide crucial hints in the formation process of complex organic molecules. The lack of data about this molecule, only studied up to 50 GHz, is mainly due to two reasons. First, this is not commercially available, the synthesis should be perform. Second, the most stable conformer is the gauche one. This exhibits large amplitude motion due to the two equivalent configurations possible. Due to tunneling effect, each level is split into 0^+ and 0^- substates. This makes the analysis of the spectra delicate. We will report here the very first results obtained. This work was supported by the CNES and the Action sur Projets de l'INSU, PCMI. Danger, G. et al.ApJ {756}, (2012) 11 Danger, G. et al.A&A {549}, (2012) A93 Cazzoli, G. et al.J. Chem. Soc., Faraday Trans. 2 {69}, (1973) 569

Conformational dynamics of L-lysine, L-arginine, L-ornithine binding protein reveals ligand-dependent plasticity.

PubMed

Silva, Daniel-Adriano; Domínguez-Ramírez, Lenin; Rojo-Domínguez, Arturo; Sosa-Peinado, Alejandro

2011-07-01

The molecular basis of multiple ligand binding affinity for amino acids in periplasmic binding proteins (PBPs) and in the homologous domain for class C G-protein coupled receptors is an unsolved question. Here, using unrestrained molecular dynamic simulations, we studied the ligand binding mechanism present in the L-lysine, L-arginine, L-ornithine binding protein. We developed an analysis based on dihedral angles for the description of the conformational changes upon ligand binding. This analysis has an excellent correlation with each of the two main movements described by principal component analysis (PCA) and it's more convenient than RMSD measurements to describe the differences in the conformational ensembles observed. Furthermore, an analysis of hydrogen bonds showed specific interactions for each ligand studied as well as the ligand interaction with the aromatic residues Tyr-14 and Phe-52. Using uncharged histidine tautomers, these interactions are not observed. On the basis of these results, we propose a model in which hydrogen bond interactions place the ligand in the correct orientation to induce a cation-π interaction with Tyr-14 and Phe-52 thereby stabilizing the closed state. Our results also show that this protein adopts slightly different closed conformations to make available specific hydrogen bond interactions for each ligand thus, allowing a single mechanism to attain multiple ligand specificity. These results shed light on the experimental evidence for ligand-dependent conformational plasticity not explained by the previous crystallographic data. Copyright © 2011 Wiley-Liss, Inc.

Conformation-selective inhibitors reveal differences in the activation and phosphate-binding loops of the tyrosine kinases Abl and Src

PubMed Central

Hari, Sanjay B.; Perera, B. Gayani K.; Ranjitkar, Pratistha; Seeliger, Markus A.; Maly, Dustin J.

2013-01-01

Over the last decade, an increasingly diverse array of potent and selective inhibitors that target the ATP-binding sites of protein kinases have been developed. Many of these inhibitors, like the clinically approved drug imatinib (Gleevec), stabilize a specific catalytically inactive ATP-binding site conformation of their kinases targets. Imatinib is notable in that it is highly selective for its kinase target, Abl, over other closely-related tyrosine kinases, like Src. In addition, imatinib is highly sensitive to the phosphorylation state of Abl's activation loop, which is believed to be a general characteristic of all inhibitors that stabilize a similar inactive ATP-binding site conformation. In this report, we perform a systematic analysis of a diverse series of ATP-competitive inhibitors that stabilize a similar inactive ATP-binding site conformation as imatinib with the tyrosine kinases Src and Abl. In contrast to imatinib, many of these inhibitors have very similar potencies against Src and Abl. Furthermore, only a subset of this class of inhibitors is sensitive to the phosphorylation state of the activation loop of these kinases. In attempting to explain this observation, we have uncovered an unexpected correlation between Abl's activation loop and another flexible active site feature, called the phosphate-binding loop (p-loop). These studies shed light on how imatinib is able to obtain its high target selectivity and reveal how the conformational preference of flexible active site regions can vary between closely related kinases. PMID:24106839

Structure of an intermediate conformer of the spindle checkpoint protein Mad2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hara, Mayuko; Özkan, Engin; Sun, Hongbin

2015-08-24

The spindle checkpoint senses unattached kinetochores during prometaphase and inhibits the anaphase-promoting complex or cyclosome (APC/C), thus ensuring accurate chromosome segregation. The checkpoint protein mitotic arrest deficient 2 (Mad2) is an unusual protein with multiple folded states. Mad2 adopts the closed conformation (C-Mad2) in a Mad1–Mad2 core complex. In mitosis, kinetochore-bound Mad1–C-Mad2 recruits latent, open Mad2 (O-Mad2) from the cytosol and converts it to an intermediate conformer (I-Mad2), which can then bind and inhibit the APC/C activator cell division cycle 20 (Cdc20) as C-Mad2. In this paper, we report the crystal structure and NMR analysis of I-Mad2 bound to C-Mad2.more » Although I-Mad2 retains the O-Mad2 fold in crystal and in solution, its core structural elements undergo discernible rigid-body movements and more closely resemble C-Mad2. Residues exhibiting methyl chemical shift changes in I-Mad2 form a contiguous, interior network that connects its C-Mad2–binding site to the conformationally malleable C-terminal region. Mutations of residues at the I-Mad2–C-Mad2 interface hinder I-Mad2 formation and impede the structural transition of Mad2. Finally, our study provides insight into the conformational activation of Mad2 and establishes the basis of allosteric communication between two distal sites in Mad2.« less

Three Dimensional Architecture of Membrane-Embedded MscS in the Closed Conformation

PubMed Central

Vásquez, Valeria; Sotomayor, Marcos; Cortes, D. Marien; Roux, Benoît; Schulten, Klaus; Perozo, Eduardo

2009-01-01

The mechanosensitive channel of small conductance (MscS) is part of a coordinated response to osmotic challenges in E. coli. MscS opens as a result of membrane tension changes, thereby releasing small solutes and effectively acting as an osmotic safety valve. Both, the functional state depicted by its crystal structure and its gating mechanism remain unclear. Here, we combine site-directed spin labeling, electron paramagnetic resonance (EPR) spectroscopy, and molecular dynamics simulations with novel energy restraints based on experimental EPR data to investigate the native transmembrane and periplasmic molecular architecture of closed MscS in a lipid bilayer. In the closed conformation, MscS shows a more compact transmembrane domain than in the crystal structure, characterized by a realignment of the transmembrane segments towards the normal of the membrane. The previously unresolved NH2-terminus forms a short helical hairpin capping the extracellular ends of TM1 and TM2 and in close interaction with the bilayer interface. The present three-dimensional model of membrane-embedded MscS in the closed state represents a key step in determining the molecular mechanism of MscS gating. PMID:18343404

40 CFR 98.438 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... substations, circuit breakers, other switchgear, gas-insulated lines, or power transformers. Fluorinated GHG... transformers containing a fluorinated GHG prior to sale or distribution, or offer for sale or distribution in...

40 CFR 98.438 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... substations, circuit breakers, other switchgear, gas-insulated lines, or power transformers. Fluorinated GHG... transformers containing a fluorinated GHG prior to sale or distribution, or offer for sale or distribution in...

40 CFR 98.438 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... substations, circuit breakers, other switchgear, gas-insulated lines, or power transformers. Fluorinated GHG... transformers containing a fluorinated GHG prior to sale or distribution, or offer for sale or distribution in...

Feasibility study of wireless power transmission systems

NASA Technical Reports Server (NTRS)

Robinson, W. J., Jr.

1968-01-01

Wireless microwave or laser energy transfers power from a manned earth-orbiting central station to unmanned astronomical substations. More efficient systems are required for the microwave power transmission.

36 CFR 14.78 - Applications.

Code of Federal Regulations, 2011 CFR

2011-07-01

... application should include a one-line diagram of the proposed line and the immediate interconnecting facilities including power plants and substations, a power flow diagram for proposed line and connecting...

36 CFR 14.78 - Applications.

Code of Federal Regulations, 2014 CFR

2014-07-01

... application should include a one-line diagram of the proposed line and the immediate interconnecting facilities including power plants and substations, a power flow diagram for proposed line and connecting...

36 CFR 14.78 - Applications.

Code of Federal Regulations, 2012 CFR

2012-07-01

... application should include a one-line diagram of the proposed line and the immediate interconnecting facilities including power plants and substations, a power flow diagram for proposed line and connecting...

36 CFR 14.78 - Applications.

Code of Federal Regulations, 2013 CFR

2013-07-01

... application should include a one-line diagram of the proposed line and the immediate interconnecting facilities including power plants and substations, a power flow diagram for proposed line and connecting...

Ligand-Induced Conformational Change in the α7 Nicotinic Receptor Ligand Binding Domain

PubMed Central

Henchman, Richard H.; Wang, Hai-Long; Sine, Steven M.; Taylor, Palmer; McCammon, J. Andrew

2005-01-01

Molecular dynamics simulations of a homology model of the ligand binding domain of the α7 nicotinic receptor are conducted with a range of bound ligands to induce different conformational states. Four simulations of 15 ns each are run with no ligand, antagonist d-tubocurarine (dTC), agonist acetylcholine (ACh), and agonist ACh with potentiator Ca2+, to give insight into the conformations of the active and inactive states of the receptor and suggest the mechanism for conformational change. The main structural factor distinguishing the active and inactive states is that a more open, symmetric arrangement of the five subunits arises for the two agonist simulations, whereas a more closed and asymmetric arrangement results for the apo and dTC cases. Most of the difference arises in the lower portion of the ligand binding domain near its connection to the adjacent transmembrane domain. The transfer of the more open state to the transmembrane domain could then promote ion flow through the channel. Variation in how subunits pack together with no ligand bound appears to give rise to asymmetry in the apo case. The presence of dTC expands the receptor but induces rotations in alternate directions in adjacent subunits that lead to an asymmetric arrangement as in the apo case. Ca2+ appears to promote a slightly greater expansion in the subunits than ACh alone by stabilizing the C-loop and ACh positions. Although the simulations are unlikely to be long enough to view the full conformational changes between open and closed states, a collection of different motions at a range of length scales are observed that are likely to participate in the conformational change. PMID:15665135

Dynamic Equilibrium of Cardiac Troponin C's Hydrophobic Cleft and Its Modulation by Ca2+ Sensitizers and a Ca2+ Sensitivity Blunting Phosphomimic, cTnT(T204E).

PubMed

Schlecht, William; Dong, Wen-Ji

2017-10-18

Several studies have suggested that conformational dynamics are important in the regulation of thin filament activation in cardiac troponin C (cTnC); however, little direct evidence has been offered to support these claims. In this study, a dye homodimerization approach is developed and implemented that allows the determination of the dynamic equilibrium between open and closed conformations in cTnC's hydrophobic cleft. Modulation of this equilibrium by Ca 2+ , cardiac troponin I (cTnI), cardiac troponin T (cTnT), Ca 2+ -sensitizers, and a Ca 2+ -desensitizing phosphomimic of cTnT (cTnT(T204E) is characterized. Isolated cTnC contained a small open conformation population in the absence of Ca 2+ that increased significantly upon the addition of saturating levels of Ca 2+ . This suggests that the Ca 2+ -induced activation of thin filament arises from an increase in the probability of hydrophobic cleft opening. The inclusion of cTnI increased the population of open cTnC, and the inclusion of cTnT had the opposite effect. Samples containing Ca 2+ -desensitizing cTnT(T204E) showed a slight but insignificant decrease in open conformation probability compared to samples with cardiac troponin T, wild type [cTnT(wt)], while Ca 2+ sensitizer treated samples generally increased open conformation probability. These findings show that an equilibrium between the open and closed conformations of cTnC's hydrophobic cleft play a significant role in tuning the Ca 2+ sensitivity of the heart.

Geometric Patterns for Neighboring Bases Near the Stacked State in Nucleic Acid Strands.

PubMed

Sedova, Ada; Banavali, Nilesh K

2017-03-14

Structural variation in base stacking has been analyzed frequently in isolated double helical contexts for nucleic acids, but not as often in nonhelical geometries or in complex biomolecular environments. In this study, conformations of two neighboring bases near their stacked state in any environment are comprehensively characterized for single-strand dinucleotide (SSD) nucleic acid crystal structure conformations. An ensemble clustering method is used to identify a reduced set of representative stacking geometries based on pairwise distances between select atoms in consecutive bases, with multiple separable conformational clusters obtained for categories divided by nucleic acid type (DNA/RNA), SSD sequence, stacking face orientation, and the presence or absence of a protein environment. For both DNA and RNA, SSD conformations are observed that are either close to the A-form, or close to the B-form, or intermediate between the two forms, or further away from either form, illustrating the local structural heterogeneity near the stacked state. Among this large variety of distinct conformations, several common stacking patterns are observed between DNA and RNA, and between nucleic acids in isolation or in complex with proteins, suggesting that these might be stable stacking orientations. Noncanonical face/face orientations of the two bases are also observed for neighboring bases in the same strand, but their frequency is much lower, with multiple SSD sequences across categories showing no occurrences of such unusual stacked conformations. The resulting reduced set of stacking geometries is directly useful for stacking-energy comparisons between empirical force fields, prediction of plausible localized variations in single-strand structures near their canonical states, and identification of analogous stacking patterns in newly solved nucleic acid containing structures.

Rapid Prototyping across the Spectrum: RF to Optical 3D Electromagnetic Structures

DTIC Science & Technology

2015-11-17

34Imprintable, Bendable, and Shape-Conformable Polymer Electrolytes for Versatile-Shaped Lithium - Ion Batteries ," Advanced Materials, vol. 25, pp. 1395-1400...center; and (d) close-up of light aperture etched with a focused ion beam [104] ............ 22 Figure 16: (a) Conformal antenna patterned by...where the features are defined using focused ion beam milling (e.g. fishnet patterns) [20], standard micro-/nano- lithography processes that are

Genetic parameters for carcass weight, conformation and fat in five beef cattle breeds.

PubMed

Kause, A; Mikkola, L; Strandén, I; Sirkko, K

2015-01-01

Profitability of beef production can be increased by genetically improving carcass traits. To construct breeding value evaluations for carcass traits, breed-specific genetic parameters were estimated for carcass weight, carcass conformation and carcass fat in five beef cattle breeds in Finland (Hereford, Aberdeen Angus, Simmental, Charolais and Limousin). Conformation and fat were visually scored using the EUROP carcass classification. Each breed was separately analyzed using a multitrait animal model. A total of 6879-19 539 animals per breed had phenotypes. For the five breeds, heritabilities were moderate for carcass weight (h 2=0.39 to 0.48, s.e.=0.02 to 0.04) and slightly lower for conformation (h 2=0.30 to 0.44, s.e.=0.02 to 0.04) and carcass fat (h 2=0.29 to 0.44, s.e.=0.02 to 0.04). The genetic correlation between carcass weight and conformation was favorable in all breeds (r G=0.37 to 0.53, s.e.=0.04 to 0.05), heavy carcasses being genetically more conformed. The phenotypic correlation between carcass weight and carcass fat was moderately positive in all breeds (r P=0.21 to 0.32), implying that increasing carcass weight was related to increasing fat levels. The respective genetic correlation was the strongest in Hereford (r G=0.28, s.e.=0.05) and Angus (r G=0.15, s.e.=0.05), the two small body-sized British breeds with the lowest conformation and the highest fat level. The correlation was weaker in the other breeds (r G=0.08 to 0.14). For Hereford, Angus and Simmental, more conformed carcasses were phenotypically fatter (r P=0.11 to 0.15), but the respective genetic correlations were close to zero (r G=-0.05 to 0.04). In contrast, in the two large body-sized and muscular French breeds, the genetic correlation between conformation and fat was negative and the phenotypic correlation was close to zero or negative (Charolais: r G=-0.18, s.e.=0.06, r P=0.02; Limousin: r G=-0.56, s.e.=0.04, r P=-0.13). The results indicate genetic variation for the genetic improvement of the carcass traits, favorable correlations for the simultaneous improvement of carcass weight and conformation in all breeds, and breed differences in the correlations of carcass fat.

7 CFR 1726.14 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... electric system, e.g., a substation transformer, heat exchanger or a transmission structure. Force account... which is combined with equipment to form an electric system, e.g., poles, insulators, or conductors...

7 CFR 1726.14 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... electric system, e.g., a substation transformer, heat exchanger or a transmission structure. Force account... which is combined with equipment to form an electric system, e.g., poles, insulators, or conductors...

7 CFR 1726.14 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... electric system, e.g., a substation transformer, heat exchanger or a transmission structure. Force account... which is combined with equipment to form an electric system, e.g., poles, insulators, or conductors...

7 CFR 1726.14 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... electric system, e.g., a substation transformer, heat exchanger or a transmission structure. Force account... which is combined with equipment to form an electric system, e.g., poles, insulators, or conductors...

7 CFR 1726.14 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... electric system, e.g., a substation transformer, heat exchanger or a transmission structure. Force account... which is combined with equipment to form an electric system, e.g., poles, insulators, or conductors...

30 CFR 75.380 - Escapeways; bituminous and lignite mines.

Code of Federal Regulations, 2010 CFR

2010-07-01

...) Underground transformer stations, battery charging stations, substations, and rectifiers except— (A) Where... rectifiers and power centers with transformers that are either dry-type or contain nonflammable liquid...

Variation in Vaccination Data Available at School Entry Across the United States.

PubMed

Leslie, Timothy F; Street, Erica J; Delamater, Paul L; Yang, Y Tony; Jacobsen, Kathryn H

2016-12-01

To compile substate-level data on US school-age children's vaccination rates. For states that did not have suitable data online, in 2015 we submitted information requests to the state health department and followed up with the state's Freedom of Information Act when necessary. The accessibility, scale, and types of vaccination data varied considerably. Whereas 26 states provided data online, 14 released data only after a Freedom of Information Act request. School or school-district data were available for 24 states, 19 at the county level, 2 at the health department level, and 6 provided no substate-level data. Effective vaccination policy requires a robust understanding of vaccination behavior. Some states make it difficult to access data or provide low-resolution data of limited value for identifying vaccination behavior.

Experience in the installation of a microprocessor system for controlling converter units of the Vyborg substation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gusakovskii, K. B.; Zmaznov, E. Yu.; Katantsev, S. V.

The experience in the installation of modern digital systems for controlling converter units at the Vyborg converter substation on the basis of advanced microprocessor devices is considered. It is shown that debugging of a control and protection system on mathematical and physical models does not guarantee optimum control of actual converter devices. Examples of advancing the control and protection system are described, the necessity for which has become obvious in tests of actual equipment. Comparison of oscillograms of processes before optimization of the control system and after its optimization and adjustment shows that the digital control system makes it possiblemore » to improve substantially the algorithms of control and protection in the short term and without changing the hardware component.« less

View southeast of main supervisory board showing panels 3 through ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

View southeast of main supervisory board showing panels 3 through 11; panel 3 at far left contains meters for monitoring power in the system; panel 4 contains controls for controlling heaters to keep track twitches free of ice and snow; panels 5, 6, and 7 date to the 1935 installation and control the catenary in the area of the station yard. These work on 120 volts direct current; panel 8 contains circuit breakers (rupture switches) which control power to individual tracks in the station area; panels 9 and 10 house controls for the West Philadelphia sub-station; panel 11 controls sub-station 13 in South Wilmington Delaware and miscellaneous meters - Thirtieth Street Station, Power Director Center, Thirtieth & Market Streets in Amtrak Railroad Station, Philadelphia, Philadelphia County, PA

Conformational fluctuation of Synaptotagmin-1 observed with single molecule fluorescence resonance energy transfer (smFRET)

NASA Astrophysics Data System (ADS)

Choi, Ucheor; Weninger, Keith

2008-10-01

Calcium dependent neurotransmitter release at the synapses involves a synaptic vesicle protein synaptotagmin-1, a calcium sensor, to regulate exocytosis. It has been known that Synaptotagmin-1 interacts with assembled SNARE complexes, but it is unclear how their molecular mechanisms are coupled. X-ray studies in the absence of calcium revealed a closed conformation of synaptotagmin-1 and with calcium bound to the C2 domains of synaptotagmin-3 found extensive interactions holding the domains open. Suggesting the two conformations can be the key to the two functions of synaptotagmin in regulating neurotransmission. Here we use single molecule fluorescence resonance energy transfer (smFRET) to study synaptotagmin interactions with SNARE complexes and the spontaneous conformational changes of synaptotagmin-1 when calcium is induced.

Mechanosensitive channel activation by diffusio-osmotic force.

PubMed

Bonthuis, Douwe Jan; Golestanian, Ramin

2014-10-03

For ion channel gating, the appearance of two distinct conformational states and the discrete transitions between them are essential, and therefore of crucial importance to all living organisms. We show that the physical interplay between two structural elements that are commonly present in bacterial mechanosensitive channels--namely, a charged vestibule and a hydrophobic constriction--creates two distinct conformational states, open and closed, as well as the gating between them. We solve the nonequilibrium Stokes-Poisson-Nernst-Planck equations, extended to include a molecular potential of mean force, and show that a first order transition between the closed and open states arises naturally from the diffusio-osmotic stress caused by the ions and the water inside the channel and the elastic restoring force from the membrane.

Cyclo-biphenalenyl biradicaloid molecular materials: conformation, tautomerization, magnetism, and thermochromism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Jingsong; Sumpter, Bobby G; Meunier, Vincent

2011-01-01

Phenalenyl and its derivatives have recently attracted a great deal of interest as a result of a 2-electron multicenter (2e/mc) covalent pi-pi bonding between two pi-stacked phenalenyl units. The 2e/mc bonded pi-dimers are close in energy to the sigma-dimers of phenalenyl and therefore fickle properties may emerge from bond fluctuation, yielding smart pi-functional materials. Here we examine the valence tautomerization of two cyclo-biphenalenyl biradicaloid molecular materials with chair- and boat-conformations by spin-restricted (R) and unrestricted (U) DFT using the M06 and B3LYP functionals. We found that the chair-conformation involves a 2e/4c pi-pi bonded structure while the boat-conformation involves a 2e/12cmore » pi-pi bonded structure on their potential energy surfaces. The global minimum for the chair-conformation is the sigma-bonded structure while it is the pi-pi bonded structure for the boat-conformation. The chair-conformation exhibits a stepwise [3,3]-sigmatropic rearrangement, and calculations predict a negligible paramagnetic susceptibility near room temperature. In comparison, the paramagnetism of the boat-conformation should be observable by SQUID and/or ESR. According to the difference of the global minima of the two conformations and the parameterized UV-Vis calculations, the color of the chair-conformation is expected to become darker while that of the boat-conformation become lighter with increasing temperature.« less

Conformal electronics for longitudinal bio-sensing in at-home assistive and rehabilitative devices.

PubMed

Batchelor, John C; Yeates, Stephen G; Casson, Alexander J

2016-08-01

Wearable electronics are revolutionizing personalized and preventative healthcare by allowing the easy, unobtrusive, and long term monitoring of a range of body parameters. Conformal electronics which attach directly to the skin in a very robust and long term manner are envisioned as the next generation of highly portable miniaturized computing devices, beyond wearables. In this paper we overview the state-of-the-art in conformal electronics created using silver nanoparticle inkjet printed techniques for home assistive and rehabilitative devices. The barriers to wider adaption, particularly the challenges of high performance antenna design when placed close to the body, are discussed in detail.

Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins.

PubMed

Harada, Ryuhei; Takano, Yu; Shigeta, Yasuteru

2014-03-28

A powerful conformational sampling method for accelerating structural transitions of proteins, "Fluctuation Flooding Method (FFM)," is proposed. In FFM, cycles of the following steps enhance the transitions: (i) extractions of largely fluctuating snapshots along anisotropic modes obtained from trajectories of multiple independent molecular dynamics (MD) simulations and (ii) conformational re-sampling of the snapshots via re-generations of initial velocities when re-starting MD simulations. In an application to bacteriophage T4 lysozyme, FFM successfully accelerated the open-closed transition with the 6 ns simulation starting solely from the open state, although the 1-μs canonical MD simulation failed to sample such a rare event.

Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins

NASA Astrophysics Data System (ADS)

Harada, Ryuhei; Takano, Yu; Shigeta, Yasuteru

2014-03-01

A powerful conformational sampling method for accelerating structural transitions of proteins, "Fluctuation Flooding Method (FFM)," is proposed. In FFM, cycles of the following steps enhance the transitions: (i) extractions of largely fluctuating snapshots along anisotropic modes obtained from trajectories of multiple independent molecular dynamics (MD) simulations and (ii) conformational re-sampling of the snapshots via re-generations of initial velocities when re-starting MD simulations. In an application to bacteriophage T4 lysozyme, FFM successfully accelerated the open-closed transition with the 6 ns simulation starting solely from the open state, although the 1-μs canonical MD simulation failed to sample such a rare event.