Crystal Structures of Trypanosoma cruzi UDP-Galactopyranose Mutase Implicate Flexibility of the Histidine Loop in Enzyme Activation

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

Dhatwalia, Richa; Singh, Harkewal; Oppenheimer, Michelle

2012-11-01

Chagas disease is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi. Here we report crystal structures of the galactofuranose biosynthetic enzyme UDP-galactopyranose mutase (UGM) from T. cruzi, which are the first structures of this enzyme from a protozoan parasite. UGM is an attractive target for drug design because galactofuranose is absent in humans but is an essential component of key glycoproteins and glycolipids in trypanosomatids. Analysis of the enzyme-UDP noncovalent interactions and sequence alignments suggests that substrate recognition is exquisitely conserved among eukaryotic UGMs and distinct from that of bacterial UGMs. This observation has implications for inhibitormore » design. Activation of the enzyme via reduction of the FAD induces profound conformational changes, including a 2.3 {angstrom} movement of the histidine loop (Gly60-Gly61-His62), rotation and protonation of the imidazole of His62, and cooperative movement of residues located on the si face of the FAD. Interestingly, these changes are substantially different from those described for Aspergillus fumigatus UGM, which is 45% identical to T. cruzi UGM. The importance of Gly61 and His62 for enzymatic activity was studied with the site-directed mutant enzymes G61A, G61P, and H62A. These mutations lower the catalytic efficiency by factors of 10-50, primarily by decreasing k{sub cat}. Considered together, the structural, kinetic, and sequence data suggest that the middle Gly of the histidine loop imparts flexibility that is essential for activation of eukaryotic UGMs. Our results provide new information about UGM biochemistry and suggest a unified strategy for designing inhibitors of UGMs from the eukaryotic pathogens.« less

Crystal Structures of Trypanosoma cruzi UDP-Galactopyranose Mutase Implicate Flexibility of the Histidine Loop in Enzyme Activation

PubMed Central

Dhatwalia, Richa; Singh, Harkewal; Oppenheimer, Michelle; Sobrado, Pablo; Tanner, John J.

2012-01-01

Chagas disease is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi. Here we report crystal structures of the galactofuranose biosynthetic enzyme UDP-galactopyranose mutase (UGM) from T. cruzi, which are the first structures of this enzyme from a protozoan parasite. UGM is an attractive target for drug design because galactofuranose is absent in humans but is an essential component of key glycoproteins and glycolipids in trypanosomatids. Analysis of the enzyme-UDP noncovalent interactions and sequence alignments suggests that substrate recognition is exquisitely conserved among eukaryotic UGMs and distinct from that of bacterial UGMs. This observation has implications for inhibitor design. Activation of the enzyme via reduction of the FAD induces profound conformational changes, including a 2.3-Å movement of the histidine loop (Gly60-Gly61-His62), rotation and protonation of the imidazole of His62, and cooperative movement of residues located on the si face of the FAD. Interestingly, these changes are substantially different from those described for Aspergillus fumigatus UGM, which is 45 % identical to T. cruzi UGM. The importance of Gly61 and His62 for enzymatic activity was studied with the site-directed mutant enzymes G61A, G61P, and H62A. These mutations lower the catalytic efficiency by factors of 10–50, primarily by decreasing kcat. Considered together, the structural, kinetic, and sequence data suggest that the middle Gly of the histidine loop imparts flexibility that is essential for activation of eukaryotic UGMs. Our results provide new information about UGM biochemistry and suggest a unified strategy for designing inhibitors of UGMs from the eukaryotic pathogens. PMID:22646091

Crystal structures of Trypanosoma cruzi UDP-galactopyranose mutase implicate flexibility of the histidine loop in enzyme activation.

PubMed

Dhatwalia, Richa; Singh, Harkewal; Oppenheimer, Michelle; Sobrado, Pablo; Tanner, John J

2012-06-19

Chagas disease is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi. Here we report crystal structures of the galactofuranose biosynthetic enzyme UDP-galactopyranose mutase (UGM) from T. cruzi, which are the first structures of this enzyme from a protozoan parasite. UGM is an attractive target for drug design because galactofuranose is absent in humans but is an essential component of key glycoproteins and glycolipids in trypanosomatids. Analysis of the enzyme-UDP noncovalent interactions and sequence alignments suggests that substrate recognition is exquisitely conserved among eukaryotic UGMs and distinct from that of bacterial UGMs. This observation has implications for inhibitor design. Activation of the enzyme via reduction of the FAD induces profound conformational changes, including a 2.3 Å movement of the histidine loop (Gly60-Gly61-His62), rotation and protonation of the imidazole of His62, and cooperative movement of residues located on the si face of the FAD. Interestingly, these changes are substantially different from those described for Aspergillus fumigatus UGM, which is 45% identical to T. cruzi UGM. The importance of Gly61 and His62 for enzymatic activity was studied with the site-directed mutant enzymes G61A, G61P, and H62A. These mutations lower the catalytic efficiency by factors of 10-50, primarily by decreasing k(cat). Considered together, the structural, kinetic, and sequence data suggest that the middle Gly of the histidine loop imparts flexibility that is essential for activation of eukaryotic UGMs. Our results provide new information about UGM biochemistry and suggest a unified strategy for designing inhibitors of UGMs from the eukaryotic pathogens.

Modulation of HIV Protease Flexibility by the T80N Mutation

PubMed Central

Zhou, Hao; Li, Shangyang; Badger, John; Nalivaika, Ellen; Cai, Yufeng; Foulkes-Murzycki, Jennifer; Schiffer, Celia; Makowski, Lee

2015-01-01

The flexibility of HIV protease plays a critical role in enabling enzymatic activity and is required for substrate access to the active site. While the importance of flexibility in the flaps that cover the active site is well known, flexibility in other parts of the enzyme is also critical for function. One key region is a loop containing Thr 80 which forms the walls of the active site. Although not situated within the active site, amino acid Thr80 is absolutely conserved. The mutation T80N preserves the structure of the enzyme but catalytic activity is completely lost. To investigate the potential influence of the T80N mutation on HIVp flexibility, wide-angle scattering (WAXS) data was measured for a series of HIV protease variants. Starting with a calculated WAXS pattern from a rigid atomic model, the modulations in the intensity distribution caused by structural fluctuations in the protein were predicted by simple analytic methods and compared to the experimental data. An analysis of T80N WAXS data shows that this variant is significantly more rigid than the WT across all length scales. The effects of this single point mutation extend throughout the protein, so as to alter the mobility of amino acids in the enzymatic core. These results support the contentions that significant protein flexibility extends throughout HIV protease and is critical to catalytic function. PMID:25488402

Relationship of Catalysis and Active Site Loop Dynamics in the (βα)8-Barrel Enzyme Indole-3-glycerol Phosphate Synthase.

PubMed

Schlee, Sandra; Klein, Thomas; Schumacher, Magdalena; Nazet, Julian; Merkl, Rainer; Steinhoff, Heinz-Jürgen; Sterner, Reinhard

2018-03-08

It is important to understand how the catalytic activity of enzymes is related to their conformational flexibility. We have studied this activity-flexibility correlation using the example of indole-3-glycerol phosphate synthase from Sulfolobus solfataricus (ssIGPS), which catalyzes the fifth step in the biosynthesis of tryptophan. ssIGPS is a thermostable representative of enzymes with the frequently encountered and catalytically versatile (βα) 8 -barrel fold. Four variants of ssIGPS with increased catalytic turnover numbers were analyzed by transient kinetics at 25 °C, and wild-type ssIGPS was likewise analyzed both at 25 °C and at 60 °C. Global fitting with a minimal three-step model provided the individual rate constants for substrate binding, chemical transformation, and product release. The results showed that in both cases, namely, the application of activating mutations and temperature increase, the net increase in the catalytic turnover number is afforded by acceleration of the product release rate relative to the chemical transformation steps. Measurements of the solvent viscosity effect at 25 °C versus 60 °C confirmed this change in the rate-determining step with temperature, which is in accordance with a kink in the Arrhenius diagram of ssIGPS at ∼40 °C. When rotational diffusion rates of electron paramagnetic spin-labels attached to active site loop β1α1 are plotted in the form of an Arrhenius diagram, kinks are observed at the same temperature. These findings, together with molecular dynamics simulations, demonstrate that a different degree of loop mobility correlates with different rate-limiting steps in the catalytic mechanism of ssIGPS.

Flexibility and Stability Trade-Off in Active Site of Cold-Adapted Pseudomonas mandelii Esterase EstK.

PubMed

Truongvan, Ngoc; Jang, Sei-Heon; Lee, ChangWoo

2016-06-28

Cold-adapted enzymes exhibit enhanced conformational flexibility, especially in their active sites, as compared with their warmer-temperature counterparts. However, the mechanism by which cold-adapted enzymes maintain their active site stability is largely unknown. In this study, we investigated the role of conserved D308-Y309 residues located in the same loop as the catalytic H307 residue in the cold-adapted esterase EstK from Pseudomonas mandelii. Mutation of D308 and/or Y309 to Ala or deletion resulted in increased conformational flexibility. Particularly, the D308A or Y309A mutant showed enhanced substrate affinity and catalytic rate, as compared with wild-type EstK, via enlargement of the active site. However, all mutant EstK enzymes exhibited reduced thermal stability. The effect of mutation was greater for D308 than Y309. These results indicate that D308 is not preferable for substrate selection and catalytic activity, whereas hydrogen bond formation involving D308 is critical for active site stabilization. Taken together, conformation of the EstK active site is constrained via flexibility-stability trade-off for enzyme catalysis and thermal stability. Our study provides further insights into active site stabilization of cold-adapted enzymes.

Heterodimer Autorepression Loop: A Robust and Flexible Pulse-Generating Genetic Module

NASA Astrophysics Data System (ADS)

Lannoo, B.; Carlon, E.; Lefranc, M.

2016-07-01

We investigate the dynamics of the heterodimer autorepression loop (HAL), a small genetic module in which a protein A acts as an autorepressor and binds to a second protein B to form an A B dimer. For suitable values of the rate constants, the HAL produces pulses of A alternating with pulses of B . By means of analytical and numerical calculations, we show that the duration of A pulses is extremely robust against variation of the rate constants while the duration of the B pulses can be flexibly adjusted. The HAL is thus a minimal genetic module generating robust pulses with a tunable duration, an interesting property for cellular signaling.

Automated stopped-in-dual-loop flow analysis system for catalytic determination of vanadium in drinking water.

PubMed

Teshima, Norio; Kuno, Masami; Ueda, Minoru; Ueda, Hisashi; Ohno, Shinsuke; Sakai, Tadao

2009-07-15

An automated stopped-in-dual-loop flow analysis (SIDL-FA) system is proposed for the determination of vanadium in drinking water. The chemistry is based on the vanadium-catalyzed oxidation reaction of p-anisidine by bromate in the presence of Tiron as an activator to produce a dye (lambda(max)=510 nm). A SIDL-FA system basically consists of a selection valve, three pumps (one is for delivering of standard/sample, and others are for reagents), two six-way injection valves, a spectrophotometric detector and a data acquisition device. A 100-microL coiled loop around a heated device is fitted onto each six-way injection valve. A well-mixed solution containing reagents and standard/sample is loaded into the first loop on a six-way valve, and then the same solution is loaded into the second loop on another six-way valve. The solutions are isolated by switching these two six-way valves, so that the catalytic reaction can be promoted. The net waste can be zero in this stage, because all pumps are turned off. Then each resulting solution is dispensed to the detector with suitable time lag. A touchscreen controller is developed to automatically carry out the original SIDL-FA protocol. The proposed SIDL-FA method allows vanadium to be quantified in the range of 0.1-2 microg L(-1) and is applied to the determination of vanadium in drinking water samples.

Experimental Study of Flexible Plate Vibration Control by Using Two-Loop Sliding Mode Control Strategy

NASA Astrophysics Data System (ADS)

Yang, Jingyu; Lin, Jiahui; Liu, Yuejun; Yang, Kang; Zhou, Lanwei; Chen, Guoping

2017-08-01

It is well known that intelligent control theory has been used in many research fields, novel modeling method (DROMM) is used for flexible rectangular active vibration control, and then the validity of new model is confirmed by comparing finite element model with new model. In this paper, taking advantage of the dynamics of flexible rectangular plate, a two-loop sliding mode (TSM) MIMO approach is introduced for designing multiple-input multiple-output continuous vibration control system, which can overcome uncertainties, disturbances or unstable dynamics. An illustrative example is given in order to show the feasibility of the method. Numerical simulations and experiment confirm the effectiveness of the proposed TSM MIMO controller.

Active site loop dynamics of a class IIa fructose 1,6-bisphosphate aldolase from M. tuberculosis

PubMed Central

Pegan, Scott D.; Rukseree, Kamolchanok; Capodagli, Glenn C.; Baker, Erica A; Krasnykh, Olga; Franzblau, Scott G; Mesecar, Andrew D

2014-01-01

Class II fructose 1,6-bisphosphate aldolases (FBA; E.C. 4.1.2.13) comprise one of two families of aldolases. Instead of forming a Schiff-base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs has been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies on class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria and protozoa have been reported, the structure of the active site loop responsible for catalyzing the protonation/deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI/DHAP bound form of the enzyme and determined the X-ray structure of MtFBA-PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information plus site-directed mutagenesis and kinetic studies conducted on a series of residues within the active-site loop revealed that E169 facilitates a water mediated deprotonation/protonation step of the MtFBA reaction mechanism. Also, secondary isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form. PMID:23298222

Active site loop dynamics of a class IIa fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis.

PubMed

Pegan, Scott D; Rukseree, Kamolchanok; Capodagli, Glenn C; Baker, Erica A; Krasnykh, Olga; Franzblau, Scott G; Mesecar, Andrew D

2013-02-05

Class II fructose 1,6-bisphosphate aldolases (FBAs, EC 4.1.2.13) comprise one of two families of aldolases. Instead of forming a Schiff base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate, forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs have been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies of class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria, and protozoa have been reported, the structure of the active site loop responsible for catalyzing the protonation-deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI- and DHAP-bound form of the enzyme and determined the X-ray structure of the MtFBA-PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information and site-directed mutagenesis and kinetic studies conducted on a series of residues within the active site loop revealed that E169 facilitates a water-mediated deprotonation-protonation step of the MtFBA reaction mechanism. Also, solvent isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form.

Flexibility and mutagenic resiliency of glycosyltransferases.

PubMed

Bay, Marie Lund; Cuesta-Seijo, Jose A; Weadge, Joel T; Persson, Mattias; Palcic, Monica M

2014-10-01

The human blood group A and B antigens are synthesized by two highly homologous enzymes, glycosyltransferase A (GTA) and glycosyltransferase B (GTB), respectively. These enzymes catalyze the transfer of either GalNAc or Gal from their corresponding UDP-donors to αFuc1-2βGal-R terminating acceptors. GTA and GTB differ at only four of 354 amino acids (R176G, G235S, L266M, G268A), which alter the donor specificity from UDP-GalNAc to UDP-Gal. Blood type O individuals synthesize truncated or non-functional enzymes. The cloning, crystallization and X-ray structure elucidations for GTA and GTB have revealed key residues responsible for donor discrimination and acceptor binding. Structural studies suggest that numerous conformational changes occur during the catalytic cycle. Over 300 ABO alleles are tabulated in the blood group antigen mutation database (BGMUT) that provides a framework for structure-function studies. Natural mutations are found in all regions of GTA and GTB from the active site, flexible loops, stem region and surfaces remote from the active site. Our characterizations of natural mutants near a flexible loop (V175M), on a remote surface site (P156L), in the metal binding motif (M212V) and near the acceptor binding site (L232P) demonstrate the resiliency of GTA and GTB to mutagenesis.

Efficient Computation of Closed-loop Frequency Response for Large Order Flexible Systems

NASA Technical Reports Server (NTRS)

Maghami, Peiman G.; Giesy, Daniel P.

1997-01-01

An efficient and robust computational scheme is given for the calculation of the frequency response function of a large order, flexible system implemented with a linear, time invariant control system. Advantage is taken of the highly structured sparsity of the system matrix of the plant based on a model of the structure using normal mode coordinates. The computational time per frequency point of the new computational scheme is a linear function of system size, a significant improvement over traditional, full-matrix techniques whose computational times per frequency point range from quadratic to cubic functions of system size. This permits the practical frequency domain analysis of systems of much larger order than by traditional, full-matrix techniques. Formulations are given for both open and closed loop loop systems. Numerical examples are presented showing the advantages of the present formulation over traditional approaches, both in speed and in accuracy. Using a model with 703 structural modes, a speed-up of almost two orders of magnitude was observed while accuracy improved by up to 5 decimal places.

Improving the reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase through stabilizing a long loop in domain B.

PubMed

Li, Zhu; Duan, Xuguo; Chen, Sheng; Wu, Jing

2017-01-01

The reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase were improved through site-directed mutagenesis. By using multiple sequence alignment and PoPMuSiC algorithm, Ser187 and Asn188, which located within a long loop in Domain B of Bacillus licheniformis α-amylase, were selected for mutation. In addition, Ala269, which is adjacent to Ser187 and Asn188, was also investigated. Seven mutants carrying the mutations S187D, N188T, N188S, A269K, A269K/S187D, S187D/N188T, and A269K/S187D/N188T were generated and characterized. The most thermostable mutant, A269K/S187D/N188T, exhibited a 9-fold improvement in half-life at 95°C and pH 5.5, compared with that of the wild-type enzyme. Mutant A269K/S187D/N188T also exhibited improved catalytic efficiency. The catalytic efficiency of mutant A269K/S187D/N188T reached 5.87×103±0.17 g·L-1·s-1 at pH 5.5, which is 1.84-fold larger than the corresponding value determined for the wild-type enzyme. Furthermore, the structure analysis showed that immobilization of the loop containing Ser187 and Asn188 plays a significant role in developing the properties of Bacillus licheniformis α-amylase.

Improving the reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase through stabilizing a long loop in domain B

PubMed Central

Li, Zhu; Duan, Xuguo; Chen, Sheng; Wu, Jing

2017-01-01

The reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase were improved through site-directed mutagenesis. By using multiple sequence alignment and PoPMuSiC algorithm, Ser187 and Asn188, which located within a long loop in Domain B of Bacillus licheniformis α-amylase, were selected for mutation. In addition, Ala269, which is adjacent to Ser187 and Asn188, was also investigated. Seven mutants carrying the mutations S187D, N188T, N188S, A269K, A269K/S187D, S187D/N188T, and A269K/S187D/N188T were generated and characterized. The most thermostable mutant, A269K/S187D/N188T, exhibited a 9-fold improvement in half-life at 95°C and pH 5.5, compared with that of the wild-type enzyme. Mutant A269K/S187D/N188T also exhibited improved catalytic efficiency. The catalytic efficiency of mutant A269K/S187D/N188T reached 5.87×103±0.17 g·L-1·s-1 at pH 5.5, which is 1.84-fold larger than the corresponding value determined for the wild-type enzyme. Furthermore, the structure analysis showed that immobilization of the loop containing Ser187 and Asn188 plays a significant role in developing the properties of Bacillus licheniformis α-amylase. PMID:28253342

Active Site Loop Dynamics of a Class IIa Fructose 1,6-Bisphosphate Aldolase from Mycobacterium tuberculosis

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

Pegan, Scott D.; Rukseree, Kamolchanok; Capodagli, Glenn C.

The class II fructose 1,6-bisphosphate aldolases (FBAs, EC 4.1.2.13) comprises one of two families of aldolases. Instead of forming a Schiff base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate, forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs have been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies of class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria, and protozoa have been reported,more » the structure of the active site loop responsible for catalyzing the protonation–deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI- and DHAP-bound form of the enzyme and determined the X-ray structure of the MtFBA–PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information and site-directed mutagenesis and kinetic studies conducted on a series of residues within the active site loop revealed that E169 facilitates a water-mediated deprotonation–protonation step of the MtFBA reaction mechanism. Furthermore, solvent isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form.« less

Flexibility of Catalytic Zinc Coordination in Thermolysin and HDAC8: A Born-Oppenheimer ab initio QM/MM Molecular Dynamics Study

PubMed Central

Wu, Ruibo; Hu, Po; Wang, Shenglong; Cao, Zexing; Zhang, Yingkai

2009-01-01

Abstracs The different coordination modes and fast ligand exchange of zinc coordination has been suggested to be one key catalytic feature of the zinc ion which makes it an invaluable metal in biological catalysis. However, partly due to the well known difficulties for zinc to be characterized by spectroscopy methods, evidence for dynamic nature of the catalytic zinc coordination has so far mainly been indirect. In this work, Born-Oppenheimer ab initio QM/MM molecular dynamics simulation has been employed, which allows for a first-principle description of the dynamics of the metal active site while properly including effects of the heterogeneous and fluctuating protein environment. Our simulations have provided direct evidence regarding inherent flexibility of the catalytic zinc coordination shell in Thermolysin (TLN) and Histone Deacetylase 8 (HDAC8). We have observed different coordination modes and fast ligand exchange during the picosecond's time-scale. For TLN, the coordination of the carboxylate group of Glu166 to Zinc is found to continuously change between monodentate and bidentate manner dynamically; while for HDAC8, the flexibility mainly comes from the coordination to a non-amino-acid ligand. Such distinct dynamics in the zinc coordination shell between two enzymes suggests that the catalytic role of Zinc in TLN and HDAC8 is likely to be different in spite of the fact that both catalyze the hydrolysis of amide bond. Meanwhile, considering that such Born-Oppenheimer ab initio QM/MM MD simulations are very much desired but are widely considered to be too computationally expensive to be feasible, our current study demonstrates the viability and powerfulness of this state-of-the-art approach in simulating metalloenzymes. PMID:20161624

Negative Factor from SIV Binds to the Catalytic Subunit of the V-ATPase to Internalize CD4 and to Increase Viral Infectivity

PubMed Central

Mandic, Robert; Fackler, Oliver T.; Geyer, Matthias; Linnemann, Thomas; Zheng, Yong-Hui; Peterlin, B. Matija

2001-01-01

The accessory protein negative factor (Nef) from human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) is required for optimal viral infectivity and the progression to acquired immunodeficiency syndrome (AIDS). Nef interacts with the endocytic machinery, resulting in the down-regulation of cluster of differentiation antigen 4 (CD4) and major histocompatibility complex class I (MHCI) molecules on the surface of infected cells. Mutations in the C-terminal flexible loop of Nef result in a lower rate of internalization by this viral protein. However, no loop-dependent binding of Nef to adaptor protein-2 (AP-2), which is the adaptor protein complex that is required for the internalization of proteins from the plasma membrane, could be demonstrated. In this study we investigated the relevance of different motifs in Nef from SIVmac239 for its internalization, CD4 down-regulation, binding to components of the trafficking machinery, and viral infectivity. Our data suggest that the binding of Nef to the catalytic subunit H of the vacuolar membrane ATPase (V-ATPase) facilitates its internalization. This binding depends on the integrity of the whole flexible loop. Subsequent studies on Nef mutant viruses revealed that the flexible loop is essential for optimal viral infectivity. Therefore, our data demonstrate how Nef contacts the endocytic machinery in the absence of its direct binding to AP-2 and suggest an important role for subunit H of the V-ATPase in viral infectivity. PMID:11179428

HRD Motif as the Central Hub of the Signaling Network for Activation Loop Autophosphorylation in Abl Kinase.

PubMed

La Sala, Giuseppina; Riccardi, Laura; Gaspari, Roberto; Cavalli, Andrea; Hantschel, Oliver; De Vivo, Marco

2016-11-08

A number of structural factors modulate the activity of Abelson (Abl) tyrosine kinase, whose deregulation is often related to oncogenic processes. First, only the open conformation of the Abl kinase domain's activation loop (A-loop) favors ATP binding to the catalytic cleft. In this regard, the trans-autophosphorylation of the Y412 residue, which is located along the A-loop, favors the stability of the open conformation, in turn enhancing Abl activity. Another key factor for full Abl activity is the formation of active conformations of the catalytic DFG motif in the Abl kinase domain. Furthermore, binding of the SH2 domain to the N-lobe of the Abl kinase was recently demonstrated to have a long-range allosteric effect on the stabilization of the A-loop open state. Intriguingly, these distinct structural factors imply a complex signal transmission network for controlling the A-loop's flexibility and conformational preference for optimal Abl function. However, the exact dynamical features of this signal transmission network structure remain unclear. Here, we report on microsecond-long molecular dynamics coupled with enhanced sampling simulations of multiple Abl model systems, in the presence or absence of the SH2 domain and with the DFG motif flipped in two ways (in or out conformation). Through comparative analysis, our simulations augment the interpretation of the existing Abl experimental data, revealing a dynamical network of interactions that interconnect SH2 domain binding with A-loop plasticity and Y412 autophosphorylation in Abl. This signaling network engages the DFG motif and, importantly, other conserved structural elements of the kinase domain, namely, the EPK-ELK H-bond network and the HRD motif. Our results show that the signal propagation for modulating the A-loop spatial localization is highly dependent on the HRD motif conformation, which thus acts as the central hub of this (allosteric) signaling network controlling Abl activation and function.

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

Three critical hydrogen bonds determine the catalytic activity of the Diels–Alderase ribozyme

PubMed Central

Kraut, Stefanie; Bebenroth, Dirk; Nierth, Alexander; Kobitski, Andrei Y.; Nienhaus, G. Ulrich; Jäschke, Andres

2012-01-01

Compared to protein enzymes, our knowledge about how RNA accelerates chemical reactions is rather limited. The crystal structures of a ribozyme that catalyzes Diels–Alder reactions suggest a rich tertiary architecture responsible for catalysis. In this study, we systematically probe the relevance of crystallographically observed ground-state interactions for catalytic function using atomic mutagenesis in combination with various analytical techniques. The largest energetic contribution apparently arises from the precise shape complementarity between transition state and catalytic pocket: A single point mutant that folds correctly into the tertiary structure but lacks one H-bond that normally stabilizes the pocket is completely inactive. In the rate-limiting chemical step, the dienophile is furthermore activated by two weak H-bonds that contribute ∼7–8 kJ/mol to transition state stabilization, as indicated by the 25-fold slower reaction rates of deletion mutants. These H-bonds are also responsible for the tight binding of the Diels–Alder product by the ribozyme that causes product inhibition. For high catalytic activity, the ribozyme requires a fine-tuned balance between rigidity and flexibility that is determined by the combined action of one inter-strand H-bond and one magnesium ion. A sharp 360° turn reminiscent of the T-loop motif observed in tRNA is found to be important for catalytic function. PMID:21976731

Structure-function analysis of water-soluble inhibitors of the catalytic domain of exotoxin A from Pseudomonas aeruginosa.

PubMed

Yates, Susan P; Taylor, Patricia L; Jørgensen, René; Ferraris, Dana; Zhang, Jie; Andersen, Gregers R; Merrill, A Rod

2005-02-01

The mono-ADPRT (mono-ADP-ribosyltransferase), Pseudomonas aeruginosa ETA (exotoxin A), catalyses the transfer of ADP-ribose from NAD+ to its protein substrate. A series of water-soluble compounds that structurally mimic the nicotinamide moiety of NAD+ was investigated for their inhibition of the catalytic domain of ETA. The importance of an amide locked into a hetero-ring structure and a core hetero-ring system that is planar was a trend evident by the IC50 values. Also, the weaker inhibitors have core ring structures that are less planar and thus more flexible. One of the most potent inhibitors, PJ34, was further characterized and shown to exhibit competitive inhibition with an inhibition constant K(i) of 140 nM. We also report the crystal structure of the catalytic domain of ETA in complex with PJ34, the first example of a mono-ADPRT in complex with an inhibitor. The 2.1 A (1 A=0.1 nm) resolution structure revealed that PJ34 is bound within the nicotinamide-binding pocket and forms stabilizing hydrogen bonds with the main chain of Gly-441 and to the side-chain oxygen of Gln-485, a member of a proposed catalytic loop. Structural comparison of this inhibitor complex with diphtheria toxin (a mono-ADPRT) and with PARPs [poly(ADP-ribose) polymerases] shows similarity of the catalytic residues; however, a loop similar to that found in ETA is present in diphtheria toxin but not in PARP. The present study provides insight into the important features required for inhibitors that mimic NAD+ and their binding to the mono-ADPRT family of toxins.

A competent catalytic active site is necessary for substrate induced dimer assembly in triosephosphate isomerase.

PubMed

Jimenez-Sandoval, Pedro; Vique-Sanchez, Jose Luis; Hidalgo, Marisol López; Velazquez-Juarez, Gilberto; Diaz-Quezada, Corina; Arroyo-Navarro, Luis Fernando; Moran, Gabriela Montero; Fattori, Juliana; Jessica Diaz-Salazar, A; Rudiño-Pinera, Enrique; Sotelo-Mundo, Rogerio; Figueira, Ana Carolina Migliorini; Lara-Gonzalez, Samuel; Benítez-Cardoza, Claudia G; Brieba, Luis G

2017-11-01

The protozoan parasite Trichomonas vaginalis contains two nearly identical triosephosphate isomerases (TvTIMs) that dissociate into stable monomers and dimerize upon substrate binding. Herein, we compare the role of the "ball and socket" and loop 3 interactions in substrate assisted dimer assembly in both TvTIMs. We found that point mutants at the "ball" are only 39 and 29-fold less catalytically active than their corresponding wild-type counterparts, whereas Δloop 3 deletions are 1502 and 9400-fold less active. Point and deletion mutants dissociate into stable monomers. However, point mutants assemble as catalytic competent dimers upon binding of the transition state substrate analog PGH, whereas loop 3 deletions remain monomeric. A comparison between crystal structures of point and loop 3 deletion monomeric mutants illustrates that the catalytic residues in point mutants and wild-type TvTIMs are maintained in the same orientation, whereas the catalytic residues in deletion mutants show an increase in thermal mobility and present structural disorder that may hamper their catalytic role. The high enzymatic activity present in monomeric point mutants correlates with the formation of dimeric TvTIMs upon substrate binding. In contrast, the low activity and lack of dimer assembly in deletion mutants suggests a role of loop 3 in promoting the formation of the active site as well as dimer assembly. Our results suggest that in TvTIMs the active site is assembled during dimerization and that the integrity of loop 3 and ball and socket residues is crucial to stabilize the dimer. Copyright © 2017 Elsevier B.V. All rights reserved.

Identifying Functional Requirements for Flexible Airspace Management Concept Using Human-In-The-Loop Simulations

NASA Technical Reports Server (NTRS)

Lee, Paul U.; Bender, Kim; Pagan, Danielle

2011-01-01

Flexible Airspace Management (FAM) is a mid- term Next Generation Air Transportation System (NextGen) concept that allows dynamic changes to airspace configurations to meet the changes in the traffic demand. A series of human-in-the-loop (HITL) studies have identified procedures and decision support requirements needed to implement FAM. This paper outlines a suggested FAM procedure and associated decision support functionality based on these HITL studies. A description of both the tools used to support the HITLs and the planned NextGen technologies available in the mid-term are presented and compared. The mid-term implementation of several NextGen capabilities, specifically, upgrades to the Traffic Management Unit (TMU), the initial release of an en route automation system, the deployment of a digital data communication system, a more flexible voice communications network, and the introduction of a tool envisioned to manage and coordinate networked ground systems can support the implementation of the FAM concept. Because of the variability in the overall deployment schedule of the mid-term NextGen capabilities, the dependency of the individual NextGen capabilities are examined to determine their impact on a mid-term implementation of FAM. A cursory review of the different technologies suggests that new functionality slated for the new en route automation system is a critical enabling technology for FAM, as well as the functionality to manage and coordinate networked ground systems. Upgrades to the TMU are less critical but important nonetheless for FAM to be fully realized. Flexible voice communications network and digital data communication system could allow more flexible FAM operations but they are not as essential.

Geometrical flexibility of platinum nanoclusters: impacts on catalytic decomposition of ethylene glycol.

PubMed

Mahmoodinia, Mehdi; Trinh, Thuat T; Åstrand, Per-Olof; Tran, Khanh-Quang

2017-11-01

Catalytic decomposition of ethylene glycol on the Pt 13 cluster was studied as a model system for hydrogen production from a lignocellulosic material. Ethylene glycol was chosen as a starting material because of two reasons, it is the smallest oxygenate with a 1 : 1 carbon to oxygen ratio and it contains the C-H, O-H, C-C, and C-O bonds also present in biomass. Density functional theory calculations were employed for predictions of reaction pathways for C-H, O-H, C-C and C-O cleavages, and Brønsted-Evans-Polanyi relationships were established between the final state and the transition state for all mechanisms. The results show that Pt 13 catalyzes the cleavage reactions of ethylene glycol more favourably than a Pt surface. The flexibility of Pt 13 clusters during the reactions is the key factor in reducing the activation barrier. Overall, the results demonstrate that ethylene glycol and thus biomass can be efficiently converted into hydrogen using platinum nanoclusters as catalysts.

Visualizing Active-Site Dynamics in Single Crystals of HePTP: Opening of the WPD Loop Involves Coordinated Movement of the E Loop

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

D Critton; L Tautz; R Page

2011-12-31

Phosphotyrosine hydrolysis by protein tyrosine phosphatases (PTPs) involves substrate binding by the PTP loop and closure over the active site by the WPD loop. The E loop, located immediately adjacent to the PTP and WPD loops, is conserved among human PTPs in both sequence and structure, yet the role of this loop in substrate binding and catalysis is comparatively unexplored. Hematopoietic PTP (HePTP) is a member of the kinase interaction motif (KIM) PTP family. Compared to other PTPs, KIM-PTPs have E loops that are unique in both sequence and structure. In order to understand the role of the E loopmore » in the transition between the closed state and the open state of HePTP, we identified a novel crystal form of HePTP that allowed the closed-state-to-open-state transition to be observed within a single crystal form. These structures, which include the first structure of the HePTP open state, show that the WPD loop adopts an 'atypically open' conformation and, importantly, that ligands can be exchanged at the active site, which is critical for HePTP inhibitor development. These structures also show that tetrahedral oxyanions bind at a novel secondary site and function to coordinate the PTP, WPD, and E loops. Finally, using both structural and kinetic data, we reveal a novel role for E-loop residue Lys182 in enhancing HePTP catalytic activity through its interaction with Asp236 of the WPD loop, providing the first evidence for the coordinated dynamics of the WPD and E loops in the catalytic cycle, which, as we show, is relevant to multiple PTP families.« less

The Ω-loop lid domain of phosphoenolpyruvate carboxykinase is essential for catalytic function

PubMed Central

Johnson, Troy A.; Holyoak, Todd

2012-01-01

Phosphoenolpyruvate carboxykinase (PEPCK) is an essential metabolic enzyme operating in the gluconeogenesis and glyceroneogenesis pathways. Recent studies have demonstrated that the enzyme contains a mobile active site lid domain that transitions between an open/disorded conformation to a closed/ordered conformation as the enzyme progresses through the catalytic cycle. The understanding of how this mobile domain functions in catalysis is incomplete. Previous studies show that the closure of the lid domain stabilizes the reaction intermediate and protects the reactive intermediate from spurious protonation and thus contributes to the fidelity of the enzyme. In order to more fully investigate the roles of the lid domain in PEPCK function we created three mutations that replaced the 11-residue lid domain with one, two or three glycine residues. Kinetic analysis of the mutant enzymes demonstrates that none of the enzyme constructs exhibit any measurable kinetic activity resulting in a decrease in the catalytic parameters by at least 106. Structural characterization of the mutants in complexes representing the catalytic cycle suggest that the inactivity is due to a role for the lid domain in the formation of the fully closed state of the enzyme that is required for catalytic function. In the absence of the lid domain, the enzyme is unable to achieve the fully closed state and is rendered inactive despite possessing all of the residues and substrates required for catalytic function. This work demonstrates how enzyme catalytic function can be abolished through the alteration of conformational equilibria despite all elements required for chemical conversion of substrates to products remaining intact. PMID:23127136

Substituting Tyr138 in the active site loop of human phenylalanine hydroxylase affects catalysis and substrate activation.

PubMed

Leandro, João; Stokka, Anne J; Teigen, Knut; Andersen, Ole A; Flatmark, Torgeir

2017-07-01

Mammalian phenylalanine hydroxylase (PAH) is a key enzyme in l-phenylalanine (l-Phe) metabolism and is active as a homotetramer. Biochemical and biophysical work has demonstrated that it cycles between two states with a variably low and a high activity, and that the substrate l-Phe is the key player in this transition. X-ray structures of the catalytic domain have shown mobility of a partially intrinsically disordered Tyr 138 -loop to the active site in the presence of l-Phe. The mechanism by which the loop dynamics are coupled to substrate binding at the active site in tetrameric PAH is not fully understood. We have here conducted functional studies of four Tyr 138 point mutants. A high linear correlation ( r 2 = 0.99) was observed between their effects on the catalytic efficiency of the catalytic domain dimers and the corresponding effect on the catalytic efficiency of substrate-activated full-length tetramers. In the tetramers, a correlation ( r 2 = 0.96) was also observed between the increase in catalytic efficiency (activation) and the global conformational change (surface plasmon resonance signal response) at the same l-Phe concentration. The new data support a similar functional importance of the Tyr 138 -loop in the catalytic domain and the full-length enzyme homotetramer.

Flexible stator control on the Galileo spacecraft

NASA Technical Reports Server (NTRS)

Kopf, E. H.; Brown, T. K.; Marsh, E. L.

1979-01-01

Galileo is a dual-spin spacecraft designed to deliver a probe to Jupiter and then orbit the planet. The stator, or despun section, contains four flexible modes below 10 Hz and the despun actuator is separated from the inertial sensors by this flexibility. Control loop separation by bandwidth proved unacceptable due to performance requirements. To obtain the desired performance, a control scheme was devised which consists of three parts. First, flexibility damping and control notch filtering are accomplished by phase locked loop techniques. Second, slewing maneuvers are produced by torque profiles which are nonexcitatory to the structure. Finally, a low bandwidth perturbation controller is supplied to remove spacecraft disturbances.

Stopped-in-loop flow analysis of trace vanadium in water.

PubMed

Teshima, Norio; Ohno, Shinsuke; Sakai, Tadao

2007-01-01

The new concept of stopped-in-loop flow analysis (SIL-FA) is proposed, and an SIL-FA method for the catalytic determination of vanadium is demonstrated. In an SIL format, a sample solution merges with reagent(s), and the well-mixed solution is loaded into a loop. The solution in the loop is separated by a six-way switching valve from the main stream. While the reaction proceeds in the stationary loop, the SIL-FA system does not need to establish a baseline continuously. This leads to a reduction in reagent consumption and waste generation compared with traditional flow injection analysis.

Rigidification of the autolysis loop enhances Na[superscript +] binding to thrombin

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

Pozzi, Nicola; Chen, Raymond; Chen, Zhiwei

2011-09-20

Binding of Na{sup +} to thrombin ensures high activity toward physiological substrates and optimizes the procoagulant and prothrombotic roles of the enzyme in vivo. Under physiological conditions of pH and temperature, the binding affinity of Na{sup +} is weak due to large heat capacity and enthalpy changes associated with binding, and the K{sub d} = 80 mM ensures only 64% saturation of the site at the concentration of Na{sup +} in the blood (140 mM). Residues controlling Na{sup +} binding and activation have been identified. Yet, attempts to improve the interaction of Na{sup +} with thrombin and possibly increase catalyticmore » activity under physiological conditions have so far been unsuccessful. Here we report how replacement of the flexible autolysis loop of human thrombin with the homologous rigid domain of the murine enzyme results in a drastic (up to 10-fold) increase in Na{sup +} affinity and a significant improvement in the catalytic activity of the enzyme. Rigidification of the autolysis loop abolishes the heat capacity change associated with Na{sup +} binding observed in the wild-type and also increases the stability of thrombin. These findings have general relevance to protein engineering studies of clotting proteases and trypsin-like enzymes.« less

Calmodulin fishing with a structurally disordered bait triggers CyaA catalysis

PubMed Central

O’Brien, Darragh P.; Durand, Dominique; Voegele, Alexis; Hourdel, Véronique; Davi, Marilyne; Chamot-Rooke, Julia; Vachette, Patrice; Brier, Sébastien; Ladant, Daniel

2017-01-01

Once translocated into the cytosol of target cells, the catalytic domain (AC) of the adenylate cyclase toxin (CyaA), a major virulence factor of Bordetella pertussis, is potently activated by binding calmodulin (CaM) to produce supraphysiological levels of cAMP, inducing cell death. Using a combination of small-angle X-ray scattering (SAXS), hydrogen/deuterium exchange mass spectrometry (HDX-MS), and synchrotron radiation circular dichroism (SR-CD), we show that, in the absence of CaM, AC exhibits significant structural disorder, and a 75-residue-long stretch within AC undergoes a disorder-to-order transition upon CaM binding. Beyond this local folding, CaM binding induces long-range allosteric effects that stabilize the distant catalytic site, whilst preserving catalytic loop flexibility. We propose that the high enzymatic activity of AC is due to a tight balance between the CaM-induced decrease of structural flexibility around the catalytic site and the preservation of catalytic loop flexibility, allowing for fast substrate binding and product release. The CaM-induced dampening of AC conformational disorder is likely relevant to other CaM-activated enzymes. PMID:29287065

Closing loop base pairs in RNA loop-loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations.

PubMed

Golebiowski, Jérôme; Antonczak, Serge; Fernandez-Carmona, Juan; Condom, Roger; Cabrol-Bass, Daniel

2004-12-01

Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the loop of an RNA in complementary interaction with HIV-1 TAR. The simulations reveal that the mismatch GA base, mediated by a water molecule, leads to a complex that presents the best compromise between flexibility and energetic contributions. The mismatch CU base pair, in spite of the presence of an inserted water molecule, is too short to achieve a tight interaction at the closing-loop junction and seems to force TAR to reorganize upon binding. An energetic analysis has allowed us to quantify the strength of the interactions of the closing and the loop-loop pairs throughout the simulations. Although the water-mediated GA closing base pair presents an interaction energy similar to that found on fully geometry-optimized structure, the water-mediated CU closing base pair energy interaction reaches less than half the optimal value.

On the structural context and identification of enzyme catalytic residues.

PubMed

Chien, Yu-Tung; Huang, Shao-Wei

2013-01-01

Enzymes play important roles in most of the biological processes. Although only a small fraction of residues are directly involved in catalytic reactions, these catalytic residues are the most crucial parts in enzymes. The study of the fundamental and unique features of catalytic residues benefits the understanding of enzyme functions and catalytic mechanisms. In this work, we analyze the structural context of catalytic residues based on theoretical and experimental structure flexibility. The results show that catalytic residues have distinct structural features and context. Their neighboring residues, whether sequence or structure neighbors within specific range, are usually structurally more rigid than those of noncatalytic residues. The structural context feature is combined with support vector machine to identify catalytic residues from enzyme structure. The prediction results are better or comparable to those of recent structure-based prediction methods.

Thumb-loops up for catalysis: a structure/function investigation of a functional loop movement in a GH11 xylanase

PubMed Central

Paës, Gabriel; Cortés, Juan; Siméon, Thierry; O'Donohue, Michael J.; Tran, Vinh

2012-01-01

Dynamics is a key feature of enzyme catalysis. Unfortunately, current experimental and computational techniques do not yet provide a comprehensive understanding and description of functional macromolecular motions. In this work, we have extended a novel computational technique, which combines molecular modeling methods and robotics algorithms, to investigate functional motions of protein loops. This new approach has been applied to study the functional importance of the so-called thumb-loop in the glycoside hydrolase family 11 xylanase from Thermobacillus xylanilyticus (Tx-xyl). The results obtained provide new insight into the role of the loop in the glycosylation/deglycosylation catalytic cycle, and underline the key importance of the nature of the residue located at the tip of the thumb-loop. The effect of mutations predicted in silico has been validated by in vitro site-directed mutagenesis experiments. Overall, we propose a comprehensive model of Tx-xyl catalysis in terms of substrate and product dynamics by identifying the action of the thumb-loop motion during catalysis. PMID:24688637

Catalytic Exhaust Gas Recirculation-Loop Reforming for High Efficiency in a Stoichiometric Spark-Ignited Engine through Thermochemical Recuperation and Dilution Limit Extension, Part 2: Engine Performance

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

Chang, Yan; Szybist, James P.; Pihl, Josh A.

This is the second part of a two-part investigation of on-board catalytic fuel reforming to increase the brake efficiency of a multicylinder, stoichiometric spark-ignited (SI) engine. In Part 1 of the investigation, we analytically and experimentally characterized the energetics and kinetics of a candidate reforming catalyst over a range of reforming equivalence ratios and oxygen concentration conditions to identify the best conditions for efficient reforming. In the present part of our investigation, we studied an engine strategy that combined exhaust gas recirculation (EGR)–loop reforming with dilution limit extension of the combustion. In our experiments, we found that, under an enginemore » operating condition of 2000 rpm and brake mean effective pressure (4 bar), catalytic EGR reforming made it possible to sustain stable combustion with a volumetric equivalent of 45%–55% EGR. Under this same operating condition with stoichiometric engine exhaust (and no reforming), we were only able to sustain stable combustion with EGR under 25%. In conclusion, these results indicate that multicylinder gasoline engine efficiency can be increased substantially with catalytic reforming combined with and higher EGR operation, resulting in a decrease of more than 8% in fuel consumption, compared to baseline operation.« less

Catalytic Exhaust Gas Recirculation-Loop Reforming for High Efficiency in a Stoichiometric Spark-Ignited Engine through Thermochemical Recuperation and Dilution Limit Extension, Part 2: Engine Performance

DOE PAGES

Chang, Yan; Szybist, James P.; Pihl, Josh A.; ...

2018-01-17

This is the second part of a two-part investigation of on-board catalytic fuel reforming to increase the brake efficiency of a multicylinder, stoichiometric spark-ignited (SI) engine. In Part 1 of the investigation, we analytically and experimentally characterized the energetics and kinetics of a candidate reforming catalyst over a range of reforming equivalence ratios and oxygen concentration conditions to identify the best conditions for efficient reforming. In the present part of our investigation, we studied an engine strategy that combined exhaust gas recirculation (EGR)–loop reforming with dilution limit extension of the combustion. In our experiments, we found that, under an enginemore » operating condition of 2000 rpm and brake mean effective pressure (4 bar), catalytic EGR reforming made it possible to sustain stable combustion with a volumetric equivalent of 45%–55% EGR. Under this same operating condition with stoichiometric engine exhaust (and no reforming), we were only able to sustain stable combustion with EGR under 25%. In conclusion, these results indicate that multicylinder gasoline engine efficiency can be increased substantially with catalytic reforming combined with and higher EGR operation, resulting in a decrease of more than 8% in fuel consumption, compared to baseline operation.« less

Intracellular segment between transmembrane helices S0 and S1 of BK channel α subunit contains two amphipathic helices connected by a flexible loop

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

Shi, Pan; High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui, 230031; Li, Dong

2013-08-02

Highlights: •The loop between S0 and S1 of BK channel was overexpressed and purified in DPC. •NMR studies indicated BK-IS1 contained two helices connected by a flexible loop. •Mg{sup 2+} titration of BK-IS1 indicated two possible binding sites of divalent ions. -- Abstract: The BK channel, a tetrameric potassium channel with very high conductance, has a central role in numerous physiological functions. The BK channel can be activated by intracellular Ca{sup 2+} and Mg{sup 2+}, as well as by membrane depolarization. Unlike other tetrameric potassium channels, the BK channel has seven transmembrane helices (S0–S6) including an extra helix S0. Themore » intracellular segment between S0 and S1 (BK-IS1) is essential to BK channel functions and Asp99 in BK-IS1 is reported to be responsible for Mg{sup 2+} coordination. In this study, BK-IS1 (44–113) was over-expressed using a bacterial system and purified in the presence of detergent micelles for multidimensional heteronuclear nuclear magnetic resonance (NMR) structural studies. Backbone resonance assignment and secondary structure analysis showed that BK-IS1 contains two amphipathic helices connected by a 36-residue loop. Amide {sup 1}H–{sup 15}N heteronuclear NOE analysis indicated that the loop is very flexible, while the two amphipathic helices are possibly stabilized through interaction with the membrane. A solution NMR-based titration assay of BK-IS1 was performed with various concentrations of Mg{sup 2+}. Two residues (Thr45 and Leu46) with chemical shift changes were observed but no, or very minor, chemical shift difference was observed for Asp99, indicating a possible site for binding divalent ions or other modulation partners.« less

Investigation of Inner Loop Flight Control Strategies for High-Speed Research

NASA Technical Reports Server (NTRS)

Newman, Brett; Kassem, Ayman

1999-01-01

This report describes the activities and findings conducted under contract NAS1-19858 with NASA Langley Research Center. Subject matter is the investigation of suitable flight control design methodologies and solutions for large, flexible high-speed vehicles. Specifically, methodologies are to address the inner control loops used for stabilization and augmentation of a highly coupled airframe system possibly involving rigid-body motion, structural vibrations, unsteady aerodynamics, and actuator dynamics. Techniques considered in this body of work are primarily conventional-based, and the vehicle of interest is the High-Speed Civil Transport (HSCT). Major findings include 1) current aeroelastic vehicle modeling procedures require further emphasis and refinement, 2) traditional and nontraditional inner loop flight control strategies employing a single feedback loop do not appear sufficient for highly flexible HSCT class vehicles, 3) inner loop flight control systems will, in all likelihood, require multiple interacting feedback loops, and 4) Ref. H HSCT configuration presents major challenges to designing acceptable closed-loop flight dynamics.

Role of the DELSEED Loop in Torque Transmission of F1-ATPase

PubMed Central

Tanigawara, Mizue; Tabata, Kazuhito V.; Ito, Yuko; Ito, Jotaro; Watanabe, Rikiya; Ueno, Hiroshi; Ikeguchi, Mitsunori; Noji, Hiroyuki

2012-01-01

F1-ATPase is an ATP-driven rotary motor that generates torque at the interface between the catalytic β-subunits and the rotor γ-subunit. The β-subunit inwardly rotates the C-terminal domain upon nucleotide binding/dissociation; hence, the region of the C-terminal domain that is in direct contact with γ—termed the DELSEED loop—is thought to play a critical role in torque transmission. We substituted all the DELSEED loop residues with alanine to diminish specific DELSEED loop-γ interactions and with glycine to disrupt the loop structure. All the mutants rotated unidirectionally with kinetic parameters comparable to those of the wild-type F1, suggesting that the specific interactions between DELSEED loop and γ is not involved in cooperative interplays between the catalytic β-subunits. Glycine substitution mutants generated half the torque of the wild-type F1, whereas the alanine mutant generated comparable torque. Fluctuation analyses of the glycine/alanine mutants revealed that the γ-subunit was less tightly held in the α3β3-stator ring of the glycine mutant than in the wild-type F1 and the alanine mutant. Molecular dynamics simulation showed that the DELSEED loop was disordered by the glycine substitution, whereas it formed an α-helix in the alanine mutant. Our results emphasize the importance of loop rigidity for efficient torque transmissions. PMID:23009846

Multiple substitutions lead to increased loop flexibility and expanded specificity in Acinetobacter baumannii carbapenemase OXA-239.

PubMed

Harper, Thomas M; June, Cynthia M; Taracila, Magdalena A; Bonomo, Robert A; Powers, Rachel A; Leonard, David A

2018-01-11

OXA-239 is a class D carbapenemase isolated from an Acinetobacter baumannii strain found in Mexico. This enzyme is a variant of OXA-23 with three amino acid substitutions in or near the active site. These substitutions cause OXA-239 to hydrolyze late-generation cephalosporins and the monobactam aztreonam with greater efficiency than OXA-23. OXA-239 activity against the carbapenems doripenem and imipenem is reduced ∼3-fold and 20-fold, respectively. Further analysis demonstrated that two of the substitutions (P225S and D222N) are largely responsible for the observed alteration of kinetic parameters, while the third (S109L) may serve to stabilize the protein. Structures of OXA-239 with cefotaxime, doripenem and imipenem bound as acyl-intermediates were determined. These structures reveal that OXA-239 has increased flexibility in a loop that contains P225S and D222N. When carbapenems are bound, the conformation of this loop is essentially identical with that observed previously for OXA-23, with a narrow active site that makes extensive contacts to the ligand. When cefotaxime is bound, the loop can adopt a different conformation that widens the active site to allow binding of that bulky drug. This alternate conformation is made possible by P225S and further stabilized by D222N. Taken together, these results suggest that the three substitutions were selected to expand the substrate specificity profile of OXA-23 to cephalosporins and monobactams. The loss of activity against imipenem, however, suggests that there may be limits to the plasticity of class D enzymes with regard to evolving active sites that can effectively bind multiple classes of β-lactam drugs. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Catalytic site interactions in yeast OMP synthase.

PubMed

Hansen, Michael Riis; Barr, Eric W; Jensen, Kaj Frank; Willemoës, Martin; Grubmeyer, Charles; Winther, Jakob R

2014-01-15

The enigmatic kinetics, half-of-the-sites binding, and structural asymmetry of the homodimeric microbial OMP synthases (orotate phosphoribosyltransferase, EC 2.4.2.10) have been proposed to result from an alternating site mechanism in these domain-swapped enzymes [R.W. McClard et al., Biochemistry 45 (2006) 5330-5342]. This behavior was investigated in the yeast enzyme by mutations in the conserved catalytic loop and 5-phosphoribosyl-1-diphosphate (PRPP) binding motif. Although the reaction is mechanistically sequential, the wild-type (WT) enzyme shows parallel lines in double reciprocal initial velocity plots. Replacement of Lys106, the postulated intersubunit communication device, produced intersecting lines in kinetic plots with a 2-fold reduction of kcat. Loop (R105G K109S H111G) and PRPP-binding motif (D131N D132N) mutant proteins, each without detectable enzymatic activity and ablated ability to bind PRPP, complemented to produce a heterodimer with a single fully functional active site showing intersecting initial velocity plots. Equilibrium binding of PRPP and orotidine 5'-monophosphate showed a single class of two binding sites per dimer in WT and K106S enzymes. Evidence here shows that the enzyme does not follow half-of-the-sites cooperativity; that interplay between catalytic sites is not an essential feature of the catalytic mechanism; and that parallel lines in steady-state kinetics probably arise from tight substrate binding. Copyright © 2013. Published by Elsevier Inc.

Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations

PubMed Central

McDowell, S. Elizabeth; Jun, Jesse M.; Walter, Nils G.

2010-01-01

Enzymes generally are thought to derive their functional activity from conformational motions. The limited chemical variation in RNA suggests that such structural dynamics may play a particularly important role in RNA function. Minimal hammerhead ribozymes are known to cleave efficiently only in ∼10-fold higher than physiologic concentrations of Mg2+ ions. Extended versions containing native loop–loop interactions, however, show greatly enhanced catalytic activity at physiologically relevant Mg2+ concentrations, for reasons that are still ill-understood. Here, we use Mg2+ titrations, activity assays, ensemble, and single molecule fluorescence resonance energy transfer (FRET) approaches, combined with molecular dynamics (MD) simulations, to ask what influence the spatially distant tertiary loop–loop interactions of an extended hammerhead ribozyme have on its structural dynamics. By comparing hammerhead variants with wild-type, partially disrupted, and fully disrupted loop–loop interaction sequences we find that the tertiary interactions lead to a dynamic motional sampling that increasingly populates catalytically active conformations. At the global level the wild-type tertiary interactions lead to more frequent, if transient, encounters of the loop-carrying stems, whereas at the local level they lead to an enrichment in favorable in-line attack angles at the cleavage site. These results invoke a linkage between RNA structural dynamics and function and suggest that loop–loop interactions in extended hammerhead ribozymes—and Mg2+ ions that bind to minimal ribozymes—may generally allow more frequent access to a catalytically relevant conformation(s), rather than simply locking the ribozyme into a single active state. PMID:20921269

Creating stable stem regions for loop elongation in Fcabs - insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations.

PubMed

Hasenhindl, Christoph; Lai, Balder; Delgado, Javier; Traxlmayr, Michael W; Stadlmayr, Gerhard; Rüker, Florian; Serrano, Luis; Oostenbrink, Chris; Obinger, Christian

2014-09-01

Fcabs (Fc antigen binding) are crystallizable fragments of IgG where the C-terminal structural loops of the CH3 domain are engineered for antigen binding. For the design of libraries it is beneficial to know positions that will permit loop elongation to increase the potential interaction surface with antigen. However, the insertion of additional loop residues might impair the immunoglobulin fold. In the present work we have probed whether stabilizing mutations flanking the randomized and elongated loop region improve the quality of Fcab libraries. In detail, 13 libraries were constructed having the C-terminal part of the EF loop randomized and carrying additional residues (1, 2, 3, 5 or 10, respectively) in the absence and presence of two flanking mutations. The latter have been demonstrated to increase the thermal stability of the CH3 domain of the respective solubly expressed proteins. Assessment of the stability of the libraries expressed on the surface of yeast cells by flow cytometry demonstrated that loop elongation was considerably better tolerated in the stabilized libraries. By using in silico loop reconstruction and mimicking randomization together with MD simulations the underlying molecular dynamics were investigated. In the presence of stabilizing stem residues the backbone flexibility of the engineered EF loop as well as the fluctuation between its accessible conformations were decreased. In addition the CD loop (but not the AB loop) and most of the framework regions were rigidified. The obtained data are discussed with respect to the design of Fcabs and available data on the relation between flexibility and affinity of CDR loops in Ig-like molecules. Copyright © 2014. Published by Elsevier B.V.

Loop-loop interactions govern multiple steps in indole-3-glycerol phosphate synthase catalysis

PubMed Central

Zaccardi, Margot J; O'Rourke, Kathleen F; Yezdimer, Eric M; Loggia, Laura J; Woldt, Svenja; Boehr, David D

2014-01-01

Substrate binding, product release, and likely chemical catalysis in the tryptophan biosynthetic enzyme indole-3-glycerol phosphate synthase (IGPS) are dependent on the structural dynamics of the β1α1 active-site loop. Statistical coupling analysis and molecular dynamic simulations had previously indicated that covarying residues in the β1α1 and β2α2 loops, corresponding to Arg54 and Asn90, respectively, in the Sulfolobus sulfataricus enzyme (ssIGPS), are likely important for coordinating functional motions of these loops. To test this hypothesis, we characterized site mutants at these positions for changes in catalytic function, protein stability and structural dynamics for the thermophilic ssIGPS enzyme. Although there were only modest changes in the overall steady-state kinetic parameters, solvent viscosity and solvent deuterium kinetic isotope effects indicated that these amino acid substitutions change the identity of the rate-determining step across multiple temperatures. Surprisingly, the N90A substitution had a dramatic effect on the general acid/base catalysis of the dehydration step, as indicated by the loss of the descending limb in the pH rate profile, which we had previously assigned to Lys53 on the β1α1 loop. These changes in enzyme function are accompanied with a quenching of ps-ns and µs-ms timescale motions in the β1α1 loop as measured by nuclear magnetic resonance studies. Altogether, our studies provide structural, dynamic and functional rationales for the coevolution of residues on the β1α1 and β2α2 loops, and highlight the multiple roles that the β1α1 loop plays in IGPS catalysis. Thus, substitution of covarying residues in the active-site β1α1 and β2α2 loops of indole-3-glycerol phosphate synthase results in functional, structural, and dynamic changes, highlighting the multiple roles that the β1α1 loop plays in enzyme catalysis and the importance of regulating the structural dynamics of this loop through noncovalent

Refined molecular hinge between allosteric and catalytic domain determines allosteric regulation and stability of fungal chorismate mutase

PubMed Central

Helmstaedt, Kerstin; Heinrich, Gabriele; Lipscomb, William N.; Braus, Gerhard H.

2002-01-01

The yeast chorismate mutase is regulated by tyrosine as feedback inhibitor and tryptophan as crosspathway activator. The monomer consists of a catalytic and a regulatory domain covalently linked by the loop L220s (212–226), which functions as a molecular hinge. Two monomers form the active dimeric enzyme stabilized by hydrophobic interactions in the vicinity of loop L220s. The role of loop L220s and its environment for enzyme regulation, dimerization, and stability was analyzed. Substitution of yeast loop L220s in place of the homologous loop from the corresponding and similarly regulated Aspergillus enzyme (and the reverse substitution) changed tyrosine inhibition to activation. Yeast loop L220s substituted into the Aspergillus enzyme resulted in a tryptophan-inhibitable enzyme. Monomeric yeast chorismate mutases could be generated by substituting two hydrophobic residues in and near the hinge region. The resulting Thr-212→Asp–Phe-28→Asp enzyme was as stable as wild type, but lost allosteric regulation and showed reduced catalytic activity. These results underline the crucial role of this molecular hinge for inhibition, activation, quaternary structure, and stability of yeast chorismate mutase. PMID:11997452

Low and medium heating value coal gas catalytic combustor characterization

NASA Technical Reports Server (NTRS)

Schwab, J. A.

1982-01-01

Catalytic combustion with both low and medium heating value coal gases obtained from an operating gasifier was demonstrated. A practical operating range for efficient operation was determined, and also to identify potential problem areas were identified for consideration during stationary gas turbine engine design. The test rig consists of fuel injectors, a fuel-air premixing section, a catalytic reactor with thermocouple instrumentation and a single point, water cooled sample probe. The test rig included inlet and outlet transition pieces and was designed for installation into an existing test loop.

Controlled-Root Approach To Digital Phase-Locked Loops

NASA Technical Reports Server (NTRS)

Stephens, Scott A.; Thomas, J. Brooks

1995-01-01

Performance tailored more flexibly and directly to satisfy design requirements. Controlled-root approach improved method for analysis and design of digital phase-locked loops (DPLLs). Developed rigorously from first principles for fully digital loops, making DPLL theory and design simpler and more straightforward (particularly for third- or fourth-order DPLL) and controlling performance more accurately in case of high gain.

Crystal structure of a polyhistidine-tagged recombinant catalytic subunit of cAMP-dependent protein kinase complexed with the peptide inhibitor PKI(5-24) and adenosine.

PubMed

Narayana, N; Cox, S; Shaltiel, S; Taylor, S S; Xuong, N

1997-04-15

The crystal structure of the hexahistidine-tagged mouse recombinant catalytic subunit (H6-rC) of cAMP-dependent protein kinase (cAPK), complexed with a 20-residue peptide inhibitor from the heat-stable protein kinase inhibitor PKI(5-24) and adenosine, was determined at 2.2 A resolution. Novel crystallization conditions were required to grow the ternary complex crystals. The structure was refined to a final crystallographic R-factor of 18.2% with good stereochemical parameters. The "active" enzyme adopts a "closed" conformation as found in rC:PKI(5-24) [Knighton et al. (1991a,b) Science 253, 407-414, 414-420] and packs in a similar manner with the peptide providing a major contact surface. This structure clearly defines the subsites of the unique nucleotide binding site found in the protein kinase family. The adenosine occupies a mostly hydrophobic pocket at the base of the cleft between the two lobes and is completely buried. The missing triphosphate moiety of ATP is filled with a water molecule (Wtr 415) which replaces the gamma-phosphate of ATP. The glycine-rich loop between beta1 and beta2 helps to anchor the phosphates while the ribose ring is buried beneath beta-strand 2. Another ordered water molecule (Wtr 375) is pentacoordinated with polar atoms from adenosine, Leu 49 in beta-strand 1, Glu 127 in the linker strand between the two lobes, Tyr 330, and a third water molecule, Wtr 359. The conserved nucleotide fold can be defined as a lid comprised of beta-strand 1, the glycine-rich loop, and beta-strand 2. The adenine ring is buried beneath beta-strand 1 and the linker strand (120-127) that joins the small and large lobes. The C-terminal tail containing Tyr 330, a segment that lies outside the conserved core, covers this fold and anchors it in a closed conformation. The main-chain atoms of the flexible glycine-rich loop (residues 50-55) in the ATP binding domain have a mean B-factor of 41.4 A2. This loop is quite mobile, in striking contrast to the other

Creating stable stem regions for loop elongation in Fcabs — Insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations

PubMed Central

Hasenhindl, Christoph; Lai, Balder; Delgado, Javier; Traxlmayr, Michael W.; Stadlmayr, Gerhard; Rüker, Florian; Serrano, Luis; Oostenbrink, Chris; Obinger, Christian

2014-01-01

Fcabs (Fc antigen binding) are crystallizable fragments of IgG where the C-terminal structural loops of the CH3 domain are engineered for antigen binding. For the design of libraries it is beneficial to know positions that will permit loop elongation to increase the potential interaction surface with antigen. However, the insertion of additional loop residues might impair the immunoglobulin fold. In the present work we have probed whether stabilizing mutations flanking the randomized and elongated loop region improve the quality of Fcab libraries. In detail, 13 libraries were constructed having the C-terminal part of the EF loop randomized and carrying additional residues (1, 2, 3, 5 or 10, respectively) in the absence and presence of two flanking mutations. The latter have been demonstrated to increase the thermal stability of the CH3 domain of the respective solubly expressed proteins. Assessment of the stability of the libraries expressed on the surface of yeast cells by flow cytometry demonstrated that loop elongation was considerably better tolerated in the stabilized libraries. By using in silico loop reconstruction and mimicking randomization together with MD simulations the underlying molecular dynamics were investigated. In the presence of stabilizing stem residues the backbone flexibility of the engineered EF loop as well as the fluctuation between its accessible conformations were decreased. In addition the CD loop (but not the AB loop) and most of the framework regions were rigidified. The obtained data are discussed with respect to the design of Fcabs and available data on the relation between flexibility and affinity of CDR loops in Ig-like molecules. PMID:24792385

A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation.

PubMed

Ruff, Emily F; Muretta, Joseph M; Thompson, Andrew R; Lake, Eric W; Cyphers, Soreen; Albanese, Steven K; Hanson, Sonya M; Behr, Julie M; Thomas, David D; Chodera, John D; Levinson, Nicholas M

2018-02-21

Many eukaryotic protein kinases are activated by phosphorylation on a specific conserved residue in the regulatory activation loop, a post-translational modification thought to stabilize the active DFG-In state of the catalytic domain. Here we use a battery of spectroscopic methods that track different catalytic elements of the kinase domain to show that the ~100 fold activation of the mitotic kinase Aurora A (AurA) by phosphorylation occurs without a population shift from the DFG-Out to the DFG-In state, and that the activation loop of the activated kinase remains highly dynamic. Instead, molecular dynamics simulations and electron paramagnetic resonance experiments show that phosphorylation triggers a switch within the DFG-In subpopulation from an autoinhibited DFG-In substate to an active DFG-In substate, leading to catalytic activation. This mechanism raises new questions about the functional role of the DFG-Out state in protein kinases. © 2018, Ruff et al.

Flexibility Correlation between Active Site Regions Is Conserved across Four AmpC β-Lactamase Enzymes.

PubMed

Brown, Jenna R; Livesay, Dennis R

2015-01-01

β-lactamases are bacterial enzymes that confer resistance to β-lactam antibiotics, such as penicillins and cephalosporins. There are four classes of β-lactamase enzymes, each with characteristic sequence and structure properties. Enzymes from class A are the most common and have been well characterized across the family; however, less is known about how physicochemical properties vary across the C and D families. In this report, we compare the dynamical properties of four AmpC (class C) β-lactamases using our distance constraint model (DCM). The DCM reliably predicts thermodynamic and mechanical properties in an integrated way. As a consequence, quantitative stability/flexibility relationships (QSFR) can be determined and compared across the whole family. The DCM calculates a large number of QSFR metrics. Perhaps the most useful is the flexibility index (FI), which quantifies flexibility along the enzyme backbone. As typically observed in other systems, FI is well conserved across the four AmpC enzymes. Cooperativity correlation (CC), which quantifies intramolecular couplings within structure, is rarely conserved across protein families; however, it is in AmpC. In particular, the bulk of each structure is composed of a large rigid cluster, punctuated by three flexibly correlated regions located at the active site. These regions include several catalytic residues and the Ω-loop. This evolutionary conservation combined with active their site location strongly suggests that these coupled dynamical modes are important for proper functioning of the enzyme.

Flexibility Correlation between Active Site Regions Is Conserved across Four AmpC β-Lactamase Enzymes

PubMed Central

Brown, Jenna R.; Livesay, Dennis R.

2015-01-01

β-lactamases are bacterial enzymes that confer resistance to β-lactam antibiotics, such as penicillins and cephalosporins. There are four classes of β-lactamase enzymes, each with characteristic sequence and structure properties. Enzymes from class A are the most common and have been well characterized across the family; however, less is known about how physicochemical properties vary across the C and D families. In this report, we compare the dynamical properties of four AmpC (class C) β-lactamases using our distance constraint model (DCM). The DCM reliably predicts thermodynamic and mechanical properties in an integrated way. As a consequence, quantitative stability/flexibility relationships (QSFR) can be determined and compared across the whole family. The DCM calculates a large number of QSFR metrics. Perhaps the most useful is the flexibility index (FI), which quantifies flexibility along the enzyme backbone. As typically observed in other systems, FI is well conserved across the four AmpC enzymes. Cooperativity correlation (CC), which quantifies intramolecular couplings within structure, is rarely conserved across protein families; however, it is in AmpC. In particular, the bulk of each structure is composed of a large rigid cluster, punctuated by three flexibly correlated regions located at the active site. These regions include several catalytic residues and the Ω-loop. This evolutionary conservation combined with active their site location strongly suggests that these coupled dynamical modes are important for proper functioning of the enzyme. PMID:26018804

Falcon: a highly flexible open-source software for closed-loop neuroscience.

PubMed

Ciliberti, Davide; Kloosterman, Fabian

2017-08-01

Closed-loop experiments provide unique insights into brain dynamics and function. To facilitate a wide range of closed-loop experiments, we created an open-source software platform that enables high-performance real-time processing of streaming experimental data. We wrote Falcon, a C++ multi-threaded software in which the user can load and execute an arbitrary processing graph. Each node of a Falcon graph is mapped to a single thread and nodes communicate with each other through thread-safe buffers. The framework allows for easy implementation of new processing nodes and data types. Falcon was tested both on a 32-core and a 4-core workstation. Streaming data was read from either a commercial acquisition system (Neuralynx) or the open-source Open Ephys hardware, while closed-loop TTL pulses were generated with a USB module for digital output. We characterized the round-trip latency of our Falcon-based closed-loop system, as well as the specific latency contribution of the software architecture, by testing processing graphs with up to 32 parallel pipelines and eight serial stages. We finally deployed Falcon in a task of real-time detection of population bursts recorded live from the hippocampus of a freely moving rat. On Neuralynx hardware, round-trip latency was well below 1 ms and stable for at least 1 h, while on Open Ephys hardware latencies were below 15 ms. The latency contribution of the software was below 0.5 ms. Round-trip and software latencies were similar on both 32- and 4-core workstations. Falcon was used successfully to detect population bursts online with ~40 ms average latency. Falcon is a novel open-source software for closed-loop neuroscience. It has sub-millisecond intrinsic latency and gives the experimenter direct control of CPU resources. We envisage Falcon to be a useful tool to the neuroscientific community for implementing a wide variety of closed-loop experiments, including those requiring use of complex data structures and real

Falcon: a highly flexible open-source software for closed-loop neuroscience

NASA Astrophysics Data System (ADS)

Ciliberti, Davide; Kloosterman, Fabian

2017-08-01

Objective. Closed-loop experiments provide unique insights into brain dynamics and function. To facilitate a wide range of closed-loop experiments, we created an open-source software platform that enables high-performance real-time processing of streaming experimental data. Approach. We wrote Falcon, a C++ multi-threaded software in which the user can load and execute an arbitrary processing graph. Each node of a Falcon graph is mapped to a single thread and nodes communicate with each other through thread-safe buffers. The framework allows for easy implementation of new processing nodes and data types. Falcon was tested both on a 32-core and a 4-core workstation. Streaming data was read from either a commercial acquisition system (Neuralynx) or the open-source Open Ephys hardware, while closed-loop TTL pulses were generated with a USB module for digital output. We characterized the round-trip latency of our Falcon-based closed-loop system, as well as the specific latency contribution of the software architecture, by testing processing graphs with up to 32 parallel pipelines and eight serial stages. We finally deployed Falcon in a task of real-time detection of population bursts recorded live from the hippocampus of a freely moving rat. Main results. On Neuralynx hardware, round-trip latency was well below 1 ms and stable for at least 1 h, while on Open Ephys hardware latencies were below 15 ms. The latency contribution of the software was below 0.5 ms. Round-trip and software latencies were similar on both 32- and 4-core workstations. Falcon was used successfully to detect population bursts online with ~40 ms average latency. Significance. Falcon is a novel open-source software for closed-loop neuroscience. It has sub-millisecond intrinsic latency and gives the experimenter direct control of CPU resources. We envisage Falcon to be a useful tool to the neuroscientific community for implementing a wide variety of closed-loop experiments, including those

Single link flexible beam testbed project. Thesis

NASA Technical Reports Server (NTRS)

Hughes, Declan

1992-01-01

This thesis describes the single link flexible beam testbed at the CLaMS laboratory in terms of its hardware, software, and linear model, and presents two controllers, each including a hub angle proportional-derivative (PD) feedback compensator and one augmented by a second static gain full state feedback loop, based upon a synthesized strictly positive real (SPR) output, that increases specific flexible mode pole damping ratios w.r.t the PD only case and hence reduces unwanted residual oscillation effects. Restricting full state feedback gains so as to produce a SPR open loop transfer function ensures that the associated compensator has an infinite gain margin and a phase margin of at least (-90, 90) degrees. Both experimental and simulation data are evaluated in order to compare some different observer performance when applied to the real testbed and to the linear model when uncompensated flexible modes are included.

Analysis of flexible aircraft longitudinal dynamics and handling qualities. Volume 1: Analysis methods

NASA Technical Reports Server (NTRS)

Waszak, M. R.; Schmidt, D. S.

1985-01-01

As aircraft become larger and lighter due to design requirements for increased payload and improved fuel efficiency, they will also become more flexible. For highly flexible vehicles, the handling qualities may not be accurately predicted by conventional methods. This study applies two analysis methods to a family of flexible aircraft in order to investigate how and when structural (especially dynamic aeroelastic) effects affect the dynamic characteristics of aircraft. The first type of analysis is an open loop model analysis technique. This method considers the effects of modal residue magnitudes on determining vehicle handling qualities. The second method is a pilot in the loop analysis procedure that considers several closed loop system characteristics. Volume 1 consists of the development and application of the two analysis methods described above.

Plastic flexible films waste management - A state of art review.

PubMed

Horodytska, O; Valdés, F J; Fullana, A

2018-04-21

Plastic flexible films are increasingly used in many applications due to their lightness and versatility. In 2014, the amount of plastic films represented 34% of total plastic packaging produced in UK. The flexible film waste generation rises according to the increase in number of applications. Currently, in developed countries, about 50% of plastics in domestic waste are films. Moreover, about 615,000 tonnes of agricultural flexible waste are generated in the EU every year. A review of plastic films recycling has been conducted in order to detect the shortcomings and establish guidelines for future research. This paper reviews plastic films waste management technologies from two different sources: post-industrial and post-consumer. Clean and homogeneous post-industrial waste is recycled through closed-loop or open-loop mechanical processes. The main differences between these methods are the quality and the application of the recycled materials. Further research should be focused on closing the loops to obtain the highest environmental benefits of recycling. This could be accomplished through minimizing the material degradation during mechanical processes. Regarding post-consumer waste, flexible films from agricultural and packaging sectors have been assessed. The agricultural films and commercial and industrial flexible packaging are recycled through open-loop mechanical recycling due to existing selective waste collection routes. Nevertheless, the contamination from the use phase adversely affects the quality of recycled plastics. Therefore, upgrading of current washing lines is required. On the other hand, household flexible packaging shows the lowest recycling rates mainly because of inefficient sorting technologies. Delamination and compatibilization methods should be further developed to ensure the recycling of multilayer films. Finally, Life Cycle Assessment (LCA) studies on waste management have been reviewed. A lack of thorough LCA on plastic films waste

A Redox 2-Cys Mechanism Regulates the Catalytic Activity of Divergent Cyclophilins1[W

PubMed Central

Campos, Bruna Medéia; Sforça, Mauricio Luis; Ambrosio, Andre Luis Berteli; Domingues, Mariane Noronha; Brasil de Souza, Tatiana de Arruda Campos; Barbosa, João Alexandre Ribeiro Gonçalvez; Leme, Adriana Franco Paes; Perez, Carlos Alberto; Whittaker, Sara Britt-Marie; Murakami, Mario Tyago; Zeri, Ana Carolina de Matos; Benedetti, Celso Eduardo

2013-01-01

The citrus (Citrus sinensis) cyclophilin CsCyp is a target of the Xanthomonas citri transcription activator-like effector PthA, required to elicit cankers on citrus. CsCyp binds the citrus thioredoxin CsTdx and the carboxyl-terminal domain of RNA polymerase II and is a divergent cyclophilin that carries the additional loop KSGKPLH, invariable cysteine (Cys) residues Cys-40 and Cys-168, and the conserved glutamate (Glu) Glu-83. Despite the suggested roles in ATP and metal binding, the functions of these unique structural elements remain unknown. Here, we show that the conserved Cys residues form a disulfide bond that inactivates the enzyme, whereas Glu-83, which belongs to the catalytic loop and is also critical for enzyme activity, is anchored to the divergent loop to maintain the active site open. In addition, we demonstrate that Cys-40 and Cys-168 are required for the interaction with CsTdx and that CsCyp binds the citrus carboxyl-terminal domain of RNA polymerase II YSPSAP repeat. Our data support a model where formation of the Cys-40-Cys-168 disulfide bond induces a conformational change that disrupts the interaction of the divergent and catalytic loops, via Glu-83, causing the active site to close. This suggests a new type of allosteric regulation in divergent cyclophilins, involving disulfide bond formation and a loop-displacement mechanism. PMID:23709667

RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

PubMed Central

Huang, Po-Ssu; Ban, Yih-En Andrew; Richter, Florian; Andre, Ingemar; Vernon, Robert; Schief, William R.; Baker, David

2011-01-01

We describe RosettaRemodel, a generalized framework for flexible protein design that provides a versatile and convenient interface to the Rosetta modeling suite. RosettaRemodel employs a unified interface, called a blueprint, which allows detailed control over many aspects of flexible backbone protein design calculations. RosettaRemodel allows the construction and elaboration of customized protocols for a wide range of design problems ranging from loop insertion and deletion, disulfide engineering, domain assembly, loop remodeling, motif grafting, symmetrical units, to de novo structure modeling. PMID:21909381

Numerical Analysis of a Flexible Dual Loop Coil and its Experimental Validation for pre-Clinical Magnetic Resonance Imaging of Rodents at 7 T

NASA Astrophysics Data System (ADS)

Solis-Najera, S.; Vazquez, F.; Hernandez, R.; Marrufo, O.; Rodriguez, A. O.

2016-12-01

A surface radio frequency coil was developed for small animal image acquisition in a pre-clinical magnetic resonance imaging system at 7 T. A flexible coil composed of two circular loops was developed to closely cover the object to be imaged. Electromagnetic numerical simulations were performed to evaluate its performance before the coil construction. An analytical expression of the mutual inductance for the two circular loops as a function of the separation between them was derived and used to validate the simulations. The RF coil is composed of two circular loops with a 5 cm external diameter and was tuned to 300 MHz and 50 Ohms matched. The angle between the loops was varied and the Q factor was obtained from the S11 simulations for each angle. B1 homogeneity was also evaluated using the electromagnetic simulations. The coil prototype was designed and built considering the numerical simulation results. To show the feasibility of the coil and its performance, saline-solution phantom images were acquired. A correlation of the simulations and imaging experimental results was conducted showing a concordance of 0.88 for the B1 field. The best coil performance was obtained at the 90° aperture angle. A more realistic phantom was also built using a formaldehyde-fixed rat phantom for ex vivo imaging experiments. All images showed a good image quality revealing clearly defined anatomical details of an ex vivo rat.

Structural consequences of cutting a binding loop: two circularly permuted variants of streptavidin

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

Le Trong, Isolde; University of Washington, Box 357742, Seattle, WA 98195-7742; Chu, Vano

2013-06-01

The crystal structures of two circularly permuted streptavidins probe the role of a flexible loop in the tight binding of biotin. Molecular-dynamics calculations for one of the mutants suggests that increased fluctuations in a hydrogen bond between the protein and biotin are associated with cleavage of the binding loop. Circular permutation of streptavidin was carried out in order to investigate the role of a main-chain amide in stabilizing the high-affinity complex of the protein and biotin. Mutant proteins CP49/48 and CP50/49 were constructed to place new N-termini at residues 49 and 50 in a flexible loop involved in stabilizing themore » biotin complex. Crystal structures of the two mutants show that half of each loop closes over the binding site, as observed in wild-type streptavidin, while the other half adopts the open conformation found in the unliganded state. The structures are consistent with kinetic and thermodynamic data and indicate that the loop plays a role in enthalpic stabilization of the bound state via the Asn49 amide–biotin hydrogen bond. In wild-type streptavidin, the entropic penalties of immobilizing a flexible portion of the protein to enhance binding are kept to a manageable level by using a contiguous loop of medium length (six residues) which is already constrained by its anchorage to strands of the β-barrel protein. A molecular-dynamics simulation for CP50/49 shows that cleavage of the binding loop results in increased structural fluctuations for Ser45 and that these fluctuations destabilize the streptavidin–biotin complex.« less

Control-structure interaction in precision pointing servo loops

NASA Technical Reports Server (NTRS)

Spanos, John T.

1989-01-01

The control-structure interaction problem is addressed via stability analysis of a generic linear servo loop model. With the plant described by the rigid body mode and a single elastic mode, structural flexibility is categorized into one of three types: (1) appendage, (2) in-the-loop minimum phase, and (3) in-the-loop nonminimum phase. Closing the loop with proportional-derivative (PD) control action and introducing sensor roll-off dynamics in the feedback path, stability conditions are obtained. Trade studies are conducted with modal frequency, modal participation, modal damping, loop bandwidth, and sensor bandwidth treated as free parameters. Results indicate that appendage modes are most likely to produce instability if they are near the sensor rolloff, whereas in-the-loop modes are most dangerous near the loop bandwidth. The main goal of this paper is to provide a fundamental understanding of the control-structure interaction problem so that it may benefit the design of complex spacecraft and pointing system servo loops. In this framework, the JPL Pathfinder gimbal pointer is considered as an example.

A Distal Disulfide Bridge in OXA-1 β-Lactamase Stabilizes the Catalytic Center and Alters the Dynamics of the Specificity Determining Ω Loop

DOE PAGES

Simakov, Nikolay; Leonard, David A.; Smith, Jeremy C.; ...

2016-09-26

Widespread antibiotic resistance, particularly when mediated by broad-spectrum β-lactamases, has major implications for public health. Substitutions in the active site often allow broad-spectrum enzymes to accommodate diverse types of β-lactams. Substitutions observed outside the active site are thought to compensate for the loss of thermal stability. The OXA-1 clade of class D β-lactamases contains a pair of conserved cysteines located outside the active site that forms a disulfide bond in the periplasm. In this paper, the effect of the distal disulfide bond on the structure and dynamics of OXA-1 was investigated via 4 μs molecular dynamics simulations. The results revealmore » that the disulfide promotes the preorganized orientation of the catalytic residues and affects the conformation of the functionally important Ω loop. Furthermore, principal component analysis reveals differences in the global dynamics between the oxidized and reduced forms, especially in the motions involving the Ω loop. A dynamical network analysis indicates that, in the oxidized form, in addition to its role in ligand binding, the KTG family motif is a central hub of the global dynamics. Finally, as activity of OXA-1 has been measured only in the reduced form, we suggest that accurate assessment of its functional profile would require oxidative conditions mimicking periplasm.« less

MD simulation of the Tat/Cyclin T1/CDK9 complex revealing the hidden catalytic cavity within the CDK9 molecule upon Tat binding.

PubMed

Asamitsu, Kaori; Hirokawa, Takatsugu; Okamoto, Takashi

2017-01-01

In this study, we applied molecular dynamics (MD) simulation to analyze the dynamic behavior of the Tat/CycT1/CDK9 tri-molecular complex and revealed the structural changes of P-TEFb upon Tat binding. We found that Tat could deliberately change the local flexibility of CycT1. Although the structural coordinates of the H1 and H2 helices did not substantially change, H1', H2', and H3' exhibited significant changes en masse. Consequently, the CycT1 residues involved in Tat binding, namely Tat-recognition residues (TRRs), lost their flexibility with the addition of Tat to P-TEFb. In addition, we clarified the structural variation of CDK9 in complex with CycT1 in the presence or absence of Tat. Interestingly, Tat addition significantly reduced the structural variability of the T-loop, thus consolidating the structural integrity of P-TEFb. Finally, we deciphered the formation of the hidden catalytic cavity of CDK9 upon Tat binding. MD simulation revealed that the PITALRE signature sequence of CDK9 flips the inactive kinase cavity of CDK9 into the active form by connecting with Thr186, which is crucial for its activity, thus presumably recruiting the substrate peptide such as the C-terminal domain of RNA pol II. These findings provide vital information for the development of effective novel anti-HIV drugs with CDK9 catalytic activity as the target.

Multiple loop conformations of peptides predicted by molecular dynamics simulations are compatible with nuclear magnetic resonance.

PubMed

Carstens, Heiko; Renner, Christian; Milbradt, Alexander G; Moroder, Luis; Tavan, Paul

2005-03-29

The affinity and selectivity of protein-protein interactions can be fine-tuned by varying the size, flexibility, and amino acid composition of involved surface loops. As a model for such surface loops, we study the conformational landscape of an octapeptide, whose flexibility is chemically steered by a covalent ring closure integrating an azobenzene dye into and by a disulfide bridge additionally constraining the peptide backbone. Because the covalently integrated azobenzene dyes can be switched by light between a bent cis state and an elongated trans state, six cyclic peptide models of strongly different flexibilities are obtained. The conformational states of these peptide models are sampled by NMR and by unconstrained molecular dynamics (MD) simulations. Prototypical conformations and the free-energy landscapes in the high-dimensional space spanned by the phi/psi angles at the peptide backbone are obtained by clustering techniques from the MD trajectories. Multiple open-loop conformations are shown to be predicted by MD particularly in the very flexible cases and are shown to comply with the NMR data despite the fact that such open-loop conformations are missing in the refined NMR structures.

CD and NMR conformational studies of a peptide encompassing the Mid Loop interface of Ship2-Sam.

PubMed

Mercurio, Flavia A; Scognamiglio, Pasqualina L; Di Natale, Concetta; Marasco, Daniela; Pellecchia, Maurizio; Leone, Marilisa

2014-11-01

The lipid phosphatase Ship2 is a protein that intervenes in several diseases such as diabetes, cancer, neurodegeneration, and atherosclerosis. It is made up of a catalytic domain and several protein docking modules such as a C-terminal Sam (Sterile alpha motif) domain. The Sam domain of Ship2 (Ship2-Sam) binds to the Sam domains of the EphA2 receptor (EphA2-Sam) and the PI3K effector protein Arap3 (Arap3-Sam). These heterotypic Sam-Sam interactions occur through formation of dimers presenting the canonical "Mid Loop/End Helix" binding mode. The central region of Ship2-Sam, spanning the C-terminal end of α2, the α3 and α4 helices together with the α2α3 and α3α4 interhelical loops, forms the Mid Loop surface that is needed to bind partners Sam domains. A peptide encompassing most of the Ship2-Sam Mid Loop interface (Shiptide) capable of binding to both EphA2-Sam and Arap3-Sam, was previously identified. Here we investigated the conformational features of this peptide, through solution CD and NMR studies in different conditions. These studies reveal that the peptide is highly flexible in aqueous buffer, while it adopts a helical conformation in presence of 2,2,2-trifluoroethanol. The discovered structural insights and in particular the identification of a helical motif, may lead to the design of more constrained and possibly cell permeable Shiptide analogs that could work as efficient antagonists of Ship2-Sam heterotypic interactions and embrace therapeutic applications. © 2014 Wiley Periodicals, Inc.

Deletion of loop fragment adjacent to active site diminishes the stability and activity of exo-inulinase.

PubMed

Arjomand, Maryam Rezaei; Habibi-Rezaei, Mehran; Ahmadian, Gholamreza; Hassanzadeh, Malihe; Karkhane, Ali Asghar; Asadifar, Mandana; Amanlou, Massoud

2016-11-01

Inulinases are classified as hydrolases and widely used in the food and medical industries. Here, we report the deletion of a six-membered adjacent active site loop fragment ( 74 YGSDVT 79 sequence) from third Ω-loop of the exo-inulinase containing aspartate residue from Aspergillus niger to study its structural and functional importance. Site-directed mutagenesis was used to create the mutant of the exo-inulinase (Δ6SL). To investigate the stability of the region spanning this loop, MD simulations were performed 80ns for 20-85 residues. Molecular docking was performed to compare the interactions in the active sites of enzymes with fructose as a ligand. Accordingly, the functional thermostability of the exo-inulinase was significantly decreased upon loop fragment deletion. Evaluation of the kinetics parameters (V max , K m , k cat and, k cat /K m ) and activation energy (E a ) of the catalysis of enzymes indicated the importance of the deleted sequence on the catalytic performance of the enzyme. In conclusion, six-membered adjacent active site loop fragment not only plays a crucial role in the stability of the enzyme, but also it involves in the enzyme catalysis through lowering the activation energy of the catalysis and effective improving the catalytic performance. Copyright © 2016. Published by Elsevier B.V.

The Catalytic and Non-catalytic Functions of the Brahma Chromatin-Remodeling Protein Collaborate to Fine-Tune Circadian Transcription in Drosophila

PubMed Central

Kwok, Rosanna S.; Li, Ying H.; Lei, Anna J.; Edery, Isaac; Chiu, Joanna C.

2015-01-01

Daily rhythms in gene expression play a critical role in the progression of circadian clocks, and are under regulation by transcription factor binding, histone modifications, RNA polymerase II (RNAPII) recruitment and elongation, and post-transcriptional mechanisms. Although previous studies have shown that clock-controlled genes exhibit rhythmic chromatin modifications, less is known about the functions performed by chromatin remodelers in animal clockwork. Here we have identified the Brahma (Brm) complex as a regulator of the Drosophila clock. In Drosophila, CLOCK (CLK) is the master transcriptional activator driving cyclical gene expression by participating in an auto-inhibitory feedback loop that involves stimulating the expression of the main negative regulators, period (per) and timeless (tim). BRM functions catalytically to increase nucleosome density at the promoters of per and tim, creating an overall restrictive chromatin landscape to limit transcriptional output during the active phase of cycling gene expression. In addition, the non-catalytic function of BRM regulates the level and binding of CLK to target promoters and maintains transient RNAPII stalling at the per promoter, likely by recruiting repressive and pausing factors. By disentangling its catalytic versus non-catalytic functions at the promoters of CLK target genes, we uncovered a multi-leveled mechanism in which BRM fine-tunes circadian transcription. PMID:26132408

Chimeric Proton-Pumping Rhodopsins Containing the Cytoplasmic Loop of Bovine Rhodopsin

PubMed Central

Sasaki, Kengo; Yamashita, Takahiro; Yoshida, Kazuho; Inoue, Keiichi; Shichida, Yoshinori; Kandori, Hideki

2014-01-01

G-protein-coupled receptors (GPCRs) transmit stimuli to intracellular signaling systems. Rhodopsin (Rh), which is a prototypical GPCR, possesses an 11-cis retinal. Photoisomerization of 11-cis to all-trans leads to structural changes in the protein of cytoplasmic loops, activating G-protein. Microbial rhodopsins are similar heptahelical membrane proteins that function as bacterial sensors, light-driven ion-pumps, or light-gated channels. They possess an all-trans retinal, and photoisomerization to 13-cis triggers structural changes in protein. Despite these similarities, there is no sequence homology between visual and microbial rhodopsins, and microbial rhodopsins do not activate G-proteins. In this study, new chimeric proton-pumping rhodopsins, proteorhodopsin (PR) and Gloeobacter rhodopsin (GR) were designed by replacing cytoplasmic loops with bovine Rh loops. Although G-protein was not activated by the PR chimeras, all 12 GR chimeras activated G-protein. The GR chimera containing the second cytoplasmic loop of bovine Rh did not activate G-protein. However, the chimera with a second and third double-loop further enhanced G-protein activation. Introduction of an E132Q mutation slowed the photocycle 30-fold and enhanced activation. The highest catalytic activity of the GR chimera was still 3,200 times lower than bovine Rh but only 64 times lower than amphioxus Go-rhodopsin. This GR chimera showed a strong absorption change of the amide-I band on a light-minus-dark difference FTIR spectrum which could represent a larger helical opening, important for G-protein activation. The light-dependent catalytic activity of this GR chimera makes it a potential optogenetic tool for enzymatic activation by light. PMID:24621599

Adsorption of finite semiflexible polymers and their loop and tail distributions

NASA Astrophysics Data System (ADS)

Kampmann, Tobias A.; Kierfeld, Jan

2017-07-01

We discuss the adsorption of semiflexible polymers to a planar attractive wall and focus on the questions of the adsorption threshold for polymers of finite length and their loop and tail distributions using both Monte Carlo simulations and analytical arguments. For the adsorption threshold, we find three regimes: (i) a flexible or Gaussian regime if the persistence length is smaller than the adsorption potential range, (ii) a semiflexible regime if the persistence length is larger than the potential range, and (iii) for finite polymers, a novel crossover to a rigid rod regime if the deflection length exceeds the contour length. In the flexible and semiflexible regimes, finite size corrections arise because the correlation length exceeds the contour length. In the rigid rod regime, however, it is essential how the global orientational or translational degrees of freedom are restricted by grafting or confinement. We discuss finite size corrections for polymers grafted to the adsorbing surface and for polymers confined by a second (parallel) hard wall. Based on these results, we obtain a method to analyze adsorption data for finite semiflexible polymers such as filamentous actin. For the loop and tail distributions, we find power laws with an exponential decay on length scales exceeding the correlation length. We derive and confirm the loop and tail power law exponents for flexible and semiflexible polymers. This allows us to explain that, close to the transition, semiflexible polymers have significantly smaller loops and both flexible and semiflexible polymers desorb by expanding their tail length. The tail distribution allows us to extract the free energy per length of adsorption for actin filaments from experimental data [D. Welch et al., Soft Matter 11, 7507 (2015)].

Isolated and coupled superquadric loop antennas for mobile communications applications

NASA Technical Reports Server (NTRS)

Jensen, Michael A.; Rahmat-Samii, Yahya

1993-01-01

This work provides an investigation of the performance of loop antennas for use in mobile communications applications. The analysis tools developed allow for high flexibility by representing the loop antenna as a superquadric curve, which includes the case of circular, elliptical, and rectangular loops. The antenna may be in an isolated environment, located above an infinite ground plane, or placed near a finite conducting plate or box. In cases where coupled loops are used, the two loops may have arbitrary relative positions and orientations. Several design examples are included to illustrate the versatility of the analysis capabilities. The performance of coupled loops arranged in a diversity scheme is also evaluated, and it is found that high diversity gain can be achieved even when the antennas are closely spaced.

Fault Accommodation in Control of Flexible Systems

NASA Technical Reports Server (NTRS)

Maghami, Peiman G.; Sparks, Dean W., Jr.; Lim, Kyong B.

1998-01-01

New synthesis techniques for the design of fault accommodating controllers for flexible systems are developed. Three robust control design strategies, static dissipative, dynamic dissipative and mu-synthesis, are used in the approach. The approach provides techniques for designing controllers that maximize, in some sense, the tolerance of the closed-loop system against faults in actuators and sensors, while guaranteeing performance robustness at a specified performance level, measured in terms of the proximity of the closed-loop poles to the imaginary axis (the degree of stability). For dissipative control designs, nonlinear programming is employed to synthesize the controllers, whereas in mu-synthesis, the traditional D-K iteration is used. To demonstrate the feasibility of the proposed techniques, they are applied to the control design of a structural model of a flexible laboratory test structure.

Closed-Loop Neuromorphic Benchmarks

PubMed Central

Stewart, Terrence C.; DeWolf, Travis; Kleinhans, Ashley; Eliasmith, Chris

2015-01-01

Evaluating the effectiveness and performance of neuromorphic hardware is difficult. It is even more difficult when the task of interest is a closed-loop task; that is, a task where the output from the neuromorphic hardware affects some environment, which then in turn affects the hardware's future input. However, closed-loop situations are one of the primary potential uses of neuromorphic hardware. To address this, we present a methodology for generating closed-loop benchmarks that makes use of a hybrid of real physical embodiment and a type of “minimal” simulation. Minimal simulation has been shown to lead to robust real-world performance, while still maintaining the practical advantages of simulation, such as making it easy for the same benchmark to be used by many researchers. This method is flexible enough to allow researchers to explicitly modify the benchmarks to identify specific task domains where particular hardware excels. To demonstrate the method, we present a set of novel benchmarks that focus on motor control for an arbitrary system with unknown external forces. Using these benchmarks, we show that an error-driven learning rule can consistently improve motor control performance across a randomly generated family of closed-loop simulations, even when there are up to 15 interacting joints to be controlled. PMID:26696820

Top3-Rmi1 dissolve Rad51-mediated D loops by a topoisomerase-based mechanism.

PubMed

Fasching, Clare L; Cejka, Petr; Kowalczykowski, Stephen C; Heyer, Wolf-Dietrich

2015-02-19

The displacement loop (D loop) is a DNA strand invasion product formed during homologous recombination. Disruption of nascent D loops prevents recombination, and during synthesis-dependent strand annealing (SDSA), disruption of D loops extended by DNA polymerase ensures a non-crossover outcome. The proteins implicated in D loop disruption are DNA motor proteins/helicases that act by moving DNA junctions. Here we report that D loops can also be disrupted by DNA topoisomerase 3 (Top3), and this disruption depends on Top3's catalytic activity. Yeast Top3 specifically disrupts D loops mediated by yeast Rad51/Rad54; protein-free D loops or D loop mediated by bacterial RecA protein or human RAD51/RAD54 resist dissolution. Also, the human Topoisomerase IIIa-RMI1-RMI2 complex is capable of dissolving D loops. Consistent with genetic data, we suggest that the extreme growth defect and hyper-recombination phenotype of Top3-deficient yeast cells is partially a result of unprocessed D loops. Copyright © 2015 Elsevier Inc. All rights reserved.

Analysis of flexible aircraft longitudinal dynamics and handling qualities. Volume 2: Data

NASA Technical Reports Server (NTRS)

Waszak, M. R.; Schmidt, D. K.

1985-01-01

Two analysis methods are applied to a family of flexible aircraft in order to investigate how and when structural (especially dynamic aeroelastic) effects affect the dynamic characteristics of aircraft. The first type of analysis is an open loop modal analysis technique. This method considers the effect of modal residue magnitudes on determining vehicle handling qualities. The second method is a pilot in the loop analysis procedure that considers several closed loop system characteristics. Both analyses indicated that dynamic aeroelastic effects caused a degradation in vehicle tracking performance, based on the evaluation of some simulation results. Volume 2 consists of the presentation of the state variable models of the flexible aircraft configurations used in the analysis applications mode shape plots for the structural modes, numerical results from the modal analysis frequency response plots from the pilot in the loop analysis and a listing of the modal analysis computer program.

Connecting Active-Site Loop Conformations and Catalysis in Triosephosphate Isomerase: Insights from a Rare Variation at Residue 96 in the Plasmodial Enzyme.

PubMed

Pareek, Vidhi; Samanta, Moumita; Joshi, Niranjan V; Balaram, Hemalatha; Murthy, Mathur R N; Balaram, Padmanabhan

2016-04-01

Despite extensive research into triosephosphate isomerases (TIMs), there exists a gap in understanding of the remarkable conjunction between catalytic loop-6 (residues 166-176) movement and the conformational flip of Glu165 (catalytic base) upon substrate binding that primes the active site for efficient catalysis. The overwhelming occurrence of serine at position 96 (98% of the 6277 unique TIM sequences), spatially proximal to E165 and the loop-6 residues, raises questions about its role in catalysis. Notably, Plasmodium falciparum TIM has an extremely rare residue--phenylalanine--at this position whereas, curiously, the mutant F96S was catalytically defective. We have obtained insights into the influence of residue 96 on the loop-6 conformational flip and E165 positioning by combining kinetic and structural studies on the PfTIM F96 mutants F96Y, F96A, F96S/S73A, and F96S/L167V with sequence conservation analysis and comparative analysis of the available apo and holo structures of the enzyme from diverse organisms. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Conformational Sampling in Template-Free Protein Loop Structure Modeling: An Overview

PubMed Central

Li, Yaohang

2013-01-01

Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a “mini protein folding problem” under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the approaches of sampling loop conformation space, which is a critical step to obtain high resolution models in template-free methods. We review the potential energy functions for loop modeling, loop buildup mechanisms to satisfy geometric constraints, and loop conformation sampling algorithms. The recent loop modeling results are also summarized. PMID:24688696

Conformational sampling in template-free protein loop structure modeling: an overview.

PubMed

Li, Yaohang

2013-01-01

Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a "mini protein folding problem" under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the approaches of sampling loop conformation space, which is a critical step to obtain high resolution models in template-free methods. We review the potential energy functions for loop modeling, loop buildup mechanisms to satisfy geometric constraints, and loop conformation sampling algorithms. The recent loop modeling results are also summarized.

The Role of the β5-α11 Loop in the Active-Site Dynamics of Acylated Penicillin-Binding Protein A from Mycobacterium tuberculosis

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

Fedarovich, Alena; Nicholas, Robert A.; Davies, Christopher

Penicillin-binding protein A (PBPA) is a class B penicillin-binding protein that is important for cell division in Mycobacterium tuberculosis. We have determined a second crystal structure of PBPA in apo form and compared it with an earlier structure of apoenzyme. Significant structural differences in the active site region are apparent, including increased ordering of a β-hairpin loop and a shift of the SxN active site motif such that it now occupies a position that appears catalytically competent. Using two assays, including one that uses the intrinsic fluorescence of a tryptophan residue, we have also measured the second-order acylation rate constantsmore » for the antibiotics imipenem, penicillin G, and ceftriaxone. Of these, imipenem, which has demonstrable anti-tubercular activity, shows the highest acylation efficiency. Crystal structures of PBPA in complex with the same antibiotics were also determined, and all show conformational differences in the β5–α11 loop near the active site, but these differ for each β-lactam and also for each of the two molecules in the crystallographic asymmetric unit. Overall, these data reveal the β5–α11 loop of PBPA as a flexible region that appears important for acylation and provide further evidence that penicillin-binding proteins in apo form can occupy different conformational states.« less

Closed Loop System Identification with Genetic Algorithms

NASA Technical Reports Server (NTRS)

Whorton, Mark S.

2004-01-01

High performance control design for a flexible space structure is challenging since high fidelity plant models are di.cult to obtain a priori. Uncertainty in the control design models typically require a very robust, low performance control design which must be tuned on-orbit to achieve the required performance. Closed loop system identi.cation is often required to obtain a multivariable open loop plant model based on closed-loop response data. In order to provide an accurate initial plant model to guarantee convergence for standard local optimization methods, this paper presents a global parameter optimization method using genetic algorithms. A minimal representation of the state space dynamics is employed to mitigate the non-uniqueness and over-parameterization of general state space realizations. This control-relevant system identi.cation procedure stresses the joint nature of the system identi.cation and control design problem by seeking to obtain a model that minimizes the di.erence between the predicted and actual closed-loop performance.

Geometrical criteria for characterizing open and closed states of WPD-loop in PTP1B

NASA Astrophysics Data System (ADS)

Shinde, Ranajit Nivrutti; Elizabeth Sobhia, M.

2012-06-01

Distinctive movement of WPD-loop occurs during the catalysis of phosphotyrosine by protein tyrosine phosphatase 1B (PTP1B). This loop is in the "open" state in apo-form whereas it is catalytically competent in the "closed" state. During the closure of this loop, unique hydrogen bond interactions are formed between different residues of the PTP1B. Present study examines such interactions from the available 118 crystal structures of PTP1B. It gives insights into the five novel hydrogen bonds essentially formed in the "closed" loop structures. Additionally, the study provides distance ranges between the atoms involved in the hydrogen bonds. This information can be used as a geometrical criterion in the characterization of conformational state of the WPD-loop especially in the molecular dynamics simulations.

Higgs mass prediction in the MSSM at three-loop level in a pure \\overline{{ {DR}}} context

NASA Astrophysics Data System (ADS)

Harlander, Robert V.; Klappert, Jonas; Voigt, Alexander

2017-12-01

The impact of the three-loop effects of order α _tα _s^2 on the mass of the light CP-even Higgs boson in the { {MSSM}} is studied in a pure \\overline{{ {DR}}} context. For this purpose, we implement the results of Kant et al. (JHEP 08:104, 2010) into the C++ module Himalaya and link it to FlexibleSUSY, a Mathematica and C++ package to create spectrum generators for BSM models. The three-loop result is compared to the fixed-order two-loop calculations of the original FlexibleSUSY and of FeynHiggs, as well as to the result based on an EFT approach. Aside from the expected reduction of the renormalization scale dependence with respect to the lower-order results, we find that the three-loop contributions significantly reduce the difference from the EFT prediction in the TeV-region of the { {SUSY}} scale {M_S}. Himalaya can be linked also to other two-loop \\overline{{ {DR}}} codes, thus allowing for the elevation of these codes to the three-loop level.

Stopped-in-loop flow analysis system for successive determination of trace vanadium and iron in drinking water using their catalytic reactions.

PubMed

Ayala Quezada, Alejandro; Ohara, Keisuke; Ratanawimarnwong, Nuanlaor; Nacapricha, Duangjai; Murakami, Hiroya; Teshima, Norio; Sakai, Tadao

2015-11-01

An automated stopped-in-loop flow analysis (SILFA) system is proposed for the successive catalytic determination of vanadium and iron. The determination of vanadium was based on the p-anisidine oxidation by potassium bromate in the presence of Tiron as an activator to form a reddish dye, which has an absorption maximum at 510 nm. The selectivity of the vanadium determination was greatly improved by adding diphosphate as a masking agent of iron. For the iron determination, an iron-catalyzed oxidative reaction of p-anisidine by hydrogen peroxide with 1,10-phenanthroline as an activator to produce a reddish dye (510 nm) was employed. The SILFA system consisted of two peristaltic pumps, two six-port injection valves, a four-port selection valve, a heater device, a spectrophotometric detector and a data acquisition device. One six-port injection valve was used for the isolation of a mixed solution of standard/sample and reagent to promote each catalytic reaction, and another six-port injection valve was used for switching the reagent for vanadium or iron to achieve selective determination of each analyte. The above mentioned four-port selection valve was used to select standard solutions or sample. These three valves and the two peristaltic pumps were controlled by a built-in programmable logic controller in a touchscreen controller. The obtained results showed that the proposed SILFA monitoring system constituted an effective approach for the selective determination of vanadium and iron. The limits of detection, 0.052 and 0.55 µg L(-1), were obtained for vanadium and iron, respectively. The proposed system was successfully applied to drinking water samples without any preconcentration procedures. Copyright © 2015 Elsevier B.V. All rights reserved.

Top3-Rmi1 dissolve Rad51-mediated D-loops by a topoisomerase-based mechanism

PubMed Central

Fasching, Clare L.; Cejka, Petr; Kowalczykowski, Stephen C.; Heyer, Wolf-Dietrich

2015-01-01

Summary The displacement loop (D-loop) is the DNA strand invasion product formed during homologous recombination. Disruption of nascent D-loops represents a mechanism of anti-recombination. During Synthesis-Dependent Strand Annealing D-loop disruption after extension of the invading strand is an integral step of the pathway and ensures a non-crossover outcome. The proteins implicated in D-loop disruption are DNA motor proteins/helicases acting by migrating DNA junctions. Here we report an unanticipated mechanism of D-loop dissolution mediated by DNA topoisomerase 3 (Top3) and dependent on its catalytic activity. D-loop dissolution catalyzed by yeast Top3 is highly specific for yeast Rad51/Rad54-mediated D-loops, whereas protein-free D-loops or D-loop mediated by bacterial RecA protein or human RAD51/RAD54 resist dissolution. Also the human Topoisomerase IIIα-RMI1–RMI2 complex is capable of dissolving D-loops. Consistent with genetic data, we suggest that the extreme growth defect and hyper-recombination phenotype of Top3-deficient yeast cells is in part a result of unprocessed D-loops. PMID:25699708

Highly flexible, transparent and conducting CuS-nanosheet networks for flexible quantum-dot solar cells.

PubMed

Xu, Zijie; Li, Teng; Zhang, Fayin; Hong, Xiaodan; Xie, Shuyao; Ye, Meidan; Guo, Wenxi; Liu, Xiangyang

2017-03-17

The rapid development of modern electronics has given rise to a higher demand for flexible and wearable energy sources. Flexible transparent conducting electrodes (TCEs) are one of the essential components of flexible/wearable thin-film solar cells (SCs). In this regard, we present highly transparent and conducting CuS-nanosheet (NS) networks with an optimized sheet resistance (R s ) as low as 50 Ω sq -1 at 85% transmittance as a counter electrode (CE) for flexible quantum-dot solar cells (QDSCs). The CuS NS network electrode exhibits remarkable mechanical flexibility under bending tests compared to traditional ITO/plastic substrates and sputtered CuS films. Herein, CuS NS networks not only served as conducting films for collecting electrons from the external circuit, but also served as superior catalysts for reducing polysulfide (S 2- /S x 2- ) electrolytes. A power conversion efficiency (PCE) up to 3.25% was achieved for the QDSCs employing CuS NS networks as CEs, which was much higher than those of the devices based on Pt networks and sputtered CuS films. We believe that such CuS network TCEs with high flexibility, transparency, conductivity and catalytic activity could be widely used in making wearable electronic products.

Rice Cellulose SynthaseA8 Plant-Conserved Region Is a Coiled-Coil at the Catalytic Core Entrance1[OPEN

PubMed Central

Rushton, Phillip S.; Olek, Anna T.; Makowski, Lee; Badger, John

2017-01-01

The crystallographic structure of a rice (Oryza sativa) cellulose synthase, OsCesA8, plant-conserved region (P-CR), one of two unique domains in the catalytic domain of plant CesAs, was solved to 2.4 Å resolution. Two antiparallel α-helices form a coiled-coil domain linked by a large extended connector loop containing a conserved trio of aromatic residues. The P-CR structure was fit into a molecular envelope for the P-CR domain derived from small-angle X-ray scattering data. The P-CR structure and molecular envelope, combined with a homology-based chain trace of the CesA8 catalytic core, were modeled into a previously determined CesA8 small-angle X-ray scattering molecular envelope to produce a detailed topological model of the CesA8 catalytic domain. The predicted position for the P-CR domain from the molecular docking models places the P-CR connector loop into a hydrophobic pocket of the catalytic core, with the coiled-coil aligned near the entrance of the substrate UDP-glucose into the active site. In this configuration, the P-CR coiled-coil alone is unlikely to regulate substrate access to the active site, but it could interact with other domains of CesA, accessory proteins, or other CesA catalytic domains to control substrate delivery. PMID:27879387

SpalLoop

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

Sabau, Adrian; Wright, Ian

Boiler tubes in steam power plants experience tube blockages due to exfoliation of oxide grown on the inner side of the tubes. In extreme cases, significant tube blockages can lead to forced power plant outages. It is thus desired to predict through modeling the amount of tube blockage in order to inform power plant operators of possible forced outages. SpalLoop solves for the stress-strain equations in an axisymmetric geometry, tracking the stress/strain evolution during boiler operation including outages for the entire boiler tube length. At each operational outage, i.e., temperature excursions down to room temperature, the amount of exfoliated areamore » for the entire tube loop is estimated the amount of tube blockage is predicted based assumed blockage geometry and site. The SpaLLoop code contains modules developed for oxide growth, stress analysis, tube loop geometry, blockage area by taking into account the following phenomena and features, (a) Plant operation schedule with periodic alternate full-load and partial-load regimes and shut-downs, i.e., temperature excursions from high-load to room temperature, (b) axisymmetric formulation for cylindrical tubes, (c) oxide growth in a temperature gradient with multiple oxide layers, (d) geometry of a boiler tube with a single tube loop or two tube loops, (e) temperature variation along the tube length based on hot gas temperature distribution outside the tube and inlet steam temperature, (f) non-uniform oxide growth along the tube length according to the local steam tube temperature, (g) exfoliated area module: at each operational outage considered, the amount of exfoliated area and exfoliated volume along the tube is estimated, (h) blockage module: at each operational outage considered, the exfoliated volume/mass for each tube loop is estimated from which the amount of tube blockage is predicted based on given blockage geometry (length, location, and geometry). The computer program is written in FORTRAN90. Its

Voltage-dependent motion of the catalytic region of voltage-sensing phosphatase monitored by a fluorescent amino acid

PubMed Central

Sakata, Souhei; Jinno, Yuka; Kawanabe, Akira; Okamura, Yasushi

2016-01-01

The cytoplasmic region of voltage-sensing phosphatase (VSP) derives the voltage dependence of its catalytic activity from coupling to a voltage sensor homologous to that of voltage-gated ion channels. To assess the conformational changes in the cytoplasmic region upon activation of the voltage sensor, we genetically incorporated a fluorescent unnatural amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap), into the catalytic region of Ciona intestinalis VSP (Ci-VSP). Measurements of Anap fluorescence under voltage clamp in Xenopus oocytes revealed that the catalytic region assumes distinct conformations dependent on the degree of voltage-sensor activation. FRET analysis showed that the catalytic region remains situated beneath the plasma membrane, irrespective of the voltage level. Moreover, Anap fluorescence from a membrane-facing loop in the C2 domain showed a pattern reflecting substrate turnover. These results indicate that the voltage sensor regulates Ci-VSP catalytic activity by causing conformational changes in the entire catalytic region, without changing their distance from the plasma membrane. PMID:27330112

Voltage-dependent motion of the catalytic region of voltage-sensing phosphatase monitored by a fluorescent amino acid.

PubMed

Sakata, Souhei; Jinno, Yuka; Kawanabe, Akira; Okamura, Yasushi

2016-07-05

The cytoplasmic region of voltage-sensing phosphatase (VSP) derives the voltage dependence of its catalytic activity from coupling to a voltage sensor homologous to that of voltage-gated ion channels. To assess the conformational changes in the cytoplasmic region upon activation of the voltage sensor, we genetically incorporated a fluorescent unnatural amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap), into the catalytic region of Ciona intestinalis VSP (Ci-VSP). Measurements of Anap fluorescence under voltage clamp in Xenopus oocytes revealed that the catalytic region assumes distinct conformations dependent on the degree of voltage-sensor activation. FRET analysis showed that the catalytic region remains situated beneath the plasma membrane, irrespective of the voltage level. Moreover, Anap fluorescence from a membrane-facing loop in the C2 domain showed a pattern reflecting substrate turnover. These results indicate that the voltage sensor regulates Ci-VSP catalytic activity by causing conformational changes in the entire catalytic region, without changing their distance from the plasma membrane.

Maneuvering and control of flexible space robots

NASA Technical Reports Server (NTRS)

Meirovitch, Leonard; Lim, Seungchul

1994-01-01

This paper is concerned with a flexible space robot capable of maneuvering payloads. The robot is assumed to consist of two hinge-connected flexible arms and a rigid end-effector holding a payload; the robot is mounted on a rigid platform floating in space. The equations of motion are nonlinear and of high order. Based on the assumption that the maneuvering motions are one order of magnitude larger than the elastic vibrations, a perturbation approach permits design of controls for the two types of motion separately. The rigid-body maneuvering is carried out open loop, but the elastic motions are controlled closed loop, by means of discrete-time linear quadratic regulator theory with prescribed degree of stability. A numerical example demonstrates the approach. In the example, the controls derived by the perturbation approach are applied to the original nonlinear system and errors are found to be relatively small.

Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification

PubMed Central

Jeliazkov, Jeliazko R.; Sljoka, Adnan; Kuroda, Daisuke; Tsuchimura, Nobuyuki; Katoh, Naoki; Tsumoto, Kouhei; Gray, Jeffrey J.

2018-01-01

Antibodies can rapidly evolve in specific response to antigens. Affinity maturation drives this evolution through cycles of mutation and selection leading to enhanced antibody specificity and affinity. Elucidating the biophysical mechanisms that underlie affinity maturation is fundamental to understanding B-cell immunity. An emergent hypothesis is that affinity maturation reduces the conformational flexibility of the antibody’s antigen-binding paratope to minimize entropic losses incurred upon binding. In recent years, computational and experimental approaches have tested this hypothesis on a small number of antibodies, often observing a decrease in the flexibility of the complementarity determining region (CDR) loops that typically comprise the paratope and in particular the CDR-H3 loop, which contributes a plurality of antigen contacts. However, there were a few exceptions and previous studies were limited to a small handful of cases. Here, we determined the structural flexibility of the CDR-H3 loop for thousands of recent homology models of the human peripheral blood cell antibody repertoire using rigidity theory. We found no clear delineation in the flexibility of naïve and antigen-experienced antibodies. To account for possible sources of error, we additionally analyzed hundreds of human and mouse antibodies in the Protein Data Bank through both rigidity theory and B-factor analysis. By both metrics, we observed only a slight decrease in the CDR-H3 loop flexibility when comparing affinity matured antibodies to naïve antibodies, and the decrease was not as drastic as previously reported. Further analysis, incorporating molecular dynamics simulations, revealed a spectrum of changes in flexibility. Our results suggest that rigidification may be just one of many biophysical mechanisms for increasing affinity. PMID:29545810

Large planar maneuvers for articulated flexible manipulators

NASA Technical Reports Server (NTRS)

Huang, Jen-Kuang; Yang, Li-Farn

1988-01-01

An articulated flexible manipulator carried on a translational cart is maneuvered by an active controller to perform certain position control tasks. The nonlinear dynamics of the articulated flexible manipulator are derived and a transformation matrix is formulated to localize the nonlinearities within the inertia matrix. Then a feedback linearization scheme is introduced to linearize the dynamic equations for controller design. Through a pole placement technique, a robust controller design is obtained by properly assigning a set of closed-loop desired eigenvalues to meet performance requirements. Numerical simulations for the articulated flexible manipulators are given to demonstrate the feasibility and effectiveness of the proposed position control algorithms.

Stepwise Loop Insertion Strategy for Active Site Remodeling to Generate Novel Enzyme Functions.

PubMed

Hoque, Md Anarul; Zhang, Yong; Chen, Liuqing; Yang, Guangyu; Khatun, Mst Afroza; Chen, Haifeng; Hao, Liu; Feng, Yan

2017-05-19

The remodeling of active sites to generate novel biocatalysts is an attractive and challenging task. We developed a stepwise loop insertion strategy (StLois), in which randomized residue pairs are inserted into active site loops. The phosphotriesterase-like lactonase from Geobacillus kaustophilus (GkaP-PLL) was used to investigate StLois's potential for changing enzyme function. By inserting six residues into active site loop 7, the best variant ML7-B6 demonstrated a 16-fold further increase in catalytic efficiency toward ethyl-paraoxon compared with its initial template, that is a 609-fold higher, >10 7 fold substrate specificity shift relative to that of wild-type lactonase. The remodeled variants displayed 760-fold greater organophosphate hydrolysis activity toward the organophosphates parathion, diazinon, and chlorpyrifos. Structure and docking computations support the source of notably inverted enzyme specificity. Considering the fundamental importance of active site loops, the strategy has potential for the rapid generation of novel enzyme functions by loop remodeling.

Flexibility Matters: Cooperative Active Sites in Covalent Organic Framework and Threaded Ionic Polymer.

PubMed

Sun, Qi; Aguila, Briana; Perman, Jason; Nguyen, Nicholas; Ma, Shengqian

2016-12-07

The combination of two or more reactive centers working in concert on a substrate to facilitate the reaction is now considered state of the art in catalysis, yet there still remains a tremendous challenge. Few heterogeneous systems of this sort have been exploited, as the active sites spatially separated within the rigid framework are usually difficult to cooperate. It is now shown that this roadblock can be surpassed. The underlying principle of the strategy presented here is the integration of catalytic components with excellent flexibility and porous heterogeneous catalysts, as demonstrated by the placement of linear ionic polymers in close proximity to surface Lewis acid active sites anchored on the walls of a covalent organic framework (COF). Using the cycloaddition of the epoxides and CO 2 as a model reaction, dramatic activity improvements have been achieved for the composite catalysts in relation to the individual catalytic component. Furthermore, they also clearly outperform the benchmark catalytic systems formed by the combination of the molecular organocatalysts and heterogeneous Lewis acid catalysts, while affording additional recyclability. The extraordinary flexibility and enriched concentration of the catalytically active moieties on linear polymers facilitate the concerted catalysis, thus leading to superior catalytic performance. This work therefore uncovers an entirely new strategy for designing bifunctional catalysts with double-activation behavior and opens a new avenue in the design of multicapable systems that mimic biocatalysis.

Functional Loop Dynamics of the Streptavidin-Biotin Complex

PubMed Central

Song, Jianing; Li, Yongle; Ji, Changge; Zhang, John Z. H.

2015-01-01

Accelerated molecular dynamics (aMD) simulation is employed to study the functional dynamics of the flexible loop3-4 in the strong-binding streptavidin-biotin complex system. Conventional molecular (cMD) simulation is also performed for comparison. The present study reveals the following important properties of the loop dynamics: (1) The transition of loop3-4 from open to closed state is observed in 200 ns aMD simulation. (2) In the absence of biotin binding, the open-state streptavidin is more stable, which is consistent with experimental evidences. The free energy (ΔG) difference is about 5 kcal/mol between two states. But with biotin binding, the closed state is more stable due to electrostatic and hydrophobic interactions between the loop3-4 and biotin. (3) The closure of loop3-4 is concerted to the stable binding of biotin to streptavidin. When the loop3-4 is in its open-state, biotin moves out of the binding pocket, indicating that the interactions between the loop3-4 and biotin are essential in trapping biotin in the binding pocket. (4) In the tetrameric streptavidin system, the conformational change of the loop3-4 in each monomer is independent of each other. That is, there is no cooperative binding for biotin bound to the four subunits of the tetramer. PMID:25601277

Catalytic multi-stage process for hydroconversion and refining hydrocarbon feeds

DOEpatents

Comolli, Alfred G.; Lee, Lap-Keung

2001-01-01

A multi-stage catalytic hydrogenation and hydroconversion process for heavy hydrocarbon feed materials such as coal, heavy petroleum fractions, and plastic waste materials. In the process, the feedstock is reacted in a first-stage, back-mixed catalytic reactor with a highly dispersed iron-based catalyst having a powder, gel or liquid form. The reactor effluent is pressure-reduced, vapors and light distillate fractions are removed overhead, and the heavier liquid fraction is fed to a second stage back-mixed catalytic reactor. The first and second stage catalytic reactors are operated at 700-850.degree. F. temperature, 1000-3500 psig hydrogen partial pressure and 20-80 lb./hr per ft.sup.3 reactor space velocity. The vapor and light distillates liquid fractions removed from both the first and second stage reactor effluent streams are combined and passed to an in-line, fixed-bed catalytic hydrotreater for heteroatom removal and for producing high quality naphtha and mid-distillate or a full-range distillate product. The remaining separator bottoms liquid fractions are distilled at successive atmospheric and vacuum pressures, low and intermediate-boiling hydrocarbon liquid products are withdrawn, and heavier distillate fractions are recycled and further upgraded to provide additional low-boiling hydrocarbon liquid products. This catalytic multistage hydrogenation process provides improved flexibility for hydroprocessing the various carbonaceous feedstocks and adjusting to desired product structures and for improved economy of operations.

Implementing Audio Digital Feedback Loop Using the National Instruments RIO System

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

Huang, G.; Byrd, J. M.

2006-11-20

Development of system for high precision RF distribution and laser synchronization at Berkeley Lab has been ongoing for several years. Successful operation of these systems requires multiple audio bandwidth feedback loops running at relatively high gains. Stable operation of the feedback loops requires careful design of the feedback transfer function. To allow for flexible and compact implementation, we have developed digital feedback loops on the National Instruments Reconfigurable Input/Output (RIO) platform. This platform uses an FPGA and multiple I/Os that can provide eight parallel channels running different filters. We present the design and preliminary experimental results of this system.

Crystal Structure of the Catalytic Domain of a Serine Threonine Protein Phosphatase

NASA Technical Reports Server (NTRS)

Swinglel, Mark; Honkanel, Richard; Ciszak, Ewa

2003-01-01

Reversible phosphorylation of serine and threonine residues is a well-recognized mechanism in eukaryotic cells for the regulation of cell-cycle progression, cell growth and metabolism. Human serine/threonine phosphatases can be placed into two major families, PPP and PPM. To date the structure on one PPP family member (PPl) has been determined. Here we present the structure of a 323-residue catalytic domain of a second phosphatase belonging to the PPP family of enzyme. catalytic domain of the enzyme has been determined to 1.60Angstrom resolution and refined to R=17.5 and Rfree = 20.8%. The catalytic domain possesses a unique fold consisting of a largely monolithic structure, divisible into closely-associated helical and sheet regions. The catalytic site contains two manganese ions that are involved in substrate binding and catalysis. The enzyme crystallizes as a dimer that completely buries catalytic surfaces of both monomers, Also, the structure shows evidence of some flexibility around the active site cleft that may be related to substrate specificity of this enzyme.

A random-walk/giant-loop model for interphase chromosomes.

PubMed Central

Sachs, R K; van den Engh, G; Trask, B; Yokota, H; Hearst, J E

1995-01-01

Fluorescence in situ hybridization data on distances between defined genomic sequences are used to construct a quantitative model for the overall geometric structure of a human chromosome. We suggest that the large-scale geometry during the G0/G1 part of the cell cycle may consist of flexible chromatin loops, averaging approximately 3 million bp, with a random-walk backbone. A fully explicit, three-parametric polymer model of this random-walk/giant-loop structure can account well for the data. More general models consistent with the data are briefly discussed. PMID:7708711

Loop engineering reveals the importance of active-site-decorating loops and gating residue in substrate affinity modulation of arginine deiminase (an anti-tumor enzyme).

PubMed

Cheng, Feng; Yang, Jianhua; Bocola, Marco; Schwaneberg, Ulrich; Zhu, Leilei

2018-05-05

Protein engineering of enzyme loop regions is an effective strategy to improve enzymatic properties. Previous studies that aimed to boost the activity of PpADI (an arginine deiminase from Pseudomonas plecoglossicida) under physiological conditions yielded several significantly improved variants that harbor substitutions predominantly located in active-site-decorating loops. A multi-site saturation mutagenesis at four positions in loop 1 (37, 38, 42, and 43) and three positions in loop 4 (402, 403, and 404) was performed to elucidate the importance of these loops in modulating the substrate affinity of PpADI. The identified "best" variant (M6-L1-4) showed a decreased S 0.5 ('K M ') of 0.48 mM compared with the parent M6 (0.81 mM). Subsequently, a rational design to recombine beneficial substitutions within loops 1 and 4 yielded variant L6 with a substantially decreased S 0.5 value (0.17 mM). A comprehensive simulation analysis resulted in a conclusion that high loop flexibility (especially the gating residue Arg400) is beneficial for substrate affinity due to less efficient blocking of the active site. Copyright © 2018 Elsevier Inc. All rights reserved.

Search for Functional Flexible Regions in the G-protein Family: New Reading of the FoldUnfold Program.

PubMed

Galzitskaya, Oxana; Deryusheva, Eugenia; Machulin, Andrey; Nemashkalova, Ekaterina; Glyakina, Anna

2018-06-21

High prediction accuracy of flexible loops in different protein families is a challenge because of the crucial functions associated with these regions. Results of the currently available programs for prediction of loops vary from protein to protein. For prediction of flexible regions in the G-domain for 23 representatives of G-proteins with the known 3D structure we have used eight programs. The results of predictions demonstrate that the FoldUnfold program predicts better loop positions than the PONDR, RОNN, DisEMBL, IUPred, GlobPlot 2, FoldIndex, and MobiDB programs. When classifying the predicted loops (rigid/flexible) according to the Debye-Waller fluctuation factors, our data reveal the existing weak correlation between the B-factors and the average number of closed residues according to the FoldUnfold program; the percentage of overlapping characteristics (residue fold/unfold status) of the protein residues from the two methods is about 60-70%. According to the FoldUnfold program, for G-proteins with the posttranslational modifications, the surrounding binding site residues by disordered-promoting glycine and alanine residues conduces to a more flexible position of the binding sites for fatty acid, while methionine, cysteine and isoleucine residues provide more rigid binding sites. Thus, our research demonstrates additional possibilities of the FoldUnfold program for prediction of flexible regions and characteristics of individual residues in a different protein family. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

A control system design approach for flexible spacecraft

NASA Technical Reports Server (NTRS)

Silverberg, L. M.

1985-01-01

A control system design approach for flexible spacecraft is presented. The control system design is carried out in two steps. The first step consists of determining the ideal control system in terms of a desirable dynamic performance. The second step consists of designing a control system using a limited number of actuators that possess a dynamic performance that is close to the ideal dynamic performance. The effects of using a limited number of actuators is that the actual closed-loop eigenvalues differ from the ideal closed-loop eigenvalues. A method is presented to approximate the actual closed-loop eigenvalues so that the calculation of the actual closed-loop eigenvalues can be avoided. Depending on the application, it also may be desirable to apply the control forces as impulses. The effect of digitizing the control to produce the appropriate impulses is also examined.

A mobile loop near the active site acts as a switch between the dual activities of a viral protease/deubiquitinase

PubMed Central

Ayach, Maya; Fieulaine, Sonia

2017-01-01

The positive-strand RNA virus Turnip yellow mosaic virus (TYMV) encodes an ovarian tumor (OTU)-like protease/deubiquitinase (PRO/DUB) protein domain involved both in proteolytic processing of the viral polyprotein through its PRO activity, and in removal of ubiquitin chains from ubiquitylated substrates through its DUB activity. Here, the crystal structures of TYMV PRO/DUB mutants and molecular dynamics simulations reveal that an idiosyncratic mobile loop participates in reversibly constricting its unusual catalytic site by adopting "open", "intermediate" or "closed" conformations. The two cis-prolines of the loop form a rigid flap that in the most closed conformation zips up against the other side of the catalytic cleft. The intermediate and closed conformations also correlate with a reordering of the TYMV PRO/DUB catalytic dyad, that then assumes a classical, yet still unusually mobile, OTU DUB alignment. Further structure-based mutants designed to interfere with the loop's mobility were assessed for enzymatic activity in vitro and in vivo, and were shown to display reduced DUB activity while retaining PRO activity. This indicates that control of the switching between the dual PRO/DUB activities resides prominently within this loop next to the active site. Introduction of mutations into the viral genome revealed that the DUB activity contributes to the extent of viral RNA accumulation both in single cells and in whole plants. In addition, the conformation of the mobile flap was also found to influence symptoms severity in planta. Such mutants now provide powerful tools with which to study the specific roles of reversible ubiquitylation in viral infection. PMID:29117247

Regulative Loops, Step Loops and Task Loops

ERIC Educational Resources Information Center

VanLehn, Kurt

2016-01-01

This commentary suggests a generalization of the conception of the behavior of tutoring systems, which the target article characterized as having an outer loop that was executed once per task and an inner loop that was executed once per step of the task. A more general conception sees these two loops as instances of regulative loops, which…

Flexible Metal-Fabric Radiators

NASA Technical Reports Server (NTRS)

Cross, Cynthia; Nguyen, Hai D.; Ruemmele, Warren; Andish, Kambiz K.; McCalley, Sean

2005-01-01

Flexible metal-fabric radiators have been considered as alternative means of dissipating excess heat from spacecraft and space suits. The radiators also may be useful in such special terrestrial applications as rejecting heat from space-suit-like protective suits worn in hot work environments. In addition to flexibility and consequent ease of deployment and installation on objects of varying sizes and shapes, the main advantages of these radiators over conventional rigid radiators are that they weigh less and occupy less volume for a given amount of cooling capacity. A radiator of this type includes conventional stainless-steel tubes carrying a coolant fluid. The main radiating component consists of a fabric of interwoven aluminum-foil strips bonded to the tubes by use of a proprietary process. The strip/tube bonds are strong and highly thermally conductive. Coolant is fed to and from the tubes via flexible stainless-steel manifolds designed to accommodate flexing of, and minimize bending forces on, the fabric. The manifolds are sized to minimize pressure drops and distribute the flow of coolant evenly to all the tubes. The tubes and manifolds are configured in two independent flow loops for operational flexibility and protective redundancy.

Impact of magnetic isolation on pointing system performance in the presence of structural flexibility

NASA Technical Reports Server (NTRS)

Seller, J.

1985-01-01

The inertial pointing stability of a gimbal pointing system (AGS) was compared with a magnetic pointing/gimbal followup system (ASPS), under certain conditions of system structural flexibility and disturbance inputs from the gimbal support structure. Separate 3 degree-of-freedom (3DOF) linear models based on NASTRAN modal flexibility data for the gimbal and support structures were generated for the ASPS configurations. Using the models inertial pointing control loops providing 6dB of gain margin and 45 deg of phase margin were defined for each configuration. The pointing loop bandwidth obtained for the ASPS is more than twice the level achieved for the AGS configuration. The AGS limit is attributed to the gimbal and support structure flexibility. As a result of the higher ASPS pointing loop bandwidth and the disturbance rejection provided by the magnetic isolation ASPS pointing performane is significantly better than that of the AGS system. The low frequency peak of the ASPS transfer function from base disturbance to payload angular motion is almost 60dB lower than AGS low frequency peak.

The Natively Disordered Loop of Bcl-2 Undergoes Phosphorylation-Dependent Conformational Change and Interacts with Pin1

PubMed Central

Kang, CongBao; Bharatham, Nagakumar; Chia, Joel; Mu, Yuguang; Baek, Kwanghee; Yoon, Ho Sup

2012-01-01

Bcl-2 plays a central role in the regulation of apoptosis. Structural studies of Bcl-2 revealed the presence of a flexible and natively disordered loop that bridges the Bcl-2 homology motifs, BH3 and BH4. This loop is phosphorylated on multiple sites in response to a variety of external stimuli, including the microtubule-targeting drugs, paclitaxel and colchicine. Currently, the underlying molecular mechanism of Bcl-2 phosphorylation and its biological significance remain elusive. In this study, we investigated the molecular characteristics of this anti-apoptotic protein. To this end, we generated synthetic peptides derived from the Bcl-2 loop, and multiple Bcl-2 loop truncation mutants that include the phosphorylation sites. Our results demonstrate that S87 in the flexible loop of Bcl-2 is the primary phosphorylation site for JNK and ERK2, suggesting some sequence or structural specificity for the phosphorylation by these kinases. Our NMR studies and molecular dynamics simulation studies support indicate that phosphorylation of S87 induces a conformational change in the peptide. Finally, we show that the phosphorylated peptides of the Bcl-2 loop can bind Pin1, further substantiating the phosphorylation-mediated conformation change of Bcl-2. PMID:23272207

Surface NMR imaging with simultaneously energized transmission loops

NASA Astrophysics Data System (ADS)

Irons, T. P.; Kass, A.; Parsekian, A.

2016-12-01

Surface nuclear magnetic resonance (sNMR) is a unique geophysical technique which allows for the direct detection of liquid-phase water. In saturated media the sNMR response also provides estimates of hydrologic properties including porosity and permeability. The most common survey deployment consists of a single coincident loop performing both transmission and receiving. Because the sNMR method is relatively slow, tomography using coincident loops is time-intensive. Surveys using multiple receiver loops (but a single transmitter) provide additional sensitivity; however, they still require iterating transmission over the loops, and do not decrease survey acquisition time. In medical rotating frame imaging, arrays of transmitters are employed in order to decrease acquisition time, whilst optimizing image resolving power-a concept which we extend to earth's field imaging. Using simultaneously energized transmission loops decreases survey time linearly with the number of channels. To demonstrate the efficacy and benefits of multiple transmission loops, we deployed simultaneous sNMR transmission arrays using minimally coupled loops and a specially modified instrument at the Red Buttes Hydrogeophysics Experiment Site-a well-characterized location near Laramie, Wyoming. The proposed survey proved capable of acquiring multiple-channel imaging data with comparable noise levels to figure-eight configurations. Finally, the channels can be combined after acquisition or inverted simultaneously to provide composite datasets and images. This capability leverages the improved near surface resolving power of small loops but retains sensitivity to deep media through the use of synthetic aperature receivers. As such, simultaneously acquired loop arrays provide a great deal of flexibility.

A decoupled recursive approach for constrained flexible multibody system dynamics

NASA Technical Reports Server (NTRS)

Lai, Hao-Jan; Kim, Sung-Soo; Haug, Edward J.; Bae, Dae-Sung

1989-01-01

A variational-vector calculus approach is employed to derive a recursive formulation for dynamic analysis of flexible multibody systems. Kinematic relationships for adjacent flexible bodies are derived in a companion paper, using a state vector notation that represents translational and rotational components simultaneously. Cartesian generalized coordinates are assigned for all body and joint reference frames, to explicitly formulate deformation kinematics under small deformation kinematics and an efficient flexible dynamics recursive algorithm is developed. Dynamic analysis of a closed loop robot is performed to illustrate efficiency of the algorithm.

Enzymatic properties of a GH19 chitinase isolated from rice lacking a major loop structure involved in chitin binding.

PubMed

Tanaka, Jun; Fukamizo, Tamo; Ohnuma, Takayuki

2017-05-01

The catalytic domains of family GH19 chitinases have been found to consist of a conserved, α-helical core-region and different numbers (1-6) of loop structures, located at both ends of the substrate-binding groove and which extend over the glycon- and aglycon-binding sites. We expressed, purified and enzymatically characterized a GH19 chitinase from rice, Oryza sativa L. cv. Nipponbare (OsChia2a), lacking a major loop structure (loop III) connected to the functionally important β-stranded region. The new enzyme thus contained the five remaining loop structures (loops I, II, IV, V and C-term). The OsChia2a recombinant protein catalyzed hydrolysis of chitin oligosaccharides, (GlcNAc)n (n = 3-6), with inversion of anomeric configuration, indicating that OsChia2a correctly folded without loop III. From thermal unfolding experiments and calorimetric titrations using the inactive OsChia2a mutant (OsChia2a-E68Q), in which the catalytic residue Glu68 was mutated to glutamine, we found that the binding affinities towards (GlcNAc)n (n = 2-6) were almost proportional to the degree of polymerization of (GlcNAc)n, but were much lower than those obtained for a moss GH19 chitinase having only loop III [Ohnuma T, Sørlie M, Fukuda T, Kawamoto N, Taira T, Fukamizo T. 2011. Chitin oligosaccharide binding to a family GH19 chitinase from the moss, Bryum coronatum. FEBS J. 278:3991-4001]. Nevertheless, OsChia2a exhibited significant antifungal activity. It appears that loop III connected to the β-stranded region is important for (GlcNAc)n binding, but is not essential for antifungal activity. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Conservative Tryptophan Mutants of the Protein Tyrosine Phosphatase YopH Exhibit Impaired WPD-Loop Function and Crystallize with Divanadate Esters in Their Active Sites

PubMed Central

Moise, Gwendolyn; Gallup, Nathan M.; Alexandrova, Anastassia N.; Hengge, Alvan C.; Johnson, Sean J.

2016-01-01

Catalysis in protein tyrosine phosphatases (PTPs) involves movement of a protein loop called the WPD loop that brings a conserved aspartic acid into the active site to function as a general acid. Mutation of the tryptophan in the WPD loop of the PTP YopH to any other residue with a planar, aromatic side chain (phenylalanine, tyrosine, or histidine) disables general acid catalysis. Crystal structures reveal these conservative mutations leave this critical loop in a catalytically unproductive, quasi-open position. Although the loop positions in crystal structures are similar for all three conservative mutants, the reasons inhibiting normal loop closure differ for each mutant. In the W354F and W354Y mutants, steric clashes result from six-membered rings occupying the position of the five-membered ring of the native indole side chain. The histidine mutant dysfunction results from new hydrogen bonds stabilizing the unproductive position. The results demonstrate how even modest modifications can disrupt catalytically important protein dynamics. Crystallization of all the catalytically compromised mutants in the presence of vanadate gave rise to vanadate dimers at the active site. In W354Y and W354H, a divanadate ester with glycerol is observed. Such species have precedence in solution and are known from the small molecule crystal database. Such species have not been observed in the active site of a phosphatase, as a functional phosphatase would rapidly catalyze their decomposition. The compromised functionality of the mutants allows the trapping of species that undoubtedly form in solution and are capable of binding at the active sites of PTPs, and, presumably, other phosphatases. In addition to monomeric vanadate, such higher-order vanadium-based molecules are likely involved in the interaction of vanadate with PTPs in solution. PMID:26445170

DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation

PubMed Central

Boedicker, James Q.; Garcia, Hernan G.; Johnson, Stephanie; Phillips, Rob

2014-01-01

As the chief informational molecule of life, DNA is subject to extensive physical manipulations. The energy required to deform double-helical DNA depends on sequence, and this mechanical code of DNA influences gene regulation, such as through nucleosome positioning. Here we examine the sequence-dependent flexibility of DNA in bacterial transcription factor-mediated looping, a context for which the role of sequence remains poorly understood. Using a suite of synthetic constructs repressed by the Lac repressor and two well-known sequences that show large flexibility differences in vitro, we make precise statistical mechanical predictions as to how DNA sequence influences loop formation and test these predictions using in vivo transcription and in vitro single-molecule assays. Surprisingly, sequence-dependent flexibility does not affect in vivo gene regulation. By theoretically and experimentally quantifying the relative contributions of sequence and the DNA-bending protein HU to DNA mechanical properties, we reveal that bending by HU dominates DNA mechanics and masks intrinsic sequence-dependent flexibility. Such a quantitative understanding of how mechanical regulatory information is encoded in the genome will be a key step towards a predictive understanding of gene regulation at single-base pair resolution. PMID:24231252

Precise control of flexible manipulators

NASA Technical Reports Server (NTRS)

Cannon, R. H., Jr.; Bindford, T. O.; Schmitz, E.

1984-01-01

The design and experimental testing of end point position controllers for a very flexible one link lightweight manipulator are summarized. The latest upgraded version of the experimental set up, and the basic differences between conventional joint angle feedback and end point position feedback are described. A general procedure for application of modern control methods to the problem is outlined. The relationship between weighting parameters and the bandwidth and control stiffness of the resulting end point position closed loop system is shown. It is found that joint rate angle feedback in addition to the primary end point position sensor is essential for adequate disturbance rejection capability of the closed loop system. The use of a low order multivariable compensator design computer code; called Sandy is documented. A solution to the problem of control mode switching between position sensor sets is outlined. The proof of concept for endpoint position feedback for a one link flexible manipulator was demonstrated. The bandwidth obtained with the experimental end point position controller is about twice as fast as the beam's first natural cantilevered frequency, and comes within a factor of four of the absolute physical speed limit imposed by the wave propagation time of the beam.

Remote Exosites of the Catalytic Domain of Matrix Metalloproteinase-12 Enhance Elastin Degradation┼

PubMed Central

Fulcher, Yan G.; Van Doren, Steven R.

2011-01-01

How does matrix metalloproteinase-12 (MMP-12 or metalloelastase) degrade elastin with high specific activity? NMR suggested soluble elastin to cover surfaces of MMP-12 far from its active site. Two of these surfaces have been found, by mutagenesis guided by the BINDSIght approach, to affect degradation and affinity for elastin substrates but not a small peptide substrate. Main exosite 1 has been extended out to Asp124 that binds calcium. Novel exosite 2 comprises residues from the II–III loop and β-strand I near the back of the catalytic domain. The high exposure of these distal exosites may make them accessible to elastin made more flexible by partial hydrolysis. Importantly, combination of a lesion at each of exosites 1 and 2 and active site decreased catalytic competence towards soluble elastin by 13- to 18-fold to the level of MMP-3, homologue and poor elastase. Double mutant cycle analysis of conservative mutations of Met156 (exosite 2) and either Asp124 (exosite 1) or Ile180 (active site) had additive effects. Compared to polar substitutions observed in other MMPs, Met156 enhanced affinity and Ile180 kcat for soluble elastin. Both residues detracted from the higher folding stability with polar mutations. This resembles the trend in enzymes of an inverse relationship between folding stability and activity. Restoring Asp124 from combination mutants enhanced kcat for soluble elastin. In elastin degradation, exosites 1 and 2 contributed independently of each other and Ile180 at the active site, but with partial coupling to Ala182 near the active site. The concept of weak, separated interactions coalescing somewhat independently can be extended to this proteolytic digestion of a protein from fibrils. PMID:21967233

Unbiased, scalable sampling of protein loop conformations from probabilistic priors.

PubMed

Zhang, Yajia; Hauser, Kris

2013-01-01

Protein loops are flexible structures that are intimately tied to function, but understanding loop motion and generating loop conformation ensembles remain significant computational challenges. Discrete search techniques scale poorly to large loops, optimization and molecular dynamics techniques are prone to local minima, and inverse kinematics techniques can only incorporate structural preferences in adhoc fashion. This paper presents Sub-Loop Inverse Kinematics Monte Carlo (SLIKMC), a new Markov chain Monte Carlo algorithm for generating conformations of closed loops according to experimentally available, heterogeneous structural preferences. Our simulation experiments demonstrate that the method computes high-scoring conformations of large loops (>10 residues) orders of magnitude faster than standard Monte Carlo and discrete search techniques. Two new developments contribute to the scalability of the new method. First, structural preferences are specified via a probabilistic graphical model (PGM) that links conformation variables, spatial variables (e.g., atom positions), constraints and prior information in a unified framework. The method uses a sparse PGM that exploits locality of interactions between atoms and residues. Second, a novel method for sampling sub-loops is developed to generate statistically unbiased samples of probability densities restricted by loop-closure constraints. Numerical experiments confirm that SLIKMC generates conformation ensembles that are statistically consistent with specified structural preferences. Protein conformations with 100+ residues are sampled on standard PC hardware in seconds. Application to proteins involved in ion-binding demonstrate its potential as a tool for loop ensemble generation and missing structure completion.

Unbiased, scalable sampling of protein loop conformations from probabilistic priors

PubMed Central

2013-01-01

Background Protein loops are flexible structures that are intimately tied to function, but understanding loop motion and generating loop conformation ensembles remain significant computational challenges. Discrete search techniques scale poorly to large loops, optimization and molecular dynamics techniques are prone to local minima, and inverse kinematics techniques can only incorporate structural preferences in adhoc fashion. This paper presents Sub-Loop Inverse Kinematics Monte Carlo (SLIKMC), a new Markov chain Monte Carlo algorithm for generating conformations of closed loops according to experimentally available, heterogeneous structural preferences. Results Our simulation experiments demonstrate that the method computes high-scoring conformations of large loops (>10 residues) orders of magnitude faster than standard Monte Carlo and discrete search techniques. Two new developments contribute to the scalability of the new method. First, structural preferences are specified via a probabilistic graphical model (PGM) that links conformation variables, spatial variables (e.g., atom positions), constraints and prior information in a unified framework. The method uses a sparse PGM that exploits locality of interactions between atoms and residues. Second, a novel method for sampling sub-loops is developed to generate statistically unbiased samples of probability densities restricted by loop-closure constraints. Conclusion Numerical experiments confirm that SLIKMC generates conformation ensembles that are statistically consistent with specified structural preferences. Protein conformations with 100+ residues are sampled on standard PC hardware in seconds. Application to proteins involved in ion-binding demonstrate its potential as a tool for loop ensemble generation and missing structure completion. PMID:24565175

Managing Demand and Capacity Using Multi-Sector Planning and Flexible Airspace: Human-in-the-Loop Evaluation of NextGen

NASA Technical Reports Server (NTRS)

Lee, Paul U.; Smith, Nancy M.; Prevot, Thomas; Homola, Jeffrey R.

2010-01-01

When demand for an airspace sector exceeds capacity, the balance can be re-established by reducing the demand, increasing the capacity, or both. The Multi-Sector Planner (MSP) concept has been proposed to better manage traffic demand by modifying trajectories across multiple sectors. A complementary approach to MSP, called Flexible Airspace Management (FAM), reconfigures the airspace such that capacity can be reallocated dynamically to balance the traffic demand across multiple sectors, resulting in fewer traffic management initiatives. The two concepts have been evaluated with a series of human-in-the-loop simulations at the Airspace Operations Laboratory to examine and refine the roles of the human operators in these concepts, as well as their tools and procedural requirements. So far MSP and FAM functions have been evaluated individually but the integration of the two functions is desirable since there are significant overlaps in their goals, geographic/temporal scope of the problem space, and the implementation timeframe. Ongoing research is planned to refine the humans roles in the integrated concept.

Mutational analysis of the active site flap (20s loop) of mandelate racemase.

PubMed

Bourque, Jennifer R; Bearne, Stephen L

2008-01-15

Mandelate racemase from Pseudomonas putida catalyzes the Mg2+-dependent 1,1-proton transfer that interconverts the enantiomers of mandelate. Residues of the 20s and 50s loops determine, in part, the topology and polarity of the active site and hence the substrate specificity. Previously, we proposed that, during racemization, the phenyl ring of mandelate moves between an S-pocket comprised of residues from the 50s loop and an R-pocket comprised of residues from the 20s loop [Siddiqi, F., Bourque, J. R., Jiang, H., Gardner, M., St. Maurice, M., Blouin, C., and Bearne, S. L. (2005) Biochemistry 44, 9013-9021]. The 20s loop constitutes a mobile beta-meander flap that covers the active site cavity shielding it from solvent and controlling entry and egress of ligands. To understand the role of the 20s loop in catalysis and substrate specificity, we constructed a series of mutants (V22A, V22I, V22F, T24S, A25V, V26A, V26L, V26F, V29A, V29L, V29F, V26A/V29L, and V22I/V29L) in which the sizes of hydrophobic side chains of the loop residues were varied. Catalytic efficiencies (kcat/Km) for all mutants were reduced between 6- and 40-fold with the exception of those of V22I, V26A, V29L, and V22I/V29L which had near wild-type efficiencies with mandelate. Thr 24 and Ala 25, located at the tip of the 20s loop, were particularly sensitive to minor alterations in the size of their hydrophobic side chains; however, most mutations were tolerated quite well, suggesting that flap mobility could compensate for increases in the steric bulk of hydrophobic side chains. With the exception of V29L, with mandelate as the substrate, and V22F and V26A/V29L, with 2-naphthylglycolate (2-NG) as the substrate, the values of kcat and Km were not altered in a manner consistent with steric obstruction of the R-pocket, perhaps due to flap mobility compensating for the increased size of the hydrophobic side chains. Surprisingly, V22I and V29L catalyzed the racemization of the bulkier substrate 2-NG

Molecular dynamics simulations of the Bcl-2 protein to predict the structure of its unordered flexible loop domain.

PubMed

Raghav, Pawan Kumar; Verma, Yogesh Kumar; Gangenahalli, Gurudutta U

2012-05-01

B-cell lymphoma (Bcl-2) protein is an anti-apoptotic member of the Bcl-2 family. It is functionally demarcated into four Bcl-2 homology (BH) domains: BH1, BH2, BH3, BH4, one flexible loop domain (FLD), a transmembrane domain (TM), and an X domain. Bcl-2's BH domains have clearly been elucidated from a structural perspective, whereas the conformation of FLD has not yet been predicted, despite its important role in regulating apoptosis through its interactions with JNK-1, PKC, PP2A phosphatase, caspase 3, MAP kinase, ubiquitin, PS1, and FKBP38. Many important residues that regulate Bcl-2 anti-apoptotic activity are present in this domain, for example Asp34, Thr56, Thr69, Ser70, Thr74, and Ser87. The structural elucidation of the FLD would likely help in attempts to accurately predict the effect of mutating these residues on the overall structure of the protein and the interactions of other proteins in this domain. Therefore, we have generated an increased quality model of the Bcl-2 protein including the FLD through modeling. Further, molecular dynamics (MD) simulations were used for FLD optimization, to predict the flexibility, and to determine the stability of the folded FLD. In addition, essential dynamics (ED) was used to predict the collective motions and the essential subspace relevant to Bcl-2 protein function. The predicted average structure and ensemble of MD-simulated structures were submitted to the Protein Model Database (PMDB), and the Bcl-2 structures obtained exhibited enhanced quality. This study should help to elucidate the structural basis for Bcl-2 anti-apoptotic activity regulation through its binding to other proteins via the FLD.

Reversible Regulation of Catalytic Activity of Gold Nanoparticles with DNA Nanomachines

NASA Astrophysics Data System (ADS)

Zhou, Peipei; Jia, Sisi; Pan, Dun; Wang, Lihua; Gao, Jimin; Lu, Jianxin; Shi, Jiye; Tang, Zisheng; Liu, Huajie

2015-09-01

Reversible catalysis regulation has gained much attention and traditional strategies utilized reversible ligand coordination for switching catalyst’s conformations. However, it remains challenging to regulate the catalytic activity of metal nanoparticle-based catalysts. Herein, we report a new DNA nanomachine-driven reversible nano-shield strategy for circumventing this problem. The basic idea is based on the fact that the conformational change of surface-attached DNA nanomachines will cause the variation of the exposed surface active area on metal nanoparticles. As a proof-of-concept study, we immobilized G-rich DNA strands on gold nanoparticles (AuNPs) which have glucose oxidase (GOx) like activity. Through the reversible conformational change of the G-rich DNA between a flexible single-stranded form and a compact G-quadruplex form, the catalytic activity of AuNPs has been regulated reversibly for several cycles. This strategy is reliable and robust, which demonstrated the possibility of reversibly adjusting catalytic activity with external surface coverage switching, rather than coordination interactions.

Smart Braid Feedback for the Closed-Loop Control of Soft Robotic Systems.

PubMed

Felt, Wyatt; Chin, Khai Yi; Remy, C David

2017-09-01

This article experimentally investigates the potential of using flexible, inductance-based contraction sensors in the closed-loop motion control of soft robots. Accurate motion control remains a highly challenging task for soft robotic systems. Precise models of the actuation dynamics and environmental interactions are often unavailable. This renders open-loop control impossible, while closed-loop control suffers from a lack of suitable feedback. Conventional motion sensors, such as linear or rotary encoders, are difficult to adapt to robots that lack discrete mechanical joints. The rigid nature of these sensors runs contrary to the aspirational benefits of soft systems. As truly soft sensor solutions are still in their infancy, motion control of soft robots has so far relied on laboratory-based sensing systems such as motion capture, electromagnetic (EM) tracking, or Fiber Bragg Gratings. In this article, we used embedded flexible sensors known as Smart Braids to sense the contraction of McKibben muscles through changes in inductance. We evaluated closed-loop control on two systems: a revolute joint and a planar, one degree of freedom continuum manipulator. In the revolute joint, our proposed controller compensated for elasticity in the actuator connections. The Smart Braid feedback allowed motion control with a steady-state root-mean-square (RMS) error of [1.5]°. In the continuum manipulator, Smart Braid feedback enabled tracking of the desired tip angle with a steady-state RMS error of [1.25]°. This work demonstrates that Smart Braid sensors can provide accurate position feedback in closed-loop motion control suitable for field applications of soft robotic systems.

Highly flexible sub-1 nm tungsten oxide nanobelts as efficient desulfurization catalysts.

PubMed

He, Jie; Liu, Huiling; Xu, Biao; Wang, Xun

2015-03-01

Ultrathin tungsten oxide nanobelts are successfully synthesized via a facile solvothermal method. Sub-1 nm thickness and hydrophobic surface property endow the nanobelts with flexibility, viscosity, gelation, and good catalytic performance in oxidative desulfurization. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Vibration and Control of Flexible Rotor Supported by Magnetic Bearings

NASA Technical Reports Server (NTRS)

Nonami, Kenzou

1988-01-01

Active vibration control of flexible rotors supported by magnetic bearings is discussed. Using a finite-element method for a mathematical model of the flexible rotor, the eigenvalue problem is formulated taking into account the interaction between a mechanical system of the flexible rotor and an electrical system of the magnetic bearings and the controller. However, for the sake of simplicity, gyroscopic effects are disregarded. It is possible to adapt this formulation to a general flexible rotor-magnetic bearing system. Controllability with and without collocation sensors and actuators located at the same distance along the rotor axis is discussed for the higher order flexible modes of the test rig. In conclusion, it is proposed that it is necessary to add new active control loops for the higher flexible modes even in the case of collocation. Then it is possible to stabilize for the case of uncollocation by means of this method.

Flexible pile thermal barrier insulator

NASA Technical Reports Server (NTRS)

Anderson, G. E.; Fell, D. M.; Tesinsky, J. S. (Inventor)

1978-01-01

A flexible pile thermal barrier insulator included a plurality of upstanding pile yarns. A generally planar backing section supported the upstanding pile yarns. The backing section included a plurality of filler yarns forming a mesh in a first direction. A plurality of warp yarns were looped around said filler yarns and pile yarns in the backing section and formed a mesh in a second direction. A binder prevented separation of the yarns in the backing section.

The DUSP–Ubl domain of USP4 enhances its catalytic efficiency by promoting ubiquitin exchange

PubMed Central

Clerici, Marcello; Luna-Vargas, Mark P. A.; Faesen, Alex C.; Sixma, Titia K.

2014-01-01

Ubiquitin-specific protease USP4 is emerging as an important regulator of cellular pathways, including the TGF-β response, NF-κB signalling and splicing, with possible roles in cancer. Here we show that USP4 has its catalytic triad arranged in a productive conformation. Nevertheless, it requires its N-terminal DUSP–Ubl domain to achieve full catalytic turnover. Pre-steady-state kinetics measurements reveal that USP4 catalytic domain activity is strongly inhibited by slow dissociation of ubiquitin after substrate hydrolysis. The DUSP–Ubl domain is able to enhance ubiquitin dissociation, hence promoting efficient turnover. In a mechanism that requires all USP4 domains, binding of the DUSP–Ubl domain promotes a change of a switching loop near the active site. This ‘allosteric regulation of product discharge’ provides a novel way of regulating deubiquitinating enzymes that may have relevance for other enzyme classes. PMID:25404403

PA-Tb-Cu MOF as luminescent nanoenzyme for catalytic assay of hydrogen peroxide.

PubMed

Qi, Zewan; Wang, Li; You, Qi; Chen, Yang

2017-10-15

Metal organic frameworks (MOFs) with flexible structures and components have aroused great interest in designing functional materials. In this work, we designed and made a kind of PA-Tb-Cu MOF nanoenzyme capable of emitting fluorescence for the catalytic reaction of hydrogen peroxide (H 2 O 2 ). Luminescent Tb 3+ , catalytic Cu 2+ and bridging ligand were assembled and integrated into a single material nanoenzyme. This PA-Tb-Cu MOF nanoenzyme not only possessed excellent catalytic activity comparable to horseradish peroxidase but also can real-time fluorescently indicate the concentration of H 2 O 2 as low as 0.2µM during catalysis. Luminescent PA-Tb-Cu MOF nanoenzyme did not need a common combined use of natural/artificial enzymes and chromogenic reactions for the quantification of H 2 O 2 in widely-used enzyme-catalytic reactions. The present strategy assembled directly from functional ions/molecules provides a new way for the design and development of smart, multifunctional artificial enzymes for wide applications in biocatalysis, bioassays and nano-biomedicine. Copyright © 2017 Elsevier B.V. All rights reserved.

Variation of wave speed determined by the PU-loop with proximity to a reflection site.

PubMed

Li, Ye; Borlotti, Alessandra; Parker, Kim H; Khir, Ashraf W

2011-01-01

Wave speed is directly related to arterial distensibility and is widely used by clinicians to assess arterial stiffness. The PU-loop method for determining wave speed is based on the water hammer equation for flow in flexible tubes and artery using the method of characteristics. This technique determines wave speed using simultaneous measurements of pressure and velocity at a single point. The method shows that during the early part of systole, the relationship between pressure and velocity is generally linear, and the initial slope of the PU-loop is proportional to wave speed. In this work, we designed an in-vitro experiment to investigate the effect of proximity to a reflection site on the wave speed determined by the PU-loop through varying the distance between the measurement and reflection sites. Measurements were made in a flexible tube with a reflection site at the distal end formed by joining the tube to another tube with a different diameter and material properties. Six different flexible tubes were used to generate both positive and negative reflection coefficients of different magnitudes. We found that the wave speed determined by the PU-loop did not change when the measurement site was far from the reflection site but did change as the distance to the reflection site decreased. The calculated wave speed increased with positive reflections and decreased with negative reflections. The magnitude of the change in wave speed at a fixed distance from the reflection site increased with increasing the value of the reflection coefficient.

Hard real-time closed-loop electrophysiology with the Real-Time eXperiment Interface (RTXI)

PubMed Central

George, Ansel; Dorval, Alan D.; Christini, David J.

2017-01-01

The ability to experimentally perturb biological systems has traditionally been limited to static pre-programmed or operator-controlled protocols. In contrast, real-time control allows dynamic probing of biological systems with perturbations that are computed on-the-fly during experimentation. Real-time control applications for biological research are available; however, these systems are costly and often restrict the flexibility and customization of experimental protocols. The Real-Time eXperiment Interface (RTXI) is an open source software platform for achieving hard real-time data acquisition and closed-loop control in biological experiments while retaining the flexibility needed for experimental settings. RTXI has enabled users to implement complex custom closed-loop protocols in single cell, cell network, animal, and human electrophysiology studies. RTXI is also used as a free and open source, customizable electrophysiology platform in open-loop studies requiring online data acquisition, processing, and visualization. RTXI is easy to install, can be used with an extensive range of external experimentation and data acquisition hardware, and includes standard modules for implementing common electrophysiology protocols. PMID:28557998

Analysis of the bacterial luciferase mobile loop by replica-exchange molecular dynamics.

PubMed

Campbell, Zachary T; Baldwin, Thomas O; Miyashita, Osamu

2010-12-15

Bacterial luciferase contains an extended 29-residue mobile loop. Movements of this loop are governed by binding of either flavin mononucleotide (FMNH2) or polyvalent anions. To understand this process, loop dynamics were investigated using replica-exchange molecular dynamics that yielded conformational ensembles in either the presence or absence of FMNH2. The resulting data were analyzed using clustering and network analysis. We observed the closed conformations that are visited only in the simulations with the ligand. Yet the mobile loop is intrinsically flexible, and FMNH2 binding modifies the relative populations of conformations. This model provides unique information regarding the function of a crystallographically disordered segment of the loop near the binding site. Structures at or near the fringe of this network were compatible with flavin binding or release. Finally, we demonstrate that the crystallographically observed conformation of the mobile loop bound to oxidized flavin was influenced by crystal packing. Thus, our study has revealed what we believe are novel conformations of the mobile loop and additional context for experimentally determined structures. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket.

PubMed

Keiper, Sonja; Bebenroth, Dirk; Seelig, Burckhard; Westhof, Eric; Jäschke, Andres

2004-09-01

Artificial ribozymes catalyze a variety of chemical reactions. Their structures and reaction mechanisms are largely unknown. We have analyzed a ribozyme catalyzing Diels-Alder cycloaddition reactions by comprehensive mutation analysis and a variety of probing techniques. New tertiary interactions involving base pairs between nucleotides of the 5' terminus and a large internal loop forming a pseudoknot fold were identified. The probing data indicate a preformed tertiary structure that shows no major changes on substrate or product binding. Based on these observations, a molecular architecture featuring a Y-shaped arrangement is proposed. The tertiary structure is formed in a rather unusual way; that is, the opposite sides of the asymmetric internal loop are clamped by the four 5'-terminal nucleotides, forming two adjacent two base-pair helices. It is proposed that the catalytic pocket is formed by a wedge within one of these helices.

Active control of flexible structures using a fuzzy logic algorithm

NASA Astrophysics Data System (ADS)

Cohen, Kelly; Weller, Tanchum; Ben-Asher, Joseph Z.

2002-08-01

This study deals with the development and application of an active control law for the vibration suppression of beam-like flexible structures experiencing transient disturbances. Collocated pairs of sensors/actuators provide active control of the structure. A design methodology for the closed-loop control algorithm based on fuzzy logic is proposed. First, the behavior of the open-loop system is observed. Then, the number and locations of collocated actuator/sensor pairs are selected. The proposed control law, which is based on the principles of passivity, commands the actuator to emulate the behavior of a dynamic vibration absorber. The absorber is tuned to a targeted frequency, whereas the damping coefficient of the dashpot is varied in a closed loop using a fuzzy logic based algorithm. This approach not only ensures inherent stability associated with passive absorbers, but also circumvents the phenomenon of modal spillover. The developed controller is applied to the AFWAL/FIB 10 bar truss. Simulated results using MATLAB© show that the closed-loop system exhibits fairly quick settling times and desirable performance, as well as robustness characteristics. To demonstrate the robustness of the control system to changes in the temporal dynamics of the flexible structure, the transient response to a considerably perturbed plant is simulated. The modal frequencies of the 10 bar truss were raised as well as lowered substantially, thereby significantly perturbing the natural frequencies of vibration. For these cases, too, the developed control law provides adequate settling times and rates of vibrational energy dissipation.

Engineering a hyper-catalytic enzyme by photo-activated conformation modulation

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

Agarwal, Pratul K

2012-01-01

Enzyme engineering for improved catalysis has wide implications. We describe a novel chemical modification of Candida antarctica lipase B that allows modulation of the enzyme conformation to promote catalysis. Computational modeling was used to identify dynamical enzyme regions that impact the catalytic mechanism. Surface loop regions located distal to active site but showing dynamical coupling to the reaction were connected by a chemical bridge between Lys136 and Pro192, containing a derivative of azobenzene. The conformational modulation of the enzyme was achieved using two sources of light that alternated the azobenzene moiety in cis and trans conformations. Computational model predicted thatmore » mechanical energy from the conformational fluctuations facilitate the reaction in the active-site. The results were consistent with predictions as the activity of the engineered enzyme was found to be enhanced with photoactivation. Preliminary estimations indicate that the engineered enzyme achieved 8-52 fold better catalytic activity than the unmodulated enzyme.« less

Rational engineering of the Neurospora VS ribozyme to allow substrate recognition via different kissing-loop interactions.

PubMed

Lacroix-Labonté, Julie; Girard, Nicolas; Dagenais, Pierre; Legault, Pascale

2016-08-19

The Neurospora VS ribozyme is a catalytic RNA that has the unique ability to specifically recognize and cleave a stem-loop substrate through formation of a highly stable kissing-loop interaction (KLI). In order to explore the engineering potential of the VS ribozyme to cleave alternate substrates, we substituted the wild-type KLI by other known KLIs using an innovative engineering method that combines rational and combinatorial approaches. A bioinformatic search of the protein data bank was initially performed to identify KLIs that are structurally similar to the one found in the VS ribozyme. Next, substrate/ribozyme (S/R) pairs that incorporate these alternative KLIs were kinetically and structurally characterized. Interestingly, several of the resulting S/R pairs allowed substrate cleavage with substantial catalytic efficiency, although with reduced activity compared to the reference S/R pair. Overall, this study describes an innovative approach for RNA engineering and establishes that the KLI of the trans VS ribozyme can be adapted to cleave other folded RNA substrates. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Exploration of alternate catalytic mechanisms and optimization strategies for retroaldolase design.

PubMed

Bjelic, Sinisa; Kipnis, Yakov; Wang, Ling; Pianowski, Zbigniew; Vorobiev, Sergey; Su, Min; Seetharaman, Jayaraman; Xiao, Rong; Kornhaber, Gregory; Hunt, John F; Tong, Liang; Hilvert, Donald; Baker, David

2014-01-09

Designed retroaldolases have utilized a nucleophilic lysine to promote carbon-carbon bond cleavage of β-hydroxy-ketones via a covalent Schiff base intermediate. Previous computational designs have incorporated a water molecule to facilitate formation and breakdown of the carbinolamine intermediate to give the Schiff base and to function as a general acid/base. Here we investigate an alternative active-site design in which the catalytic water molecule was replaced by the side chain of a glutamic acid. Five out of seven designs expressed solubly and exhibited catalytic efficiencies similar to previously designed retroaldolases for the conversion of 4-hydroxy-4-(6-methoxy-2-naphthyl)-2-butanone to 6-methoxy-2-naphthaldehyde and acetone. After one round of site-directed saturation mutagenesis, improved variants of the two best designs, RA114 and RA117, exhibited among the highest kcat (>10(-3)s(-1)) and kcat/KM (11-25M(-1)s(-1)) values observed for retroaldolase designs prior to comprehensive directed evolution. In both cases, the >10(5)-fold rate accelerations that were achieved are within 1-3 orders of magnitude of the rate enhancements reported for the best catalysts for related reactions, including catalytic antibodies (kcat/kuncat=10(6) to 10(8)) and an extensively evolved computational design (kcat/kuncat>10(7)). The catalytic sites, revealed by X-ray structures of optimized versions of the two active designs, are in close agreement with the design models except for the catalytic lysine in RA114. We further improved the variants by computational remodeling of the loops and yeast display selection for reactivity of the catalytic lysine with a diketone probe, obtaining an additional order of magnitude enhancement in activity with both approaches. © 2013.

Experimental and Theoretical Study of the Movement of the Wpd Flexible Loop of Human Protein Tyrosine Phosphatase PTP1B in Complex with Halide Ions

NASA Astrophysics Data System (ADS)

Katz, Aline; Saenz-Méndez, Patricia; Cousido-Siah, Alexandra; Podjarny, Alberto D.; Ventura, Oscar N.

2012-11-01

Protein tyrosine phosphorylation is a post-translational modification mechanism, crucial for the regulation of nearly all aspects of cell life. This dynamic, reversible process is regulated by the balanced opposing activity of protein tyrosine kinases and protein tyrosine phosphatases. In particular, the protein tyrosine phosphatase 1B (PTP1B) is implicated in the regulation of the insulin-receptor activity, leptin-stimulated signal transduction pathways and other clinically relevant metabolic routes, and it has been found overexpressed or overregulated in human breasts, colon and ovary cancers. The WPD loop of the enzyme presents an inherent flexibility, and it plays a fundamental role in the enzymatic catalysis, turning it into a potential target in the design of new efficient PTP1B inhibitors. In order to determine the interactions that control the spatial conformation adopted by the WPD loop, complexes between the enzyme and halide ions (Br- and I- in particular) were crystallized and their crystallographic structure determined, and the collective movements of the aforementioned complexes were studied through Molecular Dynamics (MD) simulations. Both studies yielded concordant results, indicating the existence of a relationship between the identity of the ion present in the complex and the strength of the interactions it establishes with the surrounding protein residues.

Robust fuel- and time-optimal control of uncertain flexible space structures

NASA Technical Reports Server (NTRS)

Wie, Bong; Sinha, Ravi; Sunkel, John; Cox, Ken

1993-01-01

The problem of computing open-loop, fuel- and time-optimal control inputs for flexible space structures in the face of modeling uncertainty is investigated. Robustified, fuel- and time-optimal pulse sequences are obtained by solving a constrained optimization problem subject to robustness constraints. It is shown that 'bang-off-bang' pulse sequences with a finite number of switchings provide a practical tradeoff among the maneuvering time, fuel consumption, and performance robustness of uncertain flexible space structures.

Kinetics of interior loop formation in semiflexible chains.

PubMed

Hyeon, Changbong; Thirumalai, D

2006-03-14

Loop formation between monomers in the interior of semiflexible chains describes elementary events in biomolecular folding and DNA bending. We calculate analytically the interior distance distribution function for semiflexible chains using a mean field approach. Using the potential of mean force derived from the distance distribution function we present a simple expression for the kinetics of interior looping by adopting Kramers theory. For the parameters, that are appropriate for DNA, the theoretical predictions in comparison with the case are in excellent agreement with explicit Brownian dynamics simulations of wormlike chain (WLC) model. The interior looping times (tauIC) can be greatly altered in the cases when the stiffness of the loop differs from that of the dangling ends. If the dangling end is stiffer than the loop then tauIC increases for the case of the WLC with uniform persistence length. In contrast, attachment of flexible dangling ends enhances rate of interior loop formation. The theory also shows that if the monomers are charged and interact via screened Coulomb potential then both the cyclization (tauc) and interior looping (tauIC) times greatly increase at low ionic concentration. Because both tauc and tauIC are determined essentially by the effective persistence length [lp(R)] we computed lp(R) by varying the range of the repulsive interaction between the monomers. For short range interactions lp(R) nearly coincides with the bare persistence length which is determined largely by the backbone chain connectivity. This finding rationalizes the efficacy of describing a number of experimental observations (response of biopolymers to force and cyclization kinetics) in biomolecules using WLC model with an effective persistence length.

Analysis of virtual passive controllers for flexible space structures

NASA Technical Reports Server (NTRS)

Williams, Trevor W.

1992-01-01

The dynamics of flexible spacecraft are not usually well known before launch. This makes it important to develop controllers for such systems that can never be destabilized by perturbations in the structural model. Virtual passive controllers, or active vibration absorbers, possess this guaranteed stability property; they mimic a fictitious flexible structure attached to the true physical one. This report analyzes the properties of such controllers, and shows that disturbance absorption behavior can be naturally described in terms of a set of virtual zeros that they introduce into the closed-loop dynamics of the system. Based on this analysis, techniques are then derived for selecting the active vibration absorber internal parameters, i.e., the gain matrices of such controllers, so as to achieve specified control objectives. Finally, the effects on closed-loop stability of small delays in the feedback loop are investigated. Such delays would typically be introduced by a digital implementation of an active vibration absorber. It is shown that these delays only affect the real parts of the eigenvalues of a lightly-damped structure. Furthermore, it is only the high-frequency modes that are destabilized by delays; low-frequency modes are actually made more heavily damped. Eigenvalue perturbation methods are used to obtain accurate predictions of the critical delay at which a given system will become unstable; these methods also determine which mode is critical.

Closed Loop Experiment Manager (CLEM)-An Open and Inexpensive Solution for Multichannel Electrophysiological Recordings and Closed Loop Experiments.

PubMed

Hazan, Hananel; Ziv, Noam E

2017-01-01

There is growing need for multichannel electrophysiological systems that record from and interact with neuronal systems in near real-time. Such systems are needed, for example, for closed loop, multichannel electrophysiological/optogenetic experimentation in vivo and in a variety of other neuronal preparations, or for developing and testing neuro-prosthetic devices, to name a few. Furthermore, there is a need for such systems to be inexpensive, reliable, user friendly, easy to set-up, open and expandable, and possess long life cycles in face of rapidly changing computing environments. Finally, they should provide powerful, yet reasonably easy to implement facilities for developing closed-loop protocols for interacting with neuronal systems. Here, we survey commercial and open source systems that address these needs to varying degrees. We then present our own solution, which we refer to as Closed Loop Experiments Manager (CLEM). CLEM is an open source, soft real-time, Microsoft Windows desktop application that is based on a single generic personal computer (PC) and an inexpensive, general-purpose data acquisition board. CLEM provides a fully functional, user-friendly graphical interface, possesses facilities for recording, presenting and logging electrophysiological data from up to 64 analog channels, and facilities for controlling external devices, such as stimulators, through digital and analog interfaces. Importantly, it includes facilities for running closed-loop protocols written in any programming language that can generate dynamic link libraries (DLLs). We describe the application, its architecture and facilities. We then demonstrate, using networks of cortical neurons growing on multielectrode arrays (MEA) that despite its reliance on generic hardware, its performance is appropriate for flexible, closed-loop experimentation at the neuronal network level.

Catalytic Combustion for Ultra-Low NOx Hydrogen Turbines

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

Etemad, Shahrokh; Baird, Benjamin; Alavandi, Sandeep

2011-06-30

Precision Combustion, Inc., (PCI) in close collaboration with Solar Turbines, Incorporated, has developed and demonstrated a combustion system for hydrogen fueled turbines that reduces NOx to low single digit level while maintaining or improving current levels of efficiency and eliminating emissions of carbon dioxide. Full scale Rich Catalytic Hydrogen (RCH1) injector was developed and successfully tested at Solar Turbines, Incorporated high pressure test facility demonstrating low single digit NOx emissions for hydrogen fuel in the range of 2200F-2750F. This development work was based on initial subscale development for faster turnaround and reduced cost. Subscale testing provided promising results for 42%more » and 52% H2 with NOx emissions of less than 2 ppm with improved flame stability. In addition, catalytic reactor element testing for substrate oxidation, thermal cyclic injector testing to simulate start-stop operation in a gas turbine environment, and steady state 15 atm. operation testing were performed successfully. The testing demonstrated stable and robust catalytic element component life for gas turbine conditions. The benefit of the catalytic hydrogen combustor technology includes capability of delivering near-zero NOx without costly post-combustion controls and without requirement for added sulfur control. In addition, reduced acoustics increase gas turbine component life. These advantages advances Department of Energy (DOE’s) objectives for achievement of low single digit NOx emissions, improvement in efficiency vs. postcombustion controls, fuel flexibility, a significant net reduction in Integrated Gasification Combined Cycle (IGCC) system net capital and operating costs, and a route to commercialization across the power generation field from micro turbines to industrial and utility turbines.« less

On the feasibility of closed-loop control of intra-aortic balloon pumping

NASA Technical Reports Server (NTRS)

Clark, J. W., Jr.; Bourland, H. M.; Kane, G. R.

1973-01-01

A closed-loop control scheme for the control of intra-aortic balloon pumping has been developed and tested in dog experiments. A performance index reflecting the general objectives of balloon-assist pumping is developed and a modified steepest ascent control algorithm is utilized for the selection of a proper operating point for the balloon during its pumping cycle. This paper attempts to indicate the feasibility of closed-loop control of balloon pumping, and particularly its flexibility in achieving both diastolic augmentation of mean aortic pressure and control of the level of end-diastolic pressure (EDP) an important factor in reducing heart work.

Inherent conformational flexibility of F1-ATPase α-subunit.

PubMed

Hahn-Herrera, Otto; Salcedo, Guillermo; Barril, Xavier; García-Hernández, Enrique

2016-09-01

The core of F1-ATPase consists of three catalytic (β) and three noncatalytic (α) subunits, forming a hexameric ring in alternating positions. A wealth of experimental and theoretical data has provided a detailed picture of the complex role played by catalytic subunits. Although major conformational changes have only been seen in β-subunits, it is clear that α-subunits have to respond to these changes in order to be able to transmit information during the rotary mechanism. However, the conformational behavior of α-subunits has not been explored in detail. Here, we have combined unbiased molecular dynamics (MD) simulations and calorimetrically measured thermodynamic signatures to investigate the conformational flexibility of isolated α-subunits, as a step toward deepening our understanding of its function inside the α3β3 ring. The simulations indicate that the open-to-closed conformational transition of the α-subunit is essentially barrierless, which is ideal to accompany and transmit the movement of the catalytic subunits. Calorimetric measurements of the recombinant α-subunit from Geobacillus kaustophilus indicate that the isolated subunit undergoes no significant conformational changes upon nucleotide binding. Simulations confirm that the nucleotide-free and nucleotide-bound subunits show average conformations similar to that observed in the F1 crystal structure, but they reveal an increased conformational flexibility of the isolated α-subunit upon MgATP binding, which might explain the evolutionary conserved capacity of α-subunits to recognize nucleotides with considerable strength. Furthermore, we elucidate the different dependencies that α- and β-subunits show on Mg(II) for recognizing ATP. Copyright © 2016 Elsevier B.V. All rights reserved.

Energy Conversion Loop: A Testbed for Nuclear Hybrid Energy Systems Use in Biomass Pyrolysis

NASA Astrophysics Data System (ADS)

Verner, Kelley M.

Nuclear hybrid energy systems are a possible solution for contemporary energy challenges. Nuclear energy produces electricity without greenhouse gas emissions. However, nuclear power production is not as flexible as electrical grids demand and renewables create highly variable electricity. Nuclear hybrid energy systems are able to address both of these problems. Wasted heat can be used in processes such as desalination, hydrogen production, or biofuel production. This research explores the possible uses of nuclear process heat in bio-oil production via biomass pyrolysis. The energy conversion loop is a testbed designed and built to mimic the heat from a nuclear reactor. Small scale biomass pyrolysis experiments were performed and compared to results from the energy conversion loop tests to determine future pyrolysis experimentation with the energy conversion loop. Further improvements must be made to the energy conversion loop before more complex experiments may be performed. The current conditions produced by the energy conversion loop are not conducive for current biomass pyrolysis experimentation.tion.

Inhibition of a type III secretion system by the deletion of a short loop in one of its membrane proteins

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

Meshcheryakov, Vladimir A.; Kitao, Akio; Core Research for Evolutionary Science and Technology, Tokyo 113-0032

2013-05-01

Crystal structures of the cytoplasmic domain of FlhB from S. typhimurium and A. aeolicus were solved at 2.45 and 2.55 Å resolution, respectively. The deletion of a short loop in the cytoplasmic domain of Salmonella FlhB completely abolishes secretion by the type III secretion system. A molecular-dynamics simulation shows that the deletion of the loop affects the flexibility of a linker between the transmembrane and cytoplasmic domains of FlhB. The membrane protein FlhB is a highly conserved component of the flagellar secretion system. It is composed of an N-terminal transmembrane domain and a C-terminal cytoplasmic domain (FlhB{sub C}). Here, themore » crystal structures of FlhB{sub C} from Salmonella typhimurium and Aquifex aeolicus are described at 2.45 and 2.55 Å resolution, respectively. These flagellar FlhB{sub C} structures are similar to those of paralogues from the needle type III secretion system, with the major difference being in a linker that connects the transmembrane and cytoplasmic domains of FlhB. It was found that deletion of a short flexible loop in a globular part of Salmonella FlhB{sub C} leads to complete inhibition of secretion by the flagellar secretion system. Molecular-dynamics calculations demonstrate that the linker region is the most flexible part of FlhB{sub C} and that the deletion of the loop reduces this flexibility. These results are in good agreement with previous studies showing the importance of the linker in the function of FlhB and provide new insight into the relationship between the different parts of the FlhB{sub C} molecule.« less

Dynamics of knotted flexible loops settling under a constant force in a viscous fluid

NASA Astrophysics Data System (ADS)

Gruziel, Magdalena; Thyagarajan, Krishnan; Dietler, Giovanni; Szymczak, Piotr; Ekiel-Jezewska, Maria

2017-11-01

Sedimenting chains of metal beads knotted to a topology of a torus knot tend to stabilize in the form of extended, flat, tightly interwound loops. In this configuration they perform an oscillatory motion of the loops swirling periodically around each other. Stokesian dynamics simulations of elastic fibers confirm the long-lasting character of the traveling wave-like swirling motion and show also the accompanying rotation of the system. Moreover, the periodic motion shows striking resemblance to the stable solutions for the evolution of vortices of torus knot topology. Using the results of the simulations we study the dependence of the frequencies and sedimentation velocities on the length of the fiber. We also notice the dependence of the knot dynamics on the bending stiffness of the fiber and the knot rank. NCN-2015/19/D/ST8/03199.

Mining protein loops using a structural alphabet and statistical exceptionality

PubMed Central

2010-01-01

Background Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. Results We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 Å). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a

Mining protein loops using a structural alphabet and statistical exceptionality.

PubMed

Regad, Leslie; Martin, Juliette; Nuel, Gregory; Camproux, Anne-Claude

2010-02-04

Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 A). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of

Closed Loop Experiment Manager (CLEM)—An Open and Inexpensive Solution for Multichannel Electrophysiological Recordings and Closed Loop Experiments

PubMed Central

Hazan, Hananel; Ziv, Noam E.

2017-01-01

There is growing need for multichannel electrophysiological systems that record from and interact with neuronal systems in near real-time. Such systems are needed, for example, for closed loop, multichannel electrophysiological/optogenetic experimentation in vivo and in a variety of other neuronal preparations, or for developing and testing neuro-prosthetic devices, to name a few. Furthermore, there is a need for such systems to be inexpensive, reliable, user friendly, easy to set-up, open and expandable, and possess long life cycles in face of rapidly changing computing environments. Finally, they should provide powerful, yet reasonably easy to implement facilities for developing closed-loop protocols for interacting with neuronal systems. Here, we survey commercial and open source systems that address these needs to varying degrees. We then present our own solution, which we refer to as Closed Loop Experiments Manager (CLEM). CLEM is an open source, soft real-time, Microsoft Windows desktop application that is based on a single generic personal computer (PC) and an inexpensive, general-purpose data acquisition board. CLEM provides a fully functional, user-friendly graphical interface, possesses facilities for recording, presenting and logging electrophysiological data from up to 64 analog channels, and facilities for controlling external devices, such as stimulators, through digital and analog interfaces. Importantly, it includes facilities for running closed-loop protocols written in any programming language that can generate dynamic link libraries (DLLs). We describe the application, its architecture and facilities. We then demonstrate, using networks of cortical neurons growing on multielectrode arrays (MEA) that despite its reliance on generic hardware, its performance is appropriate for flexible, closed-loop experimentation at the neuronal network level. PMID:29093659

Improvement in the thermostability of chitosanase from Bacillus ehimensis by introducing artificial disulfide bonds.

PubMed

Sheng, Jun; Ji, Xiaofeng; Zheng, Yuan; Wang, Zhipeng; Sun, Mi

2016-10-01

To determine the effects of artificial disulfide bridges on the thermostability and catalytic efficiency of chitosanase EAG1. Five artificial disulfide bridges were designed based on the structural information derived from the three-dimensional (3-D) model of chitosanase EAG1. Two beneficial mutants (G113C/D116C, A207C-L286C) were located in the flexible surface loop region, whereas the similar substitutions introduced in α-helices regions had a negligible effect. Mut5, the most active mutant, had a longer half-life at 50 °C (from 10.5 to 69.3 min) and a 200 % higher catalytic efficiency (K cat/K m) than that of the original EAG1. The contribution of disulfide bridges to enzyme thermostability is mainly dependent on its location within the polypeptide chain. Strategical placement of a disulfide bridge in flexible regions provides a rigid support and creation of a protected microenvironment, which is effective in improving enzyme's thermostability and catalytic efficiency.

Two stage catalytic combustor

NASA Technical Reports Server (NTRS)

Alvin, Mary Anne (Inventor); Bachovchin, Dennis (Inventor); Smeltzer, Eugene E. (Inventor); Lippert, Thomas E. (Inventor); Bruck, Gerald J. (Inventor)

2010-01-01

A catalytic combustor (14) includes a first catalytic stage (30), a second catalytic stage (40), and an oxidation completion stage (49). The first catalytic stage receives an oxidizer (e.g., 20) and a fuel (26) and discharges a partially oxidized fuel/oxidizer mixture (36). The second catalytic stage receives the partially oxidized fuel/oxidizer mixture and further oxidizes the mixture. The second catalytic stage may include a passageway (47) for conducting a bypass portion (46) of the mixture past a catalyst (e.g., 41) disposed therein. The second catalytic stage may have an outlet temperature elevated sufficiently to complete oxidation of the mixture without using a separate ignition source. The oxidation completion stage is disposed downstream of the second catalytic stage and may recombine the bypass portion with a catalyst exposed portion (48) of the mixture and complete oxidation of the mixture. The second catalytic stage may also include a reticulated foam support (50), a honeycomb support, a tube support or a plate support.

A bacterial acyl aminoacyl peptidase couples flexibility and stability as a result of cold adaptation.

PubMed

Brocca, Stefania; Ferrari, Cristian; Barbiroli, Alberto; Pesce, Alessandra; Lotti, Marina; Nardini, Marco

2016-12-01

Life in cold environments requires an overall increase in the flexibility of macromolecular and supramolecular structures to allow biological processes to take place at low temperature. Conformational flexibility supports high catalytic rates of enzymes in the cold but in several cases is also a cause of instability. The three-dimensional structure of the psychrophilic acyl aminoacyl peptidase from Sporosarcina psychrophila (SpAAP) reported in this paper highlights adaptive molecular changes resulting in a fine-tuned trade-off between flexibility and stability. In its functional form SpAAP is a dimer, and an increase in flexibility is achieved through loosening of intersubunit hydrophobic interactions. The release of subunits from the quaternary structure is hindered by an 'arm exchange' mechanism, in which a tiny structural element at the N terminus of one subunit inserts into the other subunit. Mutants lacking the 'arm' are monomeric, inactive and highly prone to aggregation. Another feature of SpAAP cold adaptation is the enlargement of the tunnel connecting the exterior of the protein with the active site. Such a wide channel might compensate for the reduced molecular motions occurring in the cold and allow easy and direct access of substrates to the catalytic site, rendering transient movements between domains unnecessary. Thus, cold-adapted SpAAP has developed a molecular strategy unique within this group of proteins: it is able to enhance the flexibility of each functional unit while still preserving sufficient stability. Structural data are available in the Protein Data Bank under the accession number 5L8S. © 2016 Federation of European Biochemical Societies.

Catalytic efficiency and thermostability improvement of Suc2 invertase through rational site-directed mutagenesis.

PubMed

Mohandesi, Nooshin; Haghbeen, Kamahldin; Ranaei, Omid; Arab, Seyed Shahriar; Hassani, Sorour

2017-01-01

Engineering of invertases has come to attention because of increasing demand for possible applications of invertases in various industrial processes. Due to the known physicochemical properties, invertases from micro-organisms such as Saccharomyces cerevisiae carrying SUC2 gene are considered as primary models. To improve thermostability and catalytic efficiency of SUC2 invertase (SInv), six influential residues with Relative Solvent Accessibility<5% were selected through multiple-sequence alignments, molecular modelling, structural and computational analyses. Consequently, SInv and 5 mutants including three mutants with single point substitution [Mut1=P152V, Mut2=S85V and Mut3=K153F)], one mutant with two points [Mut4=S305V-N463V] and one mutant with three points [Mut5=S85V-K153F-T271V] were developed via site-directed mutagenesis and produced using Pichia pastoris as the host. Physicochemical studies on these enzymes indicated that the selected amino acids which were located in the active site region mainly influenced catalytic efficiency. The best improvement belonged to Mut1 (54% increase in K cat /K m ) and Mut3 exhibited the worst effect (90% increase in K m ). These results suggest that Pro152 and Lys153 play key role in preparation of the right substrate lodging in the active site of SInv. The best thermostability improvement (16%) was observed for Mut4 in which two hydrophilic residues located on the loops, far from the active site, were replaced by Valines. These results suggest that tactful simultaneous substitution of influential hydrophilic residues in both active site region and peripheral loops with hydrophobic amino acids could result in more thermostable invertases with enhanced catalytic efficiency. Copyright © 2016 Elsevier Inc. All rights reserved.

Control of large flexible systems via eigenvalue relocation

NASA Technical Reports Server (NTRS)

Denman, E. D.; Jeon, G. J.

1985-01-01

For the vibration control of large flexible systems, a control scheme by which the eigenvalues of the closed-loop systems are assigned to predetermined locations within the feasible region through velocity-only feedback is presented. Owing to the properties of second-order lambda-matrices and an efficient model decoupling technique, the control scheme makes it possible that selected modes are damped with the rest of the modes unchanged.

Tackling Critical Catalytic Residues in Helicobacter pylori l-Asparaginase

PubMed Central

Maggi, Maristella; Chiarelli, Laurent R; Valentini, Giovanna; Scotti, Claudia

2015-01-01

Bacterial asparaginases (amidohydrolases, EC 3.5.1.1) are important enzymes in cancer therapy, especially for Acute Lymphoblastic Leukemia. They are tetrameric enzymes able to catalyze the deamination of l-ASN and, to a variable extent, of l-GLN, on which leukemia cells are dependent for survival. In contrast to other known l-asparaginases, Helicobacter pylori CCUG 17874 type II enzyme (HpASNase) is cooperative and has a low affinity towards l-GLN. In this study, some critical amino acids forming the active site of HpASNase (T16, T95 and E289) have been tackled by rational engineering in the attempt to better define their role in catalysis and to achieve a deeper understanding of the peculiar cooperative behavior of this enzyme. Mutations T16E, T95D and T95H led to a complete loss of enzymatic activity. Mutation E289A dramatically reduced the catalytic activity of the enzyme, but increased its thermostability. Interestingly, E289 belongs to a loop that is very variable in l-asparaginases from the structure, sequence and length point of view, and which could be a main determinant of their different catalytic features. PMID:25826146

Tackling Critical Catalytic Residues in Helicobacter pylori L-Asparaginase.

PubMed

Maggi, Maristella; Chiarelli, Laurent R; Valentini, Giovanna; Scotti, Claudia

2015-03-27

Bacterial asparaginases (amidohydrolases, EC 3.5.1.1) are important enzymes in cancer therapy, especially for Acute Lymphoblastic Leukemia. They are tetrameric enzymes able to catalyze the deamination of L-ASN and, to a variable extent, of L-GLN, on which leukemia cells are dependent for survival. In contrast to other known L-asparaginases, Helicobacter pylori CCUG 17874 type II enzyme (HpASNase) is cooperative and has a low affinity towards L-GLN. In this study, some critical amino acids forming the active site of HpASNase (T16, T95 and E289) have been tackled by rational engineering in the attempt to better define their role in catalysis and to achieve a deeper understanding of the peculiar cooperative behavior of this enzyme. Mutations T16E, T95D and T95H led to a complete loss of enzymatic activity. Mutation E289A dramatically reduced the catalytic activity of the enzyme, but increased its thermostability. Interestingly, E289 belongs to a loop that is very variable in L-asparaginases from the structure, sequence and length point of view, and which could be a main determinant of their different catalytic features.

Reversible amorphization and the catalytically active state of crystalline Co3O4 during oxygen evolution

PubMed Central

Bergmann, Arno; Martinez-Moreno, Elias; Teschner, Detre; Chernev, Petko; Gliech, Manuel; de Araújo, Jorge Ferreira; Reier, Tobias; Dau, Holger; Strasser, Peter

2015-01-01

Water splitting catalysed by earth-abundant materials is pivotal for global-scale production of non-fossil fuels, yet our understanding of the active catalyst structure and reactivity is still insufficient. Here we report on the structurally reversible evolution of crystalline Co3O4 electrocatalysts during oxygen evolution reaction identified using advanced in situ X-ray techniques. At electrode potentials facilitating oxygen evolution, a sub-nanometre shell of the Co3O4 is transformed into an X-ray amorphous CoOx(OH)y which comprises di-μ-oxo-bridged Co3+/4+ ions. Unlike irreversible amorphizations, here, the formation of the catalytically-active layer is reversed by re-crystallization upon return to non-catalytic electrode conditions. The Co3O4 material thus combines the stability advantages of a controlled, stable crystalline material with high catalytic activity, thanks to the structural flexibility of its active amorphous oxides. We propose that crystalline oxides may be tailored for generating reactive amorphous surface layers at catalytic potentials, just to return to their stable crystalline state under rest conditions. PMID:26456525

Reversible amorphization and the catalytically active state of crystalline Co3O4 during oxygen evolution.

PubMed

Bergmann, Arno; Martinez-Moreno, Elias; Teschner, Detre; Chernev, Petko; Gliech, Manuel; de Araújo, Jorge Ferreira; Reier, Tobias; Dau, Holger; Strasser, Peter

2015-10-12

Water splitting catalysed by earth-abundant materials is pivotal for global-scale production of non-fossil fuels, yet our understanding of the active catalyst structure and reactivity is still insufficient. Here we report on the structurally reversible evolution of crystalline Co3O4 electrocatalysts during oxygen evolution reaction identified using advanced in situ X-ray techniques. At electrode potentials facilitating oxygen evolution, a sub-nanometre shell of the Co3O4 is transformed into an X-ray amorphous CoOx(OH)y which comprises di-μ-oxo-bridged Co(3+/4+) ions. Unlike irreversible amorphizations, here, the formation of the catalytically-active layer is reversed by re-crystallization upon return to non-catalytic electrode conditions. The Co3O4 material thus combines the stability advantages of a controlled, stable crystalline material with high catalytic activity, thanks to the structural flexibility of its active amorphous oxides. We propose that crystalline oxides may be tailored for generating reactive amorphous surface layers at catalytic potentials, just to return to their stable crystalline state under rest conditions.

A double-headed cathepsin B inhibitor devoid of warhead

PubMed Central

Schenker, Patricia; Alfarano, Pietro; Kolb, Peter; Caflisch, Amedeo; Baici, Antonio

2008-01-01

Most synthetic inhibitors of peptidases have been targeted to the active site for inhibiting catalysis through reversible competition with the substrate or by covalent modification of catalytic groups. Cathepsin B is unique among the cysteine peptidase for the presence of a flexible segment, known as the occluding loop, which can block the primed subsites of the substrate binding cleft. With the occluding loop in the open conformation cathepsin B acts as an endopeptidase, and it acts as an exopeptidase when the loop is closed. We have targeted the occluding loop of human cathepsin B at its surface, outside the catalytic center, using a high-throughput docking procedure. The aim was to identify inhibitors that would interact with the occluding loop thereby modulating enzyme activity without the help of chemical warheads against catalytic residues. From a large library of compounds, the in silico approach identified [2-[2-(2,4-dioxo-1,3-thiazolidin-3-yl)ethylamino]-2-oxoethyl] 2-(furan-2-carbonylamino) acetate, which fulfills the working hypothesis. This molecule possesses two distinct binding moieties and behaves as a reversible, double-headed competitive inhibitor of cathepsin B by excluding synthetic and protein substrates from the active center. The kinetic mechanism of inhibition suggests that the occluding loop is stabilized in its closed conformation, mainly by hydrogen bonds with the inhibitor, thus decreasing endoproteolytic activity of the enzyme. Furthermore, the dioxothiazolidine head of the compound sterically hinders binding of the C-terminal residue of substrates resulting in inhibition of the exopeptidase activity of cathepsin B in a physiopathologically relevant pH range. PMID:18796695

Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg2+ Bound Structure in the Presence of Monovalent Ions

PubMed Central

2015-01-01

The Varkud Satellite RNA contains a self-cleaving ribozyme that has been shown to function independently of its surroundings. This 160 nucleotide ribozyme adopts a catalytically active tertiary structure that includes a kissing hairpin complex formed by stem-loop I and stem-loop V (SLV). The five-nucleotide 5′-rUGACU loop of the isolated SLV has been shown to adopt a Mg2+-dependent U-turn structure by solution NMR. This U-turn hairpin is examined here by molecular dynamics simulations in the presence of monovalent and divalent ions. Simulations confirm on an all-atom level the hypotheses for the role of the Mg2+ ions in stabilizing the loop, as well as the role of the solvent exposed U700 base. Additionally, these simulations suggest the Mg2+-free stem-loop adopts a wide range of structures, including energetically favorable structures similar to the Mg2+-bound loop structure. We propose this structure is a “gatekeeper” or precursor to Mg2+ binding when those ions are present. PMID:26328924

Adaptive control strategies for flexible robotic arm

NASA Technical Reports Server (NTRS)

Bialasiewicz, Jan T.

1993-01-01

The motivation of this research came about when a neural network direct adaptive control scheme was applied to control the tip position of a flexible robotic arm. Satisfactory control performance was not attainable due to the inherent non-minimum phase characteristics of the flexible robotic arm tip. Most of the existing neural network control algorithms are based on the direct method and exhibit very high sensitivity if not unstable closed-loop behavior. Therefore a neural self-tuning control (NSTC) algorithm is developed and applied to this problem and showed promising results. Simulation results of the NSTC scheme and the conventional self-tuning (STR) control scheme are used to examine performance factors such as control tracking mean square error, estimation mean square error, transient response, and steady state response.

Hydrogen bonds between the alpha and beta subunits of the F1-ATPase allow communication between the catalytic site and the interface of the beta catch loop and the gamma subunit.

PubMed

Boltz, Kathryn W; Frasch, Wayne D

2006-09-19

F(1)-ATPase mutations in Escherichia coli that changed the strength of hydrogen bonds between the alpha and beta subunits in a location that links the catalytic site to the interface between the beta catch loop and the gamma subunit were examined. Loss of the ability to form the hydrogen bonds involving alphaS337, betaD301, and alphaD335 lowered the k(cat) of ATPase and decreased its susceptibility to Mg(2+)-ADP-AlF(n) inhibition, while mutations that maintain or strengthen these bonds increased the susceptibility to Mg(2+)-ADP-AlF(n) inhibition and lowered the k(cat) of ATPase. These data suggest that hydrogen bonds connecting alphaS337 to betaD301 and betaR323 and connecting alphaD335 to alphaS337 are important to transition state stabilization and catalytic function that may result from the proper alignment of catalytic site residues betaR182 and alphaR376 through the VISIT sequence (alpha344-348). Mutations betaD301E, betaR323K, and alphaR282Q changed the rate-limiting step of the reaction as determined by an isokinetic plot. Hydrophobic mutations of betaR323 decreased the susceptibility to Mg(2+)-ADP-AlF(n)() inhibition and lowered the number of interactions required in the rate-limiting step yet did not affect the k(cat) of ATPase, suggesting that betaR323 is important to transition state formation. The decreased rate of ATP synthase-dependent growth and decreased level of lactate-dependent quenching observed with alphaD335, betaD301, and alphaE283 mutations suggest that these residues may be important to the formation of an alternative set of hydrogen bonds at the interface of the alpha and beta subunits that permits the release of intersubunit bonds upon the binding of ATP, allowing gamma rotation in the escapement mechanism.

Vibration suppression in flexible structures via the sliding-mode control approach

NASA Technical Reports Server (NTRS)

Drakunov, S.; Oezguener, Uemit

1994-01-01

Sliding mode control became very popular recently because it makes the closed loop system highly insensitive to external disturbances and parameter variations. Sliding algorithms for flexible structures have been used previously, but these were based on finite-dimensional models. An extension of this approach for differential-difference systems is obtained. That makes if possible to apply sliding-mode control algorithms to the variety of nondispersive flexible structures which can be described as differential-difference systems. The main idea of using this technique for dispersive structures is to reduce the order of the controlled part of the system by applying an integral transformation. We can say that transformation 'absorbs' the dispersive properties of the flexible structure as the controlled part becomes dispersive.

Significance of the enzymatic properties of yeast S39A enolase to the catalytic mechanism.

PubMed

Brewer, J M; Glover, C V; Holland, M J; Lebioda, L

1998-04-02

The S39A mutant of yeast enolase (isozyme 1), prepared by site-directed mutagenesis, has a relative Vmax of 0.01% and an activation constant for Mg2+ ca. 10-fold higher, compared with native enzyme. It is correctly folded. There is little effect of solvent viscosity on activity. We think that the loop Ser36-His43 fails to move to the 'closed' position upon catalytic Mg2+ binding, weakening several electrostatic interactions involved in the mechanism.

On actuator placement for robust time-optimal control of uncertain flexible spacecraft

NASA Technical Reports Server (NTRS)

Wie, Bong; Sinha, Ravi; Liu, Qiang

1992-01-01

The problem of computing open-loop, on-off jet firing logic for flexible spacecraft in the face of plant modeling uncertainty is investigated. The primary control objective is to achieve a fast maneuvering time with a minimum of structural vibrations during and/or after a maneuver. This paper is also concerned with the problem of selecting a proper pair of jets for practical trade-offs among the maneuvering time, fuel consumption, structural mode excitation, and performance robustness. A time-optimal control problem subject to parameter robustness constraints is formulated. A three-mass-spring model of flexible spacecraft with a rigid-body mode and two flexible modes is used to illustrate the concept.

Structures of apo IRF-3 and IRF-7 DNA binding domains: effect of loop L1 on DNA binding

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

De Ioannes, Pablo; Escalante, Carlos R.; Aggarwal, Aneel K.

2013-11-20

Interferon regulatory factors IRF-3 and IRF-7 are transcription factors essential in the activation of interferon-{beta} (IFN-{beta}) gene in response to viral infections. Although, both proteins recognize the same consensus IRF binding site AANNGAAA, they have distinct DNA binding preferences for sites in vivo. The X-ray structures of IRF-3 and IRF-7 DNA binding domains (DBDs) bound to IFN-{beta} promoter elements revealed flexibility in the loops (L1-L3) and the residues that make contacts with the target sequence. To characterize the conformational changes that occur on DNA binding and how they differ between IRF family members, we have solved the X-ray structures ofmore » IRF-3 and IRF-7 DBDs in the absence of DNA. We found that loop L1, carrying the conserved histidine that interacts with the DNA minor groove, is disordered in apo IRF-3 but is ordered in apo IRF-7. This is reflected in differences in DNA binding affinities when the conserved histidine in loop L1 is mutated to alanine in the two proteins. The stability of loop L1 in IRF-7 derives from a unique combination of hydrophobic residues that pack against the protein core. Together, our data show that differences in flexibility of loop L1 are an important determinant of differential IRF-DNA binding.« less

A curved RNA helix incorporating an internal loop with G·A and A·A non-Watson–Crick base pairing

PubMed Central

Baeyens, Katrien J.; De Bondt, Hendrik L.; Pardi, Arthur; Holbrook, Stephen R.

1996-01-01

The crystal structure of the RNA dodecamer 5′-GGCC(GAAA)GGCC-3′ has been determined from x-ray diffraction data to 2.3-Å resolution. In the crystal, these oligomers form double helices around twofold symmetry axes. Four consecutive non-Watson–Crick base pairs make up an internal loop in the middle of the duplex, including sheared G·A pairs and novel asymmetric A·A pairs. This internal loop sequence produces a significant curvature and narrowing of the double helix. The helix is curved by 34° from end to end and the diameter is narrowed by 24% in the internal loop. A Mn2+ ion is bound directly to the N7 of the first guanine in the Watson–Crick region following the internal loop and the phosphate of the preceding residue. This Mn2+ location corresponds to a metal binding site observed in the hammerhead catalytic RNA. PMID:8917508

Raney nickel catalytic device

DOEpatents

O'Hare, Stephen A.

1978-01-01

A catalytic device for use in a conventional coal gasification process which includes a tubular substrate having secured to its inside surface by expansion a catalytic material. The catalytic device is made by inserting a tubular catalytic element, such as a tubular element of a nickel-aluminum alloy, into a tubular substrate and heat-treating the resulting composite to cause the tubular catalytic element to irreversibly expand against the inside surface of the substrate.

Speed-accuracy trade-off in skilled typewriting: decomposing the contributions of hierarchical control loops.

PubMed

Yamaguchi, Motonori; Crump, Matthew J C; Logan, Gordon D

2013-06-01

Typing performance involves hierarchically structured control systems: At the higher level, an outer loop generates a word or a series of words to be typed; at the lower level, an inner loop activates the keystrokes comprising the word in parallel and executes them in the correct order. The present experiments examined contributions of the outer- and inner-loop processes to the control of speed and accuracy in typewriting. Experiments 1 and 2 involved discontinuous typing of single words, and Experiments 3 and 4 involved continuous typing of paragraphs. Across experiments, typists were able to trade speed for accuracy but were unable to type at rates faster than 100 ms/keystroke, implying limits to the flexibility of the underlying processes. The analyses of the component latencies and errors indicated that the majority of the trade-offs were due to inner-loop processing. The contribution of outer-loop processing to the trade-offs was small, but it resulted in large costs in error rate. Implications for strategic control of automatic processes are discussed. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

Structural Basis for Inactivation of the Human Pyruvate Dehydrogenase Complex by Phosphorylation: Role of Disordered Phosphorylation Loops

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

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

2009-09-11

We report the crystal structures of the phosporylated pyruvate dehydrogenase (E1p) component of the human pyruvate dehydrogenase complex (PDC). The complete phosphorylation at Ser264-{alpha} (site 1) of a variant E1p protein was achieved using robust pyruvate dehydrogenase kinase 4 free of the PDC core. We show that unlike its unmodified counterpart, the presence of a phosphoryl group at Ser264-{alpha} prevents the cofactor thiamine diphosphate-induced ordering of the two loops carrying the three phosphorylation sites. The disordering of these phosphorylation loops is caused by a previously unrecognized steric clash between the phosphoryl group at site 1 and a nearby Ser266-{alpha}, whichmore » nullifies a hydrogen-bonding network essential for maintaining the loop conformations. The disordered phosphorylation loops impede the binding of lipoyl domains of the PDC core to E1p, negating the reductive acetylation step. This results in the disruption of the substrate channeling in the PDC, leading to the inactivation of this catalytic machine.« less

Plasticity of 150-loop in influenza neuraminidase explored by Hamiltonian replica exchange molecular dynamics simulations.

PubMed

Han, Nanyu; Mu, Yuguang

2013-01-01

Neuraminidase (NA) of influenza is a key target for antiviral inhibitors, and the 150-cavity in group-1 NA provides new insight in treating this disease. However, NA of 2009 pandemic influenza (09N1) was found lacking this cavity in a crystal structure. To address the issue of flexibility of the 150-loop, Hamiltonian replica exchange molecular dynamics simulations were performed on different groups of NAs. Free energy landscape calculated based on the volume of 150-cavity indicates that 09N1 prefers open forms of 150-loop. The turn A (residues 147-150) of the 150-loop is discovered as the most dynamical motif which induces the inter-conversion of this loop among different conformations. In the turn A, the backbone dynamic of residue 149 is highly related with the shape of 150-loop, thus can function as a marker for the conformation of 150-loop. As a contrast, the closed conformation of 150-loop is more energetically favorable in N2, one of group-2 NAs. The D147-H150 salt bridge is found having no correlation with the conformation of 150-loop. Instead the intimate salt bridge interaction between the 150 and 430 loops in N2 variant contributes the stabilizing factor for the closed form of 150-loop. The clustering analysis elaborates the structural plasticity of the loop. This enhanced sampling simulation provides more information in further structural-based drug discovery on influenza virus.

Plasticity of 150-Loop in Influenza Neuraminidase Explored by Hamiltonian Replica Exchange Molecular Dynamics Simulations

PubMed Central

Han, Nanyu; Mu, Yuguang

2013-01-01

Neuraminidase (NA) of influenza is a key target for antiviral inhibitors, and the 150-cavity in group-1 NA provides new insight in treating this disease. However, NA of 2009 pandemic influenza (09N1) was found lacking this cavity in a crystal structure. To address the issue of flexibility of the 150-loop, Hamiltonian replica exchange molecular dynamics simulations were performed on different groups of NAs. Free energy landscape calculated based on the volume of 150-cavity indicates that 09N1 prefers open forms of 150-loop. The turn A (residues 147–150) of the 150-loop is discovered as the most dynamical motif which induces the inter-conversion of this loop among different conformations. In the turn A, the backbone dynamic of residue 149 is highly related with the shape of 150-loop, thus can function as a marker for the conformation of 150-loop. As a contrast, the closed conformation of 150-loop is more energetically favorable in N2, one of group-2 NAs. The D147-H150 salt bridge is found having no correlation with the conformation of 150-loop. Instead the intimate salt bridge interaction between the 150 and 430 loops in N2 variant contributes the stabilizing factor for the closed form of 150-loop. The clustering analysis elaborates the structural plasticity of the loop. This enhanced sampling simulation provides more information in further structural-based drug discovery on influenza virus. PMID:23593372

Flexible manipulator control experiments and analysis

NASA Technical Reports Server (NTRS)

Yurkovich, S.; Ozguner, U.; Tzes, A.; Kotnik, P. T.

1987-01-01

Modeling and control design for flexible manipulators, both from an experimental and analytical viewpoint, are described. From the application perspective, an ongoing effort within the laboratory environment at the Ohio State University, where experimentation on a single link flexible arm is underway is described. Several unique features of this study are described here. First, the manipulator arm is slewed by a direct drive dc motor and has a rigid counterbalance appendage. Current experimentation is from two viewpoints: (1) rigid body slewing and vibration control via actuation with the hub motor, and (2) vibration suppression through the use of structure-mounted proof-mass actuation at the tip. Such an application to manipulator control is of interest particularly in design of space-based telerobotic control systems, but has received little attention to date. From an analytical viewpoint, parameter estimation techniques within the closed-loop for self-tuning adaptive control approaches are discussed. Also introduced is a control approach based on output feedback and frequency weighting to counteract effects of spillover in reduced-order model design. A model of the flexible manipulator based on experimental measurements is evaluated for such estimation and control approaches.

Enhanced performance of flexible dye-sensitized solar cells using flexible Ag@ZrO2/C nanofiber film as low-cost counter electrode

NASA Astrophysics Data System (ADS)

Yin, Xin; Xie, Xueyao; Song, Lixin; Zhai, Jifeng; Du, Pingfan; Xiong, Jie

2018-05-01

Highly flexible ZrO2/C nanofibers (NFs) coated with Ag nanoparticles (NPs) have been fabricated by a combination of electrospinning, carbonization and hydrothermal treatment. The obtained Ag@ZrO2/C NFs serve as low-cost counter electrodes (CEs) for flexible dye-sensitized solar cells (FDSSCs). A considerable power conversion efficiency of 4.77% is achieved, which is 27.9% higher than the η of ZrO2/C NFs CEs (3.73%) and reaches about 90% of that of Pt CE (5.26%). It can be ascribed to the fact that the introduction of Ag NPs provides a large number of accessible reaction sites for electrolyte ions to rapidly participate in the I3-/I- reaction. Moreover, the Ag NPs can produce synergistic effect with ZrO2/C NFs to further enhance transport capacity and electro-catalytic activity of the Ag@ZrO2/C film. Therefore, the considerable performance together with characteristics of simple preparation, low cost and flexibility suggests the Ag@ZrO2/C film can be promising candidate for the future generation of FDSSC.

Modeling and control for vibration suppression of a flexible smart structure

NASA Technical Reports Server (NTRS)

Dosch, J.; Leo, D.; Inman, D.

1993-01-01

Theoretical and experimental results of the modeling and control of a flexible ribbed antenna are presented. The antenna consists of eight flexible ribs which constitutes a smart antenna in the sense that the actuator and sensors are an integral part of the structure. The antenna exhibits closely space and repeated modes, thus multi-input multi-output (MIMO) control is necessary for controllability and observability of the structure. The structure also exhibits mode localization phenomenon and contains post buckled members making an accurate finite element model of the structure difficult to obtain. An identified MIMO minimum order model of the antenna is synthesized from identified single-input single-output (SISO) transfer functions curve fit in the frequency domain. The identified model is used to design a positive position feedback (PPF) controller that increases damping in all of the modes in the targeted frequency range. Due to the accuracy of the open loop model of the antenna, the closed loop response predicted by the identified model correlates well wtih experimental results.

Delineating Substrate Diversity of Disparate Short-Chain Dehydrogenase Reductase from Debaryomyces hansenii.

PubMed

Ghatak, Arindam; Bharatham, Nagakumar; Shanbhag, Anirudh P; Datta, Santanu; Venkatraman, Janani

2017-01-01

Short-chain dehydrogenase reductases (SDRs) have been utilized for catalyzing the reduction of many aromatic/aliphatic prochiral ketones to their respective alcohols. However, there is a paucity of data that elucidates their innate biological role and diverse substrate space. In this study, we executed an in-depth biochemical characterization and substrate space mapping (with 278 prochiral ketones) of an unannotated SDR (DHK) from Debaryomyces hansenii and compared it with structurally and functionally characterized SDR Synechococcus elongatus. PCC 7942 FabG to delineate its industrial significance. It was observed that DHK was significantly more efficient than FabG, reducing a diverse set of ketones albeit at higher conversion rates. Comparison of the FabG structure with a homology model of DHK and a docking of substrate to both structures revealed the presence of additional flexible loops near the substrate binding site of DHK. The comparative elasticity of the cofactor and substrate binding site of FabG and DHK was experimentally substantiated using differential scanning fluorimetry. It is postulated that the loop flexibility may account for the superior catalytic efficiency of DHK although the positioning of the catalytic triad is conserved.

Delineating Substrate Diversity of Disparate Short-Chain Dehydrogenase Reductase from Debaryomyces hansenii

PubMed Central

Ghatak, Arindam; Bharatham, Nagakumar; Shanbhag, Anirudh P.; Datta, Santanu; Venkatraman, Janani

2017-01-01

Short-chain dehydrogenase reductases (SDRs) have been utilized for catalyzing the reduction of many aromatic/aliphatic prochiral ketones to their respective alcohols. However, there is a paucity of data that elucidates their innate biological role and diverse substrate space. In this study, we executed an in-depth biochemical characterization and substrate space mapping (with 278 prochiral ketones) of an unannotated SDR (DHK) from Debaryomyces hansenii and compared it with structurally and functionally characterized SDR Synechococcus elongatus. PCC 7942 FabG to delineate its industrial significance. It was observed that DHK was significantly more efficient than FabG, reducing a diverse set of ketones albeit at higher conversion rates. Comparison of the FabG structure with a homology model of DHK and a docking of substrate to both structures revealed the presence of additional flexible loops near the substrate binding site of DHK. The comparative elasticity of the cofactor and substrate binding site of FabG and DHK was experimentally substantiated using differential scanning fluorimetry. It is postulated that the loop flexibility may account for the superior catalytic efficiency of DHK although the positioning of the catalytic triad is conserved. PMID:28107498

Closed Loop Software Control of the MIDEX Power System

NASA Technical Reports Server (NTRS)

Castell, Karen; Hernandez-Pellerano, Amri; Wismer, Margaret

1998-01-01

The Microwave Anisotropy Probe (MAP) is a follow-on to the Differential Microwave Radiometer (DMR) instrument on the Cosmic Background Explorer (COBE) spacecraft. The design and analysis of the MAP attitude control system (ACS) have been refined since work previously reported. The full spacecraft and instrument flexible model was developed in NASTRAN, and the resulting flexible modes were plotted and reduced with the Modal Significance Analysis Package (MSAP). The reduced-order model was used to perform the linear stability analysis for each control mode, the results of which are presented in this paper. Although MAP is going to a relatively disturbance-free Lissajous orbit around the Earth-Sun L2 Lagrange point, a detailed disturbance-torque analysis is required because there are only a small number of opportunities for momentum unloading each year. Environmental torques, including solar pressure at L2, and aerodynamic and gravity gradient during phasing-loop orbits, were calculated and simulated. A simple model of fuel slosh was derived to model its effect on the motion of the spacecraft. In addition, a thruster mode linear impulse controller was developed to meet the accuracy requirements of the phasing loop burns. A dynamic attitude error limiter was added to improve the performance of the ACS during large attitude slews. The result of this analysis is a stable ACS subsystem that meets all of the mission's requirements.

A family of asymptotically stable control laws for flexible robots based on a passivity approach

NASA Technical Reports Server (NTRS)

Lanari, Leonardo; Wen, John T.

1991-01-01

A general family of asymptotically stabilizing control laws is introduced for a class of nonlinear Hamiltonian systems. The inherent passivity property of this class of systems and the Passivity Theorem are used to show the closed-loop input/output stability which is then related to the internal state space stability through the stabilizability and detectability condition. Applications of these results include fully actuated robots, flexible joint robots, and robots with link flexibility.

Conformational flexibility in the catalytic triad revealed by the high-resolution crystal structure of Streptomyces erythraeus trypsin in an unliganded state

PubMed Central

Blankenship, Elise; Vukoti, Krishna; Miyagi, Masaru; Lodowski, David T.

2014-01-01

With more than 500 crystal structures determined, serine proteases make up greater than one-third of all proteases structurally examined to date, making them among the best biochemically and structurally characterized enzymes. Despite the numerous crystallographic and biochemical studies of trypsin and related serine proteases, there are still considerable shortcomings in the understanding of their catalytic mechanism. Streptomyces erythraeus trypsin (SET) does not exhibit autolysis and crystallizes readily at physiological pH; hence, it is well suited for structural studies aimed at extending the understanding of the catalytic mechanism of serine proteases. While X-ray crystallographic structures of this enzyme have been reported, no coordinates have ever been made available in the Protein Data Bank. Based on this, and observations on the extreme stability and unique properties of this particular trypsin, it was decided to crystallize it and determine its structure. Here, the first sub-angstrom resolution structure of an unmodified, unliganded trypsin crystallized at physiological pH is reported. Detailed structural analysis reveals the geometry and structural rigidity of the catalytic triad in the unoccupied active site and comparison to related serine proteases provides a context for interpretation of biochemical studies of catalytic mechanism and activity. PMID:24598752

Conformational flexibility in the catalytic triad revealed by the high-resolution crystal structure of Streptomyces erythraeus trypsin in an unliganded state.

PubMed

Blankenship, Elise; Vukoti, Krishna; Miyagi, Masaru; Lodowski, David T

2014-03-01

With more than 500 crystal structures determined, serine proteases make up greater than one-third of all proteases structurally examined to date, making them among the best biochemically and structurally characterized enzymes. Despite the numerous crystallographic and biochemical studies of trypsin and related serine proteases, there are still considerable shortcomings in the understanding of their catalytic mechanism. Streptomyces erythraeus trypsin (SET) does not exhibit autolysis and crystallizes readily at physiological pH; hence, it is well suited for structural studies aimed at extending the understanding of the catalytic mechanism of serine proteases. While X-ray crystallographic structures of this enzyme have been reported, no coordinates have ever been made available in the Protein Data Bank. Based on this, and observations on the extreme stability and unique properties of this particular trypsin, it was decided to crystallize it and determine its structure. Here, the first sub-angstrom resolution structure of an unmodified, unliganded trypsin crystallized at physiological pH is reported. Detailed structural analysis reveals the geometry and structural rigidity of the catalytic triad in the unoccupied active site and comparison to related serine proteases provides a context for interpretation of biochemical studies of catalytic mechanism and activity.

Packing loops into annular cavities.

PubMed

Sobral, T A; Gomes, M A F

2017-02-01

The continuous packing of a flexible rod in two-dimensional cavities yields a countable set of interacting domains that resembles nonequilibrium cellular systems and belongs to a new class of lightweight material. However, the link between the length of the rod and the number of domains requires investigation, especially in the case of non-simply connected cavities, where the number of avoided regions emulates an effective topological temperature. In the present article we report the results of an experiment of injection of a single flexible rod into annular cavities in order to find the total length needed to insert a given number of loops (domains of one vertex). Using an exponential model to describe the experimental data we quite minutely analyze the initial conditions, the intermediary behavior, and the tight packing limit. This method allows the observation of a new fluctuation phenomenon associated with instabilities in the dynamic evolution of the packing process. Furthermore, the fractal dimension of the global pattern enters the discussion under a novel point of view. A comparison with the classical problems of the random close packing of disks and jammed disk packings is made.

Packing loops into annular cavities

NASA Astrophysics Data System (ADS)

Sobral, T. A.; Gomes, M. A. F.

2017-02-01

The continuous packing of a flexible rod in two-dimensional cavities yields a countable set of interacting domains that resembles nonequilibrium cellular systems and belongs to a new class of lightweight material. However, the link between the length of the rod and the number of domains requires investigation, especially in the case of non-simply connected cavities, where the number of avoided regions emulates an effective topological temperature. In the present article we report the results of an experiment of injection of a single flexible rod into annular cavities in order to find the total length needed to insert a given number of loops (domains of one vertex). Using an exponential model to describe the experimental data we quite minutely analyze the initial conditions, the intermediary behavior, and the tight packing limit. This method allows the observation of a new fluctuation phenomenon associated with instabilities in the dynamic evolution of the packing process. Furthermore, the fractal dimension of the global pattern enters the discussion under a novel point of view. A comparison with the classical problems of the random close packing of disks and jammed disk packings is made.

Conformational Flexibility of Metazoan Fatty Acid Synthase Enables Catalysis

PubMed Central

Brignole, Edward J.; Smith, Stuart; Asturias, Francisco J.

2008-01-01

The metazoan cytosolic fatty acid synthase (FAS) contains all of the enzymes required for de novo fatty acid biosynthesis covalently linked around two reaction chambers. While the 3D architecture of FAS has been mostly defined, it is unclear how reaction intermediates can transfer between distant catalytic domains. Using single-particle electron microscopy we have identified a near continuum of conformations consistent with remarkable flexibility of FAS. The distribution of conformations was influenced by the presence of substrates and altered by different catalytic mutations suggesting a direct correlation between conformation and specific enzymatic activities. 3D reconstructions were interpreted by docking high-resolution structures of individual domains and illustrate that the substrate loading and condensation domains dramatically swing and swivel to access substrates within either reaction chamber. Concomitant rearrangement of the β-carbon processing domains synchronizes acyl-chain reduction in one chamber with acyl-chain elongation in the other. PMID:19151726

Water Stream "Loop-the-Loop"

ERIC Educational Resources Information Center

Jefimenko, Oleg

1974-01-01

Discusses the design of a modified loop-the-loop apparatus in which a water stream is used to illustrate centripetal forces and phenomena of high-velocity hydrodynamics. Included are some procedures of carrying out lecture demonstrations. (CC)

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.

Single-crystal-like, c-axis oriented BaTiO3 thin films with high-performance on flexible metal templates for ferroelectric applications

NASA Astrophysics Data System (ADS)

Shin, Junsoo; Goyal, Amit; Jesse, Stephen; Kim, Dae Ho

2009-06-01

Epitaxial, c-axis oriented BaTiO3 thin films were deposited using pulsed laser ablation on flexible, polycrystalline Ni alloy tape with biaxially textured oxide buffer multilayers. The high quality of epitaxial BaTiO3 thin films with P4mm group symmetry was confirmed by x-ray diffraction. The microscopic ferroelectric domain structure and the piezoelectric domain switching in these films were confirmed via spatially resolved piezoresponse mapping and local hysteresis loops. Macroscopic measurements demonstrate that the films have well-saturated hysteresis loops with a high remanent polarization of ˜11.5 μC/cm2. Such high-quality, single-crystal-like BaTiO3 films on low-cost, polycrystalline, flexible Ni alloy substrates are attractive for applications in flexible lead-free ferroelectric devices.

Modeling the Lac repressor-operator assembly: The influence of DNA looping on Lac repressor conformation

PubMed Central

Swigon, David; Coleman, Bernard D.; Olson, Wilma K.

2006-01-01

Repression of transcription of the Escherichia coli Lac operon by the Lac repressor (LacR) is accompanied by the simultaneous binding of LacR to two operators and the formation of a DNA loop. A recently developed theory of sequence-dependent DNA elasticity enables one to relate the fine structure of the LacR–DNA complex to a wide range of heretofore-unconnected experimental observations. Here, that theory is used to calculate the configuration and free energy of the DNA loop as a function of its length and base-pair sequence, its linking number, and the end conditions imposed by the LacR tetramer. The tetramer can assume two types of conformations. Whereas a rigid V-shaped structure is observed in the crystal, EM images show extended forms in which two dimer subunits are flexibly joined. Upon comparing our computed loop configurations with published experimental observations of permanganate sensitivities, DNase I cutting patterns, and loop stabilities, we conclude that linear DNA segments of short-to-medium chain length (50–180 bp) give rise to loops with the extended form of LacR and that loops formed within negatively supercoiled plasmids induce the V-shaped structure. PMID:16785444

Activation loop targeting strategy for design of receptor-interacting protein kinase 2 (RIPK2) inhibitors.

PubMed

Suebsuwong, Chalada; Pinkas, Daniel M; Ray, Soumya S; Bufton, Joshua C; Dai, Bing; Bullock, Alex N; Degterev, Alexei; Cuny, Gregory D

2018-02-15

Development of selective kinase inhibitors remains a challenge due to considerable amino acid sequence similarity among family members particularly in the ATP binding site. Targeting the activation loop might offer improved inhibitor selectivity since this region of kinases is less conserved. However, the strategy presents difficulties due to activation loop flexibility. Herein, we report the design of receptor-interacting protein kinase 2 (RIPK2) inhibitors based on pan-kinase inhibitor regorafenib that aim to engage basic activation loop residues Lys169 or Arg171. We report development of CSR35 that displayed >10-fold selective inhibition of RIPK2 versus VEGFR2, the target of regorafenib. A co-crystal structure of CSR35 with RIPK2 revealed a resolved activation loop with an ionic interaction between the carboxylic acid installed in the inhibitor and the side-chain of Lys169. Our data provides principle feasibility of developing activation loop targeting type II inhibitors as a complementary strategy for achieving improved selectivity. Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.

The dynamics and control of large flexible space structures - 12, supplement 11

NASA Technical Reports Server (NTRS)

Bainum, Peter M.; Reddy, A. S. S. R.; Li, Feiyue; Xu, Jianke

1989-01-01

The rapid 2-D slewing and vibrational control of the unsymmetrical flexible SCOLE (Spacecraft Control Laboratory Experiment) with multi-bounded controls is considered. Pontryagin's Maximum Principle is applied to the nonlinear equations of the system to derive the necessary conditions for the optimal control. The resulting two point boundary value problem is then solved by using the quasilinearization technique, and the near minimum time is obtained by sequentially shortening the slewing time until the controls are near the bang-bang type. The tradeoff between the minimum time and the minimum flexible amplitude requirements is discussed. The numerical results show that the responses of the nonlinear system are significantly different from those of the linearized system for rapid slewing. The SCOLE station-keeping closed loop dynamics are re-examined by employing a slightly different method for developing the equations of motion in which higher order terms in the expressions for the mast modal shape functions are now included. A preliminary study on the effect of actuator mass on the closed loop dynamics of large space systems is conducted. A numerical example based on a coupled two-mass two-spring system illustrates the effect of changes caused in the mass and stiffness matrices on the closed loop system eigenvalues. In certain cases the need for redesigning control laws previously synthesized, but not accounting for actuator masses, is indicated.

Loop technique.

PubMed

Seeburger, Joerg; Noack, Thilo; Winkfein, Michael; Ender, Joerg; Mohr, Friedrich Wilhelm

2010-01-01

The loop technique facilitates mitral valve repair for leaflet prolapse by implantation of Gore-Tex neo-chordae. The key feature of the technique is a premade bundle of four loops made out of one suture. The loops are available in different lengths ranging from 10 to 26 mm. After assessment of the ideal length of neo-chordae with a caliper the loops are then secured to the body of the papillary muscle over an additional felt pledget. In the following step, the free ends of the loops are distributed along the free margin of the prolapsing segment using one additional suture for each loop.

Control of nonlinear flexible space structures

NASA Astrophysics Data System (ADS)

Shi, Jianjun

With the advances made in computer technology and efficiency of numerical algorithms over last decade, the MPC strategies have become quite popular among control community. However, application of MPC or GPC to flexible space structure control has not been explored adequately in the literature. The work presented in this thesis primarily focuses on application of GPC to control of nonlinear flexible space structures. This thesis is particularly devoted to the development of various approximate dynamic models, design and assessment of candidate controllers, and extensive numerical simulations for a realistic multibody flexible spacecraft, namely, Jupiter Icy Moons Orbiter (JIMO)---a Prometheus class of spacecraft proposed by NASA for deep space exploratory missions. A stable GPC algorithm is developed for Multi-Input-Multi-Output (MIMO) systems. An end-point weighting (penalty) is used in the GPC cost function to guarantee the nominal stability of the closed-loop system. A method is given to compute the desired end-point state from the desired output trajectory. The methodologies based on Fake Algebraic Riccati Equation (FARE) and constrained nonlinear optimization, are developed for synthesis of state weighting matrix. This makes this formulation more practical. A stable reconfigurable GPC architecture is presented and its effectiveness is demonstrated on both aircraft as well as spacecraft model. A representative in-orbit maneuver is used for assessing the performance of various control strategies using various design models. Different approximate dynamic models used for analysis include linear single body flexible structure, nonlinear single body flexible structure, and nonlinear multibody flexible structure. The control laws evaluated include traditional GPC, feedback linearization-based GPC (FLGPC), reconfigurable GPC, and nonlinear dissipative control. These various control schemes are evaluated for robust stability and robust performance in the presence of

Engineering the thermostability of β-glucuronidase from Penicillium purpurogenum Li-3 by loop transplant.

PubMed

Feng, Xudong; Tang, Heng; Han, Beijia; Zhang, Liang; Lv, Bo; Li, Chun

2016-12-01

In this study, we proposed a loop transplant strategy to improve the thermostability of Penicillium purpurogenum Li-3 β-glucuronidase expressed in Escherichia coli (abbreviated to PGUS-E). Firstly, three unstable surface loops of PGUS-E to be replaced were identified with regards to B-factor values and in-depth structure analysis: loops 205-211, 258-263, and 25-31. Then, based on B-factor analysis, eight stable loops for substitution were selected from two typical thermophilic glycosidases which had low homology with PGUS-E (less than 25 %). By analyzing the common features of these stable loops, it was found that they shared a common residue skeleton DXXTX(X)R, based on this, three chimera loops were also manually designed: RSQTSND, RSSTQRD, and DDQTSR. All these loops were introduced to replace the unstable loops of PGUS-E by homology structure modeling, and only mutants with increased hydrogen bonds number and good compatibility with the local mutated region were further subjected to experimental verification. By using this strategy, 10 mutants were experimentally generated, among which three mutants, M1, M3, and M8, were obtained which showed 11.8, 3.3, and 9.4 times higher half-life at 70 °C than that of wild-type (8.5 min). Finally, the MD simulation indicated that the increased hydrogen bonds, decreased flexibility of N-terminal, and increased π-π stacking interaction were responsible for the improved thermostability.

Activation Loop Dynamics Determine the Different Catalytic Efficiencies of B Cell- and T Cell-Specific Tec Kinases

PubMed Central

Joseph, Raji E.; Kleino, Iivari; Wales, Thomas E.; Xie, Qian; Fulton, D. Bruce; Engen, John R.; Berg, Leslie J.; Andreotti, Amy H.

2014-01-01

Itk and Btk are nonreceptor tyrosine kinases of the Tec family that signal downstream of the T cell receptor (TCR) and B cell receptor (BCR), respectively. Despite their high sequence similarity and related signaling roles, Btk is a substantially more active kinase than Itk. We showed that substitution of six of the 619 amino acid residues of Itk with those of Btk was sufficient to completely switch the activities of Itk and Btk. The substitutions responsible for the swap in activity are all localized to the activation segment of the kinase domain. Nuclear magnetic resonance and hydrogen-deuterium exchange mass spectrometry analyses revealed that Itk and Btk had distinct protein dynamics in this region, which could explain the observed differences in catalytic efficiency between these kinases. Introducing Itk with enhanced activity into T cells led to enhanced and prolonged TCR signaling compared to that in cells with wild-type Itk. These findings imply that evolutionary pressures have led to Tec kinases having distinct enzymatic properties depending on the cellular context. We suggest that the weaker catalytic activities observed for T cell–specific kinases is one mechanism to regulate cellular activation and prevent aberrant immune responses. PMID:23982207

Evidence That GH115 α-Glucuronidase Activity, Which Is Required to Degrade Plant Biomass, Is Dependent on Conformational Flexibility*

PubMed Central

Rogowski, Artur; Baslé, Arnaud; Farinas, Cristiane S.; Solovyova, Alexandra; Mortimer, Jennifer C.; Dupree, Paul; Gilbert, Harry J.; Bolam, David N.

2014-01-01

The microbial degradation of the plant cell wall is an important biological process that is highly relevant to environmentally significant industries such as the bioenergy and biorefining sectors. A major component of the wall is glucuronoxylan, a β1,4-linked xylose polysaccharide that is decorated with α-linked glucuronic and/or methylglucuronic acid (GlcA/MeGlcA). Recently three members of a glycoside hydrolase family, GH115, were shown to hydrolyze MeGlcA side chains from the internal regions of xylan, an activity that has not previously been described. Here we show that a dominant member of the human microbiota, Bacteroides ovatus, contains a GH115 enzyme, BoAgu115A, which displays glucuronoxylan α-(4-O-methyl)-glucuronidase activity. The enzyme is significantly more active against substrates in which the xylose decorated with GlcA/MeGlcA is flanked by one or more xylose residues. The crystal structure of BoAgu115A revealed a four-domain protein in which the active site, comprising a pocket that abuts a cleft-like structure, is housed in the second domain that adopts a TIM barrel-fold. The third domain, a five-helical bundle, and the C-terminal β-sandwich domain make inter-chain contacts leading to protein dimerization. Informed by the structure of the enzyme in complex with GlcA in its open ring form, in conjunction with mutagenesis studies, the potential substrate binding and catalytically significant amino acids were identified. Based on the catalytic importance of residues located on a highly flexible loop, the enzyme is required to undergo a substantial conformational change to form a productive Michaelis complex with glucuronoxylan. PMID:24214982

Flexible Airspace Management (FAM) Research 2010 Human-in-the-Loop Simulation

NASA Technical Reports Server (NTRS)

Lee, Paul U.; Brasil, Connie; Homola, Jeffrey; Kessell, Angela; Prevot, Thomas; Smith, Nancy

2011-01-01

A human-in-the-Ioop (HITL) simulation was conducted to assess potential user and system benefits of Flexible Airspace Management (FAM) concept, as well as designing role definitions, procedures, and tools to support the FAM operations in the mid-term High Altitude Airspace (HAA) environment. The study evaluated the benefits and feasibility of flexible airspace reconfiguration in response to traffic overload caused by weather deviations, and compared them to those in a baseline condition without the airspace reconfiguration. The test airspace consisted of either four sectors in one Area of Specialization or seven sectors across two Areas. The test airspace was assumed to be at or above FL340 and fully equipped Vvith data communications (Data Comm). Other assumptions were consistent with those of the HAA concept. Overall, results showed that FAM operations with multiple Traffic Management Coordinators, Area Supervisors, and controllers worked remarkably well. The results showed both user and system benefits, some of which include the increased throughput, decreased flight distance, more manageable sector loads, and better utilized airspace. Also, the roles, procedures, airspace designs, and tools were all very well received. Airspace configuration options that resulted from a combination of algorithm-generated airspace configurations with manual modifications were well acceptec and posed little difficuIty and/or workload during airspace reconfiguration process. The results suggest a positive impact of FAM operations in HAA. Further investigation would be needed to evaluate if the benefits and feasibility would extend in either non-HAA or mixed equipage environment.

Rich catalytic injection

DOEpatents

Veninger, Albert [Coventry, CT

2008-12-30

A gas turbine engine includes a compressor, a rich catalytic injector, a combustor, and a turbine. The rich catalytic injector includes a rich catalytic device, a mixing zone, and an injection assembly. The injection assembly provides an interface between the mixing zone and the combustor. The injection assembly can inject diffusion fuel into the combustor, provides flame aerodynamic stabilization in the combustor, and may include an ignition device.

Mapping flexible protein domains at subnanometer resolution with the atomic force microscope.

PubMed

Müller, D J; Fotiadis, D; Engel, A

1998-06-23

The mapping of flexible protein domains with the atomic force microscope is reviewed. Examples discussed are the bacteriorhodopsin from Halobacterium salinarum, the head-tail-connector from phage phi29, and the hexagonally packed intermediate layer from Deinococcus radiodurans which all were recorded in physiological buffer solution. All three proteins undergo reversible structural changes that are reflected in standard deviation maps calculated from aligned topographs of individual protein complexes. Depending on the lateral resolution (up to 0.8 nm) flexible surface regions can ultimately be correlated with individual polypeptide loops. In addition, multivariate statistical classification revealed the major conformations of the protein surface.

Development Specification for the Portable Life Support System (PLSS) Thermal Loop Pump

NASA Technical Reports Server (NTRS)

Anchondo, Ian; Campbell, Colin

2017-01-01

The AEMU Thermal Loop Pump Development Specification establishes the requirements for design, performance, and testing of the Water Pump as part of the Thermal System of the Advanced Portable Life Support System (PLSS). It is envisioned that the Thermal Loop Pump is a positive displacement pump that provides a repeatable volume of flow against a given range of back-pressures provided by the various applications. The intention is to operate the pump at a fixed speed for the given application. The primary system is made up of two identical and redundant pumps of which only one is in operation at given time. The Auxiliary Loop Pump is an identical pump design to the primary pumps but is operated at half the flow rate. Inlet positive pressure to the pumps is provided by the upstream Flexible Supply Assembly (FSA-431 and FSA-531) which are physically located inside the suit volume and pressurized by suit pressure. An integrated relief valve, placed in parallel to the pump's inlet and outlet protects the pump and loop from over-pressurization. An integrated course filter is placed upstream of the pump's inlet to provide filtration and prevent potential debris from damaging the pump.

Flexible Connectors between Capsomer Subunits that Regulate Capsid Assembly.

PubMed

Hasek, Mary L; Maurer, Joshua B; Hendrix, Roger W; Duda, Robert L

2017-08-04

Viruses build icosahedral capsids of specific size and shape by regulating the spatial arrangement of the hexameric and pentameric protein capsomers in the growing shell during assembly. In the T=7 capsids of Escherichia coli bacteriophage HK97 and other phages, 60 capsomers are hexons, while the rest are pentons that are correctly positioned during assembly. Assembly of the HK97 capsid to the correct size and shape has been shown to depend on specific ionic contacts between capsomers. We now describe additional ionic interactions within capsomers that also regulate assembly. Each is between the long hairpin, the "E-loop," that extends from one subunit to the adjacent subunit within the same capsomer. Glutamate E153 on the E-loop and arginine R210 on the adjacent subunit's backbone alpha-helix form salt bridges in hexamers and pentamers. Mutations that disrupt these salt bridges were lethal for virus production, because the mutant proteins assembled into tubes or sheets instead of capsids. X-ray structures show that the E153-R210 links are flexible and maintained during maturation despite radical changes in capsomer shape. The E153-R210 links appear to form early in assembly to enable capsomers to make programmed changes in their shape during assembly. The links also prevent flattening of capsomers and premature maturation. Mutant phenotypes and modeling support an assembly model in which flexible E153-R210 links mediate capsomer shape changes that control where pentons are placed to create normal-sized capsids. The E-loop may be conserved in other systems in order to play similar roles in regulating assembly. Copyright © 2017 Elsevier Ltd. All rights reserved.

Control and trajectory design of a highly flexible air vehicle with a distributed sensing architecture

NASA Astrophysics Data System (ADS)

Pachikara, Abraham James

Next generational aircraft are becoming very flexible due to efforts to reduce weight and increase aerodynamic efficiency. As a result, flight control systems and trajectories that were designed with traditional rigid body assumptions may no longer become valid. When an aircraft becomes more flexible, the shape of the aircraft can deform significantly due to the aeroservoelastic dynamics. No longer are few sensors located at the CG and elsewhere will be enough to maximize performance. Instead, a full suite of sensors will be needed all throughout the aircraft to accurately measure the complete aerodynamic distribution and dynamics. First, a parametric study will be conducted to understand how flexibility impacts both the open-loop and closed-loop dynamics of a generic micro air vehicle (MAV). Once the impact of flexibility on the MAV's aeroservoelastic dynamics is well understood, an aeroservoelastic flight controller will be designed that leverages a "Fly-By-Feel" sensor architecture. A sensor architecture will be developed that uses several sensors to estimate the MAV's full aerodynamic and inertial distribution along with inertial sensors at the CG. A modal filtering approach will be used for the relevant sensor management and to extract useful modal characteristics from the sensor data. Once that is done, a controller will be designed for maneuver tracking. Once a flight controller has been designed, a set of representative motion primitives for the MAV can be developed that model how the aircraft moves for trajectory generation. Then trajectories can be developed for the flexible vehicle. Analysis will then be conducted to understand how flexibility impacts the creation of trajectories and MAV performance metrics.

Digital tracking loops for a programmable digital modem

NASA Technical Reports Server (NTRS)

Poklemba, John J.

1992-01-01

In this paper, an analysis and hardware emulation of the tracking loops for a very flexible programmable digital modem (PDM) will be presented. The modem is capable of being programmed for 2, 4, 8, 16-PSK, 16-QAM, MSK, and Offset-QPSK modulation schemes over a range of data rates from 2.34 to 300 Mbps with programmable spectral occupancy from 1.2 to 1.8 times the symbol rate; these operational parameters are executable in burst or continuous mode. All of the critical processing in both the modulator and demodulator is done at baseband with very high-speed digital hardware and memory. Quadrature analog front-ends are used for translation between baseband and the IF center frequency. The modulator is based on a table lookup approach, where precomputed samples are stored in memory and clocked out according to the incoming data pattern. The sample values are predistorted to counteract the effects of the other filtering functions in the link as well as any transmission impairments. The demodulator architecture was adapted from a joint estimator-detector (JED) mathematical analysis. Its structure is applicable to most signalling formats that can be represented in a two-dimensional space. The JED realization uses interdependent, mutually aiding tracking loops with post-detection data feedback. To expedite and provide for more reliable synchronization, initial estimates for these loops are computed in a parallel acquisition processor. The cornerstone of the demodulator realization is the pre-averager received data filter which allows operation over a broad range of data rates without any hardware changes and greatly simplifies the implementation complexity. The emulation results confirmed tracking loop operation over the entire range of operational parameters listed above, as well as the capability of achieving and maintaining synchronization at BER's in excess of 10(exp -1). The emulation results also showed very close agreement with the tracking loop analysis, and

A passivity based control methodology for flexible joint robots with application to a simplified shuttle RMS arm

NASA Technical Reports Server (NTRS)

Sicard, Pierre; Wen, John T.

1991-01-01

The main goal is to develop a general theory for the control of flexible robots, including flexible joint robots, flexible link robots, rigid bodies with flexible appendages, etc. As part of the validation, the theory is applied to the control law development for a test example which consists of a three-link arm modeled after the shoulder yaw joint of the space shuttle remote manipulator system (RMS). The performance of the closed loop control system is then compared with the performance of the existing RMS controller to demonstrate the effectiveness of the proposed approach. The theoretical foundation of this new approach to the control of flexible robots is presented and its efficacy is demonstrated through simulation results on the three-link test arm.

Dynamic interplay between catalytic and lectin domains of GalNAc-transferases modulates protein O-glycosylation

NASA Astrophysics Data System (ADS)

Lira-Navarrete, Erandi; de Las Rivas, Matilde; Compañón, Ismael; Pallarés, María Carmen; Kong, Yun; Iglesias-Fernández, Javier; Bernardes, Gonçalo J. L.; Peregrina, Jesús M.; Rovira, Carme; Bernadó, Pau; Bruscolini, Pierpaolo; Clausen, Henrik; Lostao, Anabel; Corzana, Francisco; Hurtado-Guerrero, Ramon

2015-05-01

Protein O-glycosylation is controlled by polypeptide GalNAc-transferases (GalNAc-Ts) that uniquely feature both a catalytic and lectin domain. The underlying molecular basis of how the lectin domains of GalNAc-Ts contribute to glycopeptide specificity and catalysis remains unclear. Here we present the first crystal structures of complexes of GalNAc-T2 with glycopeptides that together with enhanced sampling molecular dynamics simulations demonstrate a cooperative mechanism by which the lectin domain enables free acceptor sites binding of glycopeptides into the catalytic domain. Atomic force microscopy and small-angle X-ray scattering experiments further reveal a dynamic conformational landscape of GalNAc-T2 and a prominent role of compact structures that are both required for efficient catalysis. Our model indicates that the activity profile of GalNAc-T2 is dictated by conformational heterogeneity and relies on a flexible linker located between the catalytic and the lectin domains. Our results also shed light on how GalNAc-Ts generate dense decoration of proteins with O-glycans.

Ca-asp bound X-ray structure and inhibition of Bacillus anthracis dihydroorotase (DHOase).

PubMed

Rice, Amy J; Lei, Hao; Santarsiero, Bernard D; Lee, Hyun; Johnson, Michael E

2016-10-01

Dihydroorotase (DHOase) is the third enzyme in the de novo pyrimidine synthesis pathway and is responsible for the reversible cyclization of carbamyl-aspartate (Ca-asp) to dihydroorotate (DHO). DHOase is further divided into two classes based on several structural characteristics, one of which is the length of the flexible catalytic loop that interacts with the substrate, Ca-asp, regulating the enzyme activity. Here, we present the crystal structure of Class I Bacillus anthracis DHOase with Ca-asp in the active site, which shows the peptide backbone of glycine in the shorter loop forming the necessary hydrogen bonds with the substrate, in place of the two threonines found in Class II DHOases. Despite the differences in the catalytic loop, the structure confirms that the key interactions between the substrate and active site residues are similar between Class I and Class II DHOase enzymes, which we further validated by mutagenesis studies. B. anthracis DHOase is also a potential antibacterial drug target. In order to identify prospective inhibitors, we performed high-throughput screening against several libraries using a colorimetric enzymatic assay and an orthogonal fluorescence thermal binding assay. Surface plasmon resonance was used for determining binding affinity (KD) and competition analysis with Ca-asp. Our results highlight that the primary difference between Class I and Class II DHOase is the catalytic loop. We also identify several compounds that can potentially be further optimized as potential B. anthracis inhibitors. Copyright © 2016 Elsevier Ltd. All rights reserved.

A classical model for closed-loop diagrams of binary liquid mixtures

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

Schnitzler, J.v.; Prausnitz, J.M.

1994-03-01

A classical lattice model for closed-loop temperature-composition phase diagrams has been developed. It considers the effect of specific interactions, such as hydrogen bonding, between dissimilar components. This van Laar-type model includes a Flory-Huggins term for the excess entropy of mixing. It is applied to several liquid-liquid equilibria of nonelectrolytes, where the molecules of the two components differ in size. The model is able to represent the observed data semi-quantitatively, but in most cases it is not flexible enough to predict all parts of the closed loop quantitatively. The ability of the model to represent different binary systems is discussed. Finally,more » attention is given to a correction term, concerning the effect of concentration fluctuations near the upper critical solution temperature.« less

The role of proline substitutions within flexible regions on thermostability of luciferase.

PubMed

Yu, Haoran; Zhao, Yang; Guo, Chao; Gan, Yiru; Huang, He

2015-01-01

Improving the stability of firefly luciferase has been a critical issue for its wider industrial applications. Studies about hyperthermophile proteins show that flexibility could be an effective indicator to find out weak spots to engineering thermostability of proteins. However, the relationship among flexibility, activity and stability in most of proteins is unclear. Proline is the most rigid residue and can be introduced to rigidify flexible regions to enhance thermostability of proteins. We firstly apply three different methods, molecular dynamics (MD) simulation, B-FITTER and framework rigidity optimized dynamics algorithm (FRODA) to determine the flexible regions of Photinus pyralis luciferase: Fragment 197-207; Fragment 471-481 and Fragment 487-495. Then, introduction of proline is used to rigidify these flexible regions. Two mutants D476P and H489P within most flexible regions are finally designed. In the results, H489P mutant shows improved thermostability while maintaining its catalytic efficiency compared to that of wild type luciferase. Flexibility analysis confirms that the overall rigidity and local rigidity of H489P mutant are greatly strengthened. D476P mutant shows decreased thermosatbility and the reason for this is elucidated at the molecular level. S307P mutation is randomly chosen outside the flexible regions as a control. Thermostability analysis shows that S307P mutation has decreased kinetic stability and enhanced thermodynamic stability. Copyright © 2014 Elsevier B.V. All rights reserved.

Clean catalytic combustor program

NASA Technical Reports Server (NTRS)

Ekstedt, E. E.; Lyon, T. F.; Sabla, P. E.; Dodds, W. J.

1983-01-01

A combustor program was conducted to evolve and to identify the technology needed for, and to establish the credibility of, using combustors with catalytic reactors in modern high-pressure-ratio aircraft turbine engines. Two selected catalytic combustor concepts were designed, fabricated, and evaluated. The combustors were sized for use in the NASA/General Electric Energy Efficient Engine (E3). One of the combustor designs was a basic parallel-staged double-annular combustor. The second design was also a parallel-staged combustor but employed reverse flow cannular catalytic reactors. Subcomponent tests of fuel injection systems and of catalytic reactors for use in the combustion system were also conducted. Very low-level pollutant emissions and excellent combustor performance were achieved. However, it was obvious from these tests that extensive development of fuel/air preparation systems and considerable advancement in the steady-state operating temperature capability of catalytic reactor materials will be required prior to the consideration of catalytic combustion systems for use in high-pressure-ratio aircraft turbine engines.

Steam reformer with catalytic combustor

DOEpatents

Voecks, Gerald E.

1990-03-20

A steam reformer is disclosed having an annular steam reforming catalyst bed formed by concentric cylinders and having a catalytic combustor located at the center of the innermost cylinder. Fuel is fed into the interior of the catalytic combustor and air is directed at the top of the combustor, creating a catalytic reaction which provides sufficient heat so as to maintain the catalytic reaction in the steam reforming catalyst bed. Alternatively, air is fed into the interior of the catalytic combustor and a fuel mixture is directed at the top. The catalytic combustor provides enhanced radiant and convective heat transfer to the reformer catalyst bed.

Steam reformer with catalytic combustor

NASA Technical Reports Server (NTRS)

Voecks, Gerald E. (Inventor)

1990-01-01

A steam reformer is disclosed having an annular steam reforming catalyst bed formed by concentric cylinders and having a catalytic combustor located at the center of the innermost cylinder. Fuel is fed into the interior of the catalytic combustor and air is directed at the top of the combustor, creating a catalytic reaction which provides sufficient heat so as to maintain the catalytic reaction in the steam reforming catalyst bed. Alternatively, air is fed into the interior of the catalytic combustor and a fuel mixture is directed at the top. The catalytic combustor provides enhanced radiant and convective heat transfer to the reformer catalyst bed.

A flexible and miniaturized hair dye based photodetector via chemiluminescence pathway.

PubMed

Lin, Ching-Chang; Sun, Da-Shiuan; Lin, Ya-Lin; Tsai, Tsung-Tso; Cheng, Chieh; Sun, Wen-Hsien; Ko, Fu-Hsiang

2017-04-15

A flexible and miniaturized metal semiconductor metal (MSM) biomolecular photodetector was developed as the core photocurrent system through chemiluminescence for hydrogen peroxide sensing. The flexible photocurrent sensing system was manufactured on a 30-µm-thick crystalline silicon chip by chemical etching process, which produced a flexible silicon chip. A surface texturization design on the flexible device enhanced the light-trapping effect and minimized reflectivity losses from the incident light. The model protein streptavidin bound to horseradish peroxidase (HRP) was successfully immobilized onto the sensor surface through high-affinity conjugation with biotin. The luminescence reaction occurred with luminol, hydrogen peroxide and HRP enzyme, and the emission of light from the catalytic reaction was detected by underlying flexible photodetector. The chemiluminescence in the miniaturized photocurrent sensing system was successfully used to determine the hydrogen peroxide concentration in real-time analyses. The hydrogen peroxide detection limit of the flexible MSM photodetector was 2.47mM. The performance of the flexible MSM photodetector maintained high stability under bending at various bending radii. Moreover, for concave bending, a significant improvement in detection signal intensity (14.5% enhancement compared with a flat configuration) was observed because of the increased photocurrent, which was attributed to enhancement of light trapping. Additionally, this detector was used to detect hydrogen peroxide concentrations in commercial hair dye products, which is a significant issue in the healthcare field. The development of this novel, flexible and miniaturized MSM biomolecular photodetector with excellent mechanical flexibility and high sensitivity demonstrates the applicability of this approach to future wearable sensor development efforts. Copyright © 2016 Elsevier B.V. All rights reserved.

Reduced modeling of flexible structures for decentralized control

NASA Technical Reports Server (NTRS)

Yousuff, A.; Tan, T. M.; Bahar, L. Y.; Konstantinidis, M. F.

1986-01-01

Based upon the modified finite element-transfer matrix method, this paper presents a technique for reduced modeling of flexible structures for decentralized control. The modeling decisions are carried out at (finite-) element level, and are dictated by control objectives. A simply supported beam with two sets of actuators and sensors (linear force actuator and linear position and velocity sensors) is considered for illustration. In this case, it is conjectured that the decentrally controlled closed loop system is guaranteed to be at least marginally stable.

Renormalization of loop functions for all loops

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

Brandt, R.A.; Neri, F.; Sato, M.

1981-08-15

It is shown that the vacuum expectation values W(C/sub 1/,xxx, C/sub n/) of products of the traces of the path-ordered phase factors P exp(igcontour-integral/sub C/iA/sub ..mu../(x)dx/sup ..mu../) are multiplicatively renormalizable in all orders of perturbation theory. Here A/sub ..mu../(x) are the vector gauge field matrices in the non-Abelian gauge theory with gauge group U(N) or SU(N), and C/sub i/ are loops (closed paths). When the loops are smooth (i.e., differentiable) and simple (i.e., non-self-intersecting), it has been shown that the generally divergent loop functions W become finite functions W when expressed in terms of the renormalized coupling constant and multipliedmore » by the factors e/sup -K/L(C/sub i/), where K is linearly divergent and L(C/sub i/) is the length of C/sub i/. It is proved here that the loop functions remain multiplicatively renormalizable even if the curves have any finite number of cusps (points of nondifferentiability) or cross points (points of self-intersection). If C/sub ..gamma../ is a loop which is smooth and simple except for a single cusp of angle ..gamma.., then W/sub R/(C/sub ..gamma../) = Z(..gamma..)W(C/sub ..gamma../) is finite for a suitable renormalization factor Z(..gamma..) which depends on ..gamma.. but on no other characteristic of C/sub ..gamma../. This statement is made precise by introducing a regularization, or via a loop-integrand subtraction scheme specified by a normalization condition W/sub R/(C-bar/sub ..gamma../) = 1 for an arbitrary but fixed loop C-bar/sub ..gamma../. Next, if C/sub ..beta../ is a loop which is smooth and simple except for a cross point of angles ..beta.., then W(C/sub ..beta../) must be renormalized together with the loop functions of associated sets S/sup i//sub ..beta../ = )C/sup i//sub 1/,xxx, C/sup i//sub p/i) (i = 2,xxx,I) of loops C/sup i//sub q/ which coincide with certain parts of C/sub ..beta../equivalentC/sup 1//sub 1/. Then W/sub R/(S/sup i//sub ..beta../) = Z/sup i

The catalytic mechanism of hairpin ribozyme studied by hydrostatic pressure

PubMed Central

Tobé, Sylvia; Heams, Thomas; Vergne, Jacques; Hervé, Guy; Maurel, Marie-Christine

2005-01-01

The discovery of ribozymes strengthened the RNA world hypothesis, which assumes that these precursors of modern life both stored information and acted as catalysts. For the first time among extensive studies on ribozymes, we have investigated the influence of hydrostatic pressure on the hairpin ribozyme catalytic activity. High pressures are of interest when studying life under extreme conditions and may help to understand the behavior of macromolecules at the origins of life. Kinetic studies of the hairpin ribozyme self-cleavage were performed under high hydrostatic pressure. The activation volume of the reaction (34 ± 5 ml/mol) calculated from these experiments is of the same order of magnitude as those of common protein enzymes, and reflects an important compaction of the RNA molecule during catalysis, associated to a water release. Kinetic studies were also carried out under osmotic pressure and confirmed this interpretation and the involvement of water movements (78 ± 4 water molecules per RNA molecule). Taken together, these results are consistent with structural studies indicating that loops A and B of the ribozyme come into close contact during the formation of the transition state. While validating baro-biochemistry as an efficient tool for investigating dynamics at work during RNA catalysis, these results provide a complementary view of ribozyme catalytic mechanisms. PMID:15870387

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.

Vibration control of a manipulator tip on a flexible body

NASA Technical Reports Server (NTRS)

Xu, J.; Bainum, P. M.; Li, F.

1992-01-01

Vibration control of a rigid manipulator tip on a main flexible uniform beam is examined. It is proposed to add a compensator between the manipulator and the beam to rotate and extend/retrieve the manipulator during the control period. The 2D station-keeping maneuvers within the linear range without gravity and damping are considered. The compensatory open-loop control law, which depends on the amplitudes of the beam's flexible deformations at the connection joint, is synthesized using linear quadratic regulator techniques. After introducing the compensatory control into the system, system control is still stable, and the tip coordinates of the manipulator can be made to closely follow the rigid beam motion, which is assumed to be a desired motion.

Catalytic nanoporous membranes

DOEpatents

Pellin, Michael J; Hryn, John N; Elam, Jeffrey W

2013-08-27

A nanoporous catalytic membrane which displays several unique features Including pores which can go through the entire thickness of the membrane. The membrane has a higher catalytic and product selectivity than conventional catalysts. Anodic aluminum oxide (AAO) membranes serve as the catalyst substrate. This substrate is then subjected to Atomic Layer Deposition (ALD), which allows the controlled narrowing of the pores from 40 nm to 10 nm in the substrate by deposition of a preparatory material. Subsequent deposition of a catalytic layer on the inner surfaces of the pores reduces pore sizes to less than 10 nm and allows for a higher degree of reaction selectivity. The small pore sizes allow control over which molecules enter the pores, and the flow-through feature can allow for partial oxidation of reactant species as opposed to complete oxidation. A nanoporous separation membrane, produced by ALD is also provided for use in gaseous and liquid separations. The membrane has a high flow rate of material with 100% selectivity. Also provided is a method for producing a catalytic membrane having flow-through pores and discreet catalytic clusters adhering to the inside surfaces of the pores.

De novo design, synthesis and characterisation of MP3, a new catalytic four-helix bundle hemeprotein.

PubMed

Faiella, Marina; Maglio, Ornella; Nastri, Flavia; Lombardi, Angela; Lista, Liliana; Hagen, Wilfred R; Pavone, Vincenzo

2012-12-07

A new artificial metalloenzyme, MP3 (MiniPeroxidase 3), designed by combining the excellent structural properties of four-helix bundle protein scaffolds with the activity of natural peroxidases, was synthesised and characterised. This new hemeprotein model was developed by covalently linking the deuteroporphyrin to two peptide chains of different compositions to obtain an asymmetric helix-loop-helix/heme/helix-loop-helix sandwich arrangement, characterised by 1) a His residue on one chain that acts as an axial ligand to the iron ion; 2) a vacant distal site that is able to accommodate exogenous ligands or substrates; and 3) an Arg residue in the distal site that should assist in hydrogen peroxide activation to give an HRP-like catalytic process. MP3 was synthesised and characterised as its iron complex. CD measurements revealed the high helix-forming propensity of the peptide, confirming the appropriateness of the model procedure; UV/Vis, MCD and EPR experiments gave insights into the coordination geometry and the spin state of the metal. Kinetic experiments showed that Fe(III)-MP3 possesses peroxidase-like activity comparable to R38A-hHRP, highlighting the possibility of mimicking the functional features of natural enzymes. The synergistic application of de novo design methods, synthetic procedures, and spectroscopic characterisation, described herein, demonstrates a method by which to implement and optimise catalytic activity for an enzyme mimetic. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Catalytic cracking process

DOEpatents

Lokhandwala, Kaaeid A.; Baker, Richard W.

2001-01-01

Processes and apparatus for providing improved catalytic cracking, specifically improved recovery of olefins, LPG or hydrogen from catalytic crackers. The improvement is achieved by passing part of the wet gas stream across membranes selective in favor of light hydrocarbons over hydrogen.

Role of Loop-Clamping Side Chains in Catalysis by Triosephosphate Isomerase.

PubMed

Zhai, Xiang; Amyes, Tina L; Richard, John P

2015-12-09

The side chains of Y208 and S211 from loop 7 of triosephosphate isomerase (TIM) form hydrogen bonds to backbone amides and carbonyls from loop 6 to stabilize the caged enzyme-substrate complex. The effect of seven mutations [Y208T, Y208S, Y208A, Y208F, S211G, S211A, Y208T/S211G] on the kinetic parameters for TIM catalyzed reactions of the whole substrates dihydroxyacetone phosphate and d-glyceraldehyde 3-phosphate [(k(cat)/K(m))(GAP) and (k(cat)/K(m))DHAP] and of the substrate pieces glycolaldehyde and phosphite dianion (k(cat)/K(HPi)K(GA)) are reported. The linear logarithmic correlation between these kinetic parameters, with slope of 1.04 ± 0.03, shows that most mutations of TIM result in an identical change in the activation barriers for the catalyzed reactions of whole substrate and substrate pieces, so that the transition states for these reactions are stabilized by similar interactions with the protein catalyst. The second linear logarithmic correlation [slope = 0.53 ± 0.16] between k(cat) for isomerization of GAP and K(d)(⧧) for phosphite dianion binding to the transition state for wildtype and many mutant TIM-catalyzed reactions of substrate pieces shows that ca. 50% of the wildtype TIM dianion binding energy, eliminated by these mutations, is expressed at the wildtype Michaelis complex, and ca. 50% is only expressed at the wildtype transition state. Negative deviations from this correlation are observed when the mutation results in a decrease in enzyme reactivity at the catalytic site. The main effect of Y208T, Y208S, and Y208A mutations is to cause a reduction in the total intrinsic dianion binding energy, but the effect of Y208F extends to the catalytic site.

Flexible graphene-PZT ferroelectric nonvolatile memory.

PubMed

Lee, Wonho; Kahya, Orhan; Toh, Chee Tat; Ozyilmaz, Barbaros; Ahn, Jong-Hyun

2013-11-29

We report the fabrication of a flexible graphene-based nonvolatile memory device using Pb(Zr0.35,Ti0.65)O3 (PZT) as the ferroelectric material. The graphene and PZT ferroelectric layers were deposited using chemical vapor deposition and sol–gel methods, respectively. Such PZT films show a high remnant polarization (Pr) of 30 μC cm−2 and a coercive voltage (Vc) of 3.5 V under a voltage loop over ±11 V. The graphene–PZT ferroelectric nonvolatile memory on a plastic substrate displayed an on/off current ratio of 6.7, a memory window of 6 V and reliable operation. In addition, the device showed one order of magnitude lower operation voltage range than organic-based ferroelectric nonvolatile memory after removing the anti-ferroelectric behavior incorporating an electrolyte solution. The devices showed robust operation in bent states of bending radii up to 9 mm and in cycling tests of 200 times. The devices exhibited remarkable mechanical properties and were readily integrated with plastic substrates for the production of flexible circuits.

Thermal Vacuum Testing of a Proto-flight Miniature Loop Heat Pipe with Two Evaporators and Two Condensers

NASA Technical Reports Server (NTRS)

Ku, Jentung; Ottenstein, Laura

2011-01-01

This paper describes thermal vacuum testing of a proto-flight miniature loop heat pipe (MLHP) with two evaporators and two condensers designed for future small systems applications requiring low mass, low power and compactness. Each evaporator contains a wick with an outer diameter of 6.35 mm, and each has its own integral compensation chamber (CC). Miniaturization of the loop components reduces the volume and mass of the thermal system. Multiple evaporators provide flexibility for placement of instruments that need to be maintained at the same temperature, and facilitate heat load sharing among instruments, reducing the auxiliary heater power requirement. A flow regulator is used to regulate heat dissipations between the two condensers, allowing flexible placement of radiators on the spacecraft. A thermoelectric converter (TEC) is attached to each CC for control of the operating temperature and enhancement of start-up success. Tests performed include start-up, power cycle, sink temperature cycle, high power and low power operation, heat load sharing, and operating temperature control. The proto-flight MLHP demonstrated excellent performance in the thermal vacuum test. The loop started successfully and operated stably under various evaporator heat loads and condenser sink temperatures. The TECs were able to maintain the loop operating temperature within b1K of the desired set point temperature at all power levels and all sink temperatures. The un-powered evaporator would automatically share heat from the other powered evaporator. The flow regulator was able to regulate the heat dissipation among the radiators and prevent vapor from flowing into the liquid line.

A voice coil actuator driven active vibration isolation system with the consideration of flexible modes.

PubMed

Park, Kyihwan; Choi, Dongyoub; Ozer, Abdullah; Kim, Sangyoo; Lee, Yongkwan; Joo, Dongik

2008-06-01

We develop a four-mount active vibration isolation system (AVIS) using voice coil actuators. The flexible body modes in the upper plate of the AVIS can cause an instability problem due to control signal whose frequency is close to the resonant frequency of the flexible modes. The loop shaping technique is applied to reduce the amplitude of the control signal. We investigate the performances of the active vibration isolation system proposed in the word in the time domain and frequency domain by comparing to the passive isolation system.

Two-loop hard-thermal-loop thermodynamics with quarks

NASA Astrophysics Data System (ADS)

Andersen, Jens O.; Petitgirard, Emmanuel; Strickland, Michael

2004-08-01

We calculate the quark contribution to the free energy of a hot quark-gluon plasma to two-loop order using hard-thermal-loop (HTL) perturbation theory. All ultraviolet divergences can be absorbed into renormalizations of the vacuum energy and the HTL quark and gluon mass parameters. The quark and gluon HTL mass parameters are determined self-consistently by a variational prescription. Combining the quark contribution with the two-loop HTL perturbation theory free energy for pure glue we obtain the total two-loop QCD free energy. Comparisons are made with lattice estimates of the free energy for Nf=2 and with exact numerical results obtained in the large-Nf limit.

FlexibleSUSY-A spectrum generator generator for supersymmetric models

NASA Astrophysics Data System (ADS)

Athron, Peter; Park, Jae-hyeon; Stöckinger, Dominik; Voigt, Alexander

2015-05-01

We introduce FlexibleSUSY, a Mathematica and C++ package, which generates a fast, precise C++ spectrum generator for any SUSY model specified by the user. The generated code is designed with both speed and modularity in mind, making it easy to adapt and extend with new features. The model is specified by supplying the superpotential, gauge structure and particle content in a SARAH model file; specific boundary conditions e.g. at the GUT, weak or intermediate scales are defined in a separate FlexibleSUSY model file. From these model files, FlexibleSUSY generates C++ code for self-energies, tadpole corrections, renormalization group equations (RGEs) and electroweak symmetry breaking (EWSB) conditions and combines them with numerical routines for solving the RGEs and EWSB conditions simultaneously. The resulting spectrum generator is then able to solve for the spectrum of the model, including loop-corrected pole masses, consistent with user specified boundary conditions. The modular structure of the generated code allows for individual components to be replaced with an alternative if available. FlexibleSUSY has been carefully designed to grow as alternative solvers and calculators are added. Predefined models include the MSSM, NMSSM, E6SSM, USSM, R-symmetric models and models with right-handed neutrinos.

(1,3;1,4)-β-Glucan Biosynthesis by the CSLF6 Enzyme: Position and Flexibility of Catalytic Residues Influence Product Fine Structure.

PubMed

Dimitroff, George; Little, Alan; Lahnstein, Jelle; Schwerdt, Julian G; Srivastava, Vaibhav; Bulone, Vincent; Burton, Rachel A; Fincher, Geoffrey B

2016-04-05

Cellulose synthase-like F6 (CslF6) genes encode polysaccharide synthases responsible for (1,3;1,4)-β-glucan biosynthesis in cereal grains. However, it is not clear how both (1,3)- and (1,4)-linkages are incorporated into a single polysaccharide chain and how the frequency and arrangement of the two linkage types that define the fine structure of the polysaccharide are controlled. Through transient expression in Nicotiana benthamiana leaves, two CSLF6 orthologs from different cereal species were shown to mediate the synthesis of (1,3;1,4)-β-glucans with very different fine structures. Chimeric cDNA constructs with interchanged sections of the barley and sorghum CslF6 genes were developed to identify regions of the synthase enzyme responsible for these differences. A single amino acid residue upstream of the TED motif in the catalytic region was shown to dramatically change the fine structure of the polysaccharide produced. The structural basis of this effect can be rationalized by reference to a homology model of the enzyme and appears to be related to the position and flexibility of the TED motif in the active site of the enzyme. The region and amino acid residue identified provide opportunities to manipulate the solubility of (1,3;1,4)-β-glucan in grains and vegetative tissues of the grasses and, in particular, to enhance the solubility of dietary fibers that are beneficial to human health.

The mitochondrial intermembrane loop region of rat carnitine palmitoyltransferase 1A is a major determinant of its malonyl-CoA sensitivity.

PubMed

Borthwick, Karen; Jackson, Vicky N; Price, Nigel T; Zammit, Victor A

2006-11-03

Carnitine palmitoyltransferase (CPT) 1A adopts a polytopic conformation within the mitochondrial outer membrane, having both the N- and C-terminal segments on the cytosolic aspect of the membrane and a loop region connecting the two transmembrane (TM) segments protruding into the inter membrane space. In this study we demonstrate that the loop exerts major effects on the sensitivity of the enzyme to its inhibitor, malonyl-CoA. Insertion of a 16-residue spacer between the C-terminal part of the loop sequence (i.e. between residues 100 and 101) and TM2 (which is predicted to start at residue 102) increased the sensitivity to malonyl-CoA inhibition of the resultant mutant protein by more than 10-fold. By contrast, the same insertion made between TM1 and the loop had no effects on the kinetic properties of the enzyme, indicating that effects on the catalytic C-terminal segment were specifically induced by loop-TM2 interactions. Enhanced sensitivity was also observed in all mutants in which the native TM2-loop pairing was disrupted either by making chimeras in which the loops and TM2 segments of CPT 1A and CPT 1B were exchanged or by deleting successive 9-residue segments from the loop sequence. The data suggest that the sequence spanning the loop-TM2 boundary determines the disposition of this TM in the membrane so as to alter the conformation of the C-terminal segment and thus affect its interaction with malonyl-CoA.

Global and local molecular dynamics of a bacterial carboxylesterase provide insight into its catalytic mechanism

PubMed Central

Yu, Xiaozhen; Sigler, Sara C.; Hossain, Delwar; Wierdl, Monika; Gwaltney, Steven R.; Potter, Philip M.; Wadkins, Randy M.

2013-01-01

Carboxylesterases (CEs) are ubiquitous enzymes responsible for the detoxification of xenobiotics. In humans, substrates for these enzymes are far-ranging, and include the street drug heroin and the anticancer agent irinotecan. Hence, their ability to bind and metabolize substrates is of broad interest to biomedical science. In this study, we focused our attention on dynamic motions of a CE from B. subtilis (pnbCE), with emphasis on the question of what individual domains of the enzyme might contribute to its catalytic activity. We used a 10 ns all-atom molecular dynamics simulation, normal mode calculations, and enzyme kinetics to understand catalytic consequences of structural changes within this enzyme. Our results shed light on how molecular motions are coupled with catalysis. During molecular dynamics, we observed a distinct C-C bond rotation between two conformations of Glu310. Such a bond rotation would alternately facilitate and impede protonation of the active site His399 and act as a mechanism by which the enzyme alternates between its active and inactive conformation. Our normal mode results demonstrate that the distinct low-frequency motions of two loops in pnbCE, coil_5 and coil_21, are important in substrate conversion and seal the active site. Mutant CEs lacking these external loops show significantly reduced rates of substrate conversion, suggesting this sealing motion prevents escape of substrate. Overall, the results of our studies give new insight into the structure-function relationship of CEs and have implications for the entire family of α/β fold family of hydrolases, of which this CE is a member. PMID:22127613

Arabidopsis thaliana dehydroascorbate reductase 2: Conformational flexibility during catalysis

NASA Astrophysics Data System (ADS)

Bodra, Nandita; Young, David; Astolfi Rosado, Leonardo; Pallo, Anna; Wahni, Khadija; de Proft, Frank; Huang, Jingjing; van Breusegem, Frank; Messens, Joris

2017-02-01

Dehydroascorbate reductase (DHAR) catalyzes the glutathione (GSH)-dependent reduction of dehydroascorbate and plays a direct role in regenerating ascorbic acid, an essential plant antioxidant vital for defense against oxidative stress. DHAR enzymes bear close structural homology to the glutathione transferase (GST) superfamily of enzymes and contain the same active site motif, but most GSTs do not exhibit DHAR activity. The presence of a cysteine at the active site is essential for the catalytic functioning of DHAR, as mutation of this cysteine abolishes the activity. Here we present the crystal structure of DHAR2 from Arabidopsis thaliana with GSH bound to the catalytic cysteine. This structure reveals localized conformational differences around the active site which distinguishes the GSH-bound DHAR2 structure from that of DHAR1. We also unraveled the enzymatic step in which DHAR releases oxidized glutathione (GSSG). To consolidate our structural and kinetic findings, we investigated potential conformational flexibility in DHAR2 by normal mode analysis and found that subdomain mobility could be linked to GSH binding or GSSG release.

Arabidopsis thaliana dehydroascorbate reductase 2: Conformational flexibility during catalysis

PubMed Central

Bodra, Nandita; Young, David; Astolfi Rosado, Leonardo; Pallo, Anna; Wahni, Khadija; De Proft, Frank; Huang, Jingjing; Van Breusegem, Frank; Messens, Joris

2017-01-01

Dehydroascorbate reductase (DHAR) catalyzes the glutathione (GSH)-dependent reduction of dehydroascorbate and plays a direct role in regenerating ascorbic acid, an essential plant antioxidant vital for defense against oxidative stress. DHAR enzymes bear close structural homology to the glutathione transferase (GST) superfamily of enzymes and contain the same active site motif, but most GSTs do not exhibit DHAR activity. The presence of a cysteine at the active site is essential for the catalytic functioning of DHAR, as mutation of this cysteine abolishes the activity. Here we present the crystal structure of DHAR2 from Arabidopsis thaliana with GSH bound to the catalytic cysteine. This structure reveals localized conformational differences around the active site which distinguishes the GSH-bound DHAR2 structure from that of DHAR1. We also unraveled the enzymatic step in which DHAR releases oxidized glutathione (GSSG). To consolidate our structural and kinetic findings, we investigated potential conformational flexibility in DHAR2 by normal mode analysis and found that subdomain mobility could be linked to GSH binding or GSSG release. PMID:28195196

Catalytic distillation process

DOEpatents

Smith, Jr., Lawrence A.

1982-01-01

A method for conducting chemical reactions and fractionation of the reaction mixture comprising feeding reactants to a distillation column reactor into a feed zone and concurrently contacting the reactants with a fixed bed catalytic packing to concurrently carry out the reaction and fractionate the reaction mixture. For example, a method for preparing methyl tertiary butyl ether in high purity from a mixed feed stream of isobutene and normal butene comprising feeding the mixed feed stream to a distillation column reactor into a feed zone at the lower end of a distillation reaction zone, and methanol into the upper end of said distillation reaction zone, which is packed with a properly supported cationic ion exchange resin, contacting the C.sub.4 feed and methanol with the catalytic distillation packing to react methanol and isobutene, and concurrently fractionating the ether from the column below the catalytic zone and removing normal butene overhead above the catalytic zone.

Catalytic distillation process

DOEpatents

Smith, L.A. Jr.

1982-06-22

A method is described for conducting chemical reactions and fractionation of the reaction mixture comprising feeding reactants to a distillation column reactor into a feed zone and concurrently contacting the reactants with a fixed bed catalytic packing to concurrently carry out the reaction and fractionate the reaction mixture. For example, a method for preparing methyl tertiary butyl ether in high purity from a mixed feed stream of isobutene and normal butene comprising feeding the mixed feed stream to a distillation column reactor into a feed zone at the lower end of a distillation reaction zone, and methanol into the upper end of said distillation reaction zone, which is packed with a properly supported cationic ion exchange resin, contacting the C[sub 4] feed and methanol with the catalytic distillation packing to react methanol and isobutene, and concurrently fractionating the ether from the column below the catalytic zone and removing normal butene overhead above the catalytic zone.

The SH2 Domain Regulates c-Abl Kinase Activation by a Cyclin-Like Mechanism and Remodulation of the Hinge Motion

PubMed Central

Dölker, Nicole; Górna, Maria W.; Sutto, Ludovico; Torralba, Antonio S.; Superti-Furga, Giulio; Gervasio, Francesco L.

2014-01-01

Regulation of the c-Abl (ABL1) tyrosine kinase is important because of its role in cellular signaling, and its relevance in the leukemiogenic counterpart (BCR-ABL). Both auto-inhibition and full activation of c-Abl are regulated by the interaction of the catalytic domain with the Src Homology 2 (SH2) domain. The mechanism by which this interaction enhances catalysis is not known. We combined computational simulations with mutagenesis and functional analysis to find that the SH2 domain conveys both local and global effects on the dynamics of the catalytic domain. Locally, it regulates the flexibility of the αC helix in a fashion reminiscent of cyclins in cyclin-dependent kinases, reorienting catalytically important motifs. At a more global level, SH2 binding redirects the hinge motion of the N and C lobes and changes the conformational equilibrium of the activation loop. The complex network of subtle structural shifts that link the SH2 domain with the activation loop and the active site may be partially conserved with other SH2-domain containing kinases and therefore offer additional parameters for the design of conformation-specific inhibitors. PMID:25299346

The SH2 domain regulates c-Abl kinase activation by a cyclin-like mechanism and remodulation of the hinge motion.

PubMed

Dölker, Nicole; Górna, Maria W; Sutto, Ludovico; Torralba, Antonio S; Superti-Furga, Giulio; Gervasio, Francesco L

2014-10-01

Regulation of the c-Abl (ABL1) tyrosine kinase is important because of its role in cellular signaling, and its relevance in the leukemiogenic counterpart (BCR-ABL). Both auto-inhibition and full activation of c-Abl are regulated by the interaction of the catalytic domain with the Src Homology 2 (SH2) domain. The mechanism by which this interaction enhances catalysis is not known. We combined computational simulations with mutagenesis and functional analysis to find that the SH2 domain conveys both local and global effects on the dynamics of the catalytic domain. Locally, it regulates the flexibility of the αC helix in a fashion reminiscent of cyclins in cyclin-dependent kinases, reorienting catalytically important motifs. At a more global level, SH2 binding redirects the hinge motion of the N and C lobes and changes the conformational equilibrium of the activation loop. The complex network of subtle structural shifts that link the SH2 domain with the activation loop and the active site may be partially conserved with other SH2-domain containing kinases and therefore offer additional parameters for the design of conformation-specific inhibitors.

Adjustment of Conformational Flexibility is a Key Event in the Thermal Adaptation of Proteins

NASA Astrophysics Data System (ADS)

Zavodszky, Peter; Kardos, Jozsef; Svingor, Adam; Petsko, Gregory A.

1998-06-01

3-Isopropylmalate dehydrogenase (IPMDH, E.C. 1.1.1.85) from the thermophilic bacterium Thermus thermophilus HB8 is homologous to IPMDH from the mesophilic Escherichia coli, but has an approximately 17 degrees C higher melting temperature. Its temperature optimum is 22-25 degrees C higher than that of the E. coli enzyme; however, it is hardly active at room temperature. The increased conformational rigidity required to stabilize the thermophilic enzyme against heat denaturation might explain its different temperature-activity profile. Hydrogen/deuterium exchange studies were performed on this thermophilic-mesophilic enzyme pair to compare their conformational flexibilities. It was found that Th. thermophilus IPMDH is significantly more rigid at room temperature than E. coli IPMDH, whereas the enzymes have nearly identical flexibilities under their respective optimal working conditions, suggesting that evolutionary adaptation tends to maintain a ``corresponding state'' regarding conformational flexibility. These observations confirm that conformational fluctuations necessary for catalytic function are restricted at room temperature in the thermophilic enzyme, suggesting a close relationship between conformational flexibility and enzyme function.

Evolution of catalytic function

NASA Technical Reports Server (NTRS)

Joyce, G. F.

1993-01-01

An RNA-based evolution system was constructed in the laboratory and used to develop RNA enzymes with novel catalytic function. By controlling the nature of the catalytic task that the molecules must perform in order to survive, it is possible to direct the evolving population toward the expression of some desired catalytic behavior. More recently, this system has been coupled to an in vitro translation procedure, raising the possibility of evolving protein enzymes in the laboratory to produce novel proteins with desired catalytic properties. The aim of this line of research is to reduce darwinian evolution, the fundamental process of biology, to a laboratory procedure that can be made to operate in the service of organic synthesis.

Behaviour of fractional loop delay zero crossing digital phase locked loop (FR-ZCDPLL)

NASA Astrophysics Data System (ADS)

Nasir, Qassim

2018-01-01

This article analyses the performance of the first-order zero crossing digital phase locked loops (FR-ZCDPLL) when fractional loop delay is added to loop. The non-linear dynamics of the loop is presented, analysed and examined through bifurcation behaviour. Numerical simulation of the loop is conducted to proof the mathematical analysis of the loop operation. The results of the loop simulation show that the proposed FR-ZCDPLL has enhanced the performance compared to the conventional zero crossing DPLL in terms of wider lock range, captured range and stable operation region. In addition, extensive experimental simulation was conducted to find the optimum loop parameters for different loop environmental conditions. The addition of the fractional loop delay network in the conventional loop also reduces the phase jitter and its variance especially when the signal-to-noise ratio is low.

An auto-inhibitory helix in CTP:phosphocholine cytidylyltransferase hijacks the catalytic residue and constrains a pliable, domain-bridging helix pair

PubMed Central

Ramezanpour, Mohsen; Lee, Jaeyong; Taneva, Svetla G.; Tieleman, D. Peter; Cornell, Rosemary B.

2018-01-01

The activity of CTP:phosphocholine cytidylyltransferase (CCT), a key enzyme in phosphatidylcholine synthesis, is regulated by reversible interactions of a lipid-inducible amphipathic helix (domain M) with membrane phospholipids. When dissociated from membranes, a portion of the M domain functions as an auto-inhibitory (AI) element to suppress catalysis. The AI helix from each subunit binds to a pair of α helices (αE) that extend from the base of the catalytic dimer to create a four-helix bundle. The bound AI helices make intimate contact with loop L2, housing a key catalytic residue, Lys122. The impacts of the AI helix on active-site dynamics and positioning of Lys122 are unknown. Extensive MD simulations with and without the AI helix revealed that backbone carbonyl oxygens at the point of contact between the AI helix and loop L2 can entrap the Lys122 side chain, effectively competing with the substrate, CTP. In silico, removal of the AI helices dramatically increased αE dynamics at a predicted break in the middle of these helices, enabling them to splay apart and forge new contacts with loop L2. In vitro cross-linking confirmed the reorganization of the αE element upon membrane binding of the AI helix. Moreover, when αE bending was prevented by disulfide engineering, CCT activation by membrane binding was thwarted. These findings suggest a novel two-part auto-inhibitory mechanism for CCT involving capture of Lys122 and restraint of the pliable αE helices. We propose that membrane binding enables bending of the αE helices, bringing the active site closer to the membrane surface. PMID:29519816

A review of tin oxide-based catalytic systems: Preparation, characterization and catalytic behavior

NASA Technical Reports Server (NTRS)

Hoflund, Gar B.

1987-01-01

This paper reviews the important aspects of the preparation, characterization and catalytic behavior of tin oxide-based catalytic systems including doped tin oxide, mixed oxides which contain tin oxide, Pt supported on tin oxide and Pt/Sn supported on alumina. These systems have a broad range of applications and are continually increasing in importance. However, due to their complex nature, much remains to be understood concerning how they function catalytically.

Flexible body stability analysis of Space Shuttle ascent flight control system by using lambda matrix solution techniques

NASA Technical Reports Server (NTRS)

Bown, R. L.; Christofferson, A.; Lardas, M.; Flanders, H.

1980-01-01

A lambda matrix solution technique is being developed to perform an open loop frequency analysis of a high order dynamic system. The procedure evaluates the right and left latent vectors corresponding to the respective latent roots. The latent vectors are used to evaluate the partial fraction expansion formulation required to compute the flexible body open loop feedback gains for the Space Shuttle Digital Ascent Flight Control System. The algorithm is in the final stages of development and will be used to insure that the feedback gains meet the design specification.

Kinetic and Binding Analysis of the Catalytic Involvement of Ribose Moieties of a trans-Acting δ Ribozyme*

PubMed Central

Fiola, Karine; Perreault, Jean-Pierre

2010-01-01

We have identified ribose 2′-hydroxyl groups (2′-OHs) that are critical for the activity of a trans-cleaving δ ribozyme derived from the antigenomic strand of the hepatitis δ virus. Initially, an RNA-DNA mixed ribozyme composed of 26 deoxyribo- (specifically the nucleotides forming the P2 stem and the P4 stem-loop) and 31 ribonucleotides (those forming the catalytic center) was engineered. This mixed ribozyme catalyzed the cleavage of a small substrate with kinetic parameters virtually identical to those of the all-RNA ribozyme. The further substitution of deoxyribose for ribose residues permitted us to investigate the contribution of all 2′-OHs to catalysis. Determination of the kinetic parameters for the cleavage reaction of the resulting ribozymes revealed (i) 10 2′-OH groups appear to be important in supporting the formation of several hydrogen bonds within the catalytic core, (ii) none of the important 2′-OHs seem to coordinate a magnesium cation, and (iii) 1 of the tested RNA-DNA mixed polymers appeared to stabilize the ribozyme-substrate transition-state complex, resulting in an improvement over the all-RNA counterpart. The contribution of the 2′-OHs to the catalytic mechanism is discussed, and differences with the crystal structure of a genomic δ self-cleaved product are explained. Clearly, the 2′-OHs are essential components of the network of interactions involved in the formation of the catalytic center of the δ ribozyme. PMID:12015324

Varietal Loops

NASA Image and Video Library

2016-09-15

A series of active regions stretched along the right side of the sun exhibited a wide variety of loops cascading above them (Sept. 12-14, 2016). The active region near the center has tightly coiled loops, while the region rotating over the right edge has some elongated and some very stretched loops above it. The loops are actually charged particles spiraling along magnetic field lines, observed here in a wavelength of extreme ultraviolet light. Near the middle of the video the Earth quickly passes in front of a portion of the sun as viewed by SDO. http://photojournal.jpl.nasa.gov/catalog/PIA16997

Catalytic bioreactors and methods of using same

DOEpatents

Worden, Robert Mark; Liu, Yangmu Chloe

2017-07-25

Various embodiments provide a bioreactor for producing a bioproduct comprising one or more catalytically active zones located in a housing and adapted to keep two incompatible gaseous reactants separated when in a gas phase, wherein each of the one or more catalytically active zones may comprise a catalytic component retainer and a catalytic component retained within and/or thereon. Each of the catalytically active zones may additionally or alternatively comprise a liquid medium located on either side of the catalytic component retainer. Catalytic component may include a microbial cell culture located within and/or on the catalytic component retainer, a suspended catalytic component suspended in the liquid medium, or a combination thereof. Methods of using various embodiments of the bioreactor to produce a bioproduct, such as isobutanol, are also provided.

An improved output feedback control of flexible large space structures

NASA Technical Reports Server (NTRS)

Lin, Y. H.; Lin, J. G.

1980-01-01

A special output feedback control design technique for flexible large space structures is proposed. It is shown that the technique will increase both the damping and frequency of selected modes for more effective control. It is also able to effect integrated control of elastic and rigid-body modes and, in particular, closed-loop system stability and robustness to modal truncation and parameter variation. The technique is seen as marking an improvement over previous work concerning large space structures output feedback control.

Catalytic hydrotreating process

DOEpatents

Karr, Jr., Clarence; McCaskill, Kenneth B.

1978-01-01

Carbonaceous liquids boiling above about 300.degree. C such as tars, petroleum residuals, shale oils and coal-derived liquids are catalytically hydrotreated by introducing the carbonaceous liquid into a reaction zone at a temperature in the range of 300.degree. to 450.degree. C and a pressure in the range of 300 to 4000 psig for effecting contact between the carbonaceous liquid and a catalytic transition metal sulfide in the reaction zone as a layer on a hydrogen permeable transition metal substrate and then introducing hydrogen into the reaction zone by diffusing the hydrogen through the substrate to effect the hydrogenation of the carbonaceous liquid in the presence of the catalytic sulfide layer.

Conformational Changes in a Hyperthermostable Glycoside Hydrolase: Enzymatic Activity Is a Consequence of the Loop Dynamics and Protonation Balance

PubMed Central

de Oliveira, Leandro C.; da Silva, Viviam M.; Colussi, Francieli; Cabral, Aline D.; de Oliveira Neto, Mario; Squina, Fabio M.; Garcia, Wanius

2015-01-01

Endo-β-1, 4-mannanase from Thermotoga petrophila (TpMan) is a modular hyperthermostable enzyme involved in the degradation of mannan-containing polysaccharides. The degradation of these polysaccharides represents a key step for several industrial applications. Here, as part of a continuing investigation of TpMan, the region corresponding to the GH5 domain (TpManGH5) was characterized as a function of pH and temperature. The results indicated that the enzymatic activity of the TpManGH5 is pH-dependent, with its optimum activity occurring at pH 6. At pH 8, the studies demonstrated that TpManGH5 is a molecule with a nearly spherical tightly packed core displaying negligible flexibility in solution, and with size and shape very similar to crystal structure. However, TpManGH5 experiences an increase in radius of gyration in acidic conditions suggesting expansion of the molecule. Furthermore, at acidic pH values, TpManGH5 showed a less globular shape, probably due to a loop region slightly more expanded and flexible in solution (residues Y88 to A105). In addition, molecular dynamics simulations indicated that conformational changes caused by pH variation did not change the core of the TpManGH5, which means that only the above mentioned loop region presents high degree of fluctuations. The results also suggested that conformational changes of the loop region may facilitate polysaccharide and enzyme interaction. Finally, at pH 6 the results indicated that TpManGH5 is slightly more flexible at 65°C when compared to the same enzyme at 20°C. The biophysical characterization presented here is well correlated with the enzymatic activity and provide new insight into the structural basis for the temperature and pH-dependent activity of the TpManGH5. Also, the data suggest a loop region that provides a starting point for a rational design of biotechnological desired features. PMID:25723179

Acetyl group coordinated progression through the catalytic cycle of an arylalkylamine N-acetyltransferase.

PubMed

Aboalroub, Adam A; Bachman, Ashleigh B; Zhang, Ziming; Keramisanou, Dimitra; Merkler, David J; Gelis, Ioannis

2017-01-01

The transfer of an acetyl group from acetyl-CoA to an acceptor amine is a ubiquitous biochemical transformation catalyzed by Gcn5-related N-acetyltransferases (GNATs). Although it is established that the reaction proceeds through a sequential ordered mechanism, the role of the acetyl group in driving the ordered formation of binary and ternary complexes remains elusive. Herein, we show that CoA and acetyl-CoA alter the conformation of the substrate binding site of an arylalkylamine N-acetyltransferase (AANAT) to facilitate interaction with acceptor substrates. However, it is the presence of the acetyl group within the catalytic funnel that triggers high affinity binding. Acetyl group occupancy is relayed through a conserved salt bridge between the P-loop and the acceptor binding site, and is manifested as differential dynamics in the CoA and acetyl-CoA-bound states. The capacity of the acetyl group carried by an acceptor to promote its tight binding even in the absence of CoA, but also its mutually exclusive position to the acetyl group of acetyl-CoA underscore its importance in coordinating the progression of the catalytic cycle.

Acetyl group coordinated progression through the catalytic cycle of an arylalkylamine N-acetyltransferase

PubMed Central

Aboalroub, Adam A.; Bachman, Ashleigh B.; Zhang, Ziming; Keramisanou, Dimitra; Merkler, David J.

2017-01-01

The transfer of an acetyl group from acetyl-CoA to an acceptor amine is a ubiquitous biochemical transformation catalyzed by Gcn5-related N-acetyltransferases (GNATs). Although it is established that the reaction proceeds through a sequential ordered mechanism, the role of the acetyl group in driving the ordered formation of binary and ternary complexes remains elusive. Herein, we show that CoA and acetyl-CoA alter the conformation of the substrate binding site of an arylalkylamine N-acetyltransferase (AANAT) to facilitate interaction with acceptor substrates. However, it is the presence of the acetyl group within the catalytic funnel that triggers high affinity binding. Acetyl group occupancy is relayed through a conserved salt bridge between the P-loop and the acceptor binding site, and is manifested as differential dynamics in the CoA and acetyl-CoA-bound states. The capacity of the acetyl group carried by an acceptor to promote its tight binding even in the absence of CoA, but also its mutually exclusive position to the acetyl group of acetyl-CoA underscore its importance in coordinating the progression of the catalytic cycle. PMID:28486510

Bio-Inspired Controller on an FPGA Applied to Closed-Loop Diaphragmatic Stimulation

PubMed Central

Zbrzeski, Adeline; Bornat, Yannick; Hillen, Brian; Siu, Ricardo; Abbas, James; Jung, Ranu; Renaud, Sylvie

2016-01-01

Cervical spinal cord injury can disrupt connections between the brain respiratory network and the respiratory muscles which can lead to partial or complete loss of ventilatory control and require ventilatory assistance. Unlike current open-loop technology, a closed-loop diaphragmatic pacing system could overcome the drawbacks of manual titration as well as respond to changing ventilation requirements. We present an original bio-inspired assistive technology for real-time ventilation assistance, implemented in a digital configurable Field Programmable Gate Array (FPGA). The bio-inspired controller, which is a spiking neural network (SNN) inspired by the medullary respiratory network, is as robust as a classic controller while having a flexible, low-power and low-cost hardware design. The system was simulated in MATLAB with FPGA-specific constraints and tested with a computational model of rat breathing; the model reproduced experimentally collected respiratory data in eupneic animals. The open-loop version of the bio-inspired controller was implemented on the FPGA. Electrical test bench characterizations confirmed the system functionality. Open and closed-loop paradigm simulations were simulated to test the FPGA system real-time behavior using the rat computational model. The closed-loop system monitors breathing and changes in respiratory demands to drive diaphragmatic stimulation. The simulated results inform future acute animal experiments and constitute the first step toward the development of a neuromorphic, adaptive, compact, low-power, implantable device. The bio-inspired hardware design optimizes the FPGA resource and time costs while harnessing the computational power of spike-based neuromorphic hardware. Its real-time feature makes it suitable for in vivo applications. PMID:27378844

Galactokinase promiscuity: a question of flexibility?

PubMed

McAuley, Megan; Kristiansson, Helena; Huang, Meilan; Pey, Angel L; Timson, David J

2016-02-01

Galactokinase catalyses the first committed step of the Leloir pathway, i.e. the ATP-dependent phosphorylation of α-D-galactose at C1-OH. Reduced galactokinase activity results in the inherited metabolic disease type II galactosaemia. However, inhibition of galactokinase is considered a viable approach to treating more severe forms of galactosaemia (types I and III). Considerable progress has been made in the identification of high affinity, selective inhibitors. Although the structure of galactokinase from a variety of species is known, its catalytic mechanism remains uncertain. Although the bulk of evidence suggests that the reaction proceeds via an active site base mechanism, some experimental and theoretical studies contradict this. The enzyme has potential as a biocatalyst in the production of sugar 1-phosphates. This potential is limited by its high specificity. A variety of approaches have been taken to identify galactokinase variants which are more promiscuous. These have broadened galactokinase's specificity to include a wide range of D- and L-sugars. Initial studies suggest that some of these alterations result in increased flexibility at the active site. It is suggested that modulation of protein flexibility is at least as important as structural modifications in determining the success or failure of enzyme engineering. © 2016 Authors; published by Portland Press Limited.

Loop-the-Loop: An Easy Experiment, A Challenging Explanation

NASA Astrophysics Data System (ADS)

Asavapibhop, B.; Suwonjandee, N.

2010-07-01

A loop-the-loop built by the Institute for the Promotion of Teaching Science and Technology (IPST) was used in Thai high school teachers training program to demonstrate a circular motion and investigate the concept of the conservation of mechanical energy. We took videos using high speed camera to record the motions of a spherical steel ball moving down the aluminum inclined track at different released positions. The ball then moved into the circular loop and underwent a projectile motion upon leaving the track. We then asked the teachers to predict the landing position of the ball if we changed the height of the whole loop-the-loop system. We also analyzed the videos using Tracker, a video analysis software. It turned out that most teachers did not realize the effect of the friction between the ball and the track and could not obtain the correct relationship hence their predictions were inconsistent with the actual landing positions of the ball.

Robust on-off pulse control of flexible space vehicles

NASA Technical Reports Server (NTRS)

Wie, Bong; Sinha, Ravi

1993-01-01

The on-off reaction jet control system is often used for attitude and orbital maneuvering of various spacecraft. Future space vehicles such as the orbital transfer vehicles, orbital maneuvering vehicles, and space station will extensively use reaction jets for orbital maneuvering and attitude stabilization. The proposed robust fuel- and time-optimal control algorithm is used for a three-mass spacing model of flexible spacecraft. A fuel-efficient on-off control logic is developed for robust rest-to-rest maneuver of a flexible vehicle with minimum excitation of structural modes. The first part of this report is concerned with the problem of selecting a proper pair of jets for practical trade-offs among the maneuvering time, fuel consumption, structural mode excitation, and performance robustness. A time-optimal control problem subject to parameter robustness constraints is formulated and solved. The second part of this report deals with obtaining parameter insensitive fuel- and time- optimal control inputs by solving a constrained optimization problem subject to robustness constraints. It is shown that sensitivity to modeling errors can be significantly reduced by the proposed, robustified open-loop control approach. The final part of this report deals with sliding mode control design for uncertain flexible structures. The benchmark problem of a flexible structure is used as an example for the feedback sliding mode controller design with bounded control inputs and robustness to parameter variations is investigated.

Experimental determination of frequency response function estimates for flexible joint industrial manipulators with serial kinematics

NASA Astrophysics Data System (ADS)

Saupe, Florian; Knoblach, Andreas

2015-02-01

Two different approaches for the determination of frequency response functions (FRFs) are used for the non-parametric closed loop identification of a flexible joint industrial manipulator with serial kinematics. The two applied experiment designs are based on low power multisine and high power chirp excitations. The main challenge is to eliminate disturbances of the FRF estimates caused by the numerous nonlinearities of the robot. For the experiment design based on chirp excitations, a simple iterative procedure is proposed which allows exploiting the good crest factor of chirp signals in a closed loop setup. An interesting synergy of the two approaches, beyond validation purposes, is pointed out.

Structural Insights into E. coli Porphobilinogen Deaminase during Synthesis and Exit of 1-Hydroxymethylbilane

PubMed Central

Bulusu, Gopalakrishnan

2014-01-01

Porphobilinogen deaminase (PBGD) catalyzes the formation of 1-hydroxymethylbilane (HMB), a crucial intermediate in tetrapyrrole biosynthesis, through a step-wise polymerization of four molecules of porphobilinogen (PBG), using a unique dipyrromethane (DPM) cofactor. Structural and biochemical studies have suggested residues with catalytic importance, but their specific role in the mechanism and the dynamic behavior of the protein with respect to the growing pyrrole chain remains unknown. Molecular dynamics simulations of the protein through the different stages of pyrrole chain elongation suggested that the compactness of the overall protein decreases progressively with addition of each pyrrole ring. Essential dynamics showed that domains move apart while the cofactor turn region moves towards the second domain, thus creating space for the pyrrole rings added at each stage. Residues of the flexible active site loop play a significant role in its modulation. Steered molecular dynamics was performed to predict the exit mechanism of HMB from PBGD at the end of the catalytic cycle. Based on the force profile and minimal structural changes the proposed path for the exit of HMB is through the space between the domains flanking the active site loop. Residues reported as catalytically important, also play an important role in the exit of HMB. Further, upon removal of HMB, the structure of PBGD gradually relaxes to resemble its initial stage structure, indicating its readiness to resume a new catalytic cycle. PMID:24603363

Loop-the-Loop: Bringing Theory into Practice

ERIC Educational Resources Information Center

Suwonjandee, N.; Asavapibhop, B.

2012-01-01

During the Thai high-school physics teacher training programme, we used an aluminum loop-the-loop system built by the Institute for the Promotion of Teaching Science and Technology (IPST) to demonstrate a circular motion and investigate the concept of the conservation of mechanical energy. There were 27 high-school teachers from three provinces,…

Catalytic site identification--a web server to identify catalytic site structural matches throughout PDB.

PubMed

Kirshner, Daniel A; Nilmeier, Jerome P; Lightstone, Felice C

2013-07-01

The catalytic site identification web server provides the innovative capability to find structural matches to a user-specified catalytic site among all Protein Data Bank proteins rapidly (in less than a minute). The server also can examine a user-specified protein structure or model to identify structural matches to a library of catalytic sites. Finally, the server provides a database of pre-calculated matches between all Protein Data Bank proteins and the library of catalytic sites. The database has been used to derive a set of hypothesized novel enzymatic function annotations. In all cases, matches and putative binding sites (protein structure and surfaces) can be visualized interactively online. The website can be accessed at http://catsid.llnl.gov.

Run-time scheduling and execution of loops on message passing machines

NASA Technical Reports Server (NTRS)

Crowley, Kay; Saltz, Joel; Mirchandaney, Ravi; Berryman, Harry

1989-01-01

Sparse system solvers and general purpose codes for solving partial differential equations are examples of the many types of problems whose irregularity can result in poor performance on distributed memory machines. Often, the data structures used in these problems are very flexible. Crucial details concerning loop dependences are encoded in these structures rather than being explicitly represented in the program. Good methods for parallelizing and partitioning these types of problems require assignment of computations in rather arbitrary ways. Naive implementations of programs on distributed memory machines requiring general loop partitions can be extremely inefficient. Instead, the scheduling mechanism needs to capture the data reference patterns of the loops in order to partition the problem. First, the indices assigned to each processor must be locally numbered. Next, it is necessary to precompute what information is needed by each processor at various points in the computation. The precomputed information is then used to generate an execution template designed to carry out the computation, communication, and partitioning of data, in an optimized manner. The design is presented for a general preprocessor and schedule executer, the structures of which do not vary, even though the details of the computation and of the type of information are problem dependent.

Run-time scheduling and execution of loops on message passing machines

NASA Technical Reports Server (NTRS)

Saltz, Joel; Crowley, Kathleen; Mirchandaney, Ravi; Berryman, Harry

1990-01-01

Sparse system solvers and general purpose codes for solving partial differential equations are examples of the many types of problems whose irregularity can result in poor performance on distributed memory machines. Often, the data structures used in these problems are very flexible. Crucial details concerning loop dependences are encoded in these structures rather than being explicitly represented in the program. Good methods for parallelizing and partitioning these types of problems require assignment of computations in rather arbitrary ways. Naive implementations of programs on distributed memory machines requiring general loop partitions can be extremely inefficient. Instead, the scheduling mechanism needs to capture the data reference patterns of the loops in order to partition the problem. First, the indices assigned to each processor must be locally numbered. Next, it is necessary to precompute what information is needed by each processor at various points in the computation. The precomputed information is then used to generate an execution template designed to carry out the computation, communication, and partitioning of data, in an optimized manner. The design is presented for a general preprocessor and schedule executer, the structures of which do not vary, even though the details of the computation and of the type of information are problem dependent.

Pilot modeling and closed-loop analysis of flexible aircraft in the pitch tracking task

NASA Technical Reports Server (NTRS)

Schmidt, D. K.

1983-01-01

The issue addressed in the appropriate modeling technique for pilot vehicle analysis of large flexible aircraft, when the frequency separation between the rigid-body mode and the dynamic aeroelastic modes is reduced. This situation was shown to have significant effects on pitch-tracking performance and subjective rating of the task, obtained via fixed base simulation. Further, the dynamics in these cases are not well modeled with a rigid-body-like model obtained by including only 'static elastic' effects, for example. It is shown that pilot/vehicle analysis of this data supports the hypothesis that an appropriate pilot-model structure is an optimal-control pilot model of full order. This is in contrast to the contention that a representative model is of reduced order when the subject is controlling high-order dynamics as in a flexible vehicle. The key appears to be in the correct assessment of the pilot's objective of attempting to control 'rigid-body' vehicle response, a response that must be estimated by the pilot from observations contaminated by aeroelastic dynamics. Finally, a model-based metric is shown to correlate well with the pilot's subjective ratings.

Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.

PubMed

Schudoma, Christian; May, Patrick; Nikiforova, Viktoria; Walther, Dirk

2010-01-01

The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence-structure relationships in loops. Loops differing by <25% in sequence identity fold into very similar structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts.

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics.

PubMed

Armen, Roger S; Chen, Jianhan; Brooks, Charles L

2009-10-13

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.

Modular high-voltage bias generator powered by dual-looped self-adaptive wireless power transmission.

PubMed

Xie, Kai; Huang, An-Feng; Li, Xiao-Ping; Guo, Shi-Zhong; Zhang, Han-Lu

2015-04-01

We proposed a modular high-voltage (HV) bias generator powered by a novel transmitter-sharing inductive coupled wireless power transmission technology, aimed to extend the generator's flexibility and configurability. To solve the problems caused through an uncertain number of modules, a dual-looped self-adaptive control method is proposed that is capable of tracking resonance frequency while maintaining a relatively stable induction voltage for each HV module. The method combines a phase-locked loop and a current feedback loop, which ensures an accurate resonance state and a relatively constant boost ratio for each module, simplifying the architecture of the boost stage and improving the total efficiency. The prototype was built and tested. The input voltage drop of each module is less than 14% if the module number varies from 3 to 10; resonance tracking is completed within 60 ms. The efficiency of the coupling structure reaches up to 95%, whereas the total efficiency approaches 73% for a rated output. Furthermore, this technology can be used in various multi-load wireless power supply applications.

Differences in the catalytic mechanisms of mesophilic and thermophilic indole-3-glycerol phosphate synthase enzymes at their adaptive temperatures.

PubMed

Zaccardi, Margot J; Mannweiler, Olga; Boehr, David D

2012-02-10

Thermophilic enzymes tend to be less catalytically-active at lower temperatures relative to their mesophilic counterparts, despite having very similar crystal structures. An often cited hypothesis for this general observation is that thermostable enzymes have evolved a more rigid tertiary structure in order to cope with their more extreme, natural environment, but they are also less flexible at lower temperatures, leading to their lower catalytic activity under mesophilic conditions. An alternative hypothesis, however, is that complementary thermophilic-mesophilic enzyme pairs simply operate through different evolutionary-optimized catalytic mechanisms. In this communication, we present evidence that while the steps of the catalytic mechanisms for mesophilic and thermophilic indole-3-glycerol phosphate synthase (IGPS) enzymes are fundamentally similar, the identity of the rate-determining step changes as a function of temperature. Our findings indicate that while product release is rate-determining at 25°C for thermophilic IGPS, near its adaptive temperature (75°C), a proton transfer event, involving a general acid, becomes rate-determining. The rate-determining steps for thermophilic and mesophilic IGPS enzymes are also different at their respective, adaptive temperatures with the mesophilic IGPS-catalyzed reaction being rate-limited before irreversible CO2 release, and the thermophilic IGPS-catalyzed reaction being rate limited afterwards. Copyright © 2012 Elsevier Inc. All rights reserved.

Catalytic distillation structure

DOEpatents

Smith, Jr., Lawrence A.

1984-01-01

Catalytic distillation structure for use in reaction distillation columns, a providing reaction sites and distillation structure and consisting of a catalyst component and a resilient component intimately associated therewith. The resilient component has at least about 70 volume % open space and being present with the catalyst component in an amount such that the catalytic distillation structure consist of at least 10 volume % open space.

Catalytic distillation structure

DOEpatents

Smith, L.A. Jr.

1984-04-17

Catalytic distillation structure is described for use in reaction distillation columns, and provides reaction sites and distillation structure consisting of a catalyst component and a resilient component intimately associated therewith. The resilient component has at least about 70 volume % open space and is present with the catalyst component in an amount such that the catalytic distillation structure consists of at least 10 volume % open space. 10 figs.

Simple and Flexible Self-Reproducing Structures in Asynchronous Cellular Automata and Their Dynamics

NASA Astrophysics Data System (ADS)

Huang, Xin; Lee, Jia; Yang, Rui-Long; Zhu, Qing-Sheng

2013-03-01

Self-reproduction on asynchronous cellular automata (ACAs) has attracted wide attention due to the evident artifacts induced by synchronous updating. Asynchronous updating, which allows cells to undergo transitions independently at random times, might be more compatible with the natural processes occurring at micro-scale, but the dark side of the coin is the increment in the complexity of an ACA in order to accomplish stable self-reproduction. This paper proposes a novel model of self-timed cellular automata (STCAs), a special type of ACAs, where unsheathed loops are able to duplicate themselves reliably in parallel. The removal of sheath cannot only allow various loops with more flexible and compact structures to replicate themselves, but also reduce the number of cell states of the STCA as compared to the previous model adopting sheathed loops [Y. Takada, T. Isokawa, F. Peper and N. Matsui, Physica D227, 26 (2007)]. The lack of sheath, on the other hand, often tends to cause much more complicated interactions among loops, when all of them struggle independently to stretch out their constructing arms at the same time. In particular, such intense collisions may even cause the emergence of a mess of twisted constructing arms in the cellular space. By using a simple and natural method, our self-reproducing loops (SRLs) are able to retract their arms successively, thereby disentangling from the mess successfully.

LOOP CALCULUS AND BELIEF PROPAGATION FOR Q-ARY ALPHABET: LOOP TOWER

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

CHERTKOV, MICHAEL; CHERNYAK, VLADIMIR

Loop calculus introduced in [1], [2] constitutes a new theoretical tool that explicitly expresses symbol Maximum-A-Posteriori (MAP) solution of a general statistical inference problem via a solution of the Belief Propagation (BP) equations. This finding brought a new significance to the BP concept, which in the past was thought of as just a loop-free approximation. In this paper they continue a discussion of the Loop Calculus, partitioning the results into three Sections. In Section 1 they introduce a new formulation of the Loop Calculus in terms of a set of transformations (gauges) that keeping the partition function of the problemmore » invariant. The full expression contains two terms referred to as the 'ground state' and 'excited states' contributions. The BP equations are interpreted as a special (BP) gauge fixing condition that emerges as a special orthogonality constraint between the ground state and excited states, which also selects loop contributions as the only surviving ones among the excited states. In Section 2 they demonstrate how the invariant interpretation of the Loop Calculus, introduced in Section 1, allows a natural extension to the case of a general q-ary alphabet, this is achieved via a loop tower sequential construction. The ground level in the tower is exactly equivalent to assigning one color (out of q available) to the 'ground state' and considering all 'excited' states colored in the remaining (q-1) colors, according to the loop calculus rule. Sequentially, the second level in the tower corresponds to selecting a loop from the previous step, colored in (q-1) colors, and repeating the same ground vs excited states splitting procedure into one and (q-2) colors respectively. The construction proceeds till the full (q-1)-levels deep loop tower (and the corresponding contributions to the partition function) are established. In Section 3 they discuss an ultimate relation between the loop calculus and the Bethe-Free energy variational

Flexible ceramic gasket for SOFC generator

DOEpatents

Zafred, Paolo [Murrysville, PA; Prevish, Thomas [Trafford, PA

2009-02-03

A solid oxide fuel cell generator (10) contains stacks of hollow axially elongated fuel cells (36) having an open top end (37), an oxidant inlet plenum (52), a feed fuel plenum (11), a combustion chamber (94) for combusting reacted oxidant/spent fuel; and, optionally, a fuel recirculation chamber (106) below the combustion chamber (94), where the fuel recirculation chamber (94) is in part defined by semi-porous fuel cell positioning gasket (108), all within an outer generator enclosure (8), wherein the fuel cell gasket (108) has a laminate structure comprising at least a compliant fibrous mat support layer and a strong, yet flexible woven layer, which may contain catalytic particles facing the combustion chamber, where the catalyst, if used, is effective to further oxidize exhaust fuel and protect the open top end (37) of the fuel cells.

Livermore Compiler Analysis Loop Suite

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

Hornung, R. D.

2013-03-01

LCALS is designed to evaluate compiler optimizations and performance of a variety of loop kernels and loop traversal software constructs. Some of the loop kernels are pulled directly from "Livermore Loops Coded in C", developed at LLNL (see item 11 below for details of earlier code versions). The older suites were used to evaluate floating-point performances of hardware platforms prior to porting larger application codes. The LCALS suite is geared toward assissing C++ compiler optimizations and platform performance related to SIMD vectorization, OpenMP threading, and advanced C++ language features. LCALS contains 20 of 24 loop kernels from the older Livermoremore » Loop suites, plus various others representative of loops found in current production appkication codes at LLNL. The latter loops emphasize more diverse loop constructs and data access patterns than the others, such as multi-dimensional difference stencils. The loops are included in a configurable framework, which allows control of compilation, loop sampling for execution timing, which loops are run and their lengths. It generates timing statistics for analysis and comparing variants of individual loops. Also, it is easy to add loops to the suite as desired.« less

Catalytic site identification—a web server to identify catalytic site structural matches throughout PDB

PubMed Central

Kirshner, Daniel A.; Nilmeier, Jerome P.; Lightstone, Felice C.

2013-01-01

The catalytic site identification web server provides the innovative capability to find structural matches to a user-specified catalytic site among all Protein Data Bank proteins rapidly (in less than a minute). The server also can examine a user-specified protein structure or model to identify structural matches to a library of catalytic sites. Finally, the server provides a database of pre-calculated matches between all Protein Data Bank proteins and the library of catalytic sites. The database has been used to derive a set of hypothesized novel enzymatic function annotations. In all cases, matches and putative binding sites (protein structure and surfaces) can be visualized interactively online. The website can be accessed at http://catsid.llnl.gov. PMID:23680785

Fast flux locked loop

DOEpatents

Ganther, Jr., Kenneth R.; Snapp, Lowell D.

2002-09-10

A flux locked loop for providing an electrical feedback signal, the flux locked loop employing radio-frequency components and technology to extend the flux modulation frequency and tracking loop bandwidth. The flux locked loop of the present invention has particularly useful application in read-out electronics for DC SQUID magnetic measurement systems, in which case the electrical signal output by the flux locked loop represents an unknown magnetic flux applied to the DC SQUID.

Catalytic molecularly imprinted polymer membranes: development of the biomimetic sensor for phenols detection.

PubMed

Sergeyeva, T A; Slinchenko, O A; Gorbach, L A; Matyushov, V F; Brovko, O O; Piletsky, S A; Sergeeva, L M; Elska, G V

2010-02-05

Portable biomimetic sensor devices for the express control of phenols content in water were developed. The synthetic binding sites mimicking active site of the enzyme tyrosinase were formed in the structure of free-standing molecularly imprinted polymer membranes. Molecularly imprinted polymer membranes with the catalytic activity were obtained by co-polymerization of the complex Cu(II)-catechol-urocanic acid ethyl ester with (tri)ethyleneglycoldimethacrylate, and oligourethaneacrylate. Addition of the elastic component oligourethaneacrylate provided formation of the highly cross-linked polymer with the catalytic activity in a form of thin, flexible, and mechanically stable membrane. High accessibility of the artificial catalytic sites for the interaction with the analyzed phenol molecules was achieved due to addition of linear polymer (polyethyleneglycol Mw 20,000) to the initial monomer mixture before the polymerization. As a result, typical semi-interpenetrating polymer networks (semi-IPNs) were formed. The cross-linked component of the semi-IPN was represented by the highly cross-linked catalytic molecularly imprinted polymer, while the linear one was represented by polyethyleneglycol Mw 20,000. Extraction of the linear polymer from the fully formed semi-IPN resulted in formation of large pores in the membranes' structure. Concentration of phenols in the analyzed samples was detected using universal portable device oxymeter with the oxygen electrode in a close contact with the catalytic molecularly imprinted polymer membrane as a transducer. The detection limit of phenols detection using the developed sensor system based on polymers-biomimics with the optimized composition comprised 0.063 mM, while the linear range of the sensor comprised 0.063-1 mM. The working characteristics of the portable sensor devices were investigated. Storage stability of sensor systems at room temperature comprised 12 months (87%). As compared to traditional methods of phenols

Megawatt-Scale Power Hardware-in-the-Loop Simulation Testing of a Power Conversion Module for Naval Applications

DTIC Science & Technology

2015-06-21

problem was detected . Protection elements were implemented to trigger on over- voltage , over-current, over/under-frequency, and zero-sequence voltage ...power hardware in the loop simulation of distribution networks with photovoltaic generation,” International Journal of Renewable Energy Research...source modules were intended to support both emulation of a representative gas turbine generator set, as well as a flexible, controllable voltage source

Catalytic ignition of hydrogen/oxygen

NASA Technical Reports Server (NTRS)

Green, James M.; Zurawski, Robert L.

1988-01-01

An experimental program was conducted to evaluate the catalytic ignition of gaseous hydrogen and oxygen. Shell 405 granular catalyst and a unique monolithic sponge catalyst were tested. Mixture ratio, mass flow rate, propellant inlet temperature, and back pressure were varied parametrically in testing to determine the operational limits of a catalytic igniter. The test results showed that the gaseous hydrogen/oxygen propellant combination can be ignited catalytically using Shell 405 catalyst over a wide range of mixture ratios, mass flow rates, and propellant injection temperatures. These operating conditions must be optimized to ensure reliable ignition for an extended period of time. The results of the experimental program and the established operational limits for a catalytic igniter using both the granular and monolithic catalysts are presented. The capabilities of a facility constructed to conduct the igniter testing and the advantages of a catalytic igniter over other ignition systems for gaseous hydrogen and oxygen are also discussed.

Introduction to Loop Heat Pipes

NASA Technical Reports Server (NTRS)

Ku, Jentung

2015-01-01

This is the presentation file for the short course Introduction to Loop Heat Pipes, to be conducted at the 2015 Thermal Fluids and Analysis Workshop, August 3-7, 2015, Silver Spring, Maryland. This course will discuss operating principles and performance characteristics of a loop heat pipe. Topics include: 1) pressure profiles in the loop; 2) loop operating temperature; 3) operating temperature control; 4) loop startup; 4) loop shutdown; 5) loop transient behaviors; 6) sizing of loop components and determination of fluid inventory; 7) analytical modeling; 8) examples of flight applications; and 9) recent LHP developments.

CryoEM and image sorting for flexible protein/DNA complexes.

PubMed

Villarreal, Seth A; Stewart, Phoebe L

2014-07-01

Intrinsically disordered regions of proteins and conformational flexibility within complexes can be critical for biological function. However, disorder, flexibility, and heterogeneity often hinder structural analyses. CryoEM and single particle image processing techniques offer the possibility of imaging samples with significant flexibility. Division of particle images into more homogenous subsets after data acquisition can help compensate for heterogeneity within the sample. We present the utility of an eigenimage sorting analysis for examining two protein/DNA complexes with significant conformational flexibility and heterogeneity. These complexes are integral to the non-homologous end joining pathway, and are involved in the repair of double strand breaks of DNA. Both complexes include the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and biotinylated DNA with bound streptavidin, with one complex containing the Ku heterodimer. Initial 3D reconstructions of the two DNA-PKcs complexes resembled a cryoEM structure of uncomplexed DNA-PKcs without additional density clearly attributable to the remaining components. Application of eigenimage sorting allowed division of the DNA-PKcs complex datasets into more homogeneous subsets. This led to visualization of density near the base of the DNA-PKcs that can be attributed to DNA, streptavidin, and Ku. However, comparison of projections of the subset structures with 2D class averages indicated that a significant level of heterogeneity remained within each subset. In summary, image sorting methods allowed visualization of extra density near the base of DNA-PKcs, suggesting that DNA binds in the vicinity of the base of the molecule and potentially to a flexible region of DNA-PKcs. Copyright © 2013 Elsevier Inc. All rights reserved.

Dynamic modelling and adaptive robust tracking control of a space robot with two-link flexible manipulators under unknown disturbances

NASA Astrophysics Data System (ADS)

Yang, Xinxin; Ge, Shuzhi Sam; He, Wei

2018-04-01

In this paper, both the closed-form dynamics and adaptive robust tracking control of a space robot with two-link flexible manipulators under unknown disturbances are developed. The dynamic model of the system is described with assumed modes approach and Lagrangian method. The flexible manipulators are represented as Euler-Bernoulli beams. Based on singular perturbation technique, the displacements/joint angles and flexible modes are modelled as slow and fast variables, respectively. A sliding mode control is designed for trajectories tracking of the slow subsystem under unknown but bounded disturbances, and an adaptive sliding mode control is derived for slow subsystem under unknown slowly time-varying disturbances. An optimal linear quadratic regulator method is proposed for the fast subsystem to damp out the vibrations of the flexible manipulators. Theoretical analysis validates the stability of the proposed composite controller. Numerical simulation results demonstrate the performance of the closed-loop flexible space robot system.

OPE for super loops

NASA Astrophysics Data System (ADS)

Sever, Amit; Vieira, Pedro; Wang, Tianheng

2011-11-01

We extend the Operator Product Expansion for Null Polygon Wilson loops to the Mason-Skinner-Caron-Huot super loop dual to non MHV gluon amplitudes. We explain how the known tree level amplitudes can be promoted into an infinite amount of data at any loop order in the OPE picture. As an application, we re-derive all one loop NMHV six gluon amplitudes by promoting their tree level expressions. We also present some new all loops predictions for these amplitudes.

High Performance, Robust Control of Flexible Space Structures: MSFC Center Director's Discretionary Fund

NASA Technical Reports Server (NTRS)

Whorton, M. S.

1998-01-01

Many spacecraft systems have ambitious objectives that place stringent requirements on control systems. Achievable performance is often limited because of difficulty of obtaining accurate models for flexible space structures. To achieve sufficiently high performance to accomplish mission objectives may require the ability to refine the control design model based on closed-loop test data and tune the controller based on the refined model. A control system design procedure is developed based on mixed H2/H(infinity) optimization to synthesize a set of controllers explicitly trading between nominal performance and robust stability. A homotopy algorithm is presented which generates a trajectory of gains that may be implemented to determine maximum achievable performance for a given model error bound. Examples show that a better balance between robustness and performance is obtained using the mixed H2/H(infinity) design method than either H2 or mu-synthesis control design. A second contribution is a new procedure for closed-loop system identification which refines parameters of a control design model in a canonical realization. Examples demonstrate convergence of the parameter estimation and improved performance realized by using the refined model for controller redesign. These developments result in an effective mechanism for achieving high-performance control of flexible space structures.

Role of coupled dynamics in the catalytic activity of prokaryotic-like prolyl-tRNA synthetases.

PubMed

Sanford, Brianne; Cao, Bach; Johnson, James M; Zimmerman, Kurt; Strom, Alexander M; Mueller, Robyn M; Bhattacharyya, Sudeep; Musier-Forsyth, Karin; Hati, Sanchita

2012-03-13

Prolyl-tRNA synthetases (ProRSs) have been shown to activate both cognate and some noncognate amino acids and attach them to specific tRNA(Pro) substrates. For example, alanine, which is smaller than cognate proline, is misactivated by Escherichia coli ProRS. Mischarged Ala-tRNA(Pro) is hydrolyzed by an editing domain (INS) that is distinct from the activation domain. It was previously shown that deletion of the INS greatly reduced cognate proline activation efficiency. In this study, experimental and computational approaches were used to test the hypothesis that deletion of the INS alters the internal protein dynamics leading to reduced catalytic function. Kinetic studies with two ProRS variants, G217A and E218A, revealed decreased amino acid activation efficiency. Molecular dynamics studies showed motional coupling between the INS and protein segments containing the catalytically important proline-binding loop (PBL, residues 199-206). In particular, the complete deletion of INS, as well as mutation of G217 or E218 to alanine, exhibited significant effects on the motion of the PBL. The presence of coupled dynamics between neighboring protein segments was also observed through in silico mutations and essential dynamics analysis. Altogether, this study demonstrates that structural elements at the editing domain-activation domain interface participate in coupled motions that facilitate amino acid binding and catalysis by bacterial ProRSs, which may explain why truncated or defunct editing domains have been maintained in some systems, despite the lack of catalytic activity.

The Sugar Model: Catalytic Flow Reactor Dynamics of Pyruvaldehyde Synthesis from Triose Catalyzed by Poly-L-Lysine Contained in a Dialyzer

NASA Technical Reports Server (NTRS)

Weber, Arthur L.; DeVincenzi, Donald (Technical Monitor)

2000-01-01

The formation of pyruvaldehyde from triose sugars was catalyzed by poly-L-lysine contained in a small dialyzer (100 MWCO) suspended in a much larger triose substrate reservoir. The polylysine confined in the dialyzer functioned as a catalytic flow reactor that constantly brought in triose from the substrate reservoir by diffusion to offset the drop in triose concentration within the reactor caused by its conversion to pyruvaldehyde. A 400 mM solution of poly-L-lysine contained in a 0.35 ml dialyzer placed in a 120 ml solution of triose substrate (pH 5.5, 40 C) generated pyruvaldehyde 11 -times faster than an a control reaction without the catalytic dialyzer. However, since the catalytic dialyzer's volume was 343-times smaller than the control reaction, the synthetic intensity (rate/volume) of pyruvaldehyde synthesis within the catalytic dialyzer was 3400-times greater than that of the control reaction and substrate solution. A similar result was obtained using a dialyzer with a 500 MWCO value. Acting as a catalytic flow reactor the polylysine catalytic dialyzer synthesized about 3.5 molecules of pyruvaldehyde per lysine residue in 7 days -- an amount of triose equal to twice the weight of the catalyst. At 7 days the catalytic activity of polylysine was 16% of its initial value, a result indicating catalyst-poisoning caused by reaction of pyruvaldehyde with the e-amino groups of polylysine. The dialyzer method of catalyst containment was selected it provides a simple, flexible, and easily manipulated experimental system for studying the dynamics and evolutionary development of confined autocatalytic processes related to the origin of life under anaerobic conditions.

Reducing model uncertainty effects in flexible manipulators through the addition of passive damping

NASA Technical Reports Server (NTRS)

Alberts, T. E.

1987-01-01

An important issue in the control of practical systems is the effect of model uncertainty on closed loop performance. This is of particular concern when flexible structures are to be controlled, due to the fact that states associated with higher frequency vibration modes are truncated in order to make the control problem tractable. Digital simulations of a single-link manipulator system are employed to demonstrate that passive damping added to the flexible member reduces adverse effects associated with model uncertainty. A controller was designed based on a model including only one flexible mode. This controller was applied to larger order systems to evaluate the effects of modal truncation. Simulations using a Linear Quadratic Regulator (LQR) design assuming full state feedback illustrate the effect of control spillover. Simulations of a system using output feedback illustrate the destabilizing effect of observation spillover. The simulations reveal that the system with passive damping is less susceptible to these effects than the untreated case.

Ciliate telomerase RNA loop IV nucleotides promote hierarchical RNP assembly and holoenzyme stability.

PubMed

Robart, Aaron R; O'Connor, Catherine M; Collins, Kathleen

2010-03-01

Telomerase adds simple-sequence repeats to chromosome 3' ends to compensate for the loss of repeats with each round of genome replication. To accomplish this de novo DNA synthesis, telomerase uses a template within its integral RNA component. In addition to providing the template, the telomerase RNA subunit (TER) also harbors nontemplate motifs that contribute to the specialized telomerase catalytic cycle of reiterative repeat synthesis. Most nontemplate TER motifs function through linkage with the template, but in ciliate and vertebrate telomerases, a stem-loop motif binds telomerase reverse transcriptase (TERT) and reconstitutes full activity of the minimal recombinant TERT+TER RNP, even when physically separated from the template. Here, we resolve the functional requirements for this motif of ciliate TER in physiological RNP context using the Tetrahymena thermophila p65-TER-TERT core RNP reconstituted in vitro and the holoenzyme reconstituted in vivo. Contrary to expectation based on assays of the minimal recombinant RNP, we find that none of a panel of individual loop IV nucleotide substitutions impacts the profile of telomerase product synthesis when reconstituted as physiological core RNP or holoenzyme RNP. However, loop IV nucleotide substitutions do variably reduce assembly of TERT with the p65-TER complex in vitro and reduce the accumulation and stability of telomerase RNP in endogenous holoenzyme context. Our results point to a unifying model of a conformational activation role for this TER motif in the telomerase RNP enzyme.

Method of fabricating a catalytic structure

DOEpatents

Rollins, Harry W [Idaho Falls, ID; Petkovic, Lucia M [Idaho Falls, ID; Ginosar, Daniel M [Idaho Falls, ID

2009-09-22

A precursor to a catalytic structure comprising zinc oxide and copper oxide. The zinc oxide has a sheet-like morphology or a spherical morphology and the copper oxide comprises particles of copper oxide. The copper oxide is reduced to copper, producing the catalytic structure. The catalytic structure is fabricated by a hydrothermal process. A reaction mixture comprising a zinc salt, a copper salt, a hydroxyl ion source, and a structure-directing agent is formed. The reaction mixture is heated under confined volume conditions to produce the precursor. The copper oxide in the precursor is reduced to copper. A method of hydrogenating a carbon oxide using the catalytic structure is also disclosed, as is a system that includes the catalytic structure.

The dynamics and control of large flexible space structures, 8

NASA Technical Reports Server (NTRS)

Bainum, P. M.; Reddy, A. S. S. R.; Diarra, C. M.; Ananthakrishnan, S.

1985-01-01

A development of the in plane open loop rotational equations of motion for the proposed Spacecraft Control Laboratory Experiment (SCOLE) in orbit configuration is presented based on an Eulerian formulation. The mast is considered to be a flexible beam connected to the (rigid) shuttle and the reflector. Frequencies and mode shapes are obtained for the mast vibrational appendage modes (assumed to be decoupled) for different boundary conditions based on continuum approaches and also preliminary results are obtained using a finite element representation of the mast reflector system. The linearized rotational in plane equation is characterized by periodic coefficients and open loop system stability can be examined with an application of the Floquet theorem. Numerical results are presented to illustrate the potential instability associated with actuator time delays even for delays which represent only a small fraction of the natural period of oscillation of the modes contained in the open loop model of the system. When plant and measurement noise effects are added to the previously designed deterministic model of the hoop column system, it is seen that both the system transient and steady state performance are degraded. Mission requirements can be satisfied by appropriate assignment of cost function weighting elements and changes in the ratio of plant noise to measurement noise.

Input preshaping with frequency domain information for flexible-link manipulator control

NASA Technical Reports Server (NTRS)

Tzes, Anthony; Englehart, Matthew J.; Yurkovich, Stephen

1989-01-01

The application of an input preshaping scheme to flexible manipulators is considered. The resulting control corresponds to a feedforward term that convolves in real-time the desired reference input with a sequence of impulses and produces a vibration free output. The robustness of the algorithm with respect to injected disturbances and modal frequency variations is not satisfactory and can be improved by convolving the input with a longer sequence of impulses. The incorporation of the preshaping scheme to a closed-loop plant, using acceleration feedback, offers satisfactory disturbance rejection due to feedback and cancellation of the flexible mode effects due to the preshaping. A frequency domain identification scheme is used to estimate the modal frequencies on-line and subsequently update the spacing between the impulses. The combined adaptive input preshaping scheme provides the fastest possible slew that results in a vibration free output.

Design of a facility for the in situ measurement of catalytic reaction by neutron scattering spectroscopy

NASA Astrophysics Data System (ADS)

Tan, Shuai; Cheng, Yongqiang; Daemen, Luke L.; Lutterman, Daniel A.

2018-01-01

Catalysis is a critical enabling science for future energy needs. The next frontier of catalysis is to evolve from catalyst discovery to catalyst design, and for this next step to be realized, we must develop new techniques to better understand reaction mechanisms. To do this, we must connect catalytic reaction rates and selectivities to the kinetics, energetics, and dynamics of individual elementary steps and relate these to the structure and dynamics of the catalytic sites involved. Neutron scattering spectroscopies offer unique capabilities that are difficult or impossible to match by other techniques. The current study presents the development of a compact and portable instrumental design that enables the in situ investigation of catalytic samples by neutron scattering techniques. The developed apparatus was tested at the Spallation Neutron Source (SNS) in Oak Ridge National Laboratory and includes a gas handling panel that allows for computer hookups to control the panel externally and online measurement equipment such as coupled GC-FID/TCD (Gas Chromatography-Flame Ionization Detector/Thermal Conductivity Detector) and MS (Mass Spectrometry) to characterize offgassing while the sample is in the neutron scattering spectrometer. This system is flexible, modular, compact, and portable enabling its use for many types of gas-solid and liquid-solid reactions at the various beamlines housed at the SNS.

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics

PubMed Central

Armen, Roger S.; Chen, Jianhan; Brooks, Charles L.

2009-01-01

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and “noise” that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds. PMID:20160879

A fragment-based approach applied to a highly flexible target: Insights and challenges towards the inhibition of HSP70 isoforms

NASA Astrophysics Data System (ADS)

Jones, Alan M.; Westwood, Isaac M.; Osborne, James D.; Matthews, Thomas P.; Cheeseman, Matthew D.; Rowlands, Martin G.; Jeganathan, Fiona; Burke, Rosemary; Lee, Diane; Kadi, Nadia; Liu, Manjuan; Richards, Meirion; McAndrew, Craig; Yahya, Norhakim; Dobson, Sarah E.; Jones, Keith; Workman, Paul; Collins, Ian; van Montfort, Rob L. M.

2016-10-01

The heat shock protein 70s (HSP70s) are molecular chaperones implicated in many cancers and of significant interest as targets for novel cancer therapies. Several HSP70 inhibitors have been reported, but because the majority have poor physicochemical properties and for many the exact mode of action is poorly understood, more detailed mechanistic and structural insight into ligand-binding to HSP70s is urgently needed. Here we describe the first comprehensive fragment-based inhibitor exploration of an HSP70 enzyme, which yielded an amino-quinazoline fragment that was elaborated to a novel ATP binding site ligand with different physicochemical properties to known adenosine-based HSP70 inhibitors. Crystal structures of amino-quinazoline ligands bound to the different conformational states of the HSP70 nucleotide binding domain highlighted the challenges of a fragment-based approach when applied to this particular flexible enzyme class with an ATP-binding site that changes shape and size during its catalytic cycle. In these studies we showed that Ser275 is a key residue in the selective binding of ATP. Additionally, the structural data revealed a potential functional role for the ATP ribose moiety in priming the protein for the formation of the ATP-bound pre-hydrolysis complex by influencing the conformation of one of the phosphate binding loops.

Active Site Flexibility as a Hallmark for Efficient PET Degradation by I. sakaiensis PETase.

PubMed

Fecker, Tobias; Galaz-Davison, Pablo; Engelberger, Felipe; Narui, Yoshie; Sotomayor, Marcos; Parra, Loreto P; Ramírez-Sarmiento, César A

2018-03-27

Polyethylene terephthalate (PET) is one of the most-consumed synthetic polymers, with an annual production of 50 million tons. Unfortunately, PET accumulates as waste and is highly resistant to biodegradation. Recently, fungal and bacterial thermophilic hydrolases were found to catalyze PET hydrolysis with optimal activities at high temperatures. Strikingly, an enzyme from Ideonella sakaiensis, termed PETase, was described to efficiently degrade PET at room temperature, but the molecular basis of its activity is not currently understood. Here, a crystal structure of PETase was determined at 2.02 Å resolution and employed in molecular dynamics simulations showing that the active site of PETase has higher flexibility at room temperature than its thermophilic counterparts. This flexibility is controlled by a novel disulfide bond in its active site, with its removal leading to destabilization of the catalytic triad and reduction of the hydrolase activity. Molecular docking of a model substrate predicts that PET binds to PETase in a unique and energetically favorable conformation facilitated by several residue substitutions within its active site when compared to other enzymes. These computational predictions are in excellent agreement with recent mutagenesis and PET film degradation analyses. Finally, we rationalize the increased catalytic activity of PETase at room temperature through molecular dynamics simulations of enzyme-ligand complexes for PETase and other thermophilic PET-degrading enzymes at 298, 323, and 353 K. Our results reveal that both the binding pose and residue substitutions within PETase favor proximity between the catalytic residues and the labile carbonyl of the substrate at room temperature, suggesting a more favorable hydrolytic reaction. These results are valuable for enabling detailed evolutionary analysis of PET-degrading enzymes and for rational design endeavors aiming at increasing the efficiency of PETase and similar enzymes toward plastic

Modal domain fiber optic sensor for closed loop vibration control of a flexible beam

NASA Technical Reports Server (NTRS)

Cox, D.; Thomas, D.; Reichard, K.; Lindner, D.; Claus, R. O.

1990-01-01

The use of a modal domain sensor in a vibration control experiment is described. An optical fiber is bonded along the length of a flexible beam. A control signal derived from the output of the modal domain sensor is used to suppress vibrations induced in the beam. A distributed effect model for the modal domain sensor is developed and combined with models of the beam and actuator dynamics to produce a system suitable for control design.

Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases.

PubMed

Jacques, Benoit; Coinçon, Mathieu; Sygusch, Jurgen

2018-03-28

Crystal structures of two bacterial metal (Zn) dependent D-fructose 1,6-bisphosphate (FBP) aldolases in complex with substrate, analogues, and triose-P reaction products were determined to 1.5-2.0 Å resolution. The ligand complexes cryotrapped in native or mutant H. pylori aldolase crystals enabled a novel mechanistic description of FBP C 3 -C 4 bond cleavage. The reaction mechanism uses active site remodelling during the catalytic cycle implicating relocation of the Zn cofactor that is mediated by conformational changes of active site loops. Substrate binding initiates conformational changes, triggered upon P 1 -phosphate binding, which liberates the Zn chelating His180, allowing it to act as a general base for the proton abstraction at the FBP C 4 -hydroxyl group. A second zinc chelating His83 hydrogen bonds the substrate C 4 - hydroxyl group and assists cleavage by stabilizing the developing negative charge during proton abstraction. Cleavage is concerted with relocation of the metal cofactor from an interior to a surface exposed site, thereby stabilizing the nascent enediolate form. Conserved residue Glu142 is essential for protonation of the enediolate form, prior to product release. A D-tagatose 1,6-bisphosphate enzymatic complex reveals how His180 mediated proton abstraction controls stereospecificity of the cleavage reaction. Recognition and discrimination of the reaction products, dihydroxyacetone-P and D-glyceraldehyde-3-P, occurs via charged hydrogen bonds between hydroxyl groups of the triose-Ps and conserved residues, Asp82 and Asp255, respectively, and are crucial aspects of the enzyme's role in gluconeogenesis. Conformational changes in mobile loops β5-α7 and β6-α8 (containing catalytic residues Glu142 and His180, respectively) drive active site remodelling enabling the relocation of the metal cofactor. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Substrate Specificities and Conformational Flexibility of 3-Ketosteroid 9α-Hydroxylases*

PubMed Central

Penfield, Jonathan S.; Worrall, Liam J.; Strynadka, Natalie C.; Eltis, Lindsay D.

2014-01-01

KshA is the oxygenase component of 3-ketosteroid 9α-hydroxylase, a Rieske oxygenase involved in the bacterial degradation of steroids. Consistent with its role in bile acid catabolism, KshA1 from Rhodococcus rhodochrous DSM43269 had the highest apparent specificity (kcat/Km) for steroids with an isopropyl side chain at C17, such as 3-oxo-23,24-bisnorcholesta-1,4-diene-22-oate (1,4-BNC). By contrast, the KshA5 homolog had the highest apparent specificity for substrates with no C17 side chain (kcat/Km >105 s−1 m−1 for 4-estrendione, 5α-androstandione, and testosterone). Unexpectedly, substrates such as 4-androstene-3,17-dione (ADD) and 4-BNC displayed strong substrate inhibition (KiS ∼100 μm). By comparison, the cholesterol-degrading KshAMtb from Mycobacterium tuberculosis had the highest specificity for CoA-thioesterified substrates. These specificities are consistent with differences in the catabolism of cholesterol and bile acids, respectively, in actinobacteria. X-ray crystallographic structures of the KshAMtb·ADD, KshA1·1,4-BNC-CoA, KshA5·ADD, and KshA5·1,4-BNC-CoA complexes revealed that the enzymes have very similar steroid-binding pockets with the substrate's C17 oriented toward the active site opening. Comparisons suggest Tyr-245 and Phe-297 are determinants of KshA1 specificity. All enzymes have a flexible 16-residue “mouth loop,” which in some structures completely occluded the substrate-binding pocket from the bulk solvent. Remarkably, the catalytic iron and α-helices harboring its ligands were displaced up to 4.4 Å in the KshA5·substrate complexes as compared with substrate-free KshA, suggesting that Rieske oxygenases may have a dynamic nature similar to cytochrome P450. PMID:25049233

Electrolyzers Enhancing Flexibility in Electric Grids

DOE PAGES

Mohanpurkar, Manish; Luo, Yusheng; Terlip, Danny; ...

2017-11-10

This paper presents a real-time simulation with a hardware-in-the-loop (HIL)-based approach for verifying the performance of electrolyzer systems in providing grid support. Hydrogen refueling stations may use electrolyzer systems to generate hydrogen and are proposed to have the potential of becoming smarter loads that can proactively provide grid services. On the basis of experimental findings, electrolyzer systems with balance of plant are observed to have a high level of controllability and hence can add flexibility to the grid from the demand side. A generic front end controller (FEC) is proposed, which enables an optimal operation of the load on themore » basis of market and grid conditions. This controller has been simulated and tested in a real-time environment with electrolyzer hardware for a performance assessment. It can optimize the operation of electrolyzer systems on the basis of the information collected by a communication module. Real-time simulation tests are performed to verify the performance of the FEC-driven electrolyzers to provide grid support that enables flexibility, greater economic revenue, and grid support for hydrogen producers under dynamic conditions. In conclusion, the FEC proposed in this paper is tested with electrolyzers, however, it is proposed as a generic control topology that is applicable to any load.« less

Initial Binding of Ions to the Interhelical Loops of Divalent Ion Transporter CorA: Replica Exchange Molecular Dynamics Simulation Study

PubMed Central

Zhang, Tong; Mu, Yuguang

2012-01-01

Crystal structures of Thermotoga maritima magnesium transporter CorA, reported in 2006, revealed its homo-pentameric constructions. However, the structure of the highly conserved extracellular interhelical loops remains unsolved, due to its high flexibility. We have explored the configurations of the loops through extensive replica exchange molecular dynamics simulations in explicit solvent model with the presence of either Co(III) Hexamine ions or Mg2+ ions. We found that there are multiple binding sites available on the interhelical loops in which the negatively charged residues, E316 and E320, are located notably close to the positively charged ions during the simulations. Our simulations resolved the distinct binding patterns of the two kinds of ions: Co(III) Hexamine ions were found to bind stronger with the loop than Mg2+ ions with binding free energy −7.3 kJ/mol lower, which is nicely consistent with the previous data. Our study provides an atomic basis description of the initial binding process of Mg2+ ions on the extracellular interhelical loops of CorA and the detailed inhibition mechanism of Co(III) Hexamine ions on CorA ions transportation. PMID:22952795

Catalytic nanoporous membranes

DOEpatents

Pellin, Michael J [Naperville, IL; Hryn, John N [Naperville, IL; Elam, Jeffrey W [Elmhurst, IL

2009-12-01

A nanoporous catalytic membrane which displays several unique features including pores which can go through the entire thickness of the membrane. The membrane has a higher catalytic and product selectivity than conventional catalysts. Anodic aluminum oxide (AAO) membranes serve as the catalyst substrate. This substrate is then subjected to Atomic Layer Deposition (ALD), which allows the controlled narrowing of the pores from 40 nm to 10 nm in the substrate by deposition of a preparatory material. Subsequent deposition of a catalytic layer on the inner surfaces of the pores reduces pore sizes to less than 10 nm and allows for a higher degree of reaction selectivity. The small pore sizes allow control over which molecules enter the pores, and the flow-through feature can allow for partial oxidation of reactant species as opposed to complete oxidation. A nanoporous separation membrane, produced by ALD is also provided for use in gaseous and liquid separations. The membrane has a high flow rate of material with 100% selectivity.

Multiple Flow Loop SCADA System Implemented on the Production Prototype Loop

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

Baily, Scott A.; Dalmas, Dale Allen; Wheat, Robert Mitchell

2015-11-16

The following report covers FY 15 activities to develop supervisory control and data acquisition (SCADA) system for the Northstar Moly99 production prototype gas flow loop. The goal of this effort is to expand the existing system to include a second flow loop with a larger production-sized blower. Besides testing the larger blower, this system will demonstrate the scalability of our solution to multiple flow loops.

A time domain inverse dynamic method for the end point tracking control of a flexible manipulator

NASA Technical Reports Server (NTRS)

Kwon, Dong-Soo; Book, Wayne J.

1991-01-01

The inverse dynamic equation of a flexible manipulator was solved in the time domain. By dividing the inverse system equation into the causal part and the anticausal part, we calculated the torque and the trajectories of all state variables for a given end point trajectory. The interpretation of this method in the frequency domain was explained in detail using the two-sided Laplace transform and the convolution integral. The open loop control of the inverse dynamic method shows an excellent result in simulation. For real applications, a practical control strategy is proposed by adding a feedback tracking control loop to the inverse dynamic feedforward control, and its good experimental performance is presented.

Testing the Use of Implicit Solvent in the Molecular Dynamics Modelling of DNA Flexibility

NASA Astrophysics Data System (ADS)

Mitchell, J.; Harris, S.

DNA flexibility controls packaging, looping and in some cases sequence specific protein binding. Molecular dynamics simulations carried out with a computationally efficient implicit solvent model are potentially a powerful tool for studying larger DNA molecules than can be currently simulated when water and counterions are represented explicitly. In this work we compare DNA flexibility at the base pair step level modelled using an implicit solvent model to that previously determined from explicit solvent simulations and database analysis. Although much of the sequence dependent behaviour is preserved in implicit solvent, the DNA is considerably more flexible when the approximate model is used. In addition we test the ability of the implicit solvent to model stress induced DNA disruptions by simulating a series of DNA minicircle topoisomers which vary in size and superhelical density. When compared with previously run explicit solvent simulations, we find that while the levels of DNA denaturation are similar using both computational methodologies, the specific structural form of the disruptions is different.

Control of a flexible planar truss using proof mass actuators

NASA Technical Reports Server (NTRS)

Minas, Constantinos; Garcia, Ephrahim; Inman, Daniel J.

1989-01-01

A flexible structure was modeled and actively controlled by using a single space realizable linear proof mass actuator. The NASA/UVA/UB actuator was attached to a flexible planar truss structure at an optimal location and it was considered as both passive and active device. The placement of the actuator was specified by examining the eigenvalues of the modified model that included the actuator dynamics, and the frequency response functions of the modified system. The electronic stiffness of the actuator was specified, such that the proof mass actuator system was tuned to the fourth structural mode of the truss by using traditional vibration absorber design. The active control law was limited to velocity feedback by integrating of the signals of two accelerometers attached to the structure. The two lower modes of the closed-loop structure were placed further in the LHS of the complex plane. The theoretically predicted passive and active control law was experimentally verified.

Redistribution of flexibility in stabilizing antibody fragment mutants follows Le Châtelier's principle.

PubMed

Li, Tong; Tracka, Malgorzata B; Uddin, Shahid; Casas-Finet, Jose; Jacobs, Donald J; Livesay, Dennis R

2014-01-01

Le Châtelier's principle is the cornerstone of our understanding of chemical equilibria. When a system at equilibrium undergoes a change in concentration or thermodynamic state (i.e., temperature, pressure, etc.), La Châtelier's principle states that an equilibrium shift will occur to offset the perturbation and a new equilibrium is established. We demonstrate that the effects of stabilizing mutations on the rigidity ⇔ flexibility equilibrium within the native state ensemble manifest themselves through enthalpy-entropy compensation as the protein structure adjusts to restore the global balance between the two. Specifically, we characterize the effects of mutation to single chain fragments of the anti-lymphotoxin-β receptor antibody using a computational Distance Constraint Model. Statistically significant changes in the distribution of both rigidity and flexibility within the molecular structure is typically observed, where the local perturbations often lead to distal shifts in flexibility and rigidity profiles. Nevertheless, the net gain or loss in flexibility of individual mutants can be skewed. Despite all mutants being exclusively stabilizing in this dataset, increased flexibility is slightly more common than increased rigidity. Mechanistically the redistribution of flexibility is largely controlled by changes in the H-bond network. For example, a stabilizing mutation can induce an increase in rigidity locally due to the formation of new H-bonds, and simultaneously break H-bonds elsewhere leading to increased flexibility distant from the mutation site via Le Châtelier. Increased flexibility within the VH β4/β5 loop is a noteworthy illustration of this long-range effect.

Redox competition mode of scanning electrochemical microscopy (RC-SECM) for visualisation of local catalytic activity.

PubMed

Eckhard, Kathrin; Chen, Xingxing; Turcu, Florin; Schuhmann, Wolfgang

2006-12-07

In order to locally analyse catalytic activity on modified surfaces a transient redox competition mode of scanning electrochemical microscopy (SECM) has been developed. In a bi-potentiostatic experiment the SECM tip competes with the sample for the very same analyte. This leads to a current decrease at the SECM tip, if it is positioned in close proximity to an active catalyst site on the surface. Specifically, local catalytic activity of a Pt-catalyst modified sample with respect to the catalytic reduction of molecular oxygen was investigated. At higher local catalytic activity the local 02 partial pressure within the gap between accurately positioned SECM tip and sample is depleted, leading to a noticeable tip current decrease over active sites. A flexible software module has been implemented into the SECM to adapt the competition conditions by proper definition of tip and sample potentials. A potential pulse profile enables the localised electrochemically induced generation of molecular oxygen prior to the competition detection. The current decay curves are recorded over the entire duration of the applied reduction pulse. Hence, a time resolved processing of the acquired current values provides movies of the local oxygen concentration against x,y-position. The SECM redox competition mode was verified with a macroscopic Pt-disk electrode as a test sample to demonstrate the feasibility of the approach. Moreover, highly dispersed electro-deposited spots of gold and platinum on glassy carbon were visualised using the redox competition mode of SECM. Catalyst spots of different nature as well as activity inhomogeneities within one spot caused by local variations in Pt-loading were visualised successfully.

An RNA internal loop acts as a hinge to facilitate ribozyme folding and catalysis.

PubMed Central

Szewczak, A A; Cech, T R

1997-01-01

RNA molecules commonly consist of helical regions separated by internal loops, and in many cases these internal loops have been found to assume stable structures. We have examined the function and dynamics of an internal loop, J5/5a, that joins the two halves of the P4-P6 domain of the Tetrahymena self-splicing group I intron. P4-P6 RNAs with mutations in the J5/5a region showed nondenaturing gel electrophoretic mobilities and levels of Fe(II)-EDTA cleavage protection intermediate between those of wild-type RNA and a mutant incapable of folding into the native P4-P6 tertiary structure. Mutants with the least structured J5/5a loops behaved the most like wild-type P4-P6, and required smaller amounts of Mg2+ to rescue folding. The activity of reconstituted introns containing mutant P4-P6 RNAs correlated similarly with the nature of the J5/5a mutation. Our results suggest that, in solution, the P4-P6 RNA is in a two-state equilibrium between folded and unfolded states. We conclude that this internal loop mainly acts as a flexible hinge, allowing the coaxially stacked helical regions on either side of it to interact via specific tertiary contacts. To a lesser extent, the specific bases within the loop contribute to folding. Furthermore, it is crucial that the junction remain unstructured in the unfolded state. These conclusions cannot be derived from a simple examination of the P4-P6 crystal structure (Cate JH et al., 1996, Science 273:1678-1685), showing once again that structure determination must be supplemented with mutational and thermodynamic analysis to provide a complete picture of a folded macromolecule. PMID:9257643

Modified nonlinear amplifying loop mirror for mode-locked fibre oscillators with record-high energy and high-average-power pulsed output

NASA Astrophysics Data System (ADS)

Kobtsev, Sergey; Ivanenko, Alexey; Smirnov, Sergey; Kokhanovsky, Alexey

2018-02-01

The present work proposes and studies approaches for development of new modified non-linear amplifying loop mirror (NALM) allowing flexible and dynamic control of their non-linear properties within a relatively broad range of radiation powers. Using two independently pumped active media in the loop reflector constitutes one of the most promising approaches to development of better NALM with nonlinear properties controllable independently of the intra-cavity radiation power. This work reports on experimental and theoretical studies of the proposed redesigned NALM allowing both a higher level of energy parameters of output generated by mode-locked fibre oscillators and new possibilities of switching among different mode-locked regimes.

N -loop running should be combined with N -loop matching

NASA Astrophysics Data System (ADS)

Braathen, Johannes; Goodsell, Mark D.; Krauss, Manuel E.; Opferkuch, Toby; Staub, Florian

2018-01-01

We investigate the high-scale behavior of Higgs sectors beyond the Standard Model, pointing out that the proper matching of the quartic couplings before applying the renormalization group equations (RGEs) is of crucial importance for reliable predictions at larger energy scales. In particular, the common practice of leading-order parameters in the RGE evolution is insufficient to make precise statements on a given model's UV behavior, typically resulting in uncertainties of many orders of magnitude. We argue that, before applying N -loop RGEs, a matching should even be performed at N -loop order in contrast to common lore. We show both analytical and numerical results where the impact is sizable for three minimal extensions of the Standard Model: a singlet extension, a second Higgs doublet and finally vector-like quarks. We highlight that the known two-loop RGEs tend to moderate the running of their one-loop counterparts, typically delaying the appearance of Landau poles. For the addition of vector-like quarks we show that the complete two-loop matching and RGE evolution hints at a stabilization of the electroweak vacuum at high energies, in contrast to results in the literature.

Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation

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

Xiao, Xiao; Yang, Hanjing; Arutiunian, Vagan

The catalytic activity of human cytidine deaminase APOBEC3B (A3B) has been correlated with kataegic mutational patterns within multiple cancer types. The molecular basis of how the N-terminal non-catalytic CD1 regulates the catalytic activity and consequently, biological function of A3B remains relatively unknown. Here, we report the crystal structure of a soluble human A3B-CD1 variant and delineate several structural elements of CD1 involved in molecular assembly, nucleic acid interactions and catalytic regulation of A3B. We show that (i) A3B expressed in human cells exists in hypoactive high-molecular-weight (HMW) complexes, which can be activated without apparent dissociation into low-molecular-weight (LMW) species aftermore » RNase A treatment. (ii) Multiple surface hydrophobic residues of CD1 mediate the HMW complex assembly and affect the catalytic activity, including one tryptophan residue W127 that likely acts through regulating nucleic acid binding. (iii) One of the highly positively charged surfaces on CD1 is involved in RNA-dependent attenuation of A3B catalysis. (iv) Surface hydrophobic residues of CD1 are involved in heterogeneous nuclear ribonucleoproteins (hnRNPs) binding to A3B. The structural and biochemical insights described here suggest that unique structural features on CD1 regulate the molecular assembly and catalytic activity of A3B through distinct mechanisms.« less

Unmixing Magnetic Hysteresis Loops

NASA Astrophysics Data System (ADS)

Heslop, D.; Roberts, A. P.

2012-04-01

Magnetic hysteresis loops provide important information in rock and environmental magnetic studies. Natural samples often contain an assemblage of magnetic particles composed of components with different origins. Each component potentially carries important environmental information. Hysteresis loops, however, provide information concerning the bulk magnetic assemblage, which makes it difficult to isolate the specific contributions from different sources. For complex mineral assemblages an unmixing strategy with which to separate hysteresis loops into their component parts is therefore essential. Previous methods to unmix hysteresis data have aimed at separating individual loops into their constituent parts using libraries of type-curves thought to correspond to specific mineral types. We demonstrate an alternative approach, which rather than decomposing a single loop into monomineralic contributions, examines a collection of loops to determine their constituent source materials. These source materials may themselves be mineral mixtures, but they provide a genetically meaningful decomposition of a magnetic assemblage in terms of the processes that controlled its formation. We show how an empirically derived hysteresis mixing space can be created, without resorting to type-curves, based on the co-variation within a collection of measured loops. Physically realistic end-members, which respect the expected behaviour and symmetries of hysteresis loops, can then be extracted from the mixing space. These end-members allow the measured loops to be described as a combination of invariant parts that are assumed to represent the different sources in the mixing model. Particular attention is paid to model selection and estimating the complexity of the mixing model, specifically, how many end-members should be included. We demonstrate application of this approach using lake sediments from Butte Valley, northern California. Our method successfully separates the hysteresis loops

Get Beyond Limits: From Colloidal Tectonics Concept to the Engineering of Eco-friendly Catalytic Systems

NASA Astrophysics Data System (ADS)

Leclercq, Loïc

2018-05-01

The interactions between two or more molecules or colloidal particles can be used to obtain a variety of self-assembled systems called supramolecules or supracolloids. There is a clear, but neglected, convergence between these two fields. Indeed, the packing of molecules into colloidal or supracolloidal particles emerges as a smart solution to build an infinite variety of reversible systems with predictable properties. In this respect, the molecular building blocks are called “tectons” whereas “colloidal tectonics” describes the spontaneous formation of (supra)colloidal structures using tectonic subunits. As a consequence, a bottom-up edification is allowed from tectons into (supra)colloidal particles with higher degrees of organization. These (supra)colloidal systems can be very useful to obtain catalysts with tunable amphiphilic properties. In this perspective, an overview of colloidal tectonics concept is presented as well as its use for the design of new, smart and flexible catalytic systems. Finally, the advantages of these catalytic devices are discussed and the perspective of future developments is addressed especially in the context of “green chemistry”.

Get Beyond Limits: From Colloidal Tectonics Concept to the Engineering of Eco-Friendly Catalytic Systems

PubMed Central

Leclercq, Loïc

2018-01-01

The interactions between two or more molecules or colloidal particles can be used to obtain a variety of self-assembled systems called supramolecules or supracolloids. There is a clear, but neglected, convergence between these two fields. Indeed, the packing of molecules into colloidal or supracolloidal particles emerges as a smart solution to build an infinite variety of reversible systems with predictable properties. In this respect, the molecular building blocks are called “tectons” whereas “colloidal tectonics” describes the spontaneous formation of (supra)colloidal structures using tectonic subunits. As a consequence, a bottom-up edification is allowed from tectons into (supra)colloidal particles with higher degrees of organization (Graphical Abstract). These (supra)colloidal systems can be very useful to obtain catalysts with tunable amphiphilic properties. In this perspective, an overview of colloidal tectonics concept is presented as well as its use for the design of new, smart, and flexible catalytic systems. Finally, the advantages of these catalytic devices are discussed and the perspective of future developments is addressed especially in the context of “green chemistry.”

A flexible and highly sensitive nonenzymatic glucose sensor based on DVD-laser scribed graphene substrate.

PubMed

Lin, Songyue; Feng, Wendou; Miao, Xiaofei; Zhang, Xiangxin; Chen, Sujing; Chen, Yuanqiang; Wang, Wei; Zhang, Yining

2018-07-01

Flexible and implantable glucose biosensors are emerging technologies for continuous monitoring of blood-glucose of diabetes. Developing a flexible conductive substrates with high active surface area is critical for advancing the technology. Here, we successfully fabricate a flexible and highly sensitive nonenzymatic glucose by using DVD-laser scribed graphene (LSG) as a flexible conductively substrate. Copper nanoparticles (Cu-NPs) are electrodeposited as the catalyst. The LSG/Cu-NPs sensor demonstrates excellent catalytic activity toward glucose oxidation and exhibits a linear glucose detection range from 1 μM to 4.54 mM with high sensitivity (1.518 mA mM -1 cm -2 ) and low limit of detection (0.35 μM). Moreover, the LSG/Cu-NPs sensor shows excellent reproducibility and long-term stability. It is also highly selective toward glucose oxidation under the presence of various interfering species. Excellent flexing stability is also demonstrated by the LSG/Cu-NPs sensor, which is capable of maintaining 83.9% of its initial current after being bent against a 4-mm diameter rod for 180 times. The LSG/Cu-NPs sensor shows great potential for practical application as a nonenzymatic glucose biosensor. Meanwhile, the LSG conductive substrate provides a platform for the developing next-generation flexible and potentially implantable bioelectronics and biosensors. Copyright © 2018 Elsevier B.V. All rights reserved.

Turning Potential Flexibility Into Flexible Performance: Moderating Effect of Self-Efficacy and Use of Flexible Cognition

PubMed Central

Liu, Ru-De; Wang, Jia; Star, Jon R.; Zhen, Rui; Jiang, Rong-Huan; Fu, Xin-Chen

2018-01-01

This study examined the relationship between two types of mathematical flexibility – potential flexibility, which indicates individuals’ knowledge of multiple strategies and strategy efficiency, and practical flexibility, which refers to individuals’ flexible performances when solving math problems. Both types of flexibility were assessed in the domain of linear equation solving. Furthermore, two types of beliefs – self-efficacy and use of flexible cognition (UFC) – were investigated as potential moderators between potential and practical flexibility. 121 8th grade students from China took part in this study. Results indicate that potential flexibility positively predicted practical flexibility. Additionally, self-efficacy and UFC might moderate the relationship between these two types of flexibility, suggesting that potential flexibility may lead to different degrees of practical flexibility depending on different levels of beliefs. Implications of these findings for research on mathematical flexibility and for educational practice are discussed. PMID:29780344

Ultrasonic-electrodeposition of PtPd alloy nanoparticles on ionic liquid-functionalized graphene paper: towards a flexible and versatile nanohybrid electrode

NASA Astrophysics Data System (ADS)

Sun, Yimin; Zheng, Huaming; Wang, Chenxu; Yang, Mengmeng; Zhou, Aijun; Duan, Hongwei

2016-01-01

Here we fabricate a new type of flexible and versatile nanohybrid paper electrode by ultrasonic-electrodeposition of PtPd alloy nanoparticles on freestanding ionic liquid (IL)-functionalized graphene paper, and explore its multifunctional applications in electrochemical catalysis and sensing systems. The graphene-based paper materials demonstrate intrinsic flexibility, exceptional mechanical strength and high electrical conductivity, and therefore can serve as an ideal freestanding flexible electrode for electrochemical devices. Furthermore, the functionalization of graphene with IL (i.e., 1-butyl-3-methylimidazolium tetrafluoroborate) not only increases the electroactive surface area of a graphene-based nanohybrid paper electrode, but also improves the adhesion and dispersion of metal nanoparticles on the paper surface. These unique attributes, combined with the merits of an ultrasonic-electrodeposition method, lead to the formation of PtPd alloy nanoparticles on IL-graphene paper with high loading, uniform distribution, controlled morphology and favourable size. Consequently, the resultant nanohybrid paper electrode exhibits remarkable catalytic activity as well as excellent cycle stability and improved anti-poisoning ability towards electrooxidation of fuel molecules such as methanol and ethanol. Furthermore, for nonenzymatic electrochemical sensing of some specific biomarkers such as glucose and reactive oxygen species, the nanohybrid paper electrode shows high selectivity, sensitivity and biocompatibility in these bio-catalytic processes, and can be used for real-time tracking hydrogen peroxide secretion by living human cells. All these features demonstrate its promising application as a versatile nanohybrid electrode material in flexible and lightweight electrochemical energy conversion and biosensing systems such as bendable on-chip power sources, wearable/implantable detectors and in vivo micro-biosensors.Here we fabricate a new type of flexible and

Role of Coupled-Dynamics in the Catalytic Activity of Prokaryotic-like Prolyl-tRNA Synthetases

PubMed Central

Sanford, Brianne; Cao, Bach; Johnson, James M.; Zimmerman, Kurt; Strom, Alexander M.; Mueller, Robyn M.; Bhattacharyya, Sudeep; Musier-Forsyth, Karin; Hati, Sanchita

2012-01-01

Prolyl-tRNA synthetases (ProRSs) have been shown to activate both cognate and some noncognate amino acids and attach them to specific tRNAPro substrates. For example, alanine, which is smaller than cognate proline, is misactivated by Escherichia coli ProRS. Mischarged Ala-tRNAPro is hydrolyzed by an editing domain (INS) that is distinct from the activation domain. It was previously shown that deletion of the INS greatly reduced cognate proline activation efficiency. In the present study, experimental and computational approaches were used to test the hypothesis that INS deletion alters the internal protein dynamics leading to reduce catalytic function. Kinetic studies with two ProRS variants, G217A and E218A, revealed decreased amino acid activation efficiency. Molecular dynamics studies showed motional coupling between the INS and protein segments containing the catalytically important proline-binding loop (PBL, residues 199–206). In particular, the complete deletion of INS, as well as mutation of G217 or E218 to alanine, exhibited significant effects on the motion of the PBL. The presence of coupled-dynamics between neighboring protein segments was also observed through in silico mutations and essential dynamics analysis. Taken together, the present study demonstrates that structural elements at the editing domain-activation domain interface participate in coupled motions that facilitate amino acid binding and catalysis by bacterial ProRSs, which may explain why truncated or defunct editing domains have been maintained in some systems, despite the lack of catalytic activity. PMID:22356126

Evolutionarily Conserved Linkage between Enzyme Fold, Flexibility, and Catalysis

PubMed Central

Ramanathan, Arvind; Agarwal, Pratul K.

2011-01-01

Proteins are intrinsically flexible molecules. The role of internal motions in a protein's designated function is widely debated. The role of protein structure in enzyme catalysis is well established, and conservation of structural features provides vital clues to their role in function. Recently, it has been proposed that the protein function may involve multiple conformations: the observed deviations are not random thermodynamic fluctuations; rather, flexibility may be closely linked to protein function, including enzyme catalysis. We hypothesize that the argument of conservation of important structural features can also be extended to identification of protein flexibility in interconnection with enzyme function. Three classes of enzymes (prolyl-peptidyl isomerase, oxidoreductase, and nuclease) that catalyze diverse chemical reactions have been examined using detailed computational modeling. For each class, the identification and characterization of the internal protein motions coupled to the chemical step in enzyme mechanisms in multiple species show identical enzyme conformational fluctuations. In addition to the active-site residues, motions of protein surface loop regions (>10 Å away) are observed to be identical across species, and networks of conserved interactions/residues connect these highly flexible surface regions to the active-site residues that make direct contact with substrates. More interestingly, examination of reaction-coupled motions in non-homologous enzyme systems (with no structural or sequence similarity) that catalyze the same biochemical reaction shows motions that induce remarkably similar changes in the enzyme–substrate interactions during catalysis. The results indicate that the reaction-coupled flexibility is a conserved aspect of the enzyme molecular architecture. Protein motions in distal areas of homologous and non-homologous enzyme systems mediate similar changes in the active-site enzyme–substrate interactions, thereby

Evolutionarily conserved linkage between enzyme fold, flexibility, and catalysis.

PubMed

Ramanathan, Arvind; Agarwal, Pratul K

2011-11-01

Proteins are intrinsically flexible molecules. The role of internal motions in a protein's designated function is widely debated. The role of protein structure in enzyme catalysis is well established, and conservation of structural features provides vital clues to their role in function. Recently, it has been proposed that the protein function may involve multiple conformations: the observed deviations are not random thermodynamic fluctuations; rather, flexibility may be closely linked to protein function, including enzyme catalysis. We hypothesize that the argument of conservation of important structural features can also be extended to identification of protein flexibility in interconnection with enzyme function. Three classes of enzymes (prolyl-peptidyl isomerase, oxidoreductase, and nuclease) that catalyze diverse chemical reactions have been examined using detailed computational modeling. For each class, the identification and characterization of the internal protein motions coupled to the chemical step in enzyme mechanisms in multiple species show identical enzyme conformational fluctuations. In addition to the active-site residues, motions of protein surface loop regions (>10 Å away) are observed to be identical across species, and networks of conserved interactions/residues connect these highly flexible surface regions to the active-site residues that make direct contact with substrates. More interestingly, examination of reaction-coupled motions in non-homologous enzyme systems (with no structural or sequence similarity) that catalyze the same biochemical reaction shows motions that induce remarkably similar changes in the enzyme-substrate interactions during catalysis. The results indicate that the reaction-coupled flexibility is a conserved aspect of the enzyme molecular architecture. Protein motions in distal areas of homologous and non-homologous enzyme systems mediate similar changes in the active-site enzyme-substrate interactions, thereby impacting

Study of design and control of remote manipulators. Modeling manipulator arms with distributed flexibility for design and control

NASA Technical Reports Server (NTRS)

Book, W. J.

1974-01-01

The interactions of control system and distributed flexible structural dynamics is explored for mechanical arms. A modeling process using 4 x 4 transfer matrices is described which permits the closed loop response of many current arm configurations to be evaluated. Root locus, frequency response, modal shapes, and time impulse response have all been obtained from the digital computer implementation of this model, which is oriented to arm design and allows for easy variation of the arm configuration through data cards. The model corresponds with experimentally observed natural frequencies with an average error of less than 5% in the first three flexible modes in the seven cases considered. The model was used to explore the limits imposed by structural flexibility on a nondimensionalized two link arm with one and two joints for planar motion.

Enzymatic function of loop movement in enolase: preparation and some properties of H159N, H159A, H159F, and N207A enolases.

PubMed

Brewer, John M; Glover, Claiborne V C; Holland, Michael J; Lebioda, Lukasz

2003-05-01

The hypothesis that His159 in yeast enolase moves on a polypeptide loop to protonate the phosphoryl of 2-phosphoglycerate to initiate its conversion to phosphoenolpyruvate was tested by preparing H159N, H159A, and H159F enolases. These have 0.07%-0.25% of the native activity under standard assay conditions and the pH dependence of maximum velocities of H159A and H159N mutants is markedly altered. Activation by Mg2+ is biphasic, with the smaller Mg2+ activation constant closer to that of the "catalytic" Mg2+ binding site of native enolase and the larger in the mM range in which native enolase is inhibited. A third Mg2+ may bind to the phosphoryl, functionally replacing proton donation by His159. N207A enolase lacks an intersubunit interaction that stabilizes the closed loop(s) conformation when 2-phosphoglycerate binds. It has 21% of the native activity, also exhibits biphasic Mg2+ activation, and its reaction with the aldehyde analogue of the substrate is more strongly inhibited than is its normal enzymatic reaction. Polypeptide loop(s) closure may keep a proton from His159 interacting with the substrate phosphoryl oxygen long enough to stabilize a carbanion intermediate.

Coupled dual loop absorption heat pump

DOEpatents

Sarkisian, Paul H.; Reimann, Robert C.; Biermann, Wendell J.

1985-01-01

A coupled dual loop absorption system which utilizes two separate complete loops. Each individual loop operates at three temperatures and two pressures. This low temperature loop absorber and condenser are thermally coupled to the high temperature loop evaporator, and the high temperature loop condenser and absorber are thermally coupled to the low temperature generator.

STRUCTURAL AND FUNCTIONAL CONSEQUENCES OF CIRCULAR PERMUTATION ON THE ACTIVE SITE OF OLD YELLOW ENZYME.

PubMed

Daugherty, Ashley B; Horton, John R; Cheng, Xiaodong; Lutz, Stefan

2015-02-06

Circular permutation of the NADPH-dependent oxidoreductase Old Yellow Enzyme from Saccharomyces pastorianus (OYE1) can significantly enhance the enzyme's catalytic performance. Termini relocation into four regions of the protein (sectors I-IV) near the active site has proven effective in altering enzyme function. To better understand the structural consequences and rationalize the observed functional gains in these OYE1 variants, we selected representatives from sectors I-III for further characterization by biophysical methods and X-ray crystallography. These investigations not only show trends in enzyme stability and quaternary structure as a function of termini location, but also provide a possible explanation for the catalytic gains in our top-performing OYE variant (new N-terminus at residue 303; sector III). Crystallographic analysis indicates that termini relocation into sector III affects the loop β6 region (amino acid positions: 290-310) of OYE1 which forms a lid over the active site. Peptide backbone cleavage greatly enhances local flexibility, effectively converting the loop into a tether and consequently increasing the environmental exposure of the active site. Interestingly, such active site remodeling does not negatively impact the enzyme's activity and stereoselectivity, nor does it perturb the conformation of other key active site residues with the exception of Y375. These observations were confirmed in truncation experiments, deleting all residues of the loop β6 region in our OYE variant. Intrigued by the finding that circular permutation leaves most of the key catalytic residues unchanged, we also tested OYE permutants for possible additive or synergistic effects of amino acid substitutions. Distinct functional changes in these OYE variants were detected upon mutations at W116, known in native OYE1 to cause inversion of diastereo-selectivity for ( S )-carvone reduction. Our findings demonstrate the contribution of loop β6 toward determining the

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.

Relevance of Local Flexibility Near the Active Site for Enzymatic Catalysis: Biochemical Characterization and Engineering of Cellulase Cel5A From Bacillus agaradherans.

PubMed

Saavedra, Juan M; Azócar, Mauricio A; Rodríguez, Vida; Ramírez-Sarmiento, César A; Andrews, Barbara A; Asenjo, Juan A; Parra, Loreto P

2018-03-25

Detailed molecular mechanisms underpinning enzymatic reactions are still a central problem in biochemistry. The need for active site flexibility to sustain catalytic activity constitutes a notion of wide acceptance, although its direct influence remains to be fully understood. With the aim of studying the relationship between structural dynamics and enzyme catalysis, the cellulase Cel5A from Bacillus agaradherans is used as a model for in silico comparative analysis with mesophilic and psychrophilic counterparts. Structural features that determine flexibility are related to kinetic and thermodynamic parameters of catalysis. As a result, three specific positions in the vicinity of the active site of Cel5A are selected for protein engineering via site-directed mutagenesis. Three Cel5A variants are generated, N141L, A137Y and I102A/A137Y, showing a concomitant increase in the catalytic activity at low temperatures and a decrease in activation energy and activation enthalpy, similar to cold-active enzymes. These results are interpreted in structural terms by molecular dynamics simulations, showing that disrupting a hydrogen bond network in the vicinity of the active site increases local flexibility. These results provide a structural framework for explaining the changes in thermodynamic parameters observed between homologous enzymes with varying temperature adaptations. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The diversity of H3 loops determines the antigen-binding tendencies of antibody CDR loops.

PubMed

Tsuchiya, Yuko; Mizuguchi, Kenji

2016-04-01

Of the complementarity-determining regions (CDRs) of antibodies, H3 loops, with varying amino acid sequences and loop lengths, adopt particularly diverse loop conformations. The diversity of H3 conformations produces an array of antigen recognition patterns involving all the CDRs, in which the residue positions actually in contact with the antigen vary considerably. Therefore, for a deeper understanding of antigen recognition, it is necessary to relate the sequence and structural properties of each residue position in each CDR loop to its ability to bind antigens. In this study, we proposed a new method for characterizing the structural features of the CDR loops and obtained the antigen-binding ability of each residue position in each CDR loop. This analysis led to a simple set of rules for identifying probable antigen-binding residues. We also found that the diversity of H3 loop lengths and conformations affects the antigen-binding tendencies of all the CDR loops. © 2016 The Protein Society.

Multiwalled carbon nanotube coated polyester fabric as textile based flexible counter electrode for dye sensitized solar cell.

PubMed

Arbab, Alvira Ayoub; Sun, Kyung Chul; Sahito, Iftikhar Ali; Qadir, Muhammad Bilal; Jeong, Sung Hoon

2015-05-21

Textile wearable electronics offers the combined advantages of both electronics and textile characteristics. The essential properties of these flexible electronics such as lightweight, stretchable, and wearable power sources are in strong demand. Here, we have developed a facile route to fabricate multi walled carbon nanotube (MWCNT) coated polyester fabric as a flexible counter electrode (CE) for dye sensitized solar cells (DSSCs). A variety of MWCNT and enzymes with different structures were used to generate individual enzyme-dispersed MWCNT (E-MWCNT) suspensions by non-covalent functionalization. A highly concentrated colloidal suspension of E-MWCNT was deposited on polyester fabric via a simple tape casting method using an air drying technique. In view of the E-MWCNT coating, the surface structure is represented by topologically randomly assembled tubular graphene units. This surface morphology has a high density of colloidal edge states and oxygen-containing surface groups which execute multiple catalytic sites for iodide reduction. A highly conductive E-MWCNT coated fabric electrode with a surface resistance of 15 Ω sq(-1) demonstrated 5.69% power conversion efficiency (PCE) when used as a flexible CE for DSSCs. High photo voltaic performance of our suggested system of E-MWCNT fabric-based DSSCs is associated with high sheet conductivity, low charge transfer resistance (RCT), and excellent electro catalytic activity (ECA). Such a conductive fabric demonstrated stable conductivity against bending cycles and strong mechanical adhesion of E-MWCNT on polyester fabric. Moreover, the polyester fabric is hydrophobic and, therefore, has good sealing capacity and retains the polymer gel electrolyte without seepage. This facile E-MWCNT fabric CE configuration provides a concrete fundamental background towards the development of textile-integrated solar cells.

Relative stability of the open and closed conformations of the active site loop of streptavidin

NASA Astrophysics Data System (ADS)

Ignacio J., General; Meirovitch, Hagai

2011-01-01

The eight-residue surface loop, 45-52 (Ser, Ala, Val, Gly, Asn, Ala, Glu, Ser), of the homotetrameric protein streptavidin has a "closed" conformation in the streptavidin-biotin complex, where the corresponding binding affinity is one of the strongest found in nature (ΔG ˜ -18 kcal/mol). However, in most of the crystal structures of apo (unbound) streptavidin, the loop conformation is "open" and typically exhibits partial disorder and high B-factors. Thus, it is plausible to assume that the loop structure is changed from open to closed upon binding of biotin, and the corresponding difference in free energy, ΔF = Fopen - Fclosed in the unbound protein, should therefore be considered in the total absolute free energy of binding. ΔF (which has generally been neglected) is calculated here using our "hypothetical scanning molecular-dynamics" (HSMD) method. We use a protein model in which only the atoms closest to the loop are considered (the "template") and they are fixed in the x-ray coordinates of the free protein; the x-ray conformation of the closed loop is attached to the same (unbound) template and both systems are capped with the same sphere of TIP3P water. Using the force field of the assisted model building with energy refinement (AMBER), we carry out two separate MD simulations (at temperature T = 300 K), starting from the open and closed conformations, where only the atoms of the loop and water are allowed to move (the template-water and template-loop interactions are considered). The absolute Fopen and Fclosed (of loop + water) are calculated from these trajectories, where the loop and water contributions are obtained by HSMD and a thermodynamic integration (TI) process, respectively. The combined HSMD-TI procedure leads to total (loop + water) ΔF = -27.1 ± 2.0 kcal/mol, where the entropy TΔS constitutes 34% of ΔF, meaning that the effect of S is significant and should not be ignored. Also, ΔS is positive, in accord with the high flexibility of the

Method and apparatus for a catalytic firebox reactor

DOEpatents

Smith, Lance L.; Etemad, Shahrokh; Ulkarim, Hasan; Castaldi, Marco J.; Pfefferle, William C.

2001-01-01

A catalytic firebox reactor employing an exothermic catalytic reaction channel and multiple cooling conduits for creating a partially reacted fuel/oxidant mixture. An oxidation catalyst is deposited on the walls forming the boundary between the multiple cooling conduits and the exothermic catalytic reaction channel, on the side of the walls facing the exothermic catalytic reaction channel. This configuration allows the oxidation catalyst to be backside cooled by any fluid passing through the cooling conduits. The heat of reaction is added to both the fluid in the exothermic catalytic reaction channel and the fluid passing through the cooling conduits. After discharge of the fluids from the exothermic catalytic reaction channel, the fluids mix to create a single combined flow. A further innovation in the reactor incorporates geometric changes in the exothermic catalytic reaction channel to provide streamwise variation of the velocity of the fluids in the reactor.

Importance of Loop L1 Dynamics for Substrate Capture and Catalysis in Pseudomonas aeruginosa d-Arginine Dehydrogenase.

PubMed

Ouedraogo, Daniel; Souffrant, Michael; Vasquez, Sheena; Hamelberg, Donald; Gadda, Giovanni

2017-05-16

Mobile loops located at the active site entrance in enzymes often participate in conformational changes required to shield the reaction from bulk solvent, to control the access of the substrate to the active site, and to position residues for substrate binding and catalysis. In d-arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH), previous crystallographic data suggested that residues 45-47 in the FAD-binding domain and residues 50-56 in the substrate-binding domain in loop L1 could adopt two distinct conformations. In this study, we have used molecular dynamics, kinetics, and fluorescence spectroscopy on the S45A and A46G enzyme variants of PaDADH to investigate the impact of mutations in loop L1 on the catalytic function of the enzyme. Molecular dynamics showed that the mutant enzymes have probabilities of being in open conformations that are higher than that of wild-type PaDADH of loop L1, yielding an increased level of solvent exposure of the active site. In agreement, the flavin fluorescence intensity was ∼2-fold higher in the S45A and A46G enzymes than in wild-type PaDADH, with a 9 nm bathochromic shift of the emission band. In the variant enzymes, the k cat /K m values with d-arginine were ∼13-fold lower than in wild-type PaDADH. Moreover, the pH profiles for the k cat value with d-arginine showed a hollow, consistent with restricted proton movements in catalysis, and no saturation was achieved with the alternate substrate d-leucine in the reductive half-reaction of the variant enzymes. Taken together, the computational and experimental data are consistent with the dynamics of loop L1 being important for substrate capture and catalysis in PaDADH.

Redistribution of Flexibility in Stabilizing Antibody Fragment Mutants Follows Le Châtelier’s Principle

PubMed Central

Li, Tong; Tracka, Malgorzata B.; Uddin, Shahid; Casas-Finet, Jose; Jacobs, Donald J.; Livesay, Dennis R.

2014-01-01

Le Châtelier’s principle is the cornerstone of our understanding of chemical equilibria. When a system at equilibrium undergoes a change in concentration or thermodynamic state (i.e., temperature, pressure, etc.), La Châtelier’s principle states that an equilibrium shift will occur to offset the perturbation and a new equilibrium is established. We demonstrate that the effects of stabilizing mutations on the rigidity ⇔ flexibility equilibrium within the native state ensemble manifest themselves through enthalpy-entropy compensation as the protein structure adjusts to restore the global balance between the two. Specifically, we characterize the effects of mutation to single chain fragments of the anti-lymphotoxin-β receptor antibody using a computational Distance Constraint Model. Statistically significant changes in the distribution of both rigidity and flexibility within the molecular structure is typically observed, where the local perturbations often lead to distal shifts in flexibility and rigidity profiles. Nevertheless, the net gain or loss in flexibility of individual mutants can be skewed. Despite all mutants being exclusively stabilizing in this dataset, increased flexibility is slightly more common than increased rigidity. Mechanistically the redistribution of flexibility is largely controlled by changes in the H-bond network. For example, a stabilizing mutation can induce an increase in rigidity locally due to the formation of new H-bonds, and simultaneously break H-bonds elsewhere leading to increased flexibility distant from the mutation site via Le Châtelier. Increased flexibility within the VH β4/β5 loop is a noteworthy illustration of this long-range effect. PMID:24671209

Multiple roles of mobile active center loops in the E1 component of the Escherichia coli pyruvate dehydrogenase complex - Linkage of protein dynamics to catalysis

PubMed Central

Jordan, Frank; Arjunan, Palaniappa; Kale, Sachin; Nemeria, Natalia S.; Furey, William

2009-01-01

same conditions. Furthermore, this analysis gave important insights into rate-limiting thermal loop dynamics. Overall, the results suggest that the dynamic properties correlate with catalytic events on the E1 component of the pyruvate dehydrogenase complex. PMID:20160956

Modulation format identification aided hitless flexible coherent transceiver.

PubMed

Xiang, Meng; Zhuge, Qunbi; Qiu, Meng; Zhou, Xingyu; Zhang, Fangyuan; Tang, Ming; Liu, Deming; Fu, Songnian; Plant, David V

2016-07-11

We propose a hitless flexible coherent transceiver enabled by a novel modulation format identification (MFI) scheme for dynamic agile optical networks. The modulation format transparent digital signal processing (DSP) is realized by a block-wise decision-directed least-mean-square (DD-LMS) equalizer for channel tracking, and a pilot symbol aided superscalar phase locked loop (PLL) for carrier phase estimation (CPE). For the MFI, the modulation format information is encoded onto the pilot symbols initially used for CPE. Therefore, the proposed MFI method does not require extra overhead. Moreover, it can identify arbitrary modulation formats including multi-dimensional formats, and it enables tracking of the format change for short data blocks. The performance of the proposed hitless flexible coherent transceiver is successfully evaluated with five modulation formats including QPSK, 16QAM, 64QAM, Hybrid QPSK/8QAM and set-partitioning (SP)-512-QAM. We show that the proposed MFI method induces a negligible performance penalty. Moreover, we experimentally demonstrate that such a hitless transceiver can adapt to fast block-by-block modulation format switching. Finally, the performance improvement of the proposed MFI method is experimentally verified with respect to other commonly used MFI methods.

Flexibility.

ERIC Educational Resources Information Center

Humphrey, L. Dennis

1981-01-01

Flexibility is an important aspect of all sports and recreational activities. Flexibility can be developed and maintained by stretching exercises. Exercises designed to develop flexibility in ankle joints, knees, hips, and the lower back are presented. (JN)

Development and Evaluation of an Order-N Formulation for Multi-Flexible Body Space Systems

NASA Technical Reports Server (NTRS)

Ghosh, Tushar K.; Quiocho, Leslie J.

2013-01-01

This paper presents development of a generic recursive Order-N algorithm for systems with rigid and flexible bodies, in tree or closed-loop topology, with N being the number of bodies of the system. Simulation results are presented for several test cases to verify and evaluate the performance of the code compared to an existing efficient dense mass matrix-based code. The comparison brought out situations where Order-N or mass matrix-based algorithms could be useful.

Piloted rich-catalytic lean-burn hybrid combustor

DOEpatents

Newburry, Donald Maurice

2002-01-01

A catalytic combustor assembly which includes, an air source, a fuel delivery means, a catalytic reactor assembly, a mixing chamber, and a means for igniting a fuel/air mixture. The catalytic reactor assembly is in fluid communication with the air source and fuel delivery means and has a fuel/air plenum which is coated with a catalytic material. The fuel/air plenum has cooling air conduits passing therethrough which have an upstream end. The upstream end of the cooling conduits is in fluid communication with the air source but not the fuel delivery means.

Study of Flexible Load Dispatch to Improve the Capacity of Wind Power Absorption

NASA Astrophysics Data System (ADS)

Yunlei, Yang; Shifeng, Zhang; Xiao, Chang; Da, Lei; Min, Zhang; Jinhao, Wang; Shengwen, Li; Huipeng, Li

2017-05-01

The dispatch method which track the trend of load demand by arranging the generation scheme of controllable hydro or thermal units faces great difficulties and challenges. With the increase of renewable energy sources such as wind power and photovoltaic power introduced to grid, system has to arrange much more spinning reserve units to compensate the unbalanced power. How to exploit the peak-shaving potential of flexible load which can be shifted with time or storage energy has become many scholars’ research direction. However, the modelling of different kinds of load and control strategy is considerably difficult, this paper choose the Air Conditioner with compressor which can storage energy in fact to study. The equivalent thermal parameters of Air Conditioner has been established. And with the use of “loop control” strategies, we can predict the regulated power of Air Conditioner. Then we established the Gen-Load optimal scheduling model including flexible load based on traditional optimal scheduling model. At last, an improved IEEE-30 case is used to verify. The result of simulation shows that flexible load can fast-track renewable power changes. More than that, with flexible load and reasonable incentive method to consumers, the operating cost of the system can be greatly cut down.

A reconfigurable visual-programming library for real-time closed-loop cellular electrophysiology

PubMed Central

Biró, István; Giugliano, Michele

2015-01-01

Most of the software platforms for cellular electrophysiology are limited in terms of flexibility, hardware support, ease of use, or re-configuration and adaptation for non-expert users. Moreover, advanced experimental protocols requiring real-time closed-loop operation to investigate excitability, plasticity, dynamics, are largely inaccessible to users without moderate to substantial computer proficiency. Here we present an approach based on MATLAB/Simulink, exploiting the benefits of LEGO-like visual programming and configuration, combined to a small, but easily extendible library of functional software components. We provide and validate several examples, implementing conventional and more sophisticated experimental protocols such as dynamic-clamp or the combined use of intracellular and extracellular methods, involving closed-loop real-time control. The functionality of each of these examples is demonstrated with relevant experiments. These can be used as a starting point to create and support a larger variety of electrophysiological tools and methods, hopefully extending the range of default techniques and protocols currently employed in experimental labs across the world. PMID:26157385

Structure Prediction of the Second Extracellular Loop in G-Protein-Coupled Receptors

PubMed Central

Kmiecik, Sebastian; Jamroz, Michal; Kolinski, Michal

2014-01-01

G-protein-coupled receptors (GPCRs) play key roles in living organisms. Therefore, it is important to determine their functional structures. The second extracellular loop (ECL2) is a functionally important region of GPCRs, which poses significant challenge for computational structure prediction methods. In this work, we evaluated CABS, a well-established protein modeling tool for predicting ECL2 structure in 13 GPCRs. The ECL2s (with between 13 and 34 residues) are predicted in an environment of other extracellular loops being fully flexible and the transmembrane domain fixed in its x-ray conformation. The modeling procedure used theoretical predictions of ECL2 secondary structure and experimental constraints on disulfide bridges. Our approach yielded ensembles of low-energy conformers and the most populated conformers that contained models close to the available x-ray structures. The level of similarity between the predicted models and x-ray structures is comparable to that of other state-of-the-art computational methods. Our results extend other studies by including newly crystallized GPCRs. PMID:24896119

Structure prediction of the second extracellular loop in G-protein-coupled receptors.

PubMed

Kmiecik, Sebastian; Jamroz, Michal; Kolinski, Michal

2014-06-03

G-protein-coupled receptors (GPCRs) play key roles in living organisms. Therefore, it is important to determine their functional structures. The second extracellular loop (ECL2) is a functionally important region of GPCRs, which poses significant challenge for computational structure prediction methods. In this work, we evaluated CABS, a well-established protein modeling tool for predicting ECL2 structure in 13 GPCRs. The ECL2s (with between 13 and 34 residues) are predicted in an environment of other extracellular loops being fully flexible and the transmembrane domain fixed in its x-ray conformation. The modeling procedure used theoretical predictions of ECL2 secondary structure and experimental constraints on disulfide bridges. Our approach yielded ensembles of low-energy conformers and the most populated conformers that contained models close to the available x-ray structures. The level of similarity between the predicted models and x-ray structures is comparable to that of other state-of-the-art computational methods. Our results extend other studies by including newly crystallized GPCRs. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Hard-thermal-loop perturbation theory to two loops

NASA Astrophysics Data System (ADS)

Andersen, Jens O.; Braaten, Eric; Petitgirard, Emmanuel; Strickland, Michael

2002-10-01

We calculate the pressure for pure-glue QCD at high temperature to two-loop order using hard-thermal-loop (HTL) perturbation theory. At this order, all the ultraviolet divergences can be absorbed into renormalizations of the vacuum energy density and the HTL mass parameter. We determine the HTL mass parameter by a variational prescription. The resulting predictions for the pressure fail to agree with results from lattice gauge theory at temperatures for which they are available.

Multiprotein DNA Looping

NASA Astrophysics Data System (ADS)

Vilar, Jose M. G.; Saiz, Leonor

2006-06-01

DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve it analytically in the case of identical binding. We uncover a switchlike transition between looped and unlooped phases and identify the key parameters that control this transition. Our results establish the basis for the quantitative understanding of fundamental cellular processes like DNA recombination, gene silencing, and telomere maintenance.

The Crystal Structure of the Ring-Hydroxylating Dioxygenase from Sphingomonas CHY-1

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

Jakoncic,J.; Jouanneau, Y.; Meyer, C.

The ring-hydroxylating dioxygenase (RHD) from Sphingomonas CHY-1 is remarkable due to its ability to initiate the oxidation of a wide range of polycyclic aromatic hydrocarbons (PAHs), including PAHs containing four- and five-fused rings, known pollutants for their toxic nature. Although the terminal oxygenase from CHY-1 exhibits limited sequence similarity with well characterized RHDs from the naphthalene dioxygenase family, the crystal structure determined to 1.85 {angstrom} by molecular replacement revealed the enzyme to share the same global {alpha}{sub 3}{beta}{sub 3} structural pattern. The catalytic domain distinguishes itself from other bacterial non-heme Rieske iron oxygenases by a substantially larger hydrophobic substrate bindingmore » pocket, the largest ever reported for this type of enzyme. While residues in the proximal region close to the mononuclear iron atom are conserved, the central region of the catalytic pocket is shaped mainly by the side chains of three amino acids, Phe350, Phe404 and Leu356, which contribute to the rather uniform trapezoidal shape of the pocket. Two flexible loops, LI and LII, exposed to the solvent seem to control the substrate access to the catalytic pocket and control the pocket length. Compared with other naphthalene dioxygenases residues Leu223 and Leu226, on loop LI, are moved towards the solvent, thus elongating the catalytic pocket by at least 2 {angstrom}. An 11 {angstrom} long water channel extends from the interface between the {alpha} and {beta} subunits to the catalytic site. The comparison of these structures with other known oxygenases suggests that the broad substrate specificity presented by the CHY-1 oxygenase is primarily due to the large size and particular topology of its catalytic pocket and provided the basis for the study of its reaction mechanism.« less

Closed-Loop Control Better than Open-Loop Control of Profofol TCI Guided by BIS: A Randomized, Controlled, Multicenter Clinical Trial to Evaluate the CONCERT-CL Closed-Loop System

PubMed Central

Zhang, Xuena; Wu, Anshi; Yao, Shanglong; Xue, Zhanggang; Yue, Yun

2015-01-01

Background The CONCERT-CL closed-loop infusion system designed by VERYARK Technology Co., Ltd. (Guangxi, China) is an innovation using TCI combined with closed-loop controlled intravenous anesthesia under the guide of BIS. In this study we performed a randomized, controlled, multicenter study to compare closed-loop control and open-loop control of propofol by using the CONCERT-CL closed-loop infusion system. Methods 180 surgical patients from three medical centers undergone TCI intravenous anesthesia with propofol and remifentanil were randomly assigned to propofol closed-loop group and propofol opened-loop groups. Primary outcome was global score (GS, GS = (MDAPE+Wobble)/% of time of bispectral index (BIS) 40-60). Secondary outcomes were doses of the anesthetics and emergence time from anesthesia, such as, time to tracheal extubation. Results There were 89 and 86 patients in the closed-loop and opened-loop groups, respectively. GS in the closed-loop groups (22.21±8.50) were lower than that in the opened-loop group (27.19±15.26) (p=0.009). The higher proportion of time of BIS between 40 and 60 was also observed in the closed-loop group (84.11±9.50%), while that was 79.92±13.17% in the opened-loop group, (p=0.016). No significant differences in propofol dose and time of tracheal extubation were observed. The frequency of propofol regulation in the closed-loop group (31.55±9.46 times/hr) was obverse higher than that in the opened-loop group (6.84±6.21 times/hr) (p=0.000). Conclusion The CONCERT-CL closed-loop infusion system can automatically regulate the TCI of propofol, maintain the BIS value in an adequate range and reduce the workload of anesthesiologists better than open-loop system. Trial Registration ChiCTR ChiCTR-OOR-14005551 PMID:25886041

Rational Engineering of a Cold-Adapted α-Amylase from the Antarctic Ciliate Euplotes focardii for Simultaneous Improvement of Thermostability and Catalytic Activity

PubMed Central

Yang, Guang; Yao, Hua; Mozzicafreddo, Matteo; Ballarini, Patrizia; Pucciarelli, Sandra

2017-01-01

ABSTRACT The α-amylases are endo-acting enzymes that hydrolyze starch by randomly cleaving the 1,4-α-d-glucosidic linkages between the adjacent glucose units in a linear amylose chain. They have significant advantages in a wide range of applications, particularly in the food industry. The eukaryotic α-amylase isolated from the Antarctic ciliated protozoon Euplotes focardii (EfAmy) is an alkaline enzyme, different from most of the α-amylases characterized so far. Furthermore, EfAmy has the characteristics of a psychrophilic α-amylase, such as the highest hydrolytic activity at a low temperature and high thermolability, which is the major drawback of cold-active enzymes in industrial applications. In this work, we applied site-directed mutagenesis combined with rational design to generate a cold-active EfAmy with improved thermostability and catalytic efficiency at low temperatures. We engineered two EfAmy mutants. In one mutant, we introduced Pro residues on the A and B domains in surface loops. In the second mutant, we changed Val residues to Thr close to the catalytic site. The aim of these substitutions was to rigidify the molecular structure of the enzyme. Furthermore, we also analyzed mutants containing these combined substitutions. Biochemical enzymatic assays of engineered versions of EfAmy revealed that the combination of mutations at the surface loops increased the thermostability and catalytic efficiency of the enzyme. The possible mechanisms responsible for the changes in the biochemical properties are discussed by analyzing the three-dimensional structural model. IMPORTANCE Cold-adapted enzymes have high specific activity at low and moderate temperatures, a property that can be extremely useful in various applications as it implies a reduction in energy consumption during the catalyzed reaction. However, the concurrent high thermolability of cold-adapted enzymes often limits their applications in industrial processes. The α-amylase from the

Rational Engineering of a Cold-Adapted α-Amylase from the Antarctic Ciliate Euplotes focardii for Simultaneous Improvement of Thermostability and Catalytic Activity.

PubMed

Yang, Guang; Yao, Hua; Mozzicafreddo, Matteo; Ballarini, Patrizia; Pucciarelli, Sandra; Miceli, Cristina

2017-07-01

The α-amylases are endo-acting enzymes that hydrolyze starch by randomly cleaving the 1,4-α-d-glucosidic linkages between the adjacent glucose units in a linear amylose chain. They have significant advantages in a wide range of applications, particularly in the food industry. The eukaryotic α-amylase isolated from the Antarctic ciliated protozoon Euplotes focardii ( Ef Amy) is an alkaline enzyme, different from most of the α-amylases characterized so far. Furthermore, Ef Amy has the characteristics of a psychrophilic α-amylase, such as the highest hydrolytic activity at a low temperature and high thermolability, which is the major drawback of cold-active enzymes in industrial applications. In this work, we applied site-directed mutagenesis combined with rational design to generate a cold-active Ef Amy with improved thermostability and catalytic efficiency at low temperatures. We engineered two Ef Amy mutants. In one mutant, we introduced Pro residues on the A and B domains in surface loops. In the second mutant, we changed Val residues to Thr close to the catalytic site. The aim of these substitutions was to rigidify the molecular structure of the enzyme. Furthermore, we also analyzed mutants containing these combined substitutions. Biochemical enzymatic assays of engineered versions of Ef Amy revealed that the combination of mutations at the surface loops increased the thermostability and catalytic efficiency of the enzyme. The possible mechanisms responsible for the changes in the biochemical properties are discussed by analyzing the three-dimensional structural model. IMPORTANCE Cold-adapted enzymes have high specific activity at low and moderate temperatures, a property that can be extremely useful in various applications as it implies a reduction in energy consumption during the catalyzed reaction. However, the concurrent high thermolability of cold-adapted enzymes often limits their applications in industrial processes. The α-amylase from the

Homology models of main proteinase from coronavirus associated with SARS

NASA Astrophysics Data System (ADS)

Liu, Hsuan-Liang; Lin, Jin-Chung; Ho, Yih; Chen, Chin-Wen

2005-01-01

In this study, two homology models of the main proteinase (M pro) from the novel coronavirus associated with severe acute respiratory syndrome (SARS-CoV) were constructed. These models reveal three distinct functional domains, in which an intervening loop connecting domains II and III as well as a catalytic cleft containing the substrate binding subsites S1 and S2 between domains I and II are observed. S2 exhibits structural variations more significantly than S1 during the 200 ps molecular dynamics simulations because it is located at the open mouth of the catalytic cleft and the amino acid residues lining up this subsite are least conserved. In addition, the higher structural variation of S2 makes it flexible enough to accommodate a bulky hydrophobic residue from the substrate.

Insights into substrate binding and catalysis in bacterial type I dehydroquinase.

PubMed

Maneiro, María; Peón, Antonio; Lence, Emilio; Otero, José M; Van Raaij, Mark J; Thompson, Paul; Hawkins, Alastair R; González-Bello, Concepción

2014-09-15

Structural, biochemical and computational studies to study substrate binding and the role of the conserved residues of the DHQ1 (type I dehydroquinase) enzyme active site are reported in the present paper. The crystal structure of DHQ1 from Salmonella typhi in complex with (2R)-2-methyl-3-dehydroquinic acid, a substrate analogue, was solved at 1.5 Å. The present study reveals a previously unknown key role for conserved Glu46, Phe145 and Met205 and Gln236, Pro234 and Ala233 residues, with the latter three being located in the flexible substrate-covering loop. Gln236 was shown to be responsible for the folding of this loop and for the dramatic reduction of its flexibility, which triggers active site closure. Glu46 was found to be key in bringing the substrate close to the lysine/histidine catalytic pocket to initiate catalysis. The present study could be useful in the rational design of inhibitors of this challenging and recognized target for the development of novel herbicides and antimicrobial agents.

Tryptophan as a Molecular Shovel in the Glycosyl Transfer Activity of Trypanosoma cruzi Trans-sialidase

PubMed Central

Mitchell, Felicity L.; Miles, Steven M.; Neres, João; Bichenkova, Elena V.; Bryce, Richard A.

2010-01-01

Abstract Molecular dynamics investigations into active site plasticity of Trypanosoma cruzi trans-sialidase, a protein implicated in Chagas disease, suggest that movement of the Trp312 loop plays an important role in the enzyme's sialic acid transfer mechanism. The observed Trp312 flexibility equates to a molecular shovel action, which leads to the expulsion of the donor aglycone leaving group from the catalytic site. These computational simulations provide detailed structural insights into sialyl transfer by the trans-sialidase and may aid the design of inhibitors effective against this neglected tropical disease. PMID:20441732

HIV protease drug resistance and its impact on inhibitor design.

PubMed

Ala, P J; Rodgers, J D; Chang, C H

1999-07-01

The primary cause of resistance to the currently available HIV protease inhibitors is the accumulation of multiple mutations in the viral protease. So far more than 20 substitutions have been observed in the active site, dimer interface, surface loops and flaps of the homodimer. While many mutations reduce the protease's affinity for inhibitors, others appear to enhance its catalytic efficiency. This high degree of genetic flexibility has made the protease an elusive drug target. The design of the next generation of HIV protease inhibitors will be discussed in light of the current structural information.

Advanced photonic filters based on cascaded Sagnac loop reflector resonators in silicon-on-insulator nanowires

NASA Astrophysics Data System (ADS)

Wu, Jiayang; Moein, Tania; Xu, Xingyuan; Moss, David J.

2018-04-01

We demonstrate advanced integrated photonic filters in silicon-on-insulator (SOI) nanowires implemented by cascaded Sagnac loop reflector (CSLR) resonators. We investigate mode splitting in these standing-wave (SW) resonators and demonstrate its use for engineering the spectral profile of on-chip photonic filters. By changing the reflectivity of the Sagnac loop reflectors (SLRs) and the phase shifts along the connecting waveguides, we tailor mode splitting in the CSLR resonators to achieve a wide range of filter shapes for diverse applications including enhanced light trapping, flat-top filtering, Q factor enhancement, and signal reshaping. We present the theoretical designs and compare the CSLR resonators with three, four, and eight SLRs fabricated in SOI. We achieve versatile filter shapes in the measured transmission spectra via diverse mode splitting that agree well with theory. This work confirms the effectiveness of using CSLR resonators as integrated multi-functional SW filters for flexible spectral engineering.

Perovskite-type catalytic materials for environmental applications.

PubMed

Labhasetwar, Nitin; Saravanan, Govindachetty; Kumar Megarajan, Suresh; Manwar, Nilesh; Khobragade, Rohini; Doggali, Pradeep; Grasset, Fabien

2015-06-01

Perovskites are mixed-metal oxides that are attracting much scientific and application interest owing to their low price, adaptability, and thermal stability, which often depend on bulk and surface characteristics. These materials have been extensively explored for their catalytic, electrical, magnetic, and optical properties. They are promising candidates for the photocatalytic splitting of water and have also been extensively studied for environmental catalysis applications. Oxygen and cation non-stoichiometry can be tailored in a large number of perovskite compositions to achieve the desired catalytic activity, including multifunctional catalytic properties. Despite the extensive uses, the commercial success for this class of perovskite-based catalytic materials has not been achieved for vehicle exhaust emission control or for many other environmental applications. With recent advances in synthesis techniques, including the preparation of supported perovskites, and increasing understanding of promoted substitute perovskite-type materials, there is a growing interest in applied studies of perovskite-type catalytic materials. We have studied a number of perovskites based on Co, Mn, Ru, and Fe and their substituted compositions for their catalytic activity in terms of diesel soot oxidation, three-way catalysis, N 2 O decomposition, low-temperature CO oxidation, oxidation of volatile organic compounds, etc. The enhanced catalytic activity of these materials is attributed mainly to their altered redox properties, the promotional effect of co-ions, and the increased exposure of catalytically active transition metals in certain preparations. The recent lowering of sulfur content in fuel and concerns over the cost and availability of precious metals are responsible for renewed interest in perovskite-type catalysts for environmental applications.

Perovskite-type catalytic materials for environmental applications

PubMed Central

Labhasetwar, Nitin; Saravanan, Govindachetty; Kumar Megarajan, Suresh; Manwar, Nilesh; Khobragade, Rohini; Doggali, Pradeep; Grasset, Fabien

2015-01-01

Perovskites are mixed-metal oxides that are attracting much scientific and application interest owing to their low price, adaptability, and thermal stability, which often depend on bulk and surface characteristics. These materials have been extensively explored for their catalytic, electrical, magnetic, and optical properties. They are promising candidates for the photocatalytic splitting of water and have also been extensively studied for environmental catalysis applications. Oxygen and cation non-stoichiometry can be tailored in a large number of perovskite compositions to achieve the desired catalytic activity, including multifunctional catalytic properties. Despite the extensive uses, the commercial success for this class of perovskite-based catalytic materials has not been achieved for vehicle exhaust emission control or for many other environmental applications. With recent advances in synthesis techniques, including the preparation of supported perovskites, and increasing understanding of promoted substitute perovskite-type materials, there is a growing interest in applied studies of perovskite-type catalytic materials. We have studied a number of perovskites based on Co, Mn, Ru, and Fe and their substituted compositions for their catalytic activity in terms of diesel soot oxidation, three-way catalysis, N2O decomposition, low-temperature CO oxidation, oxidation of volatile organic compounds, etc. The enhanced catalytic activity of these materials is attributed mainly to their altered redox properties, the promotional effect of co-ions, and the increased exposure of catalytically active transition metals in certain preparations. The recent lowering of sulfur content in fuel and concerns over the cost and availability of precious metals are responsible for renewed interest in perovskite-type catalysts for environmental applications. PMID:27877813

An Iron Reservoir to the Catalytic Metal

PubMed Central

Liu, Fange; Geng, Jiafeng; Gumpper, Ryan H.; Barman, Arghya; Davis, Ian; Ozarowski, Andrew; Hamelberg, Donald; Liu, Aimin

2015-01-01

The rubredoxin motif is present in over 74,000 protein sequences and 2,000 structures, but few have known functions. A secondary, non-catalytic, rubredoxin-like iron site is conserved in 3-hydroxyanthranilate 3,4-dioxygenase (HAO), from single cellular sources but not multicellular sources. Through the population of the two metal binding sites with various metals in bacterial HAO, the structural and functional relationship of the rubredoxin-like site was investigated using kinetic, spectroscopic, crystallographic, and computational approaches. It is shown that the first metal presented preferentially binds to the catalytic site rather than the rubredoxin-like site, which selectively binds iron when the catalytic site is occupied. Furthermore, an iron ion bound to the rubredoxin-like site is readily delivered to an empty catalytic site of metal-free HAO via an intermolecular transfer mechanism. Through the use of metal analysis and catalytic activity measurements, we show that a downstream metabolic intermediate can selectively remove the catalytic iron. As the prokaryotic HAO is often crucial for cell survival, there is a need for ensuring its activity. These results suggest that the rubredoxin-like site is a possible auxiliary iron source to the catalytic center when it is lost during catalysis in a pathway with metabolic intermediates of metal-chelating properties. A spare tire concept is proposed based on this biochemical study, and this concept opens up a potentially new functional paradigm for iron-sulfur centers in iron-dependent enzymes as transient iron binding and shuttling sites to ensure full metal loading of the catalytic site. PMID:25918158

Flight control synthesis for flexible aircraft using Eigenspace assignment

NASA Technical Reports Server (NTRS)

Davidson, J. B.; Schmidt, D. K.

1986-01-01

The use of eigenspace assignment techniques to synthesize flight control systems for flexible aircraft is explored. Eigenspace assignment techniques are used to achieve a specified desired eigenspace, chosen to yield desirable system impulse residue magnitudes for selected system responses. Two of these are investigated. The first directly determines constant measurement feedback gains that will yield a close-loop system eigenspace close to a desired eigenspace. The second technique selects quadratic weighting matrices in a linear quadratic control synthesis that will asymptotically yield the close-loop achievable eigenspace. Finally, the possibility of using either of these techniques with state estimation is explored. Application of the methods to synthesize integrated flight-control and structural-mode-control laws for a large flexible aircraft is demonstrated and results discussed. Eigenspace selection criteria based on design goals are discussed, and for the study case it would appear that a desirable eigenspace can be obtained. In addition, the importance of state-space selection is noted along with problems with reduced-order measurement feedback. Since the full-state control laws may be implemented with dynamic compensation (state estimation), the use of reduced-order measurement feedback is less desirable. This is especially true since no change in the transient response from the pilot's input results if state estimation is used appropriately. The potential is also noted for high actuator bandwidth requirements if the linear quadratic synthesis approach is utilized. Even with the actuator pole location selected, a problem with unmodeled modes is noted due to high bandwidth. Some suggestions for future research include investigating how to choose an eigenspace that will achieve certain desired dynamics and stability robustness, determining how the choice of measurements effects synthesis results, and exploring how the phase relationships between desired

Effects of copper-precursors on the catalytic activity of Cu/graphene catalysts for the selective catalytic oxidation of ammonia

NASA Astrophysics Data System (ADS)

Li, Jingying; Tang, Xiaolong; Yi, Honghong; Yu, Qingjun; Gao, Fengyu; Zhang, Runcao; Li, Chenlu; Chu, Chao

2017-08-01

Different copper-precursors were used to prepare Cu/graphene catalysts by an impregnation method. XRD, Raman spectra, TEM, BET, XPS, H2-TPR, NH3-TPD, DRIFTS and catalytic activity test were used to characterize and study the effect of precursors on the catalytic activity of Cu/graphene catalysts for NH3-SCO reaction. The large specific surface area of Cu/graphene catalysts and high dispersion of the metal particles on the graphene caused the well catalytic activity of NH3-SCO reaction. Compared to Cu/GE(AC), Cu/GE(N) showed better catalytic performance, and the complete NH3 removal efficiency was obtained at 250 °C with N2 selectivity of 85%. The copper-precursors had influence on the distribution of surface Cu species and further affected the catalytic activity of Cu/GE catalysts. The more amount of surface Cu species and highly dispersed CuO particles on the graphene surface formed by using copper nitrate as precursor could significantly improve the reducibility of catalysts and enhance NH3 adsorption, thereby improving the catalytic activity of Cu/graphene catalyst.

Fiber lasers with loop reflectors.

PubMed

Urquhart, P

1989-09-01

The theory of homogeneously broadened four level fiber lasers, which use fiber loops as distributed reflective elements, is examined. Such cavities can be made entirely from rare earth doped fiber. The amplifying characteristics of doped fiber loops are examined. The threshold pump power and the loop reflectivity necessary to optimize the lasing output power from an oscillator formed from two loops in series are predicted.

Decoupled and linear quadratic regulator control of a large, flexible space antenna with an observer in the control loop

NASA Technical Reports Server (NTRS)

Hamer, H. A.; Johnson, K. G.; Young, J. W.

1985-01-01

An analysis is performed to compare decoupled and linear quadratic regulator (LQR) procedures for the control of a large, flexible space antenna. Control objectives involve: (1) commanding changes in the rigid-body modes, (2) nulling initial disturbances in the rigid-body modes, or (3) nulling initial disturbances in the first three flexible modes. Control is achieved with two three-axis control-moment gyros located on the antenna column. Results are presented to illustrate various effects on control requirements for the two procedures. These effects include errors in the initial estimates of state variables, variations in the type, number, and location of sensors, and deletions of state-variable estimates for certain flexible modes after control activation. The advantages of incorporating a time lag in the control feedback are also illustrated. In addition, the effects of inoperative-control situations are analyzed with regard to control requirements and resultant modal responses. Comparisons are included which show the effects of perfect state feedback with no residual modes (ideal case). Time-history responses are presented to illustrate the various effects on the control procedures.

Catalytic ignition of hydrogen and oxygen propellants

NASA Technical Reports Server (NTRS)

Zurawski, Robert L.; Green, James M.

1988-01-01

An experimental program was conducted to evaluate the catalytic ignition of gaseous hydrogen and oxygen propellants. Shell 405 granular catalyst and a monolithic sponge catalyst were tested. Mixture ratio, mass flow rate, propellant temperature, and back pressure were varied parametrically in testing to determine the operational limits of the catalytic igniter. The test results show that the gaseous hydrogen and oxygen propellant combination can be ignited catalytically using Shell 405 catalyst over a wide range of mixture ratios, mass flow rates, and propellant injection temperatures. These operating conditions must be optimized to ensure reliable ignition for an extended period of time. A cyclic life of nearly 2000, 2 sec pulses at nominal operating conditions was demonstrated with the catalytic igniter. The results of the experimental program and the established operational limits for a catalytic igniter using the Shell 405 catalysts are presented.

Catalytic ignition of hydrogen and oxygen propellants

NASA Technical Reports Server (NTRS)

Zurawski, Robert L.; Green, James M.

1988-01-01

An experimental program was conducted to evaluate the catalytic ignition of gaseous hydrogen and oxygen propellants. Shell 405 granular catalyst and a monolithic sponge catalyst were tested. Mixture ratio, mass flow rate, propellant temperature, and back pressure were varied parametrically in testing to determine the operational limits of the catalytic igniter. The test results show that the gaseous hydrogen and oxygen propellant combination can be ignited catalytically using Shell 405 catalyst over a wide range of mixture ratios, mass flow rates, and propellant injection temperatures. These operating conditions must be optimized to ensure reliable ignition for an extended period of time. A cyclic life of nearly 2000, 2 sec pulses at nominal operating conditions was demonstrated with the catalytic igniter. The results of the experimental program and the established operational limits for a catalytic igniter using the Shell 405 catalyst are presented.

Diesel engine catalytic combustor system. [aircraft engines

NASA Technical Reports Server (NTRS)

Ream, L. W. (Inventor)

1984-01-01

A low compression turbocharged diesel engine is provided in which the turbocharger can be operated independently of the engine to power auxiliary equipment. Fuel and air are burned in a catalytic combustor to drive the turbine wheel of turbine section which is initially caused to rotate by starter motor. By opening a flapper value, compressed air from the blower section is directed to catalytic combustor when it is heated and expanded, serving to drive the turbine wheel and also to heat the catalytic element. To start, engine valve is closed, combustion is terminated in catalytic combustor, and the valve is then opened to utilize air from the blower for the air driven motor. When the engine starts, the constituents in its exhaust gas react in the catalytic element and the heat generated provides additional energy for the turbine section.

Loop-bed combustion apparatus

DOEpatents

Shang, Jer-Yu; Mei, Joseph S.; Slagle, Frank D.; Notestein, John E.

1984-01-01

The present invention is directed to a combustion apparatus in the configuration of a oblong annulus defining a closed loop. Particulate coal together with a sulfur sorbent such as sulfur or dolomite is introduced into the closed loop, ignited, and propelled at a high rate of speed around the loop. Flue gas is withdrawn from a location in the closed loop in close proximity to an area in the loop where centrifugal force imposed upon the larger particulate material maintains these particulates at a location spaced from the flue gas outlet. Only flue gas and smaller particulates resulting from the combustion and innerparticle grinding are discharged from the combustor. This structural arrangement provides increased combustion efficiency due to the essentially complete combustion of the coal particulates as well as increased sulfur absorption due to the innerparticle grinding of the sorbent which provides greater particle surface area.

Dynamics of the active site architecture in plant-type ferredoxin-NADP(+) reductases catalytic complexes.

PubMed

Sánchez-Azqueta, Ana; Catalano-Dupuy, Daniela L; López-Rivero, Arleth; Tondo, María Laura; Orellano, Elena G; Ceccarelli, Eduardo A; Medina, Milagros

2014-10-01

Kinetic isotope effects in reactions involving hydride transfer and their temperature dependence are powerful tools to explore dynamics of enzyme catalytic sites. In plant-type ferredoxin-NADP(+) reductases the FAD cofactor exchanges a hydride with the NADP(H) coenzyme. Rates for these processes are considerably faster for the plastidic members (FNR) of the family than for those belonging to the bacterial class (FPR). Hydride transfer (HT) and deuteride transfer (DT) rates for the NADP(+) coenzyme reduction of four plant-type FNRs (two representatives of the plastidic type FNRs and the other two from the bacterial class), and their temperature dependences are here examined applying a full tunnelling model with coupled environmental fluctuations. Parameters for the two plastidic FNRs confirm a tunnelling reaction with active dynamics contributions, but isotope effects on Arrhenius factors indicate a larger contribution for donor-acceptor distance (DAD) dynamics in the Pisum sativum FNR reaction than in the Anabaena FNR reaction. On the other hand, parameters for bacterial FPRs are consistent with passive environmental reorganisation movements dominating the HT coordinate and no contribution of DAD sampling or gating fluctuations. This indicates that active sites of FPRs are more organised and rigid than those of FNRs. These differences must be due to adaptation of the active sites and catalytic mechanisms to fulfil their particular metabolic roles, establishing a compromise between protein flexibility and functional optimisation. Analysis of site-directed mutants in plastidic enzymes additionally indicates the requirement of a minimal optimal architecture in the catalytic complex to provide a favourable gating contribution. Copyright © 2014 Elsevier B.V. All rights reserved.

Static Aeroelastic and Longitudinal Trim Model of Flexible Wing Aircraft Using Finite-Element Vortex-Lattice Coupled Solution

NASA Technical Reports Server (NTRS)

Ting, Eric; Nguyen, Nhan; Trinh, Khanh

2014-01-01

This paper presents a static aeroelastic model and longitudinal trim model for the analysis of a flexible wing transport aircraft. The static aeroelastic model is built using a structural model based on finite-element modeling and coupled to an aerodynamic model that uses vortex-lattice solution. An automatic geometry generation tool is used to close the loop between the structural and aerodynamic models. The aeroelastic model is extended for the development of a three degree-of-freedom longitudinal trim model for an aircraft with flexible wings. The resulting flexible aircraft longitudinal trim model is used to simultaneously compute the static aeroelastic shape for the aircraft model and the longitudinal state inputs to maintain an aircraft trim state. The framework is applied to an aircraft model based on the NASA Generic Transport Model (GTM) with wing structures allowed to flexibly deformed referred to as the Elastically Shaped Aircraft Concept (ESAC). The ESAC wing mass and stiffness properties are based on a baseline "stiff" values representative of current generation transport aircraft.

Adsorbent catalytic nanoparticles and methods of using the same

DOEpatents

Slowing, Igor Ivan; Kandel, Kapil

2017-01-31

The present invention provides an adsorbent catalytic nanoparticle including a mesoporous silica nanoparticle having at least one adsorbent functional group bound thereto. The adsorbent catalytic nanoparticle also includes at least one catalytic material. In various embodiments, the present invention provides methods of using and making the adsorbent catalytic nanoparticles. In some examples, the adsorbent catalytic nanoparticles can be used to selectively remove fatty acids from feedstocks for biodiesel, and to hydrotreat the separated fatty acids.

Takagi-Sugeno fuzzy model based robust dissipative control for uncertain flexible spacecraft with saturated time-delay input.

PubMed

Xu, Shidong; Sun, Guanghui; Sun, Weichao

2017-01-01

In this paper, the problem of robust dissipative control is investigated for uncertain flexible spacecraft based on Takagi-Sugeno (T-S) fuzzy model with saturated time-delay input. Different from most existing strategies, T-S fuzzy approximation approach is used to model the nonlinear dynamics of flexible spacecraft. Simultaneously, the physical constraints of system, like input delay, input saturation, and parameter uncertainties, are also taken care of in the fuzzy model. By employing Lyapunov-Krasovskii method and convex optimization technique, a novel robust controller is proposed to implement rest-to-rest attitude maneuver for flexible spacecraft, and the guaranteed dissipative performance enables the uncertain closed-loop system to reject the influence of elastic vibrations and external disturbances. Finally, an illustrative design example integrated with simulation results are provided to confirm the applicability and merits of the developed control strategy. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

Vibration sensing in flexible structures using a distributed-effect modal domain optical fiber sensor

NASA Technical Reports Server (NTRS)

Reichard, Karl M.; Lindner, Douglas K.; Claus, Richard O.

1991-01-01

Modal domain optical fiber sensors have recently been employed in the implementation of system identification algorithms and the closed-loop control of vibrations in flexible structures. The mathematical model of the modal domain optical fiber sensor used in these applications, however, only accounted for the effects of strain in the direction of the fiber's longitudinal axis. In this paper, we extend this model to include the effects of arbitrary stress. Using this sensor model, we characterize the sensor's sensitivity and dynamic range.

The dynamics and control of large flexible space structures-V

NASA Technical Reports Server (NTRS)

Bainum, P. M.; Reddy, A. S. S. R.; Diarra, C. M.; Kumar, V. K.

1982-01-01

A general survey of the progress made in the areas of mathematical modelling of the system dynamics, structural analysis, development of control algorithms, and simulation of environmental disturbances is presented. The use of graph theory techniques is employed to examine the effects of inherent damping associated with LSST systems on the number and locations of the required control actuators. A mathematical model of the forces and moments induced on a flexible orbiting beam due to solar radiation pressure is developed and typical steady state open loop responses obtained for the case when rotations and vibrations are limited to occur within the orbit plane. A preliminary controls analysis based on a truncated (13 mode) finite element model of the 122m. Hoop/Column antenna indicates that a minimum of six appropriately placed actuators is required for controllability. An algorithm to evaluate the coefficients which describe coupling between the rigid rotational and flexible modes and also intramodal coupling was developed and numerical evaluation based on the finite element model of Hoop/Column system is currently in progress.

Deduced catalytic mechanism of d-amino acid amidase from Ochrobactrum anthropi SV3

PubMed Central

Okazaki, Seiji; Suzuki, Atsuo; Komeda, Hidenobu; Asano, Yasuhisa; Yamane, Takashi

2008-01-01

d-Amino acid amidase (DAA) from Ochrobactrum anthropi SV3 catalyzes d-stereospecific hydrolysis of amino acid amides. DAA has attracted attention as a catalyst for the stereospecific production of d-amino acids, although the mechanism that drives the reaction has not been clear. Previously, the structure of DAA was classified into two types, a substrate-bound state with an ordered Ω loop, and a ground state with a disordered Ω loop. Because the binding of the substrate facilitates ordering, this transition was regarded to be induced fit motion. The angles and distances of hydrogen bonds at Tyr149 Oη, Ser60 Oγ and Lys63 Nζ revealed that Tyr149 Oη donates an H atom to a water molecule in the substrate-bound state, and that Tyr149 Oη donates an H atom to Ser60 Oγ or Lys63 Nζ in the ground state. Taking into consideration the locations of the H atoms of Tyr149 Oη, Ser60 Oγ and Lys63 Nζ, a catalytic mechanism of DAA activity is presented, wherein a shift of an H atom at Tyr149 Oη in the substrate-bound versus the ground state plays a significant role in the reaction. This mechanism explains well why acylation proceeds and deacylation does not proceed in the substrate-bound state. PMID:18421151

Conformational motions regulate phosphoryl transfer in related protein tyrosine phosphatases

PubMed Central

Whittier, Sean K.; Hengge, Alvan C.; Loria, J. Patrick

2014-01-01

Many studies have implicated a role for conformational motions during the catalytic cycle, acting to optimize the binding pocket or facilitate product release, but a more intimate role in the chemical reaction has not been described. We address this by monitoring active-site loop motion in two protein tyrosine phosphatases (PTPs) using NMR spectroscopy. The PTPs, YopH and PTP1B, have very different catalytic rates, however we find in both that the active-site loop closes to its catalytically competent position at rates that mirror the phosphotyrosine cleavage kinetics. This loop contains the catalytic acid, suggesting that loop closure occurs concomitantly with the protonation of the leaving group tyrosine and explains the different kinetics of two otherwise chemically and mechanistically indistinguishable enzymes. PMID:23970698

Bandwidth controller for phase-locked-loop

NASA Technical Reports Server (NTRS)

Brockman, Milton H. (Inventor)

1992-01-01

A phase locked loop utilizing digital techniques to control the closed loop bandwidth of the RF carrier phase locked loop in a receiver provides high sensitivity and a wide dynamic range for signal reception. After analog to digital conversion, a digital phase locked loop bandwidth controller provides phase error detection with automatic RF carrier closed loop tracking bandwidth control to accommodate several modes of transmission.

Measuring Pressure Volume Loops in the Mouse.

PubMed

Townsend, DeWayne

2016-05-02

Understanding the causes and progression of heart disease presents a significant challenge to the biomedical community. The genetic flexibility of the mouse provides great potential to explore cardiac function at the molecular level. The mouse's small size does present some challenges in regards to performing detailed cardiac phenotyping. Miniaturization and other advancements in technology have made many methods of cardiac assessment possible in the mouse. Of these, the simultaneous collection of pressure and volume data provides a detailed picture of cardiac function that is not available through any other modality. Here a detailed procedure for the collection of pressure-volume loop data is described. Included is a discussion of the principles underlying the measurements and the potential sources of error. Anesthetic management and surgical approaches are discussed in great detail as they are both critical to obtaining high quality hemodynamic measurements. The principles of hemodynamic protocol development and relevant aspects of data analysis are also addressed.

Human ER Oxidoreductin-1α (Ero1α) Undergoes Dual Regulation through Complementary Redox Interactions with Protein-Disulfide Isomerase.

PubMed

Kanemura, Shingo; Okumura, Masaki; Yutani, Katsuhide; Ramming, Thomas; Hikima, Takaaki; Appenzeller-Herzog, Christian; Akiyama, Shuji; Inaba, Kenji

2016-11-11

In the mammalian endoplasmic reticulum, oxidoreductin-1α (Ero1α) generates protein disulfide bonds and transfers them specifically to canonical protein-disulfide isomerase (PDI) to sustain oxidative protein folding. This oxidative process is coupled to the reduction of O 2 to H 2 O 2 on the bound flavin adenine dinucleotide cofactor. Because excessive thiol oxidation and H 2 O 2 generation cause cell death, Ero1α activity must be properly regulated. In addition to the four catalytic cysteines (Cys 94 , Cys 99 , Cys 104 , and Cys 131 ) that are located in the flexible active site region, the Cys 208 -Cys 241 pair located at the base of another flexible loop is necessary for Ero1α regulation, although the mechanistic basis is not fully understood. The present study revealed that the Cys 208 -Cys 241 disulfide was reduced by PDI and other PDI family members during PDI oxidation. Differential scanning calorimetry and small angle X-ray scattering showed that mutation of Cys 208 and Cys 241 did not grossly affect the thermal stability or overall shape of Ero1α, suggesting that redox regulation of this cysteine pair serves a functional role. Moreover, the flexible loop flanked by Cys 208 and Cys 241 provides a platform for functional interaction with PDI, which in turn enhances the oxidative activity of Ero1α through reduction of the Cys 208 -Cys 241 disulfide. We propose a mechanism of dual Ero1α regulation by dynamic redox interactions between PDI and the two Ero1α flexible loops that harbor the regulatory cysteines. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Guaranteed cost control with poles assignment for a flexible air-breathing hypersonic vehicle

NASA Astrophysics Data System (ADS)

Li, Hongyi; Si, Yulin; Wu, Ligang; Hu, Xiaoxiang; Gao, Huijun

2011-05-01

This article investigates the problem of guaranteed cost control for a flexible air-breathing hypersonic vehicle (FAHV). The FAHV includes intricate coupling between the engine and flight dynamics as well as complex interplay between flexible and rigid modes, which results in an intractable system for the control design. A longitudinal model is adopted for control design due to the complexity of the vehicle. First, for a highly nonlinear and coupled FAHV, a linearised model is established around the trim condition, which includes the state of altitude, velocity, angle of attack, pitch angle and pitch rate, etc. Secondly, by using the Lyapunov approach, performance analysis is carried out for the resulting closed-loop FAHV system, whose criterion with respect to guaranteed performance cost and poles assignment is expressed in the framework of linear matrix inequalities (LMIs). The established criterion exhibits a kind of decoupling between the Lyapunov positive-definite matrices to be determined and the FAHV system matrices, which is enabled by the introduction of additional slack matrix variables. Thirdly, a convex optimisation problem with LMI constraints is formulated for designing an admissible controller, which guarantees a prescribed performance cost with the simultaneous consideration of poles assignment for the resulting closed-loop system. Finally, some simulation results are provided to show that the guaranteed cost controller could assign the poles into the desired regional and achieve excellent reference altitude and velocity tracking performance.

Atomically Precise Metal Nanoclusters for Catalytic Application

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

Jin, Rongchao

2016-11-18

The central goal of this project is to explore the catalytic application of atomically precise gold nanoclusters. By solving the total structures of ligand-protected nanoclusters, we aim to correlate the catalytic properties of metal nanoclusters with their atomic/electronic structures. Such correlation unravel some fundamental aspects of nanocatalysis, such as the nature of particle size effect, origin of catalytic selectivity, particle-support interactions, the identification of catalytically active centers, etc. The well-defined nanocluster catalysts mediate the knowledge gap between single crystal model catalysts and real-world conventional nanocatalysts. These nanoclusters also hold great promise in catalyzing certain types of reactions with extraordinarily highmore » selectivity. These aims are in line with the overall goals of the catalytic science and technology of DOE and advance the BES mission “to support fundamental research to understand, predict, and ultimately control matter and energy at the level of electrons, atoms, and molecules”. Our group has successfully prepared different sized, robust gold nanoclusters protected by thiolates, such as Au 25(SR) 18, Au 28(SR) 20, Au 38(SR) 24, Au 99(SR) 42, Au 144(SR) 60, etc. Some of these nanoclusters have been crystallographically characterized through X-ray crystallography. These ultrasmall nanoclusters (< 2 nm diameter) exhibit discrete electronic structures due to quantum size effect, as opposed to quasicontinuous band structure of conventional metal nanoparticles or bulk metals. The available atomic structures (metal core plus surface ligands) of nanoclusters serve as the basis for structure-property correlations. We have investigated the unique catalytic properties of nanoclusters (i.e. not observed in conventional nanogold catalysts) and revealed the structure-selectivity relationships. Highlights of our works include: i) Effects of ligand, cluster charge state, and size on the catalytic

Effect of inlet cone pipe angle in catalytic converter

NASA Astrophysics Data System (ADS)

Amira Zainal, Nurul; Farhain Azmi, Ezzatul; Arifin Samad, Mohd

2018-03-01

The catalytic converter shows significant consequence to improve the performance of the vehicle start from it launched into production. Nowadays, the geometric design of the catalytic converter has become critical to avoid the behavior of backpressure in the exhaust system. The backpressure essentially reduced the performance of vehicles and increased the fuel consumption gradually. Consequently, this study aims to design various models of catalytic converter and optimize the volume of fluid flow inside the catalytic converter by changing the inlet cone pipe angles. Three different geometry angles of the inlet cone pipe of the catalytic converter were assessed. The model is simulated in Solidworks software to determine the optimum geometric design of the catalytic converter. The result showed that by decreasing the divergence angle of inlet cone pipe will upsurge the performance of the catalytic converter.

NMR studies of the backbone flexibility and structure of human growth hormone: a comparison of high and low pH conformations.

PubMed

Kasimova, Marina R; Kristensen, Søren M; Howe, Peter W A; Christensen, Thorkild; Matthiesen, Finn; Petersen, Jørgen; Sørensen, Hans H; Led, Jens J

2002-05-03

(15)N NMR relaxation parameters and amide (1)H/(2)H-exchange rates have been used to characterize the structural flexibility of human growth hormone (rhGH) at neutral and acidic pH. Our results show that the rigidity of the molecule is strongly affected by the solution conditions. At pH 7.0 the backbone dynamics parameters of rhGH are uniform along the polypeptide chain and their values are similar to those of other folded proteins. In contrast, at pH 2.7 the overall backbone flexibility increases substantially compared to neutral pH and the average order parameter approaches the lower limit expected for a folded protein. However, a significant variation of the backbone dynamics through the molecule indicates that under acidic conditions the mobility of the residues becomes more dependent on their location within the secondary structure units. In particular, the order parameters of certain loop regions decrease dramatically and become comparable to those found in unfolded proteins. Furthermore, the HN-exchange rates at low pH reveal that the residues most protected from exchange are clustered at one end of the helical bundle, forming a stable nucleus. We suggest that this nucleus maintains the overall fold of the protein under destabilizing conditions. We therefore conclude that the acid state of rhGH consists of a structurally conserved, but dynamically more flexible helical core surrounded by an aura of highly mobile, unstructured loops. However, in spite of its prominent flexibility the acid state of rhGH cannot be considered a "molten globule" state because of its high stability. It appears from our work that under certain conditions, a protein can tolerate a considerable increase in flexibility of its backbone, along with an increased penetration of water into its core, while still maintaining a stable folded conformation.

Topological entropy of catalytic sets: Hypercycles revisited

NASA Astrophysics Data System (ADS)

Sardanyés, Josep; Duarte, Jorge; Januário, Cristina; Martins, Nuno

2012-02-01

The dynamics of catalytic networks have been widely studied over the last decades because of their implications in several fields like prebiotic evolution, virology, neural networks, immunology or ecology. One of the most studied mathematical bodies for catalytic networks was initially formulated in the context of prebiotic evolution, by means of the hypercycle theory. The hypercycle is a set of self-replicating species able to catalyze other replicator species within a cyclic architecture. Hypercyclic organization might arise from a quasispecies as a way to increase the informational containt surpassing the so-called error threshold. The catalytic coupling between replicators makes all the species to behave like a single and coherent evolutionary multimolecular unit. The inherent nonlinearities of catalytic interactions are responsible for the emergence of several types of dynamics, among them, chaos. In this article we begin with a brief review of the hypercycle theory focusing on its evolutionary implications as well as on different dynamics associated to different types of small catalytic networks. Then we study the properties of chaotic hypercycles with error-prone replication with symbolic dynamics theory, characterizing, by means of the theory of topological Markov chains, the topological entropy and the periods of the orbits of unimodal-like iterated maps obtained from the strange attractor. We will focus our study on some key parameters responsible for the structure of the catalytic network: mutation rates, autocatalytic and cross-catalytic interactions.

Explaining Warm Coronal Loops

NASA Technical Reports Server (NTRS)

Klimchuk, James A.; Karpen, Judy T.; Patsourakos, Spiros

2008-01-01

One of the great mysteries of coronal physics that has come to light in the last few years is the discovery that warn (- 1 INK) coronal loops are much denser than expected for quasi-static equilibrium. Both the excess densities and relatively long lifetimes of the loops can be explained with bundles of unresolved strands that are heated impulsively to very high temperatures. Since neighboring strands are at different stages of cooling, the composite loop bundle is multi-thermal, with the distribution of temperatures depending on the details of the "nanoflare storm." Emission hotter than 2 MK is predicted, but it is not clear that such emission is always observed. We consider two possible explanations for the existence of over-dense warm loops without corresponding hot emission: (1) loops are bundles of nanoflare heated strands, but a significant fraction of the nanoflare energy takes the form of a nonthermal electron beam rather then direct plasma heating; (2) loops are bundles of strands that undergo thermal nonequilibrium that results when steady heating is sufficiently concentrated near the footpoints. We present numerical hydro simulations of both of these possibilities and explore the observational consequences, including the production of hard X-ray emission and absorption by cool material in the corona.

Application of the LQG/LTR technique to robust controller synthesis for a large flexible space antenna

NASA Technical Reports Server (NTRS)

Joshi, S. M.; Armstrong, E. S.; Sundararajan, N.

1986-01-01

The problem of synthesizing a robust controller is considered for a large, flexible space-based antenna by using the linear-quadratic-Gaussian (LQG)/loop transfer recovery (LTR) method. The study is based on a finite-element model of the 122-m hoop/column antenna, which consists of three rigid-body rotational modes and the first 10 elastic modes. A robust compensator design for achieving the required performance bandwidth in the presence of modeling uncertainties is obtained using the LQG/LTR method for loop-shaping in the frequency domain. Different sensor actuator locations are analyzed in terms of the pole/zero locations of the multivariable systems and possible best locations are indicated. The computations are performed by using the LQG design package ORACLS augmented with frequency domain singular value analysis software.

Silver nanocluster catalytic microreactors for water purification

NASA Astrophysics Data System (ADS)

Da Silva, B.; Habibi, M.; Ognier, S.; Schelcher, G.; Mostafavi-Amjad, J.; Khalesifard, H. R. M.; Tatoulian, M.; Bonn, D.

2016-07-01

A new method for the elaboration of a novel type of catalytic microsystem with a high specific area catalyst is developed. A silver nanocluster catalytic microreactor was elaborated by doping a soda-lime glass with a silver salt. By applying a high power laser beam to the glass, silver nanoclusters are obtained at one of the surfaces which were characterized by BET measurements and AFM. A microfluidic chip was obtained by sealing the silver coated glass with a NOA 81 microchannel. The catalytic activity of the silver nanoclusters was then tested for the efficiency of water purification by using catalytic ozonation to oxidize an organic pollutant. The silver nanoclusters were found to be very stable in the microreactor and efficiently oxidized the pollutant, in spite of the very short residence times in the microchannel. This opens the way to study catalytic reactions in microchannels without the need of introducing the catalyst as a powder or manufacturing complex packed bed microreactors.

Flexible Bond Wire Capacitive Strain Sensor for Vehicle Tyres

PubMed Central

Cao, Siyang; Pyatt, Simon; Anthony, Carl J.; Kubba, Ammar I.; Kubba, Ali E.; Olatunbosun, Oluremi

2016-01-01

The safety of the driving experience and manoeuvrability of a vehicle can be improved by detecting the strain in tyres. To measure strain accurately in rubber, the strain sensor needs to be flexible so that it does not deform the medium that it is measuring. In this work, a novel flexible bond wire capacitive strain sensor for measuring the strain in tyres is developed, fabricated and calibrated. An array of 25 micron diameter wire bonds in an approximately 8 mm × 8 mm area is built to create an interdigitated structure, which consists of 50 wire loops resulting in 49 capacitor pairs in parallel. Laser machining was used to pattern copper on a flexible printed circuit board PCB to make the bond pads for the wire attachment. The wire array was finally packaged and embedded in polydimethylsiloxane (PDMS), which acts as the structural material that is strained. The capacitance of the device is in a linear like relationship with respect to the strain, which can measure the strain up to at least ±60,000 micro-strain (±6%) with a resolution of ~132 micro-strain (0.013%). In-tyre testing under static loading has shown the ability of the sensor to measure large tyre strains. The technology used for sensor fabrication lends itself to mass production and so the design is considered to be consistent with low cost commercialisable strain sensing technology. PMID:27338402

Flexible Bond Wire Capacitive Strain Sensor for Vehicle Tyres.

PubMed

Cao, Siyang; Pyatt, Simon; Anthony, Carl J; Kubba, Ammar I; Kubba, Ali E; Olatunbosun, Oluremi

2016-06-21

The safety of the driving experience and manoeuvrability of a vehicle can be improved by detecting the strain in tyres. To measure strain accurately in rubber, the strain sensor needs to be flexible so that it does not deform the medium that it is measuring. In this work, a novel flexible bond wire capacitive strain sensor for measuring the strain in tyres is developed, fabricated and calibrated. An array of 25 micron diameter wire bonds in an approximately 8 mm × 8 mm area is built to create an interdigitated structure, which consists of 50 wire loops resulting in 49 capacitor pairs in parallel. Laser machining was used to pattern copper on a flexible printed circuit board PCB to make the bond pads for the wire attachment. The wire array was finally packaged and embedded in polydimethylsiloxane (PDMS), which acts as the structural material that is strained. The capacitance of the device is in a linear like relationship with respect to the strain, which can measure the strain up to at least ±60,000 micro-strain (±6%) with a resolution of ~132 micro-strain (0.013%). In-tyre testing under static loading has shown the ability of the sensor to measure large tyre strains. The technology used for sensor fabrication lends itself to mass production and so the design is considered to be consistent with low cost commercialisable strain sensing technology.

Flexible Bronchoscopy.

PubMed

Miller, Russell J; Casal, Roberto F; Lazarus, Donald R; Ost, David E; Eapen, George A

2018-03-01

Flexible bronchoscopy has changed the course of pulmonary medicine. As technology advances, the role of the flexible bronchoscope for both diagnostic and therapeutic indications is continually expanding. This article reviews the historical development of the flexible bronchoscopy, fundamental uses of the flexible bronchoscope as a tool to examine the central airways and obtain diagnostic tissue, and the indications, complications, and contraindications to flexible bronchoscopy. Copyright © 2017 Elsevier Inc. All rights reserved.

Contribution of the mu loop to the structure and function of rat glutathione transferase M1-1

PubMed Central

Hearne, Jennifer L.; Colman, Roberta F.

2006-01-01

The “mu loop,” an 11-residue loop spanning amino acid residues 33–43, is a characteristic structural feature of the mu class of glutathione transferases. To assess the contribution of the mu loop to the structure and function of rat GST M1-1, amino acid residues 35–44 (35GDAPDYDRSQ44) were excised by deletion mutagenesis, resulting in the “Deletion Enzyme.” Kinetic studies reveal that the Km values of the Deletion Enzyme are markedly increased compared with those of the wild-type enzyme: 32-fold for 1-chloro-2,4-dinitrobenzene, 99-fold for glutathione, and 880-fold for monobromobimane, while the Vmax value for each substrate is increased only modestly. Results from experiments probing the structure of the Deletion Enzyme, in comparison with that of the wild-type enzyme, suggest that the secondary and quaternary structures have not been appreciably perturbed. Thermostability studies indicate that the Deletion Enzyme is as stable as the wild-type enzyme at 4°C and 10°C, but it rapidly loses activity at 25°C, unlike the wild-type enzyme. In the temperature range of 4°C through 25°C, the loss of activity of the Deletion Enzyme is not the result of a change in its structure, as determined by circular dichroism spectroscopy and sedimentation equilibrium centrifugation. Collectively, these results indicate that the mu loop is not essential for GST M1-1 to maintain its structure nor is it required for the enzyme to retain some catalytic activity. However, it is an important determinant of the enzyme's affinity for its substrates. PMID:16672236

RCD+: Fast loop modeling server.

PubMed

López-Blanco, José Ramón; Canosa-Valls, Alejandro Jesús; Li, Yaohang; Chacón, Pablo

2016-07-08

Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards near-native conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbor-dependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop models are subsequently ranked using a fast distance-orientation dependent energy filter. Top ranked loops are refined with the Rosetta energy function to obtain accurate all-atom predictions that can be interactively inspected in an user-friendly web interface. Using standard benchmarks, the average root mean squared deviation (RMSD) is 0.8 and 1.4 Å for 8 and 12 residues loops, respectively, in the challenging modeling scenario in where the side chains of the loop environment are fully remodeled. These results are not only very competitive compared to those obtained with public state of the art methods, but also they are obtained ∼10-fold faster. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Concentric catalytic combustor

DOEpatents

Bruck, Gerald J [Oviedo, FL; Laster, Walter R [Oviedo, FL

2009-03-24

A catalytic combustor (28) includes a tubular pressure boundary element (90) having a longitudinal flow axis (e.g., 56) separating a first portion (94) of a first fluid flow (e.g., 24) from a second portion (95) of the first fluid flow. The pressure boundary element includes a wall (96) having a plurality of separate longitudinally oriented flow paths (98) annularly disposed within the wall and conducting respective portions (100, 101) of a second fluid flow (e.g., 26) therethrough. A catalytic material (32) is disposed on a surface (e.g., 102, 103) of the pressure boundary element exposed to at least one of the first and second portions of the first fluid flow.

Fragmentation of cosmic-string loops

NASA Technical Reports Server (NTRS)

York, Thomas

1989-01-01

The fragmentation of cosmic string loops is discussed, and the results of a simulation of this process are presented. The simulation can evolve any of a large class of loops essentially exactly, including allowing fragments that collide to join together. Such reconnection enhances the production of small fragments, but not drastically. With or without reconnections, the fragmentation process produces a collection of nonself-intersecting loops whose typical length is on the order of the persistence length of the initial loop.

Regulation of Catalytic and Non-catalytic Functions of the Drosophila Ste20 Kinase Slik by Activation Segment Phosphorylation.

PubMed

Panneton, Vincent; Nath, Apurba; Sader, Fadi; Delaunay, Nathalie; Pelletier, Ariane; Maier, Dominic; Oh, Karen; Hipfner, David R

2015-08-21

Protein kinases carry out important functions in cells both by phosphorylating substrates and by means of regulated non-catalytic activities. Such non-catalytic functions have been ascribed to many kinases, including some members of the Ste20 family. The Drosophila Ste20 kinase Slik phosphorylates and activates Moesin in developing epithelial tissues to promote epithelial tissue integrity. It also functions non-catalytically to promote epithelial cell proliferation and tissue growth. We carried out a structure-function analysis to determine how these two distinct activities of Slik are controlled. We find that the conserved C-terminal coiled-coil domain of Slik, which is necessary and sufficient for apical localization of the kinase in epithelial cells, is not required for Moesin phosphorylation but is critical for the growth-promoting function of Slik. Slik is auto- and trans-phosphorylated in vivo. Phosphorylation of at least two of three conserved sites in the activation segment is required for both efficient catalytic activity and non-catalytic signaling. Slik function is thus dependent upon proper localization of the kinase via the C-terminal coiled-coil domain and activation via activation segment phosphorylation, which enhances both phosphorylation of substrates like Moesin and engagement of effectors of its non-catalytic growth-promoting activity. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Engineered disulfide bonds increase active-site local stability and reduce catalytic activity of a cold-adapted alkaline phosphatase.

PubMed

Asgeirsson, Bjarni; Adalbjörnsson, Björn Vidar; Gylfason, Gudjón Andri

2007-06-01

Alkaline phosphatase is an extracellular enzyme that is membrane-bound in eukaryotes but resides in the periplasmic space of bacteria. It normally carries four cysteine residues that form two disulfide bonds, for instance in the APs of Escherichia coli and vertebrates. An AP variant from a Vibrio sp. has only one cysteine residue. This cysteine is second next to the nucleophilic serine in the active site. We have individually modified seven residues to cysteine that are on two loops predicted to be within a 5 A radius. Four of them formed a disulfide bond to the endogenous cysteine. Thermal stability was monitored by circular dichroism and activity measurements. Global stability was similar to the wild-type enzyme. However, a significant increase in heat-stability was observed for the disulfide-containing variants using activity as a measure, together with a large reduction in catalytic rates (k(cat)) and a general decrease in Km values. The results suggest that a high degree of mobility near the active site and in the helix carrying the endogenous cysteine is essential for full catalytic efficiency in the cold-adapted AP.

[Deletion of a dynamic surface loop improves thermostability of (R)-selective amine transaminase from Aspergillus terreus].

PubMed

Xie, Dongfang; Lv, Changjiang; Fang, Hui; Yang, Weikang; Hu, Sheng; Zhao, Weirui; Huang, Jun; Mei, Lehe

2017-12-25

Chiral amines are important building blocks for the synthesis of pharmaceutical products and fine chemicals. Highly stereoselective synthesis of chiral amines compounds through asymmetric amination has attracted more and more attention. ω-transaminases (ω-TAs) are a promising class of natural biocatalysts which provide an efficient and environment-friendly access to production of chiral amines with stringent enantioselectivity and excellent catalytic efficiency. Compared with (S)-ω-TA, the research focused on (R)-ω-TA was relatively less. However, increasing demand for chiral (R)-amines as pharmaceutical intermediates has rendered industrial applications of (R)-ω-TA more attractive. Improving the thermostability of (R)-ω-TA with potential biotechnological application will facilitate the preparation of chiral amines. In this study, the dynamic surface loop with higher B-factor from Aspergillus terreus (R)-ω-TA was predicted by two computer softwares (PyMOL and YASARA). Then mutant enzymes were obtained by deleting amino acid residues of a dynamic surface loop using site-directed mutagenesis. The results showed that the best two mutants R131del and P132-E133del improved thermostability by 2.6 ℃ and 0.9 ℃ in T₅₀¹⁰ (41.1 ℃ and 39.4 ℃, respectively), and 2.2-fold and 1.5-fold in half-life (t1/2) at 40 ℃ (15.0 min and 10.0 min, respectively), compared to that of wild type. Furtherly, the thermostability mechanism of the mutant enzymes was investigated by molecular dynamics (MD) simulation and intermolecular interaction analysis. R131del in the loop region has lower root mean square fluctuation (RMSF) than the wild type at 400 K for 10 ns, and mutant enzyme P132-E133del increases four hydrogen bonds in the loop region. In this study, we obtain two stability-increased mutants of (R)-ω-TA from A. terreus by deleting its dynamic surface loop and also provide methodological guidance for the use of rational design to enhance the thermal stability of

A fast and flexible panoramic virtual reality system for behavioural and electrophysiological experiments.

PubMed

Takalo, Jouni; Piironen, Arto; Honkanen, Anna; Lempeä, Mikko; Aikio, Mika; Tuukkanen, Tuomas; Vähäsöyrinki, Mikko

2012-01-01

Ideally, neuronal functions would be studied by performing experiments with unconstrained animals whilst they behave in their natural environment. Although this is not feasible currently for most animal models, one can mimic the natural environment in the laboratory by using a virtual reality (VR) environment. Here we present a novel VR system based upon a spherical projection of computer generated images using a modified commercial data projector with an add-on fish-eye lens. This system provides equidistant visual stimulation with extensive coverage of the visual field, high spatio-temporal resolution and flexible stimulus generation using a standard computer. It also includes a track-ball system for closed-loop behavioural experiments with walking animals. We present a detailed description of the system and characterize it thoroughly. Finally, we demonstrate the VR system's performance whilst operating in closed-loop conditions by showing the movement trajectories of the cockroaches during exploratory behaviour in a VR forest.

A vision-based end-point control for a two-link flexible manipulator. M.S. Thesis

NASA Technical Reports Server (NTRS)

Obergfell, Klaus

1991-01-01

The measurement and control of the end-effector position of a large two-link flexible manipulator are investigated. The system implementation is described and an initial algorithm for static end-point positioning is discussed. Most existing robots are controlled through independent joint controllers, while the end-effector position is estimated from the joint positions using a kinematic relation. End-point position feedback can be used to compensate for uncertainty and structural deflections. Such feedback is especially important for flexible robots. Computer vision is utilized to obtain end-point position measurements. A look-and-move control structure alleviates the disadvantages of the slow and variable computer vision sampling frequency. This control structure consists of an inner joint-based loop and an outer vision-based loop. A static positioning algorithm was implemented and experimentally verified. This algorithm utilizes the manipulator Jacobian to transform a tip position error to a joint error. The joint error is then used to give a new reference input to the joint controller. The convergence of the algorithm is demonstrated experimentally under payload variation. A Landmark Tracking System (Dickerson, et al 1990) is used for vision-based end-point measurements. This system was modified and tested. A real-time control system was implemented on a PC and interfaced with the vision system and the robot.

Integrated and flexible multichannel interface for electrotactile stimulation

NASA Astrophysics Data System (ADS)

Štrbac, Matija; Belić, Minja; Isaković, Milica; Kojić, Vladimir; Bijelić, Goran; Popović, Igor; Radotić, Milutin; Došen, Strahinja; Marković, Marko; Farina, Dario; Keller, Thierry

2016-08-01

Objective. The aim of the present work was to develop and test a flexible electrotactile stimulation system to provide real-time feedback to the prosthesis user. The system requirements were to accommodate the capabilities of advanced multi-DOF myoelectric hand prostheses and transmit the feedback variables (proprioception and force) using intuitive coding, with high resolution and after minimal training. Approach. We developed a fully-programmable and integrated electrotactile interface supporting time and space distributed stimulation over custom designed flexible array electrodes. The system implements low-level access to individual stimulation channels as well as a set of high-level mapping functions translating the state of a multi-DoF prosthesis (aperture, grasping force, wrist rotation) into a set of predefined dynamic stimulation profiles. The system was evaluated using discrimination tests employing spatial and frequency coding (10 able-bodied subjects) and dynamic patterns (10 able-bodied and 6 amputee subjects). The outcome measure was the success rate (SR) in discrimination. Main results. The more practical electrode with the common anode configuration performed similarly to the more usual concentric arrangement. The subjects could discriminate six spatial and four frequency levels with SR >90% after a few minutes of training, whereas the performance significantly deteriorated for more levels. The dynamic patterns were intuitive for the subjects, although amputees showed lower SR than able-bodied individuals (86% ± 10% versus 99% ± 3%). Significance. The tests demonstrated that the system was easy to setup and apply. The design and resolution of the multipad electrode was evaluated. Importantly, the novel dynamic patterns, which were successfully tested, can be superimposed to transmit multiple feedback variables intuitively and simultaneously. This is especially relevant for closing the loop in modern multifunction prostheses. Therefore, the proposed

SU-E-J-85: Leave-One-Out Perturbation (LOOP) Fitting Algorithm for Absolute Dose Film Calibration

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

Chu, A; Ahmad, M; Chen, Z

2014-06-01

Purpose: To introduce an outliers-recognition fitting routine for film dosimetry. It cannot only be flexible with any linear and non-linear regression but also can provide information for the minimal number of sampling points, critical sampling distributions and evaluating analytical functions for absolute film-dose calibration. Methods: The technique, leave-one-out (LOO) cross validation, is often used for statistical analyses on model performance. We used LOO analyses with perturbed bootstrap fitting called leave-one-out perturbation (LOOP) for film-dose calibration . Given a threshold, the LOO process detects unfit points (“outliers”) compared to other cohorts, and a bootstrap fitting process follows to seek any possibilitiesmore » of using perturbations for further improvement. After that outliers were reconfirmed by a traditional t-test statistics and eliminated, then another LOOP feedback resulted in the final. An over-sampled film-dose- calibration dataset was collected as a reference (dose range: 0-800cGy), and various simulated conditions for outliers and sampling distributions were derived from the reference. Comparisons over the various conditions were made, and the performance of fitting functions, polynomial and rational functions, were evaluated. Results: (1) LOOP can prove its sensitive outlier-recognition by its statistical correlation to an exceptional better goodness-of-fit as outliers being left-out. (2) With sufficient statistical information, the LOOP can correct outliers under some low-sampling conditions that other “robust fits”, e.g. Least Absolute Residuals, cannot. (3) Complete cross-validated analyses of LOOP indicate that the function of rational type demonstrates a much superior performance compared to the polynomial. Even with 5 data points including one outlier, using LOOP with rational function can restore more than a 95% value back to its reference values, while the polynomial fitting completely failed under the same

Suppressing Transients In Digital Phase-Locked Loops

NASA Technical Reports Server (NTRS)

Thomas, J. B.

1993-01-01

Loop of arbitrary order starts in steady-state lock. Method for initializing variables of digital phase-locked loop reduces or eliminates transients in phase and frequency typically occurring during acquisition of lock on signal or when changes made in values of loop-filter parameters called "loop constants". Enables direct acquisition by third-order loop without prior acquisition by second-order loop of greater bandwidth, and eliminates those perturbations in phase and frequency lock occurring when loop constants changed by arbitrarily large amounts.

The interdigitating loop of the enolase superfamily as a specificity binding determinant or 'flying buttress'.

PubMed

Bearne, Stephen L

2017-05-01

Enzymes of the enolase superfamily (ENS) are mechanistically diverse, yet share a common partial reaction (abstraction of the α-proton from a carboxylate substrate). While the catalytic machinery responsible for the deprotonation reaction has been conserved, divergent evolution has led to numerous ENS members that catalyze different overall reactions. This rich functional diversity has made the ENS an excellent model system for developing the approaches necessary to validate enzyme function. However, enzymes of the ENS also share a common bidomain structure ((β/α) 7 β-barrel domain and α+β capping domain) which makes validation of function from structural information challenging. This review presents a comparative survey of the structural data obtained over the past decade for enzymes from all seven subgroups that comprise the ENS. Of the seven ENS subgroups (enolase, mandelate racemase (MR), muconate lactonizing enzyme, β-methylaspartate ammonia lyase, d-glucarate dehydratase, d-mannonate dehydratase (ManD), and galactarate dehydratase 2), only enzymes of the MR and ManD subgroups exhibit an additional feature of structural complexity-an interdigitating loop. This loop emanates from one protomer of a homodimeric pair and penetrates into the adjacent, symmetry-related protomer to either contribute a binding determinant to the active site of the adjacent protomer, or act as a 'flying buttress' to support residues of the active site. The analysis presented in this review suggests that the interdigitating loop is the only gross structural element that permits functional distinction between ENS subgroups at the tertiary level of protein structure. Copyright © 2017 Elsevier B.V. All rights reserved.

Study of the Open Loop and Closed Loop Oscillator Techniques

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

Imel, George R.; Baker, Benjamin; Riley, Tony

This report presents the progress and completion of a five-year study undertaken at Idaho State University of the measurement of very small worth reactivity samples comparing open and closed loop oscillator techniques.The study conclusively demonstrated the equivalency of the two techniques with regard to uncertainties in reactivity values, i.e., limited by reactor noise. As those results are thoroughly documented in recent publications, in this report we will concentrate on the support work that was necessary. For example, we describe in some detail the construction and calibration of a pilot rod for the closed loop system. We discuss the campaign tomore » measure the required reactor parameters necessary for inverse-kinetics. Finally, we briefly discuss the transfer of the open loop technique to other reactor systems.« less

Study of the open loop and closed loop oscillator techniques

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

Baker, Benjamin; Riley, Tony; Langbehn, Adam

This paper presents some aspects of a five year study undertaken at Idaho State University of the measurement of very small worth reactivity samples comparing open and closed loop oscillator techniques. The study conclusively demonstrated the equivalency of the two techniques with regard to uncertainties in reactivity values, i.e., limited by reactor noise. As those results are thoroughly documented in recent publications, in this paper we will concentrate on the support work that was necessary. For example, we describe in some detail the construction and calibration of a pilot rod for the closed loop system. We discuss the campaign tomore » measure the required reactor parameters necessary for inverse-kinetics. Finally, we briefly discuss the transfer of the open loop technique to other reactor systems. (authors)« less

Transform methods for precision continuum and control models of flexible space structures

NASA Technical Reports Server (NTRS)

Lupi, Victor D.; Turner, James D.; Chun, Hon M.

1991-01-01

An open loop optimal control algorithm is developed for general flexible structures, based on Laplace transform methods. A distributed parameter model of the structure is first presented, followed by a derivation of the optimal control algorithm. The control inputs are expressed in terms of their Fourier series expansions, so that a numerical solution can be easily obtained. The algorithm deals directly with the transcendental transfer functions from control inputs to outputs of interest, and structural deformation penalties, as well as penalties on control effort, are included in the formulation. The algorithm is applied to several structures of increasing complexity to show its generality.

Posterior spinal osteosynthesis for cervical fracture/dislocation using a flexible multistrand cable system: technical note.

PubMed

Huhn, S L; Wolf, A L; Ecklund, J

1991-12-01

Cervical instability secondary to fracture/dislocation or traumatic subluxation involving the posterior elements may be treated by a variety of fusion techniques. The rigidity of the stainless steel wires used in posterior cervical fusions often leads to difficulty with insertion, adequate tension, and conformation of the graft construct. This report describes a technique of posterior cervical fusion employing a wire system using flexible stainless steel cables. The wire consists of a flexible, 49-strand, stainless steel cable connected on one end to a short, malleable, blunt leader with the opposite end connected to a small islet. The cable may be used in occipitocervical, atlantoaxial, facet-to-spinous process, and interspinous fusion techniques. The cable loop is secured by using a tension/crimper device that sets the desired tension in the cable. In addition to superior biomechanical strength, the flexibility of the cable allows greater ease of insertion and tension adjustment. In terms of direct operative instrumentation in posterior cervical arthrodesis, involving both the upper and lower cervical spine, the cable system appears to be a safe and efficient alternative to monofilament wires.

Ionizable Side Chains at Catalytic Active Sites of Enzymes

PubMed Central

Jimenez-Morales, David; Liang, Jie

2012-01-01

Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1072 Å3. The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes. PMID:22484856

Turning goals into results: the power of catalytic mechanisms.

PubMed

Collins, J

1999-01-01

Most executives have a big, hairy, audacious goal. They write vision statements, formalize procedures, and develop complicated incentive programs--all in pursuit of that goal. In other words, with the best of intentions, they install layers of stultifying bureaucracy. But it doesn't have to be that way. In this article, Jim Collins introduces the catalytic mechanism, a simple yet powerful managerial tool that helps translate lofty aspirations into concrete reality. Catalytic mechanisms are the crucial link between objectives and performance; they are a galvanizing, nonbureaucratic means to turn one into the other. What's the difference between catalytic mechanisms and most traditional managerial controls? Catalytic mechanisms share five characteristics. First, they produce desired results in unpredictable ways. Second, they distribute power for the benefit of the overall system, often to the discomfort of those who traditionally hold power. Third, catalytic mechanisms have teeth. Fourth, they eject "viruses"--those people who don't share the company's core values. Finally, they produce an ongoing effect. Catalytic mechanisms are just as effective for reaching individual goals as they are for corporate ones. To illustrate how catalytic mechanisms work, the author draws on examples of individuals and organizations that have relied on such mechanisms to achieve their goals. The same catalytic mechanism that works in one organization, however, will not necessarily work in another. Catalytic mechanisms must be tailored to specific goals and situations. To help readers get started, the author offers some general principles that support the process of building catalytic mechanisms effectively.

Structural and Thermodynamic Comparison of the Catalytic Domain of AMSH and AMSH-LP: Nearly Identical Fold but Different Stability

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

Davies, Christopher W.; Paul, Lake N.; Kim, Myung-Il

2012-02-07

AMSH plays a critical role in the ESCRT (endosomal sorting complexes required for transport) machinery, which facilitates the down-regulation and degradation of cell-surface receptors. It displays a high level of specificity toward cleavage of Lys63-linked polyubiquitin chains, the structural basis of which has been understood recently through the crystal structure of a highly related, but ESCRT-independent, protein AMSH-LP (AMSH-like protein). We have determined the X-ray structure of two constructs representing the catalytic domain of AMSH: AMSH244, the JAMM (JAB1/MPN/MOV34)-domain-containing polypeptide segment from residues 244 to 424, and AMSH219{sup E280A}, an active-site mutant, Glu280 to Ala, of the segment from 219more » to 424. In addition to confirming the expected zinc coordination in the protein, the structures reveal that the catalytic domains of AMSH and AMSH-LP are nearly identical; however, guanidine-hydrochloride-induced unfolding studies show that the catalytic domain of AMSH is thermodynamically less stable than that of AMSH-LP, indicating that the former is perhaps structurally more plastic. Much to our surprise, in the AMSH219{sup E280A} structure, the catalytic zinc was still held in place, by the compensatory effect of an aspartate from a nearby loop moving into a position where it could coordinate with the zinc, once again suggesting the plasticity of AMSH. Additionally, a model of AMSH244 bound to Lys63-linked diubiquitin reveals a type of interface for the distal ubiquitin significantly different from that seen in AMSH-LP. Altogether, we believe that our data provide important insight into the structural difference between the two proteins that may translate into the difference in their biological function.« less

Measures of Potential Flexibility and Practical Flexibility in Equation Solving.

PubMed

Xu, Le; Liu, Ru-De; Star, Jon R; Wang, Jia; Liu, Ying; Zhen, Rui

2017-01-01

Researchers interested in mathematical proficiency have recently begun to explore the development of strategic flexibility, where flexibility is defined as knowledge of multiple strategies for solving a problem and the ability to implement an innovative strategy for a given problem solving circumstance. However, anecdotal findings from this literature indicate that students do not consistently use an innovative strategy for solving a given problem, even when these same students demonstrate knowledge of innovative strategies. This distinction, sometimes framed in the psychological literature as competence vs. performance-has not been previously studied for flexibility. In order to explore the competence/performance distinction in flexibility, this study developed and validated measures for potential flexibility (e.g., competence, or knowledge of multiple strategies) and practical flexibility (e.g., performance, use of innovative strategies) for solving equations. The measures were administrated to a sample of 158 Chinese middle school students through a Tri-Phase Flexibility Assessment, in which the students were asked to solve each equation, generate additional strategies, and evaluate own multiple strategies. Confirmatory factor analysis supported a two-factor model of potential and practical flexibility. Satisfactory internal consistency was found for the measures. Additional validity evidence included the significant association with flexibility measured with the previous method. Potential flexibility and practical flexibility were found to be distinct but related. The theoretical and practical implications of the concepts and their measures of potential flexibility and practical flexibility are discussed.

Measures of Potential Flexibility and Practical Flexibility in Equation Solving

PubMed Central

Xu, Le; Liu, Ru-De; Star, Jon R.; Wang, Jia; Liu, Ying; Zhen, Rui

2017-01-01

Researchers interested in mathematical proficiency have recently begun to explore the development of strategic flexibility, where flexibility is defined as knowledge of multiple strategies for solving a problem and the ability to implement an innovative strategy for a given problem solving circumstance. However, anecdotal findings from this literature indicate that students do not consistently use an innovative strategy for solving a given problem, even when these same students demonstrate knowledge of innovative strategies. This distinction, sometimes framed in the psychological literature as competence vs. performance—has not been previously studied for flexibility. In order to explore the competence/performance distinction in flexibility, this study developed and validated measures for potential flexibility (e.g., competence, or knowledge of multiple strategies) and practical flexibility (e.g., performance, use of innovative strategies) for solving equations. The measures were administrated to a sample of 158 Chinese middle school students through a Tri-Phase Flexibility Assessment, in which the students were asked to solve each equation, generate additional strategies, and evaluate own multiple strategies. Confirmatory factor analysis supported a two-factor model of potential and practical flexibility. Satisfactory internal consistency was found for the measures. Additional validity evidence included the significant association with flexibility measured with the previous method. Potential flexibility and practical flexibility were found to be distinct but related. The theoretical and practical implications of the concepts and their measures of potential flexibility and practical flexibility are discussed. PMID:28848481

Structural basis for allosteric cross-talk between the asymmetric nucleotide binding sites of a heterodimeric ABC exporter.

PubMed

Hohl, Michael; Hürlimann, Lea M; Böhm, Simon; Schöppe, Jendrik; Grütter, Markus G; Bordignon, Enrica; Seeger, Markus A

2014-07-29

ATP binding cassette (ABC) transporters mediate vital transport processes in every living cell. ATP hydrolysis, which fuels transport, displays positive cooperativity in numerous ABC transporters. In particular, heterodimeric ABC exporters exhibit pronounced allosteric coupling between a catalytically impaired degenerate site, where nucleotides bind tightly, and a consensus site, at which ATP is hydrolyzed in every transport cycle. Whereas the functional phenomenon of cooperativity is well described, its structural basis remains poorly understood. Here, we present the apo structure of the heterodimeric ABC exporter TM287/288 and compare it to the previously solved structure with adenosine 5'-(β,γ-imido)triphosphate (AMP-PNP) bound at the degenerate site. In contrast to other ABC exporter structures, the nucleotide binding domains (NBDs) of TM287/288 remain in molecular contact even in the absence of nucleotides, and the arrangement of the transmembrane domains (TMDs) is not influenced by AMP-PNP binding, a notion confirmed by double electron-electron resonance (DEER) measurements. Nucleotide binding at the degenerate site results in structural rearrangements, which are transmitted to the consensus site via two D-loops located at the NBD interface. These loops owe their name from a highly conserved aspartate and are directly connected to the catalytically important Walker B motif. The D-loop at the degenerate site ties the NBDs together even in the absence of nucleotides and substitution of its aspartate by alanine is well-tolerated. By contrast, the D-loop of the consensus site is flexible and the aspartate to alanine mutation and conformational restriction by cross-linking strongly reduces ATP hydrolysis and substrate transport.

Binding modes of phosphotriesterase-like lactonase complexed with δ-nonanoic lactone and paraoxon using molecular dynamics simulations.

PubMed

Guan, Shanshan; Zhao, Li; Jin, Hanyong; Shan, Ning; Han, Weiwei; Wang, Song; Shan, Yaming

2017-02-01

Phosphotriesterase-like lactonases (PLLs) have received much attention because of their physical and chemical properties. They may have widespread applications in various fields. For example, they show potential for quorum-sensing signaling pathways and organophosphorus (OP) detoxification in agricultural science. However, the mechanism by which PLLs hydrolyze, which involves OP compounds and lactones and a variety of distinct catalytic efficiencies, has only rarely been explored. In the present study, molecular dynamics (MD) simulations were performed to characterize and contrast the structural dynamics of DrPLL, a member of the PLL superfamily in Deinococcus radiodurans, bound to two substrates, δ-nonanoic lactone and paraoxon. It has been observed that there is a 16-fold increase in the catalytic efficiency of the two mutant strains of DrPLL (F26G/C72I) vs. the wild-type enzyme toward the hydrolysis of paraoxon, but an explanation for this behavior is currently lacking. The analysis of the molecular trajectories of DrPLL bound to δ-nonanoic lactone indicated that lactone-induced conformational changes take place in loop 8, which is near the active site. Binding to paraoxon may lead to conformational displacement of loop 1 residues, which could lead to the deformation of the active site and so trigger the entry of the paraoxon into the active site. The efficiency of the F26G/C72I mutant was increased by decreasing the displacement of loop 1 residues and increasing the flexibility of loop 8 residues. These results provide a molecular-level explanation for the experimental behavior.

Choosing Sensor Configuration for a Flexible Structure Using Full Control Synthesis

NASA Technical Reports Server (NTRS)

Lind, Rick; Nalbantoglu, Volkan; Balas, Gary

1997-01-01

Optimal locations and types for feedback sensors which meet design constraints and control requirements are difficult to determine. This paper introduces an approach to choosing a sensor configuration based on Full Control synthesis. A globally optimal Full Control compensator is computed for each member of a set of sensor configurations which are feasible for the plant. The sensor configuration associated with the Full Control system achieving the best closed-loop performance is chosen for feedback measurements to an output feedback controller. A flexible structure is used as an example to demonstrate this procedure. Experimental results show sensor configurations chosen to optimize the Full Control performance are effective for output feedback controllers.

Numerical characterization of a flexible circular coil for magnetic resonance imaging

NASA Astrophysics Data System (ADS)

Bautista, T.; Hernandez, R.; Solis-Najera, S. E.; Rodriguez, A. O.

2012-10-01

Numerical simulations of the magnetic field generated by a flexible surface coil were conducted to study its behavior for applications of animal models at 7 Tesla. This coil design is able to fully cover a volume of interest. The Finite Difference Method in Time Domain (FDTD) was used because of its ability to accurately model complex problems in electromagnetism. This particular coil design is best suited for regions of interests with a spherical shape, since B1 uniformity is not significantly attenuated as in the case of a circular-loop coil. It still remains to investigate the feasibility to actually construct a coil prototype.

Gas phase oxidation downstream of a catalytic combustor

NASA Technical Reports Server (NTRS)

Tien, J. S.; Anderson, D. N.

1979-01-01

Effect of the length available for gas-phase reactions downstream of the catalytic reactor on the emission of CO and unburned hydrocarbons was investigated. A premixed, prevaporized propane/air feed to a 12/cm/diameter catalytic/reactor test section was used. The catalytic reactor was made of four 2.5 cm long monolithic catalyst elements. Four water cooled gas sampling probes were located at positions between 0 and 22 cm downstream of the catalytic reactor. Measurements of unburned hydrocarbon, CO, and CO2 were made. Tests were performed with an inlet air temperature of 800 K, a reference velocity of 10 m/s, pressures of 3 and 600,000 Pa, and fuel air equivalence ratios of 0.14 to 0.24. For very lean mixtures, hydrocarbon emissions were high and CO continued to be formed downstream of the catalytic reactor. At the highest equivalence ratios tested, hydrocarbon levels were much lower and CO was oxidized to CO2 in the gas phase downstream. To achieve acceptable emissions, a downstream region several times longer than the catalytic reactor could be required.

Loop Heat Pipe Startup Behaviors

NASA Technical Reports Server (NTRS)

Ku, Jentung

2014-01-01

A loop heat pipe must start successfully before it can commence its service. The start-up transient represents one of the most complex phenomena in the loop heat pipe operation. This paper discusses various aspects of loop heat pipe start-up behaviors. Topics include the four start-up scenarios, the initial fluid distribution between the evaporator and reservoir that determines the start-up scenario, factors that affect the fluid distribution between the evaporator and reservoir, difficulties encountered during the low power start-up, and methods to enhance the start-up success. Also addressed are the thermodynamic constraint between the evaporator and reservoir in the loop heat pipe operation, the superheat requirement for nucleate boiling, pressure spike and pressure surge during the start-up transient, and repeated cycles of loop start-up andshutdown under certain conditions.

Chemical Looping Technology: Oxygen Carrier Characteristics.

PubMed

Luo, Siwei; Zeng, Liang; Fan, Liang-Shih

2015-01-01

Chemical looping processes are characterized as promising carbonaceous fuel conversion technologies with the advantages of manageable CO2 capture and high energy conversion efficiency. Depending on the chemical looping reaction products generated, chemical looping technologies generally can be grouped into two types: chemical looping full oxidation (CLFO) and chemical looping partial oxidation (CLPO). In CLFO, carbonaceous fuels are fully oxidized to CO2 and H2O, as typically represented by chemical looping combustion with electricity as the primary product. In CLPO, however, carbonaceous fuels are partially oxidized, as typically represented by chemical looping gasification with syngas or hydrogen as the primary product. Both CLFO and CLPO share similar operational features; however, the optimum process configurations and the specific oxygen carriers used between them can vary significantly. Progress in both CLFO and CLPO is reviewed and analyzed with specific focus on oxygen carrier developments that characterize these technologies.

Transverse Oscillations of Coronal Loops

NASA Astrophysics Data System (ADS)

Ruderman, Michael S.; Erdélyi, Robert

2009-12-01

On 14 July 1998 TRACE observed transverse oscillations of a coronal loop generated by an external disturbance most probably caused by a solar flare. These oscillations were interpreted as standing fast kink waves in a magnetic flux tube. Firstly, in this review we embark on the discussion of the theory of waves and oscillations in a homogeneous straight magnetic cylinder with the particular emphasis on fast kink waves. Next, we consider the effects of stratification, loop expansion, loop curvature, non-circular cross-section, loop shape and magnetic twist. An important property of observed transverse coronal loop oscillations is their fast damping. We briefly review the different mechanisms suggested for explaining the rapid damping phenomenon. After that we concentrate on damping due to resonant absorption. We describe the latest analytical results obtained with the use of thin transition layer approximation, and then compare these results with numerical findings obtained for arbitrary density variation inside the flux tube. Very often collective oscillations of an array of coronal magnetic loops are observed. It is natural to start studying this phenomenon from the system of two coronal loops. We describe very recent analytical and numerical results of studying collective oscillations of two parallel homogeneous coronal loops. The implication of the theoretical results for coronal seismology is briefly discussed. We describe the estimates of magnetic field magnitude obtained from the observed fundamental frequency of oscillations, and the estimates of the coronal scale height obtained using the simultaneous observations of the fundamental frequency and the frequency of the first overtone of kink oscillations. In the last part of the review we summarise the most outstanding and acute problems in the theory of the coronal loop transverse oscillations.

Catalytic reaction in confined flow channel

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

Van Hassel, Bart A.

A chemical reactor comprises a flow channel, a source, and a destination. The flow channel is configured to house at least one catalytic reaction converting at least a portion of a first nanofluid entering the channel into a second nanofluid exiting the channel. The flow channel includes at least one turbulating flow channel element disposed axially along at least a portion of the flow channel. A plurality of catalytic nanoparticles is dispersed in the first nanofluid and configured to catalytically react the at least one first chemical reactant into the at least one second chemical reaction product in the flowmore » channel.« less

Coordination and Control of Flexible Building Loads for Renewable Integration; Demonstrations using VOLTTRON

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

Hao, He; Liu, Guopeng; Huang, Sen

Renewable energy resources such as wind and solar power have a high degree of uncertainty. Large-scale integration of these variable generation sources into the grid is a big challenge for power system operators. Buildings, in which we live and work, consume about 75% of the total electricity in the United States. They also have a large capacity of power flexibility due to their massive thermal capacitance. Therefore, they present a great opportunity to help the grid to manage power balance. In this report, we study coordination and control of flexible building loads for renewable integration. We first present the motivationmore » and background, and conduct a literature review on building-to-grid integration. We also compile a catalog of flexible building loads that have great potential for renewable integration, and discuss their characteristics. We next collect solar generation data from a photovoltaic panel on Pacific Northwest National Laboratory campus, and conduct data analysis to study their characteristics. We find that solar generation output has a strong uncertainty, and the uncertainty occurs at almost all time scales. Additional data from other sources are also used to verify our study. We propose two transactive coordination strategies to manage flexible building loads for renewable integration. We prove the theories that support the two transactive coordination strategies and discuss their pros and cons. In this report, we select three types of flexible building loads—air-handling unit, rooftop unit, and a population of WHs—for which we demonstrate control of the flexible load to track a dispatch signal (e.g., renewable generation fluctuation) using experiment, simulation, or hardware-in-the-loop study. More specifically, we present the system description, model identification, controller design, test bed setup, and experiment results for each demonstration. We show that coordination and control of flexible loads has a great potential to

The Structure of Coronal Loops

NASA Technical Reports Server (NTRS)

Antiochos, Spiro K.

2009-01-01

It is widely believed that the simple coronal loops observed by XUV imagers, such as EIT, TRACE, or XRT, actually have a complex internal structure consisting of many (perhaps hundreds) of unresolved, interwoven "strands". According to the nanoflare model, photospheric motions tangle the strands, causing them to reconnect and release the energy required to produce the observed loop plasma. Although the strands, themselves, are unresolved by present-generation imagers, there is compelling evidence for their existence and for the nanoflare model from analysis of loop intensities and temporal evolution. A problem with this scenario is that, although reconnection can eliminate some of the strand tangles, it cannot destroy helicity, which should eventually build up to observable scales. we consider, therefore, the injection and evolution of helicity by the nanoflare process and its implications for the observed structure of loops and the large-scale corona. we argue that helicity does survive and build up to observable levels, but on spatial and temporal scales larger than those of coronal loops. we discuss the implications of these results for coronal loops and the corona, in general .

High heat flux loop heat pipes

NASA Astrophysics Data System (ADS)

North, Mark T.; Sarraf, David B.; Rosenfeld, John H.; Maidanik, Yuri F.; Vershinin, Sergey

1997-01-01

Loop Heat Pipes (LHPs) can transport very large thermal power loads, over long distances, through flexible, small diameter tubes and against high gravitational heads. While recent LHPs have transported as much as 1500 W, the peak heat flux through a LHP's evaporator has been limited to about 0.07 MW/m2. This limitation is due to the arrangement of vapor passages next to the heat load which is one of the conditions necessary to ensure self priming of the device. This paper describes work aimed at raising this limit by threefold to tenfold. Two approaches were pursued. One optimized the vapor passage geometry for the high heat flux conditions. The geometry improved the heat flow into the wick and working fluid. This approach also employed a finer pored wick to support higher vapor flow losses. The second approach used a bidisperse wick material within the circumferential vapor passages. The bidisperse material increased the thermal conductivity and the evaporative surface area in the region of highest heat flux, while providing a flow path for the vapor. Proof-of-concept devices were fabricated and tested for each approach. Both devices operated as designed and both demonstrated operation at a heat flux of 0.70 MW/m2. This performance exceeded the known state of the art by a factor of more than six for both conventional heat pipes and for loop heat pipes using ammonia. In addition, the bidisperse-wick device demonstrated boiling heat transfer coefficients up to 100,000 W/m2.K, and the fine pored device demonstrated an orientation independence with its performance essentially unaffected by whether its evaporator was positioned above, below or level with the condenser.

An Intrinsically Disordered APLF Links Ku, DNA-PKcs, and XRCC4-DNA Ligase IV in an Extended Flexible Non-homologous End Joining Complex

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

Hammel, Michal; Yu, Yaping; Radhakrishnan, Sarvan K.

DNA double-strand break (DSB) repair by non-homologous end joining (NHEJ) in human cells is initiated by Ku heterodimer binding to a DSB, followed by recruitment of core NHEJ factors including DNA-dependent protein kinase catalytic subunit (DNA-PKcs), XRCC4-like factor (XLF), and XRCC4 (X4)-DNA ligase IV (L4). Ku also interacts with accessory factors such as aprataxin and polynucleotide kinase/phosphatase-like factor (APLF). But, how these factors interact to tether, process, and ligate DSB ends while allowing regulation and chromatin interactions remains enigmatic. Here, small angle X-ray scattering (SAXS) and mutational analyses show APLF is largely an intrinsically disordered protein that binds Ku, Ku/DNA-PKcsmore » (DNA-PK), and X4L4 within an extended flexible NHEJ core complex. X4L4 assembles with Ku heterodimers linked to DNA-PKcs via flexible Ku80 C-terminal regions (Ku80CTR) in a complex stabilized through APLF interactions with Ku, DNA-PK, and X4L4. Our collective results unveil the solution architecture of the six-protein complex and suggest cooperative assembly of an extended flexible NHEJ core complex that supports APLF accessibility while possibly providing flexible attachment of the core complex to chromatin. The resulting dynamic tethering furthermore, provides geometric access of L4 catalytic domains to the DNA ends during ligation and of DNA-PKcs for targeted phosphorylation of other NHEJ proteins as well as trans-phosphorylation of DNA-PKcs on the opposing DSB without disrupting the core ligation complex. Overall the results shed light on evolutionary conservation of Ku, X4, and L4 activities, while explaining the observation that Ku80CTR and DNA-PKcs only occur in a subset of higher eukaryotes.« less

An Intrinsically Disordered APLF Links Ku, DNA-PKcs, and XRCC4-DNA Ligase IV in an Extended Flexible Non-homologous End Joining Complex

DOE PAGES

Hammel, Michal; Yu, Yaping; Radhakrishnan, Sarvan K.; ...

2016-11-14

DNA double-strand break (DSB) repair by non-homologous end joining (NHEJ) in human cells is initiated by Ku heterodimer binding to a DSB, followed by recruitment of core NHEJ factors including DNA-dependent protein kinase catalytic subunit (DNA-PKcs), XRCC4-like factor (XLF), and XRCC4 (X4)-DNA ligase IV (L4). Ku also interacts with accessory factors such as aprataxin and polynucleotide kinase/phosphatase-like factor (APLF). But, how these factors interact to tether, process, and ligate DSB ends while allowing regulation and chromatin interactions remains enigmatic. Here, small angle X-ray scattering (SAXS) and mutational analyses show APLF is largely an intrinsically disordered protein that binds Ku, Ku/DNA-PKcsmore » (DNA-PK), and X4L4 within an extended flexible NHEJ core complex. X4L4 assembles with Ku heterodimers linked to DNA-PKcs via flexible Ku80 C-terminal regions (Ku80CTR) in a complex stabilized through APLF interactions with Ku, DNA-PK, and X4L4. Our collective results unveil the solution architecture of the six-protein complex and suggest cooperative assembly of an extended flexible NHEJ core complex that supports APLF accessibility while possibly providing flexible attachment of the core complex to chromatin. The resulting dynamic tethering furthermore, provides geometric access of L4 catalytic domains to the DNA ends during ligation and of DNA-PKcs for targeted phosphorylation of other NHEJ proteins as well as trans-phosphorylation of DNA-PKcs on the opposing DSB without disrupting the core ligation complex. Overall the results shed light on evolutionary conservation of Ku, X4, and L4 activities, while explaining the observation that Ku80CTR and DNA-PKcs only occur in a subset of higher eukaryotes.« less

Fabrication techniques for superconducting readout loops

NASA Technical Reports Server (NTRS)

Payne, J. E.

1982-01-01

Procedures for the fabrication of superconducting readout loops out of niobium on glass substrates were developed. A computer program for an existing fabrication system was developed. Both positive and negative resist procedures for the production of the readout loops were investigated. Methods used to produce satisfactory loops are described and the various parameters affecting the performance of the loops are analyzed.

Ionizable side chains at catalytic active sites of enzymes.

PubMed

Jimenez-Morales, David; Liang, Jie; Eisenberg, Bob

2012-05-01

Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1,072 Å(3). The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes.

LoopX: A Graphical User Interface-Based Database for Comprehensive Analysis and Comparative Evaluation of Loops from Protein Structures.

PubMed

Kadumuri, Rajashekar Varma; Vadrevu, Ramakrishna

2017-10-01

Due to their crucial role in function, folding, and stability, protein loops are being targeted for grafting/designing to create novel or alter existing functionality and improve stability and foldability. With a view to facilitate a thorough analysis and effectual search options for extracting and comparing loops for sequence and structural compatibility, we developed, LoopX a comprehensively compiled library of sequence and conformational features of ∼700,000 loops from protein structures. The database equipped with a graphical user interface is empowered with diverse query tools and search algorithms, with various rendering options to visualize the sequence- and structural-level information along with hydrogen bonding patterns, backbone φ, ψ dihedral angles of both the target and candidate loops. Two new features (i) conservation of the polar/nonpolar environment and (ii) conservation of sequence and conformation of specific residues within the loops have also been incorporated in the search and retrieval of compatible loops for a chosen target loop. Thus, the LoopX server not only serves as a database and visualization tool for sequence and structural analysis of protein loops but also aids in extracting and comparing candidate loops for a given target loop based on user-defined search options.

Coronal loops and active region structure

NASA Technical Reports Server (NTRS)

Webb, D. F.; Zirin, H.

1981-01-01

Synoptic H-alpha Ca K, magnetograph and Skylab soft X-ray and EUV data were compared for the purpose of identifying the basic coronal magnetic structure of loops in a 'typical' active region and studying its evolution. A complex of activity in July 1973, especially McMath 12417, was emphasized. The principal results are: (1) most of the brightest loops connected the bright f plage to either the sunspot penumbra or to p satellite spots; no non-flaring X-ray loops end in umbrae; (2) short, bright loops had one or both ends in regions of emergent flux, strong field or high field gradients; (3) stable, strongly sheared loop arcades formed over filaments; (4) EFRs were always associated with compact X-ray arcades; and (5) loops connecting to other active regions had their bases in outlying plage of weak field strength in McM 417 where H-alpha fibrils marked the direction of the loops

Fabrication of flexible oriented magnetic thin films with large in-plane uniaxial anisotropy by roll-to-roll nanoimprint lithography

NASA Astrophysics Data System (ADS)

Thantirige, Rukshan M.; John, Jacob; Pradhan, Nihar R.; Carter, Kenneth R.; Tuominen, Mark T.

2016-06-01

Here, we report wafer scale fabrication of densely packed Fe nanostripe-based magnetic thin films on a flexible substrate and their magnetic anisotropy properties. We find that Fe nanostripes exhibit large in-plane uniaxial anisotropy and nearly square hysteresis loops with energy products (BHmax) exceeding 3 MGOe at room temperature. High density Fe nanostripes were fabricated on 70 nm flexible polyethylene terephthalate (PET) gratings, which were made by a roll-to-roll (R2R) UV nanoimprint lithography technique. We observed large in-plane uniaxial anisotropies along the long dimension of nanostripes that can be attributed to the shape. Temperature dependent hysteresis measurements confirm that the magnetization reversal is driven by non-coherent rotation reversal processes.

Computing Bounds on Resource Levels for Flexible Plans

NASA Technical Reports Server (NTRS)

Muscvettola, Nicola; Rijsman, David

2009-01-01

A new algorithm efficiently computes the tightest exact bound on the levels of resources induced by a flexible activity plan (see figure). Tightness of bounds is extremely important for computations involved in planning because tight bounds can save potentially exponential amounts of search (through early backtracking and detection of solutions), relative to looser bounds. The bound computed by the new algorithm, denoted the resource-level envelope, constitutes the measure of maximum and minimum consumption of resources at any time for all fixed-time schedules in the flexible plan. At each time, the envelope guarantees that there are two fixed-time instantiations one that produces the minimum level and one that produces the maximum level. Therefore, the resource-level envelope is the tightest possible resource-level bound for a flexible plan because any tighter bound would exclude the contribution of at least one fixed-time schedule. If the resource- level envelope can be computed efficiently, one could substitute looser bounds that are currently used in the inner cores of constraint-posting scheduling algorithms, with the potential for great improvements in performance. What is needed to reduce the cost of computation is an algorithm, the measure of complexity of which is no greater than a low-degree polynomial in N (where N is the number of activities). The new algorithm satisfies this need. In this algorithm, the computation of resource-level envelopes is based on a novel combination of (1) the theory of shortest paths in the temporal-constraint network for the flexible plan and (2) the theory of maximum flows for a flow network derived from the temporal and resource constraints. The measure of asymptotic complexity of the algorithm is O(N O(maxflow(N)), where O(x) denotes an amount of computing time or a number of arithmetic operations proportional to a number of the order of x and O(maxflow(N)) is the measure of complexity (and thus of cost) of a maximumflow

ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis

PubMed Central

Li, Guipeng; Chen, Yang; Snyder, Michael P.; Zhang, Michael Q.

2017-01-01

ChIA-PET2 is a versatile and flexible pipeline for analyzing different types of ChIA-PET data from raw sequencing reads to chromatin loops. ChIA-PET2 integrates all steps required for ChIA-PET data analysis, including linker trimming, read alignment, duplicate removal, peak calling and chromatin loop calling. It supports different kinds of ChIA-PET data generated from different ChIA-PET protocols and also provides quality controls for different steps of ChIA-PET analysis. In addition, ChIA-PET2 can use phased genotype data to call allele-specific chromatin interactions. We applied ChIA-PET2 to different ChIA-PET datasets, demonstrating its significantly improved performance as well as its ability to easily process ChIA-PET raw data. ChIA-PET2 is available at https://github.com/GuipengLi/ChIA-PET2. PMID:27625391

Run-time parallelization and scheduling of loops

NASA Technical Reports Server (NTRS)

Saltz, Joel H.; Mirchandaney, Ravi; Crowley, Kay

1990-01-01

Run time methods are studied to automatically parallelize and schedule iterations of a do loop in certain cases, where compile-time information is inadequate. The methods presented involve execution time preprocessing of the loop. At compile-time, these methods set up the framework for performing a loop dependency analysis. At run time, wave fronts of concurrently executable loop iterations are identified. Using this wavefront information, loop iterations are reordered for increased parallelism. Symbolic transformation rules are used to produce: inspector procedures that perform execution time preprocessing and executors or transformed versions of source code loop structures. These transformed loop structures carry out the calculations planned in the inspector procedures. Performance results are presented from experiments conducted on the Encore Multimax. These results illustrate that run time reordering of loop indices can have a significant impact on performance. Furthermore, the overheads associated with this type of reordering are amortized when the loop is executed several times with the same dependency structure.

Coronal Loops: Observations and Modeling of Confined Plasma.

PubMed

Reale, Fabio

Coronal loops are the building blocks of the X-ray bright solar corona. They owe their brightness to the dense confined plasma, and this review focuses on loops mostly as structures confining plasma. After a brief historical overview, the review is divided into two separate but not independent parts: the first illustrates the observational framework, the second reviews the theoretical knowledge. Quiescent loops and their confined plasma are considered and, therefore, topics such as loop oscillations and flaring loops (except for non-solar ones, which provide information on stellar loops) are not specifically addressed here. The observational section discusses the classification, populations, and the morphology of coronal loops, its relationship with the magnetic field, and the loop stranded structure. The section continues with the thermal properties and diagnostics of the loop plasma, according to the classification into hot, warm, and cool loops. Then, temporal analyses of loops and the observations of plasma dynamics, hot and cool flows, and waves are illustrated. In the modeling section, some basics of loop physics are provided, supplying fundamental scaling laws and timescales, a useful tool for consultation. The concept of loop modeling is introduced and models are divided into those treating loops as monolithic and static, and those resolving loops into thin and dynamic strands. More specific discussions address modeling the loop fine structure and the plasma flowing along the loops. Special attention is devoted to the question of loop heating, with separate discussion of wave (AC) and impulsive (DC) heating. Large-scale models including atmosphere boxes and the magnetic field are also discussed. Finally, a brief discussion about stellar coronal loops is followed by highlights and open questions.

A multi-mode operation control strategy for flexible microgrid based on sliding-mode direct voltage and hierarchical controls.

PubMed

Zhang, Qinjin; Liu, Yancheng; Zhao, Youtao; Wang, Ning

2016-03-01

Multi-mode operation and transient stability are two problems that significantly affect flexible microgrid (MG). This paper proposes a multi-mode operation control strategy for flexible MG based on a three-layer hierarchical structure. The proposed structure is composed of autonomous, cooperative, and scheduling controllers. Autonomous controller is utilized to control the performance of the single micro-source inverter. An adaptive sliding-mode direct voltage loop and an improved droop power loop based on virtual negative impedance are presented respectively to enhance the system disturbance-rejection performance and the power sharing accuracy. Cooperative controller, which is composed of secondary voltage/frequency control and phase synchronization control, is designed to eliminate the voltage/frequency deviations produced by the autonomous controller and prepare for grid connection. Scheduling controller manages the power flow between the MG and the grid. The MG with the improved hierarchical control scheme can achieve seamless transitions from islanded to grid-connected mode and have a good transient performance. In addition the presented work can also optimize the power quality issues and improve the load power sharing accuracy between parallel VSIs. Finally, the transient performance and effectiveness of the proposed control scheme are evaluated by theoretical analysis and simulation results. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

Evaluation of inertial devices for the control of large, flexible, space-based telerobotic arms

NASA Technical Reports Server (NTRS)

Montgomery, Raymond C.; Kenny, Sean P.; Ghosh, Dave; Shenhar, Joram

1993-01-01

Inertial devices, including sensors and actuators, offer the potential of improving the tracking of telerobotic commands for space-based robots by smoothing payload motions and suppressing vibrations. In this paper, inertial actuators (specifically, torque-wheels and reaction-masses) are studied for that potential application. Batch simulation studies are presented which show that torque-wheels can reduce the overshoot in abrupt stop commands by 82 percent for a two-link arm. For man-in-the-loop evaluation, a real-time simulator has been developed which samples a hand-controller, solves the nonlinear equations of motion, and graphically displays the resulting motion on a computer workstation. Currently, two manipulator models, a two-link, rigid arm and a single-link, flexible arm, have been studied. Results are presented which show that, for a single-link arm, a reaction-mass/torque-wheel combination at the payload end can yield a settling time of 3 s for disturbances in the first flexible mode as opposed to 10 s using only a hub motor. A hardware apparatus, which consists of a single-link, highly flexible arm with a hub motor and a torque-wheel, has been assembled to evaluate the concept and is described herein.

Evaluation of inertial devices for the control of large, flexible, space-based telerobotic arms

NASA Astrophysics Data System (ADS)

Montgomery, Raymond C.; Kenny, Sean P.; Ghosh, Dave; Shenhar, Joram

1993-02-01

Inertial devices, including sensors and actuators, offer the potential of improving the tracking of telerobotic commands for space-based robots by smoothing payload motions and suppressing vibrations. In this paper, inertial actuators (specifically, torque-wheels and reaction-masses) are studied for that potential application. Batch simulation studies are presented which show that torque-wheels can reduce the overshoot in abrupt stop commands by 82 percent for a two-link arm. For man-in-the-loop evaluation, a real-time simulator has been developed which samples a hand-controller, solves the nonlinear equations of motion, and graphically displays the resulting motion on a computer workstation. Currently, two manipulator models, a two-link, rigid arm and a single-link, flexible arm, have been studied. Results are presented which show that, for a single-link arm, a reaction-mass/torque-wheel combination at the payload end can yield a settling time of 3 s for disturbances in the first flexible mode as opposed to 10 s using only a hub motor. A hardware apparatus, which consists of a single-link, highly flexible arm with a hub motor and a torque-wheel, has been assembled to evaluate the concept and is described herein.

On higher order discrete phase-locked loops.

NASA Technical Reports Server (NTRS)

Gill, G. S.; Gupta, S. C.

1972-01-01

An exact mathematical model is developed for a discrete loop of a general order particularly suitable for digital computation. The deterministic response of the loop to the phase step and the frequency step is investigated. The design of the digital filter for the second-order loop is considered. Use is made of the incremental phase plane to study the phase error behavior of the loop. The model of the noisy loop is derived and the optimization of the loop filter for minimum mean-square error is considered.