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Sample records for mechanical folding kinetics

  1. Kinetic partitioning mechanism of HDV ribozyme folding.

    PubMed

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing

    2014-01-14

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  2. Kinetic partitioning mechanism of HDV ribozyme folding

    SciTech Connect

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing

    2014-01-14

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  3. Kinetic partitioning mechanism of HDV ribozyme folding

    NASA Astrophysics Data System (ADS)

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing

    2014-01-01

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  4. Energy landscapes, folding mechanisms, and kinetics of RNA tetraloop hairpins.

    PubMed

    Chakraborty, Debayan; Collepardo-Guevara, Rosana; Wales, David J

    2014-12-31

    RNA hairpins play a pivotal role in a diverse range of cellular functions, and are integral components of ribozymes, mRNA, and riboswitches. However, the mechanistic and kinetic details of RNA hairpin folding, which are key determinants of most of its biological functions, are poorly understood. In this work, we use the discrete path sampling (DPS) approach to explore the energy landscapes of two RNA tetraloop hairpins, and provide insights into their folding mechanisms and kinetics in atomistic detail. Our results show that the potential energy landscapes have a distinct funnel-like bias toward the folded hairpin state, consistent with efficient structure-seeking properties. Mechanistic and kinetic information is analyzed in terms of kinetic transition networks. We find microsecond folding times, consistent with temperature jump experiments, for hairpin folding initiated from relatively compact unfolded states. This process is essentially driven by an initial collapse, followed by rapid zippering of the helix stem in the final phase. Much lower folding rates are predicted when the folding is initiated from extended chains, which undergo longer excursions on the energy landscape before nucleation events can occur. Our work therefore explains recent experiments and coarse-grained simulations, where the folding kinetics exhibit precisely this dependency on the initial conditions.

  5. Insights into Coupled Folding and Binding Mechanisms from Kinetic Studies*

    PubMed Central

    Crabtree, Michael D.; Dahal, Liza; Wicky, Basile I. M.; Clarke, Jane

    2016-01-01

    Intrinsically disordered proteins (IDPs) are characterized by a lack of persistent structure. Since their identification more than a decade ago, many questions regarding their functional relevance and interaction mechanisms remain unanswered. Although most experiments have taken equilibrium and structural perspectives, fewer studies have investigated the kinetics of their interactions. Here we review and highlight the type of information that can be gained from kinetic studies. In particular, we show how kinetic studies of coupled folding and binding reactions, an important class of signaling event, are needed to determine mechanisms. PMID:26851275

  6. Fast protein folding kinetics

    PubMed Central

    Gelman, Hannah; Gruebele, Martin

    2014-01-01

    Fast folding proteins have been a major focus of computational and experimental study because they are accessible to both techniques: they are small and fast enough to be reasonably simulated with current computational power, but have dynamics slow enough to be observed with specially developed experimental techniques. This coupled study of fast folding proteins has provided insight into the mechanisms which allow some proteins to find their native conformation well less than 1 ms and has uncovered examples of theoretically predicted phenomena such as downhill folding. The study of fast folders also informs our understanding of even “slow” folding processes: fast folders are small, relatively simple protein domains and the principles that govern their folding also govern the folding of more complex systems. This review summarizes the major theoretical and experimental techniques used to study fast folding proteins and provides an overview of the major findings of fast folding research. Finally, we examine the themes that have emerged from studying fast folders and briefly summarize their application to protein folding in general as well as some work that is left to do. PMID:24641816

  7. Mechanics of Curved Folds

    NASA Astrophysics Data System (ADS)

    Dias, Marcelo A.; Santangelo, Christian D.

    2011-03-01

    Despite an almost two thousand year history, origami, the art of folding paper, remains a challenge both artistically and scientifically. Traditionally, origami is practiced by folding along straight creases. A whole new set of shapes can be explored, however, if, instead of straight creases, one folds along arbitrary curves. We present a mechanical model for curved fold origami in which the energy of a plastically-deformed crease is balanced by the bending energy of developable regions on either side of the crease. Though geometry requires that a sheet buckle when folded along a closed curve, its shape depends on the elasticity of the sheet. NSF DMR-0846582.

  8. A New Folding Kinetic Mechanism for Human Transthyretin and the Influence of the Amyloidogenic V30M Mutation

    PubMed Central

    Jesus, Catarina S. H.; Almeida, Zaida L.; Vaz, Daniela C.; Faria, Tiago Q.; Brito, Rui M. M.

    2016-01-01

    Protein aggregation into insoluble amyloid fibrils is the hallmark of several neurodegenerative diseases, chief among them Alzheimer’s and Parkinson’s. Although caused by different proteins, these pathologies share some basic molecular mechanisms with familial amyloidotic polyneuropathy (FAP), a rare hereditary neuropathy caused by amyloid formation and deposition by transthyretin (TTR) in the peripheral and autonomic nervous systems. Among the amyloidogenic TTR mutations known, V30M-TTR is the most common in FAP. TTR amyloidogenesis (ATTR) is triggered by tetramer dissociation, followed by partial unfolding and aggregation of the low conformational stability monomers formed. Thus, tetramer dissociation kinetics, monomer conformational stability and competition between refolding and aggregation pathways do play a critical role in ATTR. Here, we propose a new model to analyze the refolding kinetics of WT-TTR and V30M-TTR, showing that at pH and protein concentrations close to physiological, a two-step mechanism with a unimolecular first step followed by a second-order second step adjusts well to the experimental data. Interestingly, although sharing the same kinetic mechanism, V30M-TTR refolds at a much slower rate than WT-TTR, a feature that may favor the formation of transient species leading to kinetic partition into amyloidogenic pathways and, thus, significantly increasing the probability of amyloid formation in vivo. PMID:27589730

  9. The early folding kinetics of apomyoglobin.

    PubMed Central

    Pappu, R. V.; Weaver, D. L.

    1998-01-01

    The folding pathway of apomyoglobin has been experimentally shown to have early kinetic intermediates involving the A, B, G, and H helices. The earliest detected kinetic events occur on a ns to micros time scale. We show that the early folding kinetics of apomyoglobin may be understood as the association of nascent helices through a network of diffusion-collision-coalescence steps G + H <--> GH + A <--> AGH + B <--> ABGH obtained by solving the diffusion-collision model in a chemical kinetics approximation. Our reproduction of the experimental results indicates that the model is a useful way to analyze folding data. One prediction from our fit is that the nascent A and H helices should be relatively more helix-like before coalescence than the other apomyoglobin helices. PMID:9521125

  10. Protein folded states are kinetic hubs

    PubMed Central

    Bowman, Gregory R.; Pande, Vijay S.

    2010-01-01

    Understanding molecular kinetics, and particularly protein folding, is a classic grand challenge in molecular biophysics. Network models, such as Markov state models (MSMs), are one potential solution to this problem. MSMs have recently yielded quantitative agreement with experimentally derived structures and folding rates for specific systems, leaving them positioned to potentially provide a deeper understanding of molecular kinetics that can lead to experimentally testable hypotheses. Here we use existing MSMs for the villin headpiece and NTL9, which were constructed from atomistic simulations, to accomplish this goal. In addition, we provide simpler, humanly comprehensible networks that capture the essence of molecular kinetics and reproduce qualitative phenomena like the apparent two-state folding often seen in experiments. Together, these models show that protein dynamics are dominated by stochastic jumps between numerous metastable states and that proteins have heterogeneous unfolded states (many unfolded basins that interconvert more rapidly with the native state than with one another) yet often still appear two-state. Most importantly, we find that protein native states are hubs that can be reached quickly from any other state. However, metastability and a web of nonnative states slow the average folding rate. Experimental tests for these findings and their implications for other fields, like protein design, are also discussed. PMID:20534497

  11. Modelling RNA folding under mechanical tension

    PubMed Central

    VIEREGG, JEFFREY R.; TINOCO, IGNACIO

    2006-01-01

    We investigate the thermodynamics and kinetics of RNA unfolding and refolding under mechanical tension. The hierarchical nature of RNA structure and the existence of thermodynamic parameters for base pair formation based on nearest-neighbour interactions allows modelling of sequence-dependent folding dynamics for any secondary structure. We calculate experimental observables such as the transition force for unfolding, the end-to-end distribution function and its variance, as well as kinetic information, for a representative RNA sequence and for a sequence containing two homopolymer segments: A.U and G.C. PMID:16969426

  12. Protein folding and misfolding: mechanism and principles.

    PubMed

    Englander, S Walter; Mayne, Leland; Krishna, Mallela M G

    2007-11-01

    Two fundamentally different views of how proteins fold are now being debated. Do proteins fold through multiple unpredictable routes directed only by the energetically downhill nature of the folding landscape or do they fold through specific intermediates in a defined pathway that systematically puts predetermined pieces of the target native protein into place? It has now become possible to determine the structure of protein folding intermediates, evaluate their equilibrium and kinetic parameters, and establish their pathway relationships. Results obtained for many proteins have serendipitously revealed a new dimension of protein structure. Cooperative structural units of the native protein, called foldons, unfold and refold repeatedly even under native conditions. Much evidence obtained by hydrogen exchange and other methods now indicates that cooperative foldon units and not individual amino acids account for the unit steps in protein folding pathways. The formation of foldons and their ordered pathway assembly systematically puts native-like foldon building blocks into place, guided by a sequential stabilization mechanism in which prior native-like structure templates the formation of incoming foldons with complementary structure. Thus the same propensities and interactions that specify the final native state, encoded in the amino-acid sequence of every protein, determine the pathway for getting there. Experimental observations that have been interpreted differently, in terms of multiple independent pathways, appear to be due to chance misfolding errors that cause different population fractions to block at different pathway points, populate different pathway intermediates, and fold at different rates. This paper summarizes the experimental basis for these three determining principles and their consequences. Cooperative native-like foldon units and the sequential stabilization process together generate predetermined stepwise pathways. Optional misfolding errors

  13. Three-state kinetic folding mechanism of the H2A/H2B histone heterodimer: the N-terminal tails affect the transition state between a dimeric intermediate and the native dimer.

    PubMed

    Placek, Brandon J; Gloss, Lisa M

    2005-01-28

    The H2A/H2B heterodimer is a component of the nucleosome core particle, the fundamental repeating unit of chromatin in all eukaryotic cells. The kinetic folding mechanism for the H2A/H2B dimer has been determined from unfolding and refolding kinetics as a function of urea using stopped-flow, circular dichroism and fluorescence methods. The kinetic data are consistent with a three-state mechanism: two unfolded monomers associate to form a dimeric intermediate in the dead-time of the SF instrument (approximately 5 ms); this intermediate is then converted to the native dimer by a slower, first-order reaction. Analysis of the burst-phase amplitudes as a function of denaturant indicates that the dimeric kinetic intermediate possesses approximately 50% of the secondary structure and approximately 60% of the surface area burial of the native dimer. The stability of the dimeric intermediate is approximately 30% of that of the native dimer at the monomer concentrations employed in the SF experiments. Folding-to-unfolding double-jump experiments were performed to monitor the formation of the native dimer as a function of folding delay times. The double-jump data demonstrate that the dimeric intermediate is on-pathway and obligatory. Formation of a transient dimeric burst-phase intermediate has been observed in the kinetic mechanism of other intertwined, segment-swapped, alpha-helical, DNA-binding dimers, such as the H3-H4 histone dimer, Escherichia coli factor for inversion stimulation and E.coli Trp repressor. The common feature of a dimeric intermediate in these folding mechanisms suggests that this intermediate may accelerate protein folding, when compared to the folding of archael histones, which do not populate a transient dimeric species and fold more slowly.

  14. Thermodynamics and kinetics of protein folding: an evolutionary perspective.

    PubMed

    Demetrius, Lloyd

    2002-08-07

    This article appeals to an evolutionary model which postulates that primordial proteins were described by small polypeptide chains which (i) lack disulfide bridges, and (ii) display slow folding rates with multi-state kinetics, to determine relations between structural properties of proteins and their folding kinetics. We parameterize the energy landscape of proteins in terms of thermodynamic activation variables. The model studies evolutionary changes in these thermodynamic parameters, and we invoke relations between these activation variables and structural properties of the protein to predict the following correspondence between protein structure and folding kinetics. 1. Proteins with inter- and intra-chain disulfide bridges: large variability in both folding rates and stability of intermediates, multi-state kinetics. 2. Proteins which lack inter and intra-chain disulfide bridges. 2.1 Single-domain chains: fast folding rates; unstable intermediates; two-state kinetics. 2.2 Multi-domain monomers: intermediate rates; metastable intermediates; multi-state kinetics. 2.3 Multi-domain oligomers: slow rates; metastable intermediates; multi-state kinetics. The evolutionary model thus provides a kinetic characterization of one important subfamily of proteins which we describe by the following properties: Folding dynamics of single-domain proteins which lack disulfide bridges are described by two-state kinetics. Folding rate of this class of proteins is positively correlated with the thermodynamic stability of the folded state.

  15. Osmolyte-induced folding of an intrinsically disordered protein: folding mechanism in the absence of ligand.

    PubMed

    Chang, Yu-Chu; Oas, Terrence G

    2010-06-29

    Understanding the interconversion between thermodynamically distinguishable states present in a protein folding pathway provides not only the kinetics and energetics of protein folding but also insights into the functional roles of these states in biological systems. The protein component of the bacterial RNase P holoenzyme from Bacillus subtilis (P protein) was previously shown to be unfolded in the absence of its cognate RNA or other anionic ligands. P protein was used in this study as a model system to explore general features of intrinsically disordered protein (IDP) folding mechanisms. The use of trimethylamine N-oxide (TMAO), an osmolyte that stabilizes the unliganded folded form of the protein, enabled us to study the folding process of P protein in the absence of ligand. Transient stopped-flow kinetic traces at various final TMAO concentrations exhibited multiphasic kinetics. Equilibrium "cotitration" experiments were performed using both TMAO and urea during the titration to produce a urea-TMAO titration surface of P protein. Both kinetic and equilibrium studies show evidence of a previously undetected intermediate state in the P protein folding process. The intermediate state is significantly populated, and the folding rate constants are relatively slow compared to those of intrinsically folded proteins similar in size and topology. The experiments and analysis described serve as a useful example for mechanistic folding studies of other IDPs.

  16. The complex kinetics of protein folding in wide temperature ranges.

    PubMed

    Wang, Jin

    2004-10-01

    The complex protein folding kinetics in wide temperature ranges is studied through diffusive dynamics on the underlying energy landscape. The well-known kinetic chevron rollover behavior is recovered from the mean first passage time, with the U-shape dependence on temperature. The fastest folding temperature T0 is found to be smaller than the folding transition temperature Tf. We found that the fluctuations of the kinetics through the distribution of first passage time show rather universal behavior, from high-temperature exponential Poissonian kinetics to the relatively low-temperature highly non-exponential kinetics. The transition temperature is at Tk and T0 < Tk < Tf. In certain low-temperature regimes, a power law behavior at long time emerges. At very low temperatures (lower than trapping transition temperature T < T0/(4 approximately 6)), the kinetics is an exponential Poissonian process again.

  17. Enhanced protein folding by removal of kinetic traps

    NASA Astrophysics Data System (ADS)

    Liu, Yanxin; Chapagain, Prem; Parra, Jose; Gerstman, Bernard

    2007-03-01

    The presence of non-native kinetic traps along the free energy landscape of a protein may significantly lengthen the overall folding time so that the folding process becomes unreliable. We used a computational 3-D lattice model to investigate the free energy landscape of a model alpha helical hairpin peptide. We used two slightly different sequences and show that strategic substitutions of only a few amino acid residues greatly enhance the folding process. These strategic substitutions prevent the formation of long-lived misfolded configurations which not only lengthen the folding time but also may cause unwanted aggregation. Detailed kinetic and thermodynamic analysis was carried out for the folding of these two sequences and the results are consistent with the experimental and molecular dynamics simulations of small helical bundle proteins.

  18. Oxidative folding of peptides with cystine-knot architectures: kinetic studies and optimization of folding conditions.

    PubMed

    Reinwarth, Michael; Glotzbach, Bernhard; Tomaszowski, Michael; Fabritz, Sebastian; Avrutina, Olga; Kolmar, Harald

    2013-01-02

    Bioactive peptides often contain several disulfide bonds that provide the main contribution to conformational rigidity and structural, thermal, or biological stability. Among them, cystine-knot peptides-commonly named "knottins"-make up a subclass with several thousand natural members. Hence, they are considered promising frameworks for peptide-based pharmaceuticals. Although cystine-knot peptides are available through chemical and recombinant synthetic routes, oxidative folding to afford the bioactive isomers still remains a crucial step. We therefore investigated the oxidative folding of ten protease-inhibiting peptides from two knottin families, as well as that of an HIV entry inhibitor and of aprotinin, under two conventional sets of folding conditions and by a newly developed procedure. Kinetic studies identified folding conditions that resulted in correctly folded miniproteins with high rates of conversion even for highly hydrophobic and aggregation-prone peptides in concentrated solutions.

  19. The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation.

    PubMed

    Shimada, J; Kussell, E L; Shakhnovich, E I

    2001-04-20

    We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding, all side-chain and backbone torsions, and uses a Go potential. In this study, we focus on the 46 residue alpha/beta protein crambin and two of its structural components, the helix and helix hairpin. For a wide range of temperatures, we recorded multiple folding events of these three structures from random coils to native conformations that differ by less than 1 A C(alpha) dRMS from their crystal structure coordinates. The thermodynamics and kinetic mechanism of the helix-coil transition obtained from our simulation shows excellent agreement with currently available experimental and molecular dynamics data. Based on insights obtained from folding its smaller structural components, a possible folding mechanism for crambin is proposed. We observed that the folding occurs via a cooperative, first order-like process, and that many folding pathways to the native state exist. One particular sequence of events constitutes a "fast-folding" pathway where kinetic traps are avoided. At very low temperatures, a kinetic trap arising from the incorrect packing of side-chains was observed. These results demonstrate that folding to the native state can be observed in a reasonable amount of time on desktop computers even when an all-atom representation is used, provided the energetics sufficiently stabilize the native state.

  20. Ion specificity in α-helical folding kinetics.

    PubMed

    von Hansen, Yann; Kalcher, Immanuel; Dzubiella, Joachim

    2010-11-04

    The influence of the salts KCl, NaCl, and NaI at molar concentrations on the α-helical folding kinetics of the alanine-based oligopeptide Ace-AEAAAKEAAAKA-Nme is investigated by means of (explicit-water) molecular dynamics simulations and a diffusional analysis. The mean first passage times for folding and unfolding are found to be highly salt-specific. In particular, the folding times increase about 1 order of magnitude for the sodium salts. The drastic slowing can be traced to long-lived, compact configurations of the partially folded peptide, in which sodium ions are tightly bound by several carbonyl and carboxylate groups. This multiple trapping leads to a nonexponential residence time distribution of the cations in the first solvation shell of the peptide. The analysis of α-helical folding in the framework of diffusion in a reduced (one-dimensional) free energy landscape further shows that the salt not only specifically modifies equilibrium properties but also induces kinetic barriers due to individual ion binding. In the sodium salts, for instance, the peptide's configurational mobility (or "diffusivity") can decrease about 1 order of magnitude. This study demonstrates the highly specific action of ions and highlights the intimate coupling of intramolecular friction and solvent effects in protein folding.

  1. Effects of mutation, truncation and temperature on the folding kinetics of a WW domain

    PubMed Central

    Maisuradze, Gia G.; Zhou, Rui; Liwo, Adam; Xiao, Yi; Scheraga, Harold A.

    2013-01-01

    The purpose of this work is to show how mutation, truncation and change of temperature can influence the folding kinetics of a protein. This is accomplished by principal component analysis (PCA) of molecular dynamics (MD)-generated folding trajectories of the triple β-strand WW domain from the Formin binding protein 28 (FBP) [PDB: 1E0L] and its full-size, and singly- and doubly-truncated mutants at temperatures below and very close to the melting point. The reasons for biphasic folding kinetics [i.e., coexistence of slow (three-state) and fast (two-state) phases], including the involvement of a solvent-exposed hydrophobic cluster and another delocalized hydrophobic core in the folding kinetics, are discussed. New folding pathways are identified in free-energy landscapes determined in terms of principal components for full-size mutants. Three-state folding is found to be a main mechanism for folding FBP28 WW domain and most of the full-size and truncated mutants. The results from the theoretical analysis are compared to those from experiment. Agreements and discrepancies between the theoretical and experimental results are discussed. Because of its importance in understanding protein kinetics and function, the diffusive mechanism by which FBP28 WW domain and its full-size and truncated mutants explore their conformational space is examined in terms of the mean-square displacement, (MSD), and PCA eigenvalue spectrum analyses. Subdiffusive behavior is observed for all studied systems. PMID:22560992

  2. Protein Folding and Mechanisms of Proteostasis

    PubMed Central

    Díaz-Villanueva, José Fernando; Díaz-Molina, Raúl; García-González, Victor

    2015-01-01

    Highly sophisticated mechanisms that modulate protein structure and function, which involve synthesis and degradation, have evolved to maintain cellular homeostasis. Perturbations in these mechanisms can lead to protein dysfunction as well as deleterious cell processes. Therefore in recent years the etiology of a great number of diseases has been attributed to failures in mechanisms that modulate protein structure. Interconnections among metabolic and cell signaling pathways are critical for homeostasis to converge on mechanisms associated with protein folding as well as for the preservation of the native structure of proteins. For instance, imbalances in secretory protein synthesis pathways lead to a condition known as endoplasmic reticulum (ER) stress which elicits the adaptive unfolded protein response (UPR). Therefore, taking this into consideration, a key part of this paper is developed around the protein folding phenomenon, and cellular mechanisms which support this pivotal condition. We provide an overview of chaperone protein function, UPR via, spatial compartmentalization of protein folding, proteasome role, autophagy, as well as the intertwining between these processes. Several diseases are known to have a molecular etiology in the malfunction of mechanisms responsible for protein folding and in the shielding of native structure, phenomena which ultimately lead to misfolded protein accumulation. This review centers on our current knowledge about pathways that modulate protein folding, and cell responses involved in protein homeostasis. PMID:26225966

  3. Periodic and stochastic thermal modulation of protein folding kinetics

    SciTech Connect

    Platkov, Max; Gruebele, Martin

    2014-07-21

    Chemical reactions are usually observed either by relaxation of a bulk sample after applying a sudden external perturbation, or by intrinsic fluctuations of a few molecules. Here we show that the two ideas can be combined to measure protein folding kinetics, either by periodic thermal modulation, or by creating artificial thermal noise that greatly exceeds natural thermal fluctuations. We study the folding reaction of the enzyme phosphoglycerate kinase driven by periodic temperature waveforms. As the temperature waveform unfolds and refolds the protein, its fluorescence color changes due to FRET (Förster resonant Energy Transfer) of two donor/acceptor fluorophores labeling the protein. We adapt a simple model of periodically driven kinetics that nicely fits the data at all temperatures and driving frequencies: The phase shifts of the periodic donor and acceptor fluorescence signals as a function of driving frequency reveal reaction rates. We also drive the reaction with stochastic temperature waveforms that produce thermal fluctuations much greater than natural fluctuations in the bulk. Such artificial thermal noise allows the recovery of weak underlying signals due to protein folding kinetics. This opens up the possibility for future detection of a stochastic resonance for protein folding subject to noise with controllable amplitude.

  4. Mechanical Models of Fault-Related Folding

    SciTech Connect

    Johnson, A. M.

    2003-01-09

    The subject of the proposed research is fault-related folding and ground deformation. The results are relevant to oil-producing structures throughout the world, to understanding of damage that has been observed along and near earthquake ruptures, and to earthquake-producing structures in California and other tectonically-active areas. The objectives of the proposed research were to provide both a unified, mechanical infrastructure for studies of fault-related foldings and to present the results in computer programs that have graphical users interfaces (GUIs) so that structural geologists and geophysicists can model a wide variety of fault-related folds (FaRFs).

  5. Kinetic Monte Carlo method applied to nucleic acid hairpin folding.

    PubMed

    Sauerwine, Ben; Widom, Michael

    2011-12-01

    Kinetic Monte Carlo on coarse-grained systems, such as nucleic acid secondary structure, is advantageous for being able to access behavior at long time scales, even minutes or hours. Transition rates between coarse-grained states depend upon intermediate barriers, which are not directly simulated. We propose an Arrhenius rate model and an intermediate energy model that incorporates the effects of the barrier between simulated states without enlarging the state space itself. Applying our Arrhenius rate model to DNA hairpin folding, we demonstrate improved agreement with experiment compared to the usual kinetic Monte Carlo model. Further improvement results from including rigidity of single-stranded stacking.

  6. Antibody-detected folding: kinetics of surface epitope formation are distinct from other folding phases.

    PubMed Central

    Raman, C. S.; Jemmerson, R.; Nall, B. T.

    2000-01-01

    The rate of macromolecular surface formation in yeast iso-2 cytochrome c and its site-specific mutant, N52I iso-2, has been studied using a monoclonal antibody that recognizes a tertiary epitope including K58 and H39. The results indicate that epitope refolding occurs after fast folding but prior to slow folding, in contrast to horse cytochrome c where surface formation occurs early. The antibody-detected (ad) kinetic phase accompanying epitope formation has k(ad) = 0.2 s(-1) and is approximately 40-fold slower than the fastest detectable event in the folding of yeast iso-2 cytochrome c (k2f approximately 8 s(-1)), but occurs prior to the absorbance- and fluorescence-detected slow folding steps (k1a approximately 0.06 s(-1); k1b approximately 0.09 s(-1)). N5I iso-2 cytochrome c exhibits similar kinetic behavior with respect to epitope formation. A detailed dissection of the mechanistic differences between the folding pathways of horse and yeast cytochromes c identifies possible reasons for the slow surface formation in the latter. Our results suggest that non-native ligation involving H33 or H39 during refolding may slow down the formation of the tertiary epitope in iso-2 cytochrome c. This study illustrates that surface formation can be coupled to early events in protein folding. Thus, the rate of macromolecular surface formation is fine tuned by the residues that make up the surface and the interactions they entertain during refolding. PMID:10739255

  7. Kinetics of chain motions within a protein-folding intermediate

    PubMed Central

    Neuweiler, Hannes; Banachewicz, Wiktor; Fersht, Alan R.

    2010-01-01

    Small proteins can fold remarkably rapidly, even in μs. What limits their rate of folding? The Engrailed homeodomain is a particularly well-characterized example, which folds ultrafast via an intermediate, I, of solved structure. It is a puzzle that the helix2-turn-helix3 motif of the 3-helix bundle forms in approximately 2 μs, but the final docking of preformed helix1 in I requires approximately 20 μs. Simulation and structural data suggest that nonnative interactions may slow down helix docking. Here we report the direct measurement of chain motions in I by using photoinduced electron transfer fluorescence-quenching correlation spectroscopy (PET-FCS). We use a mutant that traps I at physiological ionic strength but refolds at higher ionic strength. A single Trp in helix3 quenches the fluorescence of an extrinsic label on contact with it. We placed the label along the sequence to probe segmental chain motions. At high ionic strength, we found two relaxations for all probed positions on the 2- and 20-μs time scale, corresponding to the known folding processes, and a 200-ns phase attributable to loop closure kinetics in the unfolded state. At low ionic strength, we found only the 2-μs and 200-ns phase for labels in the helix2-turn-helix3 motif of I, because the native state is not significantly populated. But for labels in helix1 we observed an additional approximately 10-μs phase showing that it was moving slowly, with a rate constant similar to that for overall folding under native conditions. Folding was rate-limited by chain motions on a rough energy surface where nonnative interactions constrain motion. PMID:21135210

  8. Femtomole Mixer for Microsecond Kinetic Studies of Protein Folding

    PubMed Central

    Hertzog, David E.; Michalet, Xavier; Jäger, Marcus; Kong, Xiangxu; Santiago, Juan G.; Weiss, Shimon; Bakajin, Olgica

    2005-01-01

    We have developed a microfluidic mixer for studying protein folding and other reactions with a mixing time of 8 μs and sample consumption of femtomoles. This device enables us to access conformational changes under conditions far from equilibrium and at previously inaccessible time scales. In this paper, we discuss the design and optimization of the mixer using modeling of convective diffusion phenomena and a characterization of the mixer performance using microparticle image velocimetry, dye quenching, and Förster resonance energy-transfer (FRET) measurements of single-stranded DNA. We also demonstrate the feasibility of measuring fast protein folding kinetics using FRET with acyl-CoA binding protein. PMID:15595857

  9. Microsecond Microfluidic Mixing for Investigation of Protein Folding Kinetics

    SciTech Connect

    Hertzog, D E; Santiago, J G; Bakajin, O

    2005-02-10

    We have developed and characterized a mixer to study the reaction kinetics of protein folding on a microsecond timescale. The mixer uses hydrodynamic focusing of pressure-driven flow in a microfluidic channel to reduce diffusion times as first demonstrated by Knight et al.[1]. Features of the mixer include 1 {micro}s mixing times, sample consumptions of order 1 nl/s, loading sample volumes on the order of microliters, and the ability to manufacture in fused silica for compatibility with most spectroscopic methods.

  10. Folded membrane dialyzer with mechanically sealed edges

    DOEpatents

    Markley, Finley W.

    1976-01-01

    A semipermeable membrane is folded in accordion fashion to form a stack of pleats and the edges are sealed so as to isolate the opposite surfaces of the membrane. The stack is contained within a case that provides ports for flow of blood in contact with one surface of the membrane through channels formed by the pleats and also provides ports for flow of a dialysate through channels formed by the pleats in contact with the other surface of the membrane. The serpentine side edges of the membrane are sealed by a solidified plastic material, whereas effective mechanical means are provided to seal the end edges of the folded membrane. The mechanical means include a clamping strip which biases case sealing flanges into a sealed relationship with end portions of the membrane near the end edges, which portions extend from the stack and between the sealing flanges.

  11. Folding of a model three-helix bundle protein: a thermodynamic and kinetic analysis.

    PubMed

    Zhou, Y; Karplus, M

    1999-11-05

    The kinetics and thermodynamics of an off-lattice model for a three-helix bundle protein are investigated as a function of a bias gap parameter that determines the energy difference between native and non-native contacts. A simple dihedral potential is used to introduce the tendency to form right-handed helices. For each value of the bias parameter, 100 trajectories of up to one microsecond are performed. Such statistically valid sampling of the kinetics is made possible by the use of the discrete molecular dynamics method with square-well interactions. This permits much faster simulations for off-lattice models than do continuous potentials. It is found that major folding pathways can be defined, although ensembles with considerable structural variation are involved. The large gap models generally fold faster than those with a smaller gap. For the large gap models, the kinetic intermediates are non-obligatory, while both obligatory and non-obligatory intermediates are present for small gap models. Certain large gap intermediates have a two-helix microdomain with one helix extended outward (as in domain-swapped dimers); the small gap intermediates have more diverse structures. The importance of studying the kinetic, as well as the thermodynamics, of folding for an understanding of the mechanism is discussed and the relation between kinetic and equilibrium intermediates is examined. It is found that the behavior of this model system has aspects that encompass both the "new" view and the "old" view of protein folding.

  12. Kinetic role of helix caps in protein folding is context-dependent.

    PubMed

    Kapp, Gregory T; Richardson, Jane S; Oas, Terrence G

    2004-04-06

    Secondary structure punctuation through specific backbone and side chain interactions at the beginning and end of alpha-helices has been proposed to play a key role in hierarchical protein folding mechanisms [Baldwin, R. L., and Rose, G. D. (1999) Trends Biochem. Sci. 24, 26-33; Presta, L. G., and Rose, G. D. (1988) Science 240, 1632-1641]. We have made site-specific substitutions in the N- and C-cap motifs of the 5-helix protein monomeric lambda repressor (lambda(6-85)) and have measured the rate constants for folding and unfolding of each variant. The consequences of C-cap changes are strongly context-dependent. When the C-cap was located at the chain terminus, changes had little energetic and no kinetic effect. However, substitutions in a C-cap at the boundary between helix 4 and the subsequent interhelical loop resulted in large changes to the stability and rate constants of the variant, showing a substantial kinetic role for this interior C-cap and suggesting a general kinetic role for interior helix C-caps. Statistical preferences tabulated separately for internal and terminal C-caps also show only weak residue preferences in terminal C-caps. This kinetic distinction between interior and terminal C-caps can explain the discrepancy between the near-absence of stability and kinetic effects seen for C-caps of isolated peptides versus the very strong C-cap effects seen for proteins in statistical sequence preferences and mutational energetics. Introduction of consensus, in-register N-capping motifs resulted in increased stability, accelerated folding, and slower unfolding. The kinetic measurements indicate that some of the new native-state capping interactions remain unformed in the transition state. The accelerated folding rates could result from helix stabilization without invoking a specific role for N-caps in the folding reaction.

  13. Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory.

    PubMed

    Buchner, Ginka S; Murphy, Ronan D; Buchete, Nicolae-Viorel; Kubelka, Jan

    2011-08-01

    The problem of spontaneous folding of amino acid chains into highly organized, biologically functional three-dimensional protein structures continues to challenge the modern science. Understanding how proteins fold requires characterization of the underlying energy landscapes as well as the dynamics of the polypeptide chains in all stages of the folding process. In recent years, important advances toward these goals have been achieved owing to the rapidly growing interdisciplinary interest and significant progress in both experimental techniques and theoretical methods. Improvements in the experimental time resolution led to determination of the timescales of the important elementary events in folding, such as formation of secondary structure and tertiary contacts. Sensitive single molecule methods made possible probing the distributions of the unfolded and folded states and following the folding reaction of individual protein molecules. Discovery of proteins that fold in microseconds opened the possibility of atomic-level theoretical simulations of folding and their direct comparisons with experimental data, as well as of direct experimental observation of the barrier-less folding transition. The ultra-fast folding also brought new questions, concerning the intrinsic limits of the folding rates and experimental signatures of barrier-less "downhill" folding. These problems will require novel approaches for even more detailed experimental investigations of the folding dynamics as well as for the analysis of the folding kinetic data. For theoretical simulations of folding, a main challenge is how to extract the relevant information from overwhelmingly detailed atomistic trajectories. New theoretical methods have been devised to allow a systematic approach towards a quantitative analysis of the kinetic network of folding-unfolding transitions between various configuration states of a protein, revealing the transition states and the associated folding pathways at

  14. RNA folding pathways and kinetics using 2D energy landscapes.

    PubMed

    Senter, Evan; Dotu, Ivan; Clote, Peter

    2015-01-01

    RNA folding pathways play an important role in various biological processes, such as (i) the hok/sok (host-killing/suppression of killing) system in E. coli to check for sufficient plasmid copy number, (ii) the conformational switch in spliced leader (SL) RNA from Leptomonas collosoma, which controls trans splicing of a portion of the '5 exon, and (iii) riboswitches--portions of the 5' untranslated region of messenger RNA that regulate genes by allostery. Since RNA folding pathways are determined by the energy landscape, we describe a novel algorithm, FFTbor2D, which computes the 2D projection of the energy landscape for a given RNA sequence. Given two metastable secondary structures A, B for a given RNA sequence, FFTbor2D computes the Boltzmann probability p(x, y) = Z(x,y)/Z that a secondary structure has base pair distance x from A and distance y from B. Using polynomial interpolationwith the fast Fourier transform,we compute p(x, y) in O(n(5)) time and O(n(2)) space, which is an improvement over an earlier method, which runs in O(n(7)) time and O(n(4)) space. FFTbor2D has potential applications in synthetic biology, where one might wish to design bistable switches having target metastable structures A, B with favorable pathway kinetics. By inverting the transition probability matrix determined from FFTbor2D output, we show that L. collosoma spliced leader RNA has larger mean first passage time from A to B on the 2D energy landscape, than 97.145% of 20,000 sequences, each having metastable structures A, B. Source code and binaries are freely available for download at http://bioinformatics.bc.edu/clotelab/FFTbor2D. The program FFTbor2D is implemented in C++, with optional OpenMP parallelization primitives.

  15. When fast is better: protein folding fundamentals and mechanisms from ultrafast approaches

    PubMed Central

    Muñoz, Victor; Cerminara, Michele

    2016-01-01

    Protein folding research stalled for decades because conventional experiments indicated that proteins fold slowly and in single strokes, whereas theory predicted a complex interplay between dynamics and energetics resulting in myriad microscopic pathways. Ultrafast kinetic methods turned the field upside down by providing the means to probe fundamental aspects of folding, test theoretical predictions and benchmark simulations. Accordingly, experimentalists could measure the timescales for all relevant folding motions, determine the folding speed limit and confirm that folding barriers are entropic bottlenecks. Moreover, a catalogue of proteins that fold extremely fast (microseconds) could be identified. Such fast-folding proteins cross shallow free energy barriers or fold downhill, and thus unfold with minimal co-operativity (gradually). A new generation of thermodynamic methods has exploited this property to map folding landscapes, interaction networks and mechanisms at nearly atomic resolution. In parallel, modern molecular dynamics simulations have finally reached the timescales required to watch fast-folding proteins fold and unfold in silico. All of these findings have buttressed the fundamentals of protein folding predicted by theory, and are now offering the first glimpses at the underlying mechanisms. Fast folding appears to also have functional implications as recent results connect downhill folding with intrinsically disordered proteins, their complex binding modes and ability to moonlight. These connections suggest that the coupling between downhill (un)folding and binding enables such protein domains to operate analogically as conformational rheostats. PMID:27574021

  16. When fast is better: protein folding fundamentals and mechanisms from ultrafast approaches.

    PubMed

    Muñoz, Victor; Cerminara, Michele

    2016-09-01

    Protein folding research stalled for decades because conventional experiments indicated that proteins fold slowly and in single strokes, whereas theory predicted a complex interplay between dynamics and energetics resulting in myriad microscopic pathways. Ultrafast kinetic methods turned the field upside down by providing the means to probe fundamental aspects of folding, test theoretical predictions and benchmark simulations. Accordingly, experimentalists could measure the timescales for all relevant folding motions, determine the folding speed limit and confirm that folding barriers are entropic bottlenecks. Moreover, a catalogue of proteins that fold extremely fast (microseconds) could be identified. Such fast-folding proteins cross shallow free energy barriers or fold downhill, and thus unfold with minimal co-operativity (gradually). A new generation of thermodynamic methods has exploited this property to map folding landscapes, interaction networks and mechanisms at nearly atomic resolution. In parallel, modern molecular dynamics simulations have finally reached the timescales required to watch fast-folding proteins fold and unfold in silico All of these findings have buttressed the fundamentals of protein folding predicted by theory, and are now offering the first glimpses at the underlying mechanisms. Fast folding appears to also have functional implications as recent results connect downhill folding with intrinsically disordered proteins, their complex binding modes and ability to moonlight. These connections suggest that the coupling between downhill (un)folding and binding enables such protein domains to operate analogically as conformational rheostats.

  17. Perturbations of the denatured state ensemble: modeling their effects on protein stability and folding kinetics.

    PubMed Central

    Wrabl, J. O.; Shortle, D.

    1996-01-01

    By considering the denatured state of a protein as an ensemble of conformations with varying numbers of sequence-specific interactions, the effects on stability, folding kinetics, and aggregation of perturbing these interactions can be predicted from changes in the molecular partition function. From general considerations, the following conclusions are drawn: (1) A perturbation that enhances a native interaction in denatured state conformations always increases the stability of the native state. (2) A perturbation that promotes a non-native interaction in the denatured state always decreases the stability of the native state. (3) A change in the denatured state ensemble can alter the kinetics of aggregation and folding. (4) The loss (or increase) in stability accompanying two mutations, each of which lowers (or raises) the free energy of the denatured state, will be less than the sum of the effects of the single mutations, except in cases where both mutations affect the same set of partially folded conformations. By modeling the denatured state as the ensemble of all non-native conformations of hydrophobic-polar (HP) chains configured on a square lattice, it can be shown that the stabilization obtained from enhancement of native interactions derives in large measure from the avoidance of non-native interactions in the D state. In addition, the kinetic effects of fixing single native contacts in the denatured state or imposing linear gradients in the HH contact probabilities are found, for some sequences, to significantly enhance the efficiency of folding by a simple hydrophobic zippering algorithm. Again, the dominant mechanism appears to be avoidance of non-native interactions. These results suggest stabilization of native interactions and imposition of gradients in the stability of local structure are two plausible mechanisms involving the denatured state that could play a role in the evolution of protein folding and stability. PMID:8931153

  18. Evolution of Enzyme Kinetic Mechanisms.

    PubMed

    Ulusu, Nuriye Nuray

    2015-06-01

    This review paper discusses the reciprocal kinetic behaviours of enzymes and the evolution of structure-function dichotomy. Kinetic mechanisms have evolved in response to alterations in ecological and metabolic conditions. The kinetic mechanisms of single-substrate mono-substrate enzyme reactions are easier to understand and much simpler than those of bi-bi substrate enzyme reactions. The increasing complexities of kinetic mechanisms, as well as the increasing number of enzyme subunits, can be used to shed light on the evolution of kinetic mechanisms. Enzymes with heterogeneous kinetic mechanisms attempt to achieve specific products to subsist. In many organisms, kinetic mechanisms have evolved to aid survival in response to changing environmental factors. Enzyme promiscuity is defined as adaptation to changing environmental conditions, such as the introduction of a toxin or a new carbon source. Enzyme promiscuity is defined as adaptation to changing environmental conditions, such as the introduction of a toxin or a new carbon source. Enzymes with broad substrate specificity and promiscuous properties are believed to be more evolved than single-substrate enzymes. This group of enzymes can adapt to changing environmental substrate conditions and adjust catalysing mechanisms according to the substrate's properties, and their kinetic mechanisms have evolved in response to substrate variability.

  19. Thermal and mechanical multistate folding of ribonuclease H.

    PubMed

    Schmitt, Terry J; Clark, Jonathan E; Knotts, Thomas A

    2009-12-21

    Two different classes of experimental techniques exist by which protein folding mechanisms are ascertained. The first class, of which circular dichroism is an example, probes thermally-induced folding. The second class, which includes atomic force microscopy and optical tweezers, measures mechanically-induced folding. In this article, we investigate if proteins fold/unfold via the same mechanisms both thermally and mechanically. We do so using Ribonuclease H, a protein that has been shown to fold through a three-state mechanism using both types of experimental techniques. A detailed, molecular-level description of the states involved in thermal and mechanical folding shows that mechanisms for both types are globally similar, but small difference exist in the most unfolded conformations. Comparison to previous work suggests a universal folding behavior for proteins with a core helical bundle.

  20. Thermal and mechanical multistate folding of ribonuclease H

    NASA Astrophysics Data System (ADS)

    Schmitt, Terry J.; Clark, Jonathan E.; Knotts, Thomas A.

    2009-12-01

    Two different classes of experimental techniques exist by which protein folding mechanisms are ascertained. The first class, of which circular dichroism is an example, probes thermally-induced folding. The second class, which includes atomic force microscopy and optical tweezers, measures mechanically-induced folding. In this article, we investigate if proteins fold/unfold via the same mechanisms both thermally and mechanically. We do so using Ribonuclease H, a protein that has been shown to fold through a three-state mechanism using both types of experimental techniques. A detailed, molecular-level description of the states involved in thermal and mechanical folding shows that mechanisms for both types are globally similar, but small difference exist in the most unfolded conformations. Comparison to previous work suggests a universal folding behavior for proteins with a core helical bundle.

  1. Coupled folding and binding kinetics in the intrinsically disordered peptide IA3

    NASA Astrophysics Data System (ADS)

    Narayanan, Ranjani; Ganesh, Omjoy; Edison, Arthur; Hagen, Stephen

    2008-03-01

    IA3 is an intrinsically disordered 68 residue peptide and is an endogenous inhibitor of yeast proteinase A (YPrA). X-ray crystallography of the IA3.YPrA complex [Li et al, Nat. Struct. Biol. (7), 113-117 (2000)] indicates that the N-terminus of IA3 adopts an alpha-helical fold when it is bound to the YPrA active site. We have used equilibrium circular dichroism and multi-wavelength, nanosecond time-resolved laser temperature-jump spectroscopy to study the coupled folding and binding interaction of IA3 with YPrA. Our initial measurements of the rate of helix formation in free IA3 indicate mono-exponential folding kinetics that extrapolate to kF˜ 10^5/s at room temperature in aqueous solutions. By comparing this rate to the kinetics we observe for IA3 interacting with YPrA, we can assess possible mechanisms for the coupled folding and binding of IA3.

  2. Kinetic evidence of an on-pathway intermediate in the folding of lysozyme.

    PubMed Central

    Bai, Y.

    2000-01-01

    By means of a kinetic test, it was demonstrated that one of the folding intermediates (Ialpha) of hen lysozyme with alpha-domain folded and beta-domain unfolded is on the folding pathway under the classical definition. Ialpha folds to the native (N) state directly (unfolded (U) <==> Ialpha <==> N) without having to unfold to U and then refold to N through alternative folding pathways as in Ialpha <==> U <==> N. PMID:10739262

  3. Protein folding kinetics: barrier effects in chemical and thermal denaturation experiments

    PubMed Central

    Naganathan, Athi N.; Doshi, Urmi; Muñoz, Victor

    2008-01-01

    Recent experimental work on fast protein folding brings about an intriguing paradox. Microsecond-folding proteins are supposed to fold near or at the folding speed limit (downhill folding), but yet their folding behavior seems to comply with classical two-state analyses, which imply the crossing of high free energy barriers. However, close inspection of chemical and thermal denaturation kinetic experiments in fast-folding proteins reveals systematic deviations from two-state behavior. Using a simple one-dimensional free energy surface approach we find that such deviations are indeed diagnostic of marginal folding barriers. Furthermore, the quantitative analysis of available fast-kinetic data indicates that many microsecond-folding proteins fold downhill in native conditions. All of these proteins are then promising candidates for an atom-by-atom analysis of protein folding using nuclear magnetic resonance1. We also find that the diffusion coefficient for protein folding is strongly temperature dependent, corresponding to an activation energy of ~1 kJ.mol−1 per protein residue. As a consequence, the folding speed limit at room temperature is about an order of magnitude slower than the ~ 1μs estimates from high temperature T-jump experiments. Our analysis is quantitatively consistent with the available thermodynamic and kinetic data on two-state folding proteins, and provides a straightforward explanation for the apparent fast-folding paradox. PMID:17419630

  4. Folding mechanism of a multiple independently-folding domain protein: double B domain of protein A.

    PubMed

    Arora, Pooja; Hammes, Gordon G; Oas, Terrence G

    2006-10-10

    The antibody binding properties of staphylococcal protein A (SpA) can be attributed to the presence of five highly homologous domains (E, D, A, B, and C). Although the folding of the B domain of protein A (BdpA) is well-characterized, the folding behavior of this domain in the context of full-length SpA in the cell remains unexplored. The sequence of the B domain is 89 and 91% identical to those of domains A and C, respectively. We have fused B domain sequences (BBdpA) as a close approximation of the A-B or B-C portion of SpA. Circular dichroism and fluorescence-detected denaturation curves of BBdpA are experimentally indistinguishable from those of BdpA. The rate constants for folding and unfolding from NMR line shape analysis for the single- and double-domain proteins are the same within experimental uncertainties (+/-20%). These results support the designation of SpA as a multiple independently-folding domain (MIFD) protein. We develop a mathematical model that describes the folding thermodynamics and kinetics of MIFD proteins. The model depicts MIFD protein folding and unfolding as a parallel network and explicitly calculates the flux through all parallel pathways. These fluxes are combined to give a complete description of the global thermodynamics and kinetics of the folding and unfolding of MIFD proteins. The global rates for complete folding and unfolding of a MIFD protein and those of the individual domains depend on the stability of the protein. We show that the global unfolding rate of a MIFD protein may be many orders of magnitude slower than that of the constituent domains.

  5. Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements

    PubMed Central

    Zhou, Rui; Maisuradze, Gia G.; Suñol, David; Todorovski, Toni; Macias, Maria J.; Xiao, Yi; Scheraga, Harold A.; Czaplewski, Cezary; Liwo, Adam

    2014-01-01

    To demonstrate the utility of the coarse-grained united-residue (UNRES) force field to compare experimental and computed kinetic data for folding proteins, we have performed long-time millisecond-timescale canonical Langevin molecular dynamics simulations of the triple β-strand from the Formin binding protein 28 WW domain and six nonnatural variants, using UNRES. The results have been compared with available experimental data in both a qualitative and a quantitative manner. Complexities of the folding pathways, which cannot be determined experimentally, were revealed. The folding mechanisms obtained from the simulated folding kinetics are in agreement with experimental results, with a few discrepancies for which we have accounted. The origins of single- and double-exponential kinetics and their correlations with two- and three-state folding scenarios are shown to be related to the relative barrier heights between the various states. The rate constants obtained from time profiles of the fractions of the native, intermediate, and unfolded structures, and the kinetic equations fitted to them, correlate with the experimental values; however, they are about three orders of magnitude larger than the experimental ones for most of the systems. These differences are in agreement with the timescale extension derived by scaling down the friction of water and averaging out the fast degrees of freedom when passing from all-atom to a coarse-grained representation. Our results indicate that the UNRES force field can provide accurate predictions of folding kinetics of these WW domains, often used as models for the study of the mechanisms of proein folding. PMID:25489078

  6. Single-molecule kinetics under force: probing protein folding and enzymatic activity with optical tweezers

    NASA Astrophysics Data System (ADS)

    Wong, Wesley

    2010-03-01

    Weak non-covalent bonds between and within single molecules govern many aspects of biological structure and function (e.g. DNA base-paring, receptor-ligand binding, protein folding, etc.) In living systems, these interactions are often subject to mechanical forces, which can greatly alter their kinetics and activity. My group develops and applies novel single-molecule manipulation techniques to explore and quantify these force-dependent kinetics. Using optical tweezers, we have quantified the force-dependent unfolding and refolding kinetics of different proteins, including the cytoskeletal protein spectrin in collaboration with E. Evans's group [1], and the A2 domain of the von Willebrand factor blood clotting protein in collaboration with T. Springer's group [2]. Furthermore, we have studied the kinetics of the ADAMTS13 enzyme acting on a single A2 domain, and have shown that physiolgical forces in the circulation can act as a cofactor for enzymatic cleavage, regulating hemostatic activity [2]. References: 1. E. Evans, K. Halvorsen, K. Kinoshita, and W.P. Wong, Handbook of Single Molecule Biophysics, P. Hinterdorfer, ed., Springer (2009). 2. X. Zhang, K. Halvorsen, C.-Z. Zhang, W.P. Wong, and T.A. Springer, Science 324 (5932), 1330-1334 (2009).

  7. Folding Kinetics of Staphylococcal Nuclease Studied by Tryptophan Engineering and Rapid Mixing Methods

    PubMed Central

    Maki, Kosuke; Cheng, Hong; Dolgikh, Dimitry A.; Roder, Heinrich

    2007-01-01

    To monitor the development of tertiary structural contacts during folding, a unique tryptophan residue was introduced at seven partially buried locations (residues 15, 27, 61, 76, 91, 102 and 121) of a tryptophan-free variant of staphylococcal nuclease (P47G/P117G/H124L/W140H). Thermal unfolding measurements by circular dichroism indicate that the variants are destabilized, but maintain the ability to fold into a native-like structure. For the variants with Trp at positions 15, 27 and 61, the intrinsic fluorescence is significantly quenched in the native state due to close contact with polar side chains that act as intramolecular quenchers. All other variants exhibit enhanced fluorescence under native conditions consistent with burial of the tryptophans in an apolar environment. The kinetics of folding was observed by continuous- and stopped-flow fluorescence measurements over refolding times ranging from 100 μs to 10 s. The folding kinetics of all variants is quantitatively described by a mechanism involving a major pathway with a series of intermediate states and a minor parallel channel. The engineered tryptophans in the β-barrel and the N-terminal part of the α-helical domain become partially shielded from the solvent at an early stage (< 1 ms), indicating that this region of the protein undergoes a rapid specific collapse and remains uncoupled from the rest of the α-helical domain until the late stages of folding. For several variants, a major increase in fluorescence coincides with the rate-limiting step of folding on the 100 ms time scale, indicating that these tryptophans reach their buried native environment only during the late stages of folding. Other variants show more complex behavior with a transient increase in fluorescence during the 10 ms phase followed by a decrease during the rate-limiting phase. These observations are consistent with burial of these probes in a collapsed, but loosely packed intermediate, followed by the rate

  8. Solvent-Exposed Salt Bridges Influence the Kinetics of α-Helix Folding and Unfolding.

    PubMed

    Meuzelaar, Heleen; Tros, Martijn; Huerta-Viga, Adriana; van Dijk, Chris N; Vreede, Jocelyne; Woutersen, Sander

    2014-03-06

    Salt bridges are known to play an essential role in the thermodynamic stability of the folded conformation of many proteins, but their influence on the kinetics of folding remains largely unknown. Here, we investigate the effect of Glu-Arg salt bridges on the kinetics of α-helix folding using temperature-jump transient-infrared spectroscopy and steady-state UV circular dichroism. We find that geometrically optimized salt bridges (Glu(-) and Arg(+) are spaced four peptide units apart, and the Glu/Arg order is such that the side-chain rotameric preferences favor salt-bridge formation) significantly speed up folding and slow down unfolding, whereas salt bridges with unfavorable geometry slow down folding and slightly speed up unfolding. Our observations suggest a possible explanation for the surprising fact that many biologically active proteins contain salt bridges that do not stabilize the native conformation: these salt bridges might have a kinetic rather than a thermodynamic function.

  9. Mechanical Folding and Unfolding of Protein Barnase at the Single-Molecule Level

    PubMed Central

    Alemany, Anna; Rey-Serra, Blanca; Frutos, Silvia; Cecconi, Ciro; Ritort, Felix

    2016-01-01

    The unfolding and folding of protein barnase has been extensively investigated in bulk conditions under the effect of denaturant and temperature. These experiments provided information about structural and kinetic features of both the native and the unfolded states of the protein, and debates about the possible existence of an intermediate state in the folding pathway have arisen. Here, we investigate the folding/unfolding reaction of protein barnase under the action of mechanical force at the single-molecule level using optical tweezers. We measure unfolding and folding force-dependent kinetic rates from pulling and passive experiments, respectively, and using Kramers-based theories (e.g., Bell-Evans and Dudko-Hummer-Szabo models), we extract the position of the transition state and the height of the kinetic barrier mediating unfolding and folding transitions, finding good agreement with previous bulk measurements. Measurements of the force-dependent kinetic barrier using the continuous effective barrier analysis show that protein barnase verifies the Leffler-Hammond postulate under applied force and allow us to extract its free energy of folding, ΔG0. The estimated value of ΔG0 is in agreement with our predictions obtained using fluctuation relations and previous bulk studies. To address the possible existence of an intermediate state on the folding pathway, we measure the power spectrum of force fluctuations at high temporal resolution (50 kHz) when the protein is either folded or unfolded and, additionally, we study the folding transition-path time at different forces. The finite bandwidth of our experimental setup sets the lifetime of potential intermediate states upon barnase folding/unfolding in the submillisecond timescale. PMID:26745410

  10. Mechanical development of folded chert beds in Monterey Formation, California

    SciTech Connect

    Crowther, D.; Snyder, W.S.

    1988-03-01

    Small-scale folds in the upper siliceous facies of the Miocene Monterey Formation, at Lions Head, California (Santa Maria basin) are of tectonic origin. Folding is well developed in the chert-dominated zones and dies out rapidly in the adjacent siliceous mudstones. A tectonic origin is evidenced by the dominantly brittle deformation of the competent chert layers. Mechanically, the folds formed through a complex interrelationship between fracture and flexural slip. Opal-CT and quartz-chert layers display brittle fractures and rotated fracture blocks that responded to shortening. Thrusting of the chert layers is common in folds where fold propagation was impeded. Dilation breccia and void space occur in the hinges and reflect room problems during development of these disharmonic folds. Subsequent diagenesis has partially healed the fractures and slip surfaces, creating the erroneous appearance that ductile deformation was an important factor in the formation of the folds.

  11. The folding kinetics of the SDS-induced molten globule form of reduced cytochrome c.

    PubMed

    Chen, Eefei; Van Vranken, Vanessa; Kliger, David S

    2008-05-13

    The folding of reduced cytochrome c (redcyt c) is increasingly being recognized as undergoing a mechanism that deviates from a two-state process. In previous far-UV TRORD studies of redcyt c folding, a rapidly forming intermediate was attributed to the appearance of a molten-globule-like (MG) state [Chen, E., Goldbeck, R. A., and Kliger, D. S. (2003) J. Phys. Chem. A 107, 8149-8155]. A slow folding phase (>1 ms) was identified with the formation of native (N) secondary structure from that MG form. Here, using 0.65 mM SDS to induce the MG state in oxidized cytochrome c, folding of redcyt c was triggered with fast photoreduction and probed from early microseconds to milliseconds using far-UV TRORD spectroscopy. The kinetics of the reaction are described with a time constant of 50 +/- 16 ms, which corresponds to 1 +/- 0.6 ms upon extrapolation of the data to zero SDS concentration. The latter folding time is about 5 times faster than the calculated GuHCl-free time constant of 5.5 +/- 1.4 ms for slow-phase folding obtained in our previous study. This ratio of rates would be consistent with a scenario in which 20-30% MG that is suggested to form in the fast phase of redcyt c folding in GuHCl is an obligatory intermediate. The native state forms from this obligatory intermediate with an observed rate, k(f) = fk(G-->N) where f is the fractional population of MG and k(G-->N) is the microscopic rate for MG --> N. Calculation and comparison of the m(#)/m values show agreement within the uncertainties between the SDS ( approximately 0.5) and GuHCl ( approximately 0.3) based redcyt c folding experiments, suggesting that the two experiments report on comparable intermediates. The m values were obtained from far-UV CD SDS titration experiments, from which calculated thermodynamic parameters allowed estimation of the reduction potential for the MG state to be approximately 155 mV (-15 kJ/mol) vs NHE which, like the reduction potential for the native state, is more favorable than

  12. Mechanics of large folds in thin interfacial films

    NASA Astrophysics Data System (ADS)

    Démery, Vincent; Davidovitch, Benny; Santangelo, Christian D.

    2014-10-01

    A thin film confined to a liquid interface responds to uniaxial compression by wrinkling, and then by folding, that has been solved exactly before self-contact. Here, we address the mechanics of large folds, i.e., folds that absorb a length much larger than the wrinkle wavelength. With scaling arguments and numerical simulations, we show that the antisymmetric fold is energetically favorable and can absorb any excess length at zero pressure. Then, motivated by puzzles arising in the comparison of this simple model to experiments on lipid monolayers or capillary rafts, we discuss how to incorporate film weight, self-adhesion, or energy dissipation.

  13. The folding of spectrin domains I: wild-type domains have the same stability but very different kinetic properties.

    PubMed

    Scott, Kathryn A; Batey, Sarah; Hooton, Karen A; Clarke, Jane

    2004-11-12

    The study of proteins with the same architecture, but different sequence has proven to be a valuable tool in the protein folding field. As a prelude to studies on the folding mechanism of spectrin domains we present the kinetic characterisation of the wild-type forms of the 15th, 16th, and 17th domains of chicken brain alpha-spectrin (referred to as R15, R16 and R17, respectively). We show that the proteins all behave in a two-state manner, with different kinetic properties. The folding rate varies remarkably between different members, with a 5000-fold variation in folding rate and 3000-fold variation in unfolding rate seen for proteins differing only 1 kcal mol(-1) in stability. We show clear evidence for significant complexity in the energy landscape of R16, which shows a change in amplitude outside the stopped-flow timescale and curvature in the unfolding arm of the chevron plot. The accompanying paper describes the characterisation of the folding pathway of this domain.

  14. $\\cN$-FOLD SUPERSYMMETRY IN QUANTUM MECHANICAL MATRIX MODELS

    NASA Astrophysics Data System (ADS)

    Tanaka, Toshiaki

    2012-03-01

    We formulate Ņ-fold supersymmetry in quantum mechanical matrix models. As an example, we construct general two-by-two Hermitian matrix two-fold supersymmetric quantum mechanical systems. We find that there are two inequivalent such systems, both of which are characterized by two arbitrary scalar functions, and one of which does not reduce to the scalar system. The obtained systems are all weakly quasi-solvable.

  15. Characterization of protein folding by a Φ-value calculation with a statistical-mechanical model

    PubMed Central

    Wako, Hiroshi; Abe, Haruo

    2016-01-01

    The Φ-value analysis approach provides information about transition-state structures along the folding pathway of a protein by measuring the effects of an amino acid mutation on folding kinetics. Here we compared the theoretically calculated Φ values of 27 proteins with their experimentally observed Φ values; the theoretical values were calculated using a simple statistical-mechanical model of protein folding. The theoretically calculated Φ values reflected the corresponding experimentally observed Φ values with reasonable accuracy for many of the proteins, but not for all. The correlation between the theoretically calculated and experimentally observed Φ values strongly depends on whether the protein-folding mechanism assumed in the model holds true in real proteins. In other words, the correlation coefficient can be expected to illuminate the folding mechanisms of proteins, providing the answer to the question of which model more accurately describes protein folding: the framework model or the nucleation-condensation model. In addition, we tried to characterize protein folding with respect to various properties of each protein apart from the size and fold class, such as the free-energy profile, contact-order profile, and sensitivity to the parameters used in the Φ-value calculation. The results showed that any one of these properties alone was not enough to explain protein folding, although each one played a significant role in it. We have confirmed the importance of characterizing protein folding from various perspectives. Our findings have also highlighted that protein folding is highly variable and unique across different proteins, and this should be considered while pursuing a unified theory of protein folding.

  16. Using Kinetic Network Models To Probe Non-Native Salt-Bridge Effects on α-Helix Folding.

    PubMed

    Zhou, Guangfeng; Voelz, Vincent A

    2016-02-11

    Salt-bridge interactions play an important role in stabilizing many protein structures, and have been shown to be designable features for protein design. In this work, we study the effects of non-native salt bridges on the folding of a soluble alanine-based peptide (Fs peptide) using extensive all-atom molecular dynamics simulations performed on the Folding@home distributed computing platform. Using Markov State Models, we show how non-native salt-bridges affect the folding kinetics of Fs peptide by perturbing specific conformational states. Furthermore, we present methods for the automatic detection and analysis of such states. These results provide insight into helix folding mechanisms and useful information to guide simulation-based computational protein design.

  17. Isoprene: a photochemical kinetic mechanism

    SciTech Connect

    Killus, J.P.; Whitten, G.Z.

    1984-03-01

    A computer-modeling study has produced a photochemical kinetic mechanism for the atmospheric chemistry of isoprene, a naturally occurring common constituent of the troposphere. The kinetic mechnism is ready for use in atmospheric models because the reactions described are shown to adequately reproduce the results of a series of outdoor smog chamber experiments which encompass a wide range of precursor conditions of isoprene and NO/sub x/. Isoprene is a very reactive molecule that can contribute as much as 50% of the overall reactivity of rural air even though isoprene might be only 6% of the ambient hydrocarbon level. The major intermediate products of the atmospheric oxidation of isoprene, methyl vinyl ketone, methacrolein, methylglyoxal, and formaldehyde are also highly reactive. 25 references.

  18. The prosegment catalyzes pepsin folding to a kinetically trapped native state.

    PubMed

    Dee, Derek R; Yada, Rickey Y

    2010-01-19

    Investigations of irreversible protein unfolding often assume that alterations to the unfolded state, rather than the nature of the native state itself, are the cause of the irreversibility. However, the present study describes a less common explanation for the irreversible denaturation of pepsin, a zymogen-derived aspartic peptidase. The presence of a large folding barrier combined with the thermodynamically metastable nature of the native state, the formation of which depends on a separate prosegment (PS) domain, is the source of the irreversibility. Pepsin is unable to refold to the native state upon return from denaturing conditions due to a large folding barrier (24.6 kcal/mol) and instead forms a thermodynamically stable, yet inactive, refolded state. The native state is kinetically stabilized by an unfolding activation energy of 24.5 kcal/mol, comparable to the folding barrier, indicating that native pepsin exists as a thermodynamically metastable state. However, in the presence of the PS, the native state becomes thermodynamically stable, and the PS catalyzes pepsin folding by stabilizing the folding transition state by 14.7 kcal/mol. Once folded, the PS is removed, and the native conformation exists as a kinetically trapped state. Thus, while PS-guided folding is thermodynamically driven, without the PS the pepsin energy landscape is dominated by kinetic barriers rather than by free energy differences between native and denatured states. As pepsin is the archetype of a broad class of aspartic peptidases of similar structure and function, and many require their PS for correct folding, these results suggest that the occurrence of native states optimized for kinetic rather than thermodynamic stability may be a common feature of protein design.

  19. Protein Folding Mechanism of the Dimeric AmphiphysinII/Bin1 N-BAR Domain.

    PubMed

    Gruber, Tobias; Balbach, Jochen

    2015-01-01

    The human AmphyphisinII/Bin1 N-BAR domain belongs to the BAR domain superfamily, whose members sense and generate membrane curvatures. The N-BAR domain is a 57 kDa homodimeric protein comprising a six helix bundle. Here we report the protein folding mechanism of this protein as a representative of this protein superfamily. The concentration dependent thermodynamic stability was studied by urea equilibrium transition curves followed by fluorescence and far-UV CD spectroscopy. Kinetic unfolding and refolding experiments, including rapid double and triple mixing techniques, allowed to unravel the complex folding behavior of N-BAR. The equilibrium unfolding transition curve can be described by a two-state process, while the folding kinetics show four refolding phases, an additional burst reaction and two unfolding phases. All fast refolding phases show a rollover in the chevron plot but only one of these phases depends on the protein concentration reporting the dimerization step. Secondary structure formation occurs during the three fast refolding phases. The slowest phase can be assigned to a proline isomerization. All kinetic experiments were also followed by fluorescence anisotropy detection to verify the assignment of the dimerization step to the respective folding phase. Based on these experiments we propose for N-BAR two parallel folding pathways towards the homodimeric native state depending on the proline conformation in the unfolded state.

  20. Molecular-crowding effects on single-molecule RNA folding/unfolding thermodynamics and kinetics.

    PubMed

    Dupuis, Nicholas F; Holmstrom, Erik D; Nesbitt, David J

    2014-06-10

    The effects of "molecular crowding" on elementary biochemical processes due to high solute concentrations are poorly understood and yet clearly essential to the folding of nucleic acids and proteins into correct, native structures. The present work presents, to our knowledge, first results on the single-molecule kinetics of solute molecular crowding, specifically focusing on GAAA tetraloop-receptor folding to isolate a single RNA tertiary interaction using time-correlated single-photon counting and confocal single-molecule FRET microscopy. The impact of crowding by high-molecular-weight polyethylene glycol on the RNA folding thermodynamics is dramatic, with up to ΔΔG° ∼ -2.5 kcal/mol changes in free energy and thus >60-fold increase in the folding equilibrium constant (Keq) for excluded volume fractions of 15%. Most importantly, time-correlated single-molecule methods permit crowding effects on the kinetics of RNA folding/unfolding to be explored for the first time (to our knowledge), which reveal that this large jump in Keq is dominated by a 35-fold increase in tetraloop-receptor folding rate, with only a modest decrease in the corresponding unfolding rate. This is further explored with temperature-dependent single-molecule RNA folding measurements, which identify that crowding effects are dominated by entropic rather than enthalpic contributions to the overall free energy change. Finally, a simple "hard-sphere" treatment of the solute excluded volume is invoked to model the observed kinetic trends, and which predict ΔΔG° ∼ -5 kcal/mol free-energy stabilization at excluded volume fractions of 30%.

  1. PFD: a database for the investigation of protein folding kinetics and stability.

    PubMed

    Fulton, Kate F; Devlin, Glyn L; Jodun, Rachel A; Silvestri, Linda; Bottomley, Stephen P; Fersht, Alan R; Buckle, Ashley M

    2005-01-01

    We have developed a new database that collects all protein folding data into a single, easily accessible public resource. The Protein Folding Database (PFD) contains annotated structural, methodological, kinetic and thermodynamic data for more than 50 proteins, from 39 families. A user-friendly web interface has been developed that allows powerful searching, browsing and information retrieval, whilst providing links to other protein databases. The database structure allows visualization of folding data in a useful and novel way, with a long-term aim of facilitating data mining and bioinformatics approaches. PFD can be accessed freely at http://pfd.med.monash.edu.au.

  2. A comprehensive database of verified experimental data on protein folding kinetics

    PubMed Central

    Wagaman, Amy S; Coburn, Aaron; Brand-Thomas, Itai; Dash, Barnali; Jaswal, Sheila S

    2014-01-01

    Insights into protein folding rely increasingly on the synergy between experimental and theoretical approaches. Developing successful computational models requires access to experimental data of sufficient quantity and high quality. We compiled folding rate constants for what initially appeared to be 184 proteins from 15 published collections/web databases. To generate the highest confidence in the dataset, we verified the reported lnkf value and exact experimental construct and conditions from the original experimental report(s). The resulting comprehensive database of 126 verified entries, ACPro, will serve as a freely accessible resource (https://www.ats. amherst.edu/protein/) for the protein folding community to enable confident testing of predictive models. In addition, we provide a streamlined submission form for researchers to add new folding kinetics results, requiring specification of all the relevant experimental information according to the standards proposed in 2005 by the protein folding consortium organized by Plaxco. As the number and diversity of proteins whose folding kinetics are studied expands, our curated database will enable efficient and confident incorporation of new experimental results into a standardized collection. This database will support a more robust symbiosis between experiment and theory, leading ultimately to more rapid and accurate insights into protein folding, stability, and dynamics. PMID:25229122

  3. Prediction of folding pathway and kinetics among plant hemoglobins using an average distance map method.

    PubMed

    Nakajima, Shunsuke; Alvarez-Salgado, Emma; Kikuchi, Takeshi; Arredondo-Peter, Raúl

    2005-11-15

    Computational methods, such as the ADM (average distance map) method, have been developed to predict folding of homologous proteins. In this work we used the ADM method to predict the folding pathway and kinetics among selected plant nonsymbiotic (nsHb), symbiotic (Lb), and truncated (tHb) hemoglobins (Hbs). Results predicted that (1) folding of plant Hbs occurs throughout the formation of compact folding modules mostly formed by helices A, B, and C, and E, F, G, and H (folding modules A/C and E/H, respectively), and (2) primitive (moss) nsHbs fold in the C-->N direction, evolved (monocot and dicot) nsHbs fold either in the C-->N or N-->C direction, and Lbs and plant tHbs fold in the C-->N direction. We also predicted relative folding rates of plant Hbs from qualitative analyses of the stability of subdomains and classified plant Hbs into fast and moderate folding. ADM analysis of nsHbs predicted that prehelix A plays a role during folding of the N-terminal domain of Ceratodon nsHb, and that CD-loop plays a role in folding of primitive (Physcomitrella and Ceratodon) but not evolved nsHbs. Modeling of the rice Hb1 A/C and E/H modules showed that module E/H overlaps to the Mycobacterium tuberculosis HbO two-on-two folding. This observation suggests that module E/H is an ancient tertiary structure in plant Hbs.

  4. The X-38 V-201 Fin Fold Actuation Mechanism

    NASA Technical Reports Server (NTRS)

    Lupo, Christian; Robertson, Brandan; Gafka, George

    2004-01-01

    The X-38 Vehicle 201 (V-201) is a space flight prototype lifting body vehicle that was designed to launch to orbit in the Space Shuttle orbiter payload bay. Although the project was cancelled in May 2003, many of the systems were nearly complete. This paper will describe the fin folding actuation mechanism flight subsystems and development units as well as lessons learned in the design, assembly, development testing, and qualification testing. The two vertical tail fins must be stowed (folded inboard) to allow the orbiter payload bay doors to close. The fin folding actuation mechanism is a remotely or extravehicular activity (EVA) actuated single fault tolerant system consisting of seven subsystems capable of repeatedly deploying or stowing the fins.

  5. Microfluidic mixers for the investigation of rapid protein folding kinetics using synchrotron radiation circular dichroism spectroscopy.

    PubMed

    Kane, Avinash S; Hoffmann, Armin; Baumgärtel, Peter; Seckler, Robert; Reichardt, Gerd; Horsley, David A; Schuler, Benjamin; Bakajin, Olgica

    2008-12-15

    We have developed a microfluidic mixer optimized for rapid measurements of protein folding kinetics using synchrotron radiation circular dichroism (SRCD) spectroscopy. The combination of fabrication in fused silica and synchrotron radiation allows measurements at wavelengths below 220 nm, the typical limit of commercial instrumentation. At these wavelengths, the discrimination between the different types of protein secondary structure increases sharply. The device was optimized for rapid mixing at moderate sample consumption by employing a serpentine channel design, resulting in a dead time of less than 200 micros. Here, we discuss the design and fabrication of the mixer and quantify the mixing efficiency using wide-field and confocal epi-fluorescence microscopy. We demonstrate the performance of the device in SRCD measurements of the folding kinetics of cytochrome c, a small, fast-folding protein. Our results show that the combination of SRCD with microfluidic mixing opens new possibilities for investigating rapid conformational changes in biological macromolecules that have previously been inaccessible.

  6. Kinetic and thermodynamic origins of osmolyte-influenced nucleic acid folding.

    PubMed

    Holmstrom, Erik D; Dupuis, Nicholas F; Nesbitt, David J

    2015-03-05

    The influential role of monovalent and divalent metal cations in facilitating conformational transitions in both RNA and DNA has been a target of intense biophysical research efforts. However, organic neutrally charged cosolutes can also significantly alter nucleic acid conformational transitions. For example, highly soluble small molecules such as trimethylamine N-oxide (TMAO) and urea are occasionally utilized by organisms to regulate cellular osmotic pressure. Ensemble studies have revealed that these so-called osmolytes can substantially influence the thermodynamics of nucleic acid conformational transitions. In the present work, we exploit single-molecule FRET (smFRET) techniques to measure, for first time, the kinetic origins of these osmolyte-induced changes to the folding free energy. In particular, we focus on smFRET RNA and DNA constructs designed as model systems for secondary and tertiary structure formation. These findings reveal that TMAO preferentially stabilizes both secondary and tertiary interactions by increasing kfold and decreasing kunfold, whereas urea destabilizes both conformational transitions, resulting in the exact opposite shift in kinetic rate constants (i.e., decreasing kfold and increasing kunfold). Complementary temperature-dependent smFRET experiments highlight a thermodynamic distinction between the two different mechanisms responsible for TMAO-facilitated conformational transitions, while only a single mechanism is seen for the destabilizing osmolyte urea. Finally, these results are interpreted in the context of preferential interactions between osmolytes, and the solvent accessible surface area (SASA) associated with the (i) nucleobase, (ii) sugar, and (iii) phosphate groups of nucleic acids in order to map out structural changes that occur during the conformational transitions.

  7. Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding

    PubMed Central

    Wang, Jin; Oliveira, Ronaldo J.; Chu, Xiakun; Whitford, Paul C.; Chahine, Jorge; Han, Wei; Wang, Erkang; Onuchic, José N.; Leite, Vitor B.P.

    2012-01-01

    The energy landscape approach has played a fundamental role in advancing our understanding of protein folding. Here, we quantify protein folding energy landscapes by exploring the underlying density of states. We identify three quantities essential for characterizing landscape topography: the stabilizing energy gap between the native and nonnative ensembles δE, the energetic roughness ΔE, and the scale of landscape measured by the entropy S. We show that the dimensionless ratio between the gap, roughness, and entropy of the system accurately predicts the thermodynamics, as well as the kinetics of folding. Large Λ implies that the energy gap (or landscape slope towards the native state) is dominant, leading to more funneled landscapes. We investigate the role of topological and energetic roughness for proteins of different sizes and for proteins of the same size, but with different structural topologies. The landscape topography ratio Λ is shown to be monotonically correlated with the thermodynamic stability against trapping, as characterized by the ratio of folding temperature versus trapping temperature. Furthermore, Λ also monotonically correlates with the folding kinetic rates. These results provide the quantitative bridge between the landscape topography and experimental folding measurements. PMID:23019359

  8. The energy landscape, folding pathways and the kinetics of a knotted protein.

    PubMed

    Prentiss, Michael C; Wales, David J; Wolynes, Peter G

    2010-07-01

    The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling approach, and the resulting potential energy surface is visualized by constructing disconnectivity graphs. Owing to topological constraints, the low-lying portion of the landscape consists of three distinct regions, corresponding to the native knotted state and to configurations where either the N or C terminus is not yet folded into the knot. The fastest folding pathways from denatured states exhibit early formation of the N terminus portion of the knot and a rate-determining step where the C terminus is incorporated. The low-lying minima with the N terminus knotted and the C terminus free therefore constitute an off-pathway intermediate for this model. The insertion of both the N and C termini into the knot occurs late in the folding process, creating large energy barriers that are the rate limiting steps in the folding process. When compared to other protein folding proteins of a similar length, this system folds over six orders of magnitude more slowly.

  9. Common folds and transport mechanisms of secondary active transporters.

    PubMed

    Shi, Yigong

    2013-01-01

    Secondary active transporters exploit the electrochemical potential of solutes to shuttle specific substrate molecules across biological membranes, usually against their concentration gradient. Transporters of different functional families with little sequence similarity have repeatedly been found to exhibit similar folds, exemplified by the MFS, LeuT, and NhaA folds. Observations of multiple conformational states of the same transporter, represented by the LeuT superfamily members Mhp1, AdiC, vSGLT, and LeuT, led to proposals that structural changes are associated with substrate binding and transport. Despite recent biochemical and structural advances, our understanding of substrate recognition and energy coupling is rather preliminary. This review focuses on the common folds and shared transport mechanisms of secondary active transporters. Available structural information generally supports the alternating access model for substrate transport, with variations and extensions made by emerging structural, biochemical, and computational evidence.

  10. Highly Anomalous Energetics of Protein Cold Denaturation Linked to Folding-Unfolding Kinetics

    PubMed Central

    Romero-Romero, M. Luisa; Inglés-Prieto, Alvaro; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M.

    2011-01-01

    Despite several careful experimental analyses, it is not yet clear whether protein cold-denaturation is just a “mirror image” of heat denaturation or whether it shows unique structural and energetic features. Here we report that, for a well-characterized small protein, heat denaturation and cold denaturation show dramatically different experimental energetic patterns. Specifically, while heat denaturation is endothermic, the cold transition (studied in the folding direction) occurs with negligible heat effect, in a manner seemingly akin to a gradual, second-order-like transition. We show that this highly anomalous energetics is actually an apparent effect associated to a large folding/unfolding free energy barrier and that it ultimately reflects kinetic stability, a naturally-selected trait in many protein systems. Kinetics thus emerges as an important factor linked to differential features of cold denaturation. We speculate that kinetic stabilization against cold denaturation may play a role in cold adaptation of psychrophilic organisms. Furthermore, we suggest that folding-unfolding kinetics should be taken into account when analyzing in vitro cold-denaturation experiments, in particular those carried out in the absence of destabilizing conditions. PMID:21829584

  11. Diffusion-collision of foldons elucidates the kinetic effects of point mutations and suggests control strategies of the folding process of helical proteins.

    PubMed

    Capriotti, Emidio; Compiani, Mario

    2006-07-01

    In this article we use mutation studies as a benchmark for a minimal model of the folding process of helical proteins. The model ascribes a pivotal role to the collisional dynamics of a few crucial residues (foldons) and predicts the folding rates by exploiting information drawn from the protein sequence. We show that our model rationalizes the effects of point mutations on the kinetics of folding. The folding times of two proteins and their mutants are predicted. Stability and location of foldons have a critical role as the determinants of protein folding. This allows us to elucidate two main mechanisms for the kinetic effects of mutations. First, it turns out that the mutations eliciting the most notable effects alter protein stability through stabilization or destabilization of the foldons. Secondly, the folding rate is affected via a modification of the foldon topology by those mutations that lead to the birth or death of foldons. The few mispredicted folding rates of some mutants hint at the limits of the current version of the folding model proposed in the present article. The performance of our folding model declines in case the mutated residues are subject to strong long-range forces. That foldons are the critical targets of mutation studies has notable implications for design strategies and is of particular interest to address the issue of the kinetic regulation of single proteins in the general context of the overall dynamics of the interactome.

  12. Statistical mechanics of simple models of protein folding and design.

    PubMed Central

    Pande, V S; Grosberg, A Y; Tanaka, T

    1997-01-01

    It is now believed that the primary equilibrium aspects of simple models of protein folding are understood theoretically. However, current theories often resort to rather heavy mathematics to overcome some technical difficulties inherent in the problem or start from a phenomenological model. To this end, we take a new approach in this pedagogical review of the statistical mechanics of protein folding. The benefit of our approach is a drastic mathematical simplification of the theory, without resort to any new approximations or phenomenological prescriptions. Indeed, the results we obtain agree precisely with previous calculations. Because of this simplification, we are able to present here a thorough and self contained treatment of the problem. Topics discussed include the statistical mechanics of the random energy model (REM), tests of the validity of REM as a model for heteropolymer freezing, freezing transition of random sequences, phase diagram of designed ("minimally frustrated") sequences, and the degree to which errors in the interactions employed in simulations of either folding and design can still lead to correct folding behavior. Images FIGURE 2 FIGURE 3 FIGURE 4 FIGURE 6 PMID:9414231

  13. Kinetically coupled folding of a single HIV-1 glycoprotein 41 complex in viral membrane fusion and inhibition.

    PubMed

    Jiao, Junyi; Rebane, Aleksander A; Ma, Lu; Gao, Ying; Zhang, Yongli

    2015-06-02

    HIV-1 glycoprotein 41 (gp41) mediates viral entry into host cells by coupling its folding energy to membrane fusion. Gp41 folding is blocked by fusion inhibitors, including the commercial drug T20, to treat HIV/AIDS. However, gp41 folding intermediates, energy, and kinetics are poorly understood. Here, we identified the folding intermediates of a single gp41 trimer-of-hairpins and measured their associated energy and kinetics using high-resolution optical tweezers. We found that folding of gp41 hairpins was energetically independent but kinetically coupled: Each hairpin contributed a folding energy of ∼-23 kBT, but folding of one hairpin successively accelerated the folding rate of the next one by ∼20-fold. Membrane-mimicking micelles slowed down gp41 folding and reduced the stability of the six-helix bundle. However, the stability was restored by cooperative folding of the membrane-proximal external region. Surprisingly, T20 strongly inhibited gp41 folding by actively displacing the C-terminal hairpin strand in a force-dependent manner. The inhibition was abolished by a T20-resistant gp41 mutation. The energetics and kinetics of gp41 folding established by us provides a basis to understand viral membrane fusion, infection, and therapeutic intervention.

  14. TOPICAL REVIEW: The nucleation mechanism of protein folding: a survey of computer simulation studies

    NASA Astrophysics Data System (ADS)

    Faísca, Patrícia F. N.

    2009-09-01

    The nucleation mechanism of protein folding, originally proposed by Baldwin in the early 1970s, was firstly observed by Shakhnovich and co-workers two decades later in the context of Monte Carlo simulations of a simple lattice model. At about the same time the extensive use of phi-value analysis provided the first experimental evidence that the folding of Chymotrypsin-inhibitor 2, a small single-domain protein, which folds with two-state kinetics, is also driven by a nucleation mechanism. Since then, the nucleation mechanism is generally considered the most common form of folding mechanism amongst two-state proteins. However, recent experimental data has put forward the idea that this may not necessarily be so, since the accuracy of the experimentally determined phi values, which are used to identify the critical (i.e. nucleating) residues, is typically poor. Here, we provide a survey of in silico results on the nucleation mechanism, ranging from simple lattice Monte Carlo to more sophisticated off-lattice molecular dynamics simulations, and discuss them in light of experimental data.

  15. Demonstration of a folding after binding mechanism in the recognition between the measles virus NTAIL and X domains.

    PubMed

    Dosnon, Marion; Bonetti, Daniela; Morrone, Angela; Erales, Jenny; di Silvio, Eva; Longhi, Sonia; Gianni, Stefano

    2015-03-20

    In the past decade, a wealth of experimental data has demonstrated that a large fraction of proteins, while functional, are intrinsically disordered at physiological conditions. Many intrinsically disordered proteins (IDPs) undergo a disorder-to-order transition upon binding to their biological targets, a phenomenon known as induced folding. Induced folding may occur through two extreme mechanisms, namely conformational selection and folding after binding. Although the pre-existence of ordered structures in IDPs is a prerequisite for conformational selection, it does not necessarily commit to this latter mechanism, and kinetic studies are needed to discriminate between the two possible scenarios. So far, relatively few studies have addressed this issue from an experimental perspective. Here, we analyze the interaction kinetics between the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (NTAIL) and the X domain (XD) of the viral phosphoprotein. Data reveal that NTAIL recognizes XD by first forming a weak encounter complex in a disordered conformation, which is subsequently locked-in by a folding step; i.e., binding precedes folding. The implications of our kinetic results, in the context of previously reported equilibrium data, are discussed. These results contribute to enhancing our understanding of the molecular mechanisms by which IDPs recognize their partners and represent a paradigmatic example of the need of kinetic methods to discriminate between reaction mechanisms.

  16. The precursor of beta-lactamase: purification, properties and folding kinetics.

    PubMed

    Laminet, A A; Plückthun, A

    1989-05-01

    The precursor of Escherichia coli RTEM beta-lactamase was purified to homogeneity on a milligram scale by a procedure independent of the binding properties of the protein and refolded to an active, reduced form. For comparing the folding kinetics, the wild-type enzyme was reduced and a mutant was constructed, in which the two cysteines that form a very stable disulfide bond in the RTEM enzyme were both changed into alanines. The rate of folding was determined by directly measuring the increase in enzymatic activity. The reduced precursor folds at least 15 times more slowly than either the reduced mature enzyme or the mature Cys----Ala double mutant under identical conditions. The wild-type enzyme, the Cys----Ala double mutant and the precursor protein all had similar KM values, demonstrating a very similar native state. The slow folding of the precursor compared with the mature form may be an essential and general feature to secure a transport competent conformation necessary for the translocation through a membrane in protein export. This folding assay of a precursor by directly following its enzymatic activity may facilitate the characterization of putative folding modulators in bacterial membrane transport.

  17. Thermal stability and folding kinetics analysis of intrinsically disordered protein, securin

    NASA Astrophysics Data System (ADS)

    Chang, Chia-Ching; Chu, Hsueh-Liang; Ho, Li-Ping

    2014-03-01

    Lacking a stable tertiary structure, intrinsically disordered proteins (IDPs) possess particular functions in cell regulation, signaling, and controlling pathways. The study of their unique structure features, thermal stabilities, and folding kinetics is intriguing. In this study, an identified IDP, securin, was used as a model protein. By using a quasi-static five-step (on-path) folding process, the function of securin was restored and analyzed by isothermal titration calorimetry. Fluorescence spectroscopy and particle size analysis indicated that securin possessed a compact hydrophobic core and particle size. The glass transition of securin was characterized using differential scanning microcalorimetry. Furthermore, the folding/unfolding rates (kobs) of securin were undetectable, implying that the folding/unfolding rate is very fast and that the conformation of securin is sensitive to solvent environment change. Therefore, securin may fold properly under specific physiological conditions. In summary, the thermal glass transition behavior and undetectable kobs of folding/unfolding reactions may be two of the indices of IDP. This study was supported in part by grants NSC 97-2112-M-009-009-YM3 and NSC 100-2112-M-009-004-MY3, Taiwan, R.O.C.

  18. Mechanisms and Kinetics of Catalytic Reactions

    DTIC Science & Technology

    1990-08-01

    CHEMICAL RESEARCH, r- DEVELOPMENT 5 N ENGINEERING CRDE-R-084 "" CENTER CENER(GC-TR-1728-008) ’ 04 N MECHANISMS AND KINETICS OF CATALYTIC REACTIONS Q...and Kinetics of Catalytic Reactions &AUTHOR(S) Garlick, Stephanie M. 7. PERFORMING ORGANIZATION NAME(S) AND ADORESS(ES) . PERFORMING ORGANIZATION...Tables........................87 vi MECHANISMS AND KINETICS OF CATALYTIC REACTIONS 1. INTRODUCTION The hydrolysis of phosphate esters in microemulsion

  19. Navigating ligand protein binding free energy landscapes: universality and diversity of protein folding and molecular recognition mechanisms

    NASA Astrophysics Data System (ADS)

    Verkhivker, Gennady M.; Rejto, Paul A.; Bouzida, Djamal; Arthurs, Sandra; Colson, Anthony B.; Freer, Stephan T.; Gehlhaar, Daniel K.; Larson, Veda; Luty, Brock A.; Marrone, Tami; Rose, Peter W.

    2001-03-01

    Thermodynamic and kinetic aspects of ligand-protein binding are studied for the methotrexate-dihydrofolate reductase system from the binding free energy profile constructed as a function of the order parameter. Thermodynamic stability of the native complex and a cooperative transition to the unique native structure suggest the nucleation kinetic mechanism at the equilibrium transition temperature. Structural properties of the transition state ensemble and the ensemble of nucleation conformations are determined by kinetic simulations of the transmission coefficient and ligand-protein association pathways. Structural analysis of the transition states and the nucleation conformations reconciles different views on the nucleation mechanism in protein folding.

  20. The shape and mechanics of curved-fold origami structures

    NASA Astrophysics Data System (ADS)

    Dias, Marcelo A.; Santangelo, Christian D.

    2012-12-01

    We develop recursion equations to describe the three-dimensional shape of a sheet upon which a series of concentric curved folds have been inscribed. In the case of no stretching outside the fold, the three-dimensional shape of a single fold prescribes the shape of the entire origami structure. To better explore these structures, we derive continuum equations, valid in the limit of vanishing spacing between folds, to describe the smooth surface intersecting all the mountain folds. We find that this surface has negative Gaussian curvature with magnitude equal to the square of the fold's torsion. A series of open folds with constant fold angle generate a helicoid.

  1. Kinetic barriers to the folding of horse cytochrome C in the reduced state.

    PubMed

    Bhuyan, Abani K; Kumar, Rajesh

    2002-10-22

    To determine the kinetic barrier in the folding of horse cytochrome c, a CO-liganded derivative of cytochrome c, called carbonmonoxycytochrome c, has been prepared by exploiting the thermodynamic reversibility of ferrocytochrome c unfolding induced by guanidinium hydrochloride (GdnHCl), pH 7. The CO binding properties of unfolded ferrocytochrome c, studied by 13C NMR and optical spectroscopy, are remarkably similar to those of native myoglobin and isolated chains of human hemoglobin. Equilibrium unfolding transitions of ferrocytochrome c in the presence and the absence of CO observed by both excitation energy transfer from the lone tryptophan to the ferrous heme and far-UV circular dichroism (CD) indicate no accumulation of structural intermediates to a detectable level. Values of thermodynamic parameters obtained by two-state analysis of fluorescence transitions are DeltaG(H2O) = 11.65(+/-1.13) kcal x mol(-1) and C(m) = 3.9(+/-0.1) M GdnHCl in the presence of CO, and DeltaG(H2O)=19.3(+/-0.5) kcal x mol(-1) and C(m) = 5.1(+/-0.1) M GdnHCl in the absence of CO, indicating destabilization of ferrocytochrome c by approximately 7.65 kcal x mol(-1) due to CO binding. The native states of ferrocytochrome c and carbonmonoxycytochrome c are nearly identical in terms of structure and conformation except for the Fe2+-M80 --> Fe2+-CO replacement. Folding and unfolding kinetics as a function of GdnHCl, studied by stopped-flow fluorescence, are significantly different for the two proteins. Both refold fast, but carbonmonoxycytochrome c refolds 2-fold faster (tau = 1092 micros at 10 degrees C) than ferrocytochrome c. Linear extrapolation of the folding rates to the ordinate of the chevron plot projects this value of tau to 407 micros. The unfolding rate of the former in water, estimated by extrapolation, is faster by more than 10 orders of magnitude. Significant differences are also observed in rate-denaturant gradients in the chevron. Formation and disruption of the Fe2+-M80

  2. Role of mechanical factors in cortical folding development

    NASA Astrophysics Data System (ADS)

    Razavi, Mir Jalil; Zhang, Tuo; Li, Xiao; Liu, Tianming; Wang, Xianqiao

    2015-09-01

    Deciphering mysteries of the structure-function relationship in cortical folding has emerged as the cynosure of recent research on brain. Understanding the mechanism of convolution patterns can provide useful insight into the normal and pathological brain function. However, despite decades of speculation and endeavors the underlying mechanism of the brain folding process remains poorly understood. This paper focuses on the three-dimensional morphological patterns of a developing brain under different tissue specification assumptions via theoretical analyses, computational modeling, and experiment verifications. The living human brain is modeled with a soft structure having outer cortex and inner core to investigate the brain development. Analytical interpretations of differential growth of the brain model provide preliminary insight into the critical growth ratio for instability and crease formation of the developing brain followed by computational modeling as a way to offer clues for brain's postbuckling morphology. Especially, tissue geometry, growth ratio, and material properties of the cortex are explored as the most determinant parameters to control the morphogenesis of a growing brain model. As indicated in results, compressive residual stresses caused by the sufficient growth trigger instability and the brain forms highly convoluted patterns wherein its gyrification degree is specified with the cortex thickness. Morphological patterns of the developing brain predicted from the computational modeling are consistent with our neuroimaging observations, thereby clarifying, in part, the reason of some classical malformation in a developing brain.

  3. Electrostatic mechanism of nucleosomal array folding revealed by computer simulation

    NASA Astrophysics Data System (ADS)

    Sun, Jian; Zhang, Qing; Schlick, Tamar

    2005-06-01

    Although numerous experiments indicate that the chromatin fiber displays salt-dependent conformations, the associated molecular mechanism remains unclear. Here, we apply an irregular Discrete Surface Charge Optimization (DiSCO) model of the nucleosome with all histone tails incorporated to describe by Monte Carlo simulations salt-dependent rearrangements of a nucleosomal array with 12 nucleosomes. The ensemble of nucleosomal array conformations display salt-dependent condensation in good agreement with hydrodynamic measurements and suggest that the array adopts highly irregular 3D zig-zag conformations at high (physiological) salt concentrations and transitions into the extended "beads-on-a-string" conformation at low salt. Energy analyses indicate that the repulsion among linker DNA leads to this extended form, whereas internucleosome attraction drives the folding at high salt. The balance between these two contributions determines the salt-dependent condensation. Importantly, the internucleosome and linker DNA-nucleosome attractions require histone tails; we find that the H3 tails, in particular, are crucial for stabilizing the moderately folded fiber at physiological monovalent salt. chromatin modeling | irregular 3D zig-zag | Discrete Surface Charge Optimization model

  4. Electrostatic mechanism of nucleosomal array folding revealed by computer simulation

    PubMed Central

    Sun, Jian; Zhang, Qing; Schlick, Tamar

    2005-01-01

    Although numerous experiments indicate that the chromatin fiber displays salt-dependent conformations, the associated molecular mechanism remains unclear. Here, we apply an irregular Discrete Surface Charge Optimization (DiSCO) model of the nucleosome with all histone tails incorporated to describe by Monte Carlo simulations salt-dependent rearrangements of a nucleosomal array with 12 nucleosomes. The ensemble of nucleosomal array conformations display salt-dependent condensation in good agreement with hydrodynamic measurements and suggest that the array adopts highly irregular 3D zig-zag conformations at high (physiological) salt concentrations and transitions into the extended “beads-on-a-string” conformation at low salt. Energy analyses indicate that the repulsion among linker DNA leads to this extended form, whereas internucleosome attraction drives the folding at high salt. The balance between these two contributions determines the salt-dependent condensation. Importantly, the internucleosome and linker DNA–nucleosome attractions require histone tails; we find that the H3 tails, in particular, are crucial for stabilizing the moderately folded fiber at physiological monovalent salt. PMID:15919827

  5. Kinetics and Mechanism--A Games Approach.

    ERIC Educational Resources Information Center

    Harsch, Gunther

    1984-01-01

    Proposes an approach to chemical kinetics and mechanism using statistical games, illustrating its use in monomolecular, catalytic, autocatalytic, consecutive, and equilibrium reactions. Major features of the games are also outlined and discussed. (JN)

  6. Spin glasses and the statistical mechanics of protein folding.

    PubMed Central

    Bryngelson, J D; Wolynes, P G

    1987-01-01

    The theory of spin glasses was used to study a simple model of protein folding. The phase diagram of the model was calculated, and the results of dynamics calculations are briefly reported. The relation of these results to folding experiments, the relation of these hypotheses to previous protein folding theories, and the implication of these hypotheses for protein folding prediction schemes are discussed. PMID:3478708

  7. Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations.

    PubMed

    Zheng, Weihua; Gallicchio, Emilio; Deng, Nanjie; Andrec, Michael; Levy, Ronald M

    2011-02-17

    We present a new approach to study a multitude of folding pathways and different folding mechanisms for the 20-residue mini-protein Trp-Cage using the combined power of replica exchange molecular dynamics (REMD) simulations for conformational sampling, transition path theory (TPT) for constructing folding pathways, and stochastic simulations for sampling the pathways in a high dimensional structure space. REMD simulations of Trp-Cage with 16 replicas at temperatures between 270 and 566 K are carried out with an all-atom force field (OPLSAA) and an implicit solvent model (AGBNP). The conformations sampled from all temperatures are collected. They form a discretized state space that can be used to model the folding process. The equilibrium population for each state at a target temperature can be calculated using the weighted-histogram-analysis method (WHAM). By connecting states with similar structures and creating edges satisfying detailed balance conditions, we construct a kinetic network that preserves the equilibrium population distribution of the state space. After defining the folded and unfolded macrostates, committor probabilities (P(fold)) are calculated by solving a set of linear equations for each node in the network and pathways are extracted together with their fluxes using the TPT algorithm. By clustering the pathways into folding "tubes", a more physically meaningful picture of the diversity of folding routes emerges. Stochastic simulations are carried out on the network, and a procedure is developed to project sampled trajectories onto the folding tubes. The fluxes through the folding tubes calculated from the stochastic trajectories are in good agreement with the corresponding values obtained from the TPT analysis. The temperature dependence of the ensemble of Trp-Cage folding pathways is investigated. Above the folding temperature, a large number of diverse folding pathways with comparable fluxes flood the energy landscape. At low temperature

  8. Unfolding single RNA molecules by mechanical force: A stochastic kinetic method

    NASA Astrophysics Data System (ADS)

    Liu, Fei; Ou-Yang, Zhong-Can

    2004-10-01

    Using simple polymer elastic theory and known RNA free energies, we study the single RNA folding and unfolding on the secondary structure level under mechanical constant force by stochastic kinetic simulation. As a primary application, this method is used to simulate the experiment performed by Liphardt [Science 292, 733 (2001)]. The extension-force curves in equilibrium and kinetic reaction rate constants for folding and unfolding are calculated. Our results show that the agreement between simulation and experimental measurements is satisfactory.

  9. Kinetics of folding and association of differently glycosylated variants of invertase from Saccharomyces cerevisiae.

    PubMed Central

    Kern, G.; Kern, D.; Jaenicke, R.; Seckler, R.

    1993-01-01

    A core-glycosylated form of the dimeric enzyme invertase has been isolated from secretion mutants of Saccharomyces cerevisiae blocked in transport to the Golgi apparatus. This glycosylation variant corresponds to the form that folds and associates during biosynthesis of the protein in vivo. In the present work, its largely homogeneous subunit size and well-defined quaternary structure were utilized to characterize the folding and association pathway of this highly glycosylated protein in comparison with the nonglycosylated cytoplasmic and the high-mannose-glycosylated periplasmic forms of the same enzyme encoded by the suc2 gene. Renaturation of core-glycosylated invertase upon dilution from guanidinium-chloride solutions follows a unibimolecular reaction scheme with consecutive first-order subunit folding and second-order association reactions. The rate constant of the rate-limiting step of subunit folding, as detected by fluorescence increase, is k1 = 1.6 +/- 0.4 x 10(-3) s-1 at 20 degrees C; it is characterized by an activation enthalpy of delta H++ = 65 kJ/mol. The reaction is not catalyzed by peptidyl-prolyl cis-trans isomerase of the cyclophilin type. Reactivation of the enzyme depends on protein concentration and coincides with subunit association, as monitored by size-exclusion high-pressure liquid chromatography. The association rate constant, estimated by numerical simulation of reactivation kinetics, increases from 5 x 10(3) M-1 s-1 to 7 x 10(4) M-1 s-1 between 5 and 30 degrees C.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8268797

  10. KINETICS AND MECHANISMS OF SOIL BIOGEOCHEMICAL PROCESSES

    EPA Science Inventory

    The application of kinetic studies to soil chemistry is useful to determine reaction mechanisms and fate of nutrients and environmental contaminants. How deeply one wishes to query the mechanism depends on the detail sought. Reactions that involve chemical species in more than on...

  11. Comparative analysis of the folding dynamics and kinetics of an engineered knotted protein and its variants derived from HP0242 of Helicobacter pylori

    NASA Astrophysics Data System (ADS)

    Wang, Liang-Wei; Liu, Yu-Nan; Lyu, Ping-Chiang; Jackson, Sophie E.; Hsu, Shang-Te Danny

    2015-09-01

    Understanding the mechanism by which a polypeptide chain thread itself spontaneously to attain a knotted conformation has been a major challenge in the field of protein folding. HP0242 is a homodimeric protein from Helicobacter pylori with intertwined helices to form a unique pseudo-knotted folding topology. A tandem HP0242 repeat has been constructed to become the first engineered trefoil-knotted protein. Its small size renders it a model system for computational analyses to examine its folding and knotting pathways. Here we report a multi-parametric study on the folding stability and kinetics of a library of HP0242 variants, including the trefoil-knotted tandem HP0242 repeat, using far-UV circular dichroism and fluorescence spectroscopy. Equilibrium chemical denaturation of HP0242 variants shows the presence of highly populated dimeric and structurally heterogeneous folding intermediates. Such equilibrium folding intermediates retain significant amount of helical structures except those at the N- and C-terminal regions in the native structure. Stopped-flow fluorescence measurements of HP0242 variants show that spontaneous refolding into knotted structures can be achieved within seconds, which is several orders of magnitude faster than previously observed for other knotted proteins. Nevertheless, the complex chevron plots indicate that HP0242 variants are prone to misfold into kinetic traps, leading to severely rolled-over refolding arms. The experimental observations are in general agreement with the previously reported molecular dynamics simulations. Based on our results, kinetic folding pathways are proposed to qualitatively describe the complex folding processes of HP0242 variants.

  12. Mechanism of Coupled Folding and Binding in the siRNA-PAZ Complex.

    PubMed

    Chen, Hai-Feng

    2008-08-01

    The PAZ domain plays a key role in gene silencing pathway. The PAZ domain binds with siRNAs to form the multimeric RNA-induced silencing complex (RISC). RISC identifies mRNAs homologous to the siRNAs and promotes their degradation. It was found that binding with siRNA significantly enhances apo-PAZ folding. However, the mechanism by which folding is coupled to binding is poorly understood. Thus, the coupling relationship between binding and folding is very important for understanding the function of gene silencing. We have performed molecular dynamics (MD) of both bound and apo-PAZ to study the coupling mechanism between binding and folding in the siRNA-PAZ complex. Room-temperature MD simulations suggest that both PAZ and siRNA become more rigid and stable upon siRNA binding. Kinetic analysis of high-temperature MD simulations shows that both bound and apo-PAZ unfold via a two-state process. The unfolding pathways are different between bound and apo-PAZ: the order of helix III and helices I & II unfolding is switched. Furthermore, transition probability was used to determine the transition state ensemble for both bound and apo-PAZ. It was found that the transition state of bound PAZ is more compact than that of apo-PAZ. The predicted Φ-values suggest that the Φ-values of helix III and sheets of β3-β7 for bound PAZ are more native-like than those of apo-PAZ upon the binding of siRNA. The results can help us to understand the mechanism of gene silencing.

  13. Improvements in Mixing Time and Mixing Uniformity in Devices Designed for Studies of Protein Folding Kinetics

    SciTech Connect

    Yao, Shuhuai; Bakajin, Olgica

    2007-08-01

    Using a microfluidic laminar flow mixer designed for studies of protein folding kinetics, we demonstrate a mixing time of 1 +/- 1 micros with sample consumption on the order of femtomoles. We recognize two limitations of previously proposed designs: (1) size and shape of the mixing region, which limits mixing uniformity and (2) the formation of Dean vortices at high flow rates, which limits the mixing time. We address these limitations by using a narrow shape-optimized nozzle and by reducing the bend of the side channel streamlines. The final design, which combines both of these features, achieves the best performance. We quantified the mixing performance of the different designs by numerical simulation of coupled Navier-Stokes and convection-diffusion equations and experiments using fluorescence resonance energy-transfer (FRET)-labeled DNA.

  14. The E. coli thioredoxin folding mechanism: the key role of the C-terminal helix.

    PubMed

    Vazquez, Diego S; Sánchez, Ignacio E; Garrote, Ana; Sica, Mauricio P; Santos, Javier

    2015-02-01

    In this work, the unfolding mechanism of oxidized Escherichia coli thioredoxin (EcTRX) was investigated experimentally and computationally. We characterized seven point mutants distributed along the C-terminal α-helix (CTH) and the preceding loop. The mutations destabilized the protein against global unfolding while leaving the native structure unchanged. Global analysis of the unfolding kinetics of all variants revealed a linear unfolding route with a high-energy on-pathway intermediate state flanked by two transition state ensembles TSE1 and TSE2. The experiments show that CTH is mainly unfolded in TSE1 and the intermediate and becomes structured in TSE2. Structure-based molecular dynamics are in agreement with these experiments and provide protein-wide structural information on transient states. In our model, EcTRX folding starts with structure formation in the β-sheet, while the protein helices coalesce later. As a whole, our results indicate that the CTH is a critical module in the folding process, restraining a heterogeneous intermediate ensemble into a biologically active native state and providing the native protein with thermodynamic and kinetic stability.

  15. Entanglement in correlated random spin chains, RNA folding and kinetic roughening

    NASA Astrophysics Data System (ADS)

    Rodríguez-Laguna, Javier; Santalla, Silvia N.; Ramírez, Giovanni; Sierra, Germán

    2016-07-01

    Average block entanglement in the 1D XX-model with uncorrelated random couplings is known to grow as the logarithm of the block size, in similarity to conformal systems. In this work we study random spin chains whose couplings present long range correlations, generated as gaussian fields with a power-law spectral function. Ground states are always planar valence bond states, and their statistical ensembles are characterized in terms of their block entropy and their bond-length distribution, which follow power-laws. We conjecture the existence of a critical value for the spectral exponent, below which the system behavior is identical to the case of uncorrelated couplings. Above that critical value, the entanglement entropy violates the area law and grows as a power law of the block size, with an exponent which increases from zero to one. Interestingly, we show that XXZ models with positive anisotropy present the opposite behavior, and strong correlations in the couplings lead to lower entropies. Similar planar bond structures are also found in statistical models of RNA folding and kinetic roughening, and we trace an analogy between them and quantum valence bond states. Using an inverse renormalization procedure we determine the optimal spin-chain couplings which give rise to a given planar bond structure, and study the statistical properties of the couplings whose bond structures mimic those found in RNA folding.

  16. Deciphering the mechanisms of binding induced folding at nearly atomic resolution: The Φ value analysis applied to IDPs

    PubMed Central

    Gianni, Stefano; Dogan, Jakob; Jemth, Per

    2014-01-01

    The Φ value analysis is a method to analyze the structure of metastable states in reaction pathways. Such a methodology is based on the quantitative analysis of the effect of point mutations on the kinetics and thermodynamics of the probed reaction. The Φ value analysis is routinely used in protein folding studies and is potentially an extremely powerful tool to analyze the mechanism of binding induced folding of intrinsically disordered proteins. In this review we recapitulate the key equations and experimental advices to perform the Φ value analysis in the perspective of the possible caveats arising in intrinsically disordered systems. Finally, we briefly discuss some few examples already available in the literature.

  17. Absence of kinetic thermal stabilization in a hyperthermophile rubredoxin indicated by 40 microsecond folding in the presence of irreversible denaturation.

    PubMed

    LeMaster, David M; Tang, Jianzhong; Hernández, Griselda

    2004-10-01

    The striking kinetic stability of many proteins derived from hyperthermophilic organisms has led to the proposal that such stability may result from a heightened activation barrier for unfolding independent of a corresponding increase in the thermodynamic stability. This in turn implies a corresponding retardation of the folding reaction. A commonly cited model for kinetic thermal stabilization is the rubredoxin from Pyrococcus furiosus (Pf), which exhibits an irreversible denaturation lifetime at 100 degrees C of nearly a week. Utilizing protein resonances shifted well outside of the random coil chemical shift envelope, nuclear magnetic resonance (NMR) chemical exchange measurements on Pf rubredoxin as well as on the mesophile Clostridium pasteurianum (Cp) rubredoxin demonstrate reversible thermal transition temperatures of 144 degrees C (137 degrees C for the N-terminal modified A2K variant) and 104 degrees C, respectively, with similar (un)folding rates of approximately 25,000 s(-1), only modestly slower than the diffusion controlled rate. The absence of a substantial activation barrier to rubredoxin folding as well as the similar folding kinetics of the mesophile protein indicate that kinetic stabilization has not been utilized by the hyperthermophile rubredoxin in achieving its extreme thermal stability. The two-state folding kinetics observed for Pf rubredoxin contradict a previous assertion of multiphasic folding based on hydrogen exchange data extrapolated to an estimated midpoint of transition temperature (T(m)) of nearly 200 degrees C. This discrepancy is resolved by the observation that the base-catalyzed hydrogen exchange of the model dipeptide (N-acetyl-L-cysteine-N-methylamide)4-Cd2+ is 23-fold slower than that of the free cysteine model dipeptide used to normalize the Pf rubredoxin hydrogen exchange data.

  18. Integration of Inhibition Kinetics and Molecular Dynamics Simulations: A Urea-Mediated Folding Study on Acetaldehyde Dehydrogenase 1.

    PubMed

    Xu, Yingying; Lee, Jinhyuk; Lü, Zhi-Rong; Mu, Hang; Zhang, Qian; Park, Yong-Doo

    2016-07-01

    Understanding the mechanism of acetaldehyde dehydrogenase 1 (ALDH1) folding is important because this enzyme is directly involved in several types of cancers and other diseases. We investigated the urea-mediated unfolding of ALDH1 by integrating kinetic inhibition studies with computational molecular dynamics (MD) simulations. Conformational changes in the enzyme structure were also analyzed using intrinsic and 1-anilinonaphthalene-8-sulfonate (ANS)-binding fluorescence measurements. Kinetic studies revealed that the direct binding of urea to ALDH1 induces inactivation of ALDH1 in a manner of mixed-type inhibition. Tertiary structural changes associated with regional hydrophobic exposure of the active site were observed. The urea binding regions on ALDH1 were predicted by docking simulations and were partly shared with active site residues of ALDH1 and with interface residues of the oligomerization domain for tetramer formation. The docking results suggest that urea prevents formation of the ALDH1 normal shape for the tetramer state as well as entrance of the substrate into the active site. Our study provides insight into the structural changes that accompany urea-mediated unfolding of ALDH1 and the catalytic role associated with conformational changes.

  19. Reduced methanol kinetic mechanisms for combustion applications

    SciTech Connect

    Yalamanchili, S.; Sirignano, W.A.; Seiser, R.; Seshadri, K.

    2005-08-01

    Reduced chemical kinetic mechanisms for methanol combustion were investigated by evaluating ignition delay magnitudes and combustion in a continuously stirred reactor. Unsteady computations were made to study the characteristics of the kinetic mechanisms proposed in the literature and to compare the dependence of various parameters on methanol combustion. All computations were done under isobaric conditions, and, to capture the influence of all the reactions involved in the mechanism, a very small time step was used. Finite-difference methods were used to solve the coupled differential equations. The five-step mechanism developed by C.M. Mueller and N. Peters [in: N. Peters, B. Rogg (Eds.), Reduced Kinetic Mechanisms for Applications in Combustion Systems, Springer-Verlag, New York, 1993, pp. 143-155] for premixed flames and both the five-step mechanism and the four-step mechanisms developed by C.M. Mueller, K. Seshadri, J.Y. Chen [ibid, pp. 284-307] for non-premixed flames were considered. It was found that the Mueller et al. five-step mechanism, with some modifications, best supported the spontaneous ignition and continuous stirred reactor combustion. The results were validated by comparing calculated ignition delays with available experimental data of C.T. Bowman [Combust. Flame 25 (1975) 343-354], and calculated final steady-state concentrations with chemical equilibrium calculations [J.-Y. Chen, Combust. Sci. Technol. 78 (1991) 127]. Initial temperature and concentration and the operating pressure of the system have a major effect on the delay of methanol ignition. The residence time of the continuous stirred reactor affects ignition delay and also changes the transient characteristic of chemical composition of the fuel-vapor mixture. The computations are intended to guide and explain many combustion studies that require a methanol kinetic mechanism.

  20. The Fast-Folding Mechanism of Villin Headpiece Subdomain Studied by Multiscale Distributed Computing.

    PubMed

    Harada, Ryuhei; Kitao, Akio

    2012-01-10

    The fast-folding mechanism of a 35-residue mini-protein, villin headpiece subdomain (HP35), was investigated using folding free energy landscape analysis with the multiscale free energy landscape calculation method (MSFEL). A major and a minor folding pathway were deduced from the folding free energy landscape. In the major folding pathway, the formation of helices II and III was the rate-limiting step in the transition to an intermediate state, triggered by the folding of the PLWK motif. HP35 then folds into the native structure through the formation of the hydrophobic core located at the center of the three-helix bundle. Mutations in the motif and hydrophobic core that suppressed folding into the native state drastically changed the folding free energy landscape compared to the wild type protein. In the minor folding pathway, nucleation of the hydrophobic core preceded formation of the motif.

  1. Statistical mechanics of RNA folding: Importance of alphabet size

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, Ranjan; Emberly, Eldon; Tang, Chao; Wingreen, Ned S.

    2003-10-01

    We construct a base-stacking model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four- or six-letter alphabets. With only two kinds of bases, most sequences have many alternative folding configurations and are consequently thermally unstable. Stable ground states are found only for a small set of structures of high designability, i.e., total number of associated sequences. In contrast, sequences made from four bases, as found in nature, or six bases have far fewer competing folding configurations, resulting in a much greater average stability of the ground state.

  2. Mechanism of development of inversion folding in the subsalt

    NASA Astrophysics Data System (ADS)

    Lunev, B. V.; Lapkovsky, V. V.

    2014-01-01

    The numerical modeling of the Archimedean upwelling of a salt bed predicts that, with mature diapirs (from the finger stage and later), an about 2-km-thick zone of inversion (mirror) folding, where the suprasalt diapirs correspond to the subsalt synclines while the suprasalt inter-diapir sags correspond to the anticlines in the subsalt, should be expected immediately below the bottom of the salt deposits. These deformations decay with depth. The development of the inversion folding is exceptionally due to the flow caused by the rising of the unstable layer.

  3. Multiple-probe analysis of folding and unfolding pathways of human serum albumin. Evidence for a framework mechanism of folding.

    PubMed

    Santra, Manas Kumar; Banerjee, Abhijit; Krishnakumar, Shyam Sundar; Rahaman, Obaidur; Panda, Dulal

    2004-05-01

    The changes in the far-UV CD signal, intrinsic tryptophan fluorescence and bilirubin absorbance showed that the guanidine hydrochloride (GdnHCl)-induced unfolding of a multidomain protein, human serum albumin (HSA), followed a two-state process. However, using environment sensitive Nile red fluorescence, the unfolding and folding pathways of HSA were found to follow a three-state process and an intermediate was detected in the range 0.25-1.5 m GdnHCl. The intermediate state displayed 45% higher fluorescence intensity than that of the native state. The increase in the Nile red fluorescence was found to be due to an increase in the quantum yield of the HSA-bound Nile red. Low concentrations of GdnHCl neither altered the binding affinity of Nile red to HSA nor induced the aggregation of HSA. In addition, the secondary structure of HSA was not perturbed during the first unfolding transition (<1.5 m GdnHCl); however, the secondary structure was completely lost during the second transition. The data together showed that the half maximal loss of the tertiary structure occurred at a lower GdnHCl concentration than the loss of the secondary structure. Further kinetic studies of the refolding process of HSA using multiple spectroscopic techniques showed that the folding occurred in two phases, a burst phase followed by a slow phase. An intermediate with native-like secondary structure but only a partial tertiary structure was found to form in the burst phase of refolding. Then, the intermediate slowly folded into the native state. An analysis of the refolding data suggested that the folding of HSA could be best explained by the framework model.

  4. Mechanical Modeling and Computer Simulation of Protein Folding

    ERIC Educational Resources Information Center

    Prigozhin, Maxim B.; Scott, Gregory E.; Denos, Sharlene

    2014-01-01

    In this activity, science education and modern technology are bridged to teach students at the high school and undergraduate levels about protein folding and to strengthen their model building skills. Students are guided from a textbook picture of a protein as a rigid crystal structure to a more realistic view: proteins are highly dynamic…

  5. Evolution of ribonuclease in relation to polypeptide folding mechanisms.

    NASA Technical Reports Server (NTRS)

    Barnard, E. A.; Cohen, M. S.; Gold, M. H.; Kim, J.-K.

    1972-01-01

    Comparisons of the N-terminal region of pancreatic RNAase in seven species are presented, taking into account cow, bison, deer, rat, pig, kangaroo, and turtle. The available limited evidence on hypervariable regions indicates that there is still an evolutionary constraint on them. It is proposed that there is a selection pressure acting on all regions of a protein sequence in evolution. Mutations that tend to obstruct the folding process can lead to various intensities of selection pressure.

  6. The energy landscape of modular repeat proteins: topology determines folding mechanism in the ankyrin family.

    PubMed

    Ferreiro, Diego U; Cho, Samuel S; Komives, Elizabeth A; Wolynes, Peter G

    2005-12-02

    Proteins consisting of repeating amino acid motifs are abundant in all kingdoms of life, especially in higher eukaryotes. Repeat-containing proteins self-organize into elongated non-globular structures. Do the same general underlying principles that dictate the folding of globular domains apply also to these extended topologies? Using a simplified structure-based model capturing a perfectly funneled energy landscape, we surveyed the predicted mechanism of folding for ankyrin repeat containing proteins. The ankyrin family is one of the most extensively studied classes of non-globular folds. The model based only on native contacts reproduces most of the experimental observations on the folding of these proteins, including a folding mechanism that is reminiscent of a nucleation propagation growth. The confluence of simulation and experimental results suggests that the folding of non-globular proteins is accurately described by a funneled energy landscape, in which topology plays a determinant role in the folding mechanism.

  7. Single-molecule fluorescence resonance energy transfer studies of the human telomerase RNA pseudoknot: temperature-/urea-dependent folding kinetics and thermodynamics.

    PubMed

    Holmstrom, Erik D; Nesbitt, David J

    2014-04-10

    The ribonucleoprotein telomerase is an RNA-dependent DNA polymerase that catalyzes the repetitive addition of a short, species-specific, DNA sequence to the ends of linear eukaryotic chromosomes. The single RNA component of telomerase contains both the template sequence for DNA synthesis and a functionally critical pseudoknot motif, which can also exist as a less stable hairpin. Here we use a minimal version of the human telomerase RNA pseudoknot to study this hairpin-pseudoknot structural equilibrium using temperature-controlled single-molecule fluorescence resonance energy transfer (smFRET) experiments. The urea dependence of these experiments aids in determination of the folding kinetics and thermodynamics. The wild-type pseudoknot behavior is compared and contrasted to a mutant pseudoknot sequence implicated in a genetic disorder-dyskeratosis congenita. These findings clearly identify that this 2nt noncomplementary mutation destabilizes the folding of the wild-type pseudoknot by substantially reducing the folding rate constant (≈ 400-fold) while only nominally increasing the unfolding rate constant (≈ 5-fold). Furthermore, the urea dependence of the equilibrium and rate constants is used to develop a free energy landscape for this unimolecular equilibrium and propose details about the structure of the transition state. Finally, the urea-dependent folding experiments provide valuable physical insights into the mechanism for destabilization of RNA pseudoknots by such chemical denaturants.

  8. Kinetics and mechanism of autohydrolysis of hardwoods.

    PubMed

    Chen, Xiaowen; Lawoko, Martin; Heiningen, Adriaan van

    2010-10-01

    Autohydrolysis using water is a promising method to extract hemicelluloses from wood prior to pulping in order to make co-products such as ethanol and acetic acid besides pulp. Many studies have been carried out on the kinetics and mechanism of autohydrolysis using batch reactors. The present study was performed in a continuous mixed flow reactor where the wood chips are retained in a basket inside the reactor. This reactor is well suited to determine intrinsic kinetics of hemicellulose dissolution because the dissolved products are rapidly removed from the reactor, thus minimizing further hydrolysis and degradation of the hemicelluloses in solution. The xylan removal rate follows an S-shaped behavior. GPC analysis of the continuously removed extract shows that the dissolved xylan oligomers have a DP smaller than about 25. Lignin-free xylan oligomers and cellulose oligomers are the major components dissolved in the initial stage of autohydrolysis, while xylan covalently bound to lignin (i.e. an LCC) is the major component removed during the later stage of autohydrolysis. The molecular weight of the dissolved components decreases with time in the second stage. The kinetics of xylan removal are explained in terms of a mechanism based on recent knowledge of the ultrastructure of the cell fibre wall.

  9. Mechanism of folding chamber closure in a group II chaperonin.

    PubMed

    Zhang, Junjie; Baker, Matthew L; Schröder, Gunnar F; Douglas, Nicholai R; Reissmann, Stefanie; Jakana, Joanita; Dougherty, Matthew; Fu, Caroline J; Levitt, Michael; Ludtke, Steven J; Frydman, Judith; Chiu, Wah

    2010-01-21

    Group II chaperonins are essential mediators of cellular protein folding in eukaryotes and archaea. These oligomeric protein machines, approximately 1 megadalton, consist of two back-to-back rings encompassing a central cavity that accommodates polypeptide substrates. Chaperonin-mediated protein folding is critically dependent on the closure of a built-in lid, which is triggered by ATP hydrolysis. The structural rearrangements and molecular events leading to lid closure are still unknown. Here we report four single particle cryo-electron microscopy (cryo-EM) structures of Mm-cpn, an archaeal group II chaperonin, in the nucleotide-free (open) and nucleotide-induced (closed) states. The 4.3 A resolution of the closed conformation allowed building of the first ever atomic model directly from the single particle cryo-EM density map, in which we were able to visualize the nucleotide and more than 70% of the side chains. The model of the open conformation was obtained by using the deformable elastic network modelling with the 8 A resolution open-state cryo-EM density restraints. Together, the open and closed structures show how local conformational changes triggered by ATP hydrolysis lead to an alteration of intersubunit contacts within and across the rings, ultimately causing a rocking motion that closes the ring. Our analyses show that there is an intricate and unforeseen set of interactions controlling allosteric communication and inter-ring signalling, driving the conformational cycle of group II chaperonins. Beyond this, we anticipate that our methodology of combining single particle cryo-EM and computational modelling will become a powerful tool in the determination of atomic details involved in the dynamic processes of macromolecular machines in solution.

  10. Kinetic study and mechanism of Niclosamide degradation

    NASA Astrophysics Data System (ADS)

    Zaazaa, Hala E.; Abdelrahman, Maha M.; Ali, Nouruddin W.; Magdy, Maimana A.; Abdelkawy, M.

    2014-11-01

    A spectrophotometric kinetic study of Niclosamide alkaline degradation as a function of drug concentration, alkaline concentration and temperature has been established utilizing double divisor-ratio spectra spectrophotometric method. The developed method allowed determination of Niclosamide in presence of its alkaline degradation products; namely; 2-chloro-4-nitro aniline (DEG I) and 5-chloro salicylic acid (DEG II) with characterization of its degradation mechanism. It was found that degradation kinetic of Niclosamide followed pseudo-first order under the established experimental conditions with a degradation rate constant (k) of 0.0829 mol/h and half life (t1/2) of 8.35 h. The overall degradation rate constant as a function of the temperature under the given conditions obeyed Arrhenius equation where the activation energy was calculated to be 3.41 kcal/mol.

  11. Kinetic study and mechanism of Niclosamide degradation.

    PubMed

    Zaazaa, Hala E; Abdelrahman, Maha M; Ali, Nouruddin W; Magdy, Maimana A; Abdelkawy, M

    2014-11-11

    A spectrophotometric kinetic study of Niclosamide alkaline degradation as a function of drug concentration, alkaline concentration and temperature has been established utilizing double divisor-ratio spectra spectrophotometric method. The developed method allowed determination of Niclosamide in presence of its alkaline degradation products; namely; 2-chloro-4-nitro aniline (DEG I) and 5-chloro salicylic acid (DEG II) with characterization of its degradation mechanism. It was found that degradation kinetic of Niclosamide followed pseudo-first order under the established experimental conditions with a degradation rate constant (k) of 0.0829 mol/h and half life (t1/2) of 8.35 h. The overall degradation rate constant as a function of the temperature under the given conditions obeyed Arrhenius equation where the activation energy was calculated to be 3.41 kcal/mol.

  12. Numerical impact simulation of gradually increased kinetic energy transfer has the potential to break up folded protein structures resulting in cytotoxic brain tissue edema.

    PubMed

    von Holst, Hans; Li, Xiaogai

    2013-07-01

    Although the consequences of traumatic brain injury (TBI) and its treatment have been improved, there is still a substantial lack of understanding the mechanisms. Numerical simulation of the impact can throw further lights on site and mechanism of action. A finite element model of the human head and brain tissue was used to simulate TBI. The consequences of gradually increased kinetic energy transfer was analyzed by evaluating the impact intracranial pressure (ICP), strain level, and their potential influences on binding forces in folded protein structures. The gradually increased kinetic energy was found to have the potential to break apart bonds of Van der Waals in all impacts and hydrogen bonds at simulated impacts from 6 m/s and higher, thereby superseding the energy in folded protein structures. Further, impacts below 6 m/s showed none or very slight increase in impact ICP and strain levels, whereas impacts of 6 m/s or higher showed a gradual increase of the impact ICP and strain levels reaching over 1000 KPa and over 30%, respectively. The present simulation study shows that the free kinetic energy transfer, impact ICP, and strain levels all have the potential to initiate cytotoxic brain tissue edema by unfolding protein structures. The definition of mild, moderate, and severe TBI should thus be looked upon as the same condition and separated only by a gradual severity of impact.

  13. Direct observation of an ensemble of stable collapsed states in the mechanical folding of ubiquitin

    PubMed Central

    Garcia-Manyes, Sergi; Dougan, Lorna; Badilla, Carmen L.; Brujić, Jasna; Fernández, Julio M.

    2009-01-01

    Statistical theories of protein folding have long predicted plausible mechanisms for reducing the vast conformational space through distinct ensembles of structures. However, these predictions have remained untested by bulk techniques, because the conformational diversity of folding molecules has been experimentally unapproachable. Owing to recent advances in single molecule force-clamp spectroscopy, we are now able to probe the structure and dynamics of the small protein ubiquitin by measuring its length and mechanical stability during each stage of folding. Here, we discover that upon hydrophobic collapse, the protein rapidly selects a subset of minimum energy structures that are mechanically weak and essential precursors of the native fold. From this much reduced ensemble, the native state is acquired through a barrier-limited transition. Our results support the validity of statistical mechanics models in describing the folding of a small protein on biological timescales. PMID:19541635

  14. Studies of combustion kinetics and mechanisms

    SciTech Connect

    Gutman, D.

    1993-12-01

    The objective of the current research is to gain new quantitative knowledge of the kinetics and mechanisms of polyatomic free radicals which are important in hydrocarbon combustion processes. The special facility designed and built for these (which includes a heatable tubular reactor coupled to a photoionization mass spectrometer) is continually being improved. Where possible, these experimental studies are coupled with theoretical ones, sometimes conducted in collaboration with others, to obtain an improved understanding of the factors determining reactivity. The decomposition of acetyl radicals, isopropyl radicals, and n-propyl radicals have been studied as well as the oxidation of methylpropargyl radicals.

  15. Thermodynamics and kinetics of protein folding on the ribosome: Alteration in energy landscapes, denatured state, and transition state ensembles

    NASA Astrophysics Data System (ADS)

    O'Brien, Edward; Vendruscolo, Michele; Dobson, Christopher

    2010-03-01

    In vitro experiments examining cotranslational folding utilize ribosome-nascent chain complexes (RNCs) in which the nascent chain is stalled at different points of its biosynthesis on the ribosome. We investigate the thermodynamics, kinetics, and structural properties of RNCs containing five different globular and repeat proteins stalled at ten different nascent chain lengths using coarse grained replica exchange simulations. We find that when the proteins are stalled near the ribosome exit tunnel opening they exhibit altered folding coopserativity, quantified by the van't Hoff enthalpy criterion; a significantly altered denatured state ensemble, in terms of Rg and shape parameters (Rg tensor); and the appearance of partially folded intermediates during cotranslation, evidenced by the appearance of a third basin in the free energy profile. These trends are due in part to excluded volume (crowding) interactions between the ribosome and nascent chain. We perform in silico temperature-jump experiments on the RNCs and examine nascent chain folding kinetics and structural changes in the transition state ensemble at various stall lengths.

  16. Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy

    NASA Astrophysics Data System (ADS)

    Snow, Christopher D.; Qiu, Linlin; Du, Deguo; Gai, Feng; Hagen, Stephen J.; Pande, Vijay S.

    2004-03-01

    We studied the microsecond folding dynamics of three hairpins (Trp zippers 1-3, TZ1-TZ3) by using temperature-jump fluorescence and atomistic molecular dynamics in implicit solvent. In addition, we studied TZ2 by using time-resolved IR spectroscopy. By using distributed computing, we obtained an aggregate simulation time of 22 ms. The simulations included 150, 212, and 48 folding events at room temperature for TZ1, TZ2, and TZ3, respectively. The all-atom optimized potentials for liquid simulations (OPLSaa) potential set predicted TZ1 and TZ2 properties well; the estimated folding rates agreed with the experimentally determined folding rates and native conformations were the global potential-energy minimum. The simulations also predicted reasonable unfolding activation enthalpies. This work, directly comparing large simulated folding ensembles with multiple spectroscopic probes, revealed both the surprising predictive ability of current models as well as their shortcomings. Specifically, for TZ1-TZ3, OPLS for united atom models had a nonnative free-energy minimum, and the folding rate for OPLSaa TZ3 was sensitive to the initial conformation. Finally, we characterized the transition state; all TZs fold by means of similar, native-like transition-state conformations.

  17. Bend, buckle, and fold: mechanical engineering with nanomembranes.

    PubMed

    Kim, Dae-Hyeong; Rogers, John A

    2009-03-24

    Research on nanomembranes and graphene sheets represents the "third wave" of work on nanomaterials, following earlier studies of nanoparticles/fullerenes and, somewhat later, nanowires/nanotubes. Inorganic semiconductor nanomembranes are particularly appealing due to their materials diversity, the ease with which they can be grown with high quality over large areas, and the ability to exploit them in unique, high-performance electronic and optoelectronic systems. The mechanics of such nanomembranes and the coupling of strain to their electronic properties are topics of considerable current interest. A new paper by the Lagally group in this issue combines single-crystalline silicon nanomembranes with chemical vapor deposition techniques to form "mechano-electronic" superlattices whose properties could lead to unusual classes of electronic devices.

  18. Swelling and folding as mechanisms of 3D shape formation in thin elastic sheets

    NASA Astrophysics Data System (ADS)

    Dias, Marcelo A.

    We work with two different mechanisms to generate geometric frustration on thin elastic sheets; isotropic differential growth and folding. We describe how controlled growth and prescribing folding patterns are useful tools for designing three-dimensional objects from information printed in two dimensions. The first mechanism is inspired by the possibility to control shapes by swelling polymer films, where we propose a solution for the problem of shape formation by asking the question, “what 2D metric should be prescribed to achieve a given 3D shape?”', namely the reverse problem. We choose two different types of initial configurations of sheets, disk-like with one boundary and annular with two boundaries. We demonstrate our technique by choosing four examples of 3D axisymmetric shapes and finding the respective swelling factors to achieve the desired shape. Second, we present a mechanical model for a single curved fold that explains both the buckled shape of a closed fold and its mechanical stiffness. The buckling arises from the geometrical frustration between the prescribed crease angle and the bending energy of the sheet away from the crease. This frustration increases as the sheet's area increases. Stiff folds result in creases with constant space curvature while softer folds inherit the broken symmetry of the buckled shape. We extend the application of our numerical model to show the potential to study multiple fold structures.

  19. Characterization of the kinetic and thermodynamic landscape of RNA folding using a novel application of isothermal titration calorimetry.

    PubMed

    Vander Meulen, Kirk A; Butcher, Samuel E

    2012-03-01

    A novel isothermal titration calorimetry (ITC) method was applied to investigate RNA helical packing driven by the GAAA tetraloop-receptor interaction in magnesium and potassium solutions. Both the kinetics and thermodynamics were obtained in individual ITC experiments, and analysis of the kinetic data over a range of temperatures provided Arrhenius activation energies (ΔH(‡)) and Eyring transition state entropies (ΔS(‡)). The resulting rich dataset reveals strongly contrasting kinetic and thermodynamic profiles for this RNA folding system when stabilized by potassium versus magnesium. In potassium, association is highly exothermic (ΔH(25°C) = -41.6 ± 1.2 kcal/mol in 150 mM KCl) and the transition state is enthalpically barrierless (ΔH(‡) = -0.6 ± 0.5). These parameters are significantly positively shifted in magnesium (ΔH(25°C) = -20.5 ± 2.1 kcal/mol, ΔH(‡) = 7.3 ± 2.2 kcal/mol in 0.5 mM MgCl(2)). Mixed salt solutions approximating physiological conditions exhibit an intermediate thermodynamic character. The cation-dependent thermodynamic landscape may reflect either a salt-dependent unbound receptor conformation, or alternatively and more generally, it may reflect a small per-cation enthalpic penalty associated with folding-coupled magnesium uptake.

  20. Architecture and Folding Mechanism of the Azoarcus Group I Pre-tRNA

    SciTech Connect

    Rangan,P.; Masquida, B.; Westhof, E.; Woodson, S.

    2004-01-01

    Self-splicing RNAs must evolve to function in their specific exon context. The conformation of a group I pre-tRNA{sup ile} from the bacterium Azoarcus was probed by ribonuclease T1 and hydroxyl radical cleavage, and by native gel electrophoresis. Biochemical data and three-dimensional models of the pre-tRNA showed that the tRNA is folded, and that the tRNA and intron sequences form separate tertiary domains. Models of the active site before steps 1 and 2 of the splicing reaction predict that exchange of the external G-cofactor and the 3{prime}-terminal G is accomplished by a slight conformational change in P9.0 of the Azoarcus group I intron. Kinetic assays showed that the pre-tRNA folds in minutes, much more slowly than the intron alone. The dependence of the folding kinetics on Mg{sup 2+} and the concentration of urea, and RNase T1 experiments showed that formation of native pre-tRNA is delayed by misfolding of P3-P9, including mispairing between residues in P9 and the tRNA. Thus, although the intron and tRNA sequences form separate domains in the native pre-tRNA, their folding is coupled via metastable non-native base-pairs. This could help prevent premature processing of the 5{prime} and 3{prime} ends of unspliced pre-tRNA.

  1. Mechanical versus kinematical shortening reconstructions of the Zagros High Folded Zone (Kurdistan region of Iraq)

    NASA Astrophysics Data System (ADS)

    Frehner, Marcel; Reif, Daniel; Grasemann, Bernhard

    2012-06-01

    This paper compares kinematical and mechanical techniques for the palinspastic reconstruction of folded cross sections in collision orogens. The studied area and the reconstructed NE-SW trending, 55.5 km long cross section is located in the High Folded Zone of the Zagros fold-and-thrust belt in the Kurdistan region of Iraq. The present-day geometry of the cross section has been constructed from field as well as remote sensing data. In a first step, the structures and the stratigraphy are simplified and summarized in eight units trying to identify the main geometric and mechanical parameters. In a second step, the shortening is kinematically estimated using the dip domain method to 11%-15%. Then the same cross section is used in a numerical finite element model to perform dynamical unfolding simulations taking various rheological parameters into account. The main factor allowing for an efficient dynamic unfolding is the presence of interfacial slip conditions between the mechanically strong units. Other factors, such as Newtonian versus power law viscous rheology or the presence of a basement, affect the numerical simulations much less strongly. If interfacial slip is accounted for, fold amplitudes are reduced efficiently during the dynamical unfolding simulations, while welded layer interfaces lead to unrealistic shortening estimates. It is suggested that interfacial slip and decoupling of the deformation along detachment horizons is an important mechanical parameter that controlled the folding processes in the Zagros High Folded Zone.

  2. Mechanical versus kinematical shortening reconstructions of the Zagros High Folded Zone (Kurdistan Region of Iraq)

    NASA Astrophysics Data System (ADS)

    Frehner, M.; Reif, D.; Grasemann, B.

    2012-04-01

    Our study compares kinematical and mechanical techniques for the palinspastic reconstruction of folded cross-sections in collision orogens. The studied area and the reconstructed NE-SW-trending, 55.5 km long cross-section is located in the High Folded Zone of the Zagros fold-and-thrust belt in the Kurdistan Region of Iraq. The present-day geometry of the cross-section has been constructed from field, as well as remote sensing data. In a first step, the structures and the stratigraphy are simplified and summarized in eight units trying to identify the main geometric and mechanical parameters. In a second step, the shortening is kinematically estimated using the dip-domain method to 11%-15%. Then the same cross-section is used in a numerical finite-element model to perform dynamical unfolding simulations taking various rheological parameters into account. The main factor allowing for an efficient dynamic unfolding is the presence of interfacial slip conditions between the mechanically strong units. Other factors, such as Newtonian vs. power-law viscous rheology or the presence of a basement affect the numerical simulations much less strongly. If interfacial slip is accounted for, fold amplitudes are reduced efficiently during the dynamical unfolding simulations, while welded layer interfaces lead to unrealistic shortening estimates. It is suggested that interfacial slip and decoupling of the deformation along detachment horizons is an important mechanical parameter that controlled the folding processes in the Zagros High Folded Zone.

  3. Mesophile versus thermophile: insights into the structural mechanisms of kinetic stability.

    PubMed

    Kelch, Brian A; Agard, David A

    2007-07-20

    Obtaining detailed knowledge of folding intermediate and transition state (TS) structures is critical for understanding protein folding mechanisms. Comparisons between proteins adapted to survive extreme temperatures with their mesophilic homologs are likely to provide valuable information on the interactions relevant to the unfolding transition. For kinetically stable proteins such as alpha-lytic protease (alphaLP) and its family members, their large free energy barrier to unfolding is central to their biological function. To gain new insights into the mechanisms that underlie kinetic stability, we have determined the structure and high temperature unfolding kinetics of a thermophilic homolog, Thermobifida fusca protease A (TFPA). These studies led to the identification of a specific structural element bridging the N and C-terminal domains of the protease (the "domain bridge") proposed to be associated with the enhanced high temperature kinetic stability in TFPA. Mutagenesis experiments exchanging the TFPA domain bridge into alphaLP validate this hypothesis and illustrate key structural details that contribute to TFPA's increased kinetic thermostability. These results lead to an updated model for the unfolding transition state structure for this important class of proteases in which domain bridge undocking and unfolding occurs at or before the TS. The domain bridge appears to be a structural element that can modulate the degree of kinetic stability of the different members of this class of proteases.

  4. Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

    NASA Astrophysics Data System (ADS)

    Gao, Connie W.; Allen, Joshua W.; Green, William H.; West, Richard H.

    2016-06-01

    Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent thermodynamic and kinetic data. Models are generated using a rate-based algorithm which excludes species from the model based on reaction fluxes. RMG can generate reaction mechanisms for species involving carbon, hydrogen, oxygen, sulfur, and nitrogen. It also has capabilities for estimating transport and solvation properties, and it automatically computes pressure-dependent rate coefficients and identifies chemically-activated reaction paths. RMG is an object-oriented program written in Python, which provides a stable, robust programming architecture for developing an extensible and modular code base with a large suite of unit tests. Computationally intensive functions are cythonized for speed improvements.

  5. Kinetic mechanism of chicken liver xanthine dehydrogenase.

    PubMed Central

    Bruguera, P; Lopez-Cabrera, A; Canela, E I

    1988-01-01

    The kinetic behaviour of chicken-liver xanthine dehydrogenase (xanthine/NAD+ oxidoreductase; EC 1.2.1.37) has been studied. Steady-state results, obtained from a wide range of concentrations of substrates and products, were fitted by rational functions of degree 1:1, 1:2, 2:2 and 3:3 with respect to substrates, and 0:1, 1:1, 0:2 and 1:2 with regard to products, using a non-linear regression program which guarantees the fit. The goodness of fit was improved using a computer program that combines model discrimination, parameter refinement and sequential experimental design. The AIC and F tests were also used for model discrimination. For comparative purposes, the xanthine/oxygen oxidoreductase reaction was also studied. From the functions which give the maximum improvement, the complete rate equation was deduced. The significance of the terms was stated by the above methods. It was concluded that xanthine dehydrogenase requires a minimum mechanism of degree 1:1 for xanthine, 2:2 for NAD+, 1:1 for uric acid and 1:2 for NADH in the xanthine/NAD+ oxidoreductase reaction. These are the minimum degrees required but a rate equation of higher degree is not excluded. PMID:3422556

  6. Kinetics and Mechanisms of Nanosilver Oxysulfidation

    PubMed Central

    Liu, Jingyu; Pennell, Kelly G.; Hurt, Robert H.

    2011-01-01

    Among the many new engineered nanomaterials, nanosilver is one of the highest priority cases for environmental risk assessment. Recent analysis of field samples from water treatment facilities suggests that silver is converted to silver sulfide, whose very low solubility may limit the bioavailability and adverse impact of silver in the environment. The present study demonstrates that silver nanoparticles react with dissolved sulfide species (HS−, S2−) under relevant but controlled laboratory conditions to produce silver sulfide nanostructures similar to those observed in the field. The reaction is tracked by time-resolved sulfide depletion measurements to yield quantitative reaction rates and stoichiometries. The reaction requires dissolved oxygen, and it is sensitive to pH and natural organic matter. Focusedion-beam analysis of surface films reveals an irregular coarse-grained sulfide phase that allows deep (> 1 μm) conversion of silver surfaces without passivation. At high sulfide concentrations, nanosilver oxysulfidation occurs by a direct particle-fluid reaction. At low sulfide concentration, quantitative kinetic analysis suggests a mechanistic switch to an oxidative dissolution/precipitation mechanism, in which the biologically active Ag+ ion is generated as an intermediate. The environmental transformation pathways for nanosilver will vary depending on the media-specific competing rates of oxidative dissolution and direct oxysulfidation. PMID:21770469

  7. KINETICS AND MECHANISMS OF NOx - CHAR REDUCTION

    SciTech Connect

    Suuberg, E.M.

    1998-06-19

    This study was undertaken in order to improve understanding of several aspects of the NO-carbon reaction. This reaction is of practical importance in combustion systems, but its close examination also provides some fundamental insight into oxidizing gas-carbon reactions. As part of this study, a comprehensive literature review of earlier work on this reaction has been published (Aarna and Suuberg, Fuel, 1997, 76, 475-491). It has been thought for some time that the kinetics of the NO-carbon reaction are unusual, in that they often show a two-regime Arrhenius behavior. It has, however, turned out during this work that NO is not alone in this regard. In this laboratory, we also uncovered evidence of two kinetic regime behavior in CO{sub 2} gasification. In another laboratory, a former colleague has identified the same behavior in N{sub 2}O. The low temperature reaction regime always shows an activation energy which is lower than that in the high temperature regime, leaving little doubt that a shift in mechanism, as opposed to transport limitations, dictates the behavior. The activation energy of the low temperature regime of these reactions is typically less than 100 kJ/mol, and the activation energy of the high temperature regime is generally considerably in excess of this value. In this study, we have resolved some apparent inconsistencies in the explanation of the low temperature regime, whose rate has generally been ascribed to desorption-controlled processes. Part of the problem in characterization of the different temperature regimes is that they overlap to a high degree. It is difficult to probe the low temperature regime experimentally, because of slow relaxation of the surface oxides in that regime. Using careful experimental techniques, we were able to demonstrate that the low temperature regime is indeed characterized by zero order in NO, as it must be. A separate study is being carried out to model the behavior in this regime in NO and in other gases, and

  8. Infrared study of the stability and folding kinetics of a series of β-hairpin peptides with a common NPDG turn.

    PubMed

    Xu, Yao; Du, Deguo; Oyola, Rolando

    2011-12-29

    The thermal stability and folding kinetics of a series of 15-residue β-hairpins with a common Type I [3:5] NPDG turn were studied using Fourier transform infrared spectroscopy (FTIR) and laser-induced temperature jump (T-jump) with infrared detection, respectively. Mutations at positions 3, 5, or 13 in the peptide sequence SEXYXNPDGTWTXTE, where X represents the position of mutation, were performed to study the roles of hydrophobic interactions in determining the thermodynamic and kinetic properties of β-hairpin folding. The thermal stability studies show a broad thermal folding/unfolding transition for all the peptides. T-jump studies indicate that these β-hairpin peptides fold in less than 2 μs. In addition, both folding and unfolding rate constants decrease with increasing strength of hydrophobic interactions. Kinetically, the hydrophobic interactions have more significant influence on the unfolding rate than the folding rate. Φ-value analysis indicates that the hydrophobic interactions between the side chains are mainly formed at the latter part of the transition-state region during the folding process. In summary, the results suggest that the formation of the native structure of these β-hairpins depends on the correct topology of the hydrophobic cluster. Besides the formation of the turn region as a key process for folding as suggested by previous studies, a hydrophobic collapse process may also play a crucial role during β-hairpin folding.

  9. Modeling of the Kinetics of Metal Film Growth on 5-Fold Surfaces of Icosohedral Quasicrystals

    NASA Astrophysics Data System (ADS)

    Evans, J. W.; Unal, B.; Fournee, V.; Ghosh, C.; Liu, D.-J.; Jenks, C. J.; Thiel, P. A.

    2007-03-01

    During submonolayer deposition of metals on 5-f icosohedral Al- Pd-Mn and Al-Cu-Fe surfaces, experimental evidence for several system points to heterogeneous nucleation of islands at specific ``dark star'' trap sites. We model this phenomenon using a mean-field rate equation formulation for Ag on Al-Pd-Mn, where data is available for both the flux and temperature dependence of the island density. We also utilize a more sophisticated kinetic Monte Carlo simulation approach to analyze an atomistic lattice-gas model (for an appropriate ``disordered-bond-network'' of nearest-neighbor adsorption sites) describing nucleation of starfish islands observed by STM for Al on Al-Cu-Fe. Finally, we briefly describe multilayer growth morphologies (which can display kinetic roughening or quantum size effects), but which also generally reflect the submonolayer island distribution. B. Unal et al. PRB 75 (2007); C. Ghosh et al. Phil. Mag. 86 (2006) 831; Surf. Sci. 600 (2006) 1110; V. Fournee et al. PRL 95 (2005) 155504.

  10. Ring Separation Highlights the Protein-Folding Mechanism Used by the Phage EL-Encoded Chaperonin.

    PubMed

    Molugu, Sudheer K; Hildenbrand, Zacariah L; Morgan, David Gene; Sherman, Michael B; He, Lilin; Georgopoulos, Costa; Sernova, Natalia V; Kurochkina, Lidia P; Mesyanzhinov, Vadim V; Miroshnikov, Konstantin A; Bernal, Ricardo A

    2016-04-05

    Chaperonins are ubiquitous, ATP-dependent protein-folding molecular machines that are essential for all forms of life. Bacteriophage φEL encodes its own chaperonin to presumably fold exceedingly large viral proteins via profoundly different nucleotide-binding conformations. Our structural investigations indicate that ATP likely binds to both rings simultaneously and that a misfolded substrate acts as the trigger for ATP hydrolysis. More importantly, the φEL complex dissociates into two single rings resulting from an evolutionarily altered residue in the highly conserved ATP-binding pocket. Conformational changes also more than double the volume of the single-ring internal chamber such that larger viral proteins are accommodated. This is illustrated by the fact that φEL is capable of folding β-galactosidase, a 116-kDa protein. Collectively, the architecture and protein-folding mechanism of the φEL chaperonin are significantly different from those observed in group I and II chaperonins.

  11. Critical State Finite Element Models of Contractional Fault-Related Folding: Structural and Mechanical Analyses

    NASA Astrophysics Data System (ADS)

    Albertz, M.; Lingrey, S.; Sanz, P. F.

    2011-12-01

    Geometric/kinematic models of the common fault-related fold types (fault-bend, fault-propagation, detachment folding) typically assume a simplified flexural-slip based bed-parallel simple shear mechanism. The magnitude of local strain is a function of layer dip change irrespective of material properties. Line-lengths parallel to and layer thicknesses orthogonal to the flexural-slip surface remain constant. This study reports on a range of more complicated kinematic and mechanical responses observed in fourteen idealized forward numerical models of contractional fault-related folding. The models test the effects of material properties, initial fault dip, and the presence of weak inter-layer detachment horizons. We employ a Lagrangian finite element method with adaptive remeshing and a constitutive model that is based on critical state mechanics. This approach allows for large, volumetric deformation and realistic evolution of the failure envelope during progressive deformation. We demonstrate that material properties affect the way faults propagate and thus exert a significant control on resultant fold layer geometry. In most cases, these geometries differ from the flexural-slip based kinematic idealizations. For instance, models of uniform sandstone properties exhibit efficient strain localization and clear patterns of fault tip propagation. Uniform shale properties tends to inhibit fault propagation due to distributed plastic deformation. Models with mixed inter-layered sandstone and shale deform in a disharmonic manner, resembling lobate-cuspate arrangements that are common to many outcrop-scale folds. Inter-layer detachments accommodate shortening by bed-parallel slip, resulting in fault-bend fold kinematics, imbrication of sand layers, and a general absence of fault propagation across layers. Constant area based plane strain restoration of the deformed models recovers the first-order contractional deformation (80-90% of true contractional strain). Constant line

  12. Temperature dependence of the folding and unfolding kinetics of the GCN4 leucine zipper via 13C(alpha)-NMR.

    PubMed Central

    Holtzer, M E; Bretthorst, G L; d'Avignon, D A; Angeletti, R H; Mints, L; Holtzer, A

    2001-01-01

    Studies by one-dimensional NMR are reported on the interconversion of folded and unfolded forms of the GCN4 leucine zipper in neutral saline buffer. The peptide bears 99% 13C(alpha) labels at three sites: V9, L12, and G31. Time-domain 13C(alpha)-NMR spectra are interpreted by global Bayesian lineshape analysis to extract the rate constants for both unfolding and folding as functions of temperature in the range 47-71 degrees C. The data are well fit by the assumption that the same rate constants apply at each labeled site, confirming that only two conformational states need be considered. Results show that 1) both processes require a free energy of activation; 2) unfolding is kinetically enthalpy-opposed and entropy-driven, while folding is the opposite; and 3) the transition state dimer ensemble averages approximately 40% helical. The activation parameters for unfolding, derived from NMR data at the elevated temperatures where both conformations are populated, lead to estimates of the rate constant at low temperatures (5-15 degrees C) that agree with extant values determined by stopped-flow CD via dilution from denaturing media. However, the corresponding estimated values for the folding rate constant are larger by two to three orders of magnitude than those obtained by stopped flow. We propose that this apparent disagreement is caused by the necessity, in the stopped-flow experiment, for initiation of new helices as the highly denaturant-unfolded molecule adjusts to the newly created benign solvent conditions. This must reduce the success rate of collisions in producing the folded molecule. In the NMR determinations, however, the unfolded chains always have a small, but essential, helix content that makes such initiation unnecessary. Support for this hypothesis is adduced from recent extant experiments on the helix-coil transition in single-chain helical peptides and from demonstration that the folding rate constants for coiled coils, as obtained by stopped flow

  13. Probing Protein Folding Kinetics with High-resolution, Stabilized Optical Tweezers

    NASA Astrophysics Data System (ADS)

    Wong, Wesley; Halvorsen, Ken

    2009-03-01

    Single-molecule techniques provide a powerful means of exploring molecular transitions such as the unfolding and refolding of a protein. However, the quantification of bi-directional transitions and near-equilibrium phenomena poses unique challenges, and is often limited by the detection resolution and long-term stability of the instrument. We have developed unique optical tweezers methods that address these problems, including an interference-based method for high-resolution 3D bead tracking (˜1 nm laterally, ˜0.3 nm vertically, at > 100 Hz), and a continuous autofocus system that stabilizes the trap height to within 1-2 nm longterm [1,2]. We have used our instruments to quantify the force-dependent unfolding and refolding kinetics of single protein domains (e.g. spectrin in collaboration with E. Evans). These single-molecule studies are presented, together with the accompanying probabilistic analysis that we have developed. References: 1. W.P. Wong, V. Heinrich, E. Evans, Mat. Res. Soc. Symp. Proc., 790, P5.1-P5.10 (2004). 2. V. Heinrich, W.P. Wong, K. Halvorsen, E. Evans, Langmuir, 24, 1194-1203 (2008).

  14. Comparison of the Folding Mechanism of Highly Homologous Proteins in the Lipid-binding Protein Family

    EPA Science Inventory

    The folding mechanism of two closely related proteins in the intracellular lipid binding protein family, human bile acid binding protein (hBABP) and rat bile acid binding protein (rBABP) were examined. These proteins are 77% identical (93% similar) in sequence Both of these singl...

  15. Surface folding in metals: a mechanism for delamination wear in sliding

    PubMed Central

    Mahato, Anirban; Guo, Yang; Sundaram, Narayan K.; Chandrasekar, Srinivasan

    2014-01-01

    Using high-resolution, in situ imaging of a hard, wedge-shaped model asperity sliding against a metal surface, we demonstrate a new mechanism for particle formation and delamination wear. Damage to the residual surface is caused by the occurrence of folds on the free surface of the prow-shaped region ahead of the wedge. This damage manifests itself as shallow crack-like features and surface tears, which are inclined at very acute angles to the surface. The transformation of folds into cracks, tears and particles is directly captured. Notably, a single sliding pass is sufficient to damage the surface, and subsequent passes result in the generation of platelet-like wear particles. Tracking the folding process at every stage from surface bumps to folds to cracks/tears/particles ensures that there is no ambiguity in capturing the mechanism of wear. Because fold formation and consequent delamination are quite general, our findings have broad applicability beyond wear itself, including implications for design of surface generation and conditioning processes. PMID:25197251

  16. Mechanical restoration of large-scale folded multilayers using the finite element method: Application to the Zagros Simply Folded Belt, N-Iraq

    NASA Astrophysics Data System (ADS)

    Frehner, Marcel; Reif, Daniel; Grasemann, Bernhard

    2010-05-01

    There are a large number of numerical finite element studies concerned with modeling the evolution of folded geological layers through time. This body of research includes many aspects of folding and many different approaches, such as two- and three-dimensional studies, single-layer folding, detachment folding, development of chevron folds, Newtonian, power-law viscous and more complex rheologies, influence of anisotropy, pure-shear, simple-shear and other boundary conditions and so forth. In recent years, studies of multilayer folding emerged, thanks to more advanced mesh generator software and increased computational power. Common to all of these studies is the fact that they consider a forward directed time evolution, as in nature. Very few studies use the finite element method for reverse-time simulations. In such studies, folded geological layers are taken as initial conditions for the numerical simulation. The folding process is reversed by changing the signs of the boundary conditions that supposedly drove the folding process. In such studies, the geometry of the geological layers before the folding process is searched and the amount of shortening necessary for the final folded geometry can be calculated. In contrast to a kinematic or geometric fold restoration procedure, the described approach takes the mechanical behavior of the geological layers into account, such as rheology and the relative strength of the individual layers. This approach is therefore called mechanical restoration of folds. In this study, the concept of mechanical restoration is applied to a two-dimensional 50km long NE-SW-cross-section through the Zagros Simply Folded Belt in Iraqi Kurdistan, NE from the city of Erbil. The Simply Folded Belt is dominated by gentle to open folding and faults are either absent or record only minor offset. Therefore, this region is ideal for testing the concept of mechanical restoration. The profile used is constructed from structural field measurements

  17. Redesigning the type II' β-turn in green fluorescent protein to type I': implications for folding kinetics and stability.

    PubMed

    Madan, Bharat; Sokalingam, Sriram; Raghunathan, Govindan; Lee, Sun-Gu

    2014-10-01

    Both Type I' and Type II' β-turns have the same sense of the β-turn twist that is compatible with the β-sheet twist. They occur predominantly in two residue β-hairpins, but the occurrence of Type I' β-turns is two times higher than Type II' β-turns. This suggests that Type I' β-turns may be more stable than Type II' β-turns, and Type I' β-turn sequence and structure can be more favorable for protein folding than Type II' β-turns. Here, we redesigned the native Type II' β-turn in GFP to Type I' β-turn, and investigated its effect on protein folding and stability. The Type I' β-turns were designed based on the statistical analysis of residues in natural Type I' β-turns. The substitution of the native "GD" sequence of i+1 and i+2 residues with Type I' preferred "(N/D)G" sequence motif increased the folding rate by 50% and slightly improved the thermodynamic stability. Despite the enhancement of in vitro refolding kinetics and stability of the redesigned mutants, they showed poor soluble expression level compared to wild type. To overcome this problem, i and i + 3 residues of the designed Type I' β-turn were further engineered. The mutation of Thr to Lys at i + 3 could restore the in vivo soluble expression of the Type I' mutant. This study indicates that Type II' β-turns in natural β-hairpins can be further optimized by converting the sequence to Type I'.

  18. Single-Molecule Chemo-Mechanical Spectroscopy Provides Structural Identity of Folding Intermediates

    PubMed Central

    Motlagh, Hesam N.; Toptygin, Dmitri; Kaiser, Christian M.; Hilser, Vincent J.

    2016-01-01

    Single-molecule force spectroscopy has emerged as a powerful tool for studying the folding of biological macromolecules. Mechanical manipulation has revealed a wealth of mechanistic information on transient and intermediate states. To date, the majority of state assignment of intermediates has relied on empirical demarcation. However, performing such experiments in the presence of different osmolytes provides an alternative approach that reports on the structural properties of intermediates. Here, we analyze the folding and unfolding of T4 lysozyme with optical tweezers under a chemo-mechanical perturbation by adding osmolytes. We find that two unrelated protective osmolytes, sorbitol and trimethylamine-n-oxide, function by marginally decelerating unfolding rates and specifically modulating early events in the folding process, stabilizing formation of an on-pathway intermediate. The chemo-mechanical perturbation provides access to two independent metrics of the relevant states during folding trajectories, the contour length, and the solvent-accessible surface area. We demonstrate that the dependence of the population of the intermediate in different osmolytes, in conjunction with its measured contour length, provides the ability to discriminate between potential structural models of intermediate states. Our study represents a general strategy that may be employed in the structural modeling of equilibrium intermediate states observed in single-molecule experiments. PMID:27028638

  19. Kinetics and mechanism of olefin catalytic hydroalumination by organoaluminum compounds

    NASA Astrophysics Data System (ADS)

    Koledina, K. F.; Gubaidullin, I. M.

    2016-05-01

    The complex reaction mechanism of α-olefin catalytic hydroalumination by alkylalanes is investigated via mathematical modeling that involves plotting the kinetic models for the individual reactions that make up a complex system and a separate study of their principles. Kinetic parameters of olefin catalytic hydroalumination are estimated. Activation energies of the possible steps of the schemes of complex reaction mechanisms are compared and possible reaction pathways are determined.

  20. Kinetic and thermodynamic consequences of the removal of the Cys-77-Cys-123 disulphide bond for the folding of TEM-1 beta-lactamase.

    PubMed Central

    Vanhove, M; Guillaume, G; Ledent, P; Richards, J H; Pain, R H; Frère, J M

    1997-01-01

    Class A beta-lactamases of the TEM family contain a single disulphide bond which connects cysteine residues 77 and 123. To clarify the possible role of the disulphide bond in the stability and folding kinetics of the TEM-1 beta-lactamase, this bond was removed by introducing a Cys-77-->Ser mutation, and the enzymically active mutant protein was studied by reversible guanidine hydrochloride-induced denaturation. The unfolding and refolding rates were monitored using tryptophan fluorescence. At low guanidine hydrochloride concentrations, the refolding of the wild-type and mutant enzymes followed biphasic time courses. The characteristics of the two phases were not significantly affected by the mutation. Double-jump experiments, in which the protein was unfolded in a high concentration of guanidine hydrochloride for a short time period and then refolded by diluting out the denaturant, indicated that, for both the wild-type and mutant enzymes, the two refolding phases could be ascribed to proline isomerization reactions. Equilibrium unfolding experiments monitored by fluorescence spectroscopy and far-UV CD indicated a three-state mechanism (N<-->H<--U). Both the folded mutant protein (N) and, to a lesser extent the thermodynamically stable intermediate, H. were destabilized relative to the fully unfolded state, U. Removal of the disulphide bond resulted in a decrease of 14.2 kJ/mol (3.4 kcal/mol) in the global free energy of stabilization. Similarly, the mutation also induced a drastic increase in the rate of thermal inactivation. PMID:9020874

  1. Fractal features of a crumpling network in randomly folded thin matter and mechanics of sheet crushing.

    PubMed

    Balankin, Alexander S; Horta Rangel, Antonio; García Pérez, Gregorio; Gayosso Martinez, Felipe; Sanchez Chavez, Hugo; Martínez-González, Claudia L

    2013-05-01

    We study the static and dynamic properties of networks of crumpled creases formed in hand crushed sheets of paper. The fractal dimensionalities of crumpling networks in the unfolded (flat) and folded configurations are determined. Some other noteworthy features of crumpling networks are established. The physical implications of these findings are discussed. Specifically, we state that self-avoiding interactions introduce a characteristic length scale of sheet crumpling. A framework to model the crumpling phenomena is suggested. Mechanics of sheet crushing under external confinement is developed. The effect of compaction geometry on the crushing mechanics is revealed.

  2. Fractal features of a crumpling network in randomly folded thin matter and mechanics of sheet crushing

    NASA Astrophysics Data System (ADS)

    Balankin, Alexander S.; Horta Rangel, Antonio; García Pérez, Gregorio; Gayosso Martinez, Felipe; Sanchez Chavez, Hugo; Martínez-González, Claudia L.

    2013-05-01

    We study the static and dynamic properties of networks of crumpled creases formed in hand crushed sheets of paper. The fractal dimensionalities of crumpling networks in the unfolded (flat) and folded configurations are determined. Some other noteworthy features of crumpling networks are established. The physical implications of these findings are discussed. Specifically, we state that self-avoiding interactions introduce a characteristic length scale of sheet crumpling. A framework to model the crumpling phenomena is suggested. Mechanics of sheet crushing under external confinement is developed. The effect of compaction geometry on the crushing mechanics is revealed.

  3. Kinetic cooperativity of tyrosinase. A general mechanism.

    PubMed

    Muñoz-Muñoz, Jose Luis; Garcia-Molina, Francisco; Varon, Ramón; Tudela, Jose; Garcia-Cánovas, Francisco; Rodríguez-López, Jose N

    2011-01-01

    Tyrosinase shows kinetic cooperativity in its action on o-diphenols, but not when it acts on monophenols, confirming that the slow step is the hydroxylation of monophenols to o-diphenols. This model can be generalised to a wide range of substrates; for example, type S(A) substrates, which give rise to a stable product as the o-quinone evolves by means of a first or pseudo first order reaction (α-methyl dopa, dopa methyl ester, dopamine, 3,4-dihydroxyphenylpropionic acid, 3,4-dihydroxyphenylacetic acid, α-methyl-tyrosine, tyrosine methyl ester, tyramine, 4-hydroxyphenylpropionic acid and 4-hydroxyphenylacetic acid), type S(B) substrates, which include those whose o-quinone evolves with no clear stoichiometry (catechol, 4-methylcatechol, phenol and p-cresol) and, lastly, type S(C) substrates, which give rise to stable o-quinones (4-tert-butylcatechol/4-tert-butylphenol).

  4. Applied origami. Using origami design principles to fold reprogrammable mechanical metamaterials.

    PubMed

    Silverberg, Jesse L; Evans, Arthur A; McLeod, Lauren; Hayward, Ryan C; Hull, Thomas; Santangelo, Christian D; Cohen, Itai

    2014-08-08

    Although broadly admired for its aesthetic qualities, the art of origami is now being recognized also as a framework for mechanical metamaterial design. Working with the Miura-ori tessellation, we find that each unit cell of this crease pattern is mechanically bistable, and by switching between states, the compressive modulus of the overall structure can be rationally and reversibly tuned. By virtue of their interactions, these mechanically stable lattice defects also lead to emergent crystallographic structures such as vacancies, dislocations, and grain boundaries. Each of these structures comes from an arrangement of reversible folds, highlighting a connection between mechanical metamaterials and programmable matter. Given origami's scale-free geometric character, this framework for metamaterial design can be directly transferred to milli-, micro-, and nanometer-size systems.

  5. Chemical kinetic reaction mechanism for the combustion of propane

    NASA Technical Reports Server (NTRS)

    Jachimowski, C. J.

    1984-01-01

    A detailed chemical kinetic reaction mechanism for the combustion of propane is presented and discussed. The mechanism consists of 27 chemical species and 83 elementary chemical reactions. Ignition and combustion data as determined in shock tube studies were used to evaluate the mechanism. Numerical simulation of the shock tube experiments showed that the kinetic behavior predicted by the mechanism for stoichiometric mixtures is in good agrement with the experimental results over the entire temperature range examined (1150-2600K). Sensitivity and theoretical studies carried out using the mechanism revealed that hydrocarbon reactions which are involved in the formation of the HO2 radical and the H2O2 molecule are very important in the mechanism and that the observed nonlinear behavior of ignition delay time with decreasing temperature can be interpreted in terms of the increased importance of the HO2 and H2O2 reactions at the lower temperatures.

  6. Kinetic mechanism of protein N-terminal methyltransferase 1.

    PubMed

    Richardson, Stacie L; Mao, Yunfei; Zhang, Gang; Hanjra, Pahul; Peterson, Darrell L; Huang, Rong

    2015-05-01

    The protein N-terminal methyltransferase 1 (NTMT1) catalyzes the transfer of the methyl group from the S-adenosyl-l-methionine to the protein α-amine, resulting in formation of S-adenosyl-l-homocysteine and α-N-methylated proteins. NTMT1 is an interesting potential anticancer target because it is overexpressed in gastrointestinal cancers and plays an important role in cell mitosis. To gain insight into the biochemical mechanism of NTMT1, we have characterized the kinetic mechanism of recombinant NTMT1 using a fluorescence assay and mass spectrometry. The results of initial velocity, product, and dead-end inhibition studies indicate that methylation by NTMT1 proceeds via a random sequential Bi Bi mechanism. In addition, our processivity studies demonstrate that NTMT1 proceeds via a distributive mechanism for multiple methylations. Together, our studies provide new knowledge about the kinetic mechanism of NTMT1 and lay the foundation for the development of mechanism-based inhibitors.

  7. Evidence for a Shared Mechanism in the Formation of Urea-Induced Kinetic and Equilibrium Intermediates of Horse Apomyoglobin from Ultrarapid Mixing Experiments.

    PubMed

    Mizukami, Takuya; Abe, Yukiko; Maki, Kosuke

    2015-01-01

    In this study, the equivalence of the kinetic mechanisms of the formation of urea-induced kinetic folding intermediates and non-native equilibrium states was investigated in apomyoglobin. Despite having similar structural properties, equilibrium and kinetic intermediates accumulate under different conditions and via different mechanisms, and it remains unknown whether their formation involves shared or distinct kinetic mechanisms. To investigate the potential mechanisms of formation, the refolding and unfolding kinetics of horse apomyoglobin were measured by continuous- and stopped-flow fluorescence over a time range from approximately 100 μs to 10 s, along with equilibrium unfolding transitions, as a function of urea concentration at pH 6.0 and 8°C. The formation of a kinetic intermediate was observed over a wider range of urea concentrations (0-2.2 M) than the formation of the native state (0-1.6 M). Additionally, the kinetic intermediate remained populated as the predominant equilibrium state under conditions where the native and unfolded states were unstable (at ~0.7-2 M urea). A continuous shift from the kinetic to the equilibrium intermediate was observed as urea concentrations increased from 0 M to ~2 M, which indicates that these states share a common kinetic folding mechanism. This finding supports the conclusion that these intermediates are equivalent. Our results in turn suggest that the regions of the protein that resist denaturant perturbations form during the earlier stages of folding, which further supports the structural equivalence of transient and equilibrium intermediates. An additional folding intermediate accumulated within ~140 μs of refolding and an unfolding intermediate accumulated in <1 ms of unfolding. Finally, by using quantitative modeling, we showed that a five-state sequential scheme appropriately describes the folding mechanism of horse apomyoglobin.

  8. A β-Mannanase with a Lysozyme-like Fold and a Novel Molecular Catalytic Mechanism.

    PubMed

    Jin, Yi; Petricevic, Marija; John, Alan; Raich, Lluís; Jenkins, Huw; Portela De Souza, Leticia; Cuskin, Fiona; Gilbert, Harry J; Rovira, Carme; Goddard-Borger, Ethan D; Williams, Spencer J; Davies, Gideon J

    2016-12-28

    The enzymatic cleavage of β-1,4-mannans is achieved by endo-β-1,4-mannanases, enzymes involved in germination of seeds and microbial hemicellulose degradation, and which have increasing industrial and consumer product applications. β-Mannanases occur in a range of families of the CAZy sequence-based glycoside hydrolase (GH) classification scheme including families 5, 26, and 113. In this work we reveal that β-mannanases of the newly described GH family 134 differ from other mannanase families in both their mechanism and tertiary structure. A representative GH family 134 endo-β-1,4-mannanase from a Streptomyces sp. displays a fold closely related to that of hen egg white lysozyme but acts with inversion of stereochemistry. A Michaelis complex with mannopentaose, and a product complex with mannotriose, reveal ligands with pyranose rings distorted in an unusual inverted chair conformation. Ab initio quantum mechanics/molecular mechanics metadynamics quantified the energetically accessible ring conformations and provided evidence in support of a (1)C4 → (3)H4(‡) → (3)S1 conformational itinerary along the reaction coordinate. This work, in concert with that on GH family 124 cellulases, reveals how the lysozyme fold can be co-opted to catalyze the hydrolysis of different polysaccharides in a mechanistically distinct manner.

  9. A β-Mannanase with a Lysozyme-like Fold and a Novel Molecular Catalytic Mechanism

    PubMed Central

    2016-01-01

    The enzymatic cleavage of β-1,4-mannans is achieved by endo-β-1,4-mannanases, enzymes involved in germination of seeds and microbial hemicellulose degradation, and which have increasing industrial and consumer product applications. β-Mannanases occur in a range of families of the CAZy sequence-based glycoside hydrolase (GH) classification scheme including families 5, 26, and 113. In this work we reveal that β-mannanases of the newly described GH family 134 differ from other mannanase families in both their mechanism and tertiary structure. A representative GH family 134 endo-β-1,4-mannanase from a Streptomyces sp. displays a fold closely related to that of hen egg white lysozyme but acts with inversion of stereochemistry. A Michaelis complex with mannopentaose, and a product complex with mannotriose, reveal ligands with pyranose rings distorted in an unusual inverted chair conformation. Ab initio quantum mechanics/molecular mechanics metadynamics quantified the energetically accessible ring conformations and provided evidence in support of a 1C4 → 3H4‡ → 3S1 conformational itinerary along the reaction coordinate. This work, in concert with that on GH family 124 cellulases, reveals how the lysozyme fold can be co-opted to catalyze the hydrolysis of different polysaccharides in a mechanistically distinct manner. PMID:28058278

  10. A three-dimensional statistical mechanical model of folding double-stranded chain molecules

    NASA Astrophysics Data System (ADS)

    Zhang, Wenbing; Chen, Shi-Jie

    2001-05-01

    Based on a graphical representation of intrachain contacts, we have developed a new three-dimensional model for the statistical mechanics of double-stranded chain molecules. The theory has been tested and validated for the cubic lattice chain conformations. The statistical mechanical model can be applied to the equilibrium folding thermodynamics of a large class of chain molecules, including protein β-hairpin conformations and RNA secondary structures. The application of a previously developed two-dimensional model to RNA secondary structure folding thermodynamics generally overestimates the breadth of the melting curves [S-J. Chen and K. A. Dill, Proc. Natl. Acad. Sci. U.S.A. 97, 646 (2000)], suggesting an underestimation for the sharpness of the conformational transitions. In this work, we show that the new three-dimensional model gives much sharper melting curves than the two-dimensional model. We believe that the new three-dimensional model may give much improved predictions for the thermodynamic properties of RNA conformational changes than the previous two-dimensional model.

  11. Origami mechanical metamaterials based on the Miura-derivative fold patterns

    NASA Astrophysics Data System (ADS)

    Zhou, Xiang; Zang, Shixi; You, Zhong

    2016-07-01

    This paper presents two new types of origami-inspired mechanical metamaterials based on the Miura-derivative fold patterns that consist of non-identical parallelogram facets. The analytical models to predict dimension changes and deformation kinematics of the proposed metamaterials are developed. Furthermore, by modelling the creases as revolute hinges with certain rotational spring constants, we derived analytical models for stretching and bulk moduli. The analytical models are validated through finite-element simulation results. Numerical examples reveal that the proposed metamaterials possess some intriguing properties, including negative Poisson's ratios and bulk modulus. The work presented in this paper can provide a highly flexible framework for the design of versatile tunable mechanical metamaterials.

  12. Origami mechanical metamaterials based on the Miura-derivative fold patterns.

    PubMed

    Zhou, Xiang; Zang, Shixi; You, Zhong

    2016-07-01

    This paper presents two new types of origami-inspired mechanical metamaterials based on the Miura-derivative fold patterns that consist of non-identical parallelogram facets. The analytical models to predict dimension changes and deformation kinematics of the proposed metamaterials are developed. Furthermore, by modelling the creases as revolute hinges with certain rotational spring constants, we derived analytical models for stretching and bulk moduli. The analytical models are validated through finite-element simulation results. Numerical examples reveal that the proposed metamaterials possess some intriguing properties, including negative Poisson's ratios and bulk modulus. The work presented in this paper can provide a highly flexible framework for the design of versatile tunable mechanical metamaterials.

  13. Detailed chemical kinetic oxidation mechanism for a biodiesel surrogate

    SciTech Connect

    Herbinet, O; Pitz, W J; Westbrook, C K

    2007-09-17

    A detailed chemical kinetic mechanism has been developed and used to study the oxidation of methyl decanoate, a surrogate for biodiesel fuels. This model has been built by following the rules established by Curran et al. for the oxidation of n-heptane and it includes all the reactions known to be pertinent to both low and high temperatures. Computed results have been compared with methyl decanoate experiments in an engine and oxidation of rapeseed oil methyl esters in a jet stirred reactor. An important feature of this mechanism is its ability to reproduce the early formation of carbon dioxide that is unique to biofuels and due to the presence of the ester group in the reactant. The model also predicts ignition delay times and OH profiles very close to observed values in shock tube experiments fueled by n-decane. These model capabilities indicate that large n-alkanes can be good surrogates for large methyl esters and biodiesel fuels to predict overall reactivity, but some kinetic details, including early CO2 production from biodiesel fuels, can be predicted only by a detailed kinetic mechanism for a true methyl ester fuel. The present methyl decanoate mechanism provides a realistic kinetic tool for simulation of biodiesel fuels.

  14. Detailed chemical kinetic oxidation mechanism for a biodiesel surrogate

    SciTech Connect

    Herbinet, O; Pitz, W J; Westbrook, C K

    2007-09-20

    A detailed chemical kinetic mechanism has been developed and used to study the oxidation of methyl decanoate, a surrogate for biodiesel fuels. This model has been built by following the rules established by Curran et al. for the oxidation of n-heptane and it includes all the reactions known to be pertinent to both low and high temperatures. Computed results have been compared with methyl decanoate experiments in an engine and oxidation of rapeseed oil methyl esters in a jet stirred reactor. An important feature of this mechanism is its ability to reproduce the early formation of carbon dioxide that is unique to biofuels and due to the presence of the ester group in the reactant. The model also predicts ignition delay times and OH profiles very close to observed values in shock tube experiments fueled by n-decane. These model capabilities indicate that large n-alkanes can be good surrogates for large methyl esters and biodiesel fuels to predict overall reactivity, but some kinetic details, including early CO{sub 2} production from biodiesel fuels, can be predicted only by a detailed kinetic mechanism for a true methyl ester fuel. The present methyl decanoate mechanism provides a realistic kinetic tool for simulation of biodiesel fuels.

  15. Detailed chemical kinetic oxidation mechanism for a biodiesel surrogate

    SciTech Connect

    Herbinet, Olivier; Pitz, William J.; Westbrook, Charles K.

    2008-08-15

    A detailed chemical kinetic mechanism has been developed and used to study the oxidation of methyl decanoate, a surrogate for biodiesel fuels. This model has been built by following the rules established by Curran and co-workers for the oxidation of n-heptane and it includes all the reactions known to be pertinent to both low and high temperatures. Computed results have been compared with methyl decanoate experiments in an engine and oxidation of rapeseed oil methyl esters in a jet-stirred reactor. An important feature of this mechanism is its ability to reproduce the early formation of carbon dioxide that is unique to biofuels and due to the presence of the ester group in the reactant. The model also predicts ignition delay times and OH profiles very close to observed values in shock tube experiments fueled by n-decane. These model capabilities indicate that large n-alkanes can be good surrogates for large methyl esters and biodiesel fuels to predict overall reactivity, but some kinetic details, including early CO{sub 2} production from biodiesel fuels, can be predicted only by a detailed kinetic mechanism for a true methyl ester fuel. The present methyl decanoate mechanism provides a realistic kinetic tool for simulation of biodiesel fuels. (author)

  16. Folding to Curved Surfaces: A Generalized Design Method and Mechanics of Origami-based Cylindrical Structures

    PubMed Central

    Wang, Fei; Gong, Haoran; Chen, Xi; Chen, C. Q.

    2016-01-01

    Origami structures enrich the field of mechanical metamaterials with the ability to convert morphologically and systematically between two-dimensional (2D) thin sheets and three-dimensional (3D) spatial structures. In this study, an in-plane design method is proposed to approximate curved surfaces of interest with generalized Miura-ori units. Using this method, two combination types of crease lines are unified in one reprogrammable procedure, generating multiple types of cylindrical structures. Structural completeness conditions of the finite-thickness counterparts to the two types are also proposed. As an example of the design method, the kinematics and elastic properties of an origami-based circular cylindrical shell are analysed. The concept of Poisson’s ratio is extended to the cylindrical structures, demonstrating their auxetic property. An analytical model of rigid plates linked by elastic hinges, consistent with numerical simulations, is employed to describe the mechanical response of the structures. Under particular load patterns, the circular shells display novel mechanical behaviour such as snap-through and limiting folding positions. By analysing the geometry and mechanics of the origami structures, we extend the design space of mechanical metamaterials and provide a basis for their practical applications in science and engineering. PMID:27624892

  17. Folding to Curved Surfaces: A Generalized Design Method and Mechanics of Origami-based Cylindrical Structures.

    PubMed

    Wang, Fei; Gong, Haoran; Chen, Xi; Chen, C Q

    2016-09-14

    Origami structures enrich the field of mechanical metamaterials with the ability to convert morphologically and systematically between two-dimensional (2D) thin sheets and three-dimensional (3D) spatial structures. In this study, an in-plane design method is proposed to approximate curved surfaces of interest with generalized Miura-ori units. Using this method, two combination types of crease lines are unified in one reprogrammable procedure, generating multiple types of cylindrical structures. Structural completeness conditions of the finite-thickness counterparts to the two types are also proposed. As an example of the design method, the kinematics and elastic properties of an origami-based circular cylindrical shell are analysed. The concept of Poisson's ratio is extended to the cylindrical structures, demonstrating their auxetic property. An analytical model of rigid plates linked by elastic hinges, consistent with numerical simulations, is employed to describe the mechanical response of the structures. Under particular load patterns, the circular shells display novel mechanical behaviour such as snap-through and limiting folding positions. By analysing the geometry and mechanics of the origami structures, we extend the design space of mechanical metamaterials and provide a basis for their practical applications in science and engineering.

  18. Folding to Curved Surfaces: A Generalized Design Method and Mechanics of Origami-based Cylindrical Structures

    NASA Astrophysics Data System (ADS)

    Wang, Fei; Gong, Haoran; Chen, Xi; Chen, C. Q.

    2016-09-01

    Origami structures enrich the field of mechanical metamaterials with the ability to convert morphologically and systematically between two-dimensional (2D) thin sheets and three-dimensional (3D) spatial structures. In this study, an in-plane design method is proposed to approximate curved surfaces of interest with generalized Miura-ori units. Using this method, two combination types of crease lines are unified in one reprogrammable procedure, generating multiple types of cylindrical structures. Structural completeness conditions of the finite-thickness counterparts to the two types are also proposed. As an example of the design method, the kinematics and elastic properties of an origami-based circular cylindrical shell are analysed. The concept of Poisson’s ratio is extended to the cylindrical structures, demonstrating their auxetic property. An analytical model of rigid plates linked by elastic hinges, consistent with numerical simulations, is employed to describe the mechanical response of the structures. Under particular load patterns, the circular shells display novel mechanical behaviour such as snap-through and limiting folding positions. By analysing the geometry and mechanics of the origami structures, we extend the design space of mechanical metamaterials and provide a basis for their practical applications in science and engineering.

  19. Kinetics and Mechanisms of Calcite Reactions with Saline Waters

    SciTech Connect

    Chapman, Piers; *Morse, John W.

    2010-11-15

    1. Objective The general objective of this research was to determine the kinetics and mechanisms of calcite reactions with saline waters over a wide range of saline water composition, carbon dioxide partial pressure (pCO2), and modest ranges of T and P. This would be done by studying both reaction rates and solubility from changes in solution chemistry. Also, nanoscale observations of calcite surface morphology and composition would be made to provide an understanding of rate controlling mechanisms.

  20. Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations.

    PubMed

    Zhou, Hongyi; Zhang, Chi; Liu, Song; Zhou, Yaoqi

    2005-07-01

    We have developed the following web servers for protein structural modeling and analysis at http://theory.med.buffalo.edu: THUMBUP, UMDHMM(TMHP) and TUPS, predictors of transmembrane helical protein topology based on a mean-burial-propensity scale of amino acid residues (THUMBUP), hidden Markov model (UMDHMM(TMHP)) and their combinations (TUPS); SPARKS 2.0 and SP3, two profile-profile alignment methods, that match input query sequence(s) to structural templates by integrating sequence profile with knowledge-based structural score (SPARKS 2.0) and structure-derived profile (SP3); DFIRE, a knowledge-based potential for scoring free energy of monomers (DMONOMER), loop conformations (DLOOP), mutant stability (DMUTANT) and binding affinity of protein-protein/peptide/DNA complexes (DCOMPLEX & DDNA); TCD, a program for protein-folding rate and transition-state analysis of small globular proteins; and DOGMA, a web-server that allows comparative analysis of domain combinations between plant and other 55 organisms. These servers provide tools for prediction and/or analysis of proteins on the secondary structure, tertiary structure and interaction levels, respectively.

  1. Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway

    PubMed Central

    Bisaria, Namita; Greenfeld, Max; Limouse, Charles; Pavlichin, Dmitri S.; Mabuchi, Hideo; Herschlag, Daniel

    2016-01-01

    The past decade has seen a wealth of 3D structural information about complex structured RNAs and identification of functional intermediates. Nevertheless, developing a complete and predictive understanding of the folding and function of these RNAs in biology will require connection of individual rate and equilibrium constants to structural changes that occur in individual folding steps and further relating these steps to the properties and behavior of isolated, simplified systems. To accomplish these goals we used the considerable structural knowledge of the folded, unfolded, and intermediate states of P4-P6 RNA. We enumerated structural states and possible folding transitions and determined rate and equilibrium constants for the transitions between these states using single-molecule FRET with a series of mutant P4-P6 variants. Comparisons with simplified constructs containing an isolated tertiary contact suggest that a given tertiary interaction has a stereotyped rate for breaking that may help identify structural transitions within complex RNAs and simplify the prediction of folding kinetics and thermodynamics for structured RNAs from their parts. The preferred folding pathway involves initial formation of the proximal tertiary contact. However, this preference was only ∼10 fold and could be reversed by a single point mutation, indicating that a model akin to a protein-folding contact order model will not suffice to describe RNA folding. Instead, our results suggest a strong analogy with a modified RNA diffusion-collision model in which tertiary elements within preformed secondary structures collide, with the success of these collisions dependent on whether the tertiary elements are in their rare binding-competent conformations. PMID:27493222

  2. Direct Observation of Folding Energy Landscape of RNA Hairpin at Mechanical Loading Rates.

    PubMed

    Xu, Huizhong; Plaut, Benjamin; Zhu, Xiran; Chen, Maverick; Mavinkurve, Udit; Maiti, Anindita; Song, Guangtao; Murari, Krishna; Mandal, Maumita

    2017-03-16

    By applying a controlled mechanical load using optical tweezers, we measured the diffusive barrier crossing in a 49 nt long P5ab RNA hairpin. We find that in the free-energy landscape the barrier height (G(‡)) and transition distance (x(‡)) are dependent on the loading rate (r) along the pulling direction, x, as predicted by Bell. The barrier shifted toward the initial state, whereas ΔG(‡) reduced significantly from 50 to 5 kT, as r increased from 0 to 32 pN/s. However, the equilibrium work (ΔG) during strand separation, as estimated by Crook's fluctuation theorem, remained unchanged at different rates. Previously, helix formation and denaturation have been described as two-state (F ↔ U) transitions for P5ab. Herein, we report three intermediate states I1, I, and I2 located at 4, 11, and 16 nm respectively, from the folded conformation. The intermediates were observed only when the hairpin was subjected to an optimal r, 7.6 pN/s. The results indicate that the complementary strands in P5ab can zip and unzip through complex routes, whereby mismatches act as checkpoints and often impose barriers. The study highlights the significance of loading rates in force-spectroscopy experiments that are increasingly being used to measure the folding properties of biomolecules.

  3. Role of five-fold twin boundary on the enhanced mechanical properties of fcc Fe nanowires.

    PubMed

    Wu, J Y; Nagao, S; He, J Y; Zhang, Z L

    2011-12-14

    The role of 5-fold twin boundary on the structural and mechanical properties of fcc Fe nanowire under tension is explored by classical molecular dynamics. Twin-stabilized fcc nanowire with various diameters (6-24 nm) are examined by tension tests at several temperatures ranging from 0.01 to 1100 K. Significant increase in the Young's modulus of the smaller nanowires is revealed to originate from the central area of quinquefoliolate-like stress-distribution over the 5-fold twin, rather than from the surface tension that is often considered as the main source of such size-effects found in nanostructures. Because of the excess compressive stress caused by crossing twin-boundaries, the atoms in the center behave stiffer than those in bulk and even expand laterally under axial tension, providing locally negative Poisson's ratio. The yield strength of nanowire is also enhanced by the twin boundary that suppresses dislocation nucleation within a fcc twin-domain; therefore, the plasticity of nanowire is initiated by strain-induced fcc→bcc phase transformation that destroys the twin structure. After the yield, the nucleated bcc phase immediately spreads to the entire area, and forms a multigrain structure to realize ductile deformation followed by necking. As temperature elevated close to the critical temperature between bcc and fcc phases, the increased stability of fcc phase competes with the phase transformation under tension, and hence dislocation nucleations in fcc phase are observed exclusively at the highest temperature in our study.

  4. Redox cofactors insertion in prokaryotic molybdoenzymes occurs via a conserved folding mechanism

    PubMed Central

    Arias-Cartin, Rodrigo; Ceccaldi, Pierre; Schoepp-Cothenet, Barbara; Frick, Klaudia; Blanc, Jean-Michel; Guigliarelli, Bruno; Walburger, Anne; Grimaldi, Stéphane; Friedrich, Thorsten; Receveur-Brechot, Véronique; Magalon, Axel

    2016-01-01

    A major gap of knowledge in metalloproteins is the identity of the prefolded state of the protein before cofactor insertion. This holds for molybdoenzymes serving multiple purposes for life, especially in energy harvesting. This large group of prokaryotic enzymes allows for coordination of molybdenum or tungsten cofactors (Mo/W-bisPGD) and Fe/S clusters. Here we report the structural data on a cofactor-less enzyme, the nitrate reductase respiratory complex and characterize the conformational changes accompanying Mo/W-bisPGD and Fe/S cofactors insertion. Identified conformational changes are shown to be essential for recognition of the dedicated chaperone involved in cofactors insertion. A solvent-exposed salt bridge is shown to play a key role in enzyme folding after cofactors insertion. Furthermore, this salt bridge is shown to be strictly conserved within this prokaryotic molybdoenzyme family as deduced from a phylogenetic analysis issued from 3D structure-guided multiple sequence alignment. A biochemical analysis with a distantly-related member of the family, respiratory complex I, confirmed the critical importance of the salt bridge for folding. Overall, our results point to a conserved cofactors insertion mechanism within the Mo/W-bisPGD family. PMID:27886223

  5. Rapid three-dimensional microfluidic mixer for high viscosity solutions to unravel earlier folding kinetics of G-quadruplex under molecular crowding conditions.

    PubMed

    Liu, Chao; Li, Ying; Li, Yiwei; Chen, Peng; Feng, Xiaojun; Du, Wei; Liu, Bi-Feng

    2016-01-01

    Rapid mixing of highly viscous solutions is a great challenge, which helps to analyze the reaction kinetics in viscous liquid phase, particularly to discover the folding kinetics of macromolecules under molecular crowding conditions mimicking the conditions inside cells. Here, we demonstrated a novel microfluidic mixer based on Dean flows with three-dimensional (3D) microchannel configuration for fast mixing of high-viscosity fluids. The main structure contained three consecutive subunits, each consisting of a "U"-type channel followed by a chamber with different width and height. Thus, the two solutions injected from the two inlets would undergo a mixing in the first "U"-type channel due to the Dean flow effect, and simultaneous vortices expansions in both horizontal and vertical directions in the following chamber. Numerical simulations and experimental characterizations confirmed that the micromixer could achieve a mixing time of 122.4μs for solutions with viscosities about 33.6 times that of pure water. It was the fastest micromixer for high viscosity solutions compared with previous reports. With this highly efficient 3D microfluidic mixer, we further characterized the early folding kinetics of human telomere G-quadruplex under molecular crowding conditions, and unravelled a new folding process within 550μs.

  6. Mechanics of fold-and-thrust belts and accretionary wedges Cohesive Coulomb theory

    NASA Technical Reports Server (NTRS)

    Dahlen, F. A.; Suppe, J.; Davis, D.

    1984-01-01

    A self-consistent theory for the mechanics of thin-skinned accretionary Coulomb wedges is developed and applied to the active fold-and-thrust belt of western Taiwan. The state of stress everywhere within a critical wedge is determined by solving the static equilibrium equations subject to the appropriate boundary conditions. The influence of wedge cohesion, which gives rise to a concave curvature of the critical topographic surface and affects the orientation of the principal stresses and Coulomb fracture within the wedge, is considered. The shape of the topographic surface and the angles at which thrust faults step up from the basal decollement in the Taiwanese belt is analyzed taking into account the extensive structural and fluid-pressure data available there. It is concluded that the gross geometry and structure of the Taiwan wedge are consistent with normal laboratory frictional and fracture strengths of sedimentary rocks.

  7. Alternating access mechanisms of LeuT-fold transporters: trailblazing towards the promised energy landscapes.

    PubMed

    Kazmier, Kelli; Claxton, Derek P; Mchaourab, Hassane S

    2016-12-29

    Secondary active transporters couple the uphill translocation of substrates to electrochemical ion gradients. Transporter conformational motion, generically referred to as alternating access, enables a central ligand binding site to change its orientation relative to the membrane. Here we review themes of alternating access and the transduction of ion gradient energy to power this process in the LeuT-fold class of transporters where crystallographic, computational and spectroscopic approaches have converged to yield detailed models of transport cycles. Specifically, we compare findings for the Na(+)-coupled amino acid transporter LeuT and the Na(+)-coupled hydantoin transporter Mhp1. Although these studies have illuminated multiple aspects of transporter structures and dynamics, a number of questions remain unresolved that so far hinder understanding transport mechanisms in an energy landscape perspective.

  8. Purification and kinetic mechanism of the major glutathione S-transferase from bovine brain.

    PubMed Central

    Young, P R; Briedis, A V

    1989-01-01

    The major glutathione S-transferase isoenzyme from bovine brain was isolated and purified approx. 500-fold. The enzyme has a pI of 7.39 +/- 0.02 and consists of two non-identical subunits having apparent Mr values of 22,000 and 24,000. The enzyme is uniformly distributed in brain, and kinetic data at pH 6.5 with 1-chloro-2,4-dinitrobenzene (CDNB) as substrate suggest a random rapid-equilibrium mechanism. The kinetics of inhibition by product, by GSH analogues and by NADH are consistent with the suggested mechanism and require inhibitor binding to several different enzyme forms. Long-chain fatty acids are excellent inhibitors of the enzyme, and values of 1nKi for hexanoic acid, octanoic acid, decanoic acid and lauric acid form a linear series when plotted as a function of alkyl chain length. A free-energy change of -1900 J/mol (-455 cal/mol) per CH2 unit is calculated for the contribution of hydrophobic binding energy to the inhibition constants. The turnover number of the purified enzyme dimer is approx. 3400/min. When compared with the second-order rate constant for the reaction between CDNB and GSH, the enzyme is providing a rate acceleration of about 1000-fold. The role of entropic contributions to this small rate acceleration is discussed. PMID:2930465

  9. Effects of heme on the structure of the denatured state and folding kinetics of cytochrome b562.

    PubMed

    Garcia, Pascal; Bruix, Marta; Rico, Manuel; Ciofi-Baffoni, Simone; Banci, Lucia; Ramachandra Shastry, M C; Roder, Heinrich; de Lumley Woodyear, Thierry; Johnson, Christopher M; Fersht, Alan R; Barker, Paul D

    2005-02-11

    Heme-linked proteins, such as cytochromes, are popular subjects for protein folding studies. There is the underlying question of whether the heme affects the structure of the denatured state by cross-linking it and forming other interactions, which would perturb the folding pathway. We have studied wild-type and mutant cytochrome b562 from Escherichia coli, a 106 residue four-alpha-helical bundle. The holo protein apparently refolds with a half-life of 4 micros in its ferrous state. We have analysed the folding of the apo protein using continuous-flow fluorescence as well as stopped-flow fluorescence and CD. The apo protein folded much more slowly with a half-life of 270 micros that was unaffected by the presence of exogenous heme. We examined the nature of the denatured states of both holo and apo proteins by NMR methods over a range of concentrations of guanidine hydrochloride. The starting point for folding of the holo protein in concentrations of denaturant around the denaturation transition was a highly ordered native-like species with heme bound. Fully denatured holo protein at higher concentrations of denaturant consisted of denatured apo protein and free heme. Our results suggest that the very fast folding species of denatured holo protein is in a compact state, whereas the normal folding pathway from fully denatured holo protein consists of the slower folding of the apo protein followed by the binding of heme. These data should be considered in the analysis of folding of heme proteins.

  10. Predicting Folding Sequences Based on the Maximum Rock Strength and Mechanical Equilibrium

    NASA Astrophysics Data System (ADS)

    Cubas, N.; Souloumiac, P.; Maillot, B.; Leroy, Y. M.

    2007-12-01

    The objective is to propose and validate simple procedures, compared to the finite-element method, to select and optimize the dominant mode of folding in fold-and-thrust belts and accretionary wedges, and to determine its stress distribution. Mechanical equilibrium as well as the constraints due to the limited rock strength of the bulk material and of major discontinuities, such as décollements, are accounted for. The first part of the proposed procedure, which is at the core of the external approach of classical limit analysis, consists in estimating the least upper bound on the tectonic force by minimisation of the internal dissipation and part of the external work. The new twist to the method is that the optimization is also done with respect to the geometry of the evolving fold. If several folding events are possible, the dominant mode is the one leading to the least upper bound. The second part of the procedure is based on the Equilibrium Element Method, which is an application of the internal approach of limit analysis. The optimum stress field, obtained by spatial discretisation of the fold, provides the best lower bound on the tectonic force. The difference between the two bounds defines an error estimate of the exact unknown tectonic force. To show the merits of the proposed procedure, its first part is applied to predict the life span of a thrust within an accretionary prism, from its onset, its development with a relief build up and its arrest because of the onset of a more favorable new thrust (Cubas et al., 2007). This life span is sensitive to the friction angles over the ramp and the décollement. It is shown how the normal sequence of thrusting in a supercritical wedge is ended with the first out-of sequence event. The second part of the procedure provides the stress state over each thrust showing that the active back thrust is a narrow fan which dip is sensitive to the friction angle over the ramp and the amount of relief build up (Souloumiac et

  11. Kinetics and mechanisms of some atomic oxygen reactions

    NASA Technical Reports Server (NTRS)

    Cvetanovic, R. J.

    1987-01-01

    Mechanisms and kinetics of some reactions of the ground state of oxygen atoms, O(3P), are briefly summarized. Attention is given to reactions of oxygen atoms with several different types of organic and inorganic compounds such as alkanes, alkenes, alkynes, aromatics, and some oxygen, nitrogen, halogen and sulfur derivatives of these compounds. References to some recent compilations and critical evaluations of reaction rate constants are given.

  12. Biomineralization mechanisms: a kinetics and interfacial energy approach

    NASA Astrophysics Data System (ADS)

    Nancollas, George H.; Wu, Wenju

    2000-04-01

    The calcium phosphates and oxalates are among the most frequently encountered biomineral phases and numerous kinetics studies have been made of their crystallization and dissolution in supersaturated and undersaturated solutions, respectively. These have focused mainly on parameters such as solution composition, ionic strength, pH, temperature, and solid surface characteristics. There is considerable interest in extending such studies to solutions more closely simulating the biological milieu. The constant composition method is especially useful for investigating the mechanisms of these reactions, and in the present work, the interfacial tensions between water and each of these surfaces have been calculated from measured contact angles using surface tension component theory. Values for the calcium phosphate phases such as dicalcium phosphate dihydrate (DCPD), octacalcium phosphate (OCP), hydroxyapatite (HAP), and fluorapatite (FAP) may be compared with data calculated from dissolution kinetics experiments invoking different reaction mechanisms. Agreement between the directly measured interfacial energies and those calculated from the kinetics experiments provides valuable corroborative information about individual growth and dissolution mechanisms. For the calcium phosphates, the much smaller interfacial tensions of OCP and DCPD in contact with water as compared with those of HAP and FAP support the suggestion that the former phases are precursors in HAP and FAP biomineralization. The ability of a surface to nucleate mineral phases is closely related to the magnitude of the interfacial energies. Constant composition studies have also shown that HAP is an effective nucleator of calcium oxalate monohydrate, both of which are frequently observed in renal stones.

  13. Influence of Glu/Arg, Asp/Arg, and Glu/Lys Salt Bridges on α-Helical Stability and Folding Kinetics.

    PubMed

    Meuzelaar, Heleen; Vreede, Jocelyne; Woutersen, Sander

    2016-06-07

    Using a combination of ultraviolet circular dichroism, temperature-jump transient-infrared spectroscopy, and molecular dynamics simulations, we investigate the effect of salt bridges between different types of charged amino-acid residue pairs on α-helix folding. We determine the stability and the folding and unfolding rates of 12 alanine-based α-helical peptides, each of which has a nearly identical composition containing three pairs of positively and negatively charged residues (either Glu(-)/Arg(+), Asp(-)/Arg(+), or Glu(-)/Lys(+)). Within each set of peptides, the distance and order of the oppositely charged residues in the peptide sequence differ, such that they have different capabilities of forming salt bridges. Our results indicate that stabilizing salt bridges (in which the interacting residues are spaced and ordered such that they favor helix formation) speed up α-helix formation by up to 50% and slow down the unfolding of the α-helix, whereas salt bridges with an unfavorable geometry have the opposite effect. Comparing the peptides with different types of charge pairs, we observe that salt bridges between side chains of Glu(-) and Arg(+) are most favorable for the speed of folding, probably because of the larger conformational space of the salt-bridging Glu(-)/Arg(+) rotamer pairs compared to Asp(-)/Arg(+) and Glu(-)/Lys(+). We speculate that the observed impact of salt bridges on the folding kinetics might explain why some proteins contain salt bridges that do not stabilize the final, folded conformation.

  14. Folded Spring and Mechanically Switching SSHI for High Performance Miniature Piezoelectric Vibration Energy Harvester

    NASA Astrophysics Data System (ADS)

    Asanuma, H.; Okubo, H.; Komatsuzaki, T.; Iwata, Y.

    2016-11-01

    To downsize the clamp area and increase the output power of the harvester, we developed a miniature piezoelectric vibration energy harvester with combining a Z-shaped folded spring and a mechanically-switching SSHI (synchronized switch harvesting on inductor). The overall harvester size is 4×2×3 cm3. The FEM analysis revealed that the output power increases and the value of the 1st and 2nd resonance frequencies move closer as the angle of the Z-shaped spring decreases, therefore, the smaller angle would be more promising. The experimental results showed that the maximum output power of our harvester for the 1st (20.2 Hz) and 2nd (53.0 Hz) resonance frequencies at the applied acceleration of 4.9 m/s2 are 088 and 0.98 mW, respectively. The reason for a marked enhancement of the output power for the 2nd resonance frequency is attributed to the vertical movement of the 2nd vibrational mode which applies larger mechanical stress to the piezo ceramic and achieves better electrical contact between the tip of the Z-shaped spring and the spring plunger.

  15. Kinetic Mechanism of Protein N-terminal Methyltransferase 1*

    PubMed Central

    Richardson, Stacie L.; Mao, Yunfei; Zhang, Gang; Hanjra, Pahul; Peterson, Darrell L.; Huang, Rong

    2015-01-01

    The protein N-terminal methyltransferase 1 (NTMT1) catalyzes the transfer of the methyl group from the S-adenosyl-l-methionine to the protein α-amine, resulting in formation of S-adenosyl-l-homocysteine and α-N-methylated proteins. NTMT1 is an interesting potential anticancer target because it is overexpressed in gastrointestinal cancers and plays an important role in cell mitosis. To gain insight into the biochemical mechanism of NTMT1, we have characterized the kinetic mechanism of recombinant NTMT1 using a fluorescence assay and mass spectrometry. The results of initial velocity, product, and dead-end inhibition studies indicate that methylation by NTMT1 proceeds via a random sequential Bi Bi mechanism. In addition, our processivity studies demonstrate that NTMT1 proceeds via a distributive mechanism for multiple methylations. Together, our studies provide new knowledge about the kinetic mechanism of NTMT1 and lay the foundation for the development of mechanism-based inhibitors. PMID:25771539

  16. The carbon-bond mechanism: a condensed kinetic mechanism for photochemical smog

    SciTech Connect

    Whitten, G.Z.; Hog, H.; Killus, J.P.

    1980-06-01

    Efforts to develop a model that can simulate photochemical smog with kinetic mechanisms are discussed. The carbon-bond mechanism is a set of generalized reactions that can be used to model photochemical oxidant formation. The theoretical framework of carbon-bond mechanism is outlined. Chemical variables that are incorporated into the carbon-bond mechanism model are described. Further work that is needed on the carbon-bond mechanism model is considered. (1 diagram, 13 graphs, 30 references, 2 tables)

  17. Network measures for protein folding state discrimination

    PubMed Central

    Menichetti, Giulia; Fariselli, Piero; Remondini, Daniel

    2016-01-01

    Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there is not a first-principle model to explain this different behavior. We exploit the network properties of protein structures by introducing novel observables to address the problem of classifying the different types of folding kinetics. These observables display a plain physical meaning, in terms of vibrational modes, possible configurations compatible with the native protein structure, and folding cooperativity. The relevance of these observables is supported by a classification performance up to 90%, even with simple classifiers such as discriminant analysis. PMID:27464796

  18. A new mechanism for producing cleavage in preexisting folds: The translation mechanism. An example in the Burela section (Variscan belt, NW Spain)

    NASA Astrophysics Data System (ADS)

    Bobillo-Ares, Nilo C.; Bastida, Fernando; Aller, Jesús; Lisle, Richard J.

    2017-01-01

    An outcrop on the Cantabrian coast (Burela section) shows a long train of tight meter-scale folds developed in Cambrian siliciclastic rocks. These folds have been shortened in the axial trace direction on the fold profile, developing a cleavage in the incompetent layers which obliterates the primary cleavage and crosscuts the folds. Several mechanisms have been analyzed to explain the development and attitude of this cleavage, some of them being the same as those that have previously been proposed to form folds but operating in a reverse sense. They are: anti-flexural flow, anti-reverse tangential longitudinal strain and homogeneous strain. The sole operation of these mechanisms cannot explain this cleavage and a new one has been defined with this aim. This mechanism consists of deformation of the incompetent layers by translation of the competent ones (translation mechanism), and it involves an area decrease within the incompetent layers in the fold profile plane and, if there is no important volume decrease, a stretching in the hinge direction that must affect both competent and incompetent layers. The geometrical properties of this mechanism have been analyzed in detail and it is concluded that, combined with a small amount of homogeneous flattening, this mechanism can explain the distribution of the cleavage through the folds.

  19. Significance of first-order faults in folding mechanically isotropic layers: Evidence from the Sudbury Basin, Canada

    NASA Astrophysics Data System (ADS)

    Clark, Martin D.; Riller, Ulrich

    2017-02-01

    The Sudbury Basin is a non-cylindrical fold basin demarcated by the layered Sudbury Igneous Complex (SIC), the eastern part of which is transected by prominent curved faults. Folding of the SIC and adjacent rock units occurred in the brittle field and is peculiar due to its petrographically distinct, but initially mechanically similar layers. Overall, the layers are characterized by low levels of solid-state strain raising the question how the layer contacts acquired their curvature. We addressed this question by developing a G.I.S.-based workflow to analyze the orientation and slip vectors of the faults. Slip vectors form clusters of normal and reverse slip along a given fault. The clustering is best interpreted in terms of successive slip events during folding of the SIC. As the faults formed most likely as planar reverse faults prior to folding of the SIC they subsequently served as mechanically anisotropic elements to fold the SIC. The results contribute to (1) better understand the folding mechanisms of thick melt sheets in the upper crust, (2) explain apparently incompatible principal strain axes during progressive deformation, and (3) efficiently analyze the orientation and kinematics of fault zones close to the Earth's surface.

  20. Microwave pyrolysis of rice straw: products, mechanism, and kinetics.

    PubMed

    Huang, Yu-Fong; Chiueh, Pei-Te; Kuan, Wen-Hui; Lo, Shang-Lien

    2013-08-01

    Rice straw is an abundant resource for the production of biofuels and bio-based products. How to convert the recalcitrant lignocellulose effectually is a critical issue. The objective of this study was to investigate the products, mechanism, and kinetics of rice straw pyrolysis by using microwave heating. The highest energy densification ratio of solid residues was achieved at the microwave power level of 300 W. The atomic H/C and O/C ratios of solid residues were much lower than those of rice straw. The primary components of gaseous product were CO, H2, CO2, and CH4, whose molecular fractions were 57%, 21%, 14%, and 8%, respectively. The more gaseous product and the less solid residues were obtained at higher microwave power levels, while the liquid production remained the same and showed a maximum of about 50 wt.%. The kinetic parameters of rice straw pyrolysis were increased with increasing microwave power level.

  1. Identical folds used for distinct mechanical functions of the bacterial flagellar rod and hook

    PubMed Central

    Fujii, Takashi; Kato, Takayuki; Hiraoka, Koichi D.; Miyata, Tomoko; Minamino, Tohru; Chevance, Fabienne F. V.; Hughes, Kelly T.; Namba, Keiichi

    2017-01-01

    The bacterial flagellum is a motile organelle driven by a rotary motor, and its axial portions function as a drive shaft (rod), a universal joint (hook) and a helical propeller (filament). The rod and hook are directly connected to each other, with their subunit proteins FlgG and FlgE having 39% sequence identity, but show distinct mechanical properties; the rod is straight and rigid as a drive shaft whereas the hook is flexible in bending as a universal joint. Here we report the structure of the rod and comparison with that of the hook. While these two structures have the same helical symmetry and repeat distance and nearly identical folds of corresponding domains, the domain orientations differ by ∼7°, resulting in tight and loose axial subunit packing in the rod and hook, respectively, conferring the rigidity on the rod and flexibility on the hook. This provides a good example of versatile use of a protein structure in biological organisms. PMID:28120828

  2. Mechanisms and consequences of protein aggregation: the role of folding intermediates.

    PubMed

    Seshadri, Sangita; Oberg, Keith A; Uversky, Vladimir N

    2009-10-01

    Protein aggregation, being one of the hottest topics of modern protein science, is recognized now as a serious biomedical and biotechnological problem. Protein aggregation is considered as a causative factor (or at least an associated symptom) of a wide spectrum of human pathologies. Furthermore, aggregation and precipitation are known to trammel recombinant protein production, as well as to affect the manufacture, storage and delivery of proteinaceous drugs. Therefore, this topic attracts the serious attention of many researchers, a conclusion that follows from the average daily publication of 7-8 scientific papers dedicated to the various aspects of protein aggregation. However, the situation was rather different 15-20 years ago when it was believed that the formation of protein aggregates causing the irreversibility of unfolding or denaturation of some proteins was nothing more than an annoying experimental artifact, hampering the detailed characterization of the unfolding/denaturation processes. At that time, only a few laboratories (including the laboratory of Prof. Anthony L. Fink) seriously worked on understanding the molecular mechanisms of this "artifact". In this review, we summarize some of the early work of Tony Fink on aggregation, of protein folding intermediates and on the analysis of the structural consequences of this process.

  3. Structural insights into a unique cellulase fold and mechanism of cellulose hydrolysis.

    PubMed

    Brás, Joana L A; Cartmell, Alan; Carvalho, Ana Luísa M; Verzé, Genny; Bayer, Edward A; Vazana, Yael; Correia, Márcia A S; Prates, José A M; Ratnaparkhe, Supriya; Boraston, Alisdair B; Romão, Maria J; Fontes, Carlos M G A; Gilbert, Harry J

    2011-03-29

    Clostridium thermocellum is a well-characterized cellulose-degrading microorganism. The genome sequence of C. thermocellum encodes a number of proteins that contain type I dockerin domains, which implies that they are components of the cellulose-degrading apparatus, but display no significant sequence similarity to known plant cell wall-degrading enzymes. Here, we report the biochemical properties and crystal structure of one of these proteins, designated CtCel124. The protein was shown to be an endo-acting cellulase that displays a single displacement mechanism and acts in synergy with Cel48S, the major cellulosomal exo-cellulase. The crystal structure of CtCel124 in complex with two cellotriose molecules, determined to 1.5 Å, displays a superhelical fold in which a constellation of α-helices encircle a central helix that houses the catalytic apparatus. The catalytic acid, Glu96, is located at the C-terminus of the central helix, but there is no candidate catalytic base. The substrate-binding cleft can be divided into two discrete topographical domains in which the bound cellotriose molecules display twisted and linear conformations, respectively, suggesting that the enzyme may target the interface between crystalline and disordered regions of cellulose.

  4. Structural insights into a unique cellulase fold and mechanism of cellulose hydrolysis

    PubMed Central

    Brás, Joana L. A.; Cartmell, Alan; Carvalho, Ana Luísa M.; Verzé, Genny; Bayer, Edward A.; Vazana, Yael; Correia, Márcia A. S.; Prates, José A. M.; Ratnaparkhe, Supriya; Boraston, Alisdair B.; Romão, Maria J.; Fontes, Carlos M. G. A.; Gilbert, Harry J.

    2011-01-01

    Clostridium thermocellum is a well-characterized cellulose-degrading microorganism. The genome sequence of C. thermocellum encodes a number of proteins that contain type I dockerin domains, which implies that they are components of the cellulose-degrading apparatus, but display no significant sequence similarity to known plant cell wall–degrading enzymes. Here, we report the biochemical properties and crystal structure of one of these proteins, designated CtCel124. The protein was shown to be an endo-acting cellulase that displays a single displacement mechanism and acts in synergy with Cel48S, the major cellulosomal exo-cellulase. The crystal structure of CtCel124 in complex with two cellotriose molecules, determined to 1.5 Å, displays a superhelical fold in which a constellation of α-helices encircle a central helix that houses the catalytic apparatus. The catalytic acid, Glu96, is located at the C-terminus of the central helix, but there is no candidate catalytic base. The substrate-binding cleft can be divided into two discrete topographical domains in which the bound cellotriose molecules display twisted and linear conformations, respectively, suggesting that the enzyme may target the interface between crystalline and disordered regions of cellulose. PMID:21393568

  5. Mechanism-based corrector combination restores ΔF508-CFTR folding and function

    PubMed Central

    Okiyoneda, Tsukasa; Veit, Guido; Dekkers, Johanna F.; Bagdany, Miklos; Soya, Naoto; Xu, Haijin; Roldan, Ariel; Verkman, Alan S.; Kurth, Mark; Simon, Agnes; Hegedus, Tamas; Beekman, Jeffrey M.; Lukacs, Gergely L.

    2013-01-01

    The most common cystic fibrosis (CF) mutation, ΔF508 in the nucleotide binding domain-1 (NBD1), impairs CFTR coupled-domain folding, plasma membrane (PM) expression, function and stability. VX-809, a promising investigational corrector of ΔF508-CFTR misprocessing, has limited clinical benefit and incompletely understood mechanism, hampering drug development. Based on the effect of second site suppressor mutations, robust ΔF508-CFTR correction likely requires stabilization of NBD1 and the membrane spanning domains (MSDs)-NBD1 interface, both established primary conformational defects. Here, we elucidated the molecular targets of available correctors; class-I stabilizes the NBD1-MSD1/2 interface, class-II targets NBD2, and only chemical chaperones, surrogates of class-III correctors, stabilize the human ΔF508-NBD1. While VX-809 can correct missense mutations primarily destabilizing the NBD1-MSD1/2 interface, functional PM expression of ΔF508-CFTR also requires compounds that counteract the NBD1 and NBD2 stability defects in CF bronchial epithelial cells and intestinal organoids. Thus, structure-guided corrector combination represents an effective approach for CF therapy. PMID:23666117

  6. Atomimetic Mechanical Structures with Nonlinear Topological Domain Evolution Kinetics.

    PubMed

    Frazier, Michael J; Kochmann, Dennis M

    2017-03-21

    A mechanical metamaterial, a simple, periodic mechanical structure, is reported, which reproduces the nonlinear dynamic behavior of materials undergoing phase transitions and domain switching at the structural level. Tunable multistability is exploited to produce switching and transition phenomena whose kinetics are governed by the same Allen-Cahn law commonly used to describe material-level, structural-transition processes. The reported purely elastic mechanical system displays several key features commonly found in atomic- or mesoscale physics of solids. The rotating-mass network shows qualitatively analogous features as, e.g., ferroic ceramics or phase-transforming solids, and the discrete governing equation is shown to approach the phase field equation commonly used to simulate the above processes. This offers untapped opportunities for reproducing material-level, dissipative and diffusive kinetic phenomena at the structural level, which, in turn, invites experimental realization and paves the road for new active, intelligent, or phase-transforming mechanical metamaterials bringing small-scale processes to the macroscopically observable scale.

  7. Modeling the effect of codon translation rates on co-translational protein folding mechanisms of arbitrary complexity

    NASA Astrophysics Data System (ADS)

    Caniparoli, Luca; O'Brien, Edward P.

    2015-04-01

    In a cell, the folding of a protein molecule into tertiary structure can begin while it is synthesized by the ribosome. The rate at which individual amino acids are incorporated into the elongating nascent chain has been shown to affect the likelihood that proteins will populate their folded state, indicating that co-translational protein folding is a far from equilibrium process. Developing a theoretical framework to accurately describe this process is, therefore, crucial for advancing our understanding of how proteins acquire their functional conformation in living cells. Current state-of-the-art computational approaches, such as molecular dynamics simulations, are very demanding in terms of the required computer resources, making the simulation of co-translational protein folding difficult. Here, we overcome this limitation by introducing an efficient approach that predicts the effects that variable codon translation rates have on co-translational folding pathways. Our approach is based on Markov chains. By using as an input a relatively small number of molecular dynamics simulations, it allows for the computation of the probability that a nascent protein is in any state as a function of the translation rate of individual codons along a mRNA's open reading frame. Due to its computational efficiency and favorable scalability with the complexity of the folding mechanism, this approach could enable proteome-wide computational studies of the influence of translation dynamics on co-translational folding.

  8. Simplified jet-A kinetic mechanism for combustor application

    NASA Technical Reports Server (NTRS)

    Lee, Chi-Ming; Kundu, Krishna; Ghorashi, Bahman

    1993-01-01

    Successful modeling of combustion and emissions in gas turbine engine combustors requires an adequate description of the reaction mechanism. For hydrocarbon oxidation, detailed mechanisms are only available for the simplest types of hydrocarbons such as methane, ethane, acetylene, and propane. These detailed mechanisms contain a large number of chemical species participating simultaneously in many elementary kinetic steps. Current computational fluid dynamic (CFD) models must include fuel vaporization, fuel-air mixing, chemical reactions, and complicated boundary geometries. To simulate these conditions a very sophisticated computer model is required, which requires large computer memory capacity and long run times. Therefore, gas turbine combustion modeling has frequently been simplified by using global reaction mechanisms, which can predict only the quantities of interest: heat release rates, flame temperature, and emissions. Jet fuels are wide-boiling-range hydrocarbons with ranges extending through those of gasoline and kerosene. These fuels are chemically complex, often containing more than 300 components. Jet fuel typically can be characterized as containing 70 vol pct paraffin compounds and 25 vol pct aromatic compounds. A five-step Jet-A fuel mechanism which involves pyrolysis and subsequent oxidation of paraffin and aromatic compounds is presented here. This mechanism is verified by comparing with Jet-A fuel ignition delay time experimental data, and species concentrations obtained from flametube experiments. This five-step mechanism appears to be better than the current one- and two-step mechanisms.

  9. High temperature heterogeneous reaction kinetics and mechanisms of tungsten oxidation

    NASA Astrophysics Data System (ADS)

    Sabourin, Justin L.

    Tungsten, which is a material used in many high temperature applications, is limited by its susceptibility to oxidation at elevated temperatures. Although tungsten has the highest melting temperature of any metal, at much lower temperatures volatile oxides are formed during oxidation with oxygen containing species. This differs from many heterogeneous oxidation reactions involving metals since most reactions form very stable oxides that have higher melting or boiling points than the pure metal (e.g., aluminum, iron). Understanding heterogeneous oxidation and vaporization processes may allow for the expansion and improvement of high temperature tungsten applications. In order to increase understanding of the oxidation processes of tungsten, there is a need to develop reaction mechanisms and kinetics for oxidation processes involving oxidizers and environmental conditions of interest. Tungsten oxidation was thoroughly studied in the past, and today there is a good phenomenological understanding of these processes. However, as the design of large scale systems increasingly relies on computer modeling there becomes a need for improved descriptions of chemical reactions. With the increase in computing power over the last several decades, and the development of quantum chemistry and physics theories, heterogeneous systems can be modeled in detail at the molecular level. Thermochemical parameters that may not be measured experimentally may now be determined theoretically, a tool that was previously unavailable to scientists and engineers. Additionally, chemical kinetic modeling software is now available for both homogeneous and heterogeneous reactions. This study takes advantage of these new theoretical tools, as well as a thermogravimetric (TG) flow reactor developed as part of this study to learn about mechanisms and kinetics of tungsten oxidation. Oxidizers of interest are oxygen (O2), carbon dioxide (CO 2), water (H2O), and other oxidizers present in combustion and

  10. Kinetics and mechanism of the oxidation of amaranth with hypochlorite.

    PubMed

    Nadupalli, S; Koorbanally, N; Jonnalagadda, S B

    2011-07-14

    The reaction mechanism of the oxidation of Amaranth dye (2-hydroxy-1-(4-sulfonato-1-naphthylazo) naphthalene-3,6-disulfonate) with hypochlorite under varied pH conditions was elucidated by a kinetic approach. Under excess concentration of oxidant, the reaction followed pseudo-first-order kinetics with respect to Amaranth, and the oxidation was found to occur through two competitive reactions, initiated by hypochlorite and hypochlorous acid. The reaction order with respect to both OCl(-) ion and HOCl was unity. While the latter reaction was fast, the significance of the oxidation paths depended on the relative concentration of the two oxidizing species, which was dictated by the reaction pH. The role of the H(+) ion in the reaction was established. For the hypochlorite ion and hypochlorous acid facilitated reactions, the second-order rate coefficients were 1.9 and 23.2 M(-1) s(-1), respectively. The energy parameters were E(a) = 33.7 kJ mol(-1), ΔH(‡) = 31.2 kJ mol(-1) and ΔS(‡) = -190.6 J K(-1) mol(-1) for the OCl(-) ion-driven oxidation, and E(a) = 26.9 kJ mol(-1), ΔH(‡) = 24.3 kJ mol(-1) and ΔS(‡) = -222.8 J K(-1) mol(-1) for the reaction with HOCl-initiated oxidation. The major oxidation products for both the pathways were 3,4-dihydroxy naphthalene-2,7-disulfonic sodium salt (P(1)), dichloro-1,4-naphthoquione (P(2)) and naphtha(2,3)oxirene-2, 3-dione (P(3)). On the basis of the primary salt effect and other kinetic data, the rate law for the overall reaction and probable reaction mechanism was elucidated. The proposed mechanism was validated by simulations using Simkine-2.

  11. Mechanics of non-critical fold-thrust belts based on finite element models

    NASA Astrophysics Data System (ADS)

    Simpson, Guy

    2011-03-01

    The mechanics of fold-thrust belts and accretionary wedges is investigated using a two dimensional, plane strain, elastic-plastic (cohesive Mohr-Coulomb) mechanical model solved with the Finite Element Method. Results show that when a layer with an initially non-critical geometry is compressed from the rear, it does not form a wedge that is at failure throughout, as assumed in critical wedge theory. Rather, the wedge consists of narrow plastic shear zones that propagate sequentially outward with time, loading rocks ahead while unloading rocks behind. Not only are stress states within the wedge not everywhere at failure but principal stress orientations vary strongly in time and space, particularly across shear zones, near the basal detachment and in the hanging wall of active structures, where local surface extension may be observed. The reason the investigated wedges are not stressed to compressive failure throughout is related to strength reduction associated with strain localisation that enables material outside shear zones to unload and return to an elastic stress state. This mechanism is intrinsic to elastic-plastic materials and occurs regardless of any material degradation such as loss of cohesion. Even though the stress state of the investigated wedges is generally non-critical, the overall geometry may still be consistent with cohesionless critical wedge theory, since the local surface slope is created when a particular part of the wedge is at a limit state. Prowedge tapers display non self-similar growth through time but eventually evolve to the minimum critical taper. Retrowedges on the other hand, may get caught within this initial transient state and thus may have tapers anywhere between the minimum and maximum critical taper. However, if the basal detachment is such that lateral propagation is not kinematically inhibited, retrowedges are shown to also eventually evolve towards minimum critical tapers, resulting in a symmetrical doubly-vergent orogen

  12. Kinetic mechanism of putrescine oxidase from Rhodococcus erythropolis.

    PubMed

    Kopacz, Malgorzata M; Heuts, Dominic P H M; Fraaije, Marco W

    2014-10-01

    Putrescine oxidase from Rhodococcus erythropolis (PuO) is a flavin-containing amine oxidase from the monoamine oxidase family that performs oxidative deamination of aliphatic diamines. In this study we report pre-steady-state kinetic analyses of the enzyme with the use of single- and double-mixing stopped-flow spectroscopy and putrescine as a substrate. During the fast and irreversible reductive half-reaction no radical intermediates were observed, suggesting a direct hydride transfer from the substrate to the FAD. The rate constant of flavin reoxidation depends on the ligand binding; when the imine product was bound to the enzyme the rate constant was higher than with free enzyme species. Similar results were obtained with product-mimicking ligands and this indicates that a ternary complex is formed during catalysis. The obtained kinetic data were used together with steady-state rate equations derived for ping-pong, ordered sequential and bifurcated mechanisms to explore which mechanism is operative. The integrated analysis revealed that PuO employs a bifurcated mechanism due to comparable rate constants of product release from the reduced enzyme and reoxidation of the reduced enzyme-product complex.

  13. A Hooke׳s law-based approach to protein folding rate.

    PubMed

    Ruiz-Blanco, Yasser B; Marrero-Ponce, Yovani; Prieto, Pablo J; Salgado, Jesús; García, Yamila; Sotomayor-Torres, Clivia M

    2015-01-07

    Kinetics is a key aspect of the renowned protein folding problem. Here, we propose a comprehensive approach to folding kinetics where a polypeptide chain is assumed to behave as an elastic material described by the Hooke׳s law. A novel parameter called elastic-folding constant results from our model and is suggested to distinguish between protein with two-state and multi-state folding pathways. A contact-free descriptor, named folding degree, is introduced as a suitable structural feature to study protein-folding kinetics. This approach generalizes the observed correlations between varieties of structural descriptors with the folding rate constant. Additionally several comparisons among structural classes and folding mechanisms were carried out showing the good performance of our model with proteins of different types. The present model constitutes a simple rationale for the structural and energetic factors involved in protein folding kinetics.

  14. Kinetics and Mechanism of Bacterial Disinfection by Chlorine Dioxide1

    PubMed Central

    Benarde, Melvin A.; Snow, W. Brewster; Olivieri, Vincent P.; Davidson, Burton

    1967-01-01

    Survival data are presented for a fecal strain of Escherichia coli exposed to three concentrations of chlorine dioxide at four temperatures. Chick's first-order reaction equation is generalized to a pseudo nth-order model. Nonlinear least squares curve-fitting of the survival data to the nth order model was performed on an analogue computer. The data were observed to follow fractional order kinetics with respect to survival concentration, with an apparent activation energy of 12,000 cal/mole. Initial experiments support the thesis that the mechanism of chlorine dioxide kill occurs via disruption of protein synthesis. Images Fig. 1 Fig. 2 Fig. 3 PMID:5339839

  15. Kinetic study of the inhibition mechanism of dehaloperoxidase-hemoglobin a by 4-bromophenol.

    PubMed

    Zhao, Jing; Franzen, Stefan

    2013-07-18

    The mechanism of dehaloperoxidase-hemoglobin (DHP) inhibition by 4-bromophenol (4-BP) was investigated using Michealis-Menten and transient-state kinetic analyses. Transient-state kinetics using the stopped-flow technique to mix DHP and H2O2 in the presence of inhibitor concentrations less than 10-fold greater than the enzyme concentration show that 4-BP does not fully impede H2O2 entering the distal pocket to activate DHP. It is not clear whether an oxoferryl intermediate is formed under these conditions and there may be alternative pathways for H2O2 reaction in the 4-BP bound form of DHP. Two new species have been identified during the reaction of 4-BP bound form of DHP in the transient-state kinetic experiment by using Singular Value Decomposition (SVD) and global-fitting analysis. Rather than forming Compound ES in the unbound form, an inhibitor bound intermediate that possesses blue-shifted Soret band and a double peaked Q-band is observed. This intermediate is subsequently converted to the end-point species that is distinguished from Compound RH formed in the uninhibited enzyme. Bench-top mixing kinetics of DHP were conducted in order to determine the inhibitor binding constant and to understand the enzyme inhibition mechanism from a thermodynamic perspective. It was found that the inhibition constant, Ki, decreased from 2.56 mM to 0.15 mM over the temperature range from 283 to 298 K, which permits determination of the enthalpy and entropy for inhibitor binding as -135.5 ± 20.9 kJ/mol and 526.1 ± 71.9 J/(mol·K), respectively, leading to the conclusion that inhibitor binding is entropically driven.

  16. Kinetic analysis of the multistep aggregation mechanism of monoclonal antibodies.

    PubMed

    Nicoud, Lucrèce; Arosio, Paolo; Sozo, Margaux; Yates, Andrew; Norrant, Edith; Morbidelli, Massimo

    2014-09-11

    We investigate by kinetic analysis the aggregation mechanism of two monoclonal antibodies belonging to the IgG1 and IgG2 subclass under thermal stress. For each IgG, we apply a combination of size exclusion chromatography and light scattering techniques to resolve the time evolution of the monomer, dimer, and trimer concentrations, as well as the average molecular weight and the average hydrodynamic radius of the aggregate distribution. By combining the detailed experimental characterization with a theoretical kinetic model based on population balance equations, we extract relevant information on the contribution of the individual elementary steps on the global aggregation process. The analysis shows that the two molecules follow different aggregation pathways under the same operating conditions. In particular, while the monomer depletion of the IgG1 is found to be rate-limited by monomeric conformational changes, bimolecular collision is identified as the rate-limiting step in the IgG2 aggregation process. The measurement of the microscopic rate constants by kinetic analysis allows the quantification of the protein-protein interaction potentials expressed in terms of the Fuchs stability ratio (W). It is found that the antibody solutions exhibit large W values, which are several orders of magnitude larger than the values computed in the frame of the DLVO theory. This indicates that, besides net electrostatic repulsion, additional effects delay the aggregation kinetics of the antibody solutions with respect to diffusion-limited conditions. These effects likely include the limited efficiency of the collision events due to the presence of a limited number of specific aggregation-prone patches on the heterogeneous protein surface, and the contribution of additional repulsive non-DLVO forces to the protein-protein interaction potential, such as hydration forces.

  17. GeoFold: Topology-based protein unfolding pathways capture the effects of engineered disulfides on kinetic stability

    PubMed Central

    Ramakrishnan, Vibin; Srinivasan, Sai Praveen; Salem, Saeed M; Matthews, Suzanne J; Colón, Wilfredo; Zaki, Mohammed; Bystroff, Christopher

    2011-01-01

    Protein unfolding is modeled as an ensemble of pathways, where each step in each pathway is the addition of one topologically possible conformational degree of freedom. Starting with a known protein structure, GeoFold hierarchically partitions (cuts) the native structure into substructures using revolute joints and translations. The energy of each cut and its activation barrier are calculated using buried solvent accessible surface area, side chain entropy, hydrogen bonding, buried cavities, and backbone degrees of freedom. A directed acyclic graph is constructed from the cuts, representing a network of simultaneous equilibria. Finite difference simulations on this graph simulate native unfolding pathways. Experimentally observed changes in the unfolding rates for disulfide mutants of barnase, T4 lysozyme, dihydrofolate reductase, and factor for inversion stimulation were qualitatively reproduced in these simulations. Detailed unfolding pathways for each case explain the effects of changes in the chain topology on the folding energy landscape. GeoFold is a useful tool for the inference of the effects of disulfide engineering on the energy landscape of protein unfolding. PMID:22189917

  18. Distinguishing between sequential and nonsequentially folded proteins: implications for folding and misfolding.

    PubMed Central

    Tsai, C. J.; Maizel, J. V.; Nussinov, R.

    1999-01-01

    We describe here an algorithm for distinguishing sequential from nonsequentially folding proteins. Several experiments have recently suggested that most of the proteins that are synthesized in the eukaryotic cell may fold sequentially. This proposed folding mechanism in vivo is particularly advantageous to the organism. In the absence of chaperones, the probability that a sequentially folding protein will misfold is reduced significantly. The problem we address here is devising a procedure that would differentiate between the two types of folding patterns. Footprints of sequential folding may be found in structures where consecutive fragments of the chain interact with each other. In such cases, the folding complexity may be viewed as being lower. On the other hand, higher folding complexity suggests that at least a portion of the polypeptide backbone folds back upon itself to form three-dimensional (3D) interactions with noncontiguous portion(s) of the chain. Hence, we look at the mechanism of folding of the molecule via analysis of its complexity, that is, through the 3D interactions formed by contiguous segments on the polypeptide chain. To computationally splice the structure into consecutively interacting fragments, we either cut it into compact hydrophobic folding units or into a set of hypothetical, transient, highly populated, contiguous fragments ("building blocks" of the structure). In sequential folding, successive building blocks interact with each other from the amino to the carboxy terminus of the polypeptide chain. Consequently, the results of the parsing differentiate between sequentially vs. nonsequentially folded chains. The automated assessment of the folding complexity provides insight into both the likelihood of misfolding and the kinetic folding rate of the given protein. In terms of the funnel free energy landscape theory, a protein that truly follows the mechanism of sequential folding, in principle, encounters smoother free energy barriers

  19. Kinetics and mechanisms of reactions involving small aromatic reactive intermediates

    SciTech Connect

    Lin, M.C.

    1993-12-01

    Small aromatic radicals such as C{sub 6}H{sub 5}, C{sub 6}H{sub 5}O and C{sub 6}H{sub 4} are key prototype species of their homologs. C{sub 6}H{sub 5} and its oxidation product, C{sub 6}H{sub 5}O are believed to be important intermediates which play a pivotal role in hydrocarbon combustion, particularly with regard to soot formation. Despite their fundamental importance, experimental data on the reaction mechanisms and reactivities of these species are very limited. For C{sub 6}H{sub 5}, most kinetic data except its reactions with NO and NO{sub 2}, were obtained by relative rate measurements. For C{sub 6}H{sub 5}O, the authors have earlier measured its fragmentation reaction producing C{sub 5}H{sub 5} + CO in shock waves. For C{sub 6}H{sub 4}, the only rate constant measured in the gas phase is its recombination rate at room temperature. The authors have proposed to investigate systematically the kinetics and mechanisms of this important class of molecules using two parallel laser diagnostic techniques--laser resonance absorption (LRA) and resonance enhanced multiphoton ionization mass spectrometry (REMPI/MS). In the past two years, study has been focused on the development of a new multipass adsorption technique--the {open_quotes}cavity-ring-down{close_quotes} technique for kinetic applications. The preliminary results of this study appear to be quite good and the sensitivity of the technique is at least comparable to that of the laser-induced fluorescence method.

  20. Precursory signatures of protein folding/unfolding: From time series correlation analysis to atomistic mechanisms

    SciTech Connect

    Hsu, P. J.; Lai, S. K.; Cheong, S. A.

    2014-05-28

    Folded conformations of proteins in thermodynamically stable states have long lifetimes. Before it folds into a stable conformation, or after unfolding from a stable conformation, the protein will generally stray from one random conformation to another leading thus to rapid fluctuations. Brief structural changes therefore occur before folding and unfolding events. These short-lived movements are easily overlooked in studies of folding/unfolding for they represent momentary excursions of the protein to explore conformations in the neighborhood of the stable conformation. The present study looks for precursory signatures of protein folding/unfolding within these rapid fluctuations through a combination of three techniques: (1) ultrafast shape recognition, (2) time series segmentation, and (3) time series correlation analysis. The first procedure measures the differences between statistical distance distributions of atoms in different conformations by calculating shape similarity indices from molecular dynamics simulation trajectories. The second procedure is used to discover the times at which the protein makes transitions from one conformation to another. Finally, we employ the third technique to exploit spatial fingerprints of the stable conformations; this procedure is to map out the sequences of changes preceding the actual folding and unfolding events, since strongly correlated atoms in different conformations are different due to bond and steric constraints. The aforementioned high-frequency fluctuations are therefore characterized by distinct correlational and structural changes that are associated with rate-limiting precursors that translate into brief segments. Guided by these technical procedures, we choose a model system, a fragment of the protein transthyretin, for identifying in this system not only the precursory signatures of transitions associated with α helix and β hairpin, but also the important role played by weaker correlations in such protein

  1. Kinetics and Mechanisms of Calcite Reactions with Saline Waters

    SciTech Connect

    Gorman, Brian P

    2015-09-02

    Project Description: The general objective of the proposed research is to determine the kinetics and mechanisms of calcite reactions with saline waters over a wide range of saline water composition, pCO2, and modest ranges in T and P. This will be accomplished by studying both reaction rates and solubility from changes in solution chemistry, and making nanoscale observations of calcite precipitate surface morphology and composition at the micro-to-nano-scale to provide an understanding of controlling reaction mechanisms and pathways. The specific objectives necessary to reach the general objective are: a) determination of how pCO2, Ca2+, ionic strength and “foreign” ions influence reaction rates; and b) investigate the influence of these parameters on apparent kinetic solubility from dissolution and precipitation reactions. This information will clearly be central to the construction of reliable reaction-transport models to predict reservoir and formation response to increased CO2 in saline waters. This program was initially collaborative with John Morse at Texas A&M, however his passing shortly after the beginning of this program resulted in abbreviated research time and effort. Summary of Results: Early studies using electron microscopy and spectroscopy indicated that carbonate precipitation from natural seawater (NSW) conditions onto aragonite substrates was mediated by a surface amorphous calcium carbonate layer. It was hypothesized that this ACC layer (observed after < 5days reaction time) was responsible for the abnormal reaction kinetics and also served as a metastable seed layer for growth of epitaxial aragonite. Further studies of the ACC formation mechanism indicated a strong dependence on the Mg concentration in solution. Subsequent studies at shorter times (10 hrs) on calcite substrates and in a wide range of supersaturation conditions did not indicate any ACC layer. Instead, an epitaxial layer by layer

  2. Actin kinetics shapes cortical network structure and mechanics

    PubMed Central

    Fritzsche, Marco; Erlenkämper, Christoph; Moeendarbary, Emad; Charras, Guillaume; Kruse, Karsten

    2016-01-01

    The actin cortex of animal cells is the main determinant of cellular mechanics. The continuous turnover of cortical actin filaments enables cells to quickly respond to stimuli. Recent work has shown that most of the cortical actin is generated by only two actin nucleators, the Arp2/3 complex and the formin Diaph1. However, our understanding of their interplay, their kinetics, and the length distribution of the filaments that they nucleate within living cells is poor. Such knowledge is necessary for a thorough comprehension of cellular processes and cell mechanics from basic polymer physics principles. We determined cortical assembly rates in living cells by using single-molecule fluorescence imaging in combination with stochastic simulations. We find that formin-nucleated filaments are, on average, 10 times longer than Arp2/3-nucleated filaments. Although formin-generated filaments represent less than 10% of all actin filaments, mechanical measurements indicate that they are important determinants of cortical elasticity. Tuning the activity of actin nucleators to alter filament length distribution may thus be a mechanism allowing cells to adjust their macroscopic mechanical properties to their physiological needs. PMID:27152338

  3. Secondary Structure Propensities in Peptide Folding Simulations: A Systematic Comparison of Molecular Mechanics Interaction Schemes

    PubMed Central

    Matthes, Dirk; de Groot, Bert L.

    2009-01-01

    Abstract We present a systematic study directed toward the secondary structure propensity and sampling behavior in peptide folding simulations with eight different molecular dynamics force-field variants in explicit solvent. We report on the combinational result of force field, water model, and electrostatic interaction schemes and compare to available experimental characterization of five studied model peptides in terms of reproduced structure and dynamics. The total simulation time exceeded 18 μs and included simulations that started from both folded and extended conformations. Despite remaining sampling issues, a number of distinct trends in the folding behavior of the peptides emerged. Pronounced differences in the propensity of finding prominent secondary structure motifs in the different applied force fields suggest that problems point in particular to the balance of the relative stabilities of helical and extended conformations. PMID:19619475

  4. Kinetic mechanism of phenylacetone monooxygenase from Thermobifida fusca.

    PubMed

    Torres Pazmiño, Daniel E; Baas, Bert-Jan; Janssen, Dick B; Fraaije, Marco W

    2008-04-01

    Phenylacetone monooxygenase (PAMO) from Thermobifida fusca is a FAD-containing Baeyer-Villiger monooxygenase (BVMO). To elucidate the mechanism of conversion of phenylacetone by PAMO, we have performed a detailed steady-state and pre-steady-state kinetic analysis. In the catalytic cycle ( k cat = 3.1 s (-1)), rapid binding of NADPH ( K d = 0.7 microM) is followed by a transfer of the 4( R)-hydride from NADPH to the FAD cofactor ( k red = 12 s (-1)). The reduced PAMO is rapidly oxygenated by molecular oxygen ( k ox = 870 mM (-1) s (-1)), yielding a C4a-peroxyflavin. The peroxyflavin enzyme intermediate reacts with phenylacetone to form benzylacetate ( k 1 = 73 s (-1)). This latter kinetic event leads to an enzyme intermediate which we could not unequivocally assign and may represent a Criegee intermediate or a C4a-hydroxyflavin form. The relatively slow decay (4.1 s (-1)) of this intermediate yields fully reoxidized PAMO and limits the turnover rate. NADP (+) release is relatively fast and represents the final step of the catalytic cycle. This study shows that kinetic behavior of PAMO is significantly different when compared with that of sequence-related monooxygenases, e.g., cyclohexanone monooxygenase and liver microsomal flavin-containing monooxygenase. Inspection of the crystal structure of PAMO has revealed that residue R337, which is conserved in other BVMOs, is positioned close to the flavin cofactor. The analyzed R337A and R337K mutant enzymes were still able to form and stabilize the C4a-peroxyflavin intermediate. The mutants were unable to convert either phenylacetone or benzyl methyl sulfide. This demonstrates that R337 is crucially involved in assisting PAMO-mediated Baeyer-Villiger and sulfoxidation reactions.

  5. A multipurpose reduced chemical-kinetic mechanism for methanol combustion

    NASA Astrophysics Data System (ADS)

    Fernández-Tarrazo, Eduardo; Sánchez-Sanz, Mario; Sánchez, Antonio L.; Williams, Forman A.

    2016-07-01

    A multipurpose reduced chemical-kinetic mechanism for methanol combustion comprising 8 overall reactions and 11 reacting chemical species is presented. The development starts by investigating the minimum set of elementary reactions needed to describe methanol combustion with reasonable accuracy over a range of conditions of temperature, pressure, and composition of interest in combustion. Starting from a 27-step mechanism that has been previously tested and found to give accurate predictions of ignition processes for these conditions, it is determined that the addition of 11 elementary reactions taken from its basis (San Diego) mechanism extends the validity of the description to premixed-flame propagation, strain-induced extinction of non-premixed flames, and equilibrium composition and temperatures, giving results that compare favourably with experimental measurements and also with computations using the 247-step detailed San Diego mechanism involving 50 reactive species. Specifically, premixed-flame propagation velocities and extinction strain rates for non-premixed counterflow flames calculated with the 38-step mechanism show departures from experimental measurements and detailed-chemistry computations that are roughly on the order of 10%, comparable with expected experimental uncertainties. Similar accuracy is found in comparisons of autoignition times over the range considered, except at very high temperatures, under which conditions the computations tend to overpredict induction times for all of the chemistry descriptions tested. From this 38-step mechanism, the simplification is continued by introducing steady-state approximations for the intermediate species CH3, CH4, HCO, CH3O, CH2OH, and O, leading to an 8-step reduced mechanism that provides satisfactory accuracy for all conditions tested. The flame computations indicate that thermal diffusion has a negligible influence on methanol combustion in all cases considered and that a mixture-average species

  6. From the endoplasmic reticulum to the plasma membrane: mechanisms of CFTR folding and trafficking.

    PubMed

    Farinha, Carlos M; Canato, Sara

    2017-01-01

    CFTR biogenesis starts with its co-translational insertion into the membrane of endoplasmic reticulum and folding of the cytosolic domains, towards the acquisition of a fully folded compact native structure. Efficiency of this process is assessed by the ER quality control system that allows the exit of folded proteins but targets unfolded/misfolded CFTR to degradation. If allowed to leave the ER, CFTR is modified at the Golgi and reaches the post-Golgi compartments to be delivered to the plasma membrane where it functions as a cAMP- and phosphorylation-regulated chloride/bicarbonate channel. CFTR residence at the membrane is a balance of membrane delivery, endocytosis, and recycling. Several adaptors, motor, and scaffold proteins contribute to the regulation of CFTR stability and are involved in continuously assessing its structure through peripheral quality control systems. Regulation of CFTR biogenesis and traffic (and its dysregulation by mutations, such as the most common F508del) determine its overall activity and thus contribute to the fine modulation of chloride secretion and hydration of epithelial surfaces. This review covers old and recent knowledge on CFTR folding and trafficking from its synthesis to the regulation of its stability at the plasma membrane and highlights how several of these steps can be modulated to promote the rescue of mutant CFTR.

  7. Structural heterogeneity of 6 M GdmCl-denatured proteins: implications for the mechanism of protein folding.

    PubMed

    Chang, Jui-Yoa

    2009-10-13

    An in vitro experiment with protein folding is typically initiated with 6 M GdmCl-denatured proteins, which are generally considered fully unfolded. However, studies conducted by various laboratories have shown that many 6 M GdmCl-denatured proteins are structurally heterogeneous and still retain nativelike residual structures. The extent of conformational heterogeneity of the 6 M GdmCl-denatured protein has significant implications for the folding landscape as well as the interpretation of the observed early stage folding mechanism. Using the method of disulfide scrambling, we are able to gain rough insight into the diverse structural properties of 6 M GdmCl-denatured proteins. It demonstrates that most 6 M GdmCl-denatured proteins are approximately fully denatured, but partially unfolded. Most of them comprise diverse conformational isomers. We review here the cumulative evidence obtained from various laboratories and also provide experimental data obtained in our laboratory.

  8. The kinetics of composite particle formation during mechanical alloying

    NASA Technical Reports Server (NTRS)

    Aikin, B. J. M.; Courtney, T. H.

    1993-01-01

    The kinetics of composite particle formation during attritor milling of insoluble binary elemental powders have been examined. The effects of processing conditions (i.e., mill power, temperature, and charge ratio) on these kinetics were studied. Particle size distributions and fractions of elemental and composite particles were determined as functions of milling time and processing conditions. This allowed the deduction of phenomenological rate constants describing the propensity for fracture and welding during processing. For the mill-operating conditions investigated, the number of particles in the mill generally decreased with milling time, indicating a greater tendency for particle welding than fracture. Moreover, a bimodal size distribution is often obtained as a result of preferential welding. Copper and chromium 'alloy' primarily by encapsulation of Cr particles within Cu. This form of alloying also occurs in Cu-Nb alloys processed at low mill power and/or for short milling times. For other conditions, however, Cu-Nb alloys develop a lamellar morphology characteristic of mechanically alloyed two-phase ductile metals. Increasing mill power or charge (ball-to-powder weight) ratio (CR) increases the rate of composite particle formation.

  9. Complete kinetic mechanism for recycling of the bacterial ribosome.

    PubMed

    Borg, Anneli; Pavlov, Michael; Ehrenberg, Måns

    2016-01-01

    How EF-G and RRF act together to split a post-termination ribosomal complex into its subunits has remained obscure. Here, using stopped-flow experiments with Rayleigh light scattering detection and quench-flow experiments with radio-detection of GTP hydrolysis, we have clarified the kinetic mechanism of ribosome recycling and obtained precise estimates of its kinetic parameters. Ribosome splitting requires that EF-G binds to an already RRF-containing ribosome. EF-G binding to RRF-free ribosomes induces futile rounds of GTP hydrolysis and inhibits ribosome splitting, implying that while RRF is purely an activator of recycling, EF-G acts as both activator and competitive inhibitor of RRF in recycling of the post-termination ribosome. The ribosome splitting rate and the number of GTPs consumed per splitting event depend strongly on the free concentrations of EF-G and RRF. The maximal recycling rate, here estimated as 25 sec(-1), is approached at very high concentrations of EF-G and RRF with RRF in high excess over EF-G. The present in vitro results, suggesting an in vivo ribosome recycling rate of ∼5 sec(-1), are discussed in the perspective of rapidly growing bacterial cells.

  10. Complete kinetic mechanism for recycling of the bacterial ribosome

    PubMed Central

    Borg, Anneli; Pavlov, Michael

    2016-01-01

    How EF-G and RRF act together to split a post-termination ribosomal complex into its subunits has remained obscure. Here, using stopped-flow experiments with Rayleigh light scattering detection and quench-flow experiments with radio-detection of GTP hydrolysis, we have clarified the kinetic mechanism of ribosome recycling and obtained precise estimates of its kinetic parameters. Ribosome splitting requires that EF-G binds to an already RRF-containing ribosome. EF-G binding to RRF-free ribosomes induces futile rounds of GTP hydrolysis and inhibits ribosome splitting, implying that while RRF is purely an activator of recycling, EF-G acts as both activator and competitive inhibitor of RRF in recycling of the post-termination ribosome. The ribosome splitting rate and the number of GTPs consumed per splitting event depend strongly on the free concentrations of EF-G and RRF. The maximal recycling rate, here estimated as 25 sec−1, is approached at very high concentrations of EF-G and RRF with RRF in high excess over EF-G. The present in vitro results, suggesting an in vivo ribosome recycling rate of ∼5 sec−1, are discussed in the perspective of rapidly growing bacterial cells. PMID:26527791

  11. Sonolytic degradation of dimethoate: kinetics, mechanisms and toxic intermediates controlling.

    PubMed

    Yao, Juan-Juan; Hoffmann, Michael R; Gao, Nai-Yun; Zhang, Zhi; Li, Lei

    2011-11-15

    The sonolytic degradation of aqueous solutions of dimethoate, O,O-dimethyl S-[2-(methylamino)-2-oxoethyl]dithiophosphate, was examined. Optimal degradation rates were obtained at 619 kHz for continuous sonolysis and 406 kHz for pulse sonolysis. The primary pathways for degradation include hydroxyl radical oxidation, hydrolysis and pyrolysis on collapsing cavitation bubble interfaces. Reaction mechanisms coupled with the corresponding kinetic models are proposed to reproduce the observed concentration versus time profiles for dimethoate, omethoate and N-(methyl) mercaptoacetamide during sonolysis. The oxidation and hydrolysis of dimethoate and omethoate occurred at the water-bubble interface was the rate-determining step for sonolytic overall degradation of dimethoate. More than 90% toxicity of dimethoate was reduced within 45 min ultrasonic irradiation. Ferrous ion at micro molar level can significantly enhance the sonolytic degradation of dimethoate and effectively reduce the yields of toxic intermediate omethoate.

  12. Kinetics, products, and mechanisms of secondary organic aerosol formation.

    PubMed

    Ziemann, Paul J; Atkinson, Roger

    2012-10-07

    Secondary organic aerosol (SOA) is formed in the atmosphere when volatile organic compounds (VOCs) emitted from anthropogenic and biogenic sources are oxidized by reactions with OH radicals, O(3), NO(3) radicals, or Cl atoms to form less volatile products that subsequently partition into aerosol particles. Once in particles, these organic compounds can undergo heterogenous/multiphase reactions to form more highly oxidized or oligomeric products. SOA comprises a large fraction of atmospheric aerosol mass and can have significant effects on atmospheric chemistry, visibility, human health, and climate. Previous articles have reviewed the kinetics, products, and mechanisms of atmospheric VOC reactions and the general chemistry and physics involved in SOA formation. In this article we present a detailed review of VOC and heterogeneous/multiphase chemistry as they apply to SOA formation, with a focus on the effects of VOC molecular structure on the kinetics of initial reactions with the major atmospheric oxidants, the subsequent reactions of alkyl, alkyl peroxy, and alkoxy radical intermediates, and the composition of the resulting products. Structural features of reactants and products discussed include compound carbon number; linear, branched, and cyclic configurations; the presence of C[double bond, length as m-dash]C bonds and aromatic rings; and functional groups such as carbonyl, hydroxyl, ester, hydroxperoxy, carboxyl, peroxycarboxyl, nitrate, and peroxynitrate. The intention of this review is to provide atmospheric chemists with sufficient information to understand the dominant pathways by which the major classes of atmospheric VOCs react to form SOA products, and the further reactions of these products in particles. This will allow reasonable predictions to be made, based on molecular structure, about the kinetics, products, and mechanisms of VOC and heterogeneous/multiphase reactions, including the effects of important variables such as VOC, oxidant, and NO

  13. Domain closure in the catalytic chains of Escherichia coli aspartate transcarbamoylase influences the kinetic mechanism.

    PubMed

    Lee, B H; Ley, B W; Kantrowitz, E R; O'Leary, M H; Wedler, F C

    1995-06-30

    The closure of the two domains of the catalytic chains of Escherichia coli aspartate transcarbamoylase, which is critical for completion of the T-->R transition, is stabilized by salt-bridges between Glu-50 and both Arg-167 and Arg-234. Mutation of Glu-50 to Ala shifts the enzyme toward a low activity, low affinity state (Newton, C. J., and Kantrowitz, E. R. (1990) Biochemistry, 29, 1444-1451). Kinetic isotope effects (KIE) and equilibrium isotope exchange kinetics (EIEK) have been used to probe the dynamic properties of the Glu-50-->Ala enzyme. Unlike the behavior of the wild-type enzyme, the observed kinetic isotope effect for 13C versus 12C at the carbonyl group of carbamoyl phosphate (CP) increased upon the binding of ligands which promote the formation of the R-state (Asp, N-phosphonacetyl-L-aspartate (PALA), or ATP). The maximum rate for the [14C]Asp<-->Carbamoyl aspartate (CAsp) exchange with the Glu-50-->Ala enzyme was 500-fold slower than for the wild-type enzyme; however, the rate for the [14C]CP<-->CAsp exchange was only 50-fold slower, reversing the relative rates observed with the wild-type enzyme. In addition, upon variation of substrate pairs involving Asp or CAsp, loss of inhibition effects in the CP<-->CAsp exchange indicated that the Glu-50-->Ala substitution caused the kinetic mechanism for the mutant enzyme to shift from ordered to random. Computer simulations of the EIEK data indicate that the Glu-50-->Ala mutation specifically causes strong decreases in the rates of catalysis and association-dissociation for Asp and CAsp, with minimal effects on the CP and Pi on-off rates. With substrates bound, the Glu-50-->Ala enzyme apparently does not attain a full R-state conformation. The PALA-activated Glu-50-->Ala enzyme, however, exhibits substrate affinities comparable to those for the wild-type enzyme, but fails to restore the preferred order substrate binding. Unlike the wild-type enzyme, both the T and R-states of the Glu-50-->Ala enzyme

  14. Kinetic mechanism of rabbit muscle glycogen synthase I.

    PubMed

    Gold, A M

    1980-08-05

    The kinetic mechanism of rabbit muscle glycogen synthase I was investigated by determining isotope-exchange rates at chemical equilibrium between uridine diphosphoglucose (UDPG) and glycogen and between UDPG and uridine 5'-diphosphate (UDP). The rates were followed simultaneously by use of UDPG labeled with 14C in the glucose moiety and with 3H in the uracil group. They were found to be independent of the concentrations of glycogen and the UDPG-UDP pair, averaging 6 X 10(-9) mol min-1 mg-1, with a ratio of UDPG-glycogen exchange to UDPG-UDP exchange of 0.85-0.95. The conclusion is that glycogen synthase has a rapid equilibrium random bi bi mechanism. The previously reported slow activation of glycogen-free synthase in the presence of glycogen was examined kinetically. The activation rate appears to be independent of glycogen concentration over a wide range, while the maximum activation is related to the third or fourth root of the glycogen concentration. This suggest that the slow bimolecular reaction mechanism proposed for human polymorphonuclear leucocyte glycogen synthase I [Sølling, H., & Esmann, V. (1977) Eur. J. Biochem. 81, 129] does not apply to rabbit muscle synthase I. The rate of exchange of glycogen molecules in the complex between glycogen and rabbit muscle synthase I under conditions where the enzyme is catalytically active was estimated by a novel method. The enzyme-glycogen complex was treated with [glucose-14C]UDPG and glycogen of different molecular weight. The distribution of isotope between the two forms of glycogen was determined after their separation by agarose gel chromatography. A rate constant of 0.3 min-1 was estimated for the exchange. It can be calculated, on the basis of the specific activity of the enzyme (20 mumol min-1 mg-1) and its action pattern, that hundreds of individual chains in the glycogen molecule must be available to the enzyme during the average lifetime of the complex. A mechanism is proposed for this process.

  15. Kinetic mechanism of phenylalanine hydroxylase: intrinsic binding and rate constants from single-turnover experiments.

    PubMed

    Roberts, Kenneth M; Pavon, Jorge Alex; Fitzpatrick, Paul F

    2013-02-12

    Phenylalanine hydroxylase (PheH) catalyzes the key step in the catabolism of dietary phenylalanine, its hydroxylation to tyrosine using tetrahydrobiopterin (BH(4)) and O(2). A complete kinetic mechanism for PheH was determined by global analysis of single-turnover data in the reaction of PheHΔ117, a truncated form of the enzyme lacking the N-terminal regulatory domain. Formation of the productive PheHΔ117-BH(4)-phenylalanine complex begins with the rapid binding of BH(4) (K(d) = 65 μM). Subsequent addition of phenylalanine to the binary complex to form the productive ternary complex (K(d) = 130 μM) is approximately 10-fold slower. Both substrates can also bind to the free enzyme to form inhibitory binary complexes. O(2) rapidly binds to the productive ternary complex; this is followed by formation of an unidentified intermediate, which can be detected as a decrease in absorbance at 340 nm, with a rate constant of 140 s(-1). Formation of the 4a-hydroxypterin and Fe(IV)O intermediates is 10-fold slower and is followed by the rapid hydroxylation of the amino acid. Product release is the rate-determining step and largely determines k(cat). Similar reactions using 6-methyltetrahydropterin indicate a preference for the physiological pterin during hydroxylation.

  16. Investigation kinetics mechanisms of adsorption malachite green onto activated carbon.

    PubMed

    Onal, Y; Akmil-Başar, C; Sarici-Ozdemir, C

    2007-07-19

    Lignite was used to prepare activated carbon (T3K618) by chemical activation with KOH. Pore properties of the activated carbon such as BET surface area, pore volume, pore size distribution, and pore diameter were characterized by t-plot based on N2 adsorption isotherm. BET surface area of activated carbon is determined as 1000 m2/g. Adsorption capacity of malachite green (MG) onto T3K618 activated carbon was investigated in a batch system by considering the effects of various parameters like initial concentration (100, 150 and 200 mg/L) and temperature (25, 40 and 50 degrees C). The adsorption process was relatively fast and equilibrium was reached after about 20 min for 100, 150 mg/L at all adsorption temperature. Equilibrium time for 200 mg/L was determined as 20 min and 40 min at 298, 313 and 323 K, respectively. Simple mass and kinetic models were applied to the experimental data to examine the mechanisms of adsorption and potential rate controlling steps such as external mass transfer, intraparticle diffusion. Pseudo second-order model was found to explain the kinetics of MG adsorption most effectively. It was found that both mass transfer and pore diffusion are important in determining the adsorption rates. The intraparticle diffusion rate constant, external mass transfer coefficient, film and pore diffusion coefficient at various temperatures were evaluated. The activation energy (Ea) was determined as 48.56, 63.16, 67.93 kJ/mol for 100, 150, 200 mg/L, respectively. The Langmiur and Freundlich isotherm were used to describe the adsorption equilibrium studies at different temperatures. Langmiur isotherm shows better fit than Freundlich isotherm in the temperature range studied. The thermodynamic parameters, such as DeltaG degrees, DeltaS and DeltaH degrees were calculated. The thermodynamics of dyes-T3K618 system indicates endothermic process.

  17. A steady-state kinetic analysis of the prolyl-4-hydroxylase mechanism.

    PubMed

    Soskel, N T; Kuby, S A

    1981-01-01

    Published kinetic data by Kivirikko, et al. on the prolyl-4-hydroxylase reaction have been re-evaluated using the overall steady-state velocity equation in the forward and reverse directions for an ordered ter ter kinetic mechanism. Qualitatively, the published data for prolyl-4-hydroxylase appear to fit the predicted patterns for this kinetic mechanism. More kinetic data are needed to confirm these results and to quantitate the kinetic parameters but, tentatively, the order of substrate addition would appear to be alpha-ketoglutarate, oxygen, and peptide; and the order of product release would be hydroxylated peptide (or collagen), carbon dioxide, and succinate.

  18. Influences of heterogeneous native contact energy and many-body interactions on the prediction of protein folding mechanisms.

    PubMed

    Zhang, Zhuqing; Ouyang, Yanhua; Chen, Tao

    2016-11-16

    Since single-point mutant perturbation has been used to probe protein folding mechanisms in experiments, the ϕ-value has become a critical parameter to infer the transition state (TS) for two-state proteins. Experimentally, large scale analysis has shown a nearly single uniform ϕ-value with normally distributed error from 24 different proteins; moreover, in zero stability conditions, the intrinsic variable ϕ(0) is around 0.36. To explore how and to what extent theoretical models can capture experimental phenomena, we here use structure-based explicit chain coarse-grained models to investigate the influence of single-point mutant perturbation on protein folding for single domain two-state proteins. Our results indicate that uniform, additive contact energetic interactions cannot predict experimental Brønsted plots well. Those points deviate largely from the main data sets in Brønsted plots, are mostly hydrophobic, and are located in N- and C-terminal contacting regions. Heterogenous contact energy, which is dependent on sequence separation, can narrow the point dispersion in a Brønsted plot. Moreover, we demonstrate that combining many-body interactions with heterogeneous native contact energy can present mean ϕ-values consistent with experimental findings, with a comparable distributed error. This indicates that for more accurate elucidation of protein folding mechanisms by residue-level structure-based models, these elements should be considered.

  19. Role of folded anisotropic fabric in the failure mode of gneiss: new insights from mechanical, microseismic and microstructural laboratory data

    NASA Astrophysics Data System (ADS)

    Agliardi, Federico; Vinciguerra, Sergio; Dobbs, Marcus R.; Zanchetta, Stefano

    2015-04-01

    Fabric anisotropy is a key control of the mechanical behaviour of rocks in a variety of geological settings and on different timescales. However, the effects of inherited, tectonically folded anisotropic fabrics on the brittle strength and failure mode of foliated metamorphic rocks is yet to be fully understood. Data from laboratory uniaxial compression tests on folded gneiss (Agliardi et al., 2014, Tectonophysics) recently showed that the brittle failure mode of this rock type depends on the arrangement of two distinct anisotropies (i.e. foliation and fold axial plane anisotropy), and that rock strength correlates with failure mode. Here we investigate the effects of confining pressure on this behaviour by performing triaxial compression experiments with acoustic emission (AE) monitoring, and analyse resulting fracture mechanisms and their microfabric controls using high resolution microanalysis techniques. We tested the Monte Canale Gneiss (Austroalpine Bernina nappe, Central Italian Alps), characterized by low phyllosilicate content, compositional layering folded at the cm-scale, and absence of a well-developed axial plane foliation. We used a servo-controlled hydraulic loading system to test 19 air-dry cylindrical specimens (diameter: 54 mm) that were characterized both in terms of fold geometry and orientation of foliation and fold axial planes to the axial load direction. We instrumented the specimens with direct contact axial and circumferential strain gauges. We performed tests at confining pressures of 40 MPa and constant axial strain rates of 5*10-6 s-1, measuring acoustic emissions and P- and S-wave velocities by three wideband (350-1000 kHz) piezoelectric transceivers with 40 dB preamps, mounted in the compression platens. We carried out post-failure microscale observation of fracture mechanisms, microcrack patterns and related fabric controls on resin-impregnated samples, using X-ray MicroCT (resolution: 9 μm), optical microscopy and SEM. Samples

  20. Self-oscillating Vocal Fold Model Mechanics: Healthy, Diseased, and Aging

    NASA Astrophysics Data System (ADS)

    Hiubler, Elizabeth P.; Pollok, Lucas F. E.; Apostoli, Adam G.; Hancock, Adrienne B.; Plesniak, Michael W.

    2014-11-01

    Voice disorders have been estimated to have a substantial economic impact of 2.5 billion annually. Approximately 30% of people will suffer from a voice disorder at some point in their lives. Life-sized, self-oscillating, synthetic vocal fold (VF) models are fabricated to exhibit material properties representative of human VFs. These models are created both with and without a polyp-like structure, a pathology that has been shown to produce rich viscous flow structures not normally observed for healthy VFs during normal phonation. Pressure measurements are acquired upstream of the VFs and high-speed images are captured at varying flow rates during VF oscillation to facilitate an understanding of the characteristics of healthy and diseased VFs. The images are analyzed using a videokymography line-scan technique. Clinically-relevant parameters calculated from the volume-velocity output of a circumferentially-vented mask (Rothenberg mask) are compared to human data collected from two groups of males aged 18-30 and 60-80. This study extends the use of synthetic VF models by assessing their ability to replicate behaviors observed in human subject data to advance a means of investigating changes associated with normal, pathological, and the aging voice. Supported by the GWU Institute for Biomedical Engineering (GWIBE) and GWU Center for Biomimetics and Bioinspired Engineering (COBRE).

  1. Mechanical design of the folded waveguide for PBX-M and TFTR

    SciTech Connect

    Fogelman, C.H.; Bigelow, T.S.; Yugo, J.J.

    1995-12-31

    The folded waveguide (FWG) antenna is an advanced Cyclotron Range of Frequencies launcher being designed at Oak Ridge National Laboratory in collaboration with Princeton Plasma Physics Laboratory. The FWG offers a drastic increase in radio frequency (RF) power density over typical loop antennas. It also results in internal electric fields of much lower magnitude near the plasma. It is scheduled for installation on either the Tokamak Fusion Test Reactor (TFTR) or the Princeton Beta Experiment-Modified (PBX-M) tokamak in January 1996. The design objective is to provide an FWG that can withstand the thermal loads and disruption scenarios and meet the space constants of both machines. The design is also intended to be prototypical for the International Thermonuclear Experimental Reactor (ITER). The FWG is fully retractable, and maintenance operations can be performed while the vessel remains under vacuum. The FWG can operate in fast-wave mode, or it can be retracted, rotated 90{degrees}, and reengaged for the ion-Bernstein wave launch. The polarizing plate completely covers the front of the antenna, except for slots cut at every other gap between with plates of other configurations such as a 0-{pi} dipole plate.

  2. How Does Your Protein Fold? Elucidating the Apomyoglobin Folding Pathway.

    PubMed

    Dyson, H Jane; Wright, Peter E

    2017-01-17

    Although each type of protein fold and in some cases individual proteins within a fold classification can have very different mechanisms of folding, the underlying biophysical and biochemical principles that operate to cause a linear polypeptide chain to fold into a globular structure must be the same. In an aqueous solution, the protein takes up the thermodynamically most stable structure, but the pathway along which the polypeptide proceeds in order to reach that structure is a function of the amino acid sequence, which must be the final determining factor, not only in shaping the final folded structure, but in dictating the folding pathway. A number of groups have focused on a single protein or group of proteins, to determine in detail the factors that influence the rate and mechanism of folding in a defined system, with the hope that hypothesis-driven experiments can elucidate the underlying principles governing the folding process. Our research group has focused on the folding of the globin family of proteins, and in particular on the monomeric protein apomyoglobin. Apomyoglobin (apoMb) folds relatively slowly (∼2 s) via an ensemble of obligatory intermediates that form rapidly after the initiation of folding. The folding pathway can be dissected using rapid-mixing techniques, which can probe processes in the millisecond time range. Stopped-flow measurements detected by circular dichroism (CD) or fluorescence spectroscopy give information on the rates of folding events. Quench-flow experiments utilize the differential rates of hydrogen-deuterium exchange of amide protons protected in parts of the structure that are folded early; protection of amides can be detected by mass spectrometry or proton nuclear magnetic resonance spectroscopy (NMR). In addition, apoMb forms an intermediate at equilibrium at pH ∼ 4, which is sufficiently stable for it to be structurally characterized by solution methods such as CD, fluorescence and NMR spectroscopies, and the

  3. Determination of the elastic properties of short ssDNA molecules by mechanically folding and unfolding DNA hairpins.

    PubMed

    Alemany, Anna; Ritort, Felix

    2014-12-01

    The characterization of elastic properties of biopolymers is crucial to understand many molecular reactions determined by conformational bending fluctuations of the polymer. Direct measurement of such elastic properties using single-molecule methods is usually hindered by the intrinsic tendency of such biopolymers to form high-order molecular structures. For example, single-stranded deoxyribonucleic acids (ssDNA) tend to form secondary structures such as local double helices that prevent the direct measurement of the ideal elastic response of the ssDNA. In this work, we show how to extract the ideal elastic response in the entropic regime of short ssDNA molecules by mechanically pulling two-state DNA hairpins of different contour lengths. This is achieved by measuring the force dependence of the molecular extension and stiffness on mechanically folding and unfolding the DNA hairpin. Both quantities are fit to the worm-like chain elastic model giving values for the persistence length and the interphosphate distance. This method can be used to unravel the elastic properties of short ssDNA and RNA sequences and, more generally, any biopolymer that can exhibit a cooperative two-state transition between mechanically folded and unfolded states (such as proteins).

  4. Identification of enzyme inhibitory mechanisms from steady-state kinetics.

    PubMed

    Fange, David; Lovmar, Martin; Pavlov, Michael Y; Ehrenberg, Måns

    2011-09-01

    Enzyme inhibitors are used in many areas of the life sciences, ranging from basic research to the combat of disease in the clinic. Inhibitors are traditionally characterized by how they affect the steady-state kinetics of enzymes, commonly analyzed on the assumption that enzyme-bound and free substrate molecules are in equilibrium. This assumption, implying that an enzyme-bound substrate molecule has near zero probability to form a product rather than dissociate, is valid only for very inefficient enzymes. When it is relaxed, more complex but also more information-rich steady-state kinetics emerges. Although solutions to the general steady-state kinetics problem exist, they are opaque and have been of limited help to experimentalists. Here we reformulate the steady-state kinetics of enzyme inhibition in terms of new parameters. These allow for assessment of ambiguities of interpretation due to kinetic scheme degeneracy and provide an intuitively simple way to analyze experimental data. We illustrate the method by concrete examples of how to assess scheme degeneracy and obtain experimental estimates of all available rate and equilibrium constants. We suggest simple, complementary experiments that can remove ambiguities and greatly enhance the accuracy of parameter estimation.

  5. Intramolecular Charge Transfer Dynamics of 4-(DIMETHYLAMINO)BENZONITRILE: Ultrafast Branching Followed by a Two-Fold Decay Mechanism

    NASA Astrophysics Data System (ADS)

    Coto, Pedro B.; Serrano-Andrés, Luis; Gustavsson, Thomas; Fujiwara, Takashige; Lim, Edward C.

    2010-06-01

    4-(Dimethylamino)benzonitrile (DMABN) is a paradigm molecule system that exhibits dual fluorescence and intramolecular charge transfer (ICT) in polar solvents. Although numbers of different experimental and theoretical methods have been carried out to date for elucidating the basic mechanism of its energy relaxation, there are still some crucial problems that remain unanswered. The time-resolved transient absorption and time-resolved fluorescence upconversion will be presented, as combined with ab initio CASPT2//CASSCF calculations, which indicate that a more complex mechanism may be suggested in the ICT reaction in a polar environment. A scheme of ultrafast branching relaxation followed by two-fold decay is proposed in which, whereas the fully twisted ICT (TICT) state is responsible for the transient absorption, a distinct partially twisted ICT (pTICT) structure is for the fluorescent ICT state, both displaying clearly different decay rates.

  6. Folding Beauties

    ERIC Educational Resources Information Center

    Berman, Leah Wrenn

    2006-01-01

    This article has its genesis in an MAA mini-course on origami, where a way to get a parabola by folding paper was presented. This article discusses the methods and mathematics of other curves obtained by paper-folding.

  7. [Kinetics and mechanism of removing Microcystis aeruginosa using clay flocculation].

    PubMed

    Pan, Gang; Zhang, Mingming; Yan, Hai; Zou, Hua; Chen, Hao

    2003-09-01

    Twenty-six natural clays were studied for their kinetics of flocculating and removing algal cells of Microcystis aeruginosa. According to the 8 h equilibrium removal efficiencies and removal rates at a clay-loading of 0.7 g.L-1, all the 26 clays were classified into three categories. Type-I clay, which includes talc, ferric oxide, sepiolite, ferroferric oxide, and kaolinite, has an equilibrium removal efficiency greater than 90%, a t50 (time needed to remove 50% of the algae) of less than 30 min, and a t80 (time needed to remove 80% of the algae) of less than 2.5 h. Type-II clay, which includes argillanceous rocks, attapulgite, rectorite, illite, and argil, etc., has an equilibrium removal efficiency of 50%-80%, a t50 of less than 2.5 h, and a t80 of more than 5 h. Type-III clay consists of 14 minerals, including laterite, zeolite, mica, clinoptilolite, pumice, tripoli, feldspar and quartz, etc. with the removal efficiency less than 50%, and t50 > > 8 h. When the clay loading was decreased to 0.1-0.2 g.L-1, the 8 h equilibrium removal efficiencies for 25 clays declined to below 60%, except for sepiolite, a Type-I clay, which maintained around 90%. After the sepiolite was modified with Fe3+ to increase its surface charge (Zeta potential from -24.0 mV to +0.43 mV at pH 7.4), the initial removal rate was increased remarkably although its 8 h equilibrium removal efficiency was not improved substantially. As a comparison, the 8 h equilibrium removal efficiency of PAC was no greater than 40% at loadings of 0.02-0.2 g.L-1. Following the analysis of the flocculation mechanism it was concluded that the effect of bridging and netting may play a key role in the clay-algae flocculation processes, which may be important for selecting and modifying clays to improve significantly the removal efficiency.

  8. Sedimentary iron monosulfides: Kinetics and mechanism of formation

    NASA Astrophysics Data System (ADS)

    Pyzik, Albert J.; Sommer, Sheldon E.

    1981-05-01

    The reaction between hydrous iron oxides and aqueous sulfide species was studied at estuarine conditions of pH, total sulfide, and ionic strength to determine the kinetics and formation mechanism of the initial iron sulfide. Total, dissolved and acid extractable sulfide, thiosulfate, sulfate, and elemental sulfur were determined by spectrophotometric methods. Polysulfides, S 42- and S 52-, were determined from ultraviolet absorbance measurements and equilibrium calculations, while product hydroxyl ion was determined from pH measurements and solution buffer capacity. Elemental sulfur, as free and polysulfide sulfur, was 86% of the sulfide oxidation products; the remainder was thiosulfate. Rate expressions for the reduction and precipitation reactions were determined from analysis of electron balance and acid extractable iron monosulfide vs time, respectively, by the initial rate method. The rate of iron reduction in moles/liter/minute was given by d( reduction Fe) /dt = kS t0.5(J +) 0.5 A FeOOH1 where St was the total dissolved sulfide concentration, (H +) the hydrogen ion activity, both in moles/ liter; and AFeOOH the goethite specific surface area in square meters/liter. The rate constant, k, was 0.017 ± 0.002m -2 min -1. The rate of reduction was apparently determined by the rate of dissolution of the surface layer of ferrous hydroxide. The rate expression for the precipitation reaction was d(FeS)/dt = kS t1(H +) 1 A FeOOH1 where d(FeS)/dt was the rate of precipitation of acid extractable iron monosulfide in moles/liter/minute, and k = 82 ± 18 mol -1l2m-2 min -1. A model is proposed with the following steps: protonation of goethite surface layer; exchange of bisulfide for hydroxide in the mobile layer; reduction of surface ferric ions of goethite by dissolved bisulfide species which produces ferrous hydroxide surface layer elemental sulfur and thiosulfate; dissolution of surface layer of ferrous hydroxide; and precipitation of dissolved ferrous specie and

  9. Mechanics of neurulation: From classical to current perspectives on the physical mechanics that shape, fold, and form the neural tube.

    PubMed

    Vijayraghavan, Deepthi S; Davidson, Lance A

    2016-09-13

    Neural tube defects arise from mechanical failures in the process of neurulation. At the most fundamental level, formation of the neural tube relies on coordinated, complex tissue movements that mechanically transform the flat neural epithelium into a lumenized epithelial tube (Davidson, 2012). The nature of this mechanical transformation has mystified embryologists, geneticists, and clinicians for more than 100 years. Early embryologists pondered the physical mechanisms that guide this transformation. Detailed observations of cell and tissue movements as well as experimental embryological manipulations allowed researchers to generate and test elementary hypotheses of the intrinsic and extrinsic forces acting on the neural tissue. Current research has turned toward understanding the molecular mechanisms underlying neurulation. Genetic and molecular perturbation have identified a multitude of subcellular components that correlate with cell behaviors and tissue movements during neural tube formation. In this review, we focus on methods and conceptual frameworks that have been applied to the study of amphibian neurulation that can be used to determine how molecular and physical mechanisms are integrated and responsible for neurulation. We will describe how qualitative descriptions and quantitative measurements of strain, force generation, and tissue material properties as well as simulations can be used to understand how embryos use morphogenetic programs to drive neurulation. Birth Defects Research (Part A), 2016. © 2016 Wiley Periodicals, Inc.

  10. Kinetic isotope effects on the noncovalent flavin mutant protein of pyranose 2-oxidase reveal insights into the flavin reduction mechanism.

    PubMed

    Sucharitakul, Jeerus; Wongnate, Thanyaporn; Chaiyen, Pimchai

    2010-05-04

    Pyranose 2-oxidase (P2O) from Trametes multicolor contains a flavin adenine dinucleotide (FAD) cofactor covalently linked to the N(3) atom of His167. The enzyme catalyzes the oxidation of aldopyranoses by molecular oxygen to generate 2-keto-aldoses and H(2)O(2) as products. In this study, the transient kinetics and primary and solvent kinetic isotope effects of the mutant in which His167 has been replaced with Ala (H167A) were investigated, to elucidate the functional role of the 8a-N(3)-histidyl FAD linkage and to gain insights into the reaction mechanism of P2O. The results indicate that the covalent linkage is mainly important for a reductive half-reaction in which the FAD cofactor is reduced by d-glucose, while it is not important for an oxidative half-reaction in which oxygen reacts with the reduced FAD to generate H(2)O(2). d-Glucose binds to H167A via multiple binding modes before the formation of the active Michaelis complex, and the rate constant of flavin reduction decreases approximately 22-fold compared to that of the wild-type enzyme. The reduction of H167A using d-glucose isotopes (2-d-d-glucose, 3-d-d-glucose, and 1,2,3,4,5,6,6-d(7)-d-glucose) as substrates indicates that the primary isotope effect results only from substitution at the C2 position, implying that H167A catalyzes the oxidation of d-glucose regiospecifically at this position. No solvent kinetic isotope effect was detected during the reductive half-reaction of the wild-type or H167A enzyme, implying that the deprotonation of the d-glucose C2-OH group may occur readily upon the binding to P2O and is not synchronized with the cleavage of the d-glucose C2-H bond. The mutation has no drastic effect on the oxidative half-reaction of P2O, as H167A is very similar to the wild-type enzyme with respect to the kinetic constants and the formation of the C4a-hydroperoxyflavin intermediate. Kinetic mechanisms for both half-reactions of H167A were proposed on the basis of transient kinetic data and

  11. NMR of α-synuclein–polyamine complexes elucidates the mechanism and kinetics of induced aggregation

    PubMed Central

    Fernández, Claudio O; Hoyer, Wolfgang; Zweckstetter, Markus; Jares-Erijman, Elizabeth A; Subramaniam, Vinod; Griesinger, Christian; Jovin, Thomas M

    2004-01-01

    The aggregation of α-synuclein is characteristic of Parkinson's disease (PD) and other neurodegenerative synucleinopathies. The 140-aa protein is natively unstructured; thus, ligands binding to the monomeric form are of therapeutic interest. Biogenic polyamines promote the aggregation of α-synuclein and may constitute endogenous agents modulating the pathogenesis of PD. We characterized the complexes of natural and synthetic polyamines with α-synuclein by NMR and assigned the binding site to C-terminal residues 109–140. Dissociation constants were derived from chemical shift perturbations. Greater polyamine charge (+2 → +5) correlated with increased affinity and enhancement of fibrillation, for which we propose a simple kinetic mechanism involving a dimeric nucleation center. According to the analysis, polyamines increase the extent of nucleation by ∼104 and the rate of monomer addition ∼40-fold. Significant secondary structure is not induced in monomeric α-synuclein by polyamines at 15°C. Instead, NMR reveals changes in a region (aa 22–93) far removed from the polyamine binding site and presumed to adopt the β-sheet conformation characteristic of fibrillar α-synuclein. We conclude that the C-terminal domain acts as a regulator of α-synuclein aggregation. PMID:15103328

  12. Vitamin B2-sensitised photooxidation of the ophthalmic drugs Timolol and Pindolol: kinetics and mechanism.

    PubMed

    Criado, Susana; García, Norman A

    2004-01-01

    The kinetics and mechanistic aspects of the riboflavin-photosensitised oxidation of the topically administrable ophthalmic drugs Timolol (Tim) and Pindolol (Pin) were investigated in water-MeOH (9:1, v/v) solution employing light of wavelength > 400 nm. riboflavin, belonging to the vitamin B(2) complex, is a known human endogenous photosensitiser. The irradiation of riboflavin in the presence of ophthalmic drugs triggers a complex picture of competitive reactions which produces the photodegradation of both the drugs and the pigment itself. The mechanism was elucidated employing stationary photolysis, polarographic detection of dissolved oxygen, stationary and time-resolved fluorescence spectroscopy, and laser flash photolysis. Ophthalmic drugs quench riboflavin-excited singlet and triplet states. From the quenching of excited triplet riboflavin, the semireduced form of the pigment is generated, through an electron transfer process from the drug, with the subsequent production of superoxide anion radical (O(2)(*-)) by reaction with dissolved molecular oxygen. Through the interaction of dissolved oxygen with excited triplet riboflavin, the species singlet oxygen (O(2)((1)Delta(g))) is also generated to a lesser extent. Both O(2)(*-) and O(2)((1)Delta(g)) induce photodegradation of ophthalmic drugs, Tim being approximately 3-fold more easily photooxidisable than Pin, as estimated by oxygen consumption experiments.

  13. A Comparison of Kinetic Energy and Momentum in Special Relativity and Classical Mechanics

    ERIC Educational Resources Information Center

    Riggs, Peter J.

    2016-01-01

    Kinetic energy and momentum are indispensable dynamical quantities in both the special theory of relativity and in classical mechanics. Although momentum and kinetic energy are central to understanding dynamics, the differences between their relativistic and classical notions have not always received adequate treatment in undergraduate teaching.…

  14. Kinetics and mechanism of soot formation in hydrocarbon combustion

    NASA Technical Reports Server (NTRS)

    Frenklach, Michael

    1990-01-01

    The focus of this work was on kinetic modeling. The specific objectives were: detailed modeling of soot formation in premixed flames, elucidation of the effects of fuel structure on the pathway to soot, and the development of a numerical technique for accurate modeling of soot particle coagulation and surface growth. Those tasks were successfully completed and are briefly summarized.

  15. Renormalizing the Kinetic Energy Operator in Elementary Quantum Mechanics

    ERIC Educational Resources Information Center

    Coutinho, F. A. B.; Amaku, M.

    2009-01-01

    In this paper, we consider solutions to the three-dimensional Schrodinger equation of the form [psi](r) = u(r)/r, where u(0) [is not equal to] 0. The expectation value of the kinetic energy operator for such wavefunctions diverges. We show that it is possible to introduce a potential energy with an expectation value that also diverges, exactly…

  16. Extreme Folding

    NASA Astrophysics Data System (ADS)

    Demaine, Erik

    2012-02-01

    Our understanding of the mathematics and algorithms behind paper folding, and geometric folding in general, has increased dramatically over the past several years. These developments have found a surprisingly broad range of applications. In the art of origami, it has helped spur the technical origami revolution. In engineering and science, it has helped solve problems in areas such as manufacturing, robotics, graphics, and protein folding. On the recreational side, it has led to new kinds of folding puzzles and magic. I will give an overview of the mathematics and algorithms of folding, with a focus on new mathematics and sculpture.

  17. Protein folding by distributed computing and the denatured state ensemble.

    PubMed

    Marianayagam, Neelan J; Fawzi, Nicolas L; Head-Gordon, Teresa

    2005-11-15

    The distributed computing (DC) paradigm in conjunction with the folding@home (FH) client server has been used to study the folding kinetics of small peptides and proteins, giving excellent agreement with experimentally measured folding rates, although pathways sampled in these simulations are not always consistent with the folding mechanism. In this study, we use a coarse-grain model of protein L, whose two-state kinetics have been characterized in detail by using long-time equilibrium simulations, to rigorously test a FH protocol using approximately 10,000 short-time, uncoupled folding simulations starting from an extended state of the protein. We show that the FH results give non-Poisson distributions and early folding events that are unphysical, whereas longer folding events experience a correct barrier to folding but are not representative of the equilibrium folding ensemble. Using short-time, uncoupled folding simulations started from an equilibrated denatured state ensemble (DSE), we also do not get agreement with the equilibrium two-state kinetics because of overrepresented folding events arising from higher energy subpopulations in the DSE. The DC approach using uncoupled short trajectories can make contact with traditionally measured experimental rates and folding mechanism when starting from an equilibrated DSE, when the simulation time is long enough to sample the lowest energy states of the unfolded basin and the simulated free-energy surface is correct. However, the DC paradigm, together with faster time-resolved and single-molecule experiments, can also reveal the breakdown in the two-state approximation due to observation of folding events from higher energy subpopulations in the DSE.

  18. The effect of surface tethering on the folding of the src-SH3 protein domain

    NASA Astrophysics Data System (ADS)

    Zhuang, Zhuoyun; Jewett, Andrew I.; Soto, Patricia; Shea, Joan-Emma

    2009-03-01

    The effect of surface tethering on the folding mechanism of the src-SH3 protein domain was investigated using a coarse-grained Gō-type protein model. The protein was tethered at various locations along the protein chain and the thermodynamics and kinetics of folding were studied using replica exchange and constant temperature Langevin dynamics. Our simulations reveal that tethering in a structured part of the transition state can dramatically alter the folding mechanism, while tethering in an unstructured part leaves the folding mechanism unaltered as compared to bulk folding. Interestingly, there is only modest correlation between the tethering effect on the folding mechanism and its effect on thermodynamic stability and folding rates. We suggest locations on the protein at which tethering could be performed in single-molecule experiments so as to leave the folding mechanism unaltered from the bulk.

  19. Kinetics and Mechanism in the Oxidation of Metal Vapors

    DTIC Science & Technology

    1974-10-01

    cooled induction coil enters the furnace chamber from the bottom flange. The crucible and its holder are supported on three tantalum rods on the inlet...In an indium furnace , heated by the same induction field as the crucible containing the thorium. When thorium was allowed to react with partially...identify by block number) Kinetics Reproduced by Uranium NATtONAL TECHNICALThorium INFORMATIOtM SERVICE US Depermeht of Cm’,ner’e Springfield, VA. 22151

  20. From Mechanism and Kinetics to Precise ATRP Synthesis

    NASA Astrophysics Data System (ADS)

    Mueller, Laura; Golas, Patricia; Matyjaszewski, Krzysztof

    Controlled/living radical polymerizations (CRP) give access to polymers with precisely controlled molecular weight, narrow molecular weight distribution, well-defined architecture and composition. CRP can be applied to a wide range of monomers and are tolerant to impurities and functional groups. Atom transfer radical polymerization (ATRP) is one of the most widely used CRP techniques. The mechanistic and kinetic studies of ATRP are of fundamental importance since they give access to polymers with various functionalities, compositions, and topologies.

  1. Development of Non-Equilibrium Plasma-Flame Kinetic Mechanism and its Validation Using Gliding Arc Integrated with Counterflow Burner

    DTIC Science & Technology

    2010-02-21

    purely kinetic effect. This effect has been termed the kinetic - induced hydrodynamic enhancement. To exclude the complicated enhancement mechanism...experimental and numerical results becomes slightly larger for larger O3 concentration. This effect once again is caused by the kinetic - induced ...creates a kinetic enhancement that also induces hydrodynamic enhancement. The maximum overall flame speed enhancement in the laboratory coordinate was

  2. Development of Non-Equilibrium Plasma-Flame Kinetic Mechanism and its Validation Using Gliding Arc Integrated with Counterflow Burner

    DTIC Science & Technology

    2010-02-21

    termed the kinetic - induced hydrodynamic enhancement. To exclude the complicated enhancement mechanism caused by the hydrodynamic effects discussed...between this fuel mixture fraction gradient and the purely kinetic enhancement are indicative of the kinetic - induced hydrodynamic enhancement described...slightly larger for larger O3 concentration. This effect once again is caused by the kinetic - induced hydrodynamic enhancement for larger concentrations

  3. Kinetics and mechanism of the chlorine dioxide-trithionate reaction.

    PubMed

    Cseko, György; Horváth, Attila K

    2012-03-22

    The trithionate-chlorine dioxide reaction has been studied spectrophotometrically in a slightly acidic medium at 25.0 ± 0.1 °C in acetate/acetic acid buffer monitoring the decay of chlorine dioxide at constant ionic strength (I = 0.5 M) adjusted by sodium perchlorate. We found that under our experimental conditions two limiting stoichiometries exist and the pH, the concentration of the reactants, and even the concentration of chloride ion affects the actual stoichiometry of the reaction that can be augmented by an appropriate linear combination of these limiting processes. It is also shown that although the formal kinetic order of trithionate is strictly one that of chlorine dioxide varies between 1 and 2, depending on the actual chlorine dioxide excess and the pH. Moreover, the otherwise sluggish chloride ion, which is also a product of the reaction, slightly accelerates the initial rate of chlorine dioxide consumption and may therefore act as an autocatalyst. In addition to that, overshoot-undershoot behavior is also observed in the [(·)ClO(2)]-time curves in the presence of chloride ion at chlorine dioxide excess. On the basis of the experiments, a 13-step kinetic model with 6 fitted kinetic parameter is proposed by nonlinear parameter estimation.

  4. Kinetics and mechanism of the synthesis of a novel protein-based plastic using subcritical water.

    PubMed

    Abdelmoez, Wael; Yoshida, Hiroyuki

    2008-01-01

    We investigated the intermolecular mechanism and kinetics of the synthesis of a novel biodegradable protein-based plastic from bovine serum albumin under subcritical water conditions using batch reactors. The reaction mechanism could be viewed as a chain reaction stabilized by the formation of intermolecular disulfide bonds. The kinetic analysis was based on non-steady-state kinetics using a theoretical model developed in one of our previous works. The activation energy and pre-exponential factor were found to be 7.2 kJ/mol and 0.9 s-1, respectively. These low values signify that the reaction is relatively temperature-insensitive with some diffusion limitation.

  5. Transformation of the mechanism of triple-helix peptide folding in the absence of a C-terminal nucleation domain and its implications for mutations in collagen disorders.

    PubMed

    Buevich, Alexei V; Silva, Teresita; Brodsky, Barbara; Baum, Jean

    2004-11-05

    Folding abnormalities of the triple helix have been demonstrated in collagen diseases such as osteogenesis imperfecta in which the mutation leads to the substitution of a single Gly in the (Gly-X-Y)n sequence pattern by a larger residue. Model peptides can be used to clarify the details of normal collagen folding and the consequences of the interruption of that folding by a Gly substitution. NMR and CD studies show that placement of a (GPO)4 nucleation domain at the N terminus rather than the C terminus of a native collagen sequence allows the formation of a stable triple helix but alters the folding mechanism. Although C- to N-terminal directional folding occurs when the nucleation domain is at the C terminus, there is no preferential folding direction when the nucleation domain is at the N terminus. The lack of zipper-like directional folding does not interfere with triple-helix formation, and when a Gly residue is replaced by Ser to model an osteogenesis imperfecta mutation, the peptide with the N-terminal (GPO)4 domain can still form a good triple helix N-terminal to the mutation site. These peptide studies raise the possibility that mutant collagen could fold in a C to N direction in a zipper-like manner up to the mutation site and that completion of the triple helix N-terminal to the mutation would involve an alternative mechanism.

  6. Microsecond subdomain folding in dihydrofolate reductase.

    PubMed

    Arai, Munehito; Iwakura, Masahiro; Matthews, C Robert; Bilsel, Osman

    2011-07-08

    The characterization of microsecond dynamics in the folding of multisubdomain proteins has been a major challenge in understanding their often complex folding mechanisms. Using a continuous-flow mixing device coupled with fluorescence lifetime detection, we report the microsecond folding dynamics of dihydrofolate reductase (DHFR), a two-subdomain α/β/α sandwich protein known to begin folding in this time range. The global dimensions of early intermediates were monitored by Förster resonance energy transfer, and the dynamic properties of the local Trp environments were monitored by fluorescence lifetime detection. We found that substantial collapse occurs in both the locally connected adenosine binding subdomain and the discontinuous loop subdomain within 35 μs of initiation of folding from the urea unfolded state. During the fastest observable ∼550 μs phase, the discontinuous loop subdomain further contracts, concomitant with the burial of Trp residue(s), as both subdomains achieve a similar degree of compactness. Taken together with previous studies in the millisecond time range, a hierarchical assembly of DHFR--in which each subdomain independently folds, subsequently docks, and then anneals into the native conformation after an initial heterogeneous global collapse--emerges. The progressive acquisition of structure, beginning with a continuously connected subdomain and spreading to distal regions, shows that chain entropy is a significant organizing principle in the folding of multisubdomain proteins and single-domain proteins. Subdomain folding also provides a rationale for the complex kinetics often observed.

  7. Mechanics of the Salt Range-Potwar Plateau, Pakistan: A fold-and-thrust belt underlain by evaporites

    NASA Astrophysics Data System (ADS)

    Jaumé, Steven C.; Lillie, Robert J.

    1988-02-01

    The Salt Range and Potwar Plateau are part of the active foreland fold-and-thrust belt of the Himalaya in northern Pakistan. In this region the distance from the Main Boundary Thrust (MBT) to the front of the fold-and-thrust belt is very wide (100-150 km) because a thick evaporite sequence forms the zone of décollement. Recent studies have combined seismic reflection profiles, petroleum exploration wells, Bouguer gravity anomalies, and surface geology to construct cross sections in the eastern, central, and western Salt Range-Potwar Plateau areas. In this study the sections are compared with a model that considers the mechanics of a fold-and-thrust belt to be analogous to that of a wedge of snow or soil pushed in front of a bulldozer (Chapple, 1978; Davis et al., 1983; Dahlen et al., 1984; Dahlen, 1984). Models which include the effects of evaporites at the base (Chapple, 1978; Davis and Engelder, 1985) suggest that these thrust belts will have (1) narrow (< 1°) cross-sectional tapers, (2) larger widths than areas not underlain by evaporites, (3) symmetrical structures, and (4) changes in deformational style at the edge of the evaporite basin. The section across the eastern Potwar Plateau most closely resembles this latter model, having (1) a taper of 0.8° ± 0.1°, (2) a width of 100-150 km, (3) thrust faults that verge both to the north and south, and (4) structures rotated 30° counterclockwise with respect to the Salt Range. From the observed taper and pore fluid pressures of the eastern Potwar Plateau, estimates of the values for the yield strength of the evaporites (τo) and the coefficient of internal friction of the overlying wedge (μ) are calculated as τo = 1.33-1.50 MPa and μ = 0.95-1.04, which are then applied to the other cross sections. In the central and western sections a basement uplift, the Sargodha High, interferes with the front of the fold-and-thrust belt. This feature causes the ramping of the Salt Range Thrust and produces a relatively

  8. Detailed Chemical Kinetic Reaction Mechanisms for Incineration of Organophosphorus and Fluoro-Organophosphorus Compounds

    SciTech Connect

    Glaude, P A; Melius, C; Pitz, W J; Westbrook, C K

    2001-12-13

    A detailed chemical kinetic reaction mechanism is developed to describe incineration of the chemical warfare nerve agent sarin (GB), based on commonly used principles of bond additivity and hierarchical reaction mechanisms. The mechanism is based on previous kinetic models of organophosphorus compounds such as TMP, DMMP and DIMP that are often used as surrogates to predict incineration of GB. Kinetic models of the three surrogates and GB are then used to predict their consumption in a perfectly stirred reactor fueled by natural gas to simulate incineration of these chemicals. Computed results indicate that DIMP is the only one of these surrogates that adequately describes combustion of GB under comparable conditions. The kinetic pathways responsible for these differences in reactivity are identified and discussed. The most important reaction in GB and DIMP that makes them more reactive than TMP or DMMP is found to be a six-center molecular elimination reaction producing propene.

  9. Kinetics and Mechanism of Electron Transfer in Proteins

    NASA Astrophysics Data System (ADS)

    Kulys, J.

    1986-10-01

    The results of studies on the kinetics of the oxidation-reduction reactions of individual proteins (electron transfer agents and enzymes) are described. Attention has been concentrated on the effect of the nature of the active centres in the protein molecules and of the modification of individual aminoacid residues on the rate of electron transfer in a homogeneous medium. Questions associated with the electrochemical reactions of proteins and with the effect of the state of the interface on the rate of this process are considered in detail. Ideas concerning the theoretical calculation of the rate constants for electron transfer in proteins are described. The bibliography includes 154 references.

  10. Kinetics and mechanism of HO2 and DO2 disproportionations

    NASA Technical Reports Server (NTRS)

    Kircher, C. C.; Sander, S. P.

    1984-01-01

    A flash photolysis/UV abosrption technique was used to study the HO2 + HO2 and DO2 + DO2 reactions in the gas phase. Rate constants were measured at pressures between 100 and 700 torr of Ar and N2, and at temperatures between 230 and 420 K with up to 10 torr of added water vapor. The overall disproportionation rate constants for the reaction is given as the sum of pressure-independent and pressure-dependent terms. A kinetic analysis shows that both reactions have a zero-pressure bimolecular component and a termolecular component which is linearly dependent on pressure up to 700 torr. A priori estimates of the vibrational frequencies of the product of the HO2 + HO2 reaction suggest binding energies of 12-20 kcal per mol (for the initial association).

  11. Solid State Kinetic Parameters and Chemical Mechanism of the Dehydration of CoCl2.6H2O.

    ERIC Educational Resources Information Center

    Ribas, Joan; And Others

    1988-01-01

    Presents an experimental example illustrating the most common methods for the determination of kinetic parameters. Discusses the different theories and equations to be applied and the mechanism derived from the kinetic results. (CW)

  12. Exact results in nonequilibrium statistical mechanics: Formalism and applications in chemical kinetics and single-molecule free energy estimation

    NASA Astrophysics Data System (ADS)

    Adib, Artur B.

    In the last two decades or so, a collection of results in nonequilibrium statistical mechanics that departs from the traditional near-equilibrium framework introduced by Lars Onsager in 1931 has been derived, yielding new fundamental insights into far-from-equilibrium processes in general. Apart from offering a more quantitative statement of the second law of thermodynamics, some of these results---typified by the so-called "Jarzynski equality"---have also offered novel means of estimating equilibrium quantities from nonequilibrium processes, such as free energy differences from single-molecule "pulling" experiments. This thesis contributes to such efforts by offering three novel results in nonequilibrium statistical mechanics: (a) The entropic analog of the Jarzynski equality; (b) A methodology for estimating free energies from "clamp-and-release" nonequilibrium processes; and (c) A directly measurable symmetry relation in chemical kinetics similar to (but more general than) chemical detailed balance. These results share in common the feature of remaining valid outside Onsager's near-equilibrium regime, and bear direct applicability in protein folding kinetics as well as in single-molecule free energy estimation.

  13. Remote toehold: a mechanism for flexible control of DNA hybridization kinetics.

    PubMed

    Genot, Anthony J; Zhang, David Yu; Bath, Jonathan; Turberfield, Andrew J

    2011-02-23

    Hybridization of DNA strands can be used to build molecular devices, and control of the kinetics of DNA hybridization is a crucial element in the design and construction of functional and autonomous devices. Toehold-mediated strand displacement has proved to be a powerful mechanism that allows programmable control of DNA hybridization. So far, attempts to control hybridization kinetics have mainly focused on the length and binding strength of toehold sequences. Here we show that insertion of a spacer between the toehold and displacement domains provides additional control: modulation of the nature and length of the spacer can be used to control strand-displacement rates over at least 3 orders of magnitude. We apply this mechanism to operate displacement reactions in potentially useful kinetic regimes: the kinetic proofreading and concentration-robust regimes.

  14. Kinetic mechanism of L-α-glycerophosphate oxidase from Mycoplasma pneumoniae.

    PubMed

    Maenpuen, Somchart; Watthaisong, Pratchaya; Supon, Pacharee; Sucharitakul, Jeerus; Parsonage, Derek; Karplus, P Andrew; Claiborne, Al; Chaiyen, Pimchai

    2015-08-01

    L-α-glycerophosphate oxidase is an FAD-dependent enzyme that catalyzes the oxidation of L-α-glycerophosphate (Glp) by molecular oxygen to generate dihydroxyacetone phosphate (DHAP) and hydrogen peroxide (H2O2). The catalytic properties of recombinant His6-GlpO from Mycoplasma pneumoniae (His6-MpGlpO) were investigated through transient and steady-state kinetics and ligand binding studies. The results indicate that the reaction mechanism of His6-MpGlpO follows a ping-pong model. Double-mixing mode stopped-flow experiments show that, after flavin-mediated substrate oxidation, DHAP leaves rapidly prior to the oxygen reaction. The values determined for the individual rate constants and kcat (4.2 s(-1) at 4 °C), in addition to the finding that H2 O2 binds to the oxidized enzyme, suggest that H2O2 release is the rate-limiting step for the overall reaction. The results indicate that His6 -MpGlpO contains mixed populations of fast- and slow-reacting species. It is predominantly the fast-reacting species that participates in turnover. In contrast to other GlpO enzymes previously described, His6-MpGlpO is able to catalyze the reverse reaction of reduced enzyme and DHAP. This result may be explained by the standard reduction potential value of His6-MpGlpO (-167 ± 1 mV), which is lower than those of GlpO from other species. We found that D,L-glyceraldehyde 3-phosphate (GAP) may be used as a substrate in the His6-MpGlpO reaction, although it exhibited an approximately 100-fold lower kcat value in comparison with the reaction of Glp. These results also imply involvement of GlpO in glycolysis, as well as in lipid and glycerol metabolism. The kinetic models and distinctive properties of His6-MpGlpO reported here should be useful for future drug development against Mycoplasma pneumoniae infection.

  15. Folding mechanisms of individual beta-hairpins in a Go model of Pin1 WW domain by all-atom molecular dynamics simulations.

    PubMed

    Luo, Zhonglin; Ding, Jiandong; Zhou, Yaoqi

    2008-06-14

    This paper examines the folding mechanism of an individual beta-hairpin in the presence of other hairpins by using an off-lattice model of a small triple-stranded antiparallel beta-sheet protein, Pin1 WW domain. The turn zipper model and the hydrophobic collapse model originally developed for a single beta-hairpin in literature is confirmed to be useful in describing beta-hairpins in model Pin1 WW domain. We find that the mechanism for folding a specific hairpin is independent of whether it folds first or second, but the formation process are significantly dependent on temperature. More specifically, beta1-beta2 hairpin folds via the turn zipper model at a low temperature and the hydrophobic collapse model at a high temperature, while the folding of beta2-beta3 hairpin follows the turn zipper model at both temperatures. The change in folding mechanisms is interpreted by the interplay between contact stability (enthalpy) and loop lengths (entropy), the effect of which is temperature dependent.

  16. Reduced and Validated Kinetic Mechanisms for Hydrogen-CO-sir Combustion in Gas Turbines

    SciTech Connect

    Yiguang Ju; Frederick Dryer

    2009-02-07

    Rigorous experimental, theoretical, and numerical investigation of various issues relevant to the development of reduced, validated kinetic mechanisms for synthetic gas combustion in gas turbines was carried out - including the construction of new radiation models for combusting flows, improvement of flame speed measurement techniques, measurements and chemical kinetic analysis of H{sub 2}/CO/CO{sub 2}/O{sub 2}/diluent mixtures, revision of the H{sub 2}/O{sub 2} kinetic model to improve flame speed prediction capabilities, and development of a multi-time scale algorithm to improve computational efficiency in reacting flow simulations.

  17. Kinetic analysis of a Michaelis-Menten mechanism in which the enzyme is unstable.

    PubMed Central

    Garrido-del Solo, C; García-Cánovas, F; Havsteen, B H; Varón-Castellanos, R

    1993-01-01

    A kinetic analysis of the Michaelis-Menten mechanism is made for the cases in which the free enzyme, or the enzyme-substrate complex, or both, are unstable, either spontaneously or as a result of the addition of a reagent. The explicit time-course equations of all of the species involved has been derived under conditions of limiting enzyme concentration. The validity of these equations has been checked by using numerical simulations. An experimental design and a kinetic data analysis allowing the evaluation of the parameters and kinetic constants are recommended. PMID:8373361

  18. [Changes in the kinetics of quanta secretion-effective mechanism of synaptic transmission modulation].

    PubMed

    Bukharaeva, É A; Nikol'skiĭ, E E

    2010-08-01

    It is widely accepted that the leading presynaptic mechanisms underlying the synaptic plasticity involve changes of the number of neurotransmitter quanta released by one nerve pulse (the quantal content of postsynaptic response) and of the size of a single quantum. In addition, the existence of one more effective though previously ignored mechanism of modulation of synaptic plasticity was suggested related to the change in the time course (kinetics) of secretion of single neurotransmitter quanta forming the multiquantal response. This article reviews current data (including the authors' own results) on the kinetics of evoked neurotransmitter quanta secretion from motor nerve endings in peripheral synapses, mechanisms of their modulation and methods of quantitative analysis.

  19. Increase of ion kinetic temperature across a collisionless shock. I - A new mechanism

    NASA Technical Reports Server (NTRS)

    Lee, L. C.; Wu, C. S.; Hu, X. W.

    1986-01-01

    A simple but effective mechanism is proposed to account for the increase of ion kinetic temperature across an oblique or perpendicular shock. This mechanism is based on the nonadiabatic motion of the transmitted ions across the shock ramp, which can lead to an ion gyrophase-bunching behind the shock.

  20. Effect of experimental and sample factors on dehydration kinetics of mildronate dihydrate: mechanism of dehydration and determination of kinetic parameters.

    PubMed

    Bērziņš, Agris; Actiņš, Andris

    2014-06-01

    The dehydration kinetics of mildronate dihydrate [3-(1,1,1-trimethylhydrazin-1-ium-2-yl)propionate dihydrate] was analyzed in isothermal and nonisothermal modes. The particle size, sample preparation and storage, sample weight, nitrogen flow rate, relative humidity, and sample history were varied in order to evaluate the effect of these factors and to more accurately interpret the data obtained from such analysis. It was determined that comparable kinetic parameters can be obtained in both isothermal and nonisothermal mode. However, dehydration activation energy values obtained in nonisothermal mode showed variation with conversion degree because of different rate-limiting step energy at higher temperature. Moreover, carrying out experiments in this mode required consideration of additional experimental complications. Our study of the different sample and experimental factor effect revealed information about changes of the dehydration rate-limiting step energy, variable contribution from different rate limiting steps, as well as clarified the dehydration mechanism. Procedures for convenient and fast determination of dehydration kinetic parameters were offered.

  1. Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L.

    PubMed

    Clementi, Cecilia; García, Angel E; Onuchic, José N

    2003-02-21

    Experimental and theoretical results suggest that, since proteins are energetically minimally frustrated, the native fold, or topology, plays a primary role in determining the structure of the transition state ensemble and on-pathway intermediate states in protein folding. Although the central role of native state topology in determining the folding mechanism is thought to be a quite general result-at least for small two-state folding proteins-there are remarkable exceptions. Recent experimental findings have shown that topology alone cannot always determine the folding mechanism, and demonstrated that the balance between topology and energetics is very delicate. This balance seems to be particularly critical in proteins with a highly symmetrical native structure, such as proteins L and G, which have similar native structure topology but fold by different mechanisms. Simplified, C(alpha)-atom only protein models have shown not be sufficient to differentiate these mechanisms. An all-atom Gō model provides a valuable intermediate model between structurally simplified protein representations and all-atom protein simulations with explicit/implicit solvent descriptions. We present here a detailed study of an all-atom Gō-like representation of protein L, in close comparison with the experimental results and with the results obtained from a simple C(alpha)-atom representation of the same protein. We also perform simulations for protein G, where we obtain a folding mechanism in which the protein symmetry is broken exactly in the opposite way to protein L as has been observed experimentally. A detailed analysis for protein L also shows that the role of specific residues is correctly and quantitatively reproduced by the all-atom Gō model over almost the entire protein.

  2. The Kinetic Chain Revisited: New Concepts on Throwing Mechanics and Injury.

    PubMed

    Chu, Samuel K; Jayabalan, Prakash; Kibler, W Ben; Press, Joel

    2016-03-01

    The overhead throwing motion is a complex activity that is achieved through activation of the kinetic chain. The kinetic chain refers to the linkage of multiple segments of the body that allows for transfer of forces and motion. The lower extremities and core provide a base of support, generating energy that is transferred eventually through the throwing arm and hand, resulting in release of the ball. The kinetic chain requires optimal anatomy, physiology, and mechanics and is involved in all 6 phases of overhead throwing: windup, stride, arm cocking, acceleration, deceleration, and follow-through. Breaks or deficits in the kinetic chain can lead to injury or decreased performance. Through an understanding of the mechanics and pathomechanics seen in each phase of throwing, the clinician can better evaluate and screen for potential kinetic chain deficits in the overhead throwing athlete. The purpose of this article is to review the biomechanics of the overhead throwing motion, the role of the kinetic chain in throwing, and the clinical evaluation and management of abnormal throwing mechanics and related injuries.

  3. Microstructures, deformation mechanisms and strain patterns in a vertical profile, inner appalachian fold-thrust belt, Alabama

    NASA Astrophysics Data System (ADS)

    Wu, Schuman

    1993-02-01

    A core from the American Anniston No. 1 well, drilled in the Pell City thrust sheet, Calhoun County, Alabama, provides an excellent scientific opportunity to study in a vertical profile the deformation mechanisms and strain patterns associated with large-scale structures. The core contains stratigraphic units from Cambrian to Mississippian in age and two major thrust faults. A detailed structural analysis revealed two deformation episodes, a pre-orogenic deformation and Alleghanian orogenic deformation. In the pre-orogenic deformation, synsedimentary folds and growth faults are the characteristic early structures, and normal faults formed in lithifield rocks later. During Alleghanian deformation, earlier fractures are overprinted by later S1 penetrative structures. In limestone, shale and siltstone within thrust sheets, S1 is solution cleavage. Dolomites in the thrust sheets were deformed by fracturing, and no penetrative cleavages formed. In major fault zones, S1 mylonitic foliation formed in limestone, shale and siltstone. Fault-related dolomites were deformed cataclastically and no S surfaces formed. Strain magnitude increases towards major thrust faults in both the hanging walls and footwalls. For the typical fault configuration in the core with limestone-dolomite in the hanging wall and shale-siltstone in the footwall, strain is mainly caused by pressure solution and cataclasis in the hanging wall and by plastic deformation in the footwall.

  4. Effects of cohesion on the structural and mechanical evolution of fold and thrust belts and contractional wedges: Discrete element simulations

    NASA Astrophysics Data System (ADS)

    Morgan, Julia K.

    2015-05-01

    Particle-based numerical simulations of cohesive contractional wedges can yield important perspectives on the formation and evolution of fold and thrust belts, offering particular insights into the mechanical evolution of the systems. Results of several discrete element method simulations are presented here, demonstrating the stress and strain evolution of systems with different initial cohesive strengths. Particle assemblages consolidated under gravity, and bonded to impart cohesion, are pushed from the left at a constant velocity above a weak, unbonded décollement surface. Internal thrusting causes horizontal shortening and vertical thickening, forming wedge geometries. The mean wedge taper is similar for all simulations, consistent with their similar residual and basal sliding friction values. In all examples presented here, both forethrusts and back thrusts occur, but forethrusts accommodate most of the shortening. Fault spacing and offset increase with increasing cohesion. Significant tectonic volume strain also occurs, with the greatest incremental volume strain occurring just outboard of the deformation front. This diffuse shortening serves to strengthen the unfaulted domain in front of the deformed wedge, preconditioning these materials for brittle (dilative) failure. The reach of this volumetric strain and extent of décollement slip increase with cohesive strength, defining the extent of stress transmission. Stress paths for elements tracked through the simulations demonstrate systematic variations in shear stress in response to episodes of both décollement slip and thrust fault activity, providing a direct explanation for stress fluctuations during convergence.

  5. GroEL-mediated protein folding.

    PubMed Central

    Fenton, W. A.; Horwich, A. L.

    1997-01-01

    I. Architecture of GroEL and GroES and the reaction pathway A. Architecture of the chaperonins B. Reaction pathway of GroEL-GroES-mediated folding II. Polypeptide binding A. A parallel network of chaperones binding polypeptides in vivo B. Polypeptide binding in vitro 1. Role of hydrophobicity in recognition 2. Homologous proteins with differing recognition-differences in primary structure versus effects on folding pathway 3. Conformations recognized by GroEL a. Refolding studies b. Binding of metastable intermediates c. Conformations while stably bound at GroEL 4. Binding constants and rates of association 5. Conformational changes in the substrate protein associated with binding by GroEL a. Observations b. Kinetic versus thermodynamic action of GroEL in mediating unfolding c. Crossing the energy landscape in the presence of GroEL III. ATP binding and hydrolysis-driving the reaction cycle IV. GroEL-GroES-polypeptide ternary complexes-the folding-active cis complex A. Cis and trans ternary complexes B. Symmetric complexes C. The folding-active intermediate of a chaperonin reaction-cis ternary complex D. The role of the cis space in the folding reaction E. Folding governed by a "timer" mechanism F. Release of nonnative polypeptides during the GroEL-GroES reaction G. Release of both native and nonnative forms under physiologic conditions H. A role for ATP binding, as well as hydrolysis, in the folding cycle V. Concluding remarks. PMID:9098884

  6. Kinetics and mechanism of dimethoate chlorination during drinking water treatment.

    PubMed

    Tian, Fang; Liu, Wenjun; Guo, Guang; Qiang, Zhimin; Zhang, Can

    2014-05-01

    Dimethoate (DMT), a commonly used organophosphorus pesticide, is of great concern because of its toxicity and potentially harmful effects on water sources. The elimination of DMT as well as the toxicity and persistence of the byproducts formed during DMT degradation is most important for the safety of drinking water. This study first determined the reaction kinetics of DMT with free chlorine (FC) under typical water treatment conditions. The reaction between DMT and FC proceeded rapidly, exhibiting first-order with respect to each reactant. The degradation of DMT by FC was highly pH dependent, and the pseudo-first-order rate constant decreased obviously from 0.13 to 0.02 s(-1) with an increase in pH from 7.0 to 8.3. Bromide ion accelerated the reaction by acting as a catalyst, and the accelerated reaction rate was linearly proportional to the bromide concentration. As a ubiquitous component in natural waters, humic acid also increased the reaction rate. However, the presence of ammonium inhibited the degradation of DMT due to its rapid converting FC to chloramines. Omethoate (OMT) was identified as an important byproduct of DMT chlorination, but only accounted for ca. 28% of the DMT degraded; and other two organic byproducts were also identified. The acute toxicity of DMT solution increased after treatment with FC due to the formation of more toxic byproducts (e.g. OMT).

  7. Kinetics and mechanism of Dionaea muscipula trap closing.

    PubMed

    Volkov, Alexander G; Adesina, Tejumade; Markin, Vladislav S; Jovanov, Emil

    2008-02-01

    The Venus flytrap (Dionaea muscipula) possesses an active trapping mechanism to capture insects with one of the most rapid movements in the plant kingdom, as described by Darwin. This article presents a detailed experimental investigation of trap closure by mechanical and electrical stimuli and the mechanism of this process. Trap closure consists of three distinctive phases: a silent phase with no observable movement; an accelerated movement of the lobes; and the relaxation of the lobes in their closed state, resulting in a new equilibrium. Uncouplers and blockers of membrane channels were used to investigate the mechanisms of different phases of closing. Uncouplers increased trap closure delay and significantly decreased the speed of trap closure. Ion channel blockers and aquaporin inhibitors increased time of closing. Transmission of a single electrical charge between a lobe and the midrib causes closure of the trap and induces an electrical signal propagating between both lobes and midrib. The Venus flytrap can accumulate small subthreshold charges, and when the threshold value is reached, the trap closes. Repeated application of smaller charges demonstrates the summation of stimuli. The cumulative character of electrical stimuli points to the existence of electrical memory in the Venus flytrap. The observed fast movement can be explained by the hydroelastic curvature model without invoking buckling instability. The new hydroelastic curvature mechanism provides an accurate description of the authors' experimental data.

  8. Kinetic mechanism for the excision of hypoxanthine by Escherichia coli AlkA and evidence for binding to DNA ends.

    PubMed

    Zhao, Boyang; O'Brien, Patrick J

    2011-05-24

    The Escherichia coli 3-methyladenine DNA glycosylase II protein (AlkA) recognizes a broad range of oxidized and alkylated base lesions and catalyzes the hydrolysis of the N-glycosidic bond to initiate the base excision repair pathway. Although the enzyme was one of the first DNA repair glycosylases to be discovered more than 25 years ago and there are multiple crystal structures, the mechanism is poorly understood. Therefore, we have characterized the kinetic mechanism for the AlkA-catalyzed excision of the deaminated purine, hypoxanthine. The multiple-turnover glycosylase assays are consistent with Michaelis-Menten kinetics. However, under single-turnover conditions that are commonly employed for studying other DNA glycosylases, we observe an unusual biphasic protein saturation curve. Initially, the observed rate constant for excision increases with an increasing level of AlkA protein, but at higher protein concentrations, the rate constant decreases. This behavior can be most easily explained by tight binding to DNA ends and by crowding of multiple AlkA protamers on the DNA. Consistent with this model, crystal structures have shown the preferential binding of AlkA to DNA ends. By varying the position of the lesion, we identified an asymmetric substrate that does not show inhibition at higher concentrations of AlkA, and we performed pre-steady state and steady state kinetic analysis. Unlike the situation in other glycosylases, release of the abasic product is faster than N-glycosidic bond cleavage. Nevertheless, AlkA exhibits significant product inhibition under multiple-turnover conditions, and it binds approximately 10-fold more tightly to an abasic site than to a hypoxanthine lesion site. This tight binding could help protect abasic sites when the adaptive response to DNA alkylation is activated and very high levels of AlkA protein are present.

  9. Hierarchical folding mechanism of apomyoglobin revealed by ultra-fast H/D exchange coupled with 2D NMR.

    PubMed

    Uzawa, Takanori; Nishimura, Chiaki; Akiyama, Shuji; Ishimori, Koichiro; Takahashi, Satoshi; Dyson, H Jane; Wright, Peter E

    2008-09-16

    The earliest steps in the folding of proteins are complete on an extremely rapid time scale that is difficult to access experimentally. We have used rapid-mixing quench-flow methods to extend the time resolution of folding studies on apomyoglobin and elucidate the structural and dynamic features of members of the ensemble of intermediate states that are populated on a submillisecond time scale during this process. The picture that emerges is of a continuum of rapidly interconverting states. Even after only 0.4 ms of refolding time a compact state is formed that contains major parts of the A, G, and H helices, which are sufficiently well folded to protect amides from exchange. The B, C, and E helix regions fold more slowly and fluctuate rapidly between open and closed states as they search docking sites on this core; the secondary structure in these regions becomes stabilized as the refolding time is increased from 0.4 to 6 ms. No further stabilization occurs in the A, G, H core at 6 ms of folding time. These studies begin to time-resolve a progression of compact states between the fully unfolded and native folded states and confirm the presence an ensemble of intermediates that interconvert in a hierarchical sequence as the protein searches conformational space on its folding trajectory.

  10. Students' Misconceptions about Heat Transfer Mechanisms and Elementary Kinetic Theory

    ERIC Educational Resources Information Center

    Pathare, S. R.; Pradhan, H. C.

    2010-01-01

    Heat and thermodynamics is a conceptually rich area of undergraduate physics. In the Indian context in particular there has been little work done in this area from the point of view of misconceptions. This prompted us to undertake a study in this area. We present a study of students' misconceptions about heat transfer mechanisms, i.e. conduction,…

  11. Development of a surrogate kinetic mechanism for photochemical smog. Final report

    SciTech Connect

    Leone, J.A.; Seinfeld, J.H.

    1985-01-01

    A surrogate condensed chemical reaction mechanism for photochemical smog containing the latest available kinetic and mechanistic data is developed here and is extensively tested against experimental data from two smog-chamber facilities. In addition, a counter species analysis has shown that the prediction of the individual portions of the surrogate mechanism are in good agreement with those of a detailed explicit mechanism for photochemical smog. The new mechanism contains 20 non-steady-state species, making it compact enough for use in multidimensional grid models of urban air pollution. A major advantage of the new mechanism is the ease with which it can be modified to incorporate new kinetic or mechanistic information because of the straightforward manner in which the mechanism was formulated from the detailed explicit chemistry.

  12. Chemical Kinetics Mechanism Reduction Based on Principal Component Analysis: Development and Testing of Some New Implementations

    DTIC Science & Technology

    2013-05-01

    prediction of propulsion system performance. In addition, programs employed in this study for screening the merit of reduced mechanisms were...development of system -specific gas-phase finite-rate chemical kinetics mechanisms is a significant part of these efforts (Anderson et al., 2010; Chen and...employed to model other combustion systems . The final step involves producing a “reduced” (or skeletal) mechanism from the detailed/full one

  13. Caffeine catalyzed synthesis of tetrahydrobenzo[b]pyran derivatives: Synthesis and insight into kinetics and mechanism.

    PubMed

    Habibi-Khorassani, Sayyedmostafa; Shahraki, Mehdi; Pourpanah, Sayedeh Shadfar; Mollashahi, Ebrahim; Keshavarz, Shabnam

    2016-10-06

    In this work, synthesis and the feasibility of utilizing a modern in situ spectroscopic method (UV-vis spectrophotometry) has been demonstrated in order to investigate the reaction kinetics between arylaldehydes, malononitrile and dimedone in a mixture of ethanol and water as solvent in the presence of caffeine as a biodegradable catalyst. Attempts for mechanistic insight into the synthesis of a derivative of 4H-tetrahydrobenzo[b]pyrans included spectral kinetics approaches which revealed specific limiting conditions. The influence of various parameters (temperature, solvent and concentration) on the reaction by means of the pseudo-first order kinetic model was studied. Kinetic parameters were calculated. The initial stage of the presented mechanism is defined as a rate-determining step (k1) and is confirmed based upon the steady state approximation.

  14. Reaction Mechanism and Kinetics of Enargite Oxidation at Roasting Temperatures

    NASA Astrophysics Data System (ADS)

    Padilla, Rafael; Aracena, Alvaro; Ruiz, Maria C.

    2012-10-01

    Roasting of enargite (Cu3AsS4) in the temperature range of 648 K to 898 K (375 °C to 625 °C) in atmospheres containing variable amounts of oxygen has been studied by thermogravimetric methods. From the experimental results of weight loss/gain data and X-ray diffraction (XRD) analysis of partially reacted samples, the reaction mechanism of the enargite oxidation was determined, which occurred in three sequential stages:

  15. Remaining uncertainties in the kinetic mechanism of hydrogen combustion

    SciTech Connect

    Konnov, Alexander A.

    2008-03-15

    An analysis of the performance of an updated hydrogen combustion mechanism is presented. Particular attention was paid to different channels of reaction between H atoms and HO{sub 2} radicals, to pressure dependence of the recombination of HO{sub 2} radicals, and to the anomalous rate constant of reaction between OH and HO{sub 2} radicals. The contemporary choice of the reaction rate constants is presented with the emphasis on their uncertainties. Then the predictions of ignition, oxidation, flame burning velocities, and flame structure of hydrogen-oxygen-inert mixtures are shown. The modeling range covers ignition experiments from 950 to 2700 K and from subatmospheric pressures up to 87 atm; hydrogen oxidation in a flow reactor at temperatures around 900 K from 0.3 up to 15.7 atm; flame burning velocities in hydrogen-oxygen-inert mixtures from 0.35 up to 4 atm; and hydrogen flame structure at 1 and 10 atm. Comparison of the modeling and experiments is discussed in terms of the range of applicability of the present detailed mechanism. The necessity for analysis of the mechanism to have an exhaustive list of reactions is emphasized. (author)

  16. Kinetic method for the large-scale analysis of the binding mechanism of histone deacetylase inhibitors.

    PubMed

    Meyners, Christian; Baud, Matthias G J; Fuchter, Matthew J; Meyer-Almes, Franz-Josef

    2014-09-01

    Performing kinetic studies on protein ligand interactions provides important information on complex formation and dissociation. Beside kinetic parameters such as association rates and residence times, kinetic experiments also reveal insights into reaction mechanisms. Exploiting intrinsic tryptophan fluorescence a parallelized high-throughput Förster resonance energy transfer (FRET)-based reporter displacement assay with very low protein consumption was developed to enable the large-scale kinetic characterization of the binding of ligands to recombinant human histone deacetylases (HDACs) and a bacterial histone deacetylase-like amidohydrolase (HDAH) from Bordetella/Alcaligenes. For the binding of trichostatin A (TSA), suberoylanilide hydroxamic acid (SAHA), and two other SAHA derivatives to HDAH, two different modes of action, simple one-step binding and a two-step mechanism comprising initial binding and induced fit, were verified. In contrast to HDAH, all compounds bound to human HDAC1, HDAC6, and HDAC8 through a two-step mechanism. A quantitative view on the inhibitor-HDAC systems revealed two types of interaction, fast binding and slow dissociation. We provide arguments for the thesis that the relationship between quantitative kinetic and mechanistic information and chemical structures of compounds will serve as a valuable tool for drug optimization.

  17. Mechanism and kinetics of COS-induced diethanolamine degradation

    SciTech Connect

    Dawodu, O.F.; Meisen, A. . Dept. of Chemical Engineering)

    1994-03-01

    The degradation of aqueous diethanolamine (DEA) solutions by carbonyl sulfide was examined by using a 600-mL well-stirred reactor operating under the following conditions: DEA concentration 20--40 wt %, temperature 120--180 C, COS partial pressure 0.3--1.17 MPa. The reaction products were identified by GC/MS, and reaction mechanisms are developed which conform with experimental observations. The reaction rate constants are determined, and a mathematical model for estimating DEA degradation by COS is presented.

  18. Identification of multiple folding pathways of monellin using pulsed thiol labeling and mass spectrometry.

    PubMed

    Jha, Santosh Kumar; Dasgupta, Amrita; Malhotra, Pooja; Udgaonkar, Jayant B

    2011-04-19

    Protein folding reactions often display multiexponential kinetics of changes in intrinsic optical signals, as a manifestation of heterogeneity, either on one folding pathway or on multiple folding pathways. Delineating the origin of this heterogeneity is difficult because different coexisting structural forms of a protein cannot be easily distinguished by optical probes. In this study, the complex folding reaction of single-chain monellin has been investigated using a pulsed thiol labeling (SX) methodology in conjunction with mass spectrometry, which measures the kinetics of burial of a cysteine side chain thiol during folding. Because it can directly distinguish between unfolded and folded molecules and can measure the disappearance of the former during folding, the pulsed SX methodology is an ideal method for investigating whether multiple pathways are operative during folding. The kinetics of burial of the C42 thiol of monellin was observed to follow biexponential kinetics. To determine whether this was because the fast phase leads to the partial protection of the thiol group in all the molecules or to complete protection in only a fraction of the molecules, the duration and intensity of the labeling pulse were varied. The observation that the extent of labeling did not vary with the duration of the pulse cannot be explained by a simple sequential folding mechanism. Two parallel folding pathways are shown to be operative, with one leading to the formation of thiol-protective structure more rapidly than the other.

  19. Pleural liquid and kinetic friction coefficient of mesothelium after mechanical ventilation.

    PubMed

    Bodega, Francesca; Sironi, Chiara; Porta, Cristina; Zocchi, Luciano; Agostoni, Emilio

    2015-01-15

    Volume and protein concentration of pleural liquid in anesthetized rabbits after 1 or 3h of mechanical ventilation, with alveolar pressure equal to atmospheric at end expiration, were compared to those occurring after spontaneous breathing. Moreover, coefficient of kinetic friction between samples of visceral and parietal pleura, obtained after spontaneous or mechanical ventilation, sliding in vitro at physiological velocity under physiological load, was determined. Volume of pleural liquid after mechanical ventilation was similar to that previously found during spontaneous ventilation. This finding is contrary to expectation of Moriondo et al. (2005), based on measurement of lymphatic and interstitial pressure. Protein concentration of pleural liquid after mechanical ventilation was also similar to that occurring after spontaneous ventilation. Coefficient of kinetic friction after mechanical ventilation was 0.023±0.001, similar to that obtained after spontaneous breathing.

  20. Photochemistry of dipenylketyl radicals: spectroscopy, kinetics, and mechanisms

    SciTech Connect

    Johnston, L.J.; Lougnot, D.J.; Wintgens, V.; Scaiano, J.C.

    1988-01-20

    The photochemistry of the diphenylketyl radical has been examined in nonpolar solutions. Transient studies using two-laser techniques yield an excited-state lifetime of 3.9 ns in toluene at room temperature, while for diphenylketyl-O-d the lifetime is 8.7 ns. Dye laser irradiation (515 nm) in the ketyl's visible absorption band leads to efficient photobleaching with Phi/sub bleach/ = 0.27 +/- 0.06 for the parent radical and 0.39 and 0.26 for the 4-methyl and 4-chloro derivatives, respectively. The photobleaching reaction involves the cleavage of the O-H ketyl bond to yield benzophenone and hydrogen atoms; in cyclohexane the latter abstract hydrogen from the solvent to produce molecular hydrogen which was characterized by Raman spectroscopy. In accordance with this mechanism, two-laser experiments produce lower yields of photoreduction products than the one-laser experiments in which the ketyls are not photobleached. When the ketyl radicals are generated by reaction of tert-butoxy radicals with benzhydrol, dye laser irradiation leads to a large increase in the yield of benzophenone (now a product), although the mechanism here is somewhat more complex due to the quenching of excited ketyl radicals by di-tert-butyl peroxide (k/sub q/ = 1.9 x 10/sup 9/ M/sup -1/ s/sup -1/). Detailed studies of the fluorescence, isotope effects, temperature effects, and products are also included.

  1. Kinetics and mechanism of photopromoted oxidative dissolution of antimony trioxide.

    PubMed

    Hu, Xingyun; Kong, Linghao; He, Mengchang

    2014-12-16

    Light (sunlight, ultraviolet, simulated sunlight) irradiation was used to initiate the dissolution of antimony trioxide (Sb2O3). Dissolution rate of Sb2O3 was accelerated and dissolved trivalent antimony (Sb(III)) was oxidized in the irradiation of light. The photopromoted oxidative dissolution mechanism of Sb2O3 was studied through experiments investigating the effects of pH, free radicals scavengers, dissolved oxygen removal and Sb2O3 dosage on the release rate of antimony from Sb2O3 under simulated sunlight irradiation. The key oxidative components were hydroxyl free radicals, photogenerated holes and superoxide free radicals; their contribution ratios were roughly estimated. In addition, a conceptual model of the photocatalytic oxidation dissolution of Sb2O3 was proposed. The overall pH-dependent dissolution rate of Sb2O3 and the oxidation of Sb(III) under light irradiation were expressed by r = 0.08 ·[OH(-)](0.63) and rox = 0.10 ·[OH(-)](0.79). The present study on the mechanism of the photo-oxidation dissolution of Sb2O3 could help clarify the geochemical cycle and fate of Sb in the environment.

  2. Reduced kinetic mechanism of ignition for nonpremixed hydrogen/air in a supersonic mixing layer

    SciTech Connect

    Ju, Y.; Niioka, T. . Inst. of Fluid Science)

    1994-11-01

    Transient ignition processes in a two-dimensional spatially evolving supersonic mixing layer consisting of a parallel nonpremixed airstream and a hydrogen stream both with temperatures higher than 1,000 K were investigated numerically by using the full chemistry and its reduced chemistry. A phenomenon different from that examined in previous studies, in which ignition of hydrogen/oxygen mixtures was considered, was found in the nonpremixed case examined here. It was shown that the concentration of O was greater than that of OH before ignition, but became smaller with the development of ignition process. Fourteen important reactions for ignition were obtained and verified using sensitivity analyses of ignition delay time and radical concentrations. Several different four-step and three-step reduced kinetic mechanisms were then deduced by introducing the steady-state approximation to different species. Comparison of these reduced kinetic mechanisms with the full chemistry showed that the steady-state approximation of O used in previous studies caused serious errors in the prediction of ignition delay time in supersonic flow, in which nonpremixed character is predominant and the transport phenomenon is important. Ignition locations predicted with the proper four-step and three-step reduced kinetic mechanisms were within 5% and 20% of those predicted with the full chemistry. Finally, these two reduced mechanisms were used to evaluate the effect of viscous dissipation on ignition in the supersonic shear layer. Good agreements between the results of the present reduced kinetic mechanisms and those of the full chemistry were obtained.

  3. Evolving Stress State and Deformation Mechanism in the Himalayan Foreland Fold-and-Thrust Belt, Northern Pakistan

    NASA Astrophysics Data System (ADS)

    Ahmad, I.; Dasti, N.

    2010-12-01

    Crustal deformation along with shortening due to northward under-thrusting of the Indian plate beneath the Eurasian plate continues to create active tectonic features on the northern fringes of the Indian craton since major collision began in the Eocene. Here the study provides insights on the evolving stress state and deformation mechanism of the Salt Range and Potwar area of Northern Pakistan. This part of Himalayan foreland fold-and-thrust-belt has severe history of deformation during 5.1 Ma and 2 Ma. This foreland area lies between Main Boundary Thrust (MBT) in the north, Himalayan Frontal Thrust (HFT) in the south and Jhelum fault of sinistral nature in the east & Kalabagh fault of dextral nature in the west. An integrated data from seismic reflection profiles and drilling logs reveal that the subsurface deformation encompasses pop-ups, imbricates, duplexes with in-sequence and out-of-sequence thrusting. It also depicts that intensity of deformation increases from the northern margin of Soan geosyncline towards north due to lacking of evaporites while in the south it decreases due to gradual increase in salt thickness. Surface geologic mapping glimpses a series of thrust sheets and anticlines trending ENE-SWS in the eastern and central part of the study area; whereas in the western part, the trend is almost E-W. This variation in the trend of structures is the result of counter clock rotational behaviour (~10°deviation from north to the west) of north-western part of the Indian lithospheric plate. Current outcrop-scale natural fracture data collected from selected anticlinal structures of the study area is presented to manifest the stress evolution and deformation styles under the established tectonic framework. Collected data is analysed for the evaluation of tectonic stress direction and deformation mechanism. The genetic arrangement and types of fractures observed in the study area indicate that the whole area is under compression. The data also testify

  4. Distinct folding pathways of two homologous disulfide proteins: bovine pancreatic trypsin inhibitor and tick anticoagulant peptide.

    PubMed

    Chang, Jui-Yoa

    2011-01-01

    The folding pathways of disulfide proteins vary substantially (Arolas et al., Trends Biochem Sci 31: 292-301, 2006). The diversity is mainly manifested by (a) the extent of heterogeneity of folding intermediates, (b) the extent of presence of native-like intermediates, and (c) the variation of folding kinetics. Even among structurally similar proteins, the difference can be enormous. This is demonstrated in this concise review with two structurally homologous kunitz-type protease inhibitors, bovine pancreatic trypsin inhibitor and tick anticoagulant peptide, as well as a group of cystine knot proteins. The diversity of their folding mechanisms is illustrated with two different folding techniques: (a) the conventional method of disulfide oxidation (oxidative folding), and (b) the novel method of disulfide scrambling (Chang, J Biol Chem 277: 120-126, 2002). This review also highlights the convergence of folding models concluded form the conventional conformational folding and those obtained by oxidative folding.

  5. G2 chromatid aberrations: Kinetics and possible mechanisms

    SciTech Connect

    Bryant, P.E.; Slijepcevic, P. )

    1993-01-01

    Chromatid breaks and exchanges are induced by radiation in G2 mammalian cells. Breaks are at a maximum number at about 30 min after irradiation and decrease apparently exponentially with time between irradiation and sampling. Few breaks are observed immediately following exposure, probably as a result of selection of mitotic cells where chromosomes are condensed and there is consequently a lack of time for expression of damage. The change in frequency of breaks with time, from 30 min after radiation exposure and onwards, can be interpreted in two possible ways: either in terms of a repair process or in terms of a change in radiosensitivity through G2. However, the results with an inhibitor of repair of DNA double-strand breaks (ara A) and with [open quotes]transient hypothermia[close quotes] which extends the G2 phase, argue for an interpretation based on rejoining of chromatid breaks, possibly reflecting the repair of a subclass of dsb. Data from experiments with irradiated and restriction endonuclease treated radiosensitive mutant rodent lines indicate that enhanced levels of conversion of dsb into chromosomal aberrations may be largely independent of repair rates of bulk dsb. In CHO cells and in human lymphocytes exchanges initially increase rapidly with time and then remain at a constant frequency, supporting the notion of a uniform chromosomal radiosensitivity throughout most of G2 and providing further evidence that the mechanism for misjoining broken chromatids (leading to exchanges) is different from that for rejoining of chromatid breaks. Ratios of breaks to exchanges were found to vary in different cell lines and at different times during treatment with inhibitors or at altered temperatures, possibly (in different cell lines) indicating different levels of enzymes involved in misjoining, but suggesting that the mechanisms of chromosomal rejoining and misjoining are independent, at least to some degree. 19 refs., 11 figs., 1 tab.

  6. Kinetic mechanism and fidelity of nick sealing by Escherichia coli NAD+-dependent DNA ligase (LigA)

    PubMed Central

    Chauleau, Mathieu; Shuman, Stewart

    2016-01-01

    Escherichia coli DNA ligase (EcoLigA) repairs 3′-OH/5′-PO4 nicks in duplex DNA via reaction of LigA with NAD+ to form a covalent LigA-(lysyl-Nζ)–AMP intermediate (step 1); transfer of AMP to the nick 5′-PO4 to form an AppDNA intermediate (step 2); and attack of the nick 3′-OH on AppDNA to form a 3′-5′ phosphodiester (step 3). A distinctive feature of EcoLigA is its stimulation by ammonium ion. Here we used rapid mix-quench methods to analyze the kinetic mechanism of single-turnover nick sealing by EcoLigA–AMP. For substrates with correctly base-paired 3′-OH/5′-PO4 nicks, kstep2 was fast (6.8–27 s−1) and similar to kstep3 (8.3–42 s−1). Absent ammonium, kstep2 and kstep3 were 48-fold and 16-fold slower, respectively. EcoLigA was exquisitely sensitive to 3′-OH base mispairs and 3′ N:abasic lesions, which elicited 1000- to >20000-fold decrements in kstep2. The exception was the non-canonical 3′ A:oxoG configuration, which EcoLigA accepted as correctly paired for rapid sealing. These results underscore: (i) how EcoLigA requires proper positioning of the nick 3′ nucleoside for catalysis of 5′ adenylylation; and (ii) EcoLigA's potential to embed mutations during the repair of oxidative damage. EcoLigA was relatively tolerant of 5′-phosphate base mispairs and 5′ N:abasic lesions. PMID:26857547

  7. Site-specific experiments on folding/unfolding of Jun coiled coils: thermodynamic and kinetic parameters from spin inversion transfer nuclear magnetic resonance at leucine-18.

    PubMed

    d'Avignon, D André; Bretthorst, G Larry; Holtzer, Marilyn Emerson; Schwarz, Kathleen A; Angeletti, Ruth Hogue; Mints, Lisa; Holtzer, Alfred

    2006-10-15

    The 32-residue leucine zipper subsequence, called here Jun-lz, associates in benign media to form a parallel two-stranded coiled coil. Studies are reported of its thermal unfolding/folding transition by circular dichroism (CD) on samples of natural isotopic abundance and by both equilibrium and spin inversion transfer (SIT) nuclear magnetic resonance (NMR) on samples labeled at the leucine-18 alpha-carbon with 99% 13C. The data cover a wide range of temperature and concentration, and show that Jun-lz unfolds below room temperature, being far less stable than some other leucine zippers such as GCN4. 13C-NMR shows two well-separated resonances. We ascribe the upfield one to 13C spins on unfolded single chains and the downfield one to 13C spins on coiled-coil dimers. Their relative intensities provide a measure of the unfolding equilibrium constant. In SIT NMR, the recovery of the equilibrium magnetization after one resonance is inverted is modulated in part by the unfolding and folding rate constants, which are accessible from the data. Global Bayesian analysis of the equilibrium and SIT NMR data provide values for the standard enthalpy, entropy, and heat capacity of unfolding, and show the latter to be unusually large. The CD results are compatible with the NMR findings. Global Bayesian analysis of the SIT NMR data yields the corresponding activation parameters for unfolding and folding. The results show that both reaction directions are activated processes. Activation for unfolding is entropy driven, enthalpy opposed. Activation for folding is strongly enthalpy opposed and somewhat entropy opposed, falsifying the idea that the barrier for folding is solely due to a purely entropic search for properly registered partners. The activation heat capacity is much larger for folding, so almost the entire overall change is due to the folding direction. This latter finding, if it applies to GCN4 leucine zippers, clears up an extant apparent disagreement between folding rate

  8. Kinetics and Mechanism of Iodide Oxidation by Iron(III): A Clock Reaction Approach

    ERIC Educational Resources Information Center

    Bauer, Jurica; Tomisic, Vladislav; Vrkljan, Petar B. A.

    2008-01-01

    A simple method for studying the kinetics of a chemical reaction is described and the significance of reaction orders in deducing reaction mechanisms is demonstrated. In this student laboratory experiment, oxidation of iodide by iron(III) ions in an acidic medium is transformed into a clock reaction. By means of the initial rates method, it is…

  9. Detailed Chemical Kinetic Reaction Mechanism for Biodiesel Components Methyl Stearate and Methyl Oleate

    SciTech Connect

    Naik, C; Westbrook, C K; Herbinet, O; Pitz, W J; Mehl, M

    2010-01-22

    New chemical kinetic reaction mechanisms are developed for two of the five major components of biodiesel fuel, methyl stearate and methyl oleate. The mechanisms are produced using existing reaction classes and rules for reaction rates, with additional reaction classes to describe other reactions unique to methyl ester species. Mechanism capabilities were examined by computing fuel/air autoignition delay times and comparing the results with more conventional hydrocarbon fuels for which experimental results are available. Additional comparisons were carried out with measured results taken from jet-stirred reactor experiments for rapeseed methyl ester fuels. In both sets of computational tests, methyl oleate was found to be slightly less reactive than methyl stearate, and an explanation of this observation is made showing that the double bond in methyl oleate inhibits certain low temperature chain branching reaction pathways important in methyl stearate. The resulting detailed chemical kinetic reaction mechanism includes more approximately 3500 chemical species and more than 17,000 chemical reactions.

  10. Programmed folding of DNA origami structures through single-molecule force control

    NASA Astrophysics Data System (ADS)

    Bae, Wooli; Kim, Kipom; Min, Duyoung; Ryu, Je-Kyung; Hyeon, Changbong; Yoon, Tae-Young

    2014-12-01

    Despite the recent development in the design of DNA origami, its folding yet relies on thermal or chemical annealing methods. We here demonstrate mechanical folding of the DNA origami structure via a pathway that has not been accessible to thermal annealing. Using magnetic tweezers, we stretch a single scaffold DNA with mechanical tension to remove its secondary structures, followed by base pairing of the stretched DNA with staple strands. When the force is subsequently quenched, folding of the DNA nanostructure is completed through displacement between the bound staple strands. Each process in the mechanical folding is well defined and free from kinetic traps, enabling us to complete folding within 10 min. We also demonstrate parallel folding of DNA nanostructures through multiplexed manipulation of the scaffold DNAs. Our results suggest a path towards programmability of the folding pathway of DNA nanostructures.

  11. Kinetics and mechanism of the catalytic reaction between alcohols and dimethyl carbonate

    NASA Astrophysics Data System (ADS)

    Koledina, K. F.; Koledin, S. N.; Shchadneva, N. A.; Gubaidullin, I. M.

    2017-03-01

    The mechanism of the reaction between alcohols and dimethyl carbonate, catalyzed by dicobalt octacarbonyl Co2(CO)8, is studied by means of mathematical modeling. Kinetic models for possible schemes of chemical transformations are constructed at different initial concentrations of the catalyst. Based on a comparative analysis of activation energies of possible stages of chemical transformations, possible reaction pathways are determined and an appropriate mechanism is selected.

  12. Folding of beta-sandwich proteins: three-state transition of a fibronectin type III module.

    PubMed Central

    Cota, E.; Clarke, J.

    2000-01-01

    An analysis of the folding of the 94 residue tenth fibronectin type III (fnIII) domain of human fibronectin (FNfn10) is presented. Use of guanidine isothiocyanate as a denaturant allows us to obtain equilibrium and kinetic data across a broad range of denaturant concentrations that are unavailable in guanidine hydrochloride. Equilibrium unfolding experiments show that FNfn10 is significantly more stable than has been reported previously. Comparison of equilibrium and kinetic parameters reveals the presence of an intermediate that accumulates at low denaturant concentrations. This is the first demonstration of three-state folding kinetics for a fnIII domain. We have previously shown that a homologous domain from human tenascin (TNfn3) folds by a two-state mechanism, but this does not necessarily indicate that the two proteins fold by different folding pathways. PMID:10739253

  13. A Chemical Kinetic Mechanism for the Ignition of Silane/Hydrogen Mixtures

    NASA Technical Reports Server (NTRS)

    Jachimowski, C. J.; Mclain, A. G.

    1983-01-01

    A chemical kinetic reaction mechanism for the oxidation of silane/hydrogen mixtures is presented and discussed. Shock-tube ignition delay time data were used to evaluate and refine the mechanism. Good agreement between experimental results and the results predicted by the mechanism was obtained by adjusting the rate coefficient for the reaction SiH3 + O2 yields SiH2O + OH. The reaction mechanism was used to theoretically investigate the ignition characteristics of silane/hydrogen mixtures. The results revealed that over the entire range of temperature examined (800 K to 1200 K), substantial reduction in ignition delay times is obtained when silane is added to hydrogen.

  14. Roles of the Kinetic and Dynamic Mechanisms in the Lp -Ep Relation

    NASA Astrophysics Data System (ADS)

    Qin, Yi-Ping; Chen, Zhi-Fu

    2013-04-01

    The Lp -Ep relation is a well-known relation in gamma-ray bursts (GRBs). Its implication remains unclear. We propose to investigate the underlying mechanisms of this relation by considering the corresponding kinetic and dynamic mechanisms separately. In this way, one can tell how much the kinetic or dynamic mechanism contributes to the index of the relationship. Our analysis gives rise to several conclusions. (1) The index of the kinetic effect in the Lp -Ep relation can simply be derived from the theory of special relativity, which is generally larger than 2, depending on the situation concerned. (2) The index of the dynamic effect in the relation can be deduced from observation once a model of jets is adopted. According to current GRB data, we find that the dynamic effect alone tends to give rise to an anti-correlation between Lp and Ep ; in terms of statistics, the dynamic effect is obviously smaller than the kinetic effect; in the situation of jets with moving discrete radio clouds that move directly toward the observer, the index of the dynamic effect is currently constrained within (- 1.6, -1), while in other situations of jets, the constraints are different; both internal and external shocks can account for the current data.

  15. Evaluating endoglucanase Cel7B-lignin interaction mechanisms and kinetics using quartz crystal microgravimetry.

    PubMed

    Pfeiffer, Katherine A; Sorek, Hagit; Roche, Christine M; Strobel, Kathryn L; Blanch, Harvey W; Clark, Douglas S

    2015-11-01

    The kinetics and mechanisms of protein interactions with solid surfaces are important to fields as diverse as industrial biocatalysis, biomedical engineering, food science, and cell biology. The nonproductive adsorption of cellulase enzymes to lignin, a plant cell wall polymer, reduces their effectiveness in saccharifying biomass. Cellulase has been shown to interact with lignin, but the heterogeneity of lignin surfaces, challenges in measuring irreversible components of these interactions, and fast adsorption rates make quantifying the reaction kinetics difficult. This work employs quartz crystal microgravimetry with dissipation monitoring (QCM-D) for real-time measurement of adsorbed mass on a flat lignin surface. We have developed a method for casting homogeneous lignin films that are chemically similar to lignin found in pretreated biomass, and used QCM-D to compare three models of reversible-irreversible binding behavior: a single-site transition model, a transition model with changing adsorbate footprint, and a two-site transition model. Of the three models tested, the two-site transition model provides the only kinetic mechanism able to describe the behavior of Cel7B binding to lignin. While the direct implications of lignin-cellulase interactions may be limited to biomass deconstruction for renewable energy and green chemistry, the analytical and experimental methods demonstrated in this work are relevant to any system in which the kinetics and reaction mechanism of reversible and irreversible protein adsorption at a solid-liquid interface are important.

  16. Folding funnels, binding funnels, and protein function.

    PubMed Central

    Tsai, C. J.; Kumar, S.; Ma, B.; Nussinov, R.

    1999-01-01

    Folding funnels have been the focus of considerable attention during the last few years. These have mostly been discussed in the general context of the theory of protein folding. Here we extend the utility of the concept of folding funnels, relating them to biological mechanisms and function. In particular, here we describe the shape of the funnels in light of protein synthesis and folding; flexibility, conformational diversity, and binding mechanisms; and the associated binding funnels, illustrating the multiple routes and the range of complexed conformers. Specifically, the walls of the folding funnels, their crevices, and bumps are related to the complexity of protein folding, and hence to sequential vs. nonsequential folding. Whereas the former is more frequently observed in eukaryotic proteins, where the rate of protein synthesis is slower, the latter is more frequent in prokaryotes, with faster translation rates. The bottoms of the funnels reflect the extent of the flexibility of the proteins. Rugged floors imply a range of conformational isomers, which may be close on the energy landscape. Rather than undergoing an induced fit binding mechanism, the conformational ensembles around the rugged bottoms argue that the conformers, which are most complementary to the ligand, will bind to it with the equilibrium shifting in their favor. Furthermore, depending on the extent of the ruggedness, or of the smoothness with only a few minima, we may infer nonspecific, broad range vs. specific binding. In particular, folding and binding are similar processes, with similar underlying principles. Hence, the shape of the folding funnel of the monomer enables making reasonable guesses regarding the shape of the corresponding binding funnel. Proteins having a broad range of binding, such as proteolytic enzymes or relatively nonspecific endonucleases, may be expected to have not only rugged floors in their folding funnels, but their binding funnels will also behave similarly

  17. The interplay of fold mechanisms and basement weaknesses at the transition between Laramide basement-involved arches, north-central Wyoming, USA

    NASA Astrophysics Data System (ADS)

    Neely, Thomas G.; Erslev, Eric A.

    2009-09-01

    Horizontally-shortened, basement-involved foreland orogens commonly exhibit anastomosing networks of bifurcating basement highs (here called arches) whose structural culminations are linked by complex transition zones of diversely-oriented faults and folds. The 3D geometry and kinematics of the southern Beartooth arch transition zone of north-central Wyoming were studied to understand the fold mechanisms and control on basement-involved arches. Data from 1581 slickensided minor faults are consistent with a single regional shortening direction of 065°. Evidence for oblique-slip, vertical axis rotations and stress refraction at anomalously-oriented folds suggests formation over reactivated pre-existing weaknesses. Restorable cross-sections and 3D surfaces, constrained by surface, well, and seismic data, document blind, ENE-directed basement thrusting and associated thin-skinned backthrusting and folding along the Beartooth and Oregon Basin fault systems. Between these systems, the basement-cored Rattlesnake Mountain backthrust followed basement weaknesses and rotated a basement chip toward the basin before the ENE-directed Line Creek fault system broke through and connected the Beartooth and Oregon Basin fault systems. Slip was transferred at the terminations of the Rattlesnake Mountain fault block by pivoting to the north and tear faulting to the south. In summary, unidirectional Laramide compression and pre-existing basement weaknesses combined with fault-propagation and rotational fault-bend folding to create an irregular yet continuous basement arch transition.

  18. Regulatory motifs on ISWI chromatin remodelers: molecular mechanisms and kinetic proofreading

    NASA Astrophysics Data System (ADS)

    Brysbaert, Guillaume; Lensink, Marc F.; Blossey, Ralf

    2015-02-01

    Recently, kinetic proofreading scenarios have been proposed for the regulation of chromatin remodeling, first on purely theoretical grounds (Blossey and Schiessel 2008 HFSP J. 2 167-70) and deduced from experiments on the ISWI/ACF system (Narlikar 2010 Curr. Opin. Chem. Biol. 14 660). In the kinetic proofreading scenario of chromatin remodeling, the combination of the recognition of a histone tail state and ATP-hydrolysis in the remodeler motor act together to select (i.e. proofread) a nucleosomal substrate. ISWI remodelers have recently been shown to have an additional level of regulation as they contain auto-inhibitory motifs which need to be inactivated through an interaction with the nucleosome. In this paper we show that the auto-regulatory effect enhances substrate recognition in kinetic proofreading. We further report some suggestive additional insights into the molecular mechanism underlying ISWI-autoregulation.

  19. Mechanisms and Kinetics of Tellurium Precipitation in CdTe-based Materials

    NASA Astrophysics Data System (ADS)

    Lordi, Vincenzo

    2012-02-01

    CdTe and related alloys are important materials for solar photovoltaic application as well as for high-resolution room-temperature gamma radiation detectors. However, the performance of devices, particularly in high-energy applications, is limited by various material defects. Among the most important defects are Te precipitates of various sizes caused by non-stoichiometric growth conditions. In this work, we study the kinetics of Te aggregation and precipitation at the atomic scale. Density functional theory is used to compute the energetics, migration rates, and binding energies of point defects involved in Te aggregation, which include various interstitials, vacancies, and anti-site defects. Kinetic Monte Carlo is then used to simulate the aggregation process leading to precipitation nuclei. The mechanisms and kinetics of formation of these Te-rich regions are analyzed for various conditions. Prepared by LLNL under Contract DE-AC52-07NA27344.

  20. Controlling Self-Assembly Kinetics of DNA-Functionalized Liposomes Using Toehold Exchange Mechanism.

    PubMed

    Parolini, Lucia; Kotar, Jurij; Di Michele, Lorenzo; Mognetti, Bortolo M

    2016-02-23

    The selectivity of Watson-Crick base pairing has allowed the design of DNA-based functional materials bearing an unprecedented level of accuracy. Examples include DNA origami, made of tiles assembling into arbitrarily complex shapes, and DNA coated particles featuring rich phase behaviors. Frequently, the realization of conceptual DNA-nanotechnology designs has been hampered by the lack of strategies for effectively controlling relaxations. In this article, we address the problem of kinetic control on DNA-mediated interactions between Brownian objects. We design a kinetic pathway based on toehold-exchange mechanisms that enables rearrangement of DNA bonds without the need for thermal denaturation, and test it on suspensions of DNA-functionalized liposomes, demonstrating tunability of aggregation rates over more than 1 order of magnitude. While the possibility to design complex phase behaviors using DNA as a glue is already well recognized, our results demonstrate control also over the kinetics of such systems.

  1. New mechanism of kinetic exchange interaction induced by strong magnetic anisotropy

    PubMed Central

    Iwahara, Naoya; Chibotaru, Liviu F.

    2016-01-01

    It is well known that the kinetic exchange interaction between single-occupied magnetic orbitals (s-s) is always antiferromagnetic, while between single- and double-occupied orbitals (s-d) is always ferromagnetic and much weaker. Here we show that the exchange interaction between strongly anisotropic doublets of lanthanides, actinides and transition metal ions with unquenched orbital momentum contains a new s-d kinetic contribution equal in strength with the s-s one. In non-collinear magnetic systems, this s-d kinetic mechanism can cause an overall ferromagnetic exchange interaction which can become very strong for transition metal ions. These findings are fully confirmed by DFT based analysis of exchange interaction in several Ln3+ complexes. PMID:27098292

  2. Chemical Kinetic Reaction Mechanisms for Combustion of Hydrocarbon and Other Types of Chemical Fuels

    DOE Data Explorer

    The central feature of the Combustion Chemistry project at LLNL is the development, validation, and application of detailed chemical kinetic reaction mechanisms for the combustion of hydrocarbon and other types of chemical fuels. For the past 30 years, LLNL's Chemical Sciences Division has built hydrocarbon mechanisms for fuels from hydrogen and methane through much larger fuels including heptanes and octanes. Other classes of fuels for which models have been developed include flame suppressants such as halons and organophosphates, and air pollutants such as soot and oxides of nitrogen and sulfur. Reaction mechanisms have been tested and validated extensively through comparisons between computed results and measured data from laboratory experiments (e.g., shock tubes, laminar flames, rapid compression machines, flow reactors, stirred reactors) and from practical systems (e.g., diesel engines, spark-ignition engines, homogeneous charge, compression ignition (HCCI) engines). These kinetic models are used to examine a wide range of combustion systems.

  3. Single-Molecule Folding Mechanisms of the apo- and Mg2+-Bound States of Human Neuronal Calcium Sensor-1

    PubMed Central

    Naqvi, Mohsin M.; Heidarsson, Pétur O.; Otazo, Mariela R.; Mossa, Alessandro; Kragelund, Birthe B.; Cecconi, Ciro

    2015-01-01

    Neuronal calcium sensor-1 (NCS-1) is the primordial member of a family of proteins responsible primarily for sensing changes in neuronal Ca2+ concentration. NCS-1 is a multispecific protein interacting with a number of binding partners in both calcium-dependent and independent manners, and acting in a variety of cellular processes in which it has been linked to a number of disorders such as schizophrenia and autism. Despite extensive studies on the Ca2+-activated state of NCS proteins, little is known about the conformational dynamics of the Mg2+-bound and apo states, both of which are populated, at least transiently, at resting Ca2+ conditions. Here, we used optical tweezers to study the folding behavior of individual NCS-1 molecules in the presence of Mg2+ and in the absence of divalent ions. Under tension, the Mg2+-bound state of NCS-1 unfolds and refolds in a three-state process by populating one intermediate state consisting of a folded C-domain and an unfolded N-domain. The interconversion at equilibrium between the different molecular states populated by NCS-1 was monitored in real time through constant-force measurements and the energy landscapes underlying the observed transitions were reconstructed through hidden Markov model analysis. Unlike what has been observed with the Ca2+-bound state, the presence of Mg2+ allows both the N- and C-domain to fold through all-or-none transitions with similar refolding rates. In the absence of divalent ions, NCS-1 unfolds and refolds reversibly in a two-state reaction involving only the C-domain, whereas the N-domain has no detectable transitions. Overall, the results allowed us to trace the progression of NCS-1 folding along its energy landscapes and provided a solid platform for understanding the conformational dynamics of similar EF-hand proteins. PMID:26153708

  4. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation.

    PubMed

    Zheng, Wenjun; Glenn, Paul

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant--while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  5. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    NASA Astrophysics Data System (ADS)

    Zheng, Wenjun; Glenn, Paul

    2015-01-01

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  6. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    SciTech Connect

    Zheng, Wenjun Glenn, Paul

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  7. Information from folds: A review

    NASA Astrophysics Data System (ADS)

    Hudleston, Peter J.; Treagus, Susan H.

    2010-12-01

    Folds are spectacular geological structures that are seen in layered rock on many different scales. To mark 30 years of the Journal of Structural Geology, we review the information that can be gained from studies of folds in theory, experiment and nature. We first review theoretical considerations and modeling, from classical approaches to current developments. The subject is dominated by single-layer fold theory, with the assumption of perfect layer-parallel shortening, but we also review multilayer fold theory and modeling, and folding of layers that are oblique to principal stresses and strains. This work demonstrates that viscosity ratio, degree of non-linearity of the flow law, anisotropy, and the thickness and spacing distribution of layers of different competence are all important in determining the nature and strength of the folding instability. Theory and modeling provide the basis for obtaining rheological information from natural folds, through analysis of wavelength/thickness ratios of single layer folds, and fold shapes. They also provide a basis for estimating the bulk strain from folded layers. Information about folding mechanisms can be obtained by analysis of cleavage and fabric patterns in folded rocks, and the history of deformation can be revealed by understanding how asymmetry can develop in folds, by how folds develop in shear zones, and how folds develop in more complex three-dimensional deformations.

  8. The Kinetic Reaction Mechanism of the Vibrio cholerae Sodium-dependent NADH Dehydrogenase*♦

    PubMed Central

    Tuz, Karina; Mezic, Katherine G.; Xu, Tianhao; Barquera, Blanca; Juárez, Oscar

    2015-01-01

    The sodium-dependent NADH dehydrogenase (Na+-NQR) is the main ion transporter in Vibrio cholerae. Its activity is linked to the operation of the respiratory chain and is essential for the development of the pathogenic phenotype. Previous studies have described different aspects of the enzyme, including the electron transfer pathways, sodium pumping structures, cofactor and subunit composition, among others. However, the mechanism of the enzyme remains to be completely elucidated. In this work, we have studied the kinetic mechanism of Na+-NQR with the use of steady state kinetics and stopped flow analysis. Na+-NQR follows a hexa-uni ping-pong mechanism, in which NADH acts as the first substrate, reacts with the enzyme, and the oxidized NAD leaves the catalytic site. In this conformation, the enzyme is able to capture two sodium ions and transport them to the external side of the membrane. In the last step, ubiquinone is bound and reduced, and ubiquinol is released. Our data also demonstrate that the catalytic cycle involves two redox states, the three- and five-electron reduced forms. A model that gathers all available information is proposed to explain the kinetic mechanism of Na+-NQR. This model provides a background to understand the current structural and functional information. PMID:26004776

  9. The Kinetic Reaction Mechanism of the Vibrio cholerae Sodium-dependent NADH Dehydrogenase.

    PubMed

    Tuz, Karina; Mezic, Katherine G; Xu, Tianhao; Barquera, Blanca; Juárez, Oscar

    2015-08-14

    The sodium-dependent NADH dehydrogenase (Na(+)-NQR) is the main ion transporter in Vibrio cholerae. Its activity is linked to the operation of the respiratory chain and is essential for the development of the pathogenic phenotype. Previous studies have described different aspects of the enzyme, including the electron transfer pathways, sodium pumping structures, cofactor and subunit composition, among others. However, the mechanism of the enzyme remains to be completely elucidated. In this work, we have studied the kinetic mechanism of Na(+)-NQR with the use of steady state kinetics and stopped flow analysis. Na(+)-NQR follows a hexa-uni ping-pong mechanism, in which NADH acts as the first substrate, reacts with the enzyme, and the oxidized NAD leaves the catalytic site. In this conformation, the enzyme is able to capture two sodium ions and transport them to the external side of the membrane. In the last step, ubiquinone is bound and reduced, and ubiquinol is released. Our data also demonstrate that the catalytic cycle involves two redox states, the three- and five-electron reduced forms. A model that gathers all available information is proposed to explain the kinetic mechanism of Na(+)-NQR. This model provides a background to understand the current structural and functional information.

  10. Detailed chemical kinetic mechanism for the oxidation of biodiesel fuels blend surrogate.

    SciTech Connect

    Herbinet, O; Pitz, W J; Westbrook, C K

    2009-07-21

    Detailed chemical kinetic mechanisms were developed and used to study the oxidation of two large unsaturated esters: methyl-5-decenoate and methyl-9-decenoate. These models were built from a previous methyl decanoate mechanism and were compared with rapeseed oil methyl esters oxidation experiments in a jet stirred reactor. A comparative study of the reactivity of these three oxygenated compounds was performed and the differences in the distribution of the products of the reaction were highlighted showing the influence of the presence and the position of a double bond in the chain. Blend surrogates, containing methyl decanoate, methyl-5-decenoate, methyl-9-decenoate and n-alkanes, were tested against rapeseed oil methyl esters and methyl palmitate/n-decane experiments. These surrogate models are realistic kinetic tools allowing the study of the combustion of biodiesel fuels in diesel and homogeneous charge compression ignition engines.

  11. Detailed chemical kinetic mechanism for the oxidation of biodiesel fuels blend surrogate

    SciTech Connect

    Herbinet, Olivier; Pitz, William J.; Westbrook, Charles K.

    2010-05-15

    Detailed chemical kinetic mechanisms were developed and used to study the oxidation of two large unsaturated esters: methyl-5-decenoate and methyl-9-decenoate. These models were built from a previous methyl decanoate mechanism and were compared with rapeseed oil methyl esters oxidation experiments in a jet-stirred reactor. A comparative study of the reactivity of these three oxygenated compounds was performed and the differences in the distribution of the products of the reaction were highlighted showing the influence of the presence and the position of a double bond in the chain. Blend surrogates, containing methyl decanoate, methyl-5-decenoate, methyl-9-decenoate and n-alkanes, were tested against rapeseed oil methyl esters and methyl palmitate/n-decane experiments. These surrogate models are realistic kinetic tools allowing the study of the combustion of biodiesel fuels in diesel and homogeneous charge compression ignition engines. (author)

  12. Study of the kinetics and mechanism of the thermal nitridation of SiO2

    NASA Technical Reports Server (NTRS)

    Vasquez, R. P.; Madhukar, A.; Grunthaner, F. J.; Naiman, M. L.

    1985-01-01

    X-ray photoelectron spectroscopy (XPS) has been used to study the nitridation time and temperature dependence of the nitrogen distribution in thermally nitrided SiO2 films. The XPS data show that the maximum nitrogen concentration near the (SiO(x)N(y)/Si interface is initially at the interface, but moves 20-25 A away from the interface with increasing nitridation time. Computer modeling of the kinetic processes involved is carried out and reveals a mechanism in which diffusing species, initially consisting primarily of nitrogen, react with the substrate, followed by formation of the oxygen-rich oxynitride due to reaction of the diffusing oxygen displaced by the slower nitridation of the SiO2. The data are consistent with this mechanism provided the influence of the interfacial strain on the nitridation and oxidation kinetics is explicitly accounted for.

  13. Darkening mechanism and kinetics of humification process in catechol-Maillard system.

    PubMed

    Zhang, Yingchao; Yue, Dongbei; Ma, Hong

    2015-07-01

    Humic acids, products of humification process, are capable of interacting with contaminants and can be applied to environmental remediation. Browning mechanisms of humification is critical to understand and further control the process. This study aimed to investigate the mechanism of abiotic humification by tracking the fate of the precursors in systems containing glucose, glycine, and various CT concentrations, which were promoted by MnO2. Results show that the N-containing organic molecules significantly contributed in controlling the darkening effect. Increasing CT promoted the formation of Fulvic-like acids (FLAs) and Humic-like acids (HLAs). The entire reaction could be divided into two steps following pseudo-second-order kinetics equation and pseudo-zero-order kinetics equation. Moreover, increasing CT contributed to the increase of the degree of unsaturation in HLAs.

  14. Tungsten solution kinetics and amorphization of nickel in mechanically alloyed Ni-W alloys

    NASA Technical Reports Server (NTRS)

    Aning, A. O.; Wang, Z.; Courtney, T. H.

    1993-01-01

    The kinetics of solution of W, and the subsequent amorphization of Ni, in mechanically alloyed Ni-W alloys has been investigated. As W is a highly abrasive material in the energy intensive devices used for mechanical alloying, we studied the above reactions in different mills. One used hardened steel balls as the grinding media, and the other Al2O3. Abrasion is common to both mills, but Fe wear debris from the hardened steel enters into solution in the Ni rich phases whereas Al2O3 debris is present as small dispersoids. The kinetics of W solution and those of subsequent amorphization do not appear strongly affected by the Fe in solution or the Al2O3 dispersoid. Tungsten dissolves in crystalline Ni in amounts in excess of the equilibrium solubility during alloying. Amorphization of the Ni phase occurs if the W content in this phase exceeds ca. 28 at. pct.

  15. Mechanism of Folding and Activation of Subtilisin Kexin Isozyme-1 (SKI-1)/Site-1 Protease (S1P).

    PubMed

    da Palma, Joel Ramos; Cendron, Laura; Seidah, Nabil Georges; Pasquato, Antonella; Kunz, Stefan

    2016-01-29

    The proprotein convertase subtilisin kexin isozyme-1 (SKI-1)/site-1 protease (S1P) is implicated in lipid homeostasis, the unfolded protein response, and lysosome biogenesis. The protease is further hijacked by highly pathogenic emerging viruses for the processing of their envelope glycoproteins. Zymogen activation of SKI-1/S1P requires removal of an N-terminal prodomain, by a multistep process, generating the mature enzyme. Here, we uncover a modular structure of the human SKI-1/S1P prodomain and define its function in folding and activation. We provide evidence that the N-terminal AB fragment of the prodomain represents an autonomous structural and functional unit that is necessary and sufficient for folding and partial activation. In contrast, the C-terminal BC fragment lacks a defined structure but is crucial for autoprocessing and full catalytic activity. Phylogenetic analysis revealed that the sequence of the AB domain is highly conserved, whereas the BC fragment shows considerable variation and seems even absent in some species. Notably, SKI-1/S1P of arthropods, like the fruit fly Drosophila melanogaster, contains a shorter prodomain comprised of full-length AB and truncated BC regions. Swapping the prodomain fragments between fly and human resulted in a fully mature and active SKI-1/S1P chimera. Our study suggests that primordial SKI-1/S1P likely contained a simpler prodomain consisting of the highly conserved AB fragment that represents an independent folding unit. The BC region appears as a later evolutionary acquisition, possibly allowing more subtle fine-tuning of the maturation process.

  16. Mechanism of Folding and Activation of Subtilisin Kexin Isozyme-1 (SKI-1)/Site-1 Protease (S1P)*

    PubMed Central

    da Palma, Joel Ramos; Cendron, Laura; Seidah, Nabil Georges; Pasquato, Antonella; Kunz, Stefan

    2016-01-01

    The proprotein convertase subtilisin kexin isozyme-1 (SKI-1)/site-1 protease (S1P) is implicated in lipid homeostasis, the unfolded protein response, and lysosome biogenesis. The protease is further hijacked by highly pathogenic emerging viruses for the processing of their envelope glycoproteins. Zymogen activation of SKI-1/S1P requires removal of an N-terminal prodomain, by a multistep process, generating the mature enzyme. Here, we uncover a modular structure of the human SKI-1/S1P prodomain and define its function in folding and activation. We provide evidence that the N-terminal AB fragment of the prodomain represents an autonomous structural and functional unit that is necessary and sufficient for folding and partial activation. In contrast, the C-terminal BC fragment lacks a defined structure but is crucial for autoprocessing and full catalytic activity. Phylogenetic analysis revealed that the sequence of the AB domain is highly conserved, whereas the BC fragment shows considerable variation and seems even absent in some species. Notably, SKI-1/S1P of arthropods, like the fruit fly Drosophila melanogaster, contains a shorter prodomain comprised of full-length AB and truncated BC regions. Swapping the prodomain fragments between fly and human resulted in a fully mature and active SKI-1/S1P chimera. Our study suggests that primordial SKI-1/S1P likely contained a simpler prodomain consisting of the highly conserved AB fragment that represents an independent folding unit. The BC region appears as a later evolutionary acquisition, possibly allowing more subtle fine-tuning of the maturation process. PMID:26645686

  17. Kinetics and mechanism of styrene epoxidation by chlorite: role of chlorine dioxide.

    PubMed

    Leigh, Jessica K; Rajput, Jonathan; Richardson, David E

    2014-07-07

    An investigation of the kinetics and mechanism for epoxidation of styrene and para-substituted styrenes by chlorite at 25 °C in the pH range of 5-6 is described. The proposed mechanism in water and water/acetonitrile includes seven oxidation states of chlorine (-I, 0, I, II, III, IV, and V) to account for the observed kinetics and product distributions. The model provides an unusually detailed quantitative mechanism for the complex reactions that occur in mixtures of chlorine species and organic substrates, particularly when the strong oxidant chlorite is employed. Kinetic control of the reaction is achieved by the addition of chlorine dioxide to the reaction mixture, thereby eliminating a substantial induction period observed when chlorite is used alone. The epoxidation agent is identified as chlorine dioxide, which is continually formed by the reaction of chlorite with hypochlorous acid that results from ClO produced by the epoxidation reaction. The overall stoichiometry is the result of two competing chain reactions in which the reactive intermediate ClO reacts with either chlorine dioxide or chlorite ion to produce hypochlorous acid and chlorate or chloride, respectively. At high chlorite ion concentrations, HOCl is rapidly eliminated by reaction with chlorite, minimizing side reactions between HOCl and Cl2 with the starting material. Epoxide selectivity (>90% under optimal conditions) is accurately predicted by the kinetic model. The model rate constant for direct reaction of styrene with ClO2(aq) to produce epoxide is (1.16 ± 0.07) × 10(-2) M(-1) s(-1) for 60:40 water/acetonitrile with 0.20 M acetate buffer. Rate constants for para substituted styrenes (R = -SO3(-), -OMe, -Me, -Cl, -H, and -NO2) with ClO2 were determined. The results support the radical addition/elimination mechanism originally proposed by Kolar and Lindgren to account for the formation of styrene oxide in the reaction of styrene with chlorine dioxide.

  18. Kinetics and mechanism of the oxidation process of two-component Fe-Al alloys

    NASA Technical Reports Server (NTRS)

    Przewlocka, H.; Siedlecka, J.

    1982-01-01

    The oxidation process of two-component Fe-Al alloys containing up to 7.2% Al and from 18 to 30% Al was studied. Kinetic measurements were conducted using the isothermal gravimetric method in the range of 1073-1223 K and 1073-1373 K for 50 hours. The methods used in studies of the mechanism of oxidation included: X-ray microanalysis, X-ray structural analysis, metallographic analysis and marker tests.

  19. Dissecting the Catalytic Mechanism of Trypanosoma brucei Trypanothione Synthetase by Kinetic Analysis and Computational Modeling*

    PubMed Central

    Leroux, Alejandro E.; Haanstra, Jurgen R.; Bakker, Barbara M.; Krauth-Siegel, R. Luise

    2013-01-01

    In pathogenic trypanosomes, trypanothione synthetase (TryS) catalyzes the synthesis of both glutathionylspermidine (Gsp) and trypanothione (bis(glutathionyl)spermidine (T(SH)2)). Here we present a thorough kinetic analysis of Trypanosoma brucei TryS in a newly developed phosphate buffer system at pH 7.0 and 37 °C, mimicking the physiological environment of the enzyme in the cytosol of bloodstream parasites. Under these conditions, TryS displays Km values for GSH, ATP, spermidine, and Gsp of 34, 18, 687, and 32 μm, respectively, as well as Ki values for GSH and T(SH)2 of 1 mm and 360 μm, respectively. As Gsp hydrolysis has a Km value of 5.6 mm, the in vivo amidase activity is probably negligible. To obtain deeper insight in the molecular mechanism of TryS, we have formulated alternative kinetic models, with elementary reaction steps represented by linear kinetic equations. The model parameters were fitted to the extensive matrix of steady-state data obtained for different substrate/product combinations under the in vivo-like conditions. The best model describes the full kinetic profile and is able to predict time course data that were not used for fitting. This system's biology approach to enzyme kinetics led us to conclude that (i) TryS follows a ter-reactant mechanism, (ii) the intermediate Gsp dissociates from the enzyme between the two catalytic steps, and (iii) T(SH)2 inhibits the enzyme by remaining bound at its product site and, as does the inhibitory GSH, by binding to the activated enzyme complex. The newly detected concerted substrate and product inhibition suggests that TryS activity is tightly regulated. PMID:23814051

  20. Kinetic mix mechanisms in shock-driven inertial confinement fusion implosions

    DOE PAGES

    Rinderknecht, H. G.; Sio, H.; Li, C. K.; ...

    2014-05-19

    Shock-driven implosions of thin-shell capsules, or ''exploding pushers,'' generate low-density, high-temperature plasmas in which hydrodynamic instability growth is negligible and kinetic effects can play an important role. Data from implosions of thin deuterated-plastic shells with hydroequivalent D3He gas fills ranging from pure deuterium to pure 3He [H. G. Rinderknecht et al., Phys. Rev. Lett. 112, 135001 (2014)] were obtained to evaluate non-hydrodynamic fuel-shell mix mechanisms. Simulations of the experiments including reduced ion kinetic models support ion diffusion as an explanation for these data. Several additional kinetic mechanisms are investigated and compared to the data to determine which are important inmore » the experiments. Shock acceleration of shell deuterons is estimated to introduce mix less than or comparable to the amount required to explain the data. Beam-target mechanisms are found to produce yields at most an order of magnitude less than the observations« less

  1. Kinetic mechanism of the detoxification of the organophosphate paraoxon by human serum A-esterase.

    PubMed

    Vitarius, J A; Sultatos, L G

    1994-01-01

    The mammalian detoxification of certain organophosphates, such as paraoxon [O,O-diethyl (p-nitrophenyl) phosphate], is catalyzed by the enzyme A-esterase. In this study, incubations of human serum in 50 mM glycine buffer (pH 10.5) with paraoxon resulted in the nonlinear production of p-nitrophenol, characterized by a rapid initial phase for the first several minutes of the incubation, followed by a second, slower phase in which the velocity approached constancy. Production of p-nitrophenol could be accurately fitted to the velocity equation for an Ordered Uni Bi kinetic mechanism with initial-burst activity, yielding estimates of appk2, appk3, and appE, for 10 human subjects. Increasing calcium concentration in the incubation resulted in increases in appk3 and appE, without affecting appk2. Conversely, addition of 1 M sodium chloride decreased the appk3 and appE, but did not alter appk2. And finally, a continuous system computer model was constructed based on the differential equations descriptive of an Ordered Uni Bi kinetic mechanism. This model accurately simulated production of p-nitrophenol from human serum, providing further support that A-esterase hydrolyzes paraoxon by an Ordered Uni Bi kinetic mechanism with initial-burst activity.

  2. Kinetic gating mechanism of DNA damage recognition by Rad4/XPC

    NASA Astrophysics Data System (ADS)

    Chen, Xuejing; Velmurugu, Yogambigai; Zheng, Guanqun; Park, Beomseok; Shim, Yoonjung; Kim, Youngchang; Liu, Lili; van Houten, Bennett; He, Chuan; Ansari, Anjum; Min, Jung-Hyun

    2015-01-01

    The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. How XPC detects structurally diverse lesions embedded within normal DNA is unknown. Here we present a crystal structure that captures the yeast XPC orthologue (Rad4) on a single register of undamaged DNA. The structure shows that a disulphide-tethered Rad4 flips out normal nucleotides and adopts a conformation similar to that seen with damaged DNA. Contrary to many DNA repair enzymes that can directly reject non-target sites as structural misfits, our results suggest that Rad4/XPC uses a kinetic gating mechanism whereby lesion selectivity arises from the kinetic competition between DNA opening and the residence time of Rad4/XPC per site. This mechanism is further supported by measurements of Rad4-induced lesion-opening times using temperature-jump perturbation spectroscopy. Kinetic gating may be a general mechanism used by site-specific DNA-binding proteins to minimize time-consuming interrogations of non-target sites.

  3. Kinetic gating mechanism of DNA damage recognition by Rad4/XPC

    PubMed Central

    Chen, Xuejing; Velmurugu, Yogambigai; Zheng, Guanqun; Park, Beomseok; Shim, Yoonjung; Kim, Youngchang; Liu, Lili; Van Houten, Bennett; He, Chuan; Ansari, Anjum; Min, Jung-Hyun

    2015-01-01

    The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. How XPC detects structurally diverse lesions embedded within normal DNA is unknown. Here we present a crystal structure that captures the yeast XPC orthologue (Rad4) on a single register of undamaged DNA. The structure shows that a disulphide-tethered Rad4 flips out normal nucleotides and adopts a conformation similar to that seen with damaged DNA. Contrary to many DNA repair enzymes that can directly reject non-target sites as structural misfits, our results suggest that Rad4/XPC uses a kinetic gating mechanism whereby lesion selectivity arises from the kinetic competition between DNA opening and the residence time of Rad4/XPC per site. This mechanism is further supported by measurements of Rad4-induced lesion-opening times using temperature-jump perturbation spectroscopy. Kinetic gating may be a general mechanism used by site-specific DNA-binding proteins to minimize time-consuming interrogations of non-target sites. PMID:25562780

  4. Kinetic gating mechanism of DNA damage recognition by Rad4/XPC

    DOE PAGES

    Chen, Xuejing; Velmurugu, Yogambigai; Zheng, Guanqun; ...

    2015-01-06

    The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. How XPC detects structurally diverse lesions embedded within normal DNA is unknown. Here we present a crystal structure that captures the yeast XPC orthologue (Rad4) on a single register of undamaged DNA. The structure shows that a disulphide-tethered Rad4 flips out normal nucleotides and adopts a conformations similar to that seen with damaged DNA. Contrary to many DNA repair enzymes that can directly reject non-target sites as structural misfits, our results suggest that Rad4/XPC uses a kinetic gating mechanism whereby lesion selectivitymore » arises from the kinetic competition between DNA opening and the residence time of Rad4/XPC per site. This mechanism is further supported by measurements of Rad4-induced lesion-opening times using temperature-jump pertubation spectroscopy. Kinetic gating may be a general mechanism used by site-specific DNA-binding proteins to minimize time-consuming interrogations of non-target sites.« less

  5. Elemental Mercury Oxidation over Fe-Ti-Mn Spinel: Performance, Mechanism, and Reaction Kinetics.

    PubMed

    Xiong, Shangchao; Xiao, Xin; Huang, Nan; Dang, Hao; Liao, Yong; Zou, Sijie; Yang, Shijian

    2017-01-03

    The design of a high-performance catalyst for Hg(0) oxidation and predicting the extent of Hg(0) oxidation are both extremely limited due to the uncertainties of the reaction mechanism and the reaction kinetics. In this work, Fe-Ti-Mn spinel was developed as a high-performance catalyst for Hg(0) oxidation, and the reaction mechanism and the reaction kinetics of Hg(0) oxidation over Fe-Ti-Mn spinel were studied. The reaction orders of Hg(0) oxidation over Fe-Ti-Mn spinel with respect to gaseous Hg(0) concentration and gaseous HCl concentration were approximately 1 and 0, respectively. Therefore, Hg(0) oxidation over Fe-Ti-Mn spinel mainly followed the Eley-Rideal mechanism (i.e., the reaction of gaseous Hg(0) with adsorbed HCl), and the rate of Hg(0) oxidation mainly depended on Cl(•) concentration on the surface. As H2O, SO2, and NO not only inhibited Cl(•) formation on the surface but also interfered with the interface reaction between gaseous Hg(0) and Cl(•) on the surface, Hg(0) oxidation over Fe-Ti-Mn spinel was obviously inhibited in the presence of H2O, SO2, and NO. Furthermore, the extent of Hg(0) oxidation over Fe-Ti-Mn spinel can be predicted according to the kinetic parameter kE-R, and the predicted result was consistent with the experimental result.

  6. Kinetic gating mechanism of DNA damage recognition by Rad4/XPC

    SciTech Connect

    Chen, Xuejing; Velmurugu, Yogambigai; Zheng, Guanqun; Park, Beomseok; Shim, Yoonjung; Kim, Youngchang; Liu, Lili; Van Houten, Bennett; He, Chuan; Ansari, Anjum; Min, Jung -Hyun

    2015-01-06

    The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. How XPC detects structurally diverse lesions embedded within normal DNA is unknown. Here we present a crystal structure that captures the yeast XPC orthologue (Rad4) on a single register of undamaged DNA. The structure shows that a disulphide-tethered Rad4 flips out normal nucleotides and adopts a conformations similar to that seen with damaged DNA. Contrary to many DNA repair enzymes that can directly reject non-target sites as structural misfits, our results suggest that Rad4/XPC uses a kinetic gating mechanism whereby lesion selectivity arises from the kinetic competition between DNA opening and the residence time of Rad4/XPC per site. This mechanism is further supported by measurements of Rad4-induced lesion-opening times using temperature-jump pertubation spectroscopy. Kinetic gating may be a general mechanism used by site-specific DNA-binding proteins to minimize time-consuming interrogations of non-target sites.

  7. Staphylococcus aureus sortase transpeptidase SrtA: insight into the kinetic mechanism and evidence for a reverse protonation catalytic mechanism.

    PubMed

    Frankel, Brenda A; Kruger, Ryan G; Robinson, Dana E; Kelleher, Neil L; McCafferty, Dewey G

    2005-08-23

    The Staphylococcus aureus transpeptidase SrtA catalyzes the covalent attachment of LPXTG-containing virulence and colonization-associated proteins to cell-wall peptidoglycan in Gram-positive bacteria. Recent structural characterizations of staphylococcal SrtA, and related transpeptidases SrtB from S. aureus and Bacillus anthracis, provide many details regarding the active site environment, yet raise questions with regard to the nature of catalysis and active site cysteine thiol activation. Here we re-evaluate the kinetic mechanism of SrtA and shed light on aspects of its catalytic mechanism. Using steady-state, pre-steady-state, bisubstrate kinetic studies, and high-resolution electrospray mass spectrometry, revised steady-state kinetic parameters and a ping-pong hydrolytic shunt kinetic mechanism were determined for recombinant SrtA. The pH dependencies of kinetic parameters k(cat)/K(m) and k(cat) for the substrate Abz-LPETG-Dap(Dnp)-NH(2) were bell-shaped with pK(a) values of 6.3 +/- 0.2 and 9.4 +/- 0.2 for k(cat) and 6.2 +/- 0.2 and 9.4 +/- 0.2 for k(cat)/K(m). Solvent isotope effect (SIE) measurements revealed inverse behavior, with a (D)2(O)k(cat) of 0.89 +/- 0.01 and a (D)2(O)(k(cat)/K(m)) of 0.57 +/- 0.03 reflecting an equilibrium SIE. In addition, SIE measurements strongly implicated Cys184 participation in the isotope-sensitive rate-determining chemical step when considered in conjunction with an inverse linear proton inventory for k(cat). Last, the pH dependence of SrtA inactivation by iodoacetamide revealed a single ionization for inactivation. These studies collectively provide compelling evidence for a reverse protonation mechanism where a small fraction (ca. 0.06%) of SrtA is competent for catalysis at physiological pH, yet is highly active with an estimated k(cat)/K(m) of >10(5) M(-)(1) s(-)(1).

  8. Kinetics of Inhibitory Feedback from Horizontal Cells to Photoreceptors: Implications for an Ephaptic Mechanism

    PubMed Central

    Warren, Ted J.; Van Hook, Matthew J.; Tranchina, Daniel

    2016-01-01

    Inhibitory feedback from horizontal cells (HCs) to cones generates center-surround receptive fields and color opponency in the retina. Mechanisms of HC feedback remain unsettled, but one hypothesis proposes that an ephaptic mechanism may alter the extracellular electrical field surrounding photoreceptor synaptic terminals, thereby altering Ca2+ channel activity and photoreceptor output. An ephaptic voltage change produced by current flowing through open channels in the HC membrane should occur with no delay. To test for this mechanism, we measured kinetics of inhibitory feedback currents in Ambystoma tigrinum cones and rods evoked by hyperpolarizing steps applied to synaptically coupled HCs. Hyperpolarizing HCs stimulated inward feedback currents in cones that averaged 8–9 pA and exhibited a biexponential time course with time constants averaging 14–17 ms and 120–220 ms. Measurement of feedback-current kinetics was limited by three factors: (1) HC voltage-clamp speed, (2) cone voltage-clamp speed, and (3) kinetics of Ca2+ channel activation or deactivation in the photoreceptor terminal. These factors totaled ∼4–5 ms in cones meaning that the true fast time constants for HC-to-cone feedback currents were 9–13 ms, slower than expected for ephaptic voltage changes. We also compared speed of feedback to feedforward glutamate release measured at the same cone/HC synapses and found a latency for feedback of 11–14 ms. Inhibitory feedback from HCs to rods was also significantly slower than either measurement kinetics or feedforward release. The finding that inhibitory feedback from HCs to photoreceptors involves a significant delay indicates that it is not due to previously proposed ephaptic mechanisms. SIGNIFICANCE STATEMENT Lateral inhibitory feedback from horizontal cells (HCs) to photoreceptors creates center-surround receptive fields and color-opponent interactions. Although underlying mechanisms remain unsettled, a longstanding hypothesis proposes that

  9. Role of solvent on nonenzymatic peptide bond formation mechanisms and kinetic isotope effects.

    PubMed

    Świderek, Katarzyna; Tuñón, Iñaki; Martí, Sergio; Moliner, Vicent; Bertrán, Juan

    2013-06-12

    Based on the hypothesis that similar mechanisms are involved in the peptide bond formation in aqueous solution and in the ribosome, the aminolysis of esters in aqueous solution has been the subject of numerous studies as the reference reaction for the catalyzed process. The mechanisms proposed in the literature have been explored in the present paper by hybrid QM/MM molecular dynamics simulations. The free energy profiles have been computed with the QM region of the system described at semiempirical AM1 level and by DFT within the M06-2X functional. According to the results, the formation of adduct zwitterion species is a preliminary step required for all possible mechanisms. Then, from different conformers of this species, four different paths were found: three of them taking place through concerted mechanisms of four-, six- and eight-membered ring transition states, and a stepwise mechanism through a neutral intermediate. Comparison of the free energy profiles indicates that the concerted mechanisms would be kinetically favored, with free energy barriers in very good agreement with experimental data. Calculations of kinetic isotope effects, when including the solute interactions with the first solvation shell, show that the 8-membered ring TS renders values in better agreement with available experimental data. Quantitative discrepancies can be attributed to different employed models in experiments and calculations.

  10. Permanganate oxidation of diclofenac: The pH-dependent reaction kinetics and a ring-opening mechanism.

    PubMed

    Cheng, Hanyang; Song, Dean; Liu, Huijuan; Qu, Jiuhui

    2015-10-01

    In this work, the fate of diclofenac (DCF) during permanganate (Mn(VII)) oxidation was investigated at environmentally relevant pH conditions (from 5 to 9). The batch experiments showed that the kinetics of the Mn(VII)/DCF reaction follows a second-order rate law with an apparent rate constant of 1.57±0.02 M(-1) s(-1) at pH 7 and 20 °C. The half-value of DCF was calculated to be 37.5 min, when the concentration of Mn(VII) (0.4 mM) was 20-fold excess of DCF. The pH-dependence of the reaction kinetics was investigated, and the DCF reactivity with Mn(VII) was found to decrease with increasing pH. The second-order rate constants were then quantitatively described by incorporating the species distribution of DCF. A lower reactivity of the anionic DCF (DCF(-)) in comparison with its neutral counterpart (DCF(0)) was most likely attributable to the interaction between the ionized carboxylate group and amine nitrogen position, which can reduce the nucleophilicity of amine nitrogen by inductive and resonance effects. Moreover, a range of degradation products and the corresponding structures were proposed on the basis of the LC-Q-TOF-MS analysis. A detailed ring-opening reaction mechanism was proposed as follows: Mn(VII) acts as an electrophile to attack the amine moiety, leading to the formation of the primary intermediate products 2,6-dichloroaniline and 5-hydroxy-diclofenac, which can be further transformed. The further degradation proceeded through a multistep process including ring-opening, decarboxylation, hydroxylation, and cyclation reactions.

  11. Solvent–amino acid interaction energies in three-dimensional-lattice Monte Carlo simulations of a model 27-mer protein: Folding thermodynamics and kinetics

    PubMed Central

    Leonhard, Kai; Prausnitz, John M.; Radke, Clayton J.

    2004-01-01

    Amino acid residue–solvent interactions are required for lattice Monte Carlo simulations of model proteins in water. In this study, we propose an interaction-energy scale that is based on the interaction scale by Miyazawa and Jernigan. It permits systematic variation of the amino acid–solvent interactions by introducing a contrast parameter for the hydrophobicity, Cs, and a mean attraction parameter for the amino acids, ω. Changes in the interaction energies strongly affect many protein properties. We present an optimized energy parameter set for best representing realistic behavior typical for many proteins (fast folding and high cooperativity for single chains). Our optimal parameters feature a much weaker hydrophobicity contrast and mean attraction than does the original interaction scale. The proposed interaction scale is designed for calculating the behavior of proteins in bulk and at interfaces as a function of solvent characteristics, as well as protein size and sequence. PMID:14739322

  12. Evolutionary Optimization of Protein Folding

    PubMed Central

    Debès, Cédric; Wang, Minglei; Caetano-Anollés, Gustavo; Gräter, Frauke

    2013-01-01

    Nature has shaped the make up of proteins since their appearance, 3.8 billion years ago. However, the fundamental drivers of structural change responsible for the extraordinary diversity of proteins have yet to be elucidated. Here we explore if protein evolution affects folding speed. We estimated folding times for the present-day catalog of protein domains directly from their size-modified contact order. These values were mapped onto an evolutionary timeline of domain appearance derived from a phylogenomic analysis of protein domains in 989 fully-sequenced genomes. Our results show a clear overall increase of folding speed during evolution, with known ultra-fast downhill folders appearing rather late in the timeline. Remarkably, folding optimization depends on secondary structure. While alpha-folds showed a tendency to fold faster throughout evolution, beta-folds exhibited a trend of folding time increase during the last 1.5 billion years that began during the “big bang” of domain combinations. As a consequence, these domain structures are on average slow folders today. Our results suggest that fast and efficient folding of domains shaped the universe of protein structure. This finding supports the hypothesis that optimization of the kinetic and thermodynamic accessibility of the native fold reduces protein aggregation propensities that hamper cellular functions. PMID:23341762

  13. Mechanisms and Kinetics of Environmentally Assisted Cracking: Current Status, Issues, and Suggestions for Further Work

    NASA Astrophysics Data System (ADS)

    Lynch, S. P.

    2013-03-01

    Mechanisms and kinetics of metal-induced embrittlement, hydrogen-embrittlement, and stress-corrosion cracking are discussed, and long-standing controversies are addressed by reviewing critical observations. Recommendations are also made regarding further work (including repetition of previous work using more advanced measurement and characterisation techniques) that should be carried out in order to resolve some of the contentious issues. The evidence to date suggests that adsorption-based mechanisms, involving weakening of substrate interatomic bonds so that dislocation emission or decohesion is facilitated, accounts for embrittlement in many systems. Embrittling adsorbed species include some metal atoms, hydrogen, and complex ions produced by de-alloying. Other viable mechanisms of embrittlement include those based on (1) dissolution of anodic grain-boundary regions, and (2) decohesion at grain boundaries owing to segregated hydrogen and impurities. The hydrogen-enhanced localised-plasticity mechanism, based on solute hydrogen facilitating dislocation activity in the plastic zone ahead of cracks, makes a contribution in some cases, but is relatively unimportant compared with these other mechanisms for most fracture modes. The film-induced cleavage mechanism, proposed especially for stress-corrosion cracking in systems involving de-alloying at crack tips, is questionable on numerous grounds, and is probably not viable. Rate-controlling processes for environmentally assisted cracking are not well established, except for solid-metal induced embrittlement where surface self-diffusion of embrittling atoms to crack tips controls cracking kinetics. In some systems, adsorption kinetics are probably rate-controlling for liquid-metal embrittlement, hydrogen-environment embrittlement, and stress-corrosion cracking. In other cases, rate-controlling processes could include the rate of anodic or cathodic reactions at and behind crack tips (responsible for producing embrittling

  14. Mechanisms of starch digestion by α-amylase-Structural basis for kinetic properties.

    PubMed

    Dhital, Sushil; Warren, Frederick J; Butterworth, Peter J; Ellis, Peter R; Gidley, Michael J

    2017-03-24

    Recent studies of the mechanisms determining the rate and extent of starch digestion by α-amylase are reviewed in the light of current widely-used classifications for (a) the proportions of rapidly-digestible (RDS), slowly-digestible (SDS), and resistant starch (RS) based on in vitro digestibility, and (b) the types of resistant starch (RS 1,2,3,4…) based on physical and/or chemical form. Based on methodological advances and new mechanistic insights, it is proposed that both classification systems should be modified. Kinetic analysis of digestion profiles provides a robust set of parameters that should replace the classification of starch as a combination of RDS, SDS, and RS from a single enzyme digestion experiment. This should involve determination of the minimum number of kinetic processes needed to describe the full digestion profile, together with the proportion of starch involved in each process, and the kinetic properties of each process. The current classification of resistant starch types as RS1,2,3,4 should be replaced by one which recognizes the essential kinetic nature of RS (enzyme digestion rate vs. small intestinal passage rate), and that there are two fundamental origins for resistance based on (i) rate-determining access/binding of enzyme to substrate and (ii) rate-determining conversion of substrate to product once bound.

  15. Kinetic, Thermodynamic, and Structural Insight into the Mechanism of Phosphopantetheine Adenylyltransferase from Mycobacterium tuberculosis

    SciTech Connect

    Wubben, Thomas J.; Mesecar, Andrew D.

    2012-05-29

    Phosphopantetheine adenylyltransferase (PPAT) catalyzes the penultimate step in the coenzyme A (CoA) biosynthetic pathway, reversibly transferring an adenylyl group from ATP to 4'-phosphopantetheine (PhP) to form dephosphocoenzyme A. This reaction sits at the branch point between the de novo pathway and the salvage pathway, and has been shown to be a rate-limiting step in the biosynthesis of CoA. Importantly, bacterial and mammalian PPATs share little sequence homology, making the enzyme a potential target for antibiotic development. A series of steady-state kinetic, product inhibition, and direct binding studies with Mycobacterium tuberculosis PPAT (MtPPAT) was conducted and suggests that the enzyme utilizes a nonrapid-equilibrium random bi-bi mechanism. The kinetic response of MtPPAT to the binding of ATP was observed to be sigmoidal under fixed PhP concentrations, but substrate inhibition was observed at high PhP concentrations under subsaturating ATP concentrations, suggesting a preferred pathway to ternary complex formation. Negative cooperativity in the kinetic response of MtPPAT to PhP binding was observed under certain conditions and confirmed thermodynamically by isothermal titration calorimetry, suggesting the formation of an asymmetric quaternary structure during sequential ligation of substrates. Asymmetry in binding was also observed in isothermal titration calorimetry experiments with dephosphocoenzyme A and CoA. X-ray structures of MtPPAT in complex with PhP and the nonhydrolyzable ATP analogue adenosine-5'-[({alpha},{beta})-methyleno]triphosphate were solved to 1.57 {angstrom} and 2.68 {angstrom}, respectively. These crystal structures reveal small conformational changes in enzyme structure upon ligand binding, which may play a role in the nonrapid-equilibrium mechanism. We suggest that the proposed kinetic mechanism and asymmetric character in MtPPAT ligand binding may provide a means of reaction and pathway regulation in addition to that of the

  16. Kinetic and Chemical Mechanism of the Dihydrofolate Reductase from Mycobacterium tuberculosis

    PubMed Central

    Czekster, Clarissa M.; Vandemeulebroucke, An; Blanchard, John S.

    2010-01-01

    Dihydrofolate reductase from Mycobacterium tuberculosis catalyzes the NAD(P)H dependent reduction of dihydrofolate, yielding NAD(P)+ and tetrahydrofolate, the primary one carbon unit carrier in biology. Tetrahydrofolate needs to be recycled so that reactions involved in dTMP synthesis and purine metabolism are maintained. In this work, we report the kinetic characterization of the MtDHFR. This enzyme has a sequential steady-state random kinetic mechanism, probably with a preferred pathway with NADPH binding first. A pKa value for an enzymic acid of approximately 7.0 was identified from the pH dependence of V, and the analysis of the primary kinetic isotope effects revealed that the hydride transfer step is at least partly rate limiting throughout the pH range analyzed. Additionally, the determination and analysis of solvent, and multiple kinetic isotope effects was conducted, and equilibrium isotope effects were measured on the equilibrium constant. D2OV and D2OV/K[4R-4-2H]-NADH were slightly inverse at pH 6.0, and inverse values for D2OV[4R-4-2H]-NADH and D2OV/K[4R-4-2H]-NADH suggested that a pre-equilibrium protonation is occurring before the hydride transfer step, indicating a stepwise mechanism for proton and hydride transfer. The same value was obtained for DkH at pH values of 5.5 and 7.5, reaffirming the rate-limiting nature of the hydride transfer step. A chemical mechanism is proposed based on the results obtained here. PMID:21138249

  17. Modelling "reality" in tectonics: Simulation of the mechanical evolution of the Jura Mountains-Molasse Basin system, and routes to forward-inverse modelling of fold thrust belts.

    NASA Astrophysics Data System (ADS)

    Hindle, David; Kley, Jonas

    2016-04-01

    The ultimate validation of any numerical model of any geological process comes when it can accurately forward model a case study from the geological record. However, as the example of the Jura-Molasse fold thrust belt demonstrates, geological information on even the most basic aspects of the present day state of such systems is highly incomplete and usually known only with large uncertainties. Fold thrust-belts are studied and understood by geologists in an iterative process of constructing their subsurface geometries and structures (folds, faults, bedding etc) based on limited subsurface information from boreholes, tunnels or seismic data where available, and surface information on outcrops of different layers and their dips. This data is usually processed through geometric models which involve conservation of line length of different beds over the length of an entire cross section. Constructing such sections is the art of cross section balancing. A balanced cross section can be easily restored to its pre-deformation state, assuming (usually) originally horizontal bedding to remove the effects of folding and faulting. Such a pre-deformation state can then form an initial condition for a forward mechanical model of the section. A mechanical model introduces new parameters into the system such as rock elasticity, cohesion, and frictional properties. However, a forward mechanical model can also potentially show the continuous evolution of a fold thrust belt, including dynamic quantities like stress. Moreover, a forward mechanical model, if correct in most aspects, should match in its final state, the present day geological cross section it is simulating. However, when attempting to achieve a match between geometric and mechanical models, it becomes clear that many more aspects of the geodynamic history of a fold thrust belt have to be taken into account. Erosion of the uppermost layers of an evolving thrust belt is the most obvious one of these. This can potentially

  18. Dissecting Ubiquitin Folding Using the Self-Organized Polymer Model.

    PubMed

    Reddy, Govardhan; Thirumalai, D

    2015-08-27

    Folding of Ubiquitin (Ub), a functionally important protein found in eukaryotic organisms, is investigated at low and neutral pH at different temperatures using simulations of the coarse-grained self-organized-polymer model with side chains (SOP-SC). The melting temperatures (Tm's), identified with the peaks in the heat capacity curves, decrease as pH decreases, in qualitative agreement with experiments. The calculated radius of gyration, showing dramatic variations with pH, is in excellent agreement with scattering experiments. At Tm, Ub folds in a two-state manner at low and neutral pH. Clustering analysis of the conformations sampled in equilibrium folding trajectories at Tm, with multiple transitions between the folded and unfolded states, shows a network of metastable states connecting the native and unfolded states. At low and neutral pH, Ub folds with high probability through a preferred set of conformations resulting in a pH-dependent dominant folding pathway. Folding kinetics reveal that Ub assembly at low pH occurs by multiple pathways involving a combination of nucleation-collapse and diffusion collision mechanism. The mechanism by which Ub folds is dictated by the stability of the key secondary structural elements responsible for establishing long-range contacts and collapse of Ub. Nucleation collapse mechanism holds if the stability of these elements are marginal, as would be the case at elevated temperatures. If the lifetimes associated with these structured microdomains are on the order of hundreds of microseconds, then Ub folding follows the diffusion-collision mechanism with intermediates, many of which coincide with those found in equilibrium. Folding at neutral pH is a sequential process with a populated intermediate resembling that sampled at equilibrium. The transition state structures, obtained using a Pfold analysis, are homogeneous and globular with most of the secondary and tertiary structures being native-like. Many of our findings for

  19. Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model

    NASA Astrophysics Data System (ADS)

    Bordner, Andrew J.; Zorman, Barry; Abagyan, Ruben

    2011-10-01

    Membrane proteins comprise a significant fraction of the proteomes of sequenced organisms and are the targets of approximately half of marketed drugs. However, in spite of their prevalence and biomedical importance, relatively few experimental structures are available due to technical challenges. Computational simulations can potentially address this deficit by providing structural models of membrane proteins. Solvation within the spatially heterogeneous membrane/solvent environment provides a major component of the energetics driving protein folding and association within the membrane. We have developed an implicit solvation model for membranes that is both computationally efficient and accurate enough to enable molecular mechanics predictions for the folding and association of peptides within the membrane. We derived the new atomic solvation model parameters using an unbiased fitting procedure to experimental data and have applied it to diverse problems in order to test its accuracy and to gain insight into membrane protein folding. First, we predicted the positions and orientations of peptides and complexes within the lipid bilayer and compared the simulation results with solid-state NMR structures. Additionally, we performed folding simulations for a series of host-guest peptides with varying propensities to form alpha helices in a hydrophobic environment and compared the structures with experimental measurements. We were also able to successfully predict the structures of amphipathic peptides as well as the structures for dimeric complexes of short hexapeptides that have experimentally characterized propensities to form beta sheets within the membrane. Finally, we compared calculated relative transfer energies with data from experiments measuring the effects of mutations on the free energies of translocon-mediated insertion of proteins into lipid bilayers and of combined folding and membrane insertion of a beta barrel protein.

  20. Transport in semiconductor nanowire superlattices described by coupled quantum mechanical and kinetic models.

    PubMed

    Alvaro, M; Bonilla, L L; Carretero, M; Melnik, R V N; Prabhakar, S

    2013-08-21

    In this paper we develop a kinetic model for the analysis of semiconductor superlattices, accounting for quantum effects. The model consists of a Boltzmann-Poisson type system of equations with simplified Bhatnagar-Gross-Krook collisions, obtained from the general time-dependent Schrödinger-Poisson model using Wigner functions. This system for superlattice transport is supplemented by the quantum mechanical part of the model based on the Ben-Daniel-Duke form of the Schrödinger equation for a cylindrical superlattice of finite radius. The resulting energy spectrum is used to characterize the Fermi-Dirac distribution that appears in the Bhatnagar-Gross-Krook collision, thereby coupling the quantum mechanical and kinetic parts of the model. The kinetic model uses the dispersion relation obtained by the generalized Kronig-Penney method, and allows us to estimate radii of quantum wire superlattices that have the same miniband widths as in experiments. It also allows us to determine more accurately the time-dependent characteristics of superlattices, in particular their current density. Results, for several experimentally grown superlattices, are discussed in the context of self-sustained coherent oscillations of the current density which are important in an increasing range of current and potential applications.

  1. Structural and kinetic insights into the mechanism of 5-hydroxyisourate hydrolase from Klebsiella pneumoniae

    SciTech Connect

    French, Jarrod B.; Ealick, Steven E.

    2011-08-01

    The crystal structure of 5-hydroxyisourate hydrolase from K. pneumoniae and the steady-state kinetic parameters of the native enzyme as well as several mutants provide insights into the catalytic mechanism of this enzyme and the possible roles of the active-site residues. The stereospecific oxidative degradation of uric acid to (S)-allantoin has recently been demonstrated to proceed via two unstable intermediates and requires three separate enzymatic reactions. The second step of this reaction, the conversion of 5-hydroxyisourate (HIU) to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline, is catalyzed by HIU hydrolase (HIUH). The high-resolution crystal structure of HIUH from the opportunistic pathogen Klebsiella pneumoniae (KpHIUH) has been determined. KpHIUH is a homotetrameric protein that, based on sequence and structural similarity, belongs to the transthyretin-related protein family. In addition, the steady-state kinetic parameters for this enzyme and four active-site mutants have been measured. These data provide valuable insight into the functional roles of the active-site residues. Based upon the structural and kinetic data, a mechanism is proposed for the KpHIUH-catalyzed reaction.

  2. Mechanical disassembly of single virus particles reveals kinetic intermediates predicted by theory.

    PubMed

    Castellanos, Milagros; Pérez, Rebeca; Carrillo, Pablo J P; de Pablo, Pedro J; Mateu, Mauricio G

    2012-06-06

    New experimental approaches are required to detect the elusive transient intermediates predicted by simulations of virus assembly or disassembly. Here, an atomic force microscope (AFM) was used to mechanically induce partial disassembly of single icosahedral T=1 capsids and virions of the minute virus of mice. The kinetic intermediates formed were imaged by AFM. The results revealed that induced disassembly of single minute-virus-of-mice particles is frequently initiated by loss of one of the 20 equivalent capsomers (trimers of capsid protein subunits) leading to a stable, nearly complete particle that does not readily lose further capsomers. With lower frequency, a fairly stable, three-fourths-complete capsid lacking one pentamer of capsomers and a free, stable pentamer were obtained. The intermediates most frequently identified (capsids missing one capsomer, capsids missing one pentamer of capsomers, and free pentamers of capsomers) had been predicted in theoretical studies of reversible capsid assembly based on thermodynamic-kinetic models, molecular dynamics, or oligomerization energies. We conclude that mechanical manipulation and imaging of simple virus particles by AFM can be used to experimentally identify kinetic intermediates predicted by simulations of assembly or disassembly.

  3. Mechanical Disassembly of Single Virus Particles Reveals Kinetic Intermediates Predicted by Theory

    PubMed Central

    Castellanos, Milagros; Pérez, Rebeca; Carrillo, Pablo J.P.; de Pablo, Pedro J.; Mateu, Mauricio G.

    2012-01-01

    New experimental approaches are required to detect the elusive transient intermediates predicted by simulations of virus assembly or disassembly. Here, an atomic force microscope (AFM) was used to mechanically induce partial disassembly of single icosahedral T = 1 capsids and virions of the minute virus of mice. The kinetic intermediates formed were imaged by AFM. The results revealed that induced disassembly of single minute-virus-of-mice particles is frequently initiated by loss of one of the 20 equivalent capsomers (trimers of capsid protein subunits) leading to a stable, nearly complete particle that does not readily lose further capsomers. With lower frequency, a fairly stable, three-fourths-complete capsid lacking one pentamer of capsomers and a free, stable pentamer were obtained. The intermediates most frequently identified (capsids missing one capsomer, capsids missing one pentamer of capsomers, and free pentamers of capsomers) had been predicted in theoretical studies of reversible capsid assembly based on thermodynamic-kinetic models, molecular dynamics, or oligomerization energies. We conclude that mechanical manipulation and imaging of simple virus particles by AFM can be used to experimentally identify kinetic intermediates predicted by simulations of assembly or disassembly. PMID:22713577

  4. Kinetic Analysis of the Metal Binding Mechanism of Escherichia coli Manganese Superoxide Dismutase

    PubMed Central

    Whittaker, Mei M.; Mizuno, Kazunori; Bächinger, Hans Peter; Whittaker, James W.

    2006-01-01

    The acquisition of a catalytic metal cofactor is an essential step in the maturation of every metalloenzyme, including manganese superoxide dismutase (MnSOD). In this study, we have taken advantage of the quenching of intrinsic protein fluorescence by bound metal ions to continuously monitor the metallation reaction of Escherichia coli MnSOD in vitro, permitting a detailed kinetic characterization of the uptake mechanism. Apo-MnSOD metallation kinetics are “gated”, zero order in metal ion for both the native Mn2+ and a nonnative metal ion (Co2+) used as a spectroscopic probe to provide greater sensitivity to metal binding. Cobalt-binding time courses measured over a range of temperatures (35–50°C) reveal two exponential kinetic processes (fast and slow phases) associated with metal binding. The amplitude of the fast phase increases rapidly as the temperature is raised, reflecting the fraction of Apo-MnSOD in an “open” conformation, and its temperature dependence allows thermodynamic parameters to be estimated for the “closed” to “open” conformational transition. The sensitivity of the metallated protein to exogenously added chelator decreases progressively with time, consistent with annealing of an initially formed metalloprotein complex (kanneal = 0.4 min−1). A domain-separation mechanism is proposed for metal uptake by apo-MnSOD. PMID:16258041

  5. Kinetics and fracture resistance of lithiated silicon nanostructure pairs controlled by their mechanical interaction

    NASA Astrophysics Data System (ADS)

    Lee, Seok Woo; Lee, Hyun-Wook; Ryu, Ill; Nix, William D.; Gao, Huajian; Cui, Yi

    2015-06-01

    Following an explosion of studies of silicon as a negative electrode for Li-ion batteries, the anomalous volumetric changes and fracture of lithiated single Si particles have attracted significant attention in various fields, including mechanics. However, in real batteries, lithiation occurs simultaneously in clusters of Si in a confined medium. Hence, understanding how the individual Si structures interact during lithiation in a closed space is necessary. Here, we demonstrate physical and mechanical interactions of swelling Si structures during lithiation using well-defined Si nanopillar pairs. Ex situ SEM and in situ TEM studies reveal that compressive stresses change the reaction kinetics so that preferential lithiation occurs at free surfaces when the pillars are mechanically clamped. Such mechanical interactions enhance the fracture resistance of lithiated Si by lessening the tensile stress concentrations in Si structures. This study will contribute to improved design of Si structures at the electrode level for high-performance Li-ion batteries.

  6. Kinetics and fracture resistance of lithiated silicon nanostructure pairs controlled by their mechanical interaction

    SciTech Connect

    Lee, Seok Woo; Lee, Hyun -Wook; Ryu, Ill; Nix, William D.; Gao, Huajian; Cui, Yi

    2015-06-26

    Following an explosion of studies of silicon as a negative electrode for Li-ion batteries, the anomalous volumetric changes and fracture of lithiated single Si particles have attracted significant attention in various fields, including mechanics. However, in real batteries, lithiation occurs simultaneously in clusters of Si in a confined medium. Hence, understanding how the individual Si structures interact during lithiation in a closed space is necessary. Here, we demonstrate physical and mechanical interactions of swelling Si structures during lithiation using well-defined Si nanopillar pairs. Ex situ SEM and in situ TEM studies reveal that compressive stresses change the reaction kinetics so that preferential lithiation occurs at free surfaces when the pillars are mechanically clamped. Such mechanical interactions enhance the fracture resistance of lithiated Si by lessening the tensile stress concentrations in Si structures. Lastly, this study will contribute to improved design of Si structures at the electrode level for high-performance Li-ion batteries.

  7. Mechano-chemical energy transduction in biological systems. The effect of mechanical stimulation on the polymerization of actin: a kinetic study.

    PubMed Central

    Ferri, A; Grazi, E

    1982-01-01

    Mechanical stimulation (forced circulation in narrow tubing) accelerates as much as 10-fold the rate of polymerization of actin. The increase in the rate is proportional to the intensity of the stimulation for flow rates between 0 and 3 cm/s. This supports the hypothesis that a statistical factor (the orientation of the flowing particles) is influenced by the flow. Comparison of the kinetics of the polymerization of resting and of mechanically stimulated actin solutions shows that both the nucleation and the elongation steps are accelerated. It is thus concluded that flow orients not only the oligomeric structures but also the actin monomers. The elongation reaction, also in the flow-stimulated samples, occurs always by the addition of ATP--G-actin (or ATP-containing oligomers) and not by the fusion of ADP-containing oligomeric structures. PMID:7138502

  8. Structural and kinetic insights into the mechanism of 5-hydroxyisourate hydrolase from Klebsiella pneumoniae

    SciTech Connect

    French, Jarrod B.; Ealick, Steven E.

    2011-07-19

    The stereospecific oxidative degradation of uric acid to (S)-allantoin has recently been demonstrated to proceed via two unstable intermediates and requires three separate enzymatic reactions. The second step of this reaction, the conversion of 5-hydroxyisourate (HIU) to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline, is catalyzed by HIU hydrolase (HIUH). The high-resolution crystal structure of HIUH from the opportunistic pathogen Klebsiella pneumoniae (KpHIUH) has been determined. KpHIUH is a homotetrameric protein that, based on sequence and structural similarity, belongs to the transthyretin-related protein family. In addition, the steady-state kinetic parameters for this enzyme and four active-site mutants have been measured. These data provide valuable insight into the functional roles of the active-site residues. Based upon the structural and kinetic data, a mechanism is proposed for the KpHIUH-catalyzed reaction.

  9. Mechanism and kinetics of Pb(II) adsorption on ultrathin nanocrystalline titania coatings.

    PubMed

    Yang, Zheng-peng; Zhang, Chun-jing

    2009-12-30

    Pb(II) is a highly toxic substance, exposure to which can cause various diseases. To better understand the application of titania as an adsorbent for removing Pb(II) from wastewater, quartz crystal microbalance (QCM) technique was employed to investigate the adsorption behavior of Pb(II) on ultrathin nanocrystalline titania coatings. The present study focused on the mechanism and kinetics of Pb(II) adsorption. The obtained results show that the driving force of Pb(II) adsorption on titania coatings is electrostatic interaction, and that Pb(II) is adsorbed onto titania coatings by Pb(II) ions coordinating with hydroxyl groups of titania surface. In terms of the in situ frequency measurements of QCM, the adsorption kinetic parameter is estimated to be 4.12x10(5)L/mol. QCM measurement provides a useful method for monitoring the adsorption process of Pb(II) on titania coatings.

  10. Effect and kinetic mechanism of ultrasonic vibration on solidification of 7050 aluminum alloy

    NASA Astrophysics Data System (ADS)

    Jiang, Ripeng; Li, Xiaoqian; Chen, Pinghu; Li, Ruiqing; Zhang, Xue

    2014-07-01

    The work described in this paper dealt with the effect of ultrasonic vibration on the solidification of 7050 aluminum alloy. Two experiments were carried out through introducing ultrasound into the semi-continuous direct-chill (DC) casting of aluminum alloy and into alloy solidifying in a crucible, respectively. Results show that ultrasonic vibration can refine grains in the whole cross-section of a billet in the first experiment and is able to increase the cooling rate within the temperature range from 625 °C to 590 °C in the other one. The mechanism of particle resonance caused by ultrasonic vibration was illustrated on the basis of theoretical analysis of the kinetics and energy conversion during the solidification. It is demonstrated that the kinetic energy of resonant particles are mainly from the latent heat energy of solidification, which can shorten the cooling time, inhibit the crystal growth and then lead to the grain refinement.

  11. Photodegradation of naproxen in water under simulated solar radiation: mechanism, kinetics, and toxicity variation.

    PubMed

    Ma, Dujuan; Liu, Guoguang; Lv, Wenying; Yao, Kun; Zhang, Xiangdan; Xiao, Huahua

    2014-01-01

    The main objective of this study was to investigate the degradation mechanism, the reaction kinetics, and the evolution of toxicity of naproxen in waters under simulated solar radiation. These criteria were investigated by conducting quenching experiments with reactive oxygen species (ROS), oxygen concentration experiments, and toxicity evaluations with Vibrio fischeri bacteria. The results indicated that the degradation of naproxen proceeds via pseudo first-order kinetics in all cases and that photodegradation included degradation by direct photolysis and by self-sensitization via ROS; the contribution rates of self-sensitized photodegradation were 1.4%, 65.8%, and 31.7% via ·OH, (1)O₂ and O₂(•-), respectively. Furthermore, the oxygen concentration experiments indicated that dissolved oxygen inhibited the direct photodegradation of naproxen, and the higher the oxygen content, the more pronounced the inhibitory effect. The toxicity evaluation illustrated that some of the intermediate products formed were more toxic than naproxen.

  12. Understanding the Broad Substrate Repertoire of Nitroreductase Based on Its Kinetic Mechanism*

    PubMed Central

    Pitsawong, Warintra; Hoben, John P.; Miller, Anne-Frances

    2014-01-01

    The oxygen-insensitive nitroreductase from Enterobacter cloacae (NR) catalyzes two-electron reduction of nitroaromatics to the corresponding nitroso compounds and, subsequently, to hydroxylamine products. NR has an unusually broad substrate repertoire, which may be related to protein dynamics (flexibility) and/or a simple non-selective kinetic mechanism. To investigate the possible role of mechanism in the broad substrate repertoire of NR, the kinetics of oxidation of NR by para-nitrobenzoic acid (p-NBA) were investigated using stopped-flow techniques at 4 °C. The results revealed a hyperbolic dependence on the p-NBA concentration with a limiting rate of 1.90 ± 0.09 s−1, indicating one-step binding before the flavin oxidation step. There is no evidence for a distinct binding step in which specificity might be enforced. The reduction of p-NBA is rate-limiting in steady-state turnover (1.7 ± 0.3 s−1). The pre-steady-state reduction kinetics of NR by NADH indicate that NADH reduces the enzyme with a rate constant of 700 ± 20 s−1 and a dissociation constant of 0.51 ± 0.04 mm. Thus, we demonstrate simple transient kinetics in both the reductive and oxidative half-reactions that help to explain the broad substrate repertoire of NR. Finally, we tested the ability of NR to reduce para-hydroxylaminobenzoic acid, demonstrating that the corresponding amine does not accumulate to significant levels even under anaerobic conditions. Thus E. cloacae NR is not a good candidate for enzymatic production of aromatic amines. PMID:24706760

  13. Proton-pumping mechanism of cytochrome c oxidase: a kinetic master-equation approach.

    PubMed

    Kim, Young C; Hummer, Gerhard

    2012-04-01

    Cytochrome c oxidase is an efficient energy transducer that reduces oxygen to water and converts the released chemical energy into an electrochemical membrane potential. As a true proton pump, cytochrome c oxidase translocates protons across the membrane against this potential. Based on a wealth of experiments and calculations, an increasingly detailed picture of the reaction intermediates in the redox cycle has emerged. However, the fundamental mechanism of proton pumping coupled to redox chemistry remains largely unresolved. Here we examine and extend a kinetic master-equation approach to gain insight into redox-coupled proton pumping in cytochrome c oxidase. Basic principles of the cytochrome c oxidase proton pump emerge from an analysis of the simplest kinetic models that retain essential elements of the experimentally determined structure, energetics, and kinetics, and that satisfy fundamental physical principles. The master-equation models allow us to address the question of how pumping can be achieved in a system in which all reaction steps are reversible. Whereas proton pumping does not require the direct modulation of microscopic reaction barriers, such kinetic gating greatly increases the pumping efficiency. Further efficiency gains can be achieved by partially decoupling the proton uptake pathway from the active-site region. Such a mechanism is consistent with the proposed Glu valve, in which the side chain of a key glutamic acid shuttles between the D channel and the active-site region. We also show that the models predict only small proton leaks even in the absence of turnover. The design principles identified here for cytochrome c oxidase provide a blueprint for novel biology-inspired fuel cells, and the master-equation formulation should prove useful also for other molecular machines. .

  14. Kinetics and mechanism of oxidation of chondroitin-4-sulfate polysaccharide by chromic acid in aqueous perchlorate solutions.

    PubMed

    Hassan, Refat; Ibrahim, Samia; Dahy, Abdel Rahman; Zaafarany, Ishaq; Tirkistani, Fahd; Takagi, Hideo

    2013-02-15

    The kinetics of chromic acid oxidation of chondroitin-4-sulfate polysaccharide as sulfated carbohydrates at a constant ionic strength of 4.0 mol dm(-3) has been investigated, spectrophotometrically. The reaction kinetics showed a first-order dependence in chromic acid and fractional-first-order kinetics with respect to the chondroitin-4-sulfate concentration. The influence of [H(+)] on the reaction rates showed that the oxidation process is acid-catalyzed. Added Mn(2+) ions indicated the formation of Cr(IV) as intermediate species. A kinetic evidence for formation of 1:1 intermediate complex was revealed. The kinetic parameters have been evaluated and a tentative reaction mechanism in good consistent with the kinetic results obtained is discussed.

  15. Kinetic Reaction Mechanism of Sinapic Acid Scavenging NO2 and OH Radicals: A Theoretical Study

    PubMed Central

    Lu, Yang; Wang, AiHua; Shi, Peng; Zhang, Hui; Li, ZeSheng

    2016-01-01

    The mechanism and kinetics underlying reactions between the naturally-occurring antioxidant sinapic acid (SA) and the very damaging ·NO2 and ·OH were investigated through the density functional theory (DFT). Two most possible reaction mechanisms were studied: hydrogen atom transfer (HAT) and radical adduct formation (RAF). Different reaction channels of neutral and anionic sinapic acid (SA-) scavenging radicals in both atmosphere and water medium were traced independently, and the thermodynamic and kinetic parameters were calculated. We find the most active site of SA/SA- scavenging ·NO2 and ·OH is the –OH group in benzene ring by HAT mechanism, while the RAF mechanism for SA/SA- scavenging ·NO2 seems thermodynamically unfavorable. In water phase, at 298 K, the total rate constants of SA eliminating ·NO2 and ·OH are 1.30×108 and 9.20×109 M-1 S-1 respectively, indicating that sinapic acid is an efficient scavenger for both ·NO2 and ·OH. PMID:27622460

  16. Crystallization mechanism and kinetics of mayenite glass prepared by aerodynamic levitation method

    NASA Astrophysics Data System (ADS)

    Duan, Jiao; Liu, Yan; Gu, Yanjing; Pan, Xiuhong; Zheng, Xiaojie; Wang, Wei; Yu, Huimei; Yu, Jianding

    2016-05-01

    The mayenite glass with a wide high-temperature stability (ΔT=131∘C) was innovatively synthesized by the aerodynamic levitation (ADL) containerless technique without conventional glass-forming addictives. The crystallization mechanism and kinetics of mayenite glass were studied by X-ray diffraction (XRD), scaning electron microscopy (SEM), Raman spectra and differential scanning calorimetry (DSC) analysis. The crystallization mechanism study revealed that structure and morphology mainly evolved near the crystallization peak temperature by the networking process of isolated AlO4 tetrahedra units, resulting in the growth mechanism changing from “two-dimensional” to “three-dimensional”. Crystallization kinetics calculations based on the non-isothermal Matusita model indicated that the activation energy for the crystallization of mayenite glass was 844kJṡmol-1. The calculated growth morphology parameters (m and n) also confirmed the surface crystallization along with bulk crystallization mechanism for the mayenite glass. This present study supplied a thermal-physical understanding about the crystallization of mayenite glass, which could be further applied in the exploitation of glass/glass-ceramics in the CaO-Al2O3 binary system.

  17. Influence of environmental conditions on the kinetics and mechanism of dehydration of carbamazepine dihydrate.

    PubMed

    Han, J; Suryanarayanan, R

    1998-11-01

    The object of this project was to study the influence of temperature and water vapor pressure on the kinetics and mechanism of dehydration of carbamazepine dihydrate and to establish the relationship between the dehydration mechanism and the solid-state of the anhydrous phase formed. Three experimental techniques were utilized to study the kinetics of dehydration of carbamazepine dihydrate (C15H12N2O.2H2O)-thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) and variable temperature powder X-ray diffractometry (VTXRD). These techniques respectively provide information about the changes in weight, heat flow and solid-state (phase) during the dehydration process. The instrumental setup was modified so that simultaneous control of both the temperature and the water vapor pressure was possible. The experiments were carried out at different temperatures, ranging from 26 to 64 degrees C. In the absence of water vapor, the dehydration followed the 2-dimensional phase boundary controlled model at all the temperatures studied. In the next stage, the water vapor pressure was altered while the studies were carried out at a single temperature of 44 degrees C. The dehydration was 2-dimensional phase boundary controlled at water vapor pressures < or = 5.1 torr while the Avrami-Erofeev kinetics (3-dimensional nucleation) was followed at water vapor pressures > or = 12.0 torr. In the former case, the anhydrous phase formed was X-ray amorphous while it was the crystalline anhydrous gamma-carbamazepine in the latter. Thus a relationship between the mechanism of dehydration and the solid-state of the product phase was evident. The dehydration conditions influence not only the mechanism but also the solid-state of the anhydrous phase formed. While the techniques of TGA and DSC have found extensive use in studying dehydration reactions, VTXRD proved to be an excellent complement in characterizing the solid-states of the reactant and product phases.

  18. Single molecule RNA folding studied with optical trapping

    NASA Astrophysics Data System (ADS)

    Vieregg, Jeffrey Robert

    The RNA folding problem (predicting the equilibrium structure and folding pathway of an RNA molecule from its sequence) is one of the classic problems of biophysics. Recent discoveries of many new functions for RNA have increased its importance, and new instrumental techniques have provided new ways to characterize molecular behavior. In particular, optical trapping (optical tweezers) allows controlled mechanical force to be applied to single RNA molecules while their end-to-end extension is monitored in real time. This enables characterization of RNA folding dynamics at a level unreachable by traditional bulk methods. Furthermore, recent advances in statistical mechanics make it possible to recover equilibrium quantities such as free energy from reactions which occur away from equilibrium. This dissertation describes the application of optical trapping and non-equilibrium statistical mechanics to quantitatively characterize folding of RNA secondary structures. By measuring the folding free energy of several specially designed hairpins in solutions containing various amounts of sodium and potassium, we were able to determine that RNA secondary structure thermodynamics depends not only on monovalent cation concentration but also surprisingly, on species. We also investigated the temperature dependence of hairpin folding thermodynamics and kinetics, which provided a direct measurement of enthalpy and entropy for RNA folding at physiological temperatures. We found that the folding pathway was quite sensitive to both salt and temperature, as measured by the folding success rate of a biologically important hairpin from the HIV-1 viral genome. Finally, I discuss modeling of force-induced RNA folding and unfolding, as well as a series of efforts which have dramatically improved the performance of our optical trapping instrument.

  19. Changes in the folding landscape of the WW domain provide a molecular mechanism for an inherited genetic syndrome

    PubMed Central

    Pucheta-Martinez, Encarna; D’Amelio, Nicola; Lelli, Moreno; Martinez-Torrecuadrada, Jorge L.; Sudol, Marius; Saladino, Giorgio; Gervasio, Francesco Luigi

    2016-01-01

    WW domains are small domains present in many human proteins with a wide array of functions and acting through the recognition of proline-rich sequences. The WW domain belonging to polyglutamine tract-binding protein 1 (PQBP1) is of particular interest due to its direct involvement in several X chromosome-linked intellectual disabilities, including Golabi-Ito-Hall (GIH) syndrome, where a single point mutation (Y65C) correlates with the development of the disease. The mutant cannot bind to its natural ligand WBP11, which regulates mRNA processing. In this work we use high-field high-resolution NMR and enhanced sampling molecular dynamics simulations to gain insight into the molecular causes the disease. We find that the wild type protein is partially unfolded exchanging among multiple beta-strand-like conformations in solution. The Y65C mutation further destabilizes the residual fold and primes the protein for the formation of a disulphide bridge, which could be at the origin of the loss of function. PMID:27456546

  20. The Crystal Structure of Dehi Reveals a New A-Haloacid Dehalogenase Fold And Active Site Mechanism

    SciTech Connect

    Schmidberger, J.W.; Wilce, J.A.; Weightman, A.J.; Whisstock, J.C.; Wilce, M.C.J.

    2009-05-27

    Haloacid dehalogenases catalyse the removal of halides from organic haloacids and are of interest for bioremediation and for their potential use in the synthesis of industrial chemicals. We present the crystal structure of the homodimer DehI from Pseudomonas putida strain PP3, the first structure of a group I {alpha}-haloacid dehalogenase that can process both L- and D-substrates. The structure shows that the DehI monomer consists of two domains of {approx}130 amino acids that have {approx}16% sequence identity yet adopt virtually identical and unique folds that form a pseudo-dimer. Analysis of the active site reveals the likely binding mode of both L- and D-substrates with respect to key catalytic residues. Asp189 is predicted to activate a water molecule for nucleophilic attack of the substrate chiral centre resulting in an inversion of configuration of either L- or D-substrates in contrast to D-only enzymes. These details will assist with future bioengineering of dehalogenases.

  1. Changes in the folding landscape of the WW domain provide a molecular mechanism for an inherited genetic syndrome

    NASA Astrophysics Data System (ADS)

    Pucheta-Martinez, Encarna; D’Amelio, Nicola; Lelli, Moreno; Martinez-Torrecuadrada, Jorge L.; Sudol, Marius; Saladino, Giorgio; Gervasio, Francesco Luigi

    2016-07-01

    WW domains are small domains present in many human proteins with a wide array of functions and acting through the recognition of proline-rich sequences. The WW domain belonging to polyglutamine tract-binding protein 1 (PQBP1) is of particular interest due to its direct involvement in several X chromosome-linked intellectual disabilities, including Golabi-Ito-Hall (GIH) syndrome, where a single point mutation (Y65C) correlates with the development of the disease. The mutant cannot bind to its natural ligand WBP11, which regulates mRNA processing. In this work we use high-field high-resolution NMR and enhanced sampling molecular dynamics simulations to gain insight into the molecular causes the disease. We find that the wild type protein is partially unfolded exchanging among multiple beta-strand-like conformations in solution. The Y65C mutation further destabilizes the residual fold and primes the protein for the formation of a disulphide bridge, which could be at the origin of the loss of function.

  2. Theory of RNA Folding: From Hairpins to Ribozymes

    NASA Astrophysics Data System (ADS)

    Thirumalai, D.; Hyeon, Changbong

    The rugged nature of the RNA folding landscape is determined by a number of conflicting interactions like repulsive electrostatic potential between the charges on the phosphate groups, constraints due to loop entropy, base stacking, and hydrogen bonding that operate on various length scales. As a result the kinetics of self-assembly of RNA is complex, but can be easily modulated by varying the concentrations, sizes, and shapes of the counterions. Here, we provide a theoretical description of RNA folding that is rooted in the energy landscape perspective and polyelectrolyte theory. A consequence of the rugged folding landscape is that, self-assembly of RNA into compact three-dimensional structures occurs by parallel routes, and is best described by the kinetic partitioning mechanism (KPM). According to KPM one fraction of molecules (Φ) folds rapidly while the remaining gets trapped in one of several competing basins of attraction. The partition factor Φ can be altered by point mutations as well as by changing the initial conditions such as ion concentration, size and valence of ions. We show that even hairpin formation, either by temperature or force quench, captures much of the features of folding of large RNA molecules. Despite the complexity of the folding process, we show that the KPM concepts from polyelectrolyte theory, and charge density of ions can be used to explain the stability, pathways and their diversity, and the plastiCity of the transition State ensemble of RNA self-assembly.

  3. THEORY OF PROTEIN FOLDING: The Energy Landscape Perspective

    NASA Astrophysics Data System (ADS)

    Onuchic, Jose Nelson; Luthey-Schulten, Zaida; Wolynes, Peter G.

    1997-10-01

    The energy landscape theory of protein folding is a statistical description of a protein's potential surface. It assumes that folding occurs through organizing an ensemble of structures rather than through only a few uniquely defined structural intermediates. It suggests that the most realistic model of a protein is a minimally frustrated heteropolymer with a rugged funnel-like landscape biased toward the native structure. This statistical description has been developed using tools from the statistical mechanics of disordered systems, polymers, and phase transitions of finite systems. We review here its analytical background and contrast the phenomena in homopolymers, random heteropolymers, and protein-like heteropolymers that are kinetically and thermodynamically capable of folding. The connection between these statistical concepts and the results of minimalist models used in computer simulations is discussed. The review concludes with a brief discussion of how the theory helps in the interpretation of results from fast folding experiments and in the practical task of protein structure prediction.

  4. Mechanism and Kinetics of Mechanical Alloying in an Immiscible Fe-Mg System

    NASA Astrophysics Data System (ADS)

    Yelsukov, E. P.; Dorofeev, G. A.; Ulyanov, A. L.

    2005-07-01

    Mössbauer spectroscopy, X-ray diffraction, Auger spectroscopy, secondary ion mass-spectrometry and chemical analysis were used to study mechanical alloying of Fe and Mg powder mixture with the atomic ratio of 93:7. It has been shown that the process of mechanical alloying involves the formation of nanostructure in α-Fe particles, penetration and segregation of Mg atoms along the α-Fe grain boundaries, formation of the α-Fe(Mg) supersaturated solid solution.

  5. Flexibility damps macromolecular crowding effects on protein folding dynamics: Application to the murine prion protein (121-231)

    NASA Astrophysics Data System (ADS)

    Bergasa-Caceres, Fernando; Rabitz, Herschel A.

    2014-01-01

    A model of protein folding kinetics is applied to study the combined effects of protein flexibility and macromolecular crowding on protein folding rate and stability. It is found that the increase in stability and folding rate promoted by macromolecular crowding is damped for proteins with highly flexible native structures. The model is applied to the folding dynamics of the murine prion protein (121-231). It is found that the high flexibility of the native isoform of the murine prion protein (121-231) reduces the effects of macromolecular crowding on its folding dynamics. The relevance of these findings for the pathogenic mechanism are discussed.

  6. Pre-steady-state Kinetic Analysis of a Family D DNA Polymerase from Thermococcus sp. 9°N Reveals Mechanisms for Archaeal Genomic Replication and Maintenance.

    PubMed

    Schermerhorn, Kelly M; Gardner, Andrew F

    2015-09-04

    Family D DNA polymerases (polDs) have been implicated as the major replicative polymerase in archaea, excluding the Crenarchaeota branch, and bear little sequence homology to other DNA polymerase families. Here we report a detailed kinetic analysis of nucleotide incorporation and exonuclease activity for a Family D DNA polymerase from Thermococcus sp. 9°N. Pre-steady-state single-turnover nucleotide incorporation assays were performed to obtain the kinetic parameters, kpol and Kd, for correct nucleotide incorporation, incorrect nucleotide incorporation, and ribonucleotide incorporation by exonuclease-deficient polD. Correct nucleotide incorporation kinetics revealed a relatively slow maximal rate of polymerization (kpol ∼ 2.5 s(-1)) and especially tight nucleotide binding (Kd (dNTP) ∼ 1.7 μm), compared with DNA polymerases from Families A, B, C, X, and Y. Furthermore, pre-steady-state nucleotide incorporation assays revealed that polD prevents the incorporation of incorrect nucleotides and ribonucleotides primarily through reduced nucleotide binding affinity. Pre-steady-state single-turnover assays on wild-type 9°N polD were used to examine 3'-5' exonuclease hydrolysis activity in the presence of Mg(2+) and Mn(2+). Interestingly, substituting Mn(2+) for Mg(2+) accelerated hydrolysis rates > 40-fold (kexo ≥ 110 s(-1) versus ≥ 2.5 s(-1)). Preference for Mn(2+) over Mg(2+) in exonuclease hydrolysis activity is a property unique to the polD family. The kinetic assays performed in this work provide critical insight into the mechanisms that polD employs to accurately and efficiently replicate the archaeal genome. Furthermore, despite the unique properties of polD, this work suggests that a conserved polymerase kinetic pathway is present in all known DNA polymerase families.

  7. Pre-steady-state Kinetic Analysis of a Family D DNA Polymerase from Thermococcus sp. 9°N Reveals Mechanisms for Archaeal Genomic Replication and Maintenance*

    PubMed Central

    Schermerhorn, Kelly M.; Gardner, Andrew F.

    2015-01-01

    Family D DNA polymerases (polDs) have been implicated as the major replicative polymerase in archaea, excluding the Crenarchaeota branch, and bear little sequence homology to other DNA polymerase families. Here we report a detailed kinetic analysis of nucleotide incorporation and exonuclease activity for a Family D DNA polymerase from Thermococcus sp. 9°N. Pre-steady-state single-turnover nucleotide incorporation assays were performed to obtain the kinetic parameters, kpol and Kd, for correct nucleotide incorporation, incorrect nucleotide incorporation, and ribonucleotide incorporation by exonuclease-deficient polD. Correct nucleotide incorporation kinetics revealed a relatively slow maximal rate of polymerization (kpol ∼2.5 s−1) and especially tight nucleotide binding (Kd(dNTP) ∼1.7 μm), compared with DNA polymerases from Families A, B, C, X, and Y. Furthermore, pre-steady-state nucleotide incorporation assays revealed that polD prevents the incorporation of incorrect nucleotides and ribonucleotides primarily through reduced nucleotide binding affinity. Pre-steady-state single-turnover assays on wild-type 9°N polD were used to examine 3′-5′ exonuclease hydrolysis activity in the presence of Mg2+ and Mn2+. Interestingly, substituting Mn2+ for Mg2+ accelerated hydrolysis rates >40-fold (kexo ≥110 s−1 versus ≥2.5 s−1). Preference for Mn2+ over Mg2+ in exonuclease hydrolysis activity is a property unique to the polD family. The kinetic assays performed in this work provide critical insight into the mechanisms that polD employs to accurately and efficiently replicate the archaeal genome. Furthermore, despite the unique properties of polD, this work suggests that a conserved polymerase kinetic pathway is present in all known DNA polymerase families. PMID:26160179

  8. Interaction of lipoprotein lipase with p-nitrophenyl N-alkylcarbamates: kinetics, mechanism, and analogy to the acylenzyme mechanism.

    PubMed

    Shin, H C; Quinn, D M

    1992-01-28

    The interaction of lipoprotein lipase with p-nitrophenyl N-alkylcarbamates [PNPOC(=O)-NHCnH2n+1; n = 4, 8, and 12] proceeds by the three-stage mechanism shown below. After reversible [formula: see text] formation of the enzyme-carbamate complex (EC), rapid carbamylation (kc) precedes slow decarbamylation. Therefore, in short-term assays (less than or equal to 30 min) of lipoprotein lipase catalyzed hydrolysis of p-nitrophenyl butyrate, activity is rapidly lost. The inhibition by p-nitrophenyl N-butylcarbamate follows saturation kinetics, which allows determination of Kc = 5.4 +/- 0.9 microM and kc = (4.9 +/- 0.7) x 10(-2)s-1. Saturation kinetics are not observed for the longer inhibitors p-nitrophenyl N-octylcarbamate and p-nitrophenyl N-dodecylcarbamate. Rather, plots of the pseudo-first-order rate constant for activity loss versus inhibitor concentration are concave upward, consistent with inhibitor binding to two sites on the enzyme. The inhibition phase is sufficiently rapid that p-nitrophenyl N-octylcarbamate can be used to titrate enzyme active sites. On the other hand, long-term assays (greater than 5 h) show sequential inhibition and activity return phases, and from the activity return phase kd is calculated. The long-term activity time course is accurately simulated by Runge-Kutta integration of the differential equations for the three-stage mechanism. These approaches have been used to characterize the kinetics of interaction of the enzyme with the carbamate inhibitors.(ABSTRACT TRUNCATED AT 250 WORDS)

  9. One- and two-electron oxidation of thiols: mechanisms, kinetics and biological fates.

    PubMed

    Trujillo, Madia; Alvarez, Beatriz; Radi, Rafael

    2016-01-01

    The oxidation of biothiols participates not only in the defense against oxidative damage but also in enzymatic catalytic mechanisms and signal transduction processes. Thiols are versatile reductants that react with oxidizing species by one- and two-electron mechanisms, leading to thiyl radicals and sulfenic acids, respectively. These intermediates, depending on the conditions, participate in further reactions that converge on different stable products. Through this review, we will describe the biologically relevant species that are able to perform these oxidations and we will analyze the mechanisms and kinetics of the one- and two-electron reactions. The processes undergone by typical low-molecular-weight thiols as well as the particularities of specific thiol proteins will be described, including the molecular determinants proposed to account for the extraordinary reactivities of peroxidatic thiols. Finally, the main fates of the thiyl radical and sulfenic acid intermediates will be summarized.

  10. High-speed PIV measurements of the flow downstream of a dynamic mechanical model of the human vocal folds

    NASA Astrophysics Data System (ADS)

    Triep, M.; Brücker, Ch.; Schröder, W.

    2005-08-01

    The objective of the present study is the detailed analysis of the unsteady vortex dynamics downstream of the human glottis during phonation at typical fundamental frequencies of the male voice of about 120 Hz. A hydraulic respiratory mock circuit has been built, including a factor of three up-scaled realistic dynamic model of the vocal folds. Time-resolving flow measurements were carried out downstream of the glottis by means of high-speed particle image velocimetry (PIV). The function of the human glottis is reproduced by two counter-rotating cams, each of which is covered with a stretched silicone membrane. The three-dimensional (3-D) geometry of the cams is designed such that the rotation leads to a realistic time-varying motion and profile of the glottis and waveform of the glottal cycle. Using high-speed PIV, the velocity field is captured with high spatial and temporal resolution to investigate the unsteady vortex dynamics of the cyclic jet-like flow in the vocal tract. The results help us to understand the vorticity interaction within the pulsating jet and, consequently, the generated sound in a human voice. In addition, changing the 3-D contours of the cams enables us to investigate basic pathological differences of the glottis function and the resulting alterations of the velocity and vorticity field in the vocal tract. The results are presented for typical physiological flow conditions in the human glottis. The frequencies of periodic vortex structures generated downstream of the glottis are fivefold higher than the fundamental frequency of the vocal folds’ oscillation. The highest vorticity fluctuations have a phase shift of 35% relative to the opening of the glottis. Finally, the flow field in the vocal tract is identified to be highly three-dimensional.

  11. Electrostatically accelerated encounter and folding for facile recognition of intrinsically disordered proteins.

    PubMed

    Ganguly, Debabani; Zhang, Weihong; Chen, Jianhan

    2013-01-01

    Achieving facile specific recognition is essential for intrinsically disordered proteins (IDPs) that are involved in cellular signaling and regulation. Consideration of the physical time scales of protein folding and diffusion-limited protein-protein encounter has suggested that the frequent requirement of protein folding for specific IDP recognition could lead to kinetic bottlenecks. How IDPs overcome such potential kinetic bottlenecks to viably function in signaling and regulation in general is poorly understood. Our recent computational and experimental study of cell-cycle regulator p27 (Ganguly et al., J. Mol. Biol. (2012)) demonstrated that long-range electrostatic forces exerted on enriched charges of IDPs could accelerate protein-protein encounter via "electrostatic steering" and at the same time promote "folding-competent" encounter topologies to enhance the efficiency of IDP folding upon encounter. Here, we further investigated the coupled binding and folding mechanisms and the roles of electrostatic forces in the formation of three IDP complexes with more complex folded topologies. The surface electrostatic potentials of these complexes lack prominent features like those observed for the p27/Cdk2/cyclin A complex to directly suggest the ability of electrostatic forces to facilitate folding upon encounter. Nonetheless, similar electrostatically accelerated encounter and folding mechanisms were consistently predicted for all three complexes using topology-based coarse-grained simulations. Together with our previous analysis of charge distributions in known IDP complexes, our results support a prevalent role of electrostatic interactions in promoting efficient coupled binding and folding for facile specific recognition. These results also suggest that there is likely a co-evolution of IDP folded topology, charge characteristics, and coupled binding and folding mechanisms, driven at least partially by the need to achieve fast association kinetics for cellular

  12. Kinetics and Mechanisms of γ‧ Reprecipitation in a Ni-based Superalloy

    NASA Astrophysics Data System (ADS)

    Masoumi, F.; Shahriari, D.; Jahazi, M.; Cormier, J.; Devaux, A.

    2016-06-01

    The reprecipitation mechanisms and kinetics of γ‧ particles during cooling from supersolvus and subsolvus temperatures were studied in AD730TM Ni-based superalloy using Differential Thermal Analysis (DTA). The evolution in the morphology and distribution of reprecipitated γ‧ particles was investigated using Field Emission Gun Scanning Electron Microscopy (FEG-SEM). Depending on the cooling rate, γ‧ particles showed multi or monomodal distribution. The irregularity growth characteristics observed at lower cooling rates were analyzed in the context of Mullins and Sekerka theory, and allowed the determination of a critical size of γ‧ particles above which morphological instability appears. Precipitation kinetics parameters were determined using a non-isothermal JMA model and DTA data. The Avrami exponent was determined to be in the 1.5–2.3 range, suggesting spherical or irregular growth. A methodology was developed to take into account the temperature dependence of the rate coefficient k(T) in the non-isothermal JMA equation. In that regard, a function for k(T) was developed. Based on the results obtained, reprecipitation kinetics models for low and high cooling rates are proposed to quantify and predict the volume fraction of reprecipitated γ‧ particles during the cooling process.

  13. Molecular-Level Investigations of Nucleation Mechanisms and Kinetics of Formation of Environmental Nanoparticles

    SciTech Connect

    Young-Shin Jun; Glenn A. Waychunas

    2007-04-19

    Environmental nanoparticles are often poorly-crystalline or metastable structures, whose kinetics of formation and growth are poorly understood. Further, the sorption or growth of nanoparticles on mineral surfaces may control the mineral surface's reactivity and modify its ability to influence contaminant transport. Due to the characteristic length scale, a holistic understanding of the nucleation mechanisms and kinetics of nanoparticle formation on mineral surfaces is difficult to achieve with traditional methodology. In this work, our intent is to determine the molecular nature of nucleation on surfaces, the kinetics of surface nucleation and growth, and the effect of crystal surface topology using new synchrotron-based techniques. We have approached these objectives by: (1) combining state-of-the-art crystal-truncation rod diffraction (CTR) and grazing incidence x-ray absorption fine structure spectroscopy (GIXAS) techniques to investigate the three-dimensional molecular-scale geometry of silicate monomer sorption on the r-plane of hematite; and (2) developing a new grazing-incidence small angle x-ray scattering (GISAXS) setup at SSRL (0.08 nm{sup -1} < q < 8 nm{sup -1}) to explore the initial development of environmental nanoparticles on various mineral surfaces. This study also includes complementary techniques such as atomic force microscopy (AFM), bulk SAXS, dynamic light scattering (DLS), XRD, and TEM.

  14. Kinetics and Mechanisms of γ′ Reprecipitation in a Ni-based Superalloy

    PubMed Central

    Masoumi, F.; Shahriari, D.; Jahazi, M.; Cormier, J.; Devaux, A.

    2016-01-01

    The reprecipitation mechanisms and kinetics of γ′ particles during cooling from supersolvus and subsolvus temperatures were studied in AD730TM Ni-based superalloy using Differential Thermal Analysis (DTA). The evolution in the morphology and distribution of reprecipitated γ′ particles was investigated using Field Emission Gun Scanning Electron Microscopy (FEG-SEM). Depending on the cooling rate, γ′ particles showed multi or monomodal distribution. The irregularity growth characteristics observed at lower cooling rates were analyzed in the context of Mullins and Sekerka theory, and allowed the determination of a critical size of γ′ particles above which morphological instability appears. Precipitation kinetics parameters were determined using a non-isothermal JMA model and DTA data. The Avrami exponent was determined to be in the 1.5–2.3 range, suggesting spherical or irregular growth. A methodology was developed to take into account the temperature dependence of the rate coefficient k(T) in the non-isothermal JMA equation. In that regard, a function for k(T) was developed. Based on the results obtained, reprecipitation kinetics models for low and high cooling rates are proposed to quantify and predict the volume fraction of reprecipitated γ′ particles during the cooling process. PMID:27338868

  15. Carter constant induced mechanism for generation of anisotropic kinetic equilibria in collisionless N-body systems

    NASA Astrophysics Data System (ADS)

    Cremaschini, Claudio; Stuchlík, Zdeněk

    A new intrinsically-relativistic kinetic mechanism for generation of nonisotropic relativistic kinetic equilibria in collisionless N-body systems is pointed out. The theory is developed in the framework of the covariant Vlasov statistical description. The new effect is based on the constraints placed by the conservation laws of neutral single-particle dynamics in prescribed background curved-spacetimes demonstrating existence of Killing tensors. As an illustration, the particular case of the Kerr spacetime admitting the so-called Carter constant for the particle geodesic motion is considered. The general functional form of the equilibrium kinetic distribution function (KDF) is determined and an explicit realization in terms of Gaussian-like distributions is provided. It is shown that, due to the Carter constant, these equilibrium KDFs exhibit an anisotropic phase-space functional dependence in terms of the single-particle 4-velocity components, giving rise to corresponding nonisotropic continuum fluid fields. The qualitative properties of the equilibrium stress-energy tensor associated with these systems are discussed, with a particular emphasis on the related occurrence of temperature anisotropy effects. The theory is susceptible of astrophysical applications, including in particular the statistical properties of dark matter (DM) halos around stellar-mass or galactic-center black holes.

  16. Thymidine kinase 2 enzyme kinetics elucidate the mechanism of thymidine-induced mitochondrial DNA depletion.

    PubMed

    Sun, Ren; Wang, Liya

    2014-10-07

    Mitochondrial thymidine kinase 2 (TK2) is a nuclear gene-encoded protein, synthesized in the cytosol and subsequently translocated into the mitochondrial matrix, where it catalyzes the phosphorylation of thymidine (dT) and deoxycytidine (dC). The kinetics of dT phosphorylation exhibits negative cooperativity, but dC phosphorylation follows hyperbolic Michaelis-Menten kinetics. The two substrates compete with each other in that dT is a competitive inhibitor of dC phosphorylation, while dC acts as a noncompetitive inhibitor of dT phosphorylation. In addition, TK2 is feedback inhibited by dTTP and dCTP. TK2 also phosphorylates a number of pyrimidine nucleoside analogues used in antiviral and anticancer therapy and thus plays an important role in mitochondrial toxicities caused by nucleoside analogues. Deficiency in TK2 activity due to genetic alterations causes devastating mitochondrial diseases, which are characterized by mitochondrial DNA (mtDNA) depletion or multiple deletions in the affected tissues. Severe TK2 deficiency is associated with early-onset fatal mitochondrial DNA depletion syndrome, while less severe deficiencies result in late-onset phenotypes. In this review, studies of the enzyme kinetic behavior of TK2 enzyme variants are used to explain the mechanism of mtDNA depletion caused by TK2 mutations, thymidine overload due to thymidine phosphorylase deficiency, and mitochondrial toxicity caused by antiviral thymidine analogues.

  17. Kinetics and mechanism of thermal degradation of pentose- and hexose-based carbohydrate polymers.

    PubMed

    Akbar, Jamshed; Iqbal, Mohammad S; Massey, Shazma; Masih, Rashid

    2012-10-15

    This work aims at study of thermal degradation kinetics and mechanism of pentose- and hexose-based carbohydrate polymers isolated from Plantago ovata (PO), Salvia aegyptiaca (SA) and Ocimum basilicum (OB). The analysis was performed by isoconversional method. The materials exhibited mainly two-stage degradation. The weight loss at ambient-115°C characterized by low activation energy corresponds to loss of moisture. The kinetic triplets consisting of E, A and g(α) model of the materials were determined. The major degradation stage represents a loss of high boiling volatile components. This stage is exothermic in nature. Above 340°C complete degradation takes place leaving a residue of 10-15%. The master plots of g(α) function clearly differentiated the degradation mechanism of hexose-based OB and SA polymers and pentose-based PO polymer. The pentose-based carbohydrate polymer showed D(4) type and the hexose-based polymers showed A(4) type degradation mechanism.

  18. Kinetic theory approach to modeling of cellular repair mechanisms under genome stress.

    PubMed

    Qi, Jinpeng; Ding, Yongsheng; Zhu, Ying; Wu, Yizhi

    2011-01-01

    Under acute perturbations from outer environment, a normal cell can trigger cellular self-defense mechanism in response to genome stress. To investigate the kinetics of cellular self-repair process at single cell level further, a model of DNA damage generating and repair is proposed under acute Ion Radiation (IR) by using mathematical framework of kinetic theory of active particles (KTAP). Firstly, we focus on illustrating the profile of Cellular Repair System (CRS) instituted by two sub-populations, each of which is made up of the active particles with different discrete states. Then, we implement the mathematical framework of cellular self-repair mechanism, and illustrate the dynamic processes of Double Strand Breaks (DSBs) and Repair Protein (RP) generating, DSB-protein complexes (DSBCs) synthesizing, and toxins accumulating. Finally, we roughly analyze the capability of cellular self-repair mechanism, cellular activity of transferring DNA damage, and genome stability, especially the different fates of a certain cell before and after the time thresholds of IR perturbations that a cell can tolerate maximally under different IR perturbation circumstances.

  19. Mechanical-Kinetic Modeling of a Molecular Walker from a Modular Design Principle

    NASA Astrophysics Data System (ADS)

    Hou, Ruizheng; Loh, Iong Ying; Li, Hongrong; Wang, Zhisong

    2017-02-01

    Artificial molecular walkers beyond burnt-bridge designs are complex nanomachines that potentially replicate biological walkers in mechanisms and functionalities. Improving the man-made walkers up to performance for widespread applications remains difficult, largely because their biomimetic design principles involve entangled kinetic and mechanical effects to complicate the link between a walker's construction and ultimate performance. Here, a synergic mechanical-kinetic model is developed for a recently reported DNA bipedal walker, which is based on a modular design principle, potentially enabling many directional walkers driven by a length-switching engine. The model reproduces the experimental data of the walker, and identifies its performance-limiting factors. The model also captures features common to the underlying design principle, including counterintuitive performance-construction relations that are explained by detailed balance, entropy production, and bias cancellation. While indicating a low directional fidelity for the present walker, the model suggests the possibility of improving the fidelity above 90% by a more powerful engine, which may be an improved version of the present engine or an entirely new engine motif, thanks to the flexible design principle. The model is readily adaptable to aid these experimental developments towards high-performance molecular walkers.

  20. Drug Release Kinetics and Transport Mechanisms of Non-degradable and Degradable Polymeric Delivery Systems

    PubMed Central

    Fu, Yao; Kao, Weiyuan John

    2010-01-01

    Importance of the field The advancement in material design and engineering has led to the rapid development of novel materials with increasing complexity and functions. Both non-degradable and degradable polymers have found wide applications in the controlled delivery field. Studies on drug release kinetics provide important information into the function of material systems. To elucidate the detailed transport mechanism and the structure-function relationship of a material system, it is critical to bridge the gap between the macroscopic data and the transport behavior at the molecular level. Areas covered in this review The structure and function information of selected non-degradable and degradable polymers have been collected and summarized from literatures published after 1990s. The release kinetics of selected drug compounds from various material systems will be discussed in case studies. Recent progresses in the mathematical models based on different transport mechanisms will be highlighted. What the reader will gain This article aims to provide an overview of structure-function relationships of selected non-degradable and degradable polymers as drug delivery matrices. Take home message Understanding the structure-function relationship of the material system is key to the successful design of a delivery system for a particular application. Moreover, developing complex polymeric matrices requires more robust mathematical models to elucidate the solute transport mechanisms. PMID:20331353

  1. DNA-Binding Kinetics Determines the Mechanism of Noise-Induced Switching in Gene Networks.

    PubMed

    Tse, Margaret J; Chu, Brian K; Roy, Mahua; Read, Elizabeth L

    2015-10-20

    Gene regulatory networks are multistable dynamical systems in which attractor states represent cell phenotypes. Spontaneous, noise-induced transitions between these states are thought to underlie critical cellular processes, including cell developmental fate decisions, phenotypic plasticity in fluctuating environments, and carcinogenesis. As such, there is increasing interest in the development of theoretical and computational approaches that can shed light on the dynamics of these stochastic state transitions in multistable gene networks. We applied a numerical rare-event sampling algorithm to study transition paths of spontaneous noise-induced switching for a ubiquitous gene regulatory network motif, the bistable toggle switch, in which two mutually repressive genes compete for dominant expression. We find that the method can efficiently uncover detailed switching mechanisms that involve fluctuations both in occupancies of DNA regulatory sites and copy numbers of protein products. In addition, we show that the rate parameters governing binding and unbinding of regulatory proteins to DNA strongly influence the switching mechanism. In a regime of slow DNA-binding/unbinding kinetics, spontaneous switching occurs relatively frequently and is driven primarily by fluctuations in DNA-site occupancies. In contrast, in a regime of fast DNA-binding/unbinding kinetics, switching occurs rarely and is driven by fluctuations in levels of expressed protein. Our results demonstrate how spontaneous cell phenotype transitions involve collective behavior of both regulatory proteins and DNA. Computational approaches capable of simulating dynamics over many system variables are thus well suited to exploring dynamic mechanisms in gene networks.

  2. Kinetics and mechanisms of cadmium carbonate heteroepitaxial growth at the calcite (10 1bar 4) surface

    NASA Astrophysics Data System (ADS)

    Xu, Man; Kovarik, Libor; Arey, Bruce W.; Felmy, Andrew R.; Rosso, Kevin M.; Kerisit, Sebastien

    2014-06-01

    Elucidating the kinetics and mechanisms of heteroepitaxial nucleation and growth at mineral-water interfaces is essential to understanding surface reactivity in geochemical systems. In the present work, the formation of heteroepitaxial cadmium carbonate coatings at calcite-water interfaces was investigated by exposing calcite (10 1bar 4) surfaces to Cd-bearing aqueous solutions. In situ atomic force microscopy (AFM) was employed as the primary technique. The AFM results indicate that the heteroepitaxial growth of cadmium carbonate proceeds via three different mechanisms depending on the initial supersaturation of the aqueous solution: advancement of existing steps, nucleation and growth of three-dimensional (3D) islands, and nucleation and spread of two-dimensional (2D) nuclei. The 3D islands and 2D nuclei exhibit different morphologies and growth kinetics. The effects of supersaturation on heteroepitaxial growth mechanisms can be interpreted in terms of the free energy barrier for nucleation. At low initial supersaturation, where 3D nucleation dominates, it is hypothesized, from the growth rate and morphology of the 3D islands observed with AFM, that the crystallization of the overgrowth follows a non-classical pathway involving the formation of a surface precursor that is not fully crystalline, whereas high supersaturation favors the formation of crystalline 2D nuclei whose morphology is based on the atomic structure of the calcite substrate. Cross-sectional transmission electron microscopy (TEM) images reveal that the atomic structure of the interface between the cadmium carbonate coating and calcite shows perfect, dislocation-free epitaxy.

  3. Kinetics and Mechanisms of Cadmium Carbonate Heteroepitaxial Growth at the Calcite (101¯4) Surface

    SciTech Connect

    Xu, Man; Kovarik, Libor; Arey, Bruce W.; Felmy, Andrew R.; Rosso, Kevin M.; Kerisit, Sebastien N.

    2014-06-01

    Elucidating the kinetics and mechanisms of heteroepitaxial nucleation and growth at mineral-water interfaces is essential to understanding surface reactivity in geochemical systems. In the present work, the formation of heteroepitaxial cadmium carbonate coatings at calcite-water interfaces was investigated by exposing calcite (10-14) surfaces to Cd-bearing aqueous solutions. In situ atomic force microscopy (AFM) was employed as the primary technique. The AFM results indicate that the heteroepitaxial growth of cadmium carbonate proceeds via three different mechanisms depending on the initial supersaturation of the aqueous solution: advancement of existing steps, nucleation and growth of three-dimensional (3D) islands, and nucleation and spread of two-dimensional (2D) nuclei. The 3D islands and 2D nuclei exhibit different morphologies and growth kinetics. The effects of supersaturation on heteroepitaxial growth mechanisms can be interpreted in terms of the free energy barrier for nucleation. At low initial supersaturation, where 3D nucleation dominates, it is hypothesized, from the growth rate and morphology of the 3D islands observed with AFM, that the crystallization of the overgrowth follows a non-classical pathway involving the formation of a surface precursor that is not fully crystalline, whereas high supersaturation favors the formation of crystalline 2D nuclei whose morphology is based on the atomic structure of the calcite substrate. Cross-sectional transmission electron microscopy (TEM) images reveal that the atomic structure of the interface between the cadmium carbonate coating and calcite shows perfect, dislocation-free epitaxy.

  4. Kinetics and mechanism of the oxidation of organic sulfides by N-bromobenzamide

    SciTech Connect

    Chowdhury, K.; Banerji, K.K. )

    1990-09-14

    Kinetics of oxidation of 34 organic sulfides by N-bromobenzamide (NBB), to yield the corresponding sulfoxides, have been studied. The reaction is first-order with respect to the sulfide, NBB, and hydrogen ions. There is no effect of added benzamide. Protonated NBB has been postulated as the reactive oxidizing species. Reactivity of the sulfides toward NBB was subjected to correlation analysis by using multiparametric equations. The polar reaction constants are negative. Steric effects play a minor inhibitory role. A mechanism involving formulation of a halogenosulfonium cation, in the rate-determining step, has been proposed.

  5. Degradation Kinetics and Mechanism of a β-Lactam Antibiotic Intermediate, 6-Aminopenicillanic Acid, in a New Integrated Production Process.

    PubMed

    Su, Min; Sun, Hua; Zhao, Yingying; Lu, Aidang; Cao, Xiaohui; Wang, Jingkang

    2016-01-01

    In an effort to promote sustainability and to reduce manufacturing costs, the traditional production process for 6-aminopenicillanic acid (6-APA) has been modified to include less processing units. The objectives of this study are to investigate the degradation kinetics of 6-APA, to propose a reasonable degradation mechanism, and to optimize the manufacturing conditions within this new process. A series of degradation kinetic studies were conducted in the presence of impurities, as well as at various chemical and physical conditions. The concentrations of 6-APA were determined by high-performance liquid chromatography. An Arrhenius-type kinetic model was established to give a more accurate prediction on the degradation rates of 6-APA. A hydrolysis degradation mechanism is shown to be the major pathway for 6-APA. The degradation mechanisms and the kinetic models for 6-APA in the new system enable the design of a good manufacturing process with optimized parameters.

  6. Graphene folding on flat substrates

    SciTech Connect

    Chen, Xiaoming; Zhao, Yadong; Ke, Changhong; Zhang, Liuyang; Wang, Xianqiao

    2014-10-28

    We present a combined experimental-theoretical study of graphene folding on flat substrates. The structure and deformation of the folded graphene sheet are experimentally characterized by atomic force microscopy. The local graphene folding behaviors are interpreted based on nonlinear continuum mechanics modeling and molecular dynamics simulations. Our study on self-folding of a trilayer graphene sheet reports a bending stiffness of about 6.57 eV, which is about four times the reported values for monolayer graphene. Our results reveal that an intriguing free sliding phenomenon occurs at the interlayer van der Waals interfaces during the graphene folding process. This work demonstrates that it is a plausible venue to quantify the bending stiffness of graphene based on its self-folding conformation on flat substrates. The findings reported in this work are useful to a better understanding of the mechanical properties of graphene and in the pursuit of its applications.

  7. Mechanical stability model of progradational carbonate platform margins under tectonic loads: Deformation of Cretaceous carbonate platforms in the Sierra Madre Oriental fold-thrust belt (east central Mexico)

    NASA Astrophysics Data System (ADS)

    Contreras, Juan; Suter, Max

    2015-02-01

    Shortening in the Sierra Madre Oriental fold-thrust belt (east central Mexico) is localized along the margins of Cretaceous carbonate platforms and controlled by mechanical stratigraphy. The platform margins are deformed by imbricate series of thrust ramps, whereas the coeval basins and platform interiors are deformed by map-scale detachment folds. Here we present a finite element model to evaluate the influence of the boundary geometry and boundary conditions on the style of deformation observed at these basinward progradational platform margins. We calculate the stress distribution in a linearly elastic platform-basin transition zone under the action of horizontal tectonic stress, taking into account changes of rock mechanical properties across the platform margin, as well as their dependence on direction, and infer the resulting fracture patterns based on the Mohr-Coulomb failure criterion. Stress concentrations are predicted at the contacts between the massive rocks of the platform margin and the well-layered rocks of both, the platform interior and the adjacent basin. Brittle failure of the platform border can be mostly attributed to three effects: mechanical coupling between the carbonate platform and a substratum of moderate to low viscosity, variations in layering and texture that governed the mechanical properties of the involved carbonates as well as their dependence on direction, and the development of sharp domain boundary corners associated with progradational facies changes. In contrast, the dip of the basement and a possible taper of the overlying Upper Cretaceous shale toward the basin appear to have little influence on the mechanical failure of the platform margin.

  8. Equilibrium collapse and the kinetic 'foldability' of proteins.

    PubMed

    Millet, Ian S; Townsley, Lara E; Chiti, Fabrizio; Doniach, Sebastian; Plaxco, Kevin W

    2002-01-08

    An important element of protein folding theory has been the identification of equilibrium parameters that might uniquely distinguish rapidly folding polypeptide sequences from those that fold slowly. One such parameter, termed sigma, is a dimensionless, equilibrium measure of the coincidence of chain compaction and folding that is predicted to be an important determinant of relative folding kinetics. To test this prediction and improve our understanding of the putative relationship between nonspecific compaction of the unfolded state and protein folding kinetics, we have used small-angle X-ray scattering and circular dichroism spectroscopy to measure the sigma of five well-characterized proteins. Consistent with theoretical predictions, we find that near-perfect coincidence of the unfolded state contraction and folding (sigma approximately 0) is associated with the rapid kinetics of these naturally occurring proteins. We do not, however, observe any significant correlation between sigma and either the relative folding rates of these proteins or the presence or absence of well-populated kinetic intermediates. Thus, while sigma approximately 0 may be a necessary condition to ensure rapid folding, differences in sigma do not account for the wide range of rates and mechanisms with which naturally occurring proteins fold.

  9. Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism

    PubMed Central

    Vital-Lopez, Francisco G.; Reifman, Jaques; Wallqvist, Anders

    2015-01-01

    A hallmark of Pseudomonas aeruginosa is its ability to establish biofilm-based infections that are difficult to eradicate. Biofilms are less susceptible to host inflammatory and immune responses and have higher antibiotic tolerance than free-living planktonic cells. Developing treatments against biofilms requires an understanding of bacterial biofilm-specific physiological traits. Research efforts have started to elucidate the intricate mechanisms underlying biofilm development. However, many aspects of these mechanisms are still poorly understood. Here, we addressed questions regarding biofilm metabolism using a genome-scale kinetic model of the P. aeruginosa metabolic network and gene expression profiles. Specifically, we computed metabolite concentration differences between known mutants with altered biofilm formation and the wild-type strain to predict drug targets against P. aeruginosa biofilms. We also simulated the altered metabolism driven by gene expression changes between biofilm and stationary growth-phase planktonic cultures. Our analysis suggests that the synthesis of important biofilm-related molecules, such as the quorum-sensing molecule Pseudomonas quinolone signal and the exopolysaccharide Psl, is regulated not only through the expression of genes in their own synthesis pathway, but also through the biofilm-specific expression of genes in pathways competing for precursors to these molecules. Finally, we investigated why mutants defective in anthranilate degradation have an impaired ability to form biofilms. Alternative to a previous hypothesis that this biofilm reduction is caused by a decrease in energy production, we proposed that the dysregulation of the synthesis of secondary metabolites derived from anthranilate and chorismate is what impaired the biofilms of these mutants. Notably, these insights generated through our kinetic model-based approach are not accessible from previous constraint-based model analyses of P. aeruginosa biofilm

  10. Kinetics and mechanism for formation of enols in reaction of hydroxide radical with propene.

    PubMed

    Zhou, Chong-Wen; Li, Ze-Rong; Li, Xiang-Yuan

    2009-03-19

    Recently, enols have been found to be the common intermediates in hydrocarbon combustion flames (Taatjes et al. Science 2005, 308, 1887), but the knowledge of kinetic properties for such species in combustion flames is rare. Therefore in this work, particular attention is paid to the formation of enols in combustion flames. Starting with HO and propene (CH(3)CH=CH(2)), the reaction mechanism involving eight product channels has been investigated systematically. It is revealed that the electrophilic addition of OH to the double bond of CH(3)CH=CH(2) is unselective and the chemically activated adducts, CH(3)CHOH=CH(2) and CH(3)CH=CH(2)OH, may undergo dissociation in competition with H-abstractions. The kinetics and product branching ratios of the HO and propene reaction have been evaluated in the temperature range of 200-3000 K by Variflex code, based on the weak collision master equation/microcanonical variational RRKM theory. Available experimental kinetic data can be quantitatively reproduced by this study, with a minor adjustment (1.0 kcal/mol) of the OH central addition barrier. From the theoretical calculations with multiple reflection correction included, the total rate constant is fitted to k(t) = 6.07 x 10(-5)T(-2.54) exp(108/T) cm(3) x molecule(-1) x s(-1) in the range of 200-800 K and k(t) = 7.11 x 10(-23)T(3.38) exp(-1097/T) cm(3) x molecule(-1) x s(-1) in the range of 800-3000 K, which are in close agreement with experimental data. The branching ratios of enol channels are consistent with the observation in low-pressure flames and hence the reaction mechanisms presented here provide valuable descriptions of enol formations in hydrocarbon combustion chemistry.

  11. Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism.

    PubMed

    Vital-Lopez, Francisco G; Reifman, Jaques; Wallqvist, Anders

    2015-10-01

    A hallmark of Pseudomonas aeruginosa is its ability to establish biofilm-based infections that are difficult to eradicate. Biofilms are less susceptible to host inflammatory and immune responses and have higher antibiotic tolerance than free-living planktonic cells. Developing treatments against biofilms requires an understanding of bacterial biofilm-specific physiological traits. Research efforts have started to elucidate the intricate mechanisms underlying biofilm development. However, many aspects of these mechanisms are still poorly understood. Here, we addressed questions regarding biofilm metabolism using a genome-scale kinetic model of the P. aeruginosa metabolic network and gene expression profiles. Specifically, we computed metabolite concentration differences between known mutants with altered biofilm formation and the wild-type strain to predict drug targets against P. aeruginosa biofilms. We also simulated the altered metabolism driven by gene expression changes between biofilm and stationary growth-phase planktonic cultures. Our analysis suggests that the synthesis of important biofilm-related molecules, such as the quorum-sensing molecule Pseudomonas quinolone signal and the exopolysaccharide Psl, is regulated not only through the expression of genes in their own synthesis pathway, but also through the biofilm-specific expression of genes in pathways competing for precursors to these molecules. Finally, we investigated why mutants defective in anthranilate degradation have an impaired ability to form biofilms. Alternative to a previous hypothesis that this biofilm reduction is caused by a decrease in energy production, we proposed that the dysregulation of the synthesis of secondary metabolites derived from anthranilate and chorismate is what impaired the biofilms of these mutants. Notably, these insights generated through our kinetic model-based approach are not accessible from previous constraint-based model analyses of P. aeruginosa biofilm

  12. Pseudoknots in RNA folding landscapes

    PubMed Central

    Kucharík, Marcel; Hofacker, Ivo L.; Stadler, Peter F.; Qin, Jing

    2016-01-01

    Motivation: The function of an RNA molecule is not only linked to its native structure, which is usually taken to be the ground state of its folding landscape, but also in many cases crucially depends on the details of the folding pathways such as stable folding intermediates or the timing of the folding process itself. To model and understand these processes, it is necessary to go beyond ground state structures. The study of rugged RNA folding landscapes holds the key to answer these questions. Efficient coarse-graining methods are required to reduce the intractably vast energy landscapes into condensed representations such as barrier trees or basin hopping graphs (BHG) that convey an approximate but comprehensive picture of the folding kinetics. So far, exact and heuristic coarse-graining methods have been mostly restricted to the pseudoknot-free secondary structures. Pseudoknots, which are common motifs and have been repeatedly hypothesized to play an important role in guiding folding trajectories, were usually excluded. Results: We generalize the BHG framework to include pseudoknotted RNA structures and systematically study the differences in predicted folding behavior depending on whether pseudoknotted structures are allowed to occur as folding intermediates or not. We observe that RNAs with pseudoknotted ground state structures tend to have more pseudoknotted folding intermediates than RNAs with pseudoknot-free ground state structures. The occurrence and influence of pseudoknotted intermediates on the folding pathway, however, appear to depend very strongly on the individual RNAs so that no general rule can be inferred. Availability and implementation: The algorithms described here are implemented in C++ as standalone programs. Its source code and Supplemental material can be freely downloaded from http://www.tbi.univie.ac.at/bhg.html. Contact: qin@bioinf.uni-leipzig.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID

  13. PREFACE Protein folding: lessons learned and new frontiers Protein folding: lessons learned and new frontiers

    NASA Astrophysics Data System (ADS)

    Pappu, Rohit V.; Nussinov, Ruth

    2009-03-01

    multi-scale dynamical problem when one considers the synergies between protein expression, spontaneous folding, chaperonin-assisted folding, protein targeting, the kinetics of post-translational modifications, protein degradation, and of course the drive to avoid aggregation. Further, there is growing recognition that cells not only tolerate but select for proteins that are intrinsically disordered. These proteins are essential for many crucial activities, and yet their inability to fold in isolation makes them prone to proteolytic processing and aggregation. In the series of papers that make up this special focus on protein folding in physical biology, leading researchers provide insights into diverse cross-sections of problems in protein folding. Barrick provides a concise review of what we have learned from the study of two-state folders and draws attention to how several unanswered questions are being approached using studies on large repeat proteins. Dissecting the contribution of hydration-mediated interactions to driving forces for protein folding and assembly has been extremely challenging. There is renewed interest in using hydrostatic pressure as a tool to access folding intermediates and decipher the role of partially hydrated states in folding, misfolding, and aggregation. Silva and Foguel review many of the nuances that have been uncovered by perturbing hydrostatic pressure as a thermodynamic parameter. As noted above, protein folding in vivo is expected to be considerably more complex than the folding of two-state proteins in dilute solutions. Lucent et al review the state-of-the-art in the development of quantitative theories to explain chaperonin-assisted folding in vivo. Additionally, they highlight unanswered questions pertaining to the processing of unfolded/misfolded proteins by the chaperone machinery. Zhuang et al present results that focus on the effects of surface tethering on transition state ensembles and folding mechanisms of a model two

  14. Isotherm, thermodynamic, kinetics and adsorption mechanism studies of methyl orange by surfactant modified silkworm exuviae.

    PubMed

    Chen, Hao; Zhao, Jie; Wu, Junyong; Dai, Guoliang

    2011-08-15

    This paper reports on the development of organo-modified silkworm exuviae (MSE) adsorbent prepared by using hexadecyltrimethylammonium bromide (HDTMAB) for removing methyl orange (MO), a model anionic dye, from aqueous solution. The natural and modified samples were characterized by scanning electron microscope (SEM), energy dispersive spectrometer (EDS) and Fourier transform infrared spectroscopy (FT-IR). Batch adsorption experiments were carried out to remove MO from its aqueous solutions using SE and MSE. It was observed that the adsorption capacity of MSE is 5-6 times of SE. The different parameters effecting on the adsorption capacity such as pH of the solution, initial dye concentration, temperature and contact time have been investigated. Analysis of adsorption results obtained at different temperatures showed that the adsorption pattern on the MSE can be described perfectly with Langmuir isotherm model compared with Freundlich and Dubinin-Radushkevich (D-R) isotherm models, and the characteristic parameters for each adsorption isotherm were also determined. The adsorption process has been found exothermic in nature and thermodynamic parameters have been calculated. The adsorption kinetic followed the pseudo-second order kinetic model. The results of FT-IR, EDS and desorption studies all suggest that methyl orange adsorption onto the MSE should be mainly controlled by the hydrophobic interaction mechanism, along with a considerable contribution of the anionic exchange mechanism. The results indicate that HDTMAB-modified silkworm exuviae could be employed as low-cost material for the removal of methyl orange anionic dye from wastewater.

  15. Anaerobic waste-activated sludge digestion - A bioconversion mechanism and kinetic model

    SciTech Connect

    Shimizu, Tatsuo; Kudo, Kenzo; Nasu, Yoshikazu )

    1993-05-01

    The anaerobic bioconversion of raw and mechanically lysed waste-activated sludge was kinetically investigated. The hydrolysis of the biopolymers, such as protein, which leaked out from the biological sludge with ultrasonic lysis, was a first-order reaction in anaerobic digestion and the rate constant was much higher than the decay rate constant of the raw waste activated sludge. An anaerobic digestion model that is capable of evaluating the effect of the mechanical sludge lysis on digestive performance was developed. The present model includes four major biological processes - the release of intracellular matter with sludge lysis; hydrolysis of biopolymers to volatile acids; the degradation of various volatile acids to acetate; and the conversion of acetate and hydrogen to methane. Each process was assumed to follow first-order kinetics. The model approximately simulated the overall process performance of the anaerobic digestion of waste-activated sludge. The model suggested that when the lysed waste-activated sludge was fed, the overall digestive performance remarkably increased in the two-phase system consisting of an acid forming process and a methanogenic process, which ensured the symbiotic growth of acetogenic and methanogenic bacteria.

  16. Integration of large chemical kinetic mechanisms via exponential methods with Krylov approximations to Jacobian matrix functions

    NASA Astrophysics Data System (ADS)

    Bisetti, Fabrizio

    2012-06-01

    Recent trends in hydrocarbon fuel research indicate that the number of species and reactions in chemical kinetic mechanisms is rapidly increasing in an effort to provide predictive capabilities for fuels of practical interest. In order to cope with the computational cost associated with the time integration of stiff, large chemical systems, a novel approach is proposed. The approach combines an exponential integrator and Krylov subspace approximations to the exponential function of the Jacobian matrix. The components of the approach are described in detail and applied to the ignition of stoichiometric methane-air and iso-octane-air mixtures, here described by two widely adopted chemical kinetic mechanisms. The approach is found to be robust even at relatively large time steps and the global error displays a nominal third-order convergence. The performance of the approach is improved by utilising an adaptive algorithm for the selection of the Krylov subspace size, which guarantees an approximation to the matrix exponential within user-defined error tolerance. The Krylov projection of the Jacobian matrix onto a low-dimensional space is interpreted as a local model reduction with a well-defined error control strategy. Finally, the performance of the approach is discussed with regard to the optimal selection of the parameters governing the accuracy of its individual components.

  17. Extracting signal from noise: kinetic mechanisms from a Michaelis-Menten-like expression for enzymatic fluctuations.

    PubMed

    Moffitt, Jeffrey R; Bustamante, Carlos

    2014-01-01

    Enzyme-catalyzed reactions are naturally stochastic, and precision measurements of these fluctuations, made possible by single-molecule methods, promise to provide fundamentally new constraints on the possible mechanisms underlying these reactions. We review some aspects of statistical kinetics: a new field with the goal of extracting mechanistic information from statistical measures of fluctuations in chemical reactions. We focus on a widespread and important statistical measure known as the randomness parameter. This parameter is remarkably simple in that it is the squared coefficient of variation of the cycle completion times, although it places significant limits on the minimal complexity of possible enzymatic mechanisms. Recently, a general expression has been introduced for the substrate dependence of the randomness parameter that is for rate fluctuations what the Michaelis-Menten expression is for the mean rate of product generation. We discuss the information provided by the new kinetic parameters introduced by this expression and demonstrate that this expression can simplify the vast majority of published models.

  18. Kinetic nanofriction: a mechanism transition from quasi-continuous to ballistic-like Brownian regime

    PubMed Central

    2012-01-01

    Surface diffusion of mobile adsorbates is not only the key to control the rate of dynamical processes on solid surfaces, e.g. epitaxial growth, but also of fundamental importance for recent technological applications, such as nanoscale electro-mechanical, tribological, and surface probing devices. Though several possible regimes of surface diffusion have been suggested, the nanoscale surface Brownian motion, especially in the technologically important low friction regimes, remains largely unexplored. Using molecular dynamics simulations, we show for the first time, that a C60 admolecule on a graphene substrate exhibits two distinct regimes of nanoscale Brownian motion: a quasi-continuous and a ballistic-like. A crossover between these two regimes is realized by changing the temperature of the system. We reveal that the underlying physical origin for this crossover is a mechanism transition of kinetic nanofriction arising from distinctive ways of interaction between the admolecule and the graphene substrate in these two regimes due to the temperature change. Our findings provide insight into surface mass transport and kinetic friction control at the nanoscale. PMID:22353343

  19. Mechanisms of antimicrobial, cytolytic, and cell-penetrating peptides: from kinetics to thermodynamics†

    PubMed Central

    Almeida, Paulo F.; Pokorny, Antje

    2009-01-01

    The mechanisms of six different antimicrobial, cytolytic, and cell-penetrating peptides, including some of their variants, are discussed and compared. The specificity of these polypeptides varies, but they all form amphipathic α-helices when bound to membranes, and there are no striking differences in their sequences. We have examined the thermodynamics and kinetics of their interaction with phospholipid vesicles, namely binding and peptide-induced dye efflux. The thermodynamics of binding calculated using the Wimley-White interfacial hydrophobicity scale are in good agreement with the values derived from experiment. The generally accepted view that binding affinity determines functional specificity is also supported by experiment in model membranes. We now propose the hypothesis that it is the thermodynamics of peptide insertion into the membrane, from a surface-bound state, that determines the mechanism. PMID:19655791

  20. Kinetic insulation as an effective mechanism for achieving pathway specificity in intracellular signaling networks

    PubMed Central

    Behar, Marcelo; Dohlman, Henrik G.; Elston, Timothy C.

    2007-01-01

    Intracellular signaling pathways that share common components often elicit distinct physiological responses. In most cases, the biochemical mechanisms responsible for this signal specificity remain poorly understood. Protein scaffolds and cross-inhibition have been proposed as strategies to prevent unwanted cross-talk. Here, we report a mechanism for signal specificity termed “kinetic insulation.” In this approach signals are selectively transmitted through the appropriate pathway based on their temporal profile. In particular, we demonstrate how pathway architectures downstream of a common component can be designed to efficiently separate transient signals from signals that increase slowly over time. Furthermore, we demonstrate that upstream signaling proteins can generate the appropriate input to the common pathway component regardless of the temporal profile of the external stimulus. Our results suggest that multilevel signaling cascades may have evolved to modulate the temporal profile of pathway activity so that stimulus information can be efficiently encoded and transmitted while ensuring signal specificity. PMID:17913886

  1. Mechanism and kinetics for the reaction of O(3P) with DMSO: A theoretical study

    NASA Astrophysics Data System (ADS)

    Mandal, Debasish; Bagchi, Sabyasachi; Das, Abhijit K.

    2012-11-01

    Mechanism and kinetics for the reaction of DMSO with O(3P) have been investigated by M06-2X/MG3S, CBS-QB3 and G4MP2 methods. Four possible reaction pathways are identified. Among them, the O(3P) addition to S-atom followed by CH3 elimination is almost exclusive. Four pre-reactive complexes have been located. AIM theory is used to determine the nature of interactions in these complexes. Considering the formation of pre-reactive complex, the rate constant for major pathway is calculated using transition state theory applied to a two-step mechanism. Enthalpies of formation at 298.15 K (ΔfH°298.15) have been calculated using the composite CBS-QB3, G4MP2 and G3B3 methods.

  2. Theoretical study on the mechanism and kinetics of acetaldehyde and hydroperoxyl radical: An important atmospheric reaction

    NASA Astrophysics Data System (ADS)

    Farnia, Solaleh; Vahedpour, Morteza; Abedi, Mostafa; Farrokhpour, Hossein

    2013-09-01

    A systematic theoretical study was performed on the mechanism and kinetics of the atmospheric reaction of acetaldehyde (CH3CHO) and hydroperoxyl radical (HO2) in the gas phase. The DFT-B3LYP/6-311++G(3df,3pd) and CCSD(T)/6-311++G(d,p) methods were employed for calculations. Based on the calculations, this reaction leads to four different products through radical addition and hydrogen abstraction mechanisms which are very important in atmospheric and combustion chemistry. The favorable reaction paths begin with α-hydroxyethylperoxy radical, CH3CH(OO)OH, in a exothermic process and finally leads to the product P1 (CH3COOH + OH). The overall rate constants for favorite reaction paths have been calculated at different temperatures (200-2500 K).

  3. BarMap: RNA folding on dynamic energy landscapes

    PubMed Central

    Hofacker, Ivo L.; Flamm, Christoph; Heine, Christian; Wolfinger, Michael T.; Scheuermann, Gerik; Stadler, Peter F.

    2010-01-01

    Dynamical changes of RNA secondary structures play an important role in the function of many regulatory RNAs. Such kinetic effects, especially in time-variable and externally triggered systems, are usually investigated by means of extensive and expensive simulations of large sets of individual folding trajectories. Here we describe the theoretical foundations of a generic approach that not only allows the direct computation of approximate population densities but also reduces the efforts required to analyze the folding energy landscapes to a one-time preprocessing step. The basic idea is to consider the kinetics on individual landscapes and to model external triggers and environmental changes as small but discrete changes in the landscapes. A “barmap” links macrostates of temporally adjacent landscapes and defines the transfer of population densities from one “snapshot” to the next. Implemented in the BarMap software, this approach makes it feasible to study folding processes at the level of basins, saddle points, and barriers for many nonstationary scenarios, including temperature changes, cotranscriptional folding, refolding in consequence to degradation, and mechanically constrained kinetics, as in the case of the translocation of a polymer through a pore. PMID:20504954

  4. Correlation of Impact Conditions, Interface Reactions, Microstructural Evolution, and Mechanical Properties in Kinetic Spraying of Metals: A Review

    NASA Astrophysics Data System (ADS)

    Kim, Jaeick; Lee, Changhee

    2016-12-01

    In the past, most studies into kinetic spraying technology focused on basic research, but a large portion of current research is devoted to industrial applications of the technology. To advance, however, studies about industrial applications of kinetic spraying require profound understanding of the scientific foundations of the kinetic spray process. Nevertheless, no one has yet provided a well-organized summary of the correlations among impact conditions, interface reactions, microstructural evolution, and mechanical properties across the whole field of kinetic spraying technology. This paper provides such an overview of these correlations for kinetic spraying of metals. For each correlation, the interactions between the given conditions and the material properties of the metal feedstock powder are the most influential. These interactions are so complicated that it is difficult to systematically classify all cases into certain types. Nonetheless, we try to explain and summarize the critical factors and their roles in each relationship.

  5. Influence of calcium on β-lactoglobulin denaturation kinetics: Implications in unfolding and aggregation mechanisms.

    PubMed

    Petit, J; Herbig, A-L; Moreau, A; Delaplace, G

    2011-12-01

    Much research dealing with the processing of milk by-products in heat exchangers has noted the key role of calcium in β-lactoglobulin (β-LG) fouling behavior. Nevertheless, the manner by which Ca affects β-LG denaturation has rarely been quantified using reliable kinetic and thermodynamic data. To this end, the influence of Ca on β-LG denaturation mechanisms in simulated lactoserum concentrates was studied on the laboratory-scale under 100°C by HPLC analysis. The heat-treated solutions were composed of 53.3g/L β-LG and were enriched in Ca at various concentrations (0, 66, 132, and 264 mg/kg). The kinetic parameters (reaction order, activation energy, and frequency factor) associated with β-LG denaturation, along with the unfolding and aggregation thermodynamic parameters were deduced from these experiments and discussed with respect to Ca content. We found that the multistage process characterizing β-LG thermal denaturation is not greatly affected by Ca addition. In fact, the general model subdividing β-LG denaturation mechanisms in 2 steps, namely, unfolding and aggregation, remained valid for all tested Ca concentrations. The change in the predominant mechanism from unfolding to aggregation was observed at 80°C across the entire Ca concentration range. Moreover, the classical 1.5 reaction order value was unaffected by the presence of Ca. Interpretation of the acquired kinetic data showed that Ca addition led to a significant increase in kinetic rate, and more so in the aggregation temperature range. This indicates that Ca principally catalyzes β-LG aggregation, by lowering the Coulombian repulsion between the negatively charged β-LG reactive species, bridging β-LG proteins, or via an ion-specific conformational change. To a lesser extent, Ca favors β-LG unfolding, probably by disturbing the noncovalent binding network of native β-LG. Simultaneously, Ca has a slight protective role on the native and unfolded β-LG species, as shown by the increase

  6. Mechanism and kinetics of Fischer-Tropsch synthesis over supported ruthenium catalysts

    SciTech Connect

    Kellner, C.S.

    1981-06-01

    A detailed study of the kinetics of the Fischer-Tropsch synthesis of hydrocarbons, methanol, and acetaldehyde, over alumina- and silica-supported ruthenium catalysts has been carried out over a broad range of reaction conditions. Based on these results and information taken from the literature, mechanisms for the formation of normal paraffins, ..cap alpha..-olefins, methanol, and acetaldehyde have been proposed. Rate data were obtained between 448 and 548K, 1 and 10 atm, and H/sub 2//CO ratios between 1 and 3, utilizing a micro flow reactor operated at very low conversions. In addition to the studies performed with H/sub 2//CO mixtures, a series of experiments were carried out utilizing D/sub 2//CO mixtures. These studies were used to help identify rate limited steps and steps that were at equilibrium. A complementary investigation, carried out by in situ infrared spectroscopy, was performed using a Fourier Transform spectrometer. The spectra obtained were used to identify the modes of CO adsorption, the CO coverage, and the relative reactivity of different forms of adsorbed CO. It was established that CO adsorbs on alumina-supported Ru in, at least, two forms: (i) Ru-CO and (ii) OC-Ru-CO. Only the first of these forms participates in CO hydrogenation. The coverage of this species is described by a simple Langmuir isotherm. A reaction mechanism is presented for interpreting the kinetics of hydrocarbon synthesis, the olefin to paraffin ratio for each product, and the probability of chain propagation. Rate expressions based on this mechanism are reasonably consistent with the experimental data. Acetaldehyde, obtained mainly over silica-supported Ru, appears to be formed by a mechanism related to that for hydroformulation of olefins. The effect of the dispersion of Ru/Al/sub 2/O/sub 3/ catalysts on their specific activity and selectivity was also investigated. The specific activity for all products decreased rapidly with increasing dispersions.

  7. 3-Fluoro-2,4-dioxa-3-phosphadecalins as inhibitors of acetylcholinesterase. A reappraisal of kinetic mechanisms and diagnostic methods.

    PubMed

    Baici, Antonio; Schenker, Patricia; Wächter, Michael; Rüedi, Peter

    2009-03-01

    A systematic survey of the acetylcholine-mimetic 2,4-dioxa-3-phosphadecalins as irreversible inhibitors of acetylcholinesterase revealed hitherto overlooked properties as far as the kinetic mechanisms of interaction are concerned. As a support to past and future work in this field, we describe the kinetics of eight reaction schemes that may be found in irreversible enzyme modification and compare them with two mechanism of reversible, slow-binding inhibition. The relevant kinetic equations and their associated graphical representations are given for all mechanisms, and concrete examples illustrate their practical use. Since irreversible inhibition is a time-dependent phenomenon, kinetic analysis is greatly facilitated by fitting the appropriate integrated rate equations to reaction-progress curves by nonlinear regression. This primary scrutiny provides kinetic parameters that are indispensable tools for diagnosing the kinetic mechanism and for calculating inhibition constants. Numerical integration of sets of differential equations is an additional useful investigation tool in critical situations, e.g., when inhibitors are unstable and/or act as irreversible modifiers only temporarily.

  8. Vacuum contact drying kinetics of Jack pine wood and its influence on mechanical properties: industrial applications

    NASA Astrophysics Data System (ADS)

    Ouertani, Sahbi; Koubaa, Ahmed; Azzouz, Soufien; Hassini, Lamine; Dhib, Kamel Ben; Belghith, Ali

    2014-12-01

    Wood can be dried rapidly using combined contact heating and low vacuum. However, the impact on Jack pine wood drying and its mechanical strength remains unclear. The aim of this paper was to determine the kinetics of vacuum contact drying of Jack pine (Pinus banksiana) wood boards (dimensions 50 × 100 × 2480 mm3) under various drying temperatures and vacuum pressures at a pilot scale. Drying temperatures and vacuum pressures ranged from 65 to 95 °C and from 169.32 to 507.96 mbar, respectively. Dried samples were subjected to flexural loading to determine mechanical strength. Results indicated that drying time decreased with higher drying temperature and vacuum pressure, where as decreased vacuum pressure increased the temperature of wood samples at a constant drying temperature. Results also indicated that the mechanical properties of dried samples were affected by drying temperature, vacuum pressure, and lumber grade. Mechanical test results were then compared to those for a conventional drying process, revealing that vacuum contact drying do not have a negative impact on the wood mechanical properties.

  9. Mechanisms and kinetics of melting of HbS aggregates studied in high concentration phosphate buffer

    NASA Astrophysics Data System (ADS)

    Aroutiounian, Svetlana

    The importance of melting kinetics in the pathogenesis of sickle cell disease originates from the inhibition of sickle hemoglobin polymer formation by the presence of oxygen. Sickle hemoglobin polymers form in the absence of oxygen or similar ligands, like carbon monoxide (CO). Melting of HbS polymers is initiated when red cells enter the lungs. Under the double nucleation mechanism, the formation of a sickle hemoglobin (HbS) polymer is composed of two events. Homogeneous nucleation with a characteristic delay time is prior to heterogeneous nucleation, which shows an avalanche-like kinetics. Two thirds of the transit time through the circulatory system, red cells spend under hypoxic conditions. In this work the role that ligand saturation plays in the kinetics of HbS polymer melting is investigated. There are two possible pathways connecting the initial and final states, direct ligation of molecules bound to the polymers followed by melting of ligated molecule, and melting of deoxy molecules followed by ligation of free molecules. Hence four kinetic rates describe the relaxation: two rates for CO binding (one to monomer phase Hb and one to polymer phase Hb) and two for Hb dissociation from polymers (one for CO-ligated Hb and for deoxyHb). We examine two models that gradually incorporate CO presence into the mechanism of polymer melting. The Homogeneous Model (HM) describes the melting of HbS polymers due to dilution and CO binding of HbS. We assume that the melting starts with the dissociation of monomers from the fiber ends. As a result the polymer concentration remains unchanged at the beginning of melting. The Simple Ends Model (SEM) describes melting from HbS fiber ends when melting is induced by diluting with deoxy buffer (DMM). The extended Ends Model (EEM) describes melting of HbS aggregates with dissociation of monomers from fiber ends when CO fully saturated buffer is applied. An additional (second) assumption is that the CO molecules bind only to free Hb

  10. Ground-state kinetics of bistable redox-active donor-acceptor mechanically interlocked molecules.

    PubMed

    Fahrenbach, Albert C; Bruns, Carson J; Li, Hao; Trabolsi, Ali; Coskun, Ali; Stoddart, J Fraser

    2014-02-18

    The ability to design and confer control over the kinetics of theprocesses involved in the mechanisms of artificial molecular machines is at the heart of the challenge to create ones that can carry out useful work on their environment, just as Nature is wont to do. As one of the more promising forerunners of prototypical artificial molecular machines, chemists have developed bistable redox-active donor-acceptor mechanically interlocked molecules (MIMs) over the past couple of decades. These bistable MIMs generally come in the form of [2]rotaxanes, molecular compounds that constitute a ring mechanically interlocked around a dumbbell-shaped component, or [2]catenanes, which are composed of two mechanically interlocked rings. As a result of their interlocked nature, bistable MIMs possess the inherent propensity to express controllable intramolecular, large-amplitude, and reversible motions in response to redox stimuli. In this Account, we rationalize the kinetic behavior in the ground state for a large assortment of these types of bistable MIMs, including both rotaxanes and catenanes. These structures have proven useful in a variety of applications ranging from drug delivery to molecular electronic devices. These bistable donor-acceptor MIMs can switch between two different isomeric states. The favored isomer, known as the ground-state co-conformation (GSCC) is in equilibrium with the less favored metastable state co-conformation (MSCC). The forward (kf) and backward (kb) rate constants associated with this ground-state equilibrium are intimately connected to each other through the ground-state distribution constant, KGS. Knowing the rate constants that govern the kinetics and bring about the equilibration between the MSCC and GSCC, allows researchers to understand the operation of these bistable MIMs in a device setting and apply them toward the construction of artificial molecular machines. The three biggest influences on the ground-state rate constants arise from

  11. In vitro kinetic studies on the mechanism of oxygen-dependent cellular uptake of copper radiopharmaceuticals

    NASA Astrophysics Data System (ADS)

    Holland, Jason P.; Giansiracusa, Jeffrey H.; Bell, Stephen G.; Wong, Luet-Lok; Dilworth, Jonathan R.

    2009-04-01

    The development of hypoxia-selective radiopharmaceuticals for use as therapeutic and/or imaging agents is of vital importance for both early identification and treatment of cancer and in the design of new drugs. Radiotracers based on copper for use in positron emission tomography have received great attention due to the successful application of copper(II) bis(thiosemicarbazonato) complexes, such as [60/62/64Cu(II)ATSM] and [60/62/64Cu(II)PTSM], as markers for tumour hypoxia and blood perfusion, respectively. Recent work has led to the proposal of a revised mechanism of hypoxia-selective cellular uptake and retention of [Cu(II)ATSM]. The work presented here describes non-steady-state kinetic simulations in which the reported pO2-dependent in vitro cellular uptake and retention of [64Cu(II)ATSM] in EMT6 murine carcinoma cells has been modelled by using the revised mechanistic scheme. Non-steady-state (NSS) kinetic analysis reveals that the model is in very good agreement with the reported experimental data with a root-mean-squared error of less than 6% between the simulated and experimental cellular uptake profiles. Estimated rate constants are derived for the cellular uptake and washout (k1 = 9.8 ± 0.59 × 10-4 s-1 and k2 = 2.9 ± 0.17 × 10-3 s-1), intracellular reduction (k3 = 5.2 ± 0.31 × 10-2 s-1), reoxidation (k4 = 2.2 ± 0.13 mol-1 dm3 s-1) and proton-mediated ligand dissociation (k5 = 9.0 ± 0.54 × 10-5 s-1). Previous mechanisms focused on the reduction and reoxidation steps. However, the data suggest that the origins of hypoxia-selective retention may reside with the stability of the copper(I) anion with respect to protonation and ligand dissociation. In vitro kinetic studies using the nicotimamide adenine dinucleotide (NADH)-dependent ferredoxin reductase enzyme PuR isolated from the bacterium Rhodopseudomonas palustris have also been conducted. NADH turnover frequencies are found to be dependent on the structure of the ligand and the results confirm

  12. Monoamine oxidase inhibitory constituents of propolis: kinetics and mechanism of inhibition of recombinant human MAO-A and MAO-B.

    PubMed

    Chaurasiya, Narayan D; Ibrahim, Mohamed A; Muhammad, Ilias; Walker, Larry A; Tekwani, Babu L

    2014-11-18

    Propolis is the resinous material that bees gather from leaf buds, flowers and vegetables. Propolis extracts contain constituents with a broad spectra of pharmacological properties and are important ingredients of popular dietary supplements. Propolis extracts were evaluated in vitro for inhibition of recombinant human monoamine oxidase (MAO)-A and MAO-B. The dichloromethane extract of propolis showed potent inhibition of human MAO-A and MAO-B. Further fractionation identified the most active fractions as rich in flavonoids. Galangin and apigenin were identified as the principal MAO-inhibitory constituents. Inhibition of MAO-A by galangin was about 36 times more selective than MAO-B, while apigenin selectivity for MAO-A vs. MAO-B was about 1.7 fold. Apigenin inhibited MAO-B significantly more potently than galangin. Galangin and apigenin were further evaluated for kinetic characteristics and the mechanism for the enzymes' inhibition. Binding of galangin and apigenin with MAO-A and -B was not time-dependent and was reversible, as suggested by enzyme-inhibitor binding and dissociation-dialysis assay. The inhibition kinetics studies suggested that galangin and apigenin inhibited MAO-A and -B by a competitive mechanism. Presence of prominent MAO inhibitory constituents in propolis products suggests their potential for eliciting pharmacological effects that might be useful in depression or other neurological disorders. The results may also have important implications in drug-dietary supplement interactions.

  13. Insights into function, catalytic mechanism, and fold evolution of selenoprotein methionine sulfoxide reductase B1 through structural analysis.

    PubMed

    Aachmann, Finn L; Sal, Lena S; Kim, Hwa-Young; Marino, Stefano M; Gladyshev, Vadim N; Dikiy, Alexander

    2010-10-22

    Methionine sulfoxide reductases protect cells by repairing oxidatively damaged methionine residues in proteins. Here, we report the first three-dimensional structure of the mammalian selenoprotein methionine sulfoxide reductase B1 (MsrB1), determined by high resolution NMR spectroscopy. Heteronuclear multidimensional spectra yielded NMR spectral assignments for the reduced form of MsrB1 in which catalytic selenocysteine (Sec) was replaced with cysteine (Cys). MsrB1 consists of a central structured core of two β-sheets and a highly flexible, disordered N-terminal region. Analysis of pH dependence of NMR signals of catalytically relevant residues, comparison with the data for bacterial MsrBs, and NMR-based structural analysis of methionine sulfoxide (substrate) and methionine sulfone (inhibitor) binding to MsrB1 at the atomic level reveal a mechanism involving catalytic Sec(95) and resolving Cys(4) residues in catalysis. The MsrB1 structure differs from the structures of Cys-containing MsrBs in the use of distal selenenylsulfide, residues needed for catalysis, and the mode in which the active form of the enzyme is regenerated. In addition, this is the first structure of a eukaryotic zinc-containing MsrB, which highlights the structural role of this metal ion bound to four conserved Cys. We integrated this information into a structural model of evolution of MsrB superfamily.

  14. New N-Acetyltransferase Fold in the Structure and Mechanism of the Phosphonate Biosynthetic Enzyme FrbF

    SciTech Connect

    Bae, Brian; Cobb, Ryan E.; DeSieno, Matthew A.; Zhao, Huimin; Nair, Satish K.

    2015-10-15

    The enzyme FrbF from Streptomyces rubellomurinus has attracted significant attention due to its role in the biosynthesis of the antimalarial phosphonate FR-900098. The enzyme catalyzes acetyl transfer onto the hydroxamate of the FR-900098 precursors cytidine 5'-monophosphate-3-aminopropylphosphonate and cytidine 5'-monophosphate-N-hydroxy-3-aminopropylphosphonate. Despite the established function as a bona fide N-acetyltransferase, FrbF shows no sequence similarity to any member of the GCN5-like N-acetyltransferase (GNAT) superfamily. Here, we present the 2.0 {angstrom} resolution crystal structure of FrbF in complex with acetyl-CoA, which demonstrates a unique architecture that is distinct from those of canonical GNAT-like acetyltransferases. We also utilized the co-crystal structure to guide structure-function studies that identified the roles of putative active site residues in the acetyltransferase mechanism. The combined biochemical and structural analyses of FrbF provide insights into this previously uncharacterized family of N-acetyltransferases and also provide a molecular framework toward the production of novel N-acyl derivatives of FR-900098.

  15. Polymer Uncrossing and Knotting in Protein Folding, and Their Role in Minimal Folding Pathways

    PubMed Central

    Mohazab, Ali R.; Plotkin, Steven S.

    2013-01-01

    We introduce a method for calculating the extent to which chain non-crossing is important in the most efficient, optimal trajectories or pathways for a protein to fold. This involves recording all unphysical crossing events of a ghost chain, and calculating the minimal uncrossing cost that would have been required to avoid such events. A depth-first tree search algorithm is applied to find minimal transformations to fold , , , and knotted proteins. In all cases, the extra uncrossing/non-crossing distance is a small fraction of the total distance travelled by a ghost chain. Different structural classes may be distinguished by the amount of extra uncrossing distance, and the effectiveness of such discrimination is compared with other order parameters. It was seen that non-crossing distance over chain length provided the best discrimination between structural and kinetic classes. The scaling of non-crossing distance with chain length implies an inevitable crossover to entanglement-dominated folding mechanisms for sufficiently long chains. We further quantify the minimal folding pathways by collecting the sequence of uncrossing moves, which generally involve leg, loop, and elbow-like uncrossing moves, and rendering the collection of these moves over the unfolded ensemble as a multiple-transformation “alignment”. The consensus minimal pathway is constructed and shown schematically for representative cases of an , , and knotted protein. An overlap parameter is defined between pathways; we find that proteins have minimal overlap indicating diverse folding pathways, knotted proteins are highly constrained to follow a dominant pathway, and proteins are somewhere in between. Thus we have shown how topological chain constraints can induce dominant pathway mechanisms in protein folding. PMID:23365638

  16. Catalytic Mechanism of Perosamine N-Acetyltransferase Revealed by High-Resolution X-ray Crystallographic Studies and Kinetic Analyses

    SciTech Connect

    Thoden, James B.; Reinhardt, Laurie A.; Cook, Paul D.; Menden, Patrick; Cleland, W.W.; Holden, Hazel M.

    2012-09-17

    N-Acetylperosamine is an unusual dideoxysugar found in the O-antigens of some Gram-negative bacteria, including the pathogenic Escherichia coli strain O157:H7. The last step in its biosynthesis is catalyzed by PerB, an N-acetyltransferase belonging to the left-handed {beta}-helix superfamily of proteins. Here we describe a combined structural and functional investigation of PerB from Caulobacter crescentus. For this study, three structures were determined to 1.0 {angstrom} resolution or better: the enzyme in complex with CoA and GDP-perosamine, the protein with bound CoA and GDP-N-acetylperosamine, and the enzyme containing a tetrahedral transition state mimic bound in the active site. Each subunit of the trimeric enzyme folds into two distinct regions. The N-terminal domain is globular and dominated by a six-stranded mainly parallel {beta}-sheet. It provides most of the interactions between the protein and GDP-perosamine. The C-terminal domain consists of a left-handed {beta}-helix, which has nearly seven turns. This region provides the scaffold for CoA binding. On the basis of these high-resolution structures, site-directed mutant proteins were constructed to test the roles of His 141 and Asp 142 in the catalytic mechanism. Kinetic data and pH-rate profiles are indicative of His 141 serving as a general base. In addition, the backbone amide group of Gly 159 provides an oxyanion hole for stabilization of the tetrahedral transition state. The pH-rate profiles are also consistent with the GDP-linked amino sugar substrate entering the active site in its unprotonated form. Finally, for this investigation, we show that PerB can accept GDP-3-deoxyperosamine as an alternative substrate, thus representing the production of a novel trideoxysugar.

  17. Kinetic Mechanism and Rate-Limiting Steps of Focal Adhesion Kinase-1

    SciTech Connect

    Schneck, Jessica L.; Briand, Jacques; Chen, Stephanie; Lehr, Ruth; McDevitt, Patrick; Zhao, Baoguang; Smallwood, Angela; Concha, Nestor; Oza, Khyati; Kirkpatrick, Robert; Yan, Kang; Villa, James P.; Meek, Thomas D.; Thrall, Sara H.

    2010-12-07

    Steady-state kinetic analysis of focal adhesion kinase-1 (FAK1) was performed using radiometric measurement of phosphorylation of a synthetic peptide substrate (Ac-RRRRRRSETDDYAEIID-NH{sub 2}, FAK-tide) which corresponds to the sequence of an autophosphorylation site in FAK1. Initial velocity studies were consistent with a sequential kinetic mechanism, for which apparent kinetic values k{sub cat} (0.052 {+-} 0.001 s{sup -1}), K{sub MgATP} (1.2 {+-} 0.1 {micro}M), K{sub iMgATP} (1.3 {+-} 0.2 {micro}M), K{sub FAK-tide} (5.6 {+-} 0.4 {micro}M), and K{sub iFAK-tide} (6.1 {+-} 1.1 {micro}M) were obtained. Product and dead-end inhibition data indicated that enzymatic phosphorylation of FAK-tide by FAK1 was best described by a random bi bi kinetic mechanism, for which both E-MgADP-FAK-tide and E-MgATP-P-FAK-tide dead-end complexes form. FAK1 catalyzed the {beta}{gamma}-bridge:{beta}-nonbridge positional oxygen exchange of [{gamma}-{sup 18}O{sub 4}]ATP in the presence of 1 mM [{gamma}-{sup 18}O{sub 4}]ATP and 1.5 mM FAK-tide with a progressive time course which was commensurate with catalysis, resulting in a rate of exchange to catalysis of k{sub x}/k{sub cat} = 0.14 {+-} 0.01. These results indicate that phosphoryl transfer is reversible and that a slow kinetic step follows formation of the E-MgADP-P-FAK-tide complex. Further kinetic studies performed in the presence of the microscopic viscosogen sucrose revealed that solvent viscosity had no effect on k{sub cat}/K{sub FAK-tide}, while k{sub cat} and k{sub cat}/K{sub MgATP} were both decreased linearly at increasing solvent viscosity. Crystallographic characterization of inactive versus AMP-PNP-liganded structures of FAK1 showed that a large conformational motion of the activation loop upon ATP binding may be an essential step during catalysis and would explain the viscosity effect observed on k{sub cat}/K{sub m} for MgATP but not on k{sub cat}/K{sub m} for FAK-tide. From the positional isotope exchange, viscosity, and

  18. A Detailed Chemical Kinetic Reaction Mechanism for Oxidation of Four Small Alkyl Esters in Laminar Premixed Flames

    SciTech Connect

    Westbrook, C K; Pitz, W J; Westmoreland, P R; Dryer, F L; Chaos, M; Osswald, P; Kohse-Hoinghaus, K; Cool, T A; Wang, J; Yang, B; Hansen, N; Kasper, T

    2008-02-08

    A detailed chemical kinetic reaction mechanism has been developed for a group of four small alkyl ester fuels, consisting of methyl formate, methyl acetate, ethyl formate and ethyl acetate. This mechanism is validated by comparisons between computed results and recently measured intermediate species mole fractions in fuel-rich, low pressure, premixed laminar flames. The model development employs a principle of similarity of functional groups in constraining the H atom abstraction and unimolecular decomposition reactions in each of these fuels. As a result, the reaction mechanism and formalism for mechanism development are suitable for extension to larger oxygenated hydrocarbon fuels, together with an improved kinetic understanding of the structure and chemical kinetics of alkyl ester fuels that can be extended to biodiesel fuels. Variations in concentrations of intermediate species levels in these flames are traced to differences in the molecular structure of the fuel molecules.

  19. Mechanical study of the Chartreuse Fold-and-Thrust Belt: relationships between fluids overpressure and decollement within the Toarcian source-rock

    NASA Astrophysics Data System (ADS)

    Berthelon, Josselin; Sassi, William; Burov, Evgueni

    2016-04-01

    Many source-rocks are shale and constitute potential detachment levels in Fold-and-Thrust Belts (FTB): the toarcian Schistes-Cartons in the French Chartreuse FTB for example. Their mechanical properties can change during their burial and thermal maturation, as for example when large amount of hydrocarbon fluids are generated. A structural reconstruction of the Chartreuse FTB geo-history places the Toarcian Formation as the major decollement horizon. In this work, a mechanical analysis integrating the fluids overpressuring development is proposed to discuss on the validity of the structural interpretation. At first, an analogue of the Chartreuse Toarcian Fm, the albanian Posidonia Schist, is documented as it can provide insights on its initial properties and composition of its kerogen content. Laboratory characterisation documents the vertical evolution of the mineralogical, geochemical and mechanical parameters of this potential decollement layer. These physical parameters (i.e. Total Organic Carbon (TOC), porosity/permeability relationship, friction coefficient) are used to address overpressure buildup in the frontal part of the Chartreuse FTB with TEMISFlow Arctem Basin modelling approach (Faille et al, 2014) and the structural emplacement of the Chartreuse thrust units using the FLAMAR thermo-mechanical model (Burov et al, 2014). The hydro-mechanical modeling results highlight the calendar, distribution and magnitude of the overpressure that developed within the source-rock in the footwall of a simple fault-bend fold structure localized in the frontal part of the Chartreuse FTB. Several key geological conditions are required to create an overpressure able to fracture the shale-rocks and induce a significant change in the rheological behaviour: high TOC, low permeability, favourable structural evolution. These models highlight the importance of modeling the impact of a diffuse natural hydraulic fracturing to explain fluids propagation toward the foreland within

  20. Kinetic mechanism for DNA unwinding by multiple molecules of Dda helicase aligned on DNA.

    PubMed

    Eoff, Robert L; Raney, Kevin D

    2010-06-01

    Helicases catalyze the separation of double-stranded nucleic acids to form single-stranded intermediates. Using transient state kinetic methods, we have determined the kinetic properties of DNA unwinding under conditions that favor a monomeric form of the Dda helicase as well as conditions that allow multiple molecules to function on the same substrate. Multiple helicase molecules can align like a train on the DNA track. The number of base pairs unwound in a single binding event for Dda is increased from approximately 19 bp for the monomeric form to approximately 64 bp when as many as four Dda molecules are aligned on the same substrate, while the kinetic step size (3.2 +/- 0.7 bp) and unwinding rate (242 +/- 25 bp/s) appear to be independent of the number of Dda molecules present on a given substrate. The data support a model in which the helicase molecules bound to the same substrate move along the DNA track independently during DNA unwinding. The observed increase in processivity arises from the increased probability that at least one of the helicases will completely unwind the DNA prior to dissociation. These results are in contrast to previous reports in which multiple Dda molecules on the same track greatly enhanced the rate and amplitude for displacement of protein blocks on the track. Therefore, only when the progress of the lead molecule in the train is impeded by some type of block, such as a protein bound to DNA, do the trailing molecules interact with the lead molecule to overcome the block. The fact that trailing helicase molecules have little impact on the lead molecule in the train during routine DNA unwinding suggests that the trailing molecules are moving at rates similar to that of the lead molecule. This result implicates a step in the translocation mechanism as contributing greatly to the overall rate-limiting step for unwinding of duplex DNA.

  1. Sandbox modelling of sequential thrusting in a mechanically two-layered system and its implications in fold-and-thrust belts

    NASA Astrophysics Data System (ADS)

    Saha, Puspendu; Bose, Santanu; Mandal, Nibir

    2016-10-01

    Many fold-and-thrust belts display multi-storied thrust sequences, characterizing a composite architecture of the thrust wedges. Despite dramatic progress in sandbox modelling over the last three decades, our understanding of such composite thrust-wedge mechanics is limited and demands a re-visit to the problem of sequential thrusting in mechanically layered systems. This study offers a new approach to sandbox modelling, designed with a two-layered sandpack simulating a mechanically weak Coulomb layer, resting coherently upon a stronger Coulomb layer. Our experimental models reproduce strikingly similar styles of the multi-storied frontal thrust sequences observed in natural fold-and- thrust belts. The upper weak horizon undergoes sequential thrusting at a high spatial frequency, forming numerous, closely spaced frontal thrusts, whereas the lower strong horizon produces widely spaced thrusts with progressive horizontal shortening. This contrasting thrust progression behaviour gives rise to composite thrust architecture in the layered sandpack. We show the evolution of such composite thrust sequences as a function of frictional strength (μb) at the basal detachment and thickness ratio (Tr) between the weak and strong layers. For any given values of Tr and μb, the two thrust sequences progress at different rates; the closely-spaced, upper thrust sequence advances forelandward at a faster rate than the widely-spaced, lower thrust sequence. Basal friction (μb) has little effects on the vergence of thrusts in the upper weak layer; they verge always towards foreland, irrespective of Tr values. But, the lower strong layer develops back-vergent thrusts when μb is low (∼0.36). In our experiments, closely spaced thrusts in the upper sequence experience intense reactivation due to their interaction with widely spaced thrusts in the lower sequence. The interaction eventually affects the wedge topography, leading to two distinct parts: inner and outer wedges

  2. Kinetics and fracture resistance of lithiated silicon nanostructure pairs controlled by their mechanical interaction

    DOE PAGES

    Lee, Seok Woo; Lee, Hyun -Wook; Ryu, Ill; ...

    2015-06-26

    Following an explosion of studies of silicon as a negative electrode for Li-ion batteries, the anomalous volumetric changes and fracture of lithiated single Si particles have attracted significant attention in various fields, including mechanics. However, in real batteries, lithiation occurs simultaneously in clusters of Si in a confined medium. Hence, understanding how the individual Si structures interact during lithiation in a closed space is necessary. Here, we demonstrate physical and mechanical interactions of swelling Si structures during lithiation using well-defined Si nanopillar pairs. Ex situ SEM and in situ TEM studies reveal that compressive stresses change the reaction kinetics somore » that preferential lithiation occurs at free surfaces when the pillars are mechanically clamped. Such mechanical interactions enhance the fracture resistance of lithiated Si by lessening the tensile stress concentrations in Si structures. Lastly, this study will contribute to improved design of Si structures at the electrode level for high-performance Li-ion batteries.« less

  3. Kinetics and fracture resistance of lithiated silicon nanostructure pairs controlled by their mechanical interaction

    SciTech Connect

    Lee, Seok Woo; Lee, Hyun-Wook; Ryu, Ill; Nix, William D.; Gao, Huajian; Cui, Yi; /Stanford U., Materials Sci. Dept. /SLAC

    2015-06-01

    Following an explosion of studies of silicon as a negative electrode for Li-ion batteries, the anomalous volumetric changes and fracture of lithiated single Si particles have attracted significant attention in various fields, including mechanics. However, in real batteries, lithiation occurs simultaneously in clusters of Si in a confined medium. Hence, understanding how the individual Si structures interact during lithiation in a closed space is necessary. Herein, we demonstrate physical/mechanical interactions of swelling Si structures during lithiation using well-defined Si nanopillar pairs. Ex situ SEM and in situ TEM studies reveal that compressive stresses change the reaction kinetics so that preferential lithiation occurs at free surfaces when the pillars are mechanically clamped. Such mechanical interactions enhance the fracture resistance of This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering, under Contract No. DE-AC02-76SF00515. SLAC-PUB-16300 2 lithiated Si by lessening the tensile stress concentrations in Si structures. This study will contribute to improved design of Si structures at the electrode level for high performance Li-ion batteries.

  4. Kinetics and mechanism of auto- and copper-catalyzed oxidation of 1,4-naphthohydroquinone.

    PubMed

    Yuan, Xiu; Miller, Christopher J; Pham, A Ninh; Waite, T David

    2014-06-01

    Although quinones represent a class of organic compounds that may exert toxic effects both in vitro and in vivo, the molecular mechanisms involved in quinone species toxicity are still largely unknown, especially in the presence of transition metals, which may both induce the transformation of the various quinone species and result in generation of harmful reactive oxygen species. In this study, the oxidation of 1,4-naphthohydroquinone (NH2Q) in the absence and presence of nanomolar concentrations of Cu(II) in 10 mM NaCl solution over a pH range of 6.5-7.5 has been investigated, with detailed kinetic models developed to describe the predominant mechanisms operative in these systems. In the absence of copper, the apparent oxidation rate of NH2Q increased with increasing pH and initial NH2Q concentration, with concomitant oxygen consumption and peroxide generation. The doubly dissociated species, NQ(2-), has been shown to be the reactive species with regard to the one-electron oxidation by O2 and comproportionation with the quinone species, both generating the semiquinone radical (NSQ(·-)). The oxidation of NSQ(·-) by O2 is shown to be the most important pathway for superoxide (O2(·-)) generation with a high intrinsic rate constant of 1.0×10(8)M(-1)s(-1). Both NSQ(·-) and O2(·-) served as chain-propagating species in the autoxidation of NH2Q. Cu(II) is capable of catalyzing the oxidation of NH2Q in the presence of O2 with the oxidation also accelerated by increasing the pH. Both the uncharged (NH2Q(0)) and the mono-anionic (NHQ(-)) species were found to be the kinetically active forms, reducing Cu(II) with an intrinsic rate constant of 4.0×10(4) and 1.2×10(7)M(-1)s(-1), respectively. The presence of O2 facilitated the catalytic role of Cu(II) by rapidly regenerating Cu(II) via continuous oxidation of Cu(I) and also by efficient removal of NSQ(·-) resulting in the generation of O2(·-). The half-cell reduction potentials of various redox couples at neutral p

  5. The mechanism and kinetic model on the OH-initiated degradation of acetofenate in the atmosphere

    NASA Astrophysics Data System (ADS)

    Kang, Lingyan; Sun, Xiaomin; Zhang, Chenxi; Zhang, Xue; Chen, Jianmin

    2015-02-01

    As an analog of DDT, acetofenate (AF), one of the organochlorine pesticides, is widely used in agricultural and mosquito sprayings. In this paper, the main reaction mechanism of AF with the OH radical and ensuing reactions are researched, including the OH-initiated reaction, oxidation reaction in the presence of O2, bimolecular reaction of AF-OH-O2 with NO/H2O, bond cleavage of aromatic ring and C7-O bond, and dehydrogenation. Among all the reaction pathways, the main products are obtained via C2-C7/C7-O bond cleavage, C3-C4/C4-C5 bond cleavage of aromatic ring, and the generation of ketene and aldehyde. The kinetic model is constructed based on the rate constants of element reactions over a temperature range of 200-600 K, which are calculated with the transition state theory method and fitted with the Arrhenius formulas. According to the kinetic model, the atmospheric lifetime of AF, is 37 days, compared to OH radical.

  6. Cr(VI) Adsorption on Red Mud Modified by Lanthanum: Performance, Kinetics and Mechanisms.

    PubMed

    Cui, You-Wei; Li, Jie; Du, Zhao-Fu; Peng, Yong-Zhen

    Water pollution caused by the highly toxic metal hexavalent chromium (Cr(VI)) creates significant human health and ecological risks. In this study, a novel adsorbent was used to treat Cr(VI)-containing wastewater; the adsorbent was prepared using red mud (RM) generated from the alumina production industry and the rare earth element lanthanum. This study explored adsorption performance, kinetics, and mechanisms. Results showed that the adsorption kinetics of the RM modified by lanthanum (La-RM), followed the pseudo-second-order model, with a rapid adsorption rate. Cr(VI) adsorption was positively associated with the absorbent dose, pH, temperature, and initial Cr(VI) concentration; coexisting anions had little impact. The maximum Cr(VI) adsorption capacity was 17.35 mg/g. Cr(VI) adsorption on La-RM was a mono-layer adsorption pattern, following the Langmuir isotherm model. Thermodynamic parameters showed the adsorption was spontaneous and endothermic. The adsorption of Cr(VI) on La-RM occurred as a result of LaOCl formation on the RM surface, which in turn further reacted with Cr(VI) in the wastewater. This study highlighted a method for converting industrial waste into a valuable material for wastewater treatment. The novel absorbent could be used as a potential adsorbent for treating Cr(VI)-contaminating wastewater, due to its cost-effectiveness and high adsorption capability.

  7. Cr(VI) Adsorption on Red Mud Modified by Lanthanum: Performance, Kinetics and Mechanisms

    PubMed Central

    Cui, You-Wei; Li, Jie; Du, Zhao-Fu; Peng, Yong-Zhen

    2016-01-01

    Water pollution caused by the highly toxic metal hexavalent chromium (Cr(VI)) creates significant human health and ecological risks. In this study, a novel adsorbent was used to treat Cr(VI)-containing wastewater; the adsorbent was prepared using red mud (RM) generated from the alumina production industry and the rare earth element lanthanum. This study explored adsorption performance, kinetics, and mechanisms. Results showed that the adsorption kinetics of the RM modified by lanthanum (La-RM), followed the pseudo-second-order model, with a rapid adsorption rate. Cr(VI) adsorption was positively associated with the absorbent dose, pH, temperature, and initial Cr(VI) concentration; coexisting anions had little impact. The maximum Cr(VI) adsorption capacity was 17.35 mg/g. Cr(VI) adsorption on La-RM was a mono-layer adsorption pattern, following the Langmuir isotherm model. Thermodynamic parameters showed the adsorption was spontaneous and endothermic. The adsorption of Cr(VI) on La-RM occurred as a result of LaOCl formation on the RM surface, which in turn further reacted with Cr(VI) in the wastewater. This study highlighted a method for converting industrial waste into a valuable material for wastewater treatment. The novel absorbent could be used as a potential adsorbent for treating Cr(VI)-contaminating wastewater, due to its cost-effectiveness and high adsorption capability. PMID:27658113

  8. Phenol adsorption on surface-functionalized iron oxide nanoparticles: modeling of the kinetics, isotherm, and mechanism

    NASA Astrophysics Data System (ADS)

    Yoon, Soon Uk; Mahanty, Biswanath; Ha, Hun Moon; Kim, Chang Gyun

    2016-06-01

    Phenol adsorption from aqueous solution was carried out using uncoated and methyl acrylic acid (MAA)-coated iron oxide nanoparticles (NPs), having size <10 nm, as adsorbents. Batch adsorption studies revealed that the phenol removal efficiency of MAA-coated NPs (950 mg g-1) is significantly higher than that of uncoated NPs (550 mg g-1) under neutral to acidic conditions. However, this improvement disappears above pH 9. The adsorption data under optimized conditions (pH 7) were modeled with pseudo-first- and pseudo-second-order kinetics and subjected to Freundlich and Langmuir isotherms. The analysis determined that pseudo-second-order kinetics and the Freundlich model are appropriate for both uncoated and MAA-coated NPs (all R 2 > 0.98). X-ray photoelectron spectroscopy analysis of pristine and phenol-adsorbed NPs revealed core-level binding energy and charge for Fe(2 s) and O(1 s) on the NP surfaces. The calculations suggest that phenol adsorption onto MAA-coated NPs is a charge transfer process, where the adsorbate (phenol) acts as an electron donor and the NP surface (Fe, O) as an electron acceptor. However, a physisorption process appears to be the relevant mechanism for uncoated NPs.

  9. Effect of ultrasonic pretreatment on kinetics of gelatin hydrolysis by collagenase and its mechanism.

    PubMed

    Yu, Zhi-Long; Zeng, Wei-Cai; Zhang, Wen-Hua; Liao, Xue-Pin; Shi, Bi

    2016-03-01

    Gelatin is a mixture of soluble proteins prepared by partial hydrolysis of native collagen. Gelatin can be enzymatically hydrolyzed to produce bioactive hydrolysates. However, the preparation of gelatin peptide with expected activity is usually a time-consuming process. The production efficiency of gelatin hydrolysates needs to be improved. In present work, effect of ultrasonic pretreatment on kinetic parameters of gelatin hydrolysis by collagenase was investigated based on an established kinetic model. With ultrasonic pretreatment, reaction rate constant and enzyme inactivation constant were increased by 27.5% and 27.8%, respectively. Meanwhile, hydrolysis activation energy and enzyme inactivation energy were reduced by 36.3% and 43.0%, respectively. In order to explore its possible mechanism, influence of sonication on structural properties of gelatin was determined using atomic force microscopy, particle size analyzer, fluorescence spectroscopy, protein solubility test and Fourier transform infrared spectroscopy. Moreover, hydrogen peroxide was used as a positive control for potential sonochemical effect. It was found that reduction of gelatin particle size was mainly caused by physical effect of ultrasound. Increased solubility and variation in β-sheet and random coil elements of gelatin were due to sonochemical effect. Both physical and chemical effects of sonication contributed to the change in α-helix and β-turn structures. The current results suggest that ultrasound can be potentially applied to stimulate the production efficiency of gelatin peptides, mainly due to its effects on modification of protein structures.

  10. Kinetic studies on photolysis-induced gelation of sickle cell hemoglobin suggest a new mechanism

    SciTech Connect

    Ferrone, F.A.; Hofrichter, J.; Sunshine, H.R.; Eaton, W.A.

    1980-10-01

    The kinetics of deoxyhemoglobin S gelation have been investigated using photolytic dissociation of the carbon monoxide complex to initiate the process. Measurements over a wide range of times, 10/sup -3/ -10/sup 4/s, show that both the concentration dependence of the tenth-time (i.e., the time required to complete one-tenth the reaction) and the time dependence of the process decrease as gelation speeds up. In slowly gelling samples, where single domains of polymers are formed in the small sample volumes employed with this technique (1 to 2 x 10/sup -9/ cm/sup 3/), there is a marked increase in the variability of the tenth-times. These results are explained by a mechanism in which gelation is initiated by homogeneous nucleation of polymers in the bulk solution phase, followed by heterogeneous nucleation on the surface of existing polymers. At the lowest concentrations, homogeneous nucleation is so improbable that stochastic behavior is observed in the small sample volumes, and heterogeneous nucleation is the dominant pathway for polymer formation, thereby accounting for the high time dependence. At the highest concentrations homogeneous nucleation becomes much more probable, and the time dependence decreases. The decrease in concentration dependence of the tenth-time with increasing concentration results from a decrease in size of both the homogeneous and heterogeneous critical nuclei. The model rationalizes the major observations on the kinetics of gelation of deoxyhemoglobin S, and is readily testable by further experiments.

  11. Kinetics and mechanism of the oxidation of arsine by halide complexes of copper(II)

    SciTech Connect

    Dorfman, Y.A.; Abdreimova, R.R.; Emel'yanova, V.S.; Kel'man, I.V.; Polimbetova, G.S.

    1985-11-01

    This paper studies the kinetics of the oxidation of arsine by copper (II) halides. It is shown that within the investigated region of concentrations of the components of the system CuX/sub 2/-HX-LiX-H/sub 2/O, /SUB C/ the oxidation of AsH/sub 3/ proceeds to As(O). First order with respect to /SUB Cu/ X/sub 2/ is observed; the order with respect to C /SUB As/ H/sub 3/ is close to first. With regard to activity in the reaction with arsine, copper(II) halides are distributed in the series. CuCl /SUB 3aq/ -kinetic activity proved to be directly correlated with the decrease in the negative charge of the halogen and the positive charge of arsine, leading to activation of the AsH/sub 3/ molecule. A mechanism of the reaction is proposed.

  12. Degradation of oxcarbazepine by UV-activated persulfate oxidation: kinetics, mechanisms, and pathways.

    PubMed

    Bu, Lingjun; Zhou, Shiqing; Shi, Zhou; Deng, Lin; Li, Guangchao; Yi, Qihang; Gao, Naiyun

    2016-02-01

    The degradation kinetics and mechanism of the antiepileptic drug oxcarbazepine (OXC) by UV-activated persulfate oxidation were investigated in this study. Results showed that UV/persulfate (UV/PS) process appeared to be more effective in degrading OXC than UV or PS alone. The OXC degradation exhibited a pseudo-first order kinetics pattern and the degradation rate constants (k obs) were affected by initial OXC concentration, PS dosage, initial pH, and humic acid concentration to different degrees. It was found that low initial OXC concentration, high persulfate dosage, and initial pH enhanced the OXC degradation. Additionally, the presence of humic acid in the solution could greatly inhibit the degradation of OXC. Moreover, hydroxyl radical (OH•) and sulfate radical (SO4 (-)••) were identified to be responsible for OXC degradation and SO4 (-)• made the predominant contribution in this study. Finally, major intermediate products were identified and a preliminary degradation pathway was proposed. Results demonstrated that UV/PS system is a potential technology to control the water pollution caused by emerging contaminants such as OXC.

  13. Kinetics and mechanism of the reaction of sodium azide with hypochlorite in aqueous solution.

    PubMed

    Betterton, Eric A; Lowry, Joe; Ingamells, Robin; Venner, Brad

    2010-10-15

    Production of toxic sodium azide (NaN(3)) surged worldwide over the past two decades to meet the demand for automobile air bag inflator propellant. Industrial activity and the return of millions of inflators to automobile recycling facilities are leading to increasing release of NaN(3) to the environment so there is considerable interest in learning more about its environmental fate. Water soluble NaN(3) could conceivably be found in drinking water supplies so here we describe the kinetics and mechanism of the reaction of azide with hypochlorite, which is often used in water treatment plants. The reaction stoichiometry is: HOCl + 2N(3)(-) = 3N(2) + Cl(-) + OH(-), and proceeds by a key intermediate chlorine azide, ClN(3), which subsequently decomposes by reaction with a second azide molecule in the rate determining step: ClN(3) + N(3)(-) --> 3N(2) + Cl(-) (k = 0.52+/-0.04 M(-1) s(-1), 25 degrees C, mu = 0.1 M). We estimate that the half-life of azide would be approximately 15 s at the point of chlorination in a water treatment plant and approximately 24 days at some point downstream where only residual chlorine remains. Hypochlorite is not recommended for treatment of concentrated azide waste due to formation of the toxic chlorine azide intermediate under acidic conditions and the slow kinetics under basic conditions.

  14. How do chaperonins fold protein?

    PubMed Central

    Motojima, Fumihiro

    2015-01-01

    Protein folding is a biological process that is essential for the proper functioning of proteins in all living organisms. In cells, many proteins require the assistance of molecular chaperones for their folding. Chaperonins belong to a class of molecular chaperones that have been extensively studied. However, the mechanism by which a chaperonin mediates the folding of proteins is still controversial. Denatured proteins are folded in the closed chaperonin cage, leading to the assumption that denatured proteins are completely encapsulated inside the chaperonin cage. In contrast to the assumption, we recently found that denatured protein interacts with hydrophobic residues at the subunit interfaces of the chaperonin, and partially protrude out of the cage. In this review, we will explain our recent results and introduce our model for the mechanism by which chaperonins accelerate protein folding, in view of recent findings. PMID:27493521

  15. Analysis of 12C+12C Elastic and Inelastic Scatterings in the Framework of the Cluster Double Folding Model and Coupled-Channels Mechanism

    NASA Astrophysics Data System (ADS)

    Hassanain, M. A.

    2011-08-01

    A double folding cluster (DFC) model is proposed for the analysis of (12) C+(12) C elastic and inelastic scatterings. The DFC procedure is performed using the alpha-clusters structure of (12) C nucleus. Angular distributions of the (12) C+(12) C elastic and inelastic scatterings in the energy range 70.7-126 MeV were analyzed using the derived DFC potentials in the framework of the coupled-channels (CC) mechanism. Successful descriptions of the data are obtained over the full measured angular range without the need to normalize the DFC potentials. Furthermore, the deduced deformation length and the quadrupole deformation parameter are quite consistent with the corresponding electromagnetic measurements.

  16. Defect thermodynamics and kinetics in thin strained ferroelectric films: The interplay of possible mechanisms

    NASA Astrophysics Data System (ADS)

    Morozovska, Anna N.; Eliseev, Eugene A.; Krishnan, P. S. Sankara Rama; Tselev, Alexander; Strelkov, Evgheny; Borisevich, Albina; Varenyk, Olexander V.; Morozovsky, Nicola V.; Munroe, Paul; Kalinin, Sergei V.; Nagarajan, Valanoor

    2014-02-01

    We present a theoretical description of the influence of misfit strain on mobile defects dynamics in thin strained ferroelectric films. Self-consistent solutions obtained by coupling the Poisson's equation for electric potential with continuity equations for mobile donor and electron concentrations and time-dependent Landau-Ginzburg-Devonshire equations reveal that the Vegard mechanism (chemical pressure) leads to the redistribution of both charged and electro-neutral defects in order to decrease the effective stress in the film. Internal electric fields, both built-in and depolarization ones, lead to a strong accumulation of screening space charges (charged defects and electrons) near the film interfaces. Importantly, the corresponding screening length is governed by the misfit strain and Vegard coefficient. Mobile defects dynamics, kinetics of polarization, and electric current reversal are defined by the complex interplay between the donor, electron and phonon relaxation times, misfit strain, finite size effect, and Vegard stresses.

  17. Theoretical investigation of the mechanism and kinetics for HCO + HCN ⇄ HCHO + CN

    NASA Astrophysics Data System (ADS)

    Wen, Lin Feng; Yan, Wang; Shao, Wen Zhang; Xian, Yong Pang

    1997-02-01

    The mechanism and kinetics for HCO + HCN ⇄ HCNO + CN have been studied theoretically. The potential energy profile along the intrinsic reaction coordinate (IRC) has been obtained at ab initio QCISD/6-31G ∗∗//UHF/6-31G ∗∗ and CCSD/6-31G ∗∗//UHF/6-31G ∗∗ levels. The forward activation barriers are about 136.45 adn 140.94 kJ mol -1 at these levels, respectively, and the reverse barriers are 2.71 and 1.26 kJ mol -1, respectively. The canonical rate constants for the forward and reverse reactions have been calculated by using statistical theory.

  18. Microscopic Mechanism and Kinetics of Ice Formation at Complex Interfaces: Zooming in on Kaolinite.

    PubMed

    Sosso, Gabriele C; Li, Tianshu; Donadio, Davide; Tribello, Gareth A; Michaelides, Angelos

    2016-07-07

    Most ice in nature forms because of impurities which boost the exceedingly low nucleation rate of pure supercooled water. However, the microscopic details of ice nucleation on these substances remain largely unknown. Here, we have unraveled the molecular mechanism and the kinetics of ice formation on kaolinite, a clay mineral playing a key role in climate science. We find that the formation of ice at strong supercooling in the presence of this clay is about 20 orders of magnitude faster than homogeneous freezing. The critical nucleus is substantially smaller than that found for homogeneous nucleation and, in contrast to the predictions of classical nucleation theory (CNT), it has a strong two-dimensional character. Nonetheless, we show that CNT describes correctly the formation of ice at this complex interface. Kaolinite also promotes the exclusive nucleation of hexagonal ice, as opposed to homogeneous freezing where a mixture of cubic and hexagonal polytypes is observed.

  19. The kinetics and mechanism of dissociation of metal carbonyls in high infrared laser fields

    NASA Astrophysics Data System (ADS)

    Langsam, Y.; Ronn, A. M.

    1981-01-01

    The method of laser induced dielectric breakdown has been used to study the dissociation of three metal carbonyls. Following non-resonant excitation by a TEA CO 2 laser, amorphous micro-metallic particles are deposited. The identity of the various species within a laser induced plasma for a series of related reactant molecules, has been determined using infrared and visible real time fluorescence techniques. Based upon the energetics of dissociation and the relative magnitudes of the rates of activation and deactivation for various collision partners of the plasma fluorescence, an energy transfer map as well as probable mechanisms are proposed. The kinetics of a variety of chemical reactions under plasma conditions are discussed in terms of elementary collision theory. It is shown that the internal vibration manifold of the metal carbonyls is equilibrated prior to the dissociation in agreement with the majority of laser induced multiphoton dissociation experiments.

  20. Microscopic Mechanism and Kinetics of Ice Formation at Complex Interfaces: Zooming in on Kaolinite

    PubMed Central

    2016-01-01

    Most ice in nature forms because of impurities which boost the exceedingly low nucleation rate of pure supercooled water. However, the microscopic details of ice nucleation on these substances remain largely unknown. Here, we have unraveled the molecular mechanism and the kinetics of ice formation on kaolinite, a clay mineral playing a key role in climate science. We find that the formation of ice at strong supercooling in the presence of this clay is about 20 orders of magnitude faster than homogeneous freezing. The critical nucleus is substantially smaller than that found for homogeneous nucleation and, in contrast to the predictions of classical nucleation theory (CNT), it has a strong two-dimensional character. Nonetheless, we show that CNT describes correctly the formation of ice at this complex interface. Kaolinite also promotes the exclusive nucleation of hexagonal ice, as opposed to homogeneous freezing where a mixture of cubic and hexagonal polytypes is observed. PMID:27269363

  1. Study on the Kinetics of Aluminum Removal from Liquid Silicon to Slag with Mechanical Stirring

    NASA Astrophysics Data System (ADS)

    Lee, Jaewoo; White, Jesse F.; Hildal, Kjetil; Sichen, Du

    2016-12-01

    The kinetics of aluminum removal from silicon melt to CaO-SiO2-Al2O3 slag was studied. A recently designed experimental setup using mechanical stirring was employed to focus the study on the chemical reaction. The slag and metal were found to reach chemical equilibrium in 300 seconds. A simple model could reproduce the experimental data satisfactorily. Both the experimental results and the model prediction further confirmed that the process was controlled by the chemical reaction, since the reaction rate constant was found to be independent of the amount of slag and the initial slag composition. The experimental data at equilibrium were compared with the model calculations. The discrepancy between the model calculations and the experimental data strongly suggests the need for careful thermodynamic measurements.

  2. Kinetic Mechanism of the Dechlorinating Flavin-dependent Monooxygenase HadA.

    PubMed

    Pimviriyakul, Panu; Thotsaporn, Kittisak; Sucharitakul, Jeerus; Chaiyen, Pimchai

    2017-03-24

    The accumulation of chlorophenols (CPs) in the environment, due to their wide use as agrochemicals, has become a serious environmental problem. These organic halides can be degraded by aerobic microorganisms, where the initial steps of various biodegradation pathways include an oxidative dechlorinating process in which chloride is replaced by a hydroxyl substituent. Harnessing these dechlorinating processes could provide an opportunity for environmental remediation, but detailed catalytic mechanisms for these enzymes are not yet known. To close this gap, we now report transient kinetics and product analysis of the dechlorinating flavin-dependent monooxygenase, HadA, from the aerobic organism Ralstonia pickettii DTP0602, identifying several mechanistic properties that differ from other enzymes in the same class. We first overexpressed and purified HadA to homogeneity. Analyses of the products from single and multiple turnover reactions demonstrated that HadA prefers 4-CP and 2-CP over CPs with multiple substituents. Stopped-flow and rapid-quench flow experiments of HadA with 4-CP show the involvement of specific intermediates (C4a-hydroperoxy-FAD and C4a-hydroxy-FAD) in the reaction, define rate constants and the order of substrate binding, and demonstrate that the hydroxylation step occurs prior to chloride elimination. The data also identify the non-productive and productive paths of the HadA reactions and demonstrate that product formation is the rate-limiting step. This is the first elucidation of the kinetic mechanism of a two-component flavin-dependent monooxygenase that can catalyze oxidative dechlorination of various CPs, and as such it will serve as the basis for future investigation of enzyme variants that will be useful for applications in detoxifying chemicals hazardous to human health.

  3. Light induced oxidative water splitting in photosynthesis: energetics, kinetics and mechanism.

    PubMed

    Renger, Gernot

    2011-01-01

    The essential steps of photosynthetic water splitting take place in Photosystem II (PSII) and comprise three different reaction sequences: (i) light induced formation of the radical pair P680(+)Q(A)(-), (ii) P680(+) driven oxidative water splitting into O(2) and four protons, and (iii) two step plastoquinone reduction to plastoquinol by Q(A)(-). This mini-review briefly summarizes our state of knowledge on energetics, kinetics and mechanism of oxidative water splitting. Essential features of the two types of reactions involved are described: (a) P680(+) reduction by the redox active tyrosine Y(z) and (b) sequence of oxidation steps induced by Y(z)(ox) in the water-oxidizing complex (WOC). The rate of the former reaction is limited by the non-adiabatic electron transfer (NET) step and the multi-phase kinetics shown to originate from a sequence of relaxation processes. In marked contrast, the rate of the stepwise oxidation by Y(z)(ox) of the WOC up to the redox level S(3) is not limited by NET but by trigger reactions which probably comprise proton shifts and/or conformational changes. The overall rate of the final reaction sequence leading to formation and release of O(2) is assumed to be limited by the electron transfer step from the S(3) state of WOC to Y(z)(ox) due to involvement of an endergonic redox equilibrium. Currently discussed controversial ideas on possible pathways are briefly outlined. Several crucial points of the mechanism of oxidative water splitting, like O-O bond formation, role of local proton shift(s), details of hydrogen bonding, are still not clarified and remain a challenging topic of future research.

  4. Chlorine dioxide oxidation of Escherichia coli in water - A study of the disinfection kinetics and mechanism.

    PubMed

    Ofori, Isaac; Maddila, Suresh; Lin, Johnson; Jonnalagadda, Sreekantha B

    2017-03-16

    This study investigated the kinetics and mechanism of chlorine dioxide (ClO2) inactivation of a Gram-negative bacteria Escherichia coli (ATCC 35218) in oxidant demand free (ODF) water in detail as a function of disinfectant concentration (0.5-5.0 mg/L), water pH (6.5-8.5), temperature variations (4-37°C) and bacterial density (10(5)-10(7) cfu/mL). The effects of ClO2 on bacterial cell morphology, outer membrane permeability, cytoplasmic membrane disruption and intracellular enzymatic activity were also studied to elucidate the mechanism of action on the cells. Increasing temperature and disinfectant concentration were proportional to the rate of cell killing, but efficacy was found to be significantly subdued at 0.5 mg/L and less dependent on the bacterial density. The bactericidal efficiency was higher at alkaline pH of 8 or above as compared to neutral and slightly acidic pH of 7 and 6.5 respectively. The disinfection kinetic curves followed a biphasic pattern of rapid inactivation within the initial 2 min which were followed by a tailing even in the presence of residual biocide. The curves were adequately described by the Cavg Hom model. Transmission Electron Microscopy images of the bacteria cells exposed to lethal concentrations of ClO2 indicated very little observable morphological damage to the outer membranes of the cells. ClO2 however was found to increase the permeability of the outer and cytoplasmic membranes leading to the leakage of membrane components such as 260 nm absorbing materials and inhibiting the activity of the intracellular enzyme β-D-galactosidase. It is suggested that the disruption of the cytoplasmic membrane and subsequent efflux of intracellular components result in the inactivation of the Gram-negative bacteria.

  5. Fundamental and semi-global kinetic mechanisms for hydrocarbon combustion. Final report, March 1977-October 1980

    SciTech Connect

    Dryer, F L; Glassman, I; Brezinsky, K

    1981-03-01

    Over the past three and one half years, substantial research efforts of the Princeton Fuels Research Group have been directed towards the development of simplified mechanisms which would accurately describe the oxidation of hydrocarbons fuels. The objectives of this combustion research included the study of semi-empirical modeling (that is an overall description) of the chemical kinetic mechanisms of simple hydrocarbon fuels. Such fuels include the alkanes: ethane, propane, butane, hexane and octane as well as the critically important alkenes: ethene, propene and butene. As an extension to this work, the study of the detailed radical species characteristics of combustion systems was initiated as another major aspect of the program, with emphasis on the role of the OH and HO/sub 2/ radicals. Finally, the studies of important alternative fuel problems linked the program to longer range approaches to the energy supply question. Studies of alternative fuels composed the major elements of this area of the program. The efforts on methanol research were completed, and while the aromatics aspects of the DOE work have been a direct extension of efforts supported by the Air Force Office of Scientific Research, they represented a significant part of the overall research effort. The emphasis in the proposed program is to provide further fundamental understanding of the oxidation of hydrocarbon fuels which will be useful in guiding engineering approaches. Although the scope of program ranges from the fundamentals of chemical kinetics to that of alternative fuel combustion, the objective in mind is to provide insight and guidance to the understanding of practical combustion environments. The key to our approach has been our understanding of the fundamental combustion chemistry and its relation to the important practical combustion problems which exist in implementing energy efficient, alternate fuels technologies.

  6. UPTAKE OF NITRATE AND NITRITE BY DITYLUM BRIGHTWELLII-KINETICS AND MECHANISMS(1) (2).

    PubMed

    Eppley, R W; Coatsworth, J L

    1968-06-01

    Ditylum brightwellii grown on NO2 - as a nitrogen source took up and assimilated NO2 - only in the light, apparently via a photosynthetic nitrite reductase. Assimilation was inhibited by dichlorophenyldimethylurea (DCMU), KCN, partially by 2,4 dinitrophenol, and by NO3 -. Kinetics of inhibition of NO2 - assimilation by NO3 - appeared to be "competitive." D. brightwellii cells grown on NO2 - took up NO3 - in both light and dark and in both cases the uptake was inhibited by p-chloromercuribenzoate, but not by DCMU, KCN, or by NO2 -. Most of the NO3 - taken up in the dark was recovered unchanged from the cells. However only 40% of NO3 - taken up in light was recovered from the cells and no NO2 - was found. This suggests that a photosynthetic nitrate reduction mechanism was active in these cells. DCMU inhibited the light-induced NO3 - reduction. This mechanism of NO3 - reduction is distinct from that involving NADH nitrate reductase in D. brightwellii since the concentration of the latter enzyme is very low in cells grown on NO2 -. Saturation kinetics were observed for NO2 - and NO3 - uptake. Half-saturation concentrations (Ks values) were 4 and 2 μM, respectively. These values are compared with those obtained for NO2 - and NO3 - assimilation by other unicellular algae. The comparisons show lower Ks values in oceanic species compared with tide-pool or freshwater algae and they support the idea that Ks values for NO3 - assimilation may provide a key to understanding species succession when this is due to declining: nitrate concentrations in the sea.

  7. Mechanism, kinetics and toxicity assessment of OH-initiated transformation of triclosan in aquatic environments.

    PubMed

    Gao, Yanpeng; Ji, Yuemeng; Li, Guiying; An, Taicheng

    2014-02-01

    The mechanisms and kinetics of OH-initiated transformation of triclosan (TCS) in aquatic environments were modeled using high-accuracy molecular orbital theory. TCS can be initially attacked by OH in two ways, OH-addition and H-abstraction. Twelve OH-addition routes were reported, and the C atom adjacent to the ether bond in the benzene ring (RaddB1) was found as the most easily attacked position by OH, producing TCS-OHB1. Seven H-abstraction routes were reported, and the OH exclusively abstracted the phenolic hydroxyl (RabsOH) H atom, to form TCS(-H). The kinetics results showed that the RaddB1 and RabsOH routes would occur preferentially in aquatic environments, and the half-life depended on the OH concentration ([OH]). At low [OH], the main intermediates, TCS-OHB1 and TCS(-H), can be converted into 2,4-dichlorophenol and polychlorinated dibenzo-p-dioxins, respectively. However, when enough OH is present, such as in advanced oxidation process (AOP) systems, they would be fully decomposed. The acute and chronic toxicities of TCS and its products were assessed at three trophic levels using the "ecological structure-activity relationships" program. The toxicity of the products decreased through the RaddB1 route, while the toxicity of the products first increased and then decreased through the other degradation routes. These results should help reveal the mechanism of TCS transformation as well as risk assessment in aquatic environments, and will help design further experimental studies and industrial application of AOPs.

  8. Regio- and stereoselective isomerization of hexabromocyclododecanes (HBCDs): kinetics and mechanism of beta-HBCD racemization.

    PubMed

    Heeb, Norbert V; Schweizer, W Bernd; Mattrel, Peter; Haag, Regula; Kohler, Martin; Schmid, Peter; Zennegg, Markus; Wolfensberger, Max

    2008-04-01

    Hexabromocyclododecanes (HBCDs) are high production volume chemicals currently produced in quantities exceeding 20000ty(-1). They are used as flame retardants for plastics and textiles. HBCDs are thermally labile compounds, rapidly decomposing at temperatures above 250 degrees C to form bromine radicals, which scavenge other radicals formed during pyrolysis. But certain HBCD stereoisomers must reach the environment without decomposition, because their levels in soils, sediments, and biota are increasing worldwide. The fate of individual HBCD stereoisomers during production, product use, disposal, and transformation in the environment remains unclear. Herein we report on the thermally induced, highly selective isomerization of (+) and (-)beta-HBCD. Regio- and stereoselective migration of only two of the six bromine atoms resulted in the racemization of both beta-HBCDs. First order rate constants (k(rac)) increased from 0.005, 0.011, 0.021, to 0.055min(-1) at 130, 140, 150, and 160 degrees C, corresponding to half life times tau(1/2) of 143, 63, 29, and 14min, respectively. From the deduced kinetic model, we conclude that any thermal treatment of enantiomerically enriched beta-HBCDs in the range of 100-160 degrees C will result in a loss of most optical activity within few hours. The simultaneous inversion of two asymmetric centers occurred with perfect stereocontrol. Selectively, vicinal dibromides with the RR- and the SS-configurations migrated at these temperatures. An intramolecular reaction mechanism with a four-center transition state is postulated, based on the obtained stereoisomer pattern and the observed reaction kinetics. Crystal structure analysis revealed that all vicinal dibromides in beta-HBCDs prefer synclinal (gauche) conformations. However, an antiperiplanar (staggered) conformation is assumed to facilitate the concerted 1.2-shifts of both bromine atoms, resulting in an inversion of both neighboring carbon atoms. First experiments with other HBCD

  9. Parallel versus Off-Pathway Michaelis-Menten Mechanism for Single-Enzyme Kinetics of a Fluctuating Enzyme.

    PubMed

    Kumar, Ashutosh; Maity, Hiranmay; Dua, Arti

    2015-07-09

    Recent fluorescence spectroscopy measurements of the turnover time distribution of single-enzyme turnover kinetics of β-galactosidase provide evidence of Michaelis-Menten kinetics at low substrate concentration. However, at high substrate concentrations, the dimensionless variance of the turnover time distribution shows systematic deviations from the Michaelis-Menten prediction. This difference is attributed to conformational fluctuations in both the enzyme and the enzyme-substrate complex and to the possibility of both parallel- and off-pathway kinetics. Here, we use the chemical master equation to model the kinetics of a single fluctuating enzyme that can yield a product through either parallel- or off-pathway mechanisms. An exact expression is obtained for the turnover time distribution from which the mean turnover time and randomness parameters are calculated. The parallel- and off-pathway mechanisms yield strikingly different dependences of the mean turnover time and the randomness parameter on the substrate concentration. In the parallel mechanism, the distinct contributions of enzyme and enzyme-substrate fluctuations are clearly discerned from the variation of the randomness parameter with substrate concentration. From these general results, we conclude that an off-pathway mechanism, with substantial enzyme-substrate fluctuations, is needed to rationalize the experimental findings of single-enzyme turnover kinetics of β-galactosidase.

  10. Crystal structure and kinetic mechanism of aminoglycoside phosphotransferase-2″-IVa

    PubMed Central

    Toth, Marta; Frase, Hilary; Antunes, Nuno Tiago; Smith, Clyde A; Vakulenko, Sergei B

    2010-01-01

    Acquired resistance to aminoglycoside antibiotics primarily results from deactivation by three families of aminoglycoside-modifying enzymes. Here, we report the kinetic mechanism and structure of the aminoglycoside phosphotransferase 2″-IVa (APH(2″)-IVa), an enzyme responsible for resistance to aminoglycoside antibiotics in clinical enterococcal and staphylococcal isolates. The enzyme operates via a Bi-Bi sequential mechanism in which the two substrates (ATP or GTP and an aminoglycoside) bind in a random manner. The APH(2″)-IVa enzyme phosphorylates various 4,6-disubstituted aminoglycoside antibiotics with catalytic efficiencies (kcat/Km) of 1.5 × 103 to 1.2 × 106 (M−1 s−1). The enzyme uses both ATP and GTP as the phosphate source, an extremely rare occurrence in the phosphotransferase and protein kinase enzymes. Based on an analysis of the APH(2″)-IVa structure, two overlapping binding templates specifically tuned for hydrogen bonding to either ATP or GTP have been identified and described. A detailed understanding of the structure and mechanism of the GTP-utilizing phosphotransferases is crucial for the development of either novel aminoglycosides or, more importantly, GTP-based enzyme inhibitors which would not be expected to interfere with crucial ATP-dependent enzymes. PMID:20556826

  11. Free radical scavenger properties of α-mangostin: thermodynamics and kinetics of HAT and RAF mechanisms.

    PubMed

    Martínez, Ana; Galano, Annia; Vargas, Rubicelia

    2011-11-03

    Mangosteen is a tropical fruit that presents beneficial effects on human health since it is rich in anthocyanins and xanthones, which are considered bioactive compounds that have been described as good free radical scavengers. One of its most active compounds is α-mangostin. In this report, a theoretical study on the free radical scavenger capacity of α-mangostin and its monoanion is analyzed using the density functional theory approximation. Two well-known reaction mechanisms are investigated: the hydrogen atom transfer (HAT) and the radical adduct formation (RAF). Two other mechanisms are also considered: sequential electron proton Transfer (SEPT) and proton coupled electron transfer (PCET). According to thermodynamics and kinetics, α-mangostin and its deprotonated form are good free radical scavenger through the HAT mechanism, with the anionic (deprotonated) form being more reactive than the neutral one. Their capacity to scavenge OOH free radical is similar to that of carotenes, higher than that of allicin, much higher than that of melatonin and N-acetylcysteine amide, and about 15 times lower than that of 2-propenesulfenic acid.

  12. Kinetics and Mechanism of the Reaction of Hydoxyl Radicals with Acetonitrile under Atmospheric Conditions

    NASA Technical Reports Server (NTRS)

    Hynes, A. J.; Wine, P. H.

    1997-01-01

    scheme to extract kinetic information about the adduct reations with O2 and branching ratios for OH regeneration. A plausible mechanism for OH regeneration in (2) involves OH addition to the nitrogen atom followed by O2 addition to the cyano carbon atom, isomeriazation and decomposition to D2CO + DOCN + OH. Our results suggest that the OH + CH3CN reaction occurs via a complex mechanism involving both bimolecular and termolecular pathways, analogous to the mechanisms for the the important atmospheric reactions of OH with CO and HNO3.

  13. PAH growth initiated by propargyl addition: mechanism development and computational kinetics.

    PubMed

    Raj, Abhijeet; Al Rashidi, Mariam J; Chung, Suk Ho; Sarathy, S Mani

    2014-04-24

    Polycyclic aromatic hydrocarbon (PAH) growth is known to be the principal pathway to soot formation during fuel combustion, as such, a physical understanding of the PAH growth mechanism is needed to effectively assess, predict, and control soot formation in flames. Although the hydrogen abstraction C2H2 addition (HACA) mechanism is believed to be the main contributor to PAH growth, it has been shown to under-predict some of the experimental data on PAHs and soot concentrations in flames. This article presents a submechanism of PAH growth that is initiated by propargyl (C3H3) addition onto naphthalene (A2) and the naphthyl radical. C3H3 has been chosen since it is known to be a precursor of benzene in combustion and has appreciable concentrations in flames. This mechanism has been developed up to the formation of pyrene (A4), and the temperature-dependent kinetics of each elementary reaction has been determined using density functional theory (DFT) computations at the B3LYP/6-311++G(d,p) level of theory and transition state theory (TST). H-abstraction, H-addition, H-migration, β-scission, and intramolecular addition reactions have been taken into account. The energy barriers of the two main pathways (H-abstraction and H-addition) were found to be relatively small if not negative, whereas the energy barriers of the other pathways were in the range of (6-89 kcal·mol(-1)). The rates reported in this study may be extrapolated to larger PAH molecules that have a zigzag site similar to that in naphthalene, and the mechanism presented herein may be used as a complement to the HACA mechanism to improve prediction of PAH and soot formation.

  14. Mainz Organics Mechanism (MOM): description and sensitivity to some estimated kinetic parameters

    NASA Astrophysics Data System (ADS)

    Taraborrelli, Domenico; Cabrera Perez, David; Sander, Rolf; Pozzer, Andrea

    2015-04-01

    Despite decades of reasearch, global atmospheric chemistry models still have significant biases compared to the estimated distribution and evolution of tropospheric ozone and hydroxyl radical. The gas-phase oxidation of volatile organic compounds (VOC) is acknowledged to play an important role among the processes affecting tropospheric ozone, methane lifetime and aerosol evolution. Thus, chemical mechanisms of very diverse complexity have been developed for the major VOCs. However, all mechanisms present shortcomings such as neglection or lumping of intermediates and estimate of many rate constants and product distributions. Here, we present a VOC oxidation mechanism of intermediate complexity called the Mainz Organics Mechanism (MOM). With about 400 species and 1500 reactions, it represents the oxidation of about 20 primarily emitted VOCs comprising small alkanes and alkenes, isoprene, pinenes and monocyclic aromatic compounds. The development protocol significantly borrows from the Master Chemical Mechanism (MCM). However, MOM distinguishes itself for a number of features. First, the structure activity relationship for estimating the rate constants involving hydroxyl radical is site-specific and dependent on temperature. Second, the alkyl nitrate yields are considered to be dependent on temperature, pressure and molecular structure. RO2 + HO2 reaction kinetics is consistent with the recent direct studies of \\chem{OH}-reformation. Isoprene chemistry includes the latest experimental advancements with respect to OH-recycling and alkyl nitrate chemistry. Pinenes chemistry is largely the one by the MCM but with some modifications according to the work of the Leuven's group. Finally, the chemistry of the aromatics is also borrowed from the MCM but with additional photolysis of ortho-nitrophenols leading to \\chem{HONO} formation. The sensitivity of the model to the temperature and pressure dependence of estimated \\chem{OH} rate constants and alkyl nitrate yields will

  15. Kinetic modeling and mathematical analysis indicate that acute phase gene expression in Hep 3B cells is regulated by both transcriptional and posttranscriptional mechanisms.

    PubMed Central

    Jiang, S L; Samols, D; Rzewnicki, D; Macintyre, S S; Greber, I; Sipe, J; Kushner, I

    1995-01-01

    To evaluate the possible role of posttranscriptional mechanisms in the acute phase response, we determined the kinetics of transcription (by nuclear run-on assay) and mRNA accumulation of five human acute phase genes in Hep 3B cells incubated with conditioned medium from LPS-stimulated monocytes. Increase in mRNA accumulation was comparable to increase in transcription rate for fibrinogen-alpha and alpha-1 protease inhibitor, suggesting largely transcriptional regulation. In contrast, mRNA accumulation was about 10-20-fold greater than transcriptional increase for serum amyloid A, C3, and factor B, suggesting participation of posttranscriptional mechanisms. Since finding a disparity between the magnitudes of increase in mRNA and transcription does not definitively establish involvement of posttranscriptional mechanisms, we subjected our data to modeling studies and dynamic mathematical analysis to evaluate this possibility more rigorously. In modeling studies, accumulation curves resembling those observed for these three mRNAs could be generated from the nuclear run-on results only if posttranscriptional regulation was assumed. Dynamic mathematical analysis of relative transcription rates and relative mRNA abundance also strongly supported participation of posttranscriptional mechanisms. These observations suggest that posttranscriptional regulation plays a substantial role in induction of some, but not all acute phase proteins. Images PMID:7883974

  16. Group I Ribozymes as a Paradigm for RNA Folding and Evolution

    NASA Astrophysics Data System (ADS)

    Woodson, Sarah A.; Chauhan, Seema

    Group I ribozymes are an ancient class of RNA catalysts that serve as a paradigm for the self-assembly of complex structures of non-coding RNA. The diversity of subtypes illustrates the modular character of RNA architecture and the potential for the evolution of new functions. The folding mechanisms of group I ribozymes illustrate the hierarchy of folding transitions and the importance of kinetic partitioning among competing folding pathways. Studies on group I splicing factors demonstrate how proteins facilitate the assembly of splicing complexes by stabilizing tertiary interactions between domains and by ATP-dependent cycles of RNA unfolding.

  17. The protein folding network

    NASA Astrophysics Data System (ADS)

    Rao, Francesco; Caflisch, Amedeo

    2004-03-01

    Networks are everywhere. The conformation space of a 20-residue antiparallel beta-sheet peptide [1], sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. As previously found for the World-Wide Web as well as for social and biological networks , the conformation space contains highly connected hubs like the native state which is the most populated free energy basin. Furthermore, the network shows a hierarchical modularity [2] which is consistent with the funnel mechanism of folding [3] and is not observed for a random heteropolymer lacking a native state. Here we show that the conformation space network describes the free energy landscape without requiring projections into arbitrarily chosen reaction coordinates. The network analysis provides a basis for understanding the heterogeneity of the folding transition state and the existence of multiple pathways. [1] P. Ferrara and A. Caflisch, Folding simulations of a three-stranded antiparallel beta-sheet peptide, PNAS 97, 10780-10785 (2000). [2] Ravasz, E. and Barabási, A. L. Hierarchical organization in complex networks. Phys. Rev. E 67, 026112 (2003). [3] Dill, K. and Chan, H From Levinthal to pathways to funnels. Nature Struct. Biol. 4, 10-19 (1997)

  18. Kinetics and mechanisms of crystal growth inhibition of indomethacin by model precipitation inhibitors

    NASA Astrophysics Data System (ADS)

    Patel, Dhaval

    Supersaturating Drug Delivery Systems (SDDS) could enhance oral bioavailability of poorly water soluble drugs (PWSD). Precipitation inhibitors (PIs) in SDDS could maintain supersaturation by inhibiting nucleation, crystal growth, or both. The mechanisms by which these effects are realized are generally unknown. The goal of this dissertation was to explore the mechanisms underpinning the effects of model PIs including hydroxypropyl beta-cyclodextrins (HP-beta-CD), hydroxypropyl methylcellulose (HPMC), and polyvinylpyrrolidone (PVP) on the crystal growth of indomethacin, a model PWSD. At high degrees of supersaturation (S), the crystal growth kinetics of indomethacin was bulk diffusion-controlled, which was attributed to a high energy form deposited on the seed crystals. At lower S, indomethacin growth kinetics was surface integration-controlled. The effect of HP-beta-CD at high S was successfully modeled using the reactive diffusion layer theory. The superior effects of PVP and HPMC as compared to HP-beta-CD at high S were attributed to a change in the rate limiting step from bulk diffusion to surface integration largely due to prevention of the high energy form formation. The effects of PIs at low S were attributed to significant retardation of the surface integration rate, a phenomenon that may reflect the adsorption of PIs onto the growing surface. PVP was selected to further understand the relationship between adsorption and crystal growth inhibition. The Langmuir adsorption isotherm model fit the adsorption isotherms of PVP and N-vinylpyrrolidone well. The affinity and extent of adsorption of PVP were significantly higher than those of N-vinylpyrrolidone, which was attributed to cooperative interactions between PVP and indomethacin. The extent of PVP adsorption on a weight-basis was greater for higher molecular weight PVP but less on a molar-basis indicating an increased percentage of loops and tails for higher molecular weight PVPs. PVP significantly inhibited

  19. Kinetics and mechanisms of degradation of chloroacetonitriles by the UV/H2O2 process.

    PubMed

    Ling, Li; Sun, Jianliang; Fang, Jingyun; Shang, Chii

    2016-08-01

    Haloacetonitriles (HANs) are emerging disinfection by-products (DBPs) that are more toxic than the regulated DBPs and widely found in the chlorinated/chloraminated water. This paper studied kinetics and mechanisms of the degradation of chloroacetonitriles (CANs) by the UV/H2O2 process at pH 6 and 7.5 and H2O2 concentrations of 1 × 10(-3) M, 5 × 10(-3) M and 1 × 10(-2) M. The degradation followed pseudo first-order degradation kinetics. The degradation rate of monochloroacetonitrile (MCAN) remained similar, while those of dichloroacetonitrile (DCAN) and trichloroacetonitrile (TCAN) increased with increasing pH and H2O2 concentrations. The different trends were attributed to the changing contributions of the two major mechanisms: the nucleophilic attack by hydroperoxide ions ( [Formula: see text] ) and the hydroxyl radical (•OH) oxidation. The second-order rate constants of [Formula: see text] towards MCAN, DCAN and TCAN were determined to be 11.8 (±0.62), 4.83 (±0.01) × 10(3), and 2.54 (±0.23) × 10(5) M(-1) s(-1), respectively, while that of •OH were 8.7 × 10(6), 4.4 × 10(6), and < 10(6) M(-1) s(-1), respectively. The degradation of TCAN was mainly attributed to the [Formula: see text] nucleophilic attack, while that of MCAN was dominated by the •OH oxidation. DCAN was degraded by both mechanisms. The nucleophilic attack increased linearly with increasing [Formula: see text] concentration as a result of increasing H2O2 concentration and/or pH, while the •OH oxidation was less dependent on H2O2 concentrations and/or pH. The nucleophilic attack mainly transformed HANs to haloacetamides, while the •OH oxidation dechlorinated HANs. This paper firstly illustrated the importance of the [Formula: see text] nucleophilic attack, in addition to the •OH oxidation, on the CAN degradation in the UV/H2O2 process.

  20. The effect of foreland palaeo-uplift on deformation mechanism in the Wupoer fold-and-thrust belt, NE Pamir: Constraints from analogue modelling

    NASA Astrophysics Data System (ADS)

    Wang, Chunyang; Cheng, Xiaogan; Chen, Hanlin; Ding, Weiwei; Lin, Xiubin; Wu, Lei; Li, Kang; Shi, Jun; Li, Yong

    2016-10-01

    Palaeo-uplifts often exist in fold-and-thrust belts. However, their effects on the deformational process have not yet been well understood. To evaluate such effects, six analogue models were systematically run based on geological features of the Wupoer fold-and-thrust belt (FTB), NE Pamir, where the Wulagen palaeo-uplift with overlying gypsum bed has been clearly identified. Our analogue results demonstrated that the palaeo-uplift (its location and inhomogenous distribution), accompanied with overlying gypsum bed that serves as ductile décollement, plays a critical role in localizing the front thrust fault and shaping it into arc form. The results indicate that the front thrust fault slides along the ductile décollement (gypsum bed), and breaks through onto the surface at the region where the palaeo-uplift develops, forming a piggy-back basin in the hanging wall. It suggests that the palaeo-uplift with consequent topographic variation of the overlying ductile décollement localizes the breakthrough point of the front thrust fault. In addition, the results indicate that the front thrust fault (Pamir Front Thrust, PFT) initially broke through in the location where it develops the Wulagen palaeo-uplift and propagated aside. This resulted in the distance between the PFT and the basement-involved fault (Main Pamir Thrust, MPT) to decrease from the region with palaeo-uplift to the areas aside without palaeo-uplift, thereby forming the arc-shaped PFT in map view. The results of this study also provide a revised geological model, which emphasizes the effect of décollement layer on absorbing the slip along the PFT. Our results provide a new mechanical interpretation of the deformation of Wupoer FTB, NE Pamir.

  1. Large variation in the Rubisco kinetics of diatoms reveals diversity among their carbon-concentrating mechanisms

    PubMed Central

    Young, Jodi N.; Heureux, Ana M.C.; Sharwood, Robert E.; Rickaby, Rosalind E.M.; Morel, François M.M.; Whitney, Spencer M.

    2016-01-01

    While marine phytoplankton rival plants in their contribution to global primary productivity, our understanding of their photosynthesis remains rudimentary. In particular, the kinetic diversity of the CO2-fixing enzyme, Rubisco, in phytoplankton remains unknown. Here we quantify the maximum rates of carboxylation (k cat c), oxygenation (k cat o), Michaelis constants (K m) for CO2 (K C) and O2 (K O), and specificity for CO2 over O2 (SC/O) for Form I Rubisco from 11 diatom species. Diatom Rubisco shows greater variation in K C (23–68 µM), SC/O (57–116mol mol−1), and K O (413–2032 µM) relative to plant and algal Rubisco. The broad range of K C values mostly exceed those of C4 plant Rubisco, suggesting that the strength of the carbon-concentrating mechanism (CCM) in diatoms is more diverse, and more effective than previously predicted. The measured k cat c for each diatom Rubisco showed less variation (2.1–3.7s−1), thus averting the canonical trade-off typically observed between K C and k cat c for plant Form I Rubisco. Uniquely, a negative relationship between K C and cellular Rubisco content was found, suggesting variation among diatom species in how they allocate their limited cellular resources between Rubisco synthesis and their CCM. The activation status of Rubisco in each diatom was low, indicating a requirement for Rubisco activase. This work highlights the need to better understand the correlative natural diversity between the Rubisco kinetics and CCM of diatoms and the underpinning mechanistic differences in catalytic chemistry among the Form I Rubisco superfamily. PMID:27129950

  2. From surfactant adsorption kinetics to asymmetric nanomembrane mechanics: pendant drop experiments with subphase exchange.

    PubMed

    Ferri, James K; Kotsmar, Csaba; Miller, Reinhard

    2010-12-15

    Adsorption equilibrium is the state in which the chemical potential of each species in the interface and bulk is the same. Dynamic phenomena at fluid-fluid interfaces in the presence of surface active species are often probed by perturbing an interface or adjoining bulk phase from the equilibrium state. Many methods designed for studying kinetics at fluid-fluid interfaces focus on removing the system from equilibrium through dilation or compression of the interface. This modifies the surface excess concentration Γ(i) and allows the species distribution in the bulk C(i) to respond. There are only a few methods available for studying fluid-fluid interfaces which seek to control C(i) and allow the interface to respond with changes to Γ(i). Subphase exchange in pendant drops can be achieved by the injection and withdrawal of liquid into a drop at constant volumetric flow rate R(E) during which the interfacial area and drop volume V(D) are controlled to be approximately constant. This can be accomplished by forming a pendant drop at the tip of two coaxial capillary tubes. Although evolution of the subphase concentration C(i)(t) is dictated by extrinsic factors such as R(E) and V(D), complete subphase exchange can always be attained when a sufficient amount of liquid is used. This provides a means to tailor driving forces for adsorption and desorption in fluid-fluid systems and in some cases, fabricate interfacial materials of well-defined composition templated at these interfaces. The coaxial capillary pendant drop (CCPD) method opens a wide variety of experimental possibilities. Experiments and theoretical frameworks are reviewed for the study of surfactant exchange kinetics, macromolecular adsorption equilibrium and dynamics, as well as the fabrication of a wide range of soft surface materials and the characterization of their mechanics. Future directions for new experiments are also discussed.

  3. Kinetics and Mechanism of Inhibition of a Serine β-Lactamase by O-Aryloxycarbonyl Hydroxamates†

    PubMed Central

    Pelto, Ryan B.; Pratt, R.F.

    2009-01-01

    The class C serine β-lactamase of Enterobacter cloacae P99 is irreversibly inhibited by O-aryloxycarbonyl hydroxamates. A series of these new inhibitors has been prepared to investigate the kinetics and mechanism of the inactivation reaction. A pH-rate profile for the reaction indicated that the reactive form of the inhibitor is neutral rather than anionic. The reaction rate is enhanced by electron-withdrawing aryloxy substituents and by hydrophobic substitution on both aryloxy and hydroxamate groups. Kinetics studies show that the rates of loss of the two possible leaving groups, aryloxide and hydroxamate are essentially the same as the rate of enzyme inactivation. Nucleophilic trapping experiments prove, however, that the aryloxide is the first to leave. It is likely, therefore, that the rate-determining step of inactivation is the initial acylation reaction, most likely of the active site serine, yielding a hydroxamoyl-enzyme intermediate. This then partitions between hydrolysis and aminolysis by Lys 315, the latter to form an inactive, cross-linked active site. A previously described crystal structure of the inactivated enzyme shows a carbamate cross-link of Ser 64 and Lys 315. Structure-activity studies of the reported compounds suggest that they do not react at the enzyme active site in the same way as normal substrates. In particular, it appears that the initial acylation by these compounds does not involve the oxyanion hole, an unprecedented departure from known and presumed reactivity. Molecular modeling suggests that an alternative oxyanion hole may have been recruited, consisting of the side chain functional groups of Tyr 150 and Lys 315. Such an alternative mode of reaction may lead to the design of novel inhibitors. PMID:18942857

  4. Kinetics and mechanism of oxidation of tryptophan by ferrate(VI).

    PubMed

    Casbeer, Erik M; Sharma, Virender K; Zajickova, Zuzana; Dionysiou, Dionysios D

    2013-05-07

    Kinetics of the oxidation of tryptophan (Trp) and kynurenine (Kyn), precursors of nitrogenous disinfection byproducts (N-DBP), by ferrate(VI) (Fe(VI)O4(2-), Fe(VI)) were investigated over the acidic to basic pH range. The second-order rate constants decreased with increase in pH, which could be described by the speciation of Fe(VI) and Trp (or Kyn). The trend of pH dependence of rates for Trp (i.e., aromatic α-amino acid) differs from that for glycine (i.e., aliphatic α-amino acid). A nonlinear relationship between transformation of Trp and the added amount of Fe(VI) was found. This suggests that the formed intermediate oxidized products (OPs), identified by LC-PDA and LC-MS techniques, could possibly compete with Trp to react with Fe(VI). N-Formylkynurenine (NFK) at pH 7.0 and 4-hydroxyquinoline (4-OH Q) and kynurenic acid (Kyn-A) at pH 9.0 were the major OPs. Tryptophan radical formation during the reaction was confirmed by the rapid-freeze quench EPR experiments. The oxygen atom transfer from Fe(VI) to NFK was demonstrated by reacting Fe(18)O4(2-) ion with Trp. A proposed mechanism explains the identified OPs at both neutral and alkaline pH. Kinetics and OPs by Fe(VI) were compared with other oxidants (chlorine, ClO2(•), O3, and (•)OH).

  5. Troilite formation kinetics and growth mechanism in the solar nebula. [Abstract only

    NASA Technical Reports Server (NTRS)

    Lauretta, D. S.; Fegley, B., Jr.

    1994-01-01

    Troilite formation via the reaction Fe(s) + H2S(g) + H2(g) is the major mechanism for S retention in grains in the solar nebula. Thermodynamic calculations predict that troilite condenses from a solar composition gas. We present experimental results on the kinetics and growth of troilite crystals on Fe metal at temperature (450-650 C) and composition (50-1000 ppm H2S in H2) conditions similar to those in the solar nebula. The fraction of Fe reacted (based on gravimetric data) is plotted at 450, 505, 575, and 650 C. The thickness change of unreacted iron (measured by optical microscopy) is plotted at 575 and 650 C vs. time. the weight change per unit area varies as the square root of time at the lower temperatures and varies linearly with time at the highest temperature. The growth behavior along the lower isotherms is due to diffusion. This behavior suggests sulfide diffusion to the metal-sulfide interface and suggests Fe(2+) diffusion to the sulfide-gas interface. The reaction along the highest isotherm appears to be interface controlled. The formation of troilite crystals is a rapid process forming measurable layers in a few hours. The crystalgrowth is complicated. Initially there are intergrowths of troilite into the pure Fe metal. As the reaction progresses two distinct layers of troilite crystals form. One is in contact with the Fe metal and consists of small randomly oriented crystals with pore space between them. The outermost layer contains large crystals that are all oriented in the same direction. The intergrowth layer is much smaller at 650 C than at 575 C. This suggest that FeS nucleation is inhibited at the higher temperature, accounting for the initially slower reaction rate. Once nucleated, the reaction kinetics are apparently controlled by the growth of the crystals at the interface.

  6. Base-catalyzed insertion of dioxygen into rhodium-hydrogen bonds: kinetics and mechanism.

    PubMed

    Szajna-Fuller, Ewa; Bakac, Andreja

    2010-02-01

    The reaction between molecular oxygen and rhodium hydrides L(OH)RhH(+) (L = (NH(3))(4), trans-L(1), and cis-L(1), where L(1) = cyclam) in basic aqueous solutions rapidly produces the corresponding hydroperoxo complexes. Over the pH range 8 < pH < 12, the kinetics exhibit a first order dependence on [OH(-)]. The dependence on [O(2)] is less than first order and approaches saturation at the highest concentrations used. These data suggest an attack by OH(-) at the hydride with k = (1.45 +/- 0.25) x 10(3) M(-1) s(-1) for trans-L(1)(OH)RhH(+) at 25 degrees C, resulting in heterolytic cleavage of the Rh-H bond and formation of a reactive Rh(I) intermediate. A competition between O(2) and H(2)O for Rh(I) is the source of the observed dependence on O(2). In support of this mechanism, there is a significant kinetic isotope effect for the initial step, L(1)(OH(D))RhH(D)(+) + OH(D)(-) k(1)/k(-1) L(1)(OH(D))Rh(I) + H(D)(2)O, k(1H)/k(1D) = 1.7, and k(-1H)/k(-1D) = 3.0. The activation parameters for k(1) for trans-L(1)(OH)RhH(+) are DeltaH(++) = 64.6 +/- 1.3 kJ mol(-1) and DeltaS(++) = 40 +/-4 J mol(-1) K(-1).

  7. Kinetic rate constant prediction supports the conformational selection mechanism of protein binding.

    PubMed

    Moal, Iain H; Bates, Paul A

    2012-01-01

    The prediction of protein-protein kinetic rate constants provides a fundamental test of our understanding of molecular recognition, and will play an important role in the modeling of complex biological systems. In this paper, a feature selection and regression algorithm is applied to mine a large set of molecular descriptors and construct simple models for association and dissociation rate constants using empirical data. Using separate test data for validation, the predicted rate constants can be combined to calculate binding affinity with accuracy matching that of state of the art empirical free energy functions. The models show that the rate of association is linearly related to the proportion of unbound proteins in the bound conformational ensemble relative to the unbound conformational ensemble, indicating that the binding partners must adopt a geometry near to that of the bound prior to binding. Mirroring the conformational selection and population shift mechanism of protein binding, the models provide a strong separate line of evidence for the preponderance of this mechanism in protein-protein binding, comple