Dynamic disorder in simple enzymatic reactions induces stochastic amplification of substrate

A growing amount of evidence points to the fact that many enzymes exhibit fluctuations in their catalytic activity, which are associated with conformational changes on a broad range of timescales. The experimental study of this phenomenon, termed dynamic disorder, has become possible due to advances in single-molecule enzymology measurement techniques, through which the catalytic activity of individual enzyme molecules can be tracked in time. The biological role and importance of these fluctuations in a system with a small number of enzymes such as a living cell have only recently started being explored. In this work, we examine a simple stochastic reaction system consisting of an inflowing substrate and an enzyme with a randomly fluctuating catalytic reaction rate that converts the substrate into an outflowing product. To describe analytically the effect of rate fluctuations on the average substrate abundance at steady-state, we derive an explicit formula that connects the relative speed of enzymatic fluctuations with the mean substrate level. We demonstrate that the relative speed of rate fluctuations can have a dramatic effect on the mean substrate, and lead to large positive deviations from predictions based on the assumption of deterministic enzyme activity. Our results also establish an interesting connection between the amplification effect and the mixing properties of the Markov process describing the enzymatic activity fluctuations, which can be used to easily predict the fluctuation speed above which such deviations become negligible. As the techniques of single-molecule enzymology continuously evolve, it may soon be possible to study the stochastic phenomena due to enzymatic activity fluctuations within living cells. Our work can be used to formulate experimentally testable hypotheses regarding the magnitude of these fluctuations, as well as their phenotypic consequences.Comment: 7 Figure

Immobilisation of enzymes to Perloza cellulose resin : this thesis was presented in partial fulfilment of the requirements for the degree of Master of Science in Biochemistry at Massey University /

The studies reported in this thesis describe the use of Perloza™ beaded cellulose resin as a solid support for enzyme immobilisation via covalent binding. The aim of the project was to extend the uses for Perloza™ and to compare the use of well known solid support activation chemistries with a recently developed one for Perloza™. Preparations such as these have potential industrial uses. Three attachment chemistries were studied. The first activation employed 1,1-carbodiimidazole (CDI) then direct attachment of enzyme. The second again used CDI activation followed by attachment of a 6-aminocaproic acid spacer arm and then the enzyme. The final method used was attachment of a diol and subsequent oxidation to an aldehyde. The diol/aldehyde method had the advantage over the CDI methods of being based on aqueous chemistries. The two CDI based methods require extensive use of dry organic solvents. The enzymes investigated in this study were trypsin, chymotrypsin. α-amylase, horseradish peroxidase (HRPO) and alcohol dehydrogenase (ADH). Trypsin was immobilised successtully by all three chemistries. All preparations retained significant activity after immobilisation at room temperature as judged by the chromogenic substrate specific for trypsin N-α-benzoyl-DL-arginine-p-nitroanilide.HC1 (BAPNA). Measurable activity was retained in different studies from between 2 to 7 days at 60°C. The activity of immobilised trypsin with a synthetic peptide substrate was comparable to the activity of free trypsin with the same substrate. Chymotrypsin was also successfully immobilised using all three chemistries. Each preparation showed significant retention of activity after immobilisation as judged by the chromogentic substrate N-glutaryl-L.-phenylalanine-p-nitroanilide (GAPNA). Stabilisation to heating at 60°C was less successful than with trypsin but significant activity was still retained for between 3 and 6 hours. The activity of immobilised preparations with a peptide substrate was comparable to free chymotrypsin. α-Amylase, horseradish peroxidase and alcohol dehydrogenase were studied less extensively than trypsin and chymotrypsin. Nevertheless all three enzymes were successfully immobilised onto Perloza™-CDI-ACA and Perloza™-Diol/Aldehyde. Difficulty was encountered in achieving significant levels of any enzyme immobilisation to Perloza™-CDI for all three enzymes. Subsequent activity assays showed HRPO and α-amylase retained significant activity on all three resin preparations. ADH showed no measurable activity on Perloza™-CDI and very little activity on Perloza™- CDI-ACA and Perloza™-Diol/Aldehyde. Investigations have shown that enzymes can be immobilised on Perloza™ with retention of significant amounts of normal activity at room temperature and improved stability compared with free enzyme at high temperature. Comparisons of the CDI activations with the diol/aldeyde chemistry showed better performance by the latter in trypsin immobilisation and similar performance for chymotrypsin immobilisation. Horseradish peroxidase and ™-amylase were successfully immobilised using CDI/ACA and diol/aldehyde chemistries with the CDI/ACA giving higher initial specific activities than the diol/aldehyde preparation. Alcohol dehydrogenase was also successfully immobilised but gave no measurable activity

Nucleotide specificity of the enzymatic and motile activities of dynein, kinesin, and heavy meromyosin.

The substrate specificities of dynein, kinesin, and myosin substrate turnover activity and cytoskeletal filament-driven translocation were examined using 15 ATP analogues. The dyneins were more selective in their substrate utilization than bovine brain kinesin or muscle heavy meromyosin, and even different types of dyneins, such as 14S and 22S dynein from Tetrahymena cilia and the beta-heavy chain-containing particle from the outer-arm dynein of sea urchin flagella, could be distinguished by their substrate specificities. Although bovine brain kinesin and muscle heavy meromyosin both exhibited broad substrate specificities, kinesin-induced microtubule translocation varied over a 50-fold range in speed among the various substrates, whereas heavy meromyosin-induced actin translocation varied only by fourfold. With both kinesin and heavy meromyosin, the relative velocities of filament translocation did not correlate well with the relative filament-activated substrate turnover rates. Furthermore, some ATP analogues that did not support the filament translocation exhibited filament-activated substrate turnover rates. Filament-activated substrate turnover and power production, therefore, appear to become uncoupled with certain substrates. In conclusion, the substrate specificities and coupling to motility are distinct for different types of molecular motor proteins. Such nucleotide "fingerprints" of enzymatic activities of motor proteins may prove useful as a tool for identifying what type of motor is involved in powering a motility-related event that can be reconstituted in vitro

Conserved Residues R420 and Q428 in a Cytoplasmic Loop of the Citrate/Malate Transporter CimH of Bacillus subtilis Are Accessible from the External Face of the Membrane

CimH of Bacillus subtilis is a secondary transporter for citrate and malate that belongs to the 2-hydroxycarboxylate transporter (2HCT) family. Conserved residues R143, R420, and Q428, located in putative cytoplasmic loops and R432, located at the cytoplasmic end of the C-terminal transmembrane segment XI were mutated to Cys to identify residues involved in binding of the substrates. R143C, R420C, and Q428C revealed kinetics similar to those of the wild-type transporter, while the activity of R432C was reduced by at least 2 orders of magnitude. Conservative replacement of R432 with Lys reduced the activity by 1 order of magnitude, by lowering the affinity for the substrate 10-fold. It is concluded that the arginine residue at position 432 in CimH interacts with one of the carboxylate groups of the substrates. Labeling of the R420C and Q428C mutants with thiol reagents inhibited citrate transport activity. Surprisingly, the cysteine residues in the cytoplasmic loops in both R420C and Q428C were accessible to the small, membrane-impermeable, negatively charged MTSES reagent from the external site of the membrane in a substrate protectable manner. The membrane impermeable reagents MTSET, which is positively charged, and AMdiS, which is negatively charged like MTSES but more bulky, did not inhibit R420C and Q428C. It is suggested that the access pathway is optimized for small, negatively charged substrates. Either the cytoplasmic loop containing residues R420 and Q428 is partly protruding to the outside, possibly in a reentrant loop like structure, or alternatively, a water-filled substrate translocation pathway extents to the cytoplasm-membrane interface.

Substrate-Induced Self-Assembly of Cooperative Catalysts

Dissipative self-assembly processes in Nature rely on chemical fuels that activate proteins for assembly through the formation of a noncovalent complex. The catalytic activity of the assemblies causes fuel degradation, resulting in the formation of an assembly in a high-energy, out-of-equilibrium state. Herein, we apply this concept to a synthetic system and demonstrate that a substrate can induce the formation of vesicular assemblies, which act as cooperative catalysts for cleavage of the same substrate

Predicting the substrate specificity of a glycosyltransferase implicated in the production of phenolic volatiles in tomato fruit

The volatile compounds that constitute the fruit aroma of ripe tomato (Solanum lycopersicum) are often sequestered in glycosylated form. A homology-based screen was used to identify the gene SlUGT5, which is a member of UDP-glycosyltransferase 72 family and shows specificity towards a range of substrates, including flavonoid, flavanols, hydroquinone, xenobiotics and chlorinated pollutants. SlUGT5 was shown to be expressed primarily in ripening fruit and flowers, and mapped to chromosome I in a region containing a QTL that affected the content of guaiacol and eugenol in tomato crosses. Recombinant SlUGT5 protein demonstrated significant activity towards guaiacol and eugenol, as well as benzyl alcohol and methyl salicylate; however, the highest in vitro activity and affinity was shown for hydroquinone and salicyl alcohol. NMR analysis identified isosalicin as the only product of salicyl alcohol glycosylation. Protein modelling and substrate docking analysis were used to assess the basis for the substrate specificity of SlUGT5. The analysis correctly predicted the interactions with SlUGT5 substrates, and also indicated that increased hydrogen bonding, due to the presence of a second hydrophilic group in methyl salicylate, guaiacol and hydroquinone, appeared to more favourably anchor these acceptors within the glycosylation site, leading to increased stability, higher activities and higher substrate affinities

Fluorescence-based incision assay for human XPF-ERCC1 activity identifies important elements of DNA junction recognition

The structure-specific endonuclease activity of the human XPF–ERCC1 complex is essential for a number of DNA processing mechanisms that help to maintain genomic integrity. XPF–ERCC1 cleaves DNA structures such as stem–loops, bubbles or flaps in one strand of a duplex where there is at least one downstream single strand. Here, we define the minimal substrate requirements for cleavage of stem–loop substrates allowing us to develop a real-time fluorescence-based assay to measure endonuclease activity. Using this assay, we show that changes in the sequence of the duplex upstream of the incision site results in up to 100-fold variation in cleavage rate of a stem-loop substrate by XPF-ERCC1. XPF–ERCC1 has a preference for cleaving the phosphodiester bond positioned on the 3′-side of a T or a U, which is flanked by an upstream T or U suggesting that a T/U pocket may exist within the catalytic domain. In addition to an endonuclease domain and tandem helix–hairpin–helix domains, XPF has a divergent and inactive DEAH helicase-like domain (HLD). We show that deletion of HLD eliminates endonuclease activity and demonstrate that purified recombinant XPF–HLD shows a preference for binding stem–loop structures over single strand or duplex alone, suggesting a role for the HLD in initial structure recognition. Together our data describe features of XPF–ERCC1 and an accepted model substrate that are important for recognition and efficient incision activity

Heat Shock Protein 20 (HSP20) is a novel substrate for Protein Kinase D1 (PKD1)

Heat shock protein 20 (HSP20) has cardioprotective qualities, which are triggered by PKA phosphorylation. PKD1 is also a binding partner for HSP20, and this prompted us to investigate whether the chaperone was a substrate for PKD1. We delineate the PKD1 binding sites on HSP20 and show for the first time HSP20 is a substrate for PKD1. Phosphorylation of HSP20 by PKD1 is diminished by pharmacological or siRNA reduction of PKD1 activity and is enhanced following PKD1 activation. Our results suggest that both PKA and PKD1 can both phosphorylate HSP20 on serine 16 but that PKA is the most dominant

Neural networks on chemically patterned "cultured probe" electrode arrays: network growth and activity patterns

A 'cultured probe' is a hybrid type of neural information transducer or prosthesis, for stimulation and/or recording of neural activity in the brain or the spinal cord (ventral motor region or dorsal sensory region). It consists of a micro electrode array (MEA) on a planar substrate, each electrode being covered and surrounded by a locally confined network of cultured neurons, obtained by chemical patterning of the substrate. The purpose of the cultured cells is that they act as intermediates for collateral sprouts from the in vivo system, thus allowing for an effective and selective neuron electrode interface. As the local neural network will become spontaneously active and has the capability of information processing, one may envisage future applications of these intermediary networks as 'front-end' signal processors. Two aspects of the development of this kind of cultured probe device are described. First, it is shown how substrates can be chemically modified to confine developing networks, cultured from dissociated rat cortex cells, to the surrounding of an electrode site. Secondly, the paper presents results on neuronal activity in such confined, circular networks and synchronized activity between two such interconnected networks