Reverse engineering a protein: the mechanochemistry of ATP synthase

ATP synthase comprises two rotary motors in one. The F(1) motor can generate a mechanical torque using the hydrolysis energy of ATP. The F(o) motor generates a rotary torque in the opposite direction, but it employs a transmembrane proton motive force. Each motor can be reversed: The F(o) motor can drive the F(1) motor in reverse to synthesize ATP, and the F(1) motor can drive the F(o) motor in reverse to pump protons. Thus ATP synthase exhibits two of the major energy transduction pathways employed by the cell to convert chemical energy into mechanical force. Here we show how a physical analysis of the F(1) and F(o) motors can provide a unified view of the mechanochemical principles underlying these energy transducers.     

Examining the large-scale convergence of photosynthesis-weighted tree leaf temperatures through stable oxygen isotope analysis of multiple data sets

The idea that photosynthesis-weighted tree canopy leaf temperature (T(canδ)) can be resolved through analysis of oxygen isotope composition in tree wood cellulose (δ(18) O(wc)) has led to the observation of boreal-to-subtropical convergence of T(canδ) to c. 20°C. To further assess the validity of the large-scale convergence of T(canδ), we used the isotope approach to perform calculation of T(canδ) for independent δ(18) O(wc) data sets that have broad coverage of climates. For the boreal-to-subtropical data sets, we found that the deviation of T(canδ) from the growing season temperature systemically increases with the decreasing mean annual temperature. Across the whole data sets we calculated a mean T(canδ) of 19.48°C and an SD of 2.05°C, while for the tropical data set, the mean T(canδ) was 26.40 ± 1.03°C, significantly higher than the boreal-to-subtropical mean. Our study thus offers independent isotopic support for the concept that boreal-to-subtropical trees display conserved T(canδ) near 20°C. The isotopic analysis cannot distinguish between the possibility that leaf temperatures are generally elevated above ambient air temperatures in cooler environments and the possibility that leaf temperature equals air temperature, whereas the leaf/air temperature at which photosynthesis occurs has a weighted average of near 20°C in cooler environments. Future work will separate these potential explanations.     

Assaying the polyadenylation state of mRNAs

The poly(A) tail present at the 3' end of most eukaryotic mRNAs can play a critical role in message translation and stability. Therefore, identifying alterations in poly(A) tail length can yield important insights into an mRNA's function and subsequent physiological impact. Here, we present three methods for assaying polyadenylation of a specific mRNA in the context of total cellular RNA. The first method described, oligo(dT)/RNase H-Northern analysis, is the classic labor-intensive assay for polyadenylation and is included for historical reference and as a potential experimental control for the poly(A) test (PAT) assays described subsequently. The PAT methods-rapid amplification of cDNA ends-PAT (RACE-PAT), and ligase-mediated PAT (LM-PAT)-are polymerase chain reaction-driven assays that allow speed, sensitivity, and length quantitation. The PAT assays can be conducted in a single day and can readily detect the poly(A) status of an mRNA present in subnanogram quantities of total cellular RNA.     

A MILP-based flux alternative generation and NMR experimental design strategy for metabolic engineering

A mixed-integer linear program (MILP) is described that can enumerate all the ways fluxes can distribute in a metabolic network while still satisfying the same constraints and objective function. The multiple solutions can be used to (1) generate alternative flux scenarios that can account for limited experimental observations, (2) forecast the potential responses to mutation (e.g., new reaction pathways may be used), and (3) (as illustrated) design (13)C NMR experiments such that different potential flux patterns in a mutant can be distinguished. The experimental design is enabled by using the MILP results as an input to an isotopomer mapping matrices (IMM)-based program, which accounts for the network circulation of (13)C from a precursor such as glucose. The IMM-based program can interface to common plotting programs with the result that the user is provided with predicted NMR spectra that are complete with splittings and Lorentzian line-shape features. The example considered is the trafficking of carbon in an Escherichia coli mutant, which has pyruvate kinase activity deleted for the purpose of eliminating acetate production. Similar yields and extracellular measurements would be manifested by the flux alternatives. The MILP-IMM results suggest how NMR experiments can be designed such that the spectra of glutamate for two flux distribution scenarios differ significantly.     

Gene identification by shotgun antisense.

Shotgun antisense is a technique to make a random set of mutant cells or organisms in such a way that one can select an interesting mutant and then sequence part of the mutated gene within a day. In addition to the fantastic rapidity with which one can identify the mutated gene, there are more advantages of this technique over other mutagenesis techniques: (1) one can identify genes that when completely repressed are lethal; (2) one can select which sets of genes will be mutated; and (3) genes that are expressed from multiple copies can be repressed and thus identified.     

CNVDetector: locating copy number variations using array CGH data

CNVDetector is a program for locating copy number variations (CNVs) in a single genome. CNVDetector has several merits: (i) it can deal with the array comparative genomic hybridization data even if the noise is not normally distributed; (ii) it has a linear time kernel; (iii) its parameters can be easily selected; (iv) it evaluates the statistical significance for each CNV calling. AVAILABILITY: CNVDetector (for Windows platform) can be downloaded from http:www.csie.ntu.edu.tw/~kmchao/tools/CNVDetector/. The manual of CNVDetector is also available.     

Production and purification of lentiviral vectors

Lentiviral vectors offer unique versatility and robustness as vehicles for gene delivery. They can transduce a wide range of cell types and integrate into the host genome in both dividing and post-mitotic cells, resulting in long-term expression of the transgene both in vitro and in vivo. This protocol describes how lentiviral vectors can be produced, purified and titrated. High titer suspensions can be routinely prepared with relative ease: a low-titer (10(6) viral particles/ml) unpurified preparation can be obtained 3 d after transfecting cells with lentiviral vector and packaging plasmids; a high-titer (10(9) viral particles/ml) purified preparation requires 2 more days.     

Demiarcs,creaons and genons

Useful insights into the representation of natural systems can be gained by decomposing directed graphs (digraphs) into elementary components. Arcs of digraphs can be split into male demiarcs (outarcs) which leave vertices and female demiarcs (inarcs) which enter demiarcs. Likewise, a vertex can be split into an input perceiving side called the creaon and an output generating side called the genon. Digraphs can be regarded as being hierarchically organized because each vertex in a level-1 digraph can be expanded into a level-2 digraph. In general, each vertex of a level-i digraph can be expanded into a level-(i+1) digraph. Arcs of a level-i digraph can be regarded as bundles of level-(i + 1) arcs which are split at the vertex boundary. These elementary graphical components are shown to be useful for depicting input-output systems such as organisms, ecosystems and societies.     

Recycling of peroxiredoxin IV provides a novel pathway for disulphide formation in the endoplasmic reticulum

Disulphide formation in the endoplasmic reticulum (ER) is catalysed by members of the protein disulphide isomerase (PDI) family. These enzymes can be oxidized by the flavoprotein ER oxidoreductin 1 (Ero1), which couples disulphide formation with reduction of oxygen to form hydrogen peroxide (H(2)O(2)). The H(2)O(2) produced can be metabolized by ER-localized peroxiredoxin IV (PrxIV). Continuous catalytic activity of PrxIV depends on reduction of a disulphide within the active site to form a free thiol, which can then react with H(2)O(2). Here, we demonstrate that several members of the PDI family are able to directly reduce this PrxIV disulphide and in the process become oxidized. Furthermore, we show that altering cellular expression of these proteins within the ER influences the efficiency with which PrxIV can be recycled. The oxidation of PDI family members by PrxIV is a highly efficient process and demonstrates how oxidation by H(2)O(2) can be coupled to disulphide formation. Oxidation of PDI by PrxIV may therefore increase efficiency of disulphide formation by Ero1 and also allows disulphide formation via alternative sources of H(2)O(2).     

Vesicles from peptidic side-chain polymers synthesized by atom transfer radical polymerization

Block copolymers can adopt a wide range of morphologies in dilute aqueous solution. There is a significant amount of interest in the use of block copolymer vesicles for a number of applications. We show that a series of oligo(valine) and oligo(phenylalanine) peptides coupled to a methacrylic group can be prepared by conventional peptide coupling techniques. These can be successfully polymerized by atom transfer radical polymerization (ATRP) in hexafluoroisopropanol (HFIP) giving access to poly(ethylene oxide)- b-poly(side-chain peptides). Many of these polymers self-assemble to form vesicles using an organic to aqueous solvent exchange. One example with a divaline hydrophobic block gives a mixture of toroids and vesicles. Circular dichroism demonstrates that secondary structuring is observed in the hydrophobic region of the vesicle walls for the valine side-chain containing polymers.     

Immunological characterization of peptide mimetics of carbohydrate antigens in vaccine design strategies.

Targeting antigens which cannot be readily addressed by genetic vectors is a major challenge in vaccine design. The inter-conversion of carbohydrate antigens into peptide mimetic forms provides a means to broaden the immune response to carbohydrate antigens. Peptides that mimic carbohydrate antigens offer new possibilities to augment immune responses to such antigens that include inducing carbohydrate reactive T-cell responses. Peptide mimeotopes can be formulated in a variety of ways that include multiple antigen peptides (MAP) and as DNA vaccines that prime for different antibody isotypes. On the immunological side we observe that: (i) depending on the immunogen formulation peptide mimetics can be processed by either CD5+ or CD5-B cells; (ii) peptide mimeotope immunization can induce cross-reactive responses to multiple carbohydrate forms; (iii) priming with peptide mimeotopes can enhance carbohydrate immune responses upon boosting and (iv) immunization with peptide mimeotopes can induce carbohydrate reactive T cells.     

SNPCEQer II: the integrated detection and analysis of SNPs in DNA sequences

SNPCEQer II is a graphical user interface (GUI)-based application that integrates single nucleotide polymorphism (SNP) detection, SNP analysis and SNP editing in the Microsoft Windows (R) environment. SNPCEQer II detects SNPs in DNA sequences generated by the Beckman CEQ TM 2000 XL DNA analysis system. It provides tools to analyse SNPs by inspecting and comparing trace data (chromatograms) around putative SNPs with that of other related DNA sequences, and it can search for those SNPs in the National Center for Biotechnology Information (NCBI) databases. SNPCEQer II can determine the mutation type of a coding SNP and generate data for submission to the dbSNP database. The SNP report can be edited and printed, as can the chromatograms. SNPCEQer II is implemented in Visual C++.     

Metal-free PP<Subscript>i</Subscript> activates hydrolysis of MgPP<Subscript>i</Subscript> by an <Emphasis Type="Italic">Escherichia coli</Emphasis> inorganic pyrophosphatase

Soluble inorganic pyrophosphatase from Escherichia coli (E-PPase) is a hexamer forming under acidic conditions the active trimers. We have earlier found that the hydrolysis of a substrate (MgPP(i)) by the trimers as well as a mutant E-PPase Asp26Ala did not obey the Michaelis-Menten equation. To explain this fact, a model has been proposed implying the existence of, aside from an active site, an effector site that can bind PP(i) and thus accelerate MgPP(i) hydrolysis. In this paper, we demonstrate that the noncompetitive activation of MgPP(i) hydrolysis by metal-free PP(i) can also explain kinetic features of hexameric forms of both the native enzyme and the specially obtained mutant E-PPase with a substituted residue Glu145 in a flexible loop 144-149. Aside from PP(i), its non-hydrolyzable analog methylene diphosphonate can also occupy the effector site resulting in the acceleration of the substrate hydrolysis. Our finding that two moles of [32P]PP(i) can bind with each enzyme subunit is direct evidence for the existence of the effector site in the native E-PPase.     

What can venom phospholipases A(2) tell us about the functional diversity of mammalian secreted phospholipases A(2)?

Most venomous animals including snakes, bees and scorpions contain a variety of venom phospholipases A(2) (vPLA(2)s) which participate in both digestion of prey and venom toxicity. So far, more than 150 vPLA(2)s have been characterized. They all have a conserved fold with several disulfide bridges, can be catalytically active or not, and several of them can display a tremendous array of toxic effects including neurotoxicity and myotoxicity. Furthermore, the molecular diversity of vPLA(2)s found within a single snake venom can result from positive Darwinian selection. Over the last decade, receptors and binding proteins for vPLA(2)s have been identified in mammals, suggesting that vPLA(2)s can exert their toxicities through specific protein-protein interactions, besides their catalytic activity. The brain N-type receptors are involved in the neurotoxicity of vPLA(2)s, but are not yet cloned. The M-type receptor has been cloned from skeletal muscle, belongs to the superfamily of C-type lectins, and interestingly, has homology with vPLA(2) inhibitors purified from snake blood. The molecular diversity of vPLA(2)s and the presence of receptors for vPLA(2)s in mammals raises the possibility that there is also a diversity of mammalian secreted PLA(2)s (msPLA(2)s) which are the normal endogenous ligands of the vPLA(2) receptors. This view led us to clone five novel msPLA(2)s (IID, IIE, IIF, III, and X msPLA(2)s), which together with the previously cloned msPLA(2)s (IB, IIA, IIC, and V), indicate that mammals also express a large diversity of sPLA(2)s. M-type receptors can have IB and IIA msPLA(2)s as natural endogenous ligands, suggesting that msPLA(2)s, like vPLA(2)s, can function as both enzymes and ligands. msPLA(2)s were first implicated in lipid digestion, and more recently in host defense mechanisms including inflammation and antibacterial defense. The growing molecular diversity of msPLA(2)s, which all have a specific tissue distribution, and the presence of receptors suggest that msPLA(2)s, like vPLA(2)s, are endowed with a wide array of biological effects which remain to be discovered.     

Functional analysis of the Xenopus frizzled 7 protein domains using chimeric receptors

Seven-transmembrane receptors of the frizzled family can interact with secreted Wnt ligands and transmit Wnt signals into the cell. Dependent on the ligand receptor combination, distinct Wnt pathways are activated. Xenopus frizzled 7 (Xfz7) and Xwnt-8b as well as Human frizzled 5 (Hfz5) and Xwnt-5a can act synergistically in the activation of Wnt/beta-catenin target genes siamois (Xsia) and nodal related 3 (Xnr3) and in the induction of ectopic axes in Xenopus embryos. In order to characterize the role of different protein domains of Xfz7 in Wnt/beta-catenin signaling, chimeric Xfz7/Hfz5 receptors were generated in which the extracellular (N5-TC7) or the intracellular domains (NT7-C5) between Xfz7 and Hfz5 were exchanged. We present evidence that the extracellular domain of Xfz7 can interact with Xwnt-5a and that the intracellular C-terminus can transmit a Wnt/beta-catenin signal. Despite these abilities, Xfz7 and Xwnt-5a do not act synergistically in the activation of Wnt/beta-catenin targets. This implies that the interaction of a frizzled receptor with different ligands can result in distinct cellular responses.