Several algorithms have been described in the literature for protein identification by searching a sequence database using mass spectrometry data. In some approaches, the experimental data are peptide molecular weights from the digestion of a protein by an enzyme. Other approaches use tandem mass spectrometry (MS/MS) data from one or more peptides. Still others combine mass data with amino acid sequence data. We present results from a new computer program, Mascot, which integrates all three types of search. The scoring algorithm is probability based, which has a number of advantages: (i) A simple rule can be used to judge whether a result is significant or not. This is particularly useful in guarding against false positives. (ii) Scores can be compared with those from other types of search, such as sequence homology. (iii) Search parameters can be readily optimised by iteration. The strengths and limitations of probability-based scoring are discussed, particularly in the context of high throughput, fully automated protein identification.

Probability-based protein identification by searching sequence databases using mass spectrometry data.

http://nhjy.hzau.edu.cn/kech/ssyy/pdf/drought/4.PDF

Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell

The three-dimensional structure of acetylcholinesterase from Torpedo californica electric organ has been determined by x-ray analysis to 2.8 angstrom resolution. The form crystallized is the glycolipid-anchored homodimer that was purified subsequent to solubilization with a bacterial phosphatidylinositol-specific phospholipase C. The enzyme monomer is an alpha/beta protein that contains 537 amino acids. It consists of a 12-stranded mixed beta sheet surrounded by 14 alpha helices and bears a striking resemblance to several hydrolase structures including dienelactone hydrolase, serine carboxypeptidase-II, three neutral lipases, and haloalkane dehalogenase. The active site is unusual because it contains Glu, not Asp, in the Ser-His-acid catalytic triad and because the relation of the triad to the rest of the protein approximates a mirror image of that seen in the serine proteases. Furthermore, the active site lies near the bottom of a deep and narrow gorge that reaches halfway into the protein. Modeling of acetylcholine binding to the enzyme suggests that the quaternary ammonium ion is bound not to a negatively charged "anionic" site, but rather to some of the 14 aromatic residues that line the gorge.

https://science.sciencemag.org/content/sci/253/5022/872.full.pdf

Atomic structure of acetylcholinesterase from Torpedo californica: a prototypic acetylcholine-binding protein

Synthesis, structure and properties of polyhydroxyalkanoates: biological polyesters

ROS signaling: the new wave?

The catalytic properties of cuckoo-pint (Arum maculatum) mitochondrial adenosine triphosphatase have been analysed. The pH profile, effect of inhibitors, cold-stability and substrate specificity are characteristic of mitochondrial adenosine triphosphatases, although a high guanosine triphosphatase activity does appear to be restricted to plant mitochondrial adenosine triphosphatases. The kinetic properties of nucleoside 5'-triphosphate hydrolysis by membrane-bound and soluble enzymes have been studied by means of double-reciprocal plots. These plots were linear in the absence of an activating anion, which may indicate that the catalytic and/or regulatory mechanism of Arum maculatum adenosine triphosphatase is different from that of other enzyme preparations. It is suggested that the differences in subunit composition of plant and mammalian adenosine triphosphatases reported previously [Dunn, Slabas & Moore (1985) Biochem. J. 225, 821-824] are structurally, rather than functionally, significant.

/pdf/characterization-of-cuckoo-pint-arum-maculatum-mitochondrial-5awk2x1iyk.pdf

Characterization of cuckoo-pint (Arum maculatum) mitochondrial adenosine triphosphatases

Currently available cultivars of high erucic acid rape (HEAR) have a theoretical maximum of 66% erucic acid (22:1, Δ13) in their seed oil due to the specificity of the membrane-bound 1-acyl-sn-glycerol-3-phosphate acyltransferase (LPA-AT) enzyme. In HEAR the LPA-AT does not incorporate erucic acid at the s n-2 position of triacylglycerols (TAG) but preferentially incorporates oleic acid (18:1, Δ9), even if this is only a minor component of the total fatty acid pool (1). However, some plant species, e.g Limnanthes, can utilise erucoyl-CoA as a substrate and effectively incorporate erucic acid at the sn-2 position (2, 3).

Engineering Trierucin into Oilseed Rape by the Introduction of a 1-Acyl-sn-Glycerol-3-Phosphate Acyltransferase from Limnanthes Douglasii

β-Ketoacyl-acyl-carrier protein synthase from developing seeds of oilseed rape ( Brassica napus )

In an attempt to rationalize the relationship between structure and substrate selectivity of glycerol-3-phosphate acyltransferase (GPAT, 1AT, EC 2.3.1.15) we have cloned a number of cDNAs into the PET overexpression system using a PCR-based approach. Following assay of the recombinant enzyme we noted that the substrate selectivity of the squash ( Cucurbita moschata ) enzyme had altered dramatically. This form of GPAT has now been crystallized and its full three-dimensional structure elucidated. Since we now have two forms of the enzyme that display different substrate selectivities this should provide a powerful tool to determine the basis of the selectivity changes. Kinetic and structural analyses are currently being performed to rationalize the changes which have taken place.

Antoni R. Slabas

Papers

Characterization of cuckoo-pint (Arum maculatum) mitochondrial adenosine triphosphatases

Engineering Trierucin into Oilseed Rape by the Introduction of a 1-Acyl-sn-Glycerol-3-Phosphate Acyltransferase from Limnanthes Douglasii

β-Ketoacyl-acyl-carrier protein synthase from developing seeds of oilseed rape ( Brassica napus )

Mutagenesis of squash (Cucurbita moschata) glycerol-3-phosphate acyltransferase (GPAT) to produce an enzyme with altered substrate selectivity.

Discovery via Proteomics of a Novel Cell Signalling Pathway in Plants Involving Extracellular ATP