Working group report: Collider Physics

This is summary of the activities of the working group on collider physics in the IXth Workshop on High Energy Physics Phenomenology (WHEPP-9) held at the Institute of Physics, Bhubaneswar, India in January 2006. Some of the work subsequently done on these problems by the subgroups formed during the workshop is included in this report.     

Incorporation of pseudoproline derivatives allows the facile synthesis of human IAPP, a highly amyloidogenic and aggregation-prone polypeptide

The efficient Fmoc solid-phase peptide synthesis of the 37-residue human Amylin and its amyloidogenic 8-37 fragment was achieved using pseudoproline (oxazolidine) dipeptide derivatives. Syntheses of hAmylin(8-37) using Fmoc amino acids produced only traces of the desired peptide. Incorporation of pseudoproline dipeptides produced the desired product with high yield and allowed for the synthesis of the full length peptide. The crude material was pure enough to allow formation of the Cys-2 to Cys-7 disulfide by air oxidation. [Structure: see text]     

Dynamic NMR line-shape analysis demonstrates that the villin headpiece subdomain folds on the microsecond time scale

There is considerable interest in small proteins that fold very rapidly. These proteins have become attractive targets for both theoretical and computational studies. The independently folded 36-residue villin headpiece subdomain has been the subject of a number of such studies and is predicted to fold quickly. We demonstrate using dynamic NMR line-shape analysis that the protein folds on the time scale of 10 mus. Folding rates were directly estimated between 56 and 78 degrees C using resolved protein resonances from three different residues at both 500 and 700 MHz. The rates estimated using different residues and different field strengths agree well with each other. The estimated folding rate lies between 0.5 and 2.0 x 105 s-1 over this temperature range. The folding rate depends only weakly on temperature.     

Efficient microwave-assisted synthesis of human islet amyloid polypeptide designed to facilitate the specific incorporation of labeled amino acids

A cost-efficient, time-reducing solid-phase synthesis of the amyloidogenic, 37 residue islet amyloid polypeptide (IAPP) is developed using two pseudoprolines (highlighted blue in sequence) in combination with microwave technology. A yield twice that obtained with conventional syntheses is realized. The utility of this protocol is demonstrated by the synthesis of a (13)C(18)O-labeled Ser-20 IAPP variant, a prohibitively expensive and chemically challenging site to label via other protocols. TEM analysis shows the peptide forms normal amyloid (abstract image).     

Separation by hydrophobic interaction chromatography and structural determination by mass spectrometry of mannosylated glycoforms of a recombinant transferrin-exendin-4 fusion protein from yeast

Obtaining sufficient amounts of pure glycoprotein variants to characterize their structures is an important goal in both functional biology and the biotechnology industry. We have developed preparative HIC conditions that resolve glycoform variants on the basis of overall carbohydrate content for a recombinant transferrin-exendin-4 fusion protein. The fusion protein was expressed from the yeast Saccharomyces cerevisiae from high density fermentation and is post-translationally modified with mannose sugars through O-glycosidic linkages. Overall hydrophobic behavior appeared to be dominated by the N-terminal 39 amino acids from the exendin-4 and linker peptide sequences as compared to the less hydrophobic behavior of human transferrin alone. In addition, using LC techniques that measure total glycans released from the pure protein combined with new high resolution technologies using mass spectrometry, we have determined the locations and chain lengths of mannose residues on specific peptides derived from tryptic maps of the transferrin-exendin-4 protein. Though the protein is large (80,488 kDa) and contains 78 possible serine and threonine residues as potential sites for sugar addition, mannosylation was observed on only two tryptic peptides located within the first 55 amino acids of the N-terminus. These glycopeptides were highly heterogeneous and contained between 1 and 10 mannose residues scattered among the various serine and threonine sites which were identified by electron transfer dissociation mass spectrometry. Glycan sequences from 1 to 6 linear mannose residues were detected, but mannose chain lengths of 3 or 4 were more common and formed 80% of the total oligosaccharides. This work introduces new technological capabilities for the purification and characterization of glycosylated variants of therapeutic recombinant proteins.     

On the singularity of Green's tensor for a perfectly conducting semi-infinite cone

This paper is intended to clarify a misunderstanding concerningthe source singularity of the electric Green's tensor for aperfectly conducting semi-infinite cone of circular cross-section.Tai's series expansion of the Green's tensor is known to lacka singular term at the source region. Jones has reconstructedthe solution to this problem and has pointed out the differencebetween his result and that of Tai. The aim of our paper isto demonstrate that, although Jones's closed-form solution iscorrect, there is a mistake in his comparison with Tai's seriessolution. We conclude that one of the two additional singularterms that Jones claims as missing from Tai's formula must beomitted. Besides, we compare Jones's closed-form solution withSmyshlyaev's solution to the very same problem. We concludethat the magnetic field expressions given by Jones and Smyshlyaevcoincide, but a singular term is missing from Smyshlyaev's expressionfor the electric field.     

Differential ordering of the protein backbone and side chains during protein folding revealed by site-specific recombinant infrared probes

The time scale for ordering of the polypeptide backbone relative to the side chains is a critical issue in protein folding. The interplay between ordering of the backbone and ordering of the side chains is particularly important for the formation of β-sheet structures, as the polypeptide chain searches for the native stabilizing cross-strand interactions. We have studied these issues in the N-terminal domain of protein L9 (NTL9), a model protein with mixed α/β structure. We have developed a general approach for introducing site-specific IR probes for the side chains (azide) and backbone ((13)C═(18)O) using recombinant protein expression. Temperature-jump time-resolved IR spectroscopy combined with site-specific labeling enables independent measurement of the respective backbone and side-chain dynamics with single residue resolution. We have found that side-chain ordering in a key region of the β-sheet structure occurs on a slower time scale than ordering of the backbone during the folding of NTL9, likely as a result of the transient formation of non-native side-chain interactions.