A phase I, randomized study of combined IL-2 and therapeutic immunisation with antiretroviral therapy

Background  

Fully functional HIV-1-specific CD8 and CD4 effector T-cell responses are vital to the containment of viral activity and disease progression. These responses are lacking in HIV-1-infected patients with progressive disease. We attempted to augment fully functional HIV-1-specific CD8 and CD4 effector T-cell responses in patients with advanced chronic HIV-1 infection.     

Photochirogenesis: photochemical models on the absolute asymmetric formation of amino acids in interstellar space

Proteins of all living organisms including plants, animals, and humans are made up of amino acid monomers that show identical stereochemical L-configuration. Hypotheses for the origin of this symmetry breaking in biomolecules include the absolute asymmetric photochemistry model by which interstellar ultraviolet (UV) circularly polarized light (CPL) induces an enantiomeric excess in chiral organic molecules in the interstellar/circumstellar media. This scenario is supported by a) the detection of amino acids in the organic residues of UV-photo-processed interstellar ice analogues, b) the occurrence of L-enantiomer-enriched amino acids in carbonaceous meteorites, and c) the observation of CPL of the same helicity over large distance scales in the massive star-forming region of Orion. These topics are of high importance in topical biophysical research and will be discussed in this review. Further evidence that amino acids and other molecules of prebiotic interest are asymmetrically formed in space comes from studies on the enantioselective photolysis of amino acids by UV-CPL. Also, experiments have been performed on the absolute asymmetric photochemical synthesis of enantiomer-enriched amino acids from mixtures of astrophysically relevant achiral precursor molecules using UV-circularly polarized photons. Both approaches are based on circular dichroic transitions of amino acids that will be highlighted here as well. These results have strong implications on our current understanding of how life's precursor molecules were possibly built and how life selected the left-handed form of proteinogenic amino acids.     

A photoimmobilisation strategy that maximises exploration of chemical space in small molecule affinity selection and target discovery

We show that the use of multiple photochemistries is necessary to ensure diverse immobilisation of small molecules for binding of polypeptides using phage display and antibody libraries.     

MALDI-TOF/TOF de novo sequence analysis of 2-D PAGE-separated proteins from Halorhodospira halophila, a bacterium with unsequenced genome

Because protein identifications rely on matches with sequence databases, high-throughput proteomics is currently largely restricted to those species for which comprehensive sequence databases are available. The identification of proteins derived from organisms with unsequenced genomes mainly depends on homology searching. Here, we report the use of a simplified, gel-based, chemical derivatization strategy for de novo sequence analysis using a MALDI-TOF/TOF mass spectrometer. This approach allows the determination of de novo peptide sequences of up to 20 amino acid residues in length. The protocol was applied on a proteomic study of 2-D PAGE-separated proteins from Halorhodospira halophila, an extremophilic eubacterium with yet unsequenced genome. Using three different homology-based search algorithms, we were able to identify more than 30 proteins from this organism using subpicomole quantities of protein.     

A case study of de novo sequence analysis of N-sulfonated peptides by MALDI TOF/TOF mass spectrometry

The simplicity and sensitivity of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry have increased its application in recent years. The most common method of "peptide mass fingerprint" analysis often does not provide robust identification. Additional sequence information, obtained by post-source decay or collision induced dissociation, provides additional constraints for database searches. However, de novo sequencing by mass spectrometry is not yet common practice, most likely because of the difficulties associated with the interpretation of high and low energy CID spectra. Success with this type of sequencing requires full sequence coverage and demands better quality spectra than those typically used for data base searching. In this report we show that full-length de novo sequencing is possible using MALDI TOF/TOF analysis. The interpretation of MS/MS data is facilitated by N-terminal sulfonation after protection of lysine side chains (Keough et al., Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 7131-7136). Reliable de novo sequence analysis has been obtained using sub-picomol quantities of peptides and peptide sequences of up to 16 amino acid residues in length have been determined. The simple, predictable fragmentation pattern allows routine de novo interpretation, either manually or using software. Characterization of the complete primary structure of a peptide is often hindered because of differences in fragmentation efficiencies and in specific fragmentation patterns for different peptides. These differences are controlled by various structural parameters including the nature of the residues present. The influence of the presence of internal Pro, acidic and basic residues on the TOF/TOF fragmentation pattern will be discussed, both for underivatized and guanidinated/sulfonated peptides.