Protein structure analysis, using

PROTEIN STRUCTURE ANALYSIS USING BIOINFORMATICS 619 Sensitive Search 1D/2D/3P Compatibility,... 

Q. Fang and I. Cosic, Protein structure analysis using the resonant recognition model and wavelet transforms,... 

The identification and quantitation of the individual amino acids in a mixture is often required in metabolic studies and investigations of protein structure. The use of thin-layer chromatography or electrophoresis may be adequate to indicate the relative amounts and number of different amino acids in a sample but the use of gas-liquid chromatography or an amino acid analyser is essential for quantitative analysis. 

Structural analysis using both curve-fitting and multivariate statistical methods can be employed to ATR-FTIR spectra. However, because disordered and helix bands may not be well resolved, band assignments in curve-fitting analysis can be difficult. PLS analysis, on the other hand, can determine the secondary structure of proteins from H2O ATR-FTIR spectra with higher accuracy because it is not necessary to assign bands using this method. 

A. S. Yang, B. Honig. An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments. J Mol Biol. 2000, 301, 691-711. 

HMMER [96] is a freely distributable collection of software for protein-sequence analysis using profile HMMs. A profile HMM [97] is a statistical model of a multiple alignment of sequences drawn from a putative protein family. It captures position-specific information about the relative degree of conservation of different columns in an alignment and the relative likelihood of particular residues occurring in specific positions. Profile HMMs can thus capture the essential features of a structural or functional domain. 

Fischer M, Kloiber K, Hausler J, Ledolter K, Konrat R, Schmid W (2007) Synthesis of a C-methyl-group-labeled methionine precursor as a useful tool for simplifying protein structural analysis by NMR spectroscopy. Chembiochem 8 610-612... 

Chemical derivatization methods provide a useful additional tool for protein structural analysis, particularly when conpled with the multistage tandem mass spectrometric capabilities of modern ion trap mass spectrometers. The objective of this chapter was to provide a brief overview of the chemical derivatization strategies that are employed currently to address the challenges associated with protein identification, characterization, and quantitative analysis as well as for the characterization of protein-protein interactions. 

Soderblom, E.J. Goshe, M.B. Collision-induced dissociative chemical cross-linking reagents and methodology applications to protein structural characterization using tandem mass spectrometry analysis. Anal. Chem. 2006, 78, 8059-8068. 

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