Proteins secondary structure and

Zvelebil, M.J., et al. Prediction of protein secondary structure and active sites using the alignment of homologous sequences. /. Mol. Biol. 195 957-961, 1987. 

Protein folding Glycosylation can effect local protein secondary structure and help direct folding of the polypeptide chain... 

A review by Dong et al. [3.57] provides an overview of how Fourier transform JR spectroscopy can be used to study protein stabilization and to prevent lyophilization- induced protein aggregation. An introduction to the study of protein secondary structures and the processing and interpretation of protein IR spectra is given. 

Johnson, W.C. 1990. Protein secondary structure and circular dichroism A practical guide. Proteins Struct., Fund, Genet. 7 205-214. 

Yang, J. T., Protein secondary structure and circular dichroism a practical guide. Chemtracts, Biochem. Mol. Biol. 1 484-490, 1990. 

O. B. Ptitsyn and A. V. Finketatein. Theory of protein secondary structure and... 

Bohr, H., Bohr, J., Brunak, S., Cotterill, R. M., Lautrup, B., Norskov, L., Olsen, O. H. Petersen, S. B. (1988). Protein secondary structure and homology by neural networks. The alpha-helices in rhodopsin. FEBS Lett 241,223-8. 

It has been observed that the use of protein tertiary structural class improved the accuracy for a 2-state secondary structure prediction (Kneller et al., 1990). A modular network architecture was proposed using separate networks (i.e., a- or P-type network) for classification of different secondary structures (Sasagawa Tajima, 1993). Recently, Chandonia Karplus (1995) trained a pair of neural networks to predict the protein secondary structure and the structural class respectively. Using predicted class information, the secondary structure prediction network realized a small increase in accuracy. 

Calculation of octanol/water partition coefficients. SciLogW for aqueous solubility prediction. SciPredictor for protein secondary structure and homology modeling. SciPolymer for polymer property estimation. PCs under Windows. CAD Gene for gene constructs. Macintosh. 

Pollastri G, Martin AJ, Mooney C, Vullo A. Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information. BMC Bioinformatics. 2007 8 201. 

E. M. Marassi, A simple approach to membrane protein secondary structure and topology based on NMR spectroscopy. Biophys. J., 2001, 80, 994—1003. 

D Correlation Spectroscopy. A simple, quahtative approach has been described for the determination of membrane protein secondary structure and topology in lipid bilayer membranes." The new approach is based on the observation of wheel-like resonance patterns in the NMR H- N/ N polarization inversion with spin exchange at the magic angle (PISEMA) and H/ N HETCOR spectra of membrane proteins in oriented lipid bilayers. These patterns, named Pisa wheels, have been previously shown to reflect helical wheel projections of residues that are characteristic of a-helices associated with membranes. This study extends the analysis of these patterns to P-strands associated with membranes and demonstrates that, as for the case of a-helices, Pisa wheels are extremely sensitive to the tilt, rotation, and twist of P-strands in the membrane and provide a sensitive, visually accessible, qualitative index of membrane protein secondary structure and topology. 

M. J. E. (1987) Prediction of Protein Secondary Structure and Active Sites using the Alignment of Homologous Sequences, J. Mol. Biol. 195 957-961. 

Complexes that feature a-helices at interfaces were studied because a-helices constitute the largest class of protein secondary structure and mediate many protein interactions [30, 51]. Helices located within the protein core are vital for the overall stability of protein tertiary structure, whereas exposed a-helices on protein surfaces constitute central bioactive regions for the recognition of numerous proteins, DNAs, and RNAs. Importantly, helix mimetics have emerged as a highly effective class of PPI inhibitors [32, 36, 44, 52-55]. 

Hydrogen bonding is clearly ubiquitous in stabilising protein secondary structures and nucleic acid double helices (by Watson-Crick base pairing between anti-parallel phosphodiester chains), and in the wide range of homoglycan secondary to quaternary structures. 

Prediction of Protein Secondary Structure and Active Sites Using the Alignment of Homologous Sequences. 

Implicit in the kinetic mechanism proposed here is the idea that a helix (probably an a-helix) is the main protein secondary structure and that all the other secondary structures arise from the breaking and destabilization of the a-helices. This new kinetic mechanism may explain the high helidty of short polypeptides that are part of jS-strands, as well as the presence of a-helical intermediates in the folding of predominantly j8-sheet proteins. The hierarchical nature of protein structure is also a natural consequence of the mechanism since that main secondary structure is present from the beginning and the tertiary structure results from the breaks and, either the packing of the helical stretches that arise in that early process, or the packing of the jS-sheets that form later when the first process happens to lead to unfavourable side chain interactions. 

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