By Raphael Guerois, Manuela López de la Paz

Protein layout: equipment and functions provides the main updated protein layout and engineering recommendations in order that readers can adopt their very own initiatives with a greatest likelihood of good fortune. The authors current built-in computational methods that require a variety of levels of computational complexity, and the most important accomplishments which have been accomplished within the layout and structural characterization of helical peptides and proteins.

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Extra resources for Protein Design (Methods in Molecular Biology)

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68. , and Vinson, C. 4kcal/mol by phosphorylation of a serine in the e position. Protein Sci. 6, 1273–1283. 69. , and Vinson, C. (1997) Phosphorylation destabilizes alpha-helices. Nat. Struct. Biol. 4, 112–114. 70. Liehr, S. and Chenault, H. K. (1999) A comparison of the α-helix forming propensities and hydrogen bonding properties of serine phosphate and α-amino-γphoshphonobutyric acid. Bioorg. Med. Chem. Lett. 9, 2759–2762. 71. Andrew, C. , Jones, G. , and Doig, A. J. (2002) Effect of phosphorylation on α-helix stability as a function of position.

13. 14. , solvent, buffer salts and the protein/peptide in question. A good starting point in our hands is a peptide concentration of roughly 20 µM with a path length of 1 mm. The cuvette should be of quartz and of CD quality. Wavelength range. Secondary structural information is obtained in the far UV wavelength range, for a typical laboratory instrument this is between 180 and 260 nm. Noise from excessive absorbance can become a problem at the lower wavelength range. This can be checked for in most instruments by monitoring the detector voltage.

Loladze, V. , and Makhatadze, G. I. (2001) Hydration of the peptide backbone largely defines the thermodynamic propensity scale of residues at the C' position of the C-capping box of α-helices. Proc. Nat. Acad. Sci. USA 98, 10670–10675. 110. , Olson, C. , Bell, A. , and Kallenbach, N. R. O H-bonding between Phe and Glu side chains in α-helical peptides. Biophys. Chem. 101–102, 267–279. 111. Smith, J. S. and Scholtz, J. M. (1998) Energetics of polar side-chain interactions in helical peptides: Salt effects on ion pairs and hydrogen bonds.

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