Protein Design (Methods in Molecular Biology)

Protein Design (Methods in Molecular Biology)

Language: English

Pages: 300

ISBN: 1588295850

Format: PDF / Kindle (mobi) / ePub

Protein Design: Methods and Applications presents the most up-to-date protein design and engineering strategies so that readers can undertake their own projects with a maximum chance of success.

The authors present integrated computational approaches that require various degrees of computational complexity, and the major accomplishments that have been achieved in the design and structural characterization of helical peptides and proteins.

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69. Szilak, L., Moitra, J., Krylov, D., 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. D., Warwicker, J., Jones, G. R., and Doig, A. J. (2002) Effect of phosphorylation on α-helix stability as a function of position.

Raghothama, S., and Balaram, P. (1998) A designed three stranded βsheet peptide. J. Am. Chem. Soc. 120, 5812–5813. 43. Das, C., Raghothama, S., and Balaram, P. (1999) A four stranded β-sheet structure in a designed synthetic polypeptide. Chem. Commun. 967–968. 44. Venkatraman, J., Naganagowda, G. A., Sudha, R., and Balaram, P. (2001) De novo design of a five-stranded β-sheet anchoring a metal-ion binding site. Chem. Commun. 2660–2661. 94 Mahalakshmi and Balaram 45. Venkatraman, J.,

• NEC Research Laboratories, Princeton, NJ CLAUDIO VITA • Département d’Ingénierie et d’Etudes des Protéines, CEA Saclay, Gif-sur-Yvette, France JUNE YOWTAK • Protein Misfolding Disorders Laboratory, Department of Neurology, University of Texas Medical Branch, Galveston, TX Structure and Stability of the α-Helix 3 1 Structure and Stability of the α-Helix Lessons for Design Neil Errington, Teuku Iqbalsyah, and Andrew J. Doig Summary The α-helix is the most abundant secondary structure in

well-characterized. This small toxin contains an Design of Bioactive Miniproteins 123 antiparallel β-sheet which is linked in the interior core to an α-helix and an extended segment by three disulfide bridges, leaving the solvent exposed face of the β-sheet available to protein design (see Note 4). 3.1.2. Choice of the Active Site Although the forces that stabilize a metal-protein interaction are not yet fully understood and cannot be treated rigorously yet by ordinary force field

or networks of, interactions present in the alignment. This has been applied to TPRs (29), and it revealed that, although the consensus TPRs are highly negatively charged, the natural sequences are mostly near neutral, often with conserved interaction networks between charged residues, lacking in the consensus sequence. Indeed, engineering one such network to the three repeat consensus TPR protein increased the thermostability significantly, even from the already high value Tm = 83°C to an

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