lec08 - MIT OpenCourseWare http:/ocw.mit.edu 7.88J Protein...

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MIT OpenCourseWare http://ocw.mit.edu 7.88J Protein Folding Problem Fall 2007 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms .
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7.88 Lecture Notes - 8 7.24/7.88J/5.48J The Protein Folding Problem S-peptide Helices Continued S-peptide Reprise Fos/Jun Helix Dipole (10 min) S peptide of ribonuclease S. (20 min) Helicity of S- peptide variants (30 min) Presta and Rose model for helix start and stop in proteins (reading) A. Reprise Fos/Jun If prepare homodimers, analyze under conditions that suppress shuffling (acidic, no S-): HPLC trace with both homodimers Now incubate (room temp, 1 hour) with redox buffer – mixture of oxidized and reduced glutathion; these conditions promote S-S >Sh + SH > S-S- Find a single peak of heterodimer: So chains exchanging, even though both species are below their melting temperatures: Classes of helices: Fibrous proteins – Insoluble, helicity deduced In globular proteins, observed by X-ray diffraction –ridges into grooves packing In coiled/coils, X-ray scattering and diffraction – is this packing ridges into groves?? Isolated?? Coiled Coils stabilized by: Hydrophobic strip Charge charge interactions/salt bridges H- bonds buried hydrophobic core Continue with investigations of actual dynamics of chain motion and folding Helix: Today we will focus on the formation of an alpha helix formation within an isolated peptide chain, non helical polypeptide chain, and the sequence specific interactions which stabilize and destabilize such species.
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B. Helix Dipoles Originally proposed by Wada (1976), Adv. in Biophysics, 9 , 1-63. Alignment of peptide dipoles, parallel to the helix axis, gives rise to a a macro-dipole of considerable strength. Each peptide bond has a dipole: about 3.6 Debye units. In a helix, these point up axis: For 10 residues 34D, as 97% of the peptide dipole points in direction of helix axis. For points near the terminus of the helix the effect of the dipoles is the equivalent of half a positive charge at the N-terminus and half a negative charge at the C-terminus. . In a number of native proteins, the charge on the helical dipole is playing a functional role in the protein. For example in the sulfate binding protein. The negatively charged SO4 -- ion is bound in a pocket defined by the amino terminus of three helices. Presumably the helix dipoles are contributing to the biding and charge neutralization. Similar in a number of enzymes that bind a phosphate, the phosphate is associated with the N-termini of alpha helices in proteins. However, what about the role of these macro-dipoles in the folding of the protein. Hol, Wim G. J., Louis M. Halie, and Christian Sander. “Dipoles of the alpha helix and
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lec08 - MIT OpenCourseWare http:/ocw.mit.edu 7.88J Protein...

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