lec05-Packing of Secondary Structures Beta-sheets and Beta-sheet Packing

Lec05-Packing of Secondary Structures Beta-sheets and Beta-sheet Packing

Info iconThis preview shows pages 1–3. Sign up to view the full content.

View Full Document Right Arrow Icon
7.88 Lecture Notes - 5 7.24/7.88J/5.48J The Protein Folding Problem Packing of Secondary Structures Packing of Helices against sheets Packing of sheets against sheets Parallel Orthogonal Table: “Amino Acid Composition of the Ten Proteins and of the Residues at the Helix to Helix Interfaces” Name Total % Total At contacts % at contacts Gly 182 9 15 4 Ala 191 9 49 12 Val 151 7 46 12 Leu 148 7 48 12 Ile 114 6 36 9 Pro 67 3 41 1 Phe 68 3 25 6 Tyr 87 6 14 4 Trp 35 2 7 2 His 45 2 18 5 ½Cys 21 1 3 1 Met 29 1 10 3 Ser 165 8 19 5 Thr 132 7 21 5 Asp 112 6 14 4 Asn 113 6 13 3 Glu 94 5 13 3 Gln 70 3 12 3 Lys 125 6 19 5 Arg 76 4 13 3 A. Factors Contributing to Stability of Correctly Folded Native State 1. Major source of stability = removal of hydrophobic side chains atoms from the solvent and burying in environment which excludes the solvent (Entropic contribution from water structure).
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
2. Formation of hydrogen bonds between buried amide and carbonyl groups is maximized 3. Retention of backbone conformations close to the minimal energies. 4. Close packing means optimal Van der Waals interactions. You have read about alpha/beta proteins in Brandon and Tooze . B. Helix to Sheet Packing Lets examine buried contacts between the helices and the sheets. First a quick review of beta sheet structure: Colored transparency: Theoretical model, not actual sheet. A very general feature of beta sheets is that the strands are twisted with respect to their own elongated axis, and that sheets represented hydrogen bonded strands, are also twisted, in all cases seen so far, to the right. This presumably represents the fact that the amino acids are all L; This twist is expressed in the negative value of the dihedral angle omega between pairs of adjacent strands. The packing of alpha helices against sheets examined carefully by: Janin, and Chothia. J. Mol. Biol. 143: 95-128. Chothia, Cyrus, Michael Levitt, and Douglas Richardson. ”Structure of Proteins: Packing of alpha-Helices and pleated sheets.” Proc. Nat. Acad. Sci. Saa 74 (1980): 4130-4134. [1977]. Very common to have alpha helices packed on the outsides of beta sheets. Examined set of well determined alpha/beta structures: In the set of proteins they examine, the average strand length was 7 residues, not very much dispersion; the shorter strands represented edge strands. Both parallel and anti-parallel sheets have a right-handed twist when viewed along axis. C-alpha separate along strands for residues on same side is 7A, and between
Background image of page 2
Image of page 3
This is the end of the preview. Sign up to access the rest of the document.

Page1 / 14

Lec05-Packing of Secondary Structures Beta-sheets and Beta-sheet Packing

This preview shows document pages 1 - 3. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online