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Protein Structure
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the protein, there is no net change in the number of hydrogen bonds (Fig 2-2) Because the actual number of hydrogen bonds does not change as the secondary structure is formed, it is often argued that hydrogen bonds don t contribute much to the stability of a protein However, hydrogen bonds that form after the protein is already organized into the correct structure may form more stable hydrogen bonds than the ones to water Hydrogen bonding does contribute somewhat to the overall stability of a protein; however, the hydrophobic interaction usually dominates the overall stability Small peptides generally do not form significant secondary structure in water (there are some that do) For small peptides that do not form stable secondary structure, there are often other favorable interactions within the peptide that stabilize the formation of the helix or sheet structure The stability of secondary structure is also influenced by surrounding structures (Fig 2-3) Secondary structure may be stabilized by interactions between the side chains and by interactions of the side chains with other structures in the protein For example, it is possible to arrange the amino acid sequence of a protein or peptide into a helix that has one face that is hydrophobic and one that is hydrophilic The helix wheel shown in Fig 2-3 illustrates how this is possible View the helix as a long cylinder The peptide backbone spirals up and around the cylinder The
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Unfolded Protein 2 H-Bonds
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Folded Protein 2 H-Bonds
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Figure 2-2 Solvation in Protein Folding
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In an unfolded protein, water makes hydrogen bonds to all the donors and acceptors As the protein folds and some polar groups find themselves inside, many of the hydrogen bonds with the solvent are replaced by hydrogen bonds between the different donors and acceptors in the protein Because hydrogen bonds are being replaced rather than gained or lost as the protein folds, there is not a large net stabilization of the protein by the hydrogen bonds
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Basic Concepts in Biochemistry
BOTTOM
TOP Ser 4 1 Gln
Met 8
Phe 1
HYDROPHOBIC FACE 5 Ala 9 Trp
Val 2 3 Ser Leu 4 5 Lys Ala 6 7 Arg Gly 8 9 Thr 7 Gln 3 HYDROPHILIC Asp FACE 10 Lys 6 Gly Arg11 2 Leu
Looking at the side of a -sheet Every other residue is on the same face of the sheet
Looking down the axis of an -helix Residue sequence is numbered The angle between residues is 3608/36 residues or 1008
Figure 2-3
SECONDARY-STRUCTURE STABILIZATION is not provided by just the hydrogen bonds On the left, you re looking at a representation of a sheet in which the amino acid side chains alternately stick up and down If every other side chain is hydrophobic, one side of the sheet will be hydrophobic and the other side will be hydrophilic Interaction of the hydrophobic side with a hydrophobic region on the protein will add stability to the sheet On the right an helix is shown with a hydrophobic and a hydrophilic face Again, putting the hydrophobic face (or surface) up against another hydrophobic region of the protein will stabilize the helix In the helix representation, there is a 100 angle (360 /36 residues) between residues Side chains would stick out from the side of the cylinder defined by the helix
side chains of the amino acid residues point out from the helix Each amino acid residue moves up the helix and around the helix at an angle of 100 (360 /turn 36 residues/turn 100 /residue) What you see in Fig 2-3 is a view looking down the helix axis The side chains are on the side of the circle (cylinder) One surface of the helix has only hydrophobic side chains, while the other side has hydrophilic side chains This is termed an amphipathic helix (or amphiphilic, depending on whether you re a lover or a hater) With these kinds of helices, the hydrophobic face is buried in the interior while the hydrophilic face is exposed to water on the surface There are two ways to look at this The formation of the helix allows it to interact in a very specific way with
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