Loops Bends

Roughly half of the residues in a "typical" globular protein reside in a helices and P sheets and half in loops, turns, bends, and other extended conformational features. Turns and bends refer to short segments of amino acids that join two units of secondary structure, such as two adjacent strands of an antiparallel P sheet. A P turn involves four aminoacyl residues, in which the first residue is hydrogen-bonded to the fourth, resulting in a tight 180-degree turn (Figure 5-7). Proline and glycine often are present in P turns.

Loops are regions that contain residues beyond the minimum number necessary to connect adjacent regions of secondary structure. Irregular in conformation, loops nevertheless serve key biologic roles. For many enzymes, the loops that bridge domains responsible for binding substrates often contain aminoacyl residues

Figure 5-4. Hydrogen bonds (dotted lines) formed between H and O atoms stabilize a polypeptide in an a-helical conformation. (Reprinted, with permission, from Haggis GH et al: Introduction to Molecular Biology. Wiley, 1964.)

that participate in catalysis. Helix-loop-helix motifs provide the oligonucleotide-binding portion of DNA-binding proteins such as repressors and transcription factors. Structural motifs such as the helix-loop-helix motif that are intermediate between secondary and tertiary structures are often termed supersecondary structures. Since many loops and bends reside on the surface of proteins and are thus exposed to solvent, they constitute readily accessible sites, or epitopes, for recognition and binding of antibodies.

While loops lack apparent structural regularity, they exist in a specific conformation stabilized through hydrogen bonding, salt bridges, and hydrophobic interactions with other portions of the protein. However, not all portions of proteins are necessarily ordered. Proteins may contain "disordered" regions, often at the extreme amino or carboxyl terminal, characterized by high con-formational flexibility. In many instances, these disor-

Figure 5-5. Spacing and bond angles of the hydrogen bonds of antiparallel and parallel pleated ß sheets. Arrows indicate the direction of each strand. The hydrogen-donating a-nitrogen atoms are shown as blue circles. Hydrogen bonds are indicated by dotted lines. For clarity in presentation, R groups and hydrogens are omitted. Top: Antiparallel ß sheet. Pairs of hydrogen bonds alternate between being close together and wide apart and are oriented approximately perpendicular to the polypeptide backbone. Bottom: Parallel ß sheet. The hydrogen bonds are evenly spaced but slant in alternate directions.

Figure 5-5. Spacing and bond angles of the hydrogen bonds of antiparallel and parallel pleated ß sheets. Arrows indicate the direction of each strand. The hydrogen-donating a-nitrogen atoms are shown as blue circles. Hydrogen bonds are indicated by dotted lines. For clarity in presentation, R groups and hydrogens are omitted. Top: Antiparallel ß sheet. Pairs of hydrogen bonds alternate between being close together and wide apart and are oriented approximately perpendicular to the polypeptide backbone. Bottom: Parallel ß sheet. The hydrogen bonds are evenly spaced but slant in alternate directions.

dered regions assume an ordered conformation upon binding of a ligand. This structural flexibility enables such regions to act as ligand-controlled switches that affect protein structure and function.

Diabetes 2

Diabetes 2

Diabetes is a disease that affects the way your body uses food. Normally, your body converts sugars, starches and other foods into a form of sugar called glucose. Your body uses glucose for fuel. The cells receive the glucose through the bloodstream. They then use insulin a hormone made by the pancreas to absorb the glucose, convert it into energy, and either use it or store it for later use. Learn more...

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