More than a half century ago, evidence began to accumulate that a major part of most proteins' folded structure consists of two regular, highly periodic arrangements, designated a and b. In 1951 researchers worked out the precise nature of these arrangements.
The key to both structures is the hydrogen bond. A hydrogen atom is nothing more than a proton with a surrounding electron cloud. When one of these atoms is chemically bonded to an electron-withdrawing atom such as nitrogen or oxygen, much of the electron cloud moves toward the nitrogen or oxygen. The proton is thus left almost bare, with its positive charge largely unshielded. If it comes close to another atom with a bit of extra negative charge (typically, an oxygen or nitrogen atom), the partial positive and negative charges will attract each other. It is this attraction that produces the hydrogen bond and stabilizes the a and b structures.
The a structure, now called a-helix, is a right-hand spiral stabilized by hydrogen bonds between each amino acid's nitrogen atom and the oxygen atom of the fourth one up the chain. This means that there are 3.6 amino acids for each turn of the helix. The main part of the amino acid (the side chain, designated "R" in the figure) sticks out from this spiral backbone like the bristles on a bottle brush.
The b structure is now called b-sheet. It is essentially flat, with the side chains sticking out on alternate sides. b-sheet is also stabilized by hydrogen bonds between nitrogen and oxygen atoms. In this case, however, the hydrogen-bonded atoms belong to different amino acid chains running alongside each other. The sheets are `parallel' if all the chains run in the same direction and are `antiparallel' if alternate chains run in opposite directions. Antiparallel sheets are often, but not always, formed by a single chain looping back upon itself.
When a single chain loops back on itself to form an antiparallel b-sheet, the one to three amino acids linking the two strands are known as a b-turn. Today, scientists recognize the b-turn as one of the fundamental elements of protein structure. All other local arrangements of amino acids are described as `random coil,' although they are random only in the sense of not being periodic.
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(A) A model alpha-helix shows the hydrogen bonds (dotted lines) between oxygen and hydrogen atoms of the fourth amino acid up the chain. (B) beta-sheets are also held together by hydrogen bonds. The transparent arrows show the direction of individual beta-strands. Chains running in the same direction (left pair) are called parallel beta sheet; strands running in opposite directions (right pair) are said to be anti-parallel beta-sheet. The atom coloring is as follows: carbon = green, oxygen = red, nitrogen = blue, and white = hydrogen. (Courtesy: Stanley Krystek, Bristol-Myers Squibb, Pharmaceutical Research Institute) |