This class deals with the fundamental structural features of proteins, which one can understand from the structure of amino acids, and how they are

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1 This class deals with the fundamental structural features of proteins, which one can understand from the structure of amino acids, and how they are put together. 1

2 A more detailed view of a single protein molecule shows that protein structures are intricate and beautiful. The long thread of amino acids (with the side chains omitted in this display) curls into helices, or stretches out straight. The folding of the amino acid chain clearly determines the shape and the properties of the protein. But how? and what determines the folding? 2

3 The movie shows the same protein in a movie sequence. 3

4 The movie shows the same protein in a movie sequence. 4

5 A more detailed view of a single protein molecule shows that protein structures are intricate and beautiful. The long thread of amino acids (with the side chains omitted in this display) curls into helices, or stretches out straight. The folding of the amino acid chain clearly determines the shape and the properties of the protein. But how? and what determines the folding? 5

6 Proteins, even of similar overall shapes, show a bewildering variety of structures. 6

7 A protein is made of a long chain of amino acids that is put together in a precise sequence. This chain then folds into a complicated structure. The sequence of amino acids (the polypeptide chain) is sometimes called the primary structure of the protein. The sequence of the amino acids in a protein is determined by the gene that encodes that particular protein. One type of protein (for example actin, or insulin, or Bet1) may be present in many copies in a cell, but all these copies have the same sequence (primary structure). The secondary structure of the protein is based on local interactions (shortrange interactions) between amino acids. These interactions induce the formation of secondary structures, such as alpha helices and beta sheets (see below). The tertiary structure of proteins is based on the long-range interactions of amino acids, i.e., the interactions between the secondary structure elements. Protein complexes which are composed of several individual proteins (subunits, polypeptide chains) even have a quaternary structure: the way in which the individual subunits are put together. 7

8 In the polypeptide chain, amino acids are linked together by peptide bonds. A peptide bond forms when two amino acids react together, one with its carboxylic acid group, the other with its amino group. Chemically speaking, a peptide bond is an amide bond. If less than 10 amino acids are put together, one tends to talk of an oligopeptide or simply peptide. One can use the Greek numerals (di-, tri-, tetra-, penta-, hexa-, hepta-,...) to tell how many amino acids are in the peptide. For example, the peptide above, made of two amino acids, would be called a dipeptide. 8

9 Every peptide has two distinct termini (ends). The amino or N terminus is the end of the peptide with the free (unbound) alphaammonium group; the carboxyl or C terminus is the end of the peptide with the free alpha-carboxylate group. The atom chain that consists of the alpha carbons (plus their hydrogens), the carboxyl carbons (plus the oxygen), and the amide nitrogens(plus their hydrogens) is called the peptide backbone of the peptide or protein. It is shown in the picture as one horizontal sequence of atoms A protein consists of the peptide backbone and the amino acid side chains. 9

10 A peptide bond, like every amide bond, is a partial double bond. That means the C N bond is somewhere between a single and a double bond in character. This is because of the two resonance forms that exist of the peptide bond, one uncharged (shown on the left) and one charged (with the oxygen carrying a negative charge and the nitrogen, doubly bonded to the carboxyl carbon, carrying a positive charge, as shown on the right). This is because the oxygen attracts the free electron pair of the nitrogen by something called a mesomeric effect. The actual structure lies between the two resonance forms so that it seems like there is a partial negative charge on the oxygen, a partial positive charge on the nitrogen, and a partial double bond between the oxygen and the carboxyl carbon, and the carboxyl carbon and the nitrogen. Importantly, this is not usually visible when the chemical bond structure of a protein backbone is drawn (see the preceding slide). This partial double bond is the reason that the peptide cannot rotate freely around the C-N bond of the peptide backbone, introducing some restraints to the shapes that the peptide molecule can assume. 10

11 The picture shows the geometry of a peptide bond. Since the peptide bond cannot rotate, there are six atoms that are always in a plane. The bonds between nitrogen and the alpha carbon, and the alpha carbon and the carboxyl carbon can be rotated; they are indicated by the circular arrows. The angle of rotation of the N-Cα bond is called phi (φ), the angle of rotation of the Cα-C bond is called psi (ψ). Thus, in the peptide backbone, there are only two variable angles for each amino acid. 11

12 The table shows the Greek alphabet and how its characters are pronounced in (American) English. 12

13 The picture shows part of a polypeptide, indicating all the bonds that can be rotated (with an arrow around them) and the planes of the peptide bonds. 13

14 Are all combinations of φ and ψ equally likely in a protein? No. the most important observation in protein structure is that amino acids in a protein cannot assume all possible combinations of ψ and φ angles. In fact, they are very much restricted. This is because of two things: on one hand, some combinations of ψ and φ would make the side chains of the amino acids clash in space like in the image; but on the other hand, some combinations of ψ and φ are especially favored since they allow the formation of stable secondary structures which are reinforced by hydrogen bonds (see the next slides). 14

15 G. Ramachandran studied all the possible angles of φ and ψ that given amino acids can adopt in a peptide bond. He organized the data into a two-dimensional graph, with the φ values on the x-axis and the ψ values on the y-axis. Every observed combination of ψ and φ values is one cross in the graph. Each color depicts the possible angle combinations for one amino acid. The 'islands' are the combinations that are most frequently found in proteins. This kind of graph is called a Ramachandran plot. 15

16 This slide shows two types of a Ramachandran plot. On the right is a plot showing all the ψ and φ conformation combinations for individual amino acids (glycine in dark green, with the highest variety, proline in pink, with the lowest variety). Certain areas of ψ and φ peptide backbone combinations correspond to certain secondary structures. 16

17 17

18 An alpha helix is the most common secondary structure found in proteins. It was discovered by Linus Pauling. In an alpha helix, the peptide backbone is wound around an imaginary axis, always in one direction, progressing with each turn. Alpha helices have 3.6 amino acids per turn. The rise of the helix (the progress along the central axis with each amino acid) is 0.15 nm. The alpha helical structure is stabilized through hydrogen bonds between an oxygen on the carboxyl carbon of one amino acid and a hydrogen on the nitrogen of an amino acid four amino acids further in the polypeptide. The hydrogen bonds (shown as dashed yellow lines in the illustration on the left) run parallel to the helix axis. This stabilization only works with a very specific set of ψ and φ angles for the peptide backbone, otherwise the stabilizing hydrogen bonds cannot form. 18

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