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Protein structure
Mar. 7th, 2015 07:15 pmConformation is the arrangement of atoms in a protein. Changes in conformation are achieved by anything that doesn't break covalent bonds, like rotation about a single bond.
Out of the gazillions of possible conformations, only a few are stable and lead to functionality. These are called native conformations, they are thermodynamically favorable, and they are stabilized largely by weak interaction, like hydrogen bonds and van der Waals bonds.
Any hydrogen atom on a protein that's exposed to water forms a hydrogen bond to a water molecule. This creates a shell, called a solvation layer, of water molecules around the protein.
This shell tends to be minimized. The hydrophobic interactions of the protein tend to hide the hydrophobic parts of the protein away from the water. This is part of what governs protein shape.
The number of hydrogen bonds within the protein is maximized.
The peptide bond forms between the C of the carboxyl group and the N of the amine group.
The 6 elements of a peptide group are the two C-alphas, the O, the N, the H, and the C of the carboxyl group.
They're all in the same plane, leading to a certain amount of rigidity. The peptide C-N bond is shorter than the C-N bond in a simple amine. There is some sharing of electrons (resonance) between the carbonyl oxygen and the amide nitrogen, leading to a double bond, leading to the prevention of rotation about that bond, leading to planarity.
In contrast, the N--C-alpha and C-alpha--C bonds can rotate about angles designated phi and psi.
The carbonyl oxygen has a partial negative charge and the amide nitrogen a partial positive charge, leading to a small electric dipole.
Even with the bonds around which rotation is permitted, not all angles are permitted, since some bring electron groups of one atom into conflict with another (steric overlap).
The simplest secondary structure a protein can achieve with the peptide bond rigid, but others free to rotate, is an alpha-helix, which makes optimal use of internal hydrogen bonds. Every peptide bond, except those near the end of the helix, participates in hydrogen bonding. Each turn in the helix is linked by 3-4 hydrogen bonds to adjacent turns.
But not all amino acids are amenable to alpha helixes. Glutamate has negatively charged side groups that repel each other so strongly they prevent hydrogen bonds from forming. Likewise, Lysine and Arginine groups are positively charged and repel each other. The polar uncharged groups can destabilize alpha helixes with their bulk and shape.
Amino acid chains are often organized so that compatible molecules occur 3-4 links away from each other on the chain, which permits the formation of an alpha-helix.
Proline has a ring that interferes with alpha helixes. Glycine has so many options for conformation that it tends to occur in different coiled structures.
The net dipoles of the helix add up, so that at the amino-terminal end, negatively charged amino acids are often found, and positively charged amino acids are found at the carboxyl-terminal end of the helical segment.
The beta-conformation involves zigzags. Beta sheets are several zigzagged lengths linked together in parallel. When beta-sheets are layered together, the R groups on the touching surfaces must be small. So Glycine and Alanine tend to predominate.
A beta turn is where the polypeptide chain reverses direction. Glycine and proline occur in beta turns, because glycine is small and flexible, and proline because of something complicated that's conducive to a tight turn.
Fibrous proteins are important for structure. Globular proteins are important for doing work.
Collagen is a really strong fibrous protein. It consists of supertwisted helixes. If an amino acid with a larger R group is substituted for glycine, the protein can't pack correctly, and it loses its structural strength, leading to defects, like loose joints.
Supersecondary structures, also called motifs or folds, are particularly stable arrangements of several elements of secondary structure and the connections between them.
It's easier to copy a smaller protein many times than to copy one large protein once. Less chance of making mistakes in transcription.
Out of the gazillions of possible conformations, only a few are stable and lead to functionality. These are called native conformations, they are thermodynamically favorable, and they are stabilized largely by weak interaction, like hydrogen bonds and van der Waals bonds.
Any hydrogen atom on a protein that's exposed to water forms a hydrogen bond to a water molecule. This creates a shell, called a solvation layer, of water molecules around the protein.
This shell tends to be minimized. The hydrophobic interactions of the protein tend to hide the hydrophobic parts of the protein away from the water. This is part of what governs protein shape.
The number of hydrogen bonds within the protein is maximized.
The peptide bond forms between the C of the carboxyl group and the N of the amine group.
The 6 elements of a peptide group are the two C-alphas, the O, the N, the H, and the C of the carboxyl group.
They're all in the same plane, leading to a certain amount of rigidity. The peptide C-N bond is shorter than the C-N bond in a simple amine. There is some sharing of electrons (resonance) between the carbonyl oxygen and the amide nitrogen, leading to a double bond, leading to the prevention of rotation about that bond, leading to planarity.
In contrast, the N--C-alpha and C-alpha--C bonds can rotate about angles designated phi and psi.
The carbonyl oxygen has a partial negative charge and the amide nitrogen a partial positive charge, leading to a small electric dipole.
Even with the bonds around which rotation is permitted, not all angles are permitted, since some bring electron groups of one atom into conflict with another (steric overlap).
The simplest secondary structure a protein can achieve with the peptide bond rigid, but others free to rotate, is an alpha-helix, which makes optimal use of internal hydrogen bonds. Every peptide bond, except those near the end of the helix, participates in hydrogen bonding. Each turn in the helix is linked by 3-4 hydrogen bonds to adjacent turns.
But not all amino acids are amenable to alpha helixes. Glutamate has negatively charged side groups that repel each other so strongly they prevent hydrogen bonds from forming. Likewise, Lysine and Arginine groups are positively charged and repel each other. The polar uncharged groups can destabilize alpha helixes with their bulk and shape.
Amino acid chains are often organized so that compatible molecules occur 3-4 links away from each other on the chain, which permits the formation of an alpha-helix.
Proline has a ring that interferes with alpha helixes. Glycine has so many options for conformation that it tends to occur in different coiled structures.
The net dipoles of the helix add up, so that at the amino-terminal end, negatively charged amino acids are often found, and positively charged amino acids are found at the carboxyl-terminal end of the helical segment.
The beta-conformation involves zigzags. Beta sheets are several zigzagged lengths linked together in parallel. When beta-sheets are layered together, the R groups on the touching surfaces must be small. So Glycine and Alanine tend to predominate.
A beta turn is where the polypeptide chain reverses direction. Glycine and proline occur in beta turns, because glycine is small and flexible, and proline because of something complicated that's conducive to a tight turn.
Fibrous proteins are important for structure. Globular proteins are important for doing work.
Collagen is a really strong fibrous protein. It consists of supertwisted helixes. If an amino acid with a larger R group is substituted for glycine, the protein can't pack correctly, and it loses its structural strength, leading to defects, like loose joints.
Supersecondary structures, also called motifs or folds, are particularly stable arrangements of several elements of secondary structure and the connections between them.
It's easier to copy a smaller protein many times than to copy one large protein once. Less chance of making mistakes in transcription.
