How does an amino acid side chain hydrogen bond with RNA? Which residues are most likely...

How does an amino acid side chain hydrogen bond with RNA?

Which residues are most likely to hydrogen bond?

Which residues are most likely to be in the hydrophobic core?

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Expert Solution

3) Hydrophobic Amino Acids

Amino acids are grouped according to what their side chains are like. The nine amino acids that have hydrophobic side chains are glycine (Gly), alanine (Ala), valine (Val), leucine (Leu), isoleucine (Ile), proline (Pro), phenylalanine (Phe), methionine (Met), and tryptophan (Trp). Shown at the right is the structure of valine. These side chains are composed mostly of carbon and hydrogen, have very small dipole moments, and tend to be repelled from water. This fact has important implications for proteins' tertiary structure (see the Proteins 2 module for a discussion of tertiary structure).

1) Hydrogen-bonding interactions often make substantial contributions to the specificity of protein-nucleic acid complexes. Using a geometric modeling approach, we previously identified 28 possible doubly hydrogen-bonded interactions to the four unpaired RNA bases. Here we present interaction energies of these models, calculated by ab initio quantum chemical methods, and describe a correlation between the computed energies and observed frequencies of the interactions. In general, interactions with charged side chains show the most favorable energies. An Asp/Glu-G interaction may be especially favorable for recognition of unpaired guanines in RNAs. Asn and Ser/Thr/Tyr side chains are calculated to make iso-energetic interactions to the Hoogsteen face of adenine, but Asn-A interactions are much more common with DNA than RNA, and Ser/Thr/Tyr-A interactions are more common with RNA than DNA. Examination of the known interactions suggests that Ser/Thr/Tyr may be accommodated in a wider variety of protein contexts at RNA-protein interfaces. With these calculated intrinsic affinities, it should be possible to better assess the contributions of bidentate hydrogen-bonding interactions to RNA- and DNA-binding specificity.

2) Hydrophobic Amino Acids. Amino acids are grouped according to what their side chains are like. The nine amino acids that have hydrophobic side chains are glycine (Gly), alanine (Ala), valine (Val), leucine(Leu), isoleucine (Ile), proline (Pro), phenylalanine (Phe), methionine(Met), and tryptophan (Trp).

queen_honey_blossom answered 1 year ago

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