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?

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 2 years ago

Which of the following amino acids has a side chain that can serve as a hydrogen...

Which of the following amino acids has a side chain that can serve as a hydrogen bond donor (but not acceptor) in its predominant form at pH 7? D K M V N

Indicate which of the amino acid residues in the following peptide sequence contains a group that...

Indicate which of the amino acid residues in the following peptide sequence contains a group that has a negative charge for its most likely charge state at pH 4. Met-Tyr-Ile-Trp-Gln-Val-Cys-Pro-Lys

1. What sorts of residues (i.e. what amino acid side chains) would one expect to find...

1. What sorts of residues (i.e. what amino acid side chains) would one expect to find on the surface of a protein with an unusually high isoelectric point (e.g. 9.5). What if the pI were unusually low (e.g. 3.4)? 2. When one talks about “protein-ligand” interactions, what sorts of molecules can be “ligands?” 3. How would you explain the conformational selection model of protein-ligand interactions to an educated lay person?

How do hydrophobic and hydrophilic amino acid residues affect how a protein is folded? Include in...

How do hydrophobic and hydrophilic amino acid residues affect how a protein is folded? Include in your response these two examples of proteins: membrane protein and cytosolic protein.

Which amino acid substitutions are most likely to affect structure/function of the protein? Question 31 options:...

Which amino acid substitutions are most likely to affect structure/function of the protein? Question 31 options: 1) Lys --> Arg 2) Leu --> Ile 3) Arg --> Glu 4) Ser --> Thr Drug A acts by competing with substrate S of the target enzyme. Drug B acts by binding only to the ES complex to form ESB (inactive). If the levels of A and B are fixed, an increase in level S (check all that applied) Question 35 options: 1)...

1. When part of a protein chain, the amino acid proline also lacks a backbone hydrogen...

1. When part of a protein chain, the amino acid proline also lacks a backbone hydrogen bond donor; mutations to proline will delete a backbone hydrogen bond. List two reasons why proline mutagenesis is problematic for selectively studying backbone hydrogen bonds. 2. Draw chemical structures for the amino acids or hydroxy acids with these abbreviations: A, α, F, ϕ 3. Draw the structure of one of the 20 canonical amino acids whose side chain contains a hydrogen bond donor group....

Explain how amino acid structure depends on side chains and pH

1)What are amino acids? Amino group, carboxyl end, what is the side chain of an amino...

1)What are amino acids? Amino group, carboxyl end, what is the side chain of an amino acid? 2)What are essential and non-essential amino acid. 3)Which are the essential amino acids? 4)Classify the amino acids based on polarity of the R group:

Any t-RNA molecule is highly selective toward the amino acid to which it is linked in...

Any t-RNA molecule is highly selective toward the amino acid to which it is linked in forming an aminoacyl t-RNA. There is one t-RNA for every amino acid and chances of obtaining t-RNA molecules linked to wrong amino acids are rare. For example, the incorporation rate of valine into Ile-tRNA is 1 in 200 but the actual mis-incorporation occurs only at about 1 in 3000. Explain the reason for this phenomenon. A. EF-Tu-GTP-aminoacyl-t-RNA halts at the GTP hydrolysis step and...

11.Which of the following sequences of amino acids is the most likely to be located on...

11.Which of the following sequences of amino acids is the most likely to be located on the exterior of a water soluble globular protein? a. Arg-Ser-Gln-Pro-His b. Met-Phe-Ile-Leu-Ala c. Val-Leu-Ser-Ala-Val d. Met-Val-Cys-Leu-Gln QUESTION 12 1. Which pair of amino acid side chains might form a London dispersion force type of van der Waals interaction in a globular protein? a. His and Ser b. Ala and Gln c. His and Met d. Val and Met QUESTION 13 1. The β-hairpin consists...

Question