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Protein Structure Assignment 1

The document summarizes three questions regarding protein structure analysis and proteomics. For question 1, it describes the intermolecular forces between amino and carbonyl groups that form peptide bonds, including electrostatic forces between positively charged NH3+ and negatively charged COO- groups, and hydrogen bonds between hydrogen and oxygen atoms. For question 2, it estimates the change in nonpolar interaction energy resulting from a decrease in interaction surface area between two binding proteins from 500 Å2 to 300 Å2 as -5 kcal/mol. For question 3, it explains that residues like glycine and proline are often outside allowed regions on Ramachandran plots due to their structural properties, with glycine having more

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80 views

Protein Structure Assignment 1

The document summarizes three questions regarding protein structure analysis and proteomics. For question 1, it describes the intermolecular forces between amino and carbonyl groups that form peptide bonds, including electrostatic forces between positively charged NH3+ and negatively charged COO- groups, and hydrogen bonds between hydrogen and oxygen atoms. For question 2, it estimates the change in nonpolar interaction energy resulting from a decrease in interaction surface area between two binding proteins from 500 Å2 to 300 Å2 as -5 kcal/mol. For question 3, it explains that residues like glycine and proline are often outside allowed regions on Ramachandran plots due to their structural properties, with glycine having more

Uploaded by

ljl010113
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© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Protein Structure Analysis and Proteomics Assignment 1.

Junlin leng 120050010

1. Provide a short, qualitative description of all intermolecular forces that could

associate between amino (NH+3) and carbonyl (C=O) groups.

There are different kinds of intermolecular forces that can join together amino and
carbonyl groups to make the peptide bond form. During the formation process, the
hydrolyzation will happen where water will be released and the N will attach to the
CO.

The first kind of force is the electrostatic forces or ionic interactions between the
positively charged NH3+ and negatively charged COO- groups. This will also form
salt bridges between amino acid sequences.

Another kind of force is the hydrogen bond formed between the hydrogen atom and
the negatively charged atom, for example the oxygen from the carbonyl group.

2. Two proteins bind each other noncovalently in an aqueous solution, with a total

interaction surface (i.e., the interface of both binding partners) of 500 Å2. A pH
change leads to conformational changes in both proteins, which results in a

decrease of their interface to 300 Å2. Estimate the resulting change in the
nonpolar interaction energy?

Nonpolar solutes tend to aggregate in water


Δ𝐺np ≈ −0.025ΔSA
Δ𝐺np is the nonpolar interaction free energy (in kcal/mol)
ΔSA is the surface area of the molecule involved in the interaction

ΔGnp= -0.025ΔSA(surface area) Å2 decrease =200


Therefore... -0.025X200 = -5 kcal/mol

3. When the 𝜙𝜙 and 𝜓𝜓 values of residues in experimentally determined proteins


are collected, some of them reside outside the ‘allowed and partially allowed’
regions of the Ramachandran plot (Figure 1.). Explain what residues and why?
Figure 1. Experimentally obtained Ramachandran plot of an enzyme. Each point on the
map is a combination of 𝜙𝜙 + 𝜓𝜓 values, corresponding to a single amino acid. Blue
and green areas represent allowed and partially allowed 𝜙𝜙 and 𝜓𝜓 combinations,
respectably. White areas represent 𝜙𝜙 and 𝜓𝜓 combinations that are disallowed.

Ramachandran diagrams range in value from -180 to +180 for phi bonds and psi bonds.
The allowed regions of the angular values of these residues represent the range where the
angular values that form the alpha-helix and β-fold secondary structures of proteins are
usually located. The angles to these values are usually naturally selected to give the protein a
stable structure due to the nature of the bond, the side chain of the ammo acid interaction, etc.

However, some residues such as amino acids glycine and proline are usually located outside
these permitted regions.
Glycine -- It doesn't have n atoms of carbohydrate, so it has no side chain. Glycine is the
smallest amino acid and has more space to rotate without experiencing any steric clashes.
Consequently, glycine has a greater range of φ and ψ rotations compared with larger amino
acids.
Proline - Proline has annular side chains, so rotation around the bond is limited by its
inclusion in the pyrrolidine ring; Phi is limited to about -60 degrees, so proline is the most
conformationally restricted amino acid residue, located outside the allowable zone

Other reasons why this value is out of the allowed range are -
- Experimental error of electron density map
- Peptide bond flexibility
- The atomic van der Waals radius in the residue changes slightly.

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