Why do most of the peptide backbones assume trans conformation

The preference for the trans conformation in peptide backbones is primarily due to steric hindrance and energetics. Here are the main reasons why trans conformation is favored:

1. Steric Hindrance: In the cis conformation, the bulky R-groups of adjacent amino acids in the peptide backbone can cause steric clashes or crowding, leading to repulsive interactions between these side chains. This steric hindrance destabilizes the cis conformation, making it less favorable compared to the trans conformation, where the R-groups are positioned on opposite sides of the peptide bond.

2. Energy Considerations: The trans conformation is energetically favored over the cis conformation due to the lower energy associated with the trans peptide bond. This is attributed to the planarity of the peptide bond in the trans conformation, which minimizes torsional strain. In contrast, the cis conformation introduces torsional strain due to the non-planarity of the peptide bond, resulting in higher energy.

3. Hydrogen Bonding: The trans conformation allows for optimal alignment of hydrogen bonding interactions between the carbonyl oxygen of one peptide bond and the amide hydrogen of another peptide bond. In the trans conformation, these hydrogen bonds can form a linear alignment, stabilizing the secondary structures such as α-helices and β-sheets. In contrast, the cis conformation disrupts the hydrogen bonding pattern, leading to reduced stability of secondary structures.

4. Conformational Rigidity: The trans conformation imparts greater conformational rigidity to the peptide backbone compared to the cis conformation. This rigidity is essential for maintaining the structural integrity of proteins and facilitating the folding process. Proteins adopt specific three-dimensional structures based on the stable arrangements of peptide bonds in the trans conformation, allowing them to perform their biological functions effectively.

Overall, the preference for the trans conformation in peptide backbones is driven by a combination of steric hindrance, energy considerations, hydrogen bonding patterns, and conformational rigidity. These factors collectively contribute to the stability and functionality of proteins in biological systems.