Question

The complete structure of Gramicidin \(\mathrm{S}\), a polypeptide with antibiotic properties, has been worked out as follows: (a) Analysis of the hydrolysis products gave an empirical formula of Leu, Orn, Phe, Pro, Val. (Ornithine, Orn, is a rare amino acid of formula \(\left.{ }^{+} \mathrm{H}_{3} \mathrm{NCH}_{2} \mathrm{CH}_{2} \mathrm{CH}_{2} \mathrm{CH}\left(\mathrm{NH}_{2}\right) \mathrm{COO}^{-} .\right)\) It is interesting that the phenylalanine has the unusual D-configuration. Measurement of the molecular weight gave an approximate value of \(1300 .\) On this basis, what is the molecular formula of Gramicidin \(\mathrm{S} ?\) (b) Analysis for the C-terminal residue was negative; analysis for the N-terminal residue using DNFB yielded only DNP-NHCH \(_{2} \mathrm{CH}_{2} \mathrm{CH}_{2} \mathrm{CH}\left(\mathrm{N}^{+} \mathrm{H}_{3}\right) \mathrm{COO}^{-}\). What structural feature must the peptide chain possess? (c) Partial hydrolysis of Gramicidin \(\mathrm{S}\) gave the following di- and tripeptides: Leu.Phe Phe.Pro Phe.Pro.Val Val.Orn.Leu \(\begin{array}{lll}\text { Orn.Leu } & \text { Val.Orn } & \text { Pro. Val.Orn }\end{array}\) What is the structure of Gramicidin \(\mathrm{S} ?\)

Short answer

The molecular formula of Gramicidin S is 2(Leu, Orn, Phe, Pro, Val), and it has a cyclic polypeptide chain structure with the amino acid sequence: Leu-Phe-Pro-Val-Orn-Leu-Val-Orn-Phe-Pro.

Step-by-step solution

Find the molecular formula based on empirical formula and molecular weight

First, we have to calculate the molecular weight of the empirical formula: Leu, Orn, Phe, Pro, and Val. Then we will multiply the empirical formula with an integer to get a molecular weight close to the given value of 1300. Molecular weight of Leu (Leucine) = 131 Molecular weight of Orn (Ornithine) = \(HNCH_2 CH_2 CH_2 CH(NH_2) COO^{-}\) = 132 (ignoring charges) Molecular weight of Phe (Phenylalanine) = 165 Molecular weight of Pro (Proline) = 115 Molecular weight of Val (Valine) = 117 Total molecular weight of empirical formula = 131 + 132 + 165 + 115 + 117 = 660. Now, we will multiply this empirical formula with an integer such that the resulting molecular weight is close to 1300. In this case, multiplying the empirical formula by 2 will give us a molecular weight of 660 × 2 = 1320, which is close to 1300. So, the molecular formula of Gramicidin S is 2(Leu, Orn, Phe, Pro, Val).

Analyze the structural feature based on the N-terminal residue result

The given information about the N-terminal residue analysis states that it only yielded the derivatized Ornithine (Orn). This indicates that the polypeptide chain does not have any free N-terminus, which is possible only if the chain is circular. Therefore, the polypeptide chain of Gramicidin S must be cyclic.

Determine the structure of Gramicidin S using partial hydrolysis data

Using the information about dipeptides and tripeptides obtained from partial hydrolysis, we will construct the cyclic structure of Gramicidin S. From the given information, we have the following peptide sequence: Leu.Phe, Phe.Pro, Phe.Pro.Val, Val.Orn.Leu, Orn.Leu, Val.Orn, Pro.Val.Orn Combining these sequences, we get the order of amino acids in the cyclic polypeptide chain as: Leu-Phe-Pro-Val-Orn-Leu-Val-Orn-Phe-Pro Hence, the structure of Gramicidin S is a cyclic polypeptide chain with the amino acid sequence: Leu-Phe-Pro-Val-Orn-Leu-Val-Orn-Phe-Pro

Key concepts

Polypeptide Chains

A polypeptide chain is a long molecule typically formed by linking amino acids together via peptide bonds. Each amino acid in this chain is called a "residue." When amino acids bond, the carboxyl group of one amino acid links to the amino group of the next, forming the backbone of the polypeptide chain.
Polypeptides differ in length, from a few amino acids up to hundreds, and they can fold into complex shapes that are crucial for their biological function.
In the context of Gramicidin S, the polypeptide is a sequence of ten amino acids that specifically forms a cyclic structure, which is unique compared to the typical linear formation of most polypeptides found in proteins.

• Linear vs Cyclic: Most polypeptides are linear, but cyclic polypeptides form a loop, joining the ends of the chain.
• Functionality: Cyclic peptides like Gramicidin S often have enhanced stability and biological activity, making them effective in unique roles such as antibiotics.

Understanding polypeptide chains is foundational to learning about protein structure and function.

Cyclic Peptides

Cyclic peptides are a distinct type of polypeptide wherein the chain forms a closed loop, which can be achieved through various linkages between the terminal ends or between side chains of the amino acids.
These structures are key in many biological processes and often found in nature with potent biological activities, like antibiotic properties in some cases.

• Structure: In Gramicidin S, the peptide chain is cyclic, meaning there is no free N-terminal or C-terminal residue. This impacts its function as an antibiotic.
• Stability: Cyclic peptides are generally more stable than their linear counterparts because the loop reduces degradation and the flexibility is decreased.
• Applications: Besides serving as antibiotics, cyclic peptides can play roles in cell signaling and enzyme inhibition due to their enhanced binding capabilities.

The cyclic nature of Gramicidin S contributes to its effectiveness in biological applications, being resistant to enzymes that usually degrade linear peptides.

Amino Acid Sequence

An amino acid sequence in a polypeptide determines both its three-dimensional structure and function. Each amino acid is a distinct building block containing an amino group, carboxyl group, and a unique side chain, which dictates its properties and the sequence's overall structure.
The sequence in Gramicidin S is crucial as it dictates the biological activity of the antibiotic. The specific sequence involves the unusual D-configuration for phenylalanine, which influences how the peptide interacts with bacterial membranes.

• Directionality: Amino acid sequences have a specific direction from the N-terminus to the C-terminus in typical polypeptides, but in cyclic peptides, this continuity loop allows for a different kind of order.
• Gramicidin S Sequence: Leu-Phe-Pro-Val-Orn-Leu-Val-Orn-Phe-Pro is the order of amino acids, creating the specific ring structure.
• Importance: The sequence is essential for the peptide's desired properties, like membrane interaction and stability against degradation.

A clear understanding of the precise amino acid sequence allows us to appreciate how Gramicidin S functions effectively in its role.