Hi Muhammad Fikri Heikal there is no better way than others when you are doing science, so long as those methods can support each other mutually. It all depends on what kind of information you want to know about protein folding. CD is sensitive to the content of secondary structures such as alpha-helix and beta-sheet of protein and can provide indicative information if the proportion of secondary structures change during the re/unfolding processes.

Raman spectroscopy provides more details about the electron vibration of functional groups (amide I, II&III) within amide plane, disulfide bond, and aromatic side chain, which is made of protein in the context of their secondary and tertiary structures.

Dear Muhammad Fikri Heikal,

I agree with Yun-Tzai. Both Raman spectroscopy and circular dichroism are powerful techniques used for analyzing protein folding and secondary structure, but they offer different types of information and have distinct advantages and limitations. I recommend you scientific articles that can illuminate for you the range of possibilities of these techniques:

Raman spectroscopy: Article Raman Spectroscopic Characterization of Secondary Structure ...

CD: Article Greenfield, N.J. Using circular dichroism spectra to estimat...

The choice between the two methods depends on the specific goals and requirements of your peptide folding analysis. Let's compare both techniques:

1. Raman Spectroscopy:

• provides information about the vibrational and rotational modes of molecules, including peptides and proteins.
• useful for investigating changes in the conformation and tertiary structure of the peptide backbone and side chains.
• can be applied to both aqueous and non-aqueous environments, making it versatile for studying different conditions.
• can be used for real-time monitoring of folding/unfolding processes, allowing for kinetic analysis.
• requires a relatively simple sample preparation and is less sensitive to the concentration of the sample.
• can be more complex to interpret compared to CD spectra, and it might require sophisticated data analysis.

2. Circular Dichroism (CD):

• measures the differential absorption of left- and right-handed circularly polarized light by chiral molecules, providing information on the secondary structure (alpha-helix, beta-sheet, random coil) of peptides and proteins.
• widely used for studying the folding and conformational changes of biomolecules in solution.
• relatively easy to interpret, as distinct patterns in the CD spectra correspond to specific secondary structure elements.
• can be performed under different conditions, including various solvents and temperatures.
• provides qualitative and quantitative information on the secondary structure content of peptides.

However, CD might not provide as much detailed structural information as Raman spectroscopy. If your primary focus is on obtaining detailed information about the vibrational modes and tertiary structure of your peptide during folding, Raman spectroscopy might be a more suitable choice. On the other hand, if you want to primarily analyze the changes in secondary structure during folding, CD would be the preferred method. In some cases, combining both techniques can provide a more comprehensive view of the folding process.

Good luck