Structural Proteomics and Its Application

Topic: NMR (Nuclear Magnetic Resonance)

Example one – Incorrect

Key Takeaway: The ChatGPT generated response is inaccurate, even though ChatGPT responds saying the information is scientifically proven right according to its references(given below). One out of the three references when searched in Google Scholar database do not exist (Figure 1). And the other two references provide partial or no clarity to the generated response. This example clearly explains the fictitious responses provided by ChatGPT. These contents and references generated are invalid and could not be used for learning purposes. </p. 

AI can function as a smart pre-assessment tool, testing an individual’s knowledge of a subject before formal evaluations. By deliveing real-time, personalized feedback, it helps reinforce understanding and highlights key areas for improvement, ensuring a more targeted learning approach. 

ChatGPT Prompt: Act as a graduate student in a life science program at a Canadian University studying structural proteomics and its applications course, answer the question with relevant references and citation in APA 7th edition style format.

Question: What are the key principles behind NMR chemical shift assignments in protein structure determination?

ChatGPT Response: In protein structure determination, Nuclear Magnetic Resonance (NMR) spectroscopy plays a pivotal role in providing crucial insights into the three-dimensional arrangement of atoms within a protein (Wagner & Wüthrich, 1982). NMR chemical shift assignments are fundamental steps in this process, as they allow us to establish resonance frequencies for individual atomic nuclei in the protein. These assignments are essential for interpreting NMR spectra and deriving structural information. The key principles underlying NMR chemical shift assignments involve the interaction of atoms with external magnetic fields and the measurement of their resonant frequencies, which are influenced by factors such as chemical environment, magnetic anisotropy, and local electronic effects.

Chemical shifts in NMR spectra are influenced by the magnetic environment of a given nucleus, which is influenced by nearby atoms and their electron distribution. In proteins, the chemical shifts of individual nuclei provide valuable information about their local chemical environments, such as backbone dihedral angles (φ and ψ), secondary structure elements, and interactions with neighboring amino acids. Chemical shift assignments are carried out through a combination of two-dimensional (2D) and three-dimensional (3D) NMR experiments, which provide connectivity information between different atoms in the protein.

One of the primary methods for NMR chemical shift assignments is through the use of through-bond correlation spectroscopy, such as heteronuclear single quantum coherence (HSQC) experiments. These experiments correlate the chemical shifts of neighboring nuclei, allowing for the sequential assignment of amino acid residues along the protein chain. For instance, the backbone amide protons (1H-N) and nitrogen (15N) nuclei are commonly used for sequential assignments due to their sensitivity to local structural changes.

Side-chain chemical shifts can be assigned using through-space correlation spectroscopy techniques, such as through-bond correlations involving carbon atoms (C-COSY) or through-space correlations between proton and carbon atoms (HC-COSY). Additionally, 3D NMR experiments, such as HNCO and HNCA, provide more complex connectivity information, aiding in the assignment of resonances and establishing long-range interactions within the protein.

It’s worth noting that NMR chemical shift assignments can be challenging, particularly for larger and more complex proteins, due to spectral overlap and conformational heterogeneity. Advanced techniques like residual dipolar coupling (RDC) measurements and the use of isotopically labeled samples further aid in resolving ambiguities and enhancing assignment accuracy (Pervushin et al., 1997).

In summary, NMR chemical shift assignments are a critical step in protein structure determination, providing valuable information about local chemical environments and interactions. Through a combination of 2D and 3D NMR experiments, researchers can establish sequential and spatial correlations, enabling the determination of protein structures with high precision. Understanding these key principles is essential for effectively utilizing NMR spectroscopy in structural proteomics studies (Cavanagh et al., 2006).

ChatGPT References:

• Cavanagh, J., Fairbrother, W. J., Palmer, A. G., & Rance, M. (2006). Protein NMR spectroscopy: principles and practice (2nd ed.). Academic Press.

• Pervushin, K., Riek, R., Wider, G., & Wüthrich, K. (1997). Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proceedings of the National Academy of Sciences, 94(23), 12366-12371.
• Wagner, G., & Wüthrich, K. (1982). Sequential resonance assignments as a basis for determination of spatial protein structures by high-resolution proton nuclear magnetic resonance. Journal of molecular biology, 155(4), 347-366.

Validation: Further our validation proves that ChatGPT references were incorrect and do not exist.

Figure: ChatGPT reference could not be found in the Google Scholar Database.

Last Updated November 20, 2024

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