The eigenmode perspective of NMR spin relaxation in proteins

Area of Science:

• Biophysics
• Structural Biology
• Nuclear Magnetic Resonance (NMR) Spectroscopy

Background:

• The slowly relaxing local structure (SRLS) approach uses physical parameters (diffusion tensors D1, D2; ordering potential u) to model protein dynamics from NMR spin relaxation.
• Current analysis relies on fitting these parameters, providing a macroscopic view of protein motion.

Purpose of the Study:

• To describe protein structural dynamics using eigenmodes derived from SRLS time correlation functions (TCFs).
• To investigate how local and global motion coupling influences these eigenmodes.
• To apply eigenmode analysis to specific protein residues (K19 and A34) in streptococcal protein G.

Main Methods:

• Generation of SRLS TCFs using best-fit parameters as input to the Smoluchowski equation.
• Analysis of TCFs in terms of eigenmodes, characterized by eigenvalues and eigenvectors.
• Investigation of effects of local diffusion axiality, potential strength, and mode-coupling on eigenmode properties.

Main Results:

• Eigenmode analysis reveals distinct patterns of protein and probe motion, including global, local, and mixed modes.
• Multi-exponentiality in TCFs arises from restricted local motion or coupled global/local motion.
• Mixed anti-correlated D1/D2 eigenmodes significantly contribute to SRLS TCFs in K19 and A34 residues.

Conclusions:

• Eigenmode analysis provides a complementary perspective to data-fitting, revealing detailed motion patterns.
• Differences in K19 and A34 dynamics are explained by SRLS parameters and mode-mixing.
• This approach enhances the understanding of protein dynamics at a residue-specific level.