Chapter 5: Problem 14

Briefly describe the technique of NMR spectroscopy as it applies to protein structure determination.

Short Answer

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Answer: The main structural information obtained in NMR studies of protein structure comes from the measurement of distances between atom pairs, based on the nuclear Overhauser effect (NOE). A large number of NOE-derived distance restraints, along with other restraints such as dihedral angles and hydrogen bonds, are used to compute the 3D structure of the protein in solution using computational methods like molecular dynamics simulations and simulated annealing.

Step by step solution

Introduction to NMR Spectroscopy

Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful technique used in chemistry, biology, and physics to study the structure, dynamics, and interactions of molecules. It is based on the magnetic properties of atomic nuclei, specifically those with an odd number of protons and/or neutrons, such as hydrogen-1 (1H), carbon-13 (13C), and nitrogen-15 (15N) nuclei.

Basic Principles of NMR

In NMR spectroscopy, the sample is placed in a magnetic field, and radiofrequency pulses are used to excite the magnetic moments of the nuclei. The nuclei then undergo relaxation and emit radiofrequency signals, which are measured and analyzed to determine the properties of the molecule. The chemical environment of each nucleus affects its resonance frequency, giving rise to characteristic NMR spectra that can be used to deduce structural information.

Multi-dimensional NMR Techniques

To study protein structure, multi-dimensional NMR techniques are used, such as 2D, 3D, and 4D NMR experiments. These experiments involve recording spectra with multiple frequency dimensions, providing correlations between different types of nuclei (e.g., 1H-1H, 1H-15N, or 1H-13C). This allows for the assignment of individual resonances to specific atoms in the protein and the determination of various structural parameters.

Determination of Protein Structure in Solution

In NMR studies of protein structure, the main structural information comes from the measurement of distances between atom pairs, based on the nuclear Overhauser effect (NOE). A large number of NOE-derived distance restraints, along with other restraints such as dihedral angles (obtained from J-couplings) and hydrogen bonds, are used to compute the 3D structure of the protein in solution using computational methods like molecular dynamics simulations and simulated annealing.

Advantages and Limitations

NMR spectroscopy has several advantages for studying protein structure, such as the ability to analyze molecules in a solution state, which allows for the investigation of protein dynamics and interactions with ligands or other proteins. Additionally, it can provide information about protein folding and aggregation. However, there are some limitations – NMR spectroscopy is generally limited to small-to-medium-sized proteins or protein domains (up to ~25-30 kDa), and the signal sensitivity decreases with increasing protein size. Moreover, it requires a large amount of well-dispersed, isotopically labeled (e.g., 13C and/or 15N labeled) protein for structural determination.

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Briefly describe the technique of NMR spectroscopy as it applies to protein structure determination.

Short Answer

Step by step solution

Introduction to NMR Spectroscopy

Basic Principles of NMR

Multi-dimensional NMR Techniques

Determination of Protein Structure in Solution

Advantages and Limitations

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