Obtaining 3D Structures of Biomolecules

Flashcards to help review key concepts from the lecture on 3D structures of biomolecules.

What are the three main experimental methods to determine protein structures?

X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy.

What is the distribution percentage of protein structures from the Protein Data Bank based on source, as of 2008?

X-ray: 85%, NMR: 14%, Electron microscopy: <1%.

What is the fundamental process used in X-ray crystallography to visualize protein structures?

Single crystal X-ray diffraction.

What must obtain to successfully carry out single crystal X-ray diffraction?

High-quality single crystals of the target protein.

How does X-ray crystallography generate a three-dimensional image of electron density?

By measuring the angle and intensity of scattered X-rays as the crystal is rotated.

What is the typical size requirement for a protein crystal to diffract strongly enough?

At least 0.2-0.3 mm in all three dimensions.

What is the first step in the protein crystallization process?

To screen precipitants and conditions promoting protein precipitation.

What is the role of precipitating agents in protein crystallization?

They monopolize water molecules, promoting protein interactions that can lead to crystal formation.

What is the significance of recovering the phase angle in X-ray crystallography?

It is necessary to reconstruct the electron density map and determine the structure.

What is the term used to describe the maximum distance at which NMR can obtain structural information?

Typically less than 5Å for observability through the Nuclear Overhauser Effect (NOE).

What is a significant advantage of NMR over X-ray crystallography?

NMR does not require the sample to be in a crystalline state.

What are the limitations of NMR for protein structure determination?

Precision is lower than X-ray crystallography, and it can only typically analyze small biomolecules (less than 300 residues).

What is one of the main uses of Cryo-electron microscopy in structural biology?

To provide molecular structural data about large biological complexes.

How does Cryo-electron microscopy protect samples during imaging?

Samples are scanned in a frozen state to prevent radiation damage.

What is one of the key limitations of electron microscopy?

It has a current resolution of about 3.5 Å, insufficient for determining amino acid side chain locations.