Structural Data

Question 1

Importance of Structural Data:

Answer 1

Understanding protein binding and recognition at the molecular level.
Studying protein-protein interactions, tertiary structures, enzyme co-factors, and
ligand-binding sites.
Linking protein sequences to their structures to predict functional sites and mutation
impacts.

Question 2

Applications:

Answer 2

Structural annotation of genomes.
Structure prediction and comparison.
Prediction of protein dynamics, interactions, and assemblies.
Mechanism of interaction with ligands (e.g., metabolites, drugs, DNA).

Question 3

PROTEIN DATA BANK (PDB)

Answer 3

Central repository for 3D structural data of biological macromolecules.
o Contains over 200 databases utilizing PDB data for various applications, including
structural, sequence, and pathway databases.
200k records

Question 4

Basics of X-Ray Crystallography:

Answer 4

Atoms and molecules scatter X-rays, creating diffraction patterns that reveal structural
details.
Essential concepts: reflection, refraction, diffraction

Question 5

Microscopy and X-Ray Production:

Answer 5

Light microscopy is limited by diffraction to around 200 nm; X-rays are needed for
higher resolution.
X-ray production methods include X-ray tubes, synchrotrons, and free-electron lasers
(FEL).

Question 6

Crystal Formation and Diffraction:

Answer 6

Proteins crystallize to create a lattice that diffracts X-rays.
The diffraction pattern is analyzed to determine the atomic structure of the protein.

Question 7

Crystallography process 3 steps:

Answer 7

Diffraction and Data Analysis:
Diffraction patterns are converted to electron density maps using Fourier transforms.The electron density map is used to build an atomic model of the protein.
Fourier Transform:
Connects real space (atomic positions) and reciprocal space (diffraction data).
Key to interpreting diffraction patterns and constructing accurate models.
Phase Problem:
The challenge of determining phase information from diffraction data.
Solved using methods like molecular replacement, de novo structure solution, and
direct methods.

Question 8

PRACTICAL CONSIDERATIONS / Xray C

Answer 8

Protein Crystallization:
Involves growing crystals under specific conditions to achieve high-quality diffraction.Requires high protein concentrations, often achieved by overexpressing proteins in
bacteria.
Resolution and Accuracy:
Higher resolution provides more detailed structural information. Accurate phase determination is critical for building precise models.