The Three-Dimensional Structure of Proteins

These flashcards cover key vocabulary and concepts related to the three-dimensional structure of proteins, as described in the lecture notes.

Noncovalent interactions

Forces that stabilize protein structures, such as hydrogen bonds, ionic interactions, and van der Waals forces.

Hydrophobic effect

The tendency of nonpolar substances to aggregate in aqueous solutions to minimize their exposure to water.

Dihedral angles (φ and ψ)

Angles that describe the configuration of peptide bonds in proteins, influencing their three-dimensional structure.

Secondary structure

The local folded structures that form within a protein due to hydrogen bonding, such as α helices and β sheets.

Tertiary structure

The overall three-dimensional shape of a single polypeptide chain, determined by interactions between side chains of amino acids.

Quaternary structure

The structure formed when two or more polypeptide chains assemble into a functional protein complex.

Proteostasis

The cellular maintenance of the concentration, conformation, and stability of proteins.

Ramachandran plot

A graphical representation that allows visualization of dihedral angles (φ and ψ) of amino acids in proteins.

Denaturation

The process by which a protein loses its native structure and function, often due to extreme conditions.

Chaperone proteins

Proteins that assist in the correct folding of other proteins and in preventing misfolding.

Amyloid fibrils

Misfolded protein aggregates associated with various neurodegenerative diseases.

α Helix

A common type of protein secondary structure characterized by a right-handed coil and stabilized by intrahelical hydrogen bonds.

β Conformation

A secondary structure in proteins in which polypeptide chains are organized into sheets stabilized by hydrogen bonds.

Proline

An amino acid that induces kinks in protein structures and is often found in turns and loops of proteins.

Glycine

An amino acid known for its flexibility, often found in turns or bends of protein structures.

Fibrous proteins

Proteins with elongated shapes that are usually structural in function.

Globular proteins

Proteins that are roughly spherical and often function as enzymes, transport proteins, or hormones.

Protein purification methods

Column Chromatography, Size-exclusion/gel chromatography, Ion-exchange chromatography, Affinity chromatography

What are the two methods of protein visualization and characterization?

Gel electrophoresis and isoelectric focusing

Methods of protein structure determination

X-ray crystallography, NMR, CryoEM

Column chromatography

Ion-exchange chromatography

Separates proteins by net charge via attraction to oppositely charged resin. Similar charges may co-elute

Cation exchange resin

Resin is negatively charged and binds positively charged proteins

Anion exchange resin

Resin is positively charged and binds negatively charged proteins

Size-exclusion chromatography

Separates proteins by size, large proteins elute first, small ones enter pores and elute later. Similar sizes may co-elute

Affinity chromatography

Separates proteins based on specific binding to a ligand. Requires a known specific ligand, binding can alter protein structure, expensive

Gel electrophoresis

Separates proteins by molecular weight and charge. Then undergoes uniform negative charge from SDS

Isoelectric focusing (IEF)

Separates proteins by isoelectric point (pI) in a pH gradient; proteins stop moving at net charge = 0

Cryo-electron microscopy (Cryo-EM)

Determines protein structure by imaging flash-frozen proteins in a near-native state using TEM. Useful for large macromolecular complexes. The resolution is low, it’s expensive.

Nuclear magnetic resonance (NMR)

Determines protein structure by analyzing magnetic properties of atomic nuclei in solution. Only works with small proteins

X-ray crystallography

Determines protein structure by analyzing X-ray diffraction patterns from protein crystals. Crystal structure can differ from native structure, only small proteins can form crystals