The Hierarchy and Determination Methods of Protein Structure

The structure of proteins is a core area of biomolecular research because their structure is closely related to their function. The structure of proteins is usually divided into four levels: primary structure, secondary structure, tertiary structure, and quaternary structure.

 

Primary Structure

1. The primary structure describes the amino acid sequence of the protein.

2. This continuous chain of amino acids is connected through peptide bonds.

3. The primary structure determines the identity of the protein and many of its biological properties.

 

Determination Methods

(1) Amino acid sequencing: For example, the Edman degradation method, which can sequentially cut and identify amino acids from one end of the protein.

(2) Mass spectrometry: In particular, tandem mass spectrometry can be used to identify and determine the amino acid sequence.

 

Secondary Structure

1. The secondary structure describes the local folding pattern of the protein, such as α-helices and β-sheets.

2. It is a local stable structure caused by hydrogen bonds, which are formed between the main chains of amino acids.

3. These patterns provide a framework for the three-dimensional structure of the protein.

 

Determination Methods

(1) Circular Dichroism (CD): Used to detect the content of α-helices, β-sheets, and random coils in proteins.

(2) Infrared Spectroscopy (IR): Can be used to analyze the secondary structure of proteins.

 

Tertiary Structure

1. The tertiary structure describes the complete three-dimensional structure of a single polypeptide chain.

2. The tertiary structure is caused by the folding due to interactions between the R groups of amino acids (such as hydrophobic interactions, ionic bonds, hydrogen bonds, and disulfide bonds).

3. It describes the overall spatial arrangement of the protein.

 

Determination Methods

(1) X-ray crystallography: Analyze purified and crystallized protein samples to obtain a high-resolution three-dimensional structure of the protein.

(2) Nuclear Magnetic Resonance (NMR) spectroscopy: Obtain three-dimensional structural information of the protein under liquid state conditions.

(3) Cryo-Electron Microscopy (Cryo-EM): Used to obtain the three-dimensional structure of large molecular complexes.

 

Quaternary Structure

1. The quaternary structure describes how multiple polypeptide chains (subunits) aggregate to form a complete protein complex.

2. Not all proteins have a quaternary structure. Only proteins composed of two or more polypeptide chains do. For example, hemoglobin is composed of 4 polypeptide chains.

 

Determination Methods

(1) X-ray crystallography and Cryo-EM: Both can be used to analyze the structure of large molecular complexes.

(2) Gel filtration chromatography and affinity chromatography: Can be used to determine the interaction and assembly between subunits.