Tertiary structures of proteins can be further subdivided based on their secondary structures. Proteins can be classified as alpha, beta and alpha/beta and further understood by their topology or how the secondary structure is connected. 
Key secondary classification:
- Beta barrels

Classification based on Secondary Protein Topology

X-ray crystallography is a technique to visualize proteins. This technique utilizes a crystal  of the desired molecule that is exposed to an X-ray beam which then displays a diffraction pattern of the atoms in the molecule. These diffractions are used to to make the 3D image of the protein. 

Drawbacks:
- X-ray only interacts with electrons not the nuclei - the amino acid chains is added to complete the picture
- Lower resolution - possible inaccuracy of the images. 

X-ray Crystallography

NMR stands for nuclear magnetic resonance. this technique allows for visualizing the 3D structure of the protein by observing the nuclei of the proteins resonating in a magnetic field and interacts with the other nearby nuclei to create a 3D image of the protein. 
Drawbacks: 
- Sometimes lower resolution of the X-ray Crystal structures 
- Limited to smaller proteins (<100kD)
- Best when used in combination with X-ray Crystal structures. 

Cryo-electron microscopy is a continually advancing technique that is consistently improving the quality and diversity of protein images. Recently, discoveries have allowed for viewing a protein at the atomic level.

“Cryo” refers to the thin layer of noncrystalline solid water called vitreous ice that is kept at liquid nitrogen temperatures. This solution holds the desired protein to be imaged. EM refers to electron microscopy which is used to create these images. 


Cryo-EM 

Combinations of the secondary structure is a motif and is another way to classify the tertiary structure of proteins. 
Common motifs in proteins:
- Beta-alpha-beta – alpha helix connecting two parallel strands 
- Beta hairpin – antiparallel strands that are joined by reverse turns
- Alpha alpha – antiparallel alpha helices 
- Greek key – froms an antiparallel Beta sheet 



Protein Motif

Large protein chains that can form two or more clusters. Each cluster is known as a domain. 

Protein Domains

Tertiary protein structure combines the folding of the secondary back bone structure and includes the positions of the side chains of each amino acid. 

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Protein structure is the 3-dimensional assembly caused by the string of amino acids translated from RNA . Protein structures varies immensely due to the assembly of the amino acids.
There are four subdivisions of proteins structures:
- Primary structure
- Secondary structure
- Tertiary structure 
- Quaternary structure 

Protein Structure 

Voet, D., Voet, J. G., & Pratt, C. W. (2013). Chapter 6: Proteins: Three-Dimensional Structure. In Fundamentals of biochemistry: Life at the molecular level (4th ed., pp. 127-175). Hoboken, NJ: Wiley. Retrieved January 05, 2021, from archive.org.

Fundamental of biochemistry: Life of the molecular level 4th edition: Chapter 6

Secondary protein structure refers to only the spatial arrangements of the polypeptide backbone that does not include the sided chain conformations. 
The most common secondary structures include:
-	Alpha helix
-	Beta sheets
- Turns

Secondary Protein Structure

Primary structure refers to the amino acid sequence, or multiple sequences of a protein. Each amino acid in a primary structure is known as a residue. Because the 20 amino acids have individual chemical and physical properties, they influence the 3D structure, the function of the protein and its chemical properties. i.e. hydrophobic and hydrophilic properties. 

Ions can additionally be found in the primary structure. Zinc and calcium ions can form complexes that are present in the protein's primary structure. 

Primary Protein Structure 

Quaternary structure refers to the proteins that are multisubunit, more than 100 kilo Daltons, and form a specific geometry. These subunits are usually linked non-covalently. 

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