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You may include any references to papers as in: the use of JSmol in Proteopedia [1] or to the article describing Jmol [2] to the rescue.
Background
Proteins are one of the four major macromolecules in biology. Present in nearly every living organism, proteins have a diverse set of functions ranging from regulating cell activity to catalyzing reactions. Proteins are primary made up of amino acids in the primary structure, which consists of the amino acid sequence. The amino acids are set in a particular order so that they perform a specific function, and this order is determined by the DNA gene that codes for amino acids. The secondary structure consists of and . These two structures are helpful in finding similar proteins that perform similar functions. The tertiary and and quaternary structures consist of the specific folding of the complete protein structure, which all comes togther in great importance when classifying proteins.
Enzymes, proteins that catalyze reactions, are grouped into seven major classes based on amino acid sequence similarity and secondary structure proportions. Proteins in each class share unique properties that can classify them into more detailed subclasses. Protein structure and protein function are closely related. This means that identifying highly conserved sequences between two proteins increases the likelihood of discovering shared functions. In this study we attempted to compare the sequence and structure of an uncharacterized protein to that of a protein with a known function in order to understand the former protein’s function. In 2000, the Protein Structure Initiative began an attempt to solve the 3D-structures of proteins with known sequences in order to begin understanding their functions. But, in 2015, the Initiative no longer had the proper funding and stopped, successfully solving 6920 structures, but leaving many structures found without their functions classified as well.
Bacterial Transformation, Protein Expression, and Protein Purification
NEB bacterial transformation protocol was performed using DH5∂ cells in order to insert the plasmid inside the cells. Next, an overnight culture was performed using to grow more bacteria. The plasmid was then purified and isolated from genomic DNA, proteins, ribosomes, and cell walls of bacteria using the Zippy miniprep protocol. After determining that T7 polymerase was the polymerase that transcribes 2QRU by computational analysis, it was necessary to use BL21(DE3) cells to transform the cells because DH5∂ does not produce T7 polymerase. NEB transformation protocol was run using BL21 cells. The Zippy miniprep protocol was then run to measure the concentration of the plasmid. NEB protein expression protocol was run using BL21 and then a liquid culture was grown.
Structural Highlights
Functional Assay
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