1 Suggest a sequence for this 16 amino acid helix and provid

SKILLEXERCISES POST ACTIVITY 1. The E2F family of transcription factors is important in regulating the cell cycle and has a role in cancer. These DNA binding proteins have conserved helix-turn-helix motifs that interact with DNA (NOTE: The DNA is represented as a stick diagram, whereas the protein is represented as helical ribbons.) Consider the protein a helix indicated by the arrow DNA This helix is approximately 16 amino acids in length and runs along side the DNA. Suggest a sequence for this 16 amino acid helix and provide a justification for your answer. Picture from Meinhart, A. et al. J. Biol. Chem. 2003;278:48267-48274 (used by permission). View this skill exercise as an opportunity to practice scientific argumentation. Therefore the justification will be the most important aspect of your answer. Your instructor may assign one or more of these questions: 2. Describe how water contributes to the favorable free energy change that makes protein folding spontaneous process. tho come structure as the same prote

Solution

Transcription factors are the proteins which bind to DNA and modulate the transcription of DNA or genes. These E2F proteins are involved in the transcription of RNA or DNA to proteins and cell cycle regulation in higher eukaryotes. E2F family has a DNA binding region or motif and generally these region are alpha helical in nature.

Proteins generally have three secondary structure components and are alpha helical, beta sheets and turns other than the randomness in the sequence. coming a step back proteins are actually divided as having primary structures like amino acids in a sequence, secondary structures like described above and tertiary structures like the hydrophobic or hydrophilic areas in the proteins formed due the aromatic and charged aminoacids present. Also quartrnary structures which comprises of domains and higher order structures.

Alpha helices are significant in DNA binding motifs as a alpha helix fits into the major groove of the DNA. Considering this a few aminoacds can be present in the helices like Ala,Leu,Met,Phe,Glu,Gln,His,Lys,Arg. these aminoacids can form intra strand hydrogen bonding and amino acid side chain should cover and protect the backbone H-bonds in the core of the helix. these aminoacids have to be having charged side chain reactive groups for interactions.

we can provide the following sequence of 13 aminoacids based on the above justification

Ala,Leu,Met,Phe,Glu,Gln,His,Lys,Arg, Ala, Phe, Gln, Met, Ala, Leu,His,