Let's get this one started! Starting out with an easy question...
Identify each of these supersecondary motifs! Sorry about the size of the images...
Re: Protein Modeling C
Posted: October 17th, 2020, 11:50 am
by azboy1910
Don't know if these answers are correct, but here goes nothing . . .
I believe the first one is a beta-alpha-beta motif, the second one is a greek key motif, and the bottom one is a beta barrel.
Re: Protein Modeling C
Posted: October 18th, 2020, 6:08 am
by EwwPhysics
azboy1910 wrote: ↑October 17th, 2020, 11:50 am
Don't know if these answers are correct, but here goes nothing . . .
I believe the first one is a beta-alpha-beta motif, the second one is a greek key motif, and the bottom one is a beta barrel.
Good job!
1.
Zinc finger motif
2.
Correct!
3.
Correct!
Your turn!
Re: Protein Modeling C
Posted: April 2nd, 2021, 10:54 am
by Ninn
1. Why is glycine commonly found in protein linkers?
2. Arginine, histidine, and lysine are all positively charged, but what makes histidine the best buffer of these three?
3. Is aspartic acid or glutamic acid more acidic, and why?
Re: Protein Modeling C
Posted: April 3rd, 2021, 10:34 am
by popcorn3
Fun questions!
1. Glycine is a very "flexible" residue due to its very small sidechain (just a hydrogen). This means the domains/proteins that the linkers connect can move around and interact with each other.
2. Histidine has the pKa closest to physiological pH, so it best acts as a buffer in biological systems.
3. Aspartic acid is more acidic. Couldn't tell you why, but my guess is induction effects, since the only difference between Asp and Glu is the sidechain's distance from the NH2 group.
Re: Protein Modeling C
Posted: April 3rd, 2021, 4:57 pm
by Ninn
popcorn3 wrote: ↑April 3rd, 2021, 10:34 am
Fun questions!
1. Glycine is a very "flexible" residue due to its very small sidechain (just a hydrogen). This means the domains/proteins that the linkers connect can move around and interact with each other.
2. Histidine has the pKa closest to physiological pH, so it best acts as a buffer in biological systems.
3. Aspartic acid is more acidic. Couldn't tell you why, but my guess is induction effects, since the only difference between Asp and Glu is the sidechain's distance from the NH2 group.
All correct! You're right regarding induction for #3 too -- the additional methylene of Glu weakens its inductive effect. The stronger the inductive effect the more acidic the compound, so like you said, Asp is more acidic :)
