Amino Acid Interactions

The cell membrane is composed of two layers of phospholipids which have a polar phosphate head and nonpolar tails. The layers are arranged so the inner portion of the membrane is comprised of nonpolar fatty acid tails while the outer phosphate head is in contact with the aqueous extracellular fluid or cytosol. Transmembrane proteins that span the membrane would most likely have which of the following amino acids in the middle portion of their transmembrane domains?

Which of the following amino acids would be found on the outside of a globular protein?

Which peptide sequence WOULDN’T be found in a transmembrane domain? 

Vasopressin increases transcription and insertion of aquaporins into the apical membrane of collecting duct epithelial cells thus allowing more water to exit the filtrate through the aquaporin. Which of the following amino acids would be found in the central portion of the pore in aquaporin that allows water to traverse the membrane?

The insulin receptor binds to insulin via a hydrophobic crevice in its L1-β₂  domain. Which amino acid on insulin is most likely going to interact with the L1-β₂ domain?

Lipid rafts are specialized membrane nanodomains that act as signaling platforms involved in a number of physiological functions under normal and pathological conditions. These small (10–200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched domains compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions. The protein-lipid interactions typically occur when amino acid residues interact with the fatty acid tails of sphingolipids. Which amino acids can facilitate small raft stabilization via protein-lipid interactions?

Adpated From: Diaz Mario et al. Genotype-induced changes in biophysical properties of frontal cortex lipid raft from APP/PS1 transgenic mice (2012), Frontiers in Physiology, Vol. 3 CC BY-SA 4.0

Apolipoproteins are specialized proteins that carry hydrophobic lipids such as triglycerides and cholesterol throughout the blood. Apolipoproteins would be mostly likely to contain which of the following lipid binding sequences? 

A cationic antigenic protein on the surface of a bacterium is the target of antibody binding. Which class of amino acids would facilitate antibody binding to the antigenic protein?

Histones are specialized proteins that bind to the backbone of DNA and facilitate the conversion of DNA from euchromatin into heterochromatin. Which of the following amino acids on histones are responsible for binding to the phosphodiester backbone of DNA?

Menin acts as a key scaffold protein with various partners, it is possible that mutations may affect the interactions between menin and other proteins. To date two specific mutations have been identified (D185A and E260K), within the menin binding pocket. These mutations replace residues directly involved in menin-protein associations, specifically the formation of complexes between human wild-type (WT) menin and JUND, MLL1 and LEDGF proteins. Based on the information above WT menin most likely binds to which of the following amino acids on JUND, MLL1, and LEDGF? 

Adapted From: C. Biancaniello et al.  Investigating the Effects of Amino Acid Variations in Human Menin, Molecules (2022), CC BY-SA 4.0

Heart type fatty acid binding proteins (HTFBP) help facilitate lipid trafficking and cellular signaling by binding to free fatty acids within the cytosol of contractile heart muscle cells. Since fatty acids are comprised of a negatively charged head and a lipophilic tail HTFBPs would need to have which of the following residues to accommodate fatty acids?