AAMC Style Paragraphs Set 1

Paragraph 1: (Questions 1-4)
pAgo forms a bilobed scaffold, with one lobe comprising the N-PAZ domains and the other the MID-PIWI domains The N-terminal domain, being the least conserved, may facilitate the separation of RNA duplexes. The PAZ domain, a small domain of approximately 140 amino acids, is involved in binding the 3′ end of the guide molecule. The MID domain houses a pocket for binding to the 5′ end of the guide. Upon target binding, the catalytically active PIWI domain mediates target strand cleavage. This domain contains a conserved tetra-amino acid residue DEDX (where X is an aspartate, histidine, or lysine residue), which can bind to the two divalent cations required for catalytic activity.

Adapted from K. Sun et al., “Prokaryotic Argonaute Proteins: A New Frontier in Point-of-Care Viral Diagnostics,” Int. J. Mol. Sci. 2023

What is the weight of the PAZ domain within the pAgo protein?

pAgo forms a bilobed scaffold, with one lobe comprising the N-PAZ domains and the other the MID-PIWI domains The N-terminal domain, being the least conserved, may facilitate the separation of RNA duplexes. The PAZ domain, a small domain of approximately 140 amino acids, is involved in binding the 3′ end of the guide molecule. The MID domain houses a pocket for binding to the 5′ end of the guide. Upon target binding, the catalytically active PIWI domain mediates target strand cleavage. This domain contains a conserved tetra-amino acid residue DEDX (where X is an aspartate, histidine, or lysine residue), which can bind to the two divalent cations required for catalytic activity.

Adapted from K. Sun et al., “Prokaryotic Argonaute Proteins: A New Frontier in Point-of-Care Viral Diagnostics,” Int. J. Mol. Sci. 2023

If the X residue in the conserved tetra-amino acid residue is lysine, what is the net charge of the tetra-amino acid residue at physiological pH?

pAgo forms a bilobed scaffold, with one lobe comprising the N-PAZ domains and the other the MID-PIWI domains The N-terminal domain, being the least conserved, may facilitate the separation of RNA duplexes. The PAZ domain, a small domain of approximately 140 amino acids, is involved in binding the 3′ end of the guide molecule. The MID domain houses a pocket for binding to the 5′ end of the guide. Upon target binding, the catalytically active PIWI domain mediates target strand cleavage. This domain contains a conserved tetra-amino acid residue DEDX (where X is an aspartate, histidine, or lysine residue), which can bind to the two divalent cations required for catalytic activity.

Adapted from K. Sun et al., “Prokaryotic Argonaute Proteins: A New Frontier in Point-of-Care Viral Diagnostics,” Int. J. Mol. Sci. 2023

Which metal ion is required for catalytic activity in pAgo during target strand cleavage?

pAgo forms a bilobed scaffold, with one lobe comprising the N-PAZ domains and the other the MID-PIWI domains The N-terminal domain, being the least conserved, may facilitate the separation of RNA duplexes. The PAZ domain, a small domain of approximately 140 amino acids, is involved in binding the 3′ end of the guide molecule. The MID domain houses a pocket for binding to the 5′ end of the guide. Upon target binding, the catalytically active PIWI domain mediates target strand cleavage. This domain contains a conserved tetra-amino acid residue DEDX (where X is an aspartate, histidine, or lysine residue), which can bind to the two divalent cations required for catalytic activity.

Adapted from K. Sun et al., “Prokaryotic Argonaute Proteins: A New Frontier in Point-of-Care Viral Diagnostics,” Int. J. Mol. Sci. 2023

In the MID domain of pAgo, which amino acid is most likely to be found within the pocket for binding to the 5′ end of the guide molecule based on the provided information?