1. Given below are protein domains and their binding specificities.
which one of the following options represents all correct matches between column X and Column Y ?- A-iii, B-i, C-ii, D-ii
- A-i, B-ii, C-iii, D-i
- A-iii, B-iii, C-i, D-ii
- A- i, B-iii, C-ii, D-i
Answer : 4. A-i, B-iii, C-ii, D-i- Domains are distinct functional or structural units within a protein. Each domain usually has a specific role or facilitates an interaction, contributing to the protein's overall function. Domains can be present in various biological contexts, and similar domains may be found in proteins that perform different functions.
- SH2 domains were first identified in proteins encoded by the genomes of tumor-causing (oncogenic) viruses. These domains are composed of approximately 100 amino acids and feature a conserved binding pocket that accommodates a phosphorylated tyrosine residue. The human genome encodes over 110 SH2 domains, which play a crucial role in mediating numerous phosphorylation-dependent protein-protein interactions.
SH2 domains specifically bind to phosphorylated tyrosine residues on other proteins, thereby modifying the function or activity of the SH2-containing protein. The specificity of these interactions is determined by the amino acid sequence that is immediately adjacent to the phosphorylated tyrosine residues. For instance, the SH2 domain of the Src protein-tyrosine kinase recognizes the sequence pTyr-Glu-Glu-Ile, while the SH2 domains of PI 3-kinase bind to the sequence pTyr-Met-X-Met, where X can be any amino acid.
Interestingly, the genome of budding yeast encodes only one protein containing an SH2 domain, which correlates with the overall lack of tyrosine kinase signaling activity in these lower single-celled eukaryotes.
The interaction between the SH2 domain of a protein and a peptide containing a phosphotyrosine residue is illustrated here. The SH2 domain is displayed in a cutaway view, with its accessible surface area represented by red dots and the polypeptide backbone depicted as a purple ribbon. The phosphotyrosine-containing heptapeptide (Pro-Asn-pTyr-Glu-Glu-Ile-Pro) is shown as a space-filling model with its green side chains and the backbone in yellow. The phosphate group is indicated in light blue.
Notably, the phosphorylated tyrosine residue and the isoleucine residue (position 3) both project into specific pockets on the surface of the SH2 domain, creating a tight-fitting interaction. This close interaction occurs only when the tyrosine residue is phosphorylated.
(Source: Gabriel Waksman et al., courtesy of John Kuriyan, Cell 72:783, 1993; with permission from Cell Press.)- Src-homology 3 (SH3) domains specifically bind to proline-rich peptides that adopt a left-handed polyproline type II helix, characterized by the minimal consensus sequence PRO-X-X-Pro. Typically, an aliphatic residue precedes each proline, and these pairs of aliphatic residues and prolines interact with a hydrophobic pocket on the SH3 domain.
- A protein domain of about 120 amino acids, the pleckstrin homology domain (PH domain) or PHIP is found in a variety of proteins that are either cytoskeleton constituents or engaged in intracellular signaling. This domain can bind proteins including the βγ-subunits of heterotrimeric G proteins and protein kinase C, as well as phosphatidylinositol lipids found in biological membranes, such as phosphatidylinositol (3,4,5)-trisphosphate and phosphatidylinositol (4,5)-bisphosphate.
- Phosphotyrosine binding (PTB) domains are modular segments consisting of 100 to 150 amino acids. These domains typically bind to motifs characterized by the sequence Asn-Pro-X-Tyr (NPXpY). In docking proteins such as Shc and IRS-1, the phosphorylation of the tyrosine residue within the NPXpY motif is crucial for effective binding. Furthermore, specific N-terminal sequences are essential for enhancing binding affinity and ensuring specificity.
Recent research has revealed that PTB domains can bind to phosphorylated tyrosine residues, usually found within the Asn-Pro-X-Tyr motif. However, the binding behavior is more intricate than it appears: some PTB domains specifically target unphosphorylated NPXpY motifs, while others bind exclusively to the phosphorylated versions. Additionally, PTB domains are not well conserved, meaning that different PTB domains may possess various residues that interact with their respective ligands.
which one of the following options represents all correct matches between column X and Column Y ?
- A-iii, B-i, C-ii, D-ii
- A-i, B-ii, C-iii, D-i
- A-iii, B-iii, C-i, D-ii
- A- i, B-iii, C-ii, D-i
Answer : 4. A-i, B-iii, C-ii, D-i
- Domains are distinct functional or structural units within a protein. Each domain usually has a specific role or facilitates an interaction, contributing to the protein's overall function. Domains can be present in various biological contexts, and similar domains may be found in proteins that perform different functions.
- SH2 domains were first identified in proteins encoded by the genomes of tumor-causing (oncogenic) viruses. These domains are composed of approximately 100 amino acids and feature a conserved binding pocket that accommodates a phosphorylated tyrosine residue. The human genome encodes over 110 SH2 domains, which play a crucial role in mediating numerous phosphorylation-dependent protein-protein interactions.
SH2 domains specifically bind to phosphorylated tyrosine residues on other proteins, thereby modifying the function or activity of the SH2-containing protein. The specificity of these interactions is determined by the amino acid sequence that is immediately adjacent to the phosphorylated tyrosine residues. For instance, the SH2 domain of the Src protein-tyrosine kinase recognizes the sequence pTyr-Glu-Glu-Ile, while the SH2 domains of PI 3-kinase bind to the sequence pTyr-Met-X-Met, where X can be any amino acid.
Interestingly, the genome of budding yeast encodes only one protein containing an SH2 domain, which correlates with the overall lack of tyrosine kinase signaling activity in these lower single-celled eukaryotes.
Notably, the phosphorylated tyrosine residue and the isoleucine residue (position 3) both project into specific pockets on the surface of the SH2 domain, creating a tight-fitting interaction. This close interaction occurs only when the tyrosine residue is phosphorylated.
(Source: Gabriel Waksman et al., courtesy of John Kuriyan, Cell 72:783, 1993; with permission from Cell Press.)
- Src-homology 3 (SH3) domains specifically bind to proline-rich peptides that adopt a left-handed polyproline type II helix, characterized by the minimal consensus sequence PRO-X-X-Pro. Typically, an aliphatic residue precedes each proline, and these pairs of aliphatic residues and prolines interact with a hydrophobic pocket on the SH3 domain.
- A protein domain of about 120 amino acids, the pleckstrin homology domain (PH domain) or PHIP is found in a variety of proteins that are either cytoskeleton constituents or engaged in intracellular signaling. This domain can bind proteins including the βγ-subunits of heterotrimeric G proteins and protein kinase C, as well as phosphatidylinositol lipids found in biological membranes, such as phosphatidylinositol (3,4,5)-trisphosphate and phosphatidylinositol (4,5)-bisphosphate.
- Phosphotyrosine binding (PTB) domains are modular segments consisting of 100 to 150 amino acids. These domains typically bind to motifs characterized by the sequence Asn-Pro-X-Tyr (NPXpY). In docking proteins such as Shc and IRS-1, the phosphorylation of the tyrosine residue within the NPXpY motif is crucial for effective binding. Furthermore, specific N-terminal sequences are essential for enhancing binding affinity and ensuring specificity.
Recent research has revealed that PTB domains can bind to phosphorylated tyrosine residues, usually found within the Asn-Pro-X-Tyr motif. However, the binding behavior is more intricate than it appears: some PTB domains specifically target unphosphorylated NPXpY motifs, while others bind exclusively to the phosphorylated versions. Additionally, PTB domains are not well conserved, meaning that different PTB domains may possess various residues that interact with their respective ligands.
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