Sandbox 35
From Proteopedia
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<Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Insert optional scene name here' /> | <Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Insert optional scene name here' /> | ||
| + | ==Adenylate Kinase== | ||
| + | Adenylate kinase, also known as "ADK", is an enzyme which speeds up the reaction which includes the interconversion of adenine nucleotides. The protein's flexibility allows it to bind to certain substrates known as ligands. | ||
| + | |||
==Structure== | ==Structure== | ||
| - | The <scene name='Sandbox_35/Secondary_structure_colored/1'>secondary structure</scene> of Adenylate Kinase has alpha helicies (purple) and beta sheets (dark pink) that circle around and enclose the non-hydrolysable part of the protein (seen in the center). | + | The <scene name='Sandbox_35/Secondary_structure_colored/1'>secondary structure</scene> of Adenylate Kinase has alpha helicies (purple) and beta sheets (dark pink) that circle around and enclose the non-hydrolysable part of the protein,(seen in the center). This is known as the ligand, which does not experience hydrolysis. These alpha helicies and beta sheets are known as the "backbone" of the protein. |
One of the main components of protein structure are the <scene name='Sandbox_35/Secondary_h_bonds2/1'>hydrogen bonds</scene> which are shown in green on this structure. The hydrogen bonds form links between adjacent amino acids, contributing to the protein structure and fold. The hydrogen bonds on the beta sheets are in an anti-parallel configuration, which offers stability for the protein. | One of the main components of protein structure are the <scene name='Sandbox_35/Secondary_h_bonds2/1'>hydrogen bonds</scene> which are shown in green on this structure. The hydrogen bonds form links between adjacent amino acids, contributing to the protein structure and fold. The hydrogen bonds on the beta sheets are in an anti-parallel configuration, which offers stability for the protein. | ||
==Hydrophobic and Hydrophilic Residue Composition== | ==Hydrophobic and Hydrophilic Residue Composition== | ||
| - | Adenylate kinase is composed of both hydrophobic and hydrophilic residues, and folds accordingly to obtain the optimum environments for the nature of both kinds of residues. The <scene name='Sandbox_35/Secondary_hydrophobs_only_gre/1'>hydrophobic residues</scene> shown in grey are buried within the folded protein, away from contact with the solvent. This action represents the hydrophobic effect taking place, which is mainly driven by entropy. | + | Adenylate kinase is composed of both hydrophobic and hydrophilic residues, and folds accordingly to obtain the optimum environments for the nature of both kinds of residues. The <scene name='Sandbox_35/Secondary_hydrophobs_only_gre/1'>hydrophobic residues</scene> shown in grey are buried within the folded protein, away from contact with the solvent. This action represents the hydrophobic effect taking place, which is mainly driven by entropy. Surrounding the outside of the protein are the <scene name='Sandbox_35/Secondary_hphobic_and_hphilic/1'>hydrophilic residues</scene> (dark green). These residues are polar and can be in caontact with the surrounding solvent in the protein's environment. These residues can either be charged or uncharged, can hydrogen bond with water, and are generally more soluble. They cover the hydrophobic amino acid residues to protect them from the solvent. |
Revision as of 00:21, 19 October 2012
| Please do NOT make changes to this Sandbox. Sandboxes 30-60 are reserved for use by Biochemistry 410 & 412 at Messiah College taught by Dr. Hannah Tims during Fall 2012 and Spring 2013. |
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Adenylate Kinase
Adenylate kinase, also known as "ADK", is an enzyme which speeds up the reaction which includes the interconversion of adenine nucleotides. The protein's flexibility allows it to bind to certain substrates known as ligands.
Structure
The of Adenylate Kinase has alpha helicies (purple) and beta sheets (dark pink) that circle around and enclose the non-hydrolysable part of the protein,(seen in the center). This is known as the ligand, which does not experience hydrolysis. These alpha helicies and beta sheets are known as the "backbone" of the protein. One of the main components of protein structure are the which are shown in green on this structure. The hydrogen bonds form links between adjacent amino acids, contributing to the protein structure and fold. The hydrogen bonds on the beta sheets are in an anti-parallel configuration, which offers stability for the protein.
Hydrophobic and Hydrophilic Residue Composition
Adenylate kinase is composed of both hydrophobic and hydrophilic residues, and folds accordingly to obtain the optimum environments for the nature of both kinds of residues. The shown in grey are buried within the folded protein, away from contact with the solvent. This action represents the hydrophobic effect taking place, which is mainly driven by entropy. Surrounding the outside of the protein are the (dark green). These residues are polar and can be in caontact with the surrounding solvent in the protein's environment. These residues can either be charged or uncharged, can hydrogen bond with water, and are generally more soluble. They cover the hydrophobic amino acid residues to protect them from the solvent.
