Sandbox 50: Difference between revisions
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The <scene name='Sandbox_50/Ak_water6/1'>solvent</scene>, which is water (blue), can be co-crystallized with the enzyme. The water can be found all around the protein but there is also some water molecules in the active site, around the ligand. This further indicates why the hydrophilic residues are found on the surface, and the nonpolar residues are buried away. The water creates a hydrophilic environment, and the hydrophobic residues aggregate together in the interior, which is the hydrophobic effect and drives the water out. So for the most part, there are not water molecules in between the secondary structure, but there are some water molecules in the open spaces between the backbone.The hydrophilic residues in the active site cause water to be present there, and also make it easier for the ligand to enter and facilitates in the reaction. | The <scene name='Sandbox_50/Ak_water6/1'>solvent</scene>, which is water (blue), can be co-crystallized with the enzyme. The water can be found all around the protein but there is also some water molecules in the active site, around the ligand. This further indicates why the hydrophilic residues are found on the surface, and the nonpolar residues are buried away. The water creates a hydrophilic environment, and the hydrophobic residues aggregate together in the interior, which is the hydrophobic effect and drives the water out. So for the most part, there are not water molecules in between the secondary structure, but there are some water molecules in the open spaces between the backbone.The hydrophilic residues in the active site cause water to be present there, and also make it easier for the ligand to enter and facilitates in the reaction. | ||
== | ==References== | ||
http://www.ncbi.nlm.nih.gov/pubmed/21365689 | http://www.ncbi.nlm.nih.gov/pubmed/21365689 | ||
http://medical-dictionary.thefreedictionary.com/adenylate+kinase | http://medical-dictionary.thefreedictionary.com/adenylate+kinase | ||
http://en.wikipedia.org/wiki/Adenylate_kinase | http://en.wikipedia.org/wiki/Adenylate_kinase | ||
http://www.ebi.ac.uk/interpro/IEntry?ac=IPR007862 | http://www.ebi.ac.uk/interpro/IEntry?ac=IPR007862 | ||
Voet, D., Voet, J., and Pratt, C. W. ''Fundamentals of Biochemistry: Life at the Molecular Level''3rd Edition. (2008) | Voet, D., Voet, J., and Pratt, C. W. ''Fundamentals of Biochemistry: Life at the Molecular Level''3rd Edition. (2008) | ||