Sandbox 81: Difference between revisions

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 UDP-galactose + glucose -+ lactose + UDP <ref name="synthetase"> Fitzgerald DK, Brodbeck URS, Kiyosawa I, Mawal R, Colvin B, Ebner KE. 1970. α-lactalbumin and the Lactose Synthetase Reaction. The Journal of Biological Chemistry. 245(8): 2103-2108. </ref>
 which takes place in the Golgi lumen and requires Mn2+ ions <ref name="structure"> Permyakov EA, Berliner LJ. α-Lactalbumin: structure and function. 2000. FEBS Letters. 473(3):269-274. </ref>.
 {{STRUCTURE_1a4v |  PDB=1a4v  |  SCENE=  }}
 == Structure ==
 α-lactalbumin is a small globular protein, with 123 residues, <ref name="PDB"> PDBSUM. http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1a4v&template=protein.html&o=DISULPHIDES&l=1&s=1&c=8&chain=A </ref>,  with two structural domains divided by a deep cleft.
-One domain is rich in α-helices and held together by two disulfide bonds, Cys 6-Cys 120 and Cys 28-Cys 111. It is made up of three major helices (residues 5-11, 23-24,and 86-98)and 2 short 3-10 helices (residues 18-20, and 115-118).  The other has a small three-stranded antiparallel beta-pleated sheet (residues 41-44, 47-50, and 55-56), a short 3-10 alpha-helix (residues 77-80), and two disulfide bonds, Cys 61-Cys 77 and Cys 73-Cys 91.   <ref name="energetics"> Hendrix TM, Griko Y, Privalov P. 1996. Energetics of structural domains in α-lactalbumin.  Protein Science. 5923-5931.</ref> The domains are held together by a calcium binding loop formed by a cysteine bridge between residues 73 and 91, and also a disulfide bridge between residues 61 and 77. <ref name="structure"> </ref>. <ref name="structure"> </ref>.
+One domain is rich in α-helices and held together by two disulfide bonds, Cys 6-Cys 120 and Cys 28-Cys 111. It is made up of three major helices (residues 5-11, 23-24,and 86-98)and 2 short 3-10 helices (residues 18-20, and 115-118).  The other has a small three-stranded antiparallel beta-pleated sheet (residues 41-44, 47-50, and 55-56), a short 3-10 alpha-helix (residues 77-80), and two disulfide bonds, Cys 61-Cys 77 and Cys 73-Cys 91.   <ref name="energetics"> Hendrix TM, Griko Y, Privalov P. 1996. Energetics of structural domains in α-lactalbumin.  Protein Science. 5923-5931.</ref> The domains are held together by a calcium binding loop formed by a cysteine bridge between residues 73 and 91, and also a disulfide bridge between residues 61 and 77. <ref name="structure"> </ref>.
 The <scene name='Sandbox_81/Secondary_structure/1'>secondary structure</scene> has nine alpha helices shown as pink rockets, and two beta sheets shown as yellow planks.<ref name="PDB"> </ref> The four disulfide bonds are shown by the yellow strings. It also has three strands, and 2 beta hairpins, and 11 beta turns.
-<scene name='Sandbox_81/Side_chains/1'>Side Chains</scene>: with nonpolar side chains in gray, polar side chains in purple, and associated water molecules in red.
+The <scene name='Sandbox_81/Side_chains/1'>side Chains</scene> are shown here with nonpolar side chains in gray, polar side chains in purple, and associated water molecules in red.  The hydrophobic side chains congregate in the center of the protein with the polar side chains on the periphery.  The water molecules are associated with the polar side chains.
-In the beta-rich domain there are two calcium binding sites, shown here are the <scene name='Sandbox_81/Ligands/2'>ligands</scene> with their amino acid contacts (water molecules are shown in pink and oxygen molecules are shown in red).  The first site, the primary site is made of three asparagine side chains and two carbonyls <ref name="PDB"> </ref>, and has a pentagonal bypyramidal coordination with active sites: LYS A  79  ASP A  82  ASP A  84  ASP A  87 ASP A  88.  The second site has a tetrahedral coordination with active sites: THR A  38  GLN A  39  LEU A  81  ASP A  83 <ref name="PDB"> </ref>.
 <scene name='Sandbox_81/Residues/1'>Polar uncharged residues</scene>:cations in blue, anions in red, hydrophobic in gray, polar uncharged in light purple, backbone in dark purple.
-== Function ==
+In the beta-rich domain there are two calcium binding sites, shown here are the <scene name='Sandbox_81/Ligands/2'>calcium ligands</scene> with their amino acid contacts (water molecules are shown in pink and oxygen molecules are shown in red).  The first site, the primary site is made of three asparagine side chains and two carbonyls <ref name="PDB"> </ref>, and has a pentagonal bypyramidal coordination with active sites: LYS A  79  ASP A  82  ASP A  84  ASP A  87 ASP A  88.  The second site has a tetrahedral coordination with active sites: THR A  38  GLN A  39  LEU A  81  ASP A  83 <ref name="PDB"> </ref>.
 == Recent Studies ==
-Tryptophan is a component of many alpha-lactalbumin proteins <ref name="whey"> Markus CR, Olivier B, de Haan EH. 2002. Whey protein rich in alpha-lactalbumin increases the ratio of plasma tryptophan to the sum of the other larger neutral amino acids and improves cognitive performance in stress vulnerable subjects. Am J Clin Nutr. 75(6):1051-1056. </ref>, the availability of which changes the ratio of plasma tryptophan to the sum of larger neutral amino acids (Trp-LNAA ratio).   Tryptophan is a serotonin precursor and proper serotonin function in the brain has been shown to promote sleep regulation and cognitive processes. <ref name="evening"> Markus CR, Jonkman LM, Lammers JH, Deutz NE, Messer MH, Rigtering N. 2005. Evening intake of alpha-lactalbumin increases plasma tryptophan availability and improves morning alertness and brain measures of attention. Am J Clin Nutr. 81(5):1026-1033. </ref>
+Tryptophan is a component of alpha-lactalbumin proteins <ref name="whey"> Markus CR, Olivier B, de Haan EH. 2002. Whey protein rich in alpha-lactalbumin increases the ratio of plasma tryptophan to the sum of the other larger neutral amino acids and improves cognitive performance in stress vulnerable subjects. Am J Clin Nutr. 75(6):1051-1056. </ref>, the availability of which changes the ratio of plasma tryptophan to the sum of larger neutral amino acids (Trp-LNAA ratio).   Tryptophan is a serotonin precursor and proper serotonin function in the brain has been shown to promote sleep regulation and cognitive processes. <ref name="evening"> Markus CR, Jonkman LM, Lammers JH, Deutz NE, Messer MH, Rigtering N. 2005. Evening intake of alpha-lactalbumin increases plasma tryptophan availability and improves morning alertness and brain measures of attention. Am J Clin Nutr. 81(5):1026-1033. </ref>
 Deficient serotonin function, possibly from chronic stress <ref name="whey"> </ref>, can result in difficulty sleeping and therefore behavioral decline.  Recent studies have shown that consumption of alpha-lactalbumin protein with enriched tryptophan content caused increased alertness and performance the morning after <ref name="evening"> </ref>.