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<Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate kinase' scene='Scene 1' />
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==Introduction==
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<scene name='Sandbox_43/Samaniego_scene/1'>Adenylate kinase</scene> is an enzyme that catalyzes the reversible reaction in which a molecule of ATP and a molecule of AMP are converted into two molecules of ADP through the following reaction scheme:
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== '''Secondary and Tertiary Structure of α-lactalbumin'''==
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ATP + AMP ⇔ 2 ADP
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α-lactalbumin is composed of nine <scene name='Sandbox_43/Adfa/1'>α-helices</scene> (purple), eleven beta turns, two beta hairpin turns, and three strands. The three strands make up an antiparallel <scene name='Sandbox_43/Beta_sheets/2'>β-sheets</scene> (blue), the nine helices are involved in 6 helix-helix interactions.<ref name="iv"> Protein Data Bank. 2009. European Bioinformatics Institute. <http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/> Retrieved Sept.19,2009.</ref> The primary structure can also been seen in the picture below. <scene name='Sandbox_43/Secondary_structures/1'>Secondary structure</scene> can be seen here in reference to the overall tertiary structure. α-helices are represented by the pink rockets, while the β-sheets are shown as golden arrows.
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[[Image:Alphalactalbumin secondary structure.gif]]<ref name="iv"> </ref>
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Adenylate kinase is integral in maintaining cellular energy homeostasis by providing ADP, which is later utilized in oxidative phosphorylation in metabolic pathways for energy production. This enzyme also possesses a unique flexibility to bind to ligands, pictured as the space filling region.
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α-lactalbumin is stabilized by four disulfide bonds (yellow lines in picture above and yellow rods in the picture to the right in its tertiary structure) and contains two structural domains. The α-domain is rich in α-helices and contains the Cys 6-Cys 120 and Cys 28-Cys 111 disulfide bond. The β-domain is rich in β-sheets and contains as Cys 61-Cys 77 and Cys 73-Cys 91 disulfide bonds.<ref name="iii">Tonya M. Hendrix, Yuri Griko, and Peter Privalov. 1996. Energetics of structural domains in a-lactalbumin. ''Protein Science'' 5923-931. </ref>
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==Structural Elements==
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The <scene name='Sandbox_43/Samaniego_scene_bg/2'>secondary structural elements</scene> of adenylate kinase show alpha helices (black) and beta sheets (blue) surrounding the non-hydrolysable substrate analogue (orange). <scene name='Sandbox_43/Samaniego_scene_hbonds/1'>Hydrogen bonds</scene> should be visible in green but may not load. These hydrogen bonds connect amino acids of alpha helices and beta sheets, which comprise the backbone of the protein. The anti-parallel configuration of the hydrogen bonds on beta sheets provides stability for the protein.
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The tertiary state of α-lactalbumin is held together by the disulfide bonds and also the hydrophobic interactions of the non-polar amino acids. You can see that the <scene name='Sandbox_43/Unpolar2/1'>hydrophobic</scene> interactions are for the most part positioned towards the center of the globular protein. The <scene name='Sandbox_43/Polar/1'>polar</scene> amino acids however are mostly on the surface of the protein covering the majority of the helices compared to the hydrophobic view.
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The <scene name='Sandbox_43/Samaniego_scene_stickswires/1'>hydrophobic residues</scene> of adenylate kinase are depicted in the black and blue ball and stick representation. These are buried on the interior of the enzyme to avoid contact with the solvent, demonstrating the hydrophobic effect. The protein is surround by <scene name='Sandbox_43/Samaniego_scene_hydrophobic/1'>hydrophilic residues</scene> depicted in the yellow portions. These hydrophilic portions can include polar and charged amino acids, which have a high affinity for the intermolecular solvent interactions in terms of hydrogen bonding and solubility.
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== '''Metal Ions associated with α-lactalbumin'''==
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==Solvent Accessibility==
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α-lactalbumin is a small protein with calcium ions as cofactors. The binding of the calcium ion increases the stability of the protein in its native conformation and makes the folding of the protein much faster. The binding of the calcium ion acts of a nucleus for the stabilization of the tertiary structure in the protein, without it the process is much slower.<ref>Natalia A. Bushmarina, Clement E. Blanchet, Gregory Vernier, and Vincent Forge. 2006. Cofactor effects on the protein folding reaction: Acceleration of a-lactalbumin refolding by metal ions ''Protein Science'' 15:659–671</ref> In α-lactalbumin native conformation the calcium ion is bound to a unique binding loop.<ref name="ii"> </ref> The calcium binding site is located in the β-domain and is formed by three Asp side chains and two mainchain carbonyls. This site the calcium ion has a pentagonal bypyramidal coordination.<ref name="iv"> </ref> <ref name="iii"> </ref> A secondary calcium binding site involves the residues Thr, Gln, Leu, and Asp. In this site the calcium ion has a tetrahedral coordination.<ref name="iv"> </ref> The <scene name='Sandbox_43/Cal_res/1'>residues</scene> that come into contact with the calcium ion are shown to the right. Protection from thermal, guanidine HCL and urea denaturation is provided by the stability given to the protein from the calcium ion binding. The calcium-binding site has also been shown to weakly bind Mg2+, Na2+, and K+ also. Removal of the calcium ion has shown to induce a conformational change. In the presence of denaturants or absence of calcium ions α-lactalbumin adopts the molten globule state and characterized by the conserved secondary structure but fluctuating tertiary structure.<ref name="ii"> </ref> α-lactalbumin, in its native state, possesses a relatively strong Zn2+ site causing subtle changes in α-lactalbumin structure upon binding to the calcium loaded protein. The Zn2+ is important in the binding of glucose in the lactose synthase complex.<ref name="ii"> </ref>
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When dissolved in <scene name='Sandbox_43/Samaniego_scene_water2/1'>water</scene> (light blue), the hydrophilic residues of adenylate kinase interact with this polar solvent to fold the protein into its most stable conformation through hydrogen bonding. It can be seen that water interacts with the ligand (green) at its center, where catalysis occurs. However, water mostly surrounds the hydrophilic exterior of the molecule, where the majority of hydrogen bonding occurs.
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=='''Research Studies'''==
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==Ligand Interactions==
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HAMLET (human a-lactalbumin made lethal to tumor cells) is made up of partially unfolded α-lactalbumin and oleic acid (shown below). HAMLET has been shown to kill a wide range of tumor cells and embryonal cells but not healthy differentiated cells. It is thought that HAMLET initiate macroautophagy in tumor cells. HAMLET was shown to affect the mitochondria and to cause an apoptotic response with Cytochrome c release, low caspase activation, phosphatidylserine exposure and DNA fragmentation. HAMLET has also been shown to have no adverse effects ''in vivo''. HAMLET translocates to the nuclei, binding to histones and disrupts the function of chromatin in tumor cells<ref>Sonja Aits, Lotta Gustafsson, Oskar Hallgren, Patrick Brest, Mattias Gustafsson, Maria Trulsson, Ann-Kristin Mossberg, Hans-Uwe Simon, Baharia Mograbi and Catharina Svanborg. 2009. HAMLET (human a-lactalbumin made lethal to tumor cells) triggers autophagic tumor cell death. ''Int. J. Cancer'' 124, 1008–1019</ref>
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Portions of adenylate kinase which interact with the ligand are shown here in purple. These are called the <scene name='Sandbox_43/Samaniego_scene_ligand2/1'>ligand contacts</scene> and have polar-charged side chains, which help to stabilize the ligand as it binds to the protein's active site. The catalytic resides (unable to be pictured) are able to directly interact/bind to the ligand.
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[[Image:Oleic_Acid2.gif]]<ref>scienceofcooking.com retrieved Sept. 20, 2009</ref>
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==Sources==
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Library CHEM410 page: http://libguides.messiah.edu/content.php?pid=279182&sid=2407875
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==References==
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Wikipedia: http://en.wikipedia.org/wiki/Adenylate_kinase
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{{Reflist}}
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European Bioinformatics Institute: http://www.ebi.ac.uk/interpro/IEntry?ac=IPR000850

Current revision

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.

Adenylate kinase

Drag the structure with the mouse to rotate

Contents

Introduction

is an enzyme that catalyzes the reversible reaction in which a molecule of ATP and a molecule of AMP are converted into two molecules of ADP through the following reaction scheme:

ATP + AMP ⇔ 2 ADP

Adenylate kinase is integral in maintaining cellular energy homeostasis by providing ADP, which is later utilized in oxidative phosphorylation in metabolic pathways for energy production. This enzyme also possesses a unique flexibility to bind to ligands, pictured as the space filling region.

Structural Elements

The of adenylate kinase show alpha helices (black) and beta sheets (blue) surrounding the non-hydrolysable substrate analogue (orange). should be visible in green but may not load. These hydrogen bonds connect amino acids of alpha helices and beta sheets, which comprise the backbone of the protein. The anti-parallel configuration of the hydrogen bonds on beta sheets provides stability for the protein.

The of adenylate kinase are depicted in the black and blue ball and stick representation. These are buried on the interior of the enzyme to avoid contact with the solvent, demonstrating the hydrophobic effect. The protein is surround by depicted in the yellow portions. These hydrophilic portions can include polar and charged amino acids, which have a high affinity for the intermolecular solvent interactions in terms of hydrogen bonding and solubility.

Solvent Accessibility

When dissolved in (light blue), the hydrophilic residues of adenylate kinase interact with this polar solvent to fold the protein into its most stable conformation through hydrogen bonding. It can be seen that water interacts with the ligand (green) at its center, where catalysis occurs. However, water mostly surrounds the hydrophilic exterior of the molecule, where the majority of hydrogen bonding occurs.

Ligand Interactions

Portions of adenylate kinase which interact with the ligand are shown here in purple. These are called the and have polar-charged side chains, which help to stabilize the ligand as it binds to the protein's active site. The catalytic resides (unable to be pictured) are able to directly interact/bind to the ligand.

Sources

Library CHEM410 page: http://libguides.messiah.edu/content.php?pid=279182&sid=2407875 Wikipedia: http://en.wikipedia.org/wiki/Adenylate_kinase European Bioinformatics Institute: http://www.ebi.ac.uk/interpro/IEntry?ac=IPR000850

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