Sandbox Reserved 595: Difference between revisions

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OCA, Student, Irma Santoro

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 <Structure load='1NFN' size='500' frame='true' align='right' caption='3-D Rendering of ApoE3 N-terminus' scene='Insert optional scene name here' />
 ==Primary Structural Features==
-Apolipoprotein E is a polymorphic glycoprotein that consists of 299 amino acids (A,F).  It has a molecular weight of 34kDa '<ref>Weisgraber et al.  1981.  Human apolipoprotein heterogeneity: cysteine-arginine interchanges in the amino acid sequence of apo-E isoforms The Journal of Biological Chemistry 256(17):9077-9083.</ref>'.  The primary structure for ApoE is rich in the amino acid <scene name='Sandbox_Reserved_595/Arginine/1'>arginine</scene>
+Apolipoprotein E is a polymorphic glycoprotein that consists of 299 amino acids '<ref>Jones, Philip B. et al.  2011.  Apoliprotein E: Isoform specific differences in tertiary structure and interaction with amyloid-beta in human alzheimer brain.  PLOS One 6(1):e14586.</ref>'(F).  It has a molecular weight of 34kDa '<ref>Weisgraber et al.  1981.  Human apolipoprotein heterogeneity: cysteine-arginine interchanges in the amino acid sequence of apo-E isoforms The Journal of Biological Chemistry 256(17):9077-9083.</ref>'.  The primary structure for ApoE is rich in the amino acid <scene name='Sandbox_Reserved_595/Arginine/1'>arginine</scene>
-ApoE folds into two independent structural domains that are connected via a hinge region (A,F,M).  The amino-terminal domain has a molecular weight of 2kDa and is comprised of the amino acid residues 1-199 (PDB entry [[1NFN]])(C,F,J,M).  It is a globular domain consisting of an antiparallel bundle of 4 amphipathic <scene name='Sandbox_Reserved_595/4-helix_bundle/1'>alpha-helices</scene>, rich in basic amino acids;  pronounced kinks are present in the helices near the end of the 4-helix bundle that correspond with the protein's lipid binding ability (C,F,J,L).  In the fourth helix, the residues between 134-150, known as the <scene name='Sandbox_Reserved_595/Ldl-r_binding_region/1'>low density lipoprotein receptor binding region</scene>, are responsible for ApoE's ability to bind to members of the LDL receptor family (C,F,J,L).  This domain also contains the variable <scene name='Sandbox_Reserved_595/Residues_112_and_158/3'>residues 112 and 158</scene> (112 blue & 158 in red), which are responsible for much of the differences between the three isoforms of apoE.
+ApoE folds into two independent structural domains that are connected via a hinge region '<ref>Jones, Philip B. et al.  2011.  Apoliprotein E: Isoform specific differences in tertiary structure and interaction with amyloid-beta in human alzheimer brain.  PLOS One 6(1):e14586.</ref>'(F,M).  The amino-terminal domain has a molecular weight of 2kDa and is comprised of the amino acid residues 1-199 (PDB entry [[1nfn]])(C,F,J,M).  It is a globular domain consisting of an antiparallel bundle of 4 amphipathic <scene name='Sandbox_Reserved_595/4-helix_bundle/1'>alpha-helices</scene>, rich in basic amino acids;  pronounced kinks are present in the helices near the end of the 4-helix bundle that correspond with the protein's lipid binding ability (C,F,J,L).  In the fourth helix, the residues between 134-150, known as the <scene name='Sandbox_Reserved_595/Ldl-r_binding_region/1'>low density lipoprotein receptor binding region</scene>, are responsible for ApoE's ability to bind to members of the LDL receptor family (C,F,J,L).  This domain also contains the variable <scene name='Sandbox_Reserved_595/Residues_112_and_158/3'>residues 112 and 158</scene> (112 blue & 158 in red), which are responsible for much of the differences between the three isoforms of apoE.
 The carboxyl-terminal domain is 10kD respectively, and consists of the residues 216-299 (C,F).  It presents a large exposed hydrophobic surface that is well-suited for interacting with multiple binding partners, including lipids, heparin sulfate proteoglycans (HSPGs), and amyloid beta peptides (Aβ) (V).  This domain harbors high-affinity lipid binding properties and is therefore capable of anchoring lipoprotein particles; it also contains sites that mediate ApoE self-association (C,D,I,J,P).  The C-terminal domain includes two kinds of amphipathic alpha helices.  The first of these alpha helices is a class A helix (residues 216-266) and the second is a class G helix (residues 273-299) (D).  Residues 230-270 in the C-terminal domain are crucial for oligomer formation(M).  Those residues that are important for the initiation of lipid binding to ApoE are 261-272 (M).
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 The heterogeneity of the three major isoforms can be attributed to small differences within the primary structure, namely cysteine - arginine interchanges, a single residue substitution '<ref>Weisgraber et al.  1981.  Human apolipoprotein heterogeneity: cysteine-arginine interchanges in the amino acid sequence of apo-E isoforms The Journal of Biological Chemistry 256(17):9077-9083.</ref>'(F).  Cysteine-arginine changes are present within the N-terminal domain (M).  Residues 112 and 158 are the positions accounting for the different isoforms.  ApoE2 has a cysteine located positioned at both the 112 and 158 residues (Cys/Cys).  Cysteine is present at residue 112 in apoE3 and arginine is present at residue 158 (Cys/Arg).  For apoE4, both 112 and 158 are filled by the amino acid arginine (Arg/Arg) '<ref>Weisgraber et al.  1981.  Human apolipoprotein heterogeneity: cysteine-arginine interchanges in the amino acid sequence of apo-E isoforms The Journal of Biological Chemistry 256(17):9077-9083.</ref>'(F).  Risk associations with diseases and disorders arise from the substitution that occurs at the 112 residue (N).  As a result of its primary structure, E4 is the most basic isoform '<ref>Weisgraber et al.  1981.  Human apolipoprotein heterogeneity: cysteine-arginine interchanges in the amino acid sequence of apo-E isoforms The Journal of Biological Chemistry 256(17):9077-9083.</ref>'.  A single pase change, due to a point mutation, at one or two sites in the ε3 gene could account for the E2 and E4 isoforms of apoE; this is a possible explanation given the fact that of the six codons specifying arginine, two of them differ from the cysteine codon merely by one base '<ref>Weisgraber et al.  1981.  Human apolipoprotein heterogeneity: cysteine-arginine interchanges in the amino acid sequence of apo-E isoforms The Journal of Biological Chemistry 256(17):9077-9083.</ref>'.  Structural differences that exist between the isoforms at higher levels of organization are distant frrom the site of cys-arg substitution (M).   With regards to other modifications within apoE, E2 and E4 show more similarity to each other than they do to E3; however, E2 is more similar in conformation E3 than E4 is to E3 (N).
-Different isoforms associate with different lipid particles in the plasma (A).  While apoE4 preferentially binds to VLDL, apoE3 and apoE2 have a higher affinity for HDL(F,H,L).  Structural stibility of the isoforms, from most stable to least stable, is as follows, E2>E3>E4 (L).  Accessibility of the hydrophobic residues was higher in apoE4 than apoE3 (F). ApoE4 also has a higher percentage of randomly coiled structure, a feature that could contribute to its greater tendency to aggregate (F). Domain interaction within apoE is stronger, causing the domains to be closer in proximity to each other, in apoE4 than in apoE; this is true under lipid-bound and lipid-free conditions (E).  Arginine 61 and glutamic acid 255 form a salt brigde that mediates the electrostatic interaction of C-T and N-T domains in apoE; the presence of arg112 in apoE4 appears to alter the salt-bridge in such as way as to enhance domain interaction (A,E,H).  Arg112 in apoE4 forms a salt-bridge with Glu109, a feature that apoE3 lacks (M).
+Different isoforms associate with different lipid particles in the plasma '<ref>Jones, Philip B. et al.  2011.  Apoliprotein E: Isoform specific differences in tertiary structure and interaction with amyloid-beta in human alzheimer brain.  PLOS One 6(1):e14586.</ref>'.  While apoE4 preferentially binds to VLDL, apoE3 and apoE2 have a higher affinity for HDL(F,H,L).  Structural stibility of the isoforms, from most stable to least stable, is as follows, E2>E3>E4 (L).  Accessibility of the hydrophobic residues was higher in apoE4 than apoE3 (F). ApoE4 also has a higher percentage of randomly coiled structure, a feature that could contribute to its greater tendency to aggregate (F). Domain interaction within apoE is stronger, causing the domains to be closer in proximity to each other, in apoE4 than in apoE; this is true under lipid-bound and lipid-free conditions (E).  Arginine 61 and glutamic acid 255 form a salt brigde that mediates the electrostatic interaction of C-T and N-T domains in apoE; the presence of arg112 in apoE4 appears to alter the salt-bridge in such as way as to enhance domain interaction '<ref>Jones, Philip B. et al.  2011.  Apoliprotein E: Isoform specific differences in tertiary structure and interaction with amyloid-beta in human alzheimer brain.  PLOS One 6(1):e14586.</ref>' (E,H).  Arg112 in apoE4 forms a salt-bridge with Glu109, a feature that apoE3 lacks (M).
 =Function=