Sandbox k11v
Toxic Amyloid Small Oligomer’s atomic view
The interactive Molecular Tour below assumes that you are familiar with the journal article[1]. IntroductionAmyloid fibrils were first assumed to be the agents of Amyloid diseases,including Alzheimer’s,Parkinson’s and the prion conditions.But studies from many laboratories suggest that the reason for this disorder are lower molecular weight entities known as small amyloid oligomers,instead of the associated protein fibrils.Segment of amyloid forming protein alpha-beta crystallin makes oligomeric complex which exhibits properties of other amyloid oligomers.They are rich in beta-sheet structure and these oligomer can be identified by a conformational antibody(A11) that binds oligomers but not fibrils,irrespective of sequence of constituent protein.This protein is a chaperone that forms amyloid fibrils.The structure of oligomer shows a cylindrical barrel,made up of six anti-parallel protein strands known as cylindrin.This segment(coloured in black) termed as K11V forms the cylindrin structure. Molecular TourOligomer forming segment of ABC were identified by inspection of its 3D structure and by applying the Rosetta-Profile algorithm to its sequence.Two segments of high amyloidogenic propensity,with sequences KVKVLG and GDVIEV (where D indicates Asp; E, Glu; G, Gly; I, Ile; K, Lys; and V, Val). The entire 11-residue segment KVKVLGDVIEV forms a hairpin loop in the 3D structure of ABC.The six residue segment GDVIEV ,termed G6V,forms fibrils and microcrystals.THe microcrystals enabled us to determine the atomic structure of G6V, which proved to be a standard class 2 steric zipper, essentially an amyloid-like protofilament.  PDB'S are K11V (3SGO), K11V-Br2 (3SGM), K11V-Br8 (3SGN), K11VV2L (3SGP), K11V-TR (3SGR), and GDVIEV (3SGS).
RelevanceNotes & Reference
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