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Title
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Structure of the hirulog 3-thrombin complex and nature of the S' subsites of substrates and inhibitors.
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Authors
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X.Qiu,
K.P.Padmanabhan,
V.E.Carperos,
A.Tulinsky,
T.Kline,
J.M.Maraganore,
J.W.Fenton.
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Ref.
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Biochemistry, 1992,
31,
11689-11697.
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PubMed id
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Abstract
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The X-ray crystallographic structure of the human alpha-thrombin complex with
hirulog 3 (a potent, noncleavable hirudin-based peptide of the "hirulog" class
containing a beta-homoarginine at the scissile bond), which is isomorphous with
that of the hirugen-thrombin crystal structure, was solved at 2.3-A resolution
by starting with a model for thrombin derived from the hirugen-thrombin complex
and was refined by restrained least squares methods (R = 0.132). Residues of
hirulog 3 were well-defined in the electron density, which included most of the
pentaglycine linker and the C-terminal helical turn that was disordered in a
related structure of thrombin with hirulog 1. The interactions of
D-Phe1'-Pro2'-beta-homoArg3' with the active site of thrombin were essentially
identical to those of related structures of PPACK- (D-Phe-Pro-Arg chloromethyl
ketone) and hirulog 1-thrombin, with the guanidinium function of the arginyl P1
residue forming a hydrogen-bonding ion pair with Asp189 of the S1 site. A
noticeable shift in the CA atom of beta-homoArg3' due to the methylene insertion
displaces the scissile bond from attack by Ser195, thus imparting proteolytic
stability to the beta-homoArg hirulog derivative. Resolution of the pentaglycine
spacer, linking N- and C-terminal functional domains into a single oligopeptide
bivalent inhibitor, permitted delineation of corresponding S' subsites of
thrombin. The position of Gly4' (P1') is stabilized by three hydrogen bonds with
His57, Lys60F, and Ser195, while the conformational angles maintained in a
strained, nonallowed configuration for non-glycyl amino acids.(ABSTRACT
TRUNCATED AT 250 WORDS)
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