High-resolution NMR studies of fibrinogen-like peptides in solution: structural basis for the bleeding disorder caused by a single mutation of Gly(12) to Val(12) in the A.alpha. chain of human fibrinogen Rouen

Ni, Feng; Konishi, Yasuo; Bullock, Lea Doerr; Rivetna, Meheryar N.; Scheraga, Harold A.

doi:10.1021/bi00433a054

Cited by 51 publications

(12 citation statements)

References 33 publications

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“…The other mutation is GlyF12+Val; as discussed, the left-handed helical conformation adopted by GlyF12 would be energetically unfavourable for this substitution; the chain might not be able to fold back in towards the active site. NMR studies of this ValF12 tnutant [49] indeed show an alternative conformation to the wild type.…”

Section: Structural Grounds For Dysfunctional Fibrinogensmentioning

confidence: 82%

The interaction of thrombin with fibrinogen

Stubbs

Oschkinat

Mayr

et al. 1992

European Journal of Biochemistry

217

303

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The structure of the ternary complex of human a-thrombin with a covalently bound analogue of fibrinopeptide A and a C-terminal hirudin peptide has been determined by X-ray diffraction methods at 0.25 nm resolution. Fibrinopeptide A folds in a compact manner, bringing together hydrophobic residues that slot into the apolar binding site of human a-thrombin. Fibrinogen residue Phe8 occupies the aryl-binding site of thrombin, adjacent to fibrinogen residues Leu9 and Val15 in the S2 subsite. The species diversity of fibrinopeptide A is analysed with respect to its conformation and its interaction with thrombin. The non-covalently attached peptide fragment hirudin(54 -65) exhibits an identical conformation to that observed in the hirudin-thrombin complex. The occupancy of the secondary fibrinogen-recognition exosite by this peptide imposes restrictions on the manner of fibrinogen binding. The surface topology of the thrombin molecule indicates positions PI' -P3', differ from those of the canonical serine-proteinase inhibitors, suggesting a mechanical model for the switching of thrombin activity from fibrinogen cleavage to protein-C activation on thrombomodulin complex formation. The multiple interactions between thrombin and fibrinogen provide an explanation for the narrow specificity of thrombin. Structural grounds can be put forward for certain congenital clotting disorders.The specific cleavage of fibrinogen by the serine proteinase thrombin initiates the polymerisation of fibrin monomers, a primary event in blood clot formation [4]. Fibrinogen (340 kDa) is a covalently linked dimer of three peptide chains, with stoichiometry (Aa, BP,y), [5]. The cleavage releases two peptides, fibrinopeptides A and B, from the N-termini of chains Aa and Bfl respectively, thereby revealing recognition sites for aggregation with the y chain.Thrombin exhibits primarily a trypsin-like specificity, i.e. a preference for P1 arginine residues [6]. The cleavage of fibrinogen by thrombin represents a very specific reaction however; of the 376 Arg/Lys-Xaa bonds in the fibrinogen molecule, thrombin cleaves only four, releasing the fibrinopeptides [6]. Residues of fibrinogen contributing to this exceptional specificity have been localised to the first 51 amino acids of the Acc chain [7, 81. This region has been further dissected to explore subsites, assigning roles (in order of im-Enzyrnr. Thrombin (EC 3.4 .21 .S).Nomencluture. The peptide and subsite nomenclature is that suggested by Schechter and Berger 111: amino acid residues of substrates are numbered P1, P2, P3 etc. towards the amino terminus, and P1 ', P2', P3' etc. towards the carboxy terminus from the reactive-sitc bond; the complementary subsites of the enzyme are numbered S1, S2, S3 etc. and SI', S2', S3' etc., respectively. Thrombin residues are numbered according to the chymotrypsinogen system [2], with inserted residues marked by a lower-case suffix [ 3 ] . Fibrinogen residues are prefixed by the letter F, hirudin residues by the letter H and uPhe-Pro-Arg-MeC1 residues by the le...

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Section: Structural Grounds For Dysfunctional Fibrinogensmentioning

confidence: 82%

The interaction of thrombin with fibrinogen

Stubbs

Oschkinat

Mayr

et al. 1992

European Journal of Biochemistry

217

303

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“…The other mutant is Gly F12 for Val; as discussed, the lefthanded helical conformation adopted by Gly F12 would be energetically unfavorable for this substitution, with the chain not able to fold back in toward the active site. NMR studies of this Val F12 mutant, 41 indeed, show an alternative conformation to the wild type.…”

Section: Fig 2 Hypothetical Model Of the 'Primed' (Post Cleavage) Smentioning

confidence: 83%

A Model for the Specificity of Fibrinogen Cleavage by Thrombin

Stubbs¹,

Bode²

1993

Semin Thromb Hemost

111

168

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The specific cleavage of fibrinogen by the serine proteinase thrombin (EC 3.4.21.5) initiates the polymer ization of fibrin monomers, a primary event in blood clot formation. 1 Fibrinogen (M r 340,000) is a covalently linked dimer of three peptide chains, with stoichiometry (Aα,Bβ,γ) 2 . 2 The cleavage releases two peptides, fibrinopeptides A (FPA) and B (FPB) from the amino-termini of chains Act and Bβ, respectively, thereby revealing recognition sites for aggregation with the 7 chain.Thrombin exhibits primarily a trypsin-like specific ity, that is, a preference for arginyl P1 residues 3 (see Bode and Stubbs in this issue of Seminars for nomencla ture). The cleavage of fibrinogen by thrombin represents a very specific reaction, however. Of the 376 Arg/LysXaa bonds in the fibrinogen molecule, thrombin cleaves in the native state only four, releasing the fibrinopeptides. 3 Residues of fibrinogen contributing to this excep tional specificity have been localized to the first 51 amino acids of the Aα-chain. 4,5 This region has been further dissected to explore subsites, assigning roles (in order of importance) to fragments F1-F23, F33-F44, and F45-F51 6 (fibrinogen residues are prefixed by the letter "F", D-phenylalanyl-L-prolyl-L-arginine chloromethyl-ketone (PPACK) residues by "I", and hirudin residues by "H"). Two separate sites in thrombin outside S1 have been proposed as conferring this additional specificityone apolar, in the unprimed region, 7 ' 8 and one basic postcleavage site (the fibrinogen recognition exosite). [9][10][11] This recognition exosite appears to be in volved in the binding of other proteins, including fibrin itself, thrombomodulin (a cell surface protein that allows thrombin activation of protein C, which in turn shuts down thrombin production) and hirudin (the potent anti coagulant from the saliva of the leech Hirudo medicinalis). 12-14 Hirugen, a sulfated dodecapeptide correspond ing to the hirudin C-terminus, and the nonsulfated C-terminal peptide hirudin (45-65) are competitive inhib itors of fibrinogen cleavage by thrombin, while allowing peptidase activity on small synthetic substrates. 15,16 These sites have recently been identified in a series of crystallographic studies 17-23 (see Bode and Stubbs in this issue). The ternary complex of human α-thrombin with peptides derived from FPA and hirudin 22 (FPA-Hthrombin) allows a structural explanation for the extreme specificity of the fibrinogen-thrombin interaction; a spec ificity whose disruption can lead to severe clotting disor ders. 24 The covalently bound (N-acetylated) decapeptide chloromethylketone (Ac-AspF7-PheF8-LeuF9-AlaF10-GluFll-GlyF12-GlyF13-GlyF14-ValF15-ArgF16-CMK) exhibits little in the way of regular secondary structure (Fig. 1). The acetylated amino-terminal points away from the enzyme, whereby the preceding six residues could extend freely into solution. Asp F7 begins a short stretch (F8-F10) of α-helical conformation with a hydro gen bond from its carboxylate O δ1 to the amide nitrogen of Ala F10. This irregularly hydr...

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“…Bottom. Structure of the same portion of wild-type fibrinogen, which contains glycine at position G12, but shown here with V12 of fibrinogen Rouen computationally replacing G12 of the wild-type protein (Ni et al 1989a, b, c). …”

Section: Figmentioning

confidence: 98%

My 65 years in protein chemistry

Scheraga

2015

Quart. Rev. Biophys.

Self Cite

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This is a tour of a physical chemist through 65 years of protein chemistry from the time when emphasis was placed on the determination of the size and shape of the protein molecule as a colloidal particle, with an early breakthrough by James Sumner, followed by Linus Pauling and Fred Sanger, that a protein was a real molecule, albeit a macromolecule. It deals with the recognition of the nature and importance of hydrogen bonds and hydrophobic interactions in determining the structure, properties, and biological function of proteins until the present acquisition of an understanding of the structure, thermodynamics, and folding pathways from a linear array of amino acids to a biological entity. Along the way, with a combination of experiment and theoretical interpretation, a mechanism was elucidated for the thrombin-induced conversion of fibrinogen to a fibrin blood clot and for the oxidative-folding pathways of ribonuclease A. Before the atomic structure of a protein molecule was determined by x-ray diffraction or nuclear magnetic resonance spectroscopy, experimental studies of the fundamental interactions underlying protein structure led to several distance constraints which motivated the theoretical approach to determine protein structure, and culminated in the Empirical Conformational Energy Program for Peptides (ECEPP), an all-atom force field, with which the structures of fibrous collagen-like proteins and the 46-residue globular staphylococcal protein A were determined. To undertake the study of larger globular proteins, a physics-based coarse-grained UNited-RESidue (UNRES) force field was developed, and applied to the protein-folding problem in terms of structure, thermodynamics, dynamics, and folding pathways. Initially, single-chain and, ultimately, multiple-chain proteins were examined, and the methodology was extended to protein–protein interactions and to nucleic acids and to protein–nucleic acid interactions. The ultimate results led to an understanding of a variety of biological processes underlying natural and disease phenomena.

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High-resolution NMR studies of fibrinogen-like peptides in solution: structural basis for the bleeding disorder caused by a single mutation of Gly(12) to Val(12) in the A.alpha. chain of human fibrinogen Rouen

Cited by 51 publications

References 33 publications

The interaction of thrombin with fibrinogen

The interaction of thrombin with fibrinogen

A Model for the Specificity of Fibrinogen Cleavage by Thrombin

My 65 years in protein chemistry

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