Supplementary Information to the paper in J. R. Soc. Interface \Model Predictions of Deformation, Embolization, and Permeability of Partially Obstructive Blood Clots under Variable Shear Flow" from Model predictions of deformation, embolization and permeability of partially obstructive blood clots under variable shear flow

Supplementary_Information_Fina

Mechanical Transition from α‑Helical Coiled Coils to β‑Sheets in Fibrin(ogen)

We characterized the α-to-β transition in α-helical coiled-coil connectors of the human fibrin­(ogen) molecule using biomolecular simulations of their forced elongation and theoretical modeling. The force (<i>F</i>)–extension (<i>X</i>) profiles show three distinct regimes: (1) the elastic regime, in which the coiled coils act as entropic springs (<i>F</i> < 100–125 pN; <i>X</i> < 7–8 nm); (2) the constant-force plastic regime, characterized by a force-plateau (<i>F</i> ≈ 150 pN; <i>X</i> ≈ 10–35 nm); and (3) the nonlinear regime (<i>F > </i>175–200 pN; <i>X</i> > 40–50 nm). In the plastic regime, the three-stranded α-helices undergo a noncooperative phase transition to form parallel three-stranded β-sheets. The critical extension of the α-helices is 0.25 nm, and the energy difference between the α-helices and β-sheets is 4.9 kcal/mol per helical pitch. The soft α-to-β phase transition in coiled coils might be a universal mechanism underlying mechanical properties of filamentous α-helical proteins

Mechanistic Basis for the Binding of RGD- and AGDV-Peptides to the Platelet Integrin αIIbβ3

Binding of soluble fibrinogen to the activated conformation of the integrin αIIbβ3 is required for platelet aggregation and is mediated exclusively by the C-terminal AGDV-containing dodecapeptide (γC-12) sequence of the fibrinogen γ chain. However, peptides containing the Arg-Gly-Asp (RGD) sequences located in two places in the fibrinogen Aα chain inhibit soluble fibrinogen binding to αIIbβ3 and make substantial contributions to αIIbβ3 binding when fibrinogen is immobilized and when it is converted to fibrin. Here, we employed optical trap-based nanomechanical measurements and computational molecular modeling to determine the kinetics, energetics, and structural details of cyclic RGDFK (cRGDFK) and γC-12 binding to αIIbβ3. Docking analysis revealed that NMR-determined solution structures of cRGDFK and γC-12 bind to both the open and closed αIIbβ3 conformers at the interface between the αIIb β-propeller domain and the β3 βI domain. The nanomechanical measurements revealed that cRGDFK binds to αIIbβ3 at least as tightly as γC-12. A subsequent analysis of molecular force profiles and the number of peptide−αIIbβ3 binding contacts revealed that both peptides form stable bimolecular complexes with αIIbβ3 that dissociate in the 60–120 pN range. The Gibbs free energy profiles of the αIIbβ3–peptide complexes revealed that the overall stability of the αIIbβ3-cRGDFK complex was comparable with that of the αIIbβ3−γC-12 complex. Thus, these results provide a mechanistic explanation for previous observations that RGD- and AGDV-containing peptides are both potent inhibitors of the αIIbβ3–fibrinogen interactions and are consistent with the observation that RGD motifs, in addition to AGDV, support interaction of αIIbβ3 with immobilized fibrinogen and fibrin