Figure 2.
Integrin headpiece hinge opening and receptor–ligand contact stability during MD equilibration. (A) After 6 ns of MD, the equilibrated integrin complex (blue, purple, and yellow) is aligned with the starting crystal structure (gray; Xiong et al., 2002) via βA domain β-strands. For clarity, the βA domain is shown in transparent surface representation with the secondary structure of select regions visible in cartoon representation. (B) A close-up of the βA/hybrid domain interface shows the location inside the hinge of the hydrogen bond between Asn303 and Lys417. This equilibrated complex, in which the Asn303–Lys417 bond broke when the hinge spontaneously increased by ∼20°, is referred to in the text as the “reference complex.” (C, middle) In all of the equilibrated FnIII10–integrin complexes we investigated, independent of structural variations, the RGD loop of FnIII10 (yellow) displayed close alignment with the conformation of the RGD sequence found in the original crystal structure (gray), and the two principle RGD–integrin binding contacts (AspRGD-MIDAS ion and ArgRGD–α-Asp218) remained stable. (C, top and bottom). In the same, but separate, views of the equilibrated complex (top) and the liganded crystal structure (bottom), two additional AspRGD-βA domain–binding contacts that have been shown by pharmacophore refinement to be vital to the RGD-αvβ3 ligand–integrin recognition process (Marinelli et al., 2003) displayed stability. These are hydrogen bonds between AspRGD–β-Arg216 and AspRGD–β-Tyr122. Bonds present in the original crystal structure complex are shown in green. Also visible is a hydrogen bond between Fn-Glu62 and β-Tyr129 (orange) that formed in the equilibrated complex and was found to promote hinge angle opening on the nanosecond time frame.