Lalaurie C J, Kulke M, Geist N, Delcea M, Dalby P A, McDonnell T C R
Division of Medicine, Rayne Building, 5 University Street, University College London WC1E 6JF London, United Kingdom.
Theoretical Biophysics, Ernst-Otto-Fischer-Str. 8, 85748 Garching b., Technical University Munich, Munich, Germany.
J Struct Biol X. 2025 Aug 20;12:100135. doi: 10.1016/j.yjsbx.2025.100135. eCollection 2025 Dec.
Beta-2-Glycoprotein I is the main target for pathogenic antiphospholipid syndrome autoantibodies. It can adopt several conformations, including an O-shape and two more linear J- and S-shapes. The existence of the O-shape is debated, and doubt remains pertaining to the pathogenic impact of each shape. Studies have shown that APS antibodies react weakly with the O-shape and bind to the linear shapes due to the exposure of a cryptic epitope in the 1st domain. How the protein transitions from O-shape to the linear shapes remains unknown. While the main epitope is widely recognised as the R39-R43 peptide, there is evidence pointing to a discontinuous epitope across domains I and II (DI & DII). We used molecular dynamics simulations to examine the potential pathways of conformational shift from the O-shape to the open forms, and the impact of plasmin clipping on these pathways. Through these studies, starting in a theorised O-shape, we identified that peptides R39-R43, T50-N56 and R63-F67 become more exposed and have increased stability in the J- and S-shapes relative to the O-shape. These changes are likely due to a shift in DII of the T106-G109 loop, which twists to form contacts with the DI K33-Y36 loop. The R39-R43 peptide is brought closer to R63-F67 suggesting a more complex DI epitope than previously theorised. These effects were observed in the wild type and plasmin clipped model, with the effect being larger in the latter. These results are in good agreement with the increased antibody binding observed experimentally for the clipped protein. We therefore suggest that we have been able to identify the structural mechanism at the residue level which results in increased antibody binding in the J-Shape, and specifically in the clipped protein.
β-2-糖蛋白I是致病性抗磷脂综合征自身抗体的主要靶点。它可以呈现多种构象，包括O形以及另外两种线性的J形和S形。O形的存在存在争议，并且每种形状的致病影响仍存疑问。研究表明，抗磷脂综合征抗体与O形反应较弱，由于第1结构域中隐蔽表位的暴露而与线性形状结合。该蛋白如何从O形转变为线性形状仍然未知。虽然主要表位被广泛认为是R39-R43肽，但有证据指向跨越结构域I和II（DI和DII）的不连续表位。我们使用分子动力学模拟来研究从O形到开放形式的构象转变的潜在途径，以及纤溶酶切割对这些途径的影响。通过这些研究，从理论上的O形开始，我们发现肽R39-R43、T50-N56和R63-F67相对于O形在J形和S形中变得更加暴露并且稳定性增加。这些变化可能是由于T106-G109环的DII发生移位，该环扭曲以与DI的K33-Y36环形成接触。R39-R43肽更靠近R63-F67，表明DI表位比先前理论的更复杂。在野生型和纤溶酶切割模型中观察到了这些效应，后者的效应更大。这些结果与实验观察到的切割蛋白抗体结合增加非常一致。因此，我们认为我们已经能够在残基水平上确定导致J形，特别是切割蛋白中抗体结合增加的结构机制。
