Trueba-Gómez Rocio, Rosenfeld-Mann Fany, Baptista-González Hector A, Domínguez-López María L, Estrada-Juárez Higinio
Instituto Nacional de Perinatología "Isidro Espinosa de los Reyes", Coordinación de Hematología Perinatal, Mexico City, Mexico.
Posgrado en Ciencias Químico Biológicas, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico.
Vox Sang. 2023 Oct;118(10):881-890. doi: 10.1111/vox.13509. Epub 2023 Aug 9.
Computational biology analyses the theoretical tertiary structure of proteins and identifies the 'topological' differences between RhD and RhCE. Our aim was to identify the theoretical structural differences between the four isoforms of RhCE and RhD using computational biological tools.
Physicochemical profile was determined by hydrophobicity and electrostatic potential analysis. Secondary and tertiary structures were generated using computational biology tools. The structures were evaluated and validated using Ramachandran algorithm, which calculates the single score, p-value and root mean square deviation (RMSD). Structures were overlaid on local refinement of 'RhAG-RhCE-ANK' (PBDID 7uzq) and RhAG to compare their spatial distribution within the membrane.
All proteins differed in surface area and electrostatic distance due to variations in hydrophobicity and electrostatic potential. The RMSD between RhD and RhCE was 0.46 ± 0.04 Å, and the comparison within RhCE was 0.57 ± 0.08 Å. The percentage of amino acids in the hydrophobic thickness was 50.24% for RhD while for RhCE it ranged between 73.08% and 76.68%. The RHAG hydrophobic thickness was 34.2 Å, and RhCE's hydrophobic thickness was 33.83 Å. We suggest that the C/c antigens differ exofacially at loops L1 and L2. For the E/e antigens, the difference lies in L6. By contrast, L4 is the same for all proteins except Rhce.
The physicochemical properties of Rh proteins made them different, although their genes are homologous. Using computational biology, we model structures with sufficient precision, similar to those obtained experimentally. An amino acid variation alters the folding of the tertiary structure and the interactions with other proteins, modifying the electrostatic environment, the spatial conformations and therefore the antigenic recognition.
计算生物学分析蛋白质的理论三级结构，并确定RhD和RhCE之间的“拓扑”差异。我们的目的是使用计算生物学工具确定RhCE和RhD四种异构体之间的理论结构差异。
通过疏水性和静电势分析确定理化特征。使用计算生物学工具生成二级和三级结构。使用Ramachandran算法对结构进行评估和验证，该算法计算单个得分、p值和均方根偏差（RMSD）。将结构叠加在“RhAG-RhCE-ANK”（PBDID 7uzq）和RhAG的局部优化结构上，以比较它们在膜内的空间分布。
由于疏水性和静电势的变化，所有蛋白质在表面积和静电距离上存在差异。RhD和RhCE之间的RMSD为0.46±0.04 Å，RhCE内部比较的RMSD为0.57±0.08 Å。RhD的疏水性厚度中氨基酸百分比为50.24%，而RhCE的疏水性厚度中氨基酸百分比在73.08%至76.68%之间。RHAG的疏水性厚度为34.2 Å，RhCE的疏水性厚度为33.83 Å。我们认为C/c抗原在环L1和L2的外表面存在差异。对于E/e抗原，差异在于L6。相比之下，除Rhce外，所有蛋白质的L4相同。
Rh蛋白的理化性质使其有所不同，尽管它们的基因是同源的。使用计算生物学，我们能够以足够的精度模拟结构，类似于通过实验获得的结构。氨基酸变异会改变三级结构的折叠以及与其他蛋白质的相互作用，从而改变静电环境、空间构象，进而改变抗原识别。
