Genome Research Chair Unit, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia.
PLoS One. 2011;6(10):e25876. doi: 10.1371/journal.pone.0025876. Epub 2011 Oct 20.
Single amino acid substitutions in the globin chain are the most common forms of genetic variations that produce hemoglobinopathies--the most widespread inherited disorders worldwide. Several hemoglobinopathies result from homozygosity or compound heterozygosity to beta-globin (HBB) gene mutations, such as that producing sickle cell hemoglobin (HbS), HbC, HbD and HbE. Several of these mutations are deleterious and result in moderate to severe hemolytic anemia, with associated complications, requiring lifelong care and management. Even though many hemoglobinopathies result from single amino acid changes producing similar structural abnormalities, there are functional differences in the generated variants. Using in silico methods, we examined the genetic variations that can alter the expression and function of the HBB gene. Using a sequence homology-based Sorting Intolerant from Tolerant (SIFT) server we have searched for the SNPs, which showed that 200 (80%) non-synonymous polymorphism were found to be deleterious. The structure-based method via PolyPhen server indicated that 135 (40%) non-synonymous polymorphism may modify protein function and structure. The Pupa Suite software showed that the SNPs will have a phenotypic consequence on the structure and function of the altered protein. Structure analysis was performed on the key mutations that occur in the native protein coded by the HBB gene that causes hemoglobinopathies such as: HbC (E→K), HbD (E→Q), HbE (E→K) and HbS (E→V). Atomic Non-Local Environment Assessment (ANOLEA), Yet Another Scientific Artificial Reality Application (YASARA), CHARMM-GUI webserver for macromolecular dynamics and mechanics, and Normal Mode Analysis, Deformation and Refinement (NOMAD-Ref) of Gromacs server were used to perform molecular dynamics simulations and energy minimization calculations on β-Chain residue of the HBB gene before and after mutation. Furthermore, in the native and altered protein models, amino acid residues were determined and secondary structures were observed for solvent accessibility to confirm the protein stability. The functional study in this investigation may be a good model for additional future studies.
单个氨基酸取代是导致血红蛋白病（全球最普遍的遗传性疾病）的最常见遗传变异形式。几种血红蛋白病是由于β-珠蛋白（HBB）基因突变的纯合子或复合杂合子引起的，例如产生镰状细胞血红蛋白（HbS）、HbC、HbD 和 HbE 的突变。这些突变中的许多是有害的，导致中度至重度溶血性贫血，并伴有相关并发症，需要终身护理和管理。尽管许多血红蛋白病是由产生相似结构异常的单个氨基酸变化引起的，但产生的变体在功能上存在差异。我们使用计算机模拟方法研究了可改变 HBB 基因表达和功能的遗传变异。使用基于序列同源性的Sorting Intolerant from Tolerant（SIFT）服务器，我们搜索了 SNP，结果显示 200（80%）个非同义多态性被认为是有害的。基于结构的方法通过 PolyPhen 服务器表明，135（40%）个非同义多态性可能会改变蛋白质的功能和结构。Pupa Suite 软件表明，SNP 将对改变的蛋白质的结构和功能产生表型后果。对 HBB 基因编码的天然蛋白质中发生的关键突变进行了结构分析，这些突变导致血红蛋白病，如：HbC（E→K）、HbD（E→Q）、HbE（E→K）和 HbS（E→V）。原子非局部环境评估（ANOLEA）、另一个科学人工现实应用程序（YASARA）、大分子动力学和力学的 CHARMM-GUI webserver 以及 Gromacs 服务器的正常模式分析、变形和细化（NOMAD-Ref）用于在突变前后对 HBB 基因β-链残基进行分子动力学模拟和能量最小化计算。此外，在天然和改变的蛋白质模型中，确定了氨基酸残基，并观察了二级结构对溶剂可及性，以确认蛋白质稳定性。本研究中的功能研究可能是未来进一步研究的良好模型。
