A distinct structural difference between them was found in the 185-207-amino acid region, where the structure in the apo-subunit is disordered whereas that in the holo-subunit consists of two α-helices. This fact proved that the NADH binding allows the helical structures to form the substrate...
为了获得更加可靠的蛋白结构用于药物设计,来自理海大学(Lehigh University)的Guterres等研究人员提出了通过搜索apo结构的holo模板,用后者来指导前者进行相应的结构优化,使得在虚拟筛选的一开始,就是使用一个接近holo态的蛋白构象,以此提高虚拟筛选的成功率。他们的工作于今年发表在美国化学会的Journal of chemical information...
是没有结合正构分子的变构共晶(apo structure)还是结合了正构分子的变构共晶(holo structure)?针对这个问题,上海交大医学院张健课题组通过对6个典型的变构蛋白的apo和holo结构做了大规模的构象采样,同时结合对接分析,得出结论:如果正构位点和变构位点的距离低于5 Å,基于holo结构来进行药物筛选更合理。该项工作最...
Therefore, the main search mode starts with a holo structure, where the user knows the ligand that will be used as a starting point. This user-specified ligand will define the binding site as well as the search and annotation of the results. Any other (non-specified) ligands in the query...
holo形式铁蛋白在每个蛋白分子腔内含有几千铁原子;一旦铁从铁蛋白腔中去除,apo形式铁蛋白形成。Holo铁蛋白可以作为铁补充剂,而apo铁蛋白可以用作递送营养物质和生物活性化合物的有前景纳米载体。至今,来自动物和植物的铁蛋白双功能已经在一些领域例如食品、营养、医药和材料得到广泛研究。该综述突出了动物和植物铁蛋白...
Simulations of apo and holo-fatty acid binding protein: Structure and dynamics of protein, ligand and internal water 2002, Journal of Molecular Biology Citation Excerpt : One recent theoretical investigation has focused on a single water molecule known from crystal diffraction studies to be buried in...
Prepare protein structure-based data suitable for training graph neural networks to predict what residues in a protein structure are likely to change conformation when pocket opening happens (apo-to-holo transition). Here, 'apo' means a protein with at least one inactive and partially or completely...
2024 Elsevier LtdA single protein structure is rarely sufficient to capture the conformational variability of a protein. Both bound and unbound (holo and apo) forms of a protein are essential for understanding its geometry and making meaningful comparisons. Nevertheless, docking or drug design studies...
X-ray structure have been computed for either MD trajectory. Calculated C a RMSD values of 0.15 nm (apo-FABP) and 0.16 nm (holo-FABP) for the last 3 ns of MD simulation indicate rather stable back- bone geometries. Likewise, the RMSD values com- ...
The crystal structure of holo-CRABPII, as a CRABPII·all-trans-RA complex, was determined at 1.9 Å, where the methylene groups of the side-chain of Arg111 are in the center of CRABPII’s hydrophobic core, and the guanidino group interacts with the carboxylate group of RA via a water...