CONSTRAINTS ON PROTEIN SECONDARY STRUCTURE PACKING

蛋白质二级结构包装的限制

• 批准号: 6347993
• 负责人: KAIZHI YUE
• 金额: $ 0.01万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2000
• 资助国家: 美国
• 起止时间: 2000-07-01 至 2001-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6347993
• 关键词: bioengineering /biomedical engineering; biomaterials; biomedical resource; statistics /biometry

One of the main problems in computational protein folding is to devise methods that can go beyond helix formation, and that can assemble secondary structures into tertiary conformations. For example, chain representations using limited phi/psi choices can not handle secondary structure assembly (SSA). In native protein structures, helices and strands that are not sequential neighbors can come close in space and pack tightly against one another. But in the representations the packing positions imposed by the limited orientation choices will result in either steric conflicts or suboptimal packing. We are developing a new search approach for tertiary assembly. Guided by standard templates of tertiary structure packing, taken from the PDB, and standardized representations of helices and strands, we extend an algorithm called Geocore, to search for good tertiary packing. To enable two such idealized secondary structures to pack, the phi/psi's of intervening loop residues are adjusted as continuous functions. In this search, in addition to the search performed in Geocore, segments of a sequence are designated as helices or strands and the secondary structure assembly is constructed by adding one secondary structure at a time. We have tested this strategy on proteins up to chain lengths of around 100 amino acids. Comparison of the steric packing predicted by the algorithm with the known native structures indicates that this strategy is promising.

计算蛋白质折叠的主要问题之一是 设计出超越螺旋形成的方法， 将二级结构组装成三级构象。 为 例如，使用有限phi/psi选择的链表示不能 处理二级结构组件（SSA）。 在天然蛋白质中 不是顺序相邻物的结构、螺旋和链可以 在空间上靠得很近，紧紧地挤在一起。 但在 有限公司规定的包装位置 取向选择将导致空间冲突， 次优包装 我们正在开发一种新的搜索方法 三级装配。 以三级结构的标准模板为指导 包装，取自PDB，和标准化的表示， 螺旋和股，我们扩展了一个算法称为Geocore，搜索 用于良好的三级填料。 为了使两个这样的理想化的次级 为了包装结构，插入环残基的phi/psi是 调整为连续函数。 在这次搜索中，除了 在Geocore中执行的搜索，序列的段被指定为 螺旋或股线，并构建二级结构组装体， 一次增加一个二级结构。 我们已经测试了这个 蛋白质链长可达100个氨基酸左右。 将该算法预测的空间堆积与 已知的天然结构表明该策略是有希望的。