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The geometrical analysis of the structure of proteins with implications for protein folding.

机译：蛋白质结构的几何分析及其对蛋白质折叠的影响。

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摘要

Although most methods used to analyze proteins of known structure agree on the general placements of secondary structures, the end points of secondary structures and perturbations within them are often ambiguous. It is not surprising, therefore, that prediction methods fail to accurately find secondary structure end points. An analysis of protein structural geometry was done using an in-house program (GASP). The 95% confidence limits were calculated for five parameters (rise, radius, angle of rotation, residues per turn and pitch) for all helical and strand-like tetrads (four consecutive α-carbons) in 112 independently solved, well resolved proteins. These statistics were used to describe secondary structure geometry and compared with traditional descriptions to ascertain where the geometry and hydrogen-bonding differed. Some tetrads within hydrogen-bonded secondary structures did not have, helical or strand-like geometry (perturbations). Some tetrads with correct geometry did not have helical or sheet hydrogen-bonding. Some of these tetrads correspond to turns, some were in extended conformation, while others appear at the ends of secondary structures (extensions).; Several ambiguous areas were studied further and appear to be conserved in homologous proteins. This indicates the phenomena are probably not artifacts of crystallography, and that Nature has a reason for having them there. Although these reasons are not always apparent, in other cases, there appear to be readily identifiable forces at work. The ambiguous areas may be residual evidence of the folding pathway, and their further study may lead us to greater understanding of folding.; Positional frequencies were calculated for amino acids in ambiguous areas and compared to those for secondary structures. Significant differences were found, which may have an impact on the prediction of secondary structure end points from sequence data.; A comparison was done between proteins solved by crystallography and NMR. Several systematic differences were found. Three pairs of proteins solved by both crystallography and NMR were studied in depth. Interesting differences were found. These findings could have an impact on the use of crystal and NMR structures in drug design, ligand docking, and modeling protein interfaces.
机译：尽管大多数用于分析已知结构蛋白质的方法都同意二级结构的一般位置，但是二级结构的终点和它们内部的扰动通常是模棱两可的。因此，毫不奇怪的是，预测方法无法准确地找到二级结构终点。使用内部程序（GASP）对蛋白质结构的几何形状进行了分析。计算了112个独立解析的，良好解析的蛋白质中所有螺旋形和股状四联体（四个连续的α-碳）的五个参数（上升，半径，旋转角度，每转残差和间距）的95％置信限。这些统计数据用于描述二级结构的几何形状，并与传统描述进行比较，以确定几何形状和氢键在何处不同。氢键键合的二级结构中的某些四分子不具有螺旋形或链状几何形状（扰动）。一些具有正确几何形状的四边形没有螺旋或片状氢键。这些四联体中的一些对应于转弯，一些处于延伸构象，而另一些则出现在二级结构的末端（延伸）。进一步研究了几个模棱两可的区域，这些区域似乎在同源蛋白中是保守的。这表明该现象可能不是晶体学的产物，并且自然界有理由将其保存在晶体中。尽管这些原因并不总是很明显，但在其他情况下，似乎在起作用的力量很容易识别。模棱两可的区域可能是折叠路径的残留证据，它们的进一步研究可能使我们对折叠产生更多的了解。计算出歧义区域氨基酸的位置频率，并将其与二级结构的位置频率进行比较。发现了显着差异，这可能对根据序列数据预测二级结构终点产生影响。在通过晶体学和NMR解析的蛋白质之间进行了比较。发现了几个系统差异。深入研究了通过晶体学和NMR解析的三对蛋白质。发现了有趣的差异。这些发现可能会影响药物设计，配体对接和蛋白质界面建模中晶体和NMR结构的使用。

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  • 作者

    Drennan, Diana Jean.;

  • 作者单位

    Rutgers The State University of New Jersey - New Brunswick.;

  • 授予单位 Rutgers The State University of New Jersey - New Brunswick.;
  • 学科 Biology Molecular.; Computer Science.; Chemistry Biochemistry.
  • 学位 Ph.D.
  • 年度 2001
  • 页码 295 p.
  • 总页数 295
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类 分子遗传学;自动化技术、计算机技术;生物化学;
  • 关键词

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