THERMODYNAMICS AND THE DESIGN OF STRUCTURED PEPTIDES

多肽序列高效折叠成稳定的结构是生物识别中最吸引人和最重要的现象之一。 这一过程的热力学研究提供了深入了解肽类药物和激素与其受体的积极结合所需的因素。 因此，人们对蛋白质样支架的从头设计和蛋白质结构域的重新设计越来越感兴趣，以达到有效自组装所需的最小尺寸。 本提案将肽结构化作为折叠优化和从头设计问题，并且还在更基本的水平上（二级结构形成的热力学和速率以及这些如何影响蛋白质折叠的速率和效率，由于微蛋白构建体中特定的疏水和H-键合相互作用而导致的deltaG增量的定量）。 建议的一些关键实验应提供：a）形成孤立的α螺旋和β发夹的热力学参数和B）疏水效应对二级结构稳定的相对重要性。 一些初步的研究将在水性氟醇介质中进行，似乎强调疏水效应。 然而，所提出的设计肽应允许将这些研究扩展到严格的水性介质。 α螺旋和β发夹形成速率的测量将采用同位素编辑的T-jump FT-IR。将被扩展和重新参数化的螺旋设计工具和几个关键问题的内在螺旋倾向和稳定增量与侧链相互作用将得到解决的实验。 提出了几种新的微蛋白折叠的研究。 一个系列由非交联的eicosamers，折叠合作，以产生一个疏水笼周围的色氨酸环。 这种结构的突变体将被用于deltadeltaG测量，作为一个模型，用于开发策略的优化疏水簇，并作为一个测试案例的计算机模拟蛋白质折叠。 一个较小的努力将是针对构建和优化的β α α微蛋白（一个平行的β片层产生的β链在每一端的α螺旋）。 这些构建体将模拟蛋白L的B1结构域的一些特征，但将具有在自然界中从未观察到的左手交叉。所描述的研究应该提供的见解和算法，将是有用的，在其他肽结构和配体/受体界面优化的努力。 色氨酸笼状折叠，这将被广泛研究，是一个独特的结合基序，是常见的分子间生物识别现象的分子内的例子。 因此，该项目将为人工酶设计更稳定的可预测结构支架提供策略，并为设计更有效的生物分子提供原则。

The efficient folding of polypeptide sequences into stable structures is one of the most fascinating and fundamentally important biorecognition phenomena. Studies of the thermodynamics of this process provide insights into the factors that are required for avid binding of peptide drugs and hormones to their receptors. As a result, there is an increasing interest in the de novo design of protein-like scaffolds and the redesign of protein domains to be of the minimum size required for efficient self-assembly. The present proposal addresses peptide structuring requisites as a fold optimization and de novo design problem and also at a more fundamental level (the thermodynamics and rates of secondary structure formation and how these influence the rates and efficiency of protein folding, the quantitation of the deltaG increments due to specific hydrophobic and H-bonding interactions in miniprotein constructs). Some of the key experiments proposed should provide: a) the thermodynamic parameters for the formation of isolated alpha helices and beta hairpins and b) the relative importance of the hydrophobic effect for the stabilization of secondary structures. Some of the initial studies will be conducted in aqueous fluoroalcohol media that appear to accentuate the hydrophobic effect. However, the designed peptides proposed should allow the extension of these studies to strictly aqueous medium. The measurements of the rates of both alpha helix and beta hairpin formation will employ isotope-edited T-jump FT-IR. Stable alpha helices are promising units of scaffolding for designed folds; the helix/coil model developed at U.W. will be extended and reparameterized as a helix design tool and several key questions concerning intrinsic helical propensities and the stabilization increments associated with sidechain interactions will be addressed experimentally. Several novel miniprotein folds are proposed for study. One series consists of non-crosslinked eicosamers that fold cooperatively to produce a hydrophobic cage about a tryptophan ring. Mutants of this structure will be employed for the deltadeltaG measurements, as a model for developing strategies for the optimization of hydrophobic clusters, and as a test case for computer simulations of protein folding. A smaller effort will be directed at the construction and optimization of a betaalphaalpha miniprotein (a parallel beta sheet resulting from the association of beta strands at each end of an alpha helix). These constructs will mimic some features of the B1 domain of protein L but will have a left-handed crossover which has never been observed in nature. The studies described should provide insights and algorithms that will be useful in other peptide structure and ligand/receptor interface optimization efforts. The tryptophan cage fold, which will be examined extensively, is a unique intramolecular example of a binding motif that is common in intermolecular biorecognition phenomena. As a result, this project will provide strategies for designing more stable scaffolds of predictable structure for artificial enzymes and principles for the design of more potent biomolecules.