RUI: Learning the Rules that Govern the Folding and Stability of Coiled Coils.

FairmanMCB-9817188：卷曲螺旋是一种基序，它涉及a-螺旋组的相互作用，主要通过排列在结构界面上的疏水氨基酸来稳定。本研究的重点是一个天然的四链卷曲螺旋模型模体从紫胶阻遏物定量序列结构关系的系统方式。 采用突变方法研究Lac阻遏物卷曲螺旋中特定位置不同氨基酸侧链的影响。 实验策略包括固相合成法合成多肽，反相色谱法纯化，生物物理学表征。 卷曲螺旋的稳定性是通过温度或化学变性过程中的低聚状态，使用圆二色性光谱偏振法的肽浓度滴定和 分析超离心 利用这种方法，一系列的实验将系统地探讨螺旋线圈的稳定性和螺旋线圈的几个定义特性之间的关系。选择用于研究的序列将测试螺旋长度和稳定性之间的关系，疏水氨基酸对稳定性和寡聚化的作用，其他七聚体位置上的侧链相互作用对四聚体稳定性的重要性，以及基于所学到的规则设计简化序列的能力。随着对定义卷曲螺旋结构的决定因素的理解，将有可能设计出可用于纳米工程的新颖结构，特别是用于长“纳米棒”的合成，并且通过适当的修改，甚至可以转化为导电材料，例如“纳米线”。“这个项目非常适合本科生实验室，因为本文描述的每种肽的合成和表征本身就是一个项目，并且可以在一年的高级研究项目的限制内轻松完成。将由本科生学习的重要技能包括蛋白质生物化学中严格的定量方法，使用生物物理方法和跨学科的方法，从生物学和化学到物理学和数学。

FairmanMCB-9817188:Coiled coils are motifs which involve the interaction of sets of a-helicesand are stabilized largely through hydrophobic amino acids that line theinterface of the structure. This study focuses on a natural four-chaincoiled coil model motif from Lac repressor to quantitate sequence-structurerelationships in a systematic fashion. A mutational approach is used tostudy the effects of different amino acid sidechains at specific positionsin the Lac repressor coiled coil. Experimental strategies involvesynthesis of peptides by solid-phase synthetic methods, purification byreversed-phase chromatography, and biophysical characterization. Coiledcoil stability is measured by the oligomeric states during temperature orchemical denaturation, peptide concentration titrations using circulardichroism spectropolarimetry and analytical ultracentrifugation. Usingsuch approaches, a series of experiments will systematically explore therelationship between coiled coil stability and several definingcharacteristics of coiled coils. Sequences chosen for study will test therelationship between helix length and stability, the role of hydrophobicamino acids on stability and oligomerization, the importance of side-chaininteractions at other heptad positions on tetramer stability, and theability to design simplified sequences based on rules so learned.With an understanding of the determinants that define coiled coilstructure, it will be possible to design novel structures that may be ofuse in nano-engineering, particularly for the synthesis of long"nanoropes", and with appropriate modifications, may even be converted intoconducting materials such as "nanowires." This project is well-suited foran undergraduate laboratory since the synthesis and characterization ofeach peptide described herein is a project unto itself and can beaccomplished easily within the constraints of a one-year senior researchproject. Important skills that will be learned by undergraduate studentsinclude rigorous quantitative methods in protein biochemistry usingbiophysical methods and cross-cutting interdisciplinary methods that spanfrom biology and chemistry to physics and mathematics.