CAREER: Modeling and Prediction of Protein and Protein/Ligand Behavior on Surfaces

PI：托马斯A. KnottsProposal编号：1054867蛋白质芯片，通过将诊断蛋白质沉积到固体表面上而创建的设备，有可能大大改善包括医疗保健，国防，环境和安全以及蛋白质组学在内的多个领域。芯片的目的是快速检测给定样品中重要分子的身份或丰度，如抗体，细菌和药物靶标。尽管有承诺的进步，这些设备的全部潜力尚未实现，因为很难获得可靠和可重复的结果。芯片的性能取决于以保持生物活性的方式将蛋白质放置在表面上的能力。这是复杂的事实，表面诱导蛋白质的结构变化，减少或消除功能，目前还没有方法来预测这种变化的程度或功能如何受到影响。智力MeritThe论文的建议是，更好的蛋白质阵列可以设计从一个改进的基本理解的影响蛋白质/表面相互作用的因素。目标是：1）创建界面模型，可以预测如何将感兴趣的蛋白质拴在各种表面上，以实现最大的配体结合能力; 2）概述一组在设计涉及蛋白质/表面相互作用的技术时使用的化学方法。由于目前的实验技术不能探测表面结合蛋白质的分子水平的分辨率，提出了一种建模和模拟的方法。基本实验计划使用先进的采样方法来探测散装和不同类型表面上的蛋白质和蛋白质/配体复合物的稳定性。工作包括研究表面拥挤的拴系蛋白质的功能，稳定性拴系时，在非循环区域，和表面拴系，多态文件夹的折叠机制的变化的影响。这项工作将最终在建模完整的蛋白A/抗体/抗原复合物，这是蛋白质芯片中的重要系统。为了实现这些目标，提出了一种新的粗粒模型，它能够捕获化学特定的蛋白质/蛋白质和蛋白质/表面相互作用的功能，目前的粗粒模型缺乏。该模型将有能力研究其他感兴趣的系统。模拟结果将使用最近的实验测量拴蛋白的稳定性和表面抗体/抗原结合，这是以前没有的验证。初步工作是非常令人鼓舞的，并首次表明，所有α，正交束蛋白表面上的稳定性可以相关的三级结构的方式，有利于合理的设计。总的来说，这项研究预计将导致一个详细的，分子水平的图片表面如何改变结构，稳定性和配体结合能力的束缚蛋白质。更广泛的影响综合研究和教育计划有许多内在的影响水平。将受益于蛋白质/表面相互作用的更好理解的领域包括药物设计，医学诊断，生物材料和蛋白质组学。通过更好的医疗保健，这些自然会给整个社会带来额外的好处。除了这些更广泛的社会影响外，这项研究还将在更多的地方层面上产生影响。两个好处，在K-12科学教育的改善和促进科学和工程作为一种职业，将产生从参与美国国家科学基金会赞助的国家中心工程和技术教育（NCETE）。通过这一努力，将创建有关蛋白质和蛋白质/表面相互作用的角色的教学模块，用于职业技术教育课程。科学教育的其他改进，以及代表性不足的群体的机会增加，将通过推广计划，以大量西班牙裔入学的当地小学发生。关于这一努力，PI建议在教务长小学建立一个科学室，里面有学习站，学生将每两周访问一次（类似于常规的图书馆日）。

PI: Thomas A. KnottsProposal Number: 1054867Protein chips, devices created by depositing diagnostic proteins onto solid surfaces, have the potential to drastically improve several fields including healthcare, defense, environment and safety, and proteomics. The purpose of the chip is to rapidly detect the identity or abundance of important molecules, such as antibodies, bacteria, and drug targets, in a given sample. Despite the promised advances, the full potential of these devices has not yet been realized as it is difficult to obtain reliable and reproducible results. Chip performance is governed by the ability to place proteins on the surface in a manner that preserves biological activity. This is complicated by the fact that surfaces induce structural changes in proteins that reduce or eliminate function, and no method currently exists to predict the extent of such changes or how function is affected. Intellectual MeritThe thesis of this proposal is that better protein arrays can be designed from an improved fundamental understanding of the factors affecting protein/surface interactions. The goals are to 1) create interfacial models that can predict how to tether proteins of interest to various surfaces to achieve maximum ligand-binding ability and 2) outline a set of heuristics to use when designing technologies involving protein/surface interactions. Because current experimental techniques cannot probe surface bound proteins with molecular-level resolution, a modeling and simulation approach is proposed. The basic experimental plan uses advanced sampling methods to probe the stability of proteins and protein/ligand complexes in the bulk and on different types of surfaces. Work includes examining the effects of surface crowding on the function of tethered proteins, stability when tethering in non-loop regions, and changes in folding mechanisms of surface tethered, multistate folders. The work will culminate in modeling complete Protein A/Antibody/Antigen complexes which are important systems in protein chips. To accomplish the goals, a novel coarse-grain model is proposed which is capable of capturing chemically-specific protein/protein and protein/surface interactions a feature that current coarse grain models lack. This model will have the capacity to investigate other systems of interest. The simulation results will be validated using recent experimental measurements of tethered-protein stabilities and surface antibody/antigen binding which have not been available previously. Preliminary work is very encouraging and has shown for the first time that the stability of all alpha, orthogonal bundle proteins on surfaces can be correlated to tertiary structure in a way that facilitates rational design. Overall, the research is expected to result in a detailed, molecular level picture of how surfaces change the structure, stability, and ligand-binding ability of tethered proteins.Broader ImpactThe integrated research and education plan has many inherent levels of impact. Areas that will benefit from an improved understanding of protein/surface interactions include drug design, medical diagnostics, biomaterials, and proteomics. From these will naturally follow additional benefits to society as a whole through better health care. Aside from these broader societal impacts, this research will have implications on a more local level. Two benefits, improvements in K-12 science education and the promotion of science and engineering as a career, will arise from participation in the NSF sponsored National Center for Engineering and Technology Education (NCETE). Through this effort, teaching modules about the roles proteins and protein/surface interactions will be created to use in the class Career & Technical Education. Other improvements to science education, as well as increased opportunities for underrepresented groups, will occur through outreach programs to local elementary schools with large Hispanic enrollments. Concerning this effort, the PI is proposing the creation of a science room,at Provost Elementary, filled with learning stations, which students will visit on a bi-weekly basis (similar to regular library days).