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

职业：蛋白质和蛋白质/配体表面行为的建模和预测

• 批准号: 1054867
• 负责人: Thomas Knotts
• 金额: $ 41.97万
• 依托单位: Brigham Young University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-03-01 至 2017-02-28
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1054867&HistoricalAwards=false
• 关键词: CAREER; Modeling; Prediction; Protein; Ligand

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).

PI: Thomas A. knotts提案号：1054867蛋白质芯片，通过将诊断蛋白质沉积到固体表面而产生的设备，有可能极大地改善几个领域，包括医疗保健，国防，环境和安全，以及蛋白质组学。该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。尽管取得了预期的进展，但这些装置的全部潜力尚未实现，因为难以获得可靠和可重复的结果。芯片的性能取决于将蛋白质以保持生物活性的方式放置在表面的能力。由于表面会引起蛋白质的结构变化，从而降低或消除蛋白质的功能，目前还没有方法可以预测这种变化的程度或功能是如何受到影响的，这使得情况变得更加复杂。本提案的论点是，通过提高对影响蛋白质/表面相互作用因素的基本理解，可以设计出更好的蛋白质阵列。目标是：1)创建界面模型，预测如何将感兴趣的蛋白质系在各种表面上，以实现最大的配体结合能力；2)概述一套启发式方法，用于设计涉及蛋白质/表面相互作用的技术。由于目前的实验技术无法以分子水平的分辨率探测表面结合蛋白，因此提出了一种建模和模拟方法。基本实验计划使用先进的采样方法来探测蛋白质和蛋白质/配体复合物在散装和不同类型表面上的稳定性。工作包括检查表面拥挤对栓系蛋白功能的影响，在非环区栓系时的稳定性，以及表面栓系的折叠机制的变化，多状态文件夹。这项工作将最终建立完整的蛋白质A/抗体/抗原复合物模型，这是蛋白质芯片中的重要系统。为了实现这一目标，提出了一种新的粗粒模型，该模型能够捕获化学特异性蛋白质/蛋白质和蛋白质/表面相互作用，这是当前粗粒模型所缺乏的特征。这个模型将有能力研究其他感兴趣的系统。模拟结果将通过最近的拴链蛋白稳定性和表面抗体/抗原结合的实验测量来验证，这是以前没有的。初步的工作是非常令人鼓舞的，并且首次表明，表面上所有α，正交束蛋白的稳定性可以以一种促进合理设计的方式与三级结构相关联。总的来说，这项研究有望产生一个详细的，分子水平的图像，表面如何改变拴蛋白的结构，稳定性和配体结合能力。更广泛的影响综合研究和教育计划具有许多内在层面的影响。从对蛋白质/表面相互作用的更好理解中受益的领域包括药物设计、医学诊断、生物材料和蛋白质组学。这些自然会通过更好的卫生保健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，这项研究还将在更局部的层面上产生影响。参与美国国家科学基金会（NSF）资助的国家工程技术教育中心（NCETE）将带来两个好处，一是改善K-12科学教育，二是促进科学与工程作为一种职业。通过这一努力，将创建有关蛋白质和蛋白质/表面相互作用的教学模块，用于职业与技术教育课程。科学教育的其他改进，以及为代表性不足的群体增加机会，将通过向当地有大量西班牙裔学生的小学推广项目来实现。关于这一努力，PI提议在教务长小学建立一个科学教室，里面充满了学习站，学生们将每两周访问一次（类似于常规的图书馆日）。