Force Field Development for Protein Absorption Modeling

蛋白质吸收建模的力场开发

基本信息

批准号：
7383812
负责人：
ROBERT A LATOUR
金额：
$ 35.07万
依托单位：
CLEMSON UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2006
资助国家：
美国
起止时间：
2006-06-01 至 2010-03-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7383812
关键词：
Address Adsorption Agreement Amber Area Behavior Benchmarking Binding Binding Sites Biochemistry Biocompatible Materials Biophysics Biotin Chemistry Circular Dichroism Class Code Collaborations Communities Complex Controlled Study Data Data Set Development Developmental Process Equilibrium Evaluation Fibronectins Foundations Free Energy Gambling Generations Goals Gold Hybrids Implant Individual Institutes Integrin Binding Integrins Interdisciplinary Study Internet Label Letters Liquid substance Mathematics Measures Medical Device Medical Device Designs Membrane Proteins Methods Modeling Modification Molecular Molecular Conformation Monoclonal Antibodies Patient Care Peptides Performance Phase Polymers Potential Energy Principal Investigator Probability Process Property Protein Fragment Proteins Purpose Regenerative Medicine Research Research Personnel Research Subjects Role Saline Sampling Science Secondary Protein Structure Series Simulate Site Solid Solutions Source Code Spectrometry, Mass, Secondary Ion Spectrum Analysis Standards of Weights and Measures Surface Surface Plasmon Resonance System Techniques Technology Testing Time Tissue Engineering USA Georgia United States National Institutes of Health Validation Water Western Asia Georgia Work absorption aqueous base biomaterial compatibility clinically relevant computer science design desire direct application experience functional group improved interest interfacial molecular modeling monolayer prevent programs research study response simulation solid solution tool

项目摘要

DESCRIPTION (provided by applicant): Because of its governing role in implant biocompatibility, the understanding and control of protein adsorption to implant surfaces continues to be one of the major areas of research in the field of biomaterials. Although greatly desired, a detailed molecular-level understanding of how protein adsorption occurs, and how to control it, are still lacking. Molecular simulation offers great potential to help address these limitations by providing a tool to accurately predict and visualize molecular-level behavior. However, before this potential can be realized, methods must be specifically developed for this application. The overall objective of the proposed R01 research program is therefore to develop molecular simulation capabilities to accurately simulate protein adsorption on surfaces, initially with polymer-like functionality . This will be accomplished by first modifying the well-established CHARMM molecular simulation program to enable two different force fields (either Class I or II type) to be used in the same simulation to separately represent the solution phase and the solid phase. This will enable both phases of an adsorption system to be accurately modeled by a force field that has been specifically developed and validated for that particular material system (e.g., protein in aqueous solution vs. a crystalline polymer). The interface between the two phases, however, must be separately tuned and validated. To accomplish this, experimental adsorption studies using surface plasmon resonance spectroscopy will be conducted using a designed host-guest peptide system to generate experimental adsorption data that will be used to evaluate, tune, and validate a CHARMM interfacial force field for the accurate simulation of protein adsorption behavior at the solid-solution interface. Once validated, the hybrid force field system will be applied to simulate the adsorption behavior for a biomedically relevant protein on functionalized surfaces and the results will be quantitatively compared with a matched set of experimental studies to demonstrate the developed capabilities to accurately simulate protein adsorption behavior. The successful development of these simulation capabilities will provide the foundations for the establishment of molecular simulation as a valuable tool for the biomaterials community for surface design to study and control protein adsorption behavior at the molecular level, with direct applications for medical device design to enhance implant biocompatibility for improved patient care.

描述（由申请人提供）：由于其在植入物生物相容性中的主导作用，对植入物表面的蛋白质吸附的理解和控制仍然是生物材料领域的主要研究领域之一。尽管人们非常渴望，但仍然缺乏对蛋白质吸附如何发生以及如何控制它的详细分子水平理解。分子模拟通过提供准确预测和可视化分子水平行为的工具，为帮助解决这些限制提供了巨大的潜力。然而，在实现这种潜力之前，必须专门为此应用开发方法。因此，拟议的 R01 研究计划的总体目标是开发分子模拟功能，以准确模拟表面上的蛋白质吸附，最初具有类似聚合物的功能。这将通过首先修改完善的 CHARMM 分子模拟程序来实现，以便在同一模拟中使用两种不同的力场（I 类或 II 类）来分别表示溶液相和固相。这将使吸附系统的两个阶段能够通过针对特定材料系统（例如，水溶液中的蛋白质与结晶聚合物）专门开发和验证的力场来精确建模。然而，两个阶段之间的接口必须单独调整和验证。为了实现这一目标，将使用设计的主客体肽系统进行使用表面等离子体共振光谱的实验吸附研究，以生成实验吸附数据，该数据将用于评估、调整和验证 CHARMM 界面力场，以准确模拟蛋白质固溶体界面的吸附行为。一旦经过验证，混合力场系统将用于模拟生物医学相关蛋白质在功能化表面上的吸附行为，并将结果与一组匹配的实验研究进行定量比较，以证明所开发的精确模拟蛋白质吸附行为的能力。这些模拟功能的成功开发将为分子模拟的建立奠定基础，作为生物材料界进行表面设计的宝贵工具，以在分子水平上研究和控制蛋白质吸附行为，并直接应用于医疗设备设计以增强植入物生物相容性可改善患者护理。