MECHANISTIC STUDY OF ECD OF OLIGOSACCHARIDES

这个子项目是利用资源的许多研究子项目之一。 由NIH/NCRR资助的中心拨款提供。对子项目的主要支持 子项目的首席调查员可能是由其他来源提供的， 包括美国国立卫生研究院的其他来源。为子项目列出的总成本可能 表示该子项目使用的中心基础设施的估计数量， 不是由NCRR赠款提供给次级项目或次级项目工作人员的直接资金。 本理论研究旨在解释各种寡糖-金属络合离子在电子俘获解离(ECD)条件下的碎裂行为。了解低聚糖的裂解机理将有助于建立一种可靠的低聚糖结构表征的质谱学方法。 由于低聚糖同分异构体的复杂性和较大的尺寸，从第一原理出发直接从理论上对实际低聚糖体系的电化学反应过程进行研究是被禁止的。目前，研究工作主要从两个方面展开： 1)用分子动力学(MD)模拟技术确定低聚糖的能量择优金属结合部位。 由于电子捕获可能发生在金属阳离子附近，ECD碎裂模式预计将受到金属结合位置的严重影响。分子动力学模拟是对柔性生物大分子进行构象空间采样的有效工具。在本研究中，使用Accelrys开发的Discovery Studio软件，应用CHARMm力场进行MD模拟。我们已经确定了麦芽六糖-钙离子络合物的一些低能构象，其中钙离子与空间上相邻的几个氧或CH2OH基团结合。目前正在研究连接和表异构体/异构体的结合位点变异。 2)模型寡糖体系的ECD机理研究。 基于ECD结果和MD模拟确定的金属-低聚糖结合部位，将设计代表实际寡糖-金属络合物的模型体系，并将进行基于从头算和密度泛函理论的高水平分子轨道计算，以阐明ECD机理。这些计算将使用高斯03量子化学代码，利用波士顿大学的超级计算设施(IBM pSeries集群和IBM BladeCenter)进行。 2010-2011年期间的最新情况可在次级项目进展一节中找到。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. This theoretical study is aimed at explaining the fragmentation behavior of various oligosaccharide-metal complex ions, under electron capture dissociation (ECD) conditions. A better understanding of the fragmentation mechanism will help to establish a reliable mass spectrometric method for structural characterization of oligosaccharides. Due to the isomeric complexity and the large size of oligosaccharides, direct theoretical approach to the ECD process of actual oligosaccharide systems from first principle is practically forbidden. Currently, the research is carried out in two aspects: 1) The determination of the energetically preferred metal-binding sites for oligosaccharides, using molecular dynamics (MD) simulation techniques. Since electron capture is likely to occur near the metal cation, the ECD fragmentation pattern is expected to be heavily influenced by the metal-binding sites. MD simulation is a useful tool to perform conformation space sampling of large flexible biomolecules. In this study, MD simulation was performed by applying the CHARMm force field, using the Discovery Studio software developed by Accelrys. We have identified some low energy conformers for the maltohexaose-Ca2+ complex, where the calcium cation is bound to several spatially adjacent oxygen or CH2OH group. Binding-site variations in linkage and epimeric/anomeric isomers are currently being investigated. 2) The mechanistic study of ECD of model oligosaccharide systems. Based on the ECD results and MD simulation determined metal-oligosaccharide binding sites, model systems representing actual oligosaccharide-metal complexes will be designed and the high level ab initio- and density functional theory-based molecular orbital calculations will be performed to elucidate the ECD mechanism. These calculations will be carried out using Gaussian 03 quantum chemistry codes, utilizing the supercomputing facilities of Boston University (IBM pSeries Cluster and IBM BladeCenter). Update for the 2010-2011 period can be found in the subproject progress section.