APPLICATION OF GLYCAM IN GENERATION OF SOLVATED POTENTIAL ENERGY SURFACES

本子项目是利用由NIH/NCRR资助的中心赠款提供的资源的众多研究子项目之一。子项目和研究者（PI）可能已经从另一个NIH来源获得了主要资金，因此可以在其他CRISP条目中表示。列出的机构是中心的，不一定是研究者的机构。构建关于两个扭键的Ramachandran图，用于预测生物分子最优选的构象，通常是在真空中进行的——使用基于分子力学或量子力学计算的势能。然而，在过去的几年里，人们已经清楚地认识到，水在决定大分子（包括碳水化合物）最稳定的结构方面发挥着不可或缺的作用。此外，在碳水化合物中，由于糖环上羟基部分的大量可旋转键，能量最小化将忽略可能的构象的数量。此外，熵效应可能在各种状态之间相互转换的能量势垒中起重要作用，但完全被忽略了。利用完全溶解的MD模拟构建自由能剖面可以弥补这些缺点。利用伞式采样测定自由能或平均力势，在过去已广泛用于研究多肽的构象，但很少用于碳水化合物（自1995年以来的文献检索仅指向两项研究）。虽然已经从这些研究中提取了有用的信息——例如从势能面得到的全球最小值可能与从平均力模拟的势得到的预测值大不相同——但从未进行过与实验的比较，因此提供的关于所使用的力场性能的信息很少。本文提出了麦芽糖糖苷间扭角F/Y的二维平均力势计算方法，该方法在理论和实验上都得到了广泛的研究。该模拟将在溶液中进行，包括数千个水分子，使用粒子网Ewald处理远程静电，并将使用最新的Glycam力场，这是AMBER包的一部分。Glycam力场可以精确地描述溶液中碳水化合物的结构和动力学。MD模拟将在F/Y糖苷间键上以10度增量进行，使用5 kcal/mol*rad2力常数的谐波偏倚势。然后使用加权直方图分析方法（WHAM）进行无偏模拟，该方法已被证明是一种鲁棒和稳定的方法，即使对于多维表面也是如此。这将为我们提供一个独特的机会来比较平均力模拟的结果与实验预测的麦芽糖结构。这也将有可能评估Glycam力场在结构预测中的表现，并提供关于水在麦芽糖的首选结构中的作用的有用信息。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The construction of a Ramachandran plot about two torsional bonds, for prediction of the most preferred conformation of biological molecules, is usually carried out typically in vacuo -- using the potential energy based on a molecular mechanics or quantum mechanical calculations. However, it has become clear over the past few years that water can play an integral part in determining the most stable structure of macromolecules, including carbohydrates. Furthermore, in carbohydrates, an energy minimization will neglect the number of possible conformations due to the large number of rotatable bonds from the hydroxyl moieties on the sugar rings. Also, entropic effects which might play an important role in the energy barrier for inter-conversion between various states, are completely neglected. The construction of a free-energy profile using fully solvated MD simulations could remedy these shortcomings. The determination of the free energy or potential of mean force, using umbrella sampling, has been extensively used in the past for studying the conformations of peptides, but has scarcely been used for carbohydrates (a search in the literature only points to two studies since 1995). While useful information has already been extracted from these studies -- such as the fact that the global minimum from the potential energy surface can be quite different from that predicted from the potential of mean force simulation -- no comparison to experiment has ever been done, providing little information about the performance of the force fields that have been used. We propose to carry out a two-dimensional potential of mean force calculations about the F/Y interglycosidic torsional angles of maltose, which has been extensively studied both theoretically and experimentally. This simulation will be carried out in solution, with several thousand water molecules included, using particle-mesh Ewald to treat long-range electrostatics and will make use of the latest Glycam forcefield, which is part of the AMBER package. The Glycam forcefield has been tailored to accurately describe the structure and dynamics of carbohydrates in solution. MD simulations will be carried out at 10 degree increments over the F/Y interglycosidic linkages using a harmonic biasing potential with a 5 kcal/mol*rad2 force constant. The simulation will then be unbiased using the weighted histogram analysis method (WHAM), which has been shown to be a robust and stable method even for multidimensional surfaces. This will provide us a unique opportunity to compare the results of the potential of mean force simulation with the experimentally predicted structure of maltose. It will also be possible to assess the performance of the Glycam forcefield in structure predictions, and provide useful information about the role of water in the preferred structure of maltose.