Structure-Energy Correlation in Proteins

描述（由申请人提供）：了解 蛋白质的结构、功能和能量学是蛋白质研究的中心问题之一 生物化学的今天静电控制着许多关键的生化过程， 因此，最重要的任务之一是要深入了解 蛋白质中的静电效应许多计算方法， 基于结构的静电能和pKas的计算已经被 但其准确性、可靠性和实用性 仍然有限。对于远离大宗商品的群体来说， 蛋白质内部或蛋白质与其他物质之间的界面处的溶剂 分子。不幸的是，这些都是最具生物学意义的案例。 这就是那些受静电控制的过程，比如催化， 氧化还原，H+和e-传导，离子选择性，以及识别和结合 药物和其他分子的作用。计算工具， 能源和功能的结构将发挥越来越重要的作用， 后基因组时代因此，需要实验数据来测试和 挑战计算方法，以及提供物理洞察力， 需要改进它们。为此，加西亚-莫雷诺博士将执行 对可电离基团pKas的位置依赖性进行了前所未有的研究 埋在3种蛋白质的内部：葡萄球菌核酸酶、RNaseH和 绿色荧光蛋白。这将需要将可电离的基团埋在 通过诱变疏水核心，用平衡法测量pKa， 并通过晶体学确定结构， 被埋葬的群体的微环境一个特定的假设， 据评估，地下沃茨比目前更为普遍 公认的，他们水合离子化基团在内部的蛋白质 非常有效。这些实验研究将回答长期存在的问题 关于蛋白质介电效应的起源、大小和意义 内部，Garcia-Moreno博士将指导所有进一步的改进， 静电效应计算方法的改进 proteins.在某种程度上，这些研究提高了我们估计 稳定性和结合亲和力的结构，加西亚-莫雷诺博士将有一个 对药物的合理和基于结构的设计产生重大影响， proteins.

DESCRIPTION (provided by applicant): Understanding the relationship between the structure, function, and energetics of proteins is one of the central problems in biochemistry today. Electrostatics govern many key biochemical processes, therefore one of the top priorities is to develop a solid understanding of electrostatic effects in proteins. Many computational methods for structure-based calculations of electrostatic energies and pKas have been developed towards this end, but their accuracy, reliability and utility is still limited. They fail most dramatically for groups secluded from bulk solvent in the protein interior or at interfaces between proteins and other molecules. Unfortunately, these are the cases of greatest biological interest. That is where processes that are governed by electrostatics, such as catalysis, redox, H+ and e- conduction, ion selectivity, and recognition and binding of drugs and other molecules, take place. Computational tools for relating structures to energy and function will play an increasingly important role in the post-genomic era. Therefore, experimental data are needed to test and challenge computational methods, as well as to provide the physical insight needed to improve them. Towards this end, Dr. Garcia-Moreno will perform unprecedented studies of the positional dependence of pKas of ionizable groups buried in the interior of 3 proteins: staphylococcal nuclease, RNaseH, and green fluorescent protein. This will entail burial of ionizable groups in the hydrophobic core by mutagenesis, measurement of pKas with equilibrium methods, and determination of structures by crystallography to characterize microenvironments of the buried group. A specific hypothesis that will be evaluated is that buried waters are more prevalent than is currently recognized, and that they hydrate ionizable groups in the interior of proteins very effectively. These experimental studies will answer longstanding questions about the origins, magnitude and meaning of dielectric effects in the protein interior, and Dr. Garcia-Moreno will guide all further refinement and improvement of existing methods for calculation of electrostatic effects in proteins. To the extent that these studies improve our ability to estimate stability and binding affinities from structure, Dr. Garcia-Moreno will have a significant impact on rational and structure-based design of drugs and proteins.