Structure-Energy Correlation in Proteins

描述(由申请人提供)：了解 蛋白质的结构、功能和能量学是研究的中心问题之一 今天的生物化学。静电学控制着许多关键的生化过程， 因此，当务之急之一是对 蛋白质中的静电效应。许多计算方法可用于计算 基于结构的静电能和pKa的计算已经被 但它们的准确性、可靠性和实用性是 仍然是有限的。对于与大宗商品隔绝的群体来说，它们失败得最厉害。 蛋白质内部或蛋白质与其他物质交界处的溶剂 分子。不幸的是，这些都是最具生物学意义的案例。 这就是由静电学控制的过程，如催化， 氧化还原，氢和电子传导，离子选择性，识别和结合 药物和其他分子就会发生。用于关联的计算工具 结构对能源和功能的作用将越来越重要 后基因组时代。因此，需要实验数据来检验和验证。 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-莫雷诺博士将表演 对电离基团pKas位置依赖性的空前研究 埋藏在3种蛋白质内部：葡萄球菌核酸酶、RNAseH和 绿色荧光蛋白。这将需要将可电离群体埋葬在 通过诱变疏水核心，用平衡法测量pKas， 并通过结晶学确定结构以表征 埋藏群的微环境。一个具体的假设，将是 被评估的是埋在地下的水比现在更普遍 并且它们在蛋白质内部水合了可电离基团 非常有效。这些实验研究将回答长期存在的问题 关于蛋白质中介电效应的起源、大小和意义 内务部，加西亚-莫雷诺博士将指导所有进一步的改进和 对现有静电效应计算方法的改进 蛋白质。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来自结构，加西亚-莫雷诺博士将拥有 对药物和药物的合理和基于结构的设计产生重大影响 蛋白质。

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.