Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain.
J Phys Chem B. 2010 Jun 3;114(21):7413-22. doi: 10.1021/jp102092m.
Peptides and proteins find an ever-increasing number of applications in the biomedical and materials engineering fields. The use of non-proteinogenic amino acids endowed with diverse physicochemical and structural features opens the possibility to design proteins and peptides with novel properties and functions. Moreover, non-proteinogenic residues are particularly useful to control the three-dimensional arrangement of peptidic chains, which is a crucial issue for most applications. However, information regarding such amino acids--also called non-coded, non-canonical, or non-standard--is usually scattered among publications specialized in quite diverse fields as well as in patents. Making all these data useful to the scientific community requires new tools and a framework for their assembly and coherent organization. We have successfully compiled, organized, and built a database (NCAD, Non-Coded Amino acids Database) containing information about the intrinsic conformational preferences of non-proteinogenic residues determined by quantum mechanical calculations, as well as bibliographic information about their synthesis, physical and spectroscopic characterization, conformational propensities established experimentally, and applications. The architecture of the database is presented in this work together with the first family of non-coded residues included, namely, alpha-tetrasubstituted alpha-amino acids. Furthermore, the NCAD usefulness is demonstrated through a test-case application example.
肽和蛋白质在生物医学和材料工程领域的应用越来越多。使用具有各种物理化学和结构特征的非蛋白氨基酸为设计具有新颖性质和功能的蛋白质和肽提供了可能性。此外，非蛋白氨基酸残基对于控制肽链的三维排列特别有用，这是大多数应用的关键问题。然而，关于这些氨基酸的信息（也称为非编码、非规范或非标准）通常分散在专门研究各种领域的出版物以及专利中。要使这些数据对科学界有用，需要新的工具以及用于组装和连贯组织它们的框架。我们已经成功地编译、组织并构建了一个数据库（NCAD，非编码氨基酸数据库），其中包含通过量子力学计算确定的非蛋白氨基酸固有构象偏好的信息，以及关于它们的合成、物理和光谱特性、实验确定的构象倾向和应用的文献信息。本文介绍了数据库的架构以及包含的第一个非编码残基家族，即α-四取代的α-氨基酸。此外，通过一个案例研究应用示例演示了 NCAD 的有用性。
