NCAD, a Database Integrating the Intrinsic Conformational Preferences of Non-Coded Amino Acids

• Published in: The journal of physical chemistry. B 2010-06, Vol.114 (21), p.7413-7422
• Main Authors: Revilla-López, Guillem, Torras, Juan, Curcó, David, Casanovas, Jordi, Calaza, M. Isabel, Zanuy, David, Jiménez, Ana I, Cativiela, Carlos, Nussinov, Ruth, Grodzinski, Piotr, Alemán, Carlos
• Format: Article
• Language: English
• Subjects: Algorithms; Amino Acids - chemistry; Anàlisi; B: Biophysical Chemistry; Bases de dades; Databases, Factual; Databases, Protein; Enginyeria química; Proteïnes; Pèptids; Química física; Àrees temàtiques de la UPC
• ISSN: 1520-6106; 1520-5207; 1520-5207
• 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, α-tetrasubstituted α-amino acids. Furthermore, the NCAD usefulness is demonstrated through a test-case application example.