Abstract
Protein structures are classically described in terms of secondary structures. However, even if the regular secondary structures have relevant physical meaning, their recognition based on atomic coordinates has a number of important limitations, such as uncertainties in the assignment of the boundaries of the helical and β-strand regions. In addition, an average of about 50% of all residues are assigned to an irregular state, i.e., the coil. These limitations have led different research teams to focus on abstracting the conformation of the protein backbone in the localized short stretches. To this end, different geometric measures are being used to cluster local stretches in protein structures in a chosen number of states. A prototype representative of the local structures in each cluster is then generally defined. These libraries of local structure prototypes are named "structural alphabets". We have developed a structural alphabet, denoted protein blocks, not only to approximate the protein structure but also to predict them from the sequence. Since its development, we and others have explored numerous new research fields using this structural alphabet. Here, we review some of the most interesting applications of this structural alphabet.
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Acknowledgments
The authors would like to thank the reviewers for their comments that help improve the manuscript. The research was supported by grants from the French Ministry of Research, University of Paris Diderot–Paris 7, University of Saint-Denis de la Réunion, French National Institute for Blood Transfusion (INTS), French Institute for Health and Medical Research (INSERM), and Indian Department of Biotechnology. APJ and GA are supported by CEFIPRA number 3903-E and Council of Scientific and Industrial Research, respectively. AB had a grant from the French Ministry of Research, MT has a post-doctoral fellowship from NIH, and HV had a post-doctoral fellowship from CEA. NS and AdB acknowledge CEFIPRA for collaborative grant (number 3903-E). BS and AdB acknowledge Partenariat Hubert Curien Barrande (2010–2011). BS is supported by grant AV0Z50520701.
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Agnel Praveen Joseph and Garima Agarwal contributed equally to this article.
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Joseph, A.P., Agarwal, G., Mahajan, S. et al. A short survey on protein blocks. Biophys Rev 2, 137–145 (2010). https://doi.org/10.1007/s12551-010-0036-1
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DOI: https://doi.org/10.1007/s12551-010-0036-1