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A structural-alphabet-based strategy for finding structural motifs across protein families

Chih Yuan Wu, Yao Chi Chen, Carmay Lim
2010 Nucleic Acids Research  
Here, without requiring a query motif or essential residues, a fully automated method for discovering 3D motifs of various sizes across protein families with different folds based on a 16-letter structural  ...  A non-specific motif was found with a 'corner' architecture that confers a stable scaffold and enables diverse interactions, making it suitable for binding not only DNA but also RNA and proteins.  ...  proteins whose structures are known on the basis that similarity in the local structure implies similarity in biological function (4, 5) ; e.g. the helix-turn-helix (HTH) motif has been used to predict  ... 
doi:10.1093/nar/gkq478 pmid:20525797 pmcid:PMC2919736 fatcat:btql476jzrf45d34khish6b5ie

Local combinational variables: an approach used in DNA-binding helix-turn-helix motif prediction with sequence information

Wenwei Xiong, Tonghua Li, Kai Chen, Kailin Tang
2009 Nucleic Acids Research  
In this work, we develop a local combinational variable approach for sequence-based helix-turn-helix (HTH) motif prediction.  ...  Sequence-based approach for motif prediction is of great interest and remains a challenge.  ...  The HTH motif part (red for a-helix and green for turn) and its binding DNA (purple part) are shown in 3D structure of molecule (i.e. PDB Id:1BDI).  ... 
doi:10.1093/nar/gkp628 pmid:19651875 pmcid:PMC2761287 fatcat:42nq4ofhv5chtcdv4zvoltz4sm

Current Approaches in Supersecondary Structures Investigation

Vladimir R. Rudnev, Liudmila I. Kulikova, Kirill S. Nikolsky, Kristina A. Malsagova, Arthur T. Kopylov, Anna L. Kaysheva
2021 International Journal of Molecular Sciences  
This work is devoted to the study of supersecondary structures of proteins and determination of their structural motifs, description of experimental methods for their detection, databases, and repositories  ...  in protein isoforms, and aberrant proteins with high productivity.  ...  Aidan Doherty et al. suggested that one, two, or four copies of the helix-hairpin-helix motif can act as a DNA-binding structure [14] .  ... 
doi:10.3390/ijms222111879 pmid:34769310 pmcid:PMC8584461 fatcat:z6htmpbf3vfajc7b24lpguy7iy

Ab Initio Structural Modeling of and Experimental Validation for Chlamydia trachomatis Protein CT296 Reveal Structural Similarity to Fe(II) 2-Oxoglutarate-Dependent Enzymes

K. E. Kemege, J. M. Hickey, S. Lovell, K. P. Battaile, Y. Zhang, P. S. Hefty
2011 Journal of Bacteriology  
Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes.  ...  Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNAinteracting proteins or motifs.  ...  ACKNOWLEDGMENTS We are very grateful for the technical assistance of Zane Jaafar.  ... 
doi:10.1128/jb.05488-11 pmid:21965559 pmcid:PMC3232896 fatcat:reqv42r54nchbn4gg7kgrlfrqa