2lq0 | pdb_00002lq0
Solution structure of de novo designed antifreeze peptide 1m
Structural highlights
Publication Abstract from PubMedExotic functions of antifreeze proteins (AFP) and antifreeze glycopeptides (AFGP) have recently been attracted with much interest to develop them as commercial products. AFPs and AFGPs inhibit ice crystal growth by lowering the water freezing point without changing the water melting point. Our group isolated the Antarctic yeast Glaciozyma antarctica that expresses antifreeze protein to assist it in its survival mechanism at sub-zero temperatures. The protein is unique and novel, indicated by its low sequence homology compared to those of other AFPs. We explore the structure-function relationship of G. antarctica AFP using various approaches ranging from protein structure prediction, peptide design and antifreeze activity assays, nuclear magnetic resonance (NMR) studies and molecular dynamics simulation. The predicted secondary structure of G. antarctica AFP shows several alpha-helices, assumed to be responsible for its antifreeze activity. We designed several peptide fragments derived from the amino acid sequences of alpha-helical regions of the parent AFP and they also showed substantial antifreeze activities, below that of the original AFP. The relationship between peptide structure and activity was explored by NMR spectroscopy and molecular dynamics simulation. NMR results show that the antifreeze activity of the peptides correlates with their helicity and geometrical straightforwardness. Furthermore, molecular dynamics simulation also suggests that the activity of the designed peptides can be explained in terms of the structural rigidity/flexibility, i.e., the most active peptide demonstrates higher structural stability, lower flexibility than that of the other peptides with lower activities, and of lower rigidity. This report represents the first detailed report of downsizing a yeast AFP into its peptide fragments with measurable antifreeze activities. Solution structures, dynamics, and ice growth inhibitory activity of Peptide fragments derived from an antarctic yeast protein.,Shah SH, Kar RK, Asmawi AA, Rahman MB, Murad AM, Mahadi NM, Basri M, Rahman RN, Salleh AB, Chatterjee S, Tejo BA, Bhunia A PLoS One. 2012;7(11):e49788. doi: 10.1371/journal.pone.0049788. Epub 2012 Nov 28. PMID:23209600[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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