2LQ0

Solution structure of de novo designed antifreeze peptide 1m

Summary for 2LQ0

• Entry DOI: 10.2210/pdb2lq0/pdb
• Related: 2LQ1 2LQ2
• NMR Information: BMRB: 18284
• Descriptor: de novo designed antifreeze peptide 1m (1 entity in total)
• Functional Keywords: afp, antifreeze protein
• Total number of polymer chains: 1
• Total formula weight: 2984.40

Authors

Bhunia, A. (deposition date: 2012-02-21, release date: 2012-10-24, Last modification date: 2024-05-15)

Primary citation

Shah, S.H.,Kar, R.K.,Asmawi, A.A.,Rahman, M.B.,Murad, A.M.,Mahadi, N.M.,Basri, M.,Rahman, R.N.,Salleh, A.B.,Chatterjee, S.,Tejo, B.A.,Bhunia, A.
Solution structures, dynamics, and ice growth inhibitory activity of Peptide fragments derived from an antarctic yeast protein
Plos One, 7:e49788-e49788, 2012

PubMed Abstract: Exotic 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 α-helices, assumed to be responsible for its antifreeze activity. We designed several peptide fragments derived from the amino acid sequences of α-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.

PubMed: 23209600
DOI: 10.1371/journal.pone.0049788

Experimental method

SOLUTION NMR