Will It Be Beneficial To Simulate the Antifreeze Proteins at Ice Freezing Condition or at Lower Temperature?
Antifreeze proteins (AFPs) enable the polar living species to survive subzero temperature conditions through effective lowering of the freezing point of body fluids. At the molecular level, AFPs directly interact with the growing seeds of ice crystals to inhibit their formation. To understand the structural and dynamic aspects of this interaction at the atomistic level, molecular dynamics (MD) simulations were carried out on several type I AFPs at multiple temperatures, including the physiologically relevant temperature of 273 K, a lower temperature of 227 K, and the conventional 300 K. A comparison of the principal component analysis (PCA) and mean squared deviation plots for Winter flounder AFP, HPLC6 (mutant of winter flounder AFP), Sculpin, and peptide 1m AFPs reveals that simulations at 273 and 227 K result in the formation of more conserved metastable states than at 300 K. Other parameters such as root-mean-square deviation (rmsd), solvent accessibility surface area (SASA), H-bonding and residual density function (RDF) also suggest the same. MD simulations with ice crystal, where AFPs are complexed to ice plane with TIP4P/ice water model, help in finding relevance of dynamic behavior, and physiological temperature becomes more pronounced. Additionally, a control study on a nonantifreeze protein (LL37) is included, which aids in exploring significant information. On the basis of this approach, it was found that AFPs at 273 and 227 K display relevant dynamic properties that appear at 300 K for nonantifreeze proteins. The present study hence emphasizes the importance of performing computational simulations for antifreeze proteins at the physiologically relevant temperature (273 K), and even at lower temperatures (like 227 K), rather than at room temperatures (300 K).
Department of Biophysics, Bose Institute , P-1/12, CIT Scheme VII M, Kolkata 700054, India.
Rajiv K
RK
Kar
Department of Biophysics, Bose Institute , P-1/12, CIT Scheme VII M, Kolkata 700054, India.|Biophysics and Department of Chemistry, University of Michigan , 930 N. University Avenue, Ann Arbor, Michigan 48109, United States.
Anirban
A
Bhunia
D021301:Antifreeze Proteins / Q000737:chemistry*; D005615:Freezing; D006860:Hydrogen Bonding; D007053:Ice; D056004:Molecular Dynamics Simulation; D025341:Principal Component Analysis; D012997:Solvents / Q000737:chemistry; D013499:Surface Properties; D013696:Temperature
D021301:Antifreeze Proteins; D007053:Ice; D012997:Solvents