Macromolecular Simulation

Molecular modeling approaches have seen an increase in its importance towards researches in many fields including chemistry, biochemistry and biotechnology. The  rapid  evolution of computing power has seen molecular-level phenomena observed in great atomic details with higher precision and longer time-scale, using vast number of methods and software. We have explored several other molecular modeling methods available to explain findings from experimental observations. Parameterization of new molecules were achieved by using ab initio molecular characterizations. Most of the research in this group are performed using the Molecular Dynamics (MD) simulations method. Simulations of proteins, peptides and DNA in aqueous solution and organic solvents (including Ionic Liquids) have been carried out to investigate the structure and dynamics properties. We observe macroscopic properties reported for enzymes in Ionic Liquids, varied by the water content in the system. DNA solvation studied showed that RTILs acted as a stabilizer and maintained the DNA structure from being denatured even at high temperature without addition of any salts. We are also trying to observe pressure-induced folding of lipase using hundreds nano-seconds (ns) of MD simulations time, with the potential to reach micro-seconds. In collaboration with the Nanodelivery group, we modeled palm-based nano-emulsion systems using several methods such as MD, Coarse-Grained MD (CGMD) and Monte Carlo (MC) simulations. The modeling was based on the results obtained experimentally. The partnership between metal ions and life in Antarctica is currently also a main focus area. Subsequent sequence-based analyses revealed that almost one-third of them are putatively bounded by metal ions, with majority are actually zinc-bounded. Further investigation on the role of metal ions in the system is currently undertaken and will provide new insights to the life of extremophiles. In addition, we also focus on predicting the macromolecular structure and function of hypothetical proteins from extremophiles. Examples of the hypothetical proteins studied were a predicted metallo β-lactamase (a wide-spectrum antibiotics-degrading enzyme) and monothiol glutaredoxin (a possible novel protein in iron homeostasis) from Bacillus lehensis G1 alkaliphile as well as the copper-chaperone CsoR-like protein from Geobacillus zalihae. Their possibility to act as novel drug targets as well as probes for metal detection is currently addressed.