In another
studies of the lipase B interfacial activation that shows the interfacial
activation of PAL B happens in a highly hydrophobic surface and it favor large,
bulky substrates (Zisis et al., 2015). From their studies, they conclude
that the interfacial activation of lipase B happened in highly hydrophobic
surface but the conformational change only happen to the large, bulky substrates.
Due to this reason, Zisis et al. (2015) write that lipase B acts like an
esterase for small substrates and acts as lipase for substrates with large
alcohol substituent. In their studies that combine both experimental and
computer simulation shows that ? helix 5 plays a crucial role on the substrate
binding to the lipase B. Where they have confirmed that ? helix 5 are the most
mobile part of the enzyme structure and they also add that it can adopt a large
range of different conformation, including transient folding.

Studies of structure-function relationships using
computational molecular simulation approaches

The advancement of the technology have developed a
platform for scientist and research to further study the complexity of the
structure – function relationship of proteins. A molecular dynamic simulation
give more information for detailed microscopic modelling on the molecular scale
and the method follows the constructive approach by mimicking the behaviour of
molecules with the use of model systems (Ali et al., 2013). Ramakrishnan et al. (2008) in their review paper write
that molecular dynamic simulation is a powerful tool to study the structure –
function relationship of proteins.

The most widely use software to perform molecular
modelling and molecular dynamic (MD) simulation are YASARA (Yet Another
Scientific Artificial Reality Application) and GROMACS.
Molecular dynamic simulation can be performed in different temperature,
pH, and solvent to study the structural adaptation of the enzyme at different
condition. The result form the simulation is analyzed through the computed root
mean square deviation (RMSd) and root mean square fluctuation (RMSf). The RMSd
and RMSf are computed for the protein backbone and residues to check the
stability and to study the flexibility of the enzyme. Besides RMSD and RMSf,
further analysis can be done to study the radius of gyration (Rgyration) and
solvent accessible surface area (SASA) (Ali et
al., 2013).

Ramakrishnan et al. (2008) in their review paper has
list out a few studies on the structural adaptation of lipase from various
microorganisms in different condition. The molecular dynamic simulations that
were perform on the Candida rugosa
lipase shows an increase in the flap movement with the increasing of the
solvent hydrophobicity. In another molecular dynamic simulation that were
perform on Pseudomonas aeruginosa lipase
revealed the presence of a double lid and the result from molecular dynamic
simulation on Rhizomucor miehei
lipase has bring out a new founding, where Rhizomucor
miehei lipase were be able to retain its active site even though its global
conformation is changing due to the presence of cyclohexane (Ramakrishnan et al., 2008).

A molecular dynamic simulation were previously
perform using YASARA software on cold – active lipase from Pseudomonas sp. strain AMS8 in water at different temperature (0°C,
5°C, 25°C, 37°C, 50°C and 100°C) to study the structural adaptation of the
enzyme at low temperature and result from the simulation shows that the
catalytic domain of the enzyme (LipAMS8) is more stable at 0°C and 5°C, while
the non catalytic domain is not stable at the same temperature (Ali et al., 2013). Previously a molecular
dynamic simulation was performed using GROMACS in water at different
temperature on the Antarctic yeast Glaciozyma
antarctica ?-mannanase and the result from the analysis shows that it has
optimum stability at 15°C Parvizpour et al., 2014).

The modelled structure of cold – active esterase
from psychrophilic marine bacterium Rhodococcus
sp. were simulated at different pH with constant temperature for 10 ns using
GROMACS software (Santi et al.,
2013). Result from the simulation shows that the enzyme is seems to be quite
stable at neutral pH and alkaline pH that make Santi et al. (2013) conclude
that the cold – active esterase are extremely alkaliphilic.

The stability and movement of the lid of lipase in
different types of solvent has also been studied. Tejo et al. (2004) in their
studies conclude that the study of the lipase stability and lid movement in
different solvents will help to improve the understanding of the lipase in organic
solvent so later it can be manipulated in the industry. In their studies of the
effect of the organic solvent to the structure and dynamics of Candida rugosa lipase has revealed that
the movement of the lid was highly constrained in the organic solvent. The
molecular dynamic simulation that were perform on the Pseudomonas fluorescens strain AMS8 lipase in different solvent;
methanol, ethanol, 2 – propanol, DMSDO, toluene and hexane shows that
hydrophobic solvent (toluene) activate the opening of the lipase lid (Yaacob et al., 2016). It is due to the strong
interaction between the non – polar organic solvent with the AMS8 lipase.


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