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No full textReductive Alkylation of Candida Rugosa Lipase: Structural Approaches
No full textThe properties of alkylated lipase are successfully explored through experimental and molecular modelling methods. Alkylation was done using aldehydes with different degree of modification to represent different levels
of hydrophobicity which is important for enzymes to work in nonaqueous environment. Far ultraviolet circular dichroism (CD) spectroscopy of the lipase in aqueous solvent shows that increasing the degree of modification from 49% to 86% resulted in loss in secondary structure which is attributed to the enzyme unfolding. The secondary structure elements of the CD spectra of native and modified lipase were analysed using the CDPro software and the K2D
program. Both methods yield the same results in that the ratio of α-helical structure is lost. This result explains why alkylated lipases have much lower activity in an aqueous environment. Molecular modelling simulations were performed to study the structural and dynamical changes of the lipase upon different levels of modification.
Simulations were run for 1 ns (300 K) with five different initial velocities to obtain better conformational sampling. Two solvent systems were used:
TIP3P water model and carbon tetrachloride (CCl4) solvent model in periodic boundary condition (PBC). Generally, lipases simulated in water are less deviated in term of root mean square deviations (rmsd) compared to lipases
simulated in CCl4. Lid movements are essential for lipase function, both in water and waterlipid environments. Analyses of lid dynamics were done using timecorrelation
function and second-order Legendre polynomial function. Lipase in water and CCl4 shows different properties of dynamics. Without alkylation, the time correlation function of lipase in water shows one slow exponential decay with a correlation time of τ = 92.8 ps. In contrast, for
simulations in CCl4 the lid has a more complex dynamics. Exponential fit of open CRL in CCl4 results in two different τ values: a fast motion τ1 = 5.6 ps and a slow motion τ2 = 163.8 ps.Upon alkylation, different levels of modification show different properties of
lid motions. In CCl4, lid region is highly stabilised upon 95% alkylation with slow motion mode of τ1 = 4.1 ps and τ2 = 577.8 ps. Slow motion effect of lid region is also observed at 63% with τ1 = 2.9 ps and τ2 = 209.2 ps and 43%
modification with τ1 = 3.4 ps and τ2 = 117.9 ps. In water, 43% and 95% modification show similar motion with unmodified lipase, with one slow exponential decay of τ = 142.8 ps and 133.6 ps, respectively. However, 63%
modification shows more complex dynamics with different τ values which mimics the dynamics properties in CCl4.
A novel lid-locking mechanism which stabilises the opening form of lid region has been observed during simulations of unmodified CRL in CCl4, i.e. a salt bridge between Lys85 and Asp284. This salt bridge is highly stabilised
on unmodified lipase with a distance of 3.3 Å compared with lipase simulated in water with a distance of 15.25 Å. Alkylation at 43% causes the salt bridge to be deformed in CCl4 with a distance of 6.03 Å; however, 63% modification stabilises the salt bridge with a distance of 3.88 and 95% modification shows the most stabilising effect with a distance of 3.19 Å
Antifreeze proteins: characteristics and potential applications
No full textThe freezing of water is usually fatal to most organisms because it causes extensive damage to cell membranes due to the formation of ice crystals. However, several structurally different classes of antifreeze proteins (AFPs) found in fish, insects, plants, and microorganisms, including bacteria, yeast, and fungi, have been found to be capable of modifying the growth of ice crystals by thermal hysteresis and ice recrystallization inhibition. This unique property could potentially be applied to medicine and the industry as it is useful when low-temperature storage is required and ice
crystallization must be avoided. However, the application of AFPs today is not economically viable due to the complexity of the large proteins, the laborious procedures required, and the low yields obtained. A wide range of peptides mimicking their parent proteins were recently successfully designed and chemically synthesized. The developed approaches present new opportunities to understand the structure–function relationship of small-structured peptides with antifreeze properties. This mini-review highlights the diversity, classification, and properties of AFPs. The emerging applications of short mimetic peptides of AFPs and their potential application are also described
Structure and dynamics of Candida rugosa lipase : the role of organic solvent
No full textThe effect of organic solvent to structure and dynamics of proteins was investigated by multiple molecular dynamics simulations (1 ns each) of Candida rugosa lipase in water and in carbon tetrachloride. The choice of solvent had only a minor structural effect. For both solvents the open and the closed conformation of the lipase were near to their experimental X-ray structures (Cα rms deviation 1-1.3 Å). However, the solvents had a highly specific effect on the flexibility of solvent-exposed side chains: polar side chains were more flexible in water, but less flexible in organic solvent. In contrast, hydrophobic residues were more flexible in organic solvent, but less flexible in water. As a major effect solvent changed the dynamics of the lid, a mobile element involved in activation of the lipase, which fluctuated as rigid body about its average position. While in water the deviations were about 1.6 Å, organic solvent reduced flexibility to 0.9 Å. This increase rigidity was caused by two salt bridges (Lys85-Asp284, Lys75-Asp79) and a stable hydrogen bond (Lys75-Asn 292) in organic solvent. Thus organic solvents stabilize the lid but render the side chains in the hydrophobic substrate binding site more mobile
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Structure and dynamics of Candida rugosa lipase: the role of organic solvent
No full textThe effect of organic solvent on the structure and dynamics of proteins was investigated by multiple molecular dynamics simulations (1 ns each) of Candida rugosa lipase in water and in carbon tetrachloride. The choice of solvent had only a minor structural effect. For both solvents the open and the closed conformation of the lipase were near to their experimental X-ray structures (Cα rms deviation 1-1.3 Å). However, the solvents had a highly specific effect on the flexibility of solvent-exposed side chains: polar side chains were more flexible in water, but less flexible in organic solvent. In contrast, hydrophobic residues were more flexible in organic solvent, but less flexible in water. As a major effect solvent changed the dynamics of the lid, a mobile element involved in activation of the lipase, which fluctuated as a rigid body about its average position. While in water the deviations were about 1.6 Å, organic solvent reduced flexibility to 0.9 Å. This increase rigidity was caused by two salt bridges (Lys85-Asp284, Lys75-Asp79) and a stable hydrogen bond (Lys75-Asn 292) in organic solvent. Thus, organic solvents stabilize the lid but render the side chains in the hydrophobic substrate-binding site more mobile. © Springer-Verlag 2004
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