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S Toxvaerd

Publications and source records attributed to S Toxvaerd.

18 recordsLinked to original sources
PubMed1999

Analysis of the dynamics of rhizomucor miehei lipase at different temperatures.

The dynamics of Rhizomucor miehei lipase has been studied by molecular dynamics simulations at temperatures ranging from 200-500K. Simulations carried out in periodic boundary conditions and using explicit water molecules were performed for 400 ps at each temperature. Our results indicate that conformational changes and internal motions in the protein are significantly influenced by the temperature increase. With increasing temperature, the number of internal hydrogen bonds decreases, while surface accessibility, radius of gyration and the number of residues in random coil conformation increase. In the temperature range studied, the motions can be described in a low dimensional subspace, whose dimensionality decreases with increasing temperature. Approximately 80% of the total motion is described by the first (i) 80 eigenvectors at T=200K, (ii) 30 eigenvectors at T=300K and (iii) 10 eigenvectors at T=400K. At high temperature, the alpha-helix covering the active site in the native Rhizomucor miehei lipase, the helix at which end the active site is located, and in particular, the loop (Gly35-Lys50) show extensive flexibility.

Lipase↗
PubMed1998

Active serine involved in the stabilization of the active site loop in the Humicola lanuginosa lipase.

We have investigated the binding properties of and dynamics in Humicola lanuginosa lipase (Hll) and the inactive mutant S146A (active Ser146 substituted with Ala) using fluorescence spectroscopy and molecular dynamics simulations, respectively. Hll and S146A show significantly different binding behavior for phosphatidylcholine (PC) and phosphatidylglycerol (PG) liposomes. Generally, higher binding affinity is observed for Hll than the S146A mutant. Furthermore, depending on the matrix, the addition of the transition state analogue benzene boronic acid increases the binding affinity of S146A, whereas only small changes are observed for Hll suggesting that the active site lid in the latter opens more easily and hence more lipase molecules are bound to the liposomes. These observations are in agreement with molecular dynamics simulations and subsequent essential dynamics analyses. The results reveal that the hinges of the active site lid are more flexible in the wild-type Hll than in S146A. In contrast, larger fluctuations are observed in the middle region of the active site loop in S146A than in Hll. These findings reveal that the single mutation (S146A) of the active site serine leads to substantial conformational alterations in the H. lanuginosa lipase and different binding affinities.

Alanine↗
PubMed1997

Computational studies of the activation of lipases and the effect of a hydrophobic environment.

We have investigated the activation pathway of three wild type lipases and three mutants using molecular dynamics techniques combined with a constrained mechanical protocol. The activation of these lipases involves a rigid body hinge-type motion of a single helix, which is displaced during activation to expose the active site and give access to the substrate. Our results suggest that the activation of lipases is enhanced in a hydrophobic environment as is generally observed in experiments. The energy gain upon activation varies between the different lipases and depends strongly on the distribution of the charged residues in the activating loop region. In a low dielectric constant medium (such as a lipid environment), the electrostatic interactions between the residues located in the vicinity of the activating loop (lipid contact zone) are dominant and determine the activation of the lipases. Calculations of the pKas qualitatively indicate that some titratable residues experience significant pK shifts upon activation. These calculations may provide sufficient details for an understanding of the origin and magnitude of a given electrostatic effect and may provide an avenue for exploring the activation pathway of lipases.

Binding Sites↗
PubMed1996

Dynamics of proteins in different solvent systems: analysis of essential motion in lipases.

We have investigated the effect of different solvents on the dynamics of Rhizomucor miehei lipase. Molecular dynamics simulations were performed in water, methyl hexanoate, and cyclohexane. Analysis of the 400-ps trajectories showed that the solvent has a pronounced effect on the geometrical properties of the protein. The radius of gyration and total accessibility surface decrease in organic solvents, whereas the number of hydrogen bonds increases. The essential motions of the protein in different solvents can be described in a low-dimensional "essential subspace," and the dynamic behavior in this subspace correlates with the polarity of the solvent. Methyl hexanoate, which is a substrate for R. miehei lipase, significantly increases the fluctuations in the active-site loop. During the simulation, a methyl hexanoate entered the active-site groove. This observation provides insight into the possible docking mechanism of the substrate.

Fungal Proteins↗
PubMed1995

Structure and dynamics of lipid monolayers: implications for enzyme catalysed lipolysis.

We have investigated the role of the substrate on the interfacial activation of lipases by an interdisciplinary study of the structure and dynamics of 1,2-sn dipalmitoylglycerol monolayers at distinct surface pressures. The diglyceride Langmuir film undergoes two phase transitions occurring at 38.3 and 39.8 A2 per molecule. The first transition is unique for diglyceride molecules and is driven by a reorganization of the headgroups causing a change in the hydrophobicity of the oil-water interface. X-ray diffraction studies of different mesophases shows that in the two highest pressure phases, the alkyl chains pack in an hexagonal structure relaxing to a distorted-hexagonal lattice in the lowest pressure phase with the alkyl chains tilted by approximately 14 degrees in a direction close to a nearest neighbour direction.

Computer Simulation↗