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Literature DB >> 8913568

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

G H Peters¹, D M van Aalten, O Edholm, S Toxvaerd, R Bywater.

Abstract

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.

Entities: Chemical Species

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Year: 1996 PMID： 8913568 PMCID： PMC1233717 DOI： 10.1016/S0006-3495(96)79428-6

Source DB: PubMed Journal: Biophys J ISSN： 0006-3495 Impact factor: 4.033

32 in total

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Authors: M K Jain; O G Berg
Journal: Biochim Biophys Acta Date: 1989-04-03

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Authors: D M van Aalten; A Amadei; A B Linssen; V G Eijsink; G Vriend; H J Berendsen
Journal: Proteins Date: 1995-05

3. The Protein Data Bank: a computer-based archival file for macromolecular structures.

Authors: F C Bernstein; T F Koetzle; G J Williams; E F Meyer; M D Brice; J R Rodgers; O Kennard; T Shimanouchi; M Tasumi
Journal: J Mol Biol Date: 1977-05-25 Impact factor: 5.469

4. Competitive inhibition of lipolytic enzymes. I. A kinetic model applicable to water-insoluble competitive inhibitors.

Authors: S Ransac; C Rivière; J M Soulié; C Gancet; R Verger; G H de Haas
Journal: Biochim Biophys Acta Date: 1990-03-12

5. Enzymatic catalysis in nonaqueous solvents.

Authors: A Zaks; A M Klibanov
Journal: J Biol Chem Date: 1988-03-05 Impact factor: 5.157

6. A model for the molecular mechanism of interfacial activation of phospholipase A2 supporting the substrate theory.

Authors: T Thuren
Journal: FEBS Lett Date: 1988-02-29 Impact factor: 4.124

7. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.

Authors: W Kabsch; C Sander
Journal: Biopolymers Date: 1983-12 Impact factor: 2.505

8. Relation of the hydrophobicity index to the thermal stability of homologous proteins.

Authors: D E Goldsack
Journal: Biopolymers Date: 1970-02 Impact factor: 2.505

9. Dynamics of the flexible loop of triosephosphate isomerase: the loop motion is not ligand gated.

Authors: J C Williams; A E McDermott
Journal: Biochemistry Date: 1995-07-04 Impact factor: 3.162

10. The control of lipase-catalysed transesterification and esterification reaction rates. Effects of substrate polarity, water activity and water molecules on enzyme activity.

Authors: M Goldberg; D Thomas; M D Legoy
Journal: Eur J Biochem Date: 1990-07-05

18 in total

1. Theoretical studies of the response of a protein structure to cavity-creating mutations.

Authors: J Lee; K Lee; S Shin
Journal: Biophys J Date: 2000-04 Impact factor: 4.033

2. Conformational substates in different crystal forms of the photoactive yellow protein--correlation with theoretical and experimental flexibility.

Authors: D M van Aalten; W Crielaard; K J Hellingwerf; L Joshua-Tor
Journal: Protein Sci Date: 2000-01 Impact factor: 6.725

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

Review 1. The kinetics of interfacial catalysis by phospholipase A2 and regulation of interfacial activation: hopping versus scooting.

2. The essential dynamics of thermolysin: confirmation of the hinge-bending motion and comparison of simulations in vacuum and water.

3. The Protein Data Bank: a computer-based archival file for macromolecular structures.

4. Competitive inhibition of lipolytic enzymes. I. A kinetic model applicable to water-insoluble competitive inhibitors.

5. Enzymatic catalysis in nonaqueous solvents.

6. A model for the molecular mechanism of interfacial activation of phospholipase A2 supporting the substrate theory.

7. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.

8. Relation of the hydrophobicity index to the thermal stability of homologous proteins.

9. Dynamics of the flexible loop of triosephosphate isomerase: the loop motion is not ligand gated.

10. The control of lipase-catalysed transesterification and esterification reaction rates. Effects of substrate polarity, water activity and water molecules on enzyme activity.

1. Theoretical studies of the response of a protein structure to cavity-creating mutations.

2. Conformational substates in different crystal forms of the photoactive yellow protein--correlation with theoretical and experimental flexibility.

3. Influence of a lipid interface on protein dynamics in a fungal lipase.

4. A model of the pressure dependence of the enantioselectivity of Candida rugosalipase towards (+/-)-menthol.

5. Orientation and conformation of a lipase at an interface studied by molecular dynamics simulations.

6. Effects of organic solvents and substrate binding on trypsin in acetonitrile and hexane media.

7. New insights in the activation of human cholesterol esterase to design potent anti-cholesterol drugs.

8. Conformational change in the activation of lipase: an analysis in terms of low-frequency normal modes.

9. Structure and dynamics of Candida rugosa lipase: the role of organic solvent.

10. Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase.