Supplementary material
Introduction- md.avi: Dynamics of a protein molecule in time. Protein atoms (spheres) change position in relation to other atoms with progress of time. Carbon - green; nitrogen - blue; oxygen - red; sulphur - yellow; hydrogen - white.
- fig01.png | fig02.png | fig03.png | fig04.png | fig05.png | fig06.png | fig07.png | fig08.png | fig09.png | fig10.png | fig11.png | fig12.png | fig13.png | fig14.png | fig15.png | fig16.png | fig17.png | fig18.png | fig19.png | fig20.png | fig21.png | fig22.png | fig23.png | fig24.png | fig25.png | fig26.png | fig27.png | fig28.png | fig29.png | fig30.png | fig31.png | fig32.png | fig33.png | fig34.png | fig35.png | fig36.png | fig37.png: All Figs from the Introduction section in PNG format.
- figs_introduction.zip: All Figs from the Introduction section for batch download.
- genbank_AF060871: Sequence of the locus of pRTL1 plasmid from Rhodococcus rhodochrous NCIMB 13064 containing dhaA gene (nucleotides 8244 - 9125) encoding for the wild-type form of haloalkane dehalogenase DhaA. Source: GenBank.
- 1cqw.pdb: X-ray crystal (XC) structure of haloalkane dehalogenase DhaA. This structure was used as the template for molecular modelling.
- dhaa_ncimb13064.pdb: Wild-type form of the haloalkane dehalogenase DhaA from Rhodococcus rhodochrous NCIMB 13064. This structure was prepared from the 1cqw.pdb by three substitutions: Val172Ala+Ile209Leu+Ala292Gly.
- 3fbw.pdb: XC structure of the Cys176Tyr mutant of the wild-type DhaA.
- 3g9x.pdb: XC structure of the Ile135Phe mutant of the wild-type DhaA.
- 3fwh.pdb: XC structure of the Ile135Phe+Cys176Tyr mutant of the wild-type DhaA.
- linearly_polarised_light.gif: Linearly polarised light. Source: Applied Photophysics.
- circularly_polarised_light_left.gif: Left circularly polarised light. Source: Applied Photophysics.
- circularly_polarised_light_right.gif: Right circularly polarised light. Source: Applied Photophysics.
- parm94.dat: Parameters of the 1994 Cornell force field. Source: The AMBER molecular dynamics package.
- parm94_kmunicek_etal_2001.dat: Parameters of the 1994 Cornell force field modified by addition of parameters for bonds, angles and dihedrals involving halogen atoms. Source: Kmunicek et al., 2001.
- ramd.in: Input parameter file for random acceleration molecular dynamics (RAMD) simulation.
- ramd_patch.zip: Modification of Sander module of AMBER 8 for RAMD simulation. Source: Molecular and Cellular modeling group.
- bfac.zip: Calculation of B-factors for protein backbone in AMBER molecular dynamics (MD) simulation.
- fpr.zip: Identification of amino acid residues lining a ligand pathway in AMBER MD simulation.
- cpr.zip: Visualisation of amino acid residues lining a ligand pathway in AMBER MD simulation by frequency of contact with the ligand.
- path.zip: Visualisation of a ligand pathway in AMBER MD simulation.
- bcp.zip: Combined visualisation of B-factors, amino acid residues lining a ligand pathway, and the ligand pathway in AMBER MD simulation.
- fig38.png | fig39.png | fig40.png | fig41.png | fig42.png | fig43.png | fig44.png | fig45.png | fig46.png | fig47.png | fig48.png | fig49.png | fig50.png | fig51.png | fig52.png | fig53.png | fig54.png | fig55.png | fig56.png | fig57.png: All Figs from the Methods section in PNG format.
- figs_methods.zip: All Figs from the Methods section for batch download.
- c01a.avi | c02.avi | c03.avi | c04.avi | c05.avi | c06.avi | c07a.avi | c08.avi | c09.avi | c10.avi | c11.avi | c12.avi | c13.avi | c14.avi | c15.avi | c16.avi | c17.avi | c18.avi: Visualisation of tunnel opening/closing and ligand (DCL, CL and water) migration in classical MD simulations of DhaA variants (5-ps window). Protein - surface representation (cross-section with tunnels and cavities coloured in dark grey); ligands - spheres represenation; carbon - cyan; oxygen - red; chlorine/chloride anion - yellow; hydrogen - white. See Table 29.
- c19.avi | c20.avi | c21.avi | c22.avi | c23.avi | c24.avi | c25.avi | c26.avi | c27.avi | c28.avi | c29.avi | c30.avi | c31.avi | c32.avi | c33.avi | c34.avi | c35.avi | c36.avi: Visualisation of tunnel opening/closing and ligand (DCL and water) migration in classical MD simulations of DhaA variants (5-ps window). Protein - surface representation (cross-section with tunnels and cavities coloured in dark grey); ligands - spheres represenation; carbon - cyan; oxygen - red; chlorine/chloride anion - yellow; hydrogen - white. See Table 30.
- r06a.avi | r09a.avi | r11a.avi | r26a.avi | r54a.avi | r58a.avi | r66a.avi | r74a.avi | r82a.avi: Visualisation of tunnel opening/closing and ligand (DCL and water) migration in RAMD simulations of DhaA variants (2-ps window). The view of r09a.avi is adjusted by 80 deg rotation to the right with respect to the rest of the "a" animations. Protein - surface representation (cross-section with tunnels and cavities coloured in dark grey); ligands - spheres represenation; carbon - cyan; oxygen - red; chlorine/chloride anion - yellow; hydrogen - white. See Table 31.
- c01b.avi | c07b.avi: p1 CL release pathway in classical MD simulations (5-ps window). Protein - ribbon representation; CL and water - spheres representation; chloride anion - yellow; oxygen - red; hydrogen - white.
- r06b.avi | r26b.avi | r66b.avi | r74b.avi | r82b.avi: Examples of p1 DCL release pathway in RAMD simulations (1-ps window). Protein - ribbon representation; DCL and water - spheres representation; chlorine - yellow; carbon - cyan; oxygen - red; hydrogen - white.
- r11b.avi: Example of p2a DCL release pathway in RAMD simulations (1-ps window). Protein- ribbon representation; DCL and water - spheres representation; chlorine - yellow; carbon - cyan; oxygen - red; hydrogen - white.
- r58b.avi: p2b DCL release pathway in RAMD simulation (1-ps window). Protein - ribbon representation; DCL and water - spheres representation; chlorine - yellow; carbon - cyan; oxygen - red; hydrogen - white.
- r54b.avi: p2c DCL release pathway in RAMD simulation (1-ps window). Protein - ribbon representation; DCL and water - spheres representation; chlorine - yellow; carbon - cyan; oxygen - red; hydrogen - white.
- r09b.avi: p3 DCL release pathway in RAMD simulations (1-ps window). Protein - ribbon representation; DCL and water - spheres representation; chlorine - yellow; carbon - cyan; oxygen - red; hydrogen - white.
- pathways.avi: All pathways identified by classical MD and RAMD simulations (p1, p2a, p2b, p2c and p3). Shown are the RAMD pathways of DCL release (trajectories r06, r09, r11, r54 and r58) mapped to the structure of wild-type DhaA (1 deg rotation angle). Protein - ribbon representation (thickness corresponds to X-ray crystallographic B-factors of the 1cqw.pdb structure); p1 - yellow; p2a - blue; p2b - red; p2c - cyan; p3 - green.
- anims_results.zip: All animations for batch download.
- fig58.png | fig59.png | fig60.png | fig61.png | fig62.png | fig63.png | fig64.png | fig65.png | fig66.png | fig67.png | fig68.png | fig69.png | fig70.png | fig71.png | fig72.png | fig73.png | fig74.png | fig75.png | fig76.png | fig77.png | fig78.png | fig79.png | fig80.png | fig81.png | fig82.png | fig83.png | fig84.png | fig85.png | fig86.png | fig87.png | fig88.png | fig89.png: All Figs from the Results section in PNG format.
- figs_results.zip: All Figs from the Results section for batch download.
- PDF files of the 664 references (see below) are available on the DVD medium attached to the printed version of the dissertation thesis; individual PDF files can be provided at request.
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