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Investigation of Domain Motions in Bacteriophage T4 Lysozyme

Arnold, Gregory E. ; Manchester, John I. ; Townsend, Benjamin D. ; Ornstein, Rick L.

Journal of biomolecular structure & dynamics, 1994-10, Vol.12 (2), p.457-474 [Periódico revisado por pares]

England: Taylor & Francis Group

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  • Título:
    Investigation of Domain Motions in Bacteriophage T4 Lysozyme
  • Autor: Arnold, Gregory E. ; Manchester, John I. ; Townsend, Benjamin D. ; Ornstein, Rick L.
  • Assuntos: Bacteriophage T4 - enzymology ; Computer Simulation ; Crystallography, X-Ray ; Models, Molecular ; Muramidase - chemistry ; Mutagenesis, Site-Directed ; phage T4 ; Protein Structure, Secondary ; Recombinant Proteins - chemistry ; Software ; Thermodynamics
  • É parte de: Journal of biomolecular structure & dynamics, 1994-10, Vol.12 (2), p.457-474
  • Notas: ObjectType-Article-2
    SourceType-Scholarly Journals-1
    ObjectType-Feature-1
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  • Descrição: Hinge-bending in T4 lysozyme has been inferred from single amino acid mutant crystalline allomorphs by Matthews and coworkers. This raises an important question: are the different conformers in the unit cell artifacts of crystal packing forces, or do they represent different solution state structures? The objective of this theoretical study is to determine whether domain motions and hinge-bending could be simulated in T4 lysozyme using molecular dynamics. An analysis of a 400 ps molecular dynamics simulation of the 164 amino acid enzyme T4 lysozyme is presented. Molecular dynamics calculations were computed using the Discover software package (Biosym Technologies). All hydrogen atoms were modeled explicitly with the inclusion of all 152 crystallographic waters at a temperature of 300 K. The native T4 lysozyme molecular dynamics simulation demonstrated hinge-bending in the protein. Relative domain motions between the N-terminal and C-terminal domains were evident. The enzyme hinge bending sites resulted from small changes in backbone atom conformations over several residues rather than rotation about a single bound. Two hinge loci were found in the simulation. One locus comprises residues 8-14 near the C-terminal of the A helix; the other site, residues 77-83 near the C-terminal of the C helix. Comparison of several snapshot structures from the dynamics trajectory clearly illustrates domain motions between the two lysozyme lobes. Time correlated atomic motions in the protein were analyzed using a dynamical cross-correlation map. We found a high degree of correlated atomic motions in each of the domains and, to a lesser extent, anticorrelated motions between the two domains. We also found that the hairpin loop in the N-terminal lobe (residues 19-24) acted as a mobile 'flap' and exhibited highly correlated dynamic motions across the cleft of the active site, especially with residue 142.
  • Editor: England: Taylor & Francis Group
  • Idioma: Inglês
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  • Realização: ABCD-USP USP   Logos de Redes Sociais: Freepik

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