Publication

Molecular dynamics simulations of structural changes during procaspase 3 activation

2004
Journal Articles

Abstract

Mol. dynamics simulations (MDS) of the structural rearrangements on the pathway leading to procaspase 3 (I) activation are presented. A retrostructural approach was used to build I from mature caspase 3 (II). The peptide bond that was cleaved during enzyme maturation was gradually reformed during the MDS and the most relevant structural changes that occurred as a consequence were analyzed. The main structural features that characterized this I model were compared with the available x-ray structure of procaspase 7 as the only zymogen structure that has been crystd. so far. The MDS indicated that in free II, the flexible selectivity loop is already pre-organized to accommodate the substrate. Such a pre-organization is not present in either monomeric II or in the I dimer, indicating that the structure of the selectivity loop is highly sensitive to perturbations. [on SciFinder (R)]

Official source

https://infoscience.epfl.ch/entities/publication/c1a00396-fe01-44c6-a37c-157613be9006

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2004
Journal Articles

Abstract

Official source

https://infoscience.epfl.ch/entities/publication/c1a00396-fe01-44c6-a37c-157613be9006

About this result

Related concepts (32)

Structure

A structure is an arrangement and organization of interrelated elements in a material object or system, or the object or system so organized. Material structures include man-made objects such as buildings and machines and natural objects such as biological organisms, minerals and chemicals. Abstract structures include data structures in computer science and musical form. Types of structure include a hierarchy (a cascade of one-to-many relationships), a network featuring many-to-many links, or a lattice featuring connections between components that are neighbors in space.

Structural engineering

Structural engineering is a sub-discipline of civil engineering in which structural engineers are trained to design the 'bones and muscles' that create the form and shape of human-made structures. Structural engineers also must understand and calculate the stability, strength, rigidity and earthquake-susceptibility of built structures for buildings and nonbuilding structures. The structural designs are integrated with those of other designers such as architects and building services engineer and often supervise the construction of projects by contractors on site.

Structural bioinformatics

Structural bioinformatics is the branch of bioinformatics that is related to the analysis and prediction of the three-dimensional structure of biological macromolecules such as proteins, RNA, and DNA. It deals with generalizations about macromolecular 3D structures such as comparisons of overall folds and local motifs, principles of molecular folding, evolution, binding interactions, and structure/function relationships, working both from experimentally solved structures and from computational models.

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Molecular dynamics simulations of structural changes during procaspase 3 activation

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