Molecular Dynamics/Book2

LUCAS J GUTIERREZ; RICARDO D. ENRIZ; HECTOR H.BALDONI

Essential Dynamics on Different Biological Systems: Fis Protein, tvMyb1 Transcriptional Factor and BACE1 Enzyme

intech

Lugar: Rijeka; Año: 2011;

Proteins and enzymes poses a non-covalent 3D structure and therefore their intrinsic 15 flexibility allows the existence of an ensemble of different conformers which are separated 16 by low-energy barriers. These ranges of available conformers for proteins in solution are 17 due to the relative movements among the different domains. Domain motions are important 18 for a variety of protein functions, including catalysis, regulation of activity, transport of 19 metabolites, formation of protein assemblies, and cellular locomotion. 20 Considering the importance of these conformational changes it is obvious that the different 21 techniques to evaluate these behaviours are very important in order to understand the 22 biological effects. In the present chapter we report molecular dynamics (MD) trajectories 23 analyzed by essential dynamics method on three different molecular systems of biological 24 interest: i) DNA-bending protein Fis (Factor for Inversion Stimulation), ii) DNA-tvMyb1 25 (Trichomonas vaginalis transcriptional factor) and iii) the BACE1 (β−site amyloid cleaving 26 enzyme 1). Although the general structural characteristics for the above systems are well 27 known, comparatively little information is available about their flexibility and dynamics. 28 This is in part due to difficulties with obtaining such information experimentally. Thus, our 29 primary interest was the comparison between the unligated and the complexed state, 30 because the corresponding conclusions may reveal motions of functional relevance.