TY - JOUR
T1 - Effects of protein-protein interactions on electron transfer: docking and electron transfer calculations for complexes between flavodoxin and c- type cytochromes
AU - Cunha, Carlos A.
AU - Romão, Maria J.
AU - Sadeghi, Sheila J.
AU - Valetti, F.
AU - Gilardi, G.
AU - Soares, Cláudio M.
PY - 1999/6/1
Y1 - 1999/6/1
N2 - Theoretical studies of protein-protein association and electron transfer were performed on the binary systems formed by Desulfovibrio vulgaris Hildenborough (D. v. H.) flavodoxin and D. v. H. cytochrome c553 and by flavodoxin and horse heart cytochrome c. Initial structures for the complexes were obtained by rigid-body docking and were refined by MD to allow for molecular flexibility. The structures thus obtained were analysed in terms of their relative stability through the calculation of excess energies. Electrostatic, van der Waals and solvation energy terms showed all to have significant contributions to the stability of complexes. In the best association solutions found for both cytochromes, these bind to different zones of flavodoxin. The binding site of flavodoxin observed for cytochrome c is in accordance with earlier works [27]. The various association modes found were characterised in terms of electron transfer using the Pathways model. For complexes between flavodoxin and horse heart cytochrome c, some correlation was observed between electron tunnelling coupling factors and conformation energy; the best conformation found for electron transfer corresponded also to the best one in terms of energy. For complexes between flavodoxin and cytochrome c553 this was not the case and a lower correlation was observed between electron tunnelling coupling factors and excess energies. These results are in accordance with the differences in the experimental dependence of electron transfer rates with ionic strength observed between these two cases.
AB - Theoretical studies of protein-protein association and electron transfer were performed on the binary systems formed by Desulfovibrio vulgaris Hildenborough (D. v. H.) flavodoxin and D. v. H. cytochrome c553 and by flavodoxin and horse heart cytochrome c. Initial structures for the complexes were obtained by rigid-body docking and were refined by MD to allow for molecular flexibility. The structures thus obtained were analysed in terms of their relative stability through the calculation of excess energies. Electrostatic, van der Waals and solvation energy terms showed all to have significant contributions to the stability of complexes. In the best association solutions found for both cytochromes, these bind to different zones of flavodoxin. The binding site of flavodoxin observed for cytochrome c is in accordance with earlier works [27]. The various association modes found were characterised in terms of electron transfer using the Pathways model. For complexes between flavodoxin and horse heart cytochrome c, some correlation was observed between electron tunnelling coupling factors and conformation energy; the best conformation found for electron transfer corresponded also to the best one in terms of energy. For complexes between flavodoxin and cytochrome c553 this was not the case and a lower correlation was observed between electron tunnelling coupling factors and excess energies. These results are in accordance with the differences in the experimental dependence of electron transfer rates with ionic strength observed between these two cases.
KW - Docking calculations
KW - Electron transfer
KW - Electron transfer calculations
KW - Ionic strength effects in electron transfer
KW - Protein-protein interactions
UR - http://www.scopus.com/inward/record.url?scp=0032788471&partnerID=8YFLogxK
U2 - 10.1007/s007750050323
DO - 10.1007/s007750050323
M3 - Article
C2 - 10439082
AN - SCOPUS:0032788471
VL - 4
SP - 360
EP - 374
JO - JBIC Journal of Biological Inorganic Chemistry
JF - JBIC Journal of Biological Inorganic Chemistry
SN - 0949-8257
IS - 3
ER -