Computer modelling of dynamics of Ser92X deoxymyoglobin mutants.
The hydrogen bond between His93 and Ser92, recently discovered in crystal structures of myoglobins (Mbs), may contribute to the oxygen storage capacity of the heme proteins through a stabilization of the proximal ligand. The possible influence of this H-bond on the geometry of the heme proximal side and ligand binding properties of Mb were computationally studied using model proteins with point mutations affecting this bond. The results of the computer modelling of Ser92X (X = Ala, Ile, Thr, Val) mutants of human (H) and sperm whale (SW) Mbs are presented. The OPLS-AMBER-CHARMM forcefield was used in the calculations. Several 10-50 ps molecular dynamics simulations (300 K, in vacuo) were performed. Our results show that the Ser92X mutants are stable molecules. In the wild types and Ser92Thr mutants, the H-bond studied is observed only for a relatively short period of time. It is expected that in both HMb and SW Mb molecules the impact of the proximal histidine interaction with the Ser92(F7) residue on the iron reactivity is rather low. However, the limited torsional flexibility of the proximal histidine imidazole ring was found in hydrogen bonding mutants. This effect may be attributed to the specific long range electrostatic interactions.
Nowak
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Institute of Physics, N. Copernicus University, Toruń, Poland. wiesiek@phys.uni.torun.pl
D000409:Alanine / Q000737:chemistry / Q000235:genetics; D000818:Animals; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D006801:Humans; D007532:Isoleucine / Q000737:chemistry / Q000235:genetics; D008958:Models, Molecular; D009211:Myoglobin / Q000031:analogs & derivatives* / Q000737:chemistry / Q000235:genetics; D017354:Point Mutation; D011487:Protein Conformation; D012694:Serine / Q000737:chemistry / Q000235:genetics*; D013912:Threonine / Q000737:chemistry / Q000235:genetics; D014633:Valine / Q000737:chemistry / Q000235:genetics; D014907:Whales
D009211:Myoglobin; C055547:deoxymyoglobin; D007532:Isoleucine; D013912:Threonine; D012694:Serine; D014633:Valine; D000409:Alanine