Acidic range titration of HEWL using a constant-pH molecular dynamics method.
In this work, we present the first application to a protein of the stochastic constant-pH molecular dynamics (MD) method with the inclusion of proton tautomerism. The acidic titration of HEWL was performed under different conditions. Both generalized reaction field (GRF) and particle mesh Ewald (PME) methods were used in the treatment of the long range electrostatics and, even though the PME simulations revealed to be more stable, the better results were obtained using GRF (pK(a) RMSD of 0.82 for GRF and 1.13 for PME). The results using PME at different dielectric constants (2, 4, and 8) also revealed that there was no significant improvement in pK(a)'s prediction upon increasing the dielectric constant. The secondary structure analysis of HEWL revealed a remarkably stable protein in the acidic pH range. The beta-sheet strands (unlike the alpha-helices) seem to be destabilized upon pH decrease, suggesting that the beta-domain is less stable than the alpha-domain. The four principal alpha-helices were also ordered according to their stability in the acidic pH range and the results (4 < 1 < 2 approximately = 3) were consistent with the ones obtained in thermal denaturation studies.
Machuqueiro
Miguel
M
Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal.
Baptista
António M
AM
D000143:Acids; D000465:Algorithms; D000818:Animals; D001671:Biochemistry / Q000379:methods*; D002645:Chickens; D004795:Enzyme Stability; D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D009113:Muramidase / Q000737:chemistry*; D017433:Protein Structure, Secondary; D055672:Static Electricity; D017186:Titrimetry
D000143:Acids; C421864:hen egg lysozyme; D009113:Muramidase