Constant pH molecular dynamics

Constant pH Molecular Dynamics Based on Discrete Protonation States... 

In recent years, a class of methods has been developed for molecular dynamics simulations to be performed with an external pH parameter, like temperature or pressure [18, 43, 44, 70], These methods treat the solution as an infinite proton bath, and are thus referred to as constant pH molecular dynamics (PHMD). In PHMD, conformational dynamics of a protein is sampled simultaneously with the protonation states as a function of pH. As a result, protein dielectric response to the... 

An alternative formalism to the acidostat method, continuous constant pH molecular dynamics (CPHMD), has been developed by Brooks and coworkers [42, 58] drawing on the flavor of the early work by Mertz and Pettitt [67], In CPHMD, each titration residue carries a titration coordinate, A j, which is a function of an unbounded variable 0j,... 

Baptista M, Teixeira VH, Soares CM (2002) Constant-pH molecular dynamics using stochastic titration. J Chem Phys 117 4184-4200. 

Dlugosz M, Antosiewicz JM (2004) Constant-pH molecular dynamics simulations A test case of succinic acid. Chem Phys 302 161-170. 

Dlugosz M, Antosiewicz JM (2005) Effects of solute-solvent proton exchange on polypeptide chain dynamics A constant-pH molecular dynamics study. J Phys Chem B 109 13777-13784. 

Khandogin J, Brooks CL III (2005) Constant pH molecular dynamics with proton tautomerism. Biophys J 89 141-157. 

Lee S, Salsbury FR Jr, Brooks CL III (2004) Constant-pH molecular dynamics using continuous titration coordinates. Proteins 56 738-752. 

Machuqueiro M, Baptista AM (2006) Constant-pH molecular dynamics with ionic strength effects Protonation-conformation coupling in decalysine. J Phys Chem B 110 2927—2933. 

Mongan J, Case DA, McCammon JA (2004) Constant pH molecular dynamics in generalized Born implicit solvent. J Comput Chem 25 2038-2048. 

Mongan, J., Case, D.A., McCammon, J.A. Constant pH molecular dynamics in Generalized Born implicit solvent. J. Comput. Chem. 2004,25,2038-48. 

Chen, Y.Z., Chen, X., Deng, Y.F. Simulating botuhnum neurotoxin with constant pH molecular dynamics in Generalized Bom implicit solvent. Comput. Phys. Commun. 2007,177,210-3. 

This report is mainly concerned with the recent development of a pH-coupled molecular dynamics technique, continuous constant pH molecular dynamics (CPHMD), [12,13] and its applications to first principles pK calculations [14] and pH-coupled biological phenomena [15]. To put this into context, we will also briefly survey other existing methods for pK predictions and pH-coupled conformational dynamics, but we refer interested readers to a recent preliminary review of this area for further details [9]. Finally, we will discuss opportunities for further development of the CPHMD method and our ongoing application studies. 

Donnini, S., Tegeler, F., Groenhof, G., and Grubmtiller, H. (2011). Constant pH molecular dynamics In explicit solvent with X-dynamics,youma/ of Chemical Theory and Computation 7, 6, pp. 1962-1978. 

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