This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Fogolari, F. Articles by Molinari, H. Search for Related Content PubMed PubMed Citation Articles by Fogolari, F. Articles by Molinari, H.

Protocol for MM/PBSA Molecular Dynamics Simulations of Proteins

Federico Fogolari ^*, Alessandro Brigo  and Henriette Molinari ^*

^*Dipartimento Scientifico e Tecnologico, Università di Verona, 37134 Verona, Italy; and Dipartimento di Scienze Farmaceutiche, Università di Padova, 35131 Padova, Italy

Correspondence: Address reprint requests to Federico Fogolari, Ca Vignal 1, Strada Le Grazie 15, 37134 Verona, Italy. Tel.: 39-045-8027906; Fax: 39-045-8027929; E-mail: fogolari{at}sci.univr.it.

Continuum solvent models have been employed in past years for understanding processes such as protein folding or biomolecular association. In the last decade, several attempts have been made to merge atomic detail molecular dynamics simulations with solvent continuum models. Among continuum models, the Poisson-Boltzmann solvent accessible surface area model is one of the oldest and most fundamental. Notwithstanding its wide usage for simulation of biomolecular electrostatic potential, the Poisson-Boltzmann equation has been very seldom used to obtain solvation forces for molecular dynamics simulation. We propose here a fast and reliable methodology to implement continuum forces in standard molecular mechanics and dynamics algorithms. Results for a totally unrestrained 1 ns molecular dynamics simulation of a small protein are quantitatively similar to results obtained by explicit solvent molecular dynamics simulations.

This article has been cited by other articles:

				S.-i. Fujiwara and T. Amisaki Identification of High Affinity Fatty Acid Binding Sites on Human Serum Albumin by MM-PBSA Method Biophys. J., January 1, 2008; 94(1): 95 - 103. [Abstract] [Full Text] [PDF]

				Q. Zhang and T. Schlick Stereochemistry and Position-Dependent Effects of Carcinogens on TATA/TBP Binding Biophys. J., March 15, 2006; 90(6): 1865 - 1877. [Abstract] [Full Text] [PDF]

				F. Fogolari and S. C.E. Tosatto Application of MM/PBSA colony free energy to loop decoy discrimination: Toward correlation between energy and root mean square deviation Protein Sci., April 1, 2005; 14(4): 889 - 901. [Abstract] [Full Text] [PDF]

				H. Lehle, J. M. Kriegl, K. Nienhaus, P. Deng, S. Fengler, and G. U. Nienhaus Probing Electric Fields in Protein Cavities by Using the Vibrational Stark Effect of Carbon Monoxide Biophys. J., March 1, 2005; 88(3): 1978 - 1990. [Abstract] [Full Text] [PDF]

				M. Trieb, C. Rauch, F. R. Wibowo, B. Wellenzohn, and K. R. Liedl Cooperative effects on the formation of intercalation sites Nucleic Acids Res., September 1, 2004; 32(15): 4696 - 4703. [Abstract] [Full Text] [PDF]