SDA
Simulation of Diffusional Association
(version 6)



The documentation is also included in the downloaded version of sda (see Availability). Please note that not all links work in the online version of this documentation. These links will then work in the downloaded version.


Introduction

SDA simulates the diffusional association of two proteins/molecules or a protein/molecule to a solid state surface. If the atomic structure of the bound complex is known, SDA can be used to calculate bimolecular association rates. It can also be used to record Brownian dynamics trajectories or encounter complexes and calculate bimolecular electron transfer rate constants. SDA may also be used for rigid-body docking to predict the structure of protein-protein encounter complexes or the orientation in which a protein binds to a surface.

To run SDA, the following programs are usually needed:

  1. ECM - Effective Charges for Macromolecules in solvent - a program to calculate partial atomic charges used for computing accurate electrostatic interaction forces and energies included in this SDA distribution.

  2. UHBD - University of Houston Brownian Dynamics program used by SDA to calculate electrostatic potentials.

    or

    APBS - Adaptive Poisson-Boltzmann Solver used by SDA to calculate electrostatic potentials.  (APBS calculated electrostatic potentials should be converted to binary UHBD format.)

For some applications of SDA, the following programs are needed:

  1. HARLEM - to calculate the electronic coupling between donor (or acceptor) atoms and accessible atoms of a protein (for electron transfer rate calculations only).

  2. NACCESS - atomic solvent accessibility calculation program.

In this SDA distribution, sda itself an be used to compute the rate of formation of a user-defined set of intermolecular contacts, the rate constants for electron transfer during diffusion of two proteins, and to perform rigid-body docking. >The other SDA programs in the distribution can be used as follows:

In addition there are various auxiliary programs for the preparation of input data and for the analysis of the output results.


Availability

    The current version of SDA (Simulation of Diffusional Association) may be downloaded from this page.

References

References describing the method

Gabdoulline RR and Wade RC.  Brownian Dynamics Simulation of Protein-Protein Encounter.  Methods (1998) 3, 329-341. (doi)
Gabdoulline RR and Wade RC.  Simulation of the Diffusional Association of Barnase and Barstar.  Biophys. J. (1997) 72, 1917-1929. (Abstract)
Describes SDA method

Gabdoulline RR and Wade RC.  Effective charges for Macromolecules in Solvent.  J. Phys. Chem. (1996) 100, 3868-3878. (doi)
Describes ECM method

ElcockAH, Gabdoulline RR, Wade RC and McCammon JA.  Computer Simulation of Protein-Protein Association Kinetics: Acetylcholinesterase-Fasciculin.  J. Mol. Biol. (1999) 291, 149-162. (doi)
Describes electrostatic desolvation term

Gabdoulline RR and Wade RC .  On the contributions of diffusion and thermal activation to electron transfer between Phormidium laminosum plastocyanin and cytochrome f : Brownian dynamics simulations with explicit modeling of nonpolar desolvation interactions and electron transfer events.   J. Am. Chem. Soc. (2009) 131, 9320-9238. (doi)
Describes nonpolar desolvation term

Kokh DB, Corni S, Winn PJ, Hoefling M, Gottschalk KE, and Wade RC .  ProMetCS: an atomistic force field for modeling protein-metal surface interactions in a continuum aqueous solvent.   J. Chem. Theory Comput. (2010) 6, 1753-1768, . (doi)
Describes the ProMetCS model of protein-metal interactions

References describing applications

  1. Harel, M., Spaar, A. and Schreiber G. Fruitful and Futile Encounters along the Association Reaction between Proteins . Biophys. J. (2009) 96, 4237-4248.

  2. Spaar, A., Floeck, D. and Helms V. Association of Cytochrome c with Membrane-Bound Cytochrome c Oxidase Proceeds Parallel to the Membrane Rather Than in Bulk Solution . Biophys. J. (2009) 96, 1721-1732.

  3. Feldman-Salit, A., Wirtz, M., Hell, R. and Wade RC. A mechanistic model of the cysteine synthase complex . J. Mol. Biol. (2009) 386, 37-59.

  4. Motiejunas D, Gabdoulline RR, Wang T, Feldman-Salit A, Johann T, Winn PJ, Wade RC. Protein-protein docking by simulating the process of association subject to biochemical constraints. Proteins (2008) 71, 1955-1969.

  5. Pachov G,  Gabdoulline RR, Wade RC. Simulation of Linker Histone-Chromatin Interactions. In  "From Computational Biophysics to Systems Biology (CBSB2007)", John von Neumann Institute for Computing, Juelich | NIC Series (2007) 36,  69-74.

  6. Blachut-Okrasinska E and Antosiewicz JM. Brownian Dynamics Simulations of Binding mRNA Cap Analogues to eIF4E Protein. J. Phys. Chem. B (2007) 111 (45), 13107-15. (doi)

  7. Spaar A, Dammer C, Gabdoulline RR, Wade RC and Helms V. Diffusional encounter of barnase and barstar.  Biophys. J. (2006) 90, 1913-1924. (Abstract)

  8. Spaar A and Helms V.  Ionic strength effects on the association funnel of barnase and barstar investigated by Brownian dynamics simulations. J. Non-Crystalline Solids (2006) 352,(42-49):4437-44. (doi)

  9. Lin J and Beratan DN. Simulation of electron transfer between cytochrome c2 and the bacterial photosynthetic reaction center: Brownian dynamics analysis of the native protein and double mutants. J. Phys. Chem. B (2005)109, 7529-7534. (doi)

  10. Flöck D, Helms V.  A Brownian dynamics study: the effect of a membrane environment on an electron transfer system. Biophys J. (2004) 87(1): 65-74. (Abstract)

  11. Wang T, Tomic S, Gabdoulline RR, Wade RC. How optimal are the binding energetics of barnase and barstar? Biophys J. (2004) 87(3): 1618-30. (Abstract)

  12. Sun J, Viadiu H, Aggarwal AK and Weinstein H. Energetic and Structural Considerations for the Mechanism of Protein Sliding along DNA in the Nonspecific BamHI-DNA Complex.  Biophys J. (2003) 84(5): 3317–25. (Abstract)

  13. Gabdoulline RR, Kummer U, Olsen LF, Wade RC. Concerted simulations reveal how peroxidase compound III formation results in cellular oscillations. Biophys J. (2003) 85(3):1421-8. (Abstract)

  14. Elcock AH. Atomistic Simulations of Competition between Substrates Binding to an Enzyme. Biophys J (2002) 82(5):  2326-32. (Abstract)

  15. Gabdoulline RR and Wade RC. Biomolecular diffusional association. Curr. Opin. Struct. Biol. (2002) 12, 204-213. (doi)

  16. De Rienzo F, Gabdoulline RR, Menziani MC, De Benedetti PG and Wade RC.  Electrostatic Analysis and Brownian Dynamics Simulation of the Association of Plastocyanin and Cytochrome F.  Biophys. J. (2001) 81, 3090-3104. (Abstract)

  17. Elcock AH and McCammon JA. Calculation of weak protein-protein interactions: The pH dependence of the second virial coefficient. Biophys J. (2001) 80(2): 613-25. (Abstract)

  18. Gabdoulline RR and Wade RC.  Protein-protein Association: Investigation of Factors Influencing Association Rates by Brownian Dynamics Simulations.  J. Mol. Biol. (2001) 306, 1139-1155. (doi)

  19. Sept D, Elcock AH and McCammon JA.  Computer Simulation of Actin Polymerization Can Explain the Barbed-Pointed Asymmetry. J.Mol.Biol. (1999) 294, 1181-1189. (doi)

  20. ElcockAH, Gabdoulline RR, Wade RC and McCammon JA.  Computer Simulation of Protein-Protein Association Kinetics: Acetylcholinesterase-Fasciculin.  J. Mol. Biol. (1999) 291, 149-162. (doi)

  21. Gabdoulline RR and Wade RC.  On the Protein-Protein Diffusional Encounter Complex.  J. Mol. Recogn. (1999) 12, 226-234. (Abstract)

  22. Gabdoulline RR and Wade RC.  Brownian Dynamics Simulation of Protein-Protein Encounter.  Methods (1998) 3, 329-341. (doi)

  23. Madura JD, Briggs JM, Wade RC and Gabdoulline RR.  Brownian Dynamics.  In "Encyclopedia of Computational Chemistry''.  Eds. Schleyer PvR., Allinger NL, Clark T, Gasteiger J, Kollman PA and Schaefer HF, Schreiner PR. John Wiley & Sons: Chichester, UK, (1998) 1, 141-154. (Link)

  24. Gabdoulline RR and Wade RC.  Simulation of the Diffusional Association of Barnase and Barstar.  Biophys. J. (1997) 72, 1917-1929. (Abstract)


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