Barnase-Barstar: From first encounter to final complex

Journal of Structural Biology

Volumn 171, Issue 1, 2010, Pages 52-63

  Hoefling, Martin ^a   Gottschalk, Kay E ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

Barnase Barstar; Electrostatic steering; Potential of Mean Force; Protein complexation

Indexed keywords

BARNASE; BARSTAR; SODIUM CHLORIDE;

ANALYTIC METHOD; ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; MUTANT; MUTATION; PRIORITY JOURNAL; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; SIMULATION;

BACTERIAL PROTEINS; BINDING SITES; KINETICS; MOLECULAR DYNAMICS SIMULATION; MUTATION; PROTEIN CONFORMATION; RIBONUCLEASES; STATIC ELECTRICITY;

EID: 77953621551     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2010.03.001     Document Type: Article

References (64)

1. Abseher R., Schreiber H., Steinhauser O. The influence of a protein on water dynamics in its vicinity investigated by molecular dynamics simulation. Proteins-Structure Function and Genetics 1996, 25:366-378.
2. Baker N.A., Sept D., Joseph S., Holst M., McCammon J.A. Electrostatics of nanosystems: application to microtubules and the ribosome. Proceedings of the National Academy of Sciences of the United States of America 2001, 98:10037-10041.
3. Bergdorf M., Peter C., Hunenberger P.H. Influence of cut-off truncation and artificial periodicity of electrostatic interactions in molecular simulations of solvated ions: a continuum electrostatics study. The Journal of Chemical Physics 2003, 119:9129-9144.
4. Bhattacharyya K., Bagchi B. Slow dynamics of constrained water in complex geometries. Journal of Physical Chemistry A 2000, 104:10603-10613.
5. Buckle A., Schreiber G., Fersht A. Protein-protein recognition - crystal structural-analysis of a Barnase-Barstar complex at 2.0-angstrom resolution. Biochemistry 1994, 33:8878-8889.
6. Cai X., Yang J. The binding potential between the cholera toxin B-oligomer and its receptor. Biochemistry 2003, 42:4028-4034.
7. Camacho C., Weng Z., Vajda S., DeLisi C. Free energy landscapes of encounter complexes in protein-protein association. Biophysical Journal 1999, 76:1166-1178.
8. Camacho C., Kimura S., DeLisi C., Vajda S. Kinetics of desolvation-mediated protein-protein binding. Biophysical Journal 2000, 78:1094-1105.
9. Chen A., Moy V. Cross-linking of cell surface receptors enhances cooperativity of molecular adhesion. Biophysical Journal 2000, 78:2814-2820.
10. Cornell W., Cieplak P., Bayly C., Gould I., Merz K., Ferguson D., Spellmeyer D., Fox T., Caldwell J., Kollman P. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules (vol. 117, p. 5179, 1995). Journal of the American Chemical Society 1996, 118:2309.
11. W. DeLano, 2009. The PyMOL User's Manual, Manual.
12. Despa F., Fernandez A., Berry R.S. Dielectric modulation of biological water. Physical Review Letters 2004, 93:228104.
13. Dong F., Zhou H.-X. Electrostatic contribution to the binding stability of protein-protein complexes. Proteins-Structure Function and Bioinformatics 2006, 65:87-102.
14. Dong F., Vijayakumar M., Zhou H. Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of Barnase and Barstar. Biophysical Journal 2003, 85:49-60.
15. Donnini S., Mark A., Juffer A., Villa A. Incorporating the effect of ionic strength in free energy calculations using explicit ions. Journal of Computational Chemistry 2005, 26:115-122.
16. Frisch C., Schreiber G., Johnson C., Fersht A. Thermodynamics of the interaction of Barnase and Barstar: changes in free energy versus changes in enthalpy on mutation. Journal of Molecular Biology 1997, 267:696-706.
17. Frisch C., Fersht A., Schreiber G. Experimental assignment of the structure of the transition state for the association of Barnase and Barstar. Journal of Molecular Biology 2001, 308:69-77.
18. Gabdoulline R.R., Wade R.C. Brownian dynamics simulation of protein-protein diffusional encounter. Methods 1998, 14:329-341.
19. Gallagher K., Sharp K. A new angle on heat capacity changes in hydrophobic solvation. Journal of the American Chemical Society 2003, 125:9853-9860.
20. Gottschalk K.-E., Kessler H. Evidence for hetero-association of transmembrane helices of integrins. FEBS Letters 2004, 557:253-258.
21. Gottschalk K.-E., Günther R., Kessler H. A three-state mechanism of integrin activation and signal transduction for integrin alpha(v)beta(3). ChemBioChem 2002, 3:470-473.
22. Gottschalk K.-E., Neuvirth H., Schreiber G. A novel method for scoring of docked protein complexes using predicted protein-protein binding sites. Protein Engineering, Design & Selection 2004, 17:183-189.
23. Grater F., Shen J., Jiang H., Grubmueller H. Mechanically induced titin kinase activation studied by force probe molecular dynamics simulations. Biophysical Journal 2005, 88:405A.
24. Hartley R.W. Barnase and Barstar: two small proteins to fold and fit together. Trends in Biochemical Sciences 1989, 14:450-454.
25. Hess B. Determining the shear viscosity of model liquids from molecular dynamics simulations. Journal of Chemical Physics 2002, 116:209-217.
26. Hess B., Kutzner C., van der Spoel D., Lindahl E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation 2008, 4:435-447.
27. Humphrey W., Dalke A., Schulten K. VMD - visual molecular dynamics. Journal of Molecular Graphics 1996, 14:33-38.
28. Janin J. The kinetics of protein-protein recognition. Proteins-Structure Function and Genetics 1997, 28:153-161.
29. Jorgensen W., TiradoRives J. The OPLS potential functions for proteins - energy minimizations for crystals of cyclic-peptides and crambin. Journal of the American Chemical Society 1988, 110:1657-1666.
30. Jorgensen W., Maxwell D., TiradoRives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. Journal of the American Chemical Society 1996, 118:11225-11236.
31. Kada G., Blayney L., Jeyakumar L., Kienberger F., Pastushenko V., Fleischer S., Schindler H., Lai F., Hinterdorfer P. Recognition force microscopy/spectroscopy of ion channels: applications to the skeletal muscle Ca2+ release channel (RYR1). Ultramicroscopy 2001, 86:129-137.
32. Kutzner C., van der Spoel D., Fechner M., Lindahl E., Schmitt U.W., Groot B.L.D., Grubmueller H. Software news and update - speeding up parallel GROMACS on high-latency networks. Journal of Computational Chemistry 2007, 28:2075-2084.
33. Lee L., Tidor B. Optimization of binding electrostatics: charge complementarity in the Barnase-Barstar protein complex. Protein Science 2001, 10:362-377.
34. Lindahl E., Hess B., van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. Journal of Molecular Modeling 2001, 7:306-317.
35. Neumann J., Gottschalk K.E. The effect of different force applications on the protein-protein complex Barnase-Barstar. Biophysical Journal 2009, 97:1687-1699.
36. Northrup S.H., Erickson H.P. Kinetics of protein-protein association explained by Brownian dynamics computer-simulation. Proceedings of the National Academy of Sciences of the United States of America 1992, 89:3338-3342.
37. Novotny J., Sharp K. Electrostatic fields in antibodies and antibody antigen complex. Progress in Biophysics and Molecular Biology 1992, 58:203-224.
38. Palla G., Derényi I., Farkas I., Vicsek T. Uncovering the overlapping community structure of complex networks in nature and society. Nature 2005, 435:814-818.
39. Palla G., Barabási A.-L., Vicsek T. Quantifying social group evolution. Nature 2007, 446:664-667.
40. Perutz M. Electrostatic effects in proteins. Science 1978, 201:1187-1191.
41. Reichmann D., Rahat O., Albeck S., Meged R., Dym O., Schreiber G. The modular architecture of protein-protein binding interfaces. Proceedings of the National Academy of Sciences of the United States of America 2005, 102:57-62.
42. Ryckaert J., Ciccotti G., Berendsen H.J.C. Numerical integration of the cartesian equations of motion of a system with constraints; molecular dynamics of n-alkanes. Journal of Computational Physics 1977, 23:327-341.
43. Sanner M.F., Olson A.J., Spehner J.C. Reduced surface. An efficient way to compute molecular surfaces. Biopolymers 1996, 38:305-320.
44. Schlitter J., Swegat W., Mulders T. Distance-type reaction coordinates for modelling activated processes. Journal of Molecular Modeling 2001, 7:171-177.
45. Schreiber G., Ferscht A.R. Energetics of protein-protein interactions - analysis of the Barnase-Barstar interface by single mutations and double mutant cycles. Journal of Molecular Biology 1995, 248:478-486.
46. Schreiber G., Fersht A.R. Rapid, electrostatically assisted association of proteins. Nature Structural Biology 1996, 3:427-431.
47. Schreiber H., Steinhauser O. Cutoff size does strongly influence molecular-dynamics results on solvated polypeptides. Biochemistry 1992, 31:5856-5860.
48. Schröder C., Rudas T., Boresch S., Steinhauser O. Simulation studies of the protein-water interface. I. Properties at the molecular resolution. The Journal of Chemical Physics 2006, 124:234907.
49. Selzer T., Schreiber G. Predicting the rate enhancement of protein complex formation from the electrostatic energy of interaction. Journal of Molecular Biology 1999, 287:409-419.
50. Selzer T., Schreiber G. New insights into the mechanism of protein-protein association. Proteins-Structure Function and Genetics 2001, 45:190-198.
51. Sheinerman F., Honig B. On the role of electrostatic interactions in the design of protein-protein interfaces. Journal of Molecular Biology 2002, 318:161-177.
52. Sheinerman F.B., Norel R., Honig B. Electrostatic aspects of protein-protein interactions. Current Opinion in Structural Biology 2000, 10:153-159.
53. SolerGonzalez A., Fersht A. Helix stability in Barstar peptides. European Journal of Biochemistry 1997, 249:724-732.
54. Spaar A., Helms V. Free energy landscape of protein-protein encounter resulting from Brownian dynamics simulations of Barnase:Barstar. Journal of Chemical Theory and Computation 2005, 1:723-736.
55. Spaar A., Dammer C., Gabdoulline R., Wade R., Helms V. Diffusional encounter of Barnase and Barstar. Biophysical Journal 2006, 90:1913-1924.
56. Strittmatter G., Janssens J., Opsomer C., Batterman J. Inhibition of fungal disease development in plants by engineering controlled cell-death. Bio-Technology 1995, 13:1085-1089.
57. Swegat W., Schlitter J., Kruger P., Wollmer A. MD simulation of protein-ligand interaction: formation and dissociation of an insulin-phenol complex. Biophysical Journal 2003, 84:1493-1506.
58. Trzesniak D., Kunz A.-P.E., Gunsteren W.F.V. A comparison of methods to compute the potential of mean force. Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry 2007, 8:162-169.
59. van der Spoel D., van Maaren P. The origin of layer structure artifacts in simulations of liquid water. Journal of Chemical Theory and Computation 2006, 2:1-11.
60. van der Spoel D., Lindahl E., Hess B., Groenhof G., Mark A., Berendsen H.J.C. GROMACS: fast, flexible, and free. Journal of Computational Chemistry 2005, 26:1701-1718.
61. Wang T., Tomic S., Gabdoulline R.R., Wade R.C. How optimal are the binding energetics of Barnase and Barstar?. Biophysical Journal 2004, 87:1618-1630.
62. Wolf M.G., Jongejan J.A., Laman J.D., de Leeuw S.W. Rapid free energy calculation of peptide self-assembly by REMD umbrella sampling. Journal of Physical Chemistry B 2008, 112:13493-13498.
63. Yang C., Sharp K.A. Hydrophobic tendency of polar group hydration as a major force in type I antifreeze protein recognition. Proteins 2005, 59:266-274.
64. Yuan C., Chen A., Kolb P., Moy V. Energy landscape of streptavidin-biotin complexes measured by atomic force microscopy. Biochemistry 2000, 39:10219-10223.