A natural interaction: Chemical engineering and molecular biophysics

AIChE Journal

Volumn 49, Issue 4, 2003, Pages 806-812

  Lenhoff, Abraham M ^a  

^a University of Delaware   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

PHYSICS;

AMINO ACID SEQUENCE; CHEMICAL ENGINEERING; ELECTROCHEMISTRY; MOLECULAR MECHANICS; MOLECULAR PHYSICS; PREDICTION; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; REVIEW; STRUCTURE ACTIVITY RELATION; THERMODYNAMICS;

EID: 0037392403     PISSN: 00011541     EISSN: None     Source Type: Journal    
DOI: 10.1002/aic.690490402     Document Type: Review

References (49)

1. Anderson, V. J., and H. N. W. Lekkerkerker, "Insights into Phase Transition Kinetics from Colloid Science," Nature, 416, 811 (2002).
2. Arnold, F. H., "Combinatorial and Computational Challenges for Biocatalyst Design," Nature, 409, 253 (2001).
3. Bailey, J. E., "Complex Biology with No Parameters," Nature Biotech., 19, 503 (2001).
4. Boonyaratanakornkit, B. B., C. B. Park, and D. S. Clark, "Pressure Effects on Intra- and Intermolecular Interactions within Proteins," Biochim. Biophys. Acta Prot. Struct. Mol. Enzymol., 1595, 235 (2002).
5. Brune, D., and S. Kim, "Predicting Protein Diffusion Coefficients," Proc. Natl. Acad. Sci. USA, 90, 3835 (1993).
6. Burley, S. K., and J. B. Bonanno, "Structuring the Universe of Proteins," Ann. Rev. Genom. Hum. Genet., 3, 243 (2002).
7. Bystroff, C., and S. Garde, "Helix Propensities of Short Peptides: Molecular Dynamics Versus Bioinformatics," Proteins: Struct. Func. Gen., 50, 552 (2003).
8. Coen, C. J., H. W. Blanch, and J. M. Prausnitz, "Salting Out of Aqueous Proteins: Phase Equilibria and Intermolecular Potentials," AIChE J., 41, 996 (1995).
9. Cohn, E. J., and J. T. Edsall, Proteins, Amino Acids and Peptides as Ions and Dipolar Ions, Reinhold Publishing Corp., New York (1943).
10. Davies, D. R., and G. H. Cohen, "Interactions of Protein Antigens with Antibodies," Proc. Natl. Acad. Sci. USA, 93, 7 (1996).
11. Dill, K. A., S. Bromberg, K. Z. Yue, K. M. Fiebig, D. P. Yee, P. D. Thomas, and H. S. Chan, "Principles of Protein Folding-A Perspective from Simple Exact Models," Prot. Sci., 4, 561 (1995).
12. Duan, Y., and P. A. Kollman, "Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution," Science, 282, 740 (1998).
13. Elcock, A. H., and J. A. McCammon, "Calculation of Weak Protein-Protein Interactions: the pH Dependence of the Second Virial Coefficient," Biophys. J., 80, 613 (2001).
14. Elcock, A. H., D. Sept, and J. A. McCammon, "Computer Simulation of Protein-Protein Interactions," J. Phys. Chem. B, 105, 1504 (2001).
15. Foguel, D., C. R. Robinson, P. C. de Sousa, J. L. Silva, and A. S. Robinson, "Hydrostatic Pressure Rescues Native Protein from Aggregates," Biotechnol. Bioeng., 63, 552 (1999).
16. George, A., and W. W. Wilson, "Predicting Protein Crystallization from a Dilute Solution Property," Acta Cryst. D, 50, 361 (1994).
17. Ghadiri, M. R., J. R. Granja, and L. Buehler, "Artificial Transmembrane Ion Channels from Self-Assembling Peptide Nanotubes," Nature, 369, 301 (1994).
18. Grant, M. L., "Effects of Thermodynamic Nonideality in Protein Crystal Growth," J. Cryst. Growth, 209, 130 (2000).
19. Hloucha, M., J. F. M. Lodge, A. M. Lenhoff, and S. I. Sandler, "A Patch-Antipatch Representation of Specific Protein Interactions," J. Cryst. Growth, 232, 195 (2001).
20. Horton, N., and M. Lewis, "Calculation of the Free Energy of Association for Protein Complexes," Prot. Sci., 1, 169 (1992).
21. Hummer, G., S. Garde, A. E. García, M. E. Paulaitis, and L. R. Pratt, "The Pressure Dependence of Hydrophobic Interactions is Consistent with the Observed Pressure Denaturation of Proteins," Proc. Nat. Acad. Sci., 95, 1552 (1998).
22. Janin, J., "Welcome to CAPRI: A Critical Assessment of Predicted Interactions," Proteins Struct. Func. Gen., 47, 257 (2002).
23. Janin, J., and F. Rodier, "Protein-Protein Interactions at Crystal Contacts," Proteins Struct. Funct. Genet., 23, 580 (1995).
24. Klepeis, J. L., H. D. Schafroth, K. M. Westerberg, and C. A. Floudas, "Deterministic Global Optimization and ab initio Approaches for the Structure Prediction of Polypeptides, Dynamics of Protein Folding, and Protein-Protein Interactions," Adv. Chem. Phys., 120, 265 (2002).
25. Lattman, E. E., ed., Fourth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction, Proteins, 45, suppl. 5 (2001).
26. Lattman, E. E., and G. D. Rose, "Protein Folding-What's the Question," Proc. Natl. Acad. Sci., 90, 439 (1993).
27. Leckband, D., and J. Israelachvili, "Intermolecular Forces in Biology," Quart. Rev. Biophys., 34, 105 (2001).
28. Levinthal, C., in Mössbauer Spectroscopy in Biological Systems, P. Debrunner, J. C. M. Tsibris, and E. Münck, eds., University of Illinois Press, Urbana, IL (1969).
29. Lomakin, A., N. Asherie, and G. B. Benedek, "Aeolotopic Interactions of Globular Proteins," Proc. Natl. Acad. Sci. USA, 96, 9465 (1999).
30. Mann, S., Biomineralization: Principles and Concepts in Bioinorganic Materials Chemistry, Oxford University Press, Oxford (2001).
31. McMillan, W. G., and J. E. Mayer, "The Statistical Thermodynamics of Multicomponent Systems," J. Chem. Phys., 13, 276 (1945).
32. McNay, J. L. M., and E. J. Fernandez, "Protein Unfolding during Reversed-Phase Chromatography: I. Effect of Surface Properties and Duration of Adsorption," Biotechnol. Bioeng., 76, 224 (2001).
33. Nagayama, K., Protein Array: An Alternative Biomolecular System, Advances in Biophysics, Japan Scientific Societies Press, Tokyo (1996).
34. Neal, B. L., D. Asthagiri, and A. M. Lenhoff, "Molecular Origins of Osmotic Second Virial Coefficients of Proteins," Biophys. J., 75, 2469 (1998).
35. Ottino, J. M., "Complex Systems," AIChE J., 49, 292 (2003).
36. Paulaitis, M. E., and L. R. Pratt, "Hydration Theory for Molecular Biophysics," Adv. Protein Chemistry, 62, 283 (2002).
37. Pauling, L., and M. Delbrück, "The Nature of Intermolecular Forces Operative in Biological Processes," Science, 92, 77 (1940).
38. Rosenbaum, D. F., and C. F. Zukoski, "Protein Interactions and Crystallization," J. Cryst. Growth, 169, 752 (1996).
39. Roth, C. M., B. L. Neal, and A. M. Lenhoff, "Van der Waals Interactions Involving Proteins," Biophys. J., 70, 977 (1996).
40. Schonbrun, J., W. J. Wedemeyer, and D. Baker, "Protein Structure Prediction in 2002," Curr. Opin. Struct. Biol., 12, 348 (2002).
41. Sear, R. P., "Phase Behavior of a Simple Model of Globular Proteins," J. Chem. Phys., 111, 4800 (1999).
42. Sharp, K. A., and B. Honig, "Electrostatic Interactions in Macromolecules: Theory and Applications," Ann. Rev. Biophys. Biophys. Chem., 19, 301 (1990).
43. Smith, A. V., and C. K. Hall, "Protein Refolding Versus Aggregation: Computer Simulations on an Intermediate-Resolution Protein Model," J. Mol. Biol., 312, 187 (2001).
44. Stephanopoulos, G., "Metabolic Engineering: Perspective of a Chemical Engineer," AIChE J., 48, 920 (2002).
45. Sternberg, M. J. E., H. A. Gabb, and R. M. Jackson, "Predictive Docking of Protein-Protein and Protein-DNA Complexes," Curr. Opin. Struct. Biol., 8, 250 (1998).
46. Tessier, P. M., A. M. Lenhoff, and S. I. Sandler, "Rapid Measurement of Protein Osmotic Second Virial Coefficients by Self-Interaction Chromatography," Biophys. J., 82, 1620 (2002).
47. Tobler, S. A., N. E. Sherman, and E. J. Fernandez, "Tracking Lysozyme Unfolding during Salt-Induced Precipitation with Hydrogen Exchange and Mass Spectrometry," Biotechnol. Bio-eng., 71, 194 (2001).
48. Tsuji, S. Y., N. Wu, and C. Khosla, "Intermodular Communication in Polyketide Syntheses: Comparing the Role of Protein-Protein Interactions to Those in Other Multidomain Proteins," Biochemistry, 40, 2317 (2001).
49. Vilker, V. L., C. K. Colton, and K. A. Smith, "The Osmotic Pressure of Concentrated Protein Solutions: Effect of Concentration and pH in Saline Solutions of Bovine Serum Albumin," J. Coll. Interf. Sci., 79, 548 (1981).