Macromolecular Forces

Part of the Biological and Medical Physics, Biomedical Engineering book series (BIOMEDICAL)


Salt Bridge Atomic Radius Electron Cloud Protein Interface Bond Axis 
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General Reference

  1. Brandon C, and Tooze J [1999]. Introduction to Protein Structure, 2nd edition. New York: Garland Science Publishing.Google Scholar

References and Further Reading Physical and Electrostatic Properties of Amino Acids and Proteins

  1. Bolen DW, and Baskakov IV [2001]. The osmophobic effect: Natural selection of a thermodynamic force in protein folding. J. Mol. Biol., 310: 955–963.CrossRefGoogle Scholar
  2. Dill KA [1990]. Dominant forces in protein folding. Biochem., 29: 7133–7155.CrossRefGoogle Scholar
  3. Myers JK, and Pace CN [1996]. Hydrogen bonding stabilizes globular proteins. Biophys. J., 71: 2033–2039.CrossRefADSGoogle Scholar
  4. Pace CN, et al. [1996]. Forces contributing to the conformational stability of proteins. FASEB J., 10: 75–83.Google Scholar
  5. Sheinerman FB, and Honig B [2002]. On the role of electrostatic interactions in the design of protein-protein interfaces. J. Mol. Biol., 318: 161–177.CrossRefGoogle Scholar
  6. Tsai J, et al. [1999]. The packing density in proteins: Standard radii and volumes. J. Mol. Biol., 290: 253–266.CrossRefGoogle Scholar

Complementarity and Interfaces

  1. Glaser F, et al. [2001]. Residue frequencies and pairing preferences at proteinprotein interfaces. Proteins, 43: 89–102.CrossRefGoogle Scholar
  2. Lo Conte L, Chothia C, and Janin J [1999]. The atomic structure of protein-protein recognition sites. J. Mol. Biol., 285: 2177–2198.CrossRefGoogle Scholar
  3. Jones S, and Thornton JM [1996]. Principles of protein-protein interactions. Proc. Natl. Acad. Sci. USA, 93: 13–20.CrossRefADSGoogle Scholar
  4. Jones S, et al. [1999]. Protein-DNA interactions: A structural analysis. J. Mol. Biol., 287: 877–896.CrossRefGoogle Scholar
  5. Nadassy K, Wodak SJ, and Janin J [1999]. Structural features of protein-nucleic acid recognition sites. Biochem., 38: 1999–2017.CrossRefGoogle Scholar
  6. Norel R, et al. [1999]. Examination of shape complementarity in docking of unbound proteins. Proteins, 36: 307–317.CrossRefGoogle Scholar
  7. Sheinerman FB, Norel R, and Honig B [2000]. Electrostatic aspects of proteinprotein interactions. Curr. Opin. Struct. Biol., 10: 153–159.CrossRefGoogle Scholar

Hot Spots

  1. Bogan AA, and Thorn KS [1998]. Anatomy of hot spots in protein interfaces. J. Mol. Biol., 280: 1–9.CrossRefGoogle Scholar
  2. Hu ZJ, et al. [2000]. Conservation of polar residues as hot spots at protein interfaces. Proteins, 39: 331–342.CrossRefGoogle Scholar

Theoretical Methods: Computer Modeling and Simulation

  1. Cornell WD, et al. [1995]. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc., 117: 5179–5197.CrossRefGoogle Scholar
  2. Elcock AH, Sept D, and McCammon JA [2001]. Computer simulation of proteinprotein interactions. J. Phys. Chem. B, 105: 1504–1518.CrossRefGoogle Scholar
  3. Honig B, and Nicholls A [1995]. Classical electrostatics in biology and chemistry. Science, 268: 1144–1149.ADSCrossRefGoogle Scholar
  4. Kollman PA, et al. [2000]. Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Acc. Chem. Res., 33: 889–897.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2005

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