Protein Structure Introduction

Part of the Interdisciplinary Applied Mathematics book series (IAM, volume 21)


The term “protein” originates from the Greek word proteios, meaning “primary” or “of first rank”. The name was adapted by Jöns Berzelius in 1838 to emphasize the importance of this class of molecules.Indeed, proteins play crucial, life-sustaining biological roles, both as constituent molecules and as triggers of physiological processes for all living things. For example, proteins provide the architectural support in muscle tissues, ligaments, tendons, bones, skin, hair, organs, and glands. Their environment-tailored structures make possible the coordinated function (motion, regulation, etc.) in some of these assemblies.


Dihedral Angle Globular Protein Nonpolar Amino Acid Fibrous Protein Turn Region 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. 16.
    B. Al-Lazikani, J. Jung, Z. Xiang, and B. Honig. Protein structure prediction. Curr.Opin. Struct. Biol., 5:51–56, 2001.CrossRefGoogle Scholar
  2. 51.
    C. B. Anfinsen, E. Haber, M. Sela, and F. H. White, Jr. The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. Proc. Natl. cad. Sci. USA, 47:1309–1314, 1961.CrossRefGoogle Scholar
  3. 68.
    J. F. Atkins and R. Gesteland. The 22nd amino acid. Science, 296:1409–1410, 2002.CrossRefGoogle Scholar
  4. 79.
    D. Baker and A. Sali. Protein structure prediction and structural genomics. Science, 294:93–96, 2001.CrossRefGoogle Scholar
  5. 173.
    J. E. Brody.What to serve for dinner, when dinner is onMars. The New York Times, pages F1–2, 19 May 1998.Google Scholar
  6. 197.
    C. R. Cantor and P. R. Schimmel. Biophysical Chemistry, volume 1–3. W. H. reeman and Company, San Francisco, 1980.Google Scholar
  7. 205.
    L. Castagnoli, M. Scarpa, M. Kokkinidis, D.W. Banner, D. Tsernoglou, and G. Cesareni. Genetic and structural analysis of the CoIE1 Rop (Rom) protein. mbo. J., 8:621–629, 1989.Google Scholar
  8. 319.
    A. R. Dinner, R. Lazaridis, and M. Karplus. Understanding β-hairpin formation. roc. Natl. Acad. Sci. USA, 96:9068–9073, 1999.CrossRefGoogle Scholar
  9. 348.
    D. J. Earl and M. W. Deem. Monte Carlo simulations. Methods Mol. Biol., 443:25–36, 2008.Google Scholar
  10. 374.
    V. A. Eyrich, D. M. Standley, and R. A. Friesner. Prediction of protein tertiary structure to low resolution: Performance for a large and structurally diverse test set. J. Mol. Biol., 14:725–742, 1999.CrossRefGoogle Scholar
  11. 384.
    S. E. Feller, Y. Zhang, R. W. Pastor, and B. R. Brooks. Constant pressure molec- ular dynamics simulation: The Langevin piston method. J. Chem. Phys., 103: 4613–4621, 1995.CrossRefGoogle Scholar
  12. 394.
    A. M. Ferrenberg, D. P. Landau, and Y. J.Wong. Monte Carlo simulations: Hidden errors from “good” random number generators. Phys. Rev. Lett., 69:3382–3384, 1992.CrossRefGoogle Scholar
  13. 462.
    P. M. W. Gill. A new expansion of the Coulomb interaction. Chem. Phys. Lett., 270:193–195, 1997.CrossRefGoogle Scholar
  14. 511.
    U. H. E. Hansmann and Y. Okamoto. New Monte Carlo algorithms for protein folding. Curr. Opin. Struct. Biol., 9:177–183, 1999.CrossRefGoogle Scholar
  15. 615.
    V. F. R. Jones. Knot theory and statistical mechanics. Sci. Amer., 263:98–103, 1990.MathSciNetCrossRefGoogle Scholar
  16. 664.
    R. D. Knight and L. F. Landweber. The early evolution of the genetic code. Cell, 101:569–572, 2000.CrossRefGoogle Scholar
  17. 680.
    K. M. Kosikov, A. A. Gorin, V. B. Zhurkin, and W. K. Olson. DNA stretching and compression: Large-scale simulations of double helical structures. J. Mol. Biol., 289:1301–1326, 1999.CrossRefGoogle Scholar
  18. 788.
    X. Lu, M. D. Simon, J. V. Chodaparambil, J. C. Hansen, K. M. Shokat, and K. Luger. The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure. Nat. Struct. Mol. Biol., 15:1122–1124, 2008.CrossRefGoogle Scholar
  19. 799.
    B. Ma, J.-H. Lii, K. Chen, and N. L. Allinger. A molecular mechanics study of the cholesteryl acetate crystal: Evaluation of interconversion among rg, rz, and bond lengths. J. Amer. Chem. Soc., 119:2570–2573, 1997.CrossRefGoogle Scholar
  20. 820.
    S. Makino, T. J. A. Ewing, and I. D. Kuntz. DREAM++: Flexible docking program for virtual combinatorial libraries. J. Comput.-Aided Mol. Design, 13:513–532, 1999.CrossRefGoogle Scholar
  21. 959.
    E. Paci and M. Karplus. Unfolding proteins by external forces and tempera- ture: The importance of topology and energetics. Proc. Natl. Acad. Sci. USA, 97:6521–6526, 2000.CrossRefGoogle Scholar
  22. 979.
    L. Pauling and R. B. Corey. A proposed structure for nucleic acids. Proc. Natl. cad. Sci. USA, 39:84–97, 1953.CrossRefGoogle Scholar
  23. 1018.
    M. Prabhakaran, S. C. Harvey, B.Mao, and J. A. McCammon. Molecular dynamics of phenylanlanine transfer RNA. J. Biomol. Struct. Dynam., 1:357–369, 1983.CrossRefGoogle Scholar
  24. 1091.
    R. S´anchez and A. ˇSali. Advances in comparative protein-structure modelling. urr. Opin. Struct. Biol., 7:206–214, 1997.Google Scholar
  25. 1098.
    J. M. Schafer, E.-S. Lee, R. C. Dardes, D. Bentrem, R. M. O’Regan, A. De Los Reyes, and V. C. Jordan. Analysis of cross-resistance of the selective estrogen re- ceptor modulators arzoxifene (LY353381) and LY117018 in tamoxifen-stimulated breast cancer xenografts. Clin. Cancer Res., 7:2505–2512, 2001.Google Scholar
  26. 1120.
    T. Schlick. Mathematical and biological scientists assess the state-of-the-art in RNA science at an IMA workshop “RNA in Biology, Bioengineering and Biotech- nology”. Intl. J. Mult. Sci. Eng., 2009. In Press; Also available as IMA report Tamar/RNAReport.pdf.Google Scholar
  27. 1254.
    R. K.-Z. Tan and S. C. Harvey. Molecular mechanics model of supercoiled DNA. . Mol. Biol., 205:573–591, 1989.Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.Courant Institute of Mathematical Sciences and Department of ChemistryNew York UniversityNew YorkUSA

Personalised recommendations