Skip to main content
SpringerLink
Log in

The “Dead-End Elimination” Theorem: A New Approach to the Side-Chain Packing Problem

  • Chapter
The Protein Folding Problem and Tertiary Structure Prediction

Abstract

The prediction of a protein’s tertiary structure is still computationally infeasible, mainly because of the huge number of a priori possible global conformations. The prediction of side-chain conformations that are attached to a given, fixed main-chain structure is considered as a less complex but still important subproblem with applications to, for instance, homology modeling (Lee and Subbiah, 1991). Nevertheless, the determination of the global minimum energy conformation (GMEC) of a set of protein side chains was up to now still limited to small, densely packed units (Ponder and Richards, 1987; Lee and Levitt, 1991).

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Artymiuk PJ, Blake CCF (1981): Refinement of human lysozyme at 1.5 Å resolution. Analysis of non-bonded and hydrogen-bond interactions. J Mol Biol 152:737–762

    Article  PubMed  CAS  Google Scholar 

  • Benedetti E, Morelli G, Némethy G, Scheraga HA (1983): Statistical and energetic analysis of side-chain conformations in Oligopeptides. Int J Peptide Protein Res 22:1–15

    Article  CAS  Google Scholar 

  • Bernstein FC, Koetzle TF, Williams GJB, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M (1977): The Protein Data Bank: A computerbased archival file for macromolecular structures. J Mol Biol 112:535–542

    Article  PubMed  CAS  Google Scholar 

  • Bhat TN, Sasisekharan V, Vijayan M (1979): An analysis of side-chain conformation in proteins. Int J Pept Protein Res 13:170–184

    Article  PubMed  CAS  Google Scholar 

  • Blow D (1983): Molecular structure. Computer cues to combat hypertension. Nature 304:213–214

    Article  PubMed  CAS  Google Scholar 

  • Blundell TL, Sibanda BL, Stemberg MJ, Thornton JM (1987): Knowledge-based prediction of protein structures and the design of novel molecules. Nature 326:347–352

    Article  PubMed  CAS  Google Scholar 

  • Bowie JU, Reidhaar-Olson JF, Lim WA, Sauer RT (1990): Deciphering the message in protein sequences: Tolerance to amino acid substitutions. Science 247:1306–1310

    Article  PubMed  CAS  Google Scholar 

  • Brooks BR, Bruccoleri R, Olafson D, States DJ, Swaminathan S, Karplus M (1983): CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187–217

    Article  CAS  Google Scholar 

  • Claessens M, Van Cutsem E, Lasters I, Wodak S (1989): Modelling the Polypeptide backbone with “spare parts” from known protein structures. Prot Eng 2:335–345

    Article  CAS  Google Scholar 

  • Desmet J, De Maeyer M, Hazes B, Lasters I (1992): The dead-end elimination theorem and its use in protein side-chain positioning. Nature 356:539–542

    Article  PubMed  CAS  Google Scholar 

  • Delhaise P, Bardiaux M, Wodak S (1984): Interactive computer animation of macromolecules. J Mol Graph 2:103–106

    Article  CAS  Google Scholar 

  • Dill KA (1987): Commentaries. Protein surgery. Prot Eng 1:369–372

    Article  CAS  Google Scholar 

  • Greer J (1981): Comparative model-building of the mammalian serine proteases. J Mol Biol 153:1027–1042

    Article  PubMed  CAS  Google Scholar 

  • Holm L, Sander C (1991): Database algorithm for generating protein backbone and side-chain coordinates from a C(alpha) trace. Application to model building and detection of coordinate errors. J Mol Biol 193:775–791

    Google Scholar 

  • IUPAC Commission on Macromolecular Nomenclature (1979): Pure Appl Chem 51:1101–1121

    Article  Google Scholar 

  • James MNG, Sielecki AR (1983): Structure and refinement of penicillopepsin at 1.8 Å resolution. J Mol Biol 163:299–361

    Article  PubMed  CAS  Google Scholar 

  • Janin J, Wodak S, Levitt M, Maigret B (1978): Conformation of amino acid sidechains in proteins. J Mol Biol 125:357–386

    Article  PubMed  CAS  Google Scholar 

  • Kabsch W, Sander C (1983): Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577–2637

    Article  PubMed  CAS  Google Scholar 

  • Lasters I, Desmet J (1993): The fuzzy-end elimination theorem: Correctly implementing the side chain placement algorithm based on the dead-end elimination theorem. Prot Eng 6:717–722

    Article  CAS  Google Scholar 

  • Lee C, Levitt M (1991): Accurate prediction of the stability and activity effects of side-directed mutagenesis on a protein core. Nature 352:448–451

    Article  PubMed  CAS  Google Scholar 

  • Lee C, Subbiah S (1991): Prediction of protein side-chain conformation by packing optimization. J Mol Biol 217:373–388

    Article  PubMed  CAS  Google Scholar 

  • Lesk AM, Chothia C (1980): How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins. J Mol Biol 136:225–270

    Article  PubMed  CAS  Google Scholar 

  • Lesk AM, Chothia C (1982): Evolution of proteins formed by beta-sheets. II. The core of the immunoglobulin domains. J Mol Biol 160:325–342

    Article  PubMed  CAS  Google Scholar 

  • Lesk AM, Chothia C (1986): Phil Trans R Soc London, Ser A, 317:345–356

    Article  CAS  Google Scholar 

  • Levinthal C (1968): Are there pathways for protein folding? J Chem Phys 65:44–45

    Google Scholar 

  • McGregor MJ, Islam SA, Sternberg MJE (1987): Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. J Mol Biol 198:295–310

    Article  PubMed  CAS  Google Scholar 

  • Miller S, Janin J, Lesk A, Chothia C (1987): Interior and surface of monomeric proteins J Mol Biol 196:641–656

    Article  PubMed  CAS  Google Scholar 

  • Moult J, James MNG (1986): An algorithm for determining the conformation of Polypeptide segments in proteins by systematic search. Proteins 1:146–163

    Article  PubMed  CAS  Google Scholar 

  • Ponder JW, Richards FM (1987): Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol 193:775–791

    Article  PubMed  CAS  Google Scholar 

  • Privalov PL (1989): Thermodynamic problems of protein structure. Annu Rev Biophys Chem 18:47–69

    Article  CAS  Google Scholar 

  • Ramanadham M, Sieker LC, Jensen LH (1989): Triclinic Lysozyme: Some Features of the Structure at 2 Angstroms Resolution, Smith-Gill S, Sercarz E, eds. Schenectady, NY: Adenine Press

    Google Scholar 

  • Reid L, Thornton JM (1989): Rebuilding flavodoxin from C coordinates: A test study. Proteins 5:170–182

    Article  PubMed  CAS  Google Scholar 

  • Reidhaar-Olson JF, Sauer RT (1990): Functionally acceptable substitutions in two alpha-helical regions of lambda repressor. Proteins 7:306–316

    Article  PubMed  CAS  Google Scholar 

  • Schellman JA, Lindorfer M, Hawkes R, Grutter M (1981): Mutations and protein stability. Biopolymers 20:1989–1999

    Article  PubMed  CAS  Google Scholar 

  • Shortle D, Meeker AK, Freire E (1988): Stability mutants of staphylococcal nuclease: Large compensating enthalpy-entropy changes for the reversible denaturation reaction. Biochemistry 27:4761–4768

    Article  PubMed  CAS  Google Scholar 

  • Summers NL, Carlson WD, Karplus M (1987): Analysis of side-chain orientations in homologous proteins. J Mol Biol 196:175–198

    Article  PubMed  CAS  Google Scholar 

  • Summers NL, Karplus M (1989): Construction of side-chains in homology modelling. Application to the C-terminal lobe of rhizopuspepsin. J Mol Biol 210:785–811

    Article  PubMed  CAS  Google Scholar 

  • Sutcliffe MJ, Hayes FRF, Blundell TL (1987): Knowledge based modelling of homologous proteins, part II: Rules for the conformations of substituted sidechains. Prot Eng 1:385–392

    Article  CAS  Google Scholar 

  • Taylor W (1992): Protein structure. New paths from dead ends. Nature 356:478–480

    Article  Google Scholar 

  • Tuffery P, Etchebest C, Hazout S, Lavery R (1991): A new approach to the rapid determination of protein side chain conformations. J Biomol Struct Dyn 8:1267–1289

    PubMed  CAS  Google Scholar 

  • Warshel A, Levitt M (1976): Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol 103:227–249

    Article  PubMed  CAS  Google Scholar 

  • Wodak SJ, De Coen JL, Edelstein SJ, Demarne H, Beuzard Y (1986): Modification of human hemoglobin by glutathione. III. Perturbations of hemoglobin conformation analyzed by computer modeling. J Biol Chem 261:14717–14724

    PubMed  CAS  Google Scholar 

Download references

Authors
  1. Johan Desmet
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Marc De Maeyer
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ignace Lasters
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Chemistry, The Pennsylvania State University, 152 Davey Laboratory, University Park, PA, 16802-6300, USA

    Kenneth M. Merz Jr.  & Scott M. Le Grand  & 

Rights and permissions

Reprints and permissions

Copyright information

© 1994 Birkhäuser Boston

About this chapter

Cite this chapter

Desmet, J., De Maeyer, M., Lasters, I. (1994). The “Dead-End Elimination” Theorem: A New Approach to the Side-Chain Packing Problem. In: Merz, K.M., Le Grand, S.M. (eds) The Protein Folding Problem and Tertiary Structure Prediction. Birkhäuser Boston. https://doi.org/10.1007/978-1-4684-6831-1_10

Download citation

  • DOI: https://doi.org/10.1007/978-1-4684-6831-1_10

  • Publisher Name: Birkhäuser Boston

  • Print ISBN: 978-1-4684-6833-5

  • Online ISBN: 978-1-4684-6831-1

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation