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Building Protein Folds Using Distance Geometry: Towards a General Modeling and Prediction Method

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The Protein Folding Problem and Tertiary Structure Prediction

Abstract

A known protein structure can be modified and manipulated to produce a model for another protein with which it shares some sequence similarity. Typical changes involve the substitution and reorientation of side chains and the remodeling of the main chain to accommodate possible insertions and deletions of sequences. Where the two sequences are clearly related (say, more than 50%), such changes are relatively minor and a model can easily be constructed automatically.

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References

  • Aszódi A, Taylor WR (1994): Secondary structure formation in model polypeptide chains. Prot Engng (Submitted)

    Google Scholar 

  • Braun W, Gō N (1985): Calculation of protein conformations by proton-proton distance constraints—a new efficient algorithm. J Mol Biol 186:611–626

    Article  PubMed  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Chan HS, Dill KA (1990): Origins of structure in globular proteins. Proc NatlAcad Sci USA 87:6388–6392

    Article  CAS  Google Scholar 

  • Cohen FE, Richmond TJ, Richards FM (1979): Protein folding: Evaluation of some simple rules for the assembly of helices into tertiary structures with myoglobin as as example. J Mol Biol 132

    Google Scholar 

  • Cohen F, Steinberg M (1980): On the use of chemically derived distance constraints in the prediction of protein structure with myoglobin as an example. J Molec Biol 137:9–22

    Article  PubMed  CAS  Google Scholar 

  • Cohen FE, Sternberg MJE, Taylor WR (1980): Analysis and prediction of protein β-sheet structures by a combinatorial approach. Nature 285:378–382

    Article  PubMed  CAS  Google Scholar 

  • Cohen FE, Steinberg MJE, Taylor WR (1981): Analysis of the tertiary structure of protein β-sheet sandwiches. J Mol Biol 148:253–272

    Article  PubMed  CAS  Google Scholar 

  • Creighton TE (1983): Proteins: Structures and Molecular Properties. New York: Freeman

    Google Scholar 

  • Crippen GM, Havel TF (1988): Distance Geometry and Molecular Conformation. Chemometrics Research Studies Press

    Google Scholar 

  • Dayhoff MO, Schwartz RM, Orcutt BC (1978): A model of evolutionary change in proteins. In Atlas of Protein Sequence and Structure. Dayhoff MO, ed. Washington, DC: Nat Biomed Res Foundation, Vol. 5, Suppl. 3, pp. 345–352

    Google Scholar 

  • Desmet J, Demaeyer 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 

  • Dill KA, Fiebig KM, Chan HS (1993): Cooperativity in protein-folding kinetics. Proc Natl Acad Sci USA 90:1942–1946

    Article  PubMed  CAS  Google Scholar 

  • Easthope PL, Havel TF (1989): Computational experience with an algorithm for tetrangle inequality bound smoothing. Bull Math Biol 51:173–194

    PubMed  CAS  Google Scholar 

  • Flory PJ (1969): Statistical Mechanics of Chain Molecules. New York: Wiley-Interscience

    Google Scholar 

  • Gregoret LM, Cohen FE (1991): Protein folding: Effect of packing density on chain conformation. J Mol Biol 219:109–122

    Article  PubMed  CAS  Google Scholar 

  • Havel TM, Crippen GM, Kuntz ID (1979): Effects of distance constraints on macromolecular conformation. II. Simulation of experimental results and theoretical predictions. Biopolymers 18:73–81

    Article  CAS  Google Scholar 

  • Jones DT, Orengo CA, Taylor WR, Thornton JM (1993): A new approach to protein fold recognition. Nature 358:86–89

    Article  Google Scholar 

  • Kuntz ID, Crippen GM, Kollman PA, Kimelman D (1976): Calculation of protein tertiary structure. J Mol Biol 106:983–994

    Article  PubMed  CAS  Google Scholar 

  • Kuntz ID, Thomason JF, Oshiro CM (1989): Distance geometry. Meth Enzymology 177:159–204

    Article  CAS  Google Scholar 

  • Levitt M (1978): Conformational preferences of amino acids in globular proteins. Biochemistry 17:4277–4285

    Article  PubMed  CAS  Google Scholar 

  • MacKay AL (1983): The numerical geometry of biological structures. In Computing in Biological Science. Geisow MJ, Barrett AN, eds. Amsterdam: Elsevier Biomedical, pp 349–392

    Google Scholar 

  • Murzin AG, Finkelstein AV (1988): General architecture of the α-helical globule. J Mol Biol 204:749–769

    Article  PubMed  CAS  Google Scholar 

  • Pearl LH, Taylor WR (1987): A structural model for the retroviral proteases. Nature 329:351–354

    Article  PubMed  CAS  Google Scholar 

  • Press WH, Flannery BP, Teukolsky SA, Vetterling WT (1986): Numerical Recipes: The Art of Scientific Computing. Cambridge: Cambridge University Press

    Google Scholar 

  • Richards FM (1974): The interpretation of protein structures: Total volume, group volume distributions and packing density. J Mol Biol 82:1–14

    Article  PubMed  CAS  Google Scholar 

  • Saitoh S, Nakai T, Nishikawa K (1993): A geometrical constraint approach for reproducing the native backbone conformation of a protein. Proteins 15:191–204

    Article  PubMed  CAS  Google Scholar 

  • Sippl MJ (1990): Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 213:859–883

    Article  PubMed  CAS  Google Scholar 

  • Skolnick J, Kolinsky A (1990): Simulations of the folding of a globular protein. Science 250:1121–1125

    Article  PubMed  CAS  Google Scholar 

  • Skolnick J, Kolinski A (1991): Dynamic Monte-Carlo simulations of a new lattice model of globular protein folding, structure and dynamics. J Mol Biol 221:499–531

    Article  PubMed  CAS  Google Scholar 

  • Taylor WR (1991a): Sequence analysis: Spinning in hyperspace. Nature 353:388–389 (News and Views)

    Article  Google Scholar 

  • Taylor WR (1991b): Towards protein tertiary fold prediction using distance and motif constraints. Prot Engng 4:853–870

    Article  CAS  Google Scholar 

  • Taylor WR (1993): Protein fold refinement: Building models from idealised folds using motif constraints and multiple sequence data. Prot Engng 6

    Google Scholar 

  • Taylor WR, Jones DT, Green NM (1994): A method for α-helical integral membrane protein fold prediction. Prot Struct Funct Genet (In press)

    Google Scholar 

  • Taylor WR, Jones DT, Segal AW (1993): A structural model for the nucleotide binding domain of the cytochrome b -245 β-chain. Protein Science

    Google Scholar 

  • Taylor WR, Orengo CA (1989): Protein structure alignment. J Molec Biol 208:1–22

    Article  PubMed  CAS  Google Scholar 

  • Taylor WR, Thornton JM, Turnell WG (1983): A elipsoidal approximation of protein shape. J Mol Graphics 1:30–38

    Article  CAS  Google Scholar 

  • Teller DC (1976): Accessible area, packing volumes and interaction surfaces of globular proteins. Nature 260:729–731

    Article  PubMed  CAS  Google Scholar 

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Authors
  1. William R. Taylor
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  2. András Aszódi
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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  & 

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© 1994 Birkhäuser Boston

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Taylor, W.R., Aszódi, A. (1994). Building Protein Folds Using Distance Geometry: Towards a General Modeling and Prediction Method. 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_6

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  • DOI: https://doi.org/10.1007/978-1-4684-6831-1_6

  • Publisher Name: Birkhäuser Boston

  • Print ISBN: 978-1-4684-6833-5

  • Online ISBN: 978-1-4684-6831-1

  • eBook Packages: Springer Book Archive

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