Helix parameters and protein structure using quaternions

Journal of Molecular Structure: THEOCHEM

Volumn 460, Issue 1-3, 1999, Pages 53-66

  Quine, J R ^a  

^a FLORIDA STATE UNIVERSITY   (United States)

Author keywords

Coiled coil; Collagen; Helix parameters; Proteins; Helix

Indexed keywords

COLLAGEN; PROTEIN;

ARTICLE; GEOMETRY; MATHEMATICAL ANALYSIS; NUCLEAR MAGNETIC RESONANCE; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SOLID STATE;

EID: 0033604993     PISSN: 01661280     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0166-1280(98)00306-6     Document Type: Article

References (23)

1. D.J. Barlow, J.M. Thornton, Helix geometry in proteins, J. Mol. Biol. 201 (1988) 601-619.
2. R. Chandrasekaran, B.V. Venkataram Prasad, The conformation of polypeptides containing alternating L- and D-amino acids, CRC Critical Reviews in Biochemistry November (1978) 125-161.
3. M. Demura, M. Minami, T. Asakura, T.A. Cross, Structure of Bombyx mori silk fibroin based on solid state NMR orientational constraints and fiber diffraction unit cell parameters, J. Am. Chem. Soc. 120 (1998) 1300-1308.
4. R.E. Dickerson, I. Geis, The Structure and Action of Proteins, Harper & Row, New York, 1969.
5. A.M. Dress, T.H. Havel, Distance geometry and geometric algebra, Found. Phys. 23 (1993) 1357-1374.
6. R.A. Engh, R. Huber, Accurate bond and angle parameters for X-ray protein structure refinement, Acta Cryst. A47 (1991) 392-400.
7. M. Gerstein, A.M. Lesk, E.N. Baker, B. Anderson, G. Norris, C. Clothia, Domain closure in Lactoferrin: two hinges produce a see-saw motion between alternative close-packed helices, J. Mol. Biol. 234 (1900) 357-372.
8. T.F. Havel, I. Najfeld, Applications of geometric algebra to the theory of molecular conformation, part 1: the optimum alignment problem, J. Mol. Struct. 308 (1994) 241-262.
9. D. Hestenes, New Foundations for Classical Mechanics, Kluwer, Dordrecht, 1986.
10. J.C. Kendrew, et al., IUPAC-IUB Commission on Biochemical Nomenclature, J. Mol. Biol. 52 (1970) 1-17.
11. R.R. Ketchum, B. Roux, T.A. Cross, High-resolution polypeptide structure in a lamellar phase lipid environment from solid state NMR derived orientational constraints, Structure 5 (1997) 1655-1669.
12. R.R. Ketchum, W. Hu, T.A. Cross, High-resolution conformation for gramicidin A in a lipid bilayer by solid-state NMR, Science 261 (1993) 1457-1460.
13. F.A. Kovacs, T.A. Cross, Transmembrane 4-helix bundle of influenza A M2 protein channel: structural implications from helix tilt and orientation, Biophysical Journal 72 (1997) 2511-2517.
14. G. Nemethy, H.A. Scheraga, Theoretical determination of sterically allowed conformations of a polypeptide chain by a computer method, Biopolymers 3 (1965) 155-184.
15. C. Ramakrishnan, Stereochemical criteria for polypeptide and protein chain conformations, Proc. Indian Acad. Sci. A59 (1964) 327-342.
16. G.N. Ramachandran, R. Chandrasekaran, Studies on dipeptide conformation and of peptides with sequences of alternating L and D residues with special reference to antibiotic and ion transport peptides, in: S. Lande (Ed.), Progress in Peptide Research, vol. 2, Gordon & Breach, New York, 1972.
17. G.N. Ramachandran, V. Sasisekerharan, Conformation of polypeptides and proteins, in: Advances in Protein Chemistry, vol. 23, Academic Press, New York, 1968.
18. G.E. Schulz, R.H. Schirmer, Principles of Protein Structure, Springer, New York, 1979.
19. T. Shimanouchi, S. Mizushima, On the helical configuration of a polymer chain, Journal of Chemical Physics 23 (1955) 707-711.
20. Z. Song, Conformational Transitions and Molecular Order in Wet-Spun Oriented DNA, Division of Physical Chemistry, University of Stockholm, Sweden, 1996.
21. S. Sternberg, Group Theory and Physics, Cambridge University Press, 1994.
22. M. Yokouchi, H. Tadokoro, Y. Chatani, Conformational and packing stability of crystalline polymers. V. A method for calculating conformational parameters of polymer chains with glide, helical, and translational symmetries, Macromolecules 7 (1994) 769-776.
23. A. Yonath, W. Traub, Polymers of tripeptides as collagen models. IV. Structure analysis of poly(L-prolyl-glycyl-L-proline), J. Mol. Biol. 43 (1969) 461-477.