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5.0 References

Selected Reading

* Baker, E. N. & Hubbard, R. E. 1984. Hydrogen Bonding in Globular Proteins. Prog. Biophys. Molec. Biol. 44, 97-179.

* Branden, C. &Tooze, J. (1991) "Introduction to Protein Structure" Garland Publishing, Inc. New York.

* Cantor, C. R. & Schimmel, P. R. 1980. Biophysical Chemistry, Parts I-III, NewYork, W. H. Freeman and Co.

* Creighton, T. E. 1992 ProteinFolding, W. H. Freeman, New York.

* Creighton, T. E. 1993 Proteins: Structures and Molecular Properties, Second ed. W. H. Freeman, New York.

* Kabsch, W. & Sander, C. 1983. Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features. Biopolymers 22, 2577-2637.

* Linderstrøm-Lang, K. U. & Schellman, J. A. (1959) Protein Structure and Enzyme Activity in "The Enzymes" Vol 1 Second Ed. 443-510 Boyer, Lardy, Myrbäk Eds. Academic Press, New York.

* Ramachandron G. N. & Sasisekharan, V. (1968) Conformation of Polypeptides and Proteins. Adv. Prot Chem. vol 23, 283-437.

* Richardson, J. S. The Anatomy and Taxonomy of Protein Structure. (1981) Adv. Protein Chem. 34, 167-339.

* Schulz, G. E. and Schirmer, R. H. 1979. Principles of Protein Structure New York, Springer Verlag.

* Wüthrich, K. (1986). NMR of Proteins and Nucleic Acids. Wiley, New York.

Cited References

Armstrong, K. M., Fairman, R. & Baldwin, R. L. The (i,i+4) Phe-His Interaction Studied in an Alanine-based alpha-helix J. Mol. Biol. 230, 284-291 (1993).

Åslund, F., Nordstrand, K., Berndt, K. D., Nikkola, M., Bergman, T., Ponstingl, H., Jörnvall, H, Otting, G., & Holmgren, A. Glutaredoxin-3 from Escherichia coli: Amino Acid Sequence, 1H and 15N NMR Assignments, and Structural Analysis Journal of Biological Chemistry, 271, 6736-6745 (1996).

Barlow, D. J. & Thornton, J. M. Helix Geometry in Proteins. J. Mol. Biol. 201, 601-619.

Berndt, K. D., Güntert, P., Orbons, L. P. M. & Wüthrich, K. Determination of a high-quality NMR solution structure of the bovine pancreatic trypsin inhibitor (BPTI) and comparison with three crystal structures. J. Mol. Biol. 227, 757-775 (1992).

Berndt, K. D., Güntert, P., & Wüthrich, K. "The NMR Structure of the Dendrotoxin K from the Venom of Dedroaspis polylepis polylepis in Solution" J. Mol. Biol., 234, 735-750 (1993).

Brag, W. L., Kendrew, J. C., & Perutz, M. F. Proc. Roy. Soc. A203, 321 (1950).

Brahms, S. & Brahms, J. Determination of Protein Secondary Structure i Solution by Vacuum Ultraviolet Circular Dichroism J. Mol. Biol. 138, 149-178 (1980).

Byler, M. & Susi, H. Biopolymers 25, 469-487 (1986).

Carson, M. J.Appl.Cryst., 24, 958-961 (1991)

DeGrado, W. F. Design of Peptides and Proteins. Adv. Prot. Chem. v. 39, 51-124, 1988.

Dyson, H. J., Rance, M., Houghton, R. A., Lerner, R. A., & Wright, P. E. Folding of Immunogenic Peptide Fragments in Water Solution: I. Sequence Requirements for the Formation of a Reverse Turn. J. Mol. Biol. 201, 161-200 (1988).

Dyson, H. J., Rance, M., Houghton, R. A., Lerner, R. A., & Wright, P. E. Folding of Immunogenic Peptide Fragments in Water Solution: II. The Nacent Helix. J. Mol. Biol. 201, 201-217, (1988).

Eisenberg, D. Weiss, R. M. & Terwilliger, T. C. The Helical Hydrophobic Moment: a Measure of the Amphiphilicity of a Helix. Nature 299, 371-374 (1982).

Ferrin, T.E., Haung, C. C., Jarvis, E., & Langridge, R. The MIDAS display system J. Mol. Graphics, 6, 13-27 (1988).

Finer-Moore & Stroud, R. M. Amphipathic Analysis and Possible Formation of the Ion Channel in an Acetocholine Receptor. Proc. Natl. Acad. Sci. USA 81, 155-159 (1984).

Hol, W. G. J., Van Duijnen, P. Th., & Berendsen, H. J. C. The Alpha-helix Dipole and the Properties of Proteins. Nature 273, 443-446 (1978)

IUPAC-IUB Commission on Biochemical Nomenclature 1970. Abbreviationa and Symbols for the Description of the Conformation of Polypeptide Chains. Biochemistry 9, 3471, published simultaneously in J. Mol. Biol. 52, 1 1970.

Johnson, W. C. Jr. Secondary Structure of Proteins Through Circular Dichroism Spectroscopy. Ann. Rev. Biophys. Biophys. Chem. 17, 145-166 (1988).

Johnson, W. C. jr. Protein Secondary Structure and Circular Dichroism: A Practical Guide. Proteins 7, 205-214 (1990).

Johnson, W. C. Jr. Analysis of Circular Dichroism Spectra. Methods Enzymol 210, 426-447 (1992).

Kauzmann, W. 1959. Some Factors in the Interpretation of Protein Denaturation. Adv. Protein Chem. 14, 1.

Kaiser, E. T. & Kezdy, F. J. Amphiphilic Secondary Structure: Design of Peptide Hormones. Science 223, 249-255.

Kendrew, J. C. et al., A three-dimensional Model of the Myoglobin Molecule Obtained by X-ray Analysis. Nature 181, 662-666 (1958).

Kraulis, P. J. (1991) J. Appl. Cryst. 24, 946-950.

Leszczynski, J. F. & Rose, G. D. Loops in Globular Proteins: a Novel Category of Secondary Structure. Science 234, 849-855.

Levitt, M., (1976), A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol. 104, 59-107.

Linderstrøm-Lang, K. U. The Lane Medical Lectures. Stanford University Press, Stanford, California. (1952).

Linderstrom-Lang, K.U. and Shellman, J.A., Protein structure and enzyme activity. The Enzymes, (P.D. Boyer, Ed.), Vol 1, 2nd ed., pp. 443-510. Academic Press, New York. (1959).

Manalavan, P. & Johnson, W. C. jr. Variable Selection Method Improves Prediction of Protein Secondary Structure from Circular Dichroism Apectra. Anal. Biochem. 167, 76-85.

Manning, M. C. Underlying Assumptions in the Estimation of Secondary Structure Content in Proteins by Circular Dichroism Spectroscopy. J. Pharm. Biomed. Anal. 7, 1103-1119 (1989).

Marquesee, S. & Baldwin, R. L. Helix Stabilization by Glu- ... Lys+ Salt Bridges in Short Peptides of de novo Design. Proc. Natl. Acad. Sci. USA 84 8898-8902 (1987).

Milner-White, E. J. Recurring Loop Motif in Proteins That Occurs in Right-handed and Left-handed Forms: Its Relationship with Alpha-helices and Beta-bulge loops. J. Mol. Biol. 199, 503-511, 1988.

Nordstrand, K. , Ponstingl, H., Holmgren, A., & Otting, G. Resonance Assignment and Structural Analysis of Acid Denatured E. coli [U-N-15]-Glutaredoxin 3 - Use of 3D N-15-HSQC-(TOCSY-NOESY)-N-15-HSQC European Biophysics Journal. 24, 179-184, (1996)

Orengo, C. A., Jones, D. T. & Thornton, J. M. Protein Superfamilies and Domain Superfolds. Nature 372, 631-634 (1994).

Palau, J. and Puigdoménech, P. The Structural Code for Proteins: Zonal Distribution of Amino Acid Residues and Stabilization of Helices by Hydrophobic Triplets. J. Mol. Biol. 88, 457-469 (1974).

Pauling, L., Corey, R. B., & Branson, H. R. Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain. Proc. Natl. Acad. Sci. U.S. 37, 205-211 (1951).

Pauling, L., Corey, R.B., Configurations of polypeptide chains with favored orientations around single bonds: Two new pleated sheets. Proc. Nat. Acad. Sci. USA 37, 729-740 (1951).

Provencher, S. W. & Glöckner, J. Estimation of Globular Protein Secondary Structure from Circular Dichroism Biochemistry 20, 33-37 (1981).

Richards, F. M. Linderstrøm-Lang and the Carlsberg Laboratory: The View of a Postdoctoral Fellow in 1954. Protein Science 1, 1721-1730 (1992).

Richardson, J. S. The Anatomy and Taxonomy of Protein Structure Adv. Prot. Chem. 34, 167-339 (1981)

Rose, G. D., Gierasch, L. M. & Smith, J. A. Turns in Peptides and Proteins Adv. Prot. Chem. 37, 1-109 (1985).

Rost, B. & Sander, C. Combining Evolutionary Information and Neural Networks to Predict Protein Secondary Structure. Proteins 19, 55-72, (1994).

Schiffer, M. & Edmundson, A. B. Use of helical Wheels to Represent the Structures of Proteins and to Identify Segments with Helical Potential. Biophysical J. 7, 121-135 (1967).

Sreerama, N. & Woody, R. W. Protein Secondary Structure from Circular Dichroism Spectroscopy: Combining Variable Selection Principle and Cluster Analysis with Neural Network, Ridge Regression and Self-consistent Methods. J. Mol. Biol. 242, 497-507 (1994).

Sumner, J.B., J. Biol. Chem. 69, 435 (1926).

Surewicz, W. K., Mantsch, H. H., & Chapman, D. Determination of Protein Secondary Structure by Fourier Transform Infrared Spectroscopy: A Critical Assessment. biochemistry 32, 389-394.

Venkatachalam, C. M. Stereochemical Criteria for Polypeptides and Proteins. V Conformation of a System of Three Linked Peptide Units. Biopolymers 6, 1425-1436.

Waterhous, D. V. & Johnson, W. C. Jr. Importance of Environment in Determining Secondary Structure in Proteins. Biochemistry 33, 2121-2128 (1994).

Wishart, D. S., Sykes, B. D., & Richards, F. M. The Chemical Shift Index: A Fast and Simple Method for the Assignment of Protein Secondary Structure through NMR Spectroscopy. Biochemistry 31, 1647-1651 (1992).

Wolfenden, R., Andersson, L., Cullis, P.M., and Southgate, C.C.B. Affinities of amino acid side chains for solvent water. Biochemistry 20, 849-855 , (1981).

Woody, R. W. Circular Dichroism of Peptides in The Peptides Volume 7 Academic Press 14-114 (1985).

Woody, R. W., "Circular Dichroism" (1995) Methods Enzymol. 246 34-71.

Selected Reading
Cited References

No Title - 31 MAY 96
written by Kurt D. Berndt, Karolinska Institute, Stockholm, Sweden
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