Conformations of Biopolymers

The full text of three related documents are included under this heading:

Abbreviations and symbols for the description of the conformation of polypeptide chains (1969)

Symbols for specifying the conformation of polysaccharide chains. Recommendations 1981

Abbreviations and symbols for the description of conformations of polynucleotide chains. Recommendations 1982

CONTENTS

• Preamble

• 1. General Principles of Notation
  • 1.1 Designation of atoms
  • 1.2 Amino acid residue numbering
  • 1.3 Peptide units
  • 1.4 Bond lengths
  • 1.5 Bond angles
  • 1.6 Torsion angles
  • 1.7 Conformational regions

• 2. The Sequence Rule, and Choice of Torsion Angle
  • 2.1. The sequence rule
  • 2.2. Choice of torsion angle and numbering of branches (tetrahedral configurations)
  • 2.3. Choice of torsion angle and numbering of branches (planar trigonal configurations)

• 3. The Main Chain (or Polypeptide Backbone)
  • 3.1. Designation of bonds
  • 3.2. Torsion angles
  • 3.3. Chain terminations

• 4. Side Chains
  • 4.1. Atoms
  • 4.2. Designation of atoms other than hydrogen
  • 4.3. Designation of branches
  • 4.4. Designation of hydrogen atoms
  • 4.5. Designation of bonds and torsion angles

• 5. Hydrogen Bonds
  • 5.l. Polarity of hydrogen bonds
  • 5.2. Dimensions of hydrogen bonds

• 6. Helical Segments
  • 6.1. Symbols
  • 6.2. Definition in terms of and
  • 6.3. Definition in terms of symmetry and hydrogen-bond arrangement

• Appendix
  • A. Conformation and Configuration
  • B. Definitions of Primary, Secondary, Tertiary, and Quaternary Structure
    • B.l. Primary Structure
    • B.2. Secondary Structure
    • B.3. Tertiary Structure
    • B.4. Quaternary Structure

• References

This is a document of the IUPAC-IUB Commission on Biochemical Nomenclature (CBN), approved by IUPAC and IUB in 1969 and published by permission of IUPAC and IUB. The members of CBN at the time of publication were: O. Hoffmann-Ostenhof (Chairman), W. E. Cohn (Secretary), A. E. Braunstein, P. Karlson, B. Keil, W. Klyne, C. Liébecq, E. C. Slater, E. C. Webb, and W. J. Whelan. The members of the subcommission were J. C. Kendrew (Chairman), W. Klyne, S. Lifson, T. Miyazawa, G. Némethy, D. C. Phillips, G. N. Ramachandran, and H. A. Scheraga. In addition, the following assisted in the work of the subcommission: R. S. Cahn, R. Diamond, J. T. Edsall, P. J. Flory, C. K. Ingold, A. Liquori, V. Prelog, and J. A. Schellman.

CONTENTS

• 1. General principles of notation
  • 1.1. Direction of numbering
  • 1.2. Monomeric unit
  • 1.3. Atom numbering
  • 1.4. Interatomic distances
  • 1.5. Bond angles
  • 1.6. Ring shape
    • 1.6.1 Endocyclic torsion angles
    • 1.6.2 General notation of residue conformation
  • 1.7. Conformation of side groups

• 2. Orientation of the glycosidic linkage
  • 2.1. Designation of bonds
  • 2.2. Torsion angles

• 3. Helix characteristics

• References

This is a document of the IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN) whose members were at the time of publication (1981) P. Karlson (chairman), H. B. F. Dixon, C. Liébecq (as chairman of the IUB Committee of Editors of Biochemical Journals), K. L. Loening. G. P. Moss, J. Reedijk, S. F. Velick and J. F. G. Vliegenthart. JCBN thanks an expert panel set up by its predecessor under the chairmanship of R. H. Marchessault (members: D. A. Brant, F. Cramer, W. Klyne, G. N. Ramachandran, D. A. Rees; consultants: S. Arnott, R. S. Cahn, W. E. Cohn, P. Corradini, L. C. Cross, O. Hoffmann-Ostenhof, D. Horton, J. C. Kendrew, R. Langridge, K. L. Loening, V. Prelog, V. S. R. Rao, K. M. Rudall, H. A. Scheraga, M. Sundaralingam, P. R. Sundarajan, R. S. Tipson) for drafting these recommendations, and a panel under the convenership of E. D. T. Atkins (members: D. B. Davies, P. Karlson, B. Lindberg, D. A. Rees) for revising them. JCBN thanks other members of the Nomenclature Committee of IUB (H. Bielka and N. Sharon) for consultation.

CONTENTS

• Introduction

• l. General principles of notation
  • 1.1 Chain direction
  • 1.2 Definition of the nucleotide unit
  • 1.3 Atom numbering
  • 1.4 Bonds, bond lengths and interatomic distances
  • l .5 Bond angles
  • 1.6 Torsion angles
  • 1.7 Conformational regions

• 2. The nucleotide unit
  • 2.1 Sugar-phosphate backbone chain
  • 2.2 Sugar ring
    • 2.2.1 Endocyclic torsion angles
    • 2.2.2 Puckered forms
    • 2.2.3 Pseudorotational analysis
  • 2.3 N-Glycosidic bond
  • 2.4 Orientations of side groups

• 3. Hydrogen bonds
  • 3.1 Polarity of hydrogen bonds
  • 3.2 Geometry of hydrogen bonds

• 4. Helical segments
  • 4.1 Base pairs
  • 4.2 Helix characteristics

• Addenda. Atom numbering in polynucleotides

• References

Document of the IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN) whose members were at the time of publication (1983) P. Karlson (chairman), H. B. F. Dixon, C. Liébecq (as chairman of the IUB Committee of Editors of Biochemical Journals), K. L. Loening, G. P. Moss, J. Reedijk, S. F. Velick and J. F. G. Vliegenthart. JCBN thanks the expert panel and many others consulted for their work in drafting the document, including other members of the Nomenclature Committee of IUB (H. Bielka and N. Sharon). The members of the panel were C. Altona, S. Arnott, S. S. Danyluk, D. B. Davies (chairman), F. E. Hruska, A. Klug, H.-D. Ludemann, B. Pullman, G. N. Ramachandran, A. Rich, W. Saenger, R. H. Sarma, M. Sundaralingam. Associate members were P. Karlson, O. Kennard, S.-H. Kim, V. Sasisekharan and H. R. Wilson. The document is based on work by a previous subcommission (chairman, F. Cramer) and by an informal committee formed at the Fifth Jerusalem Symposium on Quantum Chemistry and Biochemistry (chairman: M. Sundaralingam).