Conformation

 Nonidentical spatial arrangements of the atoms of a molecule achieved by rotation about single bonds are referred to as different conformations (1). Two molecules differing in their conformation may be referred to as conformers . Because rotations about single bonds are usually rapid, conformers are rapidly interconverted, making it difficult to separate individual conformers. Note one exception to this rule is rotation about the  single bond of the peptide bond of polypeptides, which has partial double-bond character, so it is planar and the cis and trans conformations are only slowly interconverted. The conformation of a molecule may then be largely specified by characterizing the rotations about its single bonds. These rotations are quantified by determining the torsion angle or dihedral angle. Individual torsion angles may be qualitatively described as eclipsed, gauche, or anti (Fig. 1), or more formally named syn periplanar, clinal, and anti periplanar; they are quantified, as described in Torsion angle. 

Figure 1. The common description of a conformation, illustrated by ethylene glycol. When the substituents are superimposed, the conformation is described as eclipsed; when they are staggered, the conformation is gauche if the large substituents are roughly separated by 60° and trans or anti if they are opposite.

Other common combinations of torsion angles lead to descriptive names for common groups of atoms, eg, the 2′-endo conformation of ribose describes all five of the torsion angles of the furanose ring. This practice extends to larger biomacromolecules. The conformation of a small repeating segment of a biomacromolecule is characterized by its torsion angles along the backbone. Thus specification of the phi (f) and psi (y) angles for an oligopeptide  describes its conformation as alpha-helical or beta-sheet (2). The specification of the torsion angles along the phosphodiester backbone of a polynucleotide also will determine whether the conformation is of the A, B, or Z type (3).

 A stable three-dimensional structure of a biological macromolecule is referred to as its conformation. Because rotation about single bonds is energetically easy, a unique conformation does not exist, as at least one single bond will be changing rapidly. A cooperative change of several torsion angles, such as occurs in the protein unfolding or melting of double-stranded DNA, may have a significant energetic barrier. The interconversion of the two conformations is then identified as a conformational change , where the implication is that the macromolecule has been converted from one family of conformations to an experimentally distinguishable family of conformations.

References

1. E. L. Eliel et al. (1967) Conformational Analysis, Wiley-Interscience, New York. 

2.G. E. Schulz and R. H. Schirmer (1979) "Principles of Protein Structure", Springer Advanced Texts in Chemistry (C. R. ed.), Springer-Verlag, New York. 

3. W. Saenger (1984) Principles of Nucleic Acid Structure, Springer Advanced Texts in Chemistry (C. R. Cantor, ed.), Springer-Verlag, New York.

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مواضيع ذات صلة

How AraC Protein Loops and Unloops

DNA Looping and Repression of araBAD

Binding Sites of the ara Regulatory Proteins

Endoplasmic Reticulum-Associated Degradation and the Unfolded Protein Response

Protein Folding and Modifications in the Endoplasmic Reticulum

Protein Modifications

Regulating AraC Synthesis

Repression by AraC

Detection and Isolation of AraC Protein

Genetics of the Arabinose System

The Eukaryotic Genome

Nucleic Acids and Their Organization in Eukaryotic, Prokaryotic, and Viral Genomes