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Macromolecular structure
Macromolecules are held together by a variety of forces
Covalent bonds impose geometrical restrictions on molecular shape
− the length of the bond has negligible variability
− the angle between bonds has small variability
− the dihedral angle (rotation about the bond) is least constrained
Stabilizing interactions provided by weak interactions
o Noncovalent bonds (hydrogen bonds or van der Waals forces)
o electrostatic attraction or repulsion
o hydrophobic forces
DNA backbone configuration is determined by a list of torsional angles
The dominant interaction is the stacking of base pairs.
RNA single stranded RNA can fold into variety of structures by pairing with itself
group 1
88-nucleotide RNA
construct with two
distinct folds
X-ray crystal structure of bacterial ribosome
Protein structure is to large extent determined by the polypeptide backbone
peptide bond is planar
the backbone is parametrized
by two dihedral angles per
amino acid, φ and ψ
Because of steric constraints
(molecular groups bumping
into each other) limited
combinations of φ and ψ
are possible
Main secondary structures are:
right-handed α-helix
antiparallel β-sheet