Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone. Secondary structure may alternatively be defined based on the regular pattern of backbone dihedral angles in a particular region of the Ramachandran plot regardless of whether it has the correct hydrogen bonds. The concept of secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang at Stanford in 1952. Other types of biopolymers such as nucleic acids also possess characteristic secondary structures.
Types
The most common secondary structures are alpha helices and beta sheets. Other helices, such as the 310 helix and π helix, are calculated to have energetically favorable hydrogen-bonding patterns but are rarely observed in natural proteins except at the ends of α helices due to unfavorable backbone packing in the center of the helix. Other extended structures such as the polyproline helix and alpha sheet are rare in native state proteins but are often hypothesized as important protein folding intermediates. Tight turns and loose, flexible loops link the more "regular" secondary structure elements. The random coil is not a true secondary structure, but is the class of conformations that indicate an absence of regular secondary structure. Amino acids vary in their ability to form the various secondary structure elements. Helical conformation in proteins is preferred methionine, alanine, leucine, glutamate and lysine ("MALEK" in amino-acid 1-letter codes) as well as arginine (R) and glutamine (Q); by contrast, the large aromatic residues (tryptophan, tyrosine and phenylalanine) and Cβ-branched amino acids (isoleucine, valine, and threonine) prefer to adopt β-strand conformations. Turns and bends are preferred by glycine (G), asparagine (N), proline (P), aspartate (D) and serine (S), whereas the last two amino acids, cysteine (C) and histidine (H) show no preference. Besides this, proline and glycine are sometimes known as "helix breakers" because they disrupt the regularity of the α helical backbone conformation; However, these preferences are not strong enough to produce a reliable method of predicting secondary structure from sequence alone. Low frequency collective vibrations are thought to be sensitive to local rigidity within proteins, revealing beta structures to be generically more rigid than alpha or disordered proteins. Neutron scattering measurements have directly connected the spectral feature at ~1 THz to collective motions of the secondary structure of beta-barrel protein GFP. Hydrogen bonding patterns in secondary structures may be significantly distorted, which makes automatic determination of secondary structure difficult. There are several methods for formally defining protein secondary structure (e.g., DSSP, DEFINE, STRIDE, ScrewFit, SST).
DSSP classification
The Dictionary of Protein Secondary Structure, in short DSSP, is commonly used to describe the protein secondary structure with single letter codes. The secondary structure is assigned based on hydrogen bonding patterns as those initially proposed by Pauling et al. in 1951 (before any protein structure had ever been experimentally determined). There are eight types of secondary structure that DSSP defines:
G = 3-turn helix (310 helix). Min length 3 residues. H = 4-turn helix (α helix). Minimum length 4 residues. I = 5-turn helix (π helix). Minimum length 5 residues. T = hydrogen bonded turn (3, 4 or 5 turn) E = extended strand in parallel and/or anti-parallel β-sheet conformation. Min length 2 residues. B = residue in isolated β-bridge (single pair β-sheet hydrogen bond formation) S = bend (the only non-hydrogen-bond based assignment). C = coil (residues which are not in any of the above conformations). 'Coil' is often codified as ' ' (space), C (coil) or '–' (dash). The helices (G, H and I) and sheet conformations are all required to have a reasonable length. This means that 2 adjacent residues in the primary structure must form the same hydrogen bonding pattern. If the helix or sheet hydrogen bonding pattern is too short they are designated as T or B, respectively. Other protein secondary structure assignment categories exist (sharp turns, Omega loops, etc.), but they are less frequently used. Secondary structure is defined by hydrogen bonding, so the exact definition of a hydrogen bond is critical. The standard hydrogen-bond definition for secondary structure is that of DSSP, which is a purely electrostatic model. It assigns charges of ±q1 ≈ 0.42e to the carbonyl carbon and oxygen, respectively, and charges of ±q2 ≈ 0.20e to the amide hydrogen and nitrogen, respectively. The electrostatic energy is
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