Protein Secondary Structure PDF

Protein secondary structure  Secondary structure Leninger Fig 3-13 Secondary structure reflects the arrangement of residues close in sequence Most residues in most proteins can be seen to be forming either a-helices o...

Protein secondary structure  Secondary structure Leninger Fig 3-13 Secondary structure reflects the arrangement of residues close in sequence Most residues in most proteins can be seen to be forming either a-helices or b-strands But what dictates that these arrangements predominate, and not others?  Protein backbone conformation The conformation of the backbone can be understood by examining the bonds that join one residue to the next Three bonds join each Ca to the next Ca, so a protein’s conformation can be described by three angles per residue These angles are named omega (W), phi (F), and psi (Y)  Dihedral angles –definition A D B C Given four atoms A-B-C-D connected in a row The dihedral angle is the angle made between the A-B bond and the C-D bond when looking down the B-C bond Measured in a clockwise direction Van der Waals clashes dictate single-bond dihedral angle preferences Single bonds are short ( 100 are helix Arginine 98 93 95 called formers e.g. Threonine 83 119 96 glutamate Serine 77 75 143 Residues with P(a) > 75%) The exact beginning/end of s.s. elements are often off by 1-2 a.a. Some elements are missed entirely e.g. last helix …but secondary structure depends on structural context Methods that consider local sequence can give good, but not perfect predictions Recent methods that predict the whole structure (e.g. Alphafold) also predict secondary structure These predictions are more accurate than secondary structure alone predictions (~98% accuracy)