Biochemistry terms in Rosetta

Amino Acids table

*NOTICE: Selenocysteine is not a component of natural proteins.

Atom name definition

Starting from nitrogen in $ -NH_2 $ group (defined as “N”) in the backbone, the carbon atom connected to it, that is, the central carbon, is defined as “$ C_\alpha $” or “CA”, and the adjacent carbon in $ -COOH $ group in the backbone is defined as “C”. Other carbon atoms, accroding to their distances to $ C_\alpha $, are correspondingly defined as $ C_{\beta} $(CB), $ C_{\gamma} $(CG), $ C_{\delta} $(CD), $ C_{\epsilon} $(CE), $ C_{\zeta} $(CZ), $ C_{\eta} $(CH).

Ramachandran dihedrals

The two torsion angles of the polypeptide chain, also called Ramachandran angles, describe the rotations of the polypeptide backbone around the bonds between:

1. N-Cα (angle between $ C_{i-1} $ and $ C_i $, denoted Phi, φ) and
2. Cα-C (angle between $ N_i $and $ N_{i+1} $, called Psi, ψ)
3. C-N (peptide bond, angle between $ C_{\alpha \ i-1} $and $ C_{\alpha \ i} $, denoted Omega, $ \omega $)

In most cases, $ \omega $= 180°.

In very rare cases, $ \omega $= 0° (Not energetically favorable.)

phi = −64.8°, psi = -41.0° for left handed α-helix,

phi = -135.0°, psi = 135.0° for beta-strand,

and around phi = 60°, psi = 40° for L-helix

Ramachandran angles in Rosetta： https://docs.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/MakeBundleMover

alter 1-10/, ss='H'Set No.1 - No.10 amino acids to “alpha-helix” style in PyMOL

Side-chain dihedrals

Hydrogen and disulfide bonds

Ambiguous Hydrogen

For certain amino acids, the position of a hydrogen atom can be ambiguous due to the symmetry of the sidechain or because the sidechain can adopt different rotamers.

α-helix (3.6/13-helix)

螺旋周期约为3.6个氨基酸残基，即每3.6个残基螺旋上升一圈，

Spiral period is 3.6 residues, that is, the spiral rises a turn every 3.6 residues

Average atoms per turn: 13

Pitch: ~ 5.4 Å

Rise per residue: ~ 1.5 Å

The [Peptide bond surfaces] are approximately parallel to the central axis of the helix, and the common direction of all the peptide bonds makes the whole α-helix a macro dipole, with the N-terminus ~ + 0.5 e and the C terminus ~ - 0.5 e.

Crick equation for α-helix

Introduction

Crick equation describes the geometry of one helix of helices (one helix in a super helix).

Major Parameters

1. **The super-helical radius (R0)**：the “major super halical radius”; the distances between helices, depending on the number of helices, ~3-10 Å

2. The super helical frequency (ω0): super-helix torsion; helix twists (curve) around Z axis; measured by “how each a.a. contribute to the curvature of a helix”, -2.5~2.5°(plus or minus determines the chirality)

3. Helical phase offset (Δφ1) of a helix: the angle that the helix turns around its own central axis, relative to the initial helical phase (φ1), Δφ1 = ω1·t

   NOTICE: This is delta_omega1 in Rosetta.

4. Super-helical phase offset (Δφ0) of a helix: the angle that the helix turns around the central axis of the super helix (the Z axis), relative to the initial super-helical phase (φ0), Δφ0 = ω0·t NOTICE: This is delta_omega0 in Rosetta

5. Chain axial offset (ΔZ) of a helix: the distance that a helix moves along the central Z axis of the super-helix

6. The helical radius (R1): α-helix radius, usually set to the ideal value of an α-helix

7. The helical frequency (ω1): α-helix curvature, coupled to ω0, for an ideal α-helix, ω0+ω1=100°

The equation

Parameters in Rosetta

MakeBundle

3/10-helix

Not discussed here

π-helix

Not discussed here