β-residues

Derivation from CHARMM amino acid topologies

For the convenience of prospective users, we have generated residue topologies for mono- and disubstituted β-amino acids with proteinogenic side-chains, as well as the β-alanine, employing analogies with α-amino acids wherever possible:

  1. The atom types for the peptide bond are kept the same (i.e. NH1, O, C and H)

  2. New atom types were introduced for the α- and β-carbons:

    Atom type Based on Usage
    CTA1 CT1 β-carbon with side-chain
    CTA2 CT2 α-carbon without side-chain
    CTB1 CT1 α-carbon with side-chain
    CTB2 CT2 β-carbon without side-chain

  3. Side-chain atoms were taken from the α-counterparts:

    Letter CHARMM36 base Description
    A ALA alanine
    C CYS cysteine (neutral)
    CM CYM cysteine (anionic)
    D ASP aspartate (ionic)
    DH ASPP [1] aspartic acid (protonated)
    E GLU glutamate (ionic)
    EH GLUP [1] glutamic acid (protonated)
    F PHE phenyl-alanine
    G GLY glycine (i.e. no side-chain)
    HD HSD neutral histidine, protonated on Nδ
    HE HSE neutral histidine protonated on Nε
    HH HSP protonated histidine
    I ILE isoleucine
    K LYS lysine (charged)
    KN LSN [1] lysine (neutral)
    L LEU leucine
    M MET methionine
    N ASN asparagine
    O ORP [2] ornithine (charged)
    ON ORN [2] ornithine (neutral)
    Q GLN glutamine
    R ARG arginine
    S SER serine
    T THR threonine
    V VAL valine
    W TRP tryptophan
    Y TYR tyrosine
[1](1, 2, 3) A patch residue in CHARMM36m
[2](1, 2) Does not exist in CHARMM36m, created by removing a methylene from lysine
  1. Partial charges and charge groups of backbone atoms have been assigned as follows:
    1. the backbone is divided into three charge groups:
      • N, H, CB, HB*
      • CA, HA*
      • C, O
    2. partial charges of the peptide bond:
      • peptide N: -0.470
      • peptide C: 0.51
      • peptide O: -0.51
      • peptide H: 0.310
    3. the partial charge of all aliphatic hydrogens is 0.09.
    4. partial charges on CB and CA are determined by requiring all charge groups to be neutral. I.e.:
      • β3 substituted amino-acids (i.e. β3 and β2,3): CB -> 0.07
      • not β3 substituted amino-acids (i.e. βA and β2): CB -> -0.02
      • β2 substituted amino-acids (i.e. β2 and β2,3): CA -> -0.09
      • not β2 substituted amino-acids (i.e. βA and β3): CB -> -0.18

Naming conventions

Residue names have been assigned according to the substitution:

  • βA is BALA
  • β3-amino acids: B3*, e.g. B3A, B3C, B3KN etc.
  • β2-amino acid: B2*, e.g. B2A, B2C, B2KN etc.
  • beta2,3-amino acids: a serious limitation of CHARMM is that residue names contain at most 4 uppercase alphanumeric characters (i.e. A-Z and 0-9). For residues where the side-chains can be represented with a single letter, we chose the B0XY notation, as it does not clash with any existing residue name. Thus, for example: β2,3-h(2Ala,3Phe) will be B0AF etc. Due to the limitation above, currently there is no way to represent disubstituted β-amino acids with alternate charge/protonation states.
  • No distinction is made in chirality either in residue or atom names. This has to be resolved in the molecular geometry.
Atom names mainly follow the convention of CHARMM, i.e.:

  1. the atoms of the peptide bond are named N, HN, C and O

  2. heavy (non-hydrogen) atoms are assigned Greek letters according to their distance from C, in the following sequence: ABGDEZHT

  3. when there are multiple heavy atoms with the same Greek letter, a number is added, according to the following rules:

    1. the β3 side-chain takes precedence over the β2 side-chain (i.e. the backbone β-carbon is always either CB or CB1)
    2. atoms belonging to the same side-chain inherit their precedence from the original CHARMM topology

    Thus the name of a non-peptide-bond heavy atom will conform the scheme <element><Greek letter>[<optional number>], i.e. CB1 or NE2

  4. hydrogen atoms are labeled after their ligands, by changing the first letter to H. If there are more hydrogens attached to the same atom, an additional number is appended. In case of side-chain atoms, the order is inherited from the CHARMM topology. In the backbone protons, S absolute conformation should take recedence over R