Calculation of J-coupling constants for tri- and tetrapeptides

Application of the program.: The program uses the mole fractions, φ and ψ positions and the respec2ve halfwidths of Gaussian sub-distributions as input parameters. The respective parameter values for GxG peptides were taken from previous papers. All off-diagonal correla2on parameters in the two-dimensional Gaussian formalism were set to zero, so that all basins appear elliptical with their axis along φ and ψ in the Ramachandran plot. Each Gaussian sub-distribution is associated with a secondary structure. The Ramachandran plots are calculated as the superposition of the Gaussian sub-distributions and used as probability density function to calculate the ensemble average of J-coupling constants by use of Karplus equations.

Organization of the program: AJer defining some parameters that allow the switch between different sets of Karplus equa2ons and the number of pep2des for which calcula2ons should be carried out, the input parameters are all listed. They are organized as follows:

1. The mole fractions chi(n,m), n: number of secondary structures, m: number of pep2de.

2. The phimax(n,m) and psimax(n,m) coordinates of the Gaussian sub-distribution positions in deg.

3. The wphi(n,m) and wpsi(n,m) halfwidths in deg. The off-diagonal correlation parameter cov(n,m).

4. The experimental J-coupling constants J1(m),…,J5(m) and the respective experimental uncertain2es.

5. The number is related to secondary structure as follows: n=1: pPII; n=2: β-strand, n=3: right handed helical; n=4: leJ-handed helical; n=5: can vary, options are inverse γ-or asx-turns (just check the dihedral angles), n=6-9 accounts for the boundary overlap of n=1,2, and 5. The J-coupling parameters are defined as follows: J1: ³ J(H^N H^Cα), J2: ³J(H^N C'), J3: ³J(H^Cα C'), J4: ³J(H^N C_β), and J5: ¹J(NCα) (lines 27-23745) The peptides are listed at the respective tops of the parameter list. The tetrapeptides are listed with respect to the central residue of the tripeptide. The list starts with GAG (m=1), followed by the parameters of alanine in GsAG, GdAG, GAvG and GAlG (lower case indicates neighbors of alanine, the one letter code of amino acids is used). The remainder of the parameter list is now self-explanatory. The number of peptides can be limited by the k1max number at the beginning of the program. K1max=33 means that Gaussian Ramachandran plots and J-coupling constants of all 33 peptides considered are calculated.