A repertoire of representative Val60 structures generated using the CamTube force field.

<p>A selection of 135 structures whose TM-score from respective CATH structures is larger than 0.4; a-c) examples of three CATH structures with their equivalent Val60 structures. CATH codes are given bellow the respective figures.</p

Atom pair self-avoiding sphere distances, <i>d</i>, from Eq 1.

<p>Atom pair self-avoiding sphere distances, <i>d</i>, from <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004435#pcbi.1004435.e001" target="_blank">Eq 1</a>.</p

Schematic representation of a segment of a polypeptide chain in the CamTube model.

<p>The tube-like implementation is carried out by self-avoiding spheres, which for clarity of illustration are shown here only for Cα atoms. Bond lengths (apart from the Cα-Cβ bond) and angles are taken from the Amber force field. The length of the CA-Cβ bond of Val, Pro, Thr, Ser and Cys is scaled 1.5 times; Asp, Ile, Leu and Asn 2 times; Phe 2.25 times; Glu, Gln, Met and His 2.5 times; Tyr and Trp 3 times; Lys and Arg 4 times the length of the Cα-Cβ bond in the Amber force field.</p

Parameters for Cβ-Cα-N-C' and Cβ-Cα-C'-N dihedral angles used in the CamTube force field that encode the propensity of the amino acids for different regions in the Ramachandran map.

<p>Parameters for Cβ-Cα-N-C' and Cβ-Cα-C'-N dihedral angles used in the CamTube force field that encode the propensity of the amino acids for different regions in the Ramachandran map.</p

Illustration of the repulsion between C' and H atoms introduced by the curvature term in the CamTube model.

<p>The C' and H atoms belong to the α-helix and are 2 and 3 residues apart in the sequence.</p

Steric map in the CamTube model.

<p>The map shows main steric restrictions (dashed black line) imposed by H_i-H_i+1, O_i–1-O_i and O_i–1-N_i+1 distances. Allowed regions are represented by light blue colour and they contain the range of dihedral angles present in right-handed α-helices, left-handed α-helices and β-sheets.</p

Free energy surface of Val60 in the CamTube force field.

<p>The x and y axes represent two CV variables: the number of α-helical six-residue-long fragments and the radius of gyration.</p

Input parameters used in simulations with the CamTube force field.

<p>Input parameters used in simulations with the CamTube force field.</p

Folding of GB3 using the CamTube force field.

<p>(a) CamTube energy generated from an unbiased 1 μs long molecular dynamics simulation of GB3 as a function of the RMSD from the crystal structure, PDB ID: 2OED. Representative structures sampled in different regions of (<i>energy</i>, <i>rmsd</i>) space are shown as insets. (b) Free energy of Val60 obtained from a metadynamics simulation and the CamTube force field as a function of the RMSD from the crystal structure, PDB ID: 2OED. (c) Distributions of the radius of gyration; the radius of gyration of the native state of GB3 (PDB ID: 2OED) is indicated by the red arrow. (d) Ramachandran plot for the GB3 structures generated by the CamTube force field.</p

Illustration of the directionality of the hydrogen bonds in the CamTube model.

<p>(a) The use of spherical avoidance volumes prohibits bond angles far from 180°. The C', O, H, and N atoms are shown in teal, red, grey, and blue, respectively. (b) Angular dependence of the overall hydrogen bonding potential after the inclusion of half harmonic repulsions between C'-H and O-N pairs. The potential is plotted at the optimal O-H distance of 0.2 nm using <i>ε</i>_<i>H</i> = 21 kJ mol⁻¹.</p