PLUM* validation work

Some of the validation work on the PLUM model was repeated for the PLUM* model as a test that the model continued to function properly, without unexpected changes.

The 2A3D system in PLUM*

The 2A3D triple-helix bundle is simulated in PLUM* with the same conditions as its original PLUM model simulation, in section 3.2.1. The system is found to fold to the same native state, the transition to disorder now occurring at approximately 375 K.

(a) 1 (48.9%) Residues 1 to 13 form an ↵-helix. A kink begins at residue 14, isoleucine, immediately preceding a highly alpha-disruptive proline. Residues 15 to 27 conform to a left-handed helix which is the enantiomer of the ↵-helix, maintaining i+ 4_!i hydrogen bonding. The terminal residues 28 to 30 are lysine, lysine and cys- teine, and these deviate from the left-handed helix dihedral values, suggesting just three residues of disorder.

(b) 2 (10.3%) The cluster members are

↵-helical throughout, with a ‘double kink’ centered on the proline at residue position 15. The energy penalty of the double kink is compensated for by maintenance of the favoured↵structure and non-bonded inter- actions between the two sides of the peptide, which are pulled closer.

(c) 3 (4.1%)A strict↵-helix structure per- vades the chain, with almost no variation in dihedral angles within or between structures of the cluster.

(d) 4 (3.7%) This structure is very sim- ilar to 4.1a, having an ↵-helix disrupted by a kink, leading to a left-handed↵-helix. In this case, the left-handed portion gives way to disorder beginning at residue 22. These C-terminal residues of the chain ex- hibit lower than average alpha-helicity, as made clear by fig. 4.3b.

Figure 4.1: The four top-occurring structures for n16N represented in PLUM at 300.0K are displayed. Each structure is labelled by its rank, with the percentage of frames conforming to the structure parenthesised. The N-terminus is highlighted red and kept on the right for clarity. These top four structures cumulatively occupy 67.0%of all frames with highly ordered helical structure.

(a)300K:A tight, sharp global peak is seen at the coordinates for the ↵-helix, with a secondary peak in the left-handed ↵-helix domain.

(b)325K:The↵-helix peak remains sharp and considerably dominant. The top left quadrant may have a higher overall popula- tion, however.

(c)350K:The Ramachandran plot at last becomes remi- niscent of the totally unstructured GAG molecule seen in fig. 3.5.

Figure 4.2: Ramachandran plots showing the exploration of ( , ) phase space for

a single unit of n16N at various thermostatted temperatures. Even at 325K, the

↵-helix peak is dominant and thin. Some exploration of unfolded states and left-

handed ↵-helix occurs at all temperatures shown, but an extremely high temperature

of350K is required for the global maximum to be in an unfolded region. This makes

it clear that the PLUM model is over-stabilising this form of secondary structure for the n16N molecule.

0.8 0.82 0.84 0.86 0.88 0.9 0.92 0.94 0.96 0.98 1

PLUM backbone-backbone hydrogen bond interaction strength (reduced units) 0

0.2 0.4 0.6 0.8

Occupancy of Ramachandran quadrant

PLUM bottom left quadrant PLUM top left quadrant PLUM bottom right quadrant PLUM top right quadrant Atomistic bottom left quadrant Atomistic top left quadrant Atomistic bottom right quadrant Atomistic top right quadrant

(a) Occupancy of each of the four Ramachandran quadrants. Quadrants con- taining both left- and right-handed↵-helices decline sharply as✏HBfalls. Most

sterically permitted ( , )-space exists in the top left quadrant, so naturally it increases as the propensity to form↵-helices falls.

0.8 0.82 0.84 0.86 0.88 0.9 0.92 0.94 0.96 0.98 1

PLUM backbone-backbone hydrogen bond interaction strength (reduced units)

0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 Proportion of α -helix structure

PLUM full chain

PLUM SD1 (residues 1 to 8) PLUM SD2 (residues 9 to 16) PLUM SD3 (residues 17 to 30) Atomistic full chain

Atomistic SD1 Atomistic SD2 Atomistic SD3

(b) ↵-helical structure, broken down by the regions of n16N. The decline in

↵-helical structure follows the decline in occupancy of the bottom left quad- rant shown in fig. 4.3a, and also reaches agreement with the atomistic model around a 5% decrease. However, when the level of structure is stratified by subdomain, it emerges that the PLUM model does not match the atomistic model, assigning the lowest level of ↵-helical structure to SD3.

Figure 4.3: Behaviour of the PLUM model of n16N at 300K as a function of hy-

drogen bond interaction strength ✏HB, compared to an atomistic REMD simulation

[Brown et al., 2014] with the CHARMM22* model [Piana et al., 2011; MacKerell et al., 1998] in TIPS3P water [Jorgensen et al., 1983]. The PLUM output is very sensitive to adjustments, and reaches peak similarity to the atomistic data with a

15-unit GNNQQNY system

The -sheet aggregation system was simulated again in PLUM*, using the same conditions as in section 3.2.1. While the peak in heat capacity has shifted approxi- mately from 0.96 to 0.92, the native structure below this temperature is unchanged.