Case Studies

Natural Move Monte Carlo● Requires an initial decomposition of the

structure into segments.● Natural Moves describe the collective

motion of segments.● Segments are connected by molten

zones that close the chain after each MC iteration.

Customised Natural Moves● Can be created in two ways:

○ by turning off a molten zone between two segments.

○ by turning off the sampling of selected bond angles within segments.

Modelling Functional Motions of Biological Systems by Customised Natural Moves

Introduction● One of the main challenges of simulating

functional motions in large biomolecules is the high dimensionality and the associated computational cost [1].

● Natural Move Monte Carlo (NMMC) reduces dimensionality by exploiting the modular nature of biomolecules [2].

● Traditionally, NMMC is used to explore the conformational landscape using a single set of Natural Moves.

● We use multiple sets of customised Natural Moves to test hypotheses regarding functional motions in biomolecules.

Demharter S1, Knapp B2, Deane CM2, Minary P1

Departments of Computer Science1 and Statistics2, University of Oxford

Conclusion● Our protocol enables the investigation of causal relationships in structural

mechanisms by customised Natural Moves.● We showed how our protocol can be used to investigate functional motions

in a protein and a DNA system.

Literature1. Orozco M, Chemical Society reviews, 43(14): 5051–66 (2014)2. Minary P et al., J Comp Bio, 17(8): 993–1010 (2010)3. Rabinowitz J et al., Immunity, 9(5): 699–709 (1998)4. Carven GJ et al., J Biol Chem, 279(16):16561–70 (2004)5. Pos W et al., Cell, 151(7):1557– 68 (2012)6. Thalhammer A et al., Chemical communications, 47(18):5325–7 (2011)7. Lercher L et al., Chemical communications 50(15):1794–6 (2014)

Simulations were performed with (MOSAICS) version [-3.9.2], © Peter Minary 2007, http://www.cs.ox.ac.uk/mosaics

Summary: We describe a protocol for the in silico testing of hypotheses regarding the functional motions of biological systems. We demonstrate the use of this protocol on a protein and a DNA case study.

AcknowledgmentsThis work is funded by the EPSRC as part of the Systems Biology Doctoral Training Centre at the University of Oxford. The authors would like to acknowledge the use of the Advanced Research Computing (ARC) and the STFC Hartree Centre in carrying out this work.

Email: samuel.demharter@cs.ox.ac.ukTwitter: @samdemharter

Step 0Define hypothesis

Step 1Choose Natural Moves

Step 2Generate test cases

by customising Natural Moves

Step 3Simulation & Evaluation

Generate test cases

Our Protocol

Outcome● 5hmC had a subtle effect on the structural

parameters of the 3’-adjacent G-C base pair.

● We were able to gradually amplify this effect with two different levels of customised Natural Moves. ○ By fixing the orientation of the 5hm

epigenetic mark towards the 3’-adjacent G.○ By fixing the relative orientation of the 5hmC

and the 3’-adjacent G.

Outcome● We tested the effect of three loop/kink areas

on the narrowing of the binding groove.

● In our simulations the sharp kink (β1-1) in the β1-helix made the largest contributions.

● This suggests that the β1-1 kink may be involved in the formation of a peptide-averse state in the absence of a bound peptide.

Base Pair 1

Base Pair 2

Shear 111T 001T 000T010T

Binding Groove Width

000T 001T 100T

Simulation & Evaluation

Test cases5hmC

G

Generate test cases

Simulation & Evaluation

Hypothesis: Flexibility in the β1-1 kink leads to narrowing of the MHC II binding groove.

Define hypothesis

Define hypothesisHypothesis: Flexibility in the β1-1 kink leads to narrowing of the MHC II binding groove.

Hypothesis: The 5hmC epigenetic mark has a local structural effect on the 3’-adjacent G-C base pair.

Choose Natural Moves

Structure is based on [7].MHC II structure is based on [5].

Modelling the plasticity of the MHC II binding groove

● The MHC II complex presents peptides to the adaptive immune system.

● Without peptide the MHC II takes on a peptide-averse state. Studies suggest this is due to a narrowing of the binding groove [3].

● The β1-1 kink undergoes large structural changes upon removal of peptide [4].

The structural effect of an epigenetic mark on DNA● 5-hydroxymethylcytosine (5hmC) is a

derivative of 5-methylcytosine (5mC).● 5hmC can destabilise DNA given the right

sequence context (e.g. CpG islands) [6].● No structural differences between modified and

unmodified DNA have been found [7].

G5hmC

G5hmC

CG

CG