Organic microcomposites via reactive processing

The in-situ formation of dispersed polyaramide whiskers during melt processing of polymers represents a new route to thermoplastic and elastomeric organic microcomposites. When N-(p-aminobenzoyl)-caprolactam (PAC) is injected into melts of high molecular weight polyamide-6 or dihydroxy-terminated poly(oxytetramethylene) liquid rubber, stable dispersions of polymeric whiskers are formed. At temperatures around 200 °C PAC polymerization takes place exclusively through attack of the PAC amine group at the exocyclic carbonyl group, thus eliminating caprolactam and forming whiskers being composed of highly crystalline poly(p-phenylenebenzamide). With increasing polymerization temperature, the elimination reaction is accompanied by the competing attack of the amine group at the endocyclic carbonyl group of the caprolactam ring system. This side-reaction causes ring-opening, thus incorporating 6-aminocaproic structural units into the polyaramide backbone. Moreover, the condensation reaction of PAC and N-acyl-caprolactam-functional whisker surfaces with hydroxy- or amine-endgroups affords steric stabilization of the dispersions and excellent interfacial adhesion of the microcomposites. This covalent bond formation between matrix polymer and dispersed in-situ formed polyaramide whiskers is the key to unusual property synergisms of such organic microcomposites. In most cases, small amounts of PAC as additives during processing are sufficient to improve stiffness and strength without sacrificing toughness. Morphologies, mechanical properties, and the basic structure/property relationships of in-situ formed polyaramide-reinforced polyamide-6 and of polyurethanes elastomers prepared from novel anisotropic polymer polyol dispersions and diisocyanates are reported as a function of the PAC content and polymerization conditions

Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo

Motivation: The binding between a peptide and a major histocompatibility complex (MHC) is one of the most important processes for the induction of an adaptive immune response. Many algorithms have been developed to predict peptide/MHC (pMHC) binding. However, no approach has yet been able to give structural insight into how peptides detach from the MHC. Results: In this study, we used a combination of coarse graining, hierarchical natural move Monte Carlo and stochastic conformational optimization to explore the detachment processes of 32 different peptides from HLA-A*02:01. We performed 100 independent repeats of each stochastic simulation and found that the presence of experimentally known anchor amino acids affects the detachment trajectories of our peptides. Comparison with experimental binding affinity data indicates the reliability of our approach (area under the receiver operating characteristic curve 0.85). We also compared to a 1000 ns molecular dynamics simulation of a non-binding peptide (AAAKTPVIV) and HLA-A*02:01. Even in this simulation, the longest published for pMHC, the peptide does not fully detach. Our approach is orders of magnitude faster and as such allows us to explore pMHC detachment processes in a way not possible with all-atom molecular dynamics simulations. Availability and implementation: The source code is freely available for download at http://www.cs.ox.ac.uk/mosaics/

HLA-DM stabilizes the empty MHCII binding groove: a model using customized natural move Monte Carlo

MHC class II molecules bind peptides derived from extracellular proteins that have been ingested by antigen-presenting cells and display them to the immune system. Peptide loading occurs within the antigen-presenting cell and is facilitated by HLA-DM. HLA-DM stabilises the open conformation of the MHCII binding groove when no peptide is bound. While a structure of the MHCII/HLA-DM complex exists, the mechanism of stabilisation is still largely unknown. Here, we applied customised Natural Move Monte Carlo to investigate this interaction. We found a possible long range mechanism that implicates the configuration of the membrane-proximal globular domains in stabilising the open state of the empty MHCII binding groove

HLA-DM stabilizes the empty MHCII binding groove: a model using customized natural move Monte Carlo

MHC class II molecules bind peptides derived from extracellular proteins that have been ingested by antigen-presenting cells and display them to the immune system. Peptide loading occurs within the antigen-presenting cell and is facilitated by HLA-DM. HLA-DM stabilises the open conformation of the MHCII binding groove when no peptide is bound. While a structure of the MHCII/HLA-DM complex exists, the mechanism of stabilisation is still largely unknown. Here, we applied customised Natural Move Monte Carlo to investigate this interaction. We found a possible long range mechanism that implicates the configuration of the membrane-proximal globular domains in stabilising the open state of the empty MHCII binding groove

Modelling functional motions of biological systems by customised natural moves

Simulating the functional motions of biomolecular systems requires large computational resources. We introduce a computationally inexpensive protocol for the systematic testing of hypotheses regarding the dynamic behaviour of proteins and nucleic acids. The protocol is based on natural move Monte Carlo, a highly efficient conformational sampling method with in-built customisation capabilities that allows researchers to design and perform a large number of simulations to investigate functional motions in biological systems. We demonstrate the use of this protocol on both a protein and a DNA case study. Firstly, we investigate the plasticity of a class II major-histo-compatibility complex in the absence of a bound peptide. Secondly, we study the effects of the epigenetic mark 5-hydroxymethyl on cytosine on the structure of the Dickerson-Drew dodecamer. We show how our customised natural moves protocol can be used to investigate causal relationships of functional motions in biological systems

Modelling functional motions of biological systems by customised natural moves

Simulating the functional motions of biomolecular systems requires large computational resources. We introduce a computationally inexpensive protocol for the systematic testing of hypotheses regarding the dynamic behaviour of proteins and nucleic acids. The protocol is based on Natural Move Monte Carlo, a highly efficient conformational sampling method with in-built customisation capabilities that allows researchers to design and perform a large number of simulations to investigate functionalmotions in biological systems. We demonstrate the use of this protocol on both a protein and a DNA case study. Firstly, we investigate the plasticity of a class II major-histo-compatibility complex in the absence of a bound peptide. Secondly, we study the effects of the epigenetic mark 5-hydroxymethyl on cytosine on the structure of the Dickerson-Drew dodecamer. We show how our customised Natural Moves protocol can be used to investigate causal relationships of functional motions in biological systems

In silico structural modelling of multiple epigenetic marks on DNA

Summary: There are four known epigenetic cytosine modifications in mammals: 5mC, 5hmC, 5fC and 5caC. The biological effects of 5mC are well understood but the roles of the remaining modifications remain elusive. Experimental and computational studies suggest that a single epigenetic mark has little structural effect but six of them can radically change the structure of DNA to a new form, FDNA. Investigating the collective effect of multiple epigenetic marks requires the ability to interrogate all possible combinations of epigenetic states (e.g. methylated/non-methylated) along a stretch of DNA. Experiments on such complex systems are only feasible on small, isolated examples and there currently exist no systematic computational solutions to this problem. We address this issue by extending the use of Natural Move Monte Carlo to simulate the conformations of epigenetic marks. We validate our protocol by reproducing in silico experimental observations from two recently published high-resolution crystal structures that contain epigenetic marks 5hmC and 5fC. We further demonstrate that our protocol correctly finds either the F-DNA or the B-DNA states more energetically favorable depending on the configuration of the epigenetic marks. We hope that the computational efficiency and ease of use of this novel simulation framework would form the basis for future protocols and facilitate our ability to rapidly interrogate diverse epigenetic systems. Availability: The code together with examples and tutorials are available from http://www.cs.ox.ac.uk/mosaic

In silico structural modelling of multiple epigenetic marks on DNA

Summary: There are four known epigenetic cytosine modifications in mammals: 5mC, 5hmC, 5fC and 5caC. The biological effects of 5mC are well understood but the roles of the remaining modifications remain elusive. Experimental and computational studies suggest that a single epigenetic mark has little structural effect but six of them can radically change the structure of DNA to a new form, FDNA. Investigating the collective effect of multiple epigenetic marks requires the ability to interrogate all possible combinations of epigenetic states (e.g. methylated/non-methylated) along a stretch of DNA. Experiments on such complex systems are only feasible on small, isolated examples and there currently exist no systematic computational solutions to this problem. We address this issue by extending the use of Natural Move Monte Carlo to simulate the conformations of epigenetic marks. We validate our protocol by reproducing in silico experimental observations from two recently published high-resolution crystal structures that contain epigenetic marks 5hmC and 5fC. We further demonstrate that our protocol correctly finds either the F-DNA or the B-DNA states more energetically favorable depending on the configuration of the epigenetic marks. We hope that the computational efficiency and ease of use of this novel simulation framework would form the basis for future protocols and facilitate our ability to rapidly interrogate diverse epigenetic systems. Availability: The code together with examples and tutorials are available from http://www.cs.ox.ac.uk/mosaic