Toward the atomistic simulation of T cell epitopes automated construction of MHC:peptide structures for free energy calculations

Epitopes mediated by T cells lie at the heart of the adaptive immune response and form the essential nucleus of anti-tumour peptide or epitope-based vaccines. Antigenic T cell epitopes are mediated by major histocompatibility complex (MHC) molecules, which present them to T cell receptors. Calculating the affinity between a given MHC molecule and an antigenic peptide using experimental approaches is both difficult and time consuming, thus various computational methods have been developed for this purpose. A server has been developed to allow a structural approach to the problem by generating specific MHC:peptide complex structures and providing configuration files to run molecular modelling simulations upon them. A system has been produced which allows the automated construction of MHC:peptide structure files and the corresponding configuration files required to execute a molecular dynamics simulation using NAMD. The system has been made available through a web-based front end and stand-alone scripts. Previous attempts at structural prediction of MHC:peptide affinity have been limited due to the paucity of structures and the computational expense in running large scale molecular dynamics simulations. The MHCsim server (http://igrid-ext.cryst.bbk.ac.uk/MHCsim) allows the user to rapidly generate any desired MHC:peptide complex and will facilitate molecular modelling simulation of MHC complexes on an unprecedented scale.

Free energy functional expansion as the generalized approach to the equation of state of dense fluids

A version of the thermodynamic perturbation theory based on a scaling transformation of the partition function has been applied to the statistical derivation of the equation of state in a highpressure region. Two modifications of the equations of state have been obtained on the basis of the free energy functional perturbation series. The comparative analysis of the experimental PV T- data on the isothermal compression for the supercritical fluids of inert gases has been carried out. © 2012.

Structure, dynamics, and energetics of siRNA-cationic vector complexation:a molecular dynamics study

The design and synthesis of safe and efficient nonviral vectors for gene delivery has attracted significant attention in recent years. Previous experiments have revealed that the charge density of a polycation (the carrier) plays a crucial role in complexation and the release of the gene from the complex in the cytosol. In this work, we adopt an atomistic molecular dynamics simulation approach to study the complexation of short strand duplex RNA with six cationic carrier systems of varying charge and surface topology. The simulations reveal detailed molecular-level pictures of the structures and dynamics of the RNA-polycation complexes. Estimates for the binding free energy indicate that electrostatic contributions are dominant followed by van der Waals interactions. The binding free energy between the 8(+)polymers and the RNA is found to be larger than that of the 4(+)polymers, in general agreement with previously published data. Because reliable binding free energies provide an effective index of the ability of the polycationic carrier to bind the nucleic acid and also carry implications for the process of gene release within the cytosol, these novel simulations have the potential to provide us with a much better understanding of key mechanistic aspects of gene-polycation complexation and thereby advance the rational design of nonviral gene delivery systems.

Molecular dynamics simulations:bring biomolecular structures alive on a computer

The molecular dynamics (MD) simulations play a very important role in science today. They have been used successfully in binding free-energy calculations and rational design of drugs and vaccines. MD simulations can help visualize and understand structures and dynamics at an atomistic level when combined with molecular graphics programs. The molecular and atomistic properties can be displayed on a computer in a time-dependent way, which opens a road toward a better understanding of the relationship of structure, dynamics, and function. In this chapter, the basics of MD are explained, together with a step-by-step description of setup and running an MD simulation.

Novel hydrogel copolymers and semi-interpenetraing polymer networks

Interpenetrating polymer networks (lPN's), have been defined as a combination of two polymers each in network form, at least one of which has been synthesised and / or crosslinked in the presence of the other. A semi-lPN, is formed when only one of the polymers in the system is crosslinked, the other being linear. lPN's have potential advantages over homogeneous materials presently used in biomedical applications, in that their composite nature gives them a useful combination of properties. Such materials have potential uses in the biomedical field, specifically for use in hard tissue replacements, rigid gas permeable contact lenses and dental materials. Work on simply two or three component systems in both low water containing lPN's supplemented by the study of hydrogels (water swollen hydrophilic polymers) can provide information useful in the future development of more complex systems. A range of copolymers have been synthesised using a variety of methacrylates and acrylates. Hydrogels were obtained by the addition of N-vinyl pyrrolidone to these copolymers. A selection of interpenetrants were incorporated into the samples and their effect on the copolymer properties was investigated. By studying glass transition temperatures, mechanical, surface, water binding and oxygen permeability properties samples were assessed for their suitability for use as biomaterials. In addition copolymers containing tris-(trimethylsiloxy)-y-methacryloxypropyl silane, commonly abbreviated to 'TRlS', have been investigated. This material has been shown to enhance oxygen permeability, a desirable property when considering the design of contact lenses. However, 'TRIS' has a low polar component of surface free energy and hence low wettability. Copolymerisation with a range of methacrylates has shown that significant increases in surface wettability can be obtained without a detrimental effect on oxygen permeability. To further enhance to surface wettability 4-methacryloxyethyl trimellitic anhydride was incorporated into a range of promising samples. This study has shown that by careful choice of monomers it is possible to synthesise polymers that possess a range of properties desirable in biomedical applications.

Protein deposition at polymer surfaces:the bulk and surface structure-property effects of hydrogels

The primary objective of this research has been to investigate the interfacial phenomenon of protein adsorption in relation to the bulk and surface structure-property effect s of hydrogel polymers. In order to achieve this it was first necessary to characterise the bulk and surface properties of the hydrogels, with regard to the structural chemistry of their component monomers. The bulk properties of the hydrogels were established using equilibrium water content measurements, together with water-binding studies by differential scanning calorimetry (D.S.C.). Hamilton and captive air bubble-contact angle techniques were employed to characterise the hydrogel-water interface and from which by a mathematical derivation, the interfacial free energy (ðsw) and the surface free energy components (ð psv, ðdsv, ðsv) were obtained. From the adsorption studies using the radio labelled iodinated (125I) proteins of human serum albumin (H.S.A.) and human fibrinogen (H.Fb.), it was Found that multi-layered adsorption was occurring and that the rate and type of this adsorption was dependent on the physico-chemical behaviour of the adsorbing protein (and its bulk concentration in solution), together with the surface energetics of the adsorbent polymer. A potential method for the invitro evaluation of a material's 'biocompatibility' was also investigated, based on an empirically observed relationship between the adsorption of albumin and fibrinogen and the 'biocompatibility' of polymeric materials. Furthermore, some consideration was also given to the biocompatibility problem of proteinaceous deposit formation on hydrophilic soft' contact lenses and in addition a number of potential continual wear contact lens formulations now undergoing clinical trials,were characterised by the above techniques.

Can surface energy measurements predict the impact of catalyst hydrophobicity upon fatty acid esterification over sulfonic acid functionalised periodic mesoporous organosilicas?

Sulfonic acid functionalised periodic mesoporous organosilicas (PrSO3 H-PMOs) with tunable hydrophobicity were synthesised via a surfactant-templating route, and characterised by porosimetry, TEM, XRD, XPS, inverse gas chromatography (IGC) and ammonia pulse chemisorption. IGC reveals that incorporation of ethyl or benzyl moieties into a mesoporous SBA-15 silica framework significantly increases the non-specific dispersive surface energy of adsorption for alkane adsorption, while decreasing the free energy of adsorption of methanol, reflecting increased surface hydrophobicity. The non-specific dispersive surface energy of adsorption of PMO-SO3H materials is strongly correlated with their activity towards palmitic acid esterification with methanol, demonstrating the power of IGC as an analytical tool for identifying promising solid acid catalysts for the esterification of free fatty acids. A new parameter [-ΔGCNP-P], defined as the per carbon difference in Gibbs free energy of adsorption between alkane and polar probe molecules, provides a simple predictor of surface hydrophobicity and corresponding catalyst activity in fatty acid esterification. © 2014 Elsevier B.V.

Threshold-induced phase transitions in perceptrons

Error rates of a Boolean perceptron with threshold and either spherical or Ising constraint on the weight vector are calculated for storing patterns from biased input and output distributions derived within a one-step replica symmetry breaking (RSB) treatment. For unbiased output distribution and non-zero stability of the patterns, we find a critical load, α p, above which two solutions to the saddlepoint equations appear; one with higher free energy and zero threshold and a dominant solution with non-zero threshold. We examine this second-order phase transition and the dependence of α p on the required pattern stability, κ, for both one-step RSB and replica symmetry (RS) in the spherical case and for one-step RSB in the Ising case.

Error-correcting codes on a Bethe-like lattice

We analyse Gallager codes by employing a simple mean-field approximation that distorts the model geometry and preserves important interactions between sites. The method naturally recovers the probability propagation decoding algorithm as a minimization of a proper free-energy. We find a thermodynamical phase transition that coincides with information theoretical upper-bounds and explain the practical code performance in terms of the free-energy landscape.

The effect of pH on PAMAM dendrimer-siRNA complexation:endosomal considerations as determined by molecular dynamics simulation

Intracellular degradation of genes, most notably within the endo-lysosomal compartment is considered a significant barrier to (non-viral) gene delivery in vivo. Previous reports based on in vitro studies claim that carriers possessing a mixture of primary, secondary and tertiary amines are able to buffer the acidic environment within the endosome, allowing for timely release of their contents, leading to higher transfection rates. In this report, we adopt an atomistic molecular dynamics (MD) simulation approach, comparing the complexation of 21-bp siRNA with low-generation polyamidoamine (PAMAM) dendrimers (G0 and G1) at both neutral and acidic pHs, the latter of which mimics the degradative environment within maturing 'late-endosomes'. Our simulations reveal that the time taken for the dendrimer-gene complex (dendriplex) to reach equilibrium is appreciably longer at low pH and this is accompanied by more compact packaging of the dendriplex, as compared to simulations performed at neutral pH. We also note larger absolute values of calculated binding free energies of the dendriplex at low pH, indicating a higher dendrimer-nucleic acid affinity in comparison with neutral pH. These novel simulations provide a more detailed understanding of low molecular-weight polymer-siRNA behavior, mimicking the endosomal environment and provide input of direct relevance to the "proton sponge theory", thereby advancing the rational design of non-viral gene delivery systems.

A mean field theory of coded CDMA systems

We present a mean field theory of code-division multiple access (CDMA) systems with error-control coding. On the basis of the relation between the free energy and mutual information, we obtain an analytical expression of the maximum spectral efficiency of the coded CDMA system, from which a mean field description of the coded CDMA system is provided in terms of a bank of scalar Gaussian channels whose variances in general vary at different code symbol positions. Regular low-density parity-check (LDPC)-coded CDMA systems are also discussed as an example of the coded CDMA systems.

Cellular interactions with hydrogels

An efficient means of evaluating potential biomaterials is to use the in vitro fibroblast cell culture model. However, the chemistry which influences cell adhesion on polymer substrates is poorly understood. The work in this thesis aims to rationalise several theories of current opinion and introduce new chemical techniques that may predict cellular behaviour. The keratoprosthesis is a typical example of the need to be able to manipulate cell adhesion of materials since both adhesive and non adhesive sections are needed for proper integration and optical function. Calcein AM/ethidium homodimer-1 and DAPI assays were carried out using 3T3 and EKl.BR cells. Poly(HEMA) was found to be the most cell adhesive hydrogel tested. The reactivity of monomers and the resulting sequence distribution were found to affect surface properties and this may explain the poor levels of cell adhesion seen on NVP/MMA copolymers. Surface free energy is shown to be dependent on the polar and non polar groups present along the backbone chain of the polymers. Dehydrated and hydrated contact angle measurements show the effect of rotation of surface groups around the backbone chain. This effect is most apparent on hydrogels containing methacrylic acid. Dynamic contact angle measurements confirm sequence distribution irregularities and demonstrate the mobility of surface groups. Incorporation of NVI or DEAEMA into the hydrogels does not affect the mobility of the surface groups despite their bulkiness. Foetal calf serum was used for the first time as a test solution in an attempt to mimic a biological environment during surface experiments. A Vroman effect may be present, and may involve different surface proteins for each material tested. This interdisciplinary study combines surface characterisation and biological testing to further the knowledge of the biomaterial/host interface. Surface chemistry techniques appear to be insufficiently sensitive to predict cellular behaviour. The degree of ionisation of hydrogels containing ionic groups depends on the nature of the functional groups as well as the concentration and this is an important parameter to consider when comparing charged materials.

Variational inference for diffusion processes

Diffusion processes are a family of continuous-time continuous-state stochastic processes that are in general only partially observed. The joint estimation of the forcing parameters and the system noise (volatility) in these dynamical systems is a crucial, but non-trivial task, especially when the system is nonlinear and multimodal. We propose a variational treatment of diffusion processes, which allows us to compute type II maximum likelihood estimates of the parameters by simple gradient techniques and which is computationally less demanding than most MCMC approaches. We also show how a cheap estimate of the posterior over the parameters can be constructed based on the variational free energy.

Statistical physics of error-correcting codes

In this thesis we use statistical physics techniques to study the typical performance of four families of error-correcting codes based on very sparse linear transformations: Sourlas codes, Gallager codes, MacKay-Neal codes and Kanter-Saad codes. We map the decoding problem onto an Ising spin system with many-spins interactions. We then employ the replica method to calculate averages over the quenched disorder represented by the code constructions, the arbitrary messages and the random noise vectors. We find, as the noise level increases, a phase transition between successful decoding and failure phases. This phase transition coincides with upper bounds derived in the information theory literature in most of the cases. We connect the practical decoding algorithm known as probability propagation with the task of finding local minima of the related Bethe free-energy. We show that the practical decoding thresholds correspond to noise levels where suboptimal minima of the free-energy emerge. Simulations of practical decoding scenarios using probability propagation agree with theoretical predictions of the replica symmetric theory. The typical performance predicted by the thermodynamic phase transitions is shown to be attainable in computation times that grow exponentially with the system size. We use the insights obtained to design a method to calculate the performance and optimise parameters of the high performance codes proposed by Kanter and Saad.

The design of novel antifolates against pneumocystis carinii

The pneumonia caused by Pneumocystis carinii is ultimately responsible for the death of many acquired immunodeficiency syndrome (AIDS) patients. Large doses of trimethoprim and pyrimethamine in combination with a sulphonamide and/or pentamidine suppress the infection but produce serious side-effects and seldom prevent recurrence after treatment withdrawal. However, the partial success of the aforementioned antifolates, and also trimetrexate used alone, does suggest dihydrofolate reductase (DHFR) as a target for the development of antipneumocystis agents. From the DHFR inhibitory activities of 3'-substituted pyrimethamine analogues it was suggested that the 3'-(3'',3''-dimethyltriazen-1''-yl) substituent may be responsible for the greater activity for the P.carinii over the mammalian enzyme. Crystallographic and molecular modeling studies revealed considerable geometrical and electronic differences between the triazene and the chemically related formamidine functions that may account for the differences in DHFR inhibitory profiles. Structural and electronic parameters calculated for a series of 3'-(3'',3''-disubstitutedtriazen-1''-yl) pyrimethamine analogues did not correlate with the DHFR inhibitory activities. However, the in vitro screening against P.carinii DHFR revealed that the 3''-hydroxyethyl-3''-benzyl analogue was the most active and selective. Models of the active sites of human and P.carinii DHFRs were constructed using DHFR sequence and structural homology data which had identified key residues involved in substrate and cofactor binding. Low energy conformations of the 3'',3''-dimethyl and 3''-hydroxyethyl-3''-benzyle analogues, determined from nuclear magnetic resonance studies and theoretical calculations, were docked by superimposing the diaminopyrimidine fragment onto a previously docked pyrimethamine analogue. Enzyme kinetic data supported the 3''-hydroxyethyl-3''-benzyl moiety being located in the NADPH binding groove. The 3''-benzyl substituent was able to locate to within 3 AA of a valine residue in the active site of P.carinii DHFR thereby producing a hydrophobic contact. The equivalent residue in human DHFR is threonine, more hydrophilic and less likely to be involved in such a contact. This difference may account for the greater inhibitory activity this analogue has for P.carinii DHFR and provide a basis for future drug design. From an in vivo model of PCP in immunosuppressed rats it was established that the 3"-hydroxyethyl-3"-benzyl analogue was able to reduce the.P.carinii burden more effectively with increasing doses, without causmg any visible signs of toxicity. However, equivalent doses were not as effective as pentamidine, a current treatment of choice for Pneumocystis carinii pneumonia.