Exploring the potential of 3D Zernike descriptors and SVM for protein\u2013protein interface prediction

Abstract Background The correct determination of protein–protein interaction interfaces is important for understanding disease mechanisms and for rational drug design. To date, several computational methods for the prediction of protein interfaces have been developed, but the interface prediction problem is still not fully understood. Experimental evidence suggests that the location of binding sites is imprinted in the protein structure, but there are major differences among the interfaces of the various protein types: the characterising properties can vary a lot depending on the interaction type and function. The selection of an optimal set of features characterising the protein interface and the development of an effective method to represent and capture the complex protein recognition patterns are of paramount importance for this task. Results In this work we investigate the potential of a novel local surface descriptor based on 3D Zernike moments for the interface prediction task. Descriptors invariant to roto-translations are extracted from circular patches of the protein surface enriched with physico-chemical properties from the HQI8 amino acid index set, and are used as samples for a binary classification problem. Support Vector Machines are used as a classifier to distinguish interface local surface patches from non-interface ones. The proposed method was validated on 16 classes of proteins extracted from the Protein–Protein Docking Benchmark 5.0 and compared to other state-of-the-art protein interface predictors (SPPIDER, PrISE and NPS-HomPPI). Conclusions The 3D Zernike descriptors are able to capture the similarity among patterns of physico-chemical and biochemical properties mapped on the protein surface arising from the various spatial arrangements of the underlying residues, and their usage can be easily extended to other sets of amino acid properties. The results suggest that the choice of a proper set of features characterising the protein interface is crucial for the interface prediction task, and that optimality strongly depends on the class of proteins whose interface we want to characterise. We postulate that different protein classes should be treated separately and that it is necessary to identify an optimal set of features for each protein class

Protein contour modelling and computation for complementarity detection and docking

The aim of this thesis is the development and application of a model that effectively and efficiently integrates the evaluation of geometric and electrostatic complementarity for the protein-protein docking problem. Proteins perform their biological roles by interacting with other biomolecules and forming macromolecular complexes. The structural characterization of protein complexes is important to understand the underlying biological processes. Unfortunately, there are several limitations to the available experimental techniques, leaving the vast majority of these complexes to be determined by means of computational methods such as protein-protein docking. The ultimate goal of the protein-protein docking problem is the in silico prediction of the three-dimensional structure of complexes of two or more interacting proteins, as occurring in living organisms, which can later be verified in vitro or in vivo. These interactions are highly specific and take place due to the simultaneous formation of multiple weak bonds: the geometric complementarity of the contours of the interacting molecules is a fundamental requirement in order to enable and maintain these interactions. However, shape complementarity alone cannot guarantee highly accurate docking predictions, as there are several physicochemical factors, such as Coulomb potentials, van der Waals forces and hydrophobicity, affecting the formation of protein complexes. In order to set up correct and efficient methods for the protein-protein docking, it is necessary to provide a unique representation which integrates geometric and physicochemical criteria in the complementarity evaluation. To this end, a novel local surface descriptor, capable of capturing both the shape and electrostatic distribution properties of macromolecular surfaces, has been designed and implemented. The proposed methodology effectively integrates the evaluation of geometrical and electrostatic distribution complementarity of molecular surfaces, while maintaining efficiency in the descriptor comparison phase. The descriptor is based on the 3D Zernike invariants which possess several attractive features, such as a compact representation, rotational and translational invariance and have been shown to adequately capture global and local protein surface shape similarity and naturally represent physicochemical properties on the molecular surface. Locally, the geometric similarity between two portions of protein surface implies a certain degree of complementarity, but the same cannot be stated about electrostatic distributions. Complementarity in electrostatic distributions is more complex to handle, as charges must be matched with opposite ones even if they do not have the same magnitude. The proposed method overcomes this limitation as follows. From a unique electrostatic distribution function, two separate distribution functions are obtained, one for the positive and one for the negative charges, and both functions are normalised in [0, 1]. Descriptors are computed separately for the positive and negative charge distributions, and complementarity evaluation is then done by cross-comparing descriptors of distributions of charges of opposite signs. The proposed descriptor uses a discrete voxel-based representation of the Connolly surface on which the corresponding electrostatic potentials have been mapped. Voxelised surface representations have received a lot of interest in several bioinformatics and computational biology applications as a simple and effective way of jointly representing geometric and physicochemical properties of proteins and other biomolecules by mapping auxiliary information in each voxel. Moreover, the voxel grid can be defined at different resolutions, thus giving the means to effectively control the degree of detail in the discrete representation along with the possibility of producing multiple representations of the same molecule at different resolutions. A specific algorithm has been designed for the efficient computation of voxelised macromolecular surfaces at arbitrary resolutions, starting from experimentally-derived structural data (X-ray crystallography, NMR spectroscopy or cryo-electron microscopy). Fast surface generation is achieved by adapting an approximate Euclidean Distance Transform algorithm in the Connolly surface computation step and by exploiting the geometrical relationship between the latter and the Solvent Accessible surface. This algorithm is at the base of VoxSurf (Voxelised Surface calculation program), a tool which can produce discrete representations of macromolecules at very high resolutions starting from the three-dimensional information of their corresponding PDB files. By employing compact data structures and implementing a spatial slicing protocol, the proposed tool can calculate the three main molecular surfaces at high resolutions with limited memory demands. To reduce the surface computation time without affecting the accuracy of the representation, two parallel algorithms for the computation of voxelised macromolecular surfaces, based on a spatial slicing procedure, have been introduced. The molecule is sliced in a user-defined number of parts and the portions of the overall surface can be calculated for each slice in parallel. The molecule is sliced with planes perpendicular to the abscissa axis of the Cartesian coordinate system defined in the molecule's PDB entry. The first algorithms uses an overlapping margin of one probe-sphere radius length among slices in order to guarantee the correctness of the Euclidean Distance Transform. Because of this margin, the Connolly surface can be computed nearly independently for each slice. Communications among processes are necessary only during the pocket identification procedure which ensures that pockets spanning through more than one slice are correctly identified and discriminated from solvent-excluded cavities inside the molecule. In the second parallel algorithm the size of the overlapping margin between slices has been reduced to a one-voxel length by adapting a multi-step region-growing Euclidean Distance Transform algorithm. At each step, distance values are first calculated independently for every slice, then, a small portion of the borders' information is exchanged between adjacent slices. The proposed methodologies will serve as a basis for a full-fledged protein-protein docking protocol based on local feature matching. Rigorous benchmark tests have shown that the combined geometric and electrostatic descriptor can effectively identify shape and electrostatic distribution complementarity in the binding sites of protein-protein complexes, by efficiently comparing circular surface patches and significantly decreasing the number of false positives obtained when using a purely-geometric descriptor. In the validation experiments, the contours of the two interacting proteins are divided in circular patches: all possible patch pairs from the two proteins are then evaluated in terms of complementarity and a general ranking is produced. Results show that native patch pairs obtain higher ranks when using the newly proposed descriptor, with respect to the ranks obtained when using the purely-geometric one

Spatio–temporal analysis of changes of shape for constituent bodies within biomolecular aggregates

Changes of shape are important in many situations of interest in biology at different typical length scales. Approaches for modelling the behaviour of droplets in suspension and thermallydriven motion of the molecular chains in enzymes are presented. Both models use orthogonal basis functions to describe the spatial dependences in a spherical geometry. Both models also describe the effect of time-dependent boundary data on the shape of the bodies involved, a stochastic response for the enzyme model (dimensions of the order 10−9 m) and smooth response for the colloidal model (dimensions of the order 10−6 m). The first model presented considers the behaviour of a droplet of fluid surrounded by a thin film of host fluid, both fluids being Newtonian and immiscible, with a well-defined continuous and smooth interface between these regions. The flows for the droplet and host fluid are assumed axisymmetric with small Reynold numbers. An extension of traditional lubrication theory is used to model the flow for the host fluid and a multi-modal Stokes flow is used to derive the flow within the droplet, subject to continuity conditions at the interface between the droplet and host fluid. The interface is free to move in response to the flows, under the effects of interfacial tension. Asymptotic expansions for the flow variables and interface are used to find the simplest behaviour of the system beyond the leading order. The second unique modelling approach used is the method of Zernike moments. Zernike moments are an extension of spherical harmonics to include more general radial dependence and the ability to model holes, folded layers etc. within and on the unit sphere. The method has traditionally been used to describe the shape of enzymes in a static time-independent manner. This approach is extended to give results based on the thermally-driven motion of atoms in molecules about their equilibrium positions. The displacements are assumed to be fitted by Normal probability distributions. The precision and accuracy of this model are considered and compared to similar models. Results are plotted and discussed for both regimes and further extensions, improvements and basis for further work are discussed for both approaches

Entropically driven self-assembly of pear-shaped nanoparticles

This thesis addresses the entropically driven colloidal self-assembly of pear-shaped particle ensembles, including the formation of nanostructures based on triply periodic minimal surfaces, in particular of the Ia3d gyroid. One of the key results is that the formation of the Ia3d gyroid, re-ported earlier in the so-called pear hard Gaussian overlap (PHGO) approximation and confirmed here, is due to a slight non-additivity of that potential; this phase does not form in pears with true hard-core potential. First, we computationally study the PHGO system and present the phase diagram of pears with an aspect ratio of 3 in terms of global density and particle shape (degree of taper), containing gyroid, isotropic, nematic and smectic phases. We confirm that it is adequate to interpret the gyroid as a warped smectic bilayer phase. The collective behaviour to arrange into interdigitated sheets with negative Gauss curvature, from which the gyroid results, is investigated through correlations of (Set-)Voronoi cells and local curvature. This geometric arrangement within the bilayers suggests a fundamentally different stabilisation mechanism of the pear gyroid phase compared to those found in both lipid-water and di-block copolymer systems forming the Ia3d gyroid. The PHGO model is only an approximation for hard-core interactions, and we additionally investigate, by much slower simulations, pear-assemblies with true hard-core interactions (HPR). We find that HPR phase diagram only contains isotropic and nematic phases, but neither gyroid nor smectic phases. To understand this shape sensitivity more profoundly, the depletion interactions of both models are studied in two pear-shaped colloids dissolved in a hard sphere solvent. The HPR particles act as one would expect from a geometric analysis of the excluded-volume minimisation, whereas the PHGO particles show deviations from this expectation. These differences are attributed to the unusual angle dependency of the (non-additive) contact function and, more so, to small overlaps induced by the approximation. For the PHGO model, we further demonstrate that the addition of a small concentration of hard spheres ("solvent") drives the system towards a Pn3m diamond phase. This result is explained by the greater spatial heterogeneity of the diamond geometry compared to the gyroid where additional material is needed to relieve packing frustration. In contrast to copolymer systems, however, the solvent mostly aggregates near the diamond minimal surface, driven by the non-additivity of the PHGO pears. At high solvent concentrations, the mixture phase separates into “inverse” micelle-like structures with the blunt ends at the micellar centres and thin ends pointing out-wards. The micelles themselves spontaneously cluster, indicative of a hierarchical self-assembly process for bicontinuous structures. Finally, we develop a density functional for hard solids of revolution (including pears) within the framework of fundamental measure theory. It is applied to low-density ensembles of pear-shaped particles, where we analyse their response near a hard substrate. A complex orientational ordering close to the wall is predicted, which is directly linked to the particle shape and gives insight into adsorption processes of asymmetric particles. This predicted behaviour and the differences between the PHGO and HPR model are confirmed by MC simulations

Entropie‐dominierte Selbstorganisationsprozesse birnenförmiger Teilchensysteme

The ambition to recreate highly complex and functional nanostructures found in living organisms marks one of the pillars of today‘s research in bio- and soft matter physics. Here, self-assembly has evolved into a prominent strategy in nanostructure formation and has proven to be a useful tool for many complex structures. However, it is still a challenge to design and realise particle properties such that they self-organise into a desired target configuration. One of the key design parameters is the shape of the constituent particles. This thesis focuses in particular on the shape sensitivity of liquid crystal phases by addressing the entropically driven colloidal self-assembly of tapered ellipsoids, reminiscent of „pear-shaped“ particles. Therefore, we analyse the formation of the gyroid and of the accompanying bilayer architecture, reported earlier in the so-called pear hard Gaussian overlap (PHGO) approximation, by applying various geometrical tools like Set-Voronoi tessellation and clustering algorithms. Using computational simulations, we also indicate a method to stabilise other bicontinuous structures like the diamond phase. Moreover, we investigate both computationally and theoretically(density functional theory) the influence of minor variations in shape on different pearshaped particle systems, including the stability of the PHGO gyroid phase. We show that the formation of the gyroid is due to small non-additive properties of the PHGO potential. This phase does not form in pears with a „true“ hard pear-shaped potential. Overall our results allow for a better general understanding of necessity and sufficiency of particle shape in regards to colloidal self-assembly processes. Furthermore, the pear-shaped particle system sheds light on a unique collective mechanism to generate bicontinuous phases. It suggests a new alternative pathway which might help us to solve still unknown characteristics and properties of naturally occurring gyroid-like nano- and microstructures.Ein wichtiger Bestandteil der heutigen Forschung in Bio- und Soft Matter Physik besteht daraus, Technologien zu entwickeln, um hoch komplexe und funktionelle Strukturen, die uns aus der Natur bekannt sind, nachzubilden. Hinsichtlich dessen ist vor allem die Methode der Selbstorganisation von Mikro- und Nanoteilchen hervorzuheben, durch die eine Vielzahl verschiedener Strukturen erzeugt werden konnten. Jedoch stehen wir bei diesem Verfahren noch immer vor der Herausforderung, Teilchen mit bestimmten Eigenschaften zu entwerfen, welche die spontane Anordnung der Teilchen in eine gewünschte Struktur bewirken. Einer der wichtigsten Designparameter ist dabei die Form der Bausteinteilchen. In dieser Dissertation konzentrieren wir uns besonders auf die Anfälligkeit von Flüssigkristallphasen bezüglich kleiner Änderungen der Teilchenform und nutzen dabei das Beispiel der Selbstorganisation von Entropie-dominierter Kolloide, die dem Umriss nach verjüngten Ellipsoiden oder "Birnen" ähneln. Mit Hilfe von geometrischen Werkzeugen wie z.B. Set-Voronoi Tessellation oder Cluster-Algorithmen analysieren wir insbesondere die Entstehung der Gyroidphase und der dazugehörigen Bilagenformation, welche bereits in Systemen von harten Birnen, die durch das pear hard Gaussian overlap (PHGO) Potential angenähert werden, entdeckt wurden. Des Weiteren zeigen wir durch Computersimulationen eine Strategie auf, um andere bikontinuierliche Strukturen, wie die Diamentenphase, zu stabilisieren. Schlussendlich betrachten wir sowohl rechnerisch (durch Simulationen) als auch theoretisch (durch Dichtefunktionaltheorie) die Auswirkungen kleiner Abweichungen der Teilchenform auf das Verhalten des kolloiden, birnenförmigen Teilchensystems, inklusive der Stabilität der PHGO Gyroidphase. Wir zeigen, dass die Entstehung des Gyroids auf kleinen nicht-additiven Eigenschaften des PHGO Birnenmodells beruhen. In ''echten'' harten Teilchensystemen entwickelt sich diese Struktur nicht. Insgesamt ermöglichen unsere Ergebnisse einen besseren Einblick auf das Konzept von notwendiger und hinreichender Teilchenform in Selbstorganistationsprozessen. Die birnenförmigen Teilchensysteme geben außerdem Aufschluss über einen ungewöhnlichen, kollektiven Mechanismus, um bikontinuierliche Phasen zu erzeugen. Dies deutet auf einen neuen, alternativen Konstruktionsweg hin, der uns möglicherweise hilft, noch unbekannte Eigenschaften natürlich vorkommender, gyroidähnlicher Nano- und Mikrostrukturen zu erklären

Structure formation and identification in geometrically driven soft matter systems

Subdividing space through interfaces leads to many space partitions that are relevant to soft matter self-assembly. Prominent examples include cellular media, e.g. soap froths, which are bubbles of air separated by interfaces of soap and water, but also more complex partitions such as bicontinuous minimal surfaces. Using computer simulations, this thesis analyses soft matter systems in terms of the relationship between the physical forces between the system’s constituents and the structure of the resulting interfaces or partitions. The focus is on two systems, copolymeric self-assembly and the so-called Quantizer problem, where the driving force of structure formation, the minimisation of the free-energy, is an interplay of surface area minimisation and stretching contributions, favouring cells of uniform thickness. In the first part of the thesis we address copolymeric phase formation with sharp interfaces. We analyse a columnar copolymer system “forced” to assemble on a spherical surface, where the perfect solution, the hexagonal tiling, is topologically prohibited. For a system of three-armed copolymers, the resulting structure is described by solutions of the so-called Thomson problem, the search of minimal energy configurations of repelling charges on a sphere. We find three intertwined Thomson problem solutions on a single sphere, occurring at a probability depending on the radius of the substrate. We then investigate the formation of amorphous and crystalline structures in the Quantizer system, a particulate model with an energy functional without surface tension that favours spherical cells of equal size. We find that quasi-static equilibrium cooling allows the Quantizer system to crystallise into a BCC ground state, whereas quenching and non-equilibrium cooling, i.e. cooling at slower rates then quenching, leads to an approximately hyperuniform, amorphous state. The assumed universality of the latter, i.e. independence of energy minimisation method or initial configuration, is strengthened by our results. We expand the Quantizer system by introducing interface tension, creating a model that we find to mimic polymeric micelle systems: An order-disorder phase transition is observed with a stable Frank-Caspar phase. The second part considers bicontinuous partitions of space into two network-like domains, and introduces an open-source tool for the identification of structures in electron microscopy images. We expand a method of matching experimentally accessible projections with computed projections of potential structures, introduced by Deng and Mieczkowski (1998). The computed structures are modelled using nodal representations of constant-mean-curvature surfaces. A case study conducted on etioplast cell membranes in chloroplast precursors establishes the double Diamond surface structure to be dominant in these plant cells. We automate the matching process employing deep-learning methods, which manage to identify structures with excellent accuracy

Transmission electron tomography: quality assessment and enhancement for three-dimensional imaging of nanostructures

Nanotechnology has revolutionised humanity's capability in building microscopic systems by manipulating materials on a molecular and atomic scale. Nan-osystems are becoming increasingly smaller and more complex from the chemical perspective which increases the demand for microscopic characterisation techniques. Among others, transmission electron microscopy (TEM) is an indispensable tool that is increasingly used to study the structures of nanosystems down to the molecular and atomic scale. However, despite the effectivity of this tool, it can only provide 2-dimensional projection (shadow) images of the 3D structure, leaving the 3-dimensional information hidden which can lead to incomplete or erroneous characterization. One very promising inspection method is Electron Tomography (ET), which is rapidly becoming an important tool to explore the 3D nano-world. ET provides (sub-)nanometer resolution in all three dimensions of the sample under investigation. However, the fidelity of the ET tomogram that is achieved by current ET reconstruction procedures remains a major challenge. This thesis addresses the assessment and advancement of electron tomographic methods to enable high-fidelity three-dimensional investigations. A quality assessment investigation was conducted to provide a quality quantitative analysis of the main established ET reconstruction algorithms and to study the influence of the experimental conditions on the quality of the reconstructed ET tomogram. Regular shaped nanoparticles were used as a ground-truth for this study. It is concluded that the fidelity of the post-reconstruction quantitative analysis and segmentation is limited, mainly by the fidelity of the reconstructed ET tomogram. This motivates the development of an improved tomographic reconstruction process. In this thesis, a novel ET method was proposed, named dictionary learning electron tomography (DLET). DLET is based on the recent mathematical theorem of compressed sensing (CS) which employs the sparsity of ET tomograms to enable accurate reconstruction from undersampled (S)TEM tilt series. DLET learns the sparsifying transform (dictionary) in an adaptive way and reconstructs the tomogram simultaneously from highly undersampled tilt series. In this method, the sparsity is applied on overlapping image patches favouring local structures. Furthermore, the dictionary is adapted to the specific tomogram instance, thereby favouring better sparsity and consequently higher quality reconstructions. The reconstruction algorithm is based on an alternating procedure that learns the sparsifying dictionary and employs it to remove artifacts and noise in one step, and then restores the tomogram data in the other step. Simulation and real ET experiments of several morphologies are performed with a variety of setups. Reconstruction results validate its efficiency in both noiseless and noisy cases and show that it yields an improved reconstruction quality with fast convergence. The proposed method enables the recovery of high-fidelity information without the need to worry about what sparsifying transform to select or whether the images used strictly follow the pre-conditions of a certain transform (e.g. strictly piecewise constant for Total Variation minimisation). This can also avoid artifacts that can be introduced by specific sparsifying transforms (e.g. the staircase artifacts the may result when using Total Variation minimisation). Moreover, this thesis shows how reliable elementally sensitive tomography using EELS is possible with the aid of both appropriate use of Dual electron energy loss spectroscopy (DualEELS) and the DLET compressed sensing algorithm to make the best use of the limited data volume and signal to noise inherent in core-loss electron energy loss spectroscopy (EELS) from nanoparticles of an industrially important material. Taken together, the results presented in this thesis demonstrates how high-fidelity ET reconstructions can be achieved using a compressed sensing approach

Protein Structure

Since the dawn of recorded history, and probably even before, men and women have been grasping at the mechanisms by which they themselves exist. Only relatively recently, did this grasp yield anything of substance, and only within the last several decades did the proteins play a pivotal role in this existence. In this expose on the topic of protein structure some of the current issues in this scientific field are discussed. The aim is that a non-expert can gain some appreciation for the intricacies involved, and in the current state of affairs. The expert meanwhile, we hope, can gain a deeper understanding of the topic