Dynamic protein classification: Adaptive models based on incremental learning strategies

Abstract One of the major problems in computational biology is the inability of existing classification models to incorporate expanding and new domain knowledge. This problem of static classification models is addressed in this thesis by the introduction of incremental learning for problems in bioinformatics. The tools which have been developed are applied to the problem of classifying proteins into a number of primary and putative families. The importance of this type of classification is of particular relevance due to its role in drug discovery programs and the benefit it lends to this process in terms of cost and time saving. As a secondary problem, multi–class classification is also addressed. The standard approach to protein family classification is based on the creation of committees of binary classifiers. This one-vs-all approach is not ideal, and the classification systems presented here consists of classifiers that are able to do all-vs-all classification. Two incremental learning techniques are presented. The first is a novel algorithm based on the fuzzy ARTMAP classifier and an evolutionary strategy. The second technique applies the incremental learning algorithm Learn++. The two systems are tested using three datasets: data from the Structural Classification of Proteins (SCOP) database, G-Protein Coupled Receptors (GPCR) database and Enzymes from the Protein Data Bank. The results show that both techniques are comparable with each other, giving classification abilities which are comparable to that of the single batch trained classifiers, with the added ability of incremental learning. Both the techniques are shown to be useful to the problem of protein family classification, but these techniques are applicable to problems outside this area, with applications in proteomics including the predictions of functions, secondary and tertiary structures, and applications in genomics such as promoter and splice site predictions and classification of gene microarrays

Protein engineering and pattern recognition

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1994.Includes bibliographical references (leaves 52-53).by Georg Karl-Heinz Füllen.M.S

The Role of SurA PPIase Domains in Preventing Aggregation of the Outer Membrane Proteins tOmpA and OmpT

SurA is a conserved ATP-independent periplasmic chaperone involved in the biogenesis of outer-membrane proteins (OMPs). Escherichia coli SurA has a core domain and two peptidylprolyl isomerase (PPIase) domains, the role(s) of which remain unresolved. Here we show that while SurA homologues in early proteobacteria typically contain one or no PPIase domains, the presence of two PPIase domains is common in SurA in later proteobacteria, implying an evolutionary advantage for this domain architecture. Bioinformatics analysis of > 350,000 OMP sequences showed that their length, hydrophobicity and aggregation propensity are similar across the proteobacterial classes, ruling out a simple correlation between SurA domain architecture and these properties of OMP sequences. To investigate the role of the PPIase domains in SurA activity, we deleted one or both PPIase domains from E. coli SurA and investigated the ability of the resulting proteins to bind and prevent the aggregation of tOmpA (19 kDa) and OmpT (33 kDa). The results show that wild-type SurA inhibits the aggregation of both OMPs, as do the cytoplasmic OMP chaperones trigger factor and SecB. However, while the ability of SurA to bind and prevent tOmpA aggregation does not depend on its PPIase domains, deletion of even a single PPIase domain ablates the ability of SurA to prevent OmpT aggregation. The results demonstrate that the core domain of SurA endows its generic chaperone ability, while the presence of PPIase domains enhances its chaperone activity for specific OMPs, suggesting one reason for the conservation of multiple PPIase domains in SurA in proteobacteria

Aggregation of gluten proteins - from wheat seed biology to hydrogels : scientific modelling based primarily on Monte-Carlo and HPLC methods

Gluten proteins are intrinsically disordered proteins that form extensive aggregated networks in wheat seeds, where they are stored as a nutrient source for the embryo. A modelling approach involving computational biology with Monte-Carlo algorithms and wet laboratory studies, including HPLC analysis, was applied to unravel the aggregational and hydrogelforming properties of the gluten proteins. Two of the gluten proteins, “αgliadin” and “low molecular weight glutenin subunits” (LMW-GS) were found to have similar size, folding of disordered, rigid and compact structures, elliptical shape and secondary structures of random coils and turns. Both proteins also share an evolutionarily conserved motif resulting in internal disulphide bonds, which were shown to be established through hydrophobic interactions, together with the inherent order of cysteines. In laboratory conditions and simulations, it was found that gliadins formed oligomers by hydrophobic interactions and cross-links by disulphide and lanthionine bonds at peptide sections in the C-terminal part of the protein. At the N-terminal part, the protein formed oligomers by liquid-liquid phase separation, polyproline II structures and β-sheets. Heat and alkaline treatment was shown to favour cross-linking by lanthionine, lysinoalanine and disulphide bonds among gliadins and increase their ability to absorb liquid. Thus the modelling approach successfully characterised the gluten proteins α-gliadin and LMW-GS, the mechanisms by which they form internal and external cross-links, how they merge into oligomers and how to increase their liquid absorption

Dynamic bioinformatics and isotopic evaluation of the permeome of intraerythrocytic Plasmodium falciparum parasites

The Plasmodium falciparum parasite is the causative agent of the most severe form of malaria. The increase in resistance against the majority of antimalarial compounds underpins the need for the development of new antimalarial compounds, targeting novel biological activities of the parasite. As the P. falciparum parasite develops through its life cycle stages, the parasite is exposed to different environments, resulting in both strategy-specific differences between the asexual (proliferation) and gametocyte (differentiation) stages, as well as stage-specific (i.e. ring – schizont stages; stage I - V gametocytes) differences within each strategy. These strategy- and stage-specific differences might be supported by the presence of different membrane transport proteins (MTPs) in the asexual and gametocyte stages. P. falciparum-encoded MTPs (permeome) are promising novel drug targets because they are specific to P. falciparum and essential for the survival of the P. falciparum parasite as these proteins mediate the uptake and removal of metabolites and waste products. However, to propose parasite-encoded MTPs as potential novel drug targets in the asexual and gametocyte stages, the presence of these MTPs in these stages should be investigated. The P. falciparum-encoded permeome is well characterised in the asexual stages. However, limited knowledge is available about the permeome in the gametocyte stages. Therefore, to address this knowledge gap, the strategy- and stage-specific expression of the entire complement of parasite-encoded MTPs were investigated in the asexual and gametocyte stages to infer the presence of MTP transcripts in the absence of biochemical uptake data. The transcript expression of the permeome revealed strategy-specific expression, with the entire permeome expressed during asexual stages, as expected, given the metabolic adaptations that support the high proliferation rate. By contrast, the gametocyte stages that are undergoing sexual differentiation towards transmission, as opposed to active proliferation, less than half of the permeome were expressed, indicating a reduced range of MTPs active in the gametocyte stages. Subsequently, stage-specific expression of the permeome was investigated by correlating stage-specific metabolic processes that occur within the asexual and gametocyte stages, to the expression profiles of MTP genes involved in these processes. Most of the MTPs involved in these processes showed stage-specific expression, with a few MTP genes showing no stage-specific expression within the asexual and gametocyte stages, respectively. When comparing the stage-specific expression between the asexual and gametocyte stages, it was observed that during the gametocyte stages, there was an absence of some MTPs (decreased expression) that were expressed during the asexual stages, suggesting that the gametocyte stages require only certain metabolites to maintain the investigated metabolic processes. In conclusion, these expression profiles of the permeome in the asexual and gametocyte stages suggest the differential expression of the permeome in these stages. The data presented in this study provides the first complete evaluation of expression of the permeome across P. falciparum asexual and gametocyte stages and serves as a blueprint for future biochemical investigations of transport in these stages, thereby providing a foundation for identifying novel MTP drug targets in future drug development programmes.Dissertation (MSc)--University of Pretoria, 2018.NRFBiochemistryMScUnrestricte