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Autor: Grafiati

Data publikacji: 25 lipca 2024

Data aktualizacji: 31 lipca 2024

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1

Menlove, Kit J. "Model Detection Based upon Amino Acid Properties". BYU ScholarsArchive, 2010. https://scholarsarchive.byu.edu/etd/2253.

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Similarity searches are an essential component to most bioinformatic applications. They form the bases of structural motif identification, gene identification, and insights into functional associations. With the rapid increase in the available genetic data through a wide variety of databases, similarity searches are an essential tool for accessing these data in an informative and productive way. In our chapter, we provide an overview of similarity searching approaches, related databases, and parameter options to achieve the best results for a variety of applications. We then provide a worked example and some notes for consideration. Homology detection is one of the most basic and fundamental problems at the heart of bioinformatics. It is central to problems currently under intense investigation in protein structure prediction, phylogenetic analyses, and computational drug development. Currently discriminative methods for homology detection, which are not readily interpretable, are substantially more powerful than their more interpretable counterparts, particularly when sequence identity is very low. Here I present a computational graph-based framework for homology inference using physiochemical amino acid properties which aims to both reduce the gap in accuracy between discriminative and generative methods and provide a framework for easily identifying the physiochemical basis for the structural similarity between proteins. The accuracy of my method slightly improves on the accuracy of PSI-BLAST, the most popular generative approach, and underscores the potential of this methodology given a more robust statistical foundation.

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2

Shah, Anuj R. "Improving protein remote homology detection using supervised and semi-supervised support vector machines". Online access for everyone, 2008. http://www.dissertations.wsu.edu/Dissertations/Spring2008/A_Shah_042408.pdf.

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3

Wistrand, Markus. "Hidden Markov models for remote protein homology detection /". Stockholm, 2005. http://diss.kib.ki.se/2006/91-7140-598-4/.

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4

Chelliah, Vijayalakshmi. "Functional restraints on amino acid substitution patterns : application to definition of binding sites and sequence-structure homology recognition". Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615170.

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5

Lindholm, Cecilia K. "Shb and its homologues : signaling in T lymphocytes and fibroblasts /". Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2002. http://publications.uu.se/theses/91-554-5260-4/.

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6

Santos-Ciminera, Patricia Dantas Ciminera Patricia Dantas Santos Santos Patricia. "Molecular epidemiology of epidemic severe malaria caused by Plasmodium vivax in the state of Amazonas, Brazil /". Download the dissertation in PDF, 2005. http://www.lrc.usuhs.mil/dissertations/pdf/Santos2005.pdf.

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7

Chu, Yi-wen 1962. "Amino acid sequence requirements for ornithine decarboxylase activity". Thesis, The University of Arizona, 1988. http://hdl.handle.net/10150/276838.

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ODC activity of the altered proteins was measured and compared to that of the full length 461 amino acid containing ODC. Mouse ODC cDNA sequences were deleted from either 5' or 3' ends using exonuclease III and Mung Bean nuclease treatments. An internal deletion was obtained by Hinc II and Bcl I restriction endonuclease digestion of the full length ODC cDNA. Capped mRNAs were synthesized in vitro using the resulting deleted DNA as templates, and the protein was translated in vitro. The results indicate that the protein in which translation initiates at internal AUG start codons does not have any activity. The protein with 39 amino acids deleted from carboxy-terminus maintains 12% of the activity, while deletion of greater than 79 amino acids have no activity. An internal deletion from amino acid 290 to 331 and which may contain the suspected ornithine binding site has no activity. These results suggest that the entire amino acid sequence of mouse ODC is required for full activity of the enzyme.

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8

Forsberg, Hanna. "Genetic and biochemical characterization of a novel sensor of extracellular amino acids in yeast /". Stockholm : Karolinska Univ. Press, 2001. http://diss.kib.ki.se/2001/91-89428-06-4/.

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9

Oppermann, Madalina. "Chemical and mass spectrometrical methods in protein analysis /". Stockholm, 2000. http://diss.kib.ki.se/2000/91-628-4542-x/.

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10

Gallina, Serafina. "Structural Characterization of Donkey Lactoferrin: Amino Acid Sequence and Glycan Compositions". Doctoral thesis, Università di Catania, 2016. http://hdl.handle.net/10761/3880.

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Lactoferrin, a protein showing an array of biochemical properties, including immuno-modulation, iron-binding ability, as well as antioxidant, antibacterial and antiviral activities, was isolated from donkey milk by ion exchange chromatography.The characterization of its primary structure, by means of enzymatic digestions, SPITC derivatization of tryptic digest, reversed-phase high performance liquid chromatography, electrospray and matrix-assisted laser desorption/ionization mass spectrometry, is reported. Our results allowed the almost complete characterization of donkey s lactoferrin sequence, that, at least for the covered sequence, differs from the mare s genomic deduced sequence (UniProtKB Acc. Nr. O77811) by five point substitutions located at positions 91 (Arg->His), 328 (Thr->Ile/Leu), 466 (Ala->Gly), 642 (Asn->Ser) and 668 (Ser->Ala). Glycosylation, one of the most common post-translational modifications, can modify the structural conformation of the protein and consequently its biological activity. A comprehensive glycosylation profile by chymotrypsin digestion, TiO2 and HILIC enrichment strategy, reversed-phase high performance liquid chromatography, electrospray mass spectrometry, high collision dissociation fragmentation, is reported. 26 different glycan compositions were identified, linked to the protein backbone via an amide bond to asparagine residues located at the positions 137, 281 and 476

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11

Cheng, Fang. "Development and application of strategies for the analysis of modification patterns in chondroitin and dermatana sulphate". Lund : Dept. of Cell and Molecular Biology, Lund University, 1997. http://catalog.hathitrust.org/api/volumes/oclc/39693809.html.

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12

Ganapathy, Ashwin. "Computational analysis of protein identification using peptide mass fingerprinting approach /". free to MU campus, to others for purchase, 2004. http://wwwlib.umi.com/cr/mo/fullcit?p1426056.

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13

Li, Ran. "Signal peptide prediction in the space-frequency domain". Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file 0.44 Mb., 68 p, 2006. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:1432421.

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14

Falah, Mizied. "Evolutionary studies based on the 70-kDa heat shock family of protein sequences". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape16/PQDD_0012/NQ30084.pdf.

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15

Varmeh-Ziaie, Shohreh. "Cloning and characterization of a p53-inducible gene, WIG-1 /". Stockholm : [Karolinska institutets bibl.], 2001. http://diss.kib.ki.se/2001/91-7349-079-2/.

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16

Wang, Yuqin. "Protein and lipid interactions of mammalian antibacterial peptides /". Stockholm, 2001. http://diss.kib.ki.se/2001/91-628-4698-1/.

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17

Jonsson, Andreas. "Mass spectrometry in protein structure analysis /". Stockholm, 2001. http://diss.kib.ki.se/2001/91-628-4716-3/.

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18

Liu, Agatha H. "Motif-based mining of protein sequences /". Thesis, Connect to this title online; UW restricted, 2002. http://hdl.handle.net/1773/6894.

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19

SÌŒali, Andrej. "Modelling three-dimensional structure of a protein from its amino acid sequence". Thesis, Birkbeck (University of London), 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.415316.

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20

Tung, Wai Na Viola. "Sequence analysis and modelling of the gp130 cytokines and receptors". Click to view the E-thesis via HKUTO, 2004. http://sunzi.lib.hku.hk/hkuto/record/B31972251.

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21

Tung, Wai Na Viola, i 董維娜. "Sequence analysis and modelling of the gp130 cytokines and receptors". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B31972251.

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22

Senekal, Frederick Petrus. "Protein secondary structure prediction using amino acid regularities". Diss., Pretoria : [s.n.], 2008. http://upetd.up.ac.za/thesis/available/etd-01232009-120040/.

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23

Ndhlovu, Andrew, Scott Hazelhurst i Pierre M. Durand. "Robust sequence alignment using evolutionary rates coupled with an amino acid substitution matrix". BioMed Central, 2015. http://hdl.handle.net/10150/610270.

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BACKGROUND: Selective pressures at the DNA level shape genes into profiles consisting of patterns of rapidly evolving sites and sites withstanding change. These profiles remain detectable even when protein sequences become extensively diverged. A common task in molecular biology is to infer functional, structural or evolutionary relationships by querying a database using an algorithm. However, problems arise when sequence similarity is low. This study presents an algorithm that uses the evolutionary rate at codon sites, the dN/dS (ω) parameter, coupled to a substitution matrix as an alignment metric for detecting distantly related proteins. The algorithm, called BLOSUM-FIRE couples a newer and improved version of the original FIRE (Functional Inference using Rates of Evolution) algorithm with an amino acid substitution matrix in a dynamic scoring function. The enigmatic hepatitis B virus X protein was used as a test case for BLOSUM-FIRE and its associated database EvoDB. RESULTS: The evolutionary rate based approach was coupled with a conventional BLOSUM substitution matrix. The two approaches are combined in a dynamic scoring function, which uses the selective pressure to score aligned residues. The dynamic scoring function is based on a coupled additive approach that scores aligned sites based on the level of conservation inferred from the ω values. Evaluation of the accuracy of this new implementation, BLOSUM-FIRE, using MAFFT alignment as reference alignments has shown that it is more accurate than its predecessor FIRE. Comparison of the alignment quality with widely used algorithms (MUSCLE, T-COFFEE, and CLUSTAL Omega) revealed that the BLOSUM-FIRE algorithm performs as well as conventional algorithms. Its main strength lies in that it provides greater potential for aligning divergent sequences and addresses the problem of low specificity inherent in the original FIRE algorithm. The utility of this algorithm is demonstrated using the Hepatitis B virus X (HBx) protein, a protein of unknown function, as a test case. CONCLUSION: This study describes the utility of an evolutionary rate based approach coupled to the BLOSUM62 amino acid substitution matrix in inferring protein domain function. We demonstrate that such an approach is robust and performs as well as an array of conventional algorithms.

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24

Silvia, Christopher Paul. "The isolation, partial peptide sequence, and cDNA sequence of aromatic L-amino acid decarboxylase from bovine adrenal medulla /". The Ohio State University, 1990. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487677267729241.

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25

Shenoy, Nalini. "Investigation of the replacement of cysteine residues in DOTA-(Tyr³)-octreotate synthesis, characterization and evaluation of biological activities /". Diss., Columbia, Mo. : University of Missouri-Columbia, 2006. http://hdl.handle.net/10355/4440.

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Thesis (Ph. D.) University of Missouri-Columbia, 2006.
The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on August 8, 2007) In the 520 where natIn-DOTA⁰ appears nat should be superscripted. Includes bibliographical references.

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26

McIninch, James David. "Prediction of protein coding regions in unannotated DNA sequences using an inhomogeneous Markov model of genetic information encoding". Diss., Georgia Institute of Technology, 1997. http://hdl.handle.net/1853/25224.

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27

Ko, Ming-him. "A multi-agent model for DNA analysis /". Hong Kong : University of Hong Kong, 1999. http://sunzi.lib.hku.hk/hkuto/record.jsp?B21949116.

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28

Moreland, Rodney J. "Molecular interactions in RNA polymerase II and III transcription systems /". Full-text version available from OU Domain via ProQuest Digital Dissertations, 1998.

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29

López, Ferrando Víctor. "Functional characterization of single amino acid variants". Doctoral thesis, Universitat de Barcelona, 2019. http://hdl.handle.net/10803/668545.

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Single amino acid variants (SAVs) are one of the main causes of Mendelian disorders, and play an important role in the development of many complex diseases. At the same time, they are the most common kind of variation affecting coding DNA, without generally presenting any damaging effect. With the advent of next generation sequencing technologies, the detection of these variants in patients and the general population is easier than ever, but the characterization of the functional effects of each variant remains an open challenge. It is our objective in this work to tackle this problem by developing machine learning based in silico SAVs pathology predictors. Having the PMut classic predictor as a starting point, we have rethought the entire supervised learning pipeline, elaborating new training sets, features and classifiers. PMut2017 is the first result of these efforts, a new general-purpose predictor based on SwissVar and trained on 12 different conservation scores. Its performance, evaluated bothby cross-validation and different blind tests, was in line with the best predictors published to date. Continuing our efforts in search for more accurate predictors, especially for those cases were general predictors tend to fail, we developed PMut-S, a suite of 215 protein-specific predictors. Similar to PMut in nature, Pmut-S introduced the use of co-evolution conservation features and balanced training sets, and showed improved performance, specially for those proteins that were more commonly misclassified by PMut. Comparing PMut-S to other specific predictors we proved that it is possible to train specific predictors using a unique automated pipeline and match the results of most gene specific predictors released to date. The implementation of the machine learning pipeline of both PMut and PMut-S was released as an open source Python module: PyMut, which bundles functions implementing the features computation and selection, classifier training and evaluation, plots drawing, among others. Their predictions were also made available in a rich web portal, which includes a precomputed repository with analyses of more than 700 million variants on over 100,000 human proteins, together with relevant contextual information such as 3D visualizationsof protein structures, links to databases, functional annotations, and more.
Les mutacions puntuals d’aminoàcids són la principal causa de moltes malalties mendelianes, i juguen un paper important en el desenvolupament de moltes malalties complexes. Alhora, són el tipus de variant més comuna que afecta l’ADN codificant de proteïnes, sense provocar, en general, cap efecte advers. Amb l’adveniment de la seqüenciació de nova generació, la detecció d’aquestes variants en pacients i en la població general és més fàcil que mai, però la caracterització dels efectes funcionals de cada variant segueix sent un repte. El nostre objectiu en aquest treball és abordar aquest problema desenvolupant predictors de patologia in silico basats en l’aprenentatge automàtic. Prenent el predictor clàssic PMut com a punt de partida, hem repensat tot el procés d’aprenentatge supervisat, elaborant nous conjunts d’entrenament, descriptors i classificadors. PMut2017 és el primer resultat d’aquests esforços, un nou predictor basat en SwissVar i entrenat amb 12 mètriques de conservació de seqüència. La seva precisió, mesurada mitjançant validació creuada i amb tests cecs, s’ha mostrar en línia amb els millors predictors publicats a dia d’avui. Continuant els nostres esforços en la cerca de predictors més acurats, hem desenvolupat PMut-S, un conjunt de 215 predictors específics per cada proteïna. Similar a PMut en la seva concepció, PMut-S introdueix l’ús de descriptors basats en la coevolució i conjunts d’entrenament balancejats, millorant el rendiment de PMut2017 en 0.1 punts del coeficient de correlació de Matthews. Comparant PMut-S a d’altres predictors específics hem provat que és possible entrenar predictors específics seguint un únic procediment automatitzat i assolir uns resultats tan bon com els de la majoria de predictors específics publicats. La implementació del procediment d’aprenentatge automàtic tant de PMut com de PMut-S ha sigut publicat com a un mòdul de Python de codi obert: PyMut, el qual inclou les funcions que implementen el càlcul dels descriptors i la seva selecció, l’entrenament i avaluació dels classificadors, el dibuix de diverses gràfiques... Les prediccions també estan disponibles en un portal web que inclou un repositori precalculat amb els anàlisis de més de 700 milions de variants en més de 100 mil proteïnes humanes, junt a rellevant informació de context com visualitzacions 3D de les proteïnes, enllaços a bases de dades, anotacions funcionals i molt més.

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30

Thompson, James. "Genetic algorithms applied to biological sequence analysis /". Link to online version, 2006. https://ritdml.rit.edu/dspace/handle/1850/2269.

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31

Wang, Xiao-yu. "Deduced amino acid sequence and gene sequence of microvitellogenin, a female specific hemolymph and egg protein from the tobacco hornworm, Manduca sexta". Diss., The University of Arizona, 1988. http://hdl.handle.net/10150/184329.

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Microvitellogenin is a female specific yolk protein from the tobacco hornworm moth Manduca sexta. A cDNA library was constructed from poly (A)⁺ RNA isolated from adult female fat body. cDNA clones of mRNA for microvitellogenin were isolated by screening the cDNA library with antiserum against microvitellogenin. The results of Northern blot analysis and hybrid selection indicated that the cDNA clone was specific for microvitellogenin. The complete nucleotide sequence of the 834 base pair cDNA insert has been determined by the dideoxy chain termination method. The deduced amino acid sequence was compared with the N-terminal sequence determined by Edman degradation, an amino terminal extension of 17 amino acids appeared to be a signal peptide. The cDNA sequence predicts that the mature microvitellogenin is a protein of 232 amino acids with a calculated molecular weight of 26,201. A comparison of the translated amino acid sequence with the sequences in National Biomedical Research Foundation protein library did not establish any sequence similarity with known proteins. The microvitellogenin gene begins to be expressed in the fat body on the first day of the wandering (prepupal) females as determined by using the cDNA insert as a probe to hybridize with the mRNA for microvitellogenin. The cDNA probe was also used to screen a genomic library of M. sexta, yielding three genomic clones for microvitellogenin. One of them was characterized and it contained the complete microvitellogenin gene. The gene sequence was determined. Comparison to the cDNA sequence showed that the microvitellogenin gene contains an intron near the 5'-end of the non-coding region. The 5'-flanking sequence of the gene has been compared to the same regions of yp genes of Drosophila and vitellogenin genes of locust, some similar sequences have been observed and discussed.

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32

Cronshaw, Andrew D. "Amino acid sequence studies of lysyl oxidase and TRAMP (tyrosine rich acidic matrix protein)". Thesis, University of Edinburgh, 1994. http://hdl.handle.net/1842/19663.

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Lysyl oxidase initiates crosslinking in collagens and elastin by the conversion of specific lysine (and, in collagen, hydroxylysine) residues to peptidyl α-aminoadipic-δ-semialdehyde. Porcine skin lysyl oxidase (M_r=34K) and a protein (M_r=24K) with which the enzyme co-purifies have been isolated and characterised. The 24K protein was originally thought to be a degradation product of lysyl oxidase but this study shows it to be a distinct protein. Four variants of lysyl oxidase and five variants of the 24K protein were identified by Mono Q anion-exchange Fast Protein Liquid Chromatography (FPLC). Each lysyl oxidase variant was subjected to amino acid analysis, which did not reveal any differences between variants, and by mass analysis, which showed small incremental changes between the variants. All the 24K protein variants were indistinguishable by amino acid analysis, though the protein was clearly distinct from lysyl oxidase. As with lysyl oxidase however, mass analysis showed small incremental changes between each TRAMP variant. Both lysyl oxidase and the 24K protein were found to be N-terminally blocked. A variety of cleavage methods were employed and the resulting peptides were subjected to mass and sequence analysis. Lysyl oxidase was cleaved using cyanogen bromide and the N-terminal fragment was found and sub-digested with endoproteinase-Asp-N. From these peptides it was possible to suggest the location of the N-terminus of lysyl oxidase. The 24K protein was cleaved with cyanogen bromide and digested with various enzymes which included pyroglutamate aminopeptidase, clostripain, protease V8, and endoproteinase-Asp-N.

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33

Cherry, Melissa A. "Sequence dependence of the activity of amphipathic peptides". View electronic thesis, 2008. http://dl.uncw.edu/etd/2008-2/rp/cherrym/melissacherry.pdf.

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34

Tsoi, Carrie. "Cloning and characterization of canine sulfotransferases /". Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-679-0/.

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35

McLennan, Neil F. "Studies on the carboxyl-terminal amino acid sequence of the chaperonin GroEL from Escherichia coli". Thesis, University of Edinburgh, 1993. http://hdl.handle.net/1842/11140.

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Previous work from our laboratory had suggested that the carboxyl-terminus of GroEL limited the ability of this protein to reverse the temperature-sensitive defects of dnaA^ts mutations in E. coli. This carboxyl-terminus consists of a 13 amino acid string of glycine and methionine residues, a motif that is highly conserved amongst many of the GroEL homologues sequenced so far. A clone was constructed which expressed a form of GroEL lacking this motif. Surprisingly this clone (which also expressed wild-type groES) was unable to suppress dnaA^ts mutations when overexpressed, but was able to complement groEL^ts mutations (even when present in single copy). A groE deletion mutant strain was constructed and this too was complemented by the truncated form of groEL. The resulting strain, carrying only truncated groEL, was extensively characterized and found to behave identically to an isogenic strain carrying wild type groEL, in that growth rates, temperature dependence, carbon source utilization, bacteriophage sensitivity, ethanol sensitivity, UV sensitivity and β-lactamase excretion were all found to be identical between the two strains. However, competition experiments involving co-culturing of the strains carrying groEL + groEL_trdemonstrated an advantage to the cells expressing the wild-type gene when grown at 42^oC. The advantage was found to be due to the strain encoding the truncated groEL exiting stationary phase and entering log-phase growth more slowly than cells expressing groEL+. It was also found that strains expressing groEL_trare more sensitive to the dye crystal violet, and low levels of some other biocide at 42⁰C. This suggests a role for the GroE proteins in membrane biogenesis and.or maintenance as well as an involvement of the glycine-methionine sequence.

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36

Tolliver, Benjamin M., Devaiah P. Shivakumar i Cecelia A. McIntosh. "Effects of Amino Acid Sequence Insertion on the Substrate Preference of a Citrus Paradisi Glucosyltransferase". Digital Commons @ East Tennessee State University, 2013. https://dc.etsu.edu/etsu-works/347.

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Glucosyltransferases (GTs) are enzymes which perform glucosylation reactions, which involve attaching a UDP-activated glucose molecule to acceptor molecules specifi c to the enzyme. The enzyme which our lab focuses its research on is a fl avonol-specifi c 3-OGT found in Citrus paradisi, or grapefruit (Cp3GT). This enzyme is part of the class of enzymes known as fl avonoid GTs, which are responsible for, among other things, the formation of compounds which can affect the taste of citrus. Our lab focuses its research on performing site-directed mutagenesis on Cp3GT in an attempt to discover the residues important for substrate and regiospecifi city. In this study, we are testing the basis of substrate septicity of Cp3GT. We hypothesize that incorporation of fi ve amino acids specifi c to Citrus sinensis GT (CsGT) into Cp3GT at 308th position may facilitate mCp3GT to use anthocyanidins as one of the substrates. We report our fi ndings thus far concerning the addition of specifi c residues to the Cp3GT’s amino acid sequence based on an alignment with the sequence of a putative fl avonoid GT found in Citrus sinensis.

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37

Leonchiks, Ainars. "Regulation of protein degradation by virus derived repeated amino acid sequences /". Stockholm, 2002. http://diss.kib.ki.se/2002/91-7349-206-x/.

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38

Nanuwa, Sundeep. "Investigation into the role of sequence-driven-features and amino acid indices for the prediction of structural classes of proteins". Thesis, De Montfort University, 2013. http://hdl.handle.net/2086/9033.

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The work undertaken within this thesis is towards the development of a representative set of sequence driven features for the prediction of structural classes of proteins. Proteins are biological molecules that make living things function, to determine the function of a protein the structure must be known because the structure dictates its physical capabilities. A protein is generally classified into one of the four main structural classes, namely all-α, all-β, α + β or α / β, which are based on the arrangements and gross content of the secondary structure elements. Current methods manually assign the structural classes to the protein by manual inspection, which is a slow process. In order to address the problem, this thesis is concerned with the development of automated prediction of structural classes of proteins and extraction of a small but robust set of sequence driven features by using the amino acid indices. The first main study undertook a comprehensive analysis of the largest collection of sequence driven features, which includes an existing set of 1479 descriptor values grouped by ten different feature groups. The results show that composition based feature groups are the most representative towards the four main structural classes, achieving a predictive accuracy of 63.87%. This finding led to the second main study, development of the generalised amino acid composition method (GAAC), where amino acid index values are used to weigh corresponding amino acids. GAAC method results in a higher accuracy of 68.02%. The third study was to refine the amino acid indices database, which resulted in the highest accuracy of 75.52%. The main contributions from this thesis are the development of four computationally extracted sequence driven feature-sets based on the underused amino acid indices. Two of these methods, GAAC and the hybrid method have shown improvement over the usage of traditional sequence driven features in the context of smaller and refined feature sizes and classification accuracy. The development of six non-redundant novel sets of the amino acid indices dataset, of which each are more representative than the original database. Finally, the construction of two large 25% and 40% homology datasets consisting over 5000 and 7000 protein samples, respectively. A public webserver has been developed located at http://www.generalised-protein-sequence-features.com, which allows biologists and bioinformaticians to extract GAAC sequence driven features from any inputted protein sequence.

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Maitland, Murray E. "A correlation between the distribution of biological apatite and amino acid sequence of type I collagen". Thesis, University of British Columbia, 1989. http://hdl.handle.net/2429/27591.

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The present study was undertaken to examine the distribution of biological apatite within type I collagen fibrils of calcifying turkey leg tendons. The localization of apatite was determined by both bright field and selected-area dark field electron microscopy and was correlated with specific classes of amino acids from chick type I collagen sequence data by computer modelling. These electron microscopic techniques illustrated that apatite occurs in both the gap and overlap zones at early stages of mineralization in an asymmetric pattern which corresponds to the polarized IM- to C- molecular orientation within the collagen fibril. Based on comparisons with theoretical computer images of the known amino acid sequence of collagen it was determined for early stages of mineral deposition that apatite is excluded from areas of high hydrophobic density. The gap zone is less hydrophobic than the overlap zone on average but each of these zones had areas of high density of hydrophobic amino acids which corresponded to sites of low mineral density. Conversely, regions with a high proportion of mineral were low in density of hydrophobic amino acids. The possible interactions between hydrophobic effects and the process of mineral deposition are discussed. In addition, the accommodation of collagen to the deposition of apatite in the overlap zone is discussed.
Medicine, Faculty of
Graduate

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40

Båvner, Ann. "Molecular mechanisms of transcriptional repression by the orphan receptor SHP /". Stockholm, 2005. http://diss.kib.ki.se/2005/91-7140-212-8/.

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Pinali, Cristian. "Cross-correlation of amino acid sequence data to explain fibril formation in a number of collagen subtypes". Thesis, Cardiff University, 2008. http://orca.cf.ac.uk/54916/.

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Collagen is the most abundant protein in vertebrates. In particular, fibrillar collagens are found in bone, tendon, dermis, ligament, cartilage, cornea and blood vessel walls to mention but a few. Fibrillar collagens can be thought of as rigid linear structures and therefore are relatively simple to study from a theoretical point of view. In this thesis, a study on fibrillar collagen packing is presented. Since these collagens can be represented by a linear sequence of elements, it is possible to represent the hydrophobic or the electrostatic interactions between two collagen molecules by means of a cross correlation function. In fact, in this way we represent how many amino acids with a given property face each as a function of the displacement between the two sequences they belong to. Since cross correlation can be thought of as a scoring of the interactions between two adjacent molecules we will refer to it as the scoring method. In the first instance, the scoring method was applied to a linear amino acids sequence of type I collagen to probe the hydrophobic and attractive electrostatic interactions acting on it. Then, the method was applied systematically to type II, type III type XI collagens and to mixtures of type II and type III collagens. The appearances that these collagens would have in an electron microscope were calculated by a simulated staining method, and a comparison between real collagen fibrils and the models built in accordance to the findings of the scoring method was carried out. The scoring method allowed us to predict the correct stagger for collagen fibrils in parallel configuration. It also allowed us to predict and explain the correct axial stagger between type I collagen fibrils oriented in an antiparallel fashion. The scoring method was also used to explain oblique banding patterns found in reconstituted type II collagen fibrils. When applied to type II and type III collagen fibrils oriented in an antiparallel fashion, it shed light on a possible supercoiled structure. The validity of the scoring method was confirmed by its comparison with real collagen fibrils and, in principle, it could be extended to all proteins that can be represented as a simple linear sequence of amino acids.

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Bartfeld, Neil Stuart. "Isolation, characterization, cDNA cloning and deduced amino acid sequence of transferrin from the tobacco hornworm, Manduca sexta". Diss., The University of Arizona, 1990. http://hdl.handle.net/10150/185213.

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An iron-binding 77 kilodalton glycoprotein was isolated from hemolymph of the adult sphinx moth, Manduca sexta. This protein bound a single ferric ion both in vivo and in vitro and had a secondary structure similar to that of human serum transferrin and human lactoferrin, as judged by CD spectra. Antiserum generated against this protein was used to screen a fifth instar, day four, larval fat body cDNA library. A 2.0 kilobase clone was isolated and used to probe a northern blot of both total and poly(A)⁺ RNA from fat body, revealing a message of 2.3 kilobases. The message is expressed throughout the fourth instar, fifth instar, wandering, pupal and adult stages. The 2.0 kilobase clone selected an mRNA which, when translated in vitro, produced an immunoprecipitable 77 kDa protein. The 2.0 kb clone was used as a probe to further screen the cDNA library, resulting in the isolation of three full-length clones. The complete nucleotide sequence of one 2183 base pair cDNA insert was determined. The deduced amino acid sequence contained an 18 amino acid signal sequence which, when cleaved, resulted in a mature protein sequence of 663 amino acids with a calculated molecular weight of 73,436. The first 34 residues of the mature protein were identical to those determined by Edman degradation of the intact protein. The sequence contained four consensus N-linked glycosylation sites (Asn-X-Thr/Ser). The sequence was used to search the National Biomedical Research Foundation protein database. The proteins exhibiting the greatest similarity were human serum transferrin, chicken ovotransferrin, human lactoferrin and human melanotransferrin. When the five sequences were aligned using a multiple alignment program, the insect protein contained approximately 27% identical residues when compared to each of the other transferrins. The greatest areas of similarity were around the iron binding sites. Moreover, 23 of the 24 cysteine residues in the insect protein occupied identical positions as compared to the other transferrins, indicating a similar overall tertiary structure. The insect protein also exhibited some internal homology between the N-terminal and C-terminal halves of the molecule. Ligands capable of binding an iron atom were present in the N-terminal half, but most were lacking in the C-terminal half. Based upon sequence comparisons and other structural and functional data, we believe that we have isolated and sequenced an invertebrate transferrin, the first such molecule to have its entire sequence determined.

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Zhao, Jing. "Protein Structure Prediction Based on Neural Networks". Thèse, Université d'Ottawa / University of Ottawa, 2013. http://hdl.handle.net/10393/23636.

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Proteins are the basic building blocks of biological organisms, and are responsible for a variety of functions within them. Proteins are composed of unique amino acid sequences. Some has only one sequence, while others contain several sequences that are combined together. These combined amino acid sequences fold to form a unique three-dimensional (3D) shape. Although the sequences may fold proteins into different 3D shapes in diverse environments, proteins with similar amino acid sequences typically have similar 3D shapes and functions. Knowledge of the 3D shape of a protein is important in both protein function analysis and drug design, for example when assessing the toxicity reduction associated with a given drug. Due to the complexity of protein 3D shapes and the close relationship between shapes and functions, the prediction of protein 3D shapes has become an important topic in bioinformatics. This research introduces a new approach to predict proteins’ 3D shapes, utilizing a multilayer artificial neural network. Our novel solution allows one to learn and predict the representations of the 3D shape associated with a protein by starting directly from its amino acid sequence descriptors. The input of the artificial neural network is a set of amino acid sequence descriptors we created based on a set of probability density functions. In our algorithm, the probability density functions are calculated by the correlation between the constituent amino acids, according to the substitution matrix. The output layer of the network is formed by 3D shape descriptors provided by an information retrieval system, called CAPRI. This system contains the pose invariant 3D shape descriptors, and retrieves proteins having the closest structures. The network is trained by proteins with known amino acid sequences and 3D shapes. Once the network has been trained, it is able to predict the 3D shape descriptors of the query protein. Based on the predicted 3D shape descriptors, the CAPRI system allows the retrieval of known proteins with 3D shapes closest to the query protein. These retrieved proteins may be verified as to whether they are in the same family as the query protein, since proteins in the same family generally have similar 3D shapes. The search for similar 3D shapes is done against a database of more than 45,000 known proteins. We present the results when evaluating our approach against a number of protein families of various sizes. Further, we consider a number of different neural network architectures and optimization algorithms. When the neural network is trained with proteins that are from large families where the proteins in the same family have similar amino acid sequences, the accuracy for finding proteins from the same family is 100%. When we employ proteins whose family members have dissimilar amino acid sequences, or those from a small protein family, in which case, neural networks with one hidden layer produce more promising results than networks with two hidden layers, and the performance may be improved by increasing the number of hidden nodes when the networks have one hidden layer.

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Bakeman, Valerie R. "Pacific and Atlantic coast mollusk shells chromatographic amino acid racemization kinetics and interlaboratory comparisons /". Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file 4.12 Mb., 271 p, 2006. http://catalog.hathitrust.org/api/volumes/oclc/133182881.html.

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Norin, Annika. "Medium chain dehydrogenases/reductases : alcohol dehydrogenases of novel types /". Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-675-8/.

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Ng, Pauline Crystal. "PSSMs : not just roadkill on the information superhighway /". Thesis, Connect to this title online; UW restricted, 2002. http://hdl.handle.net/1773/8116.

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Lutya, Portia Thandokazi. "Expression and purification of the novel protein domain DWNN". Thesis, University of the Western Cape, 2002. http://etd.uwc.ac.za/index.php?module=etd&amp.

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Proteins play an important role in cells, as the morphology, function and activities of the cell depend on the proteins they express. The key to understanding how different proteins function lies in an understanding of the molecular structure. The overall aim of this thesis was the determination of the structure of DWNN domains. This thesis described the preparation of samples of human DWNN suitable for structural analysis by nuclear magnetic resonance spectroscopy (NMR), as well as NMR analysis.

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Piriyapongsa, Jittima. "Origin and evolution of eukaryotic gene sequences derived from transposable elements". Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/24766.

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Thesis (Ph.D.)--Biology, Georgia Institute of Technology, 2008.
Committee Chair: Jordan, I. King; Committee Member: Borodovsky, Mark; Committee Member: Bunimovich, Leonid; Committee Member: Choi, Jung; Committee Member: McDonald, John.

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Lin, Jasper Chua. "Application of the Trp-cage motif to polypeptide folding questions /". Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/8684.

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Sankala, Marko. "Role of macrophage receptor MARCO in host defense /". Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-686-3.

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