Rozprawy doktorskie: „Protein conformation”

1

Link, Justin J. "Ultrafast Protein Conformation Dynamics". The Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=osu1230584570.

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Wang, Chu. "Improved conformational sampling for protein-protein docking /". Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/9194.

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3

Billsten, Peter. "Studies on the conformation of adsorbed proteins". Lund : Göteborg University, 1997. http://catalog.hathitrust.org/api/volumes/oclc/39776983.html.

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4

Florane, H. "Exploring protein conformation with mass spectrometry". Thesis, University of Edinburgh, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.650980.

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The first part of this thesis describes the development and viability of a phase I screening system for obtaining a rank order of affinity of novel ligands against the immunophilin, Cyclophilin A (CypA). The naturally occurring inhibitor Cyclosporin A (CsA) was used as a positive control to validate a method for calculating the dissociation constant (K_d). An HPLC autosampler and pumping system was used as a high throughput on-line electrospray ionisation (ESI)-MS sampling system. Optimised ESI conditions were then used to screen novel ligands from 3 combinatorial libraries and approaches for data analysis is discussed. Hydrogen/deuterium exchange (HDX) can be used directly and indirectly as a means for studying protein conformations. Melittin, the major component of honey bee venom is taken here as a model system for studying secondary structure in solution and the gas phase. Comprising a 26 amino acid polypeptide, melittin occupies a random coil in aqueous conditions which can be transformed into an α-helix under increasingly hydrophobic conditions. A variety of HDX techniques were utilised: i) comparing rats of deuterium (d-) uptake by direct infusion – ESI at different pDs and methanol concentrations; ii) PLIMSTEX (protein-ligand interactions by mass spectrometry, titration and HDX) at high and low salt concentrations with varying pDs; iii) gas phase exchange in an LCQ ion trap using He/d-methanol as the bath gas. Melittin was pre-incubated in a variety of methanol concentrations. Comparing results from these different approaches, α-helical retention has been shown to exist in the N-terminal half of the peptide. All the afore-mentioned techniques developed using melittin were adapted for CypA. Comparisons of d-uptake in the presence and absence of CsA shows the ligand to have a stabilising affect on the protein.

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5

Nicholls, Robert Adam. "Conformation-independent comparison of protein structures". Thesis, University of York, 2011. http://etheses.whiterose.ac.uk/2120/.

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The comparative analysis of protein structures is often performed in order to identify and explore similarities/dissimilarities present between target structures. Whilst many tools are available for structural comparison, the development of new tools providing different information is desirable. The work presented here concerns the development of ProSMART (Procrustes Structural Matching Alignment and Restraints Tool), a tool to aid the comparative analysis of protein structures. Primarily, the software is used for conformation-independent pairwise structural alignment, allowing identification of local similarities, and quantification of dissimilarities. Functionality also allows the identification and superposition of rigid substructures, providing output that allows visualisation of local dissimilarities by means of residue-based scoring. The ProSMART pairwise alignment method optimises the net agreement of local structures along the chain, using structural fragments. In order to maintain conformation-independence, the structure-based residue alignment does not enforce global rigidity of chains, nor domains. This feature makes the tool suited to the analysis of domain movement and other conformational changes, as well as for the identification of structural units conserved between seemingly different structures. Given an alignment, ProSMART can be used to generate external restraints on the distances between relatively close atoms, for use in the crystallographic refinement of macromolecules. Using one or more similar structures, the software generates restraints that are intended to help the target protein adopt a conformation that is more reasonable, whilst allowing global flexibility. Such restraints may stabilise refinement in some cases, especially at low resolution where experimental data alone may not be sufficient. We also present a method of Procrustes score normalisation, which allows the consideration of the significance of observed fragment scores. It is suggested that the resulting global scores for the overall pairwise agreement of protein structures may provide an interesting new way of viewing protein fold space.

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6

Watt, Stephen J. "Use of electrospray ionization mass spectrometry to study protein conformation and protein-protein interactions". Access electronically, 2005. http://www.library.uow.edu.au/adt-NWU/public/adt-NWU20060516.114814/index.html.

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Thesis (Ph.D.)--University of Wollongong, 2005.
Typescript. EMBARGOED-this thesis is subject to a six months embargo (07/09/06) and may only be viewed and copied with the permission of the author. For further information please Contact the Archivist. Includes bibliographical references: leaf 159-194.

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7

Rashid, Mahmood Abdur. "Heuristic Based Search for Protein Structure Prediction". Thesis, Griffith University, 2014. http://hdl.handle.net/10072/367134.

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Proteins that are essentially sequences of amino acids, adopt specific folded 3-dimensional (3D) structures to perform their specific tasks. However, misfolded proteins cause fatal diseases. Hence, protein structure prediction (PSP) has emerged as an important multi-disciplinary research problem. Given a protein sequence, the PSP problem is to find a 3D structure of the protein such that the total free energy amongst the amino acids in the sequence is minimised. In-vitro laboratory methods are time-consuming, expensive, and failure-prone. Conversely, computational methods are NP-hard even when the models are simplified by using low-resolution energy functions and lattice-based structures.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Institute for Integrated and Intelligent Systems
Science, Environment, Engineering and Technology
Full Text

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8

Chivian, Dylan Casey. "Application of information from homologous proteins for the prediction of protein structure /". Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/9264.

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9

Hosia, Waltteri. "Molecular mechanisms in amyloid fibril formation /". Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-976-5.

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10

Sandin, Sara. "Cryo-electron tomography of individual protein molecules /". Stockholm, 2005. http://diss.kib.ki.se/2005/91-7140-462-7/.

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11

Giasuddin, Abul Bashar Mohammad. "Silane Modulation of Protein Conformation and Self-Assembly". DigitalCommons@USU, 2018. https://digitalcommons.usu.edu/etd/7029.

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This research focused on development of nanoparticle- based therapeutics against amyloid fibrils. Amyloid fibrils are associated with various diseases such as Parkinson’s, Huntington’s, mad cow disease, Alzheimer’s, and cataracts. Amyloid fibrils develop when proteins change their shape from a native form to a pathogenic “misfolded” form. The misfolded proteins have the ability to recruit more native proteins into the pathogenic forms, which self-assemble into amyloid fibrils that are hallmarks of the various protein-misfolding diseases listed above. Amyloid fibrils are highly resistant to degradation, which may contribute to the symptoms of amyloid diseases. Synthetic drugs, natural compounds, and antibodies are widely explored for potential to stop pathogenic protein assembly or to promote fibril degradation and clearance, but to date have had little success in relieving symptoms in clinical trials. In this research, I have synthesized fluorine-containing silica nanoparticles (NPs), and tested their fibril-inhibiting activity against amyloid fibrils formed by a non-pathogenic protein, β-lactoglobulin (BLG). These fluoro-silica NPs prevented BLG amyloid formation, whereas non-fluorinated nanoparticle analogs did not inhibit fibrillation under the same reaction conditions. The fluoro-silica NPs interacted with the BLG protein in a manner that prevented the protein from adopting a form that could self-assemble into fibrils. Additional applications of the NPs were explored as small-molecule drug-delivery systems; such that multiple functionalities could be introduced into a single nano- therapeutic.

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12

Kim, Junghwa. "Roles of intermediate conformation and transient disulfide bonding on native folding of P22 tailspike protein". Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file 2.50 Mb., 176 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:3220719.

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13

Pothier, Laura J. "Effects of amino acid substitutions on the conformation and stability of A[beta]₁₆₋₂₂ aggregates /". Connect to online version, 2007. http://ada.mtholyoke.edu/setr/websrc/pdfs/www/2007/213.pdf.

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14

Simons, Kim T. "Deciphering the protein folding code : ab initio prediction of protein structure /". Thesis, Connect to this title online; UW restricted, 1998. http://hdl.handle.net/1773/9234.

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15

Budi, Bunarta Hendra (Akin), i akin budi@rmit edu au. "On the effects of external stresses on protein conformation". RMIT University. School of Applied Sciences, 2006. http://adt.lib.rmit.edu.au/adt/public/adt-VIT20061116.123431.

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The use of electromagnetic devices such as microwave ovens and mobile phones has certainly brought convenience to our lives. At the same time, the proliferation of said devices has increased public awareness of the potential health hazards. It is generally assumed that there is little or no risk associated with the use of electromagnetic devices, based on the small amount of power associated with those devices. However, case studies on animals indicate that the risk cannot be entirely ruled out. It has long been known that proteins are sensitive to stress, arising from various sources such as temperature, chemical, pressure, and changes in pH condition. In all of these cases, the protein exhibits clear signs of damage and distress, which range from slight unfolding to complete loss of structure. Frequently, the damage to the protein is alleviated by refolding, either by itself or by the aid of molecular chaperones. However, if the damage to the protein is too great, the protein will generally undergo proteolysis. Opinion has been divided over the implication of prolonged use of electromagnetic devices to human health. Studies conducted on animals so far have given conflicting results. The studies on the separate components, electric and magnetic fields, also give inconclusive results. This indicates that our understanding on how electric and magnetic fields interact with biological matter is incomplete. In this project, we use molecular dynamics to explore the behaviour of two forms of insulin chain-B, isolated and monomeric (in the presence of chain-A with all disulfide bonds intact), at ambient conditions and under the influence of various stress. Specifically, we focus our attention to thermal stress and electric field stress. The electric field stress considered in this study takes several forms: static and oscillating with three different frequencies. These fields have strength ranging from 1806 V/m to 109 V/m. By performing molecular dynamics simulations totalling over 500 ns, we have gained valuable insights into the effects of elevated temperature and electric field on insulin chain-B. We observed differences in the damage mechanisms by the application of static electric field and oscillating field. The application of static fields restricts the conformational freedom of a protein, whereas the application of oscillating fields increases the mobility and flexibility of the protein, similar to the effect of thermal stress. Both of these interfere with the normal behaviour of a protein. We have also observed frequency-dependent effects, with low frequency fields having static field-like characteristics in damage mechanism.

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16

Katayama, Derrick S. "Towards a mechanistic understanding of pharmaceutical protein stabilization in solution and the solid state /". Connect to full text via ProQuest. Limited to UCD Anschutz Medical Campus, 2006.

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Thesis (Ph.D. in Pharmaceutical Sciences) -- University of Colorado at Denver and Health Sciences Center, 2006.
Typescript. Includes bibliographical references (leaves 159-173). Free to UCDHSC affiliates. Online version available via ProQuest Digital Dissertations;

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17

Ngo, Jacky Chi Ki. "SR protein kinase 1 conformation, substrate recognition and catalysis /". Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2006. http://wwwlib.umi.com/cr/ucsd/fullcit?p3211379.

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Thesis (Ph. D.)--University of California, San Diego, 2006.
Title from first page of PDF file (viewed June 13, 2006). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 169-184).

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18

Marshall, R. Andrew. "Regulation of protein synthesis via changes in ribosome conformation /". May be available electronically:, 2008. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.

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19

Boussert, Stéphanie Van Dorsselaer Alain Giralt Ernest. "Structural studies of proteins and protein complexes by mass spectrometry and atomic force microscopy". Strasbourg : Université Louis Pasteur, 2008. http://eprints-scd-ulp.u-strasbg.fr:8080/977/01/BOUSSERT_Stephanie_2008.pdf.

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20

Lundell, Sandra J. "Quantum Mechanical Studies of N-H···N Hydrogen Bonding in Acetamide Derivatives and Amino Acids". DigitalCommons@USU, 2018. https://digitalcommons.usu.edu/etd/7309.

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Proteins are made of vast chains of amino acids that twist and fold into intricate designs. These structures are held in place by networks of noncovalent interactions. One of these, the hydrogen bond, forms bridges between adjacent pieces of the protein chain and is one of the most important contributors to the shape and stability of proteins. Hydrogen bonds come in all shapes and sizes and a full understanding of these not only aids in our understanding of proteins in general but can bridge the gap to finding cures to many protein-related diseases, such as sickle-cell anemia. The primary aim of this thesis is to discover if a specific type of hydrogen bond, the N-H···N bond, occurs within proteins and if so, if it contributes to the structure and stability of proteins.

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21

Zang, Chen. "Ultrafast Spectroscopic Study of Protein Conformation Dynamics and Hydration Dynamics". The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1299481658.

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22

Nilsson, Johan. "Membrane protein topology : prediction, experimental mapping and genome-wide analysis /". Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-963-3/.

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23

Sapsaman, Temsiri. "An energy landscaping approach to the protein folding problem". Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/31637.

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Thesis (Ph.D)--Mechanical Engineering, Georgia Institute of Technology, 2010.
Committee Chair: Harvey Lipkin; Committee Member: Joel S. Sokol; Committee Member: Michael J. Leamy; Committee Member: Nader Sadegh; Committee Member: Stephen C. Harvey. Part of the SMARTech Electronic Thesis and Dissertation Collection.

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24

Joseph, Agnel Praveen. "Comparison of protein folds based on similarities in local backbone conformation". Paris 7, 2011. http://www.theses.fr/2011PA077100.

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Une grande partie de mon travail de thèse porte sur le développement de méthodes efficaces pour l'alignement par paires et multiples protéines structurelles. Ceci est basé sur l'utilisation de la protéine Blocks qui est le plus largement utilisé alphabet structural [1, 2]. Une structure de la protéine complète peut être représenté par une séquence d'alphabets, où chaque alphabet correspond à un PB. L'alignement des séquences PB donne une comparaison de la structure des protéines. Basé sur des stratégies classiques d'alignement de séquences, un outil efficace pour l'alignement de séquences PB a été développé. Matrices de substitution PB raffinés et une ancre approche de programmation dynamique ont été utilisées pour améliorer l'efficacité de cette approche. Un gain significatif de la qualité de l'alignement, d'environ 82% a été obtenue et l'efficacité des mines a été amélioré de 6,8% [3, 4]. La méthode a été encore renforcée par l'ajout de poids de substitution qui correspondent à des régions structurellement similaires identifiés comme des ancres dans alignements. Comme pour iPBA, l'alignement des séquences de BPs est guidé par les équivalences entre couplée à un raffinement itératif par le logiciel Profit. La structure la plus semblable à d'autres structures au sein du groupe a été choisie comme référence lors de l'affinage 3D et de raffinements. Lorsque comparé à MULTIPROT, MUSTANG et HOMSTRAD, notre méthode d'alignement multiple basée sur les BPs (mulPBA) était meilleure dans plus de 85% des cas. La stratégie d'alignement iPBA a également été utilisée pour évaluer la performance d'une méthode de reconnaissance de la structure basée sur la séquence prédite des BPs. Les données sur les structures secondaires prédites et l'accessibilité au solvant prédite ont été utilisés pour améliorer l'exactitude de reconnaissance de la structure. L'influence des données sur les espèces sur la relation séquence-structure a également été analysées en utilisant les BPs [5]. Les relations observées dans les séquences caméléons [6] qui adoptent des conformations différentes dans les structures de protéines, ont également été étudiés en détail. Un protocole efficace et utile a également été développé pour l'attribution des hélices PolyProline II qui peuvent être facilement incorporés dans DSSP, outil largement utilisé pour l'affectation structure secondaire [7]
Protein Structure Comparison is an efficient means for function characterization and evolutionary studies. We propose an improved approach for three dimensional (3D) protein structure comparison based on similarities in local backbone conformations. A library of 16 frequently occurring penta-peptide backbone conformations, namely Protein Blocks (1,2), was used to transform 3D structural information as a sequence. This reduces the problem of structural comparison to a more classical sequence alignment. The use of an anchor based dynamic programming algorithm with specialized gap penalties resulted in a significant improvement over earlier studies based on simple global alignments. The alignment quality improved by about 82% and the efficiency in searching a structure databank for related folds was also enhanced by 6. 2% (3,4). This approach for pairwise structure comparison (iPBA) is implemented as a web server http://www. Dsimb. Inserm. Fr/dsimb tools/ipba/. IPBA was further extended to the development of a multiple structural alignment tool. A progressive alignment strategy was adopted and local weights were added for structurally similar regions (mulPBA) (Joseph et al. In peparation). Comparison with other structural alignment tools showed that both the PB based alignment approaches (iPBA & mulPBA) often give the best performance and can be placed as one of the top two methods currently available. Local conformational variations among structurally similar proteins were also studied in detail (Joseph et al. Submitted). Subtle changes are found to occur mainly in the regions comprising turns. The preference for the indel sites are also confined to a few backbone conformations involving p-turns and helix C-caps. The alignment strategy behind iPBA was also used to assess the performance of a fold recognition approach based on PB prediction. The influence of species specific data on sequence-structure relationships was also analyzed using PBs (5). Relationships observed in chameleon sequences (6) that adopt different conformations in protein structures, was studied in detail. An efficient protocol for the assignment of PolyProline-II helices, which can be easily incorporated into the DSSP secondary structure assignment tool was also developed (7)

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25

Hatcher, Kristen-Louise. "Conformation Based Reagents for the Detection of Disease-Associated Prion Protein". Case Western Reserve University School of Graduate Studies / OhioLINK, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=case1232747817.

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26

Käll, Lukas. "Predicting transmembrane topology and signal peptides with hidden Markov models /". Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-719-7/.

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27

English, William R. "Effects of calcium on conformation and stability of porcine pancreatic phospholipase Aâ†2". Thesis, University of Kent, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285981.

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28

Kallberg, Yvonne. "Bioinformatic methods in protein characterization /". Stockholm, 2002. http://diss.kib.ki.se/2002/91-7349-370-8/.

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29

Cao, Jin. "Single Molecular Spectroscopy and Atomic Force Manipulation of Protein Conformation and Dynamics". Bowling Green State University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1416588612.

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30

Wang, Fei. "Biochemical Studies Of Interactions Between Prion Protein And Lipids". The Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=osu1227725062.

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31

Devlin, Glyn L. "The mechanisms of serpin misfolding and its inhibition". Monash University, Dept. of Biochemistry and Molecular Biology, 2003. http://arrow.monash.edu.au/hdl/1959.1/9469.

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32

Strickland, Dawn Michelle. "Maximum cliques with application to protein structure alignment". Diss., Georgia Institute of Technology, 2002. http://hdl.handle.net/1853/24081.

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33

Cassel, Marika. "Studies on the Conformation of Transmembrane Polypeptides in Membrane Proteins". Doctoral thesis, Stockholm : Deptartment of Biochemistry & Biophysics, Stockholm University, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-759.

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34

Larsericsdotter, Helén. "Macromolecules at interfaces /". Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4661.

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35

Duan, Jianxin. "Protein folding, stability and recognition /". Stockholm, 2004. http://diss.kib.ki.se/2004/91-7140-098-2/.

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36

Masuda, Yuichi. "Identification of Toxic Conformation in the Aggregates of 42-residue Amyloid β-protein". Kyoto University, 2009. http://hdl.handle.net/2433/123973.

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Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第14661号
農博第1743号
新制||農||967(附属図書館)
学位論文||H21||N4434(農学部図書室)
UT51-2009-D373
京都大学大学院農学研究科食品生物科学専攻
(主査)教授入江一浩, 教授井上國世, 教授安達修二
学位規則第4条第1項該当

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37

Fears, Kenan Patrick. "Adsorption-induced changes in enzyme bioactivity correlated with adsorbed protein orientation and conformation". Connect to this title online, 2009. http://etd.lib.clemson.edu/documents/1246558493/.

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38

Mendez, Giraldez Raul. "Critical assessment of predicted interactions at atomic resolution". Doctoral thesis, Universite Libre de Bruxelles, 2007. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210664.

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Molecular Biology has allowed the characterization and manipulation of the molecules of life in the wet lab. Also the structures of those macromolecules are being continuously elucidated. During the last decades of the past century, there was an increasing interest to study how the different genes are organized into different organisms (‘genomes’) and how those genes are expressed into proteins to achieve their functions. Currently the sequences for many genes over several genomes have been determined. In parallel, the efforts to have the structure of the proteins coded by those genes go on. However it is experimentally much harder to obtain the structure of a protein, rather than just its sequence. For this reason, the number of protein structures available in databases is an order of magnitude or so lower than protein sequences. Furthermore, in order to understand how living organisms work at molecular level we need the information about the interaction of those proteins. Elucidating the structure of protein macromolecular assemblies is still more difficult. To that end, the use of computers to predict the structure of these complexes has gained interest over the last decades.

The main subject of this thesis is the evaluation of current available computational methods to predict protein – protein interactions and build an atomic model of the complex. The core of the thesis is the evaluation protocol I have developed at Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Université Libre de Bruxelles, and its computer implementation. This method has been massively used to evaluate the results on blind protein – protein interaction prediction in the context of the world-wide experiment CAPRI, which have been thoroughly reviewed in several publications [1-3]. In this experiment the structure of a protein complex (‘the target’) had to be modeled starting from the coordinates of the isolated molecules, prior to the release of the structure of the complex (this is commonly referred as ‘docking’).

The assessment protocol let us compute some parameters to rank docking models according to their quality, into 3 main categories: ‘Highly Accurate’, ‘Medium Accurate’, ‘Acceptable’ and ‘Incorrect’. The efficiency of our evaluation and ranking is clearly shown, even for borderline cases between categories. The correlation of the ranking parameters is analyzed further. In the same section where the evaluation protocol is presented, the ranking participants give to their predictions is also studied, since often, good solutions are not easily recognized among the pool of computer generated decoys.

An overview of the CAPRI results made per target structure and per participant regarding the computational method they used and the difficulty of the complex. Also in CAPRI there is a new ongoing experiment about scoring previously and anonymously generated models by other participants (the ‘Scoring’ experiment). Its promising results are also analyzed, in respect of the original CAPRI experiment. The Scoring experiment was a step towards the use of combine methods to predict the structure of protein – protein complexes. We discuss here its possible application to predict the structure of protein complexes, from a clustering study on the different results.

In the last chapter of the thesis, I present the preliminary results of an ongoing study on the conformational changes in protein structures upon complexation, as those rearrangements pose serious limitations to current computational methods predicting the structure protein complexes. Protein structures are classified according to the magnitude of its conformational re-arrangement and the involvement of interfaces and particular secondary structure elements is discussed. At the end of the chapter, some guidelines and future work is proposed to complete the survey.
Doctorat en Sciences
info:eu-repo/semantics/nonPublished

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39

Bai, Shujun. "Understanding physicochemical stability of proteins in solution and development of new analytical methods for freeze-dried protein formulations /". Connect to full text via ProQuest. Limited to UCD Anschutz Medical Campus, 2008.

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Thesis (Ph.D. in Pharmaceutical Sciences) -- University of Colorado Denver, 2008.
Typescript. Includes bibliographical references (leaves 134-146). Free to UCD Anschutz Medical Campus. Online version available via ProQuest Digital Dissertations;

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40

Bruce, Neil John. "Investigating protein conformational change via molecular dynamics simulation". Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/investigating-protein-conformational-change-via-molecular-dynamics-simulation(17145939-f643-4b23-bbb9-029cf5489c15).html.

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Accumulation and aggregation of the 42-residue amyloid-[beta] (A[beta]) protein fragment, which originates from the cleavage of amyloid precursor protein by beta and gamma secretase, correlates with the pathology of Alzheimer's disease (AD). Possible therapies for AD include peptides based on the A[beta] sequence, and recently identified small molecular weight compounds designed to mimic these, that interfere with the aggregation of A[beta] and prevent its toxic effects on neuronal cells in culture. Here, we use molecular dynamics simulations to compare the mode of interaction of an active (LPFFD) and inactive (LHFFD) [beta]-sheet breaker peptide with an A[beta] fibril structure from solid state NMR studies. We found that LHFFD had a weaker interaction with the fibril than the active peptide, LPFFD, from geometric and energetic considerations, as estimated by the MM/PBSA approach. Cluster analysis and computational alanine scanning identified important ligand-fibril contacts, including a possible difference in the effect of histidine on ligand-fibril [pi]-stacking interactions, and the role of the proline residue establishing contacts that compete with those essential for maintenance of the inter-monomer [beta]-sheet structure of the fibril. Our results show that molecular dynamics simulations can be a useful way to classify the stability of docking sites. These mechanistic insights into the ability of LPFFD to reverse aggregation of toxic A[beta] will guide the redesign of lead compounds, and aid in developing realistic therapies for AD and other diseases of protein aggregation. We have also performed long explicit solvent MD simulations of unliganded amyloid fibril in three putative protonation states, in order to better understand the energetic and mechanical features of the fibril receptor. Over 100 ns MD simulations, the trajectories where fibril has Glu11 and Glu22 side-chains protonated exhibit the least deviation from the initial solid state NMR structures. Free energy calculations on these rajectories suggest that the weakest fibril interface lies in the lateral rather than transverse direction and that there is little dependence on whether the lateral interface is situated at the edge or middle of the fibril. This agrees with recent reported steered molecular dynamics calculations. Secondly, in an effort to improve the ability of atomistic simulation techniques to directly resolve protein tertiary structure from primary amino acid sequence, we explore the use of a molecular dynamics technique based on swarm intelligence, called SWARM-MD, to identify the native states of two peptides, polyalanine and AEK17, as well as Trp-cage miniprotein. We find that the presence of cooperative swarm interactions significantly enhanced the efficiency of molecular dynamics simulations in predicting native conformation. However, it also is evident that the presence of outlying simulation replicas can adversely impact correctly folded replica structures. By slowly removing the swarm potential after folding simulations, the negative effect of the swarm potential can be alleviated and better agreement with experiment obtained.

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Phan, Jamie. "Investigating protein folding by the de novo design of an α-helix oligomer". Scholarly Commons, 2013. https://scholarlycommons.pacific.edu/uop_etds/859.

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Proteins are composed of a unique sequence of amino acids, whose order guides a protein to adopt its particular fold and perform a specific function. It has been shown that a protein's 3-dimensional structure is embedded within its primary sequence. The problem that remains elusive to biochemists is how a protein's primary sequence directs the folding to adopt such a specific conformation. In an attempt to gain a better understanding of protein folding, my research tests a novel model of protein packing using protein design. The model defines the knob-socket construct as the fundamental unit of packing within protein structure. The knob-socket model characterizes packing specificity in terms of amino acid preferences for sockets in different environments: sockets filled with a knob are involved in inter-helical interactions and free sockets are involved in intra-helical interactions. Equipped with this knowledge, I sought to design a unique protein, Ksα1.1, completely de novo. The sequence was selected to induce helix formation with a predefined tertiary packing interface. Circular dichroism showed that Ksα1.1 formed α-helical secondary structure as intended. The nuclear magnetic resonance studies demonstrated formation of a high order oligomer with increased protein concentration. These results and analysis prove that the knob-socket model is a predictive model for all α-helical protein packing. More importantly, the knob-socket model introduces a new protein design method that can potentially hold a solution to the folding problem.

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Davidson, Patricia Marie L. "Langmuir films and nanoparticle applications of a spider silk protein analog". Thesis, McGill University, 2006. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=100794.

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A synthetic analog of a spider silk protein (M4) was studied. Langmuir films were made and an inflexion in the isotherm indicated conformational changes upon compression. Deposition onto solid substrates was most successful using a hydrophobic substrate and the Langmuir-Schaeffer method. AFM was used to image the surface, which was mesh like and did not show any indication of order.
Gold nanoparticles were produced in the presence of the protein and protein solutions were added to read made nanoparticles for the purpose of displacing the weak ligands present. CD measurements were performed on the protein solutions to study its conformation. Nanoparticle size information was obtained from TEM images. DLS was used to determine if the protein was affected by the addition of the gold nanoparticles. Precipitation of the protein was shown not to affect the nanoparticles.

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Phan, Jamie. "Investigating protein folding by the de novo design of an α-helix oligomer : a thesis". Scholarly Commons, 2001. https://scholarlycommons.pacific.edu/uop_etds/859.

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Proteins are composed of a unique sequence of amino acids, whose order guides a protein to adopt its particular fold and perform a specific function. It has been shown that a protein's 3-dimensional structure is embedded within its primary sequence. The problem that remains elusive to biochemists is how a protein's primary sequence directs the folding to adopt such a specific conformation. In an attempt to gain a better understanding of protein folding, my research tests a novel model of protein packing using protein design. The model defines the knob-socket construct as the fundamental unit of packing within protein structure. The knob-socket model characterizes packing specificity in terms of amino acid preferences for sockets in different environments: sockets filled with a knob are involved in inter-helical interactions and free sockets are involved in intra-helical interactions. Equipped with this knowledge, I sought to design a unique protein, Ksα1.1, completely de novo. The sequence was selected to induce helix formation with a predefined tertiary packing interface. Circular dichroism showed that Ksα1.1 formed α-helical secondary structure as intended. The nuclear magnetic resonance studies demonstrated formation of a high order oligomer with increased protein concentration. These results and analysis prove that the knob-socket model is a predictive model for all α-helical protein packing. More importantly, the knob-socket model introduces a new protein design method that can potentially hold a solution to the folding problem.

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Estey, Tia Brie. "Protein instability associated with PLGA delivery systems and UV-induced protein oxidation /". Connect to full text via ProQuest. IP filtered, 2006.

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Thesis (Ph.D. in Pharmaceutical Sciences) -- University of Colorado, 2006.
Typescript. Includes bibliographical references (leaves 144-161). Free to UCDHSC affiliates. Online version available via ProQuest Digital Dissertations;

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Guan, Xiao, i 关晓. "NMR approaches to protein conformation and backbone dynamics: studies on hyperthermophilicacylphosphatase and neuropeptide secretoneurin". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2010. http://hub.hku.hk/bib/B44079230.

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Mermans, Daphne Maria Johanna. "Quality control of substrate conformation in the Escherichia coli twin arginine protein-targeting pathway". Thesis, University of Kent, 2018. https://kar.kent.ac.uk/69592/.

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In Escherichia coli, the twin arginine translocase (Tat) is one of the major protein translocation mechanisms. The Tat system has the ability to transport folded proteins across the inner membrane. Therefore, it has the ability to discriminate between folding states. However, it is not well understood how the Tat system senses the folding state of a substrate. In this study we probed the Tat proofreading mechanism and we investigated whether Tat substrates in E. coli are translocated by the Tat system due to their rapid folding kinetics. We demonstrate that the E. coli Tat machinery can process a de-novo designed substrate (BT6 maquette). Moreover the Tat proofreading mechanism can discriminated between different folding states of this substrate. This data and the fact that this simple four helix artificial substrate offers a lot of engineering freedom, suggests that BT6 is an ideal candidate to study the Tat proofreading mechanism (chapter 3). In chapter 4, we focussed on the Tat system’s proofreading ability by substituting substrate surfaces of BT6 maquette. Mutants with substituted surface properties were expressed in order to understand what Tat senses as folded. Expression assays showed whether the mutants were accepted or rejected by Tat. We propose that the proofreading system does not sense a global unfolded state of the substrate but has the ability to sense localised unfolded regions. Finally, we tested whether Tat substrates fold co- or post-translationally to determine the speed of the folding kinetics by using an arrest peptide-mediated force measurements assay (chapter 5). This study was to increase our understanding about the rationale for using the Tat system.

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Willis, William L. "YB-1 Stress-Response Protein Conformation Implicated in Post-transcriptional Control of Myofibroblast Differentiation". The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1376593223.

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Guo, Shenyuan. "Localization of protein segments affecting conformation of deoxyadenosine kinase from lactobacillus acidophilus r-26 /". The Ohio State University, 1998. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487949150070277.

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Brady, John Joseph. "VAPORIZATION OF BIOLOGICAL MACROMOLECULES USING INTENSE, ULTRAFAST LASERS: MECHANISM AND APPLICATION TO PROTEIN CONFORMATION". Diss., Temple University Libraries, 2011. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/211496.

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Chemistry
Ph.D.
This dissertation details the design and implementation of a state-of-the-art ambient trace analysis technique known as laser electrospray mass spectrometry. This novel technique utilizes an intense, nonresonant femtosecond laser pulse to transfer nonvolatile, fragile molecules into the gas phase from various substrates. The vaporized analyte is subsequently captured, solvated and ionized in an electrospray plume enabling mass analysis. Laser electrospray mass spectrometry is capable of analyzing samples in the liquid or solid states, mass spectral imaging of adsorbed molecules and detecting low vapor pressure analytes remotely. Experiments with biomolecules and pharmaceuticals, such as vitamin B12 and oxycodone, have demonstrated that the nonresonant femtosecond laser pulse allows for coupling into and vaporization of all molecules. This implies that sample preparation (elution, mixing with matrix and choosing samples with a particular electronic or vibrational transition) is not necessary, thus creating a universal mass analysis technique. Investigations using low vapor pressure molecules, such as lipids and proteins, led to the discovery that unfragmented molecules are transferred into the gas phase via a nonthermal mechanism. The laser electrospray mass spectrometry technique has allowed for the nonresonant femtosecond laser vaporization and mass analysis of trace amounts of a nitro-based explosive from a metal surface. The vaporization of unfragmented explosive molecules from a surface facilitates the identification of the explosive, reducing the probability of false positives and false negatives. In addition, this "soft" vaporization of molecules using nonresonant femtosecond laser pulses allows for protein to be transferred from the condensed phase into the gas phase without altering the molecule's structure, enabling ex vivo conformational analysis and possible disease typing.
Temple University--Theses

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Singh, Jaswinder. "Detection of Cis-Trans Conformation in Protein Structure using Deep Learning Neural Network Techniques". Thesis, Griffith University, 2019. http://hdl.handle.net/10072/384790.

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Proteins are important biological macromolecules that play critical roles in most biological processes. The functionality of protein depends on its three dimensional structure, which further depends on the protein's amino acid sequence. Direct prediction of 3D structure of protein from amino acid is challenging task. Therefore, prediction of three dimensional protein structure is divided into small sub-problems like one and two-dimensional properties of protein structure. The solution of these sub-problems can lead to successful three-dimensional structure prediction of protein. Accurate prediction of Cis 􀀀 Trans conformation in amino acid residues is one such sub-problem of protein structure prediction. It has been long established that cis conformations of amino acid residues play many biologically important roles and are implicated in cancer and neurodegenerative diseases, despite their exceptionally rare occurrence in protein structure (99.6% in trans). Due to this rarity, few methods have been developed for predicting cis-isomers from protein sequences, most of which are based on outdated datasets and lack the means for independent testing. This report presents several machine learning algorithm for the prediction of Cis 􀀀 Trans conformation of amino acid residues. In this research work, using a database of more than 10000 high-resolution protein structures, we update the statistics of cis-isomers available in literature and develop a sequence-based prediction technique using an ensemble of residual convolutional and Long Short-Term Memory bidirectional recurrent neural networks which allows for learning from the whole protein sequence. We show that ensembling 8 neural network models yields the maximum MCC value of approximately 0.35 for cis-Pro-isomers, and 0.1 for cis-nonPro residues. The method should be useful to prioritize functionally important residues in cis-isomers for experimental validations and improve sampling of rare protein conformations for ab initio protein structure prediction.
Thesis (Masters)
Master of Philosophy (MPhil)
School of Eng & Built Env
Science, Environment, Engineering and Technology
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