Relevant bibliographies by topics / Protein Biology

Academic literature on the topic 'Protein Biology'

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Published: 8 June 2024

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Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Journal articles on the topic "Protein Biology":

1

Prusiner, Stanley B., Michael R. Scott, Stephen J. DeArmond, and Fred E. Cohen. "Prion Protein Biology." Cell 93, no. 3 (May 1998): 337–48. http://dx.doi.org/10.1016/s0092-8674(00)81163-0.

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2

Roy, Kasturi, and Ethan P. Marin. "Lipid Modifications in Cilia Biology." Journal of Clinical Medicine 8, no. 7 (June 27, 2019): 921. http://dx.doi.org/10.3390/jcm8070921.

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Cilia are specialized cellular structures with distinctive roles in various signaling cascades. Ciliary proteins need to be trafficked to the cilium to function properly; however, it is not completely understood how these proteins are delivered to their final localization. In this review, we will focus on how different lipid modifications are important in ciliary protein trafficking and, consequently, regulation of signaling pathways. Lipid modifications can play a variety of roles, including tethering proteins to the membrane, aiding trafficking through facilitating interactions with transporter proteins, and regulating protein stability and abundance. Future studies focusing on the role of lipid modifications of ciliary proteins will help our understanding of how cilia maintain specific protein pools strictly connected to their functions.
3

Hong. "“Cell-Free Synthetic Biology”: Synthetic Biology Meets Cell-Free Protein Synthesis." Methods and Protocols 2, no. 4 (October 8, 2019): 80. http://dx.doi.org/10.3390/mps2040080.

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Since Nirenberg and Matthaei used cell-free protein synthesis (CFPS) to elucidate the genetic code in the early 1960s [1], the technology has been developed over the course of decades and applied to studying both fundamental and applied biology [2]. Cell-free synthetic biology integrating CFPS with synthetic biology has received attention as a powerful and rapid approach to characterize and engineer natural biological systems. The open nature of cell-free (or in vitro) biological platforms compared to in vivo systems brings an unprecedented level of control and freedom in design [3]. This versatile engineering toolkit has been used for debugging biological networks, constructing artificial cells, screening protein libraries, prototyping genetic circuits, developing biosensors, producing metabolites, and synthesizing complex proteins including antibodies, toxic proteins, membrane proteins, and novel proteins containing nonstandard (unnatural) amino acids. The Methods and Protocols “Cell-Free Synthetic Biology” Special Issue consists of a series of reviews, protocols, benchmarks, and research articles describing the current development and applications of cell-free synthetic biology in diverse areas. [...]
4

Birch, James, Harish Cheruvara, Nadisha Gamage, Peter J. Harrison, Ryan Lithgo, and Andrew Quigley. "Changes in Membrane Protein Structural Biology." Biology 9, no. 11 (November 16, 2020): 401. http://dx.doi.org/10.3390/biology9110401.

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Membrane proteins are essential components of many biochemical processes and are important pharmaceutical targets. Membrane protein structural biology provides the molecular rationale for these biochemical process as well as being a highly useful tool for drug discovery. Unfortunately, membrane protein structural biology is a difficult area of study due to low protein yields and high levels of instability especially when membrane proteins are removed from their native environments. Despite this instability, membrane protein structural biology has made great leaps over the last fifteen years. Today, the landscape is almost unrecognisable. The numbers of available atomic resolution structures have increased 10-fold though advances in crystallography and more recently by cryo-electron microscopy. These advances in structural biology were achieved through the efforts of many researchers around the world as well as initiatives such as the Membrane Protein Laboratory (MPL) at Diamond Light Source. The MPL has helped, provided access to and contributed to advances in protein production, sample preparation and data collection. Together, these advances have enabled higher resolution structures, from less material, at a greater rate, from a more diverse range of membrane protein targets. Despite this success, significant challenges remain. Here, we review the progress made and highlight current and future challenges that will be overcome.
5

Allen, James P. "Recent innovations in membrane-protein structural biology." F1000Research 8 (February 22, 2019): 211. http://dx.doi.org/10.12688/f1000research.16234.1.

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Innovations are expanding the capabilities of experimental investigations of the structural properties of membrane proteins. Traditionally, three-dimensional structures have been determined by measuring x-ray diffraction using protein crystals with a size of least 100 μm. For membrane proteins, achieving crystals suitable for these measurements has been a significant challenge. The availabilities of micro-focus x-ray beams and the new instrumentation of x-ray free-electron lasers have opened up the possibility of using submicrometer-sized crystals. In addition, advances in cryo-electron microscopy have expanded the use of this technique for studies of protein crystals as well as studies of individual proteins as single particles. Together, these approaches provide unprecedented opportunities for the exploration of structural properties of membrane proteins, including dynamical changes during protein function.
6

Foster, Andrew W., Tessa R. Young, Peter T. Chivers, and Nigel J. Robinson. "Protein metalation in biology." Current Opinion in Chemical Biology 66 (February 2022): 102095. http://dx.doi.org/10.1016/j.cbpa.2021.102095.

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7

Levy, Ezra, and Nikolai Slavov. "Single cell protein analysis for systems biology." Essays in Biochemistry 62, no. 4 (August 2, 2018): 595–605. http://dx.doi.org/10.1042/ebc20180014.

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The cellular abundance of proteins can vary even between isogenic single cells. This variability between single-cell protein levels can have regulatory roles, such as controlling cell fate during apoptosis induction or the proliferation/quiescence decision. Here, we review examples connecting protein levels and their dynamics in single cells to cellular functions. Such findings were made possible by the introduction of antibodies, and subsequently fluorescent proteins, for tracking protein levels in single cells. However, in heterogeneous cell populations, such as tumors or differentiating stem cells, cellular decisions are controlled by hundreds, even thousands of proteins acting in concert. Characterizing such complex systems demands measurements of thousands of proteins across thousands of single cells. This demand has inspired the development of new methods for single-cell protein analysis, and we discuss their trade-offs, with an emphasis on their specificity and coverage. We finish by highlighting the potential of emerging mass-spec methods to enable systems-level measurement of single-cell proteomes with unprecedented coverage and specificity. Combining such methods with methods for quantitating the transcriptomes and metabolomes of single cells will provide essential data for advancing quantitative systems biology.
8

Holmes, Kenneth C. "Structural biology." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 354, no. 1392 (December 29, 1999): 1977–84. http://dx.doi.org/10.1098/rstb.1999.0537.

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Protein crystallography has become a major technique for understanding cellular processes. This has come about through great advances in the technology of data collection and interpretation, particularly the use of synchrotron radiation. The ability to express eukaryotic genes in Escherichia coli is also important. Analysis of known structures shows that all proteins are built from about 1000 primeval folds. The collection of all primeval folds provides a basis for predicting structure from sequence. At present about 450 are known. Of the presently sequenced genomes only a fraction can be related to known proteins on the basis of sequence alone. Attempts are being made to determine all (or as many as possible) of the structures from some bacterial genomes in the expectation that structure will point to function more reliably than does sequence. Membrane proteins present a special problem. The next 20 years may see the experimental determination of another 40 000 protein structures. This will make considerable demands on synchrotron sources and will require many more biochemists than are currently available. The availability of massive structure databases will alter the way biochemistry is done.
9

Nehme, Zeina, Natascha Roehlen, Punita Dhawan, and Thomas F. Baumert. "Tight Junction Protein Signaling and Cancer Biology." Cells 12, no. 2 (January 6, 2023): 243. http://dx.doi.org/10.3390/cells12020243.

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Tight junctions (TJs) are intercellular protein complexes that preserve tissue homeostasis and integrity through the control of paracellular permeability and cell polarity. Recent findings have revealed the functional role of TJ proteins outside TJs and beyond their classical cellular functions as selective gatekeepers. This is illustrated by the dysregulation in TJ protein expression levels in response to external and intracellular stimuli, notably during tumorigenesis. A large body of knowledge has uncovered the well-established functional role of TJ proteins in cancer pathogenesis. Mechanistically, TJ proteins act as bidirectional signaling hubs that connect the extracellular compartment to the intracellular compartment. By modulating key signaling pathways, TJ proteins are crucial players in the regulation of cell proliferation, migration, and differentiation, all of which being essential cancer hallmarks crucial for tumor growth and metastasis. TJ proteins also promote the acquisition of stem cell phenotypes in cancer cells. These findings highlight their contribution to carcinogenesis and therapeutic resistance. Moreover, recent preclinical and clinical studies have used TJ proteins as therapeutic targets or prognostic markers. This review summarizes the functional role of TJ proteins in cancer biology and their impact for novel strategies to prevent and treat cancer.
10

Pandey, Aditya, Kyungsoo Shin, Robin E. Patterson, Xiang-Qin Liu, and Jan K. Rainey. "Current strategies for protein production and purification enabling membrane protein structural biology." Biochemistry and Cell Biology 94, no. 6 (December 2016): 507–27. http://dx.doi.org/10.1139/bcb-2015-0143.

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Membrane proteins are still heavily under-represented in the protein data bank (PDB), owing to multiple bottlenecks. The typical low abundance of membrane proteins in their natural hosts makes it necessary to overexpress these proteins either in heterologous systems or through in vitro translation/cell-free expression. Heterologous expression of proteins, in turn, leads to multiple obstacles, owing to the unpredictability of compatibility of the target protein for expression in a given host. The highly hydrophobic and (or) amphipathic nature of membrane proteins also leads to challenges in producing a homogeneous, stable, and pure sample for structural studies. Circumventing these hurdles has become possible through the introduction of novel protein production protocols; efficient protein isolation and sample preparation methods; and, improvement in hardware and software for structural characterization. Combined, these advances have made the past 10–15 years very exciting and eventful for the field of membrane protein structural biology, with an exponential growth in the number of solved membrane protein structures. In this review, we focus on both the advances and diversity of protein production and purification methods that have allowed this growth in structural knowledge of membrane proteins through X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM).
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You might also be interested in the extended bibliographies on the topic 'Protein Biology' for particular source types:
Journal articles Dissertations / Theses Books

Dissertations / Theses on the topic "Protein Biology":

1

Robinson, Ross Alexander. "Structural biology of protein - protein interactions." Thesis, University of Oxford, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.504517.

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2

Li, Wei. "Protein-protein interaction specificity of immunity proteins for DNase colicins." Thesis, University of East Anglia, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.302033.

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3

Song, Hong Chang. "The role of protein structure and heat shock protein 70 molecules in the import of peroxisomal proteins /." Thesis, McGill University, 1997. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=20867.

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Almost all peroxisomal proteins, which play significant roles in peroxisome biogenesis, are synthesized in the cytosol and imported into peroxisomes post-translationally. Failure to assemble normal peroxisomes causes detrimental disorders of peroxisome biogenesis known as peroxisomopathies. In the present study we examined (1) the peroxisomal import competency of unfolded proteins, and (2) the essential amino acid sequence of peroxisomal targeting signal type I (PTS-1) peptide. In the first part, human serum albumin (HSA) with seventeen disulfide bonds was fully reduced at 37°C and partially reduced at the room temperature. Microinjection of HSA that was unfolded, biotinylated and cross-linked with PTS-1 peptides demonstrated colocalization with peroxisomes, indicating the peroxisomal import competency. Furthermore, they induced heat shock protein (hsp) 72 which is a part of hsp 70 molecules. In the second part of our studies, we examined the essential amino acid sequence of PTS-1 by observing the peroxisomal import competency of mutated PTS-1 peptides and their inducibility of hsp 70 molecules. The hydrophobicity and basicity of the last seven amino acids from the carboxy-terminal were shown to be essential in the peroxisomal import. Furthermore, all the mutated PTS-1 peptides induced hsp 72 response. These results suggest that the ability of hsp 70 molecules to interact with the last seven amino acid sequence of the PTS-1 peptide plays a crucial role in the peroxisomal import.
4

Laos, Roberto, and Steven A. Benner. "Linking chemistry and biology: protein sequences." Revista de Química, 2016. http://repositorio.pucp.edu.pe/index/handle/123456789/99314.

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En los últimos veinte años el número de genomas completos que han sido secuenciados y depositados en bancos de datos  ha crecido dramáticamente. Esta abundancia de información de secuencias ha servido de base para la creación de una disciplina llamada paleogenética. En este artículo, sin ahondar en algoritmos complejos, presentamos algunos conceptos clave para comprender cómo las proteínas han evolucionado con el tiempo. Luego ilustraremos como la paleogenética es utilizada en biotecnología. Estos ejemplos resaltan la conexión entre la química y la biología, dos disciplinas que quizás veinte años atrás parecían ser mucho más distintas que lo que parecen ser hoy.
In the last twenty years, the number of complete genomes that have been sequenced and deposited in data banks has grown dramatically. This abundance in sequence information has supported the creation of the discipline known as  paleogenetics. In this article, without going into complex algorithms, we present some key concepts for understanding how proteins have evolved in time. We then illustrate how paleogenetic analysis can be used in biotechnology. These examples highlight the connection between chemistry and biology, two disciplines that twenty years ago seemed to be more different than what they seem to be today.
5

Strasser, Rona. "Protein-protein interactions of receptors LdPEX5 and LPEX7 with PTS1 and PTS2 cargo proteins, and with glycosomal docking protein LdPEX14 for protein import into «Leishmania donovani»." Thesis, McGill University, 2014. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=122960.

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A unique subcellular structure found in Leishmania donovani is the glycosome. This organelle compartmentalizes the enzymatic machinery required for multiple metabolic pathways, including glycolysis. Correct targeting of glycosomal enzymes is essential for parasite viability. Proteins targeted to the glycosome have either a C-terminal PTS1 or N-terminal PTS2 topogenic signal sequence, which is recognized by cytosolic receptors LdPEX5 or LPEX7, respectively. These cargo-loaded receptors interact with the peroxin protein LdPEX14, located on the cytosolic face of the glycosomal membrane, an event required for import of the cargo proteins into the glycosomal lumen. However, the complete glycosomal protein import pathway has not been fully elucidated. This work has been undertaken to better understand the protein-protein interactions involved in the trafficking of cargo proteins across the glycosomal membrane.The cytosolic fraction from L. donovani parasites was used to determine protein-protein interactions of receptors LdPEX5 and LPEX7. Size exclusion chromatography, isoelectric focusing, and affinity pull-downs showed that in the cytosol these receptors form large heterologous PTS1-LdPEX5-LPEX7-PTS2 complexes. Purified glycosomes were used to evaluate the effects of receptor-cargo complexes on glycosomal LdPEX14 conformation. Limited trypsin proteolysis showed that interaction of receptor-cargo complexes with native LdPEX14 protected this protein from digestion, whereas native LdPEX14 alone was highly sensitive to proteolysis. Protection was not dependent on membrane integrity as disruption of the lipid bilayer did not alter the effect of trypsin on these proteins. Native gel electrophoresis showed that native LdPEX14 forms large ~800 kDa complexes; however, when associated with receptor-cargo complexes the molecular weight of LdPEX14 complexes increased to ~1200 kDa. Alkaline carbonate extractions showed that native LdPEX14 acts like a peripheral glycosomal membrane protein; however loading with receptor-cargo complexes caused LdPEX14 to behave like an integral membrane protein. Furthermore, membrane insertion of LdPEX14 drove insertion of LdPEX5 and LPEX7 into the glycosomal membrane. Receptor-cargo complex association causes LdPEX14 to undergo a conformational change resulting in deeper membrane insertion and increase in complex size.Purification of recombinant LPEX7 was hampered by its association with bacterial chaperone protein GroEL. A refolding technique was developed to purify LPEX7 from inclusion bodies free of bacterial proteins. Far Western and protein-protein affinity assays showed that refolded LPEX7 specifically bound PTS2 proteins as both a monomer and a dimer, the co-receptor LdPEX5, and LdPEX14. Mapping of the interaction domains on LPEX7 showed that LPEX7-PTS2 interaction required the entire receptor protein, while LdPEX5 and LdPEX14 interaction motifs were situated in the N-terminal region of LPEX7.There are metabolites in glycosomes that are not imported via the peroxin based glycosomal import pathway but by glycosomal membrane transporters. L-arginine is one such metabolite; it is the substrate for the PTS1 glycosomal enzyme arginase, which catalyses the first step in the polyamine biosynthetic pathway. L-arginine is scavenged from the extracellular milieu and by the L-arginine transporter, amino acid permease 3 (LdAAP3). Subcellular fractionation showed that LdAAP3 localized to both the plasma and glycosomal membranes. Furthermore, L. donovani promastigotes were capable of sensing the L-arginine levels in the media and upregulated LdAAP3 expression on the plasma and glycosome membrane in the absence of L-arginine. These studies provide evidence that metabolite specific transporters are present on the glycosomal membrane.Together these studies contribute to the elucidation of glycosomal function in Leishmania donovani, and a better understanding of some of the mechanisms required for glycosomal import.
Le glycosome est une structure subcellulaire unique qui se trouve dans le parasite Leishmania donovani. Cette organelle compartimente la machinerie enzymatique requise pour de multiples voies métaboliques, y compris la glycolyse. Le bon ciblage des enzymes du glycosome est essentiel pour la viabilité du parasite. Les protéines ciblées pour le glycosome ont une séquence signal topogénique, un PTS1 C-terminale ou un PTS2 N-terminale, qui est reconnue par les récepteurs cytosoliques, le LdPEX5 ou le LPEX7, respectivement. Ces complexes de récepteurs chargés s'interagissent avec la protéine LdPEX14, située du côté cytosolique de la membrane glycosomale, un événement requis pour le transport des protéines à travers la membrane du glycosome. Cependant, la voie complète d'importation de protéines glycosomales n'a pas été totalement élucidée. Ce travail a été entrepris pour mieux comprendre ces interactions protéine-protéine.La fraction cytosolique des parasites L.donovani a été utilisée pour déterminer les interactions protéine-protéine des récepteurs LdPEX5 et LPEX7. La chromatographie d'exclusion de taille, la focalisation isoélectrique, et les interactions d'affinité proteine-proteine ont montré que, dans les cytosols, ces récepteurs forment des grands complexes hétérologues. Les glycosomes purifiés ont été utilisés pour évaluer l'effet des complexes récepteur sur la conformation du LdPEX14. Une protéolyse limitée a montré que l'interaction du LdPEX14 chargé avec les complexes récepteur l'à protèger de la digestion à la surface de la membrane. L'électrophorèse sur gel natif a montré que le LdPEX14 forme des grands complexes de ~ 800 kDa et que lorsqu'il est associé à des complexes récepteur, le poids moléculaire des complexes LdPEX14 passe à ~ 1200 kDa. Les extractions avec le carbonate alcalin a déterminé que le LdPEX14 seul s'agit comme une protéine périphérique; mais son chargement avec des complexes récepteur l'entrainer à s'agir comme une protéine membranaire intégrale. L'insertion de LdPEX14 dans la membrane du glycosome conduit à l'insertion du LdPEX5 et LPEX7 dans la membrane aussi. L'association des complexes récepteur à causer LdPEX14 à subir un changement de conformation causant l'insertion profonde dans la membrane et l'augmentation de la taille des complexes.La purification du récepteur LPEX7 recombinante été entravée par son association avec la protéine chaperonne bactérienne GroEL. Une technique de repliement a été développé pour purifier LPEX7 en évitant l'association de protéines bactériennes. Les techniques de Far Western et d'affinité protéine-protéine ont montré que ce LPEX7 replier est spécifiquement associé à des protéines PTS2, le co-récepteur LdPEX5, et le LdPEX14. La cartographie des domaines d'interaction de LPEX7 a montré que l'interaction LPEX7-PTS2 nécessit le LPEX7 entière, alors que les motifs d'interaction avec LdPEX5 et LdPEX14 étaient situés dans sa région N-terminale.Il y a des métabolites glycosomal qui ne sont pas importés par la voie de l'importation glycosomale, mais par des transporteurs membranaires du glycosome. L-arginine est un de ces métabolites, substrat de l'enzyme glycosomale PTS1 arginase. L-arginine est récupéré dans le milieu extracellulaire par son transporteur, LdAAP3. Un fractionnement subcellulaire a été utilisés pour séparer les membranes plasmiques des glycosomes, et LdAAP3 a été localisé sur les deux membranes. De plus, des promastigotes de L. donovani sont capable de detecter le niveau de L-arginine dans le millieu, ce qui provoque une régulation positive de l'expression de LdAAP3 à la fois dans la membrane plasmique et dans la membrane du glycosome. Ces études fournissent des preuves que des transporteurs de métabolites spécifique sont présent dans la membrane du glycosome.Ensemble, ces études contribuent à l'élucidation de la fonction glycosomale de Leishmania donovani, et une meilleure compréhension de certains mécanismes nécessaires pour l'importation glycosomale.
6

Le, Min. "Protein coimmobilization: Reactions of vicinal thiol groups of proteins /." The Ohio State University, 1997. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487946776021788.

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7

Rassadi, Roozbeh. "The effect of stress on nuclear protein transport : classical nuclear protein transport versus the nuclear transport of heat shock proteins." Thesis, McGill University, 1999. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=33476.

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The stress response is conserved among eukaryotes and affects different cellular functions including protein transport. Here, we have investigated the effect of different types of stress on classical nuclear protein import as well as nuclear import of Ssa4p family of heat shock proteins in Saccharomyces cerevisiae.
Under normal conditions, Aequorea victoria green fluorescent protein (GFP), carrying a classical nuclear localization sequence (cNLS-GFP) is nuclear. However, cNLS-GFP equilibrates throughout the cell upon exposure to heat, ethanol, H2O2 or starvation. Redistribution of the small GTPase Gsp1p, a soluble nuclear transport factor, correlates with cNLS-GFP equilibration. This suggests that a collapse of the Gsp1p gradient underlies the inhibition of classical nuclear protein import. In contrast to cNLS-GFP, the cytoplasmic heat shock protein Ssa4p accumulates in nuclei when classical nuclear import is inhibited. The N-terminal 236 amino acid residues of Ssa4p are sufficient for nuclear localization of Ssa4p-GFP upon heat and ethanol stress. The nuclear localization of Ssa4p(1--236)-GFP requires components of Gsp1-GTPase system, but is independent of Srp1p, the cNLS receptor.
Ssa4p(16--642)-GFP accumulates in nuclei of starving cells, mediated by a hydrophobic stretch of amino acid residues in its N-terminal domain. This nuclear localization is reversible upon addition of fresh medium and its export is sensitive to oxidants and temperature-dependent.
8

Field, James Edward John. "Engineering protein cages with synthetic biology." Thesis, Imperial College London, 2014. http://hdl.handle.net/10044/1/45404.

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Nanotechnology has the potential to revolutionise every facet of human life. One particularly exciting branch of nanotechnology involves the construction of nanodevices using protein cages. Protein cages are spherically shaped structures with large internal cavities. The research described in this thesis was conducted with the aim of rationalising the design and fabrication of protein cage-based nanodevices. Protein-based nanodevices are typically constructed by re-engineering naturally occurring protein chassis (e.g. ferritin). To rationalise the process of chassis selection, an online registry of protein cages, rings and tubes was designed and populated by computationally mining the Protein Data Bank. The resulting registry was made publically available to the research community through the website – www.nanodevice.build. The functionality of protein cage-based nanodevices can be augmented by packaging inorganic nanoparticles inside their internal cavities. The methods currently used to achieve this typically involve exposure to harsh conditions, which can cause irreversible damage to the protein cage. To address this, a strategy for efficiently packaging inorganic nanoparticles into protein cages under mild conditions was formulated and tested. These experiments were conducted using gold nanoparticles and a number of different protein cages (e.g. Bfr, FtnH and FtnL). Cholangiocarcinoma (CCA) is a deadly liver cancer for which current treatment options are limited. Therefore a CCA-targeting protein cage-based nanodevice was designed, constructed and experimentally evaluated. CCA-targeting was achieved in the context of the CCA cell line TFK-1 using an anti-mesothelin antibody as a targeting agent. Collectively, these three outputs provide a rational framework for selecting a protein cage chassis, loading it with a pre-fabricated inorganic nanoparticle and targeting the resulting device to a particular cell-type. It is hoped that by leveraging these three tools, synthetic biologists will be able to engineer a new generation of nanodevices.
9

Sonnen, Andreas Franz-Peter. "Structural biology of protein-membrane interactions and membrane protein function." Thesis, University of Oxford, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.514997.

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10

Lite, Thúy-Lan Võ. "The genetic landscape of protein-protein interaction specificity." Thesis, Massachusetts Institute of Technology, 2020. https://hdl.handle.net/1721.1/129035.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2020
Cataloged from student-submitted PDF of thesis.
Includes bibliographical references.
Protein-protein interaction specificity is often encoded at the primary sequence level, and by just a few interfacial residues. Collectively, these residues have both positive and negative roles, promoting a desired, cognate interaction and preventing non-cognate interactions, respectively. However, for most protein-protein interactions, the contributions of individual specificity residues are poorly understood and often obscured by robustness and degeneracy of protein interfaces. Using bacterial toxin-antitoxin systems as a model, we use a variant of deep mutational scanning to dissect the positive and negative contributions of antitoxin residues that dictate toxin specificity. By screening a combinatorially complete library of antitoxin variants, we uncover a distribution of fitness effects for individual interface mutations measured across hundreds of genetic backgrounds. We show that positive and negative contributions to specificity are neither inherently coupled nor mutually exclusive. Further, we argue that the wild-type antitoxin may be optimized for specificity, because mutations that further destabilize the non-cognate interaction also weaken the cognate interaction. No mutations strengthen the cognate interaction. By comparing crystal structures of paralogous complexes, we provide a structural rationale for all of these observations. Finally, we use a library approach to identify hundreds of novel systems that are insulated from their parental systems, and that carry only two mutations - a negative specificity element on the toxin, and one on the antitoxin. This result demonstrates that highly similar (and in this case, nearly identical) complexes can be insulated using compensatory mutations of individually large effect. Collectively, this work provides a generalizable approach to understanding the logic of molecular recognition.
by Thúy-Lan Võ Lite.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Department of Biology
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Books on the topic "Protein Biology":

1

T, McManus Michael, Laing William A, and Allan Andrew C, eds. Protein-protein interactions in plant biology. Sheffield: Sheffield Academic Press, 2002.

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2

Colin, Kleanthous, ed. Protein-protein recognition. Oxford: Oxford University Press, 2000.

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A, Rice Phoebe, and Correll Carl C, eds. Protein-nucleic acid interactions: Structural biology. Cambridge: RSC Pub., 2008.

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Gabriel, Waksman, ed. Proteomics and protein-protein interactions: Biology, chemistry, bionformatics, and drug design. New York: Springer, 2005.

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Arnold, Revzin, ed. The Biology of nonspecific DNA-protein interactions. Boca Raton, Fla: CRC Press, 1990.

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Donev, Rossen. Advances in protein chemistry and structural biology. Amsterdam: Elsevier, 2011.

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Anders, Liljas, ed. Textbook of structural biology. New Jersey: World Scientific, 2008.

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1948-, Walker John M., ed. New protein techniques. Clifton, N.J: Humana Press, 1988.

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Matthews, Jacqueline M. Protein dimerization and oligomerization in biology. New York: Springer Science+Business Media, 2012.

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Tropp, Burton E. Molecular biology: Genes to proteins. 3rd ed. Sudbury, MA: Jones and Bartlett, 2008.

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Book chapters on the topic "Protein Biology":

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Fung, Jia Jun, Karla Blöcher-Juárez, and Anton Khmelinskii. "High-Throughput Analysis of Protein Turnover with Tandem Fluorescent Protein Timers." In Methods in Molecular Biology, 85–100. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-1732-8_6.

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AbstractTandem fluorescent protein timers (tFTs) are versatile reporters of protein dynamics. A tFT consists of two fluorescent proteins with different maturation kinetics and provides a ratiometric readout of protein age, which can be exploited to follow intracellular trafficking, inheritance and turnover of tFT-tagged proteins. Here, we detail a protocol for high-throughput analysis of protein turnover with tFTs in yeast using fluorescence measurements of ordered colony arrays. We describe guidelines on optimization of experimental design with regard to the layout of colony arrays, growth conditions, and instrument choice. Combined with semi-automated genetic crossing using synthetic genetic array (SGA) methodology and high-throughput protein tagging with SWAp-Tag (SWAT) libraries, this approach can be used to compare protein turnover across the proteome and to identify regulators of protein turnover genome-wide.
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Keskin, Ozlem, Attila Gursoy, and Ruth Nussinov. "Principles of Protein Recognition and Properties of Protein-protein Interfaces." In Computational Biology, 53–65. London: Springer London, 2008. http://dx.doi.org/10.1007/978-1-84800-125-1_3.

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Teng, Quincy. "Protein Dynamics." In Structural Biology, 289–310. Boston, MA: Springer US, 2012. http://dx.doi.org/10.1007/978-1-4614-3964-6_8.

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Kodama, Hiroki, and Yoichi Nakata. "Protein Structures." In Theoretical Biology, 161–75. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-16-7132-6_5.

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Gamage, Nadisha, Harish Cheruvara, Peter J. Harrison, James Birch, Charlie J. Hitchman, Monika Olejnik, Raymond J. Owens, and Andrew Quigley. "High-Throughput Production and Optimization of Membrane Proteins After Expression in Mammalian Cells." In Methods in Molecular Biology, 79–118. New York, NY: Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-3147-8_5.

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AbstractHigh-quality protein samples are an essential requirement of any structural biology experiment. However, producing high-quality protein samples, especially for membrane proteins, is iterative and time-consuming. Membrane protein structural biology remains challenging due to low protein yields and high levels of instability especially when membrane proteins are removed from their native environments. Overcoming the twin problems of compositional and conformational instability requires an understanding of protein size, thermostability, and sample heterogeneity, while a parallelized approach enables multiple conditions to be analyzed simultaneously. We present a method that couples the high-throughput cloning of membrane protein constructs with the transient expression of membrane proteins in human embryonic kidney (HEK) cells and rapid identification of the most suitable conditions for subsequent structural biology applications. This rapid screening method is used routinely in the Membrane Protein Laboratory at Diamond Light Source to identify the most successful protein constructs and conditions while excluding those that will not work. The 96-well format is easily adaptable to enable the screening of constructs, pH, salts, encapsulation agents, and other additives such as lipids.
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Barth, Marie, and Carla Schmidt. "Quantitative Cross-Linking of Proteins and Protein." In Methods in Molecular Biology, 385–400. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1024-4_26.

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AbstractCross-linking, in general, involves the covalent linkage of two amino acid residues of proteins or protein complexes in close proximity. Mass spectrometry and computational analysis are then applied to identify the formed linkage and deduce structural information such as distance restraints. Quantitative cross-linking coupled with mass spectrometry is well suited to study protein dynamics and conformations of protein complexes. The quantitative cross-linking workflow described here is based on the application of isotope labelled cross-linkers. Proteins or protein complexes present in different structural states are differentially cross-linked using a “light” and a “heavy” cross-linker. The intensity ratios of cross-links (i.e., light/heavy or heavy/light) indicate structural changes or interactions that are maintained in the different states. These structural insights lead to a better understanding of the function of the proteins or protein complexes investigated. The described workflow is applicable to a wide range of research questions including, for instance, protein dynamics or structural changes upon ligand binding.
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Gonzalez, Orland. "Protein–Protein Interaction Databases." In Encyclopedia of Systems Biology, 1786–90. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-9863-7_1046.

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Lu, Long Jason, and Minlu Zhang. "Protein-Protein Interaction Networks." In Encyclopedia of Systems Biology, 1790. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-9863-7_878.

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Szklarczyk, Damian, and Lars Juhl Jensen. "Protein-Protein Interaction Databases." In Methods in Molecular Biology, 39–56. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2425-7_3.

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Neyfakh, A. A., and M. Ya Timofeeva. "Protein." In Molecular biology of development, 170–278. Boston, MA: Springer US, 1985. http://dx.doi.org/10.1007/978-1-4899-5370-4_3.

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Conference papers on the topic "Protein Biology":

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MUIR, TOM W. "EXPLORING CHROMATIN BIOLOGY USING PROTEIN CHEMISTRY." In 23rd International Solvay Conference on Chemistry. WORLD SCIENTIFIC, 2014. http://dx.doi.org/10.1142/9789814603836_0005.

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Dunbrack, Roland L., Keith Dunker, and Adam Godzik. "PROTEIN STRUCTURE PREDICTION IN BIOLOGY AND MEDICINE." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 1999. http://dx.doi.org/10.1142/9789814447331_0009.

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Shahbazi, Zahra, Horea T. Ilies¸, and Kazem Kazerounian. "Protein Molecules as Natural Nano Bio Devices: Mobility Analysis." In ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology. ASMEDC, 2010. http://dx.doi.org/10.1115/nemb2010-13021.

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Proteins are nature’s nano-robots in the form of functional molecular components of living cells. The function of these natural nano-robots often requires conformational transitions between two or more native conformations that are made possible by the intrinsic mobility of the proteins. Understanding these transitions is essential to the understanding of how proteins function, as well as to the ability to design and manipulate protein-based nano-mechanical systems [1]. Modeling protein molecules as kinematic chains provides the foundation for developing powerful approaches to the design, manipulation and fabrication of peptide based molecules and devices. Nevertheless, these models possess a high number of degrees of freedom (DOF) with considerable computational implications. On the other hand, real protein molecules appear to exhibits a much lower mobility during the folding process than what is suggested by existing kinematic models. The key contributor to the lower mobility of real proteins is the formation of Hydrogen bonds during the folding process.
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Tretyakova, A. V., E. O. Gerasimova, P. A. Krylov, and V. V. Novochadov. "Phylogenetic analysis of the lubricin protein and surfactant-associated proteins B and C." In Mathematical Biology and Bioinformatics. Pushchino: IMPB RAS - Branch of KIAM RAS, 2022. http://dx.doi.org/10.17537/icmbb22.18.

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Pedrazzini, Emanuela. "Protein-specific induction of the unfolded protein response by two maize gamma-zeins." In ASPB PLANT BIOLOGY 2020. USA: ASPB, 2020. http://dx.doi.org/10.46678/pb.20.1383050.

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Luo, Fei, Ondrej Halgas, Pratish Gawand, and Sagar Lahiri. "Animal-free protein production using precision fermentation." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/ntka8679.

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The $1.4 trillion animal industry could not sustainably scale further to feed the next billion population, as it is resource intensive, and heavy in greenhouse gas emission. The recent plant-based food movement has provided solution for more sustainable protein sources. However, the plant-based food sector faces challenges in reaching parity in texture, sensory experience (mouthfeel) and nutritional value as animal products, limiting their potential of reaching beyond the vegan and flexitarian consumers. The technical challenge behind this problem is that proteins from plants have intrinsically different amino acid compositions and structures from animal proteins, making it challenging to emulate the properties of animal products using plant-proteins alone. There is a clear and underserved need for novel protein ingredients that can complement plant-based protein ingredients to achieve parity of animal products. Fermentation is considered the third pillar of alternative protein revolution. At Liven, we focus our efforts on developing precision fermentation technology to produce functional protein ingredients that are natural replica of animal proteins. Using engineering biology, we transforms microorganisms with genes that are responsible for producing animal proteins such as collagen and gelatin. The transformed microorganisms are cultivated in fermenters to produce proteins from plant-based raw-materials. Since the protein produced are have identical amino acid sequences and structure as proteins that would be derived from animals, they provide the desired texture and sensory characteristics currently missing in plant-based formulations. For instance, our animal-free gelatin provides the functionality of thermally reversible gel. As our protein ingredients provides functionality and nutrition value of animal proteins, these ingredients could complement plant-based protein ingredients to deliver alt-protein food formulations more accurately emulate animal products, expand the market acceptance of alt-protein foods to mass consumers.
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Shi, Lei, Young-Rae Cho, and Aidong Zhang. "ANN Based Protein Function Prediction Using Integrated Protein-Protein Interaction Data." In 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing. IEEE, 2009. http://dx.doi.org/10.1109/ijcbs.2009.98.

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Kaseniit, Kristjan E., Samuel D. Perli, and Timothy K. Lu. "Designing extensible protein-DNA interactions for synthetic biology." In 2011 IEEE Biomedical Circuits and Systems Conference (BioCAS). IEEE, 2011. http://dx.doi.org/10.1109/biocas.2011.6107799.

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Mohan, Amrita, Shripad V. Bhagwat, David M. Epstein, Mark Miglarese, and Jonathan A. Pachter. "Abstract 58: Understanding target biology using protein interactomes." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-58.

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Yong-Cui Wang, Xian-Wen Ren, Chun-Hua Zhang, Nai-Yang Deng, and Xiang-Sun Zhang. "Evaluating the denoising techniques in protein-protein interaction prediction." In 2011 IEEE International Conference on Systems Biology (ISB). IEEE, 2011. http://dx.doi.org/10.1109/isb.2011.6033124.

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Reports on the topic "Protein Biology":

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Zhou, C., and A. Zemla. Computational biology for target discovery and characterization: a feasibility study in protein-protein interaction detection. Office of Scientific and Technical Information (OSTI), February 2009. http://dx.doi.org/10.2172/948981.

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Williams, Thomas. Cell Biology Boardgame: Cell Survival: Transport. University of Dundee, March 2023. http://dx.doi.org/10.20933/100001281.

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Get your mRNAs from one side of the cell to the other so they can be turned into protein. Fastest wins! This game takes a fun approach to detail findings from real life research. Great for 2-5 people age 3+, lasts around 15 mins per game.
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Rao, Christopher. Final report: The Systems Biology of Protein Acetylation in Fuel-Producing Microorganisms. Office of Scientific and Technical Information (OSTI), November 2018. http://dx.doi.org/10.2172/1483353.

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Ecker, Joseph Robert, Shelly Trigg, Renee Garza, Haili Song, Andrew MacWilliams, Joseph Nery, Joaquin Reina, et al. Next Generation Protein Interactomes for Plant Systems Biology and Biomass Feedstock Research. Office of Scientific and Technical Information (OSTI), November 2016. http://dx.doi.org/10.2172/1333859.

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Pratt, L. R., A. E. Garcia, and G. Hummer. Computer simulation of protein solvation, hydrophobic mapping, and the oxygen effect in radiation biology. Office of Scientific and Technical Information (OSTI), August 1997. http://dx.doi.org/10.2172/524859.

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Wang, X. F., and M. Schuldiner. Systems biology approaches to dissect virus-host interactions to develop crops with broad-spectrum virus resistance. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2020. http://dx.doi.org/10.32747/2020.8134163.bard.

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More than 60% of plant viruses are positive-strand RNA viruses that cause billion-dollar losses annually and pose a major threat to stable agricultural production, including cucumber mosaic virus (CMV) that infects numerous vegetables and ornamental trees. A highly conserved feature among these viruses is that they form viral replication complexes (VRCs) to multiply their genomes by hijacking host proteins and remodeling host intracellular membranes. As a conserved and indispensable process, VRC assembly also represents an excellent target for the development of antiviral strategies that can be used to control a wide-range of viruses. Using CMV and a model virus, brome mosaic virus (BMV), and relying on genomic tools and tailor-made large-scale resources specific for the project, our original objectives were to: 1) Identify host proteins that are required for viral replication complex assembly. 2) Dissect host requirements that determine viral host range. 3) Provide proof-of-concept evidence of a viral control strategy by blocking the viral replication complex-localized phospholipid synthesis. We expect to provide new ways and new concepts to control multiple viruses by targeting a conserved feature among positive-strand RNA viruses based on our results. Our work is going according to the expected timeline and we are progressing well on all aims. For Objective 1, among ~6,000 yeast genes, we have identified 96 hits that were possibly play critical roles in viral replication. These hits are involved in cellular pathways of 1) Phospholipid synthesis; 2) Membrane-shaping; 3) Sterol synthesis and transport; 4) Protein transport; 5) Protein modification, among many others. We are pursuing several genes involved in lipid metabolism and transport because cellular membranes are primarily composed of lipids and lipid compositional changes affect VRC formation and functions. For Objective 2, we have found that CPR5 proteins from monocotyledon plants promoted BMV replication while those from dicotyledon plants inhibited it, providing direct evidence that CPR5 protein determines the host range of BMV. We are currently examining the mechanisms by which dicot CPR5 genes inhibit BMV replication and expressing the dicot CPR5 genes in monocot plants to control BMV infection. For Objective 3, we have demonstrated that substitutions in a host gene involved in lipid synthesis, CHO2, prevented the VRC formation by directing BMV replication protein 1a (BMV 1a), which remodels the nuclear membrane to form VRCs, away from the nuclear membrane, and thus, no VRCs were formed. This has been reported in Journal of Biological Chemistry. Based on the results from Objective 3, we have extended our plan to demonstrate that an amphipathic alpha-helix in BMV 1a is necessary and sufficient to target BMV 1a to the nuclear membrane. We further found that the counterparts of the BMV 1a helix from a group of viruses in the alphavirus-like superfamily, such as CMV, hepatitis E virus, and Rubella virus, are sufficient to target VRCs to the designated membranes, revealing a conserved feature among the superfamily. A joint manuscript describing these exciting results and authored by the two labs will be submitted shortly. We have also successfully set up systems in tomato plants: 1) to efficiently knock down gene expression via virus-induced gene silencing so we could test effects of lacking a host gene(s) on CMV replication; 2) to overexpress any gene transiently from a mild virus (potato virus X) so we could test effects of the overexpressed gene(s) on CMV replication. In summary, we have made promising progress in all three Objectives. We have identified multiple new host proteins that are involved in VRC formation and may serve as good targets to develop antiviral strategies; have confirmed that CPR5 from dicot plants inhibited viral infection and are generating BMV-resistance rice and wheat crops by overexpressing dicot CPR5 genes; have demonstrated to block viral replication by preventing viral replication protein from targeting to the designated organelle membranes for the VRC formation and this concept can be further employed for virus control. We are grateful to BARD funding and are excited to carry on this project in collaboration.
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Sheinerman, Felix. Report on the research conducted under the funding of the Sloan foundation postdoctoral fellowship in Computational Molecular Biology [Systematic study of protein-protein complexes] Final report. Office of Scientific and Technical Information (OSTI), June 2001. http://dx.doi.org/10.2172/810580.

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Gupta, G., S. V. Santhana Mariappan, X. Chen, P. Catasti, L. A. III Silks, R. K. Moyzis, E. M. Bradbury, and A. E. Garcia. Structural biology of disease-associated repetitive DNA sequences and protein-DNA complexes involved in DNA damage and repair. Office of Scientific and Technical Information (OSTI), July 1997. http://dx.doi.org/10.2172/505319.

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Evans, John Spencer. Material lessons of biology: structure function studies of protein sequences involved in inorganic composite material formation. Final Technical Report. Office of Scientific and Technical Information (OSTI), September 2019. http://dx.doi.org/10.2172/1560814.

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Ohad, Nir, and Robert Fischer. Control of Fertilization-Independent Development by the FIE1 Gene. United States Department of Agriculture, August 2000. http://dx.doi.org/10.32747/2000.7575290.bard.

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A fundamental problem in biology is to understand how fertilization initiates reproductive development. During plant reproduction, one sperm cell fuses with the egg to form an embryo, whereas a second sperm cell fuses with the adjacent central cell nucleus to form the endosperm tissue that supports embryo and/or seedling development. To understand the mechanisms that initiate reproduction, we have isolated mutants of Arabidopsis that allow for replication of the central cell and subsequent endosperm development without fertilization. In this project we have cloned the MEA gene and showed that it encode a SET- domain polycomb protein. Such proteins are known to form chromatin-protein complexes that repress homeotic gene transcription and influence cell proliferation from Drosophylla to mammals. We propose a model whereby MEA and an additional polycomb protein we have cloned, FIE , function to suppress a critical aspect of early plant reproduction and endosperm development, until fertilization occurs. Using a molecular approach we were able to determine that FIE and MEA interact physically, suggesting that these proteins have been conserved also during the evolution of flowering plants. The analysis of MEA expression pattern revealed that it is an imprinted gene that displays parent-of- origin-dependent monoallelic expression specifically in the endosperm tissue. Silencing of the paternal MEA allele in the endosperm and the phenotype of mutant mea seeds support the parental conflict theory for the evolution of imprinting in plants and mammals. These results contribute new information on the initiation of endosperm development and provide a unique entry point to study asexual reproduction and apomixis which is expected to improve crop production.

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