Relevant bibliographies by topics / Protein-molecule interactions

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

Academic literature on the topic 'Protein-molecule interactions'

Author: Grafiati
Published: 26 October 2024

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Journal articles on the topic "Protein-molecule interactions"

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Kuusk, Ave, Helen Boyd, Hongming Chen, and Christian Ottmann. "Small-molecule modulation of p53 protein-protein interactions." Biological Chemistry 401, no. 8 (July 28, 2020): 921–31. http://dx.doi.org/10.1515/hsz-2019-0405.

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AbstractSmall-molecule modulation of protein-protein interactions (PPIs) is a very promising but also challenging area in drug discovery. The tumor suppressor protein p53 is one of the most frequently altered proteins in human cancers, making it an attractive target in oncology. 14-3-3 proteins have been shown to bind to and positively regulate p53 activity by protecting it from MDM2-dependent degradation or activating its DNA binding affinity. PPIs can be modulated by inhibiting or stabilizing specific interactions by small molecules. Whereas inhibition has been widely explored by the pharmaceutical industry and academia, the opposite strategy of stabilizing PPIs still remains relatively underexploited. This is rather interesting considering the number of natural compounds like rapamycin, forskolin and fusicoccin that exert their activity by stabilizing specific PPIs. In this review, we give an overview of 14-3-3 interactions with p53, explain isoform specific stabilization of the tumor suppressor protein, explore the approach of stabilizing the 14-3-3σ-p53 complex and summarize some promising small molecules inhibiting the p53-MDM2 protein-protein interaction.
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Ottmann, Christian. "Small-molecule modulation of protein–protein interactions." Drug Discovery Today: Technologies 10, no. 4 (December 2013): e499-e500. http://dx.doi.org/10.1016/j.ddtec.2013.08.001.

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Pollock, Julie A., Courtney L. Labrecque, Cassidy N. Hilton, Justin Airas, Alexis Blake, Kristen J. Rubenstein, and Carol A. Parish. "Small Molecule Modulation of MEMO1 Protein-Protein Interactions." Journal of the Endocrine Society 5, Supplement_1 (May 1, 2021): A1031. http://dx.doi.org/10.1210/jendso/bvab048.2110.

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Abstract MEMO1 (mediator of ErbB2-driven cell motility) is upregulated in breast tumors and has been correlated with poor prognosis in patients. As a scaffolding protein that binds to phosphorylated-tyrosine residues on receptors such as estrogen receptor and ErbB2, MEMO1 levels can influence phosphorylation cascades. Using our previously developed fluorescence polarization assay, we have identified small molecules with the ability to disrupt the interactions of MEMO1. We have performed limited structure-activity-relationship studies and computational analyses to investigate the molecular requirements for MEMO1 inhibition. The most promising compounds exhibit slowed migration of breast cancer cell lines (T47D and SKBR3) in a wound-healing assay emulating results obtained from the knockdown of MEMO1 protein. To our knowledge, these are the first small molecules targeting the MEMO1 protein-protein interface and therefore, will be invaluable tools for the investigation of the role of the MEMO1 in breast cancer and other biological contexts.
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Guo, Z. "Designing Small-Molecule Switches for Protein-Protein Interactions." Science 288, no. 5473 (June 16, 2000): 2042–45. http://dx.doi.org/10.1126/science.288.5473.2042.

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SAHA, MIRABEAU, and TIMOLÉON C. KOFANÉ. "NONLINEAR DYNAMICS OF LONG-RANGE PROTEIN-HELICOIDAL DNA INTERACTIONS." International Journal of Modern Physics B 26, no. 19 (July 16, 2012): 1250101. http://dx.doi.org/10.1142/s0217979212501019.

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The effects of long-range interactions between peptides on the protein–DNA dynamics in the long-wave limit are studied. The investigation, done at the physiological temperature, is based on a coupled spin system of DNA molecule which includes the helicoidal geometry of DNA molecule and the Kac–Baker long-range interaction between the peptides of the protein molecule. By using the Holstein–Primakoff bosonic representation of the spin operators, we show that the original discrete equations for the protein–DNA interaction dynamics can be reduced to the nonlinear Schrödinger (NLS) equation of which the dispersive and the nonlinear coefficients depend among other things on the protein long-range interaction parameter and on the helicoidal coupling coefficient. Furthermore, we find that the amplitude and the width of the resulting breather solution, in the form of the bubble moving along the DNA molecule, are strongly influenced by the long-range and helicoidal interactions. This result shows a relevant length scale for real protein–DNA interaction.
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D’Abramo, C. M. "Small Molecule Inhibitors of Human Papillomavirus Protein - Protein Interactions." Open Virology Journal 5, no. 1 (July 4, 2011): 80–95. http://dx.doi.org/10.2174/1874357901105010080.

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Linhares, Brian M., Jolanta Grembecka, and Tomasz Cierpicki. "Targeting epigenetic protein–protein interactions with small-molecule inhibitors." Future Medicinal Chemistry 12, no. 14 (July 2020): 1305–26. http://dx.doi.org/10.4155/fmc-2020-0082.

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Epigenetic protein–protein interactions (PPIs) play essential roles in regulating gene expression, and their dysregulations have been implicated in many diseases. These PPIs are comprised of reader domains recognizing post-translational modifications on histone proteins, and of scaffolding proteins that maintain integrities of epigenetic complexes. Targeting PPIs have become focuses for development of small-molecule inhibitors and anticancer therapeutics. Here we summarize efforts to develop small-molecule inhibitors targeting common epigenetic PPI domains. Potent small molecules have been reported for many domains, yet small domains that recognize methylated lysine side chains on histones are challenging in inhibitor development. We posit that the development of potent inhibitors for difficult-to-prosecute epigenetic PPIs may be achieved by interdisciplinary approaches and extensive explorations of chemical space.
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Li, Xiyan, Xin Wang, and Michael Snyder. "Systematic investigation of protein-small molecule interactions." IUBMB Life 65, no. 1 (December 7, 2012): 2–8. http://dx.doi.org/10.1002/iub.1111.

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Nemashkalo, A., M. E. Phipps, S. P. Hennelly, and P. M. Goodwin. "Real-time, single-molecule observation of biomolecular interactions inside nanophotonic zero mode waveguides." Nanotechnology 33, no. 16 (January 25, 2022): 165101. http://dx.doi.org/10.1088/1361-6528/ac467c.

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Abstract Living cells rely on numerous protein-protein, RNA-protein and DNA-protein interactions for processes such as gene expression, biomolecular assembly, protein and RNA degradation. Single-molecule microscopy and spectroscopy are ideal tools for real-time observation and quantification of nucleic acids-protein and protein-protein interactions. One of the major drawbacks of conventional single-molecule imaging methods is low throughput. Methods such as sequencing by synthesis utilizing nanofabrication and single-molecule spectroscopy have brought high throughput into the realm of single-molecule biology. The Pacific Biosciences RS2 sequencer utilizes sequencing by synthesis within nanophotonic zero mode waveguides. A number of years ago this instrument was unlocked by Pacific Biosciences for custom use by researchers allowing them to monitor biological interactions at the single-molecule level with high throughput. In this capability letter we demonstrate the use of the RS2 sequencer for real-time observation of DNA-to-RNA transcription and RNA-protein interactions. We use a relatively complex model–transcription of structured ribosomal RNA from E. coli and interactions of ribosomal RNA with ribosomal proteins. We also show evidence of observation of transcriptional pausing without the application of an external force (as is required for single-molecule pausing studies using optical traps). Overall, in the unlocked, custom mode, the RS2 sequencer can be used to address a wide variety of biological assembly and interaction questions at the single-molecule level with high throughput. This instrument is available for use at the Center for Integrated Nanotechnologies Gateway located at Los Alamos National Laboratory.
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Luo, Fang, Gege Qin, Tie Xia, and Xiaohong Fang. "Single-Molecule Imaging of Protein Interactions and Dynamics." Annual Review of Analytical Chemistry 13, no. 1 (June 12, 2020): 337–61. http://dx.doi.org/10.1146/annurev-anchem-091619-094308.

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Live-cell single-molecule fluorescence imaging has become a powerful analytical tool to investigate cellular processes that are not accessible to conventional biochemical approaches. This has greatly enriched our understanding of the behaviors of single biomolecules in their native environments and their roles in cellular events. Here, we review recent advances in fluorescence-based single-molecule bioimaging of proteins in living cells. We begin with practical considerations of the design of single-molecule fluorescence imaging experiments such as the choice of imaging modalities, fluorescent probes, and labeling methods. We then describe analytical observables from single-molecule data and the associated molecular parameters along with examples of live-cell single-molecule studies. Lastly, we discuss computational algorithms developed for single-molecule data analysis.
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Dissertations / Theses on the topic "Protein-molecule interactions"

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Napoleon, Raeanne L. "Understanding small molecule-protein interactions." Thesis, Boston University, 2012. https://hdl.handle.net/2144/31592.

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Thesis (Ph.D.)--Boston University
PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you.
The binding of small molecules to a protein is among the most important phenomena in the chemistry of life; the activity and functionality of many proteins depend critically on binding small molecules. A deep understanding of protein-small molecule interactions and the interplay between ligation and function can give valuable insight into key systems of interest. The complete characterization of any small molecule-protein interaction requires quantification of many interactions and the pursuit of such information is the purpose of this body of work. The discovery of binding regions on proteins, or "hot spots," is an important step in drug development. To this end, a highly regarded and robust fragment-based protocol has been developed for the detection of hot spots. Firstly, we use this protocol in conjunction with other computation techniques, such as homology modeling, to locate the allosteric binding site of £-phenylalanine in Phenylalanine Hydroxylase. Secondly, computational fragment mapping was employed to locate the site of allostery for Ras, an important signaling protein. Lastly, the identification of hot spots for many unligated protein targets is presented highlighting the importance of a reliable way to predict druggability computationally. The second part of this dissertation shifts focus to the development of electrostatic models of small molecules. It is widely believed that classical potentials can describe neither vibrational frequency shifts in condensed phases nor the response of vibrational frequencies to an applied electric field, the vibrational Stark effect. In this work, an improved classical molecular electrostatic model for the CO ligand was developed to faithfully model these phenomena. This model is found to predict the vibrational Stark effect and Fe-CO binding energy with unprecedented accuracy for such a classical model. As an extension of this work, a geometrically dependent water potential was developed. This work has shown that comparison of results obtained from current water models against experimentally determined proton momentum distributions is an invaluable benchmark
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Albertoni, Barbara [Verfasser]. "Biophysical analysis of protein-protein and protein-small molecule interactions / Barbara Albertoni." Bonn : Universitäts- und Landesbibliothek Bonn, 2011. http://d-nb.info/1044846909/34.

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Jackson, Matthew. "Assay development and investigation of small molecule and amyloid protein interactions." Thesis, University of Sheffield, 2014. http://etheses.whiterose.ac.uk/6549/.

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Mittal, Sumit [Verfasser], Elsa [Gutachter] Sanchez-Garcia, and Simon [Gutachter] Ebbinghaus. "Small molecule modulation of protein-protein interactions / Sumit Mittal ; Gutachter: Elsa Sanchez-Garcia, Simon Ebbinghaus." Bochum : Ruhr-Universität Bochum, 2017. http://d-nb.info/1133361854/34.

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Pérez, González Daniel Cibrán. "Single-molecule studies of nucleic acid folding and nucleic acid-protein interactions." Thesis, University of St Andrews, 2017. http://hdl.handle.net/10023/12039.

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Nucleic acids and proteins, some of the building blocks of life, are not static structures but highly dynamic entities that need to interact with one another to meet cellular demands. The work presented in this thesis focuses on the application of highly sensitive fluorescence methods, both at ensemble and single-molecule level, to determine the dynamics and structure of specific biomolecular interactions with nanometer resolution and in temporal scales from nanoseconds to minutes, which includes most biologically relevant processes. The main aims of my PhD can be classified in three areas: i) exploring new fluorescent sensors with increased specificity for certain nucleic acid structures; ii) understanding how some of these nucleic acids sense the presence of small molecules in the cellular environment and trigger gene regulation by altering their structure; and iii) understanding how certain molecular machines, such as helicase proteins, are able to unwind the DNA double helix by using chemical energy in the form of ATP hydrolysis.
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Fagiewicz, Robert Mateusz. "Structural analysis of protein-small molecule interactions by a crystallographic and spectroscopic approach." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2017. http://amslaurea.unibo.it/13892/.

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Modern spectroscopic techniques grant various methods for a protein structure determination among with a ligand interaction. This work aims at probing the structural insights of a protein-small molecule interaction with biocrystallography and optical spectroscopies. Two independent systems were investigated in the frame of this thesis. The first one involves flavoenzyme interaction with a natural nucleotide as a cofactor required for its catalytic activity and work was purely based on macromolecular crystallography. The second concerns incorporation of a synthetic fluorescent ligand into a model protein as a solution for hydrophobicity of the probe. Due to the nature of the probe optical spectroscopies (such as absorption, fluorescence lifetime, circular dichroism) were effectively employed together with the crystallographic methodology.
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Uphoff, Stephan. "Studying protein-DNA interactions in vitro and in vivo using single-molecule photoswitching." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:d0a52864-6d26-44a4-8fb7-5d12624a04ba.

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Protein-DNA interactions govern the fundamental cellular processes of DNA replication, transcription, repair, and chromosome organisation. Despite their importance, the detailed molecular mechanisms of protein-DNA interactions and their organisation in the cell remain elusive. The complexity of molecular biology demands new experimental concepts that resolve the structural and functional diversity of biomolecules. In this thesis, I describe fluorescence methods that give a direct view on protein-DNA interactions at the single-molecule level. These methods employ photoswitching to control the number of active fluorophores in the sample. Forster Resonance Energy Transfer (FRET) measures the distance between a donor and an acceptor fluorophore to report on biomolecular structure and dynamics in vitro. Because a single distance gives only limited structural information, I developed "switchable FRET" that employs photoswitching to sequentially probe multiple FRET pairs per molecule. Switchable FRET resolved two distances within static and dynamic DNA constructs and protein-DNA complexes. Towards application of switchable FRET, I investigated aspects of the nucleotide selection mechanism of DNA polymerase. I further explored application of single-molecule imaging in the complex environment of the living cell. Photoswitching was used to resolve the precise localisations of individual fluorophores. I constructed a super-resolution fluorescence microscope to image fixed cellular structures and track the movement of individual fluorescent fusion proteins in live bacteria. I applied the method to directly visualise DNA repair processes by DNA polymerase I and ligase, generating a quantitative account of their repair rates, search times, copy numbers, and spatial distribution in the cell. I validated the approach by tracking diffusion of replisome components and their association with the replication fork. Finally, super-resolution microscopy showed dense clusters of SMC (Structural Maintenance of Chromosomes) protein complexes in vivo that have previously been hidden by the limited resolution of conventional microscopy.
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Kung, Wei-Wei. "Protein-protein interactions and small molecule targeting of the multisubunit SOCS2-EloBC-Cul5-Rbx2 E3 ubiquitin ligase." Thesis, University of Dundee, 2018. https://discovery.dundee.ac.uk/en/studentTheses/b2dd4bc4-9a13-428b-a45a-bc46b1d9c116.

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The Cullin-RING E3 ligases (CRLs) are the largest subfamily of E3 ligases that participate in many biological processes determining the fate of proteins by catalysing ubiquitin transfer to specific substrates for proteasomal degradation. SOCS2 is a component of the multisubunit CRL E3 complex (CRL5SOCS2). SOCS2 plays important roles in several cancers and is involved in diabetes and inflammatory diseases. This work aims to understand the substrate recognition mechanism of SOCS2 at an atomic level and provides structural insights to guide the development of small-molecule tools and potential drug leads. Current structural information on SOCS2 is limited to apo form (no ligand bound). In the first part of the work, two novel SOCS2-ElonginB-ElonginC (SBC) structures in complex with substrate peptides of growth hormone receptor (GHR) and erythropoietin receptor (EpoR) were solved by X-ray crystallography with a goal to elucidate the SOCS2 recognition mechanism. Different interactions of the peptides were observed in the structures as a consequence of divergences in the peptide sequences, revealing residues required to catch specific interactions and a protein loop rearrangement as a result of the binding event. An alanine scanning of substrate peptides allowed cross-validation of the structures and identified critical interactions. Based on the crystal structure, five residues that interact with GHR were selected for which single-nucleotide polymorphisms (SNPs) are known in cancer. The results show that the SNPs mutants of SOCS2 located at the phosphotyrosine (pY) pocket are highly disruptive and abolish substrate recognition, suggesting a significant impact to SOCS2 mediated interactions. The second and third part of the work focused on the ligand development at the pY pocket of SOCS2 SH2 domain using a combination of X-ray crystallography and biophysical techniques. Novel crystal structures of SBC in complex with pY and pY analogues were obtained, providing a starting point for compound design. A screening cascade consisting of nuclear magnetic resonance (NMR), surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) was established and validated by an in-house small library of pY analogues. This workflow will facilitate the process of ligand characterisation and design towards a potent binder. The findings of this work unravel interactions of SOCS2 with its substrates in mechanistic detail. Together with the small molecule bound structures and biophysical screening assays, this work provides insights and tools to assist future ligand discovery for CRL5SOCS2.
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Krumm, Stefanie A. [Verfasser], and Dieter [Akademischer Betreuer] Wolf. "Protein-protein and protein-small-molecule inhibitor interactions in the measles virus replication complex / Stefanie A. Krumm. Betreuer: Dieter Wolf." Stuttgart : Universitätsbibliothek der Universität Stuttgart, 2015. http://d-nb.info/1069815470/34.

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Hofmann, Clemens. "Pigment pigment interactions and protein dynamics in light harvesting complexes a single molecule study /." [S.l.] : [s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=971750483.

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Books on the topic "Protein-molecule interactions"

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Waldmann, H., and M. Koppitz, eds. Small Molecule — Protein Interactions. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0.

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name, No. Small molecule-protein interactions. Berlin: Springer, 2003.

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H, Waldmann, and Koppitz M. 1965-, eds. Small molecule--protein interactions. Berlin: Springer, 2003.

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Vassilev, Lyubomir, and David Fry, eds. Small-Molecule Inhibitors of Protein-Protein Interactions. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-17083-6.

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Armstrong, Megan Julia. Single molecule imaging to characterize protein interactions with the environment. [New York, N.Y.?]: [publisher not identified], 2019.

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Byun, Wan Gi. Discovery of Small-Molecule Modulators of Protein–RNA Interactions for Treating Cancer and COVID-19. Singapore: Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-19-7814-2.

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Waldmann, Herbert, and Marcus Koppitz. Small Molecule - Protein Interactions. Springer, 2014.

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Waldmann, Herbert, and Marcus Koppitz. Small Molecule -- Protein Interactions. Springer London, Limited, 2013.

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Waldmann, Herbert. Small Molecule - Protein Interactions. Springer, 2012.

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Fry, David, and Lyubomir Vassilev. Small-Molecule Inhibitors of Protein-Protein Interactions. Springer London, Limited, 2011.

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Book chapters on the topic "Protein-molecule interactions"

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Reinhard-Rupp, J., and G. Wess. "Drug Discovery Opportunities." In Small Molecule — Protein Interactions, 1–10. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_1.

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Briem, H. "De Novo Design Methods." In Small Molecule — Protein Interactions, 153–66. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_10.

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Breinbauer, R., I. R. Vetter, and H. Waldmann. "From Protein Domains to Drug Candidates — Natural Products as Guiding Principles in Compound Library Design and Synthesis." In Small Molecule — Protein Interactions, 167–88. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_11.

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Weber, L. "Discovery of New MCRs, Chemical Evolution and Lead Optimization." In Small Molecule — Protein Interactions, 189–99. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_12.

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Hermkens, P. H. H., and G. Müller. "The Impact of Combinatorial Chemistry on Drug Discovery." In Small Molecule — Protein Interactions, 201–20. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_13.

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Hopkins, A. L., and C. R. Groom. "Target Analysis: A Priori Assessment of Druggability." In Small Molecule — Protein Interactions, 11–17. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_2.

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Wells, J., M. Arkin, A. Braisted, W. DeLano, B. McDowell, J. Oslob, B. Raimundo, and M. Randal. "Drug Discovery at Signaling Interfaces." In Small Molecule — Protein Interactions, 19–27. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_3.

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Willson, T. "Chemical Genomics of Orphan Nuclear Receptors." In Small Molecule — Protein Interactions, 29–42. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_4.

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Jhoti, H. "High-Throughput X-Ray Techniques and Drug Discovery." In Small Molecule — Protein Interactions, 43–58. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_5.

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Kessler, H., M. Heller, G. Gemmecker, T. Diercks, E. Planker, and M. Coles. "NMR in Medicinal Chemistry." In Small Molecule — Protein Interactions, 59–85. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_6.

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Conference papers on the topic "Protein-molecule interactions"

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Cisse, Ibrahim, Burak Okumus, Chirlmin Joo, and Taekjip Ha. "Single Molecule Studies of Protein-DNA Interactions inside Porous Nanocontainers." In Laser Science. Washington, D.C.: OSA, 2008. http://dx.doi.org/10.1364/ls.2008.ltha4.

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Ameer-Beg, Simon M., Conor Treacy, Simon Poland, Justin Aluko, Thomas Kavanagh, and Michael Boersch. "Detection of protein-protein interactions within biological nano-domains by single molecule programmable array microscopy." In Multiphoton Microscopy in the Biomedical Sciences XXIV, edited by Ammasi Periasamy, Peter T. So, and Karsten König. SPIE, 2024. http://dx.doi.org/10.1117/12.3002714.

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Garini, Yuval. "Optical method for studying DNA-protein interactions at the single-molecule level." In Imaging Systems and Applications. Washington, D.C.: OSA, 2013. http://dx.doi.org/10.1364/isa.2013.im3e.2.

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Fore, Samantha, Thomas Huser, Rod Balhorn, Monique Cosman, and Yin Yeh. "Application of Single Molecule FRET Photon-correlation Spectroscopy to Studying DNA-Protein Interactions." In Frontiers in Optics. Washington, D.C.: OSA, 2005. http://dx.doi.org/10.1364/fio.2005.fwk6.

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Kralj, Sebastjan, Milan Hodošček, Marko Jukić, and Urban Bren. "A comprehensive in silico protocol for fast automated mutagenesis and binding affinity scoring of protein-ligand complexes." In 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.674k.

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Protein-protein interactions (PPI) are critical for cellular functions, host-pathogen dynamics and are crucial with drug design efforts. The interaction of proteins is dependent on the amino acid sequence of a protein as it determines its binding affinity to various molecules, including drugs, DNA, RNA, and proteins. Polymorphisms, natural DNA variations, affect PPIs by altering protein structure and stability. Computational chemistry is vital for the prediction of ligand-protein interactions through techniques such as docking and molecular dynamics and can elucidate the changes in energy associated with such mutations. We present a user-friendly protocol that uses the INTE command of CHARMM to predict the effects of mutations on PPIs. This command-line tool automates mutation analysis and interaction energy estimation, is applicable to different ligand types (protein, DNA, RNA, ion, small molecule) and provides various other features. The energy values yield absolute and normalized heat maps that allow rapid identification of stabilizing and destabilizing mutations. Our protocol forms the basis for automated programs that facilitate studies of binding-altering mutations in host-pathogen, protein-protein, and drug-target interactions.
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Tseng, Fan-Gang. "From High Performance Protein Micro Chip Toward Ultra High Sensitive Single Molecule Nano Array." In ASME 2009 7th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2009. http://dx.doi.org/10.1115/icnmm2009-82291.

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Protein microarrays have been employed to screen tens to thousands of proteins simultaneously for the observation of the biochemical activities in the protein-protein, protein-nucleic acid and small molecule interactions. This technology allows high throughput analysis and holds great potential for basic molecular biology research, disease marker identification, toxicological response profiling and pharmaceutical target screening. However, proteins easily malfunction in harsh environments so that they are hardly preserved before the application because of their complex and fragile structures. On the other hand, identify scarce amount of proteins less than fM range is very important and challenge for disease diagnosis at very early stage. As a result, the procedures for protein micro array formation are very important for preserving protein functionality to ensure useful protein assays, as well as the improvement of the detection sensitivity up to single molecule event but with high dynamic range for disease early detection. Therefore, this paper provides a novel view from the preparation of high efficient protein micro chip toward ultra high sensitive single protein nano array through the technology integration of BioMEMS and Bio-Nanotechnology.
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Kesić, Ana S., Snežana R. Radisavljević, Jovana V. Bogojeski, and Biljana V. Petrović. "The interaction studies of novel diaminophenazine gold(III) complex and Bovine Serum Albumin (BSA-ibuprofen and BSA-Eozine Y)." In 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.407k.

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It is well known that gold(III) complexes have found applications in medicinal inorganic chemistry. Considering this, the right choice of inert ligands in the structure of Au(III) complexes is crucial for predicting their properties and reactivity, especially towards biomolecules. Here are presented the results of the study of the interactions between the new gold(III) complex [Au(DAP)Cl3], with 2,3-diaminophenazine (DAP) as an inert ligand, and BSA. Specifically, serum albumin is the main soluble protein in the circulatory system of humans. The metabolism of drugs, their distribution, free concentration, and effectiveness strongly depend on the drug-albumin interaction. Investigation of the interactions of the [Au(DAP)Cl3] complex with bovine serum albumin (BSA) under physiological conditions was performed by fluorescence spectroscopy. This method was also used to identify the binding site on the BSA molecule, with eosin Y as a marker for site I (subdomain IIA), and ibuprofen as a marker for site II (subdomain IIIA). The results have shown that the complex moderately reacts with the BSA molecule with just one binding site for the complex on the protein. Additionally, based on the results with site markers, especially with eosin Y, it can be concluded that the studied complex binds to site I of the BSA molecule.
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Jongwan, Kim, Hocheol Lim, and K. T. No. "Abstract A45: In silico drug discovery targeting Hippo pathway and YAP-TEAD protein-protein interactions for small-molecule anticancer agent." In Abstracts: AACR Special Conference on the Hippo Pathway: Signaling, Cancer, and Beyond; May 8-11, 2019; San Diego, CA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1557-3125.hippo19-a45.

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Zheng, Zhuoyuan, Akash Singh, and Yumeng Li. "Molecular Dynamic Simulation Study on Soy Protein As Drug Delivery Vehicle." In ASME 2020 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2020. http://dx.doi.org/10.1115/imece2020-23590.

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Abstract Protein-based drug carriers are promising candidates for efficient drug delivery among the available potential colloidal carrier systems, due to their low cytotoxicity, abundance, renewability, diverse functional groups and interactions, and high drug loading capacity, etc. In this study, molecular dynamics (MD) simulations are performed to study the mechanisms of 11S molecule of soy protein as drug delivery vehicle to attach allyl isothiocyanate (AITC) and doxorubicin (DOX) drugs. The intermolecular interactions between protein and drugs are investigated; and the loading capacities of the protein molecules are calculated and compared with experiments. It is found that, for the AITC system, both nonpolar and polar residues of protein have the ability to adsorb AITCs; particularly, the polar residues serve as the primary active sites for the stable attachment of the drug molecules through the electrostatic (dipole-dipole) interactions. For the DOX system, however, the main driving force become the π-π stacking (the van der Waals interactions) among the aromatic rings of DOX and protein. In addition to pristine protein, different denaturation processes are found to be able to increase the exposure of active sites, therefore, enhance the loading efficiency of the protein carriers.
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Kabir, Abbas, and Aaron Muth. "Abstract 1311: Inhibition of gankyrin-tumor suppressor protein interactions due to small molecule induced conformational change." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-1311.

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Reports on the topic "Protein-molecule interactions"

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Chamovitz, Daniel A., and Zhenbiao Yang. Chemical Genetics of the COP9 Signalosome: Identification of Novel Regulators of Plant Development. United States Department of Agriculture, January 2011. http://dx.doi.org/10.32747/2011.7699844.bard.

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This was an exploratory one-year study to identify chemical regulators of the COP9 signalosome. Chemical Genetics uses small molecules to modify or disrupt the function of specific genes/proteins. This is in contrast to classical genetics, in which mutations disrupt the function of genes. The underlying concept is that the functions of most proteins can be altered by the binding of a chemical, which can be found by screening large libraries for compounds that specifically affect a biological, molecular or biochemical process. In addition to screens for chemicals which inhibit specific biological processes, chemical genetics can also be employed to find inhibitors of specific protein-protein interactions. Small molecules altering protein-protein interactions are valuable tools in probing protein-protein interactions. In this project, we aimed to identify chemicals that disrupt the COP9 signalosome. The CSN is an evolutionarily conserved eight-subunit protein complex whose most studied role is regulation of E3 ubiquitinligase activity. Mutants in subunits of the CSN undergo photomorphogenesis in darkness and accumulate high levels of pigments in both dark- and light-grown seedlings, and are defective in a wide range of important developmental and environmental-response pathways. Our working hypothesis was that specific molecules will interact with the CSN7 protein such that binding to its various interacting proteins will be inhibited. Such a molecule would inhibit either CSN assembly, or binding of CSN-interacting proteins, and thus specifically inhibit CSN function. We used an advanced chemical genetic screen for small-molecule-inhibitors of CSN7 protein-protein interactions. In our pilot study, following the screening of ~1200 unique compounds, we isolated four chemicals which reproducibly interfere with CSN7 binding to either CSN8 or CSN6.
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Weiss, Shimon, and Xavier Michalet. Single-Molecule Methods for the Large-Scale Characterization of Expression Levels and Protein-Protein Interactions in Shewanella Oneidensis MR-1. Office of Scientific and Technical Information (OSTI), October 2008. http://dx.doi.org/10.2172/1010284.

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Yedidia, I., H. Senderowitz, and A. O. Charkowski. Small molecule cocktails designed to impair virulence targets in soft rot Erwinias. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2020. http://dx.doi.org/10.32747/2020.8134165.bard.

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Chemical signaling between beneficial or pathogenic bacteria and plants is a central factor in determining the outcome of plant-microbe interactions. Pectobacterium and Dickeya (soft rot Erwinias) are the major cause of soft rot, stem rot, and blackleg formed on potato and ornamentals, currently with no effective control. Our major aim was to establish and study specific bacterial genes/proteins as targets for anti-virulence compounds, by combining drug design tools and bioinformatics with experimental work. The approach allowed us to identify and test compounds (small molecules) that specifically interfere with the activities of these targets, by this impairing bacterial virulence. Two main targets were selected within the frame of the BARD project. The first is the ATP-binding cassette (ABC) transporters and methyl-accepting chemotaxis proteins (MCP) that have been characterized here for the first time in Pectobacteriaceae, and the second is the quorum sensing (QS) machinery of Pectobacterium with its major proteins and in particular, the AHL synthase ExpI that was identified as the preferred target for inhibition. Both systems are strongly associated with bacterial virulence and survival in planta. We found that Pectobacteriaceae, namely Dickeya and Pectobacterium, encode more ABC transporters and MCP in their genomes, compared to other bacteria in the order. For MCP, soft rot Pectobacteriaceae not only contain more than 30 MCP genes per strain, but also have more diverse ligand binding domains than other species in the Enterobacteriales. These findings suggest that both ABC transporters and MCP are important for soft rot Pectobacteriaceae pathogenicity. We now have a selection of mutants in these proteins that may be further explored to understand their direct involvement in virulence. In parallel, we studied the QS central proteins in pectobacteria, the signaling molecule N-acyl-homoserine lactone synthase, ExpI, and the response regulator ExpR, and established their phylogenetic relations within plant pathogenic Gram negative bacteria. Next, these proteins were used for virtual screening of millions of compounds in order to discover new compounds with potential to interfere with the QS machinery. Several natural compounds were tested for their interference with virulence related traits in Pectobacterium and their capability to minimize soft rot infections. Our findings using microcalorimetric binding studies have established for the first time direct interaction between the protein ExpI and two natural ligands, the plant hormone salicylic acid and the volatile compound carvacrol. These results supported a model by which plants interfere with bacterial communication through interkingdom signaling. The collaborative project yielded two research papers and a comprehensive review, which included new computational and bioinformatics data, in Annu. Rev. Phytopathol., the highest ranked journal in phytopathology. Additional two papers are in preparation. In order to transform the fundamental knowledge that have been gained during this collaborative BARD project into agricultural practice, to control soft rot bacteria, we have submitted a continual project.
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Tzfira, Tzvi, Michael Elbaum, and Sharon Wolf. DNA transfer by Agrobacterium: a cooperative interaction of ssDNA, virulence proteins, and plant host factors. United States Department of Agriculture, December 2005. http://dx.doi.org/10.32747/2005.7695881.bard.

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Agrobacteriumtumefaciensmediates genetic transformation of plants. The possibility of exchanging the natural genes for other DNA has led to Agrobacterium’s emergence as the primary vector for genetic modification of plants. The similarity among eukaryotic mechanisms of nuclear import also suggests use of its active elements as media for non-viral genetic therapy in animals. These considerations motivate the present study of the process that carries DNA of bacterial origin into the host nucleus. The infective pathway of Agrobacterium involves excision of a single-stranded DNA molecule (T-strand) from the bacterial tumor-inducing plasmid. This transferred DNA (T-DNA) travels to the host cell cytoplasm along with two virulence proteins, VirD2 and VirE2, through a specific bacteriumplant channel(s). Little is known about the precise structure and composition of the resulting complex within the host cell and even less is known about the mechanism of its nuclear import and integration into the host cell genome. In the present proposal we combined the expertise of the US and Israeli labs and revealed many of the biophysical and biological properties of the genetic transformation process, thus enhancing our understanding of the processes leading to nuclear import and integration of the Agrobacterium T-DNA. Specifically, we sought to: I. Elucidate the interaction of the T-strand with its chaperones. II. Analyzing the three-dimensional structure of the T-complex and its chaperones in vitro. III. Analyze kinetics of T-complex formation and T-complex nuclear import. During the past three years we accomplished our goals and made the following major discoveries: (1) Resolved the VirE2-ssDNA three-dimensional structure. (2) Characterized VirE2-ssDNA assembly and aggregation, along with regulation by VirE1. (3) Studied VirE2-ssDNA nuclear import by electron tomography. (4) Showed that T-DNA integrates via double-stranded (ds) intermediates. (5) Identified that Arabidopsis Ku80 interacts with dsT-DNA intermediates and is essential for T-DNA integration. (6) Found a role of targeted proteolysis in T-DNA uncoating. Our research provide significant physical, molecular, and structural insights into the Tcomplex structure and composition, the effect of host receptors on its nuclear import, the mechanism of T-DNA nuclear import, proteolysis and integration in host cells. Understanding the mechanical and molecular basis for T-DNA nuclear import and integration is an essential key for the development of new strategies for genetic transformation of recalcitrant plant species. Thus, the knowledge gained in this study can potentially be applied to enhance the transformation process by interfering with key steps of the transformation process (i.e. nuclear import, proteolysis and integration). Finally, in addition to the study of Agrobacterium-host interaction, our research also revealed some fundamental insights into basic cellular mechanisms of nuclear import, targeted proteolysis, protein-DNA interactions and DNA repair.
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