Relevant bibliographies by topics / Molecule identification

Academic literature on the topic 'Molecule identification'

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Published: 6 September 2023

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Journal articles on the topic "Molecule identification"

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Dührkop, Kai. "Computational methods for small molecule identification." it - Information Technology 61, no. 5-6 (October 25, 2019): 285–92. http://dx.doi.org/10.1515/itit-2019-0033.

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Abstract Identification of small molecules remains a central question in analytical chemistry, in particular for natural product research, metabolomics, environmental research, and biomarker discovery. Mass spectrometry is the predominant technique for high-throughput analysis of small molecules. But it reveals only information about the mass of molecules and, by using tandem mass spectrometry, about the mass of molecular fragments. Automated interpretation of mass spectra is often limited to searching in spectral libraries, such that we can only dereplicate molecules for which we have already recorded reference mass spectra. In my thesis “Computational methods for small molecule identification” we developed SIRIUS, a tool for the structural elucidation of small molecules with tandem mass spectrometry. The method first computes a hypothetical fragmentation tree using combinatorial optimization. By using a Bayesian statistical model, we can learn parameters and hyperparameters of the underlying scoring directly from data. We demonstrate that the statistical model, which was fitted on a small dataset, generalizes well across many different datasets and mass spectrometry instruments. In a second step the fragmentation tree is used to predict a molecular fingerprint using kernel support vector machines. The predicted fingerprint can be searched in a structure database to identify the molecular structure. We demonstrate that our machine learning model outperforms all other methods for this task, including its predecessor FingerID. SIRIUS is available as commandline tool and as user interface. The molecular fingerprint prediction is implemented as web service and receives over one million requests per month.
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Mills, Randell L., William R. Good, and Robert M. Shaubach. "Dihydrino Molecule Identification." Fusion Technology 25, no. 1 (January 1994): 103–19. http://dx.doi.org/10.13182/fst94-a30239.

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Bell, David C., W. Kelley Thomas, Katelyn M. Murtagh, Cheryl A. Dionne, Adam C. Graham, Jobriah E. Anderson, and William R. Glover. "DNA Base Identification by Electron Microscopy." Microscopy and Microanalysis 18, no. 5 (October 2012): 1049–53. http://dx.doi.org/10.1017/s1431927612012615.

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AbstractAdvances in DNA sequencing, based on fluorescent microscopy, have transformed many areas of biological research. However, only relatively short molecules can be sequenced by these technologies. Dramatic improvements in genomic research will require accurate sequencing of long (>10,000 base-pairs), intact DNA molecules. Our approach directly visualizes the sequence of DNA molecules using electron microscopy. This report represents the first identification of DNA base pairs within intact DNA molecules by electron microscopy. By enzymatically incorporating modified bases, which contain atoms of increased atomic number, direct visualization and identification of individually labeled bases within a synthetic 3,272 base-pair DNA molecule and a 7,249 base-pair viral genome have been accomplished. This proof of principle is made possible by the use of a dUTP nucleotide, substituted with a single mercury atom attached to the nitrogenous base. One of these contrast-enhanced, heavy-atom-labeled bases is paired with each adenosine base in the template molecule and then built into a double-stranded DNA molecule by a template-directed DNA polymerase enzyme. This modification is small enough to allow very long molecules with labels at each A-U position. Image contrast is further enhanced by using annular dark-field scanning transmission electron microscopy (ADF-STEM). Further refinements to identify additional base types and more precisely determine the location of identified bases would allow full sequencing of long, intact DNA molecules, significantly improving the pace of complex genomic discoveries.
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LEE, J., H. LI, and E. YEUNG. "Single-molecule spectroscopy for molecular identification in capillary electrophoresis." Journal of Chromatography A 1053, no. 1-2 (October 22, 2004): 173–79. http://dx.doi.org/10.1016/s0021-9673(04)01091-x.

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Li, Qingxin, and CongBao Kang. "Mechanisms of Action for Small Molecules Revealed by Structural Biology in Drug Discovery." International Journal of Molecular Sciences 21, no. 15 (July 24, 2020): 5262. http://dx.doi.org/10.3390/ijms21155262.

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Small-molecule drugs are organic compounds affecting molecular pathways by targeting important proteins. These compounds have a low molecular weight, making them penetrate cells easily. Small-molecule drugs can be developed from leads derived from rational drug design or isolated from natural resources. A target-based drug discovery project usually includes target identification, target validation, hit identification, hit to lead and lead optimization. Understanding molecular interactions between small molecules and their targets is critical in drug discovery. Although many biophysical and biochemical methods are able to elucidate molecular interactions of small molecules with their targets, structural biology is the most powerful tool to determine the mechanisms of action for both targets and the developed compounds. Herein, we reviewed the application of structural biology to investigate binding modes of orthosteric and allosteric inhibitors. It is exemplified that structural biology provides a clear view of the binding modes of protease inhibitors and phosphatase inhibitors. We also demonstrate that structural biology provides insights into the function of a target and identifies a druggable site for rational drug design.
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Jing, Nan, Jun Kameoka, Chin B. Su, Chao-Kai Chou, and Mien-Chie Hung. "Nanofluidic Devices for Single Molecule Identification." Journal of Photopolymer Science and Technology 21, no. 4 (2008): 531–36. http://dx.doi.org/10.2494/photopolymer.21.531.

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Flower, Darren R. "Systematic identification of small molecule adjuvants." Expert Opinion on Drug Discovery 7, no. 9 (June 24, 2012): 807–17. http://dx.doi.org/10.1517/17460441.2012.699958.

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Ding, Fangyuan, Maria Manosas, Michelle M. Spiering, Stephen J. Benkovic, David Bensimon, Jean-François Allemand, and Vincent Croquette. "Single-molecule mechanical identification and sequencing." Nature Methods 9, no. 4 (March 11, 2012): 367–72. http://dx.doi.org/10.1038/nmeth.1925.

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Chauhan, Ritika, Vinita Chauhan, Priyanka Sonkar, and Ram Kumar Dhaked. "Identification of Inhibitors against Botulinum Neurotoxins: 8-Hydroxyquinolines Hold Promise." Mini-Reviews in Medicinal Chemistry 19, no. 20 (December 16, 2019): 1694–706. http://dx.doi.org/10.2174/1389557519666190906120228.

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Botulinum neurotoxins (BoNTs) are the most toxic category A biological warfare agents. There is no therapeutics available for BoNT intoxication yet, necessitating the development of a medical countermeasure against these neurotoxins. The discovery of small molecule-based drugs has revolutionized in the last two decades resulting in the identification of several small molecule inhibitors of BoNTs. However, none progressed to clinical trials. 8-Hydroxyquinolines scaffold-based molecules are important ‘privileged structures’ that can be exploited as inhibitors of a diverse range of targets. In this review, our study of recent reports suggests the development of 8-hydroxyquinoline derived molecules as a potential drug may be on the horizon.
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ANTONOPOULOU, Smaragdi, A. Constantinos DEMOPOULOS, Dimitris ARGYROPOULOS, George BALTAS, Helen KOTSIFAKI, and Anthoula DIAMANTI-KIPIOTI. "Identification of a new endogenous platelet-activating factor-like molecule in gingival crevicular fluid." Biochemical Journal 330, no. 2 (March 1, 1998): 791–94. http://dx.doi.org/10.1042/bj3300791.

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Periodontal disease is an inflammatory disease and the major cause of tooth loss in adults. Bacteria and their products are the causative agents of this disease. Endogenous molecules mediate the inflammatory process and play a major role in its amplification and perpetuation as well as in the ensuing tissue destruction. The relationship between platelet-activating factor (PAF) and periodontal disease has not so far been examined thoroughly. We have isolated a phospholipid molecule with PAF-like activity from gingival crevicular fluid. This molecule, purified on HPLC, causes washed platelet aggregation with EC50 value 0.1 μM, based on phosphorus determination. It acts through PAF-receptors and is inactivated by PAF-acetylhydrolase. In addition, this phospholipid presents biological activity towards human platelets. The combination of the results obtained from the chemical and enzymic treatments, the biological assays as well as results from the electrospray analysis, leads to the conclusion that this phospholipid is a hydroxyl-PAF analogue with relative molecular mass 703. This PAF-like molecule may be implicated in periodontal disease.
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Dissertations / Theses on the topic "Molecule identification"

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Ding, Fangyuan. "Single molecule mechanical sequencing and identification." Paris 6, 2012. http://www.theses.fr/2012PA066702.

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SAINT-ESPES, CECILE. "Identification des etats de molecule molle de hcn." Paris 11, 1993. http://www.theses.fr/1993PA112479.

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A l'etat electronique fondamental, les etats vibrationnels tres excites de la molecule hcn et de son isomere cnh sont analyses a partir d'un modele adiabatique. La methodologie proposee tient compte de la reaction d'isomerisation du systeme moleculaire (h, c, n), et utilise les proprietes des chemins de reactions d'isomerisation. Elle permet en particulier de distinguer les differents types d'etats susceptibles d'exister a des energies comprises entre la barriere d'isomerisation et l'energie de dissociation du systeme, a savoir: - etats localises de hcn et de cnh: l'energie interne est concentree pour l'essentiel, dans les modes de vibrations d'elongations: - etats delocalises: le mode de pliage mis en jeu lors de la deformation du systeme est fortement excite. L'atome h navigue autour du cur diatomique cn: aucune geometrie d'equilibre unique (hcn ou cnh) ne peut etre rattachee a un tel etat de vibration. Ces etats se repartissent dans les deux categories suivantes: 1) etats composites qui proviennent d'interferences quantiques entre un etat localise de hcn et un etat localise de cnh; 2) etats mous ou flous qui presentent de l'amplitude de vibration de pliage quasiment sur tout le domaine de variation du mode de deformation du systeme. Cette amplitude s'avere maximale a la verticale de la barriere d'isomerisation
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Heaslip, Aoife. "Identification of Small Molecule Effectors of the Toxoplasma." ScholarWorks @ UVM, 2008. http://scholarworks.uvm.edu/graddis/105.

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Toxoplasma gondii is an obligate intracellular parasite that can cause lifethreatening disease in immunocompromised individuals. Host cell invasion is therefore central to the pathology of the disease and parasite survival. Unlike many intracellular pathogens, T. gondii does not enter cells by manipulating the host’s phagocytic machinery; instead, the parasite enters the cell by a process of active penetration. Gliding motility and active penetration are driven by a complex of proteins termed the glideosome. The glideosome consists of four major proteins: TgMyoA, an unconventional myosin XIV, myosin light chain (TgMLC1) and glideosome-associated proteins 45 and 50 (TgGAP45, TgGAP50). TgMyoA has been shown to be essential for parasite motility, but the role of TgMLC1 in regulating myosin function remains unknown. Our lab has identified an inhibitor of T. gondii motility and invasion that results in a post-translational modification (PTM) to TgMLC1. Using molecular genetic and mass spectrometry methods we have shown cysteine 53 and cysteine 58 of TgMLC1 are essential for the modification to occur. To determine if the TgMLC1 PTM alters TgMyoA activity, glideosomes were isolated from DMSO- and 115556-treated parasites. Using an in vitro motility assay we have shown that the TgMyoA actin filament displacement velocities are decreased after 115556 treatment. This is the first evidence that TgMLC1 plays a role in regulating TgMyoA activity. The TgMLC1 PTM is responsible, at least in part, for the invasion and motility defects seen in the parasite after compound treatment. During the course of our investigations we have shown that TgMLC1 is dimethylated on lysine 95. This is an unusual modification for cytosolic proteins and has not been previously described for MLCs. Experiments using parasites expressing a non-methylatable form of TgMLC1 (TgMLC1-K95A) show that dimethylation is not necessary for TgMLC1 peripheral localization, TgMLC1 protein-protein interactions and is not required for TgMyoA activity in vitro. However, TgMLC1-K95A does not appear to be phosphoryalted indicating that TgMLC1 dimethylation is necessary for efficient phosphorylation of TgMLC1. These experiments will provide new insight into the ways in which TgMLC1 regulates this unconventional myosin motor complex.
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Tam, Vernon Craig Goodheart. "Identification of a glycodelin-C binding molecule on humanspermatozoa." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2007. http://hub.hku.hk/bib/B39558666.

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Tam, Vernon Craig Goodheart. "Identification of a glycodelin-C binding molecule on human spermatozoa." Click to view the E-thesis via HKUTO, 2007. http://sunzi.lib.hku.hk/HKUTO/record/B39558666.

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Macaulay, Angus. "Identification of large molecule transfer in cumulus cell - oocyte intercommunication." Doctoral thesis, Université Laval, 2015. http://hdl.handle.net/20.500.11794/26444.

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Mes travaux explorent, chez la vache, le transfert entre les cellules du cumulus et l’ovocyte des transcrits d’ARN et d’autres larges molécules qui, selon notre hypothèse, pourraient être exportées des cellules somatiques à l’ovocyte, ceci afin de soutenir sa maturation. L’étude des projections transzonales (PTZ) reliant les cellules du cumulus à l’ovocyte a révélé qu’elles sont de morphologie irrégulière, qu’elles peuvent contenir des organelles (mitochondries) et des structures cellulaires (ribosomes) et qu’elles se retractent au cours de la maturation ovocytaire. Des microvésicules pouvant transférer de larges molécules ont été identifiées à la jonction entre les cellules. Pour déterminer si l’ARN est empaqueté préalablement à son transfert entre les cellules, nous avons analysé les transcrits présents dans les PTZ et avons constaté qu’ils se déplacent vers l’ovocyte en maturation. Parmi les transcrits retrouvés dans les PTZ, certains étaient commun à ceux dont l’abondance augmente dans l’ovocyte en cours de maturation de même qu’à ceux retrouvés dans les polyribosomes de l’ovocyte en maturation, suggérant ainsi le transfert et l’utilisation des transcrits provenant des cellules du cumulus. Un transcrit synthétique ajouté aux cellules du cumulus avant qu’elles ne s’attachent à l’ovocyte a été transféré à ce dernier, confirmant ainsi le potentiel des cellules à transférer des ARNm et possiblement leurs protéins associées à l’ovocyte. Nouse avons observé, sur une échelle de temps, que les transcrits sont accumulés dans les PTZ au cours des heures suivant l’abattage de l’animal, mais préalablement à l’aspiration de l’ovocyte. Le retrait des cellules du cumulus et de cette période d’accumulation des transcrits se traduit par un faible taux de maturation des ovocytes. La nécessité d’avoir des vésicules d’ARN transférées à l’ovocyte a été testée grâce à des inhibiteurs de la synthèse d’ARN, de son transport et de la formation des vésicules. L’inhibition de chacune de ces étapes a compromis la maturation des ovocytes. En se penchant sur les mécanismes impliqués dans le transfert des transcrits, nous avons découvert un candidat potentiel jouant un rôle dans l’insuffisance ovarienne précoce. Cette protéine liant les ARNm, Fragile X mental retardation (FMRP), a été retrouvée dans les cellules folliculaires et dans l’ovocyte tout au long de la folliculogenèse et de l’ovogenèse. Nous avons constaté que FMRP s’associe à la machinerie traductionnelle et aux protéines des granules d’entreposage dans l’ovocyte. L’inhibition de la protéine a significativement réduit le taux de blastocyste. En démontrant que des transcrits exogènes contribuent au développement de l’ovocyte et influencent sa maturation, nos recherches ajoutent un niveau de compréhension additionnel aux mécanismes de communication intercellulaire menant à la production de gamètes de bonne qualité. De futures expériences axées la caractérisation du transfert des transcrits et des mécanismes spécifiques en jeu contribuera à accroître notre compréhension de la compétence ovocytaire.
The reports in this thesis explored the potential for large molecule communication between the cumulus cell and the oocyte hypothesizing that large molecules, including RNA, could be transferred to the oocyte for support during maturation. Exploration of the transzonal projections (TZPs) connecting the cumulus cells to the oocyte revealed that they are irregular in shape, can contain large organelles (mitochondria) and small cellular structures (ribosomes), and that these connections retract during oocyte maturation. Microvesicles were identified at the intercellular articulations capable of sharing large molecules between the cells. To determine if RNA is transferring as cargo between cells, nascent as well as total transcripts were evaluated in the TZPs and found moving towards the oocyte during maturation. Of the transcripts found in the TZPs during maturation, some were common to those increasing in abundance in the oocyte during maturation, and on the polyribosomes of the maturing oocyte, thus suggesting transfer and use of cumulus cell transcripts. A synthetic transcript provided to some cumulus cells for reconstruction with, and transfer to the oocyte, confirmed the potential to transfer mRNA and possibly proteins. Temporally, RNA transcripts were found to accumulate in TZPs during the hours post slaughter but prior to oocyte aspiration. Removal of the cumulus cells and this period of accumulation resulted in poor oocyte maturation. The requirement of vesicle mediated RNA transfer to the oocyte was tested. Inhibitors against RNA synthesis, transport, and vesicle formation were explored and found to reduced oocyte maturation. Focusing on mechanisms that could mediate transference, we assessed an RNA binding protein candidate with implications in premature ovarian insufficiency. Fragile X mental retardation protein (FMRP) was found in follicular cells and the oocyte throughout folliculogenesis and oogenesis. Based on known roles in translation control, FMRP was shown associated with translational machinery and storage granule proteins in the oocyte. Knockdown of this protein resulted in compromised rates of blastocyst formation. Knowing that exogenous transcripts contribute to oocyte development, and influence the molecular aspects of oocyte maturation adds another layer to our understanding of intercellular communication in the production of a healthy gamete. Future characterization of the transferred transcripts and the mechanisms in control of this process will improve our understanding of oocyte health and competence.
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Saade, Khalil. "Identification of a potent anti-invasive molecule through mixed targeting design." Thesis, McGill University, 2008. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=116059.

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The altered protein expression and activity of receptor tyrosine kinases (TK) are implicated in the progression of various types of cancers. One such dysfunction is the overexpression of the epidermal growth factor receptor (EGFR) that correlates with aggressive tumor progression and poor prognosis. On the other hand, c-Src non-receptor tyrosine kinase is overexpressed and activated in a large number of human malignancies and has been strongly linked to progression to distant metastases. c-Src-induced phosphorylation of EGFR is required for EGF-mediated mitogenesis, tumorigenesis and tumour invasiveness. Thus we surmised that molecules termed "combi-molecules" designed to block both EGFR and c-Src should not only possess significant growth inhibitory potency but also strong anti-invasive properties. In this thesis, we utilized molecular modeling to design molecules containing two moieties: one that straddles the structure of the known Src inhibitor PP2 and the other that mimics the backbone of Iressa, a potent EGFR inhibitor. Of all the molecules synthesized, only SB163 containing the longest spacer between the two moieties was capable of inducing a dose dependent inhibition of both Src and EGFR. More importantly, SB163 blocked cell motility in the wound healing assay and showed significantly greater anti-invasive activity than a PP2+Iressa combination. The observation that SB163 was a less potent EGFR or Src inhibitor than Iressa and PP2 suggests that its superior potency when compared with the PP2+ Iressa combination may be at least partially attributed to mechanisms other than EGFR or Src blockade. This was also corroborated by the fact that SB163, despite its significant bulkiness (>700) could induce dose dependent inhibition of other kinase such PDFGR and Abl. The results in toto suggest that conferring multiple kinase targeting properties to single molecules can lead to highly anti-proliferative and anti-invasive agents. Traditionally, multi-kinase targeted molecules were discovered serendipitously through multi-kinase testing. Here we initiated a more rational approach to the design of single multi-targeted molecules. Cancer being a complex disease driven by tumours characterized by multiple disordered signaling pathways, this approach may well represent a novel avenue in the therapy of refractory malignancies.
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區大綱 and Tai-kong Au. "Identification of binding sites for ophiobolin a in the calmodulin molecule." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1997. http://hub.hku.hk/bib/B31236492.

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Au, Tai-kong. "Identification of binding sites for ophiobolin a in the calmodulin molecule /." Hong Kong : University of Hong Kong, 1997. http://sunzi.lib.hku.hk/hkuto/record.jsp?B19235288.

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Kilian, Karin. "Identification of novel interaction partners for the leukocyte adhesion molecule L-selectin." [S.l. : s.n.], 2002. http://www.diss.fu-berlin.de/2002/295/index.html.

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Books on the topic "Molecule identification"

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Yu lei zhong zhi fen zi jian ding ji shu: Molecule identification technique for fish genetic resources. Beijing Shi: Hai yang chu ban she, 2011.

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Zhao, Xiaoning. Identification and characterization of a homophilic binding and neuritogenic site in the cell adhesion molecule L1. Ottawa: National Library of Canada = Bibliothèque nationale du Canada, 1998.

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Gherbawy, Youssuf, and Kerstin Voigt, eds. Molecular Identification of Fungi. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-05042-8.

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Gherbawy, Youssuf, and Kerstin Voigt. Molecular identification of fungi. Berlin: Springer, 2010.

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Lajos, Ferenczy, ed. Molecular identification of fungi. Heidelberg: Springer, 2010.

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Szostak, R. Molecular sieves: Principles of synthesis and identification. New York: Van Nostrand Reinhold, 1989.

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Towner, K. J., and A. Cockayne. Molecular Methods for Microbial Identification and Typing. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1506-3.

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A, Cockayne, ed. Molecular methods for microbial identification and typing. London: Chapman & Hall, 1993.

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Molecular sieves: Principles of synthesis and identification. New York: Van Nostrand Reinhold, 1989.

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Szostak, Rosemarie. Molecular sieves: Principles of synthesis and identification. 2nd ed. London: Blackie Academic & Professional, 1998.

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Book chapters on the topic "Molecule identification"

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Lopez-Martinez, Montse, Gwenael Mercier, Kamran Sadiq, Otmar Scherzer, Magdalena Schneider, John C. Schotland, Gerhard J. Schütz, and Roger Telschow. "Inverse Problems of Single Molecule Localization Microscopy." In Time-dependent Problems in Imaging and Parameter Identification, 323–76. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-57784-1_12.

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Bevilacqua, M. P., and M. A. Gimbrone. "Identification and Characterization of Endothelial-Leukocyte Adhesion Molecule 1." In Leukocyte Adhesion Molecules, 215–23. New York, NY: Springer New York, 1990. http://dx.doi.org/10.1007/978-1-4612-3234-6_17.

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Osada, Hiroyuki, and Siro Simizu. "Identification of Protein–Small Molecule Interactions by Chemical Array." In Chembiomolecular Science, 103–11. Tokyo: Springer Japan, 2012. http://dx.doi.org/10.1007/978-4-431-54038-0_10.

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Salcius, Michael, Gregory A. Michaud, Barry Schweitzer, and Paul F. Predki. "Identification of Small Molecule Targets on Functional Protein Microarrays." In Methods in Molecular Biology, 239–48. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-304-2_15.

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Groen, Arnoud, Ludivine Thomas, Kathryn Lilley, and Claudius Marondedze. "Identification and Quantitation of Signal Molecule-Dependent Protein Phosphorylation." In Cyclic Nucleotide Signaling in Plants, 121–37. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-441-8_9.

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Drosopoulos, Konstantinos, and Spiros Linardopoulos. "Integration of RNAi and Small Molecule Screens to Identify Targets for Drug Development." In Target Identification and Validation in Drug Discovery, 33–42. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9145-7_3.

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Drosopoulos, Konstantinos, and Spiros Linardopoulos. "Integration of RNAi and Small Molecule Screens to Identify Targets for Drug Development." In Target Identification and Validation in Drug Discovery, 97–104. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-311-4_7.

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Berlin, Vivian, and M. Isabel Chiu. "Identification of Novel Cell Cycle Targets Using Small Molecule Ligands." In Cell Cycle — Materials and Methods, 145–56. Berlin, Heidelberg: Springer Berlin Heidelberg, 1996. http://dx.doi.org/10.1007/978-3-642-57783-3_13.

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Liao, Daiqing. "Identification and Characterization of Small-Molecule Inhibitors of Lysine Acetyltransferases." In Methods in Molecular Biology, 539–48. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1804-1_28.

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Connelly, Colleen M., and Alexander Deiters. "Identification of Inhibitors of MicroRNA Function from Small Molecule Screens." In Methods in Molecular Biology, 147–56. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-703-7_12.

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Conference papers on the topic "Molecule identification"

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Zolotoukhina, Tatiana, and Takeo Fukui. "Identification of Nucleobases of Single Stranded DNA by Nanopore Force Resolution at Different Film Thickness." In ASME/JSME 2011 8th Thermal Engineering Joint Conference. ASMEDC, 2011. http://dx.doi.org/10.1115/ajtec2011-44260.

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The model of the molecular translocation of all types of DNA base molecules of cytosine, thymine, adenine and guanine through the nanoporous membrane of a solid thin film has been considered from the point of view of improving the resolution of forces by changing parameters of the membrane itself. The results of simulation of translocation process were compared for all four DNA nucleotides. The molecular dynamics (MD) method with the force field potential has been used for the atomic level modeling of the cytosine (C), thymine (T), adenine (A), and guanine (G) molecules and a configuration of the nanoporous Si membrane. With the planar structure of base molecules and cylindrical symmetry of pore, the two-dimensional projection was used in the simulation. The force field between the base molecule and atoms of nanopore has been estimated. Influence of the Si surface hydrogenization and film thickness on the force resolution for each nucleobase was evaluated vs. possible signal resolution. At 5 layer thickness of the film it was possible to cut thermal fluctuations and distinguish four nucleobase types.
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Castro, Alonso, and Brooks Shera. "Electrophoresis of Single Fluorescent Molecules." In Laser Applications to Chemical Analysis. Washington, D.C.: Optica Publishing Group, 1994. http://dx.doi.org/10.1364/laca.1994.thd.3.

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The fast, efficient detection and separation of minute quantities of biologically important molecules plays a central role in a variety of fields, such as molecular biology, biotechnology, immunology, medical diagnostics, and forensic analysis. It has proven difficult to identify and separate biomolecules at such low concentrations by existing means. Thus, it is of importance to develop methods that are able to probe such low concentrations with adequate sensitivity, resolution and ease. Here, we describe a new method for detecting and identifying individual fluorescent molecules in solution. The technique involves the measurement of electrophoretic velocities of individual molecules in a mixture, and identification by comparison with the electrophoretic velocity known to be characteristic of a particular molecular species. The application of the method to the detection and size identification of DNA restriction fragments in solution at the single molecule level has been demonstrated. In a similar experiment, the electrophoretic velocities of single molecules of the protein phycoerythrin was determined. Although we have focused on the detection and identification of biologically important molecules, the technique has the potential to find applications in organic and inorganic chemical analysis.
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Kim, Jung-Ho, Jae-Seung Moon, and Sang-Kyou Lee. "Abstract A134: Identification of novel Treg-specific molecule targets." In Abstracts: Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; September 25-28, 2016; New York, NY. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/2326-6066.imm2016-a134.

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Lykke, Keith R., Peter Wurz, Deborah H. Parker, Jerry E. Hunt, Michael J. Pellin, and Dieter M. Gruen. "Molecular Surface Analysis Utilizing Laser Desorption/Laser Ionization." In Laser Applications to Chemical Analysis. Washington, D.C.: Optica Publishing Group, 1992. http://dx.doi.org/10.1364/laca.1992.thb4.

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The ability to analyze surface elemental composition has existed for some time. The various methods include Auger Electron Spectroscopy (AES), Secondary Ion Mass Spectrometry (SIMS), and many more.1 However, molecular surface analysis is only now achieving the same sensitivity and selectivity. Molecular surface analysis often utilizes various optical probes: IR Reflection Absorption Spectroscopy, Sum-Frequency (or Second Harmonic) Generation Spectroscopy on Surfaces, etc. These techniques are generally lacking species-specific information. Another approach is to remove the molecule from the surface and probe it in the gas phase, e.g., with state- of-the-art mass spectrometry. Since mass spectrometry offers high resolution and high sensitivity, the remaining problems are removal of the molecule from the surface and ionization without alteration of the molecule (e.g., fragmentation). These pose serious complications for large molecules, in particular. Furthermore, if the molecule of interest is only a minor constituent of a sample, mass resolution and sensitivity are not sufficient for species identification, and a pre- selection in the ionization is often necessary. Our solution is to employ lasers for both desorption from the sample and ionization (post-ionization) of the gas-phase species. The ability to choose the wavelength and intensity of the desorption laser and the post-ionization laser allows for proper tailoring to the needs of the investigation. This will be demonstrated with two examples. First, a vulcanizate (rubber) will be analyzed with a time-of-flight mass spectrometer for the organic additives present in minor concentrations in the near-surface region. Second, a new class of carbon molecules (fullerenes) will be examined with a Fourier transform mass spectrometer.
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Ohshiro, Takahito, Makusu Tsutsui, Kazumichi Yokota, Tomoji Kawai, and Masateru Taniguchi. "Development of single-molecule tunnel-current based nucleotide identification method." In 2014 IEEE International Nanoelectronics Conference (INEC). IEEE, 2014. http://dx.doi.org/10.1109/inec.2014.7460445.

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Ohshiro, T., M. Tsutsui, K. Yokota, T. Kawai, and M. Taniguchi. "Single-Molecule Tunnel-Current based Detection Toward Amino-Acid Identification." In 2014 International Conference on Solid State Devices and Materials. The Japan Society of Applied Physics, 2014. http://dx.doi.org/10.7567/ssdm.2014.d-6-3.

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Kasianowicz, John J., H. Wang, and J. Ettedgui. "On the detection, characterization, and identification of single molecule with nanopores." In 2018 International Symposium on VLSI Technology, Systems and Application (VLSI-TSA). IEEE, 2018. http://dx.doi.org/10.1109/vlsi-tsa.2018.8403829.

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Zin Tun, Gloria Shwe, Martin Orecchia, Graeme Wild, Kirsty Swallow, Ravishankar Sargur, Bernard Corfe, Simon E. Hufton, and Alan J. Lobo. "P211 Identification of linear and conformational epitopes on the infliximab molecule." In Abstracts of the BSG Annual Meeting, 20–23 June 2022. BMJ Publishing Group Ltd and British Society of Gastroenterology, 2022. http://dx.doi.org/10.1136/gutjnl-2022-bsg.265.

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De Angelis, Francesco. "Plasmonic solid-state nanopores: toward single-molecule protein and DNA identification." In Smart Photonic and Optoelectronic Integrated Circuits 2023, edited by Sailing He and Laurent Vivien. SPIE, 2023. http://dx.doi.org/10.1117/12.2653096.

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Kitani, Takumu, and Tatiana Zolotoukhina. "MD Evaluation of the IR Spectra of DNA Bases in the Process of Transport Through Graphene Nanopore." In ASME 2015 International Technical Conference and Exhibition on Packaging and Integration of Electronic and Photonic Microsystems collocated with the ASME 2015 13th International Conference on Nanochannels, Microchannels, and Minichannels. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/ipack2015-48298.

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Development of the 1D and 2D IR spectroscopy of small organic molecules and clusters opens yet another way of possible identification of small organic molecules in the state of motion in the graphene nanopore scanning device. With the advantage of obtaining qualitative and at least semi-quantitative information of specimens real-time and non-invasively, vibrational spectroscopy techniques, infrared (IR) and Raman have become more and more important in the analysis of biomolecular samples. At present, the sensitivity and spatial resolution of these techniques stands at the challenge of the detection and analysis of biosamples at very low concentration (single molecule) and high spatial resolution (nanometer/sub-nanometer scale). Spectral analysis requires theoretical assignment of vibrational modes to each biomolecule. We considered vibrational spectra of DNA nucleobase at the time when they are translocated through the graphene nanopore. The Fourier transform of the density of states (DOS) of each base was calculated and the spectra of the base molecules and C atoms of graphene pore edge were obtained. Translocation rate was fixed to have maximum interaction of the base with 1.5 nm pore and single orientation of nucleobases was evaluated relative to molecular plane. Whether interaction of nucleobase and nanopore is able to enhance the signal is still remains unanswered. But we have shown that the spectra of each nucleobase are different and can be considered the fingerprint of the particular molecule. The interaction forces between pore and base are structure dependent and time-limited by translocation time. In such case, transient correlation functions were utilized for the DOSes of the individual bases and forces on each atom of the particular base were sorted by intensity. The spectra of individual atoms in the bases as well as of whole molecule were compared and frequencies of most intense peaks were related to particular atoms. Molecular dynamics method is used for the DNA base and graphene nanopore calculations with the MM2/MM3 potentials for the base and REBO graphene potential. Interaction potential between the bases can simultaneously give additional information for the electronic transport calculations with possible tra and graphene are of the MM2/MM3 part of the Van der Waals interaction only has been considered. Possibility of base identification by spectral signature is confirmed. Calculated spectra are compared with results of the existing IR measurements for nucleobases.
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Reports on the topic "Molecule identification"

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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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Chavez, Jorge L., Grant M. Slusher, Joshua A. Hagen, Nancy Kelley-Loughnane, Juliann Leny, and Suzanne Witt. Plasmonic Aptamer-Gold Nanoparticle Sensors for Small Molecule Fingerprint Identification. Fort Belvoir, VA: Defense Technical Information Center, August 2014. http://dx.doi.org/10.21236/ada612730.

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Habas, Raymond, and Xi He. Identification of the Receptor of the Wnt-1 Signaling Molecule. Fort Belvoir, VA: Defense Technical Information Center, May 2000. http://dx.doi.org/10.21236/ada391915.

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Habas, Raymond, and Xi He. Identification of the Receptor of the WNT-1 Signaling Molecule. Fort Belvoir, VA: Defense Technical Information Center, May 1999. http://dx.doi.org/10.21236/ada381284.

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Wilson, D. M. III. Automated approach for the identification of functionally-relevant small molecule inhibitors. Office of Scientific and Technical Information (OSTI), February 2000. http://dx.doi.org/10.2172/15001996.

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Sibener, Steven J. Fundamental Studies of Molecule-Surface Encounters Relevant to Molecular Adsorption, Size and Chemically Selective Collection, and Trace Identification/C and L (CBT). Fort Belvoir, VA: Defense Technical Information Center, March 2011. http://dx.doi.org/10.21236/ada545390.

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Cheng, Jin Q. Identification of Small Molecule Inhibitors of microRNA Involved in Chemoresistance and Cancer Stem Cells for Ovarian Cancer Intervention. Fort Belvoir, VA: Defense Technical Information Center, March 2012. http://dx.doi.org/10.21236/ada574634.

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Cheng, Jin. Identification of Small Molecule Inhibitors of microRNA Involved in Chemoresistance and Cancer Stem Cells for Ovarian Cancer Intervention. Fort Belvoir, VA: Defense Technical Information Center, September 2013. http://dx.doi.org/10.21236/ada595907.

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Ron, Eliora, and Eugene Eugene Nester. Global functional genomics of plant cell transformation by agrobacterium. United States Department of Agriculture, March 2009. http://dx.doi.org/10.32747/2009.7695860.bard.

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The aim of this study was to carry out a global functional genomics analysis of plant cell transformation by Agrobacterium in order to define and characterize the physiology of Agrobacterium in the acidic environment of a wounded plant. We planed to study the proteome and transcriptome of Agrobacterium in response to a change in pH, from 7.2 to 5.5 and identify genes and circuits directly involved in this change. Bacteria-plant interactions involve a large number of global regulatory systems, which are essential for protection against new stressful conditions. The interaction of bacteria with their hosts has been previously studied by genetic-physiological methods. We wanted to make use of the new capabilities to study these interactions on a global scale, using transcription analysis (transcriptomics, microarrays) and proteomics (2D gel electrophoresis and mass spectrometry). The results provided extensive data on the functional genomics under conditions that partially mimic plant infection and – in addition - revealed some surprising and significant data. Thus, we identified the genes whose expression is modulated when Agrobacterium is grown under the acidic conditions found in the rhizosphere (pH 5.5), an essential environmental factor in Agrobacterium – plant interactions essential for induction of the virulence program by plant signal molecules. Among the 45 genes whose expression was significantly elevated, of special interest is the two-component chromosomally encoded system, ChvG/I which is involved in regulating acid inducible genes. A second exciting system under acid and ChvG/Icontrol is a secretion system for proteins, T6SS, encoded by 14 genes which appears to be important for Rhizobium leguminosarum nodule formation and nitrogen fixation and for virulence of Agrobacterium. The proteome analysis revealed that gamma aminobutyric acid (GABA), a metabolite secreted by wounded plants, induces the synthesis of an Agrobacterium lactonase which degrades the quorum sensing signal, N-acyl homoserine lactone (AHL), resulting in attenuation of virulence. In addition, through a transcriptomic analysis of Agrobacterium growing at the pH of the rhizosphere (pH=5.5), we demonstrated that salicylic acid (SA) a well-studied plant signal molecule important in plant defense, attenuates Agrobacterium virulence in two distinct ways - by down regulating the synthesis of the virulence (vir) genes required for the processing and transfer of the T-DNA and by inducing the same lactonase, which in turn degrades the AHL. Thus, GABA and SA with different molecular structures, induce the expression of these same genes. The identification of genes whose expression is modulated by conditions that mimic plant infection, as well as the identification of regulatory molecules that help control the early stages of infection, advance our understanding of this complex bacterial-plant interaction and has immediate potential applications to modify it. We expect that the data generated by our research will be used to develop novel strategies for the control of crown gall disease. Moreover, these results will also provide the basis for future biotechnological approaches that will use genetic manipulations to improve bacterial-plant interactions, leading to more efficient DNA transfer to recalcitrant plants and robust symbiosis. These advances will, in turn, contribute to plant protection by introducing genes for resistance against other bacteria, pests and environmental stress.
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Wisniewski, Michael, Samir Droby, John Norelli, Dov Prusky, and Vera Hershkovitz. Genetic and transcriptomic analysis of postharvest decay resistance in Malus sieversii and the identification of pathogenicity effectors in Penicillium expansum. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597928.bard.

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Use of Lqh2 mutants (produced at TAU) and rNav1.2a mutants (produced at the US side) for identifying receptor site-3: Based on the fact that binding of scorpion alpha-toxins is voltage-dependent, which suggests toxin binding at the mobile voltage-sensing region, we analyzed which of the toxin bioactive domains (Core-domain or NC-domain) interacts with the DIV Gating-module of rNav1.2a. This analysis was based on the assumption that the dissociation of toxin mutants upon depolarization would vary from that of the unmodified toxin should the substitutions affect a site of interaction with the channel Gating-module. Using a series of toxin mutants (mutations at both domains) and two channel mutants that were shown to reduce the sensitivity to scorpion alpha-toxins, and by comparison of depolarization-driven dissociation of Lqh2 derivatives off their binding site at rNav1.2a mutant channels we found that the toxin Core-domain interacts with the Gating-module of DIV. Details of the experiments and results appear in Guret al (2011). Mapping receptor site 3 at Nav1.2a by extensive channel mutagenesis (Seattle): Since previous studies with photoaffinity labeling and antibody mapping implicated domains I and IV in scorpion alpha-toxin binding, Nav1.2 channel mutants containing substitutions at these extracellular regions were expressed and tested for receptor function by whole-cell voltage clamp. Of a large number of channel mutants, T1560A, F1610A, and E1613A in domain IV had ~5.9-, ~10.7-, and ~3.9-fold lower affinities for the scorpion toxin Lqh2, respectively, and mutant E1613R had 73-fold lower affinity. Toxin dissociation was accelerated by depolarization for both wild-type and mutants, and the rates of dissociation were also increased by mutations T1560A, F1610A and E1613A. In contrast, association rates for these three mutant channels at negative membrane potentials were not significantly changed and were not voltage-dependent. These results indicated that Thr1560 in the S1-S2 loop, Phe1610 in the S3 segment, and Glu1613 in the S3-S4 loop in domain IV participate in toxin binding. T393A in the SS2-S6 loop in domain I also showed a ~3.4-fold lower affinity for Lqh2, indicating that this extracellular loop may form a secondary component of the toxin binding site. Analysis with the Rosetta-Membrane algorithm revealed a three-dimensional model of Lqh2 binding to the voltage sensor in a resting state. In this model, amino acid residues in an extracellular cleft formed by the S1-S2 and S3-S4 loops in domain IV that are important for toxin binding interact with amino acid residues on two faces of the wedge-shaped Lqh2 molecule that are important for toxin action. The conserved gating charges in the S4 transmembrane segment are in an inward position and likely form ion pairs with negatively charged amino acid residues in the S2 and S3 segments (Wang et al 2011; Gurevitz 2012; Gurevitzet al 2013).
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