[{"date_updated":"2021-01-12T08:19:35Z","status":"public","_id":"8483","intvolume":"       104","abstract":[{"lang":"eng","text":"Atom-resolved real-time studies of kinetic processes in proteins have been hampered in the past by the lack of experimental techniques that yield sufficient temporal and atomic resolution. Here we present band-selective optimized flip-angle short transient (SOFAST) real-time 2D NMR spectroscopy, a method that allows simultaneous observation of reaction kinetics for a large number of nuclear sites along the polypeptide chain of a protein with an unprecedented time resolution of a few seconds. SOFAST real-time 2D NMR spectroscopy combines fast NMR data acquisition techniques with rapid sample mixing inside the NMR magnet to initiate the kinetic event. We demonstrate the use of SOFAST real-time 2D NMR to monitor the conformational transition of α-lactalbumin from a molten globular to the native state for a large number of amide sites along the polypeptide chain. The kinetic behavior observed for the disappearance of the molten globule and the appearance of the native state is monoexponential and uniform along the polypeptide chain. This observation confirms previous findings that a single transition state ensemble controls folding of α-lactalbumin from the molten globule to the native state. In a second application, the spontaneous unfolding of native ubiquitin under nondenaturing conditions is characterized by amide hydrogen exchange rate constants measured at high pH by using SOFAST real-time 2D NMR. Our data reveal that ubiquitin unfolds in a gradual manner with distinct unfolding regimes."}],"date_published":"2007-07-03T00:00:00Z","author":[{"first_name":"Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","full_name":"Schanda, Paul"},{"first_name":"V.","full_name":"Forge, V.","last_name":"Forge"},{"first_name":"B.","full_name":"Brutscher, B.","last_name":"Brutscher"}],"publication_status":"published","type":"journal_article","month":"07","day":"03","keyword":["Multidisciplinary"],"page":"11257-11262","volume":104,"oa_version":"None","publisher":"National Academy of Sciences","publication":"Proceedings of the National Academy of Sciences","language":[{"iso":"eng"}],"extern":"1","issue":"27","article_processing_charge":"No","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"citation":{"ieee":"P. Schanda, V. Forge, and B. Brutscher, “Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy,” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 27. National Academy of Sciences, pp. 11257–11262, 2007.","short":"P. Schanda, V. Forge, B. Brutscher, Proceedings of the National Academy of Sciences 104 (2007) 11257–11262.","mla":"Schanda, Paul, et al. “Protein Folding and Unfolding Studied at Atomic Resolution by Fast Two-Dimensional NMR Spectroscopy.” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 27, National Academy of Sciences, 2007, pp. 11257–62, doi:<a href=\"https://doi.org/10.1073/pnas.0702069104\">10.1073/pnas.0702069104</a>.","apa":"Schanda, P., Forge, V., &#38; Brutscher, B. (2007). Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0702069104\">https://doi.org/10.1073/pnas.0702069104</a>","chicago":"Schanda, Paul, V. Forge, and B. Brutscher. “Protein Folding and Unfolding Studied at Atomic Resolution by Fast Two-Dimensional NMR Spectroscopy.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2007. <a href=\"https://doi.org/10.1073/pnas.0702069104\">https://doi.org/10.1073/pnas.0702069104</a>.","ama":"Schanda P, Forge V, Brutscher B. Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy. <i>Proceedings of the National Academy of Sciences</i>. 2007;104(27):11257-11262. doi:<a href=\"https://doi.org/10.1073/pnas.0702069104\">10.1073/pnas.0702069104</a>","ista":"Schanda P, Forge V, Brutscher B. 2007. Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy. Proceedings of the National Academy of Sciences. 104(27), 11257–11262."},"year":"2007","date_created":"2020-09-18T10:12:54Z","doi":"10.1073/pnas.0702069104","article_type":"original","quality_controlled":"1","title":"Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"external_id":{"pmid":["17409185"]},"language":[{"iso":"eng"}],"scopus_import":"1","oa_version":"Published Version","month":"04","author":[{"last_name":"Penterman","full_name":"Penterman, Jon","first_name":"Jon"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel","orcid":"0000-0002-0123-8649"},{"full_name":"Huh, Jin Hoe","last_name":"Huh","first_name":"Jin Hoe"},{"first_name":"Tracy","full_name":"Ballinger, Tracy","last_name":"Ballinger"},{"first_name":"Steven","full_name":"Henikoff, Steven","last_name":"Henikoff"},{"first_name":"Robert L.","full_name":"Fischer, Robert L.","last_name":"Fischer"}],"date_published":"2007-04-17T00:00:00Z","date_updated":"2021-12-14T08:55:12Z","department":[{"_id":"DaZi"}],"doi":"10.1073/pnas.0701861104","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"article_processing_charge":"No","issue":"16","extern":"1","publication":"Proceedings of the National Academy of Sciences","publisher":"National Academy of Sciences","volume":104,"page":"6752-6757","day":"17","type":"journal_article","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.0701861104"}],"_id":"9487","abstract":[{"text":"Cytosine DNA methylation is considered to be a stable epigenetic mark, but active demethylation has been observed in both plants and animals. In Arabidopsis thaliana, DNA glycosylases of the DEMETER (DME) family remove methylcytosines from DNA. Demethylation by DME is necessary for genomic imprinting, and demethylation by a related protein, REPRESSOR OF SILENCING1, prevents gene silencing in a transgenic background. However, the extent and function of demethylation by DEMETER-LIKE (DML) proteins in WT plants is not known. Using genome-tiling microarrays, we mapped DNA methylation in mutant and WT plants and identified 179 loci actively demethylated by DML enzymes. Mutations in DML genes lead to locus-specific DNA hypermethylation. Reintroducing WT DML genes restores most loci to the normal pattern of methylation, although at some loci, hypermethylated epialleles persist. Of loci demethylated by DML enzymes, >80% are near or overlap genes. Genic demethylation by DML enzymes primarily occurs at the 5′ and 3′ ends, a pattern opposite to the overall distribution of WT DNA methylation. Our results show that demethylation by DML DNA glycosylases edits the patterns of DNA methylation within the Arabidopsis genome to protect genes from potentially deleterious methylation.","lang":"eng"}],"intvolume":"       104","pmid":1,"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"DNA demethylation in the Arabidopsis genome","quality_controlled":"1","article_type":"original","date_created":"2021-06-07T09:38:21Z","year":"2007","citation":{"short":"J. Penterman, D. Zilberman, J.H. Huh, T. Ballinger, S. Henikoff, R.L. Fischer, Proceedings of the National Academy of Sciences 104 (2007) 6752–6757.","ieee":"J. Penterman, D. Zilberman, J. H. Huh, T. Ballinger, S. Henikoff, and R. L. Fischer, “DNA demethylation in the Arabidopsis genome,” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 16. National Academy of Sciences, pp. 6752–6757, 2007.","mla":"Penterman, Jon, et al. “DNA Demethylation in the Arabidopsis Genome.” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 16, National Academy of Sciences, 2007, pp. 6752–57, doi:<a href=\"https://doi.org/10.1073/pnas.0701861104\">10.1073/pnas.0701861104</a>.","ama":"Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. DNA demethylation in the Arabidopsis genome. <i>Proceedings of the National Academy of Sciences</i>. 2007;104(16):6752-6757. doi:<a href=\"https://doi.org/10.1073/pnas.0701861104\">10.1073/pnas.0701861104</a>","ista":"Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. 2007. DNA demethylation in the Arabidopsis genome. Proceedings of the National Academy of Sciences. 104(16), 6752–6757.","apa":"Penterman, J., Zilberman, D., Huh, J. H., Ballinger, T., Henikoff, S., &#38; Fischer, R. L. (2007). DNA demethylation in the Arabidopsis genome. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0701861104\">https://doi.org/10.1073/pnas.0701861104</a>","chicago":"Penterman, Jon, Daniel Zilberman, Jin Hoe Huh, Tracy Ballinger, Steven Henikoff, and Robert L. Fischer. “DNA Demethylation in the Arabidopsis Genome.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2007. <a href=\"https://doi.org/10.1073/pnas.0701861104\">https://doi.org/10.1073/pnas.0701861104</a>."},"oa":1},{"day":"23","page":"1168-1172","volume":103,"type":"journal_article","article_processing_charge":"No","publisher":"National Academy of Sciences","issue":"5","publication":"PNAS","extern":"1","status":"public","_id":"18370","abstract":[{"text":"An efficient algorithm for isometry-invariant matching of surfaces is presented. The key idea is computing the minimum-distortion mapping between two surfaces. For this purpose, we introduce the generalized multidimensional scaling, a computationally efficient continuous optimization algorithm for finding the least distortion embedding of one surface into another. The generalized multidimensional scaling algorithm allows for both full and partial surface matching. As an example, it is applied to the problem of expression-invariant three-dimensional face recognition.","lang":"eng"}],"pmid":1,"intvolume":"       103","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Generalized multidimensional scaling: A framework for isometry-invariant partial surface matching","citation":{"mla":"Bronstein, Alex M., et al. “Generalized Multidimensional Scaling: A Framework for Isometry-Invariant Partial Surface Matching.” <i>PNAS</i>, vol. 103, no. 5, National Academy of Sciences, 2006, pp. 1168–72, doi:<a href=\"https://doi.org/10.1073/pnas.0508601103\">10.1073/pnas.0508601103</a>.","short":"A.M. Bronstein, M.M. Bronstein, R. Kimmel, PNAS 103 (2006) 1168–1172.","ieee":"A. M. Bronstein, M. M. Bronstein, and R. Kimmel, “Generalized multidimensional scaling: A framework for isometry-invariant partial surface matching,” <i>PNAS</i>, vol. 103, no. 5. National Academy of Sciences, pp. 1168–1172, 2006.","ista":"Bronstein AM, Bronstein MM, Kimmel R. 2006. Generalized multidimensional scaling: A framework for isometry-invariant partial surface matching. PNAS. 103(5), 1168–1172.","ama":"Bronstein AM, Bronstein MM, Kimmel R. Generalized multidimensional scaling: A framework for isometry-invariant partial surface matching. <i>PNAS</i>. 2006;103(5):1168-1172. doi:<a href=\"https://doi.org/10.1073/pnas.0508601103\">10.1073/pnas.0508601103</a>","chicago":"Bronstein, Alex M., Michael M. Bronstein, and Ron Kimmel. “Generalized Multidimensional Scaling: A Framework for Isometry-Invariant Partial Surface Matching.” <i>PNAS</i>. National Academy of Sciences, 2006. <a href=\"https://doi.org/10.1073/pnas.0508601103\">https://doi.org/10.1073/pnas.0508601103</a>.","apa":"Bronstein, A. M., Bronstein, M. M., &#38; Kimmel, R. (2006). Generalized multidimensional scaling: A framework for isometry-invariant partial surface matching. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0508601103\">https://doi.org/10.1073/pnas.0508601103</a>"},"article_type":"original","quality_controlled":"1","year":"2006","date_created":"2024-10-15T11:20:54Z","scopus_import":"1","oa_version":"None","month":"01","external_id":{"pmid":["16432211"]},"language":[{"iso":"eng"}],"date_updated":"2024-10-21T09:09:19Z","author":[{"last_name":"Bronstein","full_name":"Bronstein, Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","first_name":"Alexander","orcid":"0000-0001-9699-8730"},{"full_name":"Bronstein, Michael M.","last_name":"Bronstein","first_name":"Michael M."},{"full_name":"Kimmel, Ron","last_name":"Kimmel","first_name":"Ron"}],"date_published":"2006-01-23T00:00:00Z","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"doi":"10.1073/pnas.0508601103"},{"volume":101,"page":"5186-5191","day":"06","type":"journal_article","article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences","issue":"suppl_1","extern":"1","publisher":"Proceedings of the National Academy of Sciences","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC387294/"}],"_id":"11877","pmid":1,"abstract":[{"lang":"eng","text":"The World Wide Web provides a unprecedented opportunity to automatically analyze a large sample of interests and activity in the world. We discuss methods for extracting knowledge from the web by randomly sampling and analyzing hosts and pages, and by analyzing the link structure of the web and how links accumulate over time. A variety of interesting and valuable information can be extracted, such as the distribution of web pages over domains, the distribution of interest in different areas, communities related to different topics, the nature of competition in different categories of sites, and the degree of communication between different communities or countries."}],"intvolume":"       101","status":"public","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Extracting knowledge from the World Wide Web","citation":{"chicago":"Henzinger, Monika, and Steve Lawrence. “Extracting Knowledge from the World Wide Web.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2004. <a href=\"https://doi.org/10.1073/pnas.0307528100\">https://doi.org/10.1073/pnas.0307528100</a>.","apa":"Henzinger, M., &#38; Lawrence, S. (2004). Extracting knowledge from the World Wide Web. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0307528100\">https://doi.org/10.1073/pnas.0307528100</a>","ista":"Henzinger M, Lawrence S. 2004. Extracting knowledge from the World Wide Web. Proceedings of the National Academy of Sciences. 101(suppl_1), 5186–5191.","ama":"Henzinger M, Lawrence S. Extracting knowledge from the World Wide Web. <i>Proceedings of the National Academy of Sciences</i>. 2004;101(suppl_1):5186-5191. doi:<a href=\"https://doi.org/10.1073/pnas.0307528100\">10.1073/pnas.0307528100</a>","ieee":"M. Henzinger and S. Lawrence, “Extracting knowledge from the World Wide Web,” <i>Proceedings of the National Academy of Sciences</i>, vol. 101, no. suppl_1. Proceedings of the National Academy of Sciences, pp. 5186–5191, 2004.","mla":"Henzinger, Monika, and Steve Lawrence. “Extracting Knowledge from the World Wide Web.” <i>Proceedings of the National Academy of Sciences</i>, vol. 101, no. suppl_1, Proceedings of the National Academy of Sciences, 2004, pp. 5186–91, doi:<a href=\"https://doi.org/10.1073/pnas.0307528100\">10.1073/pnas.0307528100</a>.","short":"M. Henzinger, S. Lawrence, Proceedings of the National Academy of Sciences 101 (2004) 5186–5191."},"oa":1,"quality_controlled":"1","article_type":"original","date_created":"2022-08-16T13:06:10Z","year":"2004","oa_version":"Published Version","scopus_import":"1","month":"04","external_id":{"pmid":["14745041"]},"language":[{"iso":"eng"}],"date_updated":"2024-11-06T12:00:20Z","author":[{"first_name":"Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Lawrence","full_name":"Lawrence, Steve","first_name":"Steve"}],"date_published":"2004-04-06T00:00:00Z","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"doi":"10.1073/pnas.0307528100"},{"date_updated":"2022-02-14T16:12:33Z","date_published":"1989-09-01T00:00:00Z","author":[{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804"},{"full_name":"Bräu, Michael","last_name":"Bräu","first_name":"Michael"},{"full_name":"Hermsteiner, Markus","last_name":"Hermsteiner","first_name":"Markus"},{"full_name":"Vogel, Werner","last_name":"Vogel","first_name":"Werner"}],"month":"09","oa_version":"Published Version","language":[{"iso":"eng"}],"external_id":{"pmid":["2550937 "]},"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"acknowledgement":"We thank Drs. C. Baumann, D. Siemen, and W. Stuhmer for reading the manuscript and Dr. F. Dreyer for the generous gift of DTX. The study was supported by the Deutsche Forschungsgemeinschaft.","doi":"10.1073/pnas.86.18.7238","status":"public","abstract":[{"text":"Amphibian myelinated nerve fibers were treated with collagenase and protease. Axons with retraction of the myelin sheath were patch-clamped in the nodal and paranodal region. One type of Na channel was found. It has a single-channel conductance of 11 pS (15 degrees C) and is blocked by tetrodotoxin. Averaged events show the typical activation and inactivation kinetics of macroscopic Na current. Three potential-dependent K channels were identified (I, F, and S channel). The I channel, being the most frequent type, has a single-channel conductance of 23 pS (inward current, 105 mM K on both sides of the membrane), activates between -60 and -30 mV, deactivates with intermediate kinetics, and is sensitive to dendrotoxin. The F channel has a conductance of 30 pS, activates between -40 and 60 mV, and deactivates with fast kinetics. The former inactivates within tens of seconds; the latter inactivates within seconds. The third type, the S channel, has a conductance of 7 pS and deactivates slowly. All three channels can be blocked by external tetraethylammonium chloride. We suggest that these distinct K channel types form the basis for the different components of macroscopic K current described previously.","lang":"eng"}],"_id":"3466","intvolume":"        86","pmid":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC298032/?tool=pubmed"}],"publication_status":"published","type":"journal_article","day":"01","page":"7238 - 7242","volume":86,"publisher":"National Academy of Sciences","publication":"PNAS","issue":"18","extern":"1","article_processing_charge":"No","oa":1,"citation":{"ama":"Jonas PM, Bräu M, Hermsteiner M, Vogel W. Single-channel recording in myelinated nerve fibers reveals one type of Na channel but different K channels. <i>PNAS</i>. 1989;86(18):7238-7242. doi:<a href=\"https://doi.org/10.1073/pnas.86.18.7238\">10.1073/pnas.86.18.7238</a>","ista":"Jonas PM, Bräu M, Hermsteiner M, Vogel W. 1989. Single-channel recording in myelinated nerve fibers reveals one type of Na channel but different K channels. PNAS. 86(18), 7238–7242.","apa":"Jonas, P. M., Bräu, M., Hermsteiner, M., &#38; Vogel, W. (1989). Single-channel recording in myelinated nerve fibers reveals one type of Na channel but different K channels. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.86.18.7238\">https://doi.org/10.1073/pnas.86.18.7238</a>","chicago":"Jonas, Peter M, Michael Bräu, Markus Hermsteiner, and Werner Vogel. “Single-Channel Recording in Myelinated Nerve Fibers Reveals One Type of Na Channel but Different K Channels.” <i>PNAS</i>. National Academy of Sciences, 1989. <a href=\"https://doi.org/10.1073/pnas.86.18.7238\">https://doi.org/10.1073/pnas.86.18.7238</a>.","mla":"Jonas, Peter M., et al. “Single-Channel Recording in Myelinated Nerve Fibers Reveals One Type of Na Channel but Different K Channels.” <i>PNAS</i>, vol. 86, no. 18, National Academy of Sciences, 1989, pp. 7238–42, doi:<a href=\"https://doi.org/10.1073/pnas.86.18.7238\">10.1073/pnas.86.18.7238</a>.","ieee":"P. M. Jonas, M. Bräu, M. Hermsteiner, and W. Vogel, “Single-channel recording in myelinated nerve fibers reveals one type of Na channel but different K channels,” <i>PNAS</i>, vol. 86, no. 18. National Academy of Sciences, pp. 7238–7242, 1989.","short":"P.M. Jonas, M. Bräu, M. Hermsteiner, W. Vogel, PNAS 86 (1989) 7238–7242."},"year":"1989","date_created":"2018-12-11T12:03:28Z","article_type":"original","quality_controlled":"1","title":"Single-channel recording in myelinated nerve fibers reveals one type of Na channel but different K channels","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","publist_id":"2921"}]