@misc{BestZhengBorgiaetal.2018,
  author    = {Best, Robert B. and Zheng, Wenwei and Borgia, Alessandro and Buholzer, Karin and Borgia, Madeleine B. and Hofmann, Hagen and Soranno, Andrea and Nettels, Daniel and Gast, Klaus and Grishaev, Alexander and Schuler, Benjamin},
  title     = {Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water"},
  series = {Science},
  volume    = {361},
  journal   = {Science},
  number    = {6405},
  publisher = {American Assoc. for the Advancement of Science},
  address   = {Washington},
  issn      = {0036-8075},
  doi       = {10.1126/science.aar7101},
  pages     = {2},
  year      = {2018},
  abstract  = {Riback et al. (Reports, 13 October 2017, p. 238) used small-angle x-ray scattering (SAXS) experiments to infer a degree of compaction for unfolded proteins in water versus chemical denaturant that is highly consistent with the results from Forster resonance energy transfer (FRET) experiments. There is thus no "contradiction" between the two methods, nor evidence to support their claim that commonly used FRET fluorophores cause protein compaction.},
  language  = {en}
}
@book{JeskeBrehmerMengeetal.2006,
  author    = {Jeske, Janin and Brehmer, Bastian and Menge, Falko and H{\"u}ttenrauch, Stefan and Adam, Christian and Sch{\"u}ler, Benjamin and Schult, Wolfgang and Rasche, Andreas and Polze, Andreas},
  title     = {Aspektorientierte Programmierung : {\"U}berblick {\"u}ber Techniken und Werkzeuge},
  series = {Technische Berichte des Hasso-Plattner-Instituts f{\"u}r Softwaresystemtechnik an der Universit{\"a}t Potsda},
  volume    = {14},
  journal   = {Technische Berichte des Hasso-Plattner-Instituts f{\"u}r Softwaresystemtechnik an der Universit{\"a}t Potsda},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {3-939469-23-8},
  issn      = {1613-5652},
  pages     = {88 S.},
  year      = {2006},
  language  = {de}
}
@article{BuscagliaSchulerLapidusetal.2003,
  author    = {Buscaglia, Marco and Schuler, Benjamin and Lapidus, Lisa J. and Eaton, Wiliam A. and Hofrichter, James},
  title     = {Kinetics of intramolecular contact formation in a denatured protein},
  issn      = {0022-2836},
  year      = {2003},
  abstract  = {Quenching of the triplet state of tryptophan by cysteine has provided a new tool for measuring the rate of forming a specific intramolecular contact in disordered polypeptides. Here, we use this technique to investigate contact formation in the denatured state of CspTm, a small cold-shock protein from Thermotoga maritima, engineered to contain a single tryptophan residue (W29) and a single cysteine residue at the C terminus (C67). At all concentrations of denaturant, the decay rate of the W29 triplet of the unfolded protein is more than tenfold faster than the rate observed for the native protein (not, vert, similar104 s;1). Experiments on the unfolded protein without the added C- terminal cysteine residue show that this faster rate results entirely from contact quenching by C67. The quenching rate in the unfolded state by C67 increases at concentrations of denaturant that favor folding, indicating a compaction of the unfolded protein as observed previously in single-molecule Foerster resonance energy transfer (FRET) experiments.},
  language  = {en}
}
@article{GoetzSuopankiSchuleretal.2005,
  author    = {Goetz, C. and Suopanki, J. and Schuler, Benjamin and Wanker, E. and Herrmann, Andreas},
  title     = {Perturbation of brain lipid membrane by soluble Huntingtin depends on its polyproline tract},
  issn      = {0006-3495},
  year      = {2005},
  language  = {en}
}
@article{SchulerLipmanSteinbachetal.2005,
  author    = {Schuler, Benjamin and Lipman, Everett A. and Steinbach, P. J. and Kumke, Michael Uwe and Eaton, W. A.},
  title     = {Polyproline and the "spectroscopic ruler" revisited with single-molecule fluorescence},
  issn      = {0027-8424},
  year      = {2005},
  abstract  = {To determine whether Forster resonance energy transfer (FRET) measurements can provide quantitative distance information in single-molecule fluorescence experiments on polypeptides, we measured FRET efficiency distributions for donor and acceptor dyes attached to the ends of freely diffusing polyproline molecules of various lengths. The observed mean FRET efficiencies agree with those determined from ensemble lifetime measurements but differ considerably from the values expected from Forster theory, with polyproline treated as a rigid rod. At donor-acceptor distances much less than the Forster radius R-o, the observed efficiencies are lower than predicted, whereas at distances comparable to and greater than R-0, they are much higher. Two possible contributions to the former are incomplete orientational averaging during the donor lifetime and, because of the large size of the dyes, breakdown of the point-dipole approximation assumed in Forster theory. End-to-end distance distributions and correlation times obtained from Langevin molecular dynamics simulations suggest that the differences for the longer polyproline peptides can be explained by chain bending, which considerably shortens the donor-acceptor distances},
  language  = {en}
}
@article{RhoadesCohenGussakovskyetal.2004,
  author    = {Rhoades, E. and Cohen, M. and Gussakovsky, E. and Schuler, Benjamin and Haran, G.},
  title     = {Single molecule protein folding},
  issn      = {0006-3495},
  year      = {2004},
  language  = {en}
}
@book{AdamBrehmerHuettenrauchetal.2006,
  author    = {Adam, Christian and Brehmer, Bastian and H{\"u}ttenrauch, Stefan and Jeske, Janin and Polze, Andreas and Rasche, Andreas and Sch{\"u}ler, Benjamin and Schult, Wolfgang},
  title     = {Aspektorientierte Programmierung : {\"U}berblick {\"u}ber Techniken und Werkzeuge},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-939469-23-0},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-33796},
  publisher      = {Universit{\"a}t Potsdam},
  pages     = {88},
  year      = {2006},
  abstract  = {Inhaltsverzeichnis 1 Einf{\"u}hrung 2 Aspektorientierte Programmierung 2.1 Ein System als Menge von Eigenschaften 2.2 Aspekte 2.3 Aspektweber 2.4 Vorteile Aspektorientierter Programmierung 2.5 Kategorisierung der Techniken und Werkzeuge f ¨ ur Aspektorientierte Programmierung 3 Techniken und Werkzeuge zur Analyse Aspektorientierter Softwareprogramme 3.1 Virtual Source File 3.2 FEAT 3.3 JQuery 3.4 Aspect Mining Tool 4 Techniken und Werkzeuge zum Entwurf Aspektorientierter Softwareprogramme 4.1 Concern Space Modeling Schema 4.2 Modellierung von Aspekten mit UML 4.3 CoCompose 4.4 Codagen Architect 5 Techniken und Werkzeuge zur Implementierung Aspektorientierter Softwareprogramme 5.1 Statische Aspektweber 5.2 Dynamische Aspektweber 6 Zusammenfassung},
  language  = {de}
}
@misc{SchulerLipmanSteinbachetal.2005,
  author    = {Schuler, Benjamin and Lipman, Everett A. and Steinbach, Peter J. and Kumke, Michael Uwe and Eaton, William A.},
  title     = {Polyproline and the "spectroscopic ruler" revisited with single-molecule fluorescence},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-12229},
  year      = {2005},
  abstract  = {To determine whether F{\"o}rster resonance energy transfer (FRET) measurements can provide quantitative distance information in single-molecule fluorescence experiments on polypeptides, we measured FRET efficiency distributions for donor and acceptor dyes attached to the ends of freely diffusing polyproline molecules of various lengths. The observed mean FRET efficiencies agree with those determined from ensemble lifetime measurements but differ considerably from the values expected from F{\"o}rster theory, with polyproline treated as a rigid rod. At donor-acceptor distances much less than the F{\"o}rster radius R0, the observed efficiencies are lower than predicted, whereas at distances comparable to and greater than R0, they are much higher. Two possible contributions to the former are incomplete orientational averaging during the donor lifetime and, because of the large size of the dyes, breakdown of the point-dipole approximation assumed in F{\"o}rster theory. End-to-end distance distributions and correlation times obtained from Langevin molecular dynamics simulations suggest that the differences for the longer polyproline peptides can be explained by chain bending, which considerably shortens the donor-acceptor distances.},
  language  = {en}
}
@article{HoffmannKaneNettelsetal.2007,
  author    = {Hoffmann, Armin S. and Kane, Avinash S. and Nettels, Daniel and Hertzog, David E. and Baumg{\"a}rtel, Peter and Lengefeld, Jan and Reichardt, Gerd and Horsley, David A. and Seckler, Robert and Bakajin, Olgica and Schuler, Benjamin},
  title     = {Mapping protein collapse with single molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy},
  issn      = {0027-8424},
  year      = {2007},
  language  = {en}
}
@article{NettelsMuellerSpaethKuesteretal.2009,
  author    = {Nettels, Daniel and M{\"u}ller-Sp{\"a}th, Sonja and K{\"u}ster, Frank and Hofmann, Hagen and Haenni, Domminik and R{\"u}egger, Stefan and Reymond, Luc and Hoffmann, Armin S. and Kubelka, Jan and Heinz, Benjamin and Gast, Klaus and Best, Robert B. and Schuler, Benjamin},
  title     = {Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins},
  issn      = {0027-8424},
  year      = {2009},
  abstract  = {We used single-molecule FRET in combination with other biophysical methods and molecular simulations to investigate the effect of temperature on the dimensions of unfolded proteins. With singlemolecule FRET, this question can be addressed even under nearnative conditions, where most molecules are folded, allowing us to probe a wide range of denaturant concentrations and temperatures. We find a compaction of the unfolded state of a small cold shock protein with increasing temperature in both the presence and the absence of denaturant, with good agreement between the results from single-molecule FRET and dynamic light scattering. Although dissociation of denaturant from the polypeptide chain with increasing temperature accounts for part of the compaction, the results indicate an important role for additional temperaturedependent interactions within the unfolded chain. The observation of a collapse of a similar extent in the extremely hydrophilic, intrinsically disordered protein prothymosin suggests that the hydrophobic effect is not the sole source of the underlying interactions. Circular dichroism spectroscopy and replica exchange molecular dynamics simulations in explicit water show changes in secondary structure content with increasing temperature and suggest a contribution of intramolecular hydrogen bonding to unfolded state collapse.},
  language  = {en}
}