Teaching
⊞ Winter Term 2014/15
Lab "Python for the Life Sciences"
Time: Tue, Feb 17th 2015 - Fri, Feb 27th 2015, 10.00 amPlace: Computer Pool Neubau Invalidenstraße 42
Lecture "Molecular Biophysics" (BioPhysics I)
| Date | Topic | Slides |
|---|---|---|
| 25./26.11.2014 | Protein Folding Kinetics & Thermodynamics | [PDF] |
| 06./07.01.2015 | Fluorescence | [PDF] |
| 13./14.01.2015 | Hydrodynamic Methods | [PDF] |
| 20./21.01.2015 | Of Heat, Atoms, Forces and Light | [PDF] |
⊟ Summer Term 2014
Lecture "Synthetic Biology" (BioPhysics XIV)
Monday 4 pm, Invalidenstraße 42, seminar room 312a| No. | Date | Topic | Lecturer | Slides |
|---|---|---|---|---|
| 1 | 14.04.2014 | Introduction, History & Ethics | Möglich | [PDF] [DFG paper] |
| -- | 21.04.2014 | Easter Monday - no lecture | -- | -- |
| 2 | 28.04.2014 | Biological Databases & Tools | Möglich | [PDF] |
| 3 | 05.05.2014 | Bioconjugate Chemistry & Total Protein Synthesis | Möglich | [PDF] |
| 4 | 12.05.2014 | DNA Manipulation and Libraries | Möglich | [PDF] |
| -- | 19.05.2014 | Conference travel - keine Vorlesung | -- | -- |
| 5 | 26.05.2014 | Laboratory-directed Evolution | Möglich | [PDF] |
| 6 | 02.06.2014 | Incorporation of Non-canonical Amino Acids Technische Universität Berlin, Building L, Room 009 Begin 4.15 pm |
Budisa | [PDF]
German: [PDF] |
| -- | 09.06.2014 | Pentecost - no lecture | -- | -- |
| 7 | 16.06.2014 | Synthetic Signal Receptors & Optogenetics | Möglich | [PDF] |
| 8 | 23.06.2014 | De novo Proteins and Enzymes | Möglich | [PDF] |
| 9 | 30.06.2014 | DNA Computation & Origami | Möglich | [PDF] |
| 10 | 07.07.2014 | Transcriptional Control & Gene-regulatory Networks | Möglich | [PDF] |
| 11 | 14.07.2014 | Metabolic Engineering & Synthetic Life | Möglich | [PDF] |
Lab "Design and Characterization of Synthetic Photoreceptors" (BioPhysics XIV)
Time window A 14.04.-25.04.2014.Start of course Monday, 14.04.2014
First meeting Monday, 14.04.2014, 9.30 am s. t. Room 304.
Seminar "Current Topics in Photobiology and Protein Design" (BioPhysics XIV)
The seminar is one component of the module 'Synthetic Biology', and each participant should present one of the papers from the below list. Pending prior approval, the seminar can also be qualified for other biophysics modules. Please choose a topic and date you are interested in, and send me an email. First come, first serve; other papers are acceptable pending approval. The seminar starts on 25.04.2014.Friday 8.15 am, Invalidenstraße 42, seminar room 312a
| Date | Paper | Lecturer(s) | Link | Slides |
|---|---|---|---|---|
| 25.04.2014 | Annaluru, N. et al. (2014) Total synthesis of a functional designer eukaryotic chromosome. Science 344(6179), 55-58. | A.M. | [Link] | [PDF] |
| 02.05.2014 | Tag nach 1. Mai -- kein Seminar | -- | -- | -- |
| 09.05.2014 | Okamoto, R., Mandal, K., Sawaya, M.R., Kajihara, Y., Yeates, T.O., Kent, S.B. (2014) (Quasi-)Racemic X-ray Structures of Glycosylated and Non-Glycosylated Forms of the Chemokine Ser-CCL1 Prepared by Total Chemical Synthesis. Angew Chemie Int Ed in press
Deng, F.K., Zhang, L., Wang, Y.T., Schneewind, O., Kent, S.B. (2014) Total Chemical Synthesis of the Enzyme Sortase AΔN59 with Full Catalytic Activity. Angew Chemie Int Ed in press Okamoto, R., Mandal, K., Ling, M., Luster, A.D., Kajihara, Y., Kent, S.B. (2014) Total Chemical Synthesis and Biological Activities of Glycosylated and Non-Glycosylated Forms of the Chemokines CCL1 and Ser-CCL1. Angew Chemie Int Ed in press |
A.M. | [Link] | [PDF] |
| 16.05.2014 | Geu-Flores, F., Nour-Eldin, H.H., Nielsen, M.T., Halkier, B.A. (2007) USER fusion: a rapid and efficient method for simultaneous fusion and cloning of multiple PCR products. Nucleic Acids Res 35(7), e55.
Villiers, B.R., Stein, V., Hollfelder, F. (2010) USER friendly DNA recombination (USERec): a simple and flexible near homology-independent method for gene library construction. Protein Eng Des Sel 23(1), 1-8. Salomonsen, B., Mortensen, U.H., Halkier, B.A. (2014) USER-derived cloning methods and their primer design. Methods Mol Biol 852, 59-72. |
Andrea Dotzler | [Link]
[Link] |
[PDF] |
| 23.05.2014 | kein Seminar | -- | -- | -- |
| 30.05.2014 | Ai, H.W., Baird, M.A., Shen, Y., Davidson, M.W., Campbell, R.E. (2014) Engineering and characterizing monomeric fluorescent proteins for live-cell imaging applications. Nat Protoc 9(4), 910-928.
Filonov, G.S., Piatkevich, K.D., Ting, L.M., Zhang, J., Kim, K., Verkhusha, V.V. (2011) Bright and stable near-infrared fluorescent protein for in vivo imaging. Nat Biotechnol 29(8), 757-761. Shcherbakova, D.M., Verkhusha, V.V. (2013) Near-infrared fluorescent proteins for multicolor in vivo imaging. Nat Methods 10(8), 751-754. |
Daniel Pawliczek | [Link] | [PDF] |
| Yi, L., Gebhard, M.C., Li, Q., Taft, J.M., Georgiou, G., Iverson, B.L. (2013) Engineering of TEV protease variants by yeast ER sequestration screening (YESS) of combinatorial libraries. Proc Natl Acad Sci U S A 110(18), 7229-7234. | N.N. | [Link] | [PDF] | |
| 06.06.2014 | Isaacs, F.J., Carr, P.A., Wang, H.H., Lajoie, M.J., Sterling, B., Kraal, L., Tolonen, A.C., Gianoulis, T.A., Goodman, D.B., Reppas, N.B., Emig, C.J., Bang, D., Hwang, S.J., Jewett, M.C., Jacobson, J.M., Church, G.M. (2011) Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 333(6040), 348-353.
Lajoie, M.J., Rovner, A.J., Goodman, D.B., Aerni, H.R., Haimovich, A.D., Kuznetsov, G., Mercer, J.A., Wang, H.H., Carr, P.A., Mosberg, J.A., Rohland, N., Schultz, P.G., Jacobson, J.M., Rinehart, J., Church, G.M., Isaacs, F.J. (2013) Genomically recoded organisms expand biological functions. Science 342(6156), 357-360. |
Marlene Lindner | [Link] | [PDF] |
| 13.06.2014 | Pfingstwoche -- kein Seminar | -- | -- | -- |
| 20.06.2014 | Yang, X., Jost, A.P., Weiner, O.D., Tang, C. (2014) A light-inducible organelle-targeting system for dynamically activating and inactivating signaling in budding yeast. Mol Biol Cell 24(15), 2419-2430. | Malte Hilsch | [Link] | [PDF] |
| Motta-Mena, L.B., Reade, A., Mallory, M.J., Glantz, S., Weiner, O.D., Lynch, K.W., Gardner, K.H. (2014) An optogenetic gene expression system with rapid activation and deactivation kinetics. Nat Chem Biol 10(3), 196-202. | Isabel Kuhnert | [Link] | [PDF] | |
| 27.06.2014 | Tinberg, C.E., Khare, S.D., Dou, J., Doyle, L., Nelson, J.W., Schena, A., Jankowski, W., Kalodimos, C.G., Johnsson, K., Stoddard, B.L., Baker, D. (2013) Computational design of ligand-binding proteins with high affinity and selectivity. Nature 501(7466), 212-216. | Lars Zerbe | [Link] | [PDF] |
| Koga, N., Tatsumi-Koga, R., Liu, G., Xiao, R., Acton, T.B., Montelione, G.T., Baker, D. (2012) Principles for designing ideal protein structures. Nature 491(7423), 222-227. | Robert-William Welke | [Link] | [PDF] | |
| 04.07.2014 | Iinuma, R., Ke, Y., Jungmann, R., Schlichthaerle, T., Woehrstein, J.B., Yin, P. (2014) Polyhedra self-assembled from DNA tripods and characterized with 3D DNA-PAINT. Science 344(6179), 65-69. | Ferdinand Krupp | [Link] | [PDF] |
| Chen, H., Weng, T.W., Riccitelli, M., Cui, Y., Irudayaraj, J., Choi, J.H. (2014) Understanding the Mechanical Properties of DNA Origami Tiles and Controlling the Kinetics of their Folding and Unfolding Reconfiguration. J Am Chem Soc in press | Wiebke Schmidt | [Link] | [PDF] | |
| 11.07.2014 | Wang, B.L., Ghaderi, A., Zhou, H., Agresti, J., Weitz, D.A., Fink, G.R., Stephanopoulos, G. (2014) Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption. Nat Biotechnol in press | Anke Vollertsen | [Link] | [PDF] |
| Ling, H., Teo, W., Chen, B., Leong, S.S., Chang, M.W. (2014) Microbial tolerance engineering toward biochemical production: from lignocellulose to products. Curr Opin Biotechnol 29C, 99-106.
Wang, X., Yomano, L.P., Lee, J.Y., York, S.W., Zheng, H., Mullinnix, M.T., Shanmugam, K.T., Ingram, L.O. (2013) Engineering furfural tolerance in Escherichia coli improves the fermentation of lignocellulosic sugars into renewable chemicals. Proc Natl Acad Sci U S A 110(10), 4021-4026. |
Tina Jaenicke | [Link] | [PDF] | |
| 18.07.2014 | Malyshev, D.A., Dhami, K., Lavergne, T., Chen, T., Dai, N., Foster, J.M., Corrêa Jr, I.R., Romesberg, F.E. (2014) A semi-synthetic organism with an expanded genetic alphabet. Nature in press | Deborah Stier | [Link] | [PDF] |
| Xiao, H., Chatterjee, A., Choi, S.H., Bajjuri, K.M., Sinha, S.C., Schultz, P.G. (2014) Genetic incorporation of multiple unnatural amino acids into proteins in mammalian cells. Angew Chem Int Ed Engl 52(52), 14080-14083.
Xiao, H., Peters, F.B., Yang, P.Y., Reed, S., Chittuluru, J.R., Schultz, P.G. (2014) Genetic Incorporation of Histidine Derivatives Using an Engineered Pyrrolysyl-tRNA Synthetase. ACS Chem Biol in press |
Maximiliano Ancina Möller | [Link] | [PDF] |
Lab "Biophysics" (B.Sc. class 3110022)
| Spektroskopische Charakterisierung von Blaulichtrezeptorproteinen | [PDF] |
| Analyse von Proteinstrukturen mit PyMOL | [PDF] |
⊞ Winter Term 2013/14
Lab "Python for the Life Sciences"
Time: Tue, Feb 4th 2014 - Fri, Feb 14th 2014Place: Computer Pool Neubau Invalidenstraße 42
More info will be available here.
Lecture "Molecular Biophysics" (BioPhysics I)
| Date | Topic | Slides |
|---|---|---|
| 26./27.11.2013 | Protein Folding Kinetics & Thermodynamics | [PDF] |
| 07./08.01.2014 | Fluorescence | [PDF] |
| 14./15.01.2014 | Hydrodynamic Methods | [PDF] |
| 21./22.01.2014 | Of Heat, Atoms, Forces and Light | [PDF] |
⊟ Summer Term 2013
Lecture "Synthetic Biology" (BioPhysics XIV)
Monday 4 pm, Invalidenstraße 42, seminar room 312a| No. | Date | Topic | Lecturer | Slides |
|---|---|---|---|---|
| 1 | 08.04.2013 | Introduction, History & Ethics | Möglich | [PDF] |
| 2 | 15.04.2013 | Biological Databases & Tools | Möglich | [PDF] |
| 3 | 22.04.2013 | Incorporation of Non-canonical Amino Acids Technical University Berlin, Building L, Room 009 |
Budisa | [PDF] |
| 4 | 29.04.2013 | Bioconjugate Chemistry & Total Protein Synthesis | Möglich | [PDF] |
| 5 | 06.05.2013 | DNA Manipulation and Libraries | Möglich | [PDF] |
| 6 | 13.05.2013 | Laboratory-directed Evolution | Möglich | [PDF] |
| -- | 20.05.2013 | Pentecost - no lecture | -- | -- |
| 7 | 27.05.2013 | Synthetic Signal Receptors & Optogenetics | Möglich | [PDF] |
| 8 | 03.06.2013 | De novo Proteins and Enzymes | Möglich | [PDF] |
| 9 | 10.06.2013 | DNA Computation & Origami | Möglich | [PDF] |
| 10 | 17.06.2013 | Transcriptional Control & Gene-regulatory Networks | Möglich | [PDF] |
| 11 | 24.06.2013 | Metabolic Engineering & Synthetic Life | Möglich | [PDF] |
Students who are enrolled in the module "Synthetic Biology" have to submit a research proposal. Details will be discussed, and instructions are available.
Lab "Design and Characterization of Synthetic Photoreceptors" (BioPhysics XIV)
Time frame A, 09.04.-20.04.2013. First meeting Tue, 02.04.2013 10.00 s. t. room 304.Seminar "Current Topics in Photobiology and Protein Design" (BioPhysics XIV)
The seminar is one component of the module 'Synthetic Biology', and each participant should present one of the papers from the below list. Pending prior approval, the seminar can also be qualified for other biophysics modules. Please choose a topic and date you are interested in, and send me an email. First come, first serve; other papers are acceptable pending approval. The seminar starts on 26.04.2013.Friday 8.15 am, Invalidenstraße 42, seminar room 312a
| Date | Topic | Lecturer(s) | Link | Slides |
|---|---|---|---|---|
| 26.04.2013 | Chatterjee, A., Xiao, H., Schultz, P.G. (2012) Evolution of multiple, mutually orthogonal prolyl-tRNA synthetase/tRNA pairs for unnatural amino acid mutagenesis in Escherichia coli. Proc Natl Acad Sci U S A 109(37), 14841-14846. Grunbeck, A., Huber, T., Sakmar, T.P. (2012) Mapping a ligand binding site using genetically encoded photoactivatable crosslinkers. Methods Enzymol 520, 307-322. |
A.M. | [Link] [PDF] |
[PDF] |
| 03.05.2013 | Yeates, T.O., Kent, S.B. (2012) Racemic Protein Crystallography. Annu Rev Biophys 41, 21-41 Mandal, K., Pentelute, B.L., Bang, D., Gates, Z.P., Torbeev, V.Y., Kent, S.B. (2012) Design, total chemical synthesis, and X-ray structure of a protein having a novel linear-loop polypeptide chain topology. Angewandte Chemie 51(6), 1481-6 |
N.N. Jakob Kottmann |
[Link] [Link] |
[PDF] |
| 10.05.2013 | Gibson, D.G., Young, L., Chuang, R.Y., Venter, J.C., Hutchison, C.A. 3rd, Smith, H.O. (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6(5), 343-345. Gibson, D.G. (2011) Enzymatic assembly of overlapping DNA fragments. Methods Enzymol 498, 349-361. Cancelled! |
N.N. | [Link] [PDF] |
[PDF] |
| 17.05.2013 | Davids, T., Schmidt, M., Böttcher, D., Bornscheuer, U.T. (2013) Strategies for the discovery and engineering of enzymes for biocatalysis. Curr Opin Chem Biol in press Larman, H.B., Xu, G.J., Pavlova, N.N., Elledge, S.J. (2012) Construction of a rationally designed antibody platform for sequencing-assisted selection. Proc Natl Acad Sci U S A 109(45), 18523-18528. |
Jürgen Arndt Manuela Denz |
[PDF] [Link] |
[PDF] |
| 24.05.2013 | Extra day after Pentecost | -- | -- | -- |
| 31.05.2013 | Müller, K., Engesser, R., Metzger, S., Schulz, S., Kämpf, M.M., Busacker, M., Steinberg, T., Tomakidi, P., Ehrbar, M., Nagy, F., Timmer, J., Zubriggen, M.D., Weber W. (2013) A red/far-red light-responsive bi-stable toggle switch to control gene expression in mammalian cells. Nucleic Acids Res in press | Roman Scholz | [Link] | [PDF] |
| 07.06.2013 | Kiss, G., Celebi-Ölçüm, N., Moretti, R., Baker, D., Houk, K.N. Computational Enzyme Design. Angew Chem Int Ed Engl in press | Rahel Frick | [Link] | [PDF] |
| 14.06.2013 | Rajendran, A., Endo, M., Hidaka, K., Sugiyama, H. (2013) Direct and real-time observation of rotary movement of a DNA nanomechanical device. J Am Chem Soc 135(3), 1117-1123. Langecker, M., Arnaut, V., Martin, T.G., List, J., Renner, S., Mayer, M., Dietz, H., Simmel, F.C. (2012) Synthetic lipid membrane channels formed by designed DNA nanostructures. Science 338(6109), 932-936. |
Laura Zeugner Hu Jingjun |
[Link] [Link] |
[PDF] |
| 21.06.2013 | Bugaj, L.J., Choksi, A.T., Mesuda, C.K., Kane, R.S., Schaffer, D.V. (2013) Optogenetic protein clustering and signaling activation in mammalian cells. Nat Methods 10(3), 249-252. Lee, J.W., Na, D., Park, J.M., Lee, J., Choi, S., Lee, S.Y. (2012) Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nat Chem Biol 8(6), 536-546. Jardine, J., Julien, J.P., Menis, S., Ota, T., Kalyuzhniy, O., McGuire, A., Sok, D., Huang, P.S., Macpherson, S., Jones, M., Nieusma, T., Mathison, J., Baker, D., Ward, A.B., Burton, D.R., Stamatatos, L., Nemazee, D., Wilson, I.A., Schief, W.R. (2013) Rational HIV Immunogen Design to Target Specific Germline B Cell Receptors. Science in press |
Julia Katharina Schlichting Tobias Wörner Ali Saitov |
[Link] [PDF] [Link] |
[PDF] |
| 28.06.2013 | Ke, Y., Ong, L.L., Shih, W.M., Yin, P. (2012) Three-dimensional structures self-assembled from DNA bricks. Science 338(6111), 1177-1183. Kimoto, M., Yamashige, R., Matsunaga, K., Yokoyama, S., Hirao, I. (2013) Generation of high-affinity DNA aptamers using an expanded genetic alphabet. Nat Biotechnol 31(5), 453-457. Siuti, P., Yazbek, J., Lu, T.K. (2013) Synthetic circuits integrating logic and memory in living cells. Nat Biotechnol 31(5), 448-452. |
Benedikt Dänekamp Jelena Pajovic Christian Wienberg |
[Link] [Link] [Link] |
[PDF] |
Lab "Biophysics" (B.Sc. course 3110022)
| Spectroscopic Characterization of Blue-Light Photoreceptor Proteins | [PDF] |
| Analysis of Protein Structures with PyMOL | [PDF] |
⊞ Winter Term 2012/13
Lab "Python for the Life Sciences"
Time: Feb 12th-22nd 2013Place: Computer Pool Neubau Invalidenstraße 42
Lecture "Molecular Biophysics" (BioPhysics I)
| Date | Topic | Slides |
|---|---|---|
| 27./28.11.2012 | Protein Folding Kinetics & Thermodynamics | [PDF] |
| 08./09.01.2013 | Fluorescence | [PDF] |
| 15./16.01.2012 | Hydrodynamic Methods & CD Spectroscopy | [PDF] |
| 05./06.02.2013 | Of Heat, Atoms, Forces and Light | [PDF] |
⊟ Summer Term 2012
Lecture "Synthetic Biology" (BioPhysics XIV)
| Nr. | Date | Topic | Lecturer | Slides |
|---|---|---|---|---|
| 1 | 16.04.2012 | Introduction, History & Ethics | Möglich | [PDF] |
| 2 | 23.04.2012 | Biological Databases & Tools | Möglich | [PDF] |
| 3 | 30.04.2012 | Incorporation of Non-canonical Amino Acids | Budisa | [PDF] |
| 4 | 07.05.2012 | Bioconjugate Chemistry & Total Protein Synthesis | Möglich | [PDF] |
| 5 | 14.05.2012 | DNA Manipulation and Libraries | Möglich | [PDF] |
| 6 | 21.05.2012 | Laboratory-directed Evolution | Möglich | [PDF] |
| -- | 28.05.2012 | Pfingsten - no lecture | -- | -- |
| 7 | 04.06.2012 | Synthetic Signal Receptors & Optogenetics | Möglich | [PDF] |
| 8 | 11.06.2012 | De novo Proteins and Enzymes | Möglich | [PDF] |
| -- | 18.06.2012 | Business trip - no lecture | -- | -- |
| 9 | 25.06.2012 | DNA Computation & Origami | Möglich | [PDF] |
| 10 | 02.07.2012 | Transcriptional Control & Gene-regulatory Networks | Möglich | [PDF] |
| 11 | 09.07.2012 | Metabolic Engineering & Synthetic Life | Möglich | [PDF] |
Lab "Design and Characterization of Synthetic Photoreceptors" (BioPhysics XIV)
First meeting Mo, 14.05.2012 14.00 s. t. seminar room 312.Seminar "Current Topics in Photobiology and Protein Design" (BioPhysics XIV)
| Date | Paper | Presenter | Link | Slides |
|---|---|---|---|---|
| 27.04.2012 | More Databases & Tools for Structure Analysis | Möglich | n/a | [PDF] |
| 04.05.2012 | Liu, C.C., Schultz, P.G. (2010) Adding new chemistries to the genetic code. Annu Rev Biochem 79:413-44 Ai, H.W. , Shen, W., Sagi, A., Chen, P.R., Schultz, P.G. (2011) Probing protein-protein interactions with a genetically encoded photo-crosslinking amino acid. ChemBioChem 12(12):1854-7 |
Möglich | [Link] [Link] |
[PDF] |
| 11.05.2012 | Yeates, T.O., Kent, S.B. (2012) Racemic Protein Crystallography. Annu Rev Biophys 41:21-41 Mandal, K., Pentelute, B.L., Bang, D., Gates, Z.P., Torbeev, V.Y., Kent, S.B. (2012) Design, total chemical synthesis, and X-ray structure of a protein having a novel linear-loop polypeptide chain topology. Angewandte Chemie 51(6):1481-6 |
Cancelled |
[Link] [Link] |
[PDF] |
| 18.05.2012 | Pinheiro, V.B., Taylor, A.I., Cozens, C., Abramov, M., Renders, M., Zhang, S., Chaput, J.C., Wengel, J., Peak-Chew, S.Y., McLaughlin, S.H., Herdewijn, P., Holliger, P. (2012) Synthetic genetic polymers capable of heredity and evolution. Science 336(6079):341-4 Joyce, G.F. (2012) Evolution. Toward an alternative biology. Science 336(6079):307-8 |
Jens Hahn | [Link] [Link] |
[PDF] |
| 25.05.2012 | Luo, Y., Xia, Y. (2012) Selection of single-chain variable fragment antibodies against fenitrothion by ribosome display. Anal Biochem 421(1):130-7 Bornscheuer, U., Kazlauskas, R.J. (2011) Survey of protein engineering strategies. Curr Protoc Protein Sci Unit26.7 |
Sonja Minniberger | [Link] [Link] |
[PDF] |
| 01.06.2012 | Extra Tag | -- | -- | -- |
| 08.06.2012 | Wang, X., Chen, X., Yang, Y. (2012) Spatiotemporal control of gene expression by a light-switchable transgene system. Nat Methods 9(3):266-9 Lungu, O.I., Hallett, R.A., Choi, E.J., Aiken, M.J., Hahn, K.M., Kuhlman, B. (2012) Designing Photoswitchable Peptides Using the AsLOV2 Domain. Chem Biol 19(4):507-17 |
Robert Streeck Philip Luxen |
[Link] [Link] |
[PDF] [PDF] |
| 15.06.2012 | Siegel, J.B., Zanghellini, A., Lovick, H.M., Kiss, G., Lambert, A.R., St Clair, J.L., Gallaher, J.L., Hilvert, D., Gelb, M.H., Stoddard, B.L., Houk, K.N., Michael, F.E., Baker, D. (2010) Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 329(5989):309-13 Khare, S.D., Kipnis, Y., Greisen, P. Jr, Takeuchi, R., Ashani, Y., Goldsmith, M., Song, Y., Gallaher, J.L., Silman, I., Leader, H., Sussman, J.L., Stoddard, B.L., Tawfik, D.S., Baker, D. (2012) Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nat Chem Biol 8(3):294-300 |
Martha Braun Frauke Dreyer |
[Link] [Link] |
[PDF] [PDF] |
| 22.06.2012 | Extra Tag | -- | -- | -- |
| 29.06.2012 | Kuzyk, A., Schreiber, R., Fan, Z., Pardatscher, G., Roller, E.M., Högele, A., Simmel, F.C., Govorov, A.O., Liedl, T. (2012) DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response. Nature 483(7389):311-4 Douglas, S.M., Bachelet, I., Church, G.M. (2012) A logic-gated nanorobot for targeted transport of molecular payloads. Science 335(6070):831-4 |
Christiane Grimm Kristin Schmidt |
[Link] [Link] |
[PDF] [PDF] |
| 06.07.2012 | Dellomonaco, C., Clomburg, J.M., Miller, E.N., Gonzalez, R. (2011) Engineered reversal of the ß-oxidation cycle for the synthesis of fuels and chemicals. Nature 476(7360):355-9 Prindle, A., Samayoa, P., Razinkov, I., Danino, T., Tsimring, L.S., Hasty, J. (2011) A sensing array of radically coupled genetic 'biopixels'. Nature 481(7379):39-44 |
Julian Appelfeller Tobias Kaufholz |
[Link] [Link] |
[PDF] [PDF] |
| 13.07.2012 | Wargacki, A.J., Leonard, E., Win, M.N., Regitsky, D.D., Santos, C.N., Kim, P.B., Cooper, S.R., Raisner, R.M., Herman, A., Sivitz, A.B., Lakshmanaswamy, A., Kashiyama, Y., Baker, D., Yoshikuni, Y. (2012) An engineered microbial platform for direct biofuel production from brown macroalgae. Science 335(6066):308-13 | Tom Lindtner | [Link] | [PDF] |
⊞ Winter Term 2011/12
Lab "Python for the Life Sciences"
Lecture "Molecular Biophysics" (BioPhysics I)
| Date | Topic | Slides |
|---|---|---|
| 10./11.01.2012 | Protein Folding Kinetics & Thermodynamics | [PDF] |
| 17./18.01.2012 | Fluorescence | [PDF] |
| 07./08.02.2012 | Hydrodynamic Methods & CD Spectroscopy | [PDF] |
⊞ Summer Term 2011
Lecture "Synthetic Biology" (BioPhysics IV or VII)
| Nr. | Date | Topic | Lecturer | Slides |
|---|---|---|---|---|
| 1 | 11.04.2011 | Introduction, History & Ethics | Möglich | [PDF] |
| 2 | 18.04.2011 | Biological Databases & Tools | Möglich | [PDF] |
| 3 | 02.05.2011 | Incorporation of Non-canonical Amino Acids | Budisa | [PDF] |
| 4 | 09.05.2011 | Bioconjugate Chemistry & Total Protein Synthesis | Möglich | [PDF] |
| 5 | 16.05.2011 | DNA Manipulation and Libraries | Möglich | [PDF] |
| 6 | 23.05.2011 | Laboratory-directed Evolution | Möglich | [PDF] |
| 7 | 30.05.2011 | Synthetic Signal Receptors & Optogenetics | Möglich | [PDF] |
| 8 | 06.06.2011 | De novo Proteins and Enzymes | Möglich | [PDF] |
| -- | 13.06.2011 | Pfingsten - no lecture | -- | -- |
| 9 | 20.06.2011 | Transcriptional Control & Gene-regulatory Networks | Möglich | [PDF] |
| 10 | 27.06.2011 | Metabolic Engineering & Synthetic Life | Möglich | [PDF] |
| 11 | 04.07.2011 | Student Presentations | -- | -- |
| 12 | 11.07.2011 | Student Presentations | -- | -- |
Important Note
To get credit for this lecture, you have to give a seminar presentation in the last two weeks of this course. You can team up as groups of 2-3 people and choose any paper that is relevant to any unit of this lecture series. Please prepare a 10-15 minutes presentation. If you have questions or need a suggestion for a suitable paper, please contact me by email.
In the below table please find the scheduled seminar presentations:
| Date | Students | Paper | Slides |
|---|---|---|---|
| 04.07.2011 | Chang Yan Claudia Beck |
Fleishman et al. (2011) Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 332:816-821 [Link] | -- |
| 04.07.2011 | Stefan Greulich Peer Schrapers |
Mascarello et al. (2010) Inhibition of Mycobacterium tuberculosis tyrosine phosphatase PtpA by synthetic chalcones: kinetics, molecular modeling, toxicity and effect on growth. Bioorg Med Chem 18:3783-3789 [Link] | [PDF] |
| 04.07.2011 | Damian Pawolski Friederike Knipping |
Blankenship et al. (2011) Comparing photosynthetic and photovoltaic efficiencies and recognizing the potential for improvement. Science 332:805-809 [Link] | -- |
| 04.07.2011 | Annabell Hillenbrand Ferdinand Greiss |
E. glowli - iGEM project Team Cambridge 2010 [Link] | -- |
| 11.07.2011 | Roman Fudim Jonas Wietek Helena Steinocher |
Sievers et al. (2011) Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation. Nature doi:10.1038/nature10154 [Link] | -- |
| 11.07.2011 | Hikan Kobayashi | Basu et al. (2005) A synthetic multicellular system for programmed pattern formation. Nature 434:1130-1134 [Link] | -- |
| 11.07.2011 | Martin Weiland Anne Pelikan Jedrzej Blaskievicz |
Anderson et al. (2006) Environmentally controlled invasion of cancer cells by engineered bacteria. J Mol Biol 355:619-627 [Link] | -- |
| 11.07.2011 | Anna Erzberger Christopher Wolff |
Ro et al. (2006) Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440:940-943 [Link] | -- |