Modelling diffusional transport in the interphase cell nucleus (2007)
Wedemeier, Annika, Merlitz, Holger, Wu, Chen-Xu, Langowski, Jörg
In this paper a lattice model for diffusional transport of particles in the interphase cell nucleus is proposed. Dense networks of chromatin fibers are created by three different methods: randomly...
Facilitated diffusion of DNA-binding proteins: Simulation of large systems (2006)
Merlitz, Holger, Klenin, Konstantin V., Wu, Chen-Xu, Langowski, Jörg
The recently introduced method of excess collisions (MEC) is modified to estimate diffusion-controlled reaction times inside systems of arbitrary size. The resulting MEC-E equations contain a set of...
Merlitz, Holger, Klenin, Konstantin V., Wu, Chen-Xu, Langowski, Jörg
In this paper, a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins. The protein enters a spherical...
In silicio stretching of chromatin (2005)
Aumann, Frank, Lankas, Filip, Caudron, Maiwen, Langowski, Jörg
We present Monte-Carlo (MC) simulations of the stretching of a single 30 nm chromatin fiber. The model approximates the DNA by a flexible polymer chain with Debye-H\"uckel electrostatics and uses a...
Bussiek, Malte, Mücke, Norbert, Langowski, Jörg
The conformations of supercoiled (sc) DNA and linear DNA bound to polylysine (PL)-coated mica were investigated by scanning force microscopy (SFM) in solution. From the polymer statistical analysis...
Vámosi, György, Bodnár, Andrea, Vereb, György, Jenei, Attila, Goldman, Carolyn K., Langowski, Jörg, ...
The private α-chains of IL-2 and IL-15 receptors (IL-2R and IL-15R) share the signaling β- and γc-subunits, resulting in both common and contrasting roles of IL-2 and IL-15 in T cell function....
Bystricky, Kerstin, Heun, Patrick, Gehlen, Lutz, Langowski, Jörg, Gasser, Susan M.
Little is known about how chromatin folds in its native state. Using optimized in situ hybridization and live imaging techniques have determined compaction ratios and fiber flexibility for interphase...
Lankas, Filip, Cheatham, Thomas E, Spacková, Nad'a, Hobza, Pavel, Langowski, Jörg, Sponer, Jirí
Unrestrained 5-20-ns explicit-solvent molecular dynamics simulations using the Cornell et al. force field have been carried out for d[GCG(N)11GCG]2 (N, purine base) considering guanine*cytosine...
Computer simulation of the 30-nanometer chromatin fiber.
Wedemann, Gero, Langowski, Jörg
A new Monte Carlo model for the structure of chromatin is presented here. Based on our previous work on superhelical DNA and polynucleosomes, it reintegrates aspects of the "solenoid" and the...
Analyzing Intracellular Binding and Diffusion with Continuous Fluorescence Photobleaching
Wachsmuth, Malte, Weidemann, Thomas, Müller, Gabriele, Hoffmann-Rohrer, Urs W., Knoch, Tobias A., Waldeck, Waldemar, ...
Transport and binding of molecules to specific sites are necessary for the assembly and function of ordered supramolecular structures in cells. For analyzing these processes in vivo, we have...
DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations
Lankaš, Filip, Šponer, Jiří, Langowski, Jörg, Cheatham, Thomas E.
The sequence-dependent DNA deformability at the basepair step level was investigated using large-scale atomic resolution molecular dynamics simulation of two 18-bp DNA oligomers:...
Kepert, Jochen Felix, Tóth, Katalin Fejes, Caudron, Maïwen, Mücke, Norbert, Langowski, Jörg, Rippe, Karsten
The conformation of mononucleosome complexes reconstituted with recombinant core histones on a 614-basepair-long DNA fragment containing the Xenopus borealis 5S rRNA nucleosome positioning sequence...
Rapid, Diffusional Shuttling of Poly(A) RNA between Nuclear Speckles and the NucleoplasmD⃞
Politz, Joan C. Ritland, Tuft, Richard A., Prasanth, Kannanganattu V., Baudendistel, Nina, Fogarty, Kevin E., Lifshitz, Larry M., ...
Speckles are nuclear bodies that contain pre-mRNA splicing factors and polyadenylated RNA. Because nuclear poly(A) RNA consists of both mRNA transcripts and nucleus-restricted RNAs, we tested whether...
Bussiek, Malte, Mücke, Norbert, Langowski, Jörg
The conformations of supercoiled (sc) DNA and linear DNA bound to polylysine (PL)-coated mica were investigated by scanning force microscopy (SFM) in solution. From the polymer statistical analysis...
Vámosi, György, Bodnár, Andrea, Vereb, György, Jenei, Attila, Goldman, Carolyn K., Langowski, Jörg, ...
The private α-chains of IL-2 and IL-15 receptors (IL-2R and IL-15R) share the signaling β- and γc-subunits, resulting in both common and contrasting roles of IL-2 and IL-15 in T cell function....
Bystricky, Kerstin, Heun, Patrick, Gehlen, Lutz, Langowski, Jörg, Gasser, Susan M.
Little is known about how chromatin folds in its native state. Using optimized in situ hybridization and live imaging techniques have determined compaction ratios and fiber flexibility for interphase...
Lankas, Filip, Cheatham, Thomas E, Spacková, Nad'a, Hobza, Pavel, Langowski, Jörg, Sponer, Jirí
Unrestrained 5-20-ns explicit-solvent molecular dynamics simulations using the Cornell et al. force field have been carried out for d[GCG(N)11GCG]2 (N, purine base) considering guanine*cytosine...
Computer simulation of the 30-nanometer chromatin fiber.
Wedemann, Gero, Langowski, Jörg
A new Monte Carlo model for the structure of chromatin is presented here. Based on our previous work on superhelical DNA and polynucleosomes, it reintegrates aspects of the "solenoid" and the...
Analyzing Intracellular Binding and Diffusion with Continuous Fluorescence Photobleaching
Wachsmuth, Malte, Weidemann, Thomas, Müller, Gabriele, Hoffmann-Rohrer, Urs W., Knoch, Tobias A., Waldeck, Waldemar, ...
Transport and binding of molecules to specific sites are necessary for the assembly and function of ordered supramolecular structures in cells. For analyzing these processes in vivo, we have...
DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations
Lankaš, Filip, Šponer, Jiří, Langowski, Jörg, Cheatham, Thomas E.
The sequence-dependent DNA deformability at the basepair step level was investigated using large-scale atomic resolution molecular dynamics simulation of two 18-bp DNA oligomers:...
Kepert, Jochen Felix, Tóth, Katalin Fejes, Caudron, Maïwen, Mücke, Norbert, Langowski, Jörg, Rippe, Karsten
The conformation of mononucleosome complexes reconstituted with recombinant core histones on a 614-basepair-long DNA fragment containing the Xenopus borealis 5S rRNA nucleosome positioning sequence...
Rapid, Diffusional Shuttling of Poly(A) RNA between Nuclear Speckles and the NucleoplasmD⃞
Politz, Joan C. Ritland, Tuft, Richard A., Prasanth, Kannanganattu V., Baudendistel, Nina, Fogarty, Kevin E., Lifshitz, Larry M., ...
Speckles are nuclear bodies that contain pre-mRNA splicing factors and polyadenylated RNA. Because nuclear poly(A) RNA consists of both mRNA transcripts and nucleus-restricted RNAs, we tested whether...
Bussiek, Malte, Müller, Gabriele, Waldeck, Waldemar, Diekmann, Stephan, Langowski, Jörg
Alpha-satellite DNA (AS) is part of centromeric DNA and could be relevant for centromeric chromatin structure: its repetitive character may generate a specifically ordered nucleosomal arrangement and...