PDF RNA - Ligand Interactions, Part A: Structural Biology Methods

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I hear that this technique is not very accessible there. It is complementary. The information that you get with small-angle scattering is very low resolution. With neutron scattering, you can use a technique which is called contrast matching, which gives you, in combination with the deuteration of certain components of your complex, many more pieces of information than the small-angle X-ray scattering. It will never give the high-resolution, atomic information that NMR gives.


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You have to know about everything. Do you see that as the general trend — the need for an interdisciplinary approach? Yes, definitely. Especially if you want to publish in high-impact journals; you need to have this interdisciplinary aspect. Nowadays, we are especially interested in exploring the possibilities that solid-state NMR offers in terms of looking at the RNA part of our complexes. In solution, we can look at large proteins or protein complexes because proteins have methyl groups and methyl groups can still be seen at very high molecular weights, but RNA is different. When we studied the structure of the RNP methylation enzyme, we could watch the proteins in action, because we had the methyl groups of the proteins.

However, we had one part of the complex, namely the RNA part, which remained obscure to us and silent. I actually always like to compare NMR spectra with the molecule talking to us. The reason for that is because there is no real chemical moiety in the RNA molecule that is still observable in molecular machines of high molecular weight. All resonances have just become too broad to be observed.

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We believe that solid-state NMR might be the only technique that is able to give us this information. We had to develop the methodology to assign the NMR resonances, collect structural restraints and solve the structure of the RNA by solid-state NMR, which we did successfully. Now, we are progressing to the next step, namely, looking at the RNA in the context of molecular machines. We have obtained really beautiful spectra of the RNA component of our large RNP methylation complex with excellent line widths and we are really excited about the possibility of now watching the RNA in the complex using solid-state NMR.

About Prof. Teresa Carlomagno Prof. Dr Teresa Carlomagno studied chemistry in Naples, Italy. She did her PhD partly in Naples and partly in Germany, in the group led by Christian Griesinger in Frankfurt, where she also stayed on for a post-doc. With Christian, Prof. With James Williamson, she wanted to learn the wet-lab part and she was particularly interested in RNA structure at the time. RNA structure was just coming up. People mostly liked to focus on proteins, but she wanted to learn how to produce RNA and how to look at RNA interactions with proteins, so she moved to the Williamson lab where she spent two years as a post-doc.

Then, she took up a group leader position at the Max Planck Institute in Goettingen. From there, she moved to the EMBL, where she also had a group leader position for about seven years. Since summer , Prof. Dr Carlomagno has been in Hannover, where she holds a professorship. Can even small increments show a big improvement? Does mass spectrometry play a role?

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Is this complementary to NMR? References Lapinaite, B. Simon, L. Skjaerven, M.

Rakwalska-Bange, F. Gabel, T. Codutti, A. Angelini, M. Grimaldi, D. Latek, P. Monecke, M. Dreyer, T. Simon, T. Simon, G. Althoff-Ospelt, T. Journal of Magnetic Resonance doi: Explore metabolic pathways maps that identify pathway components with PDB structures and homology models. Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. It also loads annotations from external databases such as Pfam and homology models information from the Protein Model Portal.

Annotations visualizing predicted regions of protein disorder and hydrophobic regions are displayed. Illustrates the correspondences between the human genome and 3D structure. Special features include support for both rigid-body and flexible alignments and detection of circular permutations. The JSmol symmetry display mode select the Symmetry button highlights global, local, and helical symmetry among subunits. The view displays the symmetry axes, a polyhedron that reflects the symmetry, and a color scheme that emphasizes the symmetry.

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Structural Changes of RNA in Complex with Proteins in the SRP

Global percentile ranks black vertical boxes are calculated with respect to all X-ray structures available prior to Resolution-specific percentile ranks white vertical boxes are calculated considering entries with similar resolution. Mutations in a gene can have profound effects on the function of a protein. This analysis tool highlights the location of a gene location i.

The new mapping tool can be used to locate this position on the UniProt sequence and 3D structure. This web server classifies interfaces present in protein crystals to distinguish biological interfaces from crystal contacts. EPPIC Version 3 enumerates all possible symmetric assemblies with a prediction of the most likely assembly based on probabilistic scores from pairwise evolutionary scoring. Enter ligand IDs separated by comma or white space. PDB is an online portal for teachers, students, and the general public to promote exploration in the world of proteins and nucleic acids. View iconic illustrations by the gifted artist Irving Geis in context with PDB structures and educational information.

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Structure 8 , — Ban, N. Ferre-D'Amare, A. Nature , — Cate, J. Butcher, S. EMBO J. Bourdeau, V. Nucleic Acids. Lowe, T. Omer, A. Latham, J.

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Christian, E. Harris, M. RNA 3 , — Ryder, S. Methods Enzymol. Stowell, M. Nucleic Acids Res. Doudna, J. USA 90 , —