Difference between revisions of "Fabry:Normal mode analysis"
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+ | == WEBnm@ == |
| + | [http://apps.cbu.uib.no/webnma/home WEBnm@] |
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| − | In this task you will analyze your protein structure using elastic network models. You will use two servers to calculate the normal modes: |
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| − | [http://apps.cbu.uib.no/webnma/home WEBnm@] and [http://www.igs.cnrs-mrs.fr/elnemo/start.html ElNemo] |
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| − | For each server, calculate and analyze the lowest five (to ten) normal modes. If possible (for ElNemo), use a cutoff for C<sub>α</sub> atom pairs of 10 Å. ''Note:'' ElNemo reads only the ATOM record from the PDB file. If your protein has a ligand which is given as HETATM, you need to change this to ATOM, if it should be accounted for in the normal mode calculation. |
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| − | * What information do the different servers provide? |
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| − | * How are the normal modes calculated, that is from which part of the structure? How many normal modes could in principle be calculated for your protein without any cutoff. |
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| − | * Visualize the modes (provided by server or using for example [http://www.pymol.org/ PyMol] or [http://www.ks.uiuc.edu/Research/vmd/ VMD]) and describe what movements you observe: hinge-movement, “breathing”… |
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| − | * Which regions of your protein are most flexible, most stable? |
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| − | * Can you identify domains for your protein? Compare to the [http://www.cathdb.info/ CATH], [http://scop.mrc-lmb.cam.ac.uk/scop/ SCOP] and [http://pfam.sanger.ac.uk/ Pfam] domains of your protein. |
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| − | * Can you observe notable differences between the normal modes calculated by the different servers? |
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| − | * For WEBnm@ try the amplitude scaling and vectors option. |
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| − | * Try the comparison/upload of second structure option, if: (i) you have PDB structures in different conformations or (ii) your protein has a bound ligand. Then either upload a structure with and one without the ligand, or delete the ligand in your structure. ''Note:'' Due to the force field that considers only C_alpha atoms, only changes in the backbone will give results. The model does not resolve changes in side-chain positions or SNPs. |
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| − | * When your MD simulations are finished, compare the lowest-frequency normal modes with your MD simulation using visualization software, e.g. PyMol or VMD. Can you observe different movements or similar dynamics? If possible, compare an overlay of the lowest-frequency modes to your MD simulation. You can superimpose the normal modes for example in VMD. |
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| − | * What are the advantages and disadvantages of NMA compared to MD? |
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| − | '''VMD''' (Visual Molecular Dynamics, version 1.9.1) is installed on i12k-biolab01 (type 'vmd' at command line). Here is a [http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/ VMD tutorial] and the [http://www.ks.uiuc.edu/Research/vmd/current/docs.html documentation]. |
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| − | '''Wiki review''' |
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| − | We will decide next week, which group is reviewing which group for this task. |
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| − | Here are some other servers: |
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| − | [http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi Anisotropic Network Model web server] |
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| − | [http://ignm.ccbb.pitt.edu/GNM_Online_Calculation-t.htm oGNM – Gaussian network model] |
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| − | [http://lorentz.dynstr.pasteur.fr/nma/submission.php NOMAD-Ref] |
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| − | == References == |
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| − | Nathalie Reuter, Konrad Hinsen & Jean-Jacques Lacapère. (2003) ''Transconformations of the SERCA1 Ca-ATPase: A Normal Mode Study.'' '''Biophys J''' 85(4): 2186–2197. |
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| − | Siv Midtun Hollup, Gisle Salensminde & Nathalie Reutercorresponding. (2005) ''WEBnm@: a web application for normal mode analyses of proteins.'' '''BMC Bioinformatics''' 6: 52. |
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| − | Karsten Suhre & Yves-Henri Sanejouand. (2004) ''ElNemo: a normal mode web-server for protein movement analysis and the generation of templates for molecular replacement.'' '''Nucleic Acids Research''' 32 (suppl 2): W610-W614. |
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| − | Silke A. Wieninger, Engin H. Serpersu & G. Matthias Ullmann. (2011) ''ATP Binding Enables Broad Antibiotic Selectivity of Aminoglycoside Phosphotransferase(3′)-IIIa: An Elastic Network Analysis.'' '''J Mol Biol''' 409(3):450-65. |
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| − | William Humphrey, Andrew Dalke & Klaus Schulten. (1996) ''VMD: visual molecular dynamics.'' '''J Mol Graph'''14(1):33-8, 27-8. |
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| − | ''The PyMOL Molecular Graphics System'', Version 1.5.0.4 '''Schrödinger, LLC'''. |
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| − | == WEBnm@ == |
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<div style="float:left; border:thin solid lightgrey; margin-right: 20px; width: 500px"> |
<div style="float:left; border:thin solid lightgrey; margin-right: 20px; width: 500px"> |
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<figtable id="tab:webnma_3hg2"> |
<figtable id="tab:webnma_3hg2"> |
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Revision as of 14:16, 5 July 2012
WEBnm@
<figtable id="tab:webnma_3hg2">
In this table are the 6 modes shown, that were calculated by WEBnm@. Depicted is the structure 3HG2, which represents the Human α-galactosidase catalytic mechanism with empty active site in cyan and the substrate binding site at position 203 to 207 highlighted in red.
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</figtable>
<figtable id="tab:webnma_3hg3"> In this table are the 6 modes shown, that were calculated by WEBnm@. Depicted is the structure 3HG3, which represents the Human α-galactosidase catalytic mechanism with bound substrate (green, α-D-Galactose with bound α-D-Glucose) in cyan and the substrate binding site at position 203 to 207 highlighted in red.
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</figtable>
