Publication date: Available online 2 May 2014 Source:Journal of Magnetic Resonance
Author(s): Fa-An Chao , Jonggul Kim , Youlin Xia , Michael Milligan , Nancy Rowe , Gianluigi Veglia
We present an enhanced version of the FLAMEnGO (Fuzzy Logic Assignment of Methyl Group) software, a structure-based method to assign methyl group resonances in large proteins. FLAMEnGO utilizes a fuzzy logic algorithm coupled with Monte Carlo sampling to obtain a probability-based assignment of the methyl group resonances. As an input, FLAMEnGO requires the protein X-ray structure or an NMR structural ensemble with data such as methyl-methyl NOESY, paramagnetic relaxation enhancement (PRE), methine-methyl TOCSY data. Version 2.0 of this software (FLAMEnGO 2.0) has a user-friendly graphic interface and presents improved modules that enable the input of partial assignments and additional NMR restraints. We tested the performance of FLAMEnGO 2.0 on maltose binding protein (MBP) and the C-subunit of the cAMP-dependent protein kinase A (PKA-C). FLAMEnGO 2.0 can be used as a standalone method or to assist in the completion of partial resonance assignments and can be downloaded at http://www.chem.umn.edu/groups/vegli...ngo2-form.html. Graphical abstract
Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR [Biophysics and Computational Biology]
Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR
Kato, H., van Ingen, H., Zhou, B.-R., Feng, H., Bustin, M., Kay, L. E., Bai, Y....
Date: 2011-07-26
Chromatin structure and function are regulated by numerous proteins through specific binding to nucleosomes. The structural basis of many of these interactions is unknown, as in the case of the high mobility group nucleosomal (HMGN) protein family that regulates various chromatin functions, including transcription. Here, we report the architecture of the HMGN2-nucleosome...
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Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR.
Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR.
Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR.
Proc Natl Acad Sci U S A. 2011 Jul 5;
Authors: Kato H, van Ingen H, Zhou BR, Feng H, Bustin M, Kay LE, Bai Y
Chromatin structure and function are regulated by numerous proteins through specific binding to nucleosomes. The structural basis of many of these interactions is unknown, as in the case of the high mobility...
[NMR paper] Sequential assignment of 1H, 15N, 13C resonances and secondary structure of human cal
Sequential assignment of 1H, 15N, 13C resonances and secondary structure of human calmodulin-like protein determined by NMR spectroscopy.
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Protein Sci. 1998 Nov;7(11):2421-30
Authors: Qian H, Rogers MS, Schleucher J, Edlund U, Strehler EE, Sethson I
Human calmodulin-like protein (CLP) is closely related to vertebrate calmodulin, yet its unique cell specific expression pattern, overlapping but...
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11-17-2010 11:15 PM
[NMR paper] Assignment of the backbone 1H,15N,13C NMR resonances and secondary structure of a dou
Assignment of the backbone 1H,15N,13C NMR resonances and secondary structure of a double-stranded RNA binding domain from the Drosophila protein staufen.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Assignment of the backbone 1H,15N,13C NMR resonances and secondary structure of a double-stranded RNA binding domain from the Drosophila protein staufen.
FEBS Lett. 1995 Apr 10;362(3):333-6
Authors: Bycroft M, Proctor M, Freund SM, St Johnston D
NMR spectroscopy has been...
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[NMR paper] Assignment of the backbone 1H and 15N NMR resonances and secondary structure characte
Assignment of the backbone 1H and 15N NMR resonances and secondary structure characterization of barstar.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Assignment of the backbone 1H and 15N NMR resonances and secondary structure characterization of barstar.
FEBS Lett. 1993 Oct 11;332(1-2):81-7
Authors: Lubienski MJ, Bycroft M, Jones DN, Fersht AR
Barstar, a polypeptide inhibitor of ribonucleases, has been studied by 2D and 3D NMR techniques using uniformly...
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[NMR paper] Automation of protein 2D proton NMR assignment by means of fuzzy mathematics and grap
Automation of protein 2D proton NMR assignment by means of fuzzy mathematics and graph theory.
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J Chem Inf Comput Sci. 1993 Sep-Oct;33(5):668-82
Authors: Xu J, Straus SK, Sanctuary BC, Trimble L
The novel methodology for protein 2D NMR assignment presented in this paper is based upon protein spin coupling graph theory analysis, fuzzy graph pattern recognition, and tree searching. The method required to formalize the whole assignment...
FLAMEnGO 2.0: An Enhanced Fuzzy Logic Algorithm for Structure-Based Assignment of Methyl Group Resonances
Linear Mode
