Abstract The MaxOcc web portal is presented for the characterization of the conformational heterogeneity of two-domain proteins, through the calculation of the Maximum Occurrence that each protein conformation can have in agreement with experimental data. Whatever the real ensemble of conformations sampled by a protein, the weight of any conformation cannot exceed the calculated corresponding Maximum Occurrence value. The present portal allows users to compute these values using any combination of restraints like pseudocontact shifts, paramagnetism-based residual dipolar couplings, paramagnetic relaxation enhancements and small angle X-ray scattering profiles, given the 3D structure of the two domains as input. MaxOcc is embedded within the NMR grid services of the WeNMR project and is available via the WeNMR gateway at http://py-enmr.cerm.unifi.it/access/index/maxocc. It can be used freely upon registration to the grid with a digital certificate.
Content Type Journal Article
Category Article
Pages 1-10
DOI 10.1007/s10858-012-9638-1
Authors
Ivano Bertini, Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, FI, Italy
Lucio Ferella, Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, FI, Italy
Claudio Luchinat, Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, FI, Italy
Giacomo Parigi, Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, FI, Italy
Maximum occurrence analysis of protein conformations for different distributions of paramagnetic metal ions within flexible two-domain proteins
Maximum occurrence analysis of protein conformations for different distributions of paramagnetic metal ions within flexible two-domain proteins
Publication year: 2012
Source:Journal of Magnetic Resonance, Volume 215</br>
Claudio Luchinat, Malini Nagulapalli, Giacomo Parigi, Luca Sgheri</br>
Multidomain proteins are composed of rigid domains connected by (flexible) linkers. Therefore, the domains may experience a large degree of reciprocal reorientation. Pseudocontact shifts and residual dipolar couplings arising from one or more paramagnetic metals successively placed...
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Maximum occurrence analysis of protein conformations for different distributions of paramagnetic metal ions within flexible two-domain proteins
Maximum occurrence analysis of protein conformations for different distributions of paramagnetic metal ions within flexible two-domain proteins
Publication year: 2011
Source: Journal of Magnetic Resonance, Available online 30 December 2011</br>
Claudio*Luchinat, Malini*Nagulapalli, Giacomo*Parigi, Luca*Sgheri</br>
Multidomain proteins are composed of rigid domains connected by (flexible) linkers. Therefore, the domains may experience a large degree of reciprocal reorientation. Pseudocontact shifts and residual dipolar couplings arising from one or more paramagnetic metals successively...
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A Grid-enabled web portal for NMR structure refinement with AMBER.
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Authors: Bertini I, Case DA, Ferella L, Giachetti A, Rosato A
MOTIVATION: The typical workflow for NMR structure determination involves collecting thousands of conformational restraints, calculating a bundle of 20-40 conformers in agreement with them and refining the energetics of these conformers. The structure calculation step employs simulated annealing based on molecular dynamics...
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MaxOcc: a web portal for maximum occurrence analysis
Linear Mode
