3D Computational Modeling of Proteins Using Sparse Paramagnetic NMR Data.
Methods Mol Biol. 2017;1526:3-21
Authors: Pilla KB, Otting G, Huber T
Abstract
Computational modeling of proteins using evolutionary or de novo approaches offers rapid structural characterization, but often suffers from low success rates in generating high quality models comparable to the accuracy of structures observed in X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. A computational/experimental hybrid approach incorporating sparse experimental restraints in computational modeling algorithms drastically improves reliability and accuracy of 3D models. This chapter discusses the use of structural information obtained from various paramagnetic NMR measurements and demonstrates computational algorithms implementing pseudocontact shifts as restraints to determine the structure of proteins at atomic resolution.
Multiscale computational modeling of (13)C DNP in liquids #DNPNMR
From The DNP-NMR Blog:
Multiscale computational modeling of (13)C DNP in liquids #DNPNMR
Kucuk, S.E. and D. Sezer, Multiscale computational modeling of (13)C DNP in liquids. Phys Chem Chem Phys, 2016. 18(14): p. 9353-7.
http://www.ncbi.nlm.nih.gov/pubmed/27001446
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Abstract
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Abstract
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Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints
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Abstract
NMR structure determination of soluble proteins depends in large part on distance restraints derived from NOE. In this study, we examined the impact of paramagnetic relaxation enhancement (PRE)-derived distance restraints on protein structure determination. A high-resolution structure of the loop-rich soluble protein Sin1 could not be determined by conventional NOE-based...
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Abstract
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Protein structure modeling using sparse NMR data [Biophysics and Computational Biology]
Protein structure modeling using sparse NMR data
Thompson, J. M., Sgourakis, N. G., Liu, G., Rossi, P., Tang, Y., Mills, J. L., Szyperski, T., Montelione, G. T., Baker, D....
Date: 2012-06-19
While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that...
3D Computational Modeling of Proteins Using Sparse Paramagnetic NMR Data.
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