Related ArticlesFree-energy calculations highlight differences in accuracy between X-ray and NMR structures and add value to protein structure prediction.
Structure. 2001 Oct;9(10):905-16
Authors: Lee MR, Kollman PA
BACKGROUND: While X-ray crystallography structures of proteins are considerably more reliable than those from NMR spectroscopy, it has been difficult to assess the inherent accuracy of NMR structures, particularly the side chains. RESULTS: For 15 small single-domain proteins, we used a molecular mechanics-/dynamics-based free-energy approach to investigate native, decoy, and fully extended alpha conformations. Decoys were all less energetically favorable than native conformations in nine of the ten X-ray structures and in none of the five NMR structures, but short 150 ps molecular dynamics simulations on the experimental structures caused them to have the lowest predicted free energy in all 15 proteins. In addition, a strong correlation exists (r(2) = 0.86) between the predicted free energy of unfolding, from native to fully extended conformations, and the number of residues. CONCLUSIONS: This work suggests that the approximate treatment of solvent used in solving NMR structures can lead NMR model conformations to be less reliable than crystal structures. This conclusion was reached because of the considerably higher calculated free energies and the extent of structural deviation during aqueous dynamics simulations of NMR models compared to those determined by X-ray crystallography. Also, the strong correlation found between protein length and predicted free energy of unfolding in this work suggests, for the first time, that a free-energy function can allow for identification of the native state based on calculations on an extended state and in the absence of an experimental structure.
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Conferences
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12-10-2011 02:38 AM
Remeasuring HEWL pK(a) values by NMR spectroscopy: Methods, analysis, accuracy, and implications for theoretical pK(a) calculations.
Remeasuring HEWL pK(a) values by NMR spectroscopy: Methods, analysis, accuracy, and implications for theoretical pK(a) calculations.
Remeasuring HEWL pK(a) values by NMR spectroscopy: Methods, analysis, accuracy, and implications for theoretical pK(a) calculations.
Proteins. 2011 Mar;79(3):685-702
Authors: Webb H, Tynan-Connolly BM, Lee GM, Farrell D, O'Meara F, Søndergaard CR, Teilum K, Hewage C, McIntosh LP, Nielsen JE
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02-03-2011 01:44 PM
Site-specific free energy changes in proteins upon ligand binding by NMR: Ca(2+) -displacement by Ln(3+) in a Ca(2+) -binding protein from Entamoeba histolytica.
Site-specific free energy changes in proteins upon ligand binding by NMR: Ca(2+) -displacement by Ln(3+) in a Ca(2+) -binding protein from Entamoeba histolytica.
Site-specific free energy changes in proteins upon ligand binding by NMR: Ca(2+) -displacement by Ln(3+) in a Ca(2+) -binding protein from Entamoeba histolytica.
Chem Biol Drug Des. 2011 Jan 14;
Authors: Chandra K, Mustafi SM, Muthukumar S, Chary KV
The study of protein-ligand interaction has been of a great interest in contemporary structural biology. The understanding of the nature...
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01-18-2011 10:22 PM
Remeasuring HEWL pK(a) values by NMR spectroscopy: Methods, analysis, accuracy, and implications for theoretical pK(a) calculations.
Remeasuring HEWL pK(a) values by NMR spectroscopy: Methods, analysis, accuracy, and implications for theoretical pK(a) calculations.
Remeasuring HEWL pK(a) values by NMR spectroscopy: Methods, analysis, accuracy, and implications for theoretical pK(a) calculations.
Proteins. 2010 Sep 17;
Authors: Webb H, Tynan-Connolly BM, Lee GM, Farrell D, O'Meara F, Søndergaard CR, Teilum K, Hewage C, McIntosh LP, Nielsen JE
Site-specific pK(a) values measured by NMR spectroscopy provide essential information on protein electrostatics, the pH-dependence of...
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12-25-2010 02:40 PM
[CNS Yahoo group] Please apply for RapiData 2011, a course on Data Collection and Stru
Please apply for RapiData 2011, a course on Data Collection and Stru
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News from other NMR forums
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12-17-2010 12:50 AM
[NMR paper] The pressure-temperature free energy-landscape of staphylococcal nuclease monitored b
The pressure-temperature free energy-landscape of staphylococcal nuclease monitored by (1)H NMR.
Related Articles The pressure-temperature free energy-landscape of staphylococcal nuclease monitored by (1)H NMR.
J Mol Biol. 2000 Apr 28;298(2):293-302
Authors: Lassalle MW, Yamada H, Akasaka K
The thermodynamic stability of staphylococcal nuclease was studied against the variation of both temperature and pressure by utilizing (1)H NMR spectroscopy at 750 MHz in 20 mM Mes buffer containing 99.9 % (2)H(2)O, pH 5.3. Equilibrium fractions of folded...
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11-18-2010 09:15 PM
[NMR paper] Elongation of helix III of the NK-2 homeodomain upon binding to DNA: a secondary stru
Elongation of helix III of the NK-2 homeodomain upon binding to DNA: a secondary structure study by NMR.
Related Articles Elongation of helix III of the NK-2 homeodomain upon binding to DNA: a secondary structure study by NMR.
Biochemistry. 1994 Dec 20;33(50):15053-60
Authors: Tsao DH, Gruschus JM, Wang LH, Nirenberg M, Ferretti JA
The secondary structure of the homeodomain encoded by the NK-2 gene from Drosophila melanogaster, in both the free and DNA-bound states, was determined in solution using two- and three-dimensional (2D and 3D) NMR...
Free-energy calculations highlight differences in accuracy between X-ray and NMR stru
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