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Comparison of the accuracy of protein solution structures derived from conventional and network-edited NOESY data.

Hoogstraten CG, Choe S, Westler WM, Markley JL
Protein Sci 4 2289-99 (1995)
Related entries: 1omt, 1tur

Cited: 29 times
EuropePMC logo PMID: 8563625

Abstract

Network-editing experiments are variants of the basic NOESY experiment that allow more accurate direct measurement of interproton distances in macromolecules by defeating specific spin-diffusion pathways. Two network-editing approaches, block-decoupled NOESY and complementary-block-decoupled-NOESY, were applied as three-dimensional, heteronuclear-edited experiments to distance measurement in a small protein, turkey ovomucoid third domain (OMTKY3). Two-hundred and twelve of the original 655 distance constraints observed in this molecule (Krezel AM et al., 1994, J Mol Biol 242:203-214) were improved by their replacement by distances derived from network-edited spectra, and distance geometry/simulated annealing solution structure calculations were performed from both the unimproved and improved distance sets. The resulting two families of structures were found to differ significantly, the most important differences being the hinge angle of a beta-turn and an expansion of the sampled conformation space in the region of the reactive-site loop. The structures calculated from network-editing data are interpreted as a more accurate model of the solution conformation of OMTKY3.

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  2. Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems. Barroso daSilva FL, Dias LG. Biophys Rev 9 699-728 (2017)

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  2. Soft protein-protein docking in internal coordinates. Fernández-Recio J, Totrov M, Abagyan R. Protein Sci 11 280-291 (2002)
  3. Constant-pH Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulation Method. Chen Y, Roux B. J Chem Theory Comput 11 3919-3931 (2015)
  4. Protein-protein binding site identification by enumerating the configurations. Guo F, Li SC, Wang L, Zhu D. BMC Bioinformatics 13 158 (2012)
  5. Generalized Born Based Continuous Constant pH Molecular Dynamics in Amber: Implementation, Benchmarking and Analysis. Huang Y, Harris RC, Shen J. J Chem Inf Model 58 1372-1383 (2018)
  6. GPU-Accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: pKa Predictions with Single-pH Simulations. Harris RC, Shen J. J Chem Inf Model 59 4821-4832 (2019)
  7. Reproducing basic pKa values for turkey ovomucoid third domain using a polarizable force field. Click TH, Kaminski GA. J Phys Chem B 113 7844-7850 (2009)
  8. Efficient implementation of constant pH molecular dynamics on modern graphics processors. Arthur EJ, Brooks CL. J Comput Chem 37 2171-2180 (2016)
  9. Accurately Predicting Protein pKa Values Using Nonequilibrium Alchemy. Wilson CJ, Karttunen M, de Groot BL, Gapsys V. J Chem Theory Comput 19 7833-7845 (2023)


Reviews citing this publication (1)

  1. Structure calculation from NMR data. Nilges M. Curr Opin Struct Biol 6 617-623 (1996)

Articles citing this publication (17)

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  2. Constant-pH molecular dynamics using continuous titration coordinates. Lee MS, Salsbury FR, Brooks CL. Proteins 56 738-752 (2004)
  3. An efficient hybrid explicit/implicit solvent method for biomolecular simulations. Lee MS, Salsbury FR, Olson MA. J Comput Chem 25 1967-1978 (2004)
  4. pH replica-exchange method based on discrete protonation states. Itoh SG, Damjanović A, Brooks BR. Proteins 79 3420-3436 (2011)
  5. SjAPI, the first functionally characterized Ascaris-type protease inhibitor from animal venoms. Chen Z, Wang B, Hu J, Yang W, Cao Z, Zhuo R, Li W, Wu Y. PLoS One 8 e57529 (2013)
  6. Cross-correlated relaxation for the measurement of angles between tensorial interactions. Reif B, Diener A, Hennig M, Maurer M, Griesinger C. J Magn Reson 143 45-68 (2000)
  7. Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods. Khandogin J, York DM. Proteins 56 724-737 (2004)
  8. The thermodynamics of protein-protein recognition as characterized by a combination of volumetric and calorimetric techniques: the binding of turkey ovomucoid third domain to alpha-chymotrypsin. Filfil R, Chalikian TV. J Mol Biol 326 1271-1288 (2003)
  9. Contribution of peptide bonds to inhibitor-protease binding: crystal structures of the turkey ovomucoid third domain backbone variants OMTKY3-Pro18I and OMTKY3-psi[COO]-Leu18I in complex with Streptomyces griseus proteinase B (SGPB) and the structure of the free inhibitor, OMTKY-3-psi[CH2NH2+]-Asp19I. Bateman KS, Huang K, Anderson S, Lu W, Qasim MA, Laskowski M, James MN. J Mol Biol 305 839-849 (2001)
  10. Functional characterization of a new non-Kunitz serine protease inhibitor from the scorpion Lychas mucronatus. Liu H, Chen J, Wang X, Yan S, Xu Y, San M, Tang W, Yang F, Cao Z, Li W, Wu Y, Chen Z. Int J Biol Macromol 72 158-162 (2015)
  11. Linear-scaling molecular orbital calculations for the pKa values of ionizable residues in proteins. Ohno K, Sakurai M. J Comput Chem 27 906-916 (2006)
  12. Structural insights into the non-additivity effects in the sequence-to-reactivity algorithm for serine peptidases and their inhibitors. Lee TW, Qasim MA, Laskowski M, James MN. J Mol Biol 367 527-546 (2007)
  13. Improved distance analysis in RNA using network-editing techniques for overcoming errors due to spin diffusion. Hoogstraten CG, Pardi A. J Biomol NMR 11 85-95 (1998)
  14. Assessment of protein solution versus crystal structure determination using spin-diffusion-suppressed NOE and heteronuclear relaxation data. LeMaster DM. J Biomol NMR 9 79-93 (1997)
  15. Intraprotein electrostatics derived from first principles: divide-and-conquer approaches for QM/MM calculations. Molina PA, Li H, Jensen JH. J Comput Chem 24 1971-1979 (2003)
  16. Properties that rank protein:protein docking poses with high accuracy. Simões ICM, Coimbra JTS, Neves RPP, Costa IPD, Ramos MJ, Fernandes PA. Phys Chem Chem Phys 20 20927-20942 (2018)
  17. Using polarizable POSSIM force field and fuzzy-border continuum solvent model to calculate pK(a) shifts of protein residues. Sharma I, Kaminski GA. J Comput Chem 38 65-80 (2017)


Related citations provided by authors (2)

  1. Solution structure of turkey ovomucoid third domain as determined from nuclear magnetic resonance data.. Krezel AM, Darba P, Robertson AD, Fejzo J, Macura S, Markley JL J Mol Biol 242 203-14 (1994)
  2. Overexpression and purification of avian ovomucoid third domains in Escherichia coli.. Hinck AP, Walkenhorst WF, Westler WM, Choe S, Markley JL Protein Eng 6 221-7 (1993)

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