Validation of the Binding Site Structure of the Cellular Retinol-Binding Protein (CRBP) by Ligand NMR Chemical Shift PerturbationsClick to copy article linkArticle link copied!
Abstract
We have calculated proton chemical shift perturbations (CSPs) of retinol in the cellular retinol-binding protein (CRBP) through the use of a recently developed computational approach (Wang et al. J. Chem. Phys.2004, 120, 11392−11400). Excellent agreement with experimental values was obtained for the X-ray structure, whereas the lack of a key hydrogen bond and the distorted isoprene tail of retinol for some NMR models lead to large CSP RMSDs. Therefore, a comparison of computed CSPs of retinol with experiment offers a convenient way to validate the structure of retinol and its orientation in the binding site for the NMR structures.
*
In papers with more than one author, the asterisk indicates the name of the author to whom inquiries about the paper should be addressed.
Cited By
This article is cited by 12 publications.
- Ricardo M. Borges, Sean M. Colby, Susanta Das, Arthur S. Edison, Oliver Fiehn, Tobias Kind, Jesi Lee, Amy T. Merrill, Kenneth M. Merz, Jr., Thomas O. Metz, Jamie R. Nunez, Dean J. Tantillo, Lee-Ping Wang, Shunyang Wang, Ryan S. Renslow. Quantum Chemistry Calculations for Metabolomics. Chemical Reviews 2021, 121
(10)
, 5633-5670. https://doi.org/10.1021/acs.chemrev.0c00901
- Kenneth M. Merz, Jr. . Using Quantum Mechanical Approaches to Study Biological Systems. Accounts of Chemical Research 2014, 47
(9)
, 2804-2811. https://doi.org/10.1021/ar5001023
- Duane E. Williams, Martin B. Peters, Bing Wang and Kenneth M. Merz, Jr.. MNDO Parameters for the Prediction of 19F NMR Chemical Shifts in Biologically Relevant Compounds. The Journal of Physical Chemistry A 2008, 112
(37)
, 8829-8838. https://doi.org/10.1021/jp801649f
- Bing Wang and, Kenneth M. Merz, Jr.. A Fast QM/MM (Quantum Mechanical/Molecular Mechanical) Approach to Calculate Nuclear Magnetic Resonance Chemical Shifts for Macromolecules. Journal of Chemical Theory and Computation 2006, 2
(1)
, 209-215. https://doi.org/10.1021/ct050212s
- Mouhmad Elayyan, Binglin Sui, Mark R. Hoffmann. Perspective on the Role of Quantum Mechanical Calculations on Cellular Molecular Interactions. 2024, 78-155. https://doi.org/10.2174/97898151790331240700005
- Alessandro Genoni, Lukas Bučinský, Nicolas Claiser, Julia Contreras‐García, Birger Dittrich, Paulina M. Dominiak, Enrique Espinosa, Carlo Gatti, Paolo Giannozzi, Jean‐Michel Gillet, Dylan Jayatilaka, Piero Macchi, Anders Ø. Madsen, Lou Massa, Chérif F. Matta, Kenneth M. Merz, Philip N. H. Nakashima, Holger Ott, Ulf Ryde, Karlheinz Schwarz, Marek Sierka, Simon Grabowsky. Quantum Crystallography: Current Developments and Future Perspectives. Chemistry – A European Journal 2018, 24
(43)
, 10881-10905. https://doi.org/10.1002/chem.201705952
- Mike P. Williamson. Using chemical shift perturbation to characterise ligand binding. Progress in Nuclear Magnetic Resonance Spectroscopy 2013, 73 , 1-16. https://doi.org/10.1016/j.pnmrs.2013.02.001
- Yan Ling, Yong Zhang. Deciphering Structural Fingerprints for Metalloproteins with Quantum Chemical Calculations. 2010, 64-77. https://doi.org/10.1016/S1574-1400(10)06005-6
- Bing Wang, Kenneth M. Merz Jr.. Importance of loop dynamics in the neocarzinostatin chromophore binding and release mechanisms. Physical Chemistry Chemical Physics 2010, 12
(14)
, 3443. https://doi.org/10.1039/b924951f
- Wei Yang, Hugh Nymeyer, Huan‐Xiang Zhou, Bernd Berg, Rafael Brüschweiler. Quantitative computer simulations of biomolecules: A snapshot. Journal of Computational Chemistry 2008, 29
(4)
, 668-672. https://doi.org/10.1002/jcc.20819
- Harren Jhoti, Anne Cleasby, Marcel Verdonk, Glyn Williams. Fragment-based screening using X-ray crystallography and NMR spectroscopy. Current Opinion in Chemical Biology 2007, 11
(5)
, 485-493. https://doi.org/10.1016/j.cbpa.2007.07.010
- Srisunder Subramaniam, Stephen L. Briggs, Allen D. Kline. Monitoring the Ligand Binding Mode by Proton NMR Chemical Shift Differences. ChemMedChem 2006, 1
(11)
, 1197-1199. https://doi.org/10.1002/cmdc.200600175
Article Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.
Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.
The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated.