Automated evaluation of chemical shift perturbation spectra: New approaches to quantitative analysis of receptor-ligand interaction NMR spectra

Chen, Peng; Unger, S. W.; Filipp, Fabian V.; Sattler, Michael; Szalma, Sándor

doi:10.1023/b:jnmr.0000034351.37982.9e

Cited by 24 publications

(24 citation statements)

References 27 publications

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“…This discrepancy can be understood considering that the measured NMR chemical shifts are weighted averages of bound and unbound protein. 60,61 Under the experimental conditions used, there is an excess of unbound protein relative to bound protein in the UbiquitinÀAuNP complex, thus resulting in a scaling down of the measured chemical shift perturbation.…”

Section: Articlementioning

confidence: 99%

Docking of Ubiquitin to Gold Nanoparticles

et al. 2012

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Protein-nanoparticle associations have important applications in nanoscience and nanotechnology such as targeted drug delivery and theranostics. However, the mechanisms by which proteins recognize nanoparticles and the determinants of specificity are still poorly understood at the microscopic level. Gold is a promising material in nanoparticles for nanobiotechnology applications because of the ease of its functionalization and its tunable optical properties. Ubiquitin is a small, cysteine-free protein (ubiquitous in eukaryotes) whose binding to gold nanoparticles has been characterized recently by nuclear magnetic resonance (NMR). To reveal the molecular basis of these protein-nanoparticle interactions, we performed simulations at multiple levels (ab initio quantum mechanics, classical molecular dynamics and Brownian dynamics) and compared the results with experimental data (circular dichroism and NMR). The results provide a model of the ensemble of structures constituting the ubiquitin-gold surface complex, and insights into the driving forces for the binding of ubiquitin to gold nanoparticles, the role of nanoparticle surfactants (citrate) in the association process, and the origin of the perturbations in the NMR chemical shifts.

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Section: Articlementioning

confidence: 99%

Docking of Ubiquitin to Gold Nanoparticles

et al. 2012

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“…For UbcH5B and histone H1, 1.0 ppm and 0.2 ppm were used for tN and t H N , respectively. This is comparable to the thresholds used by FELIX-Autoscreen [23]. Smaller thresholds of 0.75 ppm and 0.125 ppm were used for hBclXL because it has more perturbed spectra, so the chemical shift changes are expected to be more gradual.…”

Section: Peak Walking Problemmentioning

confidence: 90%

“…Nevertheless, automated methods are necessary for high-throughput drug screening. FELIX-Autoscreen [23] formulates the assignment of peaks in the reference spectrum to peaks in a perturbed spectrum as a bipartite graph matching problem, such that the sum of the chemical shift and peak shape differences is minimized. Their approach of optimizing the sum of the distances is better than choosing the peak nearest to each reference peak because the local greedy approach disregards the mappings of other peaks nearby, which results in errors.…”

Section: Introductionmentioning

confidence: 99%

Combining ambiguous chemical shift mapping with structure-based backbone and NOE assignment from ¹⁵ N-NOESY

Jang

Gao

2011

Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine

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Chemical shift mapping is an important technique in NMRbased drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule's introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically. However, automated methods are necessary for high-throughput drug screening. We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15 N-NOESY, while avoiding TOCSY experiments and 13 C-labeling, to resolve the ambiguities for a one-toone mapping. On the three proteins, it achieves an average accuracy of 94% or better.

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“…An automatic method for the processing of chemical shift perturbation on NMR spectra was proposed [215].…”

Section: Structure Determination Of Complexesmentioning

confidence: 99%

Quantitative Analysis of Biomolecular NMR Spectra: A Prerequisite for the Determination of the Structure and Dynamics of Biomolecules

Malliavin

2006

COC

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Nuclear Magnetic Resonance (NMR) became during the two last decades an important method for biomolecular structure determination. NMR permits to study biomolecules in solution and gives access to the molecular flexibility at atomic level on a complete structure: in that respect, it is occupying a unique place i n structural biology. During the first years of its development, NMR was trying to meet the requirements previously defined in X-ray crystallography. But, NMR then started to determine its own criteria for the definition of a structure. Indeed, the atomic coordinates of an NMR structure are calculated using restraints on geometrical parameters (angles and distances) of the structure, which are only indirectly related to atom positions: in that respect, NMR and X-ray crystallography are very different. The indirect relation between the NMR measurements and the molecular structure and dynamics makes critical the precision and the interpretation of the NMR parameters and the development of quantitative analysis methods. The methods published since 1997 for liquid-NMR of proteins are reviewed here. First, methods for structure determination are presented, as well as methods for spectral assignment and for structure quality assessment. Second, the quantitative analysis of structure mobility i s reviewed.

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Automated evaluation of chemical shift perturbation spectra: New approaches to quantitative analysis of receptor-ligand interaction NMR spectra

Cited by 24 publications

References 27 publications

Docking of Ubiquitin to Gold Nanoparticles

Docking of Ubiquitin to Gold Nanoparticles

Combining ambiguous chemical shift mapping with structure-based backbone and NOE assignment from ¹⁵ N-NOESY

Quantitative Analysis of Biomolecular NMR Spectra: A Prerequisite for the Determination of the Structure and Dynamics of Biomolecules

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Automated evaluation of chemical shift perturbation spectra: New approaches to quantitative analysis of receptor-ligand interaction NMR spectra

Cited by 24 publications

References 27 publications

Docking of Ubiquitin to Gold Nanoparticles

Docking of Ubiquitin to Gold Nanoparticles

Combining ambiguous chemical shift mapping with structure-based backbone and NOE assignment from 15 N-NOESY

Quantitative Analysis of Biomolecular NMR Spectra: A Prerequisite for the Determination of the Structure and Dynamics of Biomolecules

Contact Info

Product

Resources

About

Combining ambiguous chemical shift mapping with structure-based backbone and NOE assignment from ¹⁵ N-NOESY