Direct Observation of CH/CH van der Waals Interactions in Proteins by NMR

Li, Jingwen; Wang, Yefei; An, Liaoyuan; Chen, Jingfei; Yao, Lishan

doi:10.1021/jacs.7b13345

Cited by 21 publications

(23 citation statements)

References 40 publications

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“…As such, these are an order of magnitude larger than measurements by solution-state NMR of 3h J CC couplings of 0.2 to 0.3 Hz for CH···OC hydrogen bonds in α-sheet regions of a small protein as well as for J couplings due to CH···π interactions that have been observed between methyl and aromatic side chains or carbonyl groups in proteins by Plevin et al and Perras et al, where DFT calculation predicts J coupling magnitudes of ∼0.1 Hz. We further note that, following previous ab initio predictions, , J CC couplings between 0.2 and 0.5 Hz have recently been measured for through-space van der Waals interactions between aliphatic side groups of the GB3 protein …”

Section: Discussionsupporting

confidence: 74%

Weak Intermolecular CH···N Hydrogen Bonding: Determination of ¹³CH–¹⁵N Hydrogen-Bond Mediated J Couplings by Solid-State NMR Spectroscopy and First-Principles Calculations

et al. 2019

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Weak hydrogen bonds are increasingly hypothesized to play key roles in a wide range of chemistry from catalysis to gelation to polymer structure. Here, 15N/13C spin-echo magic-angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) experiments are applied to “view” intermolecular CH···N hydrogen bonding in two selectively labeled organic compounds, 4-[15N] cyano-4′-[13C2] ethynylbiphenyl (1) and [15N3,13C6]-2,4,6-triethynyl-1,3,5-triazine (2). The synthesis of 2- 15 N 3 , 13 C 6 is reported here for the first time via a multistep procedure, where the key element is the reaction of [15N3]-2,4,6-trichloro-1,3,5-triazine (5) with [13C2]-[(trimethylsilyl)ethynyl]zinc chloride (8) to afford its immediate precursor [15N3,13C6]-2,4,6-tris[(trimethylsilyl)ethynyl]-1,3,5-triazine (9). Experimentally determined hydrogen-bond-mediated 2h J CN couplings (4.7 ± 0.4 Hz (1) and 4.1 ± 0.3 Hz (2)) are compared with density functional theory (DFT) gauge-including projector augmented wave (GIPAW) calculations, whereby species-independent coupling values 2h K CN (29.0 × 1019 kg m–2 s–2 A–2 (1) and 27.9 × 1019 kg m–2 s–2 A–2 (2)) quantitatively demonstrate the J couplings for these “weak” CH···N hydrogen bonds to be of a similar magnitude to those for conventionally observed NH···O hydrogen-bonding interactions in uracil (2h K NO: 28.1 and 36.8 × 1019 kg m–2 s–2 A–2). Moreover, the GIPAW calculations show a clear correlation between increasing 2h J CN (and 3h J CN) coupling and reducing C(H)···N and H···N hydrogen-bonding distances, with the Fermi contact term accounting for at least 98% of the isotropic 2h J CN coupling.

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Section: Discussionsupporting

confidence: 74%

Weak Intermolecular CH···N Hydrogen Bonding: Determination of ¹³CH–¹⁵N Hydrogen-Bond Mediated J Couplings by Solid-State NMR Spectroscopy and First-Principles Calculations

et al. 2019

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“…However, electrostatic interactions also contribute significantly to the folding, stability, flexibility, and function of proteins [ 48 ]. Meanwhile, van der Waals interactions play a role in the stability and function of proteins [ 49 ].…”

Section: Discussionmentioning

confidence: 99%

An Insight Based on Computational Analysis of the Interaction between the Receptor-Binding Domain of the Omicron Variants and Human Angiotensin-Converting Enzyme 2

Çeli̇k

Abdellattif

Tallei

2022

Biology

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Concerns have been raised about the high number of mutations in the spike protein of the new emergence of the highly transmissible Omicron variant (B.1.1529 lineage) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This variant’s extraordinary ability to evade antibodies would significantly impair the current vaccination program. This present study aimed to computationally analyze the interaction between the receptor-binding domain (RBD) in the spike protein of Omicron variants and human angiotensin-converting enzyme 2 (hACE2). The docking results indicated that Omicron BA.2 has exceptionally strong interactions with hACE2 in comparison to Omicron BA.1, Delta, and wild-type, as indicated by various parameters such as salt bridge, hydrogen bond, and non-bonded interactions. The results of the molecular dynamics simulation study corroborate these findings, indicating that Omicron BA.2 has a strong and stable interaction with hACE2. This study provides insight into the development of an effective intervention against this variant.

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“…We took inspiration from transfer sequences used for the measurement of homonuclear J-couplings − and for protein assignment in order to design a heteronuclear sequence that retains both the starting signal (REDOR) and the transferred signal (TEDOR). The resulting transferred-rotational-echo double resonance pulse sequence (TREDOR) co-acquires the chemical shifts of both dipolar coupled nuclei (here 13 C and 15 N or 13 C and 1 H) in one indirect dimension.…”

Section: Introductionmentioning

confidence: 99%

Transferred-Rotational-Echo Double Resonance

et al. 2021

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Internuclear distance determination is the foundation for NMR-based structure calculation. However, high-precision distance measurement is a laborious process requiring lengthy data acquisitions due to the large set of multidimensional spectra needed at different mixing times. This prevents application to large or challenging molecular systems. Here, we present a new approach, transferred-rotational-echo double resonance (TREDOR), a heteronuclear transfer method in which we simultaneously detect both starting and transferred signals in a single spectrum. This co-acquisition is used to compensate for coherence decay, resulting in accurate and precise distance determination by a single parameter fit using a single spectrum recorded at an ideal mixing time. We showcase TREDOR with the microcrystalline SH3 protein using 3D spectra to resolve resonances. By combining the measured N–C and H–C distances, we calculate the structure of SH3, which converges to the correct fold, with a root-mean-square deviation of 2.1 Å compared to a reference X-ray structure. The TREDOR data used in the structure calculation were acquired in only 4 days on a 600 MHz instrument. This is achieved due to the more than 2-fold time saving afforded by co-acquisition of additional information and demonstrates TREDOR as a fast and straightforward method for determining structures via magic-angle spinning NMR.

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Direct Observation of CH/CH van der Waals Interactions in Proteins by NMR

Cited by 21 publications

References 40 publications

Weak Intermolecular CH···N Hydrogen Bonding: Determination of ¹³CH–¹⁵N Hydrogen-Bond Mediated J Couplings by Solid-State NMR Spectroscopy and First-Principles Calculations

Weak Intermolecular CH···N Hydrogen Bonding: Determination of ¹³CH–¹⁵N Hydrogen-Bond Mediated J Couplings by Solid-State NMR Spectroscopy and First-Principles Calculations

An Insight Based on Computational Analysis of the Interaction between the Receptor-Binding Domain of the Omicron Variants and Human Angiotensin-Converting Enzyme 2

Transferred-Rotational-Echo Double Resonance

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Direct Observation of CH/CH van der Waals Interactions in Proteins by NMR

Cited by 21 publications

References 40 publications

Weak Intermolecular CH···N Hydrogen Bonding: Determination of 13CH–15N Hydrogen-Bond Mediated J Couplings by Solid-State NMR Spectroscopy and First-Principles Calculations

Weak Intermolecular CH···N Hydrogen Bonding: Determination of 13CH–15N Hydrogen-Bond Mediated J Couplings by Solid-State NMR Spectroscopy and First-Principles Calculations

An Insight Based on Computational Analysis of the Interaction between the Receptor-Binding Domain of the Omicron Variants and Human Angiotensin-Converting Enzyme 2

Transferred-Rotational-Echo Double Resonance

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Product

Resources

About

Weak Intermolecular CH···N Hydrogen Bonding: Determination of ¹³CH–¹⁵N Hydrogen-Bond Mediated J Couplings by Solid-State NMR Spectroscopy and First-Principles Calculations

Weak Intermolecular CH···N Hydrogen Bonding: Determination of ¹³CH–¹⁵N Hydrogen-Bond Mediated J Couplings by Solid-State NMR Spectroscopy and First-Principles Calculations