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NMR - Publications

DEEP picker is a deep neural network for accurate deconvolution of complex two-dimensional NMR spectra

1 month 2 weeks ago
The analysis of nuclear magnetic resonance (NMR) spectra for the comprehensive and unambiguous identification and characterization of peaks is a difficult, but critically important step in all NMR analyses of complex biological molecular systems. Here, we introduce DEEP Picker, a deep neural network (DNN)-based approach for peak picking and spectral deconvolution which semi-automates the analysis of two-dimensional NMR spectra. DEEP Picker includes 8 hidden convolutional layers and was trained...
Da-Wei Li

Observation of Sub-Microsecond Protein Methyl-Side Chain Dynamics by Nanoparticle-Assisted NMR Spin Relaxation

1 month 3 weeks ago
Amino-acid side-chain properties in proteins are key determinants of protein function. NMR spin relaxation of side chains is an important source of information about local protein dynamics and flexibility. However, traditional solution NMR relaxation methods are most sensitive to sub-nanosecond dynamics lacking information on slower ns-μs time-scale motions. Nanoparticle-assisted NMR spin relaxation (NASR) of methyl-side chains is introduced here as a window into these ns-μs dynamics. NASR...
Xinyao Xiang

Increasing sensitivity and versatility in NMR supersequences with new HSQC-based modules

3 months ago
The sensitivity-enhanced HSQC, as well as HSQC-TOCSY, experiments have been modified for incorporation into NOAH (NMR by Ordered Acquisition using ¹H detection) supersequences, adding diversity for ^(13)C and ^(15)N modules. Importantly, these heteronuclear modules have been specifically tailored to preserve the magnetisation required for subsequent acquisition of other heteronuclear or homonuclear modules in a supersequence. In addition, we present protocols for optimally combining HSQC and...
Jonathan R J Yong

From Selection to Instruction and Back: Competing Conformational Selection and Induced Fit Pathways in Abiotic Hosts

4 months ago
Two limiting cases of molecular recognition, induced fit (IF) and conformational selection (CS), play a central role in allosteric regulation of natural systems. The IF paradigm states that a substrate "instructs" the host to change its shape after complexation, while CS asserts that a guest "selects" the optimal fit from an ensemble of preexisting host conformations. With no studies that quantitatively address the interplay of two limiting pathways in abiotic systems, we herein and for the...
Radoslav Z Pavlović

2D NMR-Based Metabolomics with HSQC/TOCSY NOAH Supersequences

6 months 1 week ago
Sensitivity-improved versions of two-dimensional (2D) ^(13)C-¹H HSQC (heteronuclear single quantum coherence) and HSQC-TOCSY (HSQC-total correlation spectroscopy) NMR experiments optimized for small biological molecules and their complex mixtures encountered in metabolomics are presented that preserve the magnetization of ¹H spins not directly attached to ^(13)C spins. This allows (i) the application of rapid acquisition techniques to substantially shorten measurement time and (ii) their...
Alexandar L Hansen

Degree of <em>N</em>-Methylation of Nucleosides and Metabolites Controls Binding Affinity to Pristine Silica Surfaces

10 months 2 weeks ago
Biological molecules interact with silica (SiO(2)) surfaces with binding affinities that greatly vary depending on their physical-chemical properties. However, the quantitative characterization of biological compounds adsorbed on silica surfaces, especially of compounds involved in fast, reversible interactions, has been challenging, and the driving forces are not well understood. Here, we show how carbon-13 NMR spin relaxation provides quantitative atomic-detail information about the transient...
Mouzhe Xie

Proanthocyanidin Structural Details Revealed by Ultrahigh Resolution FT-ICR MALDI-Mass Spectrometry, (1)H-(13)C HSQC NMR, and Thiolysis-HPLC-DAD

11 months ago
Proanthocyanidins (condensed tannins) are important in food chemistry, agriculture, and health, driving demand for improvements in structure determination. We used ultrahigh resolution Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) methods to determine the exact composition of individual species in heterogeneous mixtures of proanthocyanidin polymers from Sorghum bicolor grain and Neptunia lutea leaves. Fragmentation patterns obtained with FT-ICR ESI MS-MS (electrospray...
Savanah G Reeves

Rational design of cell-permeable cyclic peptides containing a d-Pro-l-Pro motif

11 months 4 weeks ago
Cyclic peptides are capable of binding to challenging targets (e.g., proteins involved in protein-protein interactions) with high affinity and specificity, but generally cannot gain access to intracellular targets because of poor membrane permeability. In this work, we discovered a conformationally constrained cyclic cell-penetrating peptide (CPP) containing a d-Pro-l-Pro motif, cyclo(AFΦrpPRRFQ) (where Φ is l-naphthylalanine, r is d-arginine, and p is d-proline). The structural constraints...
Jin Wen

4,15-Dimethyl-7,12-diazo-niatri-cyclo-[<sup>2,7</sup>]hexa-deca-1(12),2,4,6,13,15-hexa-ene dibromide monohydrate

1 year ago
The title compound, C(16)H(20)N(2) ^(2+)·2Br^(-)·H(2)O (1) is a member of the class of compounds called viologens. Viologens are quaternary salts of di-pyridyls and are especially useful as redox indicators as a result of their large negative one-electron reduction potentials. Compound 1 consists of a dication composed of a pair of 4-methyl-pyridine rings mutually joined at the 2-position, with a dihedral angle between the pyridine rings of 62.35 (4)°. In addition, the rings are tethered via the...
Edward J Behrman

Broadband Dynamics of Ubiquitin by Anionic and Cationic Nanoparticle Assisted NMR Spin Relaxation

1 year 1 month ago
The quantitative and comprehensive description of the internal dynamics of proteins is critical for understanding their function. Nanoparticle-assisted ^(15) N NMR spin relaxation spectroscopy is a new method for the observation of picosecond to microsecond dynamics of proteins when transiently interacting with the surface of the nanoparticles (NPs). The method is applied here to the protein ubiquitin in the presence of anionic and cationic silica NPs (SNPs) of different sizes. The backbone...
Stacey Wardenfelt

Quantitative Cooperative Binding Model for Intrinsically Disordered Proteins Interacting with Nanomaterials

1 year 4 months ago
Intrinsically disordered proteins (IDPs) can display a broad spectrum of binding modes and highly variable binding affinities when interacting with both biological and nonbiological materials. A quantitative model of such behavior is important for the better understanding of the function of IDPs when encountering inorganic nanomaterials with the potential to control their behavior in vivo and in vitro. Depending on their amino acid composition and chain length, binding properties can vary...
Da-Wei Li

Cytotoxic and non-cytotoxic cardiac glycosides isolated from the combined flowers, leaves, and twigs of Streblus asper

1 year 8 months ago
A new non-cytotoxic [(+)-17β-hydroxystrebloside (1)] and two known cytotoxic [(+)-3'-de-O-methylkamaloside (2) and (+)-strebloside (3)] cardiac glycosides were isolated and identified from the combined flowers, leaves, and twigs of Streblus asper collected in Vietnam, with the absolute configuration of 1 established from analysis of its ECD and NMR spectroscopic data and confirmed by computational ECD calculations. A new 14,21-epoxycardanolide (3a) was synthesized from 3 that was treated with...
Yulin Ren

Extreme Nonuniform Sampling for Protein NMR Dynamics Studies in Minimal Time

2 years ago
NMR spectroscopy is an extraordinarily rich source of quantitative dynamics of proteins in solution using spin relaxation or chemical exchange saturation transfer (CEST) experiments. However, ^(15)N-CEST measurements require prolonged multidimensional, so-called pseudo-3D HSQC experiments where the pseudo dimension is a radio frequency offset Δω of a weak ^(15)N saturation field. Nonuniform sampling (NUS) approaches have the potential to significantly speed up these measurements, but they also...
Gregory Jameson

Functional protein dynamics on uncharted time scales detected by nanoparticle-assisted NMR spin relaxation

2 years 1 month ago
Protein function depends critically on intrinsic internal dynamics, which is manifested in distinct ways, such as loop motions that regulate protein recognition and catalysis. Under physiological conditions, dynamic processes occur on a wide range of time scales from subpicoseconds to seconds. Commonly used NMR spin relaxation in solution provides valuable information on very fast and slow motions but is insensitive to the intermediate nanosecond to microsecond range that exceeds the protein...
Mouzhe Xie

Metabolic Regulation of Glycolysis and AMP Activated Protein Kinase Pathways during Black Raspberry-Mediated Oral Cancer Chemoprevention

2 years 2 months ago
Oral cancer is a public health problem with an incidence of almost 50,000 and a mortality of 10,000 each year in the USA alone. Black raspberries (BRBs) have been shown to inhibit oral carcinogenesis in several preclinical models, but our understanding of how BRB phytochemicals affect the metabolic pathways during oral carcinogenesis remains incomplete. We used a well-established rat oral cancer model to determine potential metabolic pathways impacted by BRBs during oral carcinogenesis. F344...
Thomas J Knobloch

Structural analysis of phospholipase A2 from functional perspective. 1. Functionally relevant solution structure and roles of the hydrogen-bonding network.

2 years 4 months ago
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Structural analysis of phospholipase A2 from functional perspective. 1. Functionally relevant solution structure and roles of the hydrogen-bonding network.

Biochemistry. 1999 Mar 09;38(10):2909-18

Authors: Yuan C, Byeon IJ, Li Y, Tsai MD

Bovine pancreatic phospholipase A2 (PLA2), a small (13.8 kDa) Ca2+-dependent lipolytic enzyme, is rich in functional and structural character. In an effort to examine its detailed structure-function relationship, we determined its solution structure by multidimensional nuclear magnetic resonance (NMR) spectroscopy at a functionally relevant pH. An ensemble of 20 structures generated has an average root-mean-square deviation (RMSD) of 0.62 +/- 0.08 A for backbone (N, Calpha, C) atoms and 0.98 +/- 0.09 A for all heavy atoms. The overall structure shows several notable differences from the crystal structure: the first three residues at the N-terminus, the calcium-binding loop (Y25-T36), and the surface loop (V63-N72) appear to be flexible; the alpha-helical conformation of helix B (E17-F22) is absent; helix D appears to be shorter (D59-V63 instead of D59-D66); and the hydrogen-bonding network is less defined. These differences were analyzed in relation to the function of PLA2. We then further examined the H-bonding network, because its functional role or even its existence in solution has been in dispute recently. Our results show that part of the H-bonding network (the portion away from N-terminus) clearly exists in solution, as evidenced by direct observation (at 11.1 ppm) of a strong H-bond between Y73 and D99 and an implicated interaction between D99 and H48. Analyses of a series of mutants indicated that the existence of the Y73.D99 H-bond correlates directly with the conformational stability of the mutant. Loss of this H-bond results in a loss of 2-3 kcal/mol in the conformational stability of PLA2. The unequivocal identification and demonstration of the structural importance of a specific hydrogen bond, and the magnitude of its contribution to conformational stability, are uncommon to the best of our knowledge. Our results also suggest that, while the D99.H48 catalytic diad is the key catalytic machinery of PLA2, it also helps to maintain conformational integrity.

PMID: 10074343 [PubMed - indexed for MEDLINE]

Yuan C, Byeon IJ, Li Y, Tsai MD

Identification of Unknown Metabolomics Mixture Compounds by Combining NMR, MS, and Cheminformatics

2 years 9 months ago
Metabolomics aims at the comprehensive identification of metabolites in complex mixtures to characterize the state of a biological system and elucidate their roles in biochemical pathways. For many biological samples, a large number of spectral features observed by NMR spectroscopy and mass spectrometry (MS) belong to unknowns, i.e., these features do not belong to metabolites that have been previously identified, and their spectral information is not available in databases. By combining NMR,...
Abigail Leggett

Quantitative Binding Behavior of Intrinsically Disordered Proteins to Nanoparticle Surfaces at Individual Residue Level

3 years ago
The quantitative and predictive understanding how intrinsically disordered proteins (IDPs) interact with engineered nanoparticles has potentially important implications for new therapeutics as well as nanotoxicology. Based on a recently developed solution ^(15) N NMR relaxation approach, the interactions between four representative IDPs with silica nanoparticles are reported at atomic detail. Each IDP possesses distinct binding modes, which can be quantitatively explained by the local amino-acid...
Mouzhe Xie

Time-Resolved Protein Side-Chain Motions Unraveled by High-Resolution Relaxometry and Molecular Dynamics Simulations

3 years 1 month ago
Motions of proteins are essential for the performance of their functions. Aliphatic protein side chains and their motions play critical roles in protein interactions: for recognition and binding of partner molecules at the surface or serving as an entropy reservoir within the hydrophobic core. Here, we present a new NMR method based on high-resolution relaxometry and high-field relaxation to determine quantitatively both motional amplitudes and time scales of methyl-bearing side chains in the...
Samuel F Cousin

Resonance assignments of wild-type and two cysteine-free variants of the four-helix bundle protein, Rop

3 years 1 month ago
Repressor of primer (Rop, or ROM, RNA I modulator) is a 63 amino acid four-helix bundle protein that exists in solution as an anti-parallel homodimer. This protein has been extensively studied, including by X-ray crystallography, NMR, rational design, and combinatorial mutagenesis. Previous NMR experiments with wild-type Rop were carried out at pH 2.3 and pH 6.3. In this paper, we report complete N-H backbone assignments for three variants of Rop under the same pH 6.3 conditions: wild-type Rop;...
David P Bowles
52 minutes 11 seconds ago
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