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NMR - Publications

Predicting Protein Flexibility with AlphaFold

1 week 2 days ago
AlphaFold2 has revolutionized protein structure prediction from amino-acid sequence. In addition to protein structures, high-resolution dynamics information about various protein regions is important for understanding protein function. Although AlphaFold2 has neither been designed nor trained to predict protein dynamics, it is shown here how the information returned by AlphaFold2 can be used to predict dynamic protein regions at the individual residue level. The approach, which is termed cdsAF2,...
Puyi Ma

Differential metabolism between biofilm and suspended Pseudomonas aeruginosa cultures in bovine synovial fluid by 2D NMR-based metabolomics

3 months 2 weeks ago
Total joint arthroplasty is a common surgical procedure resulting in improved quality of life; however, a leading cause of surgery failure is infection. Periprosthetic joint infections often involve biofilms, making treatment challenging. The metabolic state of pathogens in the joint space and mechanism of their tolerance to antibiotics and host defenses are not well understood. Thus, there is a critical need for increased understanding of the physiological state of pathogens in the joint space...
Abigail Leggett

NOAH-(<sup>15</sup>N/<sup>13</sup>C)-CEST NMR supersequence for dynamics studies of biomolecules

6 months ago
An NMR supersequence is introduced for the rapid acquisition of ^(15)N-CEST and methyl-^(13)C-CEST experiments in the same pulse sequence for applications to proteins. The high sensitivity and accuracy allows the simultaneous quantitative characterization of backbone and side-chain dynamics on the millisecond timescale ideal for routine screening for alternative protein states.
Rodrigo Cabrera Allpas

COLMARq: A Web Server for 2D NMR Peak Picking and Quantitative Comparative Analysis of Cohorts of Metabolomics Samples

7 months 3 weeks ago
Highly quantitative metabolomics studies of complex biological mixtures are facilitated by the resolution enhancement afforded by 2D NMR spectra such as 2D ^(13)C-¹H HSQC spectra. Here, we describe a new public web server, COLMARq, for the semi-automated analysis of sets of 2D HSQC spectra of cohorts of samples. The workflow of COLMARq includes automated peak picking using the deep neural network DEEP Picker, quantitative cross-peak volume extraction by numerical fitting using Voigt Fitter, the...
Da-Wei Li

Fundamental and practical aspects of machine learning for the peak picking of biomolecular NMR spectra

9 months 3 weeks ago
Rapid progress in machine learning offers new opportunities for the automated analysis of multidimensional NMR spectra ranging from protein NMR to metabolomics applications. Most recently, it has been demonstrated how deep neural networks (DNN) designed for spectral peak picking are capable of deconvoluting highly crowded NMR spectra rivaling the facilities of human experts. Superior DNN-based peak picking is one of a series of critical steps during NMR spectral processing, analysis, and...
Da-Wei Li

Cadaverine Is a Switch in the Lysine Degradation Pathway in <em>Pseudomonas aeruginosa</em> Biofilm Identified by Untargeted Metabolomics

10 months 3 weeks ago
There is a critical need to accurately diagnose, prevent, and treat biofilms in humans. The biofilm forming P. aeruginosa bacteria can cause acute and chronic infections, which are difficult to treat due to their ability to evade host defenses along with an inherent antibiotic-tolerance. Using an untargeted NMR-based metabolomics approach, we identified statistically significant differences in 52 metabolites between P. aeruginosa grown in the planktonic and lawn biofilm states. Among them, the...
Abigail Leggett

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

1 year 4 months 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 year 5 months 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

1 year 6 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

1 year 7 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

1 year 9 months 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

2 years 2 months 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, <sup>1</sup>H-<sup>13</sup>C HSQC NMR, and Thiolysis-HPLC-DAD

2 years 2 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

2 years 3 months 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-[10.4.0.0<sup>2,7</sup>]hexa-deca-1(12),2,4,6,13,15-hexa-ene dibromide monohydrate

2 years 4 months 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

2 years 4 months 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

2 years 8 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

3 years 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

3 years 4 months 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

3 years 5 months 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
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