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[NMR paper] Initial Primer Synthesis of a DNA Primase Monitored by Real-Time NMR Spectroscopy
Mar 28, 2024 - 7:05 AM - by nmrlearner
nmrlearner's Avatar Initial Primer Synthesis of a DNA Primase Monitored by Real-Time NMR Spectroscopy

Primases are crucial enzymes for DNA replication, as they synthesize a short primer required for initiating DNA replication. We herein present time-resolved nuclear magnetic resonance (NMR) spectroscopy in solution and in the solid state to study the initial dinucleotide formation reaction of archaeal pRN1 primase. Our findings show that the helix-bundle domain (HBD) of pRN1 primase prepares the two substrates and then hands them over to the catalytic domain to initiate the reaction. By using...

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0 Replies | 4 Views
Prediction of order parameters based on protein NMR structure ensemble and machine learning
Mar 27, 2024 - 7:01 PM - by nmrlearner
nmrlearner's Avatar Prediction of order parameters based on protein NMR structure ensemble and machine learning

Abstract

The fast motions of proteins at the picosecond to nanosecond timescale, known as fast dynamics, are closely related to protein conformational entropy and rearrangement, which in turn affect catalysis, ligand binding and protein allosteric effects. The most used NMR approach to study fast protein dynamics is the model free method, which uses order parameter S2 to describe the amplitude of the internal motion of local group. However, to obtain order parameter through NMR experiments is quite complex and lengthy. In this paper, we present a machine learning approach for predicting backbone 1H-15N order parameters based on protein NMR structure ensemble. A random forest model is used to learn the relationship between order parameters and structural features. Our method achieves high accuracy in predicting backbone 1H-15N order parameters for a test dataset of 10 proteins, with a Pearson correlation coefficient of 0.817 and a root-mean-square error of 0.131.



Source: Journal of Biomolecular NMR
0 Replies | 47 Views
[NMR paper] New Vision of Cell Walls in Aspergillus fumigatus from Solid-State NMR Spectroscopy
Mar 27, 2024 - 7:01 PM - by nmrlearner
nmrlearner's Avatar New Vision of Cell Walls in Aspergillus fumigatus from Solid-State NMR Spectroscopy

The fungal cell wall plays a critical role in regulating cellular integrity and communication, and serves as a frontline defense against stress. It is also a prime target for the development of antifungal agents. The cell wall is comprised of diverse polysaccharides and proteins and poses a challenging target for high-resolution structural characterization. Recently, the solid-state nuclear magnetic resonance (ssNMR) analysis of intact Aspergillus fumigatus cells has provided atomic-level...

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0 Replies | 17 Views
[NMR paper] Prediction of order parameters based on protein NMR structure ensemble and machine learning
Mar 27, 2024 - 6:15 AM - by nmrlearner
nmrlearner's Avatar Prediction of order parameters based on protein NMR structure ensemble and machine learning

The fast motions of proteins at the picosecond to nanosecond timescale, known as fast dynamics, are closely related to protein conformational entropy and rearrangement, which in turn affect catalysis, ligand binding and protein allosteric effects. The most used NMR approach to study fast protein dynamics is the model free method, which uses order parameter S˛ to describe the amplitude of the internal motion of local group. However, to obtain order parameter through NMR experiments is quite...

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0 Replies | 56 Views
Use of 1H NMR STD, WaterLOGSY, and Langmuir monolayer techniques for characterization of drug–zein protein ... - ScienceDirect.com
Mar 26, 2024 - 5:50 PM - by nmrlearner
nmrlearner's Avatar Use of 1H NMR STD, WaterLOGSY, and Langmuir monolayer techniques for characterization of drug–zein protein ... - ScienceDirect.com

Use of 1H NMR STD, WaterLOGSY, and Langmuir monolayer techniques for characterization of drug–zein protein ... ScienceDirect.com Read here
0 Replies | 13 Views
A suite of solid-state NMR experiments to utilize orphaned magnetization for assignment of proteins using parallel high ... - ScienceDirect.com
Mar 26, 2024 - 5:50 PM - by nmrlearner
nmrlearner's Avatar A suite of solid-state NMR experiments to utilize orphaned magnetization for assignment of proteins using parallel high ... - ScienceDirect.com

A suite of solid-state NMR experiments to utilize orphaned magnetization for assignment of proteins using parallel high ... ScienceDirect.com Read here
0 Replies | 28 Views
Accessing Methyl Groups in Proteins via 1H-detected MAS Solid-state NMR Spectroscopy Employing Random ... - Nature.com
Mar 26, 2024 - 2:00 AM - by nmrlearner
nmrlearner's Avatar Accessing Methyl Groups in Proteins via 1H-detected MAS Solid-state NMR Spectroscopy Employing Random ... - Nature.com

Accessing Methyl Groups in Proteins via 1H-detected MAS Solid-state NMR Spectroscopy Employing Random ... Nature.com Read here
0 Replies | 40 Views
[NMR paper] ASAP: An automatic sequential assignment program for congested multidimensional solid state NMR spectra
Mar 25, 2024 - 1:50 PM - by nmrlearner
nmrlearner's Avatar ASAP: An automatic sequential assignment program for congested multidimensional solid state NMR spectra

Accurate signal assignments can be challenging for congested solid-state NMR (ssNMR) spectra. We describe an automatic sequential assignment program (ASAP) to partially overcome this challenge. ASAP takes three input files: the residue type assignments (RTAs) determined from the better-resolved NCACX spectrum, the full peak list of the NCOCX spectrum, and the protein sequence. It integrates our auto-residue type assignment strategy (ARTIST) with the Monte Carlo simulated annealing (MCSA)...

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0 Replies | 162 Views
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