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	[NMR paper] Integrative Modeling of Protein-Polypeptide Complexes by Bayesian Model Selection using AlphaFold and NMR Chemical Shift Perturbation Data Integrative Modeling of Protein-Polypeptide Complexes by Bayesian Model Selection using AlphaFold and NMR Chemical Shift Perturbation Data Protein-polypeptide interactions, including those involving intrinsically-disordered peptides and intrinsically-disordered regions of protein binding partners, are crucial for many biological functions. However, experimental structure determination of protein-peptide complexes can be challenging. Computational methods, while promising, generally require experimental data for validation and refinement. Here we present CSP_Rank, an integrated modeling... nmrlearner	Yesterday 11:40 PM by nmrlearner	0	4	Journal club
	[NMR paper] Characterizing the Monomer-Dimer Equilibrium of UbcH8/Ube2L6: A Combined SAXS and NMR Study Characterizing the Monomer-Dimer Equilibrium of UbcH8/Ube2L6: A Combined SAXS and NMR Study Interferon-stimulated gene-15 (ISG15) is an interferon-induced protein with two ubiquitin-like (Ubl) domains linked by a short peptide chain and is a conjugated protein of the ISGylation system. Similar to ubiquitin and other Ubls, ISG15 is ligated to its target proteins through a series of E1, E2, and E3 enzymes known as Uba7, Ube2L6/UbcH8, and HERC5, respectively. Ube2L6/UbcH8 plays a central role in ISGylation, underscoring it as an important drug target for boosting innate antiviral... More... nmrlearner	Yesterday 11:40 PM by nmrlearner	0	3	Journal club
	[NMR paper] Insights into the molecular interactions between urease subunit gamma from MRSA and drugs: an integrative approach by STD-NMR and molecular docking studies Insights into the molecular interactions between urease subunit gamma from MRSA and drugs: an integrative approach by STD-NMR and molecular docking studies Staphylococcus aureus, an important human pathogen, is developing resistance against a wide range of antibiotics. The antibiotic resistance in S. aureus has created the need to identify new drug targets, and to develop new drugs candidates. In the current study, urease subunit gamma from Methicillin Resistant Staphylococcus aureus (MRSA 252) was studied as a potential drug target, through protein-ligand interactions. Urease is the main... nmrlearner	Yesterday 11:40 PM by nmrlearner	0	5	Journal club
	[NMR paper] Rapid Characterization of Structural and Behavioral Changes of Therapeutic Proteins by Relaxation and Diffusion (1)H-SOFAST NMR Experiments Rapid Characterization of Structural and Behavioral Changes of Therapeutic Proteins by Relaxation and Diffusion (1)H-SOFAST NMR Experiments Biologic drugs have emerged as a rapidly expanding and important modality, offering promising therapeutic solutions by interacting with previously "undruggable" targets, thus significantly expanding the range of modern pharmaceutical applications. However, the inherent complexity of these drugs also introduces liabilities and poses challenges in their development, necessitating efficient screening methods to evaluate the structural stability and... nmrlearner	Yesterday 11:40 PM by nmrlearner	0	3	Journal club
	[NMR paper] Cryogenic probe technology enables multidimensional solid-state NMR of the stratum corneum without isotope labeling Cryogenic probe technology enables multidimensional solid-state NMR of the stratum corneum without isotope labeling Solid-state NMR has great potential for investigating molecular structure, dynamics, and organization of the stratum corneum, the outer 10-20 ?m of the skin, but is hampered by the unfeasibility of isotope labelling as generally required to reach sufficient signal-to-noise ratio for the more informative multidimensional NMR techniques. In this preliminary study of pig stratum corneum at 35 °C and water-free conditions, we demonstrate that cryogenic probe technology offers... nmrlearner	Yesterday 11:40 PM by nmrlearner	0	8	Journal club
	[NMR paper] Probing substrate binding inside a paramagnetic cavity: a NMR spectroscopy toolbox for combined experimental and theoretical investigation Probing substrate binding inside a paramagnetic cavity: a NMR spectroscopy toolbox for combined experimental and theoretical investigation Protein cavities often rely on the paramagnetic metal present in their active site in order to catalyse various chemical transformations in biology. The selective detection and identification of the substrate is of fundamental importance in environmental monitoring and biological studies. Herein, a covalently linked Fe(iii)porphyrin dimer-based paramagnetic sensory cavity has been devised for the accurate detection and simultaneous identification of... nmrlearner	Yesterday 11:40 PM by nmrlearner	0	7	Journal club
	[NMR paper] NMR assignment of the conserved bacterial DNA replication protein DnaA domain IV NMR assignment of the conserved bacterial DNA replication protein DnaA domain IV Chromosomal replication is a ubiquitous and essential cellular process. In bacteria, the master replication initiator DnaA plays a key role in promoting an open complex at the origin (oriC) and recruiting helicase in a tightly regulated process. The C-terminal domain IV specifically recognises consensus sequences of double-stranded DNA in oriC, termed DnaA-boxes, thereby facilitating the initial engagement of DnaA to oriC. Here, we report the ^(13)C? and backbone ¹H, ^(15)N, and ^(13)C chemical... More... nmrlearner	Yesterday 11:40 PM by nmrlearner	0	6	Journal club
	[NMR paper] Structural changes of Natronomonas pharaonis halorhodopsin in its late photocycle revealed by solid-state NMR spectroscopy Structural changes of Natronomonas pharaonis halorhodopsin in its late photocycle revealed by solid-state NMR spectroscopy Natronomonas pharaonis halorhodopsin (NpHR) is a light-driven Cl^(-) inward pump that is widely used as an optogenetic tool. Although NpHR is previously extensively studied, its Cl^(-) uptake process is not well understood from the protein structure perspective, mainly because in crystalline lattice, it has been difficult to analyze the structural changes associated with the Cl^(-) uptake process. In this study, we used solid-state NMR to analyze NpHR both in the... nmrlearner	Yesterday 11:40 PM by nmrlearner	0	5	Journal club
	[NMR paper] Exploring the dynamics and interactions of the N-myc transactivation domain through solution NMR Exploring the dynamics and interactions of the N-myc transactivation domain through solution NMR Myc proteins are transcription factors crucial for cell proliferation. They have a C-terminal domain that mediates Max and DNA binding, and an N-terminal disordered region culminating in the transactivation domain (TAD). The TAD participates in many protein-protein interactions, notably with kinases that promote stability (Aurora-A) or degradation (ERK1, GSK3) via the ubiquitin-proteasome system. We probed the structure, dynamics and interactions of N-myc TAD using nuclear magnetic resonance...... nmrlearner	Yesterday 11:40 PM by nmrlearner	0	4	Journal club
	[NMR paper] Disentangling the Complexity in Protein Complexes Using Complementary Isotope-Labeling and Multiple-Receiver NMR Spectroscopy Disentangling the Complexity in Protein Complexes Using Complementary Isotope-Labeling and Multiple-Receiver NMR Spectroscopy Intrinsically disordered proteins are abundant in eukaryotic systems, but they remain largely elusive pharmacological targets. NMR spectroscopy proved to be a suitable method to study these proteins and their interaction with one another or with drug candidates. Although NMR can give atomistic information about these interplays, molecular complexity due to severe spectral overlap, limited sample stability, and quantity remain an issue and hamper widespread... nmrlearner	Yesterday 11:40 PM by nmrlearner	0	4	Journal club
	[NMR paper] Evaluating protocols for reproducible targeted metabolomics by NMR Evaluating protocols for reproducible targeted metabolomics by NMR Metabolomics aims to study the downstream effects of variables like diet, environment, or disease on a given biological system. However, inconsistencies in sample preparation, data acquisition/processing protocols lead to reproducibility and accuracy concerns. A systematic study was conducted to assess how sample preparation methods and data analysis platforms affect metabolite susceptibility. A targeted panel of 25 metabolites was evaluated in 69 clinical metabolomics samples prepared following... More... nmrlearner	Yesterday 11:40 PM by nmrlearner	0	4	Journal club
	[NMR paper] Ultrafast T(1)-T(1rho) NMR for Correlating Different Motional Regimes of Molecules Ultrafast T(1)-T(1rho) NMR for Correlating Different Motional Regimes of Molecules Nuclear magnetic resonance (NMR) relaxation times provide detailed information about molecular motions and local chemical environments. Longitudinal T(1) relaxation time is most often sensitive to relatively fast, nano- to picosecond ranges of molecular motion. Rotating frame T(1?) relaxation time reflects a much slower, micro- to millisecond range of motion, and the motional regime can be tuned by changing spin-lock field strength. Conventional methods for measuring T(1) and T(1?) relaxation... More... nmrlearner	Yesterday 11:40 PM by nmrlearner	0	4	Journal club
	[NMR paper] Optimization of (15)N-(13)C double-resonance NMR experiments under low temperature magic angle spinning dynamic nuclear polarization conditions Optimization of (15)N-(13)C double-resonance NMR experiments under low temperature magic angle spinning dynamic nuclear polarization conditions Dynamic nuclear polarization (DNP) enhanced magic angle spinning (MAS) solid-state NMR carried out at 25 K enables rapid acquisition of multi-dimensional ^(13)C-^(15)N correlation spectra for protein structure studies and resonance assignment. Under commonly used DNP conditions, solvent deuteration reduces ¹H-^(15)N cross polarization (CP) efficiencies, necessitates more careful optimization, and requires longer high-power ^(15)N radio-frequency... nmrlearner	Yesterday 11:40 PM by nmrlearner	0	4	Journal club
	[NMR paper] High-Sensitivity Analysis of Native Bacterial Biofilms Using Dynamic Nuclear Polarization-Enhanced Solid-State NMR High-Sensitivity Analysis of Native Bacterial Biofilms Using Dynamic Nuclear Polarization-Enhanced Solid-State NMR Bacterial biofilms cause persistent infections that are difficult to treat and contribute greatly to antimicrobial resistance. However, high-resolution structural information on native bacterial biofilms remain very limited. This limitation is primarily due to methodological constraints associated with analyzing complex native samples. Although solid-state NMR (ssNMR) is a promising method in this regard, its conventional applications typically suffer from sensitivity... nmrlearner	Yesterday 11:40 PM by nmrlearner	0	4	Journal club
	[NMR paper] Investigating Different Dynamic pHP1alpha States in Their KCl-Mediated Liquid-Liquid Phase Separation (LLPS) Using Solid-State NMR (SSNMR) and Molecular Dynamic (MD) Simulations Investigating Different Dynamic pHP1alpha States in Their KCl-Mediated Liquid-Liquid Phase Separation (LLPS) Using Solid-State NMR (SSNMR) and Molecular Dynamic (MD) Simulations Chromatin phase separation is dynamically regulated by many factors, such as post-translational modifications and effector proteins, and plays a critical role in genomic activities. The liquid-liquid phase separation (LLPS) of chromatin and/or effector proteins has been observed both in vitro and in vivo. However, the underlying mechanisms are largely unknown, and elucidating the physicochemical properties of the... nmrlearner	Yesterday 11:40 PM by nmrlearner	0	4	Journal club
	[NMR paper] Characterization of conformational states of the homodimeric enzyme fluoroacetate dehalogenase by (19)F-(13)C two-dimensional NMR Characterization of conformational states of the homodimeric enzyme fluoroacetate dehalogenase by (19)F-(13)C two-dimensional NMR Tryptophan plays a critical role in proteins by contributing to stability, allostery, and catalysis. Using fluorine (^(19)F) nuclear magnetic resonance (NMR), protein conformational dynamics and structure-activity relationships (SARs) can be studied via fluorotryptophan reporters. Tryptophan analogs such as 4-, 5-, 6-, or 7-fluorotryptophan can be routinely incorporated into proteins during heterologous expression by arresting endogenous tryptophan biosynthesis.... nmrlearner	Yesterday 11:40 PM by nmrlearner	0	27	Journal club
	New Tools Provide New Insights in NMR Studies of Protein Dynamics - Science New Tools Provide New Insights in NMR Studies of Protein Dynamics - Science New Tools Provide New Insights in NMR Studies of Protein Dynamics Science Read here nmrlearner	Yesterday 11:34 AM by nmrlearner	0	9	Online News
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