Browsing by Author "Veglia, Gianluigi"

Now showing 1 - 11 of 11
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    Binding interaction between PKA-C and RKIP and its mutant P74L
    (2022-01-03) Olivieri, Cristina; Veglia, Gianluigi; vegli001@umn.edu; Veglia, Gianluigi; University of Minnesota, BMBB Department, Structural Biology Division, Professor Gianluigi Veglia Lab
    Kinetical and structural characterization of the interaction between the RAF kinase inhibitor (RKIP) and the cAMP-dependent protein kinase A (PKA-C) by interferometry and nuclear magnetic resonance (NMR) spectroscopy analysis. Together with the analysis performed by Dr. Marsha Rosner's laboratory (University of Chicago), these studies are part of a paper that has been sent to the PNAS journal.
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    Changes in protein kinase A conformational entropy by ATP-competitive inhibitors
    (2022-05-09) Olivieri, Cristina; Veglia, Gianluigi; vegli001@umn.edu; Veglia, Gianluigi; University of Minnesota, BMBB Department, Structural Biology Division, Professor Gianluigi Veglia Lab
    NMR characterization of the structural and dynamic changes of the catalytic subunit of cAMP-dependent protein kinase A (PKA-C) in complex with balanol and H89, two ATP-competitive inhibitors. This study aims to unveil how these two inhibitors affect the PKA-C structure and dynamics and how these changes govern the enzyme binding cooperativity and conformational dynamic. These data are part of a paper that has been sent to a peer-review paper.
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    Computational Modeling of Protein Kinase A and Comparison with Nuclear Magnetic Resonance Data
    (2009-10-07) Shi, Lei; Veglia, Gianluigi
    Protein phosphorylation is fundamental in the modulation of myocardial contractility. Sarcoendoplasmic reticulum Ca2+ ATPase(SERCA) removes cytosolic Ca2+ to initiate relaxation, but the regulatory protein, phospholamban(PLN), decreases SERCA’s affinity for free Ca2+. Phosphorylation of PLN by Protein Kinase A (PKA) induces a relief of inhibition on SERCA and augments the rate of SERCA Ca2+ uptake. Here, we studied the interaction between PKA and PLN by nuclear magnetic resonance (NMR), computational docking and molecular dynamics (MD) simulations. Comparative simulations of PKA apo, binary and ternary states were performed, which provided molecular details to understand the mechanism of PKA substrate recognition.
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    Data for AI-designed NMR spectroscopy RF pulses for fast acquisition at high and ultra-high magnetic fields
    (2023-06-15) Veliparambil Subrahmanian, Manu; Veglia, Gianluigi; vegli001@umn.edu; Veglia, Gianluigi; Veglia Lab
    The data contains RF shapes for NMR spectroscopy designed using an evolutionary algorithm and artificial intelligence. These new RF pulses cover significantly broader bandwidths for 1H and 15N nuclei and allow rapid spectra acquisition. We also re-engineered the basic transverse relaxation optimized spectroscopy experiment (RAPID-TROSY) which can enhance the spectral sensitivity of well-folded proteins up to 180 kDa molecular weight.
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    Enhanced Sensitivity of 1H,1H Nuclear Overhauser Effects using Water Irradiation Devoid Pulses
    (2022-09-26) Veliparambil Subrahmanian, Manu; Veglia, Gianluigi; vegli001@umn.edu; Veglia, Gianluigi; Veglia Lab
    The nuclear Overhauser effect (NOE) is one of NMR spectroscopy's most important and versatile parameters. NOE is routinely utilized to determine the structures of medium-to-large size biomolecules and characterize protein-protein, protein-RNA, protein-DNA, and protein-ligand inter-actions. Since NMR studies of biomacromolecules are carried out in aqueous solutions, [1H,1H] NOESY pulse sequences must incorporate water suppression schemes to reduce the water signal that dominates 1H detected experiments. These pulse schemes are also designed to minimize signal intensity losses due to unwanted polarization exchange between water and labile protons. However, at high- and ultra-high magnetic fields, the excitation of the water signal during the execution of the NOESY pulse sequences may cause significant attenuation of NOE cross-peak intensities. Using an evolutionary algorithm coupled with artificial intelligence, we recently designed high-fidelity pulses [Water irrAdiation DEvoid (WADE) pulses] that elude water excitation and irradiate broader bandwidths relative to commonly used pulses. Here, we demonstrate that WADE pulses implemented into the 2D [1H,1H] NOESY experiments increase the intensity of the NOE cross-peaks for labile and, to a lesser extent, non-exchangeable protons. We applied the new [1H,1H] WADE-NOESY pulse sequence to two well-folded medium-size proteins, i.e., the K48C mutant of ubiquitin and the Raf kinase inhibitor protein (RKIP). The new pulse sequence shows a net increase of the NOE intensities varying from 30 to 170% compared to the commonly used NOESY experiments with excitation sculpting sequence as a water suppression element. The new WADE pulses can be easily implemented into 2D and 3D homo- and hetero-nuclear NOESY pulse sequences.
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    Ensembles from dynamic refinement of non-phosphorylated and phosphorylated phospholamban-SERCA complexes
    (2021-01-22) Weber, Daniel K; Sanz-Hernández, Máximo; Uddigiri, Venkateswara Reddy; Wang, Songlin; Larsen, Erik K; Gopinath, Tata; Gustavsson, Martin; Cornea, Razvan L; Thomas, David D; De Simone, Alfonso; Veglia, Gianluigi; vegli001@umn.edu; Veglia, Gianluigi; Veglia Lab
    Analysis, setup and ensembles of the dynamic refinement of phospholamban-SERCA complexes in the calcium-free E2 state. Includes trajectory files, analytic scripts, restraint files, setup files, simulation code, raw data (including OS-ssNMR data) and processed data used for the associated citations as per transparent reporting requirements.
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    GENETICS-AI pulses
    (2022-06-16) Veliparambil Subrahmanian, Manu; Veglia, Gianluigi; vegli001@umn.edu; Veglia, Gianluigi; Gianluigi Veglia Lab
    New RF shapes for applications in Nuclear magnetic resonance. These shapes are in BRUKER format and can be directly used in pulse sequences for biomolecular NMR experiments. We have generated these pulses using a new algorithm called 'GENETICS-AI', which is a combination of an evolutionary algorithm and artificial intelligence. The main advantage of GENETICS-AI is the customizability of RF shape characteristics such as pulse operation, bandwidth, RF inhomogeneity compensation level and fidelity of the operation. The submitted files include broadband universal π/2 and π pulses.
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    NMR Pulse Sequences and RF Shapes for RAPID-HMQC
    (2024-02-01) Veliparambil Subrahmanian, Manu; Veglia, Gianluigi; vegli001@umn.edu; Veglia, Gianluigi; Veglia Lab
    The dataset includes radio frequency (RF) shapes and pulse sequences for the RAPID-HMQC nuclear magnetic resonance (NMR) experiment, which were developed using an evolutionary algorithm and artificial intelligence. These novel RF pulses significantly expand the bandwidths for 1H and 15N nuclei and enable the rapid acquisition of spectra.
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    Proton and amide chemical shift list files of wild-type cAMP-dependent protein kinase a (PKA-C) and the chimeric mutant (PKA-JC) and MATLab scripts for the chemical shift analysis
    (2020-11-23) Veglia, Gianluigi; Olivieri, Cristina; Walker, Caitlin; Veliparambil Subrahmanian, Manu; vegli001@umn.edu; Veglia, Gianluigi; University of Minnesota, BMBB Department, Structural Biology Division, Professor Gianluigi Veglia Lab
    Proton and amide chemical shift list files of wild-type cAMP-dependent protein kinase a (PKA-C) and the chimeric mutant (PKA-JC) and MatLab scripts used for the CHESCA and CONCISE analysis. The chemical shift lists were obtained using standard NMR experiments (1H-15N -TROSY-HSQC). The MatLab scripts were used for the CHESCA and CONCISE analysis of the amide chemical shift. These files are part of a publication on Communication biology: "Defective Internal Allosteric Network Imparts Dysfunctional ATP/Substrate Binding Cooperativity in Oncogenic Chimera of Protein Kinase A"
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    Replica-averaged orientational-restrained ensembles of DWORF and P15A-DWORF in lipid bilayers
    (2021-05-06) Uddigiri, Venkateswara Reddy; Weber, Daniel K; Wang, Songlin; Larsen, Erik K; Gopinath, Tata; De Simone, Alfonso; Robia, Seth; Veglia, Gianluigi; vegli001@umn.edu; Veglia, Gianluigi
    Replica-averaged orientational-restrained molecular dynamics (RAOR-MD) ensembles of DWORF and the DWORF-P15A mutant in lipid bilayers. Restrained to 15N chemical shift anisotropy and 1H-15N dipolar coupling data obtained from oriented sample solid-state NMR spectroscopy.
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    The role of the αC-β4 loop in regulating cooperativity interaction in Protein Kinase A
    (2024-02-19) Olivieri, Cristina; Veglia, Gianluigi; Veliparambil Subrahmanian, Manu; Wang, Yingjie; vegli001@umn.edu; Veglia, Gianluigi; Veglia Lab
    This investigation examines the cooperative modulation of Protein Kinase A (PKA) activity by ATP and substrates, with a specialized focus on the enzyme's catalytic subunit (PKA-C), utilizing NMR-restrained molecular dynamics simulations complemented by advanced Markov Model analysis. Herein, we deposit chemical shift datasets for the PKA-C mutant F100A, both in its apo form and in complex with nucleotides and inhibitors, and activity assay data providing a comprehensive insight into the enzyme's allosteric regulation mechanisms.