This readme.txt file was generated on 2025-10-06 by Cristina Olivieri Recommended citation for the data: Olivieri, Cristina; Veliparambil Subrahmanian, Manu; Veglia, Gianluigi; De Simone, Alfonso; Biancaniello, Carmen. (2025). PKA targets transient states of RKIP: NMR and MD Data. Retrieved from the Data Repository for the University of Minnesota (DRUM), https://doi.org/10.13020/53fr-nn58. GENERAL INFORMATION ------------------- 1. Title of Dataset: PKA targets transient states of RKIP: NMR and MD Data 2. Author Information Principal Investigator Contact Information Name: Gianluigi Veglia Institution: University of Minnesota, BMBB Department Address: 321 Church Street SE, Minneapolis, MN, 55455 Email: vegli001@umn.edu ORCID: https://orcid.org/0000-0002-2795-6964 Associate or Co-investigator Contact Information Name: Cristina Olivieri Institution: University of Minnesota, BMBB Department Address: 321 Church Street SE, Minneapolis, MN, 55455 Email: colivier@umn.edu ORCID: https://orcid.org/0000-0001-6957-6743 Associate or Co-investigator Contact Information Name: Manu Veliparambil Subrahmanian Institution: University of Minnesota, BMBB Department Address: 321 Church Street SE, Minneapolis, MN, 55455 Email: mvelip@umn.edu ORCID: https://orcid.org/0000-0002-1374-2797 Associate or Co-investigator Contact Information Name: Alfonso De Simone Institution: University of Naples Federico II, Department of Pharmacy Address: Via Domenico Montesano, 49, 80131 Napoli NA Email: alfonso.desimone@unina.it ORCID: https://orcid.org/0000-0001-8789-9546 Associate or Co-investigator Contact Information Name: Bancaniello Carmen Institution: University of Naples Federico II, Department of Pharmacy Address: Via Domenico Montesano, 49, 80131 Napoli NA Email: carmen.biancaniello@unina.it ORCID: 3. Date published or finalized for release: 26 September 2025 4. Date of data collection (single date, range, approximate date) NMR data: from 2025-06-01 to 2025-07-31 MD simulation: from 2024-09-01 to 2025-05-31 5. Geographic location of data collection (where was data collected?): NMR data: Minnesota NMR Center, University of Minnesota MD data: Department of Pharmacy, University of Naples Federico II 6. Information about funding sources that supported the collection of the data: National Institute of Health (NIH), CA290129 to Gianluigi Veglia Italian Ministry for University and Research, FARE to Alfonso De Simone 7. Overview of the data (abstract): This repository provides molecular dynamics (MD) datasets, ensembles from chemical shift-restrained replica-averaged restrained molecular dynamics (CS-RARMD) simulation and fast dynamic NMR data associated with the study “Protein Kinase A Phosphorylates a Conformationally High-Energy State of Raf Kinase Inhibitory Protein.” The stored datasets include CS-RARMD simulations of Raf Kinase Inhibitory Protein (RKIP) and experimental backbone relaxation data (T₁, T₂, and heteronuclear NOE) that capture the fast-timescale dynamics of the protein. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/ 2. Links to publications that cite or use the data: Olivieri, C., Biancaniello, C., Manu, V. S., Walters, M., Masterson, L., Rosner, M. R., Simone, A. D., & Veglia, G. (2025). Protein Kinase A Phosphorylates a Conformationally High-Energy State of Raf Kinase Inhibitory Protein. Journal of Molecular Biology, Article 169466. https://doi.org/10.1016/j.jmb.2025.169466 https://www.sciencedirect.com/science/article/pii/S0022283625005327?via%3Dihub#ak005 3. Was data derived from another source? If yes, list source(s): 4. Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/policies/#drum-terms-of-use --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. AMBER-RAMD_CSI-restrained_Ensemble 1. Filename: amber_0_confout0.gro Short description: GROMACS coordinate file for the starting conformation of replica 0. 2. Filename: amber_0_confout1.gro Short description: GROMACS coordinate file for the starting conformation of replica 1. 3. Filename: amber_0_confou2.gro Short description: GROMACS coordinate file for the starting conformation of replica 2. 4. Filename: amber_0_confout1.gro Short description: GROMACS coordinate file for the starting conformation of replica 3. 5. Filename: amber_ensemble_including_models_from_the_sampling_phase_of_all_replicas.xtc Short description: Stripped AMBER-ensemble (no water or neutralizing ions) of models extracted from the last 200 ps (each 10 ps) of 100 cycles of each replica. GROMACS trajectory. 6. Filename: GROMACS configuration file for CS restrained MD sim with AMBER ff Short description: GROMACS configuration files for AMBER-RAMD simulations. 7. Filename: ssnmr Short description: GROMACS restraint files with experimental CS used for AMBER-RAMD CSI-restrained simulations. B. CHARMM-RAMD_CSI-restrained_Ensemble 1. Filename: charmm_0_confout0.gro Short description: GROMACS coordinate file for the starting conformation of replica 0. 2. Filename: charmm_0_confout1.gro Short description: GROMACS coordinate file for the starting conformation of replica 1. 3. Filename: charmm_0_confout2.gro Short description: GROMACS coordinate file for the starting conformation of replica 2. 4. Filename: charmm_0_confout1.gro Short description: GROMACS coordinate file for the starting conformation of replica 3. 5. Filename: charmm_ensemble_including_models_from_the_sampling_phase_of_all_replicas.xtc Short description: Stripped AMBER-ensemble (no water or neutralizing ions) of models extracted from the last 200 ps (each 10 ps) of 100 cycles of each replica. GROMACS trajectory. 6. Filename: GROMACS configuration file for CS restrained MD sim with CHARMM ff Short description: GROMACS configuration files for CHARMM-RAMD simulations. 7. Filename: ssnmr Short description: GROMACS restraint files with experimental CS used for CHARMM-RAMD CSI-restrained simulations. C. CHARMM-restrained_multiframe_representative_models_of_structural_basins (This directory contains multi-frame PDB files representing the three main conformational basins sampled during CHARMM CSI-restrained simulations of RKIP. 1. Filename: basin1_clustered_representative_models_multiframe.pdb Short description: Models belonging to cluster 1 (most populated basin). 2. Filename: basin2_clustered_representative_models_multiframe.pdb Short description: Models belonging to cluster 2. 3. Filename: basin3_clustered_representative_models_multiframe.pdb Short description: Models belonging to cluster 3. D. Starting_models_for_protein-protein_docking_with_Haddock 1. Filename: Closed_PKA-C.pdb Short description: model of PKA-C in closed state. 2. Filename: Open_PKA-C.pdb Short description: model of PKA-C in open state. 3. Filename: RKIP_high_energy_state_from_CHARMM-RAMD_ensamble.pdb Short description: model of RKIP in high energy state sampled from CHARMM-CSI RAMD simulations. E. CHARMM-MD of closed_PKA-C(ATP+MG)_with_high_energy_state_of_RKIP 1. Filename: Closed_PKA(ATP+MG)_with_high_energy_state_of_RKIP_400ns_traj.xtc Short description: Stripped CHARMM-ensemble (no water or neutralizing ions) of PKA-C (in closed state + ATP + MG) in complex with the high energy state of RKIP. GROMACS trajectory. 2. Filename: Closed_PKA(ATP+MG)_with_high_energy_state_of_RKIP_frame0.pdb Short description: GROMACS coordinate file for stripped ensemble (no water or neutralizing ions) of PKA-C (in closed state + ATP + MG) in complex with the high energy state of RKIP. 3. Filename: GROMACS configuration file Short description: GROMACS configuration file for CHARMM-MD of PKA-C/RKIP complex. 4. Filename: Haddock_best_docked_complex_PKA-C(closed state)-RKIP(high energy state).pdb Short description: pdb file of the best-scored PKA-C(closed-state)/RKIP(high energy state) complex obtained with HADDOCK web-server. F. CHARMM-MD_of_open_PKA-C_with_high_energy_state_of_RKIP 1. Filename: Open_PKA-C_with_high_energy_state_of_RKIP_400ns_traj.xtc Short description: Stripped CHARMM-ensemble (no water or neutralizing ions) of PKA-C (in open state) in complex with the high energy state of RKIP. GROMACS trajectory. 2. Filename: Open_PKA-C_with_high_energy_state_of_RKIP_frame0.pdb Short description: GROMACS coordinate file for stripped ensemble (no water or neutralizing ions) of PKA-C (in open state) in complex with the high energy state of RKIP. 3. Filename: GROMACS configuration file Short description: GROMACS configuration file for CHARMM-MD of PKA-C/RKIP complex. 4. Filename: Haddock_best_docked_complex_PKA-C(open state)-RKIP(high energy state).pdb Short description: pdb file of the best-scored PKA-C(open-state)/RKIP(high energy state) complex obtained with HADDOCK web-server. G. T1-T2_HX-NOE relaxation 1. Filename: RKIP_ModelFree_Data.docx Short description: Table where are reported the value of T1, T2 (expressed in frequency R1 and R2 respectively), HX-NOE values and derived order parameters (S2) with their error, 2. Filename: ModelFreeMethods.docx Short description: extensive explanation of the Model Free analysis used to generate the values of R1, R2, HX-NOE and S2 reported in file 1 -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: For the collection of the directory A,B,C,D,E,F and G a detailed description of the simulation setup is reported in the methods section of the publication 2. Methods for processing the data: For directory A,B,C,D,E, and F detailed description of data processing is reported in the methods section of the publication For directory G, the description of the procession and data analysis is described in the file ModelFreeMethods.docx 3. Instrument- or software-specific information needed to interpret the data: All the NMR data were acquired on 850 MHz spectrometer equipped with a cryogenic probe (CP TCI 850S4 H-C/N-D-05 Z) The .mdp files contain the molecular dynamics (MD) simulation parameters used in GROMACS; they can be opened and edited with this program, or viewed with any text editor such as Notepad or TextEdit (on Mac). The .xtc files are trajectory data derived from MD simulations and can be opened using software such as VMD, GROMACS, or, in some cases, MATLAB. The .pdb files can also be viewed in a text editor to inspect the numeric coordinates of the 3D structure, or alternatively, with visualization software such as PyMOL or Chimera (UCSF). 4. People involved with sample collection, processing, analysis and/or submission: Carmen Biancaniello (CA) and Alfonso De Simone (ADS) setup the MD simulation. CA run the simulation and performed the analysis and interpretation of the results. ADS supervised the analysis and helped with data interpretation Manu Veliparambil Subrahmanian (MVS) and Gianluigi Veglia (GV) prepared the sample and performed the NMR analysis. MVS performed data processing and NMR relaxation parameters calculation. Cristina Olivieri (CO) and GV participated in data interpretation. CO collected the data from CA and MVS and submitted the data ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: RKIP_ModelFree_Data ----------------------------------------- This is not applicable to directory A, B, C, D, E, and F. They are NMR simulation. Directory G:T1-T2_HX-NOE relaxation 1. Number of variables: 14 2. Number of cases/rows: 188 3. Missing data codes: NA 4. Variable List A. Name: residue Description: Amino acid composing RKIP primary sequence, identified as a single letter and residue number position B. Name: model Description: Model-free analysis is a method used in NMR relaxation studies to describe internal motions of molecules without assuming a specific motional model (like harmonic motion or diffusion in a potential).In the literature (Lipari & Szabo 1982; Clore et al. 1990), there are five standard model-free models, each corresponding to different levels of motional complexity. This column reports in which model the residues was fitted and therefore the motion associated to each residue. Below is reported table with a brief explamnation of each model | Model | Parameters Used | When Used | Description | | ------- | --------------- | ----------------------------------- | ---------------------------------------------------- | | Model 1 | S² only | Very rigid sites | No internal motion (only global tumbling). | | Model 2 | S², τₑ | Simple fast internal motion | Internal motion on ps–ns timescale. | | Model 3 | S², Rₑₓ | Rigid but affected by slow exchange | Adds µs–ms exchange to model 1. | | Model 4 | S², τₑ, Rₑₓ | Both fast and slow motion | Combines fast internal motion and chemical exchange. | | Model 5 | S_f², S_s², τₛ | Complex multi-timescale motion | Two distinct internal motions (fast + slow). | C. Name: R1 Description: value of R1 relaxation expressed in Hz, calculated using the ModelFree analysis D. Name: R1_err Description: The error corresponding to the R1 value E. Name: R2 Description: value of R2 relaxation expressed in Hz, calculated using the ModelFree analysis F. Name: R2_err Description: The error corresponding to the R2 value G. Name: NOE Description: value of Heteronuclear [¹H, ¹⁵N] Nuclear Overhauser Effects (NOEs) (HX-NOE) calculated for each protein residue H. Name: NOE_err Description: The error corresponding to the HX-NOE value I. Name: S2 Description: Value of order parameters (S2) calculated for each residue L. Name: S2_err Description: The error corresponding to the S2 value M. Name: te Description: value of the effective internal correlation time (tau-e) N. Name: te_err Description: The error corresponding to the te value O. Name: NOE_err Description: value of Rex (the chemical exchange contribution to the transverse relaxation rate R₂) for each reside P. Name: Rex_err Description:The error corresponding to the Rex value --------------------- FILE TREE --------------------- +---A) AMBER-RAMD_CSI-restrained_Ensemble | amber_0_confout0.gro | amber_0_confout1.gro | amber_0_confout2.gro | amber_0_confout3.gro | amber_ensemble_including_models_from_the_sampling_phase_of_all_replicas.xtc | GROMACS configuration file for CS restrained MD sim with AMBER ff.mdp | ssnmr | +---B) CHARMM-RAMD_CSI-restrained_Ensemble | charmm_0_confout0.gro | charmm_0_confout1.gro | charmm_0_confout2.gro | charmm_0_confout3.gro | charmm_ensemble_including_models_from_the_sampling_phase_of_all_replicas.xtc | GROMACS configuration file for CS restrained MD sim with CHARMM ff.mdp | ssnmr | +---C) CHARMM-restrained_multiframe_representative_models_of_structural_basins | basin1_clustered_representative_models_multiframe.pdb | basin2_clustered_representative_models_multiframe.pdb | basin3_clustered_represetnative_models_multiframe.pdb | +---D) Starting_models_for_protein-protein_docking_with_Haddock | Closed_PKA-C.pdb | Open_PKA-C.pdb | RKIP_high_energy_state_from_CHARMM-RAMD_ensamble.PDB | +---E) CHARMM-MD_of_closed_PKA-C(ATP+MG)_with_high_energy_state_of_RKIP | Closed_PKA(ATP+MG)_with_high_energy_state_of_RKIP_400ns_traj.xtc | Closed_PKA(ATP+MG)_with_high_energy_state_of_RKIP_frame0.pdb | GROMACS configuration file.mdp | Haddock_best_docked_complex_PKA-C(closed state)-RKIP(high energy state).pdb | +---F) CHARMM-MD_of_open_PKA-C_with_high_energy_state_of_RKIP | Haddock_best_docked_complex_PKA-C(open state)-RKIP(high energy state).pdb | Open_PKA-C_with_high_energy_state_of_RKIP_400ns_traj.xtc | Open_PKA-C_with_high_energy_state_of_RKIP_frame0.pdb | \---G)T1-T2_HX-NOE relaxation dispersion ModelFreeMethods.docx RKIP_ModelFree_Data.docx