Residual Dipolar Coupling

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Marius G Clore - One of the best experts on this subject based on the ideXlab platform.

  • xplor nih for molecular structure determination from nmr and other data sources
    Protein Science, 2018
    Co-Authors: Charles D Schwieters, Guillermo A Bermejo, Marius G Clore
    Abstract:

    Xplor-NIH is a popular software package for biomolecular structure determination from nuclear magnetic resonance (NMR) and other data sources. Here, some of Xplor-NIH's most useful data-associated energy terms are reviewed, including newer alternative options for using Residual Dipolar Coupling data in structure calculations. Further, we discuss new developments in the implementation of strict symmetry for the calculation of symmetric homo-oligomers, and in the representation of the system as an ensemble of structures to account for motional effects. Finally, the different available force fields are presented, among other Xplor-NIH capabilities. This article is protected by copyright. All rights reserved.

  • impact of phosphorylation on structure and thermodynamics of the interaction between the n terminal domain of enzyme i and the histidine phosphocarrier protein of the bacterial phosphotransferase system
    Journal of Biological Chemistry, 2008
    Co-Authors: Jeongyong Suh, Mengli Cai, Marius G Clore
    Abstract:

    Abstract The structural and thermodynamic impact of phosphorylation on the interaction of the N-terminal domain of enzyme I (EIN) and the histidine phosphocarrier protein (HPr), the two common components of all branches of the bacterial phosphotransferase system, have been examined using NMR spectroscopy and isothermal titration calorimetry. His-189 is located at the interface of the α and αβ domains of EIN, resulting in rather widespread chemical shift perturbation upon phosphorylation, in contrast to the highly localized perturbations seen for HPr, where His-15 is fully exposed to solvent. Residual Dipolar Coupling measurements, however, demonstrate unambiguously that no significant changes in backbone conformation of either protein occur upon phosphorylation: for EIN, the relative orientation of the α and αβ domains remains unchanged; for HPr, the backbone ϕ/Ψ torsion angles of the active site residues are unperturbed within experimental error. His → Glu/Asp mutations of the active site histidines designed to mimic the phosphorylated states reveal binding equilibria that favor phosphoryl transfer from EIN to HPr. Although binding of phospho-EIN to phospho-HPr is reduced by a factor of ∼21 relative to the unphosphorylated complex, Residual Dipolar Coupling measurements reveal that the structures of the unphosphorylated and biphosphorylated complexes are the same. Hence, the phosphorylation states of EIN and HPr shift the binding equilibria predominantly by modulating intermolecular electrostatic interactions without altering either the backbone scaffold or binding interface. This facilitates highly efficient phosphoryl transfer between EIN and HPr, which is estimated to occur at a rate of ∼850 s-1 from exchange spectroscopy.

  • impact of phosphorylation on structure and thermodynamics of the interaction between the n terminal domain of enzyme i and the histidine phosphocarrier protein of the bacterial phosphotransferase system
    Journal of Biological Chemistry, 2008
    Co-Authors: Jeongyong Suh, Mengli Cai, Marius G Clore
    Abstract:

    The structural and thermodynamic impact of phosphorylation on the interaction of the N-terminal domain of enzyme I (EIN) and the histidine phosphocarrier protein (HPr), the two common components of all branches of the bacterial phosphotransferase system, have been examined using NMR spectroscopy and isothermal titration calorimetry. His-189 is located at the interface of the alpha and alphabeta domains of EIN, resulting in rather widespread chemical shift perturbation upon phosphorylation, in contrast to the highly localized perturbations seen for HPr, where His-15 is fully exposed to solvent. Residual Dipolar Coupling measurements, however, demonstrate unambiguously that no significant changes in backbone conformation of either protein occur upon phosphorylation: for EIN, the relative orientation of the alpha and alphabeta domains remains unchanged; for HPr, the backbone /Psi torsion angles of the active site residues are unperturbed within experimental error. His --> Glu/Asp mutations of the active site histidines designed to mimic the phosphorylated states reveal binding equilibria that favor phosphoryl transfer from EIN to HPr. Although binding of phospho-EIN to phospho-HPr is reduced by a factor of approximately 21 relative to the unphosphorylated complex, Residual Dipolar Coupling measurements reveal that the structures of the unphosphorylated and biphosphorylated complexes are the same. Hence, the phosphorylation states of EIN and HPr shift the binding equilibria predominantly by modulating intermolecular electrostatic interactions without altering either the backbone scaffold or binding interface. This facilitates highly efficient phosphoryl transfer between EIN and HPr, which is estimated to occur at a rate of approximately 850 s(-1) from exchange spectroscopy.

  • a physical picture of atomic motions within the dickerson dna dodecamer in solution derived from joint ensemble refinement against nmr and large angle x ray scattering data
    Biochemistry, 2007
    Co-Authors: Charles D Schwieters, Marius G Clore
    Abstract:

    The structure and dynamics of the Dickerson DNA dodecamer [5‘d(CGCGAATTCGCG)2] in solution have been investigated by joint simulated annealing refinement against NMR and large-angle X-ray scattering data (extending from 0.25 to 3 A-1). The NMR data comprise an extensive set of hetero- and homonuclear Residual Dipolar Coupling and 31P chemical shift anisotropy restraints in two alignment media, supplemented by NOE and 3J Coupling data. The NMR and X-ray scattering data cannot be fully ascribed to a single structure representation, indicating the presence of anisotropic motions that impact the experimental observables in different ways. Refinement with ensemble sizes (Ne) of ≥2 to represent the atomic motions reconciles all the experimental data within measurement error. Cross validation against both the Dipolar Coupling and X-ray scattering data suggests that the optimal ensemble size required to account for the current data is 4. The resulting ensembles permit one to obtain a detailed view of the conforma...

  • a physical picture of atomic motions within the dickerson dna dodecamer in solution derived from joint ensemble refinement against nmr and large angle x ray scattering data
    Biochemistry, 2007
    Co-Authors: Charles D Schwieters, Marius G Clore
    Abstract:

    The structure and dynamics of the Dickerson DNA dodecamer [5‘d(CGCGAATTCGCG)2] in solution have been investigated by joint simulated annealing refinement against NMR and large-angle X-ray scattering data (extending from 0.25 to 3 A-1). The NMR data comprise an extensive set of hetero- and homonuclear Residual Dipolar Coupling and 31P chemical shift anisotropy restraints in two alignment media, supplemented by NOE and 3J Coupling data. The NMR and X-ray scattering data cannot be fully ascribed to a single structure representation, indicating the presence of anisotropic motions that impact the experimental observables in different ways. Refinement with ensemble sizes (Ne) of ≥2 to represent the atomic motions reconciles all the experimental data within measurement error. Cross validation against both the Dipolar Coupling and X-ray scattering data suggests that the optimal ensemble size required to account for the current data is 4. The resulting ensembles permit one to obtain a detailed view of the conforma...

James H. Prestegard - One of the best experts on this subject based on the ideXlab platform.

  • protein structure validation and identification from unassigned Residual Dipolar Coupling data using 2d pdpa
    Molecules, 2013
    Co-Authors: Arjang Fahim, James H. Prestegard, Rishi Mukhopadhyay, Ryan Yandle, Homayoun Valafar
    Abstract:

    More than 90% of protein structures submitted to the PDB each year are homologous to some previously characterized protein structure. The extensive resources that are required for structural characterization of proteins can be justified for the 10% of the novel structures, but not for the remaining 90%. This report presents the 2D-PDPA method, which utilizes unassigned Residual Dipolar Coupling in order to address the economics of structure determination of routine proteins by reducing the data acquisition and processing time. 2D-PDPA has been demonstrated to successfully identify the correct structure of an array of proteins that range from 46 to 445 residues in size from a library of 619 decoy structures by using unassigned simulated RDC data. When using experimental data, 2D-PDPA successfully identified the correct NMR structures from the same library of decoy structures. In addition, the most homologous X-ray structure was also identified as the second best structural candidate. Finally, success of 2D-PDPA in identifying and evaluating the most appropriate structure from a set of computationally predicted structures in the case of a previously uncharacterized protein Pf2048.1 has been demonstrated. This protein exhibits less than 20% sequence identity to any protein with known structure and therefore presents a compelling and practical application of our proposed work.

  • A device for the measurement of Residual chemical shift anisotropy and Residual Dipolar Coupling in soluble and membrane-associated proteins
    Journal of Biomolecular NMR, 2010
    Co-Authors: James H. Prestegard
    Abstract:

    Residual Dipolar Coupling (RDC) and Residual chemical shift anisotropy (RCSA) report on orientational properties of a Dipolar bond vector and a chemical shift anisotropy principal axis system, respectively. They can be highly complementary in the analysis of backbone structure and dynamics in proteins as RCSAs generally include a report on vectors out of a peptide plane while RDCs usually report on in-plane vectors. Both RDC and RCSA average to zero in isotropic solutions and require partial orientation in a magnetic field to become observable. While the alignment and measurement of RDC has become routine, that of RCSA is less common. This is partly due to difficulties in providing a suitable isotopic reference spectrum for the measurement of the small chemical shift offsets coming from RCSA. Here we introduce a device (modified NMR tube) specifically designed for accurate measurement of reference and aligned spectra for RCSA measurements, but with a capacity for RDC measurements as well. Applications to both soluble and membrane anchored proteins are illustrated.

  • assessment of protein alignment using 1h 1h Residual Dipolar Coupling measurements
    Journal of Magnetic Resonance, 2005
    Co-Authors: Junfeng Wang, Homayoun Valafar, James H. Prestegard
    Abstract:

    Abstract A quick and accurate method is described for assessing protein alignment from Residual Dipolar Coupling (RDC) measurements. In contrast to observing D 2 O resonance splitting, which reflects the orientational order of the alignment medium, the degree of alignment of a protein of interest can be estimated directly from 1 H– 1 H RDCs. In this study, RDCs between aromatic protons in unlabeled Cp-rubredoxin were measured from proton homonuclear J -resolved experiments with high sensitivity, and the alignment was assessed without the need of extensive resonance assignment. Since labeled proteins are not needed, this method provides an efficient way for screening alignment media. In situations where the protein structure is known, as in the case of Cp-rubredoxin, a full set of order tensor parameters can be determined, allowing further studies, such as those of ligand alignment relative to a target protein.

  • redcat a Residual Dipolar Coupling analysis tool
    Journal of Magnetic Resonance, 2004
    Co-Authors: Homayoun Valafar, James H. Prestegard
    Abstract:

    Abstract Recent advancements in the utilization of Residual Dipolar Couplings (RDCs) as a means of structure validation and elucidation have demonstrated the need for, not only a more user friendly, but also a more powerful RDC analysis tool. In this paper, we introduce a software package named Residual Dipolar Coupling Analysis Tool (REDCAT) designed to address the above issues. REDCAT is a user-friendly program with its graphical-user-interface developed in Tcl/Tk, which is highly portable. Furthermore, the computational engine behind this GUI is written in C/C++ and its computational performance is therefore excellent. The modular implementation of REDCAT’s algorithms, with separation of the computational engine from the graphical engine allows for flexible and easy command line interaction. This feature can be utilized for the design of automated data analysis sessions. Furthermore, this software package is portable to Linux clusters for high throughput applications. In addition to basic utilities to solve for order tensors and back calculate Couplings from a given order tensor and proposed structure, a number of improved algorithms have been incorporated. These include the proper sampling of the Null-space (when the system of linear equations is under-determined), more sophisticated filters for invalid order-tensor identification, error analysis for the identification of the problematic measurements and simulation of the effects of dynamic averaging processes.

  • the southeast collaboratory for structural genomics a high throughput gene to structure factory
    Accounts of Chemical Research, 2003
    Co-Authors: Michael W W Adams, James H. Prestegard, Harry A Dailey, Lawrence J Delucas, Ming Luo, John P Rose, Bicheng Wang
    Abstract:

    The Southeast Collaboratory for Structural Genomics consists of four working groups. The protein production group supplies/develops high-output production of Pyrococcus furiosus, Caenorhabditis elegans, and selected human proteins. The X-ray crystallography group conducts high-throughput structure production in parallel with production-related research/development in nanocrystallization robotics, capillary crystallization cassette, synchrotron/home X-ray instrumentation, sample mounting robotics, data processing and pipelined structure analysis, combined refinement/validation protocols, and direct use of unlabeled native crystals (Direct Crystallography). The NMR group emphasizes/develops sample screening and backbone structure determination from Residual Dipolar Coupling data. The bioinformatics group implements/develops local database interfaces, pipelined sequence/structure information search/updates, and database/bioinformatics toolkits.

Homayoun Valafar - One of the best experts on this subject based on the ideXlab platform.

  • redcraft a computational platform using Residual Dipolar Coupling nmr data for determining structures of perdeuterated proteins in solution
    PLOS Computational Biology, 2021
    Co-Authors: Casey A Cole, Gaetano T Montelione, Nourhan S Daigham, G Liu, Homayoun Valafar
    Abstract:

    Nuclear Magnetic Resonance (NMR) spectroscopy is one of the three primary experimental means of characterizing macromolecular structures, including protein structures. Structure determination by solution NMR spectroscopy has traditionally relied heavily on distance restraints derived from nuclear Overhauser effect (NOE) measurements. While structure determination of proteins from NOE-based restraints is well understood and broadly used, structure determination from Residual Dipolar Couplings (RDCs) is relatively less well developed. Here, we describe the new features of the protein structure modeling program REDCRAFT and focus on the new Adaptive Decimation (AD) feature. The AD plays a critical role in improving the robustness of REDCRAFT to missing or noisy data, while allowing structure determination of larger proteins from less data. In this report we demonstrate the successful application of REDCRAFT in structure determination of proteins ranging in size from 50 to 145 residues using experimentally collected data, and of larger proteins (145 to 573 residues) using simulated RDC data. In both cases, REDCRAFT uses only RDC data that can be collected from perdeuterated proteins. Finally, we compare the accuracy of structure determination from RDCs alone with traditional NOE-based methods for the structurally novel PF.2048.1 protein. The RDC-based structure of PF.2048.1 exhibited 1.0 A BB-RMSD with respect to a high-quality NOE-based structure. Although optimal strategies would include using RDC data together with chemical shift, NOE, and other NMR data, these studies provide proof-of-principle for robust structure determination of largely-perdeuterated proteins from RDC data alone using REDCRAFT.

  • redcraft a computational platform using Residual Dipolar Coupling nmr data for determining structures of perdeuterated proteins without noes
    bioRxiv, 2020
    Co-Authors: Casey A Cole, Nourhan S Daigham, G Liu, G T Montelione, Homayoun Valafar
    Abstract:

    Nuclear Magnetic Resonance (NMR) spectroscopy is one of the two primary experimental means of characterizing macromolecular structures, including protein structures. Structure determination by NMR spectroscopy has traditionally relied heavily on distance restraints derived from nuclear Overhauser effect (NOE) measurements. While structure determination of proteins from NOE-based restraints is well understood and broadly used, structure determination by NOEs imposes increasing quantity of data for analysis, increased cost of structure determination and is less available in the study of perdeuterated proteins. In the recent decade, Residual Dipolar Couplings (RDCs) have been investigated as an alternative source of data for structural elucidation of proteins by NMR. Several methods have been reported that utilize RDCs in addition to NOEs, and a few utilize RDC data alone. While these methods have individually demonstrated some successes, none of these methods have exposed the full potential of protein structure determination from RDCs. To date, structure determination of proteins from RDCs is limited to small proteins (less than 8.5 kDa) using RDC data from many alignment media (>3) that cannot be collected from larger proteins. Here we present the latest version of the REDCRAFT software package designed for structure determination of proteins from RDC data alone. We have demonstrated the success of REDCRAFT in structure determination of proteins ranging in size from 50 to 145 residues using experimentally collected data and large proteins (145 to 573 residues) using simulated RDC data that can be collected from perdeuterated proteins. Finally, we demonstrate the accuracy of structure determination of REDCRAFT from RDCs alone in application to the structurally novel PF.2048 protein. The RDC-based structure of PF.2048 exhibited 1.0 ? of BB-RMSD with respect to the NOE-based structure by only using a small amount of backbone RDCs (~3 restraints per residue) compared to what is required by other approaches.

  • protein fold family recognition from unassigned Residual Dipolar Coupling data
    arXiv: Biomolecules, 2019
    Co-Authors: Rishi Mukhopadhyay, Paul Shealy, Homayoun Valafar
    Abstract:

    Despite many advances in computational modeling of protein structures, these methods have not been widely utilized by experimental structural biologists. Two major obstacles are preventing the transition from a purely-experimental to a purely-computational mode of protein structure determination. The first problem is that most computational methods need a large library of computed structures that span a large variety of protein fold families, while structural genomics initiatives have slowed in their ability to provide novel protein folds in recent years. The second problem is an unwillingness to trust computational models that have no experimental backing. In this paper we test a potential solution to these problems that we have called Probability Density Profile Analysis (PDPA) that utilizes unassigned Residual Dipolar Coupling data that are relatively cheap to acquire from NMR experiments.

  • structure calculation of α α β β proteins from Residual Dipolar Coupling data using redcraft
    Emerging Trends in Applications and Infrastructures for Computational Biology Bioinformatics and Systems Biology#R##N#Systems and Applications, 2016
    Co-Authors: Casey A Cole, Mirko Hennig, D Ishimaru, Homayoun Valafar
    Abstract:

    Structure elucidation of protein structures by traditional nuclear magnetic resonance (NMR) spectroscopy (using nuclear Overhauser effects) is time-consuming and expensive. Residual Dipolar Couplings (RDCs) have become an alternate source of data for structure calculation by NMR spectroscopy. Here we report structure calculation of α, α/β, β proteins from RDC data and explore minimum data requirements and noise tolerance using the software package Residual Dipolar Coupling-based residue assembly and filter tool (REDCRAFT). Our investigations conclude that structure calculation from RDC data alone can be accomplished with as little as {N-H, C α -H α } from two alignment media. However structure calculation from {C-N, N-H, C-H} in one alignment medium and {N-N} in the second alignment medium was problematic. Here we present a discussion of such pathological conditions, in which inherent degeneracies in RDC data make successful protein structure elucidation challenging. When using {C-N, N-H, C-H, C α -H α } from two alignment media, REDCRAFT consistently reconstructed the structures to within 2.084 A of the original structures with up to 5 Hz of added noise.

  • protein structure validation and identification from unassigned Residual Dipolar Coupling data using 2d pdpa
    Molecules, 2013
    Co-Authors: Arjang Fahim, James H. Prestegard, Rishi Mukhopadhyay, Ryan Yandle, Homayoun Valafar
    Abstract:

    More than 90% of protein structures submitted to the PDB each year are homologous to some previously characterized protein structure. The extensive resources that are required for structural characterization of proteins can be justified for the 10% of the novel structures, but not for the remaining 90%. This report presents the 2D-PDPA method, which utilizes unassigned Residual Dipolar Coupling in order to address the economics of structure determination of routine proteins by reducing the data acquisition and processing time. 2D-PDPA has been demonstrated to successfully identify the correct structure of an array of proteins that range from 46 to 445 residues in size from a library of 619 decoy structures by using unassigned simulated RDC data. When using experimental data, 2D-PDPA successfully identified the correct NMR structures from the same library of decoy structures. In addition, the most homologous X-ray structure was also identified as the second best structural candidate. Finally, success of 2D-PDPA in identifying and evaluating the most appropriate structure from a set of computationally predicted structures in the case of a previously uncharacterized protein Pf2048.1 has been demonstrated. This protein exhibits less than 20% sequence identity to any protein with known structure and therefore presents a compelling and practical application of our proposed work.

Joel R. Tolman - One of the best experts on this subject based on the ideXlab platform.

  • unraveling long range Residual Dipolar Coupling networks in strongly aligned proteins
    Journal of Magnetic Resonance, 2013
    Co-Authors: Luke W Arbogast, Ananya Majumdar, Joel R. Tolman
    Abstract:

    Abstract Long-range Residual Dipolar Couplings (lrRDCs) have the potential to serve as powerful structural restraints in protein NMR spectroscopy as they can provide both distance and orientation information about nuclei separate in sequence but close in space. Current nonselective methods for their measurement are limited to moderate alignment strengths due to the sheer abundance of active Couplings at stronger alignment. This limits the overall magnitude and therefore distance across which Couplings can be measured. We have developed a double resonance technique for the inversion of individual coupled spin pairs, called Selective Inversion by Single Transition Cross Polarization (SIST-CP). This technique enables the selective reCoupling of lrRDCs, thus allowing the complex multiplets occurring in strongly aligned systems to be disentangled. This technique is demonstrated in the context of an application to the measurement of 13 C′– 1 H N lrRDCs in strongly aligned proteins.

  • de novo determination of bond orientations and order parameters from Residual Dipolar Couplings with high accuracy
    Journal of the American Chemical Society, 2003
    Co-Authors: Kathryn B Briggman, Joel R. Tolman
    Abstract:

    We report the de novo determination of 15N−1H bond orientations and motional order parameters for the protein ubiquitin with high accuracy based solely on NMR Residual Dipolar Coupling measurements made in six distinct alignment media. The resulting bond orientations are in agreement with RDC-refined orientations of either solid or solution state coordinates to within approximately 2°, which is also the estimated precision of the resulting orientations. The squared generalized order parameters, which reflect amplitudes of motion spanning the picosecond to millisecond time scales, exhibit a correlation with picosecond time scale order parameters derived from conventional NMR 15N spin relaxation methods. Provided that RDC measurements can be obtained using many different alignment media, this approach (called direct interpretation of Dipolar Couplings) may significantly impact the attainable accuracy and the molecular weight range accessible to NMR structure determination in the solution state, as well as p...

  • a novel approach to the retrieval of structural and dynamic information from Residual Dipolar Couplings using several oriented media in biomolecular nmr spectroscopy
    Journal of the American Chemical Society, 2002
    Co-Authors: Joel R. Tolman
    Abstract:

    The interpretation of Residual Dipolar Couplings in terms of molecular properties of interest is complicated because of difficulties in separating structural and dynamic effects as well as the need to estimate alignment tensor parameters a priori. An approach is introduced here that allows many of these difficulties to be circumvented when data are acquired in multiple alignment media. The method allows the simultaneous extraction of both structural and dynamic information directly from the Residual Dipolar Coupling data, in favorable cases even in the complete absence of prior structural knowledge. Application to the protein ubiquitin indicates greater amplitudes of internal motion than expected from traditional 15N spin relaxation analysis.

  • Structural and Dynamic Analysis of Residual Dipolar Coupling Data for Proteins
    Journal of the American Chemical Society, 2001
    Co-Authors: Joel R. Tolman, Hashim M. Al-hashimi, Lewis E. Kay, James H. Prestegard
    Abstract:

    The measurement of Residual Dipolar Couplings in weakly aligned proteins can potentially provide unique information on their structure and dynamics in the solution state. The challenge is to extract the information of interest from the measurements, which normally reflect a convolution of the structural and dynamic properties. We discuss here a formalism which allows a first order separation of their effects, and thus, a simultaneous extraction of structural and motional parameters from Residual Dipolar Coupling data. We introduce some terminology, namely a generalized degree of order, which is necessary for a meaningful discussion of the effects of motion on Residual Dipolar Coupling measurements. We also illustrate this new methodology using an extensive set of Residual Dipolar Coupling measurements made on 15N,13C-labeled human ubiquitin solvated in a dilute bicelle solution. Our results support a solution structure of ubiquitin which on average agrees well with the 1UBQ X-ray structure (Vijay-Kumar, e...

  • structural and dynamic analysis of Residual Dipolar Coupling data for proteins
    Journal of the American Chemical Society, 2001
    Co-Authors: Joel R. Tolman, Lewis E. Kay, Hashim M Alhashimi, James H. Prestegard
    Abstract:

    The measurement of Residual Dipolar Couplings in weakly aligned proteins can potentially provide unique information on their structure and dynamics in the solution state. The challenge is to extract the information of interest from the measurements, which normally reflect a convolution of the structural and dynamic properties. We discuss here a formalism which allows a first order separation of their effects, and thus, a simultaneous extraction of structural and motional parameters from Residual Dipolar Coupling data. We introduce some terminology, namely a generalized degree of order, which is necessary for a meaningful discussion of the effects of motion on Residual Dipolar Coupling measurements. We also illustrate this new methodology using an extensive set of Residual Dipolar Coupling measurements made on (15)N,(13)C-labeled human ubiquitin solvated in a dilute bicelle solution. Our results support a solution structure of ubiquitin which on average agrees well with the X-ray structure (Vijay-Kumar, et al., J. Mol. Biol. 1987, 194, 531--544) for the protein core. However, the data are also consistent with a dynamic model of ubiquitin, exhibiting variable amplitudes, and anisotropy, of internal motions. This work suggests the possibility of primary use of Residual Dipolar Couplings in characterizing both structure and anisotropic internal motions of proteins in the solution state.

Jikai Liu - One of the best experts on this subject based on the ideXlab platform.