POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules

Lee, Woonghee; Rahimi, Mehdi; Lee, Yeongjoon; Chiu, Abigail

doi:10.1093/bioinformatics/btab180

Cited by 97 publications

(86 citation statements)

References 10 publications

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“…4 wwPDB (7WCG) validation results [37]. 5 Xplor-NIH pseudo-potential energy and every violation of the 20 best structures were analyzed using POKY-Analyzer [38].…”

Section: Solution Structure Of Ssossb 1-114 At High Temperaturementioning

confidence: 99%

“…4 wwPDB (7WCG) validation results [37]. 5 Xplor-NIH pseudo-potential energy and every violation of the 20 best structures were analyzed using POKY-Analyzer [38]. 1 The solution structure of SsoSSB1-114 was calculated using Xplor-NIH in PONDEROSA-C/S [36].…”

Section: Solution Structure Of Ssossb 1-114 At High Temperaturementioning

confidence: 99%

“…4 wwPDB (7WCG) validation results [37]. 5 Xplor-NIH pseudo-potential energy and every violation of the 20 best structures were analyzed using POKY-Analyzer [38]. It was already known that β strands β1, β4, and β5 are broken by residues 26, 72-73, and 89, respectively, which differs from the general OB-fold domain [14].…”

Section: Solution Structure Of Ssossb 1-114 At High Temperaturementioning

confidence: 99%

“…Pseudo-3D NMR spectra were collected with relaxation delays of 20, 60, 100, 200, 400, 600, 800, 1000, 1200, and 1600 ms at 25 • C and 50 • C for the 15 N R 1 measurements, and with relaxation delays of 16.96, 33.92, 67.84, 101.76, 135.68, 203.52, 271.36, 339.2, 407.04, and 547.72 ms at 25 • C and 50 • C for the 15 N R 2 measurements. POKY was used to extract the relaxation rate constants by fitting the decay of peak height as a function of the relaxation delay to a single exponential function [38]. For the hetNOE measurement, interleaved 2D 1 H-15 N HSQC spectra were acquired with and without an initial proton saturation of 2.5 s at 25 • C and 50 • C. hetNOE values were obtained from the ratios of peak heights between pairs of spectra, calculated with a POKY script [38].…”

Section: Nmr Backbone Relaxation Experimentsmentioning

confidence: 99%

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NMR Structure and Biophysical Characterization of Thermophilic Single-Stranded DNA Binding Protein from Sulfolobus Solfataricus

Yang

Kim

Lee

et al. 2022

IJMS

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Proteins from Sulfolobus solfataricus (S. solfataricus), an extremophile, are active even at high temperatures. The single-stranded DNA (ssDNA) binding protein of S. solfataricus (SsoSSB) is overexpressed to protect ssDNA during DNA metabolism. Although SsoSSB has the potential to be applied in various areas, its structural and ssDNA binding properties at high temperatures have not been studied. We present the solution structure, backbone dynamics, and ssDNA binding properties of SsoSSB at 50 °C. The overall structure is consistent with the structures previously studied at room temperature. However, the loop between the first two β sheets, which is flexible and is expected to undergo conformational change upon ssDNA binding, shows a difference from the ssDNA bound structure. The ssDNA binding ability was maintained at high temperature, but different interactions were observed depending on the temperature. Backbone dynamics at high temperature showed that the rigidity of the structured region was well maintained. The investigation of an N-terminal deletion mutant revealed that it is important for maintaining thermostability, structure, and ssDNA binding ability. The structural and dynamic properties of SsoSSB observed at high temperature can provide information on the behavior of proteins in thermophiles at the molecular level and guide the development of new experimental techniques.

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“…4 wwPDB (7WCG) validation results [37]. 5 Xplor-NIH pseudo-potential energy and every violation of the 20 best structures were analyzed using POKY-Analyzer [38].…”

Section: Solution Structure Of Ssossb 1-114 At High Temperaturementioning

confidence: 99%

Section: Solution Structure Of Ssossb 1-114 At High Temperaturementioning

confidence: 99%

Section: Solution Structure Of Ssossb 1-114 At High Temperaturementioning

confidence: 99%

Section: Nmr Backbone Relaxation Experimentsmentioning

confidence: 99%

See 2 more Smart Citations

NMR Structure and Biophysical Characterization of Thermophilic Single-Stranded DNA Binding Protein from Sulfolobus Solfataricus

Yang

Kim

Lee

et al. 2022

IJMS

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“…32 Before submitting calculations, all unused resonances were removed by the two-letter code dr, and nomenclature and resonance deviations of chemical shift assignments were thoroughly verified using the Check Protein Nomenclature tool (ca) and the Resonance Deviation Check tool (ck) in NMRFAM-SPARKY, respectively. Chemical shifts assignments were also used to generate backbone dihedral angle constraints by TALOS-N. 36 After every calculation, distance constraints were manually validated using the Distance Constraint Validator tool in Poky Analyzer, 37 along with the manual NOE assignments. During the validations, all spectrum data and 3D atomic coordinates were visually examined.…”

Section: Structure Determinationmentioning

confidence: 99%

pH-dependent polymorphism of the structure of SARS-CoV-2 nsp7

Lee

Tonelli

Rahimi

et al. 2021

Preprint

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The solution structure of SARS-CoV-2 nonstructural protein 7 (nsp7) at pH 7.0 has been determined by NMR spectroscopy. nsp7 is conserved in the coronavirinae subfamily and is an essential co-factor of the viral RNA-dependent RNA polymerase for active and processive replication. Similar to the previously deposited structures of SARS-CoV-1 nsp7 at acidic and basic conditions, SARS-CoV-2 nsp7 has a helical bundle folding at neutral pH. Remarkably, the α4 helix shows gradual dislocation from the core α2-α3 structure as pH increases from 6.5 to 7.5. The protonation state of residue H36 contributes to the change of nsp7's intramolecular interactions, and thus, to the structural variation near-neutral pH. Spin-relaxation results revealed that all three loop regions in nsp7 possess dynamic properties associated with this structural variation.

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An NMR portrait of functional and dysfunctional allosteric cooperativity in cAMP‐dependent protein kinase A

et al. 2023

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The cAMP‐dependent protein kinase A (PKA) is the archetypical eukaryotic kinase. The catalytic subunit (PKA‐C) structure is highly conserved among the AGC‐kinase family. PKA‐C is a bilobal enzyme with a dynamic N‐lobe, harbouring the Adenosine‐5′‐triphosphate (ATP) binding site and a more rigid helical C‐lobe. The substrate‐binding groove resides at the interface of the two lobes. A distinct feature of PKA‐C is the positive binding cooperativity between nucleotide and substrate. Several PKA‐C mutations lead to the development of adenocarcinomas, myxomas, and other rare forms of liver tumours. Nuclear magnetic resonance (NMR) spectroscopy shows that these mutations disrupt the allosteric communication between the two lobes, causing a drastic decrease in binding cooperativity. The loss of cooperativity correlates with changes in substrate fidelity and reduced kinase affinity for the endogenous protein kinase inhibitor (PKI). The similarity between PKI and the inhibitory sequence of the kinase regulatory subunits suggests that the overall mechanism of regulation of the kinase may be disrupted. We surmise that a reduced or obliterated cooperativity may constitute a common trait for both orthosteric and allosteric mutations of PKA‐C that may lead to dysregulation and disease.

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POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules

Cited by 97 publications

References 10 publications

NMR Structure and Biophysical Characterization of Thermophilic Single-Stranded DNA Binding Protein from Sulfolobus Solfataricus

NMR Structure and Biophysical Characterization of Thermophilic Single-Stranded DNA Binding Protein from Sulfolobus Solfataricus

pH-dependent polymorphism of the structure of SARS-CoV-2 nsp7

An NMR portrait of functional and dysfunctional allosteric cooperativity in cAMP‐dependent protein kinase A

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