Erratum to “The Salt-dependence of a Protein–Ligand Interaction: Ion-Protein Binding Energetics” [J. Mol. Biol. (2005) 346, 895–905]

Waldron, Travis T.; Schrift, Greta L.; Murphy, Kenneth P.

doi:10.1016/j.jmb.2005.02.012

Cited by 5 publications

(6 citation statements)

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“…3C-E), 17 indicating that ions bind and stabilize the protein. 5 The nonspecific oriC and oriC-lock increased the stability of Tus-GFP only at low ionic strength (i.e. o 150 mM [KCl]) resulting in a DT m > +10 1C at 8.5 mM [KCl] (Fig.…”

Section: Salt Resistance Of Tus-ter and Tus-ter-lock Using A Fast 2d mentioning

confidence: 99%

“…An experimental approach that analyzed the effects of salt on the stability of protein-DNA complexes was developed nearly four decades ago by Record et al 1,2 It assumes that the release of counter-ions associated with free DNA is a major factor in protein-DNA complex formation. [1][2][3][4][5][6] The application of the concept of counterion condensation (CC) allows determination of the electrostatic component in a protein-DNA complex. The analysis of the salt dependence of the binding constant can also be used to determine the non-electrostatic component of the interaction, which is sequence-specific.…”

Section: Introductionmentioning

confidence: 99%

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Dissecting the salt dependence of the Tus–Ter protein–DNA complexes by high-throughput differential scanning fluorimetry of a GFP-tagged Tus

Moreau

Schaeffer

2013

Mol. BioSyst.

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The analysis of the salt dependence of protein-DNA complexes provides useful information about the non-specific electrostatic and sequence-specific parameters driving complex formation and stability. The differential scanning fluorimetry of GFP-tagged protein (DSF-GTP) assay has been geared with an automatic Tm peak recognition system and was applied for the high-throughput (HT) determination of salt-induced effects on the GFP-tagged DNA replication protein Tus in complex with various Ter and Ter-lock sequences. The system was designed to generate two-dimensional heat map profiles of Tus-GFP protein stability allowing for a comparative study of the effect of eight increasing salt concentrations on ten different Ter DNA species at once. The data obtained with the new HT DSF-GTP allowed precise dissection of the non-specific electrostatic and sequence-specific parameters driving Tus-Ter and Tus-Ter-lock complex formation and stability. The major factor increasing the thermal resistance of Tus-Ter-lock complexes in high-salt is the formation of the TT-lock, e.g. a 10-fold higher Kspe was obtained for Tus-GFP:Ter-lockB than for Tus-GFP:TerB. It is anticipated that the system can be easily adapted for the study of other protein-DNA complexes.

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Section: Salt Resistance Of Tus-ter and Tus-ter-lock Using A Fast 2d mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Dissecting the salt dependence of the Tus–Ter protein–DNA complexes by high-throughput differential scanning fluorimetry of a GFP-tagged Tus

Moreau

Schaeffer

2013

Mol. BioSyst.

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“…Recent developments in hybrid quantum mechanics (QM) and MM method created new opportunities in more accurate assessment of interaction energies [22][23][24][25]. In particular ONIOM method nicely resolved problems with QM and MM boundary and was successfully utilized in studies on mechanism of enzymatic reactions or calculations of interaction energies between proteins and their ligands [26][27][28][29][30][31].…”

Section: Introductionmentioning

confidence: 99%

Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors

Hoffmann

Eitner

Grotthuss

et al. 2006

J Comput Aided Mol Des

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The modeling of the severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain was performed using the protein structure prediction Meta Server and the 3D Jury method for model selection, which resulted in the identification of 1JPR, 1UAA and 1W36 PDB structures as suitable templates for creating a full atom 3D model. This model was further utilized to design small molecules that are expected to block an ATPase catalytic pocket thus inhibit the enzymatic activity. Binding sites for various functional groups were identified in a series of molecular dynamics calculation. Their positions in the catalytic pocket were used as constraints in the Cambridge structural database search for molecules having the pharmacophores that interacted most strongly with the enzyme in a desired position. The subsequent MD simulations followed by calculations of binding energies of the designed molecules were compared to ATP identifying the most successful candidates, for likely inhibitors - molecules possessing two phosphonic acid moieties at distal ends of the molecule.

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“…[156][157][158] An interesting combination of ITC and DSC was used for characterising the energy profile of interacting systems and for monitoring the energetics of structural changes in biomolecules and in specific complexes formed of biomolecules and their binding partners. 159,160 DSC is suitable only for tight binding complexes exhibiting affinities from 10 À9 to 10 À20 M. 145 A direct comparison was done between DSC-, ITC-and MS-measurements of K d values. 94 The K d values obtained by MS were in good agreement with the values determined by DSC and ITC, indicating that solutionphase binding affinity is reflected in the MS-based analysis.…”

Section: B Isothermal Titration Calorimetry and Differential Scanning...mentioning

confidence: 99%

Mass spectrometric studies of dissociation constants of noncovalent complexes

Erba

Zenobi

2011

Annu. Rep. Prog. Chem., Sect. C: Phys. Chem.

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Erratum to “The Salt-dependence of a Protein–Ligand Interaction: Ion-Protein Binding Energetics” [J. Mol. Biol. (2005) 346, 895–905]

Cited by 5 publications

References 0 publications

Dissecting the salt dependence of the Tus–Ter protein–DNA complexes by high-throughput differential scanning fluorimetry of a GFP-tagged Tus

Dissecting the salt dependence of the Tus–Ter protein–DNA complexes by high-throughput differential scanning fluorimetry of a GFP-tagged Tus

Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors

Mass spectrometric studies of dissociation constants of noncovalent complexes

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