Charge state effect on the zwitterion influence on stability of non‐covalent interaction of single‐stranded DNA with peptides

Alvès, Sandra; Woods, Amina S.; Tabet, Jean Claude

doi:10.1002/jms.1359

Cited by 22 publications

(23 citation statements)

References 74 publications

(113 reference statements)

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“…The increased avidity of noncovalent complexes driven by charge-charge interactions has been ob- served by others [28,32,35,[42][43][44][45][46][47]. Removal of water results in a near-covalent strength interaction between the phosphate groups of CDP and CTP to RNase A.…”

Section: Esi-ms and Ms/ms Of Ribonuclease A Binding To Cytidine Nuclementioning

confidence: 94%

Mass spectrometry of protein-ligand complexes: Enhanced gas-phase stability of ribonuclease-nucleotide complexes

Yin

Xie

Loo

2008

J. Am. Soc. Mass Spectrom.

118

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Noncovalent protein-ligand complexes are readily detected by electrospray ionization mass spectrometry (ESI-MS). Ligand binding stoichiometry can be determined easily by the ESI-MS method. The ability to detect noncovalent protein-ligand complexes depends, however, on the stability of the complexes in the gas-phase environment. Solution binding affinities may or may not be accurate predictors of their stability in vacuo. Complexes composed of cytidine nucleotides bound to ribonuclease A (RNase A) and ribonuclease S (RNase S) were detected by ESI-MS and were further analyzed by MS/MS. RNase A and RNase S share similar structures and biological activity. Subtilisin-cleavage of RNase A yields an S-peptide and an S-protein; the S-peptide and S-protein interact through hydrophobic interactions with a solution binding constant in the nanomolar range to generate an active RNase S. Cytidine nucleotides bind to the ribonucleases through electrostatic interactions with a solution binding constant in the micromolar range. Collisionally activated dissociation (CAD) of the 1:1 RNase A-CDP and CTP complexes yields cleavage of the covalent phosphate bonds of the nucleotide ligands, releasing CMP from the complex. CAD of the RNase S-CDP and CTP complexes dissociates the S-peptide from the remaining S-protein/nucleotide complex; further dissociation of the S-protein/nucleotide complex fragments a covalent phosphate bond of the nucleotide with subsequent release of CMP. Despite a solution binding constant favoring the S-protein/S-peptide complex, CDP/CTP remains electrostatically bound to the S-protein in the gas-phase dissociation experiment. This study highlights the intrinsic stability of electrostatic interactions in the gas phase and the significant differences in solution and gas-phase stabilities of noncovalent complexes that can result.

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Section: Esi-ms and Ms/ms Of Ribonuclease A Binding To Cytidine Nuclementioning

confidence: 94%

Mass spectrometry of protein-ligand complexes: Enhanced gas-phase stability of ribonuclease-nucleotide complexes

Yin

Xie

Loo

2008

J. Am. Soc. Mass Spectrom.

118

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“…Zwitterions containing amino and phosphate groups are much less studied, even though the interaction between the zwitterionic form of amino acids and phosphate groups of the DNA strand has been found [9]. Aminophosphate zwitterions are known to exist in a solid state [10], the phosphate group is known to interact with free cationic NH þ 3 groups, [11] and the protons of the phosphate group dissociate easily in water solutions [12], so it is possible for such zwitterions to exist in water solutions.…”

Section: Introductionmentioning

confidence: 99%

The pH behavior of a 2-aminoethyl dihydrogen phosphate zwitterion studied with NMR-titrations

Myller

Karhe

Haukka

et al. 2013

Journal of Molecular Structure

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“…On the other end of the stability scale, the strength of electrostatic interactions is significantly enhanced in the absence of solvent [2,10,[15][16][17][18][19]. The influence of solvent on electrostatic interactions and their role in noncovalent complexes has been described [11,20,21].…”

mentioning

confidence: 99%

Elucidating the site of protein-ATP binding by top-down mass spectrometry

Yin

Loo

2010

J. Am. Soc. Mass Spectrom.

101

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A Fourier-transform ion cyclotron resonance (FT-ICR) top-down mass spectrometry strategy for determining the adenosine triphosphate (ATP)-binding site on chicken adenylate kinase is described. Noncovalent protein-ligand complexes are readily detected by electrospray ionization mass spectrometry (ESI-MS), but the ability to detect protein-ligand complexes depends on their stability in the gas phase. Previously, we showed that collisionally activated dissociation (CAD) of protein-nucleotide triphosphate complexes yield products from the dissociation of a covalent phosphate bond of the nucleotide with subsequent release of the nucleotide monophosphate (Yin, S. et al., J. Am. Soc. Mass Spectrom. 2008, 19, 1199 -1208. The intrinsic stability of electrostatic interactions in the gas phase allows the diphosphate group to remain noncovalently bound to the protein. This feature is exploited to yield positional information on the site of ATP-binding on adenylate kinase. CAD and electron capture dissociation (ECD) of the adenylate kinase-ATP complex generate product ions bearing monoand diphosphate groups from regions previously suggested as the ATP-binding pocket by NMR and crystallographic techniques. Top-down MS may be a viable tool to determine the ATP-binding sites on protein kinases and identify previously unknown protein kinases in a functional proteomics study. (J Am Soc Mass Spectrom 2010, 21, 899 -907) © 2010 American Society for Mass Spectrometry P roteins function in biology through direct interaction with other molecules. A ligand can be a molecule, an atom, or an ion that binds to a specific site on the protein by a variety of means, including hydrogen bonding, Van der Waals interactions, and ionic forces. Determining the presence of protein-ligand interactions and the structures of proteinligand complexes are of critical importance in biology, and this knowledge is often essential for efforts to establish new molecular drug targets and to develop more potent medicines.A number of biophysical tools are available to characterize the interaction between a protein and its ligand(s). However, mass spectrometry (MS) offers potential advantages in sensitivity, specificity, and speed, especially compared with high-resolution nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. With electrospray ionization (ESI) to ionize macromolecules without disrupting covalent bonds while maintaining weak noncovalent interactions, the ESI-MS molecular mass measurement provides direct evidence for protein-ligand associations. The proteinligand interactions are often sufficiently retained upon the transition from solution to the gas phase that the complex size and binding stoichiometry can be measured [1][2][3].Although binding stoichiometry and, in many examples, the relative and absolute solution binding affinities can be measured by ESI-MS methodologies, determining the precise ligand binding site on a target protein is not easily tractable using MS directly. Tandem mass spectrometry (MS/MS) is widely applied...

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Charge state effect on the zwitterion influence on stability of non‐covalent interaction of single‐stranded DNA with peptides

Cited by 22 publications

References 74 publications

Mass spectrometry of protein-ligand complexes: Enhanced gas-phase stability of ribonuclease-nucleotide complexes

Mass spectrometry of protein-ligand complexes: Enhanced gas-phase stability of ribonuclease-nucleotide complexes

The pH behavior of a 2-aminoethyl dihydrogen phosphate zwitterion studied with NMR-titrations

Elucidating the site of protein-ATP binding by top-down mass spectrometry

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