Modeling the electrophoresis of highly charged peptides: Application to oligolysines

Wu, Hengfu; Allison, Stuart A.; Perrin, Catherine; Cottet, Hervé

doi:10.1002/jssc.201100873

Cited by 12 publications

(16 citation statements)

References 34 publications

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“…ij ij (19) and then (20) where we have also included eq 3 for i = j and δ ij is the Kronecker delta symbol. The average ⟨1/r ij ⟩ can be calculated analytically in simple cases (such as Gaussian chains and rigid rods 26,28 ), or numerically by sampling the conformational space of the polymer (the approach taken in this paper).…”

Section: The Approachmentioning

confidence: 99%

Electrophoresis of Heteropolymers. Effect of Stiffness

Chubynsky

Slater

2015

Macromolecules

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In the limit of a small Debye length, the electrophoretic mobility of a charged heteropolymer is a weighted average of the mobilities of its parts. The weights are a function of the position along the chain that depends on the properties of the polymer, such as its stiffness. It is known that for a flexible polymer the weights diverge as a power law at the ends, while for a rodlike polymer the divergence is only logarithmic. Using the Kirkwood− Riseman approximation, we study in detail the intermediate case of a semiflexible polymer. We find that for sufficiently small persistence lengths, the position dependence of the weights matches that for flexible polymers away from the ends, but crosses over to the logarithmic dependence characteristic of rods near the ends. While this crossover is broad and the exact points at which it occurs can be defined in different ways, we give an operational definition of the distance of the crossover points from the respective end that turns out to be nearly independent of the polymer length even when it is comparable to that length. This crossover distance is proportional to the "hydrodynamic Kuhn length" defined as the polymer length at which the crossover between the "rod-like" and the "coil-like" dependences of the friction coefficient occurs. Both the crossover distance for the weights and the hydrodynamic Kuhn length scale superlinearly with the persistence length of the polymer; as a result, geometrically "coil-like" semiflexible polymers can be quite "rod-like" hydrodynamically and electrophoretically. Our results are applied to the case of a diblock copolymer with one charged and one neutral part.

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Section: The Approachmentioning

confidence: 99%

Electrophoresis of Heteropolymers. Effect of Stiffness

Chubynsky

Slater

2015

Macromolecules

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“…A more refined model accounts for the detailed size, shape, and charge distribution of the peptide. Over the last nine years, we have developed a BMM to model the electrophoretic mobility of macromolecules modeled as bead arrays and this strategy has been applied extensively to peptides . Since this approach has been explained in detail in past work, the current discussion shall be kept to a minimum.…”

Section: Methodsmentioning

confidence: 99%

“…CE offers a simple but very effective way of separating peptides as well as other ionic species and nanoparticles on the basis of their size and charge. In recent years, numerous investigators employing a variety of modeling strategies have analyzed free solution CE mobility data of peptides in an attempt to determine their physicochemical properties and, in some cases, elucidate their structure . Our laboratory has played a part in these studies by developing a coarse‐grained bead modeling methodology (BMM) that partially accounts for the finite extent of peptides in modeling their electrophoretic mobility .…”

Section: Introductionmentioning

confidence: 99%

“…Our laboratory has played a part in these studies by developing a coarse‐grained bead modeling methodology (BMM) that partially accounts for the finite extent of peptides in modeling their electrophoretic mobility . Initially designed for weakly charged peptides where electrostatics are solved at the level of the linear Poisson–Boltzmann (PB) equation, it was subsequently generalized to solve the electrostatics at the level of the no linear PB equation, the BMM‐NLPB procedure, to make it applicable to highly charged peptides .…”

Section: Introductionmentioning

confidence: 99%

“…Section also discusses the BMM‐NLPB procedure. Since this has been described extensively in past work , this discussion is brief. When the BGE is Na 2 SO 4 , a discrepancy is observed between modeled (BMM‐NLPB) and experimental mobilities.…”

Section: Introductionmentioning

confidence: 99%

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Specific ion effects on the electrophoretic mobility of small, highly charged peptides: A modeling study

Allison

Bui

et al. 2014

J of Separation Science

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In this work, we use coarse-grained modeling to study the free solution electrophoretic mobility of small highly charged peptides (lysine, arginine, and short oligos thereof (up to nonapeptides)) in NaCl and Na2SO4 aqueous solutions at neutral pH and room temperature. The experimental data are taken from the literature. A bead modeling methodology that treats the electrostatics at the level of the nonlinear Poisson Boltzmann equation developed previously in our laboratory is able to account for the mobility of all peptides in NaCl, but not Na2SO4. The peptide mobilities in Na2SO4 can be accounted for by including sulfate binding in the model and this is proposed as one possible explanation for the discrepancy. Oligo arginine peptides bind more sulfate than oligo lysines and sulfate binding increases with the oligo length.

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Recent developments in capillary and microchip electroseparations of peptides (2011–2013)

Kašička

2013

Electrophoresis

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The review presents a comprehensive survey of recent developments and applications of capillary and microchip electroseparation methods (zone electrophoresis, ITP, IEF, affinity electrophoresis, EKC, and electrochromatography) for analysis, isolation, purification, and physicochemical and biochemical characterization of peptides. Advances in the investigation of electromigration properties of peptides, in the methodology of their analysis, including sample preseparation, preconcentration and derivatization, adsorption suppression and EOF control, as well as in detection of peptides, are presented. New developments in particular CE and CEC modes are reported and several types of their applications to peptide analysis are described: conventional qualitative and quantitative analysis, determination in complex (bio)matrices, monitoring of chemical and enzymatical reactions and physical changes, amino acid, sequence and chiral analysis, and peptide mapping of proteins. Some micropreparative peptide separations are shown and capabilities of CE and CEC techniques to provide relevant physicochemical characteristics of peptides are demonstrated.

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Modeling the electrophoresis of highly charged peptides: Application to oligolysines

Cited by 12 publications

References 34 publications

Electrophoresis of Heteropolymers. Effect of Stiffness

Electrophoresis of Heteropolymers. Effect of Stiffness

Specific ion effects on the electrophoretic mobility of small, highly charged peptides: A modeling study

Recent developments in capillary and microchip electroseparations of peptides (2011–2013)

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