Intermolecular ion pairs (salt bridges) are crucial for protein–DNA association. For two protein–DNA complexes, we demonstrate that the ion pairs of protein side-chain NH3+ and DNA phosphate groups undergo dynamic transitions between distinct states in which the charged moieties are either in direct contact or separated by water. While the crystal structures of the complexes show only the solvent-separated ion pair (SIP) state for some interfacial lysine side chains, our NMR hydrogen-bond scalar coupling data clearly indicate the presence of the contact ion pair (CIP) state for the same residues. The 0.6-μs molecular dynamics (MD) simulations confirm dynamic transitions between the CIP and SIP states. This behavior is consistent with our NMR order parameters and scalar coupling data for the lysine side chains. Using the MD trajectories, we also analyze the free energies of the CIP–SIP equilibria. This work illustrates the dynamic nature of short-range electrostatic interactions in DNA recognition by proteins.

Detailed modeling of the free solution electrophoresis of five proteins (bovine R-lactalbumin, hen egg white lysozyme, bovine superoxide dismutase, human carbonic anhydrase II, and hen ovalbumin) is carried out within the framework of the continuum primitive model. Protein crystal structures and translational diffusion constants are used to design and parametrize the models. The modeling results are compared with experimental mobilities of protein charge ladders, collections of protein derivatives where the number of charge groups is varied by partial acylation of lysine residues or by amidation of glutamic and aspartic acid residues. The simplest model considered is the Yoon and Kim model of a prolate/oblate ellipsoid with uniform surface potential, electrostatics treated at the level of the linear Poisson-Boltzmann equation, and distortion of the ion atmosphere from equilibrium (ion relaxation) ignored (Yoon, B. J.; Kim, S. J. Colloid Interface Sci. 1989, 128, 275). This model provides good agreement with experiment but only if the net absolute protein charge is low or the average absolute surface, or , potential is less than ∼25 mV. Boundary element (BE) modeling is also carried out in which detailed surface models are employed and the electrostatics are solved at the level of the nonlinear Poisson-Boltzmann equation. Ion relaxation is also included in some of the BE studies. All of the experimental mobilities are in good (human carbonic anhydrase II and hen ovalbumin) to excellent (bovine R-lactalbumin, hen egg white lysozyme, and bovine superoxide dismutase) agreement with BE modeling that includes ion relaxation. We believe that these results taken as a whole serve to confirm the ability of the continuum primitive model to predict, with quantitative accuracy, the free solution electrophoretic mobilities of proteins, provided the underlying models are sufficiently realistic. When a discrepancy occurs, it may be due to error in modeling either the protein charge or the solution conformation. The models described in this work also provide a useful approach for determining values of ∆Z, the change in net charge of proteins due to the chemical modification of charged groups. Knowledge of ∆Z is essential for the use of protein charge ladders in the quantitative description of the electrostatic properties and interactions of proteins. This paper supports the view that the continuum primitive model may be more appropriate for the modeling of electrokinetics than for electrostatics. The main challenge to the accurate predictions of electrophoretic mobilities may lie primarily in the modeling of electrostatics, not electrokinetics.

Basic side chains play major roles in recognition of nucleic acids by proteins. However, dynamic properties of these positively charged side chains are not well understood. In this work, we studied changes in conformational dynamics of basic side chains upon protein–DNA association for the zinc-finger protein Egr-1. By nuclear magnetic resonance (NMR) spectroscopy, we characterized the dynamics of all side-chain cationic groups in the free protein and in the complex with target DNA. Our NMR order parameters indicate that the arginine guanidino groups interacting with DNA bases are strongly immobilized, forming rigid interfaces. Despite the strong short-range electrostatic interactions, the majority of the basic side chains interacting with the DNA phosphates exhibited high mobility, forming dynamic interfaces. In particular, the lysine side-chain amino groups exhibited only small changes in the order parameters upon DNA-binding. We found a similar trend in the molecular dynamics (MD) simulations for the free Egr-1 and the Egr-1–DNA complex. Using the MD trajectories, we also analyzed side-chain conformational entropy. The interfacial arginine side chains exhibited substantial entropic loss upon binding to DNA, whereas the interfacial lysine side chains showed relatively small changes in conformational entropy. These data illustrate different dynamic characteristics of the interfacial arginine and lysine side chains.

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In this work, boundary element modeling is used to study the transport of highly charged rod-like model polyions of various length under a variety of different aqueous salt conditions. Transport properties considered include free solution electrophoretic mobility, translational diffusion, and the components of the "tether force" tensor. The model parameters are chosen to coincide with transport measurements of duplex DNA carried out under six different salt/temperature conditions. The focus of the analysis is on the length dependence of the free solution electrophoretic mobility. In a solution containing 0.04 M Tris-acetate buffer at 25 degrees C, calculated mobilities using straight rod models show a stronger dependence on fragment length than that observed experimentally. By carrying out model studies on curved rod models, it is concluded that the "leveling off" of mobility with fragment length is due, in part at least, to the finite curvature of DNA. Experimental mobilities of long duplex DNA in monovalent alkali salts are reasonably well explained once account is taken of long-range bending and the simplifying assumptions of the model studies.

Protein-DNA recognition of a nonspecific complex is modeled to understand the nature of the transient encounter states. We consider the structural and energetic features and the role of water in the DNA grooves in the process of protein-DNA recognition. Here we have used the nuclease domain of colicin E7 (N-ColE7) from Escherichia coli in complex with a 12-bp DNA duplex as the model system to consider how a protein approaches, encounters, and associates with DNA. Multiscale simulation studies using Brownian dynamics and molecular-dynamics simulations were performed to provide the binding process on multiple length- and timescales. We define the encounter states and identified the spatial and orientational aspects. For the molecular length-scales, we used molecular-dynamics simulations. Several intermediate binding states were found, which have different positions and orientations of protein around DNA including major and minor groove orientations. The results show that the contact number and the hydrated interfacial area are measures that facilitate better understanding of sequence-independent protein-DNA binding landscapes and pathways.

BackgroundIntracavitary electrocardiogram (IC ECG) guidance emerges as a new technique for peripherally inserted central catheters (PICCs) placement and demonstrates many potential advantages in recent observational studies.AimsTo determine whether IC ECG-guided PICCs provide more accurate positioning of catheter tips compared to conventional anatomical landmarks in patients with cancer undergoing chemotherapy.MethodsIn this multicenter, open-label, randomized controlled study (ClinicalTrials.gov number, NCT02409589), a total of 1,007 adult patients were assigned to receive either IC ECG guidance (n = 500) or anatomical landmark guidance (n = 507) for PICC positioning. The confirmative catheter tip positioning x-ray data were centrally interpreted by independent radiologists. All reported analyses in the overall population were performed on an intention-to-treat basis. Analyses of pre-specified subgroups and a selected large subpopulation were conducted to explore consistency and accuracy.ResultsIn the IC ECG-guided group, the first-attempt success rate was 89.2% (95% confidence interval [CI], 86.5% to 91.9%), which was significantly higher than 77.4% (95% CI, 73.7% to 81.0%) in the anatomical landmark group (P < 0.0001). This trend of superiority of IC ECG guidance was consistently noted in almost all prespecified patient subgroups and two selected large subpopulations, even when using optimal target rates for measurement. In contrast, the superiority nearly disappeared when PICCs were used via the left instead of right arms (interaction P-value = 0.021). No catheter-related adverse events were reported during the PICC intra-procedures in either group.ConclusionsOur findings indicated that the IC ECG-guided method had a more favorable positioning accuracy versus traditional anatomical landmarks for PICC placement in adult patients with cancer undergoing chemotherapy. Furthermore, there were no significant safety concerns reported for catheterization using the two techniques.

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