Dynamics of Ionic Interactions at Protein–Nucleic Acid Interfaces

Abstract

Conspectus Molecular association of proteins with nucleic acids is required for many biological processes essential to life. Electrostatic interactions via ion pairs (salt bridges) of nucleic acid phosphates and protein side chains are crucial for proteins to bind to DNA or RNA. Counterions around the macromolecules are also key constituents for the thermodynamics of protein–nucleic acid association. Until recently, there had been only a limited amount of experiment-based information about how ions and ionic moieties behave in biological macromolecular processes. In the past decade, there has been significant progress in quantitative experimental research on ionic interactions with nucleic acids and their complexes with proteins. The highly negatively charged surfaces of DNA and RNA electrostatically attract and condense cations, creating a zone called the ion atmosphere. Recent experimental studies were able to examine and validate theoretical models on ions and their mobility and interactions with macromolecules. The ionic interactions are highly dynamic. The counterions rapidly diffuse within the ion atmosphere. Some of the ions are released from the ion atmosphere when proteins bind to nucleic acids, balancing the charge via intermolecular ion pairs of positively charged side chains and negatively charged backbone phosphates. Previously, the release of counterions had been implicated indirectly by the salt-concentration dependence of the association constant. Recently, direct detection of counterion release by NMR spectroscopy has become possible and enabled more accurate and quantitative analysis of the counterion release and its entropic impact on the thermodynamics of protein–nucleic acid association. Recent studies also revealed the dynamic nature of ion pairs of protein side chains and nucleic acid phosphates. These ion pairs undergo transitions between two major states. In one of the major states, the cation and the anion are in direct contact and form hydrogen bonds. In the other major state, the cation and the anion are separated by water. Transitions between these states rapidly occur on a picosecond to nanosecond time scale. When proteins interact with nucleic acids, interfacial arginine (Arg) and lysine (Lys) side chains exhibit considerably different behaviors. Arg side chains show a higher propensity to form rigid contacts with nucleotide bases, whereas Lys side chains tend to be more mobile at the molecular interfaces. The dynamic ionic interactions may facilitate adaptive molecular recognition and play both thermodynamic and kinetic roles in protein–nucleic acid interactions.

Quantifying and visualizing weak interactions between anions and proteins

“…This protein is a DNA-binding protein that recognizes the TAATGG sequence. Charge neutralization upon protein-DNA association is known to cause a release of cations from DNA ( 25 – 27 ). In our recent NMR study using 15 NH 4 + ions, we showed that the 15-bp DNA duplex containing the Antp recognition sequence releases 10.8 cations when it forms a complex with the Antp homeodomain ( 28 ).…”

Increased alpha-helicity of a supercharged coiled-coil protein increases siRNA delivery efficiency of protein-lipid hybrid vehicle

“…The final transfection ability of the mutants appeared to be a sum of the mutations to the protein, demonstrating a “less is more” principle in the design process since seemingly synergistic mutations could actually compete against each other and not yield the desired result. Future designs should aim to further improve protein secondary structure to create even more favorable protein-siRNA interactions [30], while maintaining a favorable positive charge density [31].…”

“…In nature, the majority of nucleic acid binding proteins are alphahelical and positively charged [28, 29]. This can allow for sequence specific interactions through the orientation of side chains able to form hydrogen bonds with specific nucleic acid base pairs [30], or sequence independent interactions through electrostatic interactions between positively charged amino acids and the negatively charged nucleic acid phosphate backbone [31]. The degree of alpha-helicity is also important, as more organized alpha-helices have been shown to form more energetically favorable interactions with nucleic acid binding partners [32].…”

Discrete-state stochastic kinetic models for target DNA search by proteins: Theory and experimental applications

“…The protein molecule must transiently break all of these ions pairs when it moves from one site to another on DNA. The requirement of breaking all ion pairs could represent an energy barrier for sliding [ 70 ]. In fact, for many proteins, the 1D diffusion coefficient for the sliding on DNA is ~10 2 –10 3 fold smaller than the 3D diffusion coefficient calculated with the Stokes-Einstein equation that gives the diffusion coefficient as a function of the hydrodynamic radius, viscosity, and temperature.…”

“…Because electrostatic interactions are crucial for protein-DNA association [ 70 ], the kinetics and thermodynamics of protein-DNA interactions strongly depend on the salt concentration used in experiments [ 29 , 34 , 64 , 67 , 83 – 88 ]. The counterion condensation theory predicts a linear relationship between log K d and log[salt] for the dissociation constants of protein-DNA complexes [ 85 , 86 ] and a similar linear relationship between log k and log[salt] for some kinetic rate constants relevant to protein-DNA constants [ 89 ].…”