Chen AA, Marucho M, Baker NA, Pappu RV. Simulations of RNA interactions with monovalent ions. Methods in Enzymology, 469, 411-432, 2009.
RNA folding and binding reactions are mediated by interactions with ions that make up the surrounding aqueous electrolytic milieu. Although Mg2+ ions are often implicated as being crucial for RNA folding, it is known that folding is feasible in high concentrations of monovalent alkali-halide salts. Experiments have yielded important information regarding the salt dependence of RNA stability. Recent work has shown that molecular simulations based on explicit representations of solvent molecules and monovalent ions can also provide useful insights regarding the ionic atmospheres around model RNA systems. These insights can help rationalize intriguing observations regarding the dependence of RNA stability on cation type providing one pays attention to important considerations that go into the proper design of molecular simulations. These issues are discussed in detail and the methods are applied to an A-form RNA and B-form DNA sequence. The results of these simulations are compared to previous work on a kissing-loop system with analogous sequence. In particular, ionic atmospheres obtained from molecular simulations are compared to those obtained using the nonlinear Poisson Boltzmann model for continuum electrostatics for these three different nucleic acid systems. The comparisons indicate reasonable agreement in terms of coarse-grained observables such as the numbers of counterions accumulated around the solutes. However, details of the ionic atmospheres, captured in terms of spatial free energy density profiles, are quite different between the two approaches. These comparisons suggest the need for improvements in continuum models to capture sequence-specific effects, ion–ion correlation, and the effects of partial dehydration of ions.
Dong F, Wagoner JA, Baker NA. Assessing the performance of implicit solvation models at a nucleic acid surface. Phys Chem Chem Phys, 10, 4889-902, 2008.
Implicit solvation models are popular alternatives to explicit solvent methods due to their ability to “pre-average” solvent behavior and thus reduce the need for computationally-expensive sampling. Previously, we have demonstrated that Poisson-Boltzmann models for polar solvation and integral-based models for nonpolar solvation can reproduce explicit solvation forces in a low-charge density protein system. In the present work, we examine the ability of these continuum models to describe solvation forces at the surface of a RNA hairpin. While these models do not completely describe all of the details of solvent behavior at this highly-charged biomolecular interface, they do provide a reasonable description of average solvation forces and therefore show significant promise for developing more robust implicit descriptions of solvent around nucleic acid systems for use in biomolecular simulation and modeling. Additionally, we observe fairly good transferability in the nonpolar model parameters optimized for protein systems, suggesting its robustness for modeling general nonpolar solvation phenomena in biomolecular systems.
Wong CJ, Rice RL, Baker NA, Ju T, Lohman TM. Probing 3′-ssDNA loop formation in E. coli RecBCD/RecBC-DNA complexes using non-natural DNA: a model for “Chi” recognition complexes. J Mol Biol, 362, 26-43, 2006.
The equilibrium binding of E. coli RecBC and RecBCD helicases to duplex DNA ends containing varying lengths of polyethylene glycol (PEG) spacers within pre-formed 3′-single-stranded (ss) DNA ((dT)_n) tails were studied. These studies were designed to test a previous proposal that the 3′-(dT)_n tail can be looped out upon binding RecBC and RecBCD for 3′-ssDNA tails with n \geq 6 nucleotides. Equilibrium binding of protein to unlabeled DNA substrates with ends containing PEG-substituted 3′-ssDNA tails was examined by competition with a Cy3-labeled reference DNA which undergoes a Cy3 fluorescence enhancement upon protein binding. We find that the binding affinities of both RecBC and RecBCD for a DNA end are unaffected upon substituting PEG for the ssDNA between the sixth and the final two nucleotides of the 3′-(dT)_n tail. However, placing PEG at the end of the 3′-(dT)_n tail increases the binding affinities to their maximum values (i.e. the same as binding constants for RecBC or RecBCD to a DNA end with only a 3′-(dT)_6 tail). Equilibrium binding studies of a RecBC mutant containing a nuclease domain deletion, RecB^{\Delta nuc}C^1 suggest that looping of the 3′-tail (when n \geq 6 nucleotides) occurs even in the absence of the RecB nuclease domain, the nuclease domain stabilizes such loop formation. Computer modeling of the RecBCD-DNA complexes suggests that the loop in the 3′-ssDNA tail may form at the RecB/RecC interface. Based on these results we suggest a model for how a loop in the 3′-ssDNA tail might form upon encounter of a “Chi” recognition sequence during unwinding of DNA by the RecBCD helicase.
Showalter SA, Baker NA, Tang C, Hall KB. Iron responsive element RNA flexibility described by NMR and isotropic reorientational eigenmode dynamics. J Biomol NMR, 32, 179-193, 2005.
The first example of the application of reorientational eigenmode dynamics (RED) to RNA is shown here for the small and floppy Iron Responsive Element (IRE) RNA hairpin. Order parameters calculated for bases and riboses from a 12 ns molecular dynamics trajectory are compared to experimentally determined order parameters from 13C-1H NMR relaxation experiments, and shown to be in qualitative agreement. Given the small size of the IRE hairpin and its very flexible loop, isotropic RED (iRED) was also used to analyze the trajectory in order to describe its dynamic motions. iRED analysis shows that the global and internal dynamics of the IRE are not rigorously separable, which will result in inaccurate experimental order parameters. In addition, the iRED analysis described the many correlated motions that comprise the dynamics of the IRE RNA. The combined use of NMR relaxation, RED, and iRED provide a uniquely detailed description of IRE RNA dynamics.
Zhang D, Konecny R, Baker NA, McCammon JA. Electrostatic interaction between RNA and protein capsid in CCMV simulated by a coarse-grain RNA model and a Monte Carlo approach. Biopolymers, 75, 325-337, 2004.
Although many viruses have been crystallized and the protein capsid structures have been determined by x-ray crystallography, the nucleic acids often cannot be resolved. This is especially true for RNA viruses. The lack of information about the conformation of DNA/RNA greatly hinders our understanding of the assembly mechanism of various viruses. Here we combine a coarse-grain model and a Monte Carlo method to simulate the distribution of viral RNA inside the capsid of cowpea chlorotic mottle virus. Our results show that there is very strong interaction between the N-terminal residues of the capsid proteins, which are highly positive charged, and the viral RNA. Without these residues, the binding energy disfavors the binding of RNA by the capsid. The RNA forms a shell close to the capsid with the highest densities associated with the capsid dimers. These high-density regions are connected to each other in the shape of a continuous net of triangles. The overall icosahedral shape of the net overlaps with the capsid subunit icosahedral organization. Medium density of RNA is found under the pentamers of the capsid. These findings are consistent with experimental observations.
Vitalis A, Baker NA, McCammon JA. ISIM: a program for grand canonical Monte Carlo simulations of the ionic environment of biomolecules. Mol Sim, 30, 45-61, 2004.
In this work we present a new software package (ISIM), which represents a flexible, computational tool for simulations of electrolyte solutions via a grand canonical Monte Carlo procedure (GCMC) with a specific capability of treating biomolecules in solution. The GCMC method provides a powerful tool for studying the ionic environments of highly charged macromolecules with attention to the atomic detail of both the solute and the mobile counterions. The ISIM software differs from previous schemes mainly by treating different ion types independently and offering a new parameterization procedure for calibrating excess chemical potentials and bulk ion concentrations. Additionally, ISIM leverages the APBS software package to provide accurate descriptions of the biomolecular electrostatic potential through the efficient solution of Poisson’s equation. ISIM has been validated on a variety of test systems; we successfully reproduce elementary properties of electrolyte solutions as well as theoretical and experimental results for challenging test systems like Calmodulin and DNA.
DOI: 10.1080/08927020310001597862
Ma C, Baker NA, Joseph S, McCammon JA. Binding of aminoglycoside antibiotics to the small ribosomal subunit: a continuum electrostatics investigation. J Am Chem Soc, 124, 1438-42, 2002.
The binding of paromomycin and similar antibiotics to the small (30S) ribosomal subunit has been studied using continuum electrostatics methods. Crystallographic information from a complex of paromomycin with the 30S subunit was used as a framework to develop structures of similar antibiotics in the same ribosomal binding site. Total binding energies were calculated from electrostatic properties obtained by solution of the Poisson-Boltzmann equation combined with a surface area-dependent apolar term. These computed results showed good correlation with experimental data. Additionally, calculation of the ribosomal electrostatic potential in the paromomycin binding site provided insight into the electrostatic mechanisms for aminoglycoside binding and clues for the rational design of more effective antibiotics.
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA, 98, 10037-41, 2001.
Evaluation of the electrostatic properties of biomolecules has become a standard practice in molecular biophysics. Foremost among the models used to elucidate the electrostatic potential is the Poisson-Boltzmann equation; however, existing methods for solving this equation have limited the scope of accurate electrostatic calculations to relatively small biomolecular systems. Here we present the application of numerical methods to enable the trivially parallel solution of the Poisson-Boltzmann equation for supramolecular structures that are orders of magnitude larger in size. As a demonstration of this methodology, electrostatic potentials have been calculated for large microtubule and ribosome structures. The results point to the likely role of electrostatics in a variety of activities of these structures.
RNA folding and binding reactions are mediated by interactions with ions that make up the surrounding aqueous electrolytic milieu. Although Mg2+ ions are often implicated as being crucial for RNA folding, it is known that folding is feasible in high concentrations of monovalent alkali-halide salts. Experiments have yielded important information regarding the salt dependence of RNA stability. Recent work has shown that molecular simulations based on explicit representations of solvent molecules and monovalent ions can also provide useful insights regarding the ionic atmospheres around model RNA systems. These insights can help rationalize intriguing observations regarding the dependence of RNA stability on cation type providing one pays attention to important considerations that go into the proper design of molecular simulations. These issues are discussed in detail and the methods are applied to an A-form RNA and B-form DNA sequence. The results of these simulations are compared to previous work on a kissing-loop system with analogous sequence. In particular, ionic atmospheres obtained from molecular simulations are compared to those obtained using the nonlinear Poisson Boltzmann model for continuum electrostatics for these three different nucleic acid systems. The comparisons indicate reasonable agreement in terms of coarse-grained observables such as the numbers of counterions accumulated around the solutes. However, details of the ionic atmospheres, captured in terms of spatial free energy density profiles, are quite different between the two approaches. These comparisons suggest the need for improvements in continuum models to capture sequence-specific effects, ion–ion correlation, and the effects of partial dehydration of ions.
