iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge

Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN

The rational targeting of RNA with small molecules is hampered by our still limited understanding of RNA structural and dynamic properties. Most in silico tools for binding site identification rely on static structures and therefore cannot face the challenges posed by the dynamic nature of RNA molecules. Here, we present SHAMAN, a computational technique to identify potential small-molecule binding sites in RNA structural ensembles. SHAMAN enables exploring the conformational landscape of RNA with atomistic molecular dynamics simulations and at the same time identifying RNA pockets in an efficient way with the aid of probes and enhanced-sampling techniques. In our benchmark composed of large, structured riboswitches as well as small, flexible viral RNAs, SHAMAN successfully identifies all the experimentally resolved pockets and ranks them among the most favorite probe hotspots. Overall, SHAMAN sets a solid foundation for future drug design efforts targeting RNA with small molecules, effectively addressing the long-standing challenges in the field.

Exposing Hidden High-Affinity RNA Conformational States

RNA recognition frequently results in conformational changes that optimize intermolecular binding. As a consequence, the overall binding affinity of RNA to its binding partners depends not only on the intermolecular interactions formed in the bound state but also on the energy cost associated with changing the RNA conformational distribution. Measuring these "conformational penalties" is, however, challenging because bound RNA conformations tend to have equilibrium populations in the absence of the binding partner that fall outside detection by conventional biophysical methods. In this study we employ as a model system HIV-1 TAR RNA and its interaction with the ligand argininamide (ARG), a mimic of TAR's cognate protein binding partner, the transactivator Tat. We use NMR chemical shift perturbations and relaxation dispersion in combination with Bayesian inference to develop a detailed thermodynamic model of coupled conformational change and ligand binding. Starting from a comprehensive 12-state model of the equilibrium, we estimate the energies of six distinct detectable thermodynamic states that are not accessible by currently available methods. Our approach identifies a minimum of four RNA intermediates that differ in terms of the TAR conformation and ARG occupancy. The dominant bound TAR conformation features two bound ARG ligands and has an equilibrium population in the absence of ARG that is below detection limit. Consequently, even though ARG binds to TAR with an apparent overall weak affinity (Kdapp ≈ 0.2 mM), it binds the prefolded conformation with a Kd in the nM range. Our results show that conformational penalties can be major determinants of RNA-ligand binding affinity as well as a source of binding cooperativity, with important implications for a predictive understanding of how RNA is recognized and for RNA-targeted drug discovery.

Molecular dynamics and MM/GBSA-integrated protocol probing the correlation between biological activities and binding free energies of HIV-1 TAR RNA inhibitors

The interaction of HIV-1 transactivator protein Tat with its cognate transactivation response (TAR) RNA has emerged as a promising target for developing antiviral compounds and treating HIV infection, since it is a crucial step for efficient transcription and replication. In the present study, molecular dynamics (MD) simulations and MM/GBSA calculations have been performed on a series of neamine derivatives in order to estimate appropriate MD simulation time for acceptable correlation between ΔG_bind and experimental pIC₅₀ values. Initially, all inhibitors were docked into the active site of HIV-1 TAR RNA. Later to explore various conformations and examine the docking results, MD simulations were carried out. Finally, binding free energies were calculated using MM/GBSA method and were correlated with experimental pIC₅₀ values at different time scales (0-1 to 0-10 ns). From this study, it is clear that in case of neamine derivatives as simulation time increased the correlation between binding free energy and experimental pIC₅₀ values increased correspondingly. Therefore, the binding energies which can be interpreted at longer simulation times can be used to predict the bioactivity of new neamine derivatives. Moreover, in this work, we have identified some plausible critical nucleotide interactions with neamine derivatives that are responsible for potent inhibitory activity. Furthermore, we also provide some insights into a new class of oxadiazole-based back bone cyclic peptides designed by incorporating the structural features of neamine derivatives. On the whole, this approach can provide a valuable guidance for designing new potent inhibitors and modify the existing compounds targeting HIV-1 TAR RNA.

Insights into the mechanisms of RNA secondary structure destabilization by the HIV-1 nucleocapsid protein

The mature HIV-1 nucleocapsid protein NCp7 (NC) plays a key role in reverse transcription facilitating the two obligatory strand transfers. Several properties contribute to its efficient chaperon activity: preferential binding to single-stranded regions, nucleic acid aggregation, helix destabilization, and rapid dissociation from nucleic acids. However, little is known about the relationships between these different properties, which are complicated by the ability of the protein to recognize particular HIV-1 stem-loops, such as SL1, SL2, and SL3, with high affinity and without destabilizing them. These latter properties are important in the context of genome packaging, during which NC is part of the Gag precursor. We used NMR to investigate destabilization of the full-length TAR (trans activating response element) RNA by NC, which is involved in the first strand transfer step of reverse transcription. NC was used at a low protein:nucleotide (nt) ratio of 1:59 in these experiments. NMR data for the imino protons of TAR identified most of the base pairs destabilized by NC. These base pairs were adjacent to the loops in the upper part of the TAR hairpin rather than randomly distributed. Gel retardation assays showed that conversion from the initial TAR-cTAR complex to the fully annealed form occurred much more slowly at the 1:59 ratio than at the higher ratios classically used. Nevertheless, NC significantly accelerated the formation of the initial complex at a ratio of 1:59.

Rapid Exchange Between Free and Bound States in RNA-Dendrimer Polyplexes: Implications on the Mechanism of Delivery and Release

A combination of solution NMR, dynamic light scattering (DLS), and fluorescence quenching assays were employed to obtain insights into the dynamics and structural features of a polyplex system consisting of HIV-1 transactivation response element (TAR) and PEGylated generation 5 poly(amidoamine) dendrimer (G5-PEG). NMR chemical shift mapping and (13)C spin relaxation based dynamics measurements depict the polyplex system as a highly dynamic assembly where the RNA, with its local structure and dynamics preserved, rapidly exchanges ( Collapse

Key Words

• therapeutic rna delivery
• pamam
• pegylation
• tar
• dls
• nmr spin relaxation

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MESH Headings

• Dendrimers/chemistry
• HIV-1/chemistry
• Magnetic Resonance Spectroscopy/methods
• Polyamines/chemistry
• Polyethylene Glycols/chemistry
• RNA/chemistry
• Response Elements/genetics
• Transfection/methods

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Grants

• R01 AI066975 NIAID NIH HHS
• P50 GM103297 NIGMS NIH HHS
• R01 AI087463-01 NIAID NIH HHS
• R01 EB005028 NIBIB NIH HHS
• R01EB005028 NIBIB NIH HHS
• R01 GM089846 NIGMS NIH HHS

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Affiliation(s)

Anisha Shakya Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
Casey A. Dougherty Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
Yi Xue Department of Biochemistry and Chemistry, Duke University Medical Center, Durham, NC 27710, USA
Hashim M. Al-Hashimi Department of Biochemistry and Chemistry, Duke University Medical Center, Durham, NC 27710, USA
Mark M. Banaszak Holl Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA

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NMR Order Parameter Determination from Long Molecular Dynamics Trajectories for Objective Comparison with Experiment

Functional protein motions covering a wide range of time scales can be studied, among other techniques, by NMR and by molecular dynamics (MD) computer simulations. MD simulations of proteins now routinely extend into the hundreds of nanoseconds time scale range exceeding the overall tumbling correlation times of proteins in solution by several orders of magnitude. This provides a unique opportunity to rigorously validate these simulations by quantitative comparison with model-free order parameters derived from NMR relaxation experiments. However, presently there is no consensus on how such a comparison is best done. We address here how this can be accomplished in a way that is both efficient and objective. For this purpose, we analyze (15)N R1 and R2 and heteronuclear {(1)H}-(15)N NOE NMR relaxation parameters computed from 500 ns MD trajectories of 10 different protein systems using the model-free analysis. The resulting model-free S(2) order parameters are then used as targets for S(2) values computed directly from the trajectories by the iRED method by either averaging over blocks of variable lengths or by using exponentially weighted snapshots (wiRED). We find that the iRED results are capable of reproducing the target S(2) values with high accuracy provided that the averaging window is chosen 5 times the length of the overall tumbling correlation time. These results provide useful guidelines for the derivation of NMR order parameters from MD for a meaningful comparison with their experimental counterparts.

NMR studies of nucleic acid dynamics

Nucleic acid structures have to satisfy two diametrically opposite requirements; on one hand they have to adopt well-defined 3D structures that can be specifically recognized by proteins; on the other hand, their structures must be sufficiently flexible to undergo very large conformational changes that are required during key biochemical processes, including replication, transcription, and translation. How do nucleic acids introduce flexibility into their 3D structure without losing biological specificity? Here, I describe the development and application of NMR spectroscopic techniques in my laboratory for characterizing the dynamic properties of nucleic acids that tightly integrate a broad set of NMR measurements, including residual dipolar couplings, spin relaxation, and relaxation dispersion with sample engineering and computational approaches. This approach allowed us to obtain fundamental new insights into directional flexibility in nucleic acids that enable their structures to change in a very specific functional manner.

The interactions and recognition of cyclic peptide mimetics of Tat with HIV-1 TAR RNA: a molecular dynamics simulation study

The interaction of HIV-1 trans-activator protein Tat with its cognate trans-activation response element (TAR) RNA is critical for viral transcription and replication. Therefore, it has long been considered as an attractive target for the development of antiviral compounds. Recently, the conformationally constrained cyclic peptide mimetics of Tat have been tested to be a promising family of lead peptides. Here, we focused on two representative cyclic peptides termed as L-22 and KP-Z-41, both of which exhibit excellent inhibitory potency against Tat and TAR interaction. By means of molecular dynamics simulations, we obtained a detailed picture of the interactions between them and HIV-1 TAR RNA. In results, it is found that the binding modes of the two cyclic peptides to TAR RNA are almost identical at or near the bulge regions, whereas the binding interfaces at the apical loop exhibit large conformational heterogeneity. In addition, it is revealed that electrostatic interaction energy contributes much more to KP-Z-41 complex formation than to L-22 complex, which is the main source of energy that results in a higher binding affinity of KP-Z-41 over-22 for TAR RNA. Furthermore, we identified a conserved motif RRK (Arg-Arg-Lys) that is shown to be essential for specific binding of this class of cyclic peptides to TAR RNA. This work can provide a useful insight into the design and modification of cyclic peptide inhibitors targeting the association of HIV-1 Tat and TAR RNA.

Dominant role of the 5' TAR bulge in dimerization of HIV-1 genomic RNA, but no evidence of TAR-TAR kissing during in vivo virus assembly

The 5' untranslated region of HIV-1 genomic RNA (gRNA) contains two stem-loop structures that appear to be equally important for gRNA dimerization: the 57-nucleotide 5' TAR, at the very 5' end, and the 35-nucleotide SL1 (nucleotides 243-277). SL1 is well-known for containing the dimerization initiation site (DIS) in its apical loop. The DIS is a six-nucleotide palindrome. Here, we investigated the mechanism of TAR-directed gRNA dimerization. We found that the trinucleotide bulge (UCU24) of the 5' TAR has dominant impacts on both formation of HIV-1 RNA dimers and maturation of the formed dimers. The ΔUCU trinucleotide deletion strongly inhibited the first process and blocked the other, thus impairing gRNA dimerization as severely as deletion of the entire 5' TAR, and more severely than deletion of the DIS, inactivation of the viral protease, or most severe mutations in the nucleocapsid protein. The apical loop of TAR contains a 10-nucleotide palindrome that has been postulated to stimulate gRNA dimerization by a TAR-TAR kissing mechanism analogous to the one used by SL1 to stimulate dimerization. Using mutations that strongly destabilize formation of the TAR palindrome duplex, as well as compensatory mutations that restore duplex formation to a wild-type-like level, we found no evidence of TAR-TAR kissing, even though mutations nullifying the kissing potential of the TAR palindrome could impair dimerization by a mechanism other than hindering of SL1. However, nullifying the kissing potential of TAR had much less severe effects than ΔUCU. By not uncovering a dimerization mechanism intrinsic to TAR, our data suggest that TAR mutations exert their effect 3' of TAR, yet not on SL1, because TAR and SL1 mutations have synergistic effects on gRNA dimerization.

Examining the relationship between RNA function and motion using nuclear magnetic resonance

The biological function of proteins and nucleic acids relies on their complex structures, yet dynamics provides an additional layer of functional adaptability. Numerous studies have demonstrated that RNA is only able to perform the multitude of functions for which it is responsible by readily changing its conformation in response to binding of proteins or small molecules. Examination of RNA dynamics is therefore essential to understanding its biological function. Nuclear magnetic resonance (NMR) has emerged as a leading technique for the examination of RNA motion and conformational transitions. It can examine domain motions as well as motion with atomic level resolution over a wide range of time scales. This review examines how NMR spectroscopy can be applied to examine the relationship between function and dynamics in RNA.

HIV-1 TAR RNA spontaneously undergoes relevant apo-to-holo conformational transitions in molecular dynamics and constrained geometrical simulations

We report all-atom molecular dynamics and replica exchange molecular dynamics simulations on the unbound human immunodeficiency virus type-1 (HIV-1) transactivation responsive region (TAR) RNA structure and three TAR RNA structures in bound conformations of, in total, approximately 250 ns length. We compare the extent of observed conformational sampling with that of the conceptually simpler and computationally much cheaper constrained geometrical simulation approach framework rigidity optimized dynamic algorithm (FRODA). Atomic fluctuations obtained by replica-exchange molecular dynamics (REMD) simulations agree quantitatively with those obtained by molecular dynamics (MD) and FRODA simulations for the unbound TAR structure. Regarding the stereochemical quality of the generated conformations, backbone torsion angles and puckering modes of the sugar-phosphate backbone were reproduced equally well by MD and REMD simulations, but further improvement is needed in the case of FRODA simulations. Essential dynamics analysis reveals that all three simulation approaches show a tendency to sample bound conformations when starting from the unbound TAR structure, with MD and REMD simulations being superior with respect to FRODA. These results are consistent with the experimental view that bound TAR RNA conformations are transiently sampled in the free ensemble, following a conformation selection model. The simulation-generated TAR RNA conformations have been successfully used as receptor structures for docking. This finding has important implications for RNA-ligand docking in that docking into an ensemble of simulation-generated RNA structures is shown to be a valuable means to cope with large apo-to-holo conformational transitions of the receptor structure.

MD simulations of the dsRBP DGCR8 reveal correlated motions that may aid pri-miRNA binding

Over the past decade, microRNAs (miRNAs) have been shown to affect gene regulation by basepairing with messenger RNA, and their misregulation has been directly linked with cancer. DGCR8, a protein that contains two dsRNA-binding domains (dsRBDs) in tandem, is vital for nuclear maturation of primary miRNAs (pri-miRNAs) in connection with the RNase III enzyme Drosha. The crystal structure of the DGCR8 Core (493-720) shows a unique, well-ordered structure of the linker region between the two dsRBDs that differs from the flexible linker connecting the two dsRBDs in the antiviral response protein, PKR. To better understand the interfacial interactions between the two dsRBDs, we ran extensive MD simulations of isolated dsRBDs (505-583 and 614-691) and the Core. The simulations reveal correlated reorientations of the two domains relative to one another, with the well-ordered linker and C-terminus serving as a pivot. The results demonstrate that motions at the domain interface dynamically impact the conformation of the RNA-binding surface and may provide an adaptive separation distance that is necessary to allow interactions with a variety of different pri-miRNAs with heterogeneous structures. These results thus provide an entry point for further in vitro studies of the potentially unique RNA-binding mode of DGCR8.

Referencing strategy for the direct comparison of nuclear magnetic resonance and molecular dynamics motional parameters in RNA

Nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations are both techniques that can be used to characterize the structural dynamics of biomolecules and their underlying time scales. Comparison of relaxation parameters obtained through each methodology allows for cross validation of techniques and for complementarity in the analysis of dynamics. Here we present a combined NMR/MD study of the dynamics of HIV-1 transactivation response (TAR) RNA. We compute relaxation constants (R(1), R(2), and NOE) and model-free parameters (S(2) and tau) from a 65 ns molecular dynamics (MD) trajectory and compare them with the respective parameters measured in a domain-elongation NMR experiment. Using the elongated domain as the frame of reference for all computed parameters allows for a direct comparison between experiment and simulation. We see good agreement for many parameters and gain further insight into the nature of the local and global dynamics of TAR, which are found to be quite complex, spanning multiple time scales. For the few cases where agreement is poor, comparison of the dynamical parameters provides insight into the limits of each technique. We suggest a frequency-matching procedure that yields an upper bound for the time scale of dynamics to which the NMR relaxation experiment is sensitive.

Domain-elongation NMR spectroscopy yields new insights into RNA dynamics and adaptive recognition

By simplifying the interpretation of nuclear magnetic resonance spin relaxation and residual dipolar couplings data, recent developments involving the elongation of RNA helices are providing new atomic insights into the dynamical properties that allow RNA structures to change functionally and adaptively. Domain elongation, in concert with spin relaxation measurements, has allowed the detailed characterization of a hierarchical network of local and collective motional modes occurring at nanosecond timescale that mirror the structural rearrangements that take place following adaptive recognition. The combination of domain elongation with residual dipolar coupling measurements has allowed the experimental three-dimensional visualization of very large amplitude rigid-body helix motions in HIV-1 transactivation response element (TAR) that trace out a highly choreographed trajectory in which the helices twist and bend in a correlated manner. The dynamic trajectory allows unbound TAR to sample many of its ligand bound conformations, indicating that adaptive recognition occurs by "conformational selection" rather than "induced fit." These studies suggest that intrinsic flexibility plays essential roles directing RNA conformational changes along specific pathways.

Preparation, resonance assignment, and preliminary dynamics characterization of residue specific 13C/15N-labeled elongated DNA for the study of sequence-directed dynamics by NMR

DNA is a highly flexible molecule that undergoes functionally important structural transitions in response to external cellular stimuli. Atomic level spin relaxation NMR studies of DNA dynamics have been limited to short duplexes in which sensitivity to biologically relevant fluctuations occurring at nanosecond timescales is often inadequate. Here, we introduce a method for preparing residue-specific (13)C/(15)N-labeled elongated DNA along with a strategy for establishing resonance assignments and apply the approach to probe fast inter-helical bending motions induced by an adenine tract. Preliminary results suggest the presence of elevated A-tract independent end-fraying internal motions occurring at nanosecond timescales, which evade detection in short DNA constructs and that penetrate deep (7 bp) within the DNA helix and gradually fade away towards the helix interior.

Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs

A broad structural landscape often needs to be characterized in order to fully understand how regulatory RNAs perform their biological functions at the atomic level. We present a protocol for visualizing thermally accessible RNA conformations at atomic-resolution and with timescales extending up to milliseconds. The protocol combines molecular dynamics (MD) simulations with experimental residual dipolar couplings (RDCs) measured in partially aligned (13)C/(15)N isotopically enriched elongated RNA samples. The structural ensembles generated in this manner provide insights into RNA dynamics and its role in functionally important transitions.

Approximate reconstruction of continuous spatially complex domain motions by multialignment NMR residual dipolar couplings

NMR spectroscopy is one of the most powerful techniques for studying the internal dynamics of biomolecules. Current formalisms approximate the dynamics using simple continuous motional models or models involving discrete jumps between a small number of states. However, no approach currently exists for interpreting NMR data in terms of continuous spatially complex motional paths that may feature more than one distinct maneuver. Here, we present an approach for approximately reconstructing spatially complex continuous motions of chiral domains using NMR anisotropic interactions. The key is to express Wigner matrix elements, which can be determined experimentally using residual dipolar couplings, as a line integral over a curve in configuration space containing an ensemble of conformations and to approximate the curve using a series of geodesic segments. Using this approach and five sets of synthetic residual dipolar couplings computed for five linearly independent alignment conditions, we show that it is theoretically possible to reconstruct salient features of a multisegment interhelical motional trajectory obtained from a 65 ns molecular dynamics simulation of a stem-loop RNA. Our study shows that the 3-D atomic reconstruction of complex motions in biomolecules is within experimental reach.

Constraint counting on RNA structures: linking flexibility and function

RNA structures are highly flexible biomolecules that can undergo dramatic conformational changes required to fulfill their diverse functional roles. Constraint counting on a topological network representation of an RNA structure can provide very efficiently detailed insights into the intrinsic flexibility characteristics of the biomolecule. In the network, vertices represent atoms and edges represent covalent and strong non-covalent bonds and angle constraints. Initially, the method has been successfully applied to identify rigid and flexible regions in proteins. Here, we present recent progress in extending the approach to RNA structures. As a case study, we analyze stability characteristics of the ribosomal exit tunnel and relate these findings to the tunnel's active role in co-translational processes.

Ultrahigh resolution characterization of domain motions and correlations by multialignment and multireference residual dipolar coupling NMR

Nuclear magnetic resonance (NMR) residual dipolar couplings (RDCs) provide a unique opportunity for spatially characterizing complex motions in biomolecules with time scale sensitivity extending up to milliseconds. Up to five motionally averaged Wigner rotation elements, (D(0k)2(alphaalpha)), can be determined experimentally using RDCs measured in five linearly independent alignment conditions and applied to define motions of axially symmetric bond vectors. Here, we show that up to 25 motionally averaged Wigner rotation elements, (D(mk)2(alphabetagamma)), can be determined experimentally from multialignment RDCs and used to characterize rigid-body motions of chiral domains. The 25 (D(mk)2(alphabetagamma)) elements form a basis set that allows one to measure motions of a domain relative to an isotropic distribution of reference frames anchored on a second domain (and vice versa), thus expanding the 3D spatial resolution with which motions can be characterized. The 25 (D(mk)2(alphabetagamma)) elements can also be used to fit an ensemble consisting of up to eight equally or six unequally populated states. For more than two domains, changing the identity of the domain governing alignment allows access to new information regarding the correlated nature of the domain fluctuations. Example simulations are provided that validate the theoretical derivation and illustrate the high spatial resolution with which rigid-body domain motions can be characterized using multialignment and multireference RDCs. Our results further motivate the development of experimental approaches for both modulating alignment and anchoring it on specifically targeted domains.

Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition

We describe a strategy for constructing atomic resolution dynamical ensembles of RNA molecules, spanning up to millisecond timescales, that combines molecular dynamics (MD) simulations with NMR residual dipolar couplings (RDC) measured in elongated RNA. The ensembles are generated via a Monte Carlo procedure by selecting snap-shot from an MD trajectory that reproduce experimentally measured RDCs. Using this approach, we construct ensembles for two variants of the transactivation response element (TAR) containing three (HIV-1) and two (HIV-2) nucleotide bulges. The HIV-1 TAR ensemble reveals significant mobility in bulge residues C24 and U25 and to a lesser extent U23 and neighboring helical residue A22 that give rise to large amplitude spatially correlated twisting and bending helical motions. Omission of bulge residue C24 in HIV-2 TAR leads to a significant reduction in both the local mobility in and around the bulge and amplitude of inter-helical bending motions. In contrast, twisting motions of the helices remain comparable in amplitude to HIV-1 TAR and spatial correlations between them increase significantly. Comparison of the HIV-1 TAR dynamical ensemble and ligand bound TAR conformations reveals that several features of the binding pocket and global conformation are dynamically preformed, providing support for adaptive recognition via a ‘conformational selection’ type mechanism.

Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme

Despite numerous structural and biochemical investigations, the catalytic mechanism of hairpin ribozyme self-cleavage remains elusive. To gain insight into the coupling of active site dynamics with activity of this small catalytic RNA, we analyzed a total of approximately 300 ns of molecular dynamics (MD) simulations. Our simulations predict improved global stability for an in vitro selected "gain of function" mutation, which is validated by native gel electrophoretic mobility shift assay. We observe that active site nucleobases and water molecules stabilize a geometry favorable to catalysis through a dynamic hydrogen bonding network. Simulations in which A38 is unprotonated show its N1 move into close proximity of the active site 2'-OH, indicating that A38 may act as a general base during cleavage, a role that has generally been discounted due to the longer distances observed in crystal structures involving inactivating substrate analogs. By contrast, simulations in which N1 of A38 is protonated place N1 in close proximity to the 5'-oxygen leaving group, which supports the proposal that A38 serves as a general acid. In analogy to protein enzymes, we discuss a plausible mechanism in which A38 acts bifunctionally and shuttles a proton directly from the 2'-OH to the 5'-oxygen. Furthermore, our simulations suggest an important role for protonation of N1 of A38 in promoting a favorable geometry similar to that observed in transition-state analog crystal structures, and support previously proposed roles of A38, G8, and long residency water molecules in transition-state stabilization.

How binding of small molecule and peptide ligands to HIV-1 TAR alters the RNA motional landscape

The HIV-1 TAR RNA represents a well-known paradigm to study the role of dynamics and conformational change in RNA function. This regulatory RNA changes conformation in response to binding of Tat protein and of a variety of peptidic and small molecule ligands, indicating that its conformational flexibility and intrinsic dynamics play important roles in molecular recognition. We have used ¹³C NMR relaxation experiments to examine changes in the motional landscape of HIV-1 TAR in the presence of three ligands of different affinity and specificity. The ligands are argininamide, a linear peptide mimic of the Tat basic domain and a cyclic peptide that potently inhibits Tat-dependent activation of transcription. All three molecules induce the same motional characteristics within the three nucleotides bulge that represents the Tat-binding site. However, the cyclic peptide has a unique motional signature in the apical loop, which represents a binding site for the essential host co-factor cyclin T1. These results suggest that all peptidic mimics of Tat induce the same dynamics in TAR within this protein binding site. However, the new cyclic peptide mimic of Tat represents a new class of ligands with a unique effect on the dynamics and the structure of the apical loop.

Thermodynamic examination of trinucleotide bulged RNA in the context of HIV-1 TAR RNA

RNA structures contain many bulges and loops that are expected to be sites for inter- and intra-molecular interactions. Nucleotides in the bulge are expected to influence the structure and recognition of RNA. The same stability is assigned to all trinucleotide bulged RNA in the current secondary structure prediction models. In this study thermal denaturation experiments were performed on four trinucleotide bulged RNA, in the context of HIV-1 TAR RNA, to determine whether the bulge sequence affects RNA stability and its divalent ion interactions. Cytosine-rich bulged RNA were more stable than uracil-rich bulged RNA in 1 M KCl. Interactions of divalent ions were more favorable with uracil-rich bulged RNA by approximately 2 kcal/mol over cytosine-rich bulged RNA. The UCU-TAR RNA (wild type) is stabilized by 1.7 kcal/mol in 9.5 mM Ca(2+) as compared with 1 M KCl, whereas no additional gain in stability is measured for CCC-TAR RNA. These results have implications for base substitution experiments traditionally employed to identify metal ion binding sites. To our knowledge, this is the first systematic study to quantify the effect of small sequence changes on RNA stability upon interactions with divalent ions.

RNA in motion

Although RNA duplex regions are highly structured and inflexible, other elements of an RNA molecule are capable of dynamic motions. These flexible regions are the sites of interactions with small molecules, proteins, and other RNAs, yet there are few descriptions of these regions that include the timescale and amplitude of their motions. No one technique is sufficient to accurately describe these motions, but the combination of in vitro methods, particularly NMR relaxation methods, and more robust in silico methods, is beginning to yield the type of data that can be used to understand RNA function. Very few RNAs have been described by both techniques, and here one such RNA and one RNA:protein complex are reviewed.

Pressure effects on the ensemble dynamics of ubiquitin inspected with molecular dynamics simulations and isotropic reorientational eigenmode dynamics

According to NMR chemical shift data, the ensemble of ubiquitin is a mixture of "open" and "closed" conformations at rapid equilibrium. Pressure perturbations provide the means to study the transition between the two conformers by imposing an additional constraint on the system's partial molar volume. Here we use nanosecond-timescale molecular dynamics simulations to characterize the network of correlated motions accessible to the conformers at low- and high-pressure conditions. Using the isotropic reorientational eigenmode dynamics formalism to analyze our simulation trajectories, we reproduce NMR relaxation data without fitting any parameters of our model. Comparative analysis of our results suggests that the two conformations behave very differently. The dynamics of the "closed" conformation are almost unaffected by pressure and are dominated by large-amplitude correlated motions of residues 23-34 in the extended alpha-helix. The "open" conformation under conditions of normal pressure displays increased mobility, focused on the loop residues 17-20, 46-55, and 58-59 at the bottom of the core of the structure, as well as the C-terminal residues 69-76, that directly participate in key protein-protein interactions. For the same conformation, a pressure increase induces a loss of separability between molecular tumbling and internal dynamics, while motions between different backbone sites become uncorrelated.

Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis

The HIV-1 transactivation response element (TAR) RNA binds a variety of proteins and is a target for developing anti-HIV therapies. TAR has two primary binding sites: a UCU bulge and a CUGGGA apical loop. We used NMR residual dipolar couplings, carbon spin relaxation (R(1) and R(2)), and relaxation dispersion (R(1rho)) in conjunction with molecular dynamics and mutagenesis to characterize the dynamics of the TAR apical loop and investigate previously proposed long-range interactions with the distant bulge. Replacement of the wild-type apical loop with a UUCG loop did not significantly affect the structural dynamics at the bulge, indicating that the apical loop and the bulge act largely as independent dynamical recognition centers. The apical loop undergoes complex dynamics at multiple timescales that are likely important for adaptive recognition: U31 and G33 undergo limited motions, G32 is highly flexible at picosecond-nanosecond timescales, and G34 and C30 form a dynamic Watson-Crick basepair in which G34 and A35 undergo a slow (approximately 30 mus) likely concerted looping in and out motion, with A35 also undergoing large amplitude motions at picosecond-nanosecond timescales. Our study highlights the power of combining NMR, molecular dynamics, and mutagenesis in characterizing RNA dynamics.