Anesthetic molecules embedded in a lipid membrane: a computer simulation study

The effect of four general anesthetic molecules, i.e., chloroform, halothane, diethyl ether and enflurane, on the properties of a fully hydrated dipalmitoylphosphatidylcholine (DPPC) membrane is studied in detail by long molecular dynamics simulations. Furthermore, to address the problem of pressure reversal, the effect of pressure on the anesthetic containing membranes is also investigated. In order to ensure sufficient equilibration and adequate sampling, the simulations performed have been at least an order of magnitude longer than the studies reported previously in the literature on general anesthetics. The results obtained can help in resolving several long-standing contradictions concerning the effect of anesthetics, some of which were the consequence of too short simulation time used in several previous studies. More importantly, a number of seeming contradictions are found to originate from the fact that different anesthetic molecules affect the membrane structure differently in several respects. In particular, halothane, being able to weakly hydrogen bound to the ester group of the lipid tails, is found to behave in a markedly different way than the other three molecules considered. Besides, we also found that two changes, namely lateral expansion of the membrane and increasing local disorder in the lipid tails next to the anesthetic molecules, are clearly induced by all four anesthetic molecules tested here in the same way, and both of these effects are reverted by the increase in pressure.     

Characterization of conformational exchange of a histidine side chain: protonation, rotamerization, and tautomerization of His61 in plastocyanin from Anabaena variabilis

A model describing conformational exchange of His 61 in plastocyanin from Anabaena variabilis is presented. A detailed picture of the exchange dynamics has been obtained using solution NMR relaxation measurements, chemical shift titrations, and structural information provided by a high-resolution crystal structure of the protein. A three-site model for chemical exchange that involves interconversion among the tautomeric and protonated forms of the histidine side chain with rates that are fast on the NMR chemical shift time scale can account for all of the data. In general, in the limit of fast exchange, it is not possible to obtain separate measures of chemical shift differences and populations of the participating states using NMR. However, we show here that when the data mentioned above are combined, it is possible to extract values of all of the parameters that characterize the exchange process, including rates, populations, and chemical shift changes, and to provide cross-validations that establish their accuracy. The methodology is generally applicable to the study of histidine side chain dynamics, which can play an important functional role in many protein systems.     

Ethanol and halothane differently modulate HLA class I and class II oligomerization. A new look at the mode of action of anesthetic agents through fluorescence spectroscopy

The field of research considering the working mechanism of anesthetic agents is a complex one and the site or sites of action of general anesthetics are yet to be elucidated. Through the years, on the molecular level, the discussion has shifted from the lipid theories to the more specific interaction with the proteins responsible for the signal transduction. While this approach led to several models, they offer, at best, partial explanations for the observed phenomena. Anesthetic agents interact with many systems, of which the neuronal is best studied, leaving interaction with the immune defense system relatively unexplored. In this study we focus on the interaction of ethanol and halothane with the co-localization on the membrane of HLA I and II molecules. We show that ethanol tends to randomize the distribution of HLA I and II molecules, while halothane increases the clustering of HLA I proteins. The notion that anesthetics modulate cell function by disrupting clustering and thereby promoting a random distribution is a novel approach that may explain the general involvement of many systems during exposition to anesthetic drugs. In this study we show the disturbance of co-localization of molecules that may form a functional network. The relevance of this finding depends on the importance of these networks for extracellular and intracellular processes.     

Temperature dependence of thermodynamic activity in volatile anesthetics: correlation between anesthetic potency and activity

Temperature dependence of the saturated concentration and the activity coefficient of anesthetics (1-propanol, diethyl ether, chloroform, and halothane) in water were evaluated using vapor pressure and H NMR measurement. We found that these physical values (quantities) correlate with anesthetic potencies estimated according to the thermodynamic equilibrium model. The anesthetic potency for hydrophilic anesthetic (diethyl ether) decreased with decreasing temperature because of the temperature specificity of this saturated concentration. In contrast, potencies of hydrophobic anesthetics (chloroform and halothane) increased with decreasing temperature because of the temperature specificity of those activity coefficients. By assuming that anesthetics interact with hydrated water of cell membranes, the temperature dependence of anesthetic potencies in vivo is qualitatively explicable.     

Unravelling the Time Scale of Conformational Plasticity and Allostery in Glycan Recognition by Human Galectin-1

The interaction of human galectin-1 with a variety of oligosaccharides, from di-(N-acetyllactosamine) to tetra-saccharides (blood B type-II antigen) has been scrutinized by using a combined approach of different NMR experiments, molecular dynamics (MD) simulations, and isothermal titration calorimetry. Ligand- and receptor-based NMR experiments assisted by computational methods allowed proposing three-dimensional structures for the different complexes, which explained the lack of enthalpy gain when increasing the chemical complexity of the glycan. Interestingly, and independently of the glycan ligand, the entropy term does not oppose the binding event, a rather unusual feature for protein-sugar interactions. CLEANEX-PM and relaxation dispersion experiments revealed that sugar binding affected residues far from the binding site and described significant changes in the dynamics of the protein. In particular, motions in the microsecond-millisecond timescale in residues at the protein dimer interface were identified in the presence of high affinity ligands. The dynamic process was further explored by extensive MD simulations, which provided additional support for the existence of allostery in glycan recognition by human galectin-1.     

Steered molecular dynamics simulations of Na+ permeation across the gramicidin A channel

The potential of mean forces (PMF) governing Na+ permeation through gramicidin A (gA) channels with explicit water and membrane was characterized using steered molecular dynamics (SMD) simulations. Constant-force SMD with a steering force parallel to the channel axis revealed at least seven energy wells in each monomer of the channel dimer. Except at the channel dimer interface, each energy well is associated with at least three and at most four backbone carbonyl oxygens and two water oxygens in a pseudo-hexahedral or pseudo-octahedral coordination with the Na+ ion. Repeated constant-velocity SMD by dragging a Na+ ion from each energy well in opposite directions parallel to the channel axis allowed the computation of the PMF across the gA channel, revealing a global minimum corresponding to Na+ binding sites near the entrance of gA at +/-9.3 A from the geometric center of the channel. The effect of volatile anesthetics on the PMF was also analyzed in the presence of halothane molecules. Although the accuracy of the current PMF calculation from SMD simulations is not yet sufficient to quantify the PMF difference with and without anesthetics, the comparison of the overall PMF profiles nevertheless confirms that the anesthetics cause insignificant changes to the structural makeup of the free energy wells along the channel and the overall permeation barrier. On average, the PMF appears less rugged in the outer part of the channel in the presence of anesthetics, consistent with our earlier finding that halothane interaction with anchoring residues makes the gA channel more dynamic. A causal relationship was observed between the reorientation of the coordinating backbone carbonyl oxygen and Na+ transit from one energy well to another, suggesting the possibility that even minute changes in the conformation of pore-lining residues due to dynamic motion could be sufficient to trigger the ion permeation. Because some of the carbonyl oxygens contribute to Na+ coordination in two adjacent energy wells, our SMD results reveal that the atomic picture of ion "hopping" through a gA channel actually involves a Na+ ion being carried in a relay by the coordinating oxygens from one energy well to the next. Steered molecular dynamics complements other computational approaches as an attractive means for the atomistic interpretation of experimental permeation studies.     

Backbone motions of free and pheromone-bound major urinary protein I studied by molecular dynamics simulation

Molecular motions of free and pheromone-bound mouse major urinary protein I, previously investigated by NMR relaxation, were simulated in 30 ns molecular dynamics (MD) runs. The backbone flexibility was described in terms of order parameters and correlation times, commonly used in the NMR relaxation analysis. Special attention was paid to the effect of conformational changes on the nanosecond time scale. Time-dependent order parameters were determined in order to separate motions occurring on different time scales. As an alternative approach, slow conformational changes were identified from the backbone torsion angle variances, and "conformationally filtered" order parameters were calculated for well-defined conformation states. A comparison of the data obtained for the free and pheromone-bound protein showed that some residues are more rigid in the bound form, but a larger portion of the protein becomes more flexible upon the pheromone binding. This finding is in general agreement with the NMR results. The higher flexibility observed on the fast (fs-ps) time scale was typically observed for the residues exhibiting higher conformational freedom on the ns time scale. An inspection of the hydrogen bond network provided a structural explanation for the flexibility differences between the free and pheromone-bound proteins in the simulations.     

Binding of the general anesthetics chloroform and 2,2,2-trichloroethanol to the hydrophobic core of a four-alpha-helix bundle proteins

The structural features of general anesthetic binding sites on proteins are being examined using a defined model system consisting of a four-alpha-helix bundle scaffold with a hydrophobic core. Previous work suggested that halothane binding to the four-alpha-helix bundle was improved by (1) introducing a cavity into the hydrophobic core and (2) substituting a methionine side-chain in place of an alpha-helical heptad e position leucine. In this study, the ability of the general anesthetics chloroform and 2,2,2-trichloroethanol to bind to the hydrophobic core of the four-alpha-helix bundle (Aalpha2-L38M)2 is explored. The halogenated alkane chloroform binds with a dissociation constant (Kd) = 1.4 +/- 0.2 mM, whereas 2,2,2-trichloroethanol binds with a Kd = 19.5 +/- 1.2 mM. The affinity of both general anesthetics for the hydrophobic core of the four-alpha-helix bundle approximates their whole animal effective concentration in 50% of test subjects' (EC50) values, as shown previously for halothane. Tryptophan phosphorescence decay rates at 77 K are accelerated by a factor of 4.5 by both bound halothane and chloroform, indicating that the heavy-atom effect is responsible for a portion of the observed fluorescence quenching. Because heavy-atom effects are operative only at short distances, the findings indicate that these general anesthetics are binding in the vicinity of the indole rings of W15 in the hydrophobic core of the four-alpha-helix bundle scaffold. The results indicate that chloroform, halothane and 2,2,2-trichloroethanol may occupy the same sites on protein targets.     

Application of the 19F NMR technique to observe binding of the general anesthetic halothane to human serum albumin.

19F NMR techniques were employed to characterize the binding property of the widely used general anesthetic halothane with human serum albumin (HSA). It was found that 19F(1H) NOE and 2D 1H-19F HOESY experiments detected intermolecular NOEs between halothane 19F and HSA protons. Measurements of the diffusion coefficients for halothane were also carried out by 1H and 19F NMR, indicating the interaction of halothane with HSA. The present results indicate that these techniques are very suitable to identify a fluorine-containing ligand binding with a protein receptor in the drug-discovery process.     

Morphological transitions in model membrane systems by the addition of anesthetics

The mechanism of anesthetic action on membranes is still an open question, regardless of their extensive use in medical practice. It has been proposed that anesthetics may have the effect of promoting pore formation across membranes or at least switching transmembrane channels. In both cases this may be the result of changes in the interfacial curvature of the membrane due to the presence of anesthetic molecules. Aqueous solutions of surfactants display phases that mimic, in a simplified manner, real biological membranes. Therefore, in this study, two nonionic surfactant systems C16E6/H2O in concentrated solution and C10E3/H2O in dilute solution have been used as model membranes for the investigation of the effects of six common anesthetics (halothane, sodium thiopental, lidocaine base form and hydrochloride, prilocaine hydrochloride, and ketamine hydrochloride). Both binary surfactant-water systems exhibit phase transitions from the lamellar phase, Lalpha, that has zero spontaneous curvature and zero monolayer curvature to phases with more local interfacial curvature. These are the random mesh phase, Mh1(0), which consists of lamellae pierced by water-filled pores with local areas of positive interfacial curvature and the sponge phase, L3, that consists of the lamellar phase with interlamellae attachments, often referred to as a "melted" cubic phase, possessing negative monolayer curvature. Small-angle X-ray scattering and 2H NMR experiments upon the C16E6/2H2O system and optical observations of the C10E3/H2O system showed that all anesthetics employed in this study cause a shift in the Mh1(0) to Lalpha phase transition temperature and in the Lalpha to L3 transition temperature, respectively. All of the anesthetics studied bind to the interfacial region of the surfactant systems. Two types of behavior were observed on anesthetic addition: type I anesthetics, which decreased interfacial curvature, and type II, which increased it. However, at physiological pH both types of anesthetics decreased interfacial curvature.     

Nonexponential polymer segmental motion in the presence and absence of ions: 2H NMR multitime correlation functions for polymer electrolytes poly(propylene glycol)-LiClO4

The authors measure 2H NMR multitime correlation functions to investigate the segmental motion of poly(propylene glycol) containing various amounts of the salt LiClO4. 2H NMR two-time correlation functions indicate that addition of salt affects not only the time scale of the segmental motion, but also the degree of the nonexponential relaxation behavior. To quantify the origin of the nonexponential segmental motion, the authors analyze 2H NMR three-time correlation functions. In general, nonexponential relaxation can result from homogeneous dynamics, i.e., intrinsic nonexponentiality, and from heterogeneous dynamics, i.e., existence of a distribution of correlation times G(ln tau). For the studied high and low salt concentrations, including neat poly(propylene glycol), the analysis shows that both homogeneous and heterogeneous contributions are important. 2H NMR four-time correlation functions allow the authors to measure the lifetime of the dynamical heterogeneities. For the studied salt concentrations, the rate exchange occurs on the same time scale as the segmental motion, indicating short-lived dynamical heterogeneities. To arrive at these results, the authors reconsider the interpretation of (2)H NMR three-time correlation functions. Results of analytical calculations and computer simulations show that it is necessary to extend the previous way of analysis so as to include effects due to correlated back-and-forth jumps.     

A model for binding of inhalation anesthetics to membranes: two dose-dependent distinctly different binding modes

Inhalation anesthetics currently in clinical use, such as halothane, methoxyflurane, enflurane, isoflurane, etc., are polar hydrophobic molecules, except nitrous oxide, which is an apolar and weak anesthetic, incapable of inducing surgical stage anesthesia. Experimental data are accumulating that these potent amphipathic inhalation anesthetics preferentially bind membranes and macromolecules on the surface at clinical concentrations. The anesthetic binding to lipid membranes in the low concentration range is characterized by a saturable curve approaching to a limiting value. When the anesthetic concentration s greatly increased above the clinical range, the binding starts to exceed the limiting saturation value. Our model for anesthetic binding to membranes consists of two parts: Langmuir-type adsorption to the membrane surface at the low concentration range and penetration into the hydrophobic core at the high concentration range. The present communication provides a statistical-thermodynamic basis to analyze this twostep interaction. An expression is derived for membrane capacitance as a function of anesthetic concentration, which explains the experimental data well. Binding parameters of anesthetics are estimated according to the theory.This study was supported by NIH grants GM 25716 and GM 26950, and by the Medical Research Service of the Veterans Administration.     

Disulfide bond isomerization in basic pancreatic trypsin inhibitor: multisite chemical exchange quantified by CPMG relaxation dispersion and chemical shift modeling

Conformational changes occurring on the microsecond-millisecond time scale in basic pancreatic trypsin inhibitor (BPTI) are investigated using nuclear magnetic resonance spectroscopy. The rczz CPMG experiment (Wang, C.; Grey, M. J.; Palmer, A. G. J. Biomol. NMR 2001, 21, 361-366) is used to record (15)N spin relaxation dispersion data, R(ex)(1/tau(cp)), in which 1/tau(cp) is the pulsing rate in the CPMG sequence, at two static magnetic fields, 11.7 and 14.1 T, and three temperatures, 280, 290, and 300 K. These data are used to characterize the kinetics and mechanism of chemical exchange line broadening of the backbone (15)N spins of Cys 14, Lys 15, Cys 38, and Arg 39 in BPTI. Line broadening is found to result from two processes: the previously identified isomerization of the Cys 38 side chain between chi(1) rotamers (Otting, G.; Liepinsh, E.; Wüthrich, K. Biochemistry 1993, 32, 3571-3582) and a previously uncharacterized process on a faster time scale. At 300 K, both processes contribute significantly to the relaxation dispersion for Cys 14 and an analytical expression for a linear three-site exchange model is used to analyze the data. At 280 K, isomerization of the Cys 38 side chain is negligibly slow and the faster process dominates the relaxation dispersion for all four spins. Global analysis of the temperature and static field dependence of R(ex)(1/tau(cp)) for Cys 14 and Lys 15 is used to determine the activation parameters and chemical shift changes for the previously uncharacterized chemical exchange process. Through an analysis of a database of chemical shifts, (15)N chemical shift changes for Cys 14 and Lys 15 are interpreted to result from a chi(1) rotamer transition of Cys 14 that converts the Cys 14-Cys 38 disulfide bond between right- and left-handed conformations. At 290 K, isomerization of Cys 14 occurs with a forward and reverse rate constant of 35 s(-1) and 2500 s(-1), respectively, a time scale more than 30-fold faster than the Cys 38 chi(1) isomerization. A comparison of the kinetics and thermodynamics for the transitions between the two alternative Cys 14-Cys 38 conformations highlights the factors that affect the contribution of disulfide bonds to protein stability.     

Differential line broadening in MAS solid-state NMR due to dynamic interference

Many MAS (magic angle spinning) solid-state NMR investigations of biologically relevant protein samples are hampered by poor resolution, particularly in the 15N chemical shift dimension. We show that dynamics in the nanosecond-microsecond time scale in solid-state samples can induce significant line broadening of 15N resonances in solid-state NMR experiments. Averaging of 15NH(alpha/beta) multiplet components due to 1H decoupling induces effective relaxation of the 15N coherence in case the N-H spin pair undergoes significant motion. High resolution solid-state NMR spectra can then only be recorded by application of TROSY (Transverse Relaxation Optimized Spectroscopy) type techniques which select the narrow component of the multiplet pattern. We speculate that this effect has been the major obstacle to the NMR spectroscopic characterization of many membrane proteins and fibrillar aggregates so far. Only in very favorable cases, where dynamics are either absent or very fast (picosecond), high-resolution spectra were obtained. We expect that this approach which requires intense deuteration will have a significant impact on the quality and the rate at which solid-state NMR spectroscopic investigations will emerge in the future.     

Millisecond dynamics in glutaredoxin during catalytic turnover is dependent on substrate binding and absent in the resting states

Conformational dynamics is important for enzyme function. Which motions of enzymes determine catalytic efficiency and whether the same motions are important for all enzymes, however, are not well understood. Here we address conformational dynamics in glutaredoxin during catalytic turnover with a combination of NMR magnetization transfer, R(2) relaxation dispersion, and ligand titration experiments. Glutaredoxins catalyze a glutathione exchange reaction, forming a stable glutathinoylated enzyme intermediate. The equilibrium between the reduced state and the glutathionylated state was biochemically tuned to exchange on the millisecond time scale. The conformational changes of the protein backbone during catalysis were followed by (15)N nuclear spin relaxation dispersion experiments. A conformational transition that is well described by a two-state process with an exchange rate corresponding to the glutathione exchange rate was observed for 23 residues. Binding of reduced glutathione resulted in competitive inhibition of the reduced enzyme having kinetics similar to that of the reaction. This observation couples the motions observed during catalysis directly to substrate binding. Backbone motions on the time scale of catalytic turnover were not observed for the enzyme in the resting states, implying that alternative conformers do not accumulate to significant concentrations. These results infer that the turnover rate in glutaredoxin is governed by formation of a productive enzyme-substrate encounter complex, and that catalysis proceeds by an induced fit mechanism rather than by conformer selection driven by intrinsic conformational dynamics.     

Measurement of slow (micros-ms) time scale dynamics in protein side chains by (15)N relaxation dispersion NMR spectroscopy: application to Asn and Gln residues in a cavity mutant of T4 lysozyme.

A new NMR experiment is presented for the measurement of micros-ms time scale dynamics of Asn and Gln side chains in proteins. Exchange contributions to the (15)N line widths of side chain residues are determined via a relaxation dispersion experiment in which the effective nitrogen transverse relaxation rate is measured as a function of the number of refocusing pulses in constant-time, variable spacing CPMG intervals. The evolution of magnetization from scalar couplings and dipole-dipole cross-correlations, which has limited studies of exchange in multi-spin systems in the past, does not affect the extraction of accurate exchange parameters from relaxation profiles of NH(2) groups obtained in the present experiment. The utility of the method is demonstrated with an application to a Leu --> Ala cavity mutant of T4 lysozyme, L99A. It is shown that many of the side chain amide groups of Asn and Gln residues in the C-terminal domain of the protein are affected by a chemical exchange process which may be important in facilitating the rapid binding of hydrophobic ligands to the cavity.     

Characterization of micros-ms dynamics of proteins using a combined analysis of 15N NMR relaxation and chemical shift: conformational exchange in plastocyanin induced by histidine protonations

An approach is presented that allows a detailed, quantitative characterization of conformational exchange processes in proteins on the micros-ms time scale. The approach relies on a combined analysis of NMR relaxation rates and chemical shift changes and requires that the chemical shift of the exchanging species can be determined independently of the relaxation rates. The applicability of the approach is demonstrated by a detailed analysis of the conformational exchange processes previously observed in the reduced form of the blue copper protein, plastocyanin from the cyanobacteria Anabaena variabilis (A.v. PCu) (Ma, L.; Hass, M. A. S.; Vierick, N.; Kristensen, S. M.; Ulstrup, J.; Led, J. J. Biochemistry 2003, 42, 320-330). The R1 and R2 relaxation rates of the backbone 15N nuclei were measured at a series of pH and temperatures on an 15N labeled sample of A.v. PCu, and the 15N chemical shifts were obtained from a series of HSQC spectra recorded in the pH range from 4 to 8. From the R1 and R2 relaxation rates, the contribution, Rex, to the transverse relaxation caused by the exchanges between the different allo-states of the protein were determined. Specifically, it is demonstrated that accurate Rex terms can be obtained from the R1 and R2 rates alone in the case of relatively rigid proteins with a small rotational anisotropy. The Rex terms belonging to the same exchange process were identified on the basis of their pH dependences. Subsequently the identifications were confirmed quantitatively by the correlation between the Rex terms and the corresponding chemical shift differences of the exchanging species. By this approach, the Rex terms of 15N nuclei belonging to contiguous regions in the protein could be assigned to the same exchange process. Furthermore, the analysis of the exchange terms shows that the observed micros-ms dynamics in A.v. PCu are caused primarily by the protonation/deprotonation of two histidine residues, His92 and His61, His92 being ligated to the Cu(I) ion. Also the exchange rate of the protonation/deprotonation process of His92 and its pH and temperature dependences were determined, revealing a reaction pathway that is more complex than a simple specific-acid/base catalysis. Finally, the approach allows a differentiation between two-site and multiple-site exchange processes, thus revealing that the protonation/deprotonation of His61 is at least a three-site exchange process. Overall, the approach makes it feasible to obtain exchange rates that are sufficiently accurate and versatile for studies of the kinetics and the mechanisms of local protein dynamics on the sub-millisecond time scale.     

SHARP-TACSY: triple-band tailored correlated spectroscopy for base-to-sugar transfer in nucleic acid residues with intermediate time scale motions

Established experiments to identify the sugar-to-base connectivity in isotopically labeled RNA require long transfer periods and are inefficient for residues undergoing intermediate time scale motions (microsecond to millisecond). Here, an alternative transfer experiment is introduced, whereby the C1'-N1/9-C6/8 spin system is selectively brought to the so-called Hartmann-Hahn condition using selectiveheteronuclear planar triple-band tailored correlated spectroscopy (SHARP-TACSY). Results are shown for the fully labeled 30-mer oligonucleotide TAR RNA with particular attention placed on residues from and close to the bulge and the loop. For these residues, the faster relaxation can be attributed to exchange contributions stemming from transient stacking and unstacking of the bases and/or from the isomerization of the ribose sugar pucker. The new experiment shows improved signal-to-noise for residues exhibiting large microsecond-millisecond time scale motions with respect to established experiments, thus providing a valid alternative for resonance assignment in mobile RNA regions.     

Temperature dependence of solvation dynamics and anisotropy decay in a protein: ANS in bovine serum albumin

Temperature dependence of solvation dynamics and fluorescence anisotropy decay of 8-anilino-1-naphthalenesulfonate (ANS) bound to a protein, bovine serum albumin (BSA), are studied. Solvation dynamics of ANS bound to BSA displays a component (300 ps) which is independent of temperature in the range of 278-318 K and a long component which decreases from 5800 ps at 278 K to 3600 ps at 318 K. The temperature independent part is ascribed to a dynamic exchange of bound to free water with a low barrier. The temperature variation of the long component of solvation dynamics corresponds to an activation energy of 2.1 kcal mol(-1). The activation energy is ascribed to local segmental motion of the protein along with the associated water molecules and polar residues. The time scale of solvation dynamics is found to be very different from the time scale of anisotropy decay. The anisotropy decays are analyzed in terms of the wobbling motion of the probe (ANS) and the overall tumbling of the protein.     

Changes in dynamics of SRE-RNA on binding to the VTS1p-SAM domain studied by 13C NMR relaxation

RNA recognition by proteins is often accompanied by significant changes in RNA dynamics in addition to conformational changes. However, there are very few studies which characterize the changes in molecular motions in RNA on protein binding. We present a quantitative (13)C NMR relaxation study of the changes in RNA dynamics in the pico-nanosecond time scale and micro-millisecond time scale resulting from interaction of the stem-loop SRE-RNA with the VTS1p-SAM domain. (13)C relaxation rates of the protonated carbons of the nucleotide base and anomeric carbons have been analyzed by employing the model-free formalism, for a fully (13)C/(15)N-labeled sample of the SRE-RNA in the free and protein-bound forms. In the free RNA, the nature of molecular motions are found to be distinctly different in the stem and the loop region. On binding to the protein, the nature of motions becomes more homogeneous throughout the RNA, with many residues showing increased flexibility at the aromatic carbon sites, while the anomeric carbon sites become more rigid. Surprisingly, we also observe indications of a slow collective motion of the RNA in the binding pocket of the protein. The observation of increased motions on binding is interesting in the context of growing evidence that binding does not always lead to motional restrictions and the resulting entropy gain could favor the free energy of association.