Tryptophan sidechain dynamics in hydrophobic oligopeptides determined by use of 13C nuclear magnetic resonance spectroscopy

Quantifying the effects of long-range 13C-13C dipolar coupling on measured relaxation rates in RNA

Selective stable isotope labeling has transformed structural and dynamics analysis of RNA by NMR spectroscopy. These methods can remove ¹³C-¹³C dipolar couplings that complicate ¹³C relaxation analyses. While these phenomena are well documented for sites with adjacent ¹³C nuclei (e.g. ribose C1'), less is known about so-called isolated sites (e.g. adenosine C2). To investigate and quantify the effects of long-range (> 2 Å) ¹³C-¹³C dipolar interactions on RNA dynamics, we simulated adenosine C2 relaxation rates in uniformly [U-¹³C/¹⁵N]-ATP or selectively [2-¹³C]-ATP labeled RNAs. Our simulations predict non-negligible ¹³C-¹³C dipolar contributions from adenosine C4, C5, and C6 to C2 longitudinal (R₁) relaxation rates in [U-¹³C/¹⁵N]-ATP labeled RNAs. Moreover, these contributions increase at higher magnetic fields and molecular weights to introduce discrepancies that exceed 50%. This will become increasingly important at GHz fields. Experimental R₁ measurements in the 61 nucleotide human hepatitis B virus encapsidation signal ε RNA labeled with [U-¹³C/¹⁵N]-ATP or [2-¹³C]-ATP corroborate these simulations. Thus, in the absence of selectively labeled samples, long-range ¹³C-¹³C dipolar contributions must be explicitly taken into account when interpreting adenosine C2 R₁ rates in terms of motional models for large RNAs.

The temperature-dependent single-crystal Raman spectroscopy of a model dipeptide: L-Alanyl-L-alanine

A single-crystal of peptide L-alanyl-L-alanine (C6H12N2O3) was studied by Raman spectroscopy at low-temperature, and a tentative assignment of the normal modes was given. Evidence of a second order structural phase transition was found through Raman spectroscopy between the temperatures of 80K and 60K. Group theory considerations suggest that the transition leads the sample from the tetragonal to a monoclinic structure. Additionally, our study suggests that the mechanism for the structural phase transition is governed by the occupation of non-equivalent C1 local symmetry sites by the CH3 molecular groups. Analysis based on group theory suggests L-alanyl-L-alanine presents C2 symmetry at low temperatures.

A graphical method for the analysis of anisotropic rotational diffusion in proteins

A graphical method for the analysis of relaxation data is presented. It allows a fast estimation of the range of values of the components of the axially symmetric rotational diffusion tensor that are compatible with the experimental relaxation data. The graphical method clearly shows the contribution of different experimental relaxation parameters to the measured anisotropy. In particular, for proteins with moderate anisotropy, data from at least two N-H bonds forming angles close to 0 degrees and 90 degrees with respect to the principal axis of the rotational diffusional tensor are needed. For very anisotropic systems, combination of different relaxation parameters from a single residue is enough to characterize the local anisotropy.

Estimation of dynamic parameters from NMR relaxation data using the Lipari-Szabo model-free approach and Bayesian statistical methods

In order to analyze NMR relaxation data in terms of parameters which describe internal motion, one must first obtain a description of the overall tumbling of the macromolecule in solution. Methods currently used to estimate these global parameters may not always provide reliable estimates of their values and uncertainties. In this paper, we present a general data analysis formalism based on products of Bayesian marginal probability densities which can be used to efficiently combine the information content from multiple experiments, such as R(1), R(2), and NOE data collected at multiple magnetic field strengths, or data from cross-correlation or rotating frame relaxation dispersion experiments. Our approach allows the estimation of global tumbling and internal dynamical parameters and their uncertainties without some of the assumptions which are made in the commonly-used methods for model-selection and global parameter estimation. Compared to an equivalent classical statistical approach, the Bayesian method not only is more computationally efficient, but also provides greater insight into the information content of the data. We demonstrate that this approach can be used to estimate both the isotropic rotational correlation time in the context of the original and "extended" Lipari-Szabo formalisms [Lipari & Szabo, J. Am. Chem. Soc. 1982, 104, 4546; Clore et al., J. Am. Chem. Soc. 1990, 112, 4989], as well as the rotational diffusion coefficients for axially symmetric anisotropic tumbling.

Noncontact dipole effects on channel permeation. II. Trp conformations and dipole potentials in gramicidin A

The four Trp dipoles in the gramicidin A (gA) channel modulate channel conductance, and their side chain conformations should therefore be important, but the energies of different conformations are unknown. A conformational search for the right-handed helix based on molecular mechanics in vacuo yielded 46 conformations within 20 kcal/mol of the lowest energy conformation. The two lowest energy conformations correspond to the solid-state and solution-state NMR conformations, suggesting that interactions within the peptide determine the conformation. For representative conformations, the electrostatic potential of the Trp side chains on the channel axis was computed. A novel application of the image-series method of. Biophys. J. 9:1160-1170) was introduced to simulate the polarization of bulk water by the Trp side chains. For the experimentally observed structures, the CHARm toph19 potential energy (PE) of a cation in the channel center is -1.65 kcal/mol without images. With images, the PE is -1.9 kcal/mol, demonstrating that the images further enhance the direct dipole effect. Nonstandard conformations yielded less favorable PEs by 0.4-1.1 kcal/mol.

Propagation of experimental uncertainties using the Lipari-Szabo model-free analysis of protein dynamics

In this paper we make use of the graphical procedure previously described [Jin, D. et al. (1997) J. Am. Chem. Soc., 119, 6923-6924] to analyze NMR relaxation data using the Lipari-Szabo model-free formalism. The graphical approach is advantageous in that it allows the direct visualization of the experimental uncertainties in the motional parameter space. Some general 'rules' describing the relationship between the precision of the relaxation measurements and the precision of the model-free parameters and how this relationship changes with the overall tumbling time (tau m) are summarized. The effect of the precision in the relaxation measurements on the detection of internal motions not close to the extreme narrowing limit is analyzed. We also show that multiple timescale internal motions may be obscured by experimental uncertainty, and that the collection of relaxation data at very high field strength can improve the ability to detect such deviations from the simple Lipari-Szabo model.

13C NMR and fluorescence analysis of tryptophan dynamics in wild-type and two single-Trp variants of Escherichia coli thioredoxin

The rotational motion of tryptophan side chains in oxidized and reduced wild-type (WT) Escherichia coli thioredoxin and in two single-tryptophan variants of E. coli thioredoxin was studied in solution in the temperature range 20-50 degrees C from 13C-NMR relaxation rate measurements at 75.4 and 125.7 MHz and at 20 degrees C from steady-state and time-resolved trp fluorescence anisotropy measurements. Tryptophan enriched with 13C at the delta 1 and epsilon 3 sites of the indole ring was incorporated into WT thioredoxin and into two single-trp mutants, W31F and W28F, in which trp-28 or trp-31 of WT thioredoxin was replaced, respectively, with phenylalanine. The NMR relaxation data were interpreted using the Lipari and Szabo "model-free" approach (G. Lipari and A. Szabo. 1982. J. Amer. Chem. Soc. 104:4546-4559) with trp steady-state anisotropy data included for the variants at 20 degrees C. Values for the correlation time for the overall rotational motion (tau m) from NMR of oxidized and reduced WT thioredoxin at 35 degrees C agree well with those given by Stone et al. (Stone, M. J., K. Chandrasekhar, A. Holmgren, P. E. Wright, and H. J. Dyson. 1993. Biochemistry. 32:426-435) from 15N NMR relaxation rates, and the dependence of tau m on viscosity and temperature was in accord with the Stokes-Einstein relationship. Order parameters (S2) near 1 were obtained for the trp side chains in the WT proteins even at 50 degrees C. A slight increase in the amplitude of motion (decrease in S2) of trp-31, which is near the protein surface, but not of trp-28, which is partially buried in the protein matrix, was observed in reduced relative to oxidized WT thioredoxin. For trp-28 in W31F, order parameters near 1 (S2 > or = 0.8) at 20 degrees C were found, whereas trp-31 in W28F yielded the smallest order parameters (S2 approximately 0.6) of any of the cases. Analysis of time-resolved anisotropy decays in W28F and W31F yielded S2 values in good agreement with NMR, but gave tau m values about 60% smaller. Generally, values of tau e, the effective correlation time for the internal motion, were < or = 60 ps from NMR, whereas somewhat longer times were obtained from fluorescence. The ability of NMR and fluorescence techniques to detect subnanosecond motions in proteins reliably is examined.

A model for multiexponential tryptophan fluorescence intensity decay in proteins

Tryptophan fluorescence intensity decay in proteins is modeled by multiexponential functions characterized by lifetimes and preexponential factors. Commonly, multiple conformations of the protein are invoked to explain the recovery of two or more lifetimes from the experimental data. However, in many proteins the structure seems to preclude the possibility of multiple conformers sufficiently different from one another to justify such an inference. We present here another plausible multiexponential model based on the assumption that an energetically excited donor surrounded by N acceptor molecules decays by specific radiative and radiationless relaxation processes, and by transferring its energy to acceptors present in or close to the protein matrix. If interactions between the acceptors themselves and back energy transfer are neglected, we show that the intensity decay function contain 2N exponential components characterized by the unperturbed donor lifetime, by energy transfer rates and a probability of occurrence for the corresponding process. We applied this model to the fluorescence decay of holo- and apoazurin, ribonuclease T1, and the reduced single tryptophan mutant (W28F) of thioredoxin. Use of a multiexponential model for the analysis of the fluorescence intensity decay can therefore be justified, without invoking multiple protein conformations.

13C NMR study of the effects of mutation on the tryptophan dynamics in chymotrypsin inhibitor 2: correlations with structure and stability

Recombinant chymotrypsin inhibitor 2 (CI-2) and the three mutants Ile39-->Val, Ile39-->Leu, and Arg67-->Ala were successfully enriched with [2-13C]tryptophan at position 24 within the hydrophobic core of the protein. Carbon-13 NMR relaxation measurements were then used to investigate the effect of these mutations on the dynamics of the tryptophan residue. In addition, the stability of wild-type and mutant CI-2s was measured by their susceptibility to unfolding by guanidine hydrochloride. The mutant proteins were all found to be less stable, giving delta delta GU values relative to wild-type of 1.17, 1.96, and 1.21 kcal mol-1, respectively. The indole moiety of the tryptophan residue was found to be more mobile in all the mutants studied than in wild-type CI-2. Order parameters of 0.69, 0.60, 0.56, and 0.44 were derived for wild-type, Ile39-->Val, Ile39-->Leu, and Arg67-->Ala CI-2, respectively. It is concluded that there is a correlation between the protein stability and the picosecond dynamics within the hydrophobic core and that mutations can influence the dynamic behavior of the residues that are relatively distant in the three-dimensional structure.

Conformational dynamics of unfolded peptides as a function of chain length: a frequency domain fluorescence approach

The fluorescence emission decays of single-tryptophan-containing peptides of different chain lengths in their unfolded state were investigated in the frequency domain. The data were analyzed using different functions, i.e., exponential fit and probability-density functions of different shape. We found that unimodal Lorentzian distributions best describe the fluorescence decays. This finding agrees with the point of view, now broadly accepted, that rapid motions exist in polypeptides. As a consequence of this flexibility, a large variety of conformations, with an unequal perturbation of tryptophan in its excited state, is generated. The lifetime distribution center was independent of the length of the polypeptide chain but strongly related to the nature of the amino acid residues located in the proximity of the tryptophan in the primary structure. The full width at half maximum, W, of the lifetime distribution was found to be related to the length of unfolded polypeptide by the empirical logarithmic relationship W = 0.83 log n, where n indicates the number of residues. For short peptides, a single lifetime or a narrow range of lifetimes is observed because of the fast relaxation of the tryptophanyl environment. On peptide lengthening, the spectrum of conformations, which the peptide can assume, increases; this causes a complex fluorescence decay represented by a lifetime distribution. For long polypeptide chains, the motions of the regions far from tryptophan do not significantly perturb the chromophore environment.

Experimentally verifying molecular dynamics simulations through fluorescence anisotropy measurements

The fluorescence anisotropy decay of the single tryptophan residue in phospholipase A2 was studied by use of differential polarized phase fluorometry and computer simulations of protein dynamics. The results enable the verification of a simulated dynamic event by direct experimental measurement on the same time scale. When all hydrogen atoms are modeled explicitly, the simulations agree well with the experimental measurements. However, the measurements contradict simulations in which nonpolar hydrogens are incorporated into "extended" or "united" atoms. These simulations predict an anisotropy decay in excess of measured values and appear to seriously underestimate the electrostatic interactions occurring between water and aromatic side chains. The results support the general validity of studying protein dynamics with the molecular-mechanics approach and illustrate a potentially serious deficiency of simulations which do not explicitly model all hydrogen atoms.

Characterization of selectively 13C-labeled synthetic melittin and melittin analogues in isotropic solvents by circular dichroism, fluorescence, and NMR spectroscopy

The spectroscopic and functional characterization of 13C-labeled synthetic melittin and three analogues is described. Selectively 13C-enriched tryptophan ( [13C delta 1]-L-Trp) and glycine ( [13C alpha]Gly) were incorporated into melittin and three analogues by de novo peptide synthesis. 13C-Labeled tryptophan was incorporated into melittin at position 19 and into single-tryptophan analogues of melittin at positions 17, 11, and 9, respectively. Each of the synthetic peptides contained 13C-labeled glycine at position 12 only. The peptides were characterized functionally in a cytolytic assay, and spectroscopically by CD, fluorescence, and NMR. The behavior of 13C-labeled synthetic melittin was, in all respects, indistinguishable from that of the naturally occurring peptide. All of the analogues were found to be efficient lytic agents and thus were functionally similar to the native peptide, yet no evidence was found for formation of a melittin-like tetramer by any of the analogues in aqueous media, although there was a propensity for apparently nonspecific peptide aggregation, especially for MLT-W9. Since the analogues did exhibit fractional helicities by CD comparable to or even greater than melittin itself in the presence of methanol, we infer that tetramer assembly requires not only the ability to form alpha-helix but also a very precise packing of amino acid side chains of the constituent monomers. The 13C chemical shift of the Gly-12 C alpha was found to be a sensitive marker for helix formation in all of the peptides. For melittin itself, 13C NMR spectra revealed a downfield shift of approximately 1.8 ppm for the Gly-12 13C alpha resonance of the tetramer relative to that observed for the free monomer in D2O. In mixed samples containing melittin monomer and tetramer, two discrete Gly-12 13C alpha peaks were observed simultaneously, suggestive of slow exchange between the two species. We conclude that melittin's ability to form a soluble tetramer is not a prerequisite for cytolytic activity, nor is cytolytic potential precisely correlated with the ability to form an amphiphilic helix.

Fluorescence and 13C NMR determination of side-chain and backbone dynamics of synthetic melittin and melittin analogues in isotropic solvents

The dynamics in isotopic solvents of selectively 13C labeled synthetic melittin and three analogues have been investigated by using NMR and fluorescence techniques both separately and in combination. In conjunction with the "model-free" approach to interpretation of NMR relaxation data [Lipari, G., & Szabo, A. (1982) J. Am. Chem. Soc. 104, 4546-4570], the availability of steady-state fluorescence anisotropy and lifetime data augment T1, T2, and NOE data to provide quantitative information about fluorophore dynamics in these peptides. A method is presented for using combined fluorescence and NMR data to obtain technique- and model-independent values for parameters describing local motion of 13C-labeled fluorophores in peptides and proteins. The dynamics of melittin and melittin analogues are found to be consistent with structural characteristics inferred from CD, fluorescence, and NMR spectral information presented in the preceding paper (Weaver et al., 1989). In particular, the mobility of the random coil peptide monomers is shown to be quite similar, while side-chain as well as peptide backbone motion in the aggregated or oligomeric species differs markedly among the analogues. For melittin itself, experimentally determined overall rotational correlation times for the monomer and tetramer agree very well with values predicted on the basis of solvent-accessible protein surface area. The local dynamics of selectively 13C-labeled Trp-19 and Gly-12 residues of melittin are also found to be consistent with peptide structure. In random coil melittin monomer, a specific model for the motion indicates that the Trp side chain moves through an approximate angle of +/- 71 degrees about the beta-gamma bond with a correlation time of 159 +/- 24 ps. In melittin tetramer, the indole moiety is spatially more confined with a flip angle of +/- 37 degrees, yet demonstrates an increased rate of motion with a correlation time of 56 +/- 8 ps. The constrained mobility of the Trp-19 side chain is consistent with motional constraints inferred from the X-ray structure of melittin tetramer. These results show that protein side-chain motion, even of moieties as large as indole, can occur on the picosecond time scale and that these motions are reasonably similar to those inferred from molecular dynamics simulations.

Applications of ultrafast laser spectroscopy for the study of biological systems

The discovery of mode-locked laser operation now nearly two decades ago has started a development which enables researchers to probe the dynamics of ultrafast physical and chemical processes at the molecular level on shorter and shorter time scales. Naturally the first applications were in the fields of photophysics and photochemistry where it was then possible for the first time to probe electronic and vibrational relaxation processes on a sub-nanosecond timescale. The development went from lasers producing pulses of many picoseconds to the shortest pulses which are at present just a few femtoseconds long. Soon after their discovery ultrashort pulses were applied also to biological systems which has revealed a wealth of information contributing to our understanding of a broadrange of biological processes on the molecular level.It is the aim of this review to discuss the recent advances and point out some future trends in the study of ultrafast processes in biological systems using laser techniques. The emphasis will be mainly on new results obtained during the last 5 or 6 years. The term ultrafast means that I shall restrict myself to sub-nanosecond processes with a few exceptions.