Thermal denaturation of ribonuclease A characterized by water 17O and 2H magnetic relaxation dispersion

XylR Overexpression in Escherichia coli Alleviated Transcriptional Repression by Arabinose and Enhanced Xylitol Bioproduction from Xylose Mother Liquor

Xylitol is a polyol widely used in food, pharmaceuticals, and light industries. It is currently produced through the chemical catalytic hydrogenation of xylose and generates xylose mother liquor as a substantial byproduct in the procedure of xylose extraction. If xylose mother liquor could also be efficiently bioconverted to xylitol, the greenness and atom economy of xylitol production would be largely improved. However, xylose mother liquor contains a mixture of glucose, xylose, and arabinose, raising the issue of carbon catabolic repression in its utilization by microbial conversion. Targeting this challenge, the transcriptional activator XylR was overexpressed in a previously constructed xylitol-producing E. coli strain CPH. The resulting strain CPHR produced 16.61 g/L of xylitol in shake-flask cultures from the mixture of corn cob hydrolysate and xylose mother liquor (1:1, v/v) with a xylose conversion rate of 90.1%, which were 2.23 and 2.15 times higher than the starting strain, respectively. Furthermore, XylR overexpression upregulated the expression levels of xylE, xylF, xylG, and xylH genes by 2.08-2.72 times in arabinose-containing medium, suggesting the alleviation of transcriptional repression of xylose transport genes by arabinose. This work lays the foundation for xylitol bioproduction from xylose mother liquor.

Protein Solvent Shell Structure Provides Rapid Analysis of Hydration Dynamics

The solvation layer surrounding a protein is clearly an intrinsic part of protein structure-dynamics-function, and our understanding of how the hydration dynamics influences protein function is emerging. We have recently reported simulations indicating a correlation between regional hydration dynamics and the structure of the solvation layer around different regions of the enzyme Candida antarctica lipase B, wherein the radial distribution function (RDF) was used to calculate the pairwise entropy, providing a link between dynamics (diffusion) and thermodynamics (excess entropy) known as Rosenfeld scaling. Regions with higher RDF values/peaks in the hydration layer (the first peak, within 6 Å of the protein surface) have faster diffusion in the hydration layer. The finding thus hinted at a handle for rapid evaluation of hydration dynamics at different regions on the protein surface in molecular dynamics simulations. Such an approach may move the analysis of hydration dynamics from a specialized venture to routine analysis, enabling an informatics approach to evaluate the role of hydration dynamics in biomolecular function. This paper first confirms that the correlation between regional diffusive dynamics and hydration layer structure (via water center of mass around protein side-chain atom RDF) is observed as a general relationship across a set of proteins. Second, it seeks to devise an approach for rapid analysis of hydration dynamics, determining the minimum amount of information and computational effort required to get a reliable value of hydration dynamics from structural data in MD simulations based on the protein-water RDF. A linear regression model using the integral of the hydration layer in the water-protein RDF was found to provide statistically equivalent apparent diffusion coefficients at the 95% confidence level for a set of 92 regions within five different proteins. In summary, RDF analysis of 10 ns of data after simulation convergence is sufficient to accurately map regions of fast and slow hydration dynamics around a protein surface. Additionally, it is anticipated that a quick look at protein-water RDFs, comparing peak heights, will be useful to provide a qualitative ranking of regions of faster and slower hydration dynamics at the protein surface for rapid analysis when investigating the role of solvent dynamics in protein function.

Glutamate Induced Thermal Equilibrium Intermediate and Counteracting Effect on Chemical Denaturation of Proteins

When organisms are subjected to stress conditions, one of their adaptive responses is accumulation of small organic molecules called osmolytes. These osmolytes affect the structure and stability of the biological macromolecules including proteins. The present study examines the effect of a negatively charged amino acid osmolyte, glutamate (Glu), on two model proteins, ribonuclease A (RNase A) and α-lactalbumin (α-LA), which have positive and negative surface charges at pH 7, respectively. These proteins follow two-state unfolding transitions during both heat and chemical induced denaturation processes. The addition of Glu stabilizes the proteins against temperature and induces an early equilibrium intermediate during unfolding. The stability is found to be enthalpy-driven, and the free energy of stabilization is more for α-LA compared to RNase A. The decrease in the partial molar volume and compressibility of both of the proteins in the presence of Glu suggests that the proteins attain a more compact state through surface hydration which could provide a more stable conformation. This is also supported by molecule dynamic simulation studies which demonstrate that the water density around the proteins is increased upon the addition of Glu. Further, the intermediates could be completely destabilized by lower concentrations (∼0.5 M) of guanidinium chloride and salt. However, urea subverts the Glu-induced intermediate formed by α-LA, whereas it only slightly destabilizes in the case of RNase A which has a positive surface charge and could possess charge-charge interactions with Glu. This suggests that, apart from hydration, columbic interactions might also contribute to the stability of the intermediate. Gdm-induced denaturation of RNase A and α-LA in the absence and the presence of Glu at different temperatures was carried out. These results also show the Glu-induced stabilization of both of the proteins; however, all of the unfolding transitions followed two-state transitions during chemical denaturation. The extent of stability exerted by Glu is higher for RNase A at higher temperature, whereas it provides more stability for α-LA at lower temperature. Thus, the experiments indicate that Glu induces a thermal equilibrium intermediate and increases the thermodynamic stability of proteins irrespective of their surface charges. The extent of stability varies between the proteins in a temperature-dependent manner.

Theoretical and Experimental Investigation of the Translational Diffusion of Proteins in the Vicinity of Temperature-Induced Unfolding Transition

Translational diffusion is the most fundamental form of transport in chemical and biological systems. The diffusion coefficient is highly sensitive to changes in the size of the diffusing species; hence, it provides important information on the variety of macromolecular processes, such as self-assembly or folding-unfolding. Here, we investigate the behavior of the diffusion coefficient of a macromolecule in the vicinity of heat-induced transition from folded to unfolded state. We derive the equation that describes the diffusion coefficient of the macromolecule in the vicinity of the transition and use it to fit the experimental data from pulsed-field-gradient nuclear magnetic resonance (PFG NMR) experiments acquired for two globular proteins, lysozyme and RNase A, undergoing temperature-induced unfolding. A very good qualitative agreement between the theoretically derived diffusion coefficient and experimental data is observed.

Proteins Take up Water Before Unfolding

Proteins perform specific biological functions that strongly depend on their three-dimensional structure. This three-dimensional structure, i.e. the way the protein folds, is strongly determined by the interaction between the protein and the water solvent. We study the dynamics of water in aqueous solutions of several globular proteins at different degrees of urea-induced unfolding, using polarization-resolved femtosecond infrared spectroscopy. We observe that a fraction of the water molecules is strongly slowed down by their interaction with the protein surface. By monitoring the slow water fraction we can directly probe the amount of water-exposed protein surface. We find that at mild denaturing conditions, the water-exposed surface increases by almost 50%, while the secondary structure is still intact. This finding indicates that protein unfolding starts with the protein structure becoming less tight, thereby allowing water to enter.

(17)O relaxation times in the rat brain at 16.4 tesla

PURPOSE

Measurement of the cerebral metabolic rate of oxygen (CMRO2 ) by means of direct imaging of the (17) O signal can be a valuable tool in neuroscientific research. However, knowledge of the longitudinal and transverse relaxation times of different brain tissue types is required, which is difficult to obtain because of the low sensitivity of natural abundance H2 (17) O measurements.

METHODS

Using the improved sensitivity at a field strength of 16.4 Tesla, relaxation time measurements in the rat brain were performed in vivo and postmortem with relatively high spatial resolutions, using a chemical shift imaging sequence.

RESULTS

In vivo relaxation times of rat brain were found to be T1 = 6.84 ± 0.67 ms and T2 * = 1.77 ± 0.04 ms. Postmortem H2 (17) O relaxometry at enriched concentrations after inhalation of (17) O2 showed similar T2 * values for gray matter (1.87 ± 0.04 ms) and white matter, significantly longer than muscle (1.27 ± 0.05 ms) and shorter than cerebrospinal fluid (2.30 ± 0.16 ms).

CONCLUSION

Relaxation times of brain H2 (17) O were measured for the first time in vivo in different types of tissues with high spatial resolution. Because the relaxation times of H2 (17) O are expected to be independent of field strength, our results should help in optimizing the acquisition parameters for experiments also at other MRI field strengths.

Water-proton-spin-lattice-relaxation dispersion of paramagnetic protein solutions

The paramagnetic contributions to water-proton-spin-lattice relaxation rate constants in protein systems spin-labeled with nitroxide radicals were re-examined. As noted by others, the strength of the dipolar coupling between water protons and the protein-bound nitroxide radical often appears to be larger than physically reasonable when the relaxation is assumed to be controlled by 3-dimensional diffusive processes in the vicinity of the spin label. We examine the effects of the surface in biasing the diffusive exploration of the radical region and derive a relaxation model that incorporates 2-dimensional dynamics at the interfacial layer. However, we find that the local 2-dimensional dynamics changes the shape of the relaxation dispersion profile but does not necessarily reproduce the low-field relaxation efficiency found by experiment. We examine the contributions of long-range dipolar couplings between the paramagnetic center and protein-bound-water molecules and find that the contributions from these several long range couplings may be competitive with translational contributions because the correlation time for global rotation of the protein is approximately 1000 times longer than that for the diffusive motion of water at the interfacial region. As a result the electron-proton dipolar coupling to rare protein-bound-water-molecule protons may be significant for protein systems that accommodate long-lived-water molecules. Although the estimate of local diffusion coefficients is not seriously compromised because it derives from the Larmor frequency dependence, these several contributions confound efforts to fit relaxation data quantitatively with unique models.

Concatenated two-dimensional correlation analysis: a new possibility for generalized two-dimensional correlation spectroscopy and its application to the examination of process reversibility

We propose a new application of generalized two-dimensional (2D) correlation spectroscopy called "concatenated" 2D correlation analysis, which is useful in identifying the presence of strict similarity or very subtle difference between two spectral data sets having a similar origin. This approach is very efficient and can offer many potential applications. In this study, the detailed examination of process reversibility is explored. Two forms of concatenation, horizontal and vertical concatenation of data matrices, are introduced and the latter is discussed in detail. Concatenated 2D correlation analysis allows one to investigate directly the correlation between two independent but related spectral data sets. It can extract more detailed information, such as the comparison of effects of two different perturbations or different systems. We describe the principle of the "mirror-image concatenation" in 2D correlation analysis, which is applied to demonstrate its reliability and efficiency on three spectral models: a synthetic simulation data set; experimental Fourier transform infrared (FT-IR) spectra of the thermally induced unfolding-refolding transition of bovine pancreatic ribonuclease A (RNase A) in aqueous solution; and a set of FT-IR spectra of traditional Chinese medicines (TCM) of similar origin. The concatenated 2D correlation analysis shows its power in revealing the irreversibility of the thermally induced conformation transition of RNase A as well as the comparison of different species of TCM.

Hydration profiles of amyloidogenic molecular structures

Hydration shells of normal proteins display regions of highly structured water as well as patches of less structured bulk-like water. Recent studies suggest that isomers with larger surface densities of patches of bulk-like water have an increased propensity to aggregate. These aggregates are toxic to the cellular environment. Hence, the early detection of these toxic deposits is of paramount medical importance. We show that various morphological states of association of such isomers can be differentiated from the normal protein background based on the characteristic partition between bulk, caged, and surface hydration water and the magnetic resonance (MR) signals of this water. We derive simple mathematical equations relating the compartmentalization of water to the local hydration fraction and the packing density of the newly formed molecular assemblies. Then, we employ these equations to predict the MR response of water constrained by protein aggregation. Our results indicate that single units and compact aggregates that contain no water between constituents induce a shift of the MR signal from normal protein background to values in the hyperintensity domain (bright spots), corresponding to bulk water. In contrast, large plaques that cage significant amounts of water between constituents are likely to generate MR responses in the hypointensity domain (dark spots), typical for strongly correlated water. The implication of these results is that amyloids can display both dark and bright spots when compared to the normal gray background tissue on MR images. In addition, our findings predict that the bright spots are more likely to correspond to amyloids in their early stage of development. The results help explain the MR contrast patterns of amyloids and suggest a new approach for identifying unusual protein aggregation related to disease.

Distinct unfolding and refolding pathways of ribonuclease a revealed by heating and cooling temperature jumps

Heating and cooling temperature jumps (T-jumps) were performed using a newly developed technique to trigger unfolding and refolding of wild-type ribonuclease A and a tryptophan-containing variant (Y115W). From the linear Arrhenius plots of the microscopic folding and unfolding rate constants, activation enthalpy (DeltaH(#)), and activation entropy (DeltaS(#)) were determined to characterize the kinetic transition states (TS) for the unfolding and refolding reactions. The single TS of the wild-type protein was split into three for the Y115W variant. Two of these transition states, TS1 and TS2, characterize a slow kinetic phase, and one, TS3, a fast phase. Heating T-jumps induced protein unfolding via TS2 and TS3; cooling T-jumps induced refolding via TS1 and TS3. The observed speed of the fast phase increased at lower temperature, due to a strongly negative DeltaH(#) of the folding-rate constant. The results are consistent with a path-dependent protein folding/unfolding mechanism. TS1 and TS2 are likely to reflect X-Pro(114) isomerization in the folded and unfolded protein, respectively, and TS3 the local conformational change of the beta-hairpin comprising Trp(115). A very fast protein folding/unfolding phase appears to precede both processes. The path dependence of the observed kinetics is suggestive of a rugged energy protein folding funnel.

Magnetic resonance imaging of changes in muscle tissues after membrane trauma

A pure electroporation injury leads to cell membrane disruption and subsequent osmotic swelling of the tissue. The state of water in the injured area of a tissue is changed and differs from a healthy tissue. Magnetic resonance imaging (MRI), which is very sensitive to the quality of the interaction between mobile (water) protons and a restricted (protein) proton pool, is therefore a useful tool to characterize this injury. Here, we present a protocol designed to measure the difference between the values of the transverse magnetic relaxation time (T2) in MRIs of healthy and electrically injured tissue. In addition, we present a method to evaluate the two main contributions to the MRI contrast, the degree of structural alteration of the cellular components (including a major contribution from membrane pores), and edema. The approach is useful in assessing the level of damage that electric shocks produce in muscle tissues, in that edema will resolve in time whereas structural changes require active repair mechanisms.

Water and urea interactions with the native and unfolded forms of a beta-barrel protein

A fundamental understanding of protein stability and the mechanism of denaturant action must ultimately rest on detailed knowledge about the structure, solvation, and energetics of the denatured state. Here, we use (17)O and (2)H magnetic relaxation dispersion (MRD) to study urea-induced denaturation of intestinal fatty acid-binding protein (I-FABP). MRD is among the few methods that can provide molecular-level information about protein solvation in native as well as denatured states, and it is used here to simultaneously monitor the interactions of urea and water with the unfolding protein. Whereas CD shows an apparently two-state transition, MRD reveals a more complex process involving at least two intermediates. At least one water molecule binds persistently (with residence time >10 nsec) to the protein even in 7.5 M urea, where the large internal binding cavity is disrupted and CD indicates a fully denatured protein. This may be the water molecule buried near the small hydrophobic folding core at the D-E turn in the native protein. The MRD data also provide insights about transient (residence time <1 nsec) interactions of urea and water with the native and denatured protein. In the denatured state, both water and urea rotation is much more retarded than for a fully solvated polypeptide. The MRD results support a picture of the denatured state where solvent penetrates relatively compact clusters of polypeptide segments.

Protein reorientation and bound water molecules measured by 1H magnetic spin-lattice relaxation

The water-proton spin-lattice relaxation rate constant, 1/T(1), was measured as a function of magnetic field strength for several dilute protein solutions. By separating the intermolecular contributions from the intramolecular contributions to the water-proton spin-lattice relaxation, the number of water molecules that bind to the protein for a time long compared with the rotational correlation time may be measured. We find a good correlation between the number of long-lived water molecules and the predictions based on available free volume in the proteins studied. The rotational correlation times of these proteins are larger than predicted by the Stokes-Einstein-Debye (SED) model for a sphere reorienting in a viscous liquid. The discrepancy between experiment and theory is usually attributed to hydration effects increasing the effective radius of the particle. However, the average lifetime of water molecules at the protein interface is far too short to justify such a picture. We suggest that surface roughness may be responsible for the retardation of rotational mobility and find that the SED model provides a reasonable representation of experiment if the radius assumed for the reorienting particle is the arithmetic mean of the crystallographic packing radius and the radius deduced from the effective surface area of the protein.

Single-particle and collective dynamics of protein hydration water: a molecular dynamics study

We present an analysis based on molecular dynamics simulations of water single particle and collective density fluctuations in a protein crystal at 150 and 300 K. For the collective dynamics, the calculations predict the existence of two sound modes. The first one around 35 meV is highly dispersive and the second one around 9 meV is weakly dispersive in the k range studied here (0.5<k<4.2 A(-1)). We provide evidence that the boson peak around 4 meV in the single particle spectra arises from translational motion, is present in the coherent spectra, and is distinct from the two sound modes.

Magnetic relaxation dispersion studies of biomolecular solutions

Although the MRD method has a long record in biomolecular systems, it has undergone a renaissance in the past few years as methodological developments have provided access to new types of information. In particular, MRD studies of quadrupolar nuclei such as 17O and 23Na have yielded valuable insights about the interactions of proteins and oligonucleotides with their solvent environment. The biomolecular MRD literature is still dominated by hydration studies, but the method has also been used to study the interaction of organic cosolvents and inorganic counterions with biomolecules. The MRD method can potentially make important contributions to the understanding of the mechanisms whereby protein conformational stability is affected by nonaqueous solvent components, such as denaturants, stabilizers, and helix promoters. Residence times of water molecules and other low molecular weight species in association with biomolecules can be determined by MRD. Such residence times are of general interest for understanding the kinetics of biomolecule-ligand interactions and, when exchange is gated by the biomolecule, can be used to characterize large-scale conformational fluctuations on nanosecond-millisecond time scales. By monitoring the integrity and specific internal hydration sites as well as the global solvent exposure, the MRD method can also shed light on the structure and dynamics of biomolecules in fluctuating nonnative states. Because it does not rely on high resolution, the MRD method is also applicable to very large biomolecules and complexes and has even been used to investigate protein crystals, gels, and biological tissues. In fact, dynamic studies of solids and liquid crystals were among the earliest applications of the MRD method. In many of its diverse applications, the MRD method provides unique information, complementing that available from high-resolution NMR.

Thermal unfolding of ribonuclease A in phosphate at neutral pH: deviations from the two-state model

The thermal denaturation of ribonuclease A (RNase A) in the presence of phosphate at neutral pH was studied by differential scanning calorimetry (DSC) and a combination of optical spectroscopic techniques to probe the existence of intermediate states. Fourier transform infrared (FTIR) spectra of the amide I' band and far-uv circular dichroism (CD) spectra were used to monitor changes in the secondary structure. Changes in the tertiary structure were monitored by near-uv CD. Spectral bandshape changes with change in temperature were analyzed using factor analysis. The global unfolding curves obtained from DSC confirmed that structural changes occur in the molecule before the main thermal denaturation transition. The analysis of the far-uv CD and FTIR spectra showed that these lower temperature-induced modifications occur in the secondary structure. No pretransition changes in the tertiary structure (near-uv CD) were observed. The initial changes observed in far-uv CD were attributed to the fraying of the helical segments, which would explain the loss of spectral intensity with almost no modification of spectral bandshape. Separate analyses of different regions of the FTIR amide I' band indicate that, in addition to alpha-helix, part of the pretransitional change also occurs in the beta-strands.

The dynamics of protein hydration water: a quantitative comparison of molecular dynamics simulations and neutron-scattering experiments

We present results from an extensive molecular dynamics simulation study of water hydrating the protein Ribonuclease A, at a series of temperatures in cluster, crystal, and powder environments. The dynamics of protein hydration water appear to be very similar in crystal and powder environments at moderate to high hydration levels. Thus, we contend that experiments performed on powder samples are appropriate for discussing hydration water dynamics in native protein environments. Our analysis reveals that simulations performed on cluster models consisting of proteins surrounded by a finite water shell with free boundaries are not appropriate for the study of the solvent dynamics. Detailed comparison to available x-ray diffraction and inelastic neutron-scattering data shows that current generation force fields are capable of accurately reproducing the structural and dynamical observables. On the time scale of tens of picoseconds, at room temperature and high hydration, significant water translational diffusion and rotational motion occur. At low hydration, the water molecules are translationally confined but display appreciable rotational motion. Below the protein dynamical transition temperature, both translational and rotational motions of the water molecules are essentially arrested. Taken together, these results suggest that water translational motion is necessary for the structural relaxation that permits anharmonic and diffusive motions in proteins. Furthermore, it appears that the exchange of protein-water hydrogen bonds by water rotational/librational motion is not sufficient to permit protein structural relaxation. Rather, the complete exchange of protein-bound water molecules by translational displacement seems to be required.

A new alternative method to quantify residual structure in 'unfolded' proteins

Pig (pCSD1) and human (hCSD1) calpastatin domain 1 proteins were studied to characterize common features of the denatured state of proteins. These proteins were chosen for the present investigation, because pCSD1 was suggested previously to be unstructured in water even at 25 degrees C (1) [T. Konno et al., Biochim. Biophys. Acta 1342 (1997) 73-82]. hCSD1 could be expected to exhibit similar features on the basis of preliminary spectroscopic studies. In the present study, the experimental grounds for the estimate of residual structure in the unfolded state were differential scanning calorimetry heat capacity and circular dichroism (CD) measurements over the temperature range 10-80 degrees C. At selected temperatures, we studied also the effect of guanidinium hydrochloride (GdnHCl) which is known to promote further unfolding of the polypeptide chain. All other measurements were performed at pH 6 in pure water. The present results support the conclusion that the comparison of the experimentally obtained heat capacity data with theoretical heat capacity values calculated on the basis of a newly established increment system gives insight into the degree of hydration of the unfolded polypeptide chain. The percentage by which the experimental heat capacity of the unfolded polypeptide chain differs from the calculated heat capacity permits a quantitative estimate of the residual structure. This estimate is in good agreement with that based on CD absorption. The heat capacity approach has the advantage of comparing fully hydrated and partially hydrated residues in the same aqueous environment, whereas for example spectroscopic measurements, such as CD, are generally referred to the fully unfolded chain in concentrated urea or GdnHCl solutions. As the unfolded chains of pCSD1 and hCSD1 exhibit a smaller heat capacity than that calculated on the new peptide-based increment system [M. Häckel et al., J. Mol. Biol. 291 (1999) 197-213], we conclude that the residues in the unfolded polypeptide chain are less hydrated than the same residues in oligopeptides. This suboptimal hydration is the result of residual structure in the chain as observed in both CD and heat capacity measurements.

Protein-bound water molecule counting by resolution of (1)H spin-lattice relaxation mechanisms

Water proton spin-lattice relaxation is studied in dilute solutions of bovine serum albumin as a function of magnetic field strength, oxygen concentration, and solvent deuteration. In contrast to previous studies conducted at high protein concentrations, the observed relaxation dispersion is accurately Lorentzian with an effective correlation time of 41 +/- 3 ns when measured at low proton and low protein concentrations to minimize protein aggregation. Elimination of oxygen flattens the relaxation dispersion profile above the rotational inflection frequency, nearly eliminating the high field tail previously attributed to a distribution of exchange times for either whole water molecules or individual protons at the protein-water interface. The small high-field dispersion that remains is attributed to motion of the bound water molecules on the protein or to internal protein motions on a time scale of order one ns. Measurements as a function of isotope composition permit separation of intramolecular and intermolecular relaxation contributions. The magnitude of the intramolecular proton-proton relaxation rate constant is interpreted in terms of 25 +/- 4 water molecules that are bound rigidly to the protein for a time long compared with the rotational correlation time of 42 ns. This number of bound water molecules neglects the possibility of local motions of the water in the binding site; inclusion of these effects may increase the number of bound water molecules by 50%.

The importance of aquaporin water channel protein structures

The history of the water channel and recent structural and functional analyses of aquaporins are reviewed. These ubiquitous channels are important for bacteria, plants and animals, exhibit a pronounced sequence homology and share functional as well as structural similarities. Aquaporins allow water or small specific solutes to pass unhindered, but block the passage of ions to prevent dissipation of the transmembrane potential. Besides advances in structure determination, recent experiments suggest that many of these channels are regulated by pH variations, phosphorylation and binding of auxiliary proteins.

Dissection of the structural and functional role of a conserved hydration site in RNase T1

The reoccurrence of water molecules in crystal structures of RNase T1 was investigated. Five waters were found to be invariant in RNase T1 as well as in six other related fungal RNases. The structural, dynamical, and functional characteristics of one of these conserved hydration sites (WAT1) were analyzed by protein engineering, X-ray crystallography, and (17)O and 2H nuclear magnetic relaxation dispersion (NMRD). The position of WAT1 and its surrounding hydrogen bond network are unaffected by deletions of two neighboring side chains. In the mutant Thr93Gln, the Gln93N epsilon2 nitrogen replaces WAT1 and participates in a similar hydrogen bond network involving Cys6, Asn9, Asp76, and Thr91. The ability of WAT1 to form four hydrogen bonds may explain why evolution has preserved a water molecule, rather than a side-chain atom, at the center of this intricate hydrogen bond network. Comparison of the (17)O NMRD profiles from wild-type and Thr93Gln RNase T1 yield a mean residence time of 7 ns at 27 degrees C and an orientational order parameter of 0.45. The effects of mutations around WAT1 on the kinetic parameters of RNase T1 are small but significant and probably relate to the dynamics of the active site.

Water molecules in the binding cavity of intestinal fatty acid binding protein: dynamic characterization by water 17O and 2H magnetic relaxation dispersion

The hydration of intestinal fatty acid binding protein (IFABP) in apo-form and complexed with palmitate, oleate, and 1-anilino-8-naphthalene sulfonate (ANS) has been studied by water 17O and 2H magnetic relaxation dispersion (MRD) measurements. These ligands bind in a large internal cavity, displacing most of the crystallographically identified cavity water molecules. Unlike most other proteins, IFABP gives rise to MRD profiles with two dispersion steps. The low-frequency dispersion yields a correlation time of 7 ns at 300 K, matching the known tumbling time of IFABP. The dispersion amplitude requires only three (apo) or four (holo) long-lived and ordered water molecules (residence time 0.01-4 microseconds at 300 K). Comparison of MRD profiles from the different complexes indicates that the displaced cavity water molecules are short-lived. The few long-lived (>10 ns) water molecules required by the MRD data are tentatively assigned to crystallographic hydration sites on the basis of accessibility, positional order, and H-bonding. The amplitude of the high-frequency dispersion corresponds to 10-20 moderately ordered water molecules, with a correlation time of ca. 1 ns that may reflect a transient opening of the cavity required for exchange with external water.