Biomedical subjects

Bertil Halle

Publications and source records attributed to Bertil Halle.

At least 19 recordsLinked to original sources

PubMed2006

Hydrogen exchange and hydration dynamics in gelatin gels.

Gelatin, derived from the collagen triple helix, is the most widely used functional biopolymer and a prototype for studies of physical gels. Gelatin gels have also served as models for soft biological tissue in efforts to elucidate the molecular basis of the magnetic relaxation phenomena that govern magnetic resonance image contrast. Yet, the microstructure, hydration, and magnetic relaxation behavior of gelatin gels are not well understood. To address these issues, we report here the water 2H and 17O magnetic relaxation dispersion (MRD) profiles from gelatin gels over wide ranges of resonance frequency and pH. For the global analysis of this extensive data set, we use a generalized relaxation theory that remains valid for arbitrarily slow molecular dynamics. The strong pH dependence in the 2H profiles can be rationalized quantitatively as the result of exchange with bulk water of labile hydrogens in gelatin side chains. The global analysis of the MRD data yields hydrogen-exchange rate constants, acid dissociation constants, and orientational order parameters in agreement with independent structural, thermodynamic, and kinetic data. The MRD analysis reveals a highly mobile hydration layer at the surface of the gelatin triple helix and a small number of trapped water molecules with residence times on the order of 10(-8) s, presumably associated with structural defects and branch points in the gel. The MRD data also indicate that approximately 20% of the gelatin residues belong to flexible polypeptide chains, rather than to rigid triple-helical segments. By identifying the molecular species and motions responsible for the 2H and 17O dispersion profiles, this study takes a significant step toward a quantitative understanding of water relaxation in aqueous gels and biological tissue.

Gelatin↗

PubMed2006

Internal water molecules and magnetic relaxation in agarose gels.

Agarose gels have long been known to produce exceptionally large enhancements of the water 1H and 2H magnetic relaxation rates. The molecular basis for this effect has not been clearly established, despite its potential importance for a wide range of applications of agarose gels, including their use as biological tissue models in magnetic resonance imaging. To resolve this issue, we have measured the 2H magnetic relaxation dispersion profile from agarose gels over more than 4 frequency decades. We find a very large dispersion, which, at neutral pH, is produced entirely by internal water molecules, exchanging with bulk water on the time scale 10(-8)-10(-6) s. The most long-lived of these dominate the dispersion and give rise to a temperature maximum in the low-frequency relaxation rate. At acidic pH, there is also a low-frequency contribution from hydroxyl deuterons exchanging on a time scale of 10(-4) s. Our analysis of the dispersion profiles is based on a nonperturbative relaxation theory that remains valid outside the conventional motional-narrowing regime. The results of this analysis suggest that the internal water molecules responsible for the dispersion are located in the central cavity of the agarose double helix, as previously proposed on the basis of fiber diffraction data. The magnetic relaxation mechanism invoked here, where spin relaxation is induced directly by molecular exchange, also provides a molecular basis for understanding the water 1H relaxation behavior that governs the intrinsic magnetic resonance image contrast in biological tissue.

Gels↗

PubMed2006

Molecular basis of water proton relaxation in gels and tissue.

An extensive set of water-1H magnetic relaxation dispersion (MRD) data are presented for aqueous agarose and gelatin gels. It is demonstrated that the EMOR model, which was developed in a companion paper to this study (see Halle, this issue), accounts for the dependence of the water-1H spin-lattice relaxation rate on resonance frequency over more than four decades and on pH. The parameter values deduced from analysis of the 1H MRD data are consistent with values derived from 2H MRD profiles from the same gels and with small-molecule reference data. This agreement indicates that the water-1H relaxation dispersion in aqueous biopolymer gels is produced directly by exchange-mediated orientational randomization of internal water molecules or labile biopolymer protons, with little or no role played by collective biopolymer vibrations or coherent spin diffusion. This ubiquitous mechanism is proposed to be the principal source of water-1H spin-lattice relaxation at low magnetic fields in all aqueous systems with rotationally immobile biopolymers, including biological tissue. The same mechanism also contributes to transverse and rotating-frame relaxation and magnetization transfer at high fields.

Gelatin↗

PubMed2006

Molecular theory of field-dependent proton spin-lattice relaxation in tissue.

A molecular theory is presented for the field-dependent spin-lattice relaxation time of water in tissue. The theory attributes the large relaxation enhancement observed at low frequencies to intermediary protons in labile groups or internal water molecules that act as relaxation sinks for the bulk water protons. Exchange of intermediary protons not only transfers magnetization to bulk water protons, it also drives relaxation by a mechanism of exchange-mediated orientational randomization (EMOR). An analytical expression for T1 is derived that remains valid outside the motional-narrowing regime. Cross-relaxation between intermediary protons and polymer protons plays an important role, whereas spin diffusion among polymer protons can be neglected. For sufficiently slow exchange, the dispersion midpoint is determined by the local dipolar field rather than by molecular motions, which makes the dispersion frequency insensitive to temperature and system composition. The EMOR model differs fundamentally from previous models that identify collective polymer vibrations or hydration water dynamics as the molecular motion responsible for spin relaxation. Unlike previous models, the EMOR model accounts quantitatively for 1H magnetic relaxation dispersion (MRD) profiles from tissue model systems without invoking unrealistic parameter values.

Magnetic Resonance Spectroscopy↗

PubMed2005

Molecular origin of time-dependent fluorescence shifts in proteins.

Time-resolved fluorescence spectroscopy is used increasingly to probe molecular motions at the aqueous interfaces of biological macromolecules and membranes. By recording the time variation of the fluorescence frequency, thermal atomic fluctuations in the vicinity of the chromophore can be probed. From such fluorescence Stokes shift (FSS) experiments, it has been inferred that water motions in the hydration layer are slowed down by 1-3 orders of magnitude. To provide a more secure foundation for the interpretation of FSS data, we use molecular dynamics simulations to examine the molecular origin of the FSS from a tryptophan residue in a protein. By using linear response theory to decompose the FSS into its water and protein components, we find that the water component dominates the static FSS but decays rapidly. Thus, after a few picoseconds, the FSS essentially reflects protein dynamics, including the self-motion of the chromophore. Because of its collective nature, the FSS response is insensitive to the motion of individual water molecules. Collective water displacement by slowly fluctuating protein groups introduces a long-time tail in the water autocorrelation function, but this dynamic coupling is hardly manifested in the observed FSS. Our analysis reconciles FSS data with the picture of a highly dynamic hydration layer, derived mainly from magnetic relaxation dispersion and simulation studies, and calls for a revision of previous interpretations of FSS decays in terms of slow hydration dynamics at biomolecular and other interfaces.

Protein Conformation↗

PubMed2005

Protein self-association induced by macromolecular crowding: a quantitative analysis by magnetic relaxation dispersion.

In the presence of high concentrations of inert macromolecules, the self-association of proteins is strongly enhanced through an entropic, excluded-volume effect variously called macromolecular crowding or depletion attraction. Despite the predicted large magnitude of this universal effect and its far-reaching biological implications, few experimental studies of macromolecular crowding have been reported. Here, we introduce a powerful new technique, fast field-cycling magnetic relaxation dispersion, for investigating crowding effects on protein self-association equilibria. By recording the solvent proton spin relaxation rate over a wide range of magnetic field strengths, we determine the populations of coexisting monomers and decamers of bovine pancreatic trypsin inhibitor in the presence of dextran up to a macromolecular volume fraction of 27%. Already at a dextran volume fraction of 14%, we find a 30-fold increase of the decamer population and 510(5)-fold increase of the association constant. The analysis of these results, in terms of a statistical-mechanical model that incorporates polymer flexibility as well as the excluded volume of the protein, shows that the dramatic enhancement of bovine pancreatic trypsin inhibitor self-association can be quantitatively rationalized in terms of hard repulsive interactions.

Animals↗

PubMed2004

Accelerated exchange of a buried water molecule in selectively disulfide-reduced bovine pancreatic trypsin inhibitor.

Using magnetic relaxation dispersion (MRD), we have previously shown that the four internal water molecules in bovine pancreatic trypsin inhibitor (BPTI) exchange with bulk water on time scales between 10(-8) and 10(-4) s at room temperature. Because this exchange is controlled by the protein structure, internal water molecules can be used to probe rare conformational fluctuations. Here, we report (2)H and (17)O MRD data at three temperatures for wild-type BPTI and two BPTI variants where the 14-38 disulfide bond has been cleaved by a double Cys --> Ser mutation or by disulfide reduction and carboxamidomethylation. The MRD data show that the internal water molecules are conserved on disulfide cleavage. However, the exchange rate of the water molecule buried near the disulfide bond is enhanced by 2-4 orders of magnitude. The relation of water exchange to other dynamic processes in BPTI is discussed.

Animals↗

PubMed2004

Stabilization of internal charges in a protein: water penetration or conformational change?

The ionizable amino acid side chains of proteins are usually located at the surface. However, in some proteins an ionizable group is embedded in an apolar internal region. Such buried ionizable groups destabilize the protein and may trigger conformational changes in response to pH variations. Because of the prohibitive energetic cost of transferring a charged group from water to an apolar medium, other stabilizing factors must be invoked, such as ionization-induced water penetration or structural changes. To examine the role of water penetration, we have measured the 17O and 2H magnetic relaxation dispersions (MRD) for the V66E and V66K mutants of staphylococcal nuclease, where glutamic acid and lysine residues are buried in predominantly apolar environments. At neutral pH, where these residues are uncharged, we find no evidence of buried water molecules near the mutation site. This contrasts with a previous cryogenic crystal structure of the V66E mutant, but is consistent with the room-temperature crystal structure reported here. MRD measurements at different pH values show that ionization of Glu-66 or Lys-66 is not accompanied by penetration of long-lived water molecules. On the other hand, the MRD data are consistent with a local conformational change in response to ionization of the internal residues.

Amino Acid Substitution↗

PubMed2004

Protein hydration dynamics in solution: a critical survey.

The properties of water in biological systems have been studied for well over a century by a wide range of physical techniques, but progress has been slow and erratic. Protein hydration--the perturbation of water structure and dynamics by the protein surface--has been a particularly rich source of controversy and confusion. Our aim here is to critically examine central concepts in the description of protein hydration, and to assess the experimental basis for the current view of protein hydration, with the focus on dynamic aspects. Recent oxygen-17 magnetic relaxation dispersion (MRD) experiments have shown that the vast majority of water molecules in the protein hydration layer suffer a mere twofold dynamic retardation compared with bulk water. The high mobility of hydration water ensures that all thermally activated processes at the protein-water interface, such as binding, recognition and catalysis, can proceed at high rates. The MRD-derived picture of a highly mobile hydration layer is consistent with recent molecular dynamics simulations, but is incompatible with results deduced from intermolecular nuclear Overhauser effect spectroscopy, dielectric relaxation and fluorescence spectroscopy. It is also inconsistent with the common view of hydration effects on protein hydrodynamics. Here, we show how these discrepancies can be resolved.

Magnetics↗

PubMed2004

Competitive Na(+) and Rb(+) binding in the minor groove of DNA.

Sequence-dependent coordination of alkali ions to the nucleotide bases in the minor groove of AT-tract B-DNA has recently been inferred from X-ray crystallography, solution NMR and computer simulations. Here, we present new (23)Na and (87)Rb magnetic relaxation dispersion (MRD) data that demonstrate competitive and long-lived binding of Na(+) and Rb(+) ions in the minor groove of the B-DNA duplex [d(CGCGAATTCGCG)](2). The Na(+)/Rb(+) selectivity of the minor groove is found to be weak, consistent with local structural flexibility. The ion occupancies derived from the MRD data are substantially higher than previously reported, suggesting that groove-bound ions significantly influence the energetics and structural polymorphism of DNA in vivo. For example, in the presence of 0.20 M Na(+) and 0.56 M Rb(+) at 4 degrees C, the ApT site in the minor groove is occupied by a Rb(+) ion, a Na(+) ion, or a water molecule 40, 10, and 50% of the time, respectively. In the absence of Rb(+), the Na(+) occupancy increases to 50%. At 4 degrees C, the mean residence time of groove-bound ions is 0.2 +/- 0.1 micros for Rb(+) and 10 ns to 100 micros for Na(+). A shorter correlation time of 2 ns is attributed to counterions bridging cross-strand phosphate groups.

Base Sequence↗

PubMed2004

Biomolecular cryocrystallography: structural changes during flash-cooling.

To minimize radiation damage, crystal structures of biological macromolecules are usually determined after rapid cooling to cryogenic temperatures, some 150-200 K below the normal physiological range. The biological relevance of such structures relies on the assumption that flash-cooling is sufficiently fast to kinetically trap the macromolecule and associated solvent in a room-temperature equilibrium state. To test this assumption, we use a two-state model to calculate the structural changes expected during rapid cooling of a typical protein crystal. The analysis indicates that many degrees of freedom in a flash-cooled protein crystal are quenched at temperatures near 200 K, where local conformational and association equilibria may be strongly shifted toward low-enthalpy states. Such cryoartifacts should be most important for strongly solvent-coupled processes, such as hydration of nonpolar cavities and surface regions, conformational switching of solvent-exposed side chains, and weak ligand binding. The dynamic quenching that emerges from the model considered here can also rationalize the glass transition associated with the atomic fluctuations in the protein.

Cold Temperature↗

PubMed2004

Dynamics of protein and peptide hydration.

Biological processes often involve the surfaces of proteins, where the structural and dynamic properties of the aqueous solvent are modified. Information about the dynamics of protein hydration can be obtained by measuring the magnetic relaxation dispersion (MRD) of the water (2)H and (17)O nuclei or by recording the nuclear Overhauser effect (NOE) between water and protein protons. Here, we use the MRD method to study the hydration of the cyclic peptide oxytocin and the globular protein BPTI in deeply supercooled solutions. The results provide a detailed characterization of water dynamics in the hydration layer at the surface of these biomolecules. More than 95% of the water molecules in contact with the biomolecular surface are found to be no more than two-fold motionally retarded as compared to bulk water. In contrast to small nonpolar molecules, the retardation factor for BPTI showed little or no temperature dependence, suggesting that the exposed nonpolar residues do not induce clathrate-like hydrophobic hydration structures. New NOE data for oxytocin and published NOE data for BPTI were analyzed, and a mutually consistent interpretation of MRD and NOE results was achieved with the aid of a new theory of intermolecular dipolar relaxation that accounts explicitly for the dynamic perturbation at the biomolecular surface. The analysis indicates that water-protein NOEs are dominated by long-range dipolar couplings to bulk water, unless the monitored protein proton is near a partly or fully buried hydration site where the water molecule has a long residence time.

Aprotinin↗

PubMed2003

Trifluoroethanol-induced beta --> alpha transition in beta-lactoglobulin: hydration and cosolvent binding studied by 2H, 17O, and 19F magnetic relaxation dispersion.

Alcohols, such as 2,2,2-trifluoroethanol (TFE), have been shown to induce a cooperative transition to an open helical structure in many proteins, but the underlying molecular mechanism has not been identified. Here, we employ the technique of magnetic relaxation dispersion (MRD) to study the TFE-induced beta --> alpha transition of beta-lactoglobulin at pH 2.4. Unlike traditional techniques that focus on protein secondary structure, the MRD method directly monitors the solvent, providing quantitative information about preferential solvation and solvent penetration and about the overall size and structural integrity of the protein. In this multinuclear MRD study, we use the (2)H and (17)O resonances to examine hydration and the (19)F resonance to study TFE. The transformation from the native to the helical state via an intermediate state at 300 K is found to be accompanied by a progressive expansion of the protein and loss of specific long-lived hydration sites. The observation of (17)O and (19)F dispersions from the helical state shows that water and TFE penetrate the protein. The MRD data indicate a strong accumulation of TFE at the surface as well as in the interior of the protein. At 277 K, BLG is much less affected by TFE, remaining in the native state at 16% TFE, but adopting a nonnative structure at 30% TFE. This nonnative structure is not penetrated by long-lived water molecules. The implications of these findings for the mechanism of TFE-induced structural transformations are discussed.

Animals↗

PubMed2003

Biomolecular hydration: from water dynamics to hydrodynamics.

Thermally driven rotational and translational diffusion of proteins and other biomolecules is governed by frictional coupling to their solvent environment. Prediction of this coupling from biomolecular structures is a longstanding biophysical problem, which cannot be solved without knowledge of water dynamics in an interfacial region comparable to the dry protein in volume. Efficient algorithms have been developed for solving the hydrodynamic equations of motion for atomic-resolution biomolecular models, but experimental diffusion coefficients can be reproduced only by postulating hundreds of rigidly bound water molecules. This static picture of biomolecular hydration is fundamentally inconsistent with magnetic relaxation dispersion experiments and molecular dynamics simulations, which both reveal a highly dynamic interface where rotation and exchange of nearly all water molecules are several orders of magnitude faster than biomolecular diffusion. Here, we resolve this paradox by means of a dynamic hydration model that explicitly links protein hydrodynamics to hydration dynamics. With the aid of this model, bona fide structure-based predictions of global biomolecular dynamics become possible, as demonstrated here for a set of 16 proteins for which accurate experimental rotational diffusion coefficients are available.

Animals↗

PubMed2003

Water dynamics in the large cavity of three lipid-binding proteins monitored by (17)O magnetic relaxation dispersion.

Intracellular lipid-binding proteins contain a large binding cavity filled with water molecules. The role played by these water molecules in ligand binding is not well understood, but their energetic and dynamic properties must be important for protein function. Here, we use the magnetic relaxation dispersion (MRD) of the water 17O resonance to investigate the water molecules in the binding cavity of three different lipid-binding proteins: heart fatty acid-binding protein (H-FABP), ileal lipid-binding protein (I-LBP) and intestinal fatty acid-binding protein (I-FABP). Whereas about half of the crystallographically visible water molecules appear to be expelled by the ligand, we find that ligand binding actually increases the number of water molecules within the cavity. At 300 K, the water molecules in the cavity exchange positions on a time-scale of about 1ns and exchange with external water on longer time-scales (0.01-1 micros). Exchange of water molecules among hydration sites within the cavity should be strongly coupled to ligand motion. Whereas a recent MD simulation indicates that the structure of the cavity water resembles a bulk water droplet, the present MRD results show that its dynamics is more than two orders of magnitude slower than in the bulk. These findings may have significant implications for the strength, specificity and kinetics of lipid binding.

Animals↗

PubMed2003

Temperature-dependent hydrogen-bond geometry in liquid water.

We have determined the hydrogen-bond geometry in liquid water from 0 to 80 degrees C by combining measurements of the proton magnetic shielding tensor with ab initio density functional calculations. The resulting moments of the distributions of hydrogen-bond length and angle are direct measures of thermal disorder in the hydrogen-bond network. These moments, and the distribution functions that can be reconstructed from them, impose quantitative constraints on structural models of liquid water.

Hydrogen Bonding↗

PubMed2003

Protein self-association in solution: the bovine pancreatic trypsin inhibitor decamer.

We have used magnetic relaxation dispersion to study bovine pancreatic trypsin inhibitor (BPTI) self-association as a function of pH, salt type and concentration, and temperature. The magnetic relaxation dispersion method sensitively detects stable oligomers without being affected by other interactions. We find that BPTI decamers form cooperatively under a wide range of solution conditions with no sign of dimers or other small oligomers. Decamer formation is opposed by electrostatic repulsion among numerous cationic residues confined within a narrow channel. Accordingly, the decamer population increases with increasing pH, as cationic residues are deprotonated, and with increasing salt concentration. The salt effect cannot be described in terms of Debye screening, but involves the ion-specific sequestering of anions within the narrow channel. The lifetime of the BPTI decamer is 101 +/- 4 min at 27 degrees C. We propose that the BPTI decamer, with a heparin chain threading the decamer channel, plays a functional role in the mast cell. We also detect a higher oligomer that appears to be a subcritical nucleation cluster of 3-5 decamers. We argue that monomeric crystals form at high pH despite a high decamer population in solution, because the ion pairs that provide the critical decamer-decamer contacts are disrupted at high pH.

Animals↗

PubMed2003

Protein self-association in solution: the bovine beta -lactoglobulin dimer and octamer.

We have used proton magnetic relaxation dispersion (MRD) to study the self-association of bovine beta-lactoglobulin variant A (BLG-A) as a function of temperature at pH 4.7 (dimer-octamer equilibrium) and as a function of NaCl concentration at pH 2.5 (monomer-dimer equilibrium). The MRD method identifies coexisting oligomers from their rotational correlation times and determines their relative populations from the associated dispersion amplitudes. From MRD-derived correlation times and hydrodynamic model calculations, we confirm that BLG-A dimers associate to octamers below room temperature. The tendency for BLG-A dimers to assemble into octamers is found to be considerably weaker than in previous light scattering studies in the presence of buffer salt. At pH 2.5, the MRD data are consistent with an essentially complete transition from monomers in the absence of salt to dimers in 1 M NaCl. Because of an interfering relaxation dispersion from nanosecond water exchange, we cannot determine the oligomer populations at intermediate salt concentrations. This nanosecond dispersion may reflect intersite exchange of water molecules trapped inside the large binding cavity of BLG-A.

Animals↗