Methods of physical labels--a combined approach to the study of microstructure and dynamics in biological systems

The physical principles of several new approaches to the investigation of biological and model systems are discussed, including versions of the spin label method based on relaxation measurements, and also the methods of triplet, M?ssbauer, electron-scattering and radical-pair labels and probes. It is shown that all these methods make it possible to investigate molecular mobility of the medium with the correlation frequencies tau c-1 = 10(-3) -10(11) s-1, to measure the rate constants of collisions Ktr = 10(3) -10(10) M-1 s-1, to measure the distance between centers up to 100 A and finally, to evaluate the immersion depths of paramagnetic and chromophore centers in matrices up to 40 A. The combined approach is demonstrated with examples from studies of the structure of nitrogenase, the reaction centers of photosynthetic bacteria and sarcoplasmic reticulum membranes and from studies of the molecular dynamics of proteins and membranes.     

A simple method for determination of rotational correlation times and separation of rotational and polarity effects from EPR spectra of spin-labeled biomolecules in a wide correlation time range

A method using nitroxide radical spin labels for determining both the isotropic rotational correlation time tau R and the environmental polarity of the label is described. By means of a least square fitting method, the values of an effective hyperfine tensor A' and of an effective g value tensor g' of randomly oriented spin labels are determined from X-band EPR spectra on the basis of an effective time-independent Hamiltonian. The traces of the tensors deliver the information about the environmental polarity of the label and are not dependent on the rotational correlation time tau R. A new averaging parameter S (tau R), calculated on the basis of the principal values of the tensor A', permits the evaluation of the rotational correlation time tau R in a very wide time range between 10(-10) and 10(-6) s. An application of this method to spin-labeled methemoglobin over a large temperature range and in environments of different polarity is discussed.     

A comparative study of the alpha-subdomains of bovine and human alpha-lactalbumin reveals key differences that correlate with molten globule stability

The alpha-lactalbumins form stable molten globule states under a range of conditions, with the low pH form being the best characterized. The stability of the molten globule varies among different members of this family, but the origin of the stability difference is not clear. We compare the folding and stability of alpha-subdomain constructs of human and bovine alpha-lactalbumin. Previous studies have demonstrated that the isolated alpha-subdomain of human alpha-lactalbumin folds and forms a molten globule state. The minimum core construct has been defined to include the A, B, and D alpha-helices and the C-terminal 3(10) helix. A construct corresponding to the same region of bovine alpha-lactalbumin is much less structured and less stable than the human alpha-lactalbumin construct. Addition of the C-helix to generate a 75-residue bovine construct does not lead to a significant increase in structure or stability. This construct (AB-CD/3(10)) contains the entire alpha-subdomain of bovine alpha-lactalbumin. Thus molten globule formation in the human protein, but not in the bovine protein, can be rationalized on the basis of a stable alpha-subdomain. Interactions involving more of the protein chain are required to generate a well structured molten globule in the bovine protein. Comparison of AB-CD/3(10) to the molten globule formed by the intact protein and to the protein with the 6-120 disulfide reduced indicates that both the beta-subdomain and the 6-120 disulfide play a role in stabilizing the bovine alpha-lactalbumin molten globule.     

Intramolecular dynamics and electron transfer in photosynthetic reaction centers. A study using luminescence

The temperature dependences of fluorescence and phosphorescence spectra maxima of chromophor labels--endogenic (tryptophan) and exogenic (eosinisothiocyanate)--were measured for the preparations of photosynthetic membranes and reaction centers from Rhodospirillum rubrum. It was found that the dipole mobility of protein-lipid matrix in the vicinity of the chromophores intensified markedly with a temperature rise from 150 to 300K resulting in the corresponding relaxation time tau r decrease from 10(0) to 10(-8) s. The efficiency of direct transfer of the photomobilized electron in the system of quinone acceptors (A1- leads to A2) of reaction centers (characteristic half-times of the process being 10(-3) divided by 10(-4) s) was shown also to increase sharply at temperatures higher than 200K parallel to the enhancement of molecular motions with tau r approximately 10(-8) s. Meanwhile, changes observed in the rate of recombination of primary photoproducts, i.e. an oxidized bacteriochlorophyll dimer, P+ and a reduced acceptor, A1- (characteristic half-time of 10(-1) divided by 10(-2) s) and the activization of low-frequency motions with tau r approximately 10(-3) s in the external layers and tau r less than 1 s in the internal parts of the reaction centers protein develop over the same range of low temperatures (150-220 K). The nature of interactions which determine the dependence of the photosynthetic electron transport on the molecular mobility of the membrane proteins is discussed.     

Study of the structure of human serum albumin, liberated from fatty acids, by a tritium marker method]

To elucidate the natural fatty acids effect on the human serum albumin (HSA) structure a new method of tritium labelling was used. The main peculiarity of the method consists in the possibility to get information on the qualitative and quantitative amino acid composition of the surface layer of the protein globule at different conformational states of the globule. Defatted HSA was shown to be characterized a higher accessibility of Asx, Glx, Thr, Ser, Gly, Pro, Ile, Tyr residues while the other residues remain unchanged. Asx residues are characterized by the largest changes (about 8 folds). Full accessible protein surface during defatting increases from 39,000 to 48,000 A2. Fatty acids connected with albumin in the relation 1-3 moles/mol of protein are noted to be the factor increasing the globule compactness and stipulating for the conformational protein stability to warmth, urine and guanidine salts effect.     

Salt‐promoted protein folding,preferential binding,or electrostatic screening?

The extended coil/molten globule conformational equilibrium exhibited by ferricytochrome c in 10 to 20 mM HCl was examined using free boundary capillary electrophoresis. Addition of the osmolyte glucitol, also called sorbitol, to shift the conformational equilibrium toward the molten globule markedly diminished the mobility of the protein. This diminution can be entirely assigned to the relative viscosity of the added glucitol. The insensitivity of the viscosity corrected protein mobility to added glucitol suggests that both the extended coil and molten globule conformations of cytochrome c are free draining in an electrophoresis measurement. Addition of a neutral salt to shift the conformational equilibrium toward the molten globule conformation also markedly diminished the mobility of the protein. This diminution can be entirely assigned to the electrostatic screening afforded by the added salt. The onset of the conformational transition observed by optical measurements and the onset of electrostatic screening observed by mobility measurements appear to be in common for some but not all neutral salts. The exception suggests that preferential binding of the anion of a neutral salt to the molten globule conformation and not electrostatic screening is principally responsible for the shift in the conformational equilibrium of cytochrome c in acidic solutions.     

Water translational motion at the bilayer interface: an NMR relaxation dispersion measurement.

Nuclear magnetic relaxation rates for water protons in aqueous palmitoyloleoylphosphatidylcholine vesicle suspensions containing different nitroxide free radical spin labels are reported as a function of magnetic field strength corresponding to proton Larmor frequencies from 10 kHz to 30 MHz. Under these conditions the water proton relaxation rate is determined by the magnetic coupling between the water protons and the paramagnetic nitroxide fixed on the phospholipid. This coupling is made time-dependent by the relative translational motion of the water proton spins past the nitroxide radical. Using theories developed by Freed and others, we interpret the NMR relaxation data in terms of localized water translational motion and find that the translational diffusion constant for water within approximately 10 A of the phospholipid surface is 6 x 10(-10) m2 s(-1) at 298 K. Similar results are obtained for three different nitroxide labels positioned at different points on the lipid. The diffusion is a thermally activated process with an activation energy only slightly higher than that for bulk water.     

Luminescent analysis of the structure of human alpha-1-microglobulin

The spectra of absorption, fluorescence, and excitation of fluorescence of preparations of alpha-1-microglobulin isolated from human urea by two methods, gel chromatography and immunoaffinity chromatography with additional purification by activated charcoal, have been investigated in ultraviolet and visible regions. A possible nature of low-molecular compounds coloring alpha-1-microglobulin yellow-brown and their role in stabilizing the structure of protein globule are discussed. The action of urea (1.0-10 M) and guanidine hydrochloride (0.25-6 M) on the conformational state and the fast (nanosecond) internal dynamics of alpha-1-microglobulin has been investigated by the method of tryptophan fluorescence. It has been shown that the unfolding of alpha-1-microglobulin under the action of these denaturants is associated with a significant increase in the nanosecond internal dynamics of protein. The ability of alpha-1-microglobulin to restore the initial conformation characteristic for the native protein and the internal dynamics after the unfolding of the globule by 10 M urea and 6 M guanidine hydrochloride has been ascertained. It has been found that alpha-1-microglobulin isolated by the method of gel chromatography can exist in solution of 4-6 M urea in a thermodynamically stabile partialy folded state.     

Effects of melittin on molecular dynamics and Ca-ATPase activity in sarcoplasmic reticulum membranes: electron paramagnetic resonance.

We have performed electron paramagnetic resonance (EPR) experiments on nitroxide spin labels incorporated into rabbit skeletal sarcoplasmic reticulum (SR), in order to investigate the physical and functional interactions between melittin, a small basic membrane-binding peptide, and the Ca-ATPase of SR. Melittin binding to SR substantially inhibits Ca(2+)-dependent ATPase activity at 25 degrees C, with half-maximal inhibition at 9 mol of melittin bound per mole of Ca-ATPase. Saturation transfer EPR (ST-EPR) of maleimide spin-labeled Ca-ATPase showed that melittin decreases the submillisecond rotational mobility of the enzyme, with a 4-fold increase in the effective rotational correlation time (tau r) at a melittin/Ca-ATPase mole ratio of 10:1. This decreased rotational motion is consistent with melittin-induced aggregation of the Ca-ATPase. Conventional EPR was used to measure the submicrosecond rotational dynamics of spin-labeled stearic acid probes incorporated into SR. Melittin binding to SR at a melittin/Ca-ATPase mole ratio of 10:1 decreases lipid hydrocarbon chain mobility (fluidity) 25% near the surface of the membrane, but only 5% near the center of the bilayer. This gradient effect of melittin on SR fluidity suggests that melittin interacts primarily with the membrane surface. For all of these melittin effects (on enzymatic activity, protein mobility, and fluidity), increasing the ionic strength lessened the effect of melittin but did not alleviate it entirely. This is consistent with a melittin-SR interaction characterized by both hydrophobic and electrostatic forces. Since the effect of melittin on lipid fluidity alone is too small to account for the large inhibition of Ca-ATPase rotational mobility and enzymatic activity, we propose that melittin inhibits the ATPase primarily through its capacity to aggregate the enzyme, consistent with previous observations of decreased Ca-ATPase activity under conditions that decrease protein rotational mobility.     

Accessible and total molecular surfaces of unsmooth protein globules

A method for the calculation of accessible and total molecular surfaces of protein globules is proposed. It is based on consideration of structuring of protein globule surface. As a whole, the protein globule is approximated by ellipsoids. By computer imitations, the areas of accessible and total molecular surfaces as well as the volumes for 58 globular proteins were calculated. The calculation showed that the best agreement between the calculated areas and volumes and the experimental results is obtained at the radii of protein surface structures of 1-2 A.     

Poly(ethylene oxide) layers grafted to dopamine-melanin anchoring layer: stability and resistance to protein adsorption

In this study, we propose substrate-independent modification for creating a protein-repellent surface based on dopamine-melanin anchoring layer used for subsequent binding of poly(ethylene oxide) (PEO) from melt. We verified that the dopamine-melanin layer can be formed on literally any substrate and could serve as the anchoring layer for subsequent grafting of PEO chains. Grafting of PEO from melt in a temperature range 70-110 °C produces densely packed PEO layers showing exceptionally low protein adsorption when exposed to the whole blood serum or plasma. The PEO layers prepared from melt at 110 °C retained the protein repellent properties for as long as 10 days after their exposure to physiological-like conditions. The PEO-dopamine-melanin modification represents a simple and universal surface modification method for the preparation of protein repellent surfaces that could serve as a nonfouling background in various applications, such as optical biosensors and tissue engineering.     

Vinyl ketone reagents for covalent protein modification. Nitroxide derivatives suited to rotational diffusion studies by saturation transfer electron spin resonance, using membrane-bound Na,K-ATPase as an example

The reactivity of a series of substituted vinyl ketone nitroxides with an integral membrane protein, the Na,K-ATPase, is described. Increasing the electrophilicity of the conjugated double bond enhances reactivity markedly, with some spin labels showing higher reactivity than the conventionally used maleimide derivatives. The spectroscopic characteristics of the spin-labeled protein are also better suited for motional analysis by the saturation transfer electron spin resonance (STESR) method than with previous labeling procedures. The rotational correlation time, deduced from STESR experiments, is in the same range (100-300 microseconds) irrespective of the vinyl ketone derivative used, and the rotational mobility corresponds to an (alpha beta)2 or higher oligomer of the membrane-bound Na,K-ATPase.     

Domain formation in sphingomyelin/cholesterol mixed membranes studied by spin-label electron spin resonance spectroscopy

Interactions of palmitoylsphingomyelin with cholesterol in multilamellar vesicles have been studied over a wide range of compositions and temperatures in excess water by using electron spin resonance (ESR) spectroscopy. Spin labels bearing the nitroxide free radical group on the 5 or 14 C-atom in either the sn-2 stearoyl chain of phosphatidylcholine (predominantly 1-palmitoyl) or the N-stearoyl chain of sphingomyelin were used to determine the mobility and ordering of the lipids in the different phases. Two-component ESR spectra of the 14-position spin labels demonstrate the coexistence first of gel (L(beta)) and liquid-ordered (L(o)) phases and then of liquid-ordered and liquid-disordered (L(alpha)) phases, with progressively increasing temperature. These phase coexistences are detected over a limited range of cholesterol contents. ESR spectra of the 5-position spin labels register an abrupt increase in ordering at the L(alpha)-L(o) transition and a biphasic response at the L(beta)-L(o) transition. Differences in outer splitting between the C14-labeled sphingomyelin and phosphatidylcholine probes are attributed to partial interdigitation of the sphingomyelin N-acyl chains across the bilayer plane in the L(o) state. In the region where the two fluid phases, L(alpha) and L(o), coexist, the rate at which lipids exchange between phases (<7 x 10(7) s(-)(1)) is much slower than translational rates in the L(alpha) phase, which facilitates resolution of two-component spectra.     

Spin-trapping studies with MTDO, a dihydroquinoline type radical scavenger

The effect of MTDQ, a dihydroquinoline type free radical scavenger was studied in biological membranes, and model systems. Using spin-labelling and spin-trapping methods, it was that MTDQ induced a decrease of the mobility of spin labels attached to the thiol sites of membrane proteins, and it was a strong free radical scavenger in hydroxyl and superoxide anion free radical generating systems. The experimental results suggest that the presence of MTDQ in the cell membranes may improve the protection of membrane components against free radical attacks.     

Quantitative measurement of lipoprotein surface charge by agarose gel electrophoresis.

The electrophoretic mobilities of low density lipoprotein (LDL) and six pure proteins in a 0.5% agarose gel have been compared to literature electrophoretic mobility values determined by the Tiselius moving boundary method. There is a strong correlation (r = 0.99) between the electrophoretic mobilities determined by the two techniques. The electrophoretic behavior of charged particles smaller than very low density lipoproteins (VLDL) is not markedly perturbed by a 0.5% agarose matrix, and variations in mobility primarily reflect differences in particle valence and density of surface charge. Application of electrokinetic theory to derive protein and lipoprotein net charges from the electrophoretic mobilities in agarose yields a quantitative delineation of lipoprotein electrophoretic migration patterns wherein the beta mobility region comprises a surface potential range of -4.5 to -7.0 mV; the pre-beta region a range of -7.0 to -10.5 mV; the alpha mobility region a range of -10.5 to -12.5 mV and the serum albumin region a range of -12.5 to -14.0 mV. Because protein conformation and charge are critical in metabolic regulation, the agarose gel electrophoresis technique provides a valuable analytical tool that should help to elucidate further details of the structure-function relationships of serum lipoprotein particles.     

Nanosecond dynamics of tryptophans in different conformational states of apomyoglobin proteins

Fluorescence anisotropy kinetics were employed to quantify the nanosecond mobility of tryptophan residues in different conformational states (native, molten globule, unfolded) of apomyoglobins. Of particular interest is the similarity between the fluorescence anisotropy decays of tryptophans in the native and molten globule states. We find that, in these compact states, tryptophan residues rotate rapidly within a cone of semiangle 22-25 degrees and a correlation time of 0.5 ns, in addition to rotating together with the whole protein with a correlation time of 7-11 ns. The similar nanosecond dynamics of tryptophan residues in both states suggests that the conformation changes that distinguish the molten globule and native states of apomyoglobins originate from either subtle, slow rearrangements or fast changes distant from these tryptophans.     

DNA fragments with specific nucleotide sequences in their single-stranded termini exhibit unusual electrophoretic mobilities.

DNA restriction fragments, 120-650 base pairs (bp) in length, with 5'-GCGC-3', 5'-GGCC-3' or 3'-GCGC-5' single-stranded overhanging termini, give rise to diffuse bands of unusual electrophoretic mobility in non-denaturing polyacrylamide gels. This shift in electrophoretic mobility can be observed at 4-12 degreesC, not at higher temperatures, but is stabilized by 5-10 mM Mg2+, even at 37 degreesC. The nucleotide sequence in the abutting double-stranded part of the fragment does not affect this phenomenon, which is not caused by dimerization. The altered mobility may be due to the unusual terminal DNA structure, which is dependent on co-operative interactions among more than two neighboring G and C residues. The structure is stabilized by cytidine methylation. The biological role of such fragment structures in DNA repair and recombination is presently unknown.     

A new bifunctional spin-label suitable for saturation-transfer EPR studies of protein rotational motion

A new bifunctional spin-label (BSL) has been synthesized that can be immobilized on the surface of proteins, allowing measurement of rotational motion of proteins by saturation-transfer electron paramagnetic resonance (STEPR). The spin-label contains a photoactivatable azido moiety, a cleavable disulfide, and a nitroxide spin with restricted mobility relative to the rest of the label. The label reacts with surface lysine residues modified with beta-mercaptopropionate. Bifunctional attachment is achieved by photoactivation of the azido group. Any spin-label that remains monofunctionally attached after photolysis is removed by reduction of the disulfide. Only bifunctionally attached BSL remains on the protein. Hemoglobin was used to test the utility of the BSL in STEPR by comparison with hemoglobin modified with maleimide spin-label (MSL), a commonly used standard for the STEPR technique. MSL is a monofunctional spin-label which is fortuitously immobilized by local protein structure within hemoglobin. The BSL labeling of hemoglobin did not significantly affect the quaternary structure of hemoglobin as determined by gel filtration chromatography. The conventional EPR spectra of the mono- and bifunctionally attached BSL-hemoglobin were similar to the MSL-hemoglobin spectrum, indicating that both forms of BSL were rigidly bound to hemoglobin. In contrast, the spectrum obtained by reaction of modified hemoglobin lysine residues with MSL indicated that these labels were highly mobile. The monofunctionally attached BSL was mobilized upon octyl glucoside addition whereas bifunctionally attached BSL was only slightly mobilized, suggesting that hydrophobic interactions immobilize the monofunctionally attached label on hemoglobin. The response of STEPR spectra of mono- and bifunctionally attached BSL-hemoglobin to changes in hemoglobin rotational correlation time was similar to the MSL-hemoglobin over the range of 10(-5)-10(-3) s. The spectra of bifunctionally attached BSL indicated slightly less motion than corresponding spectra for MSL or monofunctionally attached BSL. The new BSL is a good reporter of protein rotation and does not require unique protein structures for its immobilization on the protein. Thus, the BSL should be more generally applicable for STEPR studies of membrane protein rotation than existing monofunctional spin-labels.     

Lipid protein interactions in mitochondria. VIII. Effect of general anesthetics on the mobility of spin labels in lipid vesticles and mitochondrial membranes

We have studied the effect of general anesthetics on the mobility of two stearic acid spin labels (5-doxyl stearic acid and 16-doxyl stearic acid) in bovine heart mitochondria and in phospholipid vesicles made from either mitochondrial lipids or commercial soybean phospholipids. The general anesthetics used include nonpolar compounds (alcohols, halothane, pentrane, diethyl ether, chloroform) and the amphipathic compound, ketamine. All anesthetics tested increase the mobility of the spin labels in phospholipid vesicles to a limited extent up to a concentration where the ESR spectra become those of free spin labels. On the other hand, anesthetics have a pronounced effect on mitochondrial membranes at concentrations as low as those known to produce general anesthesia; the effect is lower near the bilayer surface (5-doxyl stearic acid) and very strong in the bilayer core (16-doxyl stearic acid). The effects of anesthetics are mimicked by the detergent, Triton X-100. We suggest that the discrepancy between the action of anesthetics in mobilizing the spin labels in lipid vesicles and in membranes results from labilization of lipid protein interactions.