Pulse compression in a time variant system with application to ultrasonic vibrometry.

Pulse compression is normally applied only to time-invariant systems, as the variation of a system's properties during its interrogation violates assumptions of the compression process. However, there is an exact solution to the pulse-compression problem when the time variance satisfies two criteria, which are the same as those required for the operation of an ultrasonic vibrometer in the context of a tissue elastography system. One is that the variations be very small in comparison with the wavelength of the interrogating ultrasound. The other is that the bandwidth of the variations be within one Nyquist band as sampled by the periodic interrogation signal. The solution to this problem involves a step-wise interpolation of the static pulse-compression transfer function in the frequency domain. This technique, in conjunction with the selection of an appropriate interrogation signal, offers significant advantages in measurement time or measurement resolution for an ultrasonic vibrometer limited by additive noise at the receiver. The characteristics of optimal interrogation signals for this technique are the signal's crest factor, spectral energy distribution, and phasing. These relate to the intended compression pulse, the noise, and the static response of the system. The technique has been demonstrated analytically, experimentally, and with numerical models.

Range discrimination in ultrasonic vibrometry: theory and experiment.

A technique has been developed to demodulate periodic broadband ultrasonic interrogation signals that are returned from multiple scattering sites to simultaneously determine the low-frequency displacement time histories of each individual site. The technique employs a broadband periodic transmit signal. The motions of scattering sites are separately determined from the echoed receive signal by an algorithm involving comb filtering and pulse synthesis. This algorithm permits spatial resolution comparable to pulse-echo techniques and displacement sensitivities comparable to pure-tone techniques. A system based on this technique was used to image transient audio-frequency displacements on the order of 1-10 µm peak (≥ 50 nm/√Hz) that were produced by propagating shear waves in a tissue phantom. The system used concentric transmitting and receiving transducers and a carrier signal centered at 2.5 MHz with an 800 kHz bandwidth. The system was self-noise-limited and capable of detecting motions of strongly reflecting regions on the order of 1 nm/√Hz. System performance is limited by several factors including signal selection, component hardware, and ultrasonic propagation within the media of interest.

The 1.8 A structure of carbonmonoxy-beta 4 hemoglobin. Analysis of a homotetramer with the R quaternary structure of liganded alpha 2 beta 2 hemoglobin.

The beta-chains isolated from the human hemoglobin alpha 2 beta 2 heterotetramer self-assemble to form a beta 4 homotetramer. We report the structure of the carbonmonoxy-beta 4 (CO beta 4) tetramer refined at a resolution of 1.8 A. Compared to the three known quaternary structures of human hemoglobin, the T state, the R state and the R2 state, the quaternary structure of CO beta 4 most closely resembles the R state. While the degree of structural similarity between CO beta 4 and the R state of liganded alpha 2 beta 2 is quite high, differences between the alpha and beta-chain sequences result in interesting alternative packing arrangements at the subunit interfaces of CO beta 4. In particular, Arg40 beta and Asp99 beta interact across the CO beta 4 equivalent of the alpha 1 beta 2 interface to form two symmetry-related salt bridges that have no counterpart in either liganded or deoxyhemoglobin. Because these salt bridges are near a 2-fold symmetry axis, steric constraints prevent their simultaneous formation, and electron density images of Arg40 beta and Asp99 beta show equally populated dual conformations for the side-chains of both residues. Relative to the liganded alpha 2 beta 2 tetramer, the Arg40 beta...Asp99 beta salt bridges introduce ionic interactions that should strengthen the CO beta 4 tetramer. The CO beta 4 equivalent of the alpha 1 alpha 2 and beta 1 beta 2 interfaces strengthens the tetramer relative to the liganded alpha 2 beta 2 tetramer by tethering both ends of the central cavity. (The entrance to the central cavity is altered so that the N termini move closer together and the C termini further apart, forming an anion binding pocket that is absent in liganded alpha 2 beta 2 hemoglobin.) In contrast, analysis of the CO beta 4 counterpart of the alpha 1 beta 1 interface indicates that this interface is weakened in the CO beta 4 tetramer. These differences in interface stability provide a structural explanation for the published observation that the alpha 2 beta 2 tetramer assembles via a stable alpha 1 beta 1 dimer intermediate, whereas assembly of the CO beta 4 tetramer is characterized more accurately by a monomer-tetramer equilibrium.

The 1.9 A structure of deoxy beta 4 hemoglobin. Analysis of the partitioning of quaternary-associated and ligand-induced changes in tertiary structure.

The crystal structure of the deoxygenated form of the human hemoglobin beta 4 tetramer (deoxy beta 4) has been determined and refined at a resolution of 1.9 A. A detailed comparison of the quaternary structures of carbonmonoxy-beta 4 (CO beta 4) and deoxy beta 4 shows that ligand binding to the beta 4 tetramer produces only slight movements of the subunits relative to each other. Therefore, unlike the hemoglobin alpha 2 beta 2 tetramer, where the transition from an unliganded T state tetramer to a liganded R state tetramer results in a large change in quaternary structure, beta 4 is locked in a quaternary structure that very closely resembles the R state. By comparing the high-resolution structures of T state deoxy alpha 2 beta 2, R state deoxy beta 4 and R state CO beta 4, it is possible to partition the changes in beta subunit tertiary structure into those that arise from changes in quaternary structure and those that result solely from ligand binding. Specifically, when viewed from the heme reference frame, comparison of the structures of T state deoxy alpha 2 beta 2 and R state deoxy beta 4 shows that the T-to-R quaternary structure transition induces changes in beta subunit tertiary structure that are approximately halfway toward the tertiary structure observed in liganded beta 4 and liganded alpha 2 beta 2. When viewed from the reference frame of the globin backbone atoms, the T-to-R quaternary structure transition induces a small rotation of the heme group and a shift of the "allosteric core" (the end of the F helix, the FG corner, the beginning of the G helix, and the heme group) away from the E helix. These movements open the ligand binding pocket and place the heme in a more symmetric position relative to the proximal histidine residue. Together, these effects work in unison to give the subunits of deoxy beta 4 a tertiary structure that has high ligand affinity.

Crystallization and preliminary crystallographic studies of Saccharomyces cerevisiae alcohol dehydrogenase I.

The cytoplasmic yeast alcohol dehydrogenase I crystallized at 5 degrees C as hexagonal plates or short columns in the presence of NAD+ and 2,2,2-trifluoroethanol, in sodium N-tris(hydroxymethyl)methyl-3-aminopropanesulfonate buffer at pH 8.2 to 8.6, using polyethylene glycol 4000 as precipitant. X-ray diffraction data to 3.2 A resolution show that the crystals are hexagonal in space group P622 with unit cell dimensions a = b = 147.9 A, c = 69.1 A. There is one subunit of the tetrameric enzyme per asymmetric unit, giving a packing density of 2.9 A3/Da.

Correlation of polarized absorption spectroscopic and X-ray diffraction studies of crystalline cytosolic aspartate aminotransferase of pig hearts.

Absorption spectra of large, well-formed crystals of cytosolic aspartate aminotransferase have been recorded using plane polarized light. Making use of measurements of crystal thickness we have calculated extinction coefficients with the electric vector of the light parallel to both the a and c axes of the crystals of the enzyme in space group P2(1)2(1)2(1). The spectra have been resolved into components with lognormal distribution curves and the resulting integrated intensities have been used to calculate the c/a polarization ratios for the absorption bands of the bound co-enzyme pyridoxal 5'-phosphate. From the polarization ratio and the co-ordinates of the co-enzyme ring atoms, provided by X-ray crystallography, we have assigned principal molecular directions of the transition dipole moment within the plane of the co-enzyme ring. Of two possible orientations, only one predicts the correct crystal extinction coefficients for the 436 nm band. In this orientation, when viewed from the B face of the ring (i.e. looking into the active site of the enzyme), the transition moment is related to the N-1-C-4 axis of the ring by counterclockwise rotation by 27 degrees. A tentative assignment of the principal molecular directions of the transition moment has also been made for the 368 nm band of the high pH form of the enzyme. In each case, the plane of the co-enzyme ring was located from the atomic co-ordinates of the ring atoms and of those atoms attached directly to the ring. The projection of the N-1 to C-4 axis on to this plane was used to evaluate the orientation of the transition moment, which was presumed to lie precisely within the plane of the ring. We have tilted this plane systematically to evaluate the error in transition moment direction resulting from uncertainties in the atomic co-ordinates. When 2-methylaspartate is diffused into the crystals if forms a Schiff base with the co-enzyme in which the ring has tilted about 32 degrees from its original position and the polarization ratio of the 436 nm band drops from 1.6 in the free enzyme to about 0.38. On the assumption that the orientation of the transition moment within the co-enzyme does not change during this rotation, this value of the polarization ratio is within experimental error of that predicted from X-ray structures on the two forms. The 2-methylaspartate binds only to subunit 1.(ABSTRACT TRUNCATED AT 250 WORDS)

Site-directed mutations of human hemoglobin at residue 35beta: a residue at the intersection of the alpha1beta1, alpha1beta2, and alpha1alpha2 interfaces.

Because Tyr35beta is located at the convergence of the alpha1beta1, alpha1beta2, and alpha1alpha2 interfaces in deoxyhemoglobin, it can be argued that mutations at this position may result in large changes in the functional properties of hemoglobin. However, only small mutation-induced changes in functional and structural properties are found for the recombinant hemoglobins betaY35F and betaY35A. Oxygen equilibrium-binding studies in solution, which measure the overall oxygen affinity (the p50) and the overall cooperativity (the Hill coefficient) of a hemoglobin solution, show that removing the phenolic hydroxyl group of Tyr35beta results in small decreases in oxygen affinity and cooperativity. In contrast, removing the entire phenolic ring results in a fourfold increase in oxygen affinity and no significant change in cooperativity. The kinetics of carbon monoxide (CO) combination in solution and the oxygen-binding properties of these variants in deoxy crystals, which measure the oxygen affinity and cooperativity of just the T quaternary structure, show that the ligand affinity of the T quaternary structure decreases in betaY35F and increases in betaY35A. The kinetics of CO rebinding following flash photolysis, which provides a measure of the dissociation of the liganded hemoglobin tetramer, indicates that the stability of the liganded hemoglobin tetramer is not altered in betaY35F or betaY35A. X-ray crystal structures of deoxy betaY35F and betaY35A are highly isomorphous with the structure of wild-type deoxyhemoglobin. The betaY35F mutation repositions the carboxyl group of Asp126alpha1 so that it may form a more favorable interaction with the guanidinium group of Arg141alpha2. The betaY35A mutation results in increased mobility of the Arg141alpha side chain, implying that the interactions between Asp126alpha1 and Arg141alpha2 are weakened. Therefore, the changes in the functional properties of these 35beta mutants appear to correlate with subtle structural differences at the C terminus of the alpha-subunit.

Controlled trial of low-dose heparin and sulfinpyrazone to prevent venous thromboembolism after operation on the hip.

A randomized, double-blind controlled trial of low-dose heparin combined with sulfinpyrazone to prevent deep-vein thrombosis after operation on the hip was carried out. In a group of seventy-three patients after arthroplasty, postoperative thrombosis of the veins of the lower limbs occurred in 51 per cent of the control patients and in 36 per cent of the treated patients. In a fracture group of thirty patients, thrombosis occurred in 75 per cent of the control patients and in 36 per cent of the treated patients. These differences are of borderline statistical significance in the fracture group and are of no statistical significance in the arthroplasty group. However, a 36 per cent incidence of venous thrombosis in the drug-treated patients is too high to justify recommendation of the regimen tested without careful monitoring of patients by tests designed to detect thrombosis. Then, appropriate anticoagulant therapy can be instituted if necessary.

Measurement of the depth-dependent resonance of water-loaded human lungs.

An experiment was conducted to determine the response of the human lung to water-borne sound in the range of 20 to 500 Hz. A small pool inside a hyperbaric chamber was used to simulate four ambient pressure conditions spanning the range of recreational diving depths. Ten subjects were tested on two occasions each using three separate measures to evaluate the response of the subjects' lungs. With some notable exceptions, results were consistent between subjects and between measures. These indicate that human lungs can be reasonably modeled as a lumped single-degree-of-freedom system over the lower portion of the band of interest. Here, the surrounding fluid provides the dominant mass and the dominant stiffness is provided by the entrapped air with a small additional contribution from tissue elasticity. Measured resonances increase with the square root of ambient pressure from an average of 40 Hz with a quality factor of 1.8 at near-surface pressure to 73 Hz with a quality factor of 2.6 at an equivalent depth of 36.4 m. There is evidence of other resonances within or near the band of interest that may be attributable to nonvolumetric chest/lung modes, Helmholtz resonance, and/or resonance of gastrointestinal bubbles.

High-resolution X-ray study of deoxy recombinant human hemoglobins synthesized from beta-globins having mutated amino termini.

The crystal structures of three mutant hemoglobins reconstituted from recombinant beta chains and authentic human alpha chains have been determined in the deoxy state at 1.8-A resolution. The primary structures of the mutant hemoglobins differ at the beta-chain amino terminus. One mutant, beta Met, is characterized by the addition of a methionine at the amino terminus. The other two hemoglobins are characterized by substitution of Val 1 beta with either a methionine, beta V1M, or an alanine, beta V1A. All the mutation-induced structural perturbations are small intrasubunit changes that are localized to the immediate vicinity of the beta-chain amino terminus. In the beta Met and beta V1A mutants, the mobility of the beta-chain amino terminus increases and the electron density of an associated inorganic anion is decreased. In contrast, the beta-chain amino terminus of the beta V1M mutant becomes less mobile, and the inorganic anion binds with increased affinity. These structural differences can be correlated with functional data for the mutant hemoglobins [Doyle, M. L., Lew, G., DeYoung, A., Kwiatkowski, L., Noble, R. W., & Ackers, G. K. (1992) Biochemistry preceding paper is this issue] as well as with the properties of ruminant hemoglobins and a mechanism [Perutz, M., & Imai, K. (1980) J. Mol. Biol. 136, 183-191] that relates the intrasubunit interactions of the beta-chain amino terminus to changes in oxygen affinity. Since the structures of the mutant deoxyhemoglobins show only subtle differences from the structure of deoxyhemoglobin A, it is concluded that any of the three hemoglobins could probably function as a surrogate for hemoglobin A.(ABSTRACT TRUNCATED AT 250 WORDS)

A third quaternary structure of human hemoglobin A at 1.7-A resolution.

Previous crystallographic studies have shown that human hemoglobin A can adopt two stable quaternary structures, one for deoxyhemoglobin (the T-state) and one for liganded hemoglobin (the R-state). In this paper we report our finding of a second quaternary structure (the R2-state) for liganded hemoglobin A. The magnitudes of the spatial differences between the R- and R2-states are as large as those between the R- and T-states. Of particular interest are the structural changes that occur as a result of R-T and R-R2 transitions at the so-called "switch" region of the critical alpha 1 beta 2 interface. In the R-state, His-97 beta 2 is positioned between Thr-38 alpha 1 and Thr-41 alpha 1, whereas in transition to the T-state His 97 beta 2 must "jump" a turn in the alpha 1 C helix to form nonpolar contacts with Thr-41 alpha 1 and Pro-44 alpha 1. This facet of the R-T transition presents a major steric barrier to the quaternary structure change. In the R2-state, His-97 beta 2 simply rotates away from threonines 38 alpha 1 and 41 alpha 1, breaking contact with these residues and allowing water access to the center of the alpha 1 beta 2 interface. With the switch region in an open position in the R2-state, His-97 beta 2 should be able to move by Thr-41 alpha 1 and make the transition to the T-state with a steric barrier that is less than that for the R-T transition. Thus the R2-state may function as a stable intermediate along a R-R2-T pathway. The T-, R-, and R2-states must coexist in solution. That is, the fact that these states can be crystallized implies that they are all energetically accessible structures. What remains to be determined are the T-to-R, T-to-R2, and R-to-R2 equilibrium constants for hemoglobin under various solution conditions and ligation states. Although this may prove to be difficult, we discuss previously published results which indicate that low concentrations of inorganic anions or low pH may favor the R2-state and at least one alpha 1 beta 2 interface mutation stabilizes a quaternary structure that is very similar to the R2-state.

Crystal structure of the S-nitroso form of liganded human hemoglobin.

Although numerous reports have documented that the S-nitrosylation of cysteine residues by NO alters the activities of a wide variety of proteins, the direct visualization and the structural consequences of this reversible modification have not yet been reported for any protein. Here we describe the crystal structure of S-nitroso-nitrosylhemoglobin determined at a resolution of 1.8 A. The specific reaction of NO with Cys93beta is confirmed in this structure, and a large S-nitrosylation-induced change in the tertiary structure of the COOH-terminal dipeptides of the beta subunits provides additional insight into the stereochemical mechanism by which blood flow is regulated by the interaction of NO with hemoglobin.

Interface sliding as illustrated by the multiple quaternary structures of liganded hemoglobin.

Initial crystallographic studies suggested that fully liganded mammalian hemoglobin can adopt only a single quaternary structure, the quaternary R structure. However, more recent crystallographic studies revealed the existence of a second quaternary structure for liganded hemoglobin, the quaternary R2 structure. Since these quaternary structures can be crystallized, both must be energetically accessible structures that coexist in solution. Unanswered questions include (i) the relative abundance of the R and R2 structures under various solution conditions and (ii) whether other quaternary structures are energetically accessible for the liganded alpha(2)beta(2) hemoglobin tetramer. Although crystallographic methods cannot directly answer the first question, they represent the most direct and most accurate approach to answering the second question. We now have determined and refined three different crystal structures of bovine carbonmonoxyhemoglobin. These structures provide clear evidence that the dimer-dimer interface of liganded hemoglobin has a wide range of energetically accessible structures that are related to each other by a simple sliding motion. The dimer-dimer interface acts as a "molecular slide bearing" that allows the two alpha beta dimers to slide back and forth without greatly altering the number or the nature of the intersubunit contacts. Since the general stereochemical features of this interface are not unusual, it is likely that interface sliding of the kind displayed by fully liganded hemoglobin plays important structural and functional roles in many other protein assemblies.

Processing of acoustic signals in the auditory system of bony fish.

In order to determine unambiguously the bearing of a sound source, a fish must be able to resolve acoustic pressure and the components of the acoustic displacement vector from the signals detected by the otolithic organs. A new hypothesis for the processing of acoustical information by bony fish is presented. It is demonstrated that much of the processing required to do this may be implicit in the structure of the ear and its associated neural innervation. Possible algorithms are presented that the central nervous system might use to further process the derived information to localize a sound source and discriminate frequency and range. The hypothesis is shown to be consistent with much of what is known of the morphology and physiology of the auditory system of bony fishes.

The interaction of folylpolyglutamates with deoxyhemoglobin. Identification of the binding site.

Previous studies have shown that pteroylheptaglutamate (PteGlu7) can form a 1:1 complex with deoxyhemoglobin. The solution and crystallographic studies reported in this paper delineate the nature of the PteGlu7 binding site. We find that the three structural elements of PteGlu7 (the pteridine moiety, the p-aminobenzoyl portion, and the glutamate groups) each contribute to the binding energy by interacting with residues in the central cavity between the beta subunits and with residues at the alpha 1 beta 1 interface. Identification of the 2,3-diphosphoglycerate (DPG) binding site as part of the PteGlu7 binding site was accomplished in two ways; first by the demonstration of reduced PteGlu7 binding to hemoglobin selectively modified by pyridoxylation at this site, and second by the finding that DPG and PteGlu7 bind to deoxyhemoglobin in a competitive manner. In addition, since analogs of PteGlu7 in which the pteridine moiety is modified display reduced binding, it can be concluded that the pteridine group also contributes significantly to the binding energy. The crystallographic studies are completely consistent with the results determined in solution. A difference electron density image at 4.3 A resolution shows that the pteridine and p-aminobenzoyl groups are nestled against an interior edge of the alpha 1 beta 1 interface with the pteridine ring interacting with Phe 36 alpha 1 and the p-aminobenzoyl group positioned against a portion of the H helix between residues Lys 132 beta 1 and Ala 135 beta 1. The difference density for the glutamate residues is less well resolved (for reasons described in the text), but it is clear that some of the carboxylate side chains must interact with residues at the DPG binding site.

High-resolution X-ray study of deoxyhemoglobin Rothschild 37 beta Trp----Arg: a mutation that creates an intersubunit chloride-binding site.

The mutation site in hemoglobin Rothschild (37 beta Trp----Arg) is located in the "hinge region" of the alpha 1 beta 2 interface, a region that is critical for normal hemoglobin function. The mutation results in greatly reduced cooperativity and an oxygen affinity similar to that of hemoglobin A [Gacon, G., Belkhodja, O., Wajcman, H., & Labie, D. (1977) FEBS Lett. 82, 243-246]. Crystal were grown under "low-salt" conditions [100 mM Cl- in 10 mM phosphate buffer at pH 7.0 with poly(ethylene glycol) as a precipitating agent]. The crystal structure of deoxyhemoglobin Rothschild and the isomorphous crystal structure of deoxyhemoglobin A were refined at resolutions of 2.0 and 1.9 A, respectively. The mutation-induced structural changes were partitioned into components of (1) tetramer rotation, (2) quaternary structure rearrangement, and (3) deformations of tertiary structure. The quaternary change involves a 1 degree rotation of the alpha subunit about the "switch region" of the alpha 1 beta 2 interface. The tertiary changes are confined to residues at the alpha 1 beta 2 interface, with the largest shifts (approximately 0.4 A) located across the interface from the mutation site at the alpha subunit FG corner-G helix boundary. Most surprising was the identification of a mutation-generated anion-binding site in the alpha 1 beta 2 interface. Chloride binds at this site as a counterion for Arg 37 beta. The requirement of a counterion implies that the solution properties of hemoglobin Rothschild, in particular the dimer-tetramer equilibrium, should be very dependent upon the concentration and type of anions present.