Dynamic instability of liquidlike motions in a globular protein observed by inelastic neutron scattering.
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Journal Article↗
Biomedical subjects
S Cusack
Publications and source records attributed to S Cusack.
Temperature dependence of the low frequency dynamics of myoglobin. Measurement of the vibrational frequency distribution by inelastic neutron scattering.
Inelastic neutron scattering spectra of myoglobin hydrated to 0.33 g water (D2O)/g protein have been measured in the low frequency range (1-150 cm-1) at various temperatures between 100 and 350 K. The spectra at low temperatures show a well-resolved maximum in the incoherent dynamic structure factor Sinc(q, omega) at approximately 25 cm-1 and no elastic broadening. This maximum becomes gradually less distinct above 180 K due to the increasing amplitude of quasielastic scattering which extends out to 30 cm-1. The vibrational frequency distribution derived independently at 100 and 180 K are very similar, suggesting harmonic behavior at these temperatures. This result has been used to separate the vibrational motion from the quasielastic motion at temperatures above 180 K. The form of the density of states of myoglobin is discussed in relation to that of other amorphous systems, to theoretical calculations of low frequency modes in proteins, and to previous observations by electron-spin relaxation of fractal-like spectral properties of proteins. The onset of quasielastic scattering above 180 K is indicative of a dynamic transition of the system and correlates with an anomalous increase in the atomic mean-squared displacements observed by Mössbauer spectroscopy (Parak, F., E. W. Knapp, and D. Kucheida. 1982. J. Mol. Biol. 161: 177-194.) and inelastic neutron scattering (Doster, W., S. Cusack, and W. Petry, 1989. Nature [Lond.]. 337: 754-756.) Similar behavior is observed for a hydrated powder of lysozyme suggesting that the low frequency dynamics of globular proteins have common features.
Deuterium↗
Non-traumatic chest pain in young adults: a medical audit.
Four hundred consecutive young patients who attended an accident and emergency department with non-traumatic chest pain as their primary complaint were reviewed. They represented 0.7% of total new attendances. Most were self-referrals, but ambulance transport was requested for over 25%. The majority of investigations (mainly chest radiography and electrocardiography) performed in this group of patients were normal; however, almost one in six investigations was judged to be abnormal. Although this group of patients is at low risk for serious cardiorespiratory disease, a small but significant number of underlying (mainly non-cardiac) disorders was found and 22.5% (90) required in-patient admission. In contrast, almost one-fifth of patients received no specific diagnosis, while almost 40% were deemed to require no follow-up.
Adolescent↗
Dynamical transition of myoglobin revealed by inelastic neutron scattering.
Structural fluctuations in proteins on the picosecond timescale have been studied in considerable detail by theoretical methods such as molecular dynamics simulation, but there exist very few experimental data with which to test the conclusions. We have used the technique of inelastic neutron scattering to investigate atomic motion in hydrated myoglobin over the temperature range 4-350 K and on the molecular dynamics timescale 0.1-100 ps. At temperatures below 180 K myoglobin behaves as a harmonic solid, with essentially only vibrational motion. Above 180 K there is a striking dynamic transition arising from the excitation of nonvibrational motion, which we interpret as corresponding to torsional jumps between states of different energy, with a mean energy asymmetry of 12 kJ mol-1. This extra mobility is reflected in a strong temperature dependence of the mean-square atomic displacements, a phenomenon previously observed specifically for the heme iron by Mössbauer spectroscopy, but on a much slower timescale (10(-7) s). It also correlates with a glass-like transition in the hydration shell of myoglobin and with the temperature-dependence of ligand-binding rates at the heme iron, as monitored by flash photolysis. In contrast, the crystal structure of myoglobin determined down to 80 K shows no significant structural transition. The dynamical behaviour we find for myoglobin (and other globular proteins) suggests a coupling of fast local motions to slower collective motions, which is a characteristic feature of other dense glass-forming systems.
Algorithms↗
Inelastic neutron scattering analysis of picosecond internal protein dynamics. Comparison of harmonic theory with experiment.
The experimental inelastic neutron scattering spectrum of a protein, the bovine pancreatic trypsin inhibitor (BPTI), in a powder sample is presented together with the generalized density of states, G(omega), as a function of the frequency, omega, derived from the scattering data. The experimental results are compared with calculations from two different normal mode analyses of BPTI. One of these, based on an improved model, gives a calculated spectrum and density of states in general agreement with those obtained experimentally; the other, based on an earlier model, shows considerable disagreement. The important improvements in the newer normal mode analysis are the explicit treatment of all atoms (non-polar as well as polar hydrogens are included) and a modified truncation scheme for the long-range electrostatic interactions. The fact that the inelastic neutron scattering measurements can distinguish between the two theoretical models makes clear their utility for the analysis of protein dynamics.
Animals↗
Structure of the influenza virus haemagglutinin complexed with its receptor, sialic acid.
The three-dimensional structures of influenza virus haemagglutinins complexed with cell receptor analogues show sialic acids bound to a pocket of conserved amino acids surrounded by antibody-binding sites. Sialic acid fills the conserved pocket, demonstrating that it is the influenza virus receptor. The proximity of the antibody-binding sites suggests that antibodies neutralize virus infectivity by preventing virus-to-cell binding. The structures suggest approaches to the design of anti-viral drugs that could block attachment of viruses to cells.
Antibodies↗
Crystals of seryl-tRNA synthetase from Escherichia coli. Preliminary crystallographic data.
Crystals of seryl-tRNA synthetase from Escherichia coli can be grown from ammonium sulphate/octyl glucoside solutions in two days. The crystals appear to be very suitable for X-ray analysis, diffracting to at least 2.8 A resolution and being resistant to radiation damage. The crystals are monoclinic (space group C2) with cell parameters a = 148.2 A, b = 90.6 A, c = 69.5 A and beta = 119.0 degrees. Depending on whether the asymmetric unit is the enzyme monomer (Mr 48,414) or dimer the Vm value would be either 4.12 or 2.10 A3/dalton. Although the former would indicate a rather high solvent content, other proteins crystallized in the presence of octyl glucoside have Vm values similar to this.
Amino Acyl-tRNA Synthetases↗
Direct measurement of hydration-related dynamic changes in lysozyme using inelastic neutron scattering spectroscopy.
Inelastic neutron scattering spectroscopy is used to investigate dynamic changes in lysozyme powder at two different low D2O hydrations (0.07g D2O/g protein and 0.20 g D2O/g protein). In the higher hydration sample, the inelastic scattering between 0.8 and 4.0 cm-1 energy transfer is increased and the elastic scattering is decreased. The decreased elastic scattering suggests increased atomic amplitudes of motion and the increased 0.8 to 4.0 cm-1 scattering suggests increased motions in this frequency range. Comparison with normal mode models of lysozyme dynamics shows that the inelastic difference occurs in the frequency region predicted for the lowest frequency, largest amplitude, global modes of the molecular [M. Levitt, C. Sander and P.S. Stern, J. Mol. Biol. 181, 423 (1985). B. Brooks and M. Karplus, Proc. Natl. Acad. Sci (U.S.A) 82, 4995 (1985), R.E. Bruccoleri, M. Karplus and J.A. McCammon, Biopolymers 25 1767 (1986)]. Our results are consistent with a model in which an increased number of low frequency global modes are present in the higher hydrated sample.
Energy Transfer↗
Electron microscopy of the low pH structure of influenza virus haemagglutinin.
Influenza virus haemagglutinin mediates infection of cells by fusion of viral and endosomal membranes, triggered by low pH which induces a conformational change in the protein. We report studies of this change by electron microscopy, neutron scattering, sedimentation and photon correlation on X-31 (H3N2) haemagglutinin, both intact and bromelain cleaved, in various assemblies. HAs in all preparations showed a thinning at low pH, and a marked elongation which was removed on tryptic digestion, revealing altered features in the remaining stem portion of the molecule. A tentative model of the change is proposed, with reference to the known X-ray structure at neutral pH, in which major changes occur in the stem tertiary structure, while the top portion is only affected in its quaternary structure.
Animals↗
Structure and composition of influenza virus. A small-angle neutron scattering study.
A detailed analysis is presented of the small-angle neutron scattering curves of homogeneous solutions of influenza B virus, both intact and after treatment with bromelain, which removes the external glycoprotein spikes. The two sets of data are consistent with the following low-resolution structure: the virus particles are spherical, about 1200 A in diameter and of Mr about 180 X 10(6). The lipid bilayer is centred at a radius of 425 A, is 40 A to 50 A thick and constitutes 25% to 28% of the virus mass. The surface glycoproteins, predominantly haemagglutinin, contribute 40% to 46% of the total mass. Surprisingly little protein is found in the interior of the virus. It is suggested that the reason for this is that many particles do not contain the full complement of ribonucleoprotein complexes. These results are in good agreement with recent scanning transmission electron microscopic measurements of molecular mass and cryo-electron microscopic observations of the same preparations. Appendix 1 describes a new method of deriving spherical shell models from contrast variation neutron scattering data on viruses, in which scattering curves from all measured contrasts are used simultaneously. There is also a discussion of the assumptions and limitations implicit in the structural interpretation of such models, with emphasis on viruses containing lipid bilayers. Appendix 2 examines the effect on the scattering curves of various arrangements of the surface glycoproteins.
Bromelains↗
Three-dimensional molecular shape determination from a limited number of projections.
A real space method allowing the reconstruction of negatively stained crystalline objects from a limited number of projections is presented. The method is based on the assumption that only two density levels are required to describe an ideally negatively stained object (that of the volume occupied by the object and that of the volume occupied by the stain). The method is illustrated by the reconstruction of the asymmetric unit of catalase microcrystals using only the three principal projections. It is shown that other projections can then be predicted to a good approximation.
Animals↗
Low resolution structure of the influenza C glycoprotein determined by electron microscopy.
The influenza C glycoprotein is clearly seen to be a trimer in specimens prepared with uranyl stains. Three-dimensional reconstructions from naturally occurring hexagonal arrays show that at low resolution (approximately 30 A) the influenza C glycoprotein exhibits similar features to the haemagglutinin glycoprotein of influenza A. Both have a triangular stalk near the membrane. Further from the membrane, the stalk becomes broader and the monomers more separated, leaving an open centre. The molecule narrows at the top. The regions of greatest contact between adjacent trimers in the arrays are situated nearer the distal end of the molecule. These contact zones can be related to equivalent zones on the influenza A haemagglutinin. Differences between the structure of the influenza A haemagglutinin glycoprotein determined by X-ray analysis and reconstructions of the influenza C glycoprotein are greatest at either end of the molecule, where the reconstructions are least reliable. Ordered glycoprotein arrays have not been observed on influenza C virions incubated at low pH. The staining patterns of glycoproteins on intact virions are essentially determined by the pH at which the virus is incubated, and the stain type, but not the pH of the stain.
Humans↗
Variation of longitudinal acoustic velocity at gigahertz frequencies with water content in rat-tail tendon fibers.
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Animals↗
Neutron scattering studies of virus structure.
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Models, Structural↗
Inelastic neutron scattering studies of hexokinase in solution.
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Binding Sites↗
Structure of the Top a-t component of alfalfa mosaic virus. A non-icosahedral virion.
Neutron-scattering in combination with quasi-elastic light-scattering and electron microscopy was used to derive a model for the capsid structure of the Top a-t component of alfalfa mosaic virus (AMV-Ta-t). In the electron microscope, AMV-Ta-t appears as an irregular ellipsoidal particle with apparent dimensions 275 (+/- 31) A X 225 (+/- 22) A. Assuming that the particles are monodisperse, model calculations show that the neutron-scattering data are best explained by an oblate ellipsoidal shape for the virion with external dimensions 284 A X 284 A X 216 A. Based on this result, and in combination with the known composition of the virion, it is suggested that the capsid structure could be based on a deltahedron with 52 pointgroup symmetry and comprising 120 subunits. Such a model would imply a greater deviation from equivalent subunit interactions than normally necessary in icosahedral capsids. The neutron and photon correlation data, however, do not allow us to rule out the possibility that Top a-t is a slightly polydisperse preparation of irregular prolate shapes with mean dimensions 312 A X 232 A X 232 A. Both possibilities support the concept of alfalfa mosaic virus coat protein being capable of a wide range of intersubunit interactions, this flexibility resulting in considerable polymorphism in capsid structures.
Capsid↗
Solution scattering study on the structure of alfalfa mosaic virus strain VRU.
Neutron-scattering with contrast variation has been used to derive a model for the radial distribution of protein and RNA in the VRU strain of alfalfa mosaic virus. The RNA is distributed uniformly throughout the interior of the capsid up to a radius of 65 A and the protein coat extends from 65 to 100 A. It was found necessary to distinguish between two regions within the protein coat: one with mainly hydrophobic amino acids and another with more hydrophylic amino acids. Only a very small part of the protein penetrates into the RNA. Using X-ray scattering, no indication was found for long or short-range order in the packing of the RNA in the virion.
Medicago sativa↗