Neutron Laue macromolecular crystallography

Recent progress in neutron protein crystallography such as the use of the Laue technique and improved neutron optics and detector technologies have dramatically improved the speed and precision with which neutron protein structures can now be determined. These studies are providing unique and complementary insights on hydrogen and hydration in protein crystal structures that are not available from X-ray structures alone. Parallel improvements in modern molecular biology now allow fully (per)deuterated protein samples to be produced for neutron scattering that essentially eradicate the large-and ultimately limiting-hydrogen incoherent scattering background that has hampered such studies in the past. High quality neutron data can now be collected to near atomic resolution (approximately 2.0 A) for proteins of up to approximately 50 kDa molecular weight using crystals of volume approximately 0.1 mm3 on the Laue diffractometer at ILL. The ability to flash-cool and collect high resolution neutron data from protein crystals at cryogenic temperature (15 K) has opened the way for kinetic crystallography on freeze trapped systems. Current instrument developments now promise to reduce crystal volume requirements by a further order of magnitude, making neutron protein crystallography a more accessible and routine technique.     

High-energy neutron spectroscopy with thick silicon detectors

The high-energy neutron component of the space radiation environment in thick structures such as the International Space Station contributes to the total radiation dose received by an astronaut. Detector design constraints such as size and mass have limited the energy range of neutron spectrum measurements in orbit to about 12 MeV in Space Shuttle studies. We present a new method for high-energy neutron spectroscopy using small silicon detectors that can extend these measurements to more than 500 MeV. The methodology is based on measurement of the detector response function for high-energy neutrons and inversion of this response function with measured deposition data to deduce neutron energy spectra. We also present the results of an initial shielding study performed with the thick silicon detector system for high-energy neutrons incident on polyethylene.     

Selective deuteration of tryptophan and methionine residues in maltose binding protein: a model system for neutron scattering

We describe methods that have been developed within the ILL-EMBL Deuteration Laboratory for the production of maltose binding protein (MBP) that has been selectively labelled either with deuterated tryptophan or deuterated methionine (single labelling), or both (double labelling). MBP is used as an important model system for biophysical studies, and selective labelling can be helpful in the analysis of small-angle neutron scattering (SANS) data, neutron reflection (NR) data, and high-resolution neutron diffraction data. The selective labelling was carried out in E. coli high-cell density cultures using auxotrophic mutants in minimal medium containing the required deuterated precursors. Five types of sample were prepared and studied: (1) unmodified hydrogenated MBP (H-MBP), (2) perdeuterated MBP (D-MBP), (3) singly labelled MBP with the tryptophan residues deuterated (D-trp MBP), (4) singly labelled MBP with methionine residues deuterated (D-met MBP) and (5) doubly labelled MBP with both tryptophan and methionine residues deuterated (D-trp/met MBP). Labelled samples were characterised by size exclusion chromatography, gel electrophoresis, light scattering and mass spectroscopy. Preliminary small-angle neutron scattering (SANS) experiments have also been carried out and show measurable differences between the SANS data recorded for the various labelled analogues. More detailed SANS experiments using these labelled MBP analogues are planned; the degree to which such data could enhance structure determination by SANS is discussed.     

Neutron relative biological effectiveness for solid cancer incidence in the Japanese A-bomb survivors: an analysis considering the degree of independent effects from γ-ray and neutron absorbed doses with hierarchical partitioning

It has generally been assumed that the neutron and γ-ray absorbed doses in the data from the life span study (LSS) of the Japanese A-bomb survivors are too highly correlated for an independent separation of the all solid cancer risks due to neutrons and due to γ-rays. However, with the release of the most recent data for all solid cancer incidence and the increased statistical power over previous datasets, it is instructive to consider alternatives to the usual approaches. Simple excess relative risk (ERR) models for radiation-induced solid cancer incidence fitted to the LSS epidemiological data have been applied with neutron and γ-ray absorbed doses as separate explanatory covariables. A simple evaluation of the degree of independent effects from γ-ray and neutron absorbed doses on the all solid cancer risk with the hierarchical partitioning (HP) technique is presented here. The degree of multi-collinearity between the γ-ray and neutron absorbed doses has also been considered. The results show that, whereas the partial correlation between the neutron and γ-ray colon absorbed doses may be considered to be high at 0.74, this value is just below the level beyond which remedial action, such as adding the doses together, is usually recommended. The resulting variance inflation factor is 2.2. Applying HP indicates that just under half of the drop in deviance resulting from adding the γ-ray and neutron absorbed doses to the baseline risk model comes from the joint effects of the neutrons and γ-rays—leaving a substantial proportion of this deviance drop accounted for by individual effects of the neutrons and γ-rays. The average ERR/Gy γ-ray absorbed dose and the ERR/Gy neutron absorbed dose that have been obtained here directly for the first time, agree well with previous indirect estimates. The average relative biological effectiveness (RBE) of neutrons relative to γ-rays, calculated directly from fit parameters to the all solid cancer ERR model with both colon absorbed dose covariables, is 65 (95 %CI: 11; 170). Therefore, although the 95 % CI is quite wide, reference to the colon doses with a neutron weighting of 10 may not be optimal as the basis for the determination of all solid cancer risks. Further investigations into the neutron RBE are required, ideally based on the LSS data with organ-specific neutron and γ-ray absorbed doses for all organs rather than the RBE weighted absorbed doses currently provided. The HP method is also suggested for use in other epidemiological cohort analyses that involve correlated explanatory covariables.     

Biophysical aspects of neutron scattering from vibrational modes of proteins

This review describes a major portion of the published work on neutron scattering experiments aimed at measuring large scale motions in proteins. The importance of these motions for enzyme function and oxygen transport is indicated. The theory applicable to each type of neutron scattering measurement is given and results are discussed with a view to biological relevance. New experiments are suggested and a comparison of neutron scattering data is made with results from other techniques such as raman scattering, infrared absorption, photolysis and molecular dynamics simulations.     

Neutron-induced gamma dose from a reactor beam filter for boron neutron capture therapy

For the boron neutron capture therapy (NCT) of deep-seated metastatic melanoma, an epithermal (up to a few keV energy) neutron beam from a reactor horizontal facility could be useful if the inherent contamination from fast neutrons and gamma rays could be minimised. Calculations for ANSTO's 10 MW research reactor HIFAR have shown that, even though a filter material such as AlF3 attenuates the fast neutron dose, the beam quality improvement is counteracted by a relative increase in the gamma dose because of the gammas arising from neutron captures in the filter material, particularly the aluminium. The aluminium gammas, most of which arise from thermal neutron capture, are hard and cannot be attenuated by lead or bismuth without comparable attenuation of the epithermal neutron flux. Addition of an absorber such as 6Li to the AlF3 filter was investigated as a means of reducing the hard gamma dose, but the improvement in beam quality was small and at considerable cost to dose intensity. Dose characteristics calculations confirmed the superiority of a tangential beam over a radial beam with better results from an unfiltered tangential beam than from an AlF3 filter in a radial beam. This study showed conclusively that assessments of filter assemblies based on the effect of individual components on either the neutron or gamma dose in isolation are inadequate. In assessing any epithermal neutron filter, thermal neutron shield, and gamma shield combination, the total effect of each on the neutron, gamma, and boron-10 dose must be considered.     

Study of microdosimetric energy deposition patterns in tissue-equivalent medium due to low-energy neutron fields using a graphite-walled proportional counter

To improve radiation protection dosimetry for low-energy neutron fields encountered in nuclear power reactor environments, there is increasing interest in modeling neutron energy deposition in metrological instruments such as tissue-equivalent proportional counters (TEPCs). Along with these computational developments, there is also a need for experimental data with which to benchmark and test the results obtained from the modeling methods developed. The experimental work described in this paper is a study of the energy deposition in tissue-equivalent (TE) medium using an in-house built graphite-walled proportional counter (GPC) filled with TE gas. The GPC is a simple model of a standard TEPC because the response of the counter at these energies is almost entirely due to the neutron interactions in the sensitive volume of the counter. Energy deposition in tissue spheres of diameter 1, 2, 4 and 8 μm was measured in low-energy neutron fields below 500 keV. We have observed a continuously increasing trend in microdosimetric averages with an increase in neutron energy. The values of these averages decrease as we increase the simulated diameter at a given neutron energy. A similar trend for these microdosimetric averages has been observed for standard TEPCs and the Rossi-type, TE, spherical wall-less counter filled with propane-based TE gas in the same energy range. This implies that at the microdosimetric level, in the neutron energy range we employed in this study, the pattern of average energy deposited by starter and insider proton recoil events in the gas is similar to those generated cumulatively by crosser and stopper events originating from the counter wall plus starter and insider recoil events originating in the sensitive volume of a TEPC.     

Analytical functions to predict cosmic-ray neutron spectra in the atmosphere

Estimation of cosmic-ray neutron spectra in the atmosphere has been an essential issue in the evaluation of the aircrew doses and the soft-error rates of semiconductor devices. We therefore performed Monte Carlo simulations for estimating neutron spectra using the PHITS code in adopting the nuclear data library JENDL-High-Energy file. Excellent agreements were observed between the calculated and measured spectra for a wide altitude range even at the ground level. Based on a comprehensive analysis of the simulation results, we propose analytical functions that can predict the cosmic-ray neutron spectra for any location in the atmosphere at altitudes below 20 km, considering the influences of local geometries such as ground and aircraft on the spectra. The accuracy of the analytical functions was well verified by various experimental data.     

Neutron microscopy. The low-damage imaging of specialized organic materials

It is shown that, insofar as radiation damage is concerned, transmission neutron microscopy using neutrons in the energy range approximately 0.0001-1.0 eV is extremely attractive for the imaging of specialized organic materials. By "specialized organic materials" is meant organic specimens composed entirely of specific isotopes that have been selected on the basis of their favorable properties with regard to radiation damage. In connection with such specimens, it is demonstrated that at a resolution of, for example, 100 A, neutrons will have an advantage over soft X-rays in terms of radiation damage, provided that the inherent (neutron) bright field image contrast turns out to be greater than 10(-5). Suggestions relating to (a) the comprehensive calculation of the radiation damage sustained by specialized organic specimens under slow neutron irradiation, (b) the construction of a theory of image formation in the neutron microscope, (c) the development of neutron lenses/focusing devices, and (d) the development of a brighter neutron source (essential for neutron microscopy) are outlined in some detail. The paper concludes with two appendices, which provide important background material.     

Cancer risk estimates for gamma-rays with regard to organ-specific doses

Part I of this study presented an analysis of the solid cancer mortality data for 1950-1997 from the Japanese life-span study of the A-bomb survivors to assess the cancer risk for gamma-rays in terms of the organ-specific dose for all solid cancers combined. Compared to earlier analyses, considerably more curvature in the dose-effect relation is indicated by these computations, which now suggests a dose and dose-rate effectiveness factor of about 2. The computations are extended here in order to explore the site-specific solid cancer risks for various organs. A computational method has been developed whereby the site-specific cancer risks are all simultaneously computed with global age and gender effect modifiers. This provides a more parsimonious representation with fewer parameters and avoids the large relative standard errors which would otherwise result. The sensitivity of site-specific risks to the choices of the neutron RBE is examined. The site-specific risk estimates are quite sensitive to the neutron RBE for the least shielded organs such as the breast, bladder and oesophagus. For the deeper lying organs, such as the gallbladder, pancreas and uterus, the impact of the neutrons is much lower. With an assumed neutron RBE of 35, which is in line with results on low neutron doses in major past studies on rodents and which corresponds approximately to the current ICRP radiation weighting factor for neutrons, the neutrons appear to contribute about 40% of the observed excess cancer risk in the breast, i.e. the organ that is closest to the body surface. However, this neutron contribution fraction is only about 10% for deeper lying organs, such as the colon.     

Neutron microscopy

It is shown that, insofar as radiation damage is concerned, transmission neutron microscopy using neutrons in the energy range ≈0.0001–1.0 eV is extremely attractive for the imaging of specialized organic materials. By “specialized organic materials” is meant organic specimens composed entirely of specific isotopes that have been selected on the basis of their favorable properties with regard to radiation damage. In connection with such specimens, it is demonstrated that at a resolution of, for example, 100 Å, neutrons will have an advantage over soft X-rays in terms of radiation damage, provided that the inherent (neutron) bright field image contrast turns out to be greater than 10^?5. Suggestions relating to (a) the comprehensive calculation of the radiation damage sustained by specialized organic specimens under slow neutron irradiation, (b) the construction of a theory of image formation in the neutron microscope, (c) the development of neutron lenses/focusing devices, and (d) the development of a brighter neutron source (essential for neutron microscopy) are outlined in some detail. The paper concludes with two appendices, which provide important background material.     

Induction of DNA double-strand breaks by 157Gd neutron capture

The rationale of boron (10B) neutron capture therapy (BNCT) is based on the high thermal neutron capture cross section of 10B and the limited maximum range (about one cell diameter) of the high LET fission products of the boron neutron capture (NC) reaction. The resulting radiochemical damage is confined to the cell containing the BNC reaction. Although other nuclides have higher thermal neutron capture cross sections than 10B, NC by such nuclides results in the emission of highly penetrating gamma rays. However, gadolinium-157 (157Gd) n-gamma reaction is also accompanied by some internal conversion and, by implication, Auger electron emission. Irradiation of Gd3+-DNA complexes with thermal neutrons results in the induction of DNA double-strand (ds) breaks, but the effect is largely abrogated in the presence of EDTA. Thus, by analogy with the effects of decay of Auger electron-emitting isotopes such as 125I, the Gd NC event must take place in the close proximity of DNA in order to induce a DNA ds break. It is proposed that 157Gd-DNA ligands therefore have potential in NCT. The thermal neutron capture cross section of 157Gd, a nonradioactive isotope, is more than 50 times that of 10B.     

Metallodrug-protein interaction probed by synchrotron terahertz and neutron scattering spectroscopy

This experimental work applied coherent synchrotron-radiation terahertz spectroscopy and inelastic neutron scattering to address two processes directly associated with the mode of action of metal-based anticancer agents that can severely undermine chemotherapeutic treatment: drug binding to human serum albumin, occurring during intravenous drug transport, and intracellular coordination to thiol-containing biomolecules (such as metallothioneins) associated with acquired drug resistance. Cisplatin and two dinuclear platinum (Pt)- and palladium (Pd)-polyamine agents developed by this research group, which have yielded promising results toward some types of human cancers, were investigated. Complementary synchrotron-radiation-terahertz and inelastic neutron scattering data revealed protein metalation, through S- and N-donor ligands from cysteine, methionine, and histidine residues. A clear impact of the Pt and Pd agents was evidenced, drug binding to albumin and metallothionein having been responsible for significant changes in the overall protein conformation, as well as for an increased flexibility and possible aggregation.     

Tumor induction in BALB/c female mice after fission neutron or gamma irradiation

This study was designed to examine the dose-response relationships for tumor induction after neutron irradiation in female BALB/c mice, with emphasis on the response in the dose range 0 to 50 rad. Tumors induced after radiation exposure included ovarian tumors, lung adenocarcinomas, and mammary adenocarcinomas. For comparison the dose responses for induction of these tumors after 137Cs gamma irradiation were also examined. As previously described for the female RFM mouse, the data for ovarian tumor induction after neutron and gamma irradiation were consistent with a threshold model. For lung and mammary tumors the dose-response curve after neutron irradiation appeared to "bend over" in the dose range 10 to 20 rad. The factors responsible for this bend-over and their relative contributions to the overall form of the dose-response relationship are not presently known. However, these data strongly indicate that extrapolation from data above 50 rad could result in a significant underestimate of risks. Further, it is clear that current models of neutron carcinogenesis are inadequate, since such a bend-over is not predicted at these low dose levels.     

Problems of component discrimination in space radiation dosimetry

Resolving the LET spectrum of environmental radiation in space for assessing dose equivalents creates special problems due to superposition effects. Three components of the radiation field in space, trapped protons, tissue disintegration stars, and neutrons, contribute the bulk of the total dose equivalent. While lack of discrimination of neutron recoil and trapped primary protons does not interfere with correct determination of the combined dose equivalent as such, the simultaneous bursts of several low-energy protons and alpha particles from tissue disintegration stars completely defy LET-resolution with conventional instrumentation. So far, the tissue star dose has been determined only semiquantitatively from nuclear emulsion data. The neutron spectrum in space shows a markedly higher relative fluence in the region beyond 5 MeV than the fission neutron spectrum. Therefore, its LET spectrum centers less heavily on LET values near the proton Bragg Peak. This would call for assigning a QF value of less than 10 to the neutron dose in space. Still more serious shortcomings exist with regard to LET interpretation of heavy primaries.     

Protein kinase A targeting and activation as seen by small-angle solution scattering

We have studied the solution structures of the multi-functional protein kinase A using small-angle X-ray and neutron scattering and have found a remarkable structural diversity in the different isoforms of this multi-subunit enzyme, in spite of its having high sequence homology and a common domain organization within its sequences. The available high-resolution crystal and NMR structural data for the protein kinase A components have aided in the interpretation of the solution scattering data and enabled us to develop models that bring insights into protein kinase A activation and targeting mechanisms, such as the opening and closing of the catalytic cleft to facilitate substrate binding or inhibition, respectively, and the role of sequence segments that join functional domains in the R subunit in providing a structurally flexible scaffold for interactions with the C subunit and A kinase-anchoring proteins (AKAPs).     

Squalane is in the midplane of the lipid bilayer: implications for its function as a proton permeability barrier

A recently proposed model for proton leakage across biological membranes [Prog. Lipid Res. 40 (2001) 299] suggested that hydrocarbons specifically in the center of the lipid bilayer inhibit proton leaks. Since cellular membranes maintain a proton electrochemical gradient as a principal energy transducer, proton leakage unproductively consumes cellular energy. Hydrocarbons in the bilayer are widespread in membranes that sustain such gradients. The alkaliphiles are unique in that they contain up to 40 mol% isoprenes in their membranes including 10-11 mol% squalene [J. Bacteriol. 168 (1986) 334]. Squalene is a polyisoprene hydrocarbon without polar groups. Localizing hydrocarbons in lipid bilayers has not been trivial. A myriad of physical methods including fluorescence spectroscopy, electron-spin resonance, nuclear magnetic resonance as well as X-ray and neutron diffraction have been used to explore this question with various degrees of success and often contradictory results. Seeking unambiguous evidence for the localization of squalene in membranes or lipid bilayers, we employed neutron diffraction. We incorporated 10 mol% perdeuterated or protonated squalane, an isosteric analogue of squalene, into stacked bilayers of dioleoyl phosphatidyl choline (DOPC) doped with dioleoyl phosphatidyl glycerol (DOPG) to simulate the negative charges found on natural membranes. The neutron diffraction data clearly show that the squalane lies predominantly in the bilayer center, parallel to the plane of the membrane.     

A neutron Laue diffraction study of endothiapepsin: implications for the aspartic proteinase mechanism.

Current proposals for the catalytic mechanism of aspartic proteinases are largely based on X-ray structures of bound oligopeptide inhibitors possessing nonhydrolyzable analogues of the scissile peptide bond. However, the positions of protons on the catalytic aspartates and the ligand in these complexes have not been determined with certainty. Thus, our objective was to locate crucial protons at the active site of an inhibitor complex since this will have major implications for a detailed understanding of the mechanism of action. We have demonstrated that high-resolution neutron diffraction data can be collected from crystals of the fungal aspartic proteinase endothiapepsin bound to a transition state analogue (H261). The neutron structure of the complex has been refined at a resolution of 2.1 A to an R-factor of 23.5% and an R(free) of 27.4%. This work represents the largest protein structure studied to date by neutron crystallography at high resolution. The neutron data demonstrate that 49% of the main chain nitrogens have exchanged their hydrogen atoms with D2O in the mother liquor. The majority of residues resisting exchange are buried within core beta-sheet regions of the molecule. The neutron maps confirm that the protein has a number of buried ionized carboxylate groups which are likely to give the molecule a net negative charge even at very low pH, thereby accounting for its low pI. The functional groups at the catalytic center have clearly undergone H-D exchange despite being buried by the inhibitor occupying the active site cleft. Most importantly, the data provide convincing evidence that Asp 215 is protonated and that Asp 32 is the negatively charged residue in the transition state complex. This has an important bearing on mechanistic proposals for this class of proteinase.     

A simplified model of local structure in aqueous proline amino acid revealed by first-principles molecular dynamics simulations

Aqueous proline solutions are deceptively simple as they can take on complex roles such as protein chaperones, cryoprotectants, and hydrotropic agents in biological processes. Here, a molecular level picture of proline/water mixtures is developed. Car-Parrinello ab initio molecular dynamics (CPAIMD) simulations of aqueous proline amino acid at the B-LYP level of theory, performed using IBM's Blue Gene/L supercomputer and massively parallel software, reveal hydrogen-bonding propensities that are at odds with the predictions of the CHARMM22 empirical force field but are in better agreement with results of recent neutron diffraction experiments. In general, the CPAIMD (B-LYP) simulations predict a simplified structural model of proline/water mixtures consisting of fewer distinct local motifs. Comparisons of simulation results to experiment are made by direct evaluation of the neutron static structure factor S(Q) from CPAIMD (B-LYP) trajectories as well as to the results of the empirical potential structure refinement reverse Monte Carlo procedure applied to the neutron data.     

Assessment of ideal neutron beams for neutron capture therapy.

The discrete-ordinates transport computer code DORT has been used to develop a two-dimensional cylindrical phantom model for use as a tool to assess beam design and dose distributions for boron neutron capture therapy. The model uses an S8 approximation for angular fluxes and a P3 Legendre approximation for scattering cross sections. A one-dimensional discrete-ordinates model utilizing the computer code ANISN was used to validate the energy-group structure used in the two-dimensional calculations. In the two-dimensional model the effects of varying basic parameters such as aperture width, neutron source energy, and tissue composition have been studied. Identical results were obtained when comparing narrow beam calculations to fine-mesh higher-order Sn treatments (up to S32), and with P5 cross sections. It is shown that, when the correct assessment volume is used, narrow beams will give little or no advantage for therapy even with an optimum-energy ideal neutron beam.