New sources and instrumentation for neutrons in biology.

Neutron radiation offers significant advantages for the study of biological molecular structure and dynamics. A broad and significant effort towards instrumental and methodological development to facilitate biology experiments at neutron sources worldwide is reviewed.

Recent results on hydrogen and hydration in biology studied by neutron macromolecular crystallography.

Neutron diffraction provides an experimental method of directly locating hydrogen atoms in proteins, a technique complimentary to ultra-high-resolution [1, 2] X-ray diffraction. Three different types of neutron diffractometers for biological macromolecules have been constructed in Japan, France and the United States, and they have been used to determine the crystal structures of proteins up to resolution limits of 1.5-2.5 A. Results relating to hydrogen positions and hydration patterns in proteins have been obtained from these studies. Examples include the geometrical details of hydrogen bonds, H/D exchange in proteins and oligonucleotides, the role of hydrogen atoms in enzymatic activity and thermostability, and the dynamical behavior of hydration structures, all of which have been extracted from these structural results and reviewed. Other techniques, such as the growth of large single crystals, the preparation of fully deuterated proteins, the use of cryogenic techniques, and a data base of hydrogen and hydration in proteins, will be described.

Crystallization of a large single crystal of cubic insulin for neutron protein crystallography.

The growth of a large single crystal of cubic porcine insulin for characterization of hydrogen and hydration in cubic insulin crystals by neutron diffraction analysis is reported. Growth in D2O was investigated based on the phase diagram for cubic insulin to determine appropriate growth conditions, and a large single crystal was then successfully grown by a dialysis method to a size of 4.0 x 4.0 x 1.3 mm3. Neutron diffraction analysis of the cubic insulin crystals was carried out using a single-crystal diffractometer at the JRR-3M reactor of the Japan Atomic Energy Research Institute. In preliminary analysis, Npi appears to be protonated and Ntau deprotonated in His5 in the B-chain, whereas both Npi and Ntau are protonated in His10.

Direct observation of deuterium migration in crystalline-state reaction by single-crystal neutron diffraction. III. Photoracemization of 1-cyanoethyl cobaloxime complexes.

The H atoms bonded to the chiral C atoms (stereogenic center) of the 1-cyanoethyl groups in two cobalt complexes, [(R)-1-cyanoethyl]bis(dimethylglyoximato)(pyridine)cobalt(III) (2) and [(R,S)-1-cyanoethyl]bis(dimethylglyoximato)(piperidine)cobalt(III) (3), were replaced with D atoms, such as Co--C*D(CH(3))CN. The crystals of the two cobalt complexes were irradiated with a xenon lamp for 72 h and 27 d, respectively. The unit-cell dimensions were gradually changed with retention of the single-crystal form. The crystal structures after irradiation were determined by neutron diffraction. In each crystal the chiral 1-cyanoethyl group of one of the two crystallographically independent molecules was partly inverted to the opposite configuration, whereas that of the other molecule kept the original configuration. The C*--D bond in the inverted group was completely conserved in the process of the inversion of the chiral alkyl group. This suggests that the inversion of the chiral 1-cyanoethyl group proceeds with the rotation of the cyanoethyl radical after the Co--C bond cleavage by photo-irradiation so that the opposite side of the radical faces the Co atom. This is followed by recombination of the Co--C bond to form the inverted 1-cyanoethyl group.

Dissolution rate of hen egg-white lysozyme crystal under microgravity.

Protein crystallization under micro gravity has been already tried many times in the United States and other countries, and it is reported that about 20% of proteins were better crystallized under microgravity than on earth. This verified that microgravity is sometimes effective in protein crystallization. However, if these procedures continued to be carried out without clarifying which processes are effective, improved development of protein crystallization cannot be expected. The most effective way to study the process is to carry out protein crystallization experiments, each elementary stage of which is clearly observed. To this end, the dissolution rate of a single crystal of hen egg-white lysozyme has been measured both under microgravity and on earth in order to study the mechanism of protein crystallization. In May 1997, we had an opportunity to have an experiment on protein crystallization with use of STS-84 space shuttle missions (the time duration of which was 210 hours). The apparatus for protein crystallization by vapor diffusion techniques was available and we have tried to use it for measurement of crystal dissolution rate under microgravity. The barrels of two syringes (20 ml x 2) were filled with unsaturated protein solutions (hen egg-white lysozyme (HEWL): 0.0wt%, 0.1wt%, 0.2wt%, 0.3wt%; NaCl 3wt% aqueous solution) and a crystal (HEWL: tetragonal form; 1 mm +/- 0.2 mm in diameter) was put on the bottom of the one syringe. Dissolution of the crystal was started by extruding the unsaturated solutions onto the syringe tip with the crystal. The crystal dissoluted in 40 ml droplets that are extruded from syringes. The temperature was kept at 20 degrees C. Just before the Space Shuttle begins returning to the earth, the protein solution was withdrawn back into the syringes by the astronaut, and the melting experiment was finished. In the one syringe the incompletely melted crystal was withdrawn as well. The solution concentration in the other syringe was measured. In the flight experiment, only the initial and final solution concentrations can be measured. In the control experiment on earth the solution concentrations in the course of dissolution were also measured. 20 undersaturated solutions (40 ml in volume) were prepared and a crystal (1 mm +/- 0.2 mm in diameter) was put in each solution. The solution concentration was measured at constant time intervals. When the crystal starts to dissolute [correction of dissolue], molecules in the crystal surface leave the crystal, the concentration around the crystal becomes high and there occurs a radial concentration gradient centered on the nucleus. Molecules diffuse along the gradient and go farther from the crystal. On earth, the concentration gradient might be disturbed by convection and the high concentration around the crystal might be disturbed more quickly than under microgravity. We might therefore expect that dissolution rate on the ground should be larger than under micro-gravity. However, our experimental results show that the expectation was not correct. What might the reason be? One possible reason is that there might be Marangoni convection effects in the apparatus for protein crystallization by vapor diffusion techniques used for the melting experiment. This effect has also been observed by Chayen et al.

Direct observation of deuterium migration in crystalline-state reaction by single-crystal neutron diffraction. II. 3-1 photoisomerization of a cobal-oxime complex

Single crystal neutron diffraction analysis of photo-exposed (3-cyanopropyl-d2(alpha,alpha))-[(R)-1-phenylethylamine-d11]bis(dimethylglyoximato-d14)cobalt(III) was carried out in order to clarify the mechanism of the crystalline-state photoisomerization of the 3-cyanopropyl group bonded to the Co atom in some cobaloxime complexes. Before irradiation the two H atoms bonded to the C1 atom of the 3-cyanopropyl group were exchanged with the D atoms such as --CH2CH2CD2CN. On exposure to a xenon lamp, the cell dimensions of the crystal were gradually changed. After 7 d exposure the change became insignificantly small. The structure was analyzed by neutron diffraction. The 3-cyanopropyl group was transformed to the 1-cyanopropyl group such as --CD(CN)C(H1/2,D1/2)2CH3 with retention of the single-crystal form. This indicates that one of the D atoms bonded to C1 migrates to either position bonded to C2. The other atoms of the complex remained unchanged. These results indicate that photoisomerization proceeded in two steps: the 3-cyanopropyl group was isomerized to the 2-cyanopropyl group in the first place and then the 2-cyanopropyl group was transformed to the 1-cyanopropyl group. Moreover, it was made clear that the second-step isomerization was irreversible, since one of the D atoms was retained. The disordered structure at C2 is estimated to be caused by the interconversion between the 1-cyanopropyl group produced and its dehydrogenated olefin after the photoisomerization.

Neutrons expand the field of structural biology.

Neutron protein crystallography aids the identification of all the hydrogen atoms in biological macromolecules and has helped to establish hydration patterns in proteins. Recent technical innovations, such as the development of the neutron imaging plate, have made it possible to shorten the prohibitively long amount of time required to collect a full diffraction data set. These instrumental advances have been applied to Laue diffractometry, as well as to more conventional data collection techniques, such as those using monochromatized neutron beams.

Molecular dynamics study of femtosecond events in photoactive yellow protein after photoexcitation of the chromophore.

Molecular dynamics simulations were carried out to study what happens in a photoreceptor protein, photoactive yellow protein (PYP), immediately after the vertical transition of the chromophore from the ground to the excited state. A photon absorption simulation was performed to investigate the movement of amino acid residues upon photoexcitation. To calculate the excited state of the chromophore, SCF-CI calculation was carried out with INDO/S Hamiltonian. We observed that some amino acid residues have strong interactions with the chromophore. Most of these amino acid residues are conserved in PYPs from three different species of bacteria. This observation indicates the biological importance of these residues.

Small-angle neutron scattering and dynamic light scattering studies of N- and C-terminal fragments of ovotransferrin.

In order to rationalize the physicochemical heterogeneities between the N- and C-lobes of ovotransferrin (OTf), we have analyzed the structural characteristics of the isolated fragments corresponding to the N- and C-terminal halves of OTf (OTf/2N and OTf/2C) with and without iron by means of small-angle neutron scattering (SANS) using the contrast variation method with solvents of various D2O/H2O mixtures, and dynamic light scattering (DLS) measurements. The analyses of the internal structural characteristics from SANS data revealed that the radius of gyration (Rg) for both fragments decreased to the same extent with iron binding, and the structural distortion of OTf/2C was smaller than that of OTf/2N, decreasing with iron uptake. The DLS studies showed that the change in the diffusion coefficient induced by iron binding to OTf/2C was greater than that to OTf/2N. It was inferred that the OTf/2C molecule tends to become more compact on the whole by iron binding as compared to the OTf/2N molecule.

Neutron Laue diffractometry with an imaging plate provides an effective data collection regime for neutron protein crystallography.

Neutron quasi-Laue diffraction data (2 A resolution) from tetragonal hen egg-white lysozyme were collected in ten days with neutron imaging plates. The data processing Laue software, LAUEGEN, developed for X-ray Laue diffractometry, was adapted for neutron diffractometry with a cylindrical detector. The data analysis software, X-PLOR, was modified and used for the refinement of hydrogen atoms, and the positions of 960 hydrogen atoms in the protein and 157 bound water molecules, were determined. Several examples are given of the methods used to identify hydrogen atoms and water molecules.

Small angle neutron scattering from lysozyme solutions in unsaturated and supersaturated states (SANS from lysozyme solutions).

Small angle neutron scattering (SANS) method was used to study lysozyme solutions, with particular interest in an understanding of the crystallization process at the initial stage. It is found that (1) in the unsaturated solution, the protein molecules aggregate with a continuous increase in size when NaCl concentration is increased, and (2) in the supersaturated solution, an irreversible change, superimposed on the former process, occurs when the supersaturation is realized. These facts indicate the usefulness of SANS in detecting changes of protein molecules in solution on the nanometer scale. The reliability of the SANS results are indicated by (1) comparing them with those of small angle X-ray scattering (SAXS), and (2) comparing the effect of D(2)O and H(2)O as solvent. Since the interparticle interaction is essential in the crystallization process and a simple Guinier plot analysis is not allowed, a more rigorous framework of analyzing data with interference function is developed, through which both average interparticle distance and particle size are estimated.

Interparticle interactions and structural changes of nucleosome core particles in low-salt solution.

The structural behavior of the nucleosome core particles in the range of solvent Na+ concentration from 10.45 to 0.45 mM has been studied by small-angle neutron and synchroton radiation X-ray scattering, sedimentation, atomic absorption spectroscopy, density measurements, and circular dichroism. With decreasing salt concentration, the appearance of a scattering peak that is assignable to interparticle interactions, an intraparticle structural transition, a decrease in the sedimentation velocity of the particle, and a release of bound Na+ ions from the particle are all observed concurrently when the ratio of solvent Na+ ions per particle is below approximately 1000. These observations are interpreted to indicate that a release of bound Na+ ions from the particle brings about structural rearrangements and weakens the electrostatic shielding of the particle, and this introduces long-range repulsive ordering of the particle in low-salt solution. Analyses of the scattering data indicate that the rearrangement within the core particle in low-salt solution is slight, changing the particle's shape slightly from cylindrical to a more spherical form by moving the center of the mass of the DNA somewhat inward with accompanying small decreases in the radii of gyration of both the DNA and the histones.

Isolation of deuterated histones from yeast grown on media dissolved in 2H2O.

We have succeeded in growing Saccharomyces cerevisiae (baker's yeast) on media containing 2H2O and isolating the core histones highly deuterated in the non-exchangeable positions. The deuterated histones obtained here are of great value for their possible widespread use for structural studies of chromatin.

Small angle neutron scattering studies of the structure of nucleosome cores at low ionic strength.

Nucleosome core particles from chicken erythrocytes have been studied by small angle neutron scattering over the range from 10 to 0.04 mM Na+ at 65 and 100% D2O, and the radii of gyration of the particle were determined. A single transition in the radius of gyration was observed at either D2O concentration. With decreasing the ionic strength from 10 mM, the radius of gyration of the histones obtained at 65% D2O increased from 35 to 40A at about 1 mM ionic strength, whereas at 100% D2O the radius of gyration decreased from 39 to 36A also near 1 mM ionic strength. No loss of the secondary structure of the histones was observed by circular dichroism over the range of the ionic strength examined. These results suggest that at low ionic strength (less than or equal to 1 mM) the histones may locate outside of the nucleosome core particle accompanied by an alteration of the tertiary and/or the quaternary structure of the histone octamer.