Protein Neutron Scattering

Direct experiment-simulation quasielastic neutron scattering comparisons have been perfonned for a variety of small molecule and polymeric systems, as described in detail in Refs. 4 and 18-21. The combination of simulation and neutron scattering in the analysis of internal motions in globular proteins was reviewed in 1991 [3] and 1997 [4]. 

A dynamic transition in the internal motions of proteins is seen with increasing temperamre [22]. The basic elements of this transition are reproduced by MD simulation [23]. As the temperature is increased, a transition from harmonic to anharmonic motion is seen, evidenced by a rapid increase in the atomic mean-square displacements. Comparison of simulation with quasielastic neutron scattering experiment has led to an interpretation of the dynamics involved in terms of rigid-body motions of the side chain atoms, in a way analogous to that shown above for the X-ray diffuse scattering [24]. 

Tofield BC (1975) The Study of Covalency by Magnetic Neutron Scattering. 21 1-87 Trautwein AX, Bill E, Bominaar EL, Winkler H (1991) Iron-Containing Proteins and Related Analogs-Complementary Mossbauer, EPR and Magnetic Susceptibility Studies. 78 1-96 Trautwein AX (1974) Mossbauer-Spectroscopy on Heme Proteins. 20 101-167 Tressaud A, Dance J-M (1982) Relationships Between Structure and Low-Dimensional Magnetism in Fluorides. 52 87-146... 

Furthermore, there is a striking parallelism between these data and the neutron diffraction data from nucleosomes in 100% D 0 (Pardon et al., 1977 Suau et al., 1977), where scattering from the histone protein dominates, and from core protein in 2 M NaCl solution (Pardon et al., 1978). The above interference phenomenon may well be the explanation for the protein-dominated scattering maximum between 35 and 37 A observed for chromatin and nucleosomes in solution (Pardon et al., 1977 Suau et al., 1977). 

One of the most intriguing recent examples of disordered structure is in tomato bushy stunt virus (Harrison et ah, 1978), where at least 33 N-terminal residues from subunit types A and B, and probably an additional 50 or 60 N-terminal residues from all three subunit types (as judged from the molecular weight), project into the central cavity of the virus particle and are completely invisible in the electron density map, as is the RNA inside. Neutron scattering (Chauvin et ah, 1978) shows an inner shell of protein separated from the main coat by a 30-A shell containing mainly RNA. The most likely presumption is that the N-terminal arms interact with the RNA, probably in a quite definite local conformation, but that they are flexibly hinged and can take up many different orientations relative to the 180 subunits forming the outer shell of the virus particle. The disorder of the arms is a necessary condition for their specific interaction with the RNA, which cannot pack with the icosahedral symmetry of the protein coat subunits. 

To determine the shape of ribosomal proteins in solution, ultracentrifugation, digital densimetry, viscosity, gel filtration, quasi-elastic light scattering, and small-angle X-ray or neutron scattering have all been used. With each technique it is possible to obtain a physical characteristic of the protein. Combining these techniques should allow the size and shape of the protein to be characterized quite well. However, the values determined in various laboratories for the same ribosomal proteins differ considerably. To help understand some of the reasons we will initially discuss each method briefly as it relates to proteins and then review the size and shape of the ribosomal proteins that have been so characterized. 

The question can be raised as to whether the structure of the proteins within the ribosomal particle is the same as in the isolated state. The only direct evidence we have that the structures of proteins are not changed upon incorporation into the subunit is provided by the neutron-scattering studies of Nierhaus et al. (1983b). They showed that individual proteins in solution had radii of gyration indistinguishable from those obtained from their counterparts on the ribosomal subunits in the same buffers and under identical preparation conditions. 

For both the 30 S and 50 S subunits, additional neutron-scattering studies have been made to determine the distribution of the protein and the RNA within the subunits. It has been shown in both cases that the... 

One of the most powerful techniques by which protein-protein neighborhoods within the ribosomal particles can be elucidated is neutron scattering. When using this method to determine the relative positions of proteins in the 30 S subunit, the pardcle is reconstituted with two specific proteins that are deuterated whereas all other ribosomal components are in the protonated form (Moore, 1980). The subunits containing the two deuterated proteins give additional contributions to the scattering curves which provide information on the lengths of the vectors between the two deuterated proteins. 

Fig. 11. Map of proteins within the E. coli 30 S ribosomal subunit as determined by neutron scattering studies (Moore, 1980 Moore et al., 1984). Reproduced with permission from Wittmann (1983).

The application of neutron spin-echo spectroscopy to the analysis of the slow dynamics of biomolecules is still in its infancy, but developing fast. The few published investigations either pertain to the diffusion of globular proteins in solution [332-334] or focus on the internal subnanosecond dynamics on the length scale, <10 A as measured on wet powders [335,336]. The latter regime overlaps with other quasi-elastic neutron scattering methods as backscattering and TOE spectrometry [337-339]. 

Tofield,B.C. The Study of Covalency by Magnetic Neutron Scattering. Vol. 21, pp, 1—87. Trautwein, A. Mossbauer-Spectroscopy on Heme Proteins. Vol. 20, pp. 101—167. Truter,M.R. Structures of Organic Complexes with Alkali Metal Ions. Vol. 16, pp. 71—111. 

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