Location of platinum binding sites on bacteriorhodopsin by electron diffraction

Structural studies of bacteriorhodopsin in BC era

It marked half a century since the discovery of bacteriorhodopsin two years ago. On this occasion, I have revisited historically important diffraction studies of this membrane protein, based on my recollections. X-ray diffraction and electron diffraction, and electron microscopy, described the low-resolution structure of bacteriorhodopsin within the purple membrane. Neutron diffraction was effective to assign the helical regions in the primary structure with 7 rods revealed by low-resolution structure as well as to describe the retinal position. Substantial conformational changes upon light illumination were clarified by the structures of various photointermediates. Early trials of time-resolved studies were also introduced. Models for the mechanism of light-driven proton pump based on the low-resolution structural studies are also described. Significantly, they are not far from the today's understanding. I believe that the spirit of the early research scientists in this field and the essence of their studies, which constitute the foundations of the field, still actively fertilizes current membrane protein research.

High-resolution structural analysis of purple membrane

Two crystal forms of the purple membrane from Halobacterium halobium are being investigated. One is the native p3 form which occurs naturally, and the other is an orthorhombic p22121 form which is made artificially with detergent.

Both forms diffract to better than 3 Å resolution. They have been studied by electron diffraction at high (3 Å) resolution, and at lower resolution (6.5-7 Å) by electron microscopy. Both crystal forms occur as membrane sheets, containing a single molecular layer of protein molecules with a lipid bilayer filling the space between the protein molecules, the whole having a thickness of about 45-50 Å. The electron microscopic and diffraction analyses have been carried out in three dimensions using specimens tilted at angles of up to 60° to the incident electron beam.

The resulting Fourier maps of the two structures enable a common shape for a single molecule of bacteriorhodopsin to be determined, which is free of the ambiguity of molecular boundary normally found in crystal structure analyses at lower resolution than that required to trace the path of the polypeptide chain.

X-ray diffraction in temporally and spatially resolved biomolecular science

Time-resolved Laue protein crystallography at the European Synchrotron Radiation Facility (ESRF) opened up the field of sub-nanosecond protein crystal structure analyses. There are a limited number of such time-resolved studies in the literature. Why is this? The X-ray laser now gives us femtosecond (fs) duration pulses, typically 10 fs up to ∼50 fs. Their use is attractive for the fastest time-resolved protein crystallography studies. It has been proposed that single molecules could even be studied with the advantage of being able to measure X-ray diffraction from a 'crystal lattice free' single molecule, with or without temporal resolved structural changes. This is altogether very challenging R&D. So as to assist this effort we have undertaken studies of metal clusters that bind to proteins, both 'fresh' and after repeated X-ray irradiation to assess their X-ray-photo-dynamics, namely Ta6Br12, K2PtI6 and K2PtBr6 bound to a test protein, hen egg white lysozyme. These metal complexes have the major advantage of being very recognisable shapes (pseudo spherical or octahedral) and thereby offer a start to (probably very difficult) single molecule electron density map interpretations, both static and dynamic. A further approach is to investigate the X-ray laser beam diffraction strength of a well scattering nano-cluster; an example from nature being the iron containing ferritin. Electron crystallography and single particle electron microscopy imaging offers alternatives to X-ray structural studies; our structural studies of crustacyanin, a 320 kDa protein carotenoid complex, can be extended either by electron based techniques or with the X-ray laser representing a fascinating range of options. General outlook remarks concerning X-ray, electron and neutron macromolecular crystallography as well as 'NMR crystallography' conclude the article.

Physicochemical properties of the ternary complexes of Pt(ii) with uracil and small peptide moieties: an experimental and computational study

Interactions of Pt(Ura)(GL) with DNA.

Preparation of platinum(II) complexes with l-serine using KI. X-ray crystal structure, HPLC and 195Pt NMR spectra

The preparation of platinum(II) complexes containing L-serine using K(2)[PtCl(4)] and KI as raw materials was undertaken. The cis-trans isomer ratio of the complexes in the reaction mixture differed significantly depending on whether KI was present or absent in the reaction mixture. One of the two [Pt(L-ser-N,O)(2)] complexes (L-ser=L-serinate anion) prepared using KI crystallizes in the monoclinic space group P2(1)2(1)2(1) with unit cell dimensions a=8.710(2) A, b=9.773(3) A, c=11.355(3) A, Z=4. The crystal data revealed that this complex has a cis configuration. The other [Pt(L-ser-N,O)(2)] complex also crystallizes in the monoclinic space group P2(1)2(1)2(1) with unit cell dimensions a=7.0190(9) A, b=7.7445(6) A, c=20.946(2) A, Z=4. The crystal data revealed that this complex has a trans configuration. The 195Pt NMR chemical shifts of trans-[Pt(L-ser-N,O)(2)] and cis-[Pt(L-ser-N,O)(2)] complexes are -1632 and -1832 ppm, respectively. 195Pt NMR and HPLC measurements were conducted to monitor the reactions of the two [Pt(L-ser-N,O)(2)] complexes with HCl. Both 195Pt NMR and HPLC showed that the reactivities of cis- and trans-[Pt(L-ser-N,O)(2)] toward HCl are different: coordinated carboxyl oxygen atoms of trans-[Pt(L-ser-N,O)(2)] were detached faster than those for cis-[Pt(L-ser-N,O)(2)].

Recollections of the electron crystallographic heavy atom derivative search of purple membrane: the quest for EM structure determination

The use of multiple isomorphous replacement in protein electron crystallography for phase determination has been systematically studied only for purple membrane, even though the use of heavy atoms or heavy atom clusters has been used on many occasions in electron microscopy for locating domains or subunits in protein assemblies. The background behind the structure determination of bacteriorhodopsin, the protein component of purple membranes, is summarized and an evaluation of the strengths and weaknesses of using isomorphous replacement in electron crystallography is discussed.

The opsin family of proteins

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Undecagold clusters for site-specific labeling of biological macromolecules: simplified preparation and model applications

We report simple and rapid procedures for the synthesis of a variety of stable, water-soluble undecagold cluster, and model applications of a thiol-reactive gold cluster for the specific labeling of cysteine residues in proteins.

Location of an extrinsic label in the primary and tertiary structure of bacteriorhodopsin

We located a heavy metal label, mercurilated phenylglyoxal, in both the primary sequence and in the tertiary structure of bacteriorhodopsin. This label modified arginines 225 and 227, which are on the COOH-terminal helix (G). In the projected electron potential difference map, the major site is close to the central inner helix. From this result we conclude that helix 1 could not be the COOH-terminal helix G. We tested the multiple isomorphous replacement method for obtaining phases for purple membrane by electron diffraction.

Estimates of validity of projection approximation for three-dimensional reconstructions at high resolution

As spatial frequency increases, the electron microscope "image" deviates increasingly from a true projection of the specimen's structure. This is due to the finite radius of the Ewald sphere. Quantitative estimates of these deviations of the reconstruction from the true projection are presented for a range of accelerating voltages, spatial frequencies, specimen thicknesses, and specimen tilts.

Linking regions between helices in bacteriorhodopsin revealed

Three-dimensional electron-microscopic structural analysis requires the combination of many different tilted views of the same specimen. The relative difficulty of tilting the sample to high angles >60 degrees without introducing severe distortion due to different focal distances across the specimen entails that the observable range of electron diffraction data is often limited to this range of angles. Thus, it is generally not possible to observe the diffraction maxima that lie within the conical region of reciprocal space around the direction perpendicular to the electron microscope grid. The absence of data in this region leads to a predictable distortion in the object, and for +/-60 degrees tilting makes the resolution essentially twice as bad in the direction perpendicular to the grid as it is for the in-plane image. Constrained density map modification and refinement methods can significantly reduce these effects. A method has been developed, tested on model cases, and applied to the electron-microscopic structure determination of bacteriorhodopsin in order to visualize the location of linking regions between helices. Electron-microscopic structural analysis of bacteriorhodopsin (Henderson and Unwin. 1975 Nature [Lond.] 257:28-32.) showed that the molecule consists of seven rods of density each nearly spanning the lipid bilayer. Owing to the distortion introduced by the missing conical region of reciprocal space data, no density was visible for the polypeptide segments linking the alpha-helices. Density in the refined maps indicates the location of at least five of the extrahelical segments of the polypeptide. The total number of possible ways of interconnecting the helices is reduced from 7! (5,040) to the five most consistent possibilities without recourse to other considerations. In addition, the density for the helical regions is more uniform and cylindrical throughout their length, and the length of the helices increases from 35 to 45 A, close to the membrane thickness of 49 A obtained for membranes dried in vacuo. Only three of the five structures consistent with the location of observed linkers place the seventh helix, onto which the chromophore can be attached by reduction in the light, at a position consistent with the main peak for deuterated retinal in the structure, as derived from neutron diffraction analysis. Two of these models are also consistent with the possible location of some of the reduced chromophore on helix B, at lys 40/41 after reduction in the dark, as well as lys 216 on helix G.

Reproducibility of electron diffraction intensity data obtained from hydrated microcrystals of rat hemoglobin

Analysis of electron diffraction patterns from rat hemoglobin taken at 200 kV on a wet stage yields intensity data to a resolution of 2-3 A which are as reproducible as those from typical X-ray diffraction. Some crystals were so similar that the differences in measured intensities were insignificant (R = 0.056), but in other cases real differences between crystals were observed (R = 0.33). Dynamic scattering was insignificant under our diffraction conditions; however, exposures to electron doses as low as 10(-2) e/A2 produced detectable changes in measured intensities. Limits to the reproducibility of the data are set by radiation damage and errors in microdensitometry.

Three-dimensional structure of proteins determined by electron microscopy

Recent developments in specimen preparation and image processing techniques have made it possible to determine the three-dimensional structure of proteins by electron microscopy. Periodic supramolecular aggregates of the protein under investigation are requiring to minimize radiation damage and to maximize the signal-to-noise ratio of structural detail. Useful information about the fine structure of the protein (e.g. binding sites for interacting molecules, antigenic determinants) can often be obtained by stoichiometric labeling of the ordered arrays with interacting molecules or antibody fragments, and computing difference maps from the reconstructions of the labeled and native structures. The use of this approach to molecular structure determination of proteins will be discussed in light of our work with bacteriophage and actin.