Group-directed modification of bacteriorhodopsin by arylisothiocyanates. Labeling, identification of the binding site and topology

Location of chemically modified lysine 41 in the structure of bacteriorhodopsin by neutron diffraction

Purple membranes were prepared in which bacteriorhodopsin was labeled at lysine 41 with phenylisothiocyanate (PITC) and with perdeuterated PITC. The in-plane position of this small label containing only five deuterons was determined from the differences between the neutron diffraction intensities of the two samples. At 8.7-A resolution the Fourier difference map revealed a well-defined site between helices 3 and 4. This position was confirmed by a refinement procedure in reciprocal space. Model calculations showed that the observed difference density had the right amplitude for the label. Thus it is possible to locate a small group in a large protein structure by replacing as few as five hydrogens by deuterium. The observed location of PITC restricts the number of possibilities for the assignment of helix B in the sequence (to which lysine 41 is attached) to one of the seven helices of the structure. Taking into account the size of the label and the length of the lysine side chain our result excludes helices 1, 2, and 7 as candidates for B.

Purple membranes as microscaled nanopatterned biosubstrates for reversible attachment of biocomponents

One of the key challenges in the construction of complex bionanotechnological building blocks and devices is the controlled linkage and release of biomolecular components to and from a biomolecular surface. Here we report a versatile, easy and universally applicable method for the reversible assembly of protein-protein conjugates. The process is demonstrated using green fluorescent protein (GFP) and purple membranes (PM) as model compounds. GFP was reversibly bound to PM patches which served as a biomolecular model surface. Due to its size in the micrometre range PM is, as far as its Brownian diffusion is considered, like a solid surface. PMs comprising the mutated bacteriorhodopsin BR-D36C were employed, where aspartic acid in position 36 was replaced with cysteine. The introduced cysteine is accessible from the cytoplasmic side of the membrane. The cysteine group was first functionalized with a nitrilotriacetic acid group (NTA) and then, after loading with Ni, histidine-tagged GFP was bound to the chemically modified PM surface the well-known NTA-His complex. Binding and release of GFP from the PM surface was monitored by atomic force microscopy (AFM).

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.

Refolding and proton pumping activity of a polyethylene glycol-bacteriorhodopsin water-soluble conjugate

Bacteriorhodopsin (BR), from the purple membrane (PM) of Halobacterium halobium, was chemically modified with methoxypolyethylene glycol (m-PEG; molecular weight = 5,000 Da) succinimidyl carbonate. The polyethylene glycol-bacteriorhodopsin (m-PEG-SC-BR33) conjugate, containing one polyethylene glycol chain, was water soluble. The secondary structure of the conjugate in water appeared partially denatured, but was shown to contain alpha-helical segments by circular dichroism spectroscopy. The isolated bacteriorhodopsin conjugate, with added retinal, was refolded in a mixed detergent-lipid micelle and had an absorption maximum at 555 nm. The refolded conjugate was transferred into vesicles that pumped protons, upon illumination, as efficiently as did native BR. Modification of the PM with m-PEG did not alter the native structure or inhibit proton pumping, and therefore it is suggested that the glycol polymer is present as a moiety covalently linked to residues unnecessary for proton pumping and proper folding. The site of attachment of m-PEG was determined to be at either Lys 129 or Lys 159, with position Lys 129 the most probable site of attachment. The m-PEG-SC-BR33 could be stepwise refolded to the native conformation by the addition of trifluoroethanol to lower the dielectric constant, simulating the insertion of the BR into the phospholipid bilayer.

3-(Trifluoromethyl)-3-(m-isothiocyanophenyl)diazirine: synthesis and chemical characterization of a heterobifunctional carbene-generating crosslinking reagent

A new hydrophobic heterobifunctional photocrosslinking reagent 3-(trifluoromethyl)-3-(m-isothiocyanophenyl)diazirine (TRIMID), a carbene precursor, and its radioiodinated analogue [125I]TRIMID, have been synthesized and chemically characterized. The reagents were applied for membrane protein modification in human erythrocyte membranes and purple membranes from Halobacterium halobium. Covalent labeling of the anion transport protein (band 3) via the isothiocyanate function was confirmed. Radiolabeled TRIMID was detected in at least two thermolysin-generated transmembrane fragments of the anion transport protein, and half-maximal inhibition of the erythrocyte anion transport activity was attained with 2.2 mM reagent. In bacteriorhodopsin (BR), a common binding site for the monofunctional phenylisothiocyanate and the bifunctional crosslinking reagent was identified: preincubation of purple membranes with TRIMID suppressed phenylisothio-[14C]-cyanate binding to BR. [125I]TRIMID was recovered in V-1, the N-terminal segment of BR, which includes the phenylisothiocyanate binding site Lys-41. Light-induced intramolecular crosslinking of band 3-derived thermolytic fragments was not observed, although the carbene was generated in situ and photocrosslinking of the protease V8 fragments of BR was not detected. Chemical and physicochemical characteristics of the new reagent are discussed with regard to limitations imposed for photoinduced site-directed crosslink formation.

Analysis of high-resolution electron diffraction patterns from purple membrane labelled with heavy-atoms

Progress in the structure determination of bacteriorhodopsin, the protein component of purple membrane from Halobacterium halobium has been limited by the lack of three-dimensional phase information between 6 and 3 A resolution. By analogy with X-ray methods, it is possible that heavy-atom labelling of the membrane crystal may provide heavy-atom derivatives that can be used for phasing by the multiple isomorphous replacement method. This paper describes the screening of heavy-atom compounds as potential derivatives, and the evaluation of the data collected from these heavy-atom-labelled membranes. Improvements in the methods for collecting electron diffraction data and analysing and merging the data are presented. Diffraction patterns of purple membrane samples were taken at -120 degrees C to minimize radiation damage. About 30 heavy-atom compounds were tested for use as potential derivatives. The diffraction patterns from labelled membranes were analysed by examining 6.5 A difference Fourier maps. Two heavy-atom compounds were selected for three-dimensional data collection at 3 A resolution. In addition, a full set of native data at -120 degrees C was collected to 2.7 A resolution. The intensity merging, heavy-atom derivative evaluation, heavy-atom refinement and the calculation of phases are presented. Phases are compared to those determined by electron microscope imaging, and limitations of the method are discussed. It is concluded that, with the present accuracy of data collection and the present magnitude of delta F/F available for the derivatives, the phasing power is too small. The phases that are obtained are not sufficiently accurate to provide a reliably interpretable map. It may be possible, however, to use the heavy-atom derivative data in difference Fourier calculations in which the presence of a peak would confirm the phases calculated from a model or obtained by electron microscope imaging.

Heavy metal derivatives of membrane proteins: selective mercurilation of bacteriorhodopsin

A method is described for the selective introduction of heavy atoms into structured membrane proteins by a two step modification. The procedure is applied for the purple membrane protein bacteriorhodopsin. Selective heavy-atom modification of this protein is achieved by placing a mercury reagent of intermediate polarity into phenylthiocarbamoylated bacteriorhodopsin. Incorporation of mercury requires the selective phenylthiocarbamoylation of a lysine residue. Optical investigations including circular dichroism document unchanged chromophore-protein and protein-protein interactions in mercury labeled purple membranes.

Refolding of bacteriorhodopsin. Protease V8 fragmentation and chromophore reconstitution from proteolytic V8 fragments

Staphylococcus aureus protease V8 cleaves bacteriorhodopsin to two main fragments, V-1 and V-2. Proteolytic digestion of the purple membrane integrated protein is carried out in the presence of limited amounts of sodium dodecyl sulfate (0.5 g detergent/g bacteriorhodopsin). The fragment V-1 includes the arylisothiocyanate binding site (Lys41). The V-2 fragment comprises the two C-terminal transmembrane segments of bacteriorhodopsin. Improved renaturation of bacteriorhodopsin and the ternary complex, reformed from its V8 proteolytic fragments, is attained by peptide extraction in chloroform/methanol/0.1 M ammonium acetate and subsequent incorporation into phospholipid/detergent micelles. In the presence of retinal, V8 fragments reform chromophoric ternary complexes. Light-adapted reconstituted chromophores absorb incident light at 560 nm. Protein secondary structures are partially conserved in the course of solvent extraction and are restored in the reconstituted system. Vesicles prepared from the reconstituted complexes show light-dependent proton translocation activity.

Labelling of erythrocyte spectrin in situ with phenylisothiocyanate

The labelling of erythrocyte spectrin in situ with the hydrophobic reagent phenylisothiocyanate (Sigrist, H. and Zahler, P. (1978) FEBS Lett. 95, 116-120) is studied. Spectrin isolated from erythrocytes which have been incubated with phenylisothiocyanate is covalently modified by the probe. The modification in the spectrin molecule is stable under an excess of nucleophile in alkaline conditions. The labelling is very little or not affected by preincubation of erythrocytes of membranes with the polar, structural analogue of phenylisothiocyanate, p-sulfophenylisothiocyanate. When erythrocyte ghosts are subjected to labelling, a substantial increase in the degree of spectrin modification is observed. Subunits of labelled spectrin separated electrophoretically show similar amounts of attached label.