Silk I structure in Bombyx mori silk foams.

Single crystals of Bombyx mori silk fibroin in the metastable silk I polymorph have been produced using a new foaming technique. Foams of silk protein are generated by bubbling pure nitrogen gas through an aqueous solution of regenerated silk fibroin. The foamed material is collected, dried, and then sonicated to yield individual crystals which were examined using transmission electron microscopy and electron diffraction. It is found that slightly acidic conditions in the solution from which the foam was generated favor the formation of silk II while neutral to slightly basic solutions favor silk I formation. More dilute solutions favor the formation of silk II while more concentrated solutions (about 7 wt.% or greater) favor the formation of silk I. X-ray powder diffraction patterns from the dried silk I foams displayed features highly indicative of silk I. We also report the first single crystal electron diffraction patterns of silk I. These patterns indicate a large unit cell, possibly 22.66 x 5.70 x 20.82 A. with six chains of six residues, Gly-Ala-Gly-Ala-Gly-Ser. Although we have not fully characterized this complex structure it appears that the chain is nearly fully extended and thus our data is consistent with models possessing general features similar to those proposed by Fossey SA, Nemethy G, Gibson KD, Scheraga HA. (Biopolymers 1991;31:1529-1541).     

Crystallization of deoxyhemoglobin S by fiber alignment and fusion.

Fibers of deoxyhemoglobin S obtained directly from lysed sickled red blood cells have been compared with fibers from chromatographically pure deoxyhemoglobin S solutions of known chemical composition. Electron micrographs of negatively stained specimens reveal that the molecular packing within the fibers remains largely invariant with changes in pH, ionic strength, Mg²⁺ concentration, 2,3-diphosphoglycerate concentration, temperature or the method of deoxygenation.When solutions of chromatographically pure deoxyhemoglobin S are stirred, the fibers align into well defined fascicles. After several hours of stirring, long needles and twisted ribbons develop and in a relatively short time replace the fascicles in solution. With continued stirring all forms are replaced by small crystals. By use of electron microscopy and low-angle X-ray diffraction we have found these crystals to have cell parameters indistinguishable from those of crystals grown in polyethylene glycol and citrate/phosphate buffer at pH 5 to 6 (Wishner et al., 1975a).Our evidence indicates that crystal formation in stirred solutions of deoxyhemoglobin S is the result of a progressive alignment and fusion of the fibers, and that the molecular arrangement within the fibers is closely related to that within the crystal. The remarkable pH invariance of the molecular packing within the fiber and crystal structures is consistent with the dominance of hydrophobic bonding between molecules. The β6-valine contact observed by Wishner et al. (1975b) is apparently the pathological contact responsible for the polymerization of deoxyhemoglobin S in vivo. On the basis of our observations and knowledge of the crystal structure we propose that the deoxyhemoglobin S fiber consists of eight molecular double strands, four of which run in each direction along the length of the fiber.     

Characterization and crystal packing of three-dimensional bacteriorhodopsin crystals

The three-dimensional crystals of the integral membrane protein bacteriorhodopsin have been characterized by X-ray diffraction and freeze-fracture electron microscopy: the needle-like form A crystals belong to space group P 1 (pseudohexagonal) with seven molecules per crystallographic unit cell forming one turn of a non-crystallographic helix. The probable arrangement of the bacteriorhodopsin molecules is derived from freeze-fracture electron micrographs and chromophore orientation. Membrane-like structures are not present. The same helices of bacteriorhodopsin molecules found in crystal form A also make up the cube-like crystal form B. They are now arranged in all three mutually perpendicular directions. These cubes are always highly disordered, since the unit cell length corresponds to 6.7 molecules of the 7-fold helix. Very often, conversion of bacteriorhodopsin from the three-dimensional crystals into filamentous material occurs.     

In situ observation of elementary growth processes of protein crystals by advanced optical microscopy

To start systematically investigating the quality improvement of protein crystals, the elementary growth processes of protein crystals must be first clarified comprehensively. Atomic force microscopy (AFM) has made a tremendous contribution toward elucidating the elementary growth processes of protein crystals and has confirmed that protein crystals grow layer by layer utilizing kinks on steps, as in the case of inorganic and low-molecular-weight compound crystals. However, the scanning of the AFM cantilever greatly disturbs the concentration distribution and solution flow in the vicinity of growing protein crystals. AFM also cannot visualize the dynamic behavior of mobile solute and impurity molecules on protein crystal surfaces. To compensate for these disadvantages of AFM, in situ observation by two types of advanced optical microscopy has been recently performed. To observe the elementary steps of protein crystals noninvasively, laser confocal microscopy combined with differential interference contrast microscopy (LCM-DIM) was developed. To visualize individual mobile protein molecules, total internal reflection fluorescent (TIRF) microscopy, which is widely used in the field of biological physics, was applied to the visualization of protein crystal surfaces. In this review, recent progress in the noninvasive in situ observation of elementary steps and individual mobile protein molecules on protein crystal surfaces is outlined.     

Elucidation of the mechanism and end products of glutaraldehyde crosslinking reaction by X-ray structure analysis

Glutaraldehyde has been used for several decades as an effective crosslinking agent for many applications including sample fixation for microscopy, enzyme and cell immobilization, and stabilization of protein crystals. Despite of its common use as a crosslinking agent, the mechanism and chemistry involved in glutaraldehyde crosslinking reaction is not yet fully understood. Here we describe feasibility study and results obtained from a new approach to investigate the process of protein crystals stabilization by glutaraldehyde crosslinking. It involves exposure of a model protein crystal (Lysozyme) to glutaraldehyde in alkaline or acidic pH for different incubation periods and reaction arrest by medium exchange with crystallization medium to remove unbound glutaraldehyde. The crystals were subsequently incubated in diluted buffer affecting dissolution of un-crosslinked crystals. Samples from the resulting solution were subjected to protein composition analysis by gel electrophoresis and mass spectroscopy while crosslinked, dissolution resistant crystals were subjected to high resolution X-ray structural analysis. Data from gel electrophoresis indicated that the crosslinking process starts at specific preferable crosslinking site by lysozyme dimer formation, for both acidic and alkaline pH values. These dimer formations were followed by trimer and tetramer formations leading eventually to dissolution resistant crystals. The crosslinking initiation site and the end products obtained from glutaraldehyde crosslinking in both pH ranges resulted from reactions between lysine residues of neighboring protein molecules and the polymeric form of glutaraldehyde. Reaction rate was much faster at alkaline pH. Different reaction end products, indicating different reaction mechanisms, were identified for crosslinking taking place under alkaline or acidic conditions.     

Structural basis and dynamics of the fiber-to-crystal transition of sickle cell hemoglobin

The kinetics of the assembly of structurally distinct, polymeric aggregates constituting the fiber-to-crystal transition of sickle cell hemoglobin in slowly stirred, deoxygenated solutions has been studied with the use of electron microscopy as a function of pH, as a function of the crystal structures of mutant forms of human deoxyhemoglobins employed as nucleating seeds, and as a function of hemoglobin S chemically modified at the Cys F9 (beta 93) position. The temporal order of appearance of fibers of approximately 210 A diameter, bundles of aligned fibers, macrofibers of greater than or equal to 650 A diameter, and microcrystals is observed. Microscopic fragments of end-stage crystals formed under slowly stirred conditions and introduced as nucleating seeds enhance the rate of crystallization only when added prior to the formation of large bundles of aligned fibers, while microscopic seed crystals added after the formation of bundles of aligned fibers do not alter the rate of crystallization. Over the pH range 6.3 to 7.1, the presence of macrofibers does not influence modulation of the kinetics of the transition with seed crystal fragments. Microscopic seed crystals of deoxyhemoglobin S and deoxyhemoglobin C formed under acidic conditions (pH less than 6.5) have a comparable influence on the kinetics of the fiber-to-crystal transition to that of end-stage crystals. Microscopic seed crystals of deoxyhemoglobin C formed under alkaline conditions (pH greater than 6.5) enhance the formation of macrofibers but do not alter the rate of crystallization. Under conditions associated with enhanced formation of macrofibers, metastable microscopic crystals having axial periodicities of approximately 64 A and approximately 210 A are observed in the intermediate phase of the transition, while end-stage crystals have axial unit cell dimensions identical to those of deoxyhemoglobin S crystallized from polyethylene glycol solutions of pH less than 6.5. Although the metastable crystals may arise from fragments of macrofibers, it is shown that they cannot be transformed directly into end-stage crystals under slowly stirred conditions without undergoing dissolution. These results stipulate that the pathway of the fiber-to-crystal transition proceeds according to the reaction: (Formula: see text) wherein the rate-limiting step is the alignment of fibers into large bundles, and macrofibers are not an intermediate of the fiber-to-crystal transition.(ABSTRACT TRUNCATED AT 400 WORDS)     

Two-dimensional crystallization of Ca-ATPase by detergent removal.

By using Bio-Beads as a detergent-removing agent, it has been possible to produce detergent-depleted two-dimensional crystals of purified Ca-ATPase. The crystallinity and morphology of these different crystals were analyzed by electron microscopy under different experimental conditions. A lipid-to-protein ratio below 0.4 w/w was required for crystal formation. The rate of detergent removal critically affected crystal morphology, and large multilamellar crystalline sheets or wide unilamellar tubes were generated upon slow or fast detergent removal, respectively. Electron crystallographic analysis indicated unit cell parameters of a = 159 A, b = 54 A, and gamma = 90 degrees for both types of crystals, and projection maps at 15-A resolution were consistent with Ca-ATPase molecules alternately facing the two sides of the membrane. Crystal formation was also affected by the protein conformation. Indeed, tubular and multilamellar crystals both required the presence of Ca2+; the presence of ADP gave rise to another type of packing within the unit cell (a = 86 A, b = 77 A, and gamma = 90 degrees), while maintaining a bipolar orientation of the molecules within the bilayer. All of the results are discussed in terms of nucleation and crystal growth, and a model of crystallogenesis is proposed that may be generally true for asymmetrical proteins with a large hydrophilic cytoplasmic domain.     

High-resolution spot-scan electron microscopy of microcrystals of an alpha-helical coiled-coil protein

We describe the electron microscopy of a crystalline assembly of an alpha-helical coiled-coil protein extracted from the ootheca of the praying mantis. Electron diffraction patterns of unstained crystals show crystal lattice sampling of the coiled-coil molecular transform to a resolution beyond 1.5 A. Using a "spot-scan" method of electron imaging, micrographs of unstained crystals have been obtained that visibly diffract laser light from crystal spacings as small as 4.3 A. A projection map was calculated to 4 A using electron diffraction amplitudes and phases from computer-processed images. The projection map clearly shows modulations in density arising from the 5.1 A alpha-helical repeat, the first time this type of modulation has been revealed by electron microscopy. The crystals have p2 plane group symmetry with a = 92.4 A, b = 150.7 A, y = 92.4 degrees. Examination of tilted specimens shows that c is approximately 18 A, indicating that the unit cell is only one molecule thick. A preliminary interpretation shows tightly packed molecules some 400 A long lying with their long axes in the plane of the projection. The molecules have a coiled-coil configuration for most of their length. The possible modes of packing of the molecules in three dimensions are discussed.     

Helical crystals of sickle cell hemoglobin

Thin ribbon-like crystals are intermediates in the formation of large crystals of deoxyhemoglobin S from many individual fibers. The thin crystals show foldedover regions when observed by electron microscopy. Some crystals are sufficiently long to have several folds each separated by a distance of about 4.4 μm, suggesting that the crystals are helical in solution. The thickness of the crystals varies from 500 to 900 Å as shown by heavy-metal shadowing and by measurements of the thickness at the crossover point where an edge-on view of the crystal is obtained.     

Transmission electron microscopy as a tool for nanocrystal characterization pre- and post-injector

Recent advancements at the Linac Coherent Light Source X-ray free-electron laser (XFEL) enabling successful serial femtosecond diffraction experiments using nanometre-sized crystals (NCs) have opened up the possibility of X-ray structure determination of proteins that produce only submicrometre crystals such as many membrane proteins. Careful crystal pre-characterization including compatibility testing of the sample delivery method is essential to ensure efficient use of the limited beamtime available at XFEL sources. This work demonstrates the utility of transmission electron microscopy for detecting and evaluating NCs within the carrier solutions of liquid injectors. The diffraction quality of these crystals may be assessed by examining the crystal lattice and by calculating the fast Fourier transform of the image. Injector reservoir solutions, as well as solutions collected post-injection, were evaluated for three types of protein NCs (i) the membrane protein PTHR1, (ii) the multi-protein complex Pol II-GFP and (iii) the soluble protein lysozyme. Our results indicate that the concentration and diffraction quality of NCs, particularly those with high solvent content and sensitivity to mechanical manipulation may be affected by the delivery process.     

Ultrastructure of otolith increments and checks in the teleost fish Oreochromis niloticus

An otolith increment is composed of an incremental zone and a discontinous zone. Observation of the otoliths of Oreochromis niloticus with transmission and scanning electron microscopy reveals that organic fibers are concentrated in the discontinuous zone and are relatively scarce in the incremental zone. On the other hand, calcium carbonate crystals are chiefly packed in the incremental zone and are less dense in the discontinuous zone. Both fibers and crystals are oriented perpendicular to the growth increments. Otolith checks, or discontinuities, contain even denser fibers and fewer fine crystals than does the discontinuous zone. A higher proportion of individual fibers is prominently stained in the discontinuous zone and check than in the incremental zone. Other features of individual fibers appear to be the same among the three zones. The crystals on either side of a check or a discontinuous zone resemble each other both in size and orientation. Zonation of protein and mineral components of otoliths can be understood in terms of both incremental growth and the daily cycle of deposition.     

Mechanisms of homogeneous nucleation of polymers of sickle cell anemia hemoglobin in deoxy state

The primary pathogenic event of sickle cell anemia is the polymerization of the mutant hemoglobin (Hb) S within the red blood cells, occurring when HbS is in deoxy state in the venous circulation. Polymerization is known to start with nucleation of individual polymer fibers, followed by growth and branching via secondary nucleation, yet the mechanisms of nucleation of the primary fibers have never been subjected to dedicated tests. We implement a technique for direct determination of rates and induction times of primary nucleation of HbS fibers, based on detection of emerging HbS polymers using optical differential interference contrast microscopy after laser photolysis of CO-HbS. We show that: (i). nucleation throughout these determinations occurs homogeneously and not on foreign substrates; (ii). individual nucleation events are independent of each other; (iii). the nucleation rates are of the order of 10(6)-10(8)cm(-3)s(-1); (iv). nucleation induction times agree with an a priori prediction based on Zeldovich's theory; (v). in the probed parameter space, the nucleus contains 11 or 12 molecules. The nucleation rate values are comparable to those leading to erythrocyte sickling in vivo and suggest that the mechanisms deduced from in vitro experiments might provide physiologically relevant insights. While the statistics and dynamics of nucleation suggest mechanisms akin to those for small-molecule and protein crystals, the nucleation rate values are nine to ten orders of magnitude higher than those known for protein crystals. These high values cannot be rationalized within the current understanding of the nucleation processes.     

The formation of intracellular crystals in midgut glands of Limnoria lignorum

Certain morphological features of intracellular crystal formation within the midgut glands of Limnoria lignorum (Rathke) have been studied with the electron microscope and cytochemical methods. A correlation has been established between Golgi membranes and formation of the crystals. The Prussian blue reaction reveals quantities of iron localized in the intracellular crystals and in small granular structures seen in the apical region of the cells. These granules can be identified as accumulations of Golgi membranes, with which iron-containing particles are associated. When these membrane configurations are studied with the electron microscope, they can be classified and arranged in an assumed sequence which is thought to represent successive stages in the development of crystals. As the membrane systems become progressively specialized, increasing accumulations of dense granular material appear within their interstices. This material is rich in iron and probably represents the component responsible for the positive Prussian blue reaction. This material also appears to be a precursor substance for iron-containing protein molecules which are synthesized and arranged to make up the crystals. These iron-containing molecules are first deposited in orderly array as double rows of dense particles on certain internal membranes of the specialized Golgi complexes. The membranes later disappear and the particles form definitive crystals by rearrangement into a hexagonal close-packed pattern.     

Structure of CaATPase: electron microscopy of frozen-hydrated crystals at 6 A resolution in projection

Thin, three-dimensional crystals of CaATPase have been studied at high resolution by electron crystallography. These crystals were grown by adding purified CaATPase to appropriate concentrations of lipid, detergent and calcium. A thin film of crystals was then rapidly frozen and maintained in the frozen-hydrated state during electron microscopy. The resulting electron diffraction patterns extend to 4.1 A resolution and images contain phase data to 6 A resolution. By combining Fourier amplitudes from electron diffraction patterns with phases from images, a density map has been calculated in projection. Comparison of this map from unstained crystals with a previously determined map from negatively stained crystals reveals distinct contributions from intramembranous and extramembranous protein domains. On the basis of this distinction and of the packing of molecules in the crystal, we have proposed a specific arrangement for the ten alpha-helices that have been suggested as spanning the bilayer.     

Short and long range order of the morphology of silk from Latrodectus hesperus (Black Widow) as characterized by atomic force microscopy.

The surfaces of both stretched and unstretched silk threads from the cobweb weaver, Latrodectus hesperus (Black Widow) have been examined by atomic force microscopy (AFM). AFM images of cobweb scaffolding threads show both unordered and highly ordered regions. Two types of fibers within the threads were observed: thicker (approximately 300 nm in diameter) fibers oriented parallel to the thread axis and thinner (10-100 nm) fibrils oriented across the thread axis. While regions which lacked parallel fibers or fibrils were observed on threads at all strain values, the probability of observing fibers and/or fibrils increased with strain. High-resolution AFM images show that with increasing strain, both mean fiber and fibril diameters decrease and that fibrils align themselves more closely with the thread axis. The observation of fibers and fibrils within the cobweb threads has implications for current models of the secondary and tertiary structure and organization of spider silk.     

Tracing cellulose elements adsorbed on composite cellulose biomaterials by a new labeling method

In view of tracing the fate of cellulose fine elements added to a suspension of cellulose fibers, a novel method for specific labeling of polysaccharides in a composite material was developed. The purpose was to visualize a given cellulose material within a cellulose mixture. The method consists of generating aldehyde groups in the chain by mild periodic acid oxidation followed by biotinylation of the carbonyls. Once added to the composite, the biotinylated molecules are labeled with streptavidin conjugated to a fluorescent probe for confocal microscopy, or streptavidin-gold for electron microscopy observations. In the present work, the fate of fresh fines (never-dried) and dead fines (dried) when they were added to a purified suspension of fibers was followed by observation of the labeling in confocal and electron microscopy. The differential mode of interaction of fresh fines and dead fines with the fibers was correlated to the mechanical characteristics measured on the corresponding papers. The versatility of the new labeling method and its possible generalization to other polysaccharides incorporated to a polysaccharide or nonpolysaccharide material should be of potential interest for the study of composite microstructure.     

Molecular resolution imaging of macromolecular crystals by atomic force microscopy.

Atomic force microscopy (AFM) images at the molecular level have been obtained for a number of different protein and virus crystals. They can be utilized in some special cases to obtain information useful to crystal structure analyses by x-ray diffraction. In particular, questions of space group enantiomer, the packing of molecules within a unit cell, the number of molecules per asymmetric unit, and the dispositions of multiple molecules within the asymmetric unit may be resolved. In addition, because of the increasing sensitivity and resolution of the AFM technique, some molecular features of very large asymmetric units may be within reach. We describe here high-resolution studies, using AFM, to visualize individual molecules and viruses in their crystal lattices. These investigations included fungal lipase, lysozyme, thaumatin, canavalin, and satellite tobacco mosaic virus (STMV).     

Crystals of modified fibrinogen: Size,shape and packing of molecules

We have produced several new macroscopic crystal forms and a variety of microcrystals from modified flbrinogens. Bovine and rabbit flbrinogens crystallize after limited digestion by a bacterial protease or α-chymotrypsin. The fibrinogens making up these crystals are largely intact and highly clottable. Tentative molecular packing arrangements for two crystal forms have been deduced. The crystal morphology and cleavage planes were used in this analysis. The characteristic α-helical coiled-coil reflections arid spikes of intensity in certain directions in the crystal X-ray patterns serve as markers for the orientation of the fibrinogen molecules. Changes that occur in one of the forms during preparation for electron microscopy, as shown by comparison with X-ray experiments on crystals in various stains and solvents, support this packing model. These studies provide preliminary evidence that fibrinogen is about 450 Å in length and that the molecules bond end-to-end to form filaments making up the crystals.     

Heat denaturation of crystalline and dissolved leghemoglobin

Heat transitions in crystals of leghemoglobin (LH) are studied by means of scanning microcalorimetry and microscopy. It has been found that LH crystals do not melt and their loss of crystal lattice is due to the denaturation of protein globules inside the crystal. Peculiarities of the crystal state (as compared to the solution) are shown in an increase in the cooperative character of heat transition and relaxation time of the system. Subsequent consideration of different variants of correlation of two stages of heat absorption by LH crystals made it possible to determine the type of physical process proceeding in the object by the shape of calorimetric curve. Both observed peaks of heat absorption were grouped with intramolecular processes of different thermodynamic properties. The first peak of heat absorption is a manifestation of intramolecular mobility, both of individual protein segments in relation to each other and of individual segments of alpha-helical regions. Thus microcalorimetry allows a study of peculiar intramolecular dynamics of globular proteins precisely in the crystal state, because the crystal as if synchronizes the movement of individual molecules at the expense of the unification of their kinetic energy, surroundings and mutual orientation.     

Detection of membrane protein two-dimensional crystals in living cells

It is notoriously difficult to grow membrane protein crystals and solve membrane protein structures. Improved detection and screening of membrane protein crystals are needed. We have shown here that second-order nonlinear optical imaging of chiral crystals based on second harmonic generation can provide sensitive and selective detection of two-dimensional protein crystalline arrays with sufficiently low background to enable crystal detection within the membranes of live cells. The method was validated using bacteriorhodopsin crystals generated in live Halobacterium halobium bacteria and confirmed by electron microscopy from the isolated crystals. Additional studies of alphavirus glycoproteins indicated the presence of localized crystalline domains associated with virus budding from mammalian cells. These results suggest that in vivo crystallization may provide a means for expediting membrane protein structure determination for proteins exhibiting propensities for two-dimensional crystal formation.