X-ray diffraction studies of fibers and crystals of deoxygenated sickle cell hemoglobin

Nonclassical Nucleation—Role of Metastable Intermediate Phase in Crystal Nucleation: An Editorial Prefix

Classical nucleation theory (CNT), which was established about 90 years ago, represents the most commonly used theory in describing nucleation processes. For a fluid-to-solid phase transition, CNT states that the solutes in a supersaturated solution reversibly form small clusters. Once a cluster reaches its critical size, it becomes thermodynamically stable and is favored for further growth. One of the most important assumptions of CNT is that the nucleation process is described by one reaction coordinate and all order parameters proceed simultaneously. Recent studies in experiments, computer simulations, and theory have revealed nonclassical features in the early stage of nucleation. In particular, the decoupling of order parameters involved during a fluid-to-solid transition leads to the so-called two-step nucleation mechanism, in which a metastable intermediate phase (MIP) exists in parallel to the initial supersaturated solution and the final crystals. These MIPs can be high-density liquid phases, mesoscopic clusters, or preordered states. In this Special Issue, we focus on the role of the various MIPs in the early stage of crystal nucleation of organic materials, metals and alloys, aqueous solutions, minerals, colloids, and proteins, and thus on various scenarios of nonclassical pathways of crystallization.

Thermodynamics of amyloid fibril formation from chemical depolymerization

Amyloid fibrils are homo-molecular protein polymers that play an important role in disease and biological function. While much is known about their kinetics and mechanisms of formation, the origin and magnitude of their thermodynamic stability has received significantly less attention. This is despite the fact that the thermodynamic stability of amyloid fibrils is an important determinant of their lifetimes and processing in vivo. Here we use depolymerization by chemical denaturants of amyloid fibrils of two different proteins (PI3K-SH3 and glucagon) at different concentrations and show that the previously applied isodesmic linear polymerization model is an oversimplification that does not capture the concentration dependence of chemical depolymerization of amyloid fibrils. We show that cooperative polymerization, which is compatible with the picture of amyloid formation as a nucleated polymerization process, is able to quantitatively describe the thermodynamic data. We use this combined experimental and conceptual framework in order to probe the ionic strength dependence of amyloid fibril stability. In combination with previously published data on the ionic strength dependence of amyloid fibril growth kinetics, our results provide strong evidence for the product-like nature of the transition state of amyloid fibril growth.

Structural basis for the antipolymer activity of Hb ζ2βs2 trapped in a tense conformation

The phenotypical severity of sickle-cell disease (SCD) can be mitigated by modifying mutant hemoglobin S (Hb S, Hb α₂β^s₂) to contain embryonic ζ-globin in place of adult α-globin subunits (Hb ζ₂β^s₂). Crystallographical analyses of liganded Hb ζζ₂β^s₂, though, demonstrate a tense (T-state) quaternary structure that paradoxically predicts its participation in--rather than its exclusion from--pathological deoxyHb S polymers. We resolved this structure-function conundrum by examining the effects of α→ζ exchange on the characteristics of specific amino acids that mediate sickle polymer assembly. Superposition analyses of the β^s subunits of T-state deoxyHb α₂β^s₂ and T-state CO-liganded Hb ζ₂β^s₂ reveal significant displacements of both mutant β^sVal6 and conserved β-chain contact residues, predicting weakening of corresponding polymer-stabilizing interactions. Similar comparisons of the α- and ζ-globin subunits implicate four amino acids that are either repositioned or undergo non-conservative substitution, abrogating critical polymer contacts. CO-Hb ζ₂β^s₂ additionally exhibits a unique trimer-of-heterotetramers crystal packing that is sustained by novel intermolecular interactions involving the pathological β^sVal6, contrasting sharply with the classical double-stranded packing of deoxyHb S. Finally, the unusually large buried solvent-accessible surface area for CO-Hb ζ₂β^s₂ suggests that it does not co-assemble with deoxyHb S in vivo. In sum, the antipolymer activities of Hb ζ₂β^s₂ appear to arise from both repositioning and replacement of specific α- and β^s-chain residues, favoring an alternate T-state solution structure that is excluded from pathological deoxyHb S polymers. These data account for the antipolymer activity of Hb ζ₂β^s₂, and recommend the utility of SCD therapeutics that capitalize on α-globin exchange strategies.

Review: model peptides and the physicochemical approach to beta-amyloids

beta-Amyloid peptides are the main protein components of neuritic plaques and may be important in the pathogenesis of Alzheimer's Disease. The determination of the structure of beta-amyloid fibrils poses a challenge because of the limited solubility of beta-amyloid peptides and the noncrystalline nature of fibrils formed from these peptides. In this paper, we describe several physicochemical approaches which have been used to examine fibrils and the fibrillogenesis of peptide models of beta-amyloid. Recent advances in solid state NMR, such as the DRAWS pulse sequence, have made this approach a particularly attractive one for peptides such as beta-amyloid, which are not yet amenable to high-resolution solution phase NMR and crystallography. The application of solid state NMR techniques has yielded information on a model peptide comprising residues 10-35 of human beta-amyloid and indicates that in fibrils, this peptide assumes a parallel beta-strand conformation, with all residues in exact register. In addition, we discuss the use of block copolymers of Abeta peptides and polyethylene glycol as probes for the pathways of fibrillogenesis. These methods can be combined with other new methods, such as high-resolution synchrotron X-ray diffraction and small angle neutron and X-ray scattering, to yield structural data of relevance not only to disease, but to the broader question of protein folding and self-assembly.

Crystal structure of deoxy-human hemoglobin beta6 Glu --> Trp. Implications for the structure and formation of the sickle cell fiber

An atomic-level understanding of the interactions between hemoglobin molecules that contribute to the formation of pathological fibers in sickle cell disease remains elusive. By exploring crystal structures of mutant hemoglobins with altered polymerization properties, insight can be gained into sickle cell hemoglobin (HbS) polymerization. We present here the 2.0-A resolution deoxy crystal structure of human hemoglobin mutated to tryptophan at the beta6 position, the site of the glutamate --> valine mutation in HbS. Unlike leucine and isoleucine, which promote polymerization relative to HbS, tryptophan inhibits polymerization. Our results provide explanations for the altered polymerization properties and reveal a fundamentally different double strand that may provide a model for interactions within a fiber and/or interactions leading to heterogeneous nucleation.

Analysis of the stability of hemoglobin S double strands

The deoxyhemoglobin S (deoxy-HbS) double strand is the fundamental building block of both the crystals of deoxy-HbS and the physiologically relevant fibers present within sickle cells. To use the atomic-resolution detail of the hemoglobin-hemoglobin interaction known from the crystallography of HbS as a basis for understanding the interactions in the fibers, it is necessary to define precisely the relationship between the straight double strands in the crystal and the twisted, helical double strands in the fibers. The intermolecular contact conferring the stability of the double strand in both crystal and fiber is between the beta6 valine on one HbS molecule and residues near the EF corner of an adjacent molecule. Models for the helical double strands were constructed by a geometric transformation from crystal to fiber that preserves this critical interaction, minimizes distortion, and makes the transformation as smooth as possible. From these models, the energy of association was calculated over the range of all possible helical twists of the double strands and all possible distances of the double strands from the fiber axis. The calculated association energies reflect the fact that the axial interactions decrease as the distance between the double strand and the fiber axis increases, because of the increased length of the helical path taken by the double strand. The lateral interactions between HbS molecules in a double strand change relatively little between the crystal and possible helical double strands. If the twist of the fiber or the distance between the double strand and the fiber axis is too great, the lateral interaction is broken by intermolecular contacts in the region around the beta6 valine. Consequently, the geometry of the beta6 valine interaction and the residues surrounding it severely restricts the possible helical twist, radius, and handedness of helical aggregates constructed from the double strands. The limitations defined by this analysis establish the structural basis for the right-handed twist observed in HbS fibers and demonstrates that for a subunit twist of 8 degrees, the fiber diameter cannot be more than approximately 300 A, consistent with electron microscope observations. The energy of interaction among HbS molecules in a double strand is very slowly varying with helical pitch, explaining the variable pitch observed in HbS fibers. The analysis results in a model for the HbS double strand, for use in the analysis of interactions between double strands and for refinement of models of the HbS fibers against x-ray diffraction data.

The high resolution crystal structure of deoxyhemoglobin S

We have refined the crystal structure of deoxyhemoglobin S (beta Glu6-->Val) at 2.05 A resolution to an R-factor of 16.5% (free R=21. 5%) using crystals isomorphous to those originally grown by Wishner and Love. A predominant feature of this crystal form is a double strand of hemoglobin tetramers that has been shown by a variety of techniques to be the fundamental building block of the intracellular sickle cell fiber. The double strand is stabilized by lateral contacts involving the mutant valine interacting with a pocket between the E and F helices on another tetramer. The new structure reveals some marked differences from the previously refined 3.0 A resolution structure, including several residues in the lateral contact which have shifted by as much as 3.5 A. The lateral contact includes, in addition to the hydrophobic interactions involving the mutant valine, hydrophilic interactions and bridging water molecules at the periphery of the contact. This structure provides further insights into hemoglobin polymerization and may be useful for the structure-based design of therapeutic agents to treat sickle cell disease.

Recombinant human sickle hemoglobin expressed in yeast

Sickle hemoglobin has been expressed in the yeast Saccharomyces cerevisiae after site-directed mutagenesis of a plasmid containing normal human alpha- and beta-globin genes. Cassette mutagenesis of this plasmid was achieved by inserting a DNA fragment containing the beta-globin gene in the replicative form of M13mp18 to make a point mutation and then reconstituting the original plasmid containing the mutated beta-globin gene. Pure recombinant hemoglobin S was shown to be identical to natural sickle hemoglobin in its ultraviolet and visible absorption bands and by gel electrophoresis, isoelectric focusing, amino acid analysis, mass spectrometry, partial N-terminal sequencing, and functional properties (P50, cooperativity, and response to 2,3-bisphosphoglycerate). In yeast and in mammalian cells, cotranslational processing yields the same N-terminal valine residues of hemoglobin alpha- and beta-chains, but in bacterial expression systems the N terminus is extended by an additional amino acid because the initiator methionine residue is retained. Since the N-terminal valine residues of both chains of hemoglobin S participate in important physiological functions, such as oxygen affinity, interaction with anions, and the Bohr coefficient, the yeast expression system is preferable to the bacterial system for recombinant DNA studies. Hence, mutagenesis employing this expression system should permit definitive assignments of the role of any amino acid side chain in hemoglobin S aggregation and could suggest additional approaches to therapeutic intervention. The engineering of this system for the synthesis of sickle hemoglobin and its purification to homogeneity in a single column procedure are described.

Computer models of a new deoxy-sickle cell hemoglobin fiber based on x-ray diffraction data

A new x-ray fiber diffraction pattern from deoxygenated sickle cell erythrocytes has been observed. It displays 14 layer lines with a 109 A periodicity compared with the 64 A periodicity of the "classic" sickle cell hemoglobin (HbS) fiber. These data and association energy calculations serve as a basis for computer model building. Systematic searches over four-dimensional parameter space yielded twelve protofilament models that satisfy the following constraints: (a) two HbS molecules be related by twofold screw symmetry with a translational repeat of 109 A; (b) at least one of the substituted residues in HbS, val beta 6, should participate in intermolecular contacts; and (c) the energy of intermolecular interaction be less than -24 kcal/mol. Each of the protofilament models is a zigzag mono-strand that stands in contrast to the double-stranded protofilament of the "classic" fiber. Fiber models were constructed with each of the 12 protofilament models, pseudo-hexagonally packed. Searches of variable packing parameters showed four fiber models with minimal protofilament association energies and minimal differences between calculated transforms and observed data. The R-factor was less than 0.24 for each of these four models. In three of the fiber models the protofilament association energy is between -(93 and 130) kcal, and in a fourth, the energy is -64 kcal. One protofilament model constituted three distinct fiber models of the lower energy class, and a second protofilament model packed with a higher association energy into a fourth fiber model. The selection of a unique fiber model from among these four cannot be made because of the limited available data. Fibers models constructed with any of the ten other protofilament models do not satisfy the conditions of minimal association energy and R-factor.

Structural polymorphism correlated to surface charge in filamentous bacteriophages

Fiber diffraction studies are used to demonstrate that changes in the helical symmetry of the protein coat of filamentous bacterial viruses fd and M13 are correlated with changes in the surface charge. Comparison of the structure of M13 and fd at pH 2 and 8 indicate that surface charge affects both the helical symmetry and flexibility of the virions. The changes in helical symmetry are similar in magnitude to that observed in the Pseudomanas phage Pf1 and probably reflect an inocuous side effect of the particle flexibility required for protection of the virus particles from damage due to shear. The magnitude of the observed changes in helical symmetry appears to be limited to that which can occur without repacking of the interfaces between the alpha-helices making up the viral protein coat.

Pairings and polarities of the 14 strands in sickle cell hemoglobin fibers

Sickle cell anemia results from the formation of hemoglobin S fibers in erythrocytes, and a greater understanding of the structure of these fibers should provide insights into the basis of the disease and aid in the development of effective antisickling agents. Improved reconstructions from electron micrographs of negatively stained single hemoglobin S fibers or embedded fiber bundles reveal that the 14 strands of the fiber are organized into pairs. The strands in each of the seven pairs are half-staggered, and from longitudinal views the polarity of each pair can be determined. The positions of the pairs and their polarities (three in one orientation; four in the opposite orientation) suggest a close relationship with the crystals of deoxyhemoglobin S composed of antiparallel pairs of half-staggered strands.

Polymorphism of sickle cell hemoglobin aggregates: structural basis for limited radial growth

Fibers composed of molecules of deoxygenated sickle cell hemoglobin are the basic cause of pathology in sickle cell disease. The hemoglobin molecules in these fibers are arranged in double strands that twist around one another with a long axial repeat. These fibrous aggregates exhibit a pattern of polymorphism in which the ratio of their helical pitch to their radius is approximately constant. The observed ratio agrees with an estimate of its value calculated from the geometric properties of helical assemblies and the degree of distortion that a protein-protein interface can undergo. This agreement indicates that the radius of an aggregate is limited by the maximum possible stretching of double strands. The geometric properties limiting the radial extent of sickle hemoglobin fibers are fundamental to all cables of protein filaments and could contribute to the control of diameter in other biological fibers such as collagen or fibrin.

Fibers, crystals, and other forms of HbS polymers in deoxygenated sickle erythrocytes

We have examined by electron microscopy the formation of fibers and crystals from sickle hemoglobin within sickle erythrocytes following deoxygenation during capillary storage from 1 to 132 days. Intracellular fibers were found on the first day and throughout the period of study. The fibers exhibited a diameter (mean +/- SD) of 17.4 +/- 0.62 nm and were aligned in the cell with a fiber-to-fiber spacing of 18.6 nm (x-axis) by 22.7 nm (y-axis). Between 65 and 132 days, extracellular hemoglobin crystals developed, with a lattice periodicity of 9.63 +/- 0.6 nm. Fibers and crystals coexist as separate structures. These results suggest that crystal formation upon storage of packed deoxygenated sickle erythrocytes may proceed via a phase of fiber dissolution followed by hemoglobin reassembly into extracellular crystals, rather than by a progressive alignment and direct fusion of existing fibers.

Electrostatic effects in acylation of hemoglobin by aspirins

Carboxylate substituents added to the salicylate ring increase the effectiveness of a variety of aspirins and diaspirins in acylating hemoglobin. Even more effective are a series of monoesters of dicarboxylate derivatives. Bis(5-carbomethoxysalicyl)fumarate and -succinate at 5 mM concentrations modify approximately 100% of the hemoglobin in solution and should alter the aggregation behavior of sickle hemoglobin.

A potent new dipeptide inhibitor of cell sickling and haemoglobin S gelation

A dipeptide L-lysine-L-phenylalanine is shown to inhibit both cell sickling and the gelation of solutions of sickle-cell haemoglobin. The effect on deoxyhaemoglobin solutions and gels was followed by centrifugation; a progressive inhibition of gelation was observed up to 30 mM Lys-Phe. The haemoglobin concentration at the plateau (26 g/dl) suggests that an effect might be seen in vivo if suitable concentrations of Lys-Phe (about 20 mM) can be maintained in the blood stream. Additional studies of lag time before onset of gelation support this. Oxygen dissociation curves of sickle cells showed an effect of Lys-Phe only after incubation for 3 h before measurement, the P50 decreasing from 51 mmHg (6.8 MPa) to 41 mmHg (5.5 MPa) for cells depleted of 2,3-bisphosphoglycerate. The effect of Lys-Phe on intact sickle cells was more rapid. A marked increase in the number of unsickled cells in the presence of Lys-Phe was observed after only 15 min incubation. This result, together with measurements of uptake both into the cell and onto the cell membrane shows that the compound produces a membrane-mediated antisickling effect in addition to the effect on haemoglobin in solution within the cell. The membrane effect is not due to a change in cell volume. The properties of this dipeptide may be of value in the treatment of impending and early sickle crisis.

Sickle cell hemoglobin fiber structure altered by alpha-chain mutation

Hybrid hemoglobin molecules prepared with beta chains from hemoglobin S (beta 6 Glu leads to Val) and alpha chains from hemoglobin Sealy (alpha 47 Asp leads to His) form fibers with a novel structure. In contrast to the typical fibers of hemoglobin S with an average diameter of 22 nm and a solid cross section composed of 10 outer filaments surrounding a 4-filament core, the fibers of the alpha Sealy2 beta S2 hybrid are much larger, with a mean diameter of 32 nm and a unique double-hollow arrangement of filaments. Sealy--S fibers can be described by a model in which the two pairs of filaments most readily lost from fibers of hemoglobin S are missing to form the hollow regions, with an additional sheath of filaments added to form the overall larger structure.

Diffusion coefficients of hemoglobin by intensity fluctuation spectroscopy: effects of varying pH and ionic strength

Measurements of the mutual diffusion coefficients (D) of the liganded human hemoglobins (Hb) oxy-HbA and oxy-HbS were performed as a function of Hb concentration (CHb), pH, and ionic strength (tau) by intensity fluctuation spectroscopy (IFS). Average diffusion coefficients, (D), and normalized variances, ((D/(D) - 1)2), were recorded. Results are reported and select features are discussed quantitatively. (a) for tau = 0.15 M, the shape of the (d) vs. CHb curve is found to vary with pH. We developed a precise description of this effect in the form of an algebraic relationship between (D), CHb, and Z, the titration charge. (b) only slight differences between the (D) values of oxy-HbS and oxy-HbA are observed, at tau = 0.15 M, for CHb Less Than or Equal To 10 g%. These differences are explained by the theory of part a. (c) No evidence of aggregation is found in solutions of oxy-HbA or oxy-HbS, at tau = 0.15 M, for CHb Less Than or Equal To 10 g%. (d) Indications of aggregation appear in oxy-HbA solutions at very low concentrations of salt. An estimate is made of the extent of aggregation, and the average radius of a cluster is determined.

Kinetic studies on photolysis-induced gelation of sickle cell hemoglobin suggest a new mechanism

The kinetics of deoxyhemoglobin S gelation have been investigated using photolytic dissociation of the carbon monoxide complex to initiate the process. Measurements over a wide range of times, 10(-3)-10(4) show that both the concentration dependence of the tenth-time (i.e., the time required to complete one-tenth the reaction) and the time dependence of the process decrease as gelation speeds up. In slowly gelling samples, where single domains of polymers are formed in the small sample volumes employed with this technique (1-2 x 10(-9) cm3), there is a marked increase in the variability of the tenth-times. These results are explained by a mechanism in which gelation is initiated by homogeneous nucleation of polymers in the bulk solution phase, followed by heterogeneous nucleation on the surface of existing polymers. At the lowest concentrations, homogeneous nucleation is so improbable that stochastic behavior is observed in the small sample volumes, and heterogeneous nucleation is the dominant pathway for polymer formation, thereby accounting for the high time dependence. At the highest concentrations homogeneous nucleation becomes much more probable, and the time dependence decreases. The decrease in concentration dependence of the tenth-time with increasing concentration results from a decrease in size of both the homogeneous and heterogeneous critical nuclei. The model rationalizes the major observations on the kinetics of gelation of deoxyhemoglobin S, and is readily testable by further experiments.

Patterns in the quinary structures of proteins. Plasticity and inequivalence of individual molecules in helical arrays of sickle cell hemoglobin and tubulin

The four recognized levels of organization of protein structure (primary through quaternary) are extended to add the designation quinary structure for the interactions within helical arrays, such as found for sickle cell hemoglobin fibers or tubulin units in microtubules. For sickle cell hemoglobin the main quinary structure is a 14-filament fiber, with a number of other minor forms also encountered. Degenerate forms of the 14-filament fibers can be characterized that lack specific pairs of filaments; evidence is presented which suggests an overall organization of the 14 filaments in pairs, with particular pairs aligned in an antiparallel orientation. For tubulin, a range of quinary structures can be detected depending on the number of protofilaments and whether adjacent protofilaments composed of alternating alpha- and beta-subunits are aligned with contacts between like or unlike subunits and with parallel or antiparallel polarity. Thus, in contrast to quarternary structure, which generally involves a fixed number of subunits, the quinary structures of proteins can exhibit marked plasticity and inequivalence in the juxtaposition of constituent molecules.

Determination of deoxyhemoglobin S polymer in sickle erythrocytes upon deoxygenation

We have used 13C/1H magnetic double-resonance spectroscopy to measure the amount of sickle hemoglobin polymer within sickle erythrocytes as a function of oxygen saturation. We previously showed that the methods of cross-polarization and scalar decoupling could be used to measure accurately the polymer fraction in deoxygenated sickle hemoglobin solutions [Noguchi, C.T., Torchia, D.A. & Schechter, A.N. (1979) Proc. Natl. Acad. Sci. USA 76, 4936-4940]. Our measurements show that the amount of intracellular deoxyhemoglobin S polymer increases monotonically with decreasing oxygen saturation. Polymer can be detected at oxygen saturation values above 90%. This result can be theoretically explained by the excluded volume effect of the oxyhemoglobin S in the cell. The very high total intracellular hemoglobin concentration (34 g/dl) reduces the amount of soluble deoxyhemoglobin S to about 3 g/dl at 90% oxygen saturation. The agreement between theory and experiment indicates that the equilibrium properties of intracellular polymerization can be described by the analyses resulting from studies of concentrated sickle hemoglobin solutions. The curve for polymer formation as a function of oxygen saturation is roughly hyperbolic whereas that for cell sickling is sigmoidal; the difference is most apparent for measurements at pH 7.65. Intracellular polymer formation may in general have a different relationship to oxygen saturation than cell sickling and may be a more meaningful parameter of the pathophysiological process in sickle cell anemia than cell morphology. In addition, measurements of intracellular polymer should be useful in evaluating potential therapeutic agents.

Electron microscope study of the kinetics of the fiber-to-crystal transition of sickle cell hemoglobin

The intermediates and the rate-limiting step in the crystallization of deoxygenated sickle hemoglobin have been determined by a kinetic study with the use of electron microscopy. In slowly stirred solutions of deoxygenated hemoglobin S [Pumphrey, J. & Steinhardt, J. (1977) J. Mol. Biol. 112, 359--375], the sequential appearance of fibers have a diameter of approximately equal to 210 A, bundles of aligned fibers in well-ordered arrays, "thick" fibers of approximately equal to 470 A diameter, and microcrystals is observed. Only the fibers having a diameter of approximately equal to 210 A and bundles of aligned fibers are assigned as kinetically important intermediates of the fiber-to-crystal transition. Addition of microscopic seed crystals obtained from slowly stirred solutions of deoxyhemoglobin S to a solution composed of only fibers and hemoglobin monomers results in more rapid crystallization than in control solutions. Addition of seed crystals after the formation of bindles of aligned fibers does not alter the overall kinetics of crystallization. The results demonstrate that alignment of fibers is the rate-limiting step in the crystallization process and results in formation of nucleation sites for crystal growth.

Stereospecific inhibitors of the gelation of sickle hemoglobin

During the last decade there have been major advances in understanding the structure of the gel of deoxyhemoglobin S and the mechanism of its formation. These advances have allowed the development of a new strategy for the inhibition of gelation, i.e., stereospecific competitive inhibitors of the polymerization process. For this purpose we have used equilibrium solubility measurements to study the effects of amino acids and peptides on deoxyhemoglobin S solubility. We have found that aromatic amino acids and short peptides containing these amino acids significantly increase solubility; longer peptides, however, decrease solubility by an excluded-volume related effect. Recently we have used computer graphics projections of the surface of the hemoglobin molecules in the crystal form to design peptide inhibitors. In addition, we have developed 13C nuclear magnetic resonance spectroscopic methods to quantitate the gel of deoxyhemoglobin S in hemoglobin solutions an in cells. These spectroscopic methods allow us to study the mechanism of intracellular gelation and to test the effects of inhibitors on sickle cells.