Efficient factorial designs and the analysis of macromolecular crystal growth conditions

Application of general multilevel factorial design with formulation of fast disintegrating tablets containing croscaremellose sodium and Disintequick MCC-25

Despite the popularity of orally fast disintegrating tablets (FDTs), their formulation can sometimes be challenging, producing tablets with either poor mechanical properties or high disintegration times. The aim of this research was to enhance the properties of FDTs produced by direct compression to have both sufficient hardness to withstand manual handling, and rapid disintegration time. General multilevel factorial design was applied to optimise and evaluate main and interaction effects of independent variables (i) disintegrant concentration, (ii) % filler (Disintequick MCC-25) to mannitol on the responses hardness, tensile strength and disintegration time. In this experiment mannitol was used as a diluent, Disintequick MCC-25 (to best of our knowledge there is no publication available yet for its use with FDTs) was termed in this study as a filler and croscaremellose sodium was used as the superdisintegrant. Seven formulations were prepared following a progressive two-stage approach. Each stage involved the change in the ratio of excipients (Mannitol:Filler) (1:0), (1:0.25), (1:0.50), (1:1), (0.50:1), (0.25:1), (0:1) w/w and concentration of superdisintegrant (1%, 3%, 5%, 7%, 10% w/w). All FDTs were tested for different parameters such as diameter, hardness, tensile strength, thickness, friability and disintegration time. The results of multiple linear regression analysis show a good degree of correlation between experimental (R(2):0.84, 0.94, 0.91) and predicted response (R(2):0.83, 0.96, 0.95) for hardness, tensile strength and disintegration time respectively. The optimum formulations (regarding disintegration time with acceptable hardness and friability properties) consisted of: (i) 5% w/w disintegrant and 20% w/w filler to mannitol, showing a disintegration time of 30s, a hardness of 66.6N (6.8 kg/cm(2)) and friability of 2.2%; (ii) 7% or 10% w/w disintegrant with 33.33% w/w filler to mannitol, showing disintegration time of 84 s (for 7% disintegrant) and 107 s (for 10% disintegrant), hardness of 73.86N (for 7% disintegrant) and 72.68N (for 10% disintegrant) and friability of 1.44 (for 7% disintegrant) and 1.15% (for 10% disintegrant).

Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization

Electron crystallography is well suited for studying the structure of membrane proteins in their native lipid bilayer environment. This technique relies on electron cryomicroscopy of two-dimensional (2D) crystals, grown generally by reconstitution of purified membrane proteins into proteoliposomes under conditions favoring the formation of well-ordered lattices. Growing these crystals presents one of the major hurdles in the application of this technique. To identify conditions favoring crystallization a wide range of factors that can lead to a vast matrix of possible reagent combinations must be screened. However, in 2D crystallization these factors have traditionally been surveyed in a relatively limited fashion. To address this problem we carried out a detailed analysis of published 2D crystallization conditions for 12 β-barrel and 138 α-helical membrane proteins. From this analysis we identified the most successful conditions and applied them in the design of new sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. Using these matrices we have run 19 crystallization screens for 16 different membrane proteins totaling over 1300 individual crystallization conditions. Six membrane proteins have yielded diffracting 2D crystals suitable for structure determination, indicating that these new matrices show promise to accelerate the success rate of membrane protein 2D crystallization.

Enhanced amino acid selection in fully evolved tryptophanyl-tRNA synthetase, relative to its urzyme, requires domain motion sensed by the D1 switch, a remote dynamic packing motif

We previously showed (Li, L., and Carter, C. W., Jr. (2013) J. Biol. Chem. 288, 34736-34745) that increased specificity for tryptophan versus tyrosine by contemporary Bacillus stearothermophilus tryptophanyl-tRNA synthetase (TrpRS) over that of TrpRS Urzyme results entirely from coupling between the anticodon-binding domain and an insertion into the Rossmann-fold known as Connecting Peptide 1. We show that this effect is closely related to a long range catalytic effect, in which side chain repacking in a region called the D1 Switch, accounts fully for the entire catalytic contribution of the catalytic Mg(2+) ion. We report intrinsic and higher order interaction effects on the specificity ratio, (kcat/Km)Trp/(kcat/Km)Tyr, of 15 combinatorial mutants from a previous study (Weinreb, V., Li, L., and Carter, C. W., Jr. (2012) Structure 20, 128-138) of the catalytic role of the D1 Switch. Unexpectedly, the same four-way interaction both activates catalytic assist by Mg(2+) ion and contributes -4.4 kcal/mol to the free energy of the specificity ratio. A minimum action path computed for the induced-fit and catalytic conformation changes shows that repacking of the four residues precedes a decrease in the volume of the tryptophan-binding pocket. We suggest that previous efforts to alter amino acid specificities of TrpRS and glutaminyl-tRNA synthetase (GlnRS) by mutagenesis without extensive, modular substitution failed because mutations were incompatible with interdomain motions required for catalysis.

Full implementation of the genetic code by tryptophanyl-tRNA synthetase requires intermodular coupling

Tryptophanyl-tRNA Synthetase (TrpRS) Urzyme (fragments A and C), a 130-residue construct containing only secondary structures positioning the HIGH and KMSKS active site signatures and the specificity helix, accelerates tRNA(Trp) aminoacylation with ∼10-fold specificity toward tryptophan, relative to structurally related tyrosine. We proposed that including the 76-residue connecting peptide 1 insertion (Fragment B) might enhance tryptophan affinity and hence amino acid specificity, because that subdomain constrains the orientation of the specificity helix. We test that hypothesis by characterizing two new constructs: the catalytic domain (fragments A-C) and the Urzyme supplemented with the anticodon-binding domain (fragments A, C, and D). The three constructs, together with the full-length enzyme (fragments A-D), comprise a factorial experiment from which we deduce individual and combined contributions of the two modules to the steady-state kinetics parameters for tryptophan-dependent (32)PPi exchange, specificity for tryptophan versus tyrosine, and aminoacylation of tRNA(Trp). Factorial design directly measures the energetic coupling between the two more recent modules in the contemporary enzyme and demonstrates its functionality. Combining the TrpRS Urzyme individually in cis with each module affords an analysis of long term evolution of amino acid specificity and tRNA aminoacylation, both essential for expanding the genetic code. Either module significantly enhances tryptophan activation but unexpectedly eliminates amino acid specificity for tryptophan, relative to tyrosine, and significantly reduces tRNA aminoacylation. Exclusive dependence of both enhanced functionalities of full-length TrpRS on interdomain coupling energies between the two new modules argues that independent recruitment of connecting peptide 1 and the anticodon-binding domain during evolutionary development of Urzymes would have entailed significant losses of fitness.

Determination of soluble and membrane protein structures by X-ray crystallography

X-ray crystallography is a technique used to determine the atomic-detail structure of a biological macromolecule. The method relies on the ability to generate a three-dimensional crystal of a highly purified protein or nucleic acid for diffraction by X-rays. The extent of scattering of X-rays by the crystal determines the accuracy of the resulting structural model. Unlike electrons, X-rays cannot be refocused after they have been scattered by their target. Thus, calculations are needed to reconstruct the image of the macromolecule that builds the crystal lattice. Tremendous advances over the past 60 years in recombinant expression and purification, crystal growth methods and equipment, X-ray sources, computer processing power, programs, and graphics have taken X-ray crystallography from a highly specialized field to one increasingly accessible to researchers in the biomedical sciences. In this chapter, we review the major concepts of macromolecular X-ray crystallography, focusing mainly on techniques for crystallizing soluble and membrane proteins, and provide a protocol for the crystallization of lysozyme as a model for the crystallization of other proteins.

A deliberate approach to screening for initial crystallization conditions of biological macromolecules

A method to rationally predict crystallization conditions for a previously uncrystallized macromolecule has not yet been developed. One way around this problem is to determine initial crystallization conditions by casting a wide net, surveying a large number of chemical and physical conditions to locate crystallization leads. A facility that executes the rapid survey of crystallization lead conditions is described in detail. Results and guidelines for the initial screening of crystallization conditions, applicable to both manual and robotic setups, are discussed.

High-throughput protein crystallization

The combinatorial chemistry industry has made major advances in the handling and mixing of small volumes, and in the development of robust liquid-handling systems. In addition, developments have been made in the area of material handling for the high-throughput drug screening and combinatorial chemistry fields. Lastly, improvements in beamline optics at synchrotron sources have enabled the use of flash-frozen micron-sized (10-50 microm) crystals. The combination of these and other recent advances will make high-throughput protein crystallography possible. Further advances in high-throughput methods of protein crystallography will require application of the above developments and the accumulation of success/failure data in a more systematic manner. Major changes in crystallography technology will emerge based on the data collected by first-generation high-throughput systems.

A systematic approach to the large-scale production of protein crystals

Crystallization has recently emerged as a suitable process for the manufacture of biocatalysts in the form of cross-linked enzyme crystals (CLECs) or for the recovery of proteins from fermentation broths. In both instances it is essential to define conditions which control crystal size and habit, and that yield a reliable recovery of the active protein. Experiments to define the crystallization conditions usually depend on a factorial design (either incomplete or sparse matrix) or reverse screening techniques. In this work, we describe a simple procedure that allows the effect of three factors, for example protein concentration, precipitant concentration and pH, to be varied simultaneously and smoothly over a wide range. The results are mapped onto a simple triangular diagram where a 'window of crystallization' is immediately apparent, and that conveniently describes variations either in the crystal features, such as their yield, size, and habit, or in the recovery of biological activity. The approach is illustrated with two enzymes, yeast alcohol dehydrogenase (ADH I) and Candida rugosa lipase. For ADH the formation of two crystal habits (rod and hexagonal) could be controlled as a function of pH (6.5-10) and temperature (4-25 degrees C). At pH 7, in 10 to 16% w/v polyethylene glycol (PEG) 4000, only rod-shaped crystals formed whereas at pH 8, in 10 to 14% w/v PEG, only hexagonal crystals existed. For both enzymes, catalyst recovery was greatest at high crystallization agent concentrations and low protein concentration. For ADH, the greatest activity recovery was 87% whereas for the lipase crystals, by using 45% v/v 2-methyl-2,4-pentanediol (MPD) as the crystallization agent, a crystal recovery of 250 crystals per µl was obtained. For the lipase system, the use of crystal seeding was also shown to increase the crystal recovery by up to a factor of four. From the crystallization windows, the original conditions based on literature precedent (35% v/v MPD, 1 mM CaCl(2), 1.8 mg protein/ml) were altered (47.5% v/v MPD, 2 mM CaCl(2), 3 mg protein/ml). This led to an improved recovery of the lipase under conditions that scale reliably from 0.5 ml to 500 ml with no change in size, shape or recovery of the crystals themselves. Finally, these crystals were crosslinked with 5% v/v glutaraldehyde and mass and activity balances were calculated for the entire process of CLEC production. Up to 35% of the lipase activity present in the crude solid was finally recovered in the lipase CLECs after propan-2-ol fractionation, crystallization, and crosslinking.

SAmBA: an interactive software for optimizing the design of biological macromolecules crystallization experiments

SAmBA is a new software for the design of minimal experimental protocols using the notion of orthogonal arrays of strength 2. The main application of SAmBA is the search of protein crystallization conditions. Given a user input defining the relevant effectors/variables (e.g., pH, temperature, salts) and states (e.g., pH: 5, 6, 7 and 8), this software proposes an optimal set of experiments in which all tested variables and the pairwise interactions between them are symmetrically sampled. No a priori restrictions on the number and range of experimental variables is imposed. SAmBA consists of two complementary programs, SAm and BA, using a simulated annealing approach and a backtracking algorithm, respectively. The software is freely available as C code or as an interactive JAVA applet at http:/(/)igs-server.cnrs-mrs.fr.

Crystallization of biological macromolecules for X-ray diffraction studies

Advances in the crystallization of biological macromolecules have come not only from the application of biochemical, molecular biological and immunological principles and techniques, but also from continued efforts to understand the crystallization process. Developments in crystallization methodologies, protocols, and reagents are also facilitating crystallization efforts.

Trends and challenges in experimental macromolecular crystallography

Macromolecular X-ray crystallography underpins the vigorous field of structural molecular biology having yielded many protein, nucleic acid and virus structures in fine detail. The understanding of the recognition by these macromolecules, as receptors, of their cognate ligands involves the detailed study of the structural chemistry of their molecular interactions. Also these structural details underpin the rational design of novel inhibitors in modern drug discovery in the pharmaceutical industry. Moreover, from such structures the functional details can be inferred, such as the biological chemistry of enzyme reactivity. There is then a vast number and range of types of biological macromolecules that potentially could be studied. The completion of the protein primary sequencing of the yeast genome, and the human genome sequencing project comprising some 105proteins that is underway, raises expectations for equivalent three dimensional structural databases.

Incomplete factorial and response surface methods in experimental design: yield optimization of tRNA(Trp) from in vitro T7 RNA polymerase transcription

We have studied the yield of Escherichia coli tRNA(Trp) obtained from in vitro T7 RNA polymerase transcription using incomplete factorial and response surface methods. Incomplete factorial experiments were first used to estimate the relative impact of six variables on the yield of tRNA(Trp). Fifteen trials were performed according to a balanced and randomized design. The correlation between observed yield and all experimental variables was identified by stepwise multiple linear regression analysis. The concentrations of T7 RNA polymerase, DNA template, NTP and MgCl2 proved to be significantly correlated with the yield of tRNA(Trp). We then optimized the yield with respect to each of these four variables simultaneously with a designed, response surface experiment based on the Hardin-Sloane minimum prediction variance algorithm. Twenty experiments were performed, in duplicate, to sample the quadratic surface relating the yield to the four significant variables. Coefficients of the quadratic function with all two-factor interactions were evaluated by stepwise regression using least squares, and significant coefficients were retained. Partial differentiation of the resulting quadratic model showed it to possess an optimum. Transcription performed at the corresponding conditions yielded 6-fold more tRNA(Trp) than the initial conditions, confirming the predictive value of the experimentally determined response surface.

Crystallization and structure determination of RNA

Progress in the synthesis, purification and crystallization of RNA has resulted in the determination of several X-ray crystal structures of RNA molecules over the past few years. Methods proven and under development will lead to future structure determinations and shed light on the structural basis for RNA's many functions.

Crystallization of a membrane pore-forming protein with mosquitocidal activity from Bacillus thuringiensis subspecies kyushuensis

CytB, a membrane pore-forming toxin from Bacillus thuringiensis subspecies kyushuensis, is specifically toxic to dipteran insect larvae but broadly cytolytic in vitro. It has been purified in the protoxin form from a recombinant Escherichia coli source and crystals have been obtained which diffract X-rays to at least 2.6 A resolution. The tendency for CytB to aggregate in solution was overcome by including 50 mM of urea or 8 mM of ethanolamine during crystallization. Mutants designed to add or subtract single cysteine residues for the purpose of heavy atom derivative preparation were similarly purified and crystallized. The crystals are hexagonal bipyramids. They belong to space group P6(1)22 (or P6(5)22) with lattice constants a = b = 67.34 A, c = 170.96 A, and contain one molecule of the CytB protoxin (MW 29235) per asymmetric unit and 27% solvent by volume.

Regression analysis of factorially designed trials--a logical approach to protein crystallization

The specific composition of the mother liquor that induces the formation of protein crystal is usually quoted as the 'best condition' for crystallization. However, very little is described about how these conditions were determined. These missing and non-reported details would certainly lead to a better understanding of why a specific purified protein does not crystallize, and why crystallization seems to be a totally unpredictable enterprise. In this paper, it is shown that a simple regression model applied to a set of factorially designed experiments (comprising successful and failed experiments) is a useful tool for the analysis of crystallization outcomes. The applications of this approach to the proteins lysozyme and calmodulin yielded results that did not substantially differ from published accounts. When this procedure is applied to myelin basic protein (MBP) and to a MBP and calmodulin complex no crystals formed, which would suggest that neither is easy to crystallize. In summary, factorial design and regression analysis can be an important methodological approach for crystallizing proteins.

Purification and preliminary crystallographic studies of penicillin G acylase from Providencia rettgeri

Two isoforms of the heterodimeric enzyme penicillin G acylase (EC 3.5.1.11) from Providencia rettgeri ATCC 31052 (strain Bro1) were purified to near homogeneity. The isoforms exhibited comparable enzymatic activities but differed slightly in the molecular weight and pI of their respective alpha-subunit. The origin of this difference was traced to the partial conversion of the N-terminal Gln of the alpha-subunit to pyrrolidonecarboxylic acid (pyro-Glu). The boundaries of the mature enzyme within the translated DNA sequence of the wild-type propeptide (GenBank M86533) were determined. The results conclusively identified the length of the signal peptide and the position of the spacer cleaved from the propeptide to form the active heterodimer. The molecular weights of the alpha- and beta-subunits, based on these termini, were 23.7 and 62.2 kDa, respectively. Both isoforms were crystallized independently as hexagonal bipyramids up to 0.60 mm in diameter in either space group P6(1)22 or P6(5)22 (a = b = 140.5 A and c = 209.5 A) from ammonium sulfate solutions buffered by 50 mM potassium phosphate at pH 7.5. The presence of glycerol, although not required, facilitated crystal growth. Native and heavy atom derivative data were collected to 3.0 A resolution, and the calculation of isomorphous replacement phases is under way.

Control of nucleation of protein crystals

Control of nucleation may be needed to obtain a reliable supply of large protein crystals, when standard techniques give many small or twinned crystals. Heterogeneous nucleation may be controlled by the use of fine filters, with the elimination of airborne contaminants by working under paraffin oil. The area of contact with the supporting vessel also has an important effect. A heterogenous nucleant for lysozyme (identified earlier) has been shown to be effective for carboxypeptidase G2. Control of homogeneous nucleation (previously demonstrated by dilutions of a nucleating sample after various times of incubation) may also be achieved by incubating a sample at 1 temperature, where nucleation can occur, and changing the temperature to conditions where there is growth but no nucleation.

A glutamic acid specific serine protease utilizes a novel histidine triad in substrate binding

Proteases specific for cleavage after acidic residues have been implicated in several disease states, including epidermolysis, inflammation, and viral processing. A serine protease with specificity toward glutamic acid substrates (Glu-SGP) has been crystallized in the presence of a tetrapeptide ligand and its structure determined and refined to an R-factor of 17% at 2.0-A resolution. This structure provides an initial description of the design of proteolytic specificity for negatively charged residues. While the overall fold of Glu-SGP closely resembles that observed in the pancreatic-type serine proteases, stabilization of the negatively charged substrate when bound to this protein appears to involve a more extensive part of the protease than previously observed. The substrate carboxylate is bound to a histidine side chain, His213, which provides the primary electrostatic compensation of the negative charge on the substrate, and to two serine hydroxyls, Ser192 and Ser216. Glu-SGP displays maximum activity at pH 8.3, and assuming normal pKa's, the glutamate side chain and His213 will be negatively charged and neutral, respectively, at this pH. In order for His213 to carry a positive charge at the optimal pH, its pKa will have to be raised by at least two units. An alternative mechanism for substrate charge compensation is suggested that involves a novel histidine triad, His213, His199, and His228, not observed in any other serine protease. The C-terminal alpha-helix, ubiquitous to all pancreatic-type proteases, is directly linked to this histidine triad and may also play a role in substrate stabilization.(ABSTRACT TRUNCATED AT 250 WORDS)

Effect of polyethylene glycol-400 at low concentrations on long-term growth of muscle phosphoglucomutase crystals from concentrated salt solutions

Although rabbit muscle phosphoglucomutase occasionally deposits tetragonal crystals from solutions of ammonium sulfate at about 47% of saturation, low concentrations of polyethylene glycol-400 (PEG), 1 to 4.5% w/v, must be included to sustain crystal growth. A comparison of long-term growth rates for macroscopic crystals in the presence and absence of added PEG suggests that at high salt concentration this cosolute exerts its primary effect on disordered protein aggregates, either in the external medium or at the surface of the crystal, and thereby allows the growth of much larger crystals. Since the observed effects may arise from a PEG-induced increase in the "solubility" of the aggregate that exceeds the induced increase in solubility of the crystalline phase under these conditions, the physical basis for a cosolute-induced increase in solubility in the presence of a precipitant is considered. The applicability of such a rationale to the present system is supported by an assessment of the relative effects of polyethylene glycol and beta-octylglucoside on amorphous, salt-induced precipitates of phosphoglucomutase. PEG also produces what appears to be a differential effect on nucleation efficiency and crystal growth rate. Thus, seed crystals cannot be enlarged at a significant rate at high salt concentration without producing showers of extraneous nucleation centers when the concentration of added PEG is 3% or less. But PEG concentrations of 4.5% essentially eliminate the showering problem, ostensibly by increasing the supersaturation required for nucleation to a greater extent than that required for crystal growth. The same type of effect is observed during de novo growth. Again a solubility-based mechanism is posed. Hysteretic effects related to properties of amorphous aggregates of the protein also are described.