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X-ray crystallography and NMR spectroscopy provide the only sources of experimental data from which protein structures can be analyzed at high or even atomic resolution. The degree to which these methods complement each other as sources of structural knowledge is a matter of debate; it is often proposed that small proteins yielding high quality, readily analyzed NMR spectra are a subset of those that readily yield strongly diffracting crystals. We have examined the correlation between NMR spectral quality and success in structure determination by X-ray crystallography for 159 prokaryotic and eukaryotic proteins, prescreened to avoid proteins providing polydisperse and/or aggregated samples. This study demonstrates that, across this protein sample set, the quality of a protein's ( 15 N- 1 H)-heteronuclear correlation (HSQC) spectrum recorded under conditions generally suitable for 3D structure determination by NMR, a key predictor of the ability to determine a structure by NMR, is not correlated with successful crystallization and structure determination by X-ray crystallography. These results, together with similar results of an independent study presented in the accompanying paper (Yee, et al., J. Am. Chem. Soc., accompanying paper), demonstrate that X-ray crystallography and NMR often provide complementary sources of structural data and that both methods are required in order to optimize success for as many targets as possible in large-scale structural proteomics efforts.

The biochemical and physical factors controlling protein expression level and solubility in vivo remain incompletely characterized. To gain insight into the primary sequence features influencing these outcomes, we performed statistical analyses of results from the high-throughput protein-production pipeline of the Northeast Structural Genomics Consortium. Proteins expressed in E. coli and consistently purified were scored independently for expression and solubility levels. These parameters nonetheless show a very strong positive correlation. We used logistic regressions to determine whether they are systematically influenced by fractional amino acid composition or several bulk sequence parameters including hydrophobicity, sidechain entropy, electrostatic charge, and predicted backbone disorder. Decreasing hydrophobicity correlates with higher expression and solubility levels, but this correlation apparently derives solely from the beneficial effect of three charged amino acids, at least for bacterial proteins. In fact, the three most hydrophobic residues showed very different correlations with solubility level. Leu showed the strongest negative correlation among amino acids, while Ile showed a slightly positive correlation in most data segments. Several other amino acids also had unexpected effects. Notably, Arg correlated with decreased expression and, most surprisingly, solubility of bacterial proteins, an effect only partially attributable to rare codons. However, rare codons did significantly reduce expression despite use of a codon-enhanced strain. Additional analyses suggest that positively but not negatively charged amino acids may reduce translation efficiency in E. coli irrespective of codon usage. While some observed effects may reflect indirect evolutionary correlations, others may reflect basic physicochemical phenomena. We used these results to construct and validate predictors of expression and solubility levels and overall protein usability, and we propose new strategies to be explored for engineering improved protein expression and solubility.

Crystallization has proven to be the most significant bottleneck to high-throughput protein structure determination using diffraction methods. We have used the large-scale, systematically generated experimental results of the Northeast Structural Genomics Consortium to characterize the biophysical properties that control protein crystallization. Datamining of crystallization results combined with explicit folding studies lead to the conclusion that crystallization propensity is controlled primarily by the prevalence of well-ordered surface epitopes capable of mediating interprotein interactions and is not strongly influenced by overall thermodynamic stability. These analyses identify specific sequence features correlating with crystallization propensity that can be used to estimate the crystallization probability of a given construct. Analyses of entire predicted proteomes demonstrate substantial differences in the bulk amino acid sequence properties of human versus eubacterial proteins that reflect likely differences in their biophysical properties including crystallization propensity. Finally, our thermodynamic measurements enable critical evaluation of previous claims regarding correlations between protein stability and bulk sequence properties, which generally are not supported by our dataset.

Das helikale Starkemolekul wird durch Amylase aus Bacillus macerans so abgebaut, das Cyclodextrine mit vorzugsweise 6 oder 7 mol Glucose entstehen (α- und β-CD). Aufgrund ihrer besonderen Struktur bilden diese Cyclodextrine mit verschiedenen Molekulen Einschlusverbindungen. Die Komplexe mit Polyjodid kristallisieren in Form von „endlosen”, geldrollenahnlichen Stapeln, in deren zentralem Hohlraum lineares Polyjodid eingelagert ist; diese tief gefarbten Strukturen konnen als Modelle fur den blauen Starke-Polyjodid-Komplex angesehen werden. Je nach Gegenion kristallisieren die α-Cyclodextrin-Polyjodid-Addukte in funf verschiedenen Raumgruppen, die zu vier verschiedenen Gittertypen gehoren, wahrend mit β-Cyclodextrin zwei Raumgruppen desselben Gittertyps existieren. Die Jodketten sind aus J3- und J2 oder aus (J2…J …J2)-n-Einheiten aufgebaut. Es ist zu schliesen, das im Starke-Polyjodid-Addukt die Struktur J3- und J2 vorliegt und das die Starke-Jod-Wechselwirkungen vor allem durch Wasserstoffatome, nicht durch die Sauerstoffatome am C-4 bewirkt werden. Topography of Cyclodextrin Inclusion Compounds, IX 1). - Linear Polyiodide Chains in Cyclodextrin Channels; Crystallographic Data and Comparison with the Blue Starch-Poly-iodide Complex The helical starch molecule is degraded by Bacillus macerans amylase into cyclodextrins (cycloamyloses) with preference for ring sizes of 6 and 7 mol of glucose (α- and β-CD). Owing to their special structure the cyclodextrins form inclusion compounds with various small molecules. The complexes with polyiodide crystallize as „endless” stacks like coins in a roll, linear polyiodide being embedded their central cavity. These deeply coloured structures can be regarded as models for the well known blue starch.polyiodide complex. Depending on the counterion the α-cyclodextrin-polyiodide adducts crystallize in five different space groups belonging to four different lattice types whereas for β-cyclodextrin only two space groups of the same lattice type do exist. The polyiodide chains are composed of I3- and I2 units or of (12…I…I2)-n units. It is concluded that the former structure dominates in the starch-polyiodide complex and that the starch-iodine interactions are due to hydrogen atoms and not to the glucosidic oxygen at C-4.

Proteinase K is obtained from the fungus Tritirachium album Limber and is named after its keratin-digesting activity. The enzyme, of molecular weight 18,500, is a serine proteinase and hydrolyses proteins at the carboxyl end of hydrophobic amino acids, as does α-chymotrypsin. The amino acid composition of proteinase K was determined by standard methods and the protein was crystallized using an improved dialysis method. The crystals obtained have been characterized by X-ray diffraction methods; the space group is tetragonal, P41212 or P43212 and the cell constants are a = b = 68·3 A, c = 108·5 A; two protein molecules are found in one asymmetric unit.

Crystallization procedures and X-ray crystallographic investigations are reported for eight different crystal forms of native yeast tRNAPhe. The crystals belong to the space groups monoclinic P21 and C2, orthorhombic P21 221 and C2221, hexagonal P62 22 with two different unit cells, rhombohedral R32, and cubic I41 32. The experimental conditions under which the various forms can be obtained are defined and the question is discussed as to whether these crystal forms reflect different conformations of the tRNA molecule itself. Further, yeast tRNAPhe was modified chemically with the objective of obtaining heavy atom substitution suitable for X-ray crystal structure analysis: s4 UMP can be incorporated into position 75 of tRNAPhe by tRNA nucleotidyl transferase yielding tRNAPhepCps4 U. This modified tRNA, tRNAPhepCpCspA, and tRNAPhepCps2 CpA crystallised in suitable specimens isomorphous with native yeast tRNAPhe while the iodine analogue tRNAPhe p(i5Cpi5 CpA crystallised in small, as yet uncharacterized crystals. Attempts have been made to obtain mercury derivatives by treating the sulphur-containing tRNAs with mercurials.

The title compound crystallizes in the monoclinic space group P21 with unit cell dimensions, a = 9.091 A , b = 6.404 A , c = 10.395 A , β = 93.6°, and there are two molecules per unit cell. The crystal structure has been determined on the basis of 828 diffraction intensities measured with a four-circle diffractometer, Cu radiation, and refined by the method of least squares to a residual index of R = 0.049. The uracil residue shows the features typical for O(2) cyclic derivatives: the C(2)-N(3) bond length, 1.283 A, is characteristic of a double bond. The ribofuranose conformation is an envelope with O(1′) 0.524 A exo, and the base is oriented syn with respect to the sugar with dihedral angles C(2)-N(1)-C(1′)-O(1′) = 71.2° and C(2)-N(1)-C(1′)-C(2′) = −47.6° which results in the positioning of O(2) almost over the center of the ribose ring. The spin-coupling constants of the proton magnetic resonance spectrum of this cyclic nucleoside derivative measured in C2HCl3 solution confirm the conformation found in the solid state by X-ray methods. There are substantial differences between the experimentally observed coupling constants for the bridged nucleoside and those predicted from the X-ray structure using modified Karplus type relations derived from less strained molecules.

Adenylyl-(3′–5′-adenylyl-(3′–5′)-adenosine, ApApA, crystallised from acidic, aqueous solution as a zwitterion, Ap−A+p−A+. The molecule consists of both a helical section, Ap−A+ and a non-helical section, A+p−A+; two anti-parallel molecules are linked by base pairing between protonated adenines. Although the base pair scheme is as proposed for poly(A+).poly(A+), the ApA+pA+ duplex is not double helical.

α-CYCLODEXTRIN (cyclohexaamylose) is the smallest member of the family of Schardinger dextrins, a group of cyclic D-glucosyl oligosaccharides each consisting of six to nine α-(1→4) linked glycopyranoses. These torus shaped molecules have voids of approximate diameter 6–9 A and are capable of forming inclusion complexes with a variety of “guest” molecules1,2. In the crystalline state, these complexes can exist as either “cage” or “channel” structures, depending on whether the cyclodextrins align themselves so that the voids form continuous, extended channels. At least eight different, non-isomorphous crystalline modifications of α-cyclodextrin with various different guest molecules are known. Cyclodextrin inclusion complexes can also exist in aqueous solution. As it has been proposed3 that simultaneously with complex formation the included solvent (water) is released, for an understanding of the mechanism of complex formation it is important to determine how many and in what manner solvent molecules are bound to the interior of the cyclodextrin ring. The structure we report here is that of α-cyclodextrin · 6H2O (αCDH2O), the “empty” inclusion complex, and is of the cage type.