Edgar F. Meyer

The Protein Data Bank: a computer-based archival file for macromolecular structures.

Abstract The Protein Data Bank is a computer-based archival file for macromolecular structures. The Bank stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies. Text included in each data entry gives pertinent information for the structure at hand (e.g. species from which the molecule has been obtained, resolution of diffraction data, literature citations and specifications of secondary structure). In addition to atomic co-ordinates and connectivities, the Protein Data Bank stores structure factors and phases, although these latter data are not placed in any uniform format. Input of data to the Bank and general maintenance functions are carried out at Brookhaven National Laboratory. All data stored in the Bank are available on magnetic tape for public distribution, from Brookhaven (to laboratories in the Americas), Tokyo (Japan), and Cambridge (Europe and worldwide). A master file is maintained at Brookhaven and duplicate copies are stored in Cambridge and Tokyo. In the future, it is hoped to expand the scope of the Protein Data Bank to make available co-ordinates for standard structural types (e.g. α-helix, RNA double-stranded helix) and representative computer programs of utility in the study and interpretation of macromolecular structures.

Structure of an endoglucanase from termite, Nasutitermes takasagoensis.

Contrary to conventional wisdom, it has been shown recently that termites do not necessarily depend on symbiotic bacteria to process cellulose. They secrete their own cellulases, mainly endo-beta-1,4-glucanase and beta-1,4-glucosidase. Here, the first structure of an endogenous endoglucanase from the higher termite Nasutitermes takasagoensis (NtEgl) is reported at 1.40 A resolution. NtEgl has the general folding of an (alpha/alpha)(6) barrel, which is a common folding pattern for glycosyl hydrolase family 9. Three-dimensional structural analysis shows that the conserved Glu412 is the catalytic acid/base residue and the conserved Asp54 or Asp57 is the base. The enzyme has a Ca(2+)-binding site near its substrate-binding cleft. Comparison between the structure of the Ca(2+)-free enzyme produced by reducing the pH of the soaked crystal from 5.6 (the pH of optimum enzyme activity) to 2.5 with that of the Ca(2+)-bound enzyme did not show significant differences in the locations of the C(alpha) atoms. The main differences are in the conformation of the residue side chains ligating the Ca(2+) ion. The overall structure of NtEgl at pH 6.5 is similar to that at pH 5.6. The major change observed was in the conformation of the side chain of the catalytic acid/base Glu412, which rotates from a hydrophobic cavity to a relatively hydrophilic environment. This side-chain displacement may decrease the enzyme activity at higher pH.

X-ray diffraction analysis of the inhibition of porcine pancreatic elastase by a peptidyl trifluoromethylketone

X-ray crystallographic data to 2.57 A resolution (1 A = 0.1 nm) have been measured for the complex of a peptidyl trifluoromethylketone inhibitor with porcine pancreatic elastase (PPE); R = 0.14. The inhibitor forms a stable complex with the enzyme by means of a covalent attachment to active site Ser195O gamma, resulting in a hemiketal moiety with tetrahedral geometry. The tripeptide protion binds as an antiparallel beta-sheet, with four hydrogen bonds augmenting the active-site covalent linkage, Ki = 9.5 microM. His57 exhibits a bifurcated H-bond to both Ser195O gamma and an F atom of the inhibitor. This study is one of a series which explores the binding geometry of a variety of small substrates and inhibitors to PPE. This peptidyl-PPE complex affords insight into the binding geometry of a novel trifluoromethylketone moiety to a serine proteinase.

Determination of the structure of an endoglucanase from Aspergillus niger and its mode of inhibition by palladium chloride.

The fungus Aspergillus niger is a main source of industrial cellulase. beta-1,4-Endoglucanase is the major component of cellulase from A. niger. In spite of widespread applications, little is known about the structure of this enzyme. Here, the structure of beta-1,4-endoglucanase from A. niger (EglA) was determined at 2.1 A resolution. Although there is a low sequence identity between EglA and CelB2, another member of family 12, the three-dimensional structures of their core regions are quite similar. The structural differences are mostly found in the loop regions, where CelB2 has an extra beta-sheet (beta-sheet C) at the non-reducing end of the binding cleft of the native enzyme. Incubation of EglA with PdCl(2) irreversibly inhibits the EglA activity. Structural studies of the enzyme-palladium complex show that three Pd(2+) ions bind to each EglA molecule. One of the Pd(2+) ions forms a coordinate covalent bond with Met118 S(delta) and the nucleophilic Glu116 O(epsilon1) at the active site of the enzyme. The other two Pd(2+) ions bind on the surface of the protein. Binding of Pd(2+) ions to EglA does not change the general conformation of the backbone of the protein significantly. Based on this structural study, one can conclude that the palladium ion directly binds to and blocks the active site of EglA and thus inactivates the enzyme.

Backward binding and other structural surprises

From simple to highly complex molecules, examples are cited of ‘backward’ or retro-binding. In some cases, symmetry dictates the directions observed and in cases not treated here, statistical disorder reveals averaged forward/backward binding. In most of the cases found, both the receptor and the ligand(s) are asymmetric, so local interactions dictate the preferred binding mode. A general rationale is presented to explain some of these observations and a hypothesis derived from this review can be tested experimentally.

Mapping the atomic environment of functional groups: turning 3D scatter plots into pseudo-density contours

Abstract A 3D map of the atomic environment about a pharmacophore, or any other functional group, can be constructed by combining data from crystal structures containing that group. 3D scatter plots show the positions where nonbonded atoms interact with the group. By placing a ‘smearing’ function at each of these points, we convert the scatter plot into a density map. Contours at various densities reveal non-uniformities in the distribution, which may indicate preferred directions of chemical interaction. Quantitative comparisons between density maps are easier to make than between scatter plots. We illustrate the method by examining the distribution of anions about the trimethylammonium group, a substructure of the neurotransmitter acetylcholine.

Computer aided prediction and evaluation of the tertiary structure for rat elastase II

Predictive methods have been extended to generate a proposed tertiary structure of rat elastase II on the basis of primary amino acid sequence and structural homologies within the family of mammalian serine proteinases. Force field refinement calculations were used to relax the structure. Structurally conserved molecules of solvation were introduced and the structure was again refined by means of force-field calculations. The resulting structure suggests probable substrate cleavage preferences. An independent statistical analysis of the crystallographically refined structures of serine proteinases (0.01-0.13 A, RMS) shows a close similarity to the final predicted model of rat pancreatic elastase II (0.03-0.14 A, RMS).

syn- and anti-Conformation in oxodipyrromethenes: crystal and molecular structure of 3,4-dimethyl-2,2′-pyrromethen-5(1H)-one and its N-methyl derivative

The structure of two oxodipyrromethenes have been determined from three-dimensional diffractometer data. One is 3,4-dimethyl-2,2′-pyrromethen-5(1H)-one, C11H12N2O (I), which crystallizes in the monoclinic space group P21/n with a= 13.597(1), b= 5.809(1), c= 12.558(1)A, β= 101.29(1)°, Z= 4. The second is a derivative of this compound in which one of the pyrrole nitrogen atoms is methylated. This is 1′,3,4-trimethyl-2,2′-pyrromethen-5(1H)-one, C12H14N2O, (II). It also crystallizes in P21/n with a= 7.122(1), b= 22.873(1), c= 7.012(1)A, β= 104.64(2)°, Z= 4. Both structures were solved by direct methods and refined by full-matrix least squares. The isomers obtained both had the Z-configuration, but in (I), the nitrogen atoms are syn, while in (II), they are anti. Both compounds show relatively small deviation from planarity, but (II) shows larger deviations than (I). Both form hydrogen-bonded dimers between the lactam oxygen atom and pyrrole nitrogen atoms. A comparison of the structures in the solid state and in solution indicates the difference in energy between a planar and twisted conformation is small.

Unusual metalloporphyrins. Structure of the product from the reaction of dodecacarbonylruthenium with meso-tetraphenylporphine: ‘dicarbonyltetraphenylporphinatoruthenium(II)’

The product of a reaction of Ru3(CO)12 and meso-tetraphenylporphine, previously believed to be an ethanol adduct of a monocarbonyl derivative of ruthenium(II) tetraphenylporphine, has been found by a single crystal X-ray analysis to be a centrosymmetrical octahedral complex of dicarbonyltetraphenylporphinatoruthenium (II).

WWWWhy does nature stutter? A survey of strands of repeated amino acids

Human stuttering is a simple example of the repetition of sounds or symbols, sometimes associated with single letters, and may be used to illustrate the amazing repetition of amino acids (symbolized by a letter, e.g. W) in proteins. A survey of available databases with highly improbable strings of single amino acids is tabulated. This paper concludes with a challenge to the crystallographic community to probe the structural origins of the structure-function relationship in this neglected area. When nature stutters, we should pay attention.