Mason-Pfizer monkey virus (M-PMV), a D-type retrovirus assembling in the cytoplasm, causes simian acquired immunodeficiency syndrome (SAIDS) in rhesus monkeys. Its pepsin-like aspartic protease (retropepsin) is an integral part of the expressed retroviral polyproteins. As in all retroviral life cycles, release and dimerization of the protease (PR) is strictly required for polyprotein processing and virion maturation. Biophysical and NMR studies have indicated that in the absence of substrates or inhibitors M-PMV PR should fold into a stable monomer, but the crystal structure of this protein could not be solved by molecular replacement despite countless attempts. Ultimately, a solution was obtained in mr-rosetta using a model constructed by players of the online protein-folding game Foldit. The structure indeed shows a monomeric protein, with the N- and C-termini completely disordered. On the other hand, the flap loop, which normally gates access to the active site of homodimeric retropepsins, is clearly traceable in the electron density. The flap has an unusual curled shape and a different orientation from both the open and closed states known from dimeric retropepsins. The overall fold of the protein follows the retropepsin canon, but the C(α) deviations are large and the active-site 'DTG' loop (here NTG) deviates up to 2.7 Å from the standard conformation. This structure of a monomeric retropepsin determined at high resolution (1.6 Å) provides important extra information for the design of dimerization inhibitors that might be developed as drugs for the treatment of retroviral infections, including AIDS.

Following the failure of a wide range of attempts to solve the crystal structure of M-PMV retroviral protease by molecular replacement, we challenged players of the protein folding game Foldit to produce accurate models of the protein. Remarkably, Foldit players were able to generate models of sufficient quality for successful molecular replacement and subsequent structure determination. The refined structure provides new insights for the design of antiretroviral drugs.

The Human Proteome Organization (HUPO) Proteomics Standard Initiative has been tasked with developing file formats for storing raw data (mzML) and the results of spectral processing (protein identification and quantification) from proteomics experiments (mzIndentML). In order to fully characterize complex experiments, special data types have been designed. Standardized file formats will promote visualization, validation and dissemination of data independent of the vendor-specific binary data storage files. Innovative programmatic solutions for robust and efficient data access to standardized file formats will contribute to more rapid wide-scale acceptance of these file formats by the proteomics community.In this work, we compare algorithms for accessing spectral data in the mzML file format. As an XML file, mzML files allow efficient parsing of data structures when using XML-specific class types. These classes provide only sequential access to files. However, random access to spectral data is needed in many algorithmic applications for processing proteomics datasets. Here, we demonstrate implementation of memory streams to convert a sequential access into random access. Our application preserves the elegant XML parsing capabilities. Benchmarking file access times in sequential and random access modes show that while for small number of spectra the random access is more time efficient, when retrieving large number of spectra sequential access becomes more efficient. We also provide comparisons to other file accessing methods from academia and industry.

The Protein Data Bank and Cambridge Structural Database were analyzed with the aim of verifying whether the restraints that are most commonly used for protein structure refinement are still appropriate 15 years after their introduction. From an analysis of selected main-chain parameters in well ordered fragments of ten highest resolution protein structures, it was concluded that some of the currently used geometrical target values should be adjusted somewhat (the C-N bond and the N-C(alpha)-C angle) or applied with less emphasis (peptide planarity). It was also found that the weighting of stereochemical information in medium-resolution refinements is often overemphasized at the cost of the experimental information in the diffraction data. A correctly set balance will be reflected in root-mean-square deviations from ideal bond lengths in the range 0.015-0.020 A for structures refined to R factors of 0.15-0.20. At ultrahigh resolution, however, the diffraction terms should be allowed to dominate, with even higher acceptable deviations from idealized standards in the well defined fragments of the protein. It is postulated that modern refinement programs should accommodate variable restraint weights that are dependent on the occupancies and B factors of the atoms involved.

Studies based on ab initio optimized geometries (at B3LYP/6-311+G** and MP2/6-311+G** levels) and on experimental structures retrieved from the Cambridge Structural Database (CSD) reveal that the nucleobases constituting DNA and RNA differ significantly in their aromatic character, as shown by the geometry-based index of aromaticity HOMA that ranges from 0.466 for thymine to 0.917 for adenine, based on B3LYP/6-311+G** calculations, and 0.495-0.926, respectively, if based on the MP2/6-311+G** level. Aromaticity of the bases decreases markedly with an increase of the number of double-bond C=X (X = N, O) substituents at the rings. H-bonds involving C=O groups in Watson-Crick pairs cause an increase of the aromatic character of the rings.

The crystal structure of the title compound, alternatively called 3-[4-(benzyloxy)phenyl]-2-(N-tert-butoxycarbonyl-N-methylamino)propionic acid, C(22)H(27)NO(5), has been studied in order to examine the role of N-methylation as a determinant of peptide conformation. The conformation of the tert-butoxycarbonyl group is trans-trans. The side chain has a folded conformation and the two phenyl rings are effectively perpendicular to one another. The carboxylate hydroxyl group and the urethane carbonyl group form a strong intermolecular O[bond]H...O hydrogen bond.

In the crystal structures of N3-protonated cytidinium and 2'-deoxycytidinium salts with composite XYn anions capable of accepting hydrogen bonds through their Y atoms, the dominating motif of cytosinium...anion interactions consists of a pair of hydrogen bonds donated from the N3+-H protonation site and from the exoamino N4-H41 group cis to N3, and accepted by two Y centers of one anion. This multipoint recognition pattern is stable and robust and thus can be classified as a supramolecular synthon. In a broader group of N3-protonated, N1-substituted cytosinium salts with composite anions it occurs with 70% frequency. The C5 side of the cytosine ring mimics the N3+-H type synthon and shows a propensity to form an analogous motif in which a C5-H5...Y hydrogen bond replaces the strong N3+-H...Y interaction. Since the C-H...Y bond is much weaker, the secondary motif shows higher deformability and is less frequent (44%).

2'-Deoxycytidine hemidihydrogenphosphate has been crystallized in the hexagonal space group P6(2) with a = 25.839(3), c = 12.529(1) A. The structure has been solved using the Patterson search method. The asymmetric unit contains two protonated, base-paired 2'-deoxycytidine dimers and two H2PO4- anions. The C+.C base pairs are composed of a protonated and a neutral species each and are triple H-bonded, the central N(3)... N(3) bonds being 2.850(7) and 2.884(5) A. The conformations of the four nucleosides fall in the same category (sugar puckers 2'-endo, glycosidic links anti) but in one of them the glycosidic torsion angle is quite low with consequences in other geometrical parameters. The H2PO4- anions are located on twofold axes and form two types of tight columns with P ... P separations about 4.18 A. The neighboring units along a column are linked via two very short O ... H ... O hydrogen bonds (O ... O about 2.49 A) leading to effective equalization of the P-O bonds. The base pairs of the two dC+.dC cations are coplanar and form layers perpendicular to the phosphate columns repeating every c/3. Within the layers, the dimers form a network through O(5')... O(2) hydrogen bonds but their primary intermolecular interactions have the form of H-bond anchors [N(4)-H ... O-P and O(3')-H ... O-P] to the phosphate groups.