To address data management and data exchange problems in the nuclear magnetic resonance (NMR) community, the Collaborative Computing Project for the NMR community (CCPN) created a "Data Model" that describes all the different types of information needed in an NMR structural study, from molecular structure and NMR parameters to coordinates. This paper describes the development of a set of software applications that use the Data Model and its associated libraries, thus validating the approach. These applications are freely available and provide a pipeline for high-throughput analysis of NMR data. Three programs work directly with the Data Model: CcpNmr Analysis, an entirely new analysis and interactive display program, the CcpNmr FormatConverter, which allows transfer of data from programs commonly used in NMR to and from the Data Model, and the CLOUDS software for automated structure calculation and assignment (Carnegie Mellon University), which was rewritten to interact directly with the Data Model. The ARIA 2.0 software for structure calculation (Institut Pasteur) and the QUEEN program for validation of restraints (University of Nijmegen) were extended to provide conversion of their data to the Data Model. During these developments the Data Model has been thoroughly tested and used, demonstrating that applications can successfully exchange data via the Data Model. The software architecture developed by CCPN is now ready for new developments, such as integration with additional software applications and extensions of the Data Model into other areas of research.
Recently we have identified angiostatin, an endogenous angiogenesis inhibitor of 38 kDa which specifically blocks the growth of endothelial cells (O'Reilly, M. S., Holmgren, L., Shing, Y., Chen, C., Rosenthal, R. A., Moses, M., Lane, W. S., Cao, Y., Sage, E. H., and Folkman, J. (1994) Cell 79, 315-328; Folkman, J. (1995) Nat. Med. 1, 27-31). Angiostatin was shown to represent an internal fragment of plasminogen containing the first four kringle structures. We now report on the inhibitory effects of individual or combined kringle structures of angiostatin on capillary endothelial cell proliferation. Recombinant kringle 1 and kringle 3 exhibit potent inhibitory activity with half-maximal concentrations (ED 50 ) of 320 nM and 460 nM, respectively. Also, recombinant kringle 2 displays a significant inhibition, although decreased compared with both kringle 1 and kringle 3. In contrast, kringle 4 is an ineffective inhibitor of basic fibroblast growth factor-stimulated endothelial cell proliferation. Among the tandem kringle arrays, the recombinant kringle 2-3 fragment exerts inhibitory activity similar to kringle 2 alone. However, relative to kringle 2-3, a marked enhancement in inhibition is observed when individual kringle 2 and kringle 3 are added together to endothelial cells. This implies that it is necessary to open the cystine bridge between kringle 2 and kringle 3 to obtain the maximal inhibitory effect of kringle 2-3. An increased (<2-fold) inhibitory activity is observed for the kringle 1-3 fragment (ED 50 ؍ 70 nM) compared with kringle 1-4 (ED 50 ؍ 135 nM). These data indicate that the anti-proliferative activity of angiostatin on endothelial cells is shared by kringle 1, kringle 2, and kringle 3, but probably not by kringle 4 and that more potent inhibition results when kringle 4 is removed from angiostatin. Thus, in view of the variable lysine affinity of the homologous domains, it would appear that lysine binding capability does not correlate with the relative inhibitory effects of the kringle-containing constructs. However, as we also demonstrate, appropriate folding of kringle structures is essential for angiostatin to maintain its full anti-endothelial activity.
The thus far unexplored aliphatic region of the proton magnetic resonance spectra of ferrichrome peptides was investigated at 360 MHz. Six isomorphic diamagnetic analogues of the ferric cyclohexapeptide differing in the coordinated cation (AL3+ or Ga3+) and the amino acid composition were studied in d6‐DMSO solution. By use of a novel resolution enhancement technique which applies a sinusoidal half‐wave window to the free induction decay combined with multiplication by an increasing exponential, the proton chemical shifts and spin‐spin couplings were accurately measured. Homonuclear decoupling combined with Fourier difference spectroscopy was used to selectively extract resonances out of crowded spectral regions. The spectra revealed unique features of fine structure in the proton resonance lines. Thus, the conformation‐dependent geminal coupling constants of glycyl α‐protons were found to be constant throughout the suite of analogue peptides. A similar invariance was observed for the vicinal coupling constants between α‐, β‐, γ‐, and δ‐protons in the ornithyl side chains. Comparison of the proton spin–spin coupling constants with the crstallographic dihedral angles led to a unique stereochemical assignment of the side‐chain resonances. The combined data sets of x‐ray atomic coordinates and 1H‐nmr spin‐spin coupling parameters have been used to calibrate the coefficients for a Karplus curve related to the torsional x angles in amino acid side chains: Structurial information was also obtained for the seryl residues, where the multiplet structures of the OH resonances indicate preferred spatial arrangements of the side chains.
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