A preliminary three-dimensional structure of angiogenin.

Abstract

A preliminary three-dimensional structure of angiogenin has been computed, based on its homology to bovine pancreatic ribonuclease A. A standard-geometry structure of ribonuclease was first obtained from its x-ray coordinates. The fit of the backbone of angiogenin to that of ribonuclease was then optimized by taking account of amino acid deletions and by minimizing its conformational energy-plus-a-penalty distance function constraining its backbone to that of ribonuclease. Side-chain and backbone dihedral angles were allowed to vary throughout the cycles of energy minimization. In the last stages of minimization, the penalty distance function was removed. A low-energy structure resembling ribonuclease was obtained.Angiogenin is a basic single-chain protein of 123 amino acid residues that induces in vivo angiogenesis, the formation of blood vessels and a vascular system (1-3). The protein has been isolated in pure form from the serum-free conditioned medium of the human colorectal adenocarcinoma cell line HT-29. Both the amino acid sequence (2) and the corresponding DNA sequence (3) have been determined, showing it to have about a 35% homology with several mammalian pancreatic ribonucleases. Since the structure of bovine pancreatic ribonuclease is known (4, 5), the structure of angiogenin can be computed by minimization of its conformational energy on the assumption that it has a three-dimensional backbone structure similar to that of ribonuclease. This approach is used here to compute a preliminary three-dimensional structure of the whole angiogenin molecule. A similar procedure has been used to compute the structure of bovine a-lactalbumin (6) from that of hen egg-white lysozyme (7) and those of several snake venom inhibitors (8) from that of bovine pancreatic trypsin inhibitor (9). METHODOLOGY AND RESULTSOptimized Structure of Ribonuclease. First, a model of ribonuclease (RNase) having the standard geometry (bond lengths and bond angles) of the ECEPP (empirical conformational energy program for peptides) algorithm (10, 11) was computed from the x-ray coordinates (4, 5). The objective was to obtain an energy-minimized, standard-geometry structure for ribonuclease that would superimpose well on the known 2.0-A resolution x-ray structure and be free of any high-energy atomic overlaps. The coordinates from this standard-geometry model could then be used as input to provide a starting conformation for the backbone of angiogenin, as well as for side chains that are conserved between the two molecules. The degrees of freedom in this type of model are dihedral angles, with bond lengths and bond angles fixed at values obtained from high-resolution crystal structures of small molecules. For those dihedral angles that could be defined by the positions of four heavy atoms, initial values were computed from the neutron-and x-ray-derived Cartesian coordinates (4, 5). For the initial ECEPP model, all peptide bond dihedral angles, cl, were fixed at 1800 with the exception of those preceding proline residues, which wer...

Ribonucleolytic activity of angiogenin: essential histidine, lysine, and arginine residues.

“…It acquires additional importance for its capacity to indicate approaches for gaining a comparable understanding of angiogenin. Thus, a preliminary three-dimensional structure of angiogenin has been computed by minimization of its conformational energy based on the assumption that its backbone structure is similar to that of RNase (25). The results to date argue for conservation of the overall structural motif of RNase in the angiogenin molecule and are entirely consistent with its being a ribonucleolytic enzyme.…”

“…Chemical modifications were performed by standard procedures as described below using [14][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30] t.M angiogenin.…”

Dual site model for the organogenic activity of angiogenin.

“…A preliminary threedimensional structure of angiogenin calculated by energy minimization techniques (ref. 27; Fig. 5) suggests that the polypeptide backbone in this region forms a loop that differs substantially from that of RNase.…”

“…Angiogenin K retains full enzymatic activity toward tRNA, 28S and 18S rRNA (19), and dinucleoside phosphates ( (27). Arrows indicate the sites of cleavage for the BHK protease and endoproteinase Lys-C.…”

Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: Application in predicting the three‐dimensional structure of murine homeodomain Msx‐1

“…Homology modeling has been applied successfully to a number of proteins (see, for example, Greer, 1985Greer, , 1990Chothia et al, 1986;Palmer et al, 1986;Havel & Snow, 1991;Bruccoleri & Novotny, 1992;Bajorath et al, 1993;Brocklehurst & Perham, 1993;Fogolari et al, 1993;Havel, 1993;Srinivasan et al, 1993; for a comprehensive review see Sali, 1995). Such homology models are very useful in certain protein engineering applications that do not require an accurate high-resolution structure, and for accelerating experimental structure determinations by NMR and X-ray crystallography using molecular replacement methods.…”