Biomedical subjects

K Fidelis

Publications and source records attributed to K Fidelis.

22 records · Page 2Linked to original sources

PubMed1994

Comparison of systematic search and database methods for constructing segments of protein structure.

Two principal methods of determining the conformation of short pieces of polypeptide backbone in proteins have been developed: using a database of known structures and systematically generating all conformations. In this paper, we compare the effectiveness of these two techniques. The completeness of the database for segments of different lengths is examined and it is found to contain most conformations for segments seven residues long, but to deteriorate rapidly for longer regions. When the database segment is to be incorporated into the rest of a structure, at least seven residues are required to build four new residues, because of the need to position the segment relative to the rest of the structure. It is found that such positioning using flanking residues results in large errors in the inserted region. We conclude that the database method is currently not effective for comparative modeling, even for short segments. The systematic search procedure is found to generate almost all structures of short segments found in proteins. In contrast to the database method, low root mean square error structures are obtained for a set of trial segments embedded in the rest of a protein structure. Thus, it should be considered the method of choice.

Computer Simulation↗

PubMed1993

New jaeschkeanadiol derivatives from Ferula jaeschkeana.

Two new jaeschkeanadiol derivatives have been isolated from Ferula jaeschkeana rhizomes. These have been identified as a dichloro compound, jaeschkenol [1], and 2 alpha,3 alpha-dihydroxy-4-keto-5 alpha-p-hydroxybenzoyl-jaeschkeanadiol [2], on the basis of spectral data and the X-ray analysis of the former.

Coumarins↗

PubMed1990

Structure and molecular mechanics of ferrirhodin.

C41H64FeN9O17.7 1/2H2O, Mr = 1146.0, orthorhombic, P2(1)2(1)2(1), a = 9.740 (7), b = 16.764 (10), c = 32.632 (17) A, V = 5328 (6) A3, Z = 4, D chi = 1.43 g cm-3, Mo K alpha, lambda = 0.71069 A, mu = 3.26 cm-1, F(000) = 2428, T = 138 (2) K, R = 0.0986 for 3543 observed reflections. Ferrirhodin, a ferrichrome siderophore (iron transport agent) was isolated from low-iron cultures of Aspergillus versicolor and A. nidulans. The compound is isomeric with another microbial siderophore, ferrirubin, but is different in having cis, rather than trans, anhydromevalonic acid as acyl groups. The conformation of the molecular backbone and iron coordination geometry compares well with ferrirubin and other ferrichrome structures. The differences between the acyl groups of ferrirubin and ferrirhodin are explored using molecular-mechanics modeling.

Aspergillus↗

PubMed1990

Structure and conformations of two cycloisomeric hexapeptides: cyclo(L-Leu-L-Phe-Gly-D-Phe-L-Leu-Gly-) trihydrate and cyclo(L-Phe-L-Leu-Gly-D-Leu-L-Phe-Gly-) trihydrate.

cyclo(L-Leucyl-L-phenylalanyl-glycyl-D-phenylalanyl-L-leucyl-glycyl-) trihydrate (IV), C34H46N6O6.-3H2O, Mr = 688.8, monoclinic, P2(1), a = 11.720 (2), b = 36.354 (4), c = 8.888 (1) A, beta = 103.88 (1) degree, V = 3676.3 A3, Z = 4, Dx = 1.244 g cm-3, lambda (Cu K alpha) = 1.54178 A, mu = 7.6 cm-1, F(000) = 1480, T = 138 K, final R = 0.052 for 7661 unique reflections. cyclo(L-Phenylalanyl-L-leucyl-glycyl-D-leucyl-L-phenylalanyl-glycyl-) trihydrate (V), C34H46N6O6.-3H2O, Mr = 688.8, triclinic, P1, a = 101.54 (2), b = 19.111 (5), c = 8.527 (1) A, alpha = 101.54 (2), beta = 93.42 (2), gamma = 94.27 (2) degree, V = 1852.4 A3, Z = 2, Dx = 1.235 g cm-3, lambda (Cu K alpha) = 1.54178 A, mu = 7.5 cm-1, F(000) = 740, T = 138 K, final R = 0.063 for 7574 unique reflections. Peptides IV and V both have two independent conformers (molecules A and B). The peptide ring in each case contains one beta (I) turn and one beta (II') turn. A molecules in both structures have two transannular N--H...O hydrogen bonds, while B molecules form only one strong transannular hydrogen bond. The conformational differences between the two independent molecules (A and B) are much larger than the differences between the corresponding molecules of the two structures (A and A, and B and B). The crystal structures of the two peptides are very similar and consist of parallel bands of hydrophobic side chains and polar peptide regions. In each structure, molecules are stacked one over another with the hexapeptide ring lying perpendicular to the axis of the stack. The water molecules form well delimited solvent channels sandwiched between the layers of peptide molecules, and bridge the peptides through extensive hydrogen bonding.

Peptides, Cyclic↗