scholarly journals Computer graphics program to reveal the dependence of the gross three-dimensional structure of the B-DNA double helix on primary structure

1986 ◽  
Vol 14 (1) ◽  
pp. 381-387 ◽  
Author(s):  
Chang-Shung Tung ◽  
Stephen C. Harvey
Keyword(s):  
Computer Graphics ◽  
Primary Structure ◽  
Double Helix ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Dna Double Helix

The structure of CMS2MS2, a mitogenic protein isolated from Carica candamarcensis

2007 ◽  
Vol 388 (8) ◽  
pp. 819-822 ◽  
Author(s):  
Marco Túlio R. Gomes ◽  
Marcelo P. Bemquerer ◽  
Miriam Tereza P. Lopes ◽  
Michael Richardson ◽  
Sergio Oyama Júnior ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Primary Structure ◽  
Three Dimensional ◽  
Catalytic Triad ◽  
Dimensional Structure ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Three Dimensional Structure ◽  
Structural Differences

AbstractIn a recent study we showed that two proteinases (CMS2MS2 and CMS2MS3) fromCarica candamarcensisenhance mammalian cell proliferation. The aim of the present study is the determination of the primary structure of CMS2MS2 and prediction of its three-dimensional structure. The protein contains 214 residues, including the catalytic triad composed of Cys25, His159, and Asn175. A phylogenetic tree analysis demonstrated that CMS2MS2 ranks closer to chymopapain than to papain. The overall predicted three-dimensional structure is similar to proteinases from the papain family. These results suggest that minor structural differences within CMS2MS2 must account for its proliferative action.

Three-dimensional structure model for benzenoid musks expressed by computer graphics

1992 ◽  
Vol 17 (5) ◽  
pp. 573-582 ◽  
Author(s):  
Fumiko Yoshii ◽  
Shuichi Hirono ◽  
Qian Liu ◽  
Ikuo Moriguichi
Keyword(s):  
Computer Graphics ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Structure Model ◽  
Three Dimensional Structure

scholarly journals Intramolecular ionic interactions of lysine residues and a possible folding domain in fructose diphosphate aldolase

1977 ◽  
Vol 161 (1) ◽  
pp. 63-71 ◽  
Author(s):  
J M Lambert ◽  
R N Perham ◽  
J R Coggins
Keyword(s):  
Primary Structure ◽  
Protein Structures ◽  
Three Dimensional ◽  
Native Enzyme ◽  
Dimensional Structure ◽  
Ionic Interactions ◽  
Rabbit Muscle ◽  
Amino Groups ◽  
Three Dimensional Structure ◽  
Lysine Residues

1. Treatment with methyl acetimidate was used to probe the topography of the tetrameric fructose 1,6-diphosphate aldolase from ox liver. A single treatment with imido ester in the presence or absence of 20mM-fructose 1,6-diphosphate caused the number of amino groups in the enzyme to fall to approx. 30% of the starting number (assumed to be 30 per subunit). The catalytic activity of the aldolase modified in the presence of fructose 1,6-diphosphate was unaffected, whereas that of the enzyme modified in the absence of substrate fell by about 20%. 2. Use of methyl [1-14C]acetimidate and small-scale methods of protein chemistry showed that the amino group of lysine-27 (the numbering is that of the highly homologous rabbit muscle enzyme) is essentially unavailable for amidination in the native enzyme and is therefore predicted to be buried in a hydrophobic environment, probably in the form of an ion-pair with a negatively charged side-chain carboxyl group. All the other lysine residues that reacted poorly with methyl acetimidate in the native enzyme (a total of 7) were found to be within the primary structure bounded by lysine-107 and lysine-227. An important member of this group of lysine residues displaying aberrant reactivity is lysine-227, which is known to form an imine with the substrate as part of the catalytic mechanism of the enzyme. 3. The results of the amidination experiments can be correlated in an interesting way with previous studies of thiol-group modification in the aldolases. Taken together, and arguing in part by analogy with the results of identical experiments with glyceraldehyde 3-phosphate dehydrogenases where the three-dimensional structure is known [Lambert & Perham (1977) Biochem. 4. 161. 49-62], they suggest that the region of primary structure from residues 107-227 may form the whole or part of a three-dimensional structural feature, perhaps a folding domain. A three-dimensional structure deduced from X-ray-crystallographic analysis will be needed to interpret these findings more closely. 4. The amino groups of lysine residues are commonly thought to reside at the ‘surface’ of protein structures. The patterns of specific lysine residues in glyceraldehyde 3-phosphate dehydrogenases and in aldolases that have been found to react poorly with methyl acetimidate in the native enzymes can be attributed to intramolecular ionic interactions deep in hydrophobic pockets and at the protein ‘surface’. Such ionic interactions may contribute significantly to the stability of a given protein.

The Three-dimensional structure of frozen-hydrated nudaurelia capensis β virus

1987 ◽  
Vol 45 ◽  
pp. 650-651
Author(s):  
N. H. Olson ◽  
T. S. Baker ◽  
Wu Bo Mu ◽  
J. E. Johnson ◽  
D. A. Hendry
Keyword(s):  
South African ◽  
Rna Virus ◽  
Carbon Film ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Electron Dose ◽  
Total Electron ◽  
Three Dimensional Structure ◽  
Negative Stain ◽  
Dimensional Reconstruction

Nudaurelia capensis β virus (NβV) is an RNA virus of the South African Pine Emperor moth, Nudaurelia cytherea capensis (Lepidoptera: Saturniidae). The NβV capsid is a T = 4 icosahedron that contains 60T = 240 subunits of the coat protein (Mr = 61,000). A three-dimensional reconstruction of the NβV capsid was previously computed from visions embedded in negative stain suspended over holes in a carbon film. We have re-examined the three-dimensional structure of NβV, using cryo-microscopy to examine the native, unstained structure of the virion and to provide a initial phasing model for high-resolution x-ray crystallographic studiesNβV was purified and prepared for cryo-microscopy as described. Micrographs were recorded ∼1 - 2 μm underfocus at a magnification of 49,000X with a total electron dose of about 1800 e-/nm2.

Three Dimensional structure and organization of diploid chromosomes by optical section microscopy

1987 ◽  
Vol 45 ◽  
pp. 633-635
Author(s):  
David A. Agard ◽  
Yasushi Hiraoka ◽  
John W. Sedat
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Developmental State ◽  
Mitotic Cell ◽  
Biological Properties ◽  
Dimensional Structure ◽  
Specific Gene ◽  
Three Dimensional Structure ◽  
Complementary Techniques ◽  
Dynamic Structures

In an effort to understand the complex relationship between structure and biological function within the nucleus, we have embarked on a program to examine the three-dimensional structure and organization of Drosophila melanogaster embryonic chromosomes. Our overall goal is to determine how DNA and proteins are organized into complex and highly dynamic structures (chromosomes) and how these chromosomes are arranged in three dimensional space within the cell nucleus. Futher, we hope to be able to correlate structual data with such fundamental biological properties as stage in the mitotic cell cycle, developmental state and transcription at specific gene loci.Towards this end, we have been developing methodologies for the three-dimensional analysis of non-crystalline biological specimens using optical and electron microscopy. We feel that the combination of these two complementary techniques allows an unprecedented look at the structural organization of cellular components ranging in size from 100A to 100 microns.

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