Fractal Analysis of Tertiary Structure of Protein Molecule

1984 ◽  
Vol 53 (6) ◽  
pp. 2162-2171 ◽  
Author(s):  
Yoshinori Isogai ◽  
Toshiyuki Itoh
Keyword(s):  
Fractal Analysis ◽  
Tertiary Structure ◽  
Protein Molecule

scholarly journals An examination of the utility of photogenerated reagents by using α-chymotrypsin

1974 ◽  
Vol 143 (3) ◽  
pp. 663-668 ◽  
Author(s):  
Alex J. Bridges ◽  
Jeremy R. Knowles
Keyword(s):  
Tertiary Structure ◽  
Protein Molecule ◽  
Aryl Azide ◽  
Tryptic Fragment ◽  
High Degree ◽  
Nitrophenyl Ester ◽  
Labelling Method ◽  
Binding Locus ◽  
Covalently Bound

As a test of the labelling characteristics of photogenerated reagents, an aryl azide was photolysed in the aromatic-binding locus of a protein of known tertiary structure. The acyl-enzyme derived from the reaction of α-chymotrypsin with the p-nitrophenyl ester of p-azido[14C]cinnamate was isolated and photolysed. About 60% of the acyl group is covalently bound to the protein after photolysis and deacylation, and labelled enzyme is inactive. The covalently attached label is localized in the C chain of chymotrypsin, and there are firm indications that the major labelled tryptic fragment of the C chain is that which constitutes the aromatic-binding locus of the enzyme. The high degree of labelling of that portion of the protein molecule predicted on the basis of the known chemistry and structure of α-chymotrypsin, provides gratifying confirmation of the utility of the photo-labelling method.

Plasticity, Hydration and Accessibility in Ribonuclease A. The Structure of a New Crystal Form and its Low-Humidity Variant

1998 ◽  
Vol 54 (6) ◽  
pp. 1343-1352 ◽  
Author(s):  
C. Sadasivan ◽  
H. G. Nagendra ◽  
M. Vijayan
Keyword(s):  
Surface Area ◽  
Tertiary Structure ◽  
Detailed Comparison ◽  
Protein Molecule ◽  
Accessible Surface Area ◽  
Crystal Form ◽  
Ribonuclease A ◽  
Probe Radius ◽  
Low Humidity ◽  
Accessible Surface

The structures of a new crystal form of ribonuclease A and its low-humidity variant, each containing two crystallographically independent molecules, have been determined and refined. A detailed comparison of these structures with those of the other known crystal forms of the enzyme, which have different packing arrangements and solvent composition, leads to a meaningful delineation of the rigid and flexible regions of the protein molecule and the nature of its plasticity. Many of the water molecules which are common to all the structures are involved in bridging different regions of the protein molecule, thus emphasizing the role of water in stabilizing the tertiary structure. The analysis of the structures shows that for a given N or O atom, the level of hydration increases with accessible surface area, but levels off at an area of about 10 Å2. Generally, the hydration level tends to drop when the area increases beyond about 20 Å2. This drop correlates with an increase in the displacement parameter. The analysis also suggests that the van der Waals radii and probe radius normally used in accessible surface area calculations are not appropriate for dealing with all situations.

Cloning and Prokaryotic Expression and Structure Prediction of Prx II the Differentially Expressed Gene under AFB1 Stress

2011 ◽  
Vol 236-238 ◽  
pp. 1078-1082
Author(s):  
Zhen Hong Zhuang ◽  
Feng Zhang ◽  
Yan Yun Li ◽  
Jun Yuan ◽  
Yan Ling Yang ◽  
...  
Keyword(s):  
Signal Peptide ◽  
Prokaryotic Expression ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Differentially Expressed Gene ◽  
Protein Molecule ◽  
Helix 69 ◽  
Prokaryotic Expression Vector ◽  
Mice Liver ◽  
Α Helix

The gene, prx II, in mice liver was found to be up-regulated under the stress of AFB1 in our previous study. In this study, the total RNA from the mice liver was extracted, and followed by the synthesis of cDNA with the RNA as template by the method of reverse transcription. Then, prx II gene fragment was amplified by PCR with the cDNA as template. After double-digestion and ligation reaction, the prokaryotic expression vector pET28a (+)-prx II was successfully constructed and was transformed into E. coli BL21 (DE3). The protein- Prx II was successfully expressed when induced byIPTG, and finally, Prx II was purified by Ni2+-NTA affinity chromatography. The molecule structure of Prx II, including its signal peptide, hydrophobicity, and its secondary and tertiary structure, was predicted by bioinformatics analysis. The results showed that no signal peptide was predicted in the molecule of Prx II; Five hydrohpobic domains were predicted in the protein molecule, and the average predictive value for its hydrophobicity was -0.151; There were 35% α-helix (69 residues) and 21% β-pleated sheet (42 residues) in the molecule; The tertiary structure of the protein was constituted by seven α-helices and seven β-pleated sheets.

The stereochemical code and the logic of a protein molecule

1969 ◽  
Vol 2 (1) ◽  
pp. 65-92 ◽  
Author(s):  
A. M. Liquori
Keyword(s):  
Tertiary Structure ◽  
Polypeptide Chain ◽  
Water Solution ◽  
Storage System ◽  
Three Dimensional ◽  
Protein Molecule ◽  
Information Storage ◽  
Chemical Information ◽  
Amino Acid Residues ◽  
Surrounding Water

Like DNA and the various forms of RNA, a protein molecule is an information storage system. It contains in fact one or more polypeptide chains which may be regarded as linear sequences of twenty different types of monomer units. It is now clearly established that the chemical information corresponding to a given sequence of a polypeptide chain, containing n amino acid residues, is stored in a segment of one of the two strands of DNA containing 3n nucleotides. The transfer of such information from a gene to a polypeptide chain takes place according to the well-known process involving a transcription and a chemical translation step. This last step leads to a polymer which, in appropriate conditions, takes a three-dimensional conformation or tertiary structure which should correspond to a free-energy minimum of the molecule and its surrounding water solution.

Torus Circumference and Thickness Parameters From a Linear DNA Size Series Suggest How Toruses Self-Assemble

1985 ◽  
Vol 43 ◽  
pp. 522-523
Author(s):  
George C. Ruben ◽  
Kenneth A. Marx
Keyword(s):  
Tertiary Structure ◽  
Dna Complexes ◽  
Tertiary Structures ◽  
Self Assembling ◽  
Double Stranded Dna ◽  
Calf Thymus ◽  
Dna Organization ◽  
Condensed Dna ◽  
Dna Size

Certain double stranded DNA bacteriophage and viruses are thought to have their DNA organized into large torus shaped structures. Morphologically, these poorly understood biological DNA tertiary structures resemble spermidine-condensed DNA complexes formed in vitro in the total absence of other macromolecules normally synthesized by the pathogens for the purpose of their own DNA packaging. Therefore, we have studied the tertiary structure of these self-assembling torus shaped spermidine- DNA complexes in a series of reports. Using freeze-etch, low Pt-C metal (10-15Å) replicas, we have visualized the microscopic DNA organization of both calf Thymus( CT) and linear 0X-174 RFII DNA toruses. In these structures DNA is circumferentially wound, continuously, around the torus into a semi-crystalline, hexagonal packed array of parallel DNA helix sections.

Heterogeneity of Cerebral Blood Flow: a Fractal Approach

2000 ◽  
Vol 39 (02) ◽  
pp. 37-42 ◽  
Author(s):  
P. Hartikainen ◽  
J. T. Kuikka
Keyword(s):  
Blood Flow ◽  
Cerebral Blood Flow ◽  
Fractal Dimension ◽  
Frontal Lobe ◽  
Fractal Analysis ◽  
Relative Dispersion ◽  
Emission Computed Tomography ◽  
Brain Blood Flow ◽  
Healthy Controls ◽  
Fractal Approach

Summary Aim: We demonstrate the heterogeneity of regional cerebral blood flow using a fractal approach and singlephoton emission computed tomography (SPECT). Method: Tc-99m-labelled ethylcysteine dimer was injected intravenously in 10 healthy controls and in 10 patients with dementia of frontal lobe type. The head was imaged with a gamma camera and transaxial, sagittal and coronal slices were reconstructed. Two hundred fifty-six symmetrical regions of interest (ROIs) were drawn onto each hemisphere of functioning brain matter. Fractal analysis was used to examine the spatial heterogeneity of blood flow as a function of the number of ROIs. Results: Relative dispersion (= coefficient of variation of the regional flows) was fractal-like in healthy subjects and could be characterized by a fractal dimension of 1.17 ± 0.05 (mean ± SD) for the left hemisphere and 1.15 ± 0.04 for the right hemisphere, respectively. The fractal dimension of 1.0 reflects completely homogeneous blood flow and 1.5 indicates a random blood flow distribution. Patients with dementia of frontal lobe type had a significantly lower fractal dimension of 1.04 ± 0.03 than in healthy controls. Conclusion: Within the limits of spatial resolution of SPECT, the heterogeneity of brain blood flow is well characterized by a fractal dimension. Fractal analysis may help brain scientists to assess age-, sex- and laterality-related anatomic and physiological changes of brain blood flow and possibly to improve precision of diagnostic information available for patient care.

Air Pollution Attributable Deaths: A Global View Through Fractal Analysis

2014 ◽  
Vol 2 (1) ◽  
pp. 149-162
Author(s):  
Melvin de Castro ◽  
◽  
Tonette Villanueva ◽  
Grace Arcamo ◽  
Rayna Lynn de Castro ◽  
...  
Keyword(s):  
Air Pollution ◽  
Fractal Analysis ◽  
Global View

Structure characterization of ground calcium carbonate flocs by fractal analysis and their effects on handsheet properties

TAPPI Journal ◽  
2013 ◽  
Vol 12 (3) ◽  
pp. 17-23 ◽  
Author(s):  
WANHEE IM ◽  
HAK LAE LEE ◽  
HYE JUNG YOUN ◽  
DONGIL SEO
Keyword(s):  
Fractal Analysis ◽  
Structural Characteristics ◽  
Fractal Dimensions ◽  
Strength Loss ◽  
Structure Characterization ◽  
Uniform Size ◽  
Cross Sectional ◽  
Floc Size ◽  
Mass Fractal ◽  
Handsheet Properties

Preflocculation of filler particles before their addition to pulp stock provides the most viable and practical solution to increase filler content while minimizing strength loss. The characteristics of filler flocs, such as floc size and structure, have a strong influence on preflocculation efficiency. The influence of flocculant systems on the structural characteristics of filler flocs was examined using a mass fractal analysis method. Mass fractal dimensions of filler flocs under high shear conditions were obtained using light diffraction spectroscopy for three different flocculants. A single polymer (C-PAM), a dual cationic polymer (p-DADMAC/C-PAM) and a C-PAM/micropolymer system were used as flocculants, and their effects on handsheet properties were investigated. The C-PAM/micropolymer system gave the greatest improvement in tensile index. The mass fractal analysis showed that this can be attributed to the formation of highly dense and spherical flocs by this flocculant. A cross-sectional analysis of the handsheets showed that filler flocs with more uniform size were formed when a C-PAM/micropolymer was used. The results suggest that a better understanding of the characteristics of preflocculated fillers and their influence on the properties of paper can be gained based on a fractal analysis.

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