Phonon-like excitation in secondary and tertiary structure of hydrated protein powders

Soft Matter ◽  
2011 ◽  
Vol 7 (21) ◽  
pp. 9848 ◽  
Author(s):  
Mingda Li ◽  
Xiang-qiang Chu ◽  
Emiliano Fratini ◽  
Piero Baglioni ◽  
Ahmet Alatas ◽  
...  
Keyword(s):  
Tertiary Structure ◽  
Hydrated Protein ◽  
Secondary And Tertiary Structure

Quantitative determination of the number of secondary and tertiary structure base pairs in transfer RNA in solution

Biochemistry ◽  
1976 ◽  
Vol 15 (20) ◽  
pp. 4370-4377 ◽  
Author(s):  
P. H. Bolton ◽  
C. R. Jones ◽  
D. Bastedo-Lerner ◽  
K. L. Wong ◽  
D. R. Kearns
Keyword(s):  
Quantitative Determination ◽  
Tertiary Structure ◽  
Transfer Rna ◽  
Base Pairs ◽  
Secondary And Tertiary Structure

scholarly journals The effects of Ca2+ and Cd2+ on the secondary and tertiary structure of bovine testis calmodulin. A circular-dichroism study

1986 ◽  
Vol 238 (2) ◽  
pp. 485-490 ◽  
Author(s):  
S R Martin ◽  
P M Bayley
Keyword(s):  
Circular Dichroism ◽  
Conformational Changes ◽  
Metal Ion ◽  
Tertiary Structure ◽  
Thermal Unfolding ◽  
Apparent Effect ◽  
Thermally Induced ◽  
Circular Dichroïsm ◽  
Secondary And Tertiary Structure

Near-u.v. and far-u.v. c.d. spectra of bovine testis calmodulin and its tryptic fragments (TR1C, N-terminal half, residues 1-77, and TR2C, C-terminal half, residues 78-148) were recorded in metal-ion-free buffer and in the presence of saturating concentrations of Ca2+ or Cd2+ under a range of different solvent conditions. The results show the following: if there is any interaction between the N-terminal and C-terminal halves of calmodulin, it has not apparent effect on the secondary or tertiary structure of either half; the conformational changes induced by Ca2+ or Cd2+ are substantially greater in TR2C than they are in TR1C; the presence of Ca2+ or Cd2+ confers considerable stability with respect to urea-induced denaturation, both for the whole molecule and for either of the tryptic fragments; a thermally induced transition occurs in whole calmodulin at temperatures substantially below the temperature of major thermal unfolding, both in the presence and in the absence of added metal ion; the effects of Cd2+ are identical with those of Ca2+ under all conditions studied.

scholarly journals Digital dissection of arsenate reductase enzyme from an arsenic hyperccumulating fern Pteris vittata

2016 ◽  
Author(s):  
Zarrin Basharat ◽  
Deeba Noreen Baig ◽  
Azra Yasmin
Keyword(s):  
Neural Network ◽  
Active Site ◽  
Tertiary Structure ◽  
Pteris Vittata ◽  
Arsenate Reductase ◽  
Dynamics Simulation ◽  
Reduction Mechanism ◽  
Arsenic Reduction ◽  
Secondary And Tertiary Structure ◽  
Active Site Region

Action of arsenate reductase is crucial for the survival of an organism in arsenic polluted area. Pteris vittata, also known as Chinese ladder brake, was the first identified arsenic hyperaccumulating fern with the capability to convert [As(V)] to arsenite [As(III)]. This study aims at sequence analysis of the most important protein of the arsenic reduction mechanism in this specie. Phosphorylation potential of the protein along with possible interplay of phosphorylation with O-β-GlcNAcylation was predicted using neural network based webservers. Secondary and tertiary structure of arsenate reductase was then analysed. Active site region of the protein comprised a rhodanese-like domain. Cursory dynamics simulation revealed that folds remained conserved in the rhodanese main but variations were observed in the structure in other regions. This information sheds light on the various characteristics of the protein and may be useful to enzymologists working on the improvement of its traits for arsenic reduction.

RNA Structure Analysis: A Multifaceted Approach

1999 ◽  
Author(s):  
Bruce A. Shapiro ◽  
Wojciech Kasprzak
Keyword(s):  
Nucleic Acid ◽  
Secondary Structure ◽  
Tertiary Structure ◽  
Hammerhead Ribozyme ◽  
3D Structure ◽  
Computer Prediction ◽  
Rna Molecules ◽  
Tertiary Interactions ◽  
The One ◽  
Secondary And Tertiary Structure

Genomic information (nucleic acid and amino acid sequences) completely determines the characteristics of the nucleic acid and protein molecules that express a living organism’s function. One of the greatest challenges in which computation is playing a role is the prediction of higher order structure from the one-dimensional sequence of genes. Rules for determining macromolecule folding have been continually evolving. Specifically in the case of RNA (ribonucleic acid) there are rules and computer algorithms/systems (see below) that partially predict and can help analyze the secondary and tertiary interactions of distant parts of the polymer chain. These successes are very important for determining the structural and functional characteristics of RNA in disease processes and hi the cell life cycle. It has been shown that molecules with the same function have the potential to fold into similar structures though they might differ in their primary sequences. This fact also illustrates the importance of secondary and tertiary structure in relation to function. Examples of such constancy in secondary structure exist in transfer RNAs (tRNAs), 5s RNAs, 16s RNAs, viroid RNAs, and portions of retroviruses such as HIV. The secondary and tertiary structure of tRNA Phe (Kim et al., 1974), of a hammerhead ribozyme (Pley et al., 1994), and of Tetrahymena (Cate et al., 1996a, 1996b) have been shown by their crystal structure. Currently little is known of tertiary interactions, but studies on tRNA indicate these are weaker than secondary structure interactions (Riesner and Romer, 1973; Crothers and Cole, 1978; Jaeger et al., 1989b). It is very difficult to crystallize and/or get nuclear magnetic resonance spectrum data for large RNA molecules. Therefore, a logical place to start in determining the 3D structure of RNA is computer prediction of the secondary structure. The sequence (primary structure) of an RNA molecule is relatively easy to produce. Because experimental methods for determining RNA secondary and tertiary structure (when the primary sequence folds back on itself and forms base pairs) have not kept pace with the rapid discovery of RNA molecules and their function, use of and methods for computer prediction of secondary and tertiary structures have increasingly been developed.

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