scholarly journals Denaturation of RNA Secondary and Tertiary Structure by Urea: Simple Unfolded State Models and Free Energy Parameters Account for Measured m-Values

Biochemistry ◽  
2012 ◽  
Vol 51 (44) ◽  
pp. 9014-9026 ◽  
Author(s):  
Dominic Lambert ◽  
David E. Draper
Keyword(s):  
Free Energy ◽  
Tertiary Structure ◽  
Energy Parameters ◽  
Unfolded State ◽  
State Models ◽  
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 High stability of trehalose/maltose binding protein fromThermococcus litoralismakes it a good candidate as a sensitive element in biosensor systems for sugar control

2010 ◽  
Vol 24 (3-4) ◽  
pp. 349-353 ◽  
Author(s):  
Olga I. Povarova ◽  
Olga V. Stepanenko ◽  
Anna I. Sulatskaya ◽  
Irina M. Kuznetsova ◽  
Konstantin K. Turoverov ◽  
...  
Keyword(s):  
Free Energy ◽  
Sensitive Element ◽  
High Stability ◽  
Binding Protein ◽  
Maltose Binding Protein ◽  
Thermococcus Litoralis ◽  
Thermophilic Archaeon ◽  
Unfolded State ◽  
The Stability ◽  
Innate Ability

Fluorescence and circular dichroism in far-UV region were used to study the stability of trehalose/maltose binding protein (TMBP) from hyper thermophilic archaeonThermococcus litoralisand its complex with glucose (TMBP/Glc). The evaluation of difference between free energy of native and unfolded state for TMBP and TMBP/Glc showed that both of them are several times higher than that of proteins from mesophilic organisms. Due to the high stability and innate ability to bind glucose this protein is a good candidate as a sensitive element in biosensor systems for sugar control.

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 Thermal versus Mechanical Unfolding in a Model Protein

2019 ◽  
Author(s):  
Rafael Tapia-Rojo ◽  
Juan J. Mazo ◽  
Fernando Falo
Keyword(s):  
Free Energy ◽  
Force Spectroscopy ◽  
Reaction Coordinate ◽  
Force Extension ◽  
Thermal Dynamics ◽  
Zero Force ◽  
Protein Model ◽  
Model Protein ◽  
State Models ◽  
Competing Pathways

Force spectroscopy techniques are often used to learn about the free energy landscape of single biomolecules, typically by recovering free energy quantities that, extrapolated to zero force, are compared to those measured in bulk experiments. However, it is not always clear how the information obtained from a mechanically perturbed system can be related to that obtained using other denaturants, since tensioned molecules unfold and refold along a reaction coordinate imposed by the force, which is unlikely meaningful in its absence. Here, we explore this dichotomy by investigating the unfolding landscape of a model protein, which is first unfolded mechanically through typical force spectroscopy-like protocols, and next thermally. When unfolded by non-equilibrium force extension and constant force protocols, we recover a simple two-barrier landscape, as the protein reaches the extended conformation through a metastable intermediate. Interestingly, folding-unfolding equilibrium simulations at low forces suggested a totally different scenario, where this metastable state plays little role in the unfolding mechanism, and the protein unfolds through two competing pathways27. Finally, we use Markov state models to describe the configurational space of the unperturbed protein close to the critical temperature. The thermal dynamics is well understood by a one-dimensional landscape along an appropriate reaction coordinate, however very different from the mechanical picture. In this sense, in our protein model the mechanical and thermal descriptions provide incompatible views of the folding/unfolding landscape of the system, and the estimated quantities to zero force result hard to interpret.

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.

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