scholarly journals ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years

2020 ◽  
Vol 49 (D1) ◽  
pp. D420-D424
Author(s):  
Rahul Nikam ◽  
A Kulandaisamy ◽  
K Harini ◽  
Divya Sharma ◽  
M Michael Gromiha
Keyword(s):  
Heat Capacity ◽  
Experimental Methods ◽  
Enthalpy Change ◽  
Thermodynamic Database ◽  
Heat Capacity Change ◽  
Graphical Interface ◽  
Current Version ◽  
Literature Information ◽  
Sequence Structure ◽  
Capacity Change

Abstract ProThermDB is an updated version of the thermodynamic database for proteins and mutants (ProTherm), which has ∼31 500 data on protein stability, an increase of 84% from the previous version. It contains several thermodynamic parameters such as melting temperature, free energy obtained with thermal and denaturant denaturation, enthalpy change and heat capacity change along with experimental methods and conditions, sequence, structure and literature information. Besides, the current version of the database includes about 120 000 thermodynamic data obtained for different organisms and cell lines, which are determined by recent high throughput proteomics techniques using whole-cell approaches. In addition, we provided a graphical interface for visualization of mutations at sequence and structure levels. ProThermDB is cross-linked with other relevant databases, PDB, UniProt, PubMed etc. It is freely available at https://web.iitm.ac.in/bioinfo2/prothermdb/index.html without any login requirements. It is implemented in Python, HTML and JavaScript, and supports the latest versions of major browsers, such as Firefox, Chrome and Safari.

scholarly journals Heat capacity change for ribonuclease A folding

1999 ◽  
Vol 8 (7) ◽  
pp. 1500-1504 ◽  
Author(s):  
C. Nick Pace ◽  
Gerald R. Grimsley ◽  
Susan T. Thomas ◽  
George I. Makhatadze
Keyword(s):  
Heat Capacity ◽  
Ribonuclease A ◽  
Heat Capacity Change ◽  
Capacity Change

scholarly journals Temperature control technology by heat capacity change upon lock and key binding

2010 ◽  
Vol 375 (2) ◽  
pp. 165-169 ◽  
Author(s):  
Ken-ichi Amano ◽  
Daisuke Miyazaki ◽  
Liew Fong Fong ◽  
Paul Hilscher ◽  
Taro Sonobe
Keyword(s):  
Heat Capacity ◽  
Temperature Control ◽  
Heat Capacity Change ◽  
Control Technology ◽  
Capacity Change

scholarly journals Thermodynamics of DNA: heat capacity changes on duplex unfolding

2019 ◽  
Vol 48 (8) ◽  
pp. 773-779 ◽  
Author(s):  
Anatoliy Dragan ◽  
Peter Privalov ◽  
Colyn Crane-Robinson
Keyword(s):  
Heat Capacity ◽  
Accessible Surface Area ◽  
Solvent Accessible Surface Area ◽  
Polar Component ◽  
Heat Capacity Change ◽  
Dna Duplex ◽  
Capacity Change ◽  
Heat Capacity Changes ◽  
Accessible Surface ◽  
Lower Magnitude

Abstract The heat capacity change, ΔCp, accompanying the folding/unfolding of macromolecules reflects their changing state of hydration. Thermal denaturation of the DNA duplex is characterized by an increase in ΔCp but of much lower magnitude than observed for proteins. To understand this difference, the changes in solvent accessible surface area (ΔASA) have been determined for unfolding the B-form DNA duplex into disordered single strands. These showed that the polar component represents ~ 55% of the total increase in ASA, in contrast to globular proteins of similar molecular weight for which the polar component is only about 1/3rd of the total. As the exposure of polar surface results in a decrease of ΔCp, this explains the much reduced heat capacity increase observed for DNA and emphasizes the enhanced role of polar interactions in maintaining duplex structure. Appreciation of a non-zero ΔCp for DNA has important consequences for the calculation of duplex melting temperatures (Tm). A modified approach to Tm prediction is required and comparison is made of current methods with an alternative protocol.

Heat capacity change on isothermal vitrification during a macromolecule's growth

1993 ◽  
Vol 201 (1-3) ◽  
pp. 95-100 ◽  
Author(s):  
M. Cassettari ◽  
G. Salvetti ◽  
E. Tombari ◽  
S. Veronesi ◽  
G.P. Johari
Keyword(s):  
Heat Capacity ◽  
Heat Capacity Change ◽  
Capacity Change

scholarly journals Glucosylation of β-lactoglobulin lowers the heat capacity change of unfolding; a unique way to affect protein thermodynamics

2005 ◽  
Vol 14 (8) ◽  
pp. 2187-2194 ◽  
Author(s):  
Annemarie M.M. Van Teeffelen ◽  
Kerensa Broersen ◽  
Harmen H.J. de Jongh
Keyword(s):  
Heat Capacity ◽  
Heat Capacity Change ◽  
Protein Thermodynamics ◽  
Capacity Change ◽  
Β Lactoglobulin

Aqueous Solutions of Nonpolar Compounds. Heat-Capacity Effects

1972 ◽  
Vol 50 (2) ◽  
pp. 133-138 ◽  
Author(s):  
R. D. Wauchope ◽  
R. Haque
Keyword(s):  
Heat Capacity ◽  
Temperature Coefficient ◽  
Solution Process ◽  
Positive Temperature Coefficient ◽  
Heat Capacity Change ◽  
Positive Temperature ◽  
Capacity Change ◽  
Heat Capacity Changes ◽  
Nonpolar Compounds ◽  
Better Than

The method of Clarke and Glew has been used to obtain estimates of the precision of measurement of the thermodynamic functions for the solution of hydrocarbons, the noble gases, and inert diatomic gases in water. In some cases, the precision of the data is such that a statistically significant value for the temperature coefficient of the heat-capacity change for the solution process is obtained. Comparison with the theory of Nemethy and Scheraga shows that their calculations of heat-capacity changes at 25 °C are better than previously believed, but that their prediction of a positive temperature coefficient for this quantity is in contradiction with most data.

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