Sign convention for free energy change
In ProTherm, dG is defined as the Free Energy of Unfolding. The Free Energy Difference, ddG/ddGH2O, in either thermal or denaturant denaturation, is defined as dG(mutant) - dG(wild). Thus, if the sign is negative it indicates that the mutation destabilizes the protein whereas the positive sign corresponds to the stabilization by the mutation. Similarly, the difference of transition temperature, dTm, is defined as Tm(mutant) - Tm(wild). We try to keep the sign of free energy change uniform according to our definition. However, because some authors define ddG as dG(wild) - dG(mutant), mistakes in the sign can occur during the data input. We selected a set of data from our database which contain more than half with negative signs from the same article as we suspected them as possible errors in signs. It was from 122 articles, which we cross-checked with the database again and found the signs are correct according to our definition. However, users are advised to take adequate precautions when they use these data for their analyses as we could not cross-check whole database with corresponding original articles (February 2007).
E.Coli as Source
Many researchers use E.Coli as a vehicle to express proteins. Sometimes, the descriptions in papers are not clear whether E.Coli is the Source of proteins or used for expression. We try to trace the original Source for each protein, but E.Coli may be taken by mistake as the Source, if the original Sources are not written in the paper. We are checking those entries containing E.Coli in Source again, and we will put "unknown" if the original Source cannot be identified.
In our checking, we found that the E.coli was entered as a source for some entries by mistake and we corrected it now. These entries are 6732,6733,6736 and 6737. The correct sources are Sufolobus acidocaldarius for the entries 6732 and 6736 and Thermus thermophilus for the entries 6733 and 6737.
Two kinds of temperatures in experimental data.
Experimental data from thermal denaturation experiment could contain two kinds of temperatures: (1) transition temperature (Tm); and (2) the temperature (T) at which thermodynamic quantities such as unfolding free energy (dG), unfolding free-energy change due to mutation (ddG) and sometimes unfolding enthalpy change (dH) were calculated. These thermodynamic quantities are mostly extrapolated at room temperature or at Tm of wild type protein. dH is usually given at Tm of wild type or mutant. So far, we have placed all the temperatures at Tm column without distinguishing T from Tm for thermal denaturation experiments. If only dG/ddG is given, the temperature is supposed to corresponds to T. Otherwise, the temperature refers to Tm and the temperature (T) at which dG/ddG was calculated is given as Remark. But, it is not always the case. We are in the process of separating the dG/ddG and Tm data as different entries, and T and Tm will then be correctly distinguished for such entries.
This problem already rectified on 9 Dec. 2002. Please see What's new
Significant decimal points in energy unit conversion.
The unit of energy is either in cal or Joule, and we enter the data with the same unit as in the literature. However, the unit is unified to cal when they are entered into the database by a conversion factor 4.184. We keep the original number of decimal digit in entered data but this information is lost in the SYBASE data table. When these values are displayed in the list page after search, they appear with fixed decimal points (two decimal digits), which may be different from the original ones. However, correct decimal digits are shown in the entry page. If you are taking the values from list page, please be aware of this problem.
Lack of some experimental information.
ProTherm was started as a private database for our research purpose. At that time we did not put much effort on extracting detailed information from literature. During the development of ProTherm, we added new items in different stages, and hence the amount of information content may not be uniform among different entries. Due to this fact, some entries(especially earlier entries) lack certain experimental information necessary to interpret the data. In order to overcome this problem, we continue to add that necessary information in Remark section if it is missing.
Duplication of data.
Some papers include, for the purpose of comparison, experimental data in tables, which are the repetition of the previous work. If they mention that the data are derived from the previous work, we usually check if the data are already in ProTherm. However, the duplication may still occur by incomplete checking or if the authors did not mention that in the paper. We are checking the papers and ProTherm data again to remove such duplicated entries.
ProTherm database is a non-profit service to the scientific community. We have tried to provide accurate and up-to-date information. However, we make no warranty that the information contained is accurate or complete. Our responsibility is limited to applying best efforts in providing good programs and data. We have no responsibility for any damage resulting from the use of this database.