AUTHOR=Ahmad Faizan 

TITLE=Protein stability [determination] problems

JOURNAL=Frontiers in Molecular Biosciences

VOLUME=9

YEAR=2022

URL=https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2022.880358

DOI=10.3389/fmolb.2022.880358

ISSN=2296-889X

ABSTRACT=<p>Human health depends on the correct folding of proteins, for misfolding and aggregation lead to diseases. An unfolded (denatured) protein can refold to its original folded state. How does this occur is known as the protein folding problem. One of several related questions to this problem is that how much more stable is the folded state than the unfolded state. There are several measures of protein stability. In this article, protein stability is given a thermodynamic definition and is measured by Gibbs free energy change (<inline-formula id="inf1"><mml:math id="m1" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi mathvariant="italic">Δ</mml:mi><mml:msubsup><mml:mi>G</mml:mi><mml:mi mathvariant="normal">D</mml:mi><mml:mi mathvariant="normal">0</mml:mi></mml:msubsup></mml:mrow></mml:math></inline-formula>) associated with the equilibrium, native (N) conformation ↔ denatured (D) conformation under the physiological condition usually taken as dilute buffer (or water) at 25 °C. We show that this thermodynamic quantity (<inline-formula id="inf2"><mml:math id="m2" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi mathvariant="italic">Δ</mml:mi><mml:msubsup><mml:mi>G</mml:mi><mml:mi mathvariant="normal">D</mml:mi><mml:mi mathvariant="normal">0</mml:mi></mml:msubsup></mml:mrow></mml:math></inline-formula>), where subscript D represents transition between N and D states, and superscript 0 (zero) represents the fact that the transition occurs in the absence of denaturant, can be neither measured nor predicted under physiological conditions. However, <inline-formula id="inf3"><mml:math id="m3" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi mathvariant="italic">Δ</mml:mi><mml:msub><mml:mi>G</mml:mi><mml:mi mathvariant="normal">D</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> can be measured in the presence of strong chemical denaturants such as guanidinium chloride and urea which are shown to destroy all noncovalent interactions responsible for maintaining the folded structure. A problem with this measurement is that the estimate of <inline-formula id="inf4"><mml:math id="m4" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi mathvariant="italic">Δ</mml:mi><mml:msubsup><mml:mi>G</mml:mi><mml:mi mathvariant="normal">D</mml:mi><mml:mi mathvariant="normal">0</mml:mi></mml:msubsup></mml:mrow></mml:math></inline-formula> comes from the analysis of the plot of <inline-formula id="inf5"><mml:math id="m5" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi mathvariant="italic">Δ</mml:mi><mml:msub><mml:mi>G</mml:mi><mml:mi mathvariant="normal">D</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula><italic>versus</italic> denaturant concentration, which requires a long extrapolation of values of <inline-formula id="inf6"><mml:math id="m6" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi mathvariant="italic">Δ</mml:mi><mml:msub><mml:mi>G</mml:mi><mml:mi mathvariant="normal">D</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, and all the three methods of extrapolation give three different values of <inline-formula id="inf7"><mml:math id="m7" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi mathvariant="italic">Δ</mml:mi><mml:msubsup><mml:mi>G</mml:mi><mml:mi mathvariant="normal">D</mml:mi><mml:mi mathvariant="normal">0</mml:mi></mml:msubsup></mml:mrow></mml:math></inline-formula> for a protein. Thus, our confidence in the authentic value of <inline-formula id="inf8"><mml:math id="m8" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi mathvariant="italic">Δ</mml:mi><mml:msubsup><mml:mi>G</mml:mi><mml:mi mathvariant="normal">D</mml:mi><mml:mi mathvariant="normal">0</mml:mi></mml:msubsup></mml:mrow></mml:math></inline-formula> is eroded. Another problem with this <italic>in vitro</italic> measurement of <inline-formula id="inf9"><mml:math id="m9" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi mathvariant="italic">Δ</mml:mi><mml:msubsup><mml:mi>G</mml:mi><mml:mi mathvariant="normal">D</mml:mi><mml:mi mathvariant="normal">0</mml:mi></mml:msubsup></mml:mrow></mml:math></inline-formula> is that it is done on the pure protein sample in dilute buffer which is a very large extrapolation of the <italic>in vivo</italic> conditions, for the crowding effect on protein stability is ignored.</p>