Abstract <p>Alchemical free energy calculations using thermodynamic integration are widely used in p<InlineEquation ID="IEq3"> <EquationSource Format="TEX">$K_{\rm a}$</EquationSource> <EquationSource Format="MATHML"><math> <msub> <mi>K</mi> <mi mathvariant="normal">a</mi> </msub> </math></EquationSource> </InlineEquation> calculations, of amino acid residues within proteins. However, insufficient conformational sampling during these calculations can lead to erroneous free energy estimates. To overcome this issue, we use a combination of thermodynamic integration (TI) and Unified Free Energy Dynamics (UFED). This hybrid method, TI-UFED, is first benchmarked by computing the enantiomerization free energy of alanine dipeptide, and p<InlineEquation ID="IEq4"> <EquationSource Format="TEX">$K_{\rm a}$</EquationSource> <EquationSource Format="MATHML"><math> <msub> <mi>K</mi> <mi mathvariant="normal">a</mi> </msub> </math></EquationSource> </InlineEquation> shift of <InlineEquation ID="IEq5"> <EquationSource Format="TEX">$\hbox {Asp}_{26}$</EquationSource> <EquationSource Format="MATHML"><math> <msub> <mtext>Asp</mtext> <mn>26</mn> </msub> </math></EquationSource> </InlineEquation> in thioredoxin. Thereafter, we apply this approach to compute p<InlineEquation ID="IEq6"> <EquationSource Format="TEX">$K_{\rm a}$</EquationSource> <EquationSource Format="MATHML"><math> <msub> <mi>K</mi> <mi mathvariant="normal">a</mi> </msub> </math></EquationSource> </InlineEquation> shifts to determine the most stable protonation state of active site residues in class-C <InlineEquation ID="IEq7"> <EquationSource Format="TEX">$\beta$</EquationSource> <EquationSource Format="MATHML"><math> <mi>β</mi> </math></EquationSource> </InlineEquation>-lactamase.</p> Graphical abstract <p></p>

Protonation states of class-C $\varvec{\beta}$-lactamases determined by a combination of thermodynamic integration and unified free energy dynamics

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发表日期：

2026年2月17日

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Shivani Verma,
Nisanth N Nair

摘要

Abstract

Alchemical free energy calculations using thermodynamic integration are widely used in p $K_{\rm a}$ $K_{a}$ calculations, of amino acid residues within proteins. However, insufficient conformational sampling during these calculations can lead to erroneous free energy estimates. To overcome this issue, we use a combination of thermodynamic integration (TI) and Unified Free Energy Dynamics (UFED). This hybrid method, TI-UFED, is first benchmarked by computing the enantiomerization free energy of alanine dipeptide, and p $K_{\rm a}$ $K_{a}$ shift of $\hbox {Asp}_{26}$ ${Asp}_{26}$ in thioredoxin. Thereafter, we apply this approach to compute p $K_{\rm a}$ $K_{a}$ shifts to determine the most stable protonation state of active site residues in class-C $\beta$ $β$ -lactamase.

Graphical abstract

Protonation states of class-C \(\varvec{\beta}\)-lactamases determined by a combination of thermodynamic integration and unified free energy dynamics

摘要