Structurally Linked Dynamics in Lactate Dehydrogenases of Evolutionarily Distinct Species

Abstract

We present new findings about how primary and secondary structure affects the role of fast protein motions in the reaction coordinates of enzymatic reactions. Using transition path sampling and committor distribution analysis, we examined the difference in the role of these fast protein motions in the reaction coordinate of lactate dehydrogenases (LDHs) of Apicomplexa organisms Plasmodium falciparum and Cryptosporidium parvum. Having evolved separately from a common malate dehydrogenase ancestor, the two enzymes exhibit several important structural differences, notably a five-amino acid insertion in the active site loop of P. falciparum LDH. We find that these active site differences between the two organisms’ LDHs likely cause a decrease in the contribution of the previously determined LDH rate-promoting vibration to the reaction coordinate of P. falciparum LDH compared to that of C. parvum LDH, specifically in the coupling of the rate-promoting vibration and the hydride transfer. This effect, while subtle, directly shows how changes in structure near the active site of LDH alter catalytically important motions. Insights provided by studying these alterations would prove to be useful in identifying LDH inhibitors that specifically target the isozymes of these parasitic organisms.

Structural Dynamics Support Electrostatic Interactions in the Active Site of Adenylate Kinase

“…However, others have argued that these dynamical effects are short‐ranged (less than 6 Å) and cannot include the scaffold [5,44] . Alternatively, others suggested that the evolutionary advantage of dynamical and conformational flexibility in proteins was to accommodate different reaction mechanisms in the active site, [45,46] which enables catalytic promiscuity and facilitate the evolution of new proteins and functions [47–53] . Finally, some refer to the process by which protein dynamics influence protein activity as dynamic allostery, in analogy with allosteric regulation of protein activity upon the binding of a drug or toxin [54–56] .…”

“…[5,44] Alternatively, others suggested that the evolutionary advantage of dynamical and conformational flexibility in proteins was to accommodate different reaction mechanisms in the active site, [45,46] which enables catalytic promiscuity and facilitate the evolution of new proteins and functions. [47][48][49][50][51][52][53] Finally, some refer to the process by which protein dynamics influence protein activity as dynamic allostery, in analogy with allosteric regulation of protein activity upon the binding of a drug or toxin. [54][55][56] Although all of these theories were verified convincingly for specific examples, they often focus on parts of the catalytic cycle other than the catalytic step (substrate binding, product release, catalytic promiscuity, etc.)…”

Contribution of buried distal amino acid residues in horse liver alcohol dehydrogenase to structure and catalysis

“…They identified a conserved evolutionary motif in horse liver ADH that spans the catalytic and coenzyme binding domains (including Ser‐144, Gly‐181, Val‐203, Gly‐204, Val‐207, Glu‐267, Ile‐269, and Val‐292) and could participate in catalysis. They used transition path sampling to conclude that “protein compression” in the homologous yeast ADH “mediates a near barrier‐less hydride transfer.” They suggested that “slight changes in promoting vibrations (in lactate dehydrogenase) result in dramatic changes in enzyme chemistry.” The contribution of such fast dynamics to catalysis of hydride transfer by ADH needs experimental evaluation.…”

“…52,53 They suggested that "slight changes in promoting vibrations (in lactate dehydrogenase) result in dramatic changes in enzyme chemistry." 54,55 The contribution of such fast dynamics to catalysis of hydride transfer by ADH needs experimental evaluation.…”

Directed Evolution as a Probe of Rate Promoting Vibrations Introduced via Mutational Change

“…Significant effort has been directed to understanding the mechanism of enzymatic catalysis. Increasing evidence has shown that dynamic motions of enzymes play an important role in catalytic process. − Recent theoretical and experimental studies have shown that sub-picosecond motions, which are on the same time scale as the chemical step of enzymatic reactions, can couple with the reaction coordinate of enzymes. ,,,− These femtosecond motions are termed rate promoting vibrations (RPVs), since couplings between these motions and reaction coordinates can promote the rate of the chemical step in the reaction process. The RPV promotes the rate of the chemical step of an enzymatic reaction by dynamically modulating the height and width of the potential energy barrier .…”