What makes proteins work: exploring life inP–T–X

Abstract

Although considerable progress has been made in the molecular biophysics of proteins, it is still not possible to reliably design an enzyme for a given function. The current understanding of enzyme function is that both structure and flexibility are important. Much attention has been focused recently on protein folding and thus structure, spurred on by insights from the folding funnel concept. For experimental studies of protein folding, variations in temperature (T) and chemical composition (X) of the solution have been traditionally exploited, although more recent studies using variations in pressure (P) made possible through new instrumentation have led to a deeper understanding of the energy landscape of protein folding. Other work has shown that flexibility is also essential for enzymes, although it is still not clear what type is important. Another avenue has been to take advantage of “Nature’s laboratory” by exploring homologous proteins from organisms that live in extreme conditions, or “extremophiles”. While the most studied extremophiles live at extremes of T and X, recent exploration of deep-sea environments has led to the discovery of organisms living under high P, or “piezophiles”. An exploration of targeted enzymes from organisms with various P-T-X growth conditions coupled with advances in biophysical instrumentation and computer simulations that allow studies of these enzymes at different P-T-X conditions may lead to a better understanding of “flexibility” and to general design criteria for active enzymes. Preface Kamal Shukla’s great contribution to science has been his vision that physical sciences could bring new insights to biological sciences, and that the marriage of methodologies, particularly theoretical/computational with experimental, was needed to tackle the complexities of biology. Furthermore, his openness to new methods and different ideas outside the current fad has helped make his vision a reality. In my remarks below, I have not tried to limit myself to projects that I know Kamal had sponsored, nor have I tried to highlight all that he has sponsored. Instead, everything I mention has been influenced directly or indirectly by his efforts. Perhaps the indirect influences are most telling, because they would not have happened without Kamal.

Extreme biophysics: Enzymes under pressure

“…Fundamentally, determining the adaptations of enzymes for extreme conditions can lead to a greater understanding of enzyme structure–function relationships. Practically, understanding these adaptations can be used in biotechnology so that enzymes can be bioengineered to function under specific conditions . In addition, determining the limiting conditions where enzyme activity can be maintained could be one of the factors in defining the “limits of life,” which could guide the search for life in extreme environments such as beneath the oceanic and continental surface or even extraterrestrially.…”

Pressure Adaptations in Deep-Sea Moritella Dihydrofolate Reductases: Compressibility versus Stability

“…Mechanisms used by “extremophiles” to adapt their biological macromolecules to these extremes could assist in our understanding of these limits of life. Studying the sequence-structure-function relationship of proteins from extremophiles compared to proteins from organisms living under ambient conditions, “mesophiles,” is useful in understanding adaptations used to maintain functional enzymes under all conditions [ 1 ]. So far, studies of extremophiles have largely focused on temperature adaptation.…”

Adaptations for Pressure and Temperature in Dihydrofolate Reductases

“…The discoveries of “extremophilic” organisms that thrive under extremes of temperature, pressure, and other conditions [ 1 ] raise questions about the nature of adaptations in their biomolecules so that they can function under conditions where their counterparts from mesophiles would fail. Determining the adaptations of proteins for extreme conditions can lead to a greater fundamental understanding of structure-function relationships in proteins, as well as practical applications such as bioengineering proteins to function under specific conditions [ 2 ]. In addition, determining the limiting conditions where enzyme activity can be maintained may be useful in defining conditions for the “limits of life” to guide the search for life in extreme environments such as beneath the oceanic and continental surface or even extraterrestrially.…”