Computer aided enzyme design and catalytic concepts

Abstract

Gaining a deeper understanding of enzyme catalysis is of great practical and fundamental importance. Over the years it has become clear that despite advances made in experimental mutational studies, a quantitative understanding of enzyme catalysis will not be possible without the use of computer modeling approaches. While we believe that electrostatic preorganization is by far the most important catalytic factor, convincing the wider scientific community of this may require the demonstration of effective rational enzyme design. Here we make the point that the main current advances in enzyme design are basically advances in directed evolution and that computer aided enzyme design must involve approaches that can reproduce catalysis in well-defined test cases. Such an approach is provided by the empirical valence bond method.

Perspective: Defining and quantifying the role of dynamics in enzyme catalysis

“…At any rate, the power of the EVB has been established in studies of the effect of long range mutations, 56 in evaluating entropic effects, in studies of NQM, 68 and in exploring benchmarks for enzyme design. [172][173][174] …”

Computational strategies for the design of new enzymatic functions

“…Warshel and coworkers 45,76,77 have recently pointed out that the design of a new catalyst must be focused not only in placing the reacting fragments in proper places around the substrate but in optimizing the full environment preorganization. This preorganization accounts for the required electrostatic properties of the enzyme to lower the activation free energy of the reaction, a property that depends not only on residues of the active site.…”

“…5,7,9,11,38,39,40,41,42,43,44,45 This review will focus mainly on the advances obtained in the field of the de novo design during the last years, emphasizing the new achievements of the different computational strategies employed in the design process. The three aforementioned reactions, Kemp, Diels-Alder and retro-aldolase, will be used to illustrate these points.…”

Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin

“…To improve function, subsequent directed evolution experiments fix mutations that act to stabilize the functionally important conformations found in the broadened ensemble of the redesigned protein (Frushicheva et al, 2014). This pattern of design and selection has been performed for functions including small molecule binding (Tinberg et al, 2013) and protein-protein interaction (Karanicolas et al, 2011), the most developed examples of directed evolution changing dynamics and function emerged from enzyme design.…”