I trained as a macromolecular X-ray crystallographer and my research has contributed broadly to structural biology; experimental design; mechanistic enzymology—energetic coupling within proteins; bioinformatics; and evolutionary biology—the origin of genetic coding.
Two mysteries about enzymes have fascinated me throughout my career: how they work and where they came from. Tryptophanyl-tRNA synthetase (TrpRS) introduced my group to novel aspects of both mysteries:
Mechanistic Enzymology and Allostery
- Ligand-dependent crystal growth gave us a full set of conformations related to the mechanism (Fig. 1).
- Combinatorial mutagenesis and thermodynamic cycles allowed us to identify what we feel are the central long-range coupling between domain motion, catalysis, and specificity (Fig. 2).
- Minimum action pathways furnished computational parameters we could correlate quantitatively with both structural and functional consequences of the mutagenesis (Fig. 3).
- TrpRS illustrates the conversion of ATP hydrolysis free energy into information with the use of an “escapement mechanism” which allows it to transcend the second law of thermodynamics (Fig. 4, Fig. 5).
Origins of genetic coding
- Modular deconstruction of superposed 3D structures of the two aminoacyl-tRNA synthetase superfamilies led to the identification of successively more highly conserved motifs—Urzymes and Protozymes—that we have expressed and shown retain high catalytic proficiencies (Figure 6).
- We built sound, multidimensional support for the Rodin-Ohno hypothesis that the two aminoacyl-tRNA synthetase superfamilies descended from opposite strands of the same ancestral bidirectional gene (Figure 7).
- Bidirectional coding is a bizarre notion; it means that the unique information in a gene has two entirely different interpretations, depending on which strand is translated (Figure 8).
- We related amino acid physical chemistry to both protein folding and tRNA recognition (Figure 9).
- We uncovered the recognition signals in tRNA bases that implement the complementary duality observed in the aminoacyl-tRNA synthetases (Figure 10).
- Relationships in Figures 8 and 9 demonstrate how cognate aaRS/tRNA pairs became the molecular dictionary that translates the genetic code. They also serve as a nanosensing mechanism essential to indirect, computational genetic coding (Figure 11).
- The most important selective advantage of ancestral bidirectional coding was probably that it assured the colonization of parts of amino acid sequence space that are as distinct as possible from each other, assuring that descendants of the aaRS could generate the diversity seen in the proteome.
- They establish a convincing scenario for how the synthetases were able evolve—reflexively—as the first proteins able to enforce the rules by which they are translated (Figure 11).