Despite more than half a century of detailed studies, we still do not have a satisfactory
physical model for the enormous rate accelerations brought about by enzymes. The Klinman
group focuses on the following three aspects of this problem:
What is the direct link between protein dynamical motions and the efficiency of the chemical steps
catalyzed by enzymes? These studies are focused on two fundamental processes in nature:
hydrogen transfer (shown to occur by quantum mechanical tunneling) that is mediated by the
heavy atoms of protein and, more recently, methyl group transfer. A model is emerging in which
a conformational landscape involving motions, both distal and proximal, to the active site, leads
to the transient generation of a family of compressed active site configurations.
A representation of a subunit of a thermophilic alcohol dehydrogenase illustrating the local
protein motions (reorganization) and distal motions (pre-organization) that control
efficient H-tunneling. (Klinman (2009) Chem Phys Lett - Frontiers 471, 179-193).
Post-translational modifications abound in biology, with a very large number of these reactions
involving amino acid side chains. While reversible protein modifications play key roles in
cellular regulation, there are numerous unidirectional modifications that occur in the production
of bacterial secondary metabolites and in the biogenesis of cofactors. Our group is focused on
the range of novel enzymatic processes that generate the peptide and protein-derived quinocofactors.
Illustration of the five known protein- and peptide-derived quinocofactors. The four
derived from proteins are TPQ, LTQ, TTQ and CTQ. PQQ is the sole post-translational
process that occurs on a peptide. (Mure, Mills and Klinman (2000) Biochemistry 41,
9269-9278; Wecksler et al. (2009) Biochemistry 48, 10151-10161).
How did organisms cope with the transition from anaerobic to aerobic life? Key issues are determining
whether there are specific pathways for migration of molecular oxygen to enzyme active sites, the nature
of persistent chemical intermediates formed from oxygen, and, most importantly, how these chemical
intermediates are protected from performing undesirable side reactions that would either inactivate the
protein or lead to poor yield of product. As the major catalysts within cells, enzymes have had to cope
with reactive oxygen intermediates that can wreak havoc with protein structure and function.
A scheme for the 4e¯, 4H+ reduction of O2 to produce H2O.
The potentially damaging species are •OH > O•¯ H2O2.
(Klinman (2007) Acc Chem Res 40, 325-333).