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2016 ; 578
(ä): 273-97
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Conformational Sub-states and Populations in Enzyme Catalysis
#MMPMID27497171
Agarwal PK
; Doucet N
; Chennubhotla C
; Ramanathan A
; Narayanan C
Methods Enzymol
2016[]; 578
(ä): 273-97
PMID27497171
show ga
Enzyme function involves substrate and cofactor binding, precise positioning of
reactants in the active site, chemical turnover, and release of products. In
addition to formation of crucial structural interactions between enzyme and
substrate(s), coordinated motions within the enzyme-substrate complex allow
reaction to proceed at a much faster rate, compared to the reaction in solution
and in the absence of enzyme. An increasing number of enzyme systems show the
presence of conserved protein motions that are important for function. A wide
variety of motions are naturally sampled (over femtosecond to millisecond
time-scales) as the enzyme complex moves along the energetic landscape, driven by
temperature and dynamical events from the surrounding environment. Areas of low
energy along the landscape form conformational sub-states, which show higher
conformational populations than surrounding areas. A small number of these
protein conformational sub-states contain functionally important structural and
dynamical features, which assist the enzyme mechanism along the catalytic cycle.
Identification and characterization of these higher-energy (also called excited)
sub-states and the associated populations are challenging, as these sub-states
are very short-lived and therefore rarely populated. Specialized techniques based
on computer simulations, theoretical modeling, and nuclear magnetic resonance
have been developed for quantitative characterization of these sub-states and
populations. This chapter discusses these techniques and provides examples of
their applications to enzyme systems.
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