The self-organizing fractal theory as a universal discovery method: the phenomenon of life

A universal discovery method potentially applicable to all disciplines studying organizational phenomena has been developed. This method takes advantage of a new form of global symmetry, namely, scale-invariance of self-organizational dynamics of energy/matter at all levels of organizational hierarchy, from elementary particles through cells and organisms to the Universe as a whole. The method is based on an alternative conceptualization of physical reality postulating that the energy/matter comprising the Universe is far from equilibrium, that it exists as a flow, and that it develops via self-organization in accordance with the empirical laws of nonequilibrium thermodynamics. It is postulated that the energy/matter flowing through and comprising the Universe evolves as a multiscale, self-similar structure-process, i.e., as a self-organizing fractal. This means that certain organizational structures and processes are scale-invariant and are reproduced at all levels of the organizational hierarchy. Being a form of symmetry, scale-invariance naturally lends itself to a new discovery method that allows for the deduction of missing information by comparing scale-invariant organizational patterns across different levels of the organizational hierarchy

Coupled inter-subunit dynamics enable the fastest CO2-fixation by reductive carboxylases

Enoyl-CoA carboxylases/reductases (ECRs) are the most efficient CO2-fixing enzymes described to date, outcompeting RubisCO, the key enzyme in photosynthesis in catalytic activity by more than an order of magnitude. However, the molecular mechanisms underlying ECR’s extraordinary catalytic activity remain elusive. Here we used different crystallographic approaches, including ambient temperature X-ray Free Electron Laser (XFEL) experiments, to study the dynamic structural organization of the ECR from Kitasatospora setae. K. setae ECR is a homotetramer that differentiates into a dimer of dimers of open- and closed-form subunits in the catalytically active state, suggesting that the enzyme operates with “half-site reactivity” to achieve high catalytic rates. Using structure-based mutagenesis, we show that catalysis is synchronized in K. setae ECR across the pair of dimers by conformational coupling of catalytic domains and within individual dimers by shared substrate binding sites. Our results provide unprecedented insights into the dynamic organization and synchronized inter- and intra-subunit communications of nature’s most efficient CO2-fixing enzyme during catalysis