Mechanism of the Early Catalytic Events in the Collagenolysis by Matrix Metalloproteinase-1

Metalloproteinase-1 (MMP-1) catalyzed collagen degradation is essential for a wide variety of normal physiological processes, while at the same time contributing to several diseases in humans. Therefore, a comprehensive understanding of this process is of great importance. Although crystallographic and spectroscopic studies provided fundamental information about the structure and function of MMP-1, the precise mechanism of collagen degradation especially considering the complex and flexible structure of the substrate, remains poorly understood. In addition, how the protein environment dynamically reorganizes at the atomic scale into a catalytically active state capable of collagen hydrolysis remains unknown. In this study, we applied experimentally-guided multiscale molecular modeling methods including classical molecular dynamics (MD), well-tempered (WT) classical metadynamics (MetD), combined quantum mechanics/molecular mechanics (QM/MM) MD and QM/MM MetD simulations to explore and characterize the early catalytic events of MMP-1 collagenolysis. Importantly the study provided a complete atomic and dynamic description of the transition from the open to the closed form of the MMP-1•THP complex. Notably, the formation of catalytically active Michaelis complex competent for collagen cleavage was characterized. The study identified the changes in the coordination state of the catalytic zinc(II) associated with the conformational transformation and the formation of catalytically productive ES complex. Our results confirm the essential role of the MMP-1 catalytic domain\u27s α-helices (hA, hB and hC) and the linker region in the transition to the catalytically competent ES complex. Overall, the results provide unique mechanistic insight into the conformational transformations and associated changes in the coordination state of the catalytic zinc(II) that would be important for the design of effective MMP-1 inhibitors

Effects of different fire intensities on chemical and biological soil components and related feedbacks on a Mediterranean shrub (Phillyrea angustifolia L.)

In July 2000, six plots of Mediterranean maquis in the Castel Volturno Nature Reserve were burnt at two intensity levels to examine the effects of fire intensities on chemical and biological soil components and their relationships with ecophysiological processes of Phillyrea angustifolia L. Net photosynthesis and stomatal conductance, as well as P availability, were higher in burnt plots than in control plots, even 2 years after fire; the TM density of total soil microfungi was significantly lower in the first 8 months after fire, while xerotolerant and heat-stimulated soil microfungi were still higher 2 years after fire. Significant correlations between photosynthesis and stomatal conductance in resprouts and mycorrhizal status, as well as changes in the soil fungal components of the communities, suggest that both soil and mycorrhizal fungi play a role in immobilizing and translocating nutrients temporarily released in the below-ground system by fire. Nutrient balance interacts with physiological processes, and a feedback mechanism is well represented by stomatal conductance, which allows both the influx of water and mineral nutrients from the soil; moreover, the post-fire increase in photosynthetic activity promotes vigorous resprouting and may lead to increased availability of carbohydrates for soil biota and, consequently, to enhanced vegetation resilience