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Kuzmanic A.,Mediterranean Institute for Life Sciences | Zagrovic B.,University of Split
Biophysical Journal | Year: 2010

Root mean-square deviation (RMSD) after roto-translational least-squares fitting is a measure of global structural similarity of macromolecules used commonly. On the other hand, experimental x-ray B-factors are used frequently to study local structural heterogeneity and dynamics in macromolecules by providing direct information about root mean-square fluctuations (RMSF) that can also be calculated from molecular dynamics simulations. We provide a mathematical derivation showing that, given a set of conservative assumptions, a root mean-square ensemble-average of an all-against-all distribution of pairwise RMSD for a single molecular species, 〈RMSD2〉 1/2, is directly related to average B-factors (〈B〉) and 〈RMSF2〉1/2. We show this relationship and explore its limits of validity on a heterogeneous ensemble of structures taken from molecular dynamics simulations of villin headpiece generated using distributed-computing techniques and the Folding@Home cluster. Our results provide a basis for quantifying global structural diversity of macromolecules in crystals directly from x-ray experiments, and we show this on a large set of structures taken from the Protein Data Bank. In particular, we show that the ensemble-average pairwise backbone RMSD for a microscopic ensemble underlying a typical protein x-ray structure is ∼1.1 Å , under the assumption that the principal contribution to experimental B-factors is conformational variability. © 2010 by the Biophysical Society. Source

Slade D.,University of Paris Descartes | Radman M.,University of Paris Descartes | Radman M.,Mediterranean Institute for Life Sciences
Microbiology and Molecular Biology Reviews | Year: 2011

Deinococcus radiodurans is a robust bacterium best known for its capacity to repair massive DNA damage efficiently and accurately. It is extremely resistant to many DNA-damaging agents, including ionizing radiation and UV radiation (100 to 295 nm), desiccation, and mitomycin C, which induce oxidative damage not only to DNA but also to all cellular macromolecules via the production of reactive oxygen species. The extreme resilience of D. radiodurans to oxidative stress is imparted synergistically by an efficient protection of proteins against oxidative stress and an efficient DNA repair mechanism, enhanced by functional redundancies in both systems. D. radiodurans assets for the prevention of and recovery from oxidative stress are extensively reviewed here. Radiation- and desiccation-resistant bacteria such as D. radiodurans have substantially lower protein oxidation levels than do sensitive bacteria but have similar yields of DNA double-strand breaks. These findings challenge the concept of DNA as the primary target of radiation toxicity while advancing protein damage, and the protection of proteins against oxidative damage, as a new paradigm of radiation toxicity and survival. The protection of DNA repair and other proteins against oxidative damage is imparted by enzymatic and nonenzymatic antioxidant defense systems dominated by divalent manganese complexes. Given that oxidative stress caused by the accumulation of reactive oxygen species is associated with aging and cancer, a comprehensive outlook on D. radiodurans strategies of combating oxidative stress may open new avenues for antiaging and anticancer treatments. The study of the antioxidation protection in D. radiodurans is therefore of considerable potential interest for medicine and public health. Copyright © 2011, American Society for Microbiology. All Rights Reserved. Source

Radman M.,Mediterranean Institute for Life Sciences | Radman M.,University of Paris Descartes
DNA Repair | Year: 2016

This paper promotes a concept that protein damage determines radiation resistance and underlies aging and age-related diseases. The first bottleneck in cell recovery from radiation damage is functional (proteome) rather than informational (DNA), since prokaryotic and eukaryotic cell death correlates with incurred protein, but not DNA, damage. Proteome protection against oxidative damage determines survival after ionizing or UV irradiation, since sufficient residual proteome activity is required to turn on the DNA damage response activating DNA repair and protein renewal processes.Extreme radiation and desiccation resistance of rare bacterial and animal species is accounted for by exceptional constitutive proteome protection against oxidative damage. After excessive radiation their well-protected proteome faithfully reconstitutes a transcription-competent genome from hundreds of DNA fragments. The observation that oxidative damage targeted selectively to cellular proteins results in aging-like phenotypes suggests that aging and age-related diseases could be phenotypic consequences of proteome damage patterns progressing with age. © 2016 Elsevier B.V. Source

Elez M.,University of Paris Descartes | Radman M.,University of Paris Descartes | Radman M.,Mediterranean Institute for Life Sciences | Matic I.,University of Paris Descartes
Nucleic Acids Research | Year: 2012

Mismatch repair (MMR) is an evolutionarily conserved DNA repair system, which corrects mismatched bases arising during DNA replication. MutS recognizes and binds base pair mismatches, while the MutL protein interacts with MutS-mismatch complex and triggers MutH endonuclease activity at a distal-strand discrimination site on the DNA. The mechanism of communication between these two distal sites on the DNA is not known. We used functional fluorescent MMR proteins, MutS and MutL, in order to investigate the formation of the fluorescent MMR protein complexes on mismatches in real-time in growing Escherichia coli cells. We found that MutS and MutL proteins co-localize on unrepaired mismatches to form fluorescent foci. MutL foci were, on average, 2.7 times more intense than the MutS foci co-localized on individual mismatches. A steric block on the DNA provided by the MutHE56A mutant protein, which binds to but does not cut the DNA at the strand discrimination site, decreased MutL foci fluorescence 3-fold. This indicates that MutL accumulates from the mismatch site toward strand discrimination site along the DNA. Our results corroborate the hypothesis postulating that MutL accumulation assures the coordination of the MMR activities between the mismatch and the strand discrimination site. © 2012 The Author(s). Source

Mediterranean Institute for Life Sciences | Date: 2013-12-18

Vaccines and therapeutic proteins, including polyclonal and monoclonal antibodies, must be maximally pure and stable in their most active native form. This is a requirement for their maximal efficacy, specificity and stability as well as for precluding immune responses against erroneous or damaged moieties. Similar considerations hold for proteins used in diagnostics, industry and research. The most frequent source of damage to proteins produced in living cells is the diverse product of oxidative damage. Two main sources of protein oxidation are the level of reactive oxygen species (ROS) and even more importantly the intrinsic susceptibility of proteins to oxidative damage. Methods for avoiding oxidative protein damage are disclosed, including providing for (i) a decrease in intracellular ROS levels and (ii) an increase in the intrinsic resilience of proteins to oxidative damage. Metabolites synthesized by the most robust species provide exceptionally high levels of protection against oxidative damage from ROS. High fidelity ribosomal mutations and over-expression of diverse chaperones increase the accuracy of protein biosynthesis and of protein post-synthetic folding, both greatly contributing to increased intrinsic resistance of proteins to oxidative damage.

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