scholarly journals Thermal fluctuations of immature SOD1 lead to separate folding and misfolding pathways

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Ashok Sekhar ◽  
Jessica AO Rumfeldt ◽  
Helen R Broom ◽  
Colleen M Doyle ◽  
Guillaume Bouvignies ◽  
...  
Keyword(s):  
Structural Models ◽  
Thermal Fluctuations ◽  
Atomic Level ◽  
Native State ◽  
Dimer Interface ◽  
Starting Point ◽  
Dimeric Protein ◽  
Nmr Methods ◽  
Lateral Sclerosis

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease involving cytotoxic conformations of Cu, Zn superoxide dismutase (SOD1). A major challenge in understanding ALS disease pathology has been the identification and atomic-level characterization of these conformers. Here, we use a combination of NMR methods to detect four distinct sparsely populated and transiently formed thermally accessible conformers in equilibrium with the native state of immature SOD1 (apoSOD12SH). Structural models of two of these establish that they possess features present in the mature dimeric protein. In contrast, the other two are non-native oligomers in which the native dimer interface and the electrostatic loop mediate the formation of aberrant intermolecular interactions. Our results show that apoSOD12SH has a rugged free energy landscape that codes for distinct kinetic pathways leading to either maturation or non-native association and provide a starting point for a detailed atomic-level understanding of the mechanisms of SOD1 oligomerization.

scholarly journals Atomic-level characterization of protein–protein association

2019 ◽  
Vol 116 (10) ◽  
pp. 4244-4249 ◽  
Author(s):  
Albert C. Pan ◽  
Daniel Jacobson ◽  
Konstantin Yatsenko ◽  
Duluxan Sritharan ◽  
Thomas M. Weinreich ◽  
...  
Keyword(s):  
Structural Information ◽  
Protein Complexes ◽  
Md Simulations ◽  
Atomic Level ◽  
Conformational Ensemble ◽  
Native State ◽  
Protein Interfaces ◽  
Study Association ◽  
Functionally Diverse

Despite the biological importance of protein–protein complexes, determining their structures and association mechanisms remains an outstanding challenge. Here, we report the results of atomic-level simulations in which we observed five protein–protein pairs repeatedly associate to, and dissociate from, their experimentally determined native complexes using a molecular dynamics (MD)–based sampling approach that does not make use of any prior structural information about the complexes. To study association mechanisms, we performed additional, conventional MD simulations, in which we observed numerous spontaneous association events. A shared feature of native association for these five structurally and functionally diverse protein systems was that if the proteins made contact far from the native interface, the native state was reached by dissociation and eventual reassociation near the native interface, rather than by extensive interfacial exploration while the proteins remained in contact. At the transition state (the conformational ensemble from which association to the native complex and dissociation are equally likely), the protein–protein interfaces were still highly hydrated, and no more than 20% of native contacts had formed.

scholarly journals Atomic-level characterization of protein-protein association

2018 ◽  
Author(s):  
Albert C. Pan ◽  
Daniel Jacobson ◽  
Konstantin Yatsenko ◽  
Duluxan Sritharan ◽  
Thomas M. Weinreich ◽  
...  
Keyword(s):  
Structural Information ◽  
Protein Complexes ◽  
Md Simulations ◽  
Atomic Level ◽  
Conformational Ensemble ◽  
Native State ◽  
Protein Interfaces ◽  
Study Association ◽  
Functionally Diverse

Despite the biological importance of protein-protein complexes, determining their structures and association mechanisms remains an outstanding challenge. Here, we report the results of atomic-level simulations in which we observed five protein-protein pairs repeatedly associate to, and dissociate from, their experimentally determined native complexes using a new molecular dynamics (MD)-based sampling approach that does not make use of any prior structural information about the complexes. To study association mechanisms, we performed additional, conventional MD simulations, in which we observed numerous spontaneous association events. A shared feature of native association for these five structurally and functionally diverse protein systems was that if the proteins made contact far from the native interface, the native state was reached by dissociation and eventual re-association near the native interface, rather than by extensive interfacial exploration while the proteins remained in contact. At the transition state (the conformational ensemble from which association to the native complex and dissociation are equally likely), the protein-protein interfaces were still highly hydrated, and no more than 20% of native contacts had formed.

Voltage Gated Sodium Channel Blockers: Synthesis of Mexiletine Analogues and Homologues

2020 ◽  
Vol 27 ◽  
Author(s):  
Alessia Catalano ◽  
Carlo Franchini ◽  
Alessia Carocci
Keyword(s):  
Sodium Channel ◽  
Channel Blocker ◽  
Parent Compound ◽  
Channel Blockers ◽  
Sodium Channel Blocker ◽  
Starting Point ◽  
Channel Blocking ◽  
Blocking Activity ◽  
Synthetic Routes ◽  
Lateral Sclerosis

: Mexiletine is an antiarrhythmic drug belonging to IB class, acting as sodium channel blocker. Besides its well-known activity on arrhythmias, its usefulness in the treatment of myotonia, myotonic distrophy and amyotrophic lateral sclerosis is now widely recognized. Nevertheless, it has been retired from the market in several countries because of its undesired effects. Thus, several papers were reported in the last years about analogues and homologues of mexiletine being endowed with a wider therapeutic ratio and a more selectivity of action. Some of them showed sodium channel blocking activity higher than the parent compound. It is noteworthy that mexiletine is used in therapy as a racemate even though a difference in the activities of the two enantiomers were widely demonstrated, with (–)-(R)-enantiomer being more active: this finding led several research groups to study mexiletine and its analogues and homologues in their optically active forms. This review summarizes the different synthetic routes used to obtain these compounds. They could represent an interesting starting point to new mexiletine-like compounds without common side effects related to the use of mexiletine.

scholarly journals New Insights into the Crystal Chemistry of Elpidite, Na2Zr[Si6O15]·3H2O and (Na1+YCax□1−X−Y)Σ=2Zr[Si6O15]·(3−X)H2O, and Ab Initio Modeling of IR Spectra

Materials ◽  
2021 ◽  
Vol 14 (9) ◽  
pp. 2160
Author(s):  
Alexander Bogdanov ◽  
Ekaterina Kaneva ◽  
Roman Shendrik
Keyword(s):  
Ir Spectra ◽  
Structural Models ◽  
Chemical Characterization ◽  
Chemical Compositions ◽  
X Ray Diffraction ◽  
Special Group ◽  
X Ray ◽  
Influence Of Water ◽  
Radioactive Species

Elpidite belongs to a special group of microporous zirconosilicates, which are of great interest due to their capability to uptake various molecules and ions, e.g., some radioactive species, in their structural voids. The results of a combined electron probe microanalysis and single-crystal X-ray diffraction study of the crystals of elpidite from Burpala (Russia) and Khan-Bogdo (Mongolia) deposits are reported. Some differences in the chemical compositions are observed and substitution at several structural positions within the structure of the compounds are noted. Based on the obtained results, a detailed crystal–chemical characterization of the elpidites under study was carried out. Three different structure models of elpidite were simulated: Na2ZrSi6O15·3H2O (related to the structure of Russian elpidite), partly Ca-replaced Na1.5Ca0.25ZrSi6O15·2.75H2O (close to elpidite from Mongolia), and a hypothetical CaZrSi6O15·2H2O. The vibration spectra of the models were obtained and compared with the experimental one, taken from the literature. The strong influence of water molecule vibrations on the shape of IR spectra of studied structural models of elpidite is discussed in the paper.

scholarly journals Mass Spectrometry-Based Proteomic Characterization of Cutaneous Melanoma Ectosomes Reveals the Presence of Cancer-Related Molecules

2020 ◽  
Vol 21 (8) ◽  
pp. 2934 ◽  
Author(s):  
Magdalena Surman ◽  
Sylwia Kędracka-Krok ◽  
Dorota Hoja-Łukowicz ◽  
Urszula Jankowska ◽  
Anna Drożdż ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Protein Content ◽  
Cell Lines ◽  
Cutaneous Melanoma ◽  
Epithelial Mesenchymal Transition ◽  
Mesenchymal Transition ◽  
Starting Point ◽  
Novel Biomarkers

Cutaneous melanoma (CM) is an aggressive type of skin cancer for which effective biomarkers are still needed. Recently, the protein content of extracellular vesicles (ectosomes and exosomes) became increasingly investigated in terms of its functional role in CM and as a source of novel biomarkers; however, the data concerning the proteome of CM-derived ectosomes is very limited. We used the shotgun nanoLC–MS/MS approach to the profile protein content of ectosomes from primary (WM115, WM793) and metastatic (WM266-4, WM1205Lu) CM cell lines. Additionally, the effect exerted by CM ectosomes on recipient cells was assessed in terms of cell proliferation (Alamar Blue assay) and migratory properties (wound healing assay). All cell lines secreted heterogeneous populations of ectosomes enriched in the common set of proteins. A total of 1507 unique proteins were identified, with many of them involved in cancer cell proliferation, migration, escape from apoptosis, epithelial–mesenchymal transition and angiogenesis. Isolated ectosomes increased proliferation and motility of recipient cells, likely due to the ectosomal transfer of different cancer-promoting molecules. Taken together, these results confirm the significant role of ectosomes in several biological processes leading to CM development and progression, and might be used as a starting point for further studies exploring their diagnostic and prognostic potential.

Macro- to Atomic-Scale Tailoring of Si3N4 Ceramics to Enhance Properties

2005 ◽  
Vol 287 ◽  
pp. 233-241 ◽  
Author(s):  
Paul F. Becher ◽  
Gayle S. Painter ◽  
Naoya Shibata ◽  
Hua Tay Lin ◽  
Mattison K. Ferber
Keyword(s):  
Electronic Device ◽  
Atomic Level ◽  
Atomic Scale ◽  
Fracture Properties ◽  
Beta Particles ◽  
Preferential Segregation ◽  
Nitride Ceramics ◽  
Theoretical Predictions ◽  
The Matrix

Silicon nitride ceramics are finding uses in numerous engineering applications because of their tendency to form whisker-like microstructures that can overcome the inherent brittle nature of ceramics. Studies now establish the underlying microscopic and atomic-scale principles for engineering a tough, strong ceramic. The theoretical predictions are confirmed by macroscopic observations and atomic level characterization of preferential segregation at the interfaces between the grains and the continuous nanometer thick amorphous intergranular film (IGF). Two interrelated factors must be controlled for this to occur including the generation of the elongated reinforcing grains during sintering and debonding of the interfaces between the reinforcing grains and the matrix. The reinforcing grains can be controlled by (1) seeding with beta particles and (2) the chemistry of the additives, which also can influence the interfacial debonding conditions. In addition to modifying the morphology of the reinforcing grains, it now appears that the combination of preferential segregation and strong bonding of the additives (e.g., the rare earths, RE) to the prism planes can also result in sufficiently weakens the bond of the interface with the IGF to promote debonding. Thus atomic-scale engineering may allow us to gain further enhancements in fracture properties. This new knowledge will enable true atomic-level engineering to be joined with microscale tailoring to develop the advanced ceramics that will be required for more efficient engines, new electronic device architectures and composites.

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