Experimental Methods in Unimolecular Dissociation Studies

Author(s):  
Tomas Baer ◽  
William L. Hase

The experimental aspects of kinetic studies with state-selected reactants have played a critical role in the advancement of our understanding of unimolecular processes.

Polymers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 1760
Author(s):  
Rose K. Baimuratova ◽  
Gulzhian I. Dzhardimalieva ◽  
Evgeniy V. Vaganov ◽  
Valentina A. Lesnichaya ◽  
Gulsara D. Kugabaeva ◽  
...  

We report here our successful attempt to obtain self-healing supramolecular hydrogels with new metal-containing monomers (MCMs) with pendent 4-phenyl-2,2′:6′,2″-terpyridine metal complexes as reversible moieties by free radical copolymerization of MCMs with vinyl monomers, such as acrylic acid and acrylamide. The resulting metal-polymer hydrogels demonstrate a developed system of hydrogen, coordination and electron-complementary π–π stacking interactions, which play a critical role in achieving self-healing. Kinetic data show that the addition of a third metal-containing comonomer to the system decreases the initial polymerization rate, which is due to the specific effect of the metal group located in close proximity of the active center on the growth of radicals.


2021 ◽  
pp. 95-114
Author(s):  
Marcin Kobielusz ◽  
Joanna Kuncewicz ◽  
Taymaz Tabari ◽  
Mateusz Trochowski ◽  
Wojciech Macyk

2010 ◽  
Vol 54 (8) ◽  
pp. 3197-3204 ◽  
Author(s):  
Luisa Borgianni ◽  
Julie Vandenameele ◽  
André Matagne ◽  
Luca Bini ◽  
Robert A. Bonomo ◽  
...  

ABSTRACT Metallo-β-lactamase (MBL)-producing bacteria are emerging worldwide and represent a formidable threat to the efficacy of relevant β-lactams, including carbapenems, expanded-spectrum cephalosporins, and β-lactamase inactivator/β-lactam combinations. VIM-2 is currently the most widespread MBL and represents a primary target for MBL inhibitor research, the clinical need for which is expected to further increase in the future. Using a saturation mutagenesis approach, we probed the importance of four residues (Phe-61, Ala-64, Tyr-67, and Trp-87) located close to the VIM-2 active site and putatively relevant to the enzyme activity based on structural knowledge of the enzyme and on structure-activity relationships of the subclass B1 MBLs. The ampicillin MIC values shown by the various mutants were affected very differently depending on the randomized amino acid position. Position 64 appeared to be rather tolerant to substitution, and kinetic studies showed that the A64W mutation did not significantly affect substrate hydrolysis or binding, representing an important difference from IMP-type enzymes. Phe-61 and Tyr-67 could be replaced with several amino acids without the ampicillin MIC being significantly affected, but in contrast, Trp-87 was found to be critical for ampicillin resistance. Further kinetic and biochemical analyses of W87A and W87F variants showed that this residue is apparently important for the structure and proper folding of the enzyme but, surprisingly, not for its catalytic activity. These data support the critical role of residue 87 in the stability and folding of VIM-2 and might have strong implications for MBL inhibitor design, as this residue would represent an ideal target for interaction with small molecules.


2012 ◽  
Vol 56 (9) ◽  
pp. 4718-4728 ◽  
Author(s):  
Adeyemi O. Adedeji ◽  
Kamalendra Singh ◽  
Nicholas E. Calcaterra ◽  
Marta L. DeDiego ◽  
Luis Enjuanes ◽  
...  

ABSTRACTSevere acute respiratory syndrome (SARS) is a highly contagious disease, caused by SARS coronavirus (SARS-CoV), for which there are no approved treatments. We report the discovery of a potent inhibitor of SARS-CoV that blocks replication by inhibiting the unwinding activity of the SARS-CoV helicase (nsp13). We used a Förster resonance energy transfer (FRET)-based helicase assay to screen the Maybridge Hitfinder chemical library. We identified and validated a compound (SSYA10-001) that specifically blocks the double-stranded RNA (dsRNA) and dsDNA unwinding activities of nsp13, with 50% inhibitory concentrations (IC50s) of 5.70 and 5.30 μM, respectively. This compound also has inhibitory activity (50% effective concentration [EC50] = 8.95 μM) in a SARS-CoV replicon assay, with low cytotoxicity (50% cytotoxic concentration [CC50] = >250 μM), suggesting that the helicase plays a still unidentified critical role in the SARS-CoV life cycle. Enzyme kinetic studies on the mechanism of nsp13 inhibition revealed that SSYA10-001 acts as a noncompetitive inhibitor of nsp13 with respect to nucleic acid and ATP substrates. Moreover, SSYA10-001 does not affect ATP hydrolysis or nsp13 binding to the nucleic acid substrate. SSYA10-001 did not inhibit hepatitis C virus (HCV) helicase, other bacterial and viral RNA-dependent RNA polymerases, or reverse transcriptase. These results suggest that SSYA10-001 specifically blocks nsp13 through a novel mechanism and is less likely to interfere with the functions of cellular enzymes that process nucleic acids or ATP. Hence, it is possible that SSYA10-001 inhibits unwinding by nsp13 by affecting conformational changes during the course of the reaction or translocation on the nucleic acid. SSYA10-001 will be a valuable tool for studying the specific role of nsp13 in the SARS-CoV life cycle, which could be a model for other nidoviruses and also a candidate for further development as a SARS antiviral target.


Archaea ◽  
2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Cheryl Ingram-Smith ◽  
Jerry L. Thurman ◽  
Karen Zimowski ◽  
Kerry S. Smith

The acyl-adenylate-forming enzyme superfamily, consisting of acyl- and aryl-CoA synthetases, the adenylation domain of the nonribosomal peptide synthetases, and luciferase, has three signature motifs (I–III) and ten conserved core motifs (A1–A10), some of which overlap the signature motifs. The consensus sequence for signature motif III (core motif A7) in acetyl-CoA synthetase is Y-X-S/T/A-G-D, with an invariant fifth position, highly conserved first and fourth positions, and variable second and third positions. Kinetic studies of enzyme variants revealed that an alteration at any position resulted in a strong decrease in the catalytic rate, although the most deleterious effects were observed when the first or fifth positions were changed. Structural modeling suggests that the highly conserved Tyr in the first position plays a key role in active site architecture through interaction with a highly conserved active-site Gln, and the invariant Asp in the fifth position plays a critical role in ATP binding and catalysis through interaction with the 2′- and 3′-OH groups of the ribose moiety. Interactions between these Asp and ATP are observed in all structures available for members of the superfamily, consistent with a critical role in substrate binding and catalysis for this invariant residue.


2020 ◽  
Author(s):  
Pengkai Sun ◽  
Yan Liu ◽  
Tengfei Ma ◽  
Jianping Ding

AbstractHuman NAD-dependent isocitrate dehydrogenase or IDH3 catalyzes the decarboxylation of isocitrate into α-ketoglutarate in the TCA cycle. We here report the structure of the IDH3 holoenzyme, in which the αβ and αγ heterodimers assemble the α2βγ heterotetramer via their clasp domains, and two α2βγ heterotetramers assemble the (α2βγ)2 heterooctamer via the β and γ subunits. The functional roles of the key residues involved in the assembly and allosteric regulation are validated by mutagenesis and kinetic studies. The allosteric site plays an important role but the pseudo allosteric site plays no role in the allosteric activation; the activation signal from the allosteric site is transmitted to the active sites of both heterodimers via the clasp domains; and the N-terminus of the γ subunit plays a critical role in the formation and function of the holoenzyme. These findings reveal the molecular mechanism of the assembly and allosteric regulation of human IDH3 holoenzyme.


2018 ◽  
Vol 18 (13) ◽  
pp. 1123-1134 ◽  
Author(s):  
Sreyashi Majumdar ◽  
Abhirupa Ghosh ◽  
Sudipto Saha

Asthma is a complex, heterogeneous, airway inflammatory disorder broadly classified into atopic (IgE mediated) and non-atopic asthma. Monoclonal Antibodies (MAbs) and small chemical Protein- Protein Interaction Modulators (PPIMs) are targeted against interleukins (ILs), which play a critical role in asthma. Many MAbs are targeted against ILs and IgE. Anti IgE MAb (Omalizumab) and Anti IL- 5 MAbs (Mepolizumab, Reslizumab) have only been approved by FDA. Most of the MAbs including Tracolizumab, Lebrikizumab, Anrukinzumab (Anti IL-13 MAb), and Brodalumab (Anti IL-17 MAb) are in different phases of clinical trials. Pascolizumab (Anti IL-4 MAb), however, has failed. These MAbs are expensive and may render adverse immune response. Thus, small chemical modulators targeting ILs and their receptors (IL-Rs) are being exploited computationally and further validated experimentally. The complex ILs and IL-Rs available in PDB are best suited for these types of studies. A large number of small chemical modulators against Protein-Protein Interactions (PPIs) have been compiled in a few databases like TIMBAL, 2P2I DB and IPPIDB. Small chemical libraries are used for virtual screening to find novel modulators targeting IL-R binding interface on IL. Molecular dynamic simulations have been further used for disruption mechanism and kinetic studies. IL-2/IL-2R was targeted with clinically tested small molecule modulators like SP4206, and IL-2 levels were known to increase in non-atopic asthma. In the absence of experimentally known modulators against atopic asthma, computational tools are being explored. For example, IL-33 is a target for atopic asthma where IL-33 and its receptor complex structure is available in PDB. In summary, small chemical modulators against ILs are a complementary approach to MAbs and computational tools have been used for identifying these modulators for asthma.


2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Pengkai Sun ◽  
Yan Liu ◽  
Tengfei Ma ◽  
Jianping Ding

AbstractHuman NAD-dependent isocitrate dehydrogenase or HsIDH3 catalyzes the decarboxylation of isocitrate into α-ketoglutarate in the TCA cycle. HsIDH3 exists and functions as a heterooctamer composed of the αβ and αγ heterodimers, and is regulated allosterically and/or competitively by numerous metabolites including CIT, ADP, ATP, and NADH. In this work, we report the crystal structure of HsIDH3 containing a β mutant in apo form. In the HsIDH3 structure, the αβ and αγ heterodimers form the α2βγ heterotetramer via their clasp domains, and two α2βγ heterotetramers form the (α2βγ)2 heterooctamer through insertion of the N-terminus of the γ subunit of one heterotetramer into the back cleft of the β subunit of the other heterotetramer. The functional roles of the key residues at the allosteric site, the pseudo allosteric site, the heterodimer and heterodimer–heterodimer interfaces, and the N-terminal of the γ subunit are validated by mutagenesis and kinetic studies. Our structural and biochemical data together demonstrate that the allosteric site plays an important role but the pseudo allosteric site plays no role in the allosteric activation of the enzyme; the activation signal from the allosteric site is transmitted to the active sites of both αβ and αγ heterodimers via the clasp domains; and the N-terminal of the γ subunit plays a critical role in the formation of the heterooctamer to ensure the optimal activity of the enzyme. These findings reveal the molecular mechanism of the assembly and allosteric regulation of HsIDH3.


Author(s):  
M.R. Richter ◽  
R.V. Blystone

Dexamethasone and other synthetic analogs of corticosteroids have been employed clinically as enhancers of lung development. The mechanism(s) by which this steroid induction of later lung maturation operates is not clear. This study reports the effect on lung epithelia of dexamethasone administered at different intervals during development. White Leghorn chick embryos were used so as to remove possible maternal and placental influences on the exogenously applied steroid. Avian lung architecture does vary from mammals; however, respiratory surfactant produced by the lung epithelia serves an equally critical role in avian lung physiology.


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