scholarly journals Long-range allosteric effects - How adenine nucleotides shape the conformational landscape of the Ski2-like RNA helicase, Brr2

2021 ◽  
Author(s):  
Eva Absmeier ◽  
Karen Vester ◽  
Tahereh Ghane ◽  
Dmitry Burakovskiy ◽  
Pohl Milon ◽  
...  
Keyword(s):  
Long Range ◽  
Adenine Nucleotide ◽  
Adenine Nucleotides ◽  
High Specificity ◽  
Nucleotide Binding ◽  
Binding Pocket ◽  
Rna Helicase ◽  
Nucleotide Binding Sites ◽  
Catalytically Active ◽  
Dynamics Simulations

ABSTRACTBrr2 is an essential Ski2-like RNA helicase that exhibits a unique structure among the spliceosomal helicases. Brr2 harbors a catalytically active N-terminal helicase cassette and a structurally similar, but enzymatically inactive C-terminal helicase cassette. Both cassettes contain a nucleotide binding pocket. Here we use biophysical and computational methods to delineate the functional connectivity between the cassettes and how occupancy of the nucleotide binding sites may influence each other. Our results show that Brr2 exhibits high specificity for adenine nucleotides with both cassettes binding ADP tighter than ATP. Adenine nucleotide affinity for the inactive C-terminal cassette is more than two orders of magnitude higher than that of the active N-terminal cassette, largely determined by slow nucleotide release. Mutations at the inter-cassette surfaces and in the connecting linker diminish the affinity of adenine nucleotides for both cassettes. Abrogation of nucleotide binding at the C-terminal cassette reduces nucleotide binding at the N-terminal cassette, 70 Å away. Molecular dynamics simulations identified structural communication lines that likely mediate the long-range allosteric effects. Together, our results reveal intricate networks of intra-molecular interactions in the complex Brr2 RNA helicase, which fine-tune its nucleotide affinities and which could be exploited for regulating the enzyme during splicing.

scholarly journals ADENINE NUCLEOTIDE-INDUCED CONTRACTION OF THE INNER MITOCHONDRIAL MEMBRANE

1973 ◽  
Vol 56 (1) ◽  
pp. 65-73 ◽  
Author(s):  
Clinton D. Stoner ◽  
Howard D. Sirak
Keyword(s):  
Binding Sites ◽  
Mitochondrial Membrane ◽  
Adenine Nucleotide ◽  
Adenine Nucleotides ◽  
Nucleotide Binding ◽  
Nucleotide Exchange ◽  
Inner Mitochondrial Membrane ◽  
Inner Membrane ◽  
Nucleotide Binding Sites ◽  
Bongkrekic Acid

In bovine heart mitochondria bongkrekic acid at concentrations as low as about 4 nmol/mg protein (a) completely inhibits phosphorylation of exogenous adenosine diphosphate (ADP) and dephosphorylation of exogenous adenosine triphosphate (ATP), (b) completely reverses atractyloside inhibition of inner membrane contraction induced by exogenous adenine nucleotides, and (c) decreases the amount of adenine nucleotide required to elicit maximal exogenous adenine nucleotide-induced inner membrane contraction to a level which appears to correspond closely with the concentration of contractile, exogenous adenine nucleotide binding sites Bongkrekic acid at concentrations greater than 4 nmol/mg protein induces inner membrane contraction which seems to depend on the presence of endogenous ADP and/or ATP. The findings appear to be consistent with the interpretations (a) that the inner mitochondrial membrane contains two types of contractile, adenine nucleotide binding sites, (b) that the two sites differ markedly with regard to adenine nucleotide affinity, (c) that the high affinity site is identical with the adenine nucleotide exchange carrier, (d) that the low affinity site is accessible exclusively to endogenous adenine nucleotides and is largely unoccupied in the absence of bongkrekic acid, and (e) that bongkrekic acid increases the affinity of both sites in proportion to the amount of the antibiotic bound to the inner membrane.

scholarly journals Long-range allostery mediates cooperative adenine nucleotide binding by the Ski2-like RNA helicase Brr2

2021 ◽  
pp. 100829
Author(s):  
Eva Absmeier ◽  
Karen Vester ◽  
Tahereh Ghane ◽  
Dmitry Burakovskiy ◽  
Pohl Milon ◽  
...  
Keyword(s):  
Long Range ◽  
Adenine Nucleotide ◽  
Nucleotide Binding ◽  
Rna Helicase

scholarly journals The effect of butacaine on adenine nucleotide binding and translocation in rat liver mitochondria

1975 ◽  
Vol 148 (3) ◽  
pp. 527-531 ◽  
Author(s):  
D R Fayle ◽  
G J Barritt ◽  
F L Bygrave
Keyword(s):  
Rat Liver ◽  
Local Anaesthetic ◽  
Binding Sites ◽  
Adenine Nucleotide ◽  
Adenine Nucleotides ◽  
Nucleotide Binding ◽  
Local Anaesthetics ◽  
Liver Mitochondria ◽  
Rat Liver Mitochondria ◽  
Mitochondrial Inner Membrane

The effect of the local anaesthetic, butacaine, on adenine nucleotide binding and translocation in rat liver mitochondria partially depleted of their adenine nucleotide content was investigated. The range of butacaine concentrations that inhibit adenine nucleotide translocation and the extent of the inhibition are similar to the values obtained for native mitochondria. Butacaine does not alter either the total number of atractyloside-sensitive binding sites of depleted mitochondria, or the affinity of these sites for ADP or ATP under conditions where a partial inhibition of the rate of adenine nucleotide translocation is observed. The data are consistent with an effect of butacaine on the process by which adenine nucleotides are transported across the mitochondrial inner membrane rather than on the binding of adenine nucleotides to sites on the adenine nucleotide carrier. The results are briefly discussed in relation to the use of local anaesthetics in investigations of the mechanism of adenine nucleotide translocation.

An asparagine residue mediates intramolecular communication in nucleotide-regulated pyrophosphatase

2016 ◽  
Vol 473 (14) ◽  
pp. 2097-2107 ◽  
Author(s):  
Viktor A. Anashkin ◽  
Anu Salminen ◽  
Natalia N. Vorobjeva ◽  
Reijo Lahti ◽  
Alexander A. Baykov
Keyword(s):  
Adenine Nucleotide ◽  
Nucleotide Binding ◽  
Regulatory Domains ◽  
Hydrogen Bonding Pattern ◽  
Cbs Domain ◽  
Subunit Interface ◽  
Desulfitobacterium Hafniense ◽  
Dynamics Simulations ◽  
Cbs Domains ◽  
Asparagine Residue

Many prokaryotic soluble PPases (pyrophosphatases) contain a pair of regulatory adenine nucleotide-binding CBS (cystathionine β-synthase) domains that act as ‘internal inhibitors’ whose effect is modulated by nucleotide binding. Although such regulatory domains are found in important enzymes and transporters, the underlying regulatory mechanism has only begun to come into focus. We reported previously that CBS domains bind nucleotides co-operatively and induce positive kinetic co-operativity (non-Michaelian behaviour) in CBS-PPases (CBS domain-containing PPases). In the present study, we demonstrate that a homodimeric ehPPase (Ethanoligenens harbinense PPase) containing an inherent mutation in an otherwise conserved asparagine residue in a loop near the active site exhibits non-co-operative hydrolysis kinetics. A similar N312S substitution in ‘co-operative’ dhPPase (Desulfitobacterium hafniense PPase) abolished kinetic co-operativity while causing only minor effects on nucleotide-binding affinity and co-operativity. However, the substitution reversed the effect of diadenosine tetraphosphate, abolishing kinetic co-operativity in wild-type dhPPase, but restoring it in the variant dhPPase. A reverse serine-to-asparagine replacement restored kinetic co-operativity in ehPPase. Molecular dynamics simulations revealed that the asparagine substitution resulted in a change in the hydrogen-bonding pattern around the asparagine residue and the subunit interface, allowing greater flexibility at the subunit interface without a marked effect on the overall structure. These findings identify this asparagine residue as lying at the ‘crossroads’ of information paths connecting catalytic and regulatory domains within a subunit and catalytic sites between subunits.

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