scholarly journals A Conserved Structural Role for the Walker-A Lysine in P-Loop Containing Kinases

2021 ◽  
Vol 8 ◽  
Author(s):  
Fatlum Hajredini ◽  
Ranajeet Ghose
Keyword(s):  
Tyrosine Kinases ◽  
Specific Interaction ◽  
Enhanced Sampling ◽  
Structural Role ◽  
Catalytic Function ◽  
Key Characteristics ◽  
Optimal Coordination ◽  
Enzyme Families ◽  
Dynamics Simulations

Bacterial tyrosine kinases (BY-kinases) and shikimate kinases (SKs) comprise two structurally divergent P-loop containing enzyme families that share similar catalytic site geometries, most notably with respect to their Walker-A, Walker-B, and DxD motifs. We had previously demonstrated that in BY-kinases, a specific interaction between the Walker-A and Walker-B motifs, driven by the conserved “catalytic” lysine housed on the former, leads to a conformation that is unable to efficiently coordinate Mg2+•ATP and is therefore incapable of chemistry. Here, using enhanced sampling molecular dynamics simulations, we demonstrate that structurally similar interactions between the Walker-A and Walker-B motifs, also mediated by the catalytic lysine, stabilize a state in SKs that deviates significantly from one that is necessary for the optimal coordination of Mg2+•ATP. This structural role of the Walker-A lysine is a general feature in SKs and is found to be present in members that encode a Walker-B sequence characteristic of the family (Coxiella burnetii SK), and in those that do not (Mycobacterium tuberculosis SK). Thus, the structural role of the Walker-A lysine in stabilizing an inactive state, distinct from its catalytic function, is conserved between two distantly related P-loop containing kinase families, the SKs and the BY-kinases. The universal conservation of this element, and of the key characteristics of its associated interaction partners within the Walker motifs of P-loop containing enzymes, suggests that this structural role of the Walker-A lysine is perhaps a widely deployed regulatory mechanism within this ancient family.

scholarly journals Role of RNA Guanine Quadruplexes in Favoring the Dimerization of SARS Unique Domain in Coronaviruses

2020 ◽  
Author(s):  
Cécilia Hognon ◽  
Tom Miclot ◽  
Cristina Garcia Iriepa ◽  
Antonio Francés-Monerris ◽  
Stephanie Grandemange ◽  
...  
Keyword(s):  
Rational Design ◽  
Economic Consequences ◽  
Binding Modes ◽  
Enhanced Sampling ◽  
Present Contribution ◽  
Global Pandemic ◽  
Protein Dimer ◽  
Dynamics Simulations ◽  
Unique Domain

ABSTRACTCoronaviruses may produce severe acute respiratory syndrome (SARS). As a matter of fact, a new SARS-type virus, SARS-CoV-2, is responsible of a global pandemic in 2020 with unprecedented sanitary and economic consequences for most countries. In the present contribution we study, by all-atom equilibrium and enhanced sampling molecular dynamics simulations, the interaction between the SARS Unique Domain and RNA guanine quadruplexes, a process involved in eluding the defensive response of the host thus favoring viral infection of human cells. Our results evidence two stable binding modes involving an interaction site spanning either the protein dimer interface or only one monomer. The free energy profile unequivocally points to the dimer mode as the thermodynamically favored one. The effect of these binding modes in stabilizing the protein dimer was also assessed, being related to its biological role in assisting SARS viruses to bypass the host protective response. This work also constitutes a first step of the possible rational design of efficient therapeutic agents aiming at perturbing the interaction between SARS Unique Domain and guanine quadruplexes, hence enhancing the host defenses against the virus.TOC GRAPHICS

scholarly journals Amphiphilic silica derivatives associated with oligomeric medium in octamethylcyclotetrasiloxane polymerization

2020 ◽  
Vol 63 (8) ◽  
pp. 40-45
Author(s):  
Ruslan S. Davletbaev ◽  
◽  
Zulfia Z. Faizulina ◽  
Albina I. Akhmetova ◽  
Samat R. Izmailov ◽  
...  
Keyword(s):  
Intermolecular Interactions ◽  
Specific Interaction ◽  
Rheological Characteristics ◽  
Catalytic Function ◽  
Reduced Viscosity ◽  
Polyoxyethylene Glycol ◽  
Composition Modification ◽  
Hydrophobic Component ◽  
Derivatives Of

The amphiphilic derivatives of silica associated with oligomeric medium have been studied as modifiers of the catalyst for the octamethylcyclotetrasiloxane polymerization of anionic nature. The effect of the modifiers structure on the polymerization time of the obtained polydimethylsiloxanes was investigated. It was found that the modifier, like the initial polyoxyethylene glycol, exhibits the properties of promoters for the catalytic polymerization of octamethylcyclotetrasiloxane by the anionic mechanism. To establish the role of amphiphilic silica derivatives in the occurrence of intermolecular interactions in polydimethylsiloxanes that were obtained with them, the regularities of changes in the reduced viscosity of the obtained modified polydimethylsiloxanes were analyzed. It has been established that the reduced viscosity of polydimethylsiloxanes increases with an increase of the modifier amphiphilicity. This is due to the occurrence of intermolecular interactions because the specific interaction of amphiphilic silica derivatives with polydimethylsiloxane macromolecules. When using amphiphilic derivatives of silica as a modifier of the resulting polydimethylsiloxane to a content of 6 wt% hydrophobic fragment in their composition, modification of polydimethylsiloxanes does not affect their rheological characteristics. This is due to the presence of polyoxyethylene branches in the composition of the modifier, which creates a cavity for the trapping of K+ ions, as in the crown ether, they perform only a catalytic function, which leads to an increase in the rate of the process. However, starting from 10 % wt the content of the hydrophobic component in the composition of the modifier, the reduced viscosity of the obtained polydimethylsiloxane increases due to the occurrence of intermolecular interactions between the modifier and the obtained polydimethylsiloxane. It was noted that polydimethylsiloxane obtained using only polyoxyethylene glycol as a modifier exhibits viscosity characteristics lower than polydimethylsiloxane obtained by the anionic mechanism without using any modifiers.

scholarly journals Long-range dynamic correlations regulate the catalytic activity of the bacterial tyrosine kinase Wzc

2020 ◽  
Vol 6 (51) ◽  
pp. eabd3718
Author(s):  
Fatlum Hajredini ◽  
Andrea Piserchio ◽  
Ranajeet Ghose
Keyword(s):  
Tyrosine Kinases ◽  
Catalytic Domain ◽  
Atp Hydrolysis ◽  
Titration Calorimetry ◽  
Nucleotide Exchange ◽  
Enhanced Sampling ◽  
Futile Cycle ◽  
Dynamic Correlations ◽  
Sequence Of Events ◽  
Dynamics Simulations

BY-kinases represent a highly conserved family of protein tyrosine kinases unique to bacteria without eukaryotic orthologs. BY-kinases are regulated by oligomerization-enabled transphosphorylation on a C-terminal tyrosine cluster through a process with sparse mechanistic detail. Using the catalytic domain (CD) of the archetypal BY-kinase, Escherichia coli Wzc, and enhanced-sampling molecular dynamics simulations, isothermal titration calorimetry and nuclear magnetic resonance measurements, we propose a mechanism for its activation and nucleotide exchange. We find that the monomeric Wzc CD preferentially populates states characterized by distortions at its oligomerization interfaces and by catalytic element conformations that allow high-affinity interactions with ADP but not with ATP·Mg2+. We propose that oligomer formation stabilizes the intermonomer interfaces and results in catalytic element conformations suitable for optimally engaging ATP·Mg2+, facilitating exchange with bound ADP. This sequence of events, oligomerization, i.e., substrate binding, before engaging ATP·Mg2+, facilitates optimal autophosphorylation by preventing a futile cycle of ATP hydrolysis.

Peripheral insertion modulates the editing activity of the isolated CP1 domain of leucyl-tRNA synthetase

2011 ◽  
Vol 440 (2) ◽  
pp. 217-227 ◽  
Author(s):  
Ru-Juan Liu ◽  
Min Tan ◽  
Dao-Hai Du ◽  
Bei-Si Xu ◽  
Gilbert Eriani ◽  
...  
Keyword(s):  
Active Site ◽  
Trna Synthetase ◽  
Site Directed Mutagenesis ◽  
Aquifex Aeolicus ◽  
Trna Synthetases ◽  
Catalytic Function ◽  
Editing Activity ◽  
Domain Docking ◽  
Dynamics Simulations

A large insertion domain called CP1 (connective peptide 1) present in class Ia aminoacyl-tRNA synthetases is responsible for post-transfer editing. LeuRS (leucyl-tRNA synthetase) from Aquifex aeolicus and Giardia lamblia possess unique 20 and 59 amino acid insertions respectively within the CP1 that are crucial for editing activity. Crystal structures of AaLeuRS-CP1 [2.4 Å (1 Å=0.1 nm)], GlLeuRS-CP1 (2.6 Å) and the insertion deletion mutant AaLeuRS-CP1Δ20 (2.5 Å) were solved to understand the role of these insertions in editing. Both insertions are folded as peripheral motifs located on the opposite side of the proteins from the active-site entrance in the CP1 domain. Docking modelling and site-directed mutagenesis showed that the insertions do not interact with the substrates. Results of molecular dynamics simulations show that the intact CP1 is more dynamic than its mutant devoid of the insertion motif. Taken together, the data show that a peripheral insertion without a substrate-binding site or major structural role in the active site may modulate catalytic function of a protein, probably from protein dynamics regulation in two respective LeuRS CP1s. Further results from proline and glycine mutational analyses intended to reduce or increase protein flexibility are consistent with this hypothesis.

scholarly journals Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes

2019 ◽  
Vol 47 (14) ◽  
pp. 7276-7293 ◽  
Author(s):  
Petr Stadlbauer ◽  
Petra Kührová ◽  
Lukáš Vicherek ◽  
Pavel Banáš ◽  
Michal Otyepka ◽  
...  
Keyword(s):  
Single Molecule ◽  
Local Equilibrium ◽  
Enhanced Sampling ◽  
Loop Formation ◽  
Folding Intermediates ◽  
G4 Dna ◽  
Folding Pathways ◽  
Dynamics Simulations ◽  
Genomic Regions

Abstract Guanine quadruplexes (G4s) are non-canonical nucleic acids structures common in important genomic regions. Parallel-stranded G4 folds are the most abundant, but their folding mechanism is not fully understood. Recent research highlighted that G4 DNA molecules fold via kinetic partitioning mechanism dominated by competition amongst diverse long-living G4 folds. The role of other intermediate species such as parallel G-triplexes and G-hairpins in the folding process has been a matter of debate. Here, we use standard and enhanced-sampling molecular dynamics simulations (total length of ∼0.9 ms) to study these potential folding intermediates. We suggest that parallel G-triplex per se is rather an unstable species that is in local equilibrium with a broad ensemble of triplex-like structures. The equilibrium is shifted to well-structured G-triplex by stacked aromatic ligand and to a lesser extent by flanking duplexes or nucleotides. Next, we study propeller loop formation in GGGAGGGAGGG, GGGAGGG and GGGTTAGGG sequences. We identify multiple folding pathways from different unfolded and misfolded structures leading towards an ensemble of intermediates called cross-like structures (cross-hairpins), thus providing atomistic level of description of the single-molecule folding events. In summary, the parallel G-triplex is a possible, but not mandatory short-living (transitory) intermediate in the folding of parallel-stranded G4.

scholarly journals An evolutionary non-conserved motif in Helicobacter pylori arginase mediates positioning of the loop containing the catalytic residue for catalysis

2021 ◽  
Vol 478 (4) ◽  
pp. 871-894
Author(s):  
Ankita Dutta ◽  
Ditsa Sarkar ◽  
Pooja Murarka ◽  
Tasneem Kausar ◽  
Satya Narayan ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Structural Integrity ◽  
Double Mutation ◽  
Conserved Motif ◽  
Catalytic Function ◽  
Underlying Basis ◽  
Critical Residues ◽  
Dynamics Simulations ◽  
The Individual

The binuclear metalloenzyme Helicobacter pylori arginase is important for pathogenesis of the bacterium in the human stomach. Despite conservation of the catalytic residues, this single Trp enzyme has an insertion sequence (–153ESEEKAWQKLCSL165–) that is extremely crucial to function. This sequence contains the critical residues, which are conserved in the homolog of other Helicobacter gastric pathogens. However, the underlying basis for the role of this motif in catalytic function is not completely understood. Here, we used biochemical, biophysical and molecular dynamics simulations studies to determine that Glu155 of this stretch interacts with both Lys57 and Ser152. These interactions are essential for positioning of the motif through Trp159, which is located near Glu155 (His122–Trp159–Tyr125 contact is essential to tertiary structural integrity). The individual or double mutation of Lys57 and Ser152 to Ala considerably reduces catalytic activity with Lys57 to Ala being more significant, indicating they are crucial to function. Our data suggest that the Lys57–Glu155–Ser152 interaction influences the positioning of the loop containing the catalytic His133 so that this His can participate in catalysis, thereby providing a mechanistic understanding into the role of this motif in catalytic function. Lys57 was also found only in the arginases of other Helicobacter gastric pathogens. Based on the non-conserved motif, we found a new molecule, which specifically inhibits this enzyme. Thus, the present study not only provides a molecular basis into the role of this motif in function, but also offers an opportunity for the design of inhibitors with greater efficacy.

The Role of Hydrophobicity in the Stability and pH-Switchability of (RXDX)4 and Coumarin-RXDX Conjugate β-Sheets

2020 ◽  
Author(s):  
Ryan Weber ◽  
Martin McCullagh
Keyword(s):  
Biological Imaging ◽  
Ph Sensing ◽  
Hydrophobic Residue ◽  
Ideal Candidate ◽  
Self Assembling ◽  
Sensing Applications ◽  
Β Sheets ◽  
The Stability ◽  
Dynamics Simulations

<p>pH-switchable, self-assembling materials are of interest in biological imaging and sensing applications. Here we propose that combining the pH-switchability of RXDX (X=Ala, Val, Leu, Ile, Phe) peptides and the optical properties of coumarin creates an ideal candidate for these materials. This suggestion is tested with a thorough set of all-atom molecular dynamics simulations. We first investigate the dependence of pH-switchabiliy on the identity of the hydrophobic residue, X, in the bare (RXDX)<sub>4</sub> systems. Increasing the hydrophobicity stabilizes the fiber which, in turn, reduces the pH-switchabilty of the system. This behavior is found to be somewhat transferable to systems in which a single hydrophobic residue is replaced with a coumarin containing amino acid. In this case, conjugates with X=Ala are found to be unstable and both pHs while conjugates with X=Val, Leu, Ile and Phe are found to form stable β-sheets at least at neutral pH. The (RFDF)<sub>4</sub>-coumarin conjugate is found to have the largest relative entropy value of 0.884 +/- 0.001 between neutral and acidic coumarin ordering distributions. Thus, we posit that coumarin-(RFDF)<sub>4</sub> containing peptide sequences are ideal candidates for pH-sensing bioelectronic materials.</p>

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