Phenol sensing in nature is modulated via a conformational switch governed by dynamic allostery

Singh, Jayanti; Sahil, Mohammad; Ray, Shamayeeta; Dcosta, Criss; Panjikar, Santosh; Krishnamoorthy, G.; Mondal, Jagannath; Anand, Ruchi

doi:10.1016/j.jbc.2022.102399

Cited by 4 publications

(8 citation statements)

References 69 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…H106 exists in two different states in I2 and B states, which allow it to form a hydrogen bond with ligand initially in the I2 state and potentially drive the ligand to bound state, where ligand can form hydrogen bond with W134 also (Figure C,D, S8). This shifting of H106 marks the beginning of downstream signaling as explained in our previous work . Additionally, involvement of H106 in the I2 state also re-explains our previous observation regarding the pronounced effect of H106 as compared to W134.…”

Section: Resultssupporting

confidence: 87%

“…This shifting of H106 marks the beginning of downstream signaling as explained in our previous work. 32 Additionally, involvement of H106 in the I2 state also re-explains our previous observation regarding the pronounced effect of H106 as compared to W134. In particular, H106 (H106A K d = 7.86 ± 0.01 μM) and W134 (W134A K d = 2.87 ± 0.01 μM) form a hydrogen bond with bound phenol but have a different contribution to binding affinity.…”

Section: Statistical Model Reveals Four-state Ligand-sensing Processmentioning

confidence: 95%

See 1 more Smart Citation

Identifying Selectivity Filters in Protein Biosensor for Ligand Screening

Sahil,

Singh,

Sahu

et al. 2023

JACS Au

Self Cite

View full text Add to dashboard Cite

Specialized sensing mechanisms in bacteria enable the identification of cognate ligands with remarkable selectivity in highly xenobiotic-polluted environments where these ligands are utilized as energy sources. Here, via integrating all-atom computer simulation, biochemical assay, and isothermal titration calorimetry measurements, we determine the molecular basis of MopR, a phenol biosensor’s complex selection process of ligand entry. Our results reveal a set of strategically placed selectivity filters along the ligand entry pathway of MopR. These filters act as checkpoints, screening diverse aromatic ligands at the protein surface based on their chemical features and sizes. Ligands meeting specific criteria are allowed to enter the sensing site in an orientation-dependent manner. Sequence and structural analyses demonstrate the conservation of this ligand entry mechanism across the sensor class, with individual amino acids along the selectivity filter path playing a critical role in ligand selection. Together, this investigation highlights the importance of interactions with the ligand entry pathway, in addition to interactions within the binding pocket, in achieving ligand selectivity in biological sensing. The findings enhance our understanding of ligand selectivity in bacterial phenol biosensors and provide insights for rational expansion of the biosensor repertoire, particularly for the biotechnologically relevant class of aromatic pollutants.

show abstract

Section: Resultssupporting

confidence: 87%

Section: Statistical Model Reveals Four-state Ligand-sensing Processmentioning

confidence: 95%

Identifying Selectivity Filters in Protein Biosensor for Ligand Screening

Sahil,

Singh,

Sahu

et al. 2023

JACS Au

Self Cite

View full text Add to dashboard Cite

show abstract

“…To better understand the apparently high selectivity of the sensory domains of the PheR, PcrS, and EtpR proteins from A. aromaticum EbN1 T , insights into their ligand-binding were aimed at. For this purpose, crystal structures of the sensory domains from the known phenol sensors MopR, CapR, and PoxR from other bacteria ( 18 – 21 ) were compared with 3D models of their counterparts in PheR, PcrS, and EtpR, which were generated by applying the recently available AlphaFold tool ( 30 ).…”

Section: Resultsmentioning

confidence: 99%

“…S5B) reveals, next to overall high similarities, several conserved residues that are functionally and structurally essential for the ligand-binding pocket: (i) a dyad His and Trp anchors the hydroxy group of phenol via hydrogen bonds, (ii) several hydrophobic residues that stabilize the aromatic ring of phenol via van der Waals interactions, and (iii) three Cys and one Glu residue(s) that are involved in tetrahedral zinc coordination for maintaining structural integrity. The overall fold of the sensory domains of the MopR dimer from Acinetobacter calcoaceticus , as revealed by its crystal structure (2.30 Å resolution) ( 19 ), is shown in Fig. 5B , highlighting bound phenol and zinc as well as indicating the secondary structural elements.…”

Section: Resultsmentioning

confidence: 99%

“…Furthermore, the predicted PheR protein is homologous to the known phenol sensors MopR (from Acinetobacter calcoaceticus ), CapR (also called DmpR, from Pseudomonas putida ), and PoxR (from Ralstonia eutropha ). Their determined crystal structures revealed conserved histidine and tryptophane residues in the N-terminal V4R domain, which anchor via hydrogen bridges the hydroxy group of phenol ( 18 – 21 ). (ii) The genes ( cmh , hbd , and hcl2 ) assigned to anaerobic p -cresol degradation are intercalated by those for the predicted σ 54 -dependent two-component system PcrSR (activator), while the promotor region upstream of the cmh gene harbors a σ 54 consensus promoter ( 13 ).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Sensitive and selective phenol sensing in denitrifying Aromatoleum aromaticum EbN1 ^T

Buschen,

Lambertus,

Scheve

et al. 2023

Microbiol Spectr

View full text Add to dashboard Cite

Aromatoleum aromaticum EbN1 T anaerobically degrades phenol, p -cresol, and p -ethylphenol, each via a distinct peripheral pathway. The compound-specific regulation of each pathway is proposed to occur on the transcriptional level in the case of phenol supposedly mediated by the one-component system PheR. To confirm its predicted function, we generated an unmarked, in-frame deletion mutant (Δ pheR ). This mutant did not express the ppsA1 gene, which encodes the A1 subunit of phenol-activating phenylphosphate synthase. The expression of ppsA1 was restored by in trans complementation of pheR into the Δ pheR background. The responsiveness to phenol was studied in vivo in benzoate-limited anaerobic cultures by adding, upon benzoate depletion, single defined pulses of phenol (from 100 µM down to 0.1 nM). Time-resolved, targeted transcript profiling by qRT-PCR revealed a response threshold for ppsA1 expression of 30‒50 nM phenol. Notably, ppsA1 expression could not be induced by p -cresol or p -ethylphenol. Conversely, lack of expression was also observed for the additional target genes cmh ( p -cresol degradation) and acsA1 ( p -ethylphenol degradation) applying phenol or p -ethylphenol as well as phenol or p -cresol as stimuli. Thus, the sensory proteins PheR, PcrS, and EtpR should be highly selective for phenol, p -cresol, and p -ethylphenol, respectively. The implicated incapability of cross-stimulus binding was corroborated by comparing the predicted 3D structural models of the proteins’ sensory domains. While the ligand-binding pockets share the conserved hydroxy group-anchoring histidine and tryptophane, their distal faces in PcrS and EtpR are, compared to PheR, enlarged to accommodate the bulkier methyl ( p -cresol) and ethyl group ( p -ethylphenol), respectively. IMPORTANCE Aromatic compounds are globally abundant organic molecules with a multitude of natural and anthropogenic sources, underpinning the relevance of their biodegradation. A. aromaticum EbN1 T is a well-studied environmental betaproteobacterium specialized on the anaerobic degradation of aromatic compounds. The here studied responsiveness toward phenol in conjunction with the apparent high ligand selectivity (non-promiscuity) of its PheR sensor and those of the related p -cresol (PcrS) and p -ethylphenol (EtpR) sensors are in accord with the substrate-specificity and biochemical distinctiveness of the associated degradation pathways. Furthermore, the present findings advance our general understanding of the substrate-specific regulation of the strain’s remarkable degradation network and of the concentration thresholds below which phenolic compounds become essentially undetectable and as a consequence should escape substantial biodegradation. Furthermore, the findings may inspire biomimetic sensor designs for detecting and quantifying phenolic contaminants in wastewater or environments.

show abstract

Long-time-step molecular dynamics can retard simulation of protein-ligand recognition process

Sahil¹,

Sarkar²,

Mondal³

2023

Biophysical Journal

View full text Add to dashboard Cite

Phenol sensing in nature is modulated via a conformational switch governed by dynamic allostery

Cited by 4 publications

References 69 publications

Identifying Selectivity Filters in Protein Biosensor for Ligand Screening

Identifying Selectivity Filters in Protein Biosensor for Ligand Screening

Sensitive and selective phenol sensing in denitrifying Aromatoleum aromaticum EbN1 ^T

Long-time-step molecular dynamics can retard simulation of protein-ligand recognition process

Contact Info

Product

Resources

About

Phenol sensing in nature is modulated via a conformational switch governed by dynamic allostery

Cited by 4 publications

References 69 publications

Identifying Selectivity Filters in Protein Biosensor for Ligand Screening

Identifying Selectivity Filters in Protein Biosensor for Ligand Screening

Sensitive and selective phenol sensing in denitrifying Aromatoleum aromaticum EbN1 T

Long-time-step molecular dynamics can retard simulation of protein-ligand recognition process

Contact Info

Product

Resources

About

Sensitive and selective phenol sensing in denitrifying Aromatoleum aromaticum EbN1 ^T