Understanding the molecular behaviour of Renilla luciferase in imidazolium-based ionic liquids, a new model for the α/β fold collapse

Ghaedizadeh, Shima; Emamzadeh, Rahman; Nazari, Mahboobeh; Rasa, S. Mohamad Mahdi; Zarkesh-Esfahani, Hamid; Yousefi, Maryam

doi:10.1016/j.bej.2015.10.024

Cited by 34 publications

(35 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The essential catalytic unit of RLuc has been reported to be the catalytic triad, which consists of D120, E144 and H285. Moreover, this catalytic triad is located at the bottom of a main tunnel, which is solvent accessible and permits substrate influx and product egress during the bioluminescence reaction [20].…”

Section: The Relationship Between Mutations and Super Rluc8 Activitymentioning

confidence: 99%

Super RLuc8: A novel engineered Renilla luciferase with a red-shifted spectrum and stable light emission

Rahnama

Saffar

Kahrani

et al. 2017

Enzyme and Microbial Technology

Self Cite

View full text Add to dashboard Cite

Renilla luciferase is a bioluminescent enzyme which is broadly used as a reporter protein in molecular biosensors. In this study, a novel luciferase with desired light emission wavelength and thermostability is reported. The results indicated that the new luciferase, namely super RLuc8, had a red-shifted spectrum and showed stable light emission. Super RLuc8 showed a 10-fold (p-value=0.0084) increase in the thermostability at 37°C after 20min incubation, in comparison to the native enzyme. The optimum temperature of the mutant increased from 30 to 37°C. Molecular dynamics simulation analysis indicated that the increased thermostability was most probably caused by a better structural compactness and more local rigidity in the regions out of the emitter site.

show abstract

Section: The Relationship Between Mutations and Super Rluc8 Activitymentioning

confidence: 99%

Super RLuc8: A novel engineered Renilla luciferase with a red-shifted spectrum and stable light emission

Rahnama

Saffar

Kahrani

et al. 2017

Enzyme and Microbial Technology

Self Cite

View full text Add to dashboard Cite

show abstract

“…Although most studies are focused on the enzymes catalytic activity in presence of aromatic ILs, particularly imidazolium‐based, noncyclic and nonaromatic cations, such as phosphonium‐based ILs, could lead to relevant improvements and contribute to the design of efficient biotechnological processes . Imidazolium‐based ILs have been applied as solvents in biocatalytic processes involving reactions such as transesterification and hydrolysis . Mai et al studied the transesterification of sugar fatty acids catalyzed by Novozym 435 in presence of imidazolium‐based ILs, showing 96% of conversion of vinyl laurate with glucose in a mixture of (1:1, vol/vol) [C 4 mim][TfO]:[C 4 mim][NTf 2 ] (1‐butyl‐3‐methylimidazolium triflate:1‐butyl‐3‐methylimidazolium bistrisflamide).…”

Section: Introductionmentioning

confidence: 99%

“…After 10 cycles, the enzyme activity was 75% of its initial activity. To better understand how the Renilla luciferase activity is influenced by imidazolium‐based ILs, Ghaedizadeh et al performed a combined experimental and molecular dynamics simulation study with ILs composed of fluorinated anions, namely [C 4 mim][PF 6 ] and [C 4 mim][BF 4 ] (1‐butyl‐3‐methylimidazolium hexafluorophosphate and 1‐butyl‐3‐methylimidazolium tetrafluoroborate). The authors showed that these ILs promote changes in the protein secondary structure leading to a decrease on the enzymatic activity.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Effects of phosphonium‐based ionic liquids on the lipase activity evaluated by experimental results and molecular docking

Barbosa

Freire

Souza

et al. 2019

Biotechnology Progress

View full text Add to dashboard Cite

In this work, the effect of several phosphonium‐based ionic liquids (ILs) on the activity of lipase from Burkholderia cepacia (BCL) was evaluated by experimental assays and molecular docking. ILs comprising different cations ([P4444]+, [P444(14)]+, [P666(14)]+) and anions (Cl−, Br−, [Deca]−, [Phosp]−, [NTf2]−) were investigated to appraise the individual roles of IL ions on the BCL activity. From the activity assays, it was found that an increase in the cation alkyl chain length leads to a decrease on the BCL enzymatic activity. ILs with the anions [Phosp]− and [NTf2]− increase the BCL activity, while the remaining [P666(14)]‐based ILs with the Cl−, Br−, and [Deca]− anions display a negative effect on the BCL activity. The highest activity of BCL was identified with the IL [P666(14)][NTf2] (increase in the enzymatic activity of BCL by 61% at 0.055 mol·L−1). According to the interactions determined by molecular docking, IL cations preferentially interact with the Leu17 residue (amino acid present in the BCL oxyanion hole). The anion [Deca]− has a higher binding affinity compared to Cl− and Br−, and mainly interacts by hydrogen‐bonding with Ser87, an amino acid residue which constitutes the catalytic triad of BCL. The anions [Phosp]− and [NTf2]− have high binding energies (−6.2 and −5.6 kcal·mol−1, respectively) with BCL, and preferentially interact with the side chain amino acids of the enzyme and not with residues of the active site. Furthermore, FTIR analysis of the protein secondary structure show that ILs that lead to a decrease on the α‐helix content result in a higher BCL activity, which may be derived from an easier access of the substrate to the BCL active site.

show abstract

“…(Jaeger, Burney, & Pfaendtner, 2015; W. Li, Wang, Zhou, & Mu, 2015). Other proteins, including lipase (Burney, Nordwald, Hickman, Kaar, & Pfaendtner, 2015;Burney & Pfaendtner, 2013;Kim, Ha, Sethaphong, Koo, & Yingling, 2014;Klähn, Lim, Seduraman, & Wu, 2011;Klähn, Lim, & Wu, 2011;Latif, Micaêlo, & Rahman, 2014a), protease Latif, Tejo, Abedikargiban, Abdul Rahman, & Micaêlo, 2013;Micaêlo & Soares, 2008), lysozyme (Ghosh, Parui, Jana, & Bhattacharyya, 2015), monooxygenase (Sprenger, Choudhury, Kaar, & Pfaendtner, 2016;Tee et al, 2008), luciferase (Ghaedizadeh et al, 2016), xylanase (Jaeger & Pfaendtner, 2013), ubiquitin , and zinc finger proteins (Haberler, Schröder, & Steinhauser, 2011), have been simulated in a range of ILs and provide many hypotheses regarding candidate inactivation mechanisms. In neat ILs or highly concentrated mixtures, surface solvation can play an important role in moderating enzyme activity.…”

mentioning

confidence: 94%

Molecular dynamics simulations of cellulase homologs in aqueous 1-ethyl-3-methylimidazolium chloride

Johnson

Snow

2016

Journal of Biomolecular Structure and Dynamics

View full text Add to dashboard Cite

Pretreating biomass using ionic liquids (ILs) can decrease cellulose crystallinity and lead to improved hydrolysis. However, cellulase activity is often reduced in even low concentrations of ILs, necessitating complete washing between pretreatment and hydrolysis steps. To better understand how ILs interact with enzymes at the molecular scale, endoglucanase E1 from Acidothermus cellulolyticus was simulated in aqueous 1-ethyl-3-methylimidazolium chloride ([Emim]Cl). Homologs with differing surface charge were also simulated to assess the role of electrostatic interactions between the enzyme and the surrounding solvent. Chloride anions interacted with the enzyme surface via Coulomb or hydrogen bond interactions, while [Emim] cations primarily formed hydrophobic or ring stacking interactions. Cations strongly associated with the binding pocket of E1, potentially inhibiting the binding of substrate molecules. At elevated temperatures, cations also disrupted native hydrophobic contacts and caused some loss of secondary structure. These observations suggested that both cations and anions could influence enzyme behavior and that denaturing and inhibitory interactions might both be important in aqueous IL systems.

show abstract

Understanding the molecular behaviour of Renilla luciferase in imidazolium-based ionic liquids, a new model for the α/β fold collapse

Cited by 34 publications

References 55 publications

Super RLuc8: A novel engineered Renilla luciferase with a red-shifted spectrum and stable light emission

Super RLuc8: A novel engineered Renilla luciferase with a red-shifted spectrum and stable light emission

Effects of phosphonium‐based ionic liquids on the lipase activity evaluated by experimental results and molecular docking

Molecular dynamics simulations of cellulase homologs in aqueous 1-ethyl-3-methylimidazolium chloride

Contact Info

Product

Resources

About