Biocatalyst activity in nonaqueous environments correlates with centisecond-range protein motions

Recent Advances in Microfluidics-Based Electrochemical Sensors for Foodborne Pathogen Detection

Using pathogen-infected food that can be unhygienic can result in severe diseases and an increase in mortality rate among humans. This may arise as a serious emergency problem if not appropriately restricted at this point of time. Thus, food science researchers are concerned with precaution, prevention, perception, and immunity to pathogenic bacteria. Expensive, elongated assessment time and the need for skilled personnel are some of the shortcomings of the existing conventional methods. Developing and investigating a rapid, low-cost, handy, miniature, and effective detection technology for pathogens is indispensable. In recent times, there has been a significant scope of interest for microfluidics-based three-electrode potentiostat sensing platforms, which have been extensively used for sustainable food safety exploration because of their progressively high selectivity and sensitivity. Meticulously, scholars have made noteworthy revolutions in signal enrichment tactics, measurable devices, and portable tools, which can be used as an allusion to food safety investigation. Additionally, a device for this purpose must incorporate simplistic working conditions, automation, and miniaturization. In order to meet the critical needs of food safety for on-site detection of pathogens, point-of-care testing (POCT) has to be introduced and integrated with microfluidic technology and electrochemical biosensors. This review critically discusses the recent literature, classification, difficulties, applications, and future directions of microfluidics-based electrochemical sensors for screening and detecting foodborne pathogens.

Macromolecular Crowding Is More than Hard-Core Repulsions

Cells are crowded, but proteins are almost always studied in dilute aqueous buffer. We review the experimental evidence that crowding affects the equilibrium thermodynamics of protein stability and protein association and discuss the theories employed to explain these observations. In doing so, we highlight differences between synthetic polymers and biologically relevant crowders. Theories based on hard-core interactions predict only crowding-induced entropic stabilization. However, experiment-based efforts conducted under physiologically relevant conditions show that crowding can destabilize proteins and their complexes. Furthermore, quantification of the temperature dependence of crowding effects produced by both large and small cosolutes, including osmolytes, sugars, synthetic polymers, and proteins, reveals enthalpic effects that stabilize or destabilize proteins. Crowding-induced destabilization and the enthalpic component point to the role of chemical interactions between and among the macromolecules, cosolutes, and water. We conclude with suggestions for future studies. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The role of conformational dynamics on the activity of polymer-conjugated CalB in organic solvents

A perennial interest in enzyme catalysis has been expanding its applicability from aqueous phase where enzymes are naturally evolved to organic solvents in which the majority of industrial chemical synthesis...

Enabling biocatalysis in high-concentration organic cosolvent by enzyme gate engineering

Biocatalysis in high-concentration organic solvents (OSs) offers many advantages, but realizing this process remains a huge challenge. An R-selective ω-amine transaminase variant (AcATA_M2 ) exhibited high activity toward 50 g/L pro-sitagliptin ketone 1-[1-piperidinyl]-4-[2,4,5-trifluorophenyl]-1,3-butanedione (PTfpB). However, AcATA_M2 displayed unsatisfactory organic-cosolvent resistance against high-concentration dimethyl sulfoxide (DMSO), which is required to enhance the solubility of the hydrophobic substrate PTfpB. Located in the substrate-binding tunnel, enzyme gates are structural elements that undergo reversible conformational transitions, thus affecting the accessibility of the binding pocket to solvent molecules. Depending on the conformation of the enzyme gates, one can define an open or closed conformation on which the enzyme activity in OSs may depend. To enhance the DMSO resistance of AcATA_M2 , we identified the beneficial residues at the "enzyme gate" region via computational analysis, alanine scanning, and site-saturation mutagenesis. Two beneficial variants, namely, AcATA_M2 ^F56D and AcATA_M2 ^F56V , not only displayed improved enzyme activity but also exhibited enhanced DMSO resistance (the half-life value increased from 25.71 to 42.49 h under 60% DMSO). Molecular dynamic simulations revealed that the increase in DMSO resistance was mainly caused by the decrease in the number of DMSO molecules in the substrate-binding pocket. Moreover, in the kilogram-scale experiment, the conversion of 80 g/L substrate was increased from 50% (AcATA_M2 ) to 85% (M2^F56D in 40% DMSO) with a high e.e. of >99% within 24 h.

What do we learn from enzyme behaviors in organic solvents? - Structural functionalization of ionic liquids for enzyme activation and stabilization

Enzyme activity in nonaqueous media (e.g. conventional organic solvents) is typically lower than in water by several orders of magnitude. There is a rising interest of developing new nonaqueous solvent systems that are more "water-like" and more biocompatible. Therefore, we need to learn from the current state of nonaqueous biocatalysis to overcome its bottleneck and provide guidance for new solvent design. This review firstly focuses on the discussion of how organic solvent properties (such as polarity and hydrophobicity) influence the enzyme activity and stability, and how these properties impact the enzyme's conformation and dynamics. While hydrophobic organic solvents usually lead to the maintenance of enzyme activity, solvents carrying functional groups like hydroxys and ethers (including crown ethers and cyclodextrins) can lead to enzyme activation. Ionic liquids (ILs) are designable solvents that can conveniently incorporate these functional groups. Therefore, we systematically survey these ether- and/or hydroxy-functionalized ILs, and find most of them are highly compatible with enzymes leading to high activity and stability. In particular, ILs carrying both ether and tert-alcohol groups are among the most enzyme-activating solvents. Future direction is to learn from enzyme behaviors in both water and nonaqueous media to design biocompatible "water-like" solvents.

Production and use of immobilized lipases in/on nanomaterials: A review from the waste to biodiesel production

As a highly efficient and environmentally friendly biocatalyst, immobilized lipase has received incredible interest among the biotechnology community for the production of biodiesel. Nanomaterials possess high enzyme loading, low mass transfer limitation, and good dispersibility, making them suitable biocatalytic supports for biodiesel production. In addition to traditional nanomaterials such as nano‑silicon, magnetic nanoparticles and nano metal particles, novel nanostructured forms such as nanoflowers, carbon nanotubes, nanofibers and metal-organic frameworks (MOFs) have also been studied for biodiesel production in the recent years. However, some problems still exist that need to be overcome in achieving large-scale biodiesel production using immobilized lipase on/in nanomaterials. This article mainly presents an overview of the current and state-of-the-art research on biodiesel production by immobilized lipases in/on nanomaterials. Various immobilization strategies of lipase on various advanced nanomaterial supports and its applications in biodiesel production are highlighted. Influential factors such as source of lipase, immobilization methods, feedstocks, and production process are also critically discussed. Finally, the current challenges and future directions in developing immobilized lipase-based biocatalytic systems for high-level production of biodiesel from waste resources are also recommended.

Coupled Valence-Bond State Molecular Dynamics Description of an Enzyme-Catalyzed Reaction in a Non-Aqueous Organic Solvent

Enzymes are widely used in nonaqueous solvents to catalyze non-natural reactions. While experimental measurements showed that the solvent nature has a strong effect on the reaction kinetics, the molecular details of the catalytic mechanism in nonaqueous solvents have remained largely elusive. Here we study the transesterification reaction catalyzed by the paradigm subtilisin Carlsberg serine protease in an organic apolar solvent. The rate-limiting acylation step involves a proton transfer between active-site residues and the nucleophilic attack of the substrate to form a tetrahedral intermediate. We design the first coupled valence-bond state model that simultaneously describes both reactions in the enzymatic active site. We develop a new systematic procedure to parametrize this model on high-level ab initio QM/MM free energy calculations that account for the molecular details of the active site and for both substrate and protein conformational fluctuations. Our calculations show that the reaction energy barrier changes dramatically with the solvent and protein conformational fluctuations. We find that the mechanism of the tetrahedral intermediate formation during the acylation step is similar to that determined under aqueous conditions, and that the proton transfer and nucleophilic attack reactions occur concertedly. We identify the reaction coordinate to be mostly due to the rearrangement of some residual water molecules close to the active site.

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.

Enzyme activity in liquid lipase melts as a step towards solvent-free biology at 150 °C

Water molecules play a number of critical roles in enzyme catalysis, including mass transfer of substrates and products, nucleophilicity and proton transfer at the active site, and solvent shell-mediated dynamics for accessing catalytically competent conformations. The pervasiveness of water in enzymolysis therefore raises the question concerning whether biocatalysis can be undertaken in the absence of a protein hydration shell. Lipase-mediated catalysis has been undertaken with reagent-based solvents and lyophilized powders, but there are no examples of molecularly dispersed enzymes that catalyse reactions at sub-solvation levels within solvent-free melts. Here we describe the synthesis, properties and enzyme activity of self-contained reactive biofluids based on solvent-free melts of lipase-polymer surfactant nanoconjugates. Desiccated substrates in liquid (p-nitrophenyl butyrate) or solid (p-nitrophenyl palmitate) form can be mixed or solubilized, respectively, into the enzyme biofluids, and hydrolysed in the solvent-free state. Significantly, the efficiency of product formation increases as the temperature is raised to 150 °C.

LiCl-induced improvement of multilayer nanofibrous lipase for biodiesel synthesis

A unique method that applied a multilayer-immobilization strategy was developed to prepare nanofibrous enzymes for biosynthesis. LiCl co-electrospun with polyurethane nanofibers enabled strong physical adsorption of bovine serum albumin (BSA), forming the first layer of protein on the nanofibers; lipase AK was subsequently crosslinked to BSA as an outer layer of enzyme. The content of LiCl in nanofibers was found to be a sensitive factor affecting the activity and stability of the immobilized lipase. For biodiesel synthesis from soybean oil and methanol in isooctane, the reaction rate catalyzed by nanofibrious lipase carrying 5 wt% LiCl was 6.6-fold higher than fibers without LiCl, with a conversion of 91% was achieved within 2 h. LiCl also induced much improved enzyme stability. The nanofibrous lipase with 5% LiCl could be repeatedly used for 42 cycles without apparent activity loss, while the immobilized lipase without LiCl lost over 90% activity within 13 reuse cycles.

"Fluctuograms" reveal the intermittent intra-protein communication in subtilisin Carlsberg and correlate mechanical coupling with co-evolution

The mechanism of intra-protein communication and allosteric coupling is key to understanding the structure-property relationship of protein function. For subtilisin Carlsberg, the Ca²⁺-binding loop is distal to substrate-binding and active sites, yet the serine protease function depends on Ca²⁺ binding. The atomic molecular dynamics (MD) simulations of apo and Ca²⁺-bound subtilisin show similar structures and there is no direct evidence that subtilisin has alternative conformations. To model the intra-protein communication due to Ca²⁺ binding, we transform the sequential segments of an atomic MD trajectory into separate elastic network models to represent anharmonicity and nonlinearity effectively as the temporal and spatial variation of the mechanical coupling network. In analogy to the spectrogram of sound waves, this transformation is termed the “fluctuogram” of protein dynamics. We illustrate that the Ca²⁺-bound and apo states of subtilisin have different fluctuograms and that intra-protein communication proceeds intermittently both in space and in time. We found that residues with large mechanical coupling variation due to Ca²⁺ binding correlate with the reported mutation sites selected by directed evolution for improving the stability of subtilisin and its activity in a non-aqueous environment. Furthermore, we utilize the fluctuograms calculated from MD to capture the highly correlated residues in a multiple sequence alignment. We show that in addition to the magnitude, the variance of coupling strength is also an indicative property for the sequence correlation observed in a statistical coupling analysis. The results of this work illustrate that the mechanical coupling networks calculated from atomic details can be used to correlate with functionally important mutation sites and co-evolution.

A hallmark of protein molecules is their machine-like behaviors while carrying out biological functions. At the molecular level, molecular signals such as binding a metal ion at an action site can cause long-range effects and alter protein function. Such phenomena are often referred to as intra-protein communication or allosteric coupling. Elucidating the underlying mechanisms could lead to novel discovery of molecular modulators to regulate protein function in a more specific and effective manner. A long-standing puzzle is the roles of the anharmonicity and nonlinearity in protein dynamics. To incorporate these characters in modeling intra-protein communication, we devise a “fluctuogram” analysis to record the choreography of allosteric coupling in an atomic molecular dynamics simulation. We show that fluctuogram analysis can bridge the results of physics-based simulation and sequence alignment in bioinformatics by capturing the residues that exhibit high correlation in a multiple sequence alignment. We also show that the fluctuograms calculated from atomic details have the potential to be applied as a tool to select mutation sites for modulating protein function.

On the roles of substrate binding and hinge unfolding in conformational changes of adenylate kinase

We characterized the conformational change of adenylate kinase (AK) between open and closed forms by conducting five all-atom molecular-dynamics simulations, each of 100 ns duration. Different initial structures and substrate binding configurations were used to probe the pathways of AK conformational change in explicit solvent, and no bias potential was applied. A complete closed-to-open and a partial open-to-closed transition were observed, demonstrating the direct impact of substrate-mediated interactions on shifting protein conformation. The sampled configurations suggest two possible pathways for connecting the open and closed structures of AK, affirming the prediction made based on available x-ray structures and earlier works of coarse-grained modeling. The trajectories of the all-atom molecular-dynamics simulations revealed the complexity of protein dynamics and the coupling between different domains during conformational change. Calculations of solvent density and density fluctuations surrounding AK did not show prominent variation during the transition between closed and open forms. Finally, we characterized the effects of local unfolding of an important hinge near Pro(177) on the closed-to-open transition of AK and identified a novel mechanism by which hinge unfolding modulates protein conformational change. The local unfolding of Pro(177) hinge induces alternative tertiary contacts that stabilize the closed structure and prevent the opening transition.

Dramatic thermal stability of virus-polymer conjugates in hydrophobic solvents

We have developed a method for integrating the self-assembling tobacco mosaic virus capsid into hydrophobic solvents and hydrophobic polymers. The capsid was modified at tyrosine residues to display an array of linear poly(ethylene glycol) chains, allowing it to be transferred into chloroform. In a subsequent step, the capsids could be transferred to a variety of hydrophobic solvents, including benzyl alcohol, o-dichlorobenzene, and diglyme. The thermal stability of the material against denaturation increased from 70 °C in water to at least 160 °C in hydrophobic solvents. With a view toward material fabrication, the polymer-coated TMV rods were also incorporated into solid polystyrene and thermally cast at 110 °C. Overall, this process significantly expands the range of processing conditions for TMV-based materials, with the goal of incorporating these templated nanoscale systems into conductive polymer matrices.

Acrylonitrile quenching of trp phosphorescence in proteins: a probe of the internal flexibility of the globular fold

Quenching of Trp phosphorescence in proteins by diffusion of solutes of various molecular sizes unveils the frequency-amplitude of structural fluctuations. To cover the sizes gap between O(2) and acrylamide, we examined the potential of acrylonitrile to probe conformational flexibility of proteins. The distance dependence of the through-space acrylonitrile quenching rate was determined in a glass at 77 K, with the indole analog 2-(3-indoyl) ethyl phenyl ketone. Intensity and decay kinetics data were fitted to a rate, k(r) =k(0) exp[-(r -r(0))/r(e)], with an attenuation length r(e) = 0.03 nm and a contact rate k(0) = 3.6 x 10(10) s(-1). At ambient temperature, the bimolecular quenching rate constant (kq) was determined for a series of proteins, appositely selected to test the importance of factors such as the degree of Trp burial and structural rigidity. Relative to kq = 1.9 x 10(9) M(-1)s(-1) for free Trp in water, in proteins kq ranged from 6.5 x 10(6) M(-1)s(-1) for superficial sites to 1.3 x 10(2) M(-1)s(-1) for deep cores. The short-range nature of the interaction and the direct correlation between kq and structural flexibility attest that in the microsecond-second timescale of phosphorescence acrylonitrile readily penetrates even compact protein cores and exhibits significant sensitivity to variations in dynamical structure of the globular fold.

Activity and enantioselectivity of the hydroxynitrile lyase MeHNL in dry organic solvents

Water concentration affects both the enantioselectivity and activity of enzymes in dry organic media. Its influence has been investigated using the hydrocyanation of benzaldehyde catalyzed by hydroxynitrile lyase cross-linked enzyme aggregate (MeHNL-CLEA) as a model reaction. The enzyme displayed higher enantioselectivity at higher water concentration, thus suggesting a positive effect of enzyme flexibility on selectivity. The activity increased on reducing the solvent water content, but drastic dehydration of the enzyme resulted in a reversible loss of activity.

Effect of prolonged exposure to organic solvents on the active site environment of subtilisin Carlsberg

The potential of enzyme catalysis as a tool for organic synthesis is nowadays indisputable, as is the fact that organic solvents affect an enzyme's activity, selectivity and stability. Moreover, it was recently realized that an enzyme's initial activity is substantially decreased after prolonged exposure to organic media, an effect that further hampers their potential as catalysts for organic synthesis. Regrettably, the mechanistic reasons for these effects are still debatable. In the present study we have made an attempt to explain the reasons behind the partial loss of enzyme activity on prolonged exposure to organic solvents. Fluorescence spectroscopic studies of the serine protease subtilisin Carlsberg chemically modified with polyethylene glycol (PEG-SC) and inhibited with a Dancyl fluorophore, and dissolved in two organic solvents (acetonitrile and 1,4-dioxane) indicate that when the enzyme is initially introduced into these solvents, the active site environment is similar to that in water; however prolonged exposure to the organic medium causes this environment to resemble that of the solvent in which the enzyme is dissolved. Furthermore, kinetic studies show a reduction on both V(max) and K(M) as a result of prolonged exposure to the solvents. One interpretation of these results is that during this prolonged exposure to organic solvents the active-site fluorescent label inhibitor adopts a different binding conformation. Extrapolating this to an enzymatic reaction we argue that substrates bind in a less catalytically favorable conformation after the enzyme has been exposed to organic media for several hours.