Exploring the Promoting Mechanisms of Bovine Serum Albumin, Lignosulfonate, Polyethylene Glycol for Lignocellulose Saccharification from Perspective of Molecular Interactions with Cellulase

Background: Bovine serum albumin (BSA), polyethylene glycol (PEG) and lignosulfonate (LS) have been extensively employed as synergistic agents in lignocellulose saccharification. Nevertheless, the promoting mechanisms have not been fully understood and there are a number of controversial opinions existed. All attention has been paid to the interactions between respective additive and substrate. However, rarely attention has been paid to the interactions between additives and cellulase. The interaction between respective additive and cellulase is actually more important since cellulase interacts with the additives before it contacts with substrate.Results: This investigation showed that BSA and LS could bind to cellulase to form complexes, whereas PEG did not. However, PEG had a high affinity to lignin or lignin derivatives. The complexes of Cell-BSA consisted of one BSA and four cellulase molecules; while the complexes of Cell-LS were composed of one cellulase and four LS molecules in the testing conditions. Regarding to the enzymatic hydrolytic efficiency for Avicel and lignocellulose substrates, the results showed that BSA and PEG promoted the enzymatic hydrolysis for both substrates, while LS had a promoting effect for lignocellulose only and inhibited some extent for Avicel. Conclusions: This study showed that synergistic agents of LS, BSA, and PEG have different interaction modes with cellulase. BSA and LS can form complexes with cellulase and the formed complexes prevent them from nonproductive binding by residue lignin; what’s more, the cellulase-BSA complexes improve the hydrolytic capability of pristine enzyme whereas cellulase-LS complexes reduce. The promoting mechanism of PEG has to be attributed to two aspects: one is to prevent cellulase from nonproductive binding to residue lignin by forming a thin layer that actually serves as steric hindrance on residue lignin; the other is the structure change of substrate induced by PEG addition. This investigation will help us to understand the sophisticated interactions among the components in the complicated enzymatic system, especially the interactions between enzymes and synergistic agents. It will be helpful in the design and utilization of synergistic additives in the lignocellulose biorefinery process as well.

Comparison of the Interaction Modes Between Cellulase and Bovine Serum Albumin /Lignosulfonate /Polyethylene Glycol in Promoting Lignocellulose Saccharification

Background: Bovine serum albumin (BSA), polyethylene glycol (PEG) and lignosulfonate (LS) have been extensively employed as synergistic agents in lignocellulose saccharification, albeit it has not been fully understood how they interact with enzymes from the perspectives of molecular interactions. Herein, we attempted to unveil the promotion mechanisms of BSA, PEG and LS for lignocellulose saccharification from the perspective of their respective interaction with cellulase using Quartz Crystal Microbalance with Dissipation monitoring (QCM-D), Surface Plasmon Resonance (SPR), and Small Angle X-ray Scattering (SAXS) to investigate their respective interaction and the complex formation. In the meanwhile, we compared the effects of adding these additives into the enzymatic hydrolysis of pure cellulose (Avicel) and green liquor-pretreated lignocellulose (GL).Results: The results showed that BSA and LS could bind to cellulase to form complexes, whereas PEG did not. However, PEG had a high affinity to lignin or lignin derivatives. In term for Avicel and GL substrates, the results showed that BSA and PEG promoted the enzymatic hydrolysis of both substrates, while LS had a promoting effect for GL only and inhibited some extent for Avicel. Conclusions: This study showed that synergistic agents of LS, BSA, and PEG have different interaction modes with cellulase. BSA and LS form complexes with cellulase and the formed complexes prevent from nonproductive binding by residue lignin; whereas PEG prevents from nonproductive binding by forming a thin layer on residue lignin which actually serve as steric hindrance. This investigation will help us to understand the sophisticated interactions among the components in the complicated enzymatic system, especially the interactions between enzymes and synergistic agents. It will be helpful in the design and utilization of synergistic additives in the lignocellulose biorefinery process as well.

Structure of the SARS-CoV-2 RNA-dependent RNA polymerase in the presence of favipiravir-RTP

The RNA polymerase inhibitor favipiravir is currently in clinical trials as a treatment for infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), despite limited information about the molecular basis for its activity. Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 Å. The structure shows clear evidence for the inhibitor at the catalytic site of the enzyme, and resolves the conformation of key side chains and ions surrounding the binding pocket. Polymerase activity assays indicate that the inhibitor is weakly incorporated into the RNA primer strand, and suppresses RNA replication in the presence of natural nucleotides. The structure reveals an unusual, nonproductive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp, which explains its low rate of incorporation into the RNA primer strand. Together, these findings inform current and future efforts to develop polymerase inhibitors for SARS coronaviruses.

NMR elucidation of nonproductive binding sites of lignin models with carbohydrate-binding module of cellobiohydrolase I

Background Highly efficient enzymatic saccharification of pretreated lignocellulose is a key step in achieving lignocellulosic biorefinery. Cellobiohydrolase I (Cel7A) secreted by Trichoderma reesei is an industrially used cellulase that possesses carbohydrate-binding module 1 (TrCBM1) at the C-terminal domain. The nonproductive binding of TrCBM1 to lignin significantly decreases the enzymatic saccharification efficiency and increases the cost of biomass conversion because of the additionally required enzymes. Understanding the interaction mechanism between lignin and TrCBM1 is essential for realizing a cost-effective biofuel production; however, the binding sites in lignin have not been clearly elucidated. Results Three types of 13C-labeled β-O-4 lignin oligomer models were synthesized and characterized. The 2D 1H–13C heteronuclear single-quantum correlation (HSQC) spectra of the 13C-labeled lignin models confirmed that the three types of the 13C labels were correctly incorporated in the (1) aromatic rings and β positions, (2) α positions, and (3) methoxy groups, respectively. The TrCBM1-binding sites in lignin were analyzed by observing NMR chemical shift perturbations (CSPs) using the synthetic 13C-labeled β-O-4 lignin oligomer models. Obvious CSPs were observed in signals from the aromatic regions in oligomers bound to TrCBM1, whereas perturbations in the signals from aliphatic regions and methoxy groups were insignificant. These findings indicated that hydrophobic interactions and π–π stacking were dominating factors in nonproductive binding. The synthetic lignin models have two configurations whose terminal units were differently aligned and donated C(I) and C(II). The C(I) ring showed remarkable perturbation compared with the C(II), which indicated that the binding of TrCBM1 was markedly affected by the configuration of the lignin models. The long-chain lignin models (degree of polymerization (DP) 4.16–4.70) clearly bound to TrCBM1. The interactions of TrCBM1 with the short-chain lignin models (DP 2.64–3.12) were insignificant, indicating that a DP greater than 4 was necessary for TrCBM1 binding. Conclusion The CSP analysis using 13C-labeled β-O-4 lignin oligomer models enabled the identification of the TrCBM1 binding sites in lignins at the atomic level. This specific interaction analysis will provide insights for new molecular designs of cellulase having a controlled affinity to cellulose and lignin for a cost-effective biorefinery process.

NMR Elucidation of Nonproductive Binding Sites of Lignin Models with Carbohydrate-Binding Module of Cellobiohydrolase I

Background : Highly efficient enzymatic saccharification of pretreated lignocellulose is a key step in achieving lignocellulosic biorefinery. Cellobiohydrolase I (Cel7A) secreted by Trichoderma reesei is an industrially used cellulase that possesses carbohydrate-binding module 1 (TrCBM1) at the C-terminal domain. The nonproductive binding of TrCBM1 to lignin significantly decreases the enzymatic saccharification efficiency and increases the cost of biomass conversion because of the additionally required enzymes. Understanding the interaction mechanism between lignin and TrCBM1 is essential for realizing a cost-effective biofuel production; however, the binding sites in lignin have not been clearly elucidated.Results: Three types of 13C-labeled β-O-4 lignin oligomer models were synthesized and characterized. The 2D 1H–13C heteronuclear single-quantum correlation (HSQC) spectra of the 13C-labeled lignin models confirmed that the three types of the 13C labels were correctly incorporated in the (1) aromatic rings and β positions, (2) α positions, and (3) methoxy groups, respectively. The TrCBM1 binding sites in lignin were analyzed by observing NMR chemical shift perturbations (CSPs) using the synthetic 13C-labeled β-O-4 lignin oligomer models. Obvious CSPs were observed in signals from the aromatic regions in oligomers bound to TrCBM1, whereas perturbations in the signals from aliphatic regions and methoxy groups were insignificant. These findings indicated that hydrophobic interactions and π–π stacking were dominating factors in nonproductive binding. The synthetic lignin models have two configurations whose terminal units were differently aligned and donated C(I) and C(II) . The C(I) ring showed remarkable perturbation compared with the C(II) , which indicated that the binding of TrCBM1 was markedly affected by the configuration of the lignin models. The long-chain lignin models (degree of polymerization (DP) 4.16–4.70) clearly bound to TrCBM1. The interactions of TrCBM1 with the short-chain lignin models (DP 2.64–3.12) were insignificant, indicating that a DP greater than 4 was necessary for TrCBM1 binding.Conclusion: The CSP analysis using 13C-labeled β-O-4 lignin oligomer models enabled the identification of the TrCBM1 binding sites in lignins at the atomic level. This specific interaction analysis will provide insights for new molecular designs of cellulase having a controlled affinity to cellulose and lignin for a cost-effective biorefinery process.

The –SH Protection Method for Determining Accurate Kd Values for Enzyme-Coenzyme Complexes of NAD+-Dependent Glutamate Dehydrogenase and Engineered Mutants: Evidence for Nonproductive NADPH Complexes

Inactivation rates have been measured for clostridial glutamate dehydrogenase and several engineered mutants at various DTNB concentrations. Analysis of rate constants allowed determination of Kd for each non-covalent enzyme-DTNB complex and the rate constant for reaction to form the inactive enzyme-thionitrobenzoate adduct. Both parameters are sensitive to the mutations F238S, P262S, the double mutation F238S/P262S, and D263K, all in the coenzyme binding site. Study of the effects of NAD+, NADH and NADPH at various concentrations in protecting against inactivation by 200 μM DTNB allowed determination of Kd values for binding of these coenzymes to each protein, yielding surprising results. The mutations were originally devised to lessen discrimination against the disfavoured coenzyme NADP(H), and activity measurements showed this was achieved. However, the Kd determinations indicated that, although Kd values for NAD+ and NADH were increased considerably, Kd for NADPH was increased even more than for NADH, so that discrimination against binding of NADPH was not decreased. This apparent contradiction can only be explained if NADPH has a nonproductive binding mode that is not weakened by the mutations, and a catalytically productive mode that, though strengthened, is masked by the nonproductive binding. Awareness of the latter is important in planning further mutagenesis.