The four-helix bundle in cholinesterase dimers: Structural and energetic determinants of stability

Joint technique "parallel peptide synthesis & de novo sequencing" development for the structure verification and high-throughput activity screening of biological peptides from sea cucumber (Stichopus japonicus) intestinal hydrolysate

This study introduces a novel joint technique combining "parallel peptide synthesis" and "de novo sequencing", which facilitates the high-throughput screening and structure validation of biological peptides derived from food and traditional Chinese medicine (TCM). Sea cucumber (Stichopus japonicus) was used as a model organism, undergoing simulated gastrointestinal digestion followed by de novo sequencing to predict potential peptides. Subsequently, cost-effective filter pipette tips were innovatively employed as parallel reaction vessels, enabling efficient peptide synthesis through the microfluidic flow of amino acid solutions over the loaded resin. After high-throughput biological activity screening, peptide YPGQLT was identified as the most potent antioxidant and acetylcholinesterase (AChE) inhibitor. It was then subjected to a molecular docking study to further explore its potential ligand-receptor interactions. This synergistic effect highlights peptide YPGQLT as a promising candidate for Alzheimer's disease (AD) treatment, thereby enhancing the potential biomedical application of sea cucumber. Notably, de novo predicted sequences can be further verified by comparing their characteristics, such as retention time and MS/MS spectrum, with those from the standard reference synthesized using this parallel synthesis protocol.

Why is binding of a divalent metal cation to a structural motif containing four carboxylate residues not accompanied by a conformational change?

We earlier showed that Torpedo californica acetylcholinesterase (AChE) contains a cluster of four conserved aspartates that can strongly bind divalent cations, which we named the 4D motif. Binding of the divalent metal cations greatly increases its thermal stability. Here we systematically examined all available crystallographic structures of T. californica AChE. Two additional metal-binding sites were identified, both composed of acidic and histidine residues. Relative binding to the 4D and additional sites was studied using metadynamics simulations. It was observed that in crystal structures devoid of metal ions in the 4D site, the conformation of T. californica AChE is almost identical to that in structures in which it is occupied by a divalent metal ion. Closer examination of the 4D motif reveals that three of the four acidic residues form ion pairs with conserved basic residues surrounding them. We named this new motif the 4A/3B motif. Molecular dynamics with quantum potential simulations was used to quantify the 4D motif's binding strength compared with that of the metal-binding site in the protein fXIIIa, which consists of four aspartates, but is devoid of adjacent cationic residues. Whereas fXIIIa's 4D site, in the absence of a metal cation, expanded significantly in the simulation, that of Torpedo AChE displayed only minor periodic changes in size. Furthermore, the energy of metal ion unbinding from the two sites differs by ca. 10 kcal/mol. We identified several other proteins in the PDB that contain the 4A/3B motif, whose conformations are identical in the presence or absence of a metal ion. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at https://proteopedia.org/w/Journal:Protein_Science:4.

Conformational Stability and Denaturation Processes of Proteins Investigated by Electrophoresis under Extreme Conditions

The functional structure of proteins results from marginally stable folded conformations. Reversible unfolding, irreversible denaturation, and deterioration can be caused by chemical and physical agents due to changes in the physicochemical conditions of pH, ionic strength, temperature, pressure, and electric field or due to the presence of a cosolvent that perturbs the delicate balance between stabilizing and destabilizing interactions and eventually induces chemical modifications. For most proteins, denaturation is a complex process involving transient intermediates in several reversible and eventually irreversible steps. Knowledge of protein stability and denaturation processes is mandatory for the development of enzymes as industrial catalysts, biopharmaceuticals, analytical and medical bioreagents, and safe industrial food. Electrophoresis techniques operating under extreme conditions are convenient tools for analyzing unfolding transitions, trapping transient intermediates, and gaining insight into the mechanisms of denaturation processes. Moreover, quantitative analysis of electrophoretic mobility transition curves allows the estimation of the conformational stability of proteins. These approaches include polyacrylamide gel electrophoresis and capillary zone electrophoresis under cold, heat, and hydrostatic pressure and in the presence of non-ionic denaturing agents or stabilizers such as polyols and heavy water. Lastly, after exposure to extremes of physical conditions, electrophoresis under standard conditions provides information on irreversible processes, slow conformational drifts, and slow renaturation processes. The impressive developments of enzyme technology with multiple applications in fine chemistry, biopharmaceutics, and nanomedicine prompted us to revisit the potentialities of these electrophoretic approaches. This feature review is illustrated with published and unpublished results obtained by the authors on cholinesterases and paraoxonase, two physiologically and toxicologically important enzymes.

Molecular Simulations and Markov State Modeling Reveal Inactive Form of Quorum Sensing Regulator SdiA of Escherichia Coli

Enteropathogenic Escherichia coli remains one of the most important pathogens infecting children and it is one of the main causes of persistent diarrhea worldwide. Enteropathogenic Escherichia coli is capable of forming biofilms. Several E. coli mechanisms are regulated by quorum sensing, including virulence factors and biofilm formation. Quorum sensing is the communication system of bacteria with the ability to respond to chemical molecules known as autoinducers. Suppressor of division inhibitor (SdiA) is a quorum sensing receptor present in enteropathogenic E. coli in humans that detect acyl-homoserine lactone type autoinducers. SdiA receptor can also respond to autoinducers produced by other bacterial species that control cell division and virulence. SdiA is regulated by 1-octanoyl-rac-glycerol, which serves as an energy source, signaling molecule, and substrate for membrane biogenesis. SdiA is a potential target, which can be used as an anti-infectious technique. Current crystallographic structures for virtual screening may not be sufficient for molecular docking. So they are not very predictive, because the structures are in the active form. It has been shown that SdiA protein is not activated without a ligand. Generally, ligands bind to the ligand binding domain of SdiA. We employ Markov modeling and molecular dynamics simulations to understand the behaviour of SdiA protein and find the possible inactive form. We find an unknown conformation after 24 molecular dynamics simulation runs with random initial velocities and Markov state modeling. In summary, using molecular simulations and Markov state modeling, we have obtained an unknown conformation, which is not available in the crystallographic structures of SdiA. This unknown conformation could be the structure of the inactive form without a ligand. The obtained ensemble structures could be used for virtual screening.

Rational design and structure-based engineering of alkaline pectate lyase from Paenibacillus sp. 0602 to improve thermostability

BACKGROUND

Ramie degumming is often carried out at high temperatures; therefore, thermostable alkaline pectate lyase (PL) is beneficial for ramie degumming for industrial applications. Thermostable PLs are usually obtained by exploring new enzymes or reconstructing existing enzyme by rational design. Here, we improved the thermostability of an alkaline pectate lyase (PelN) from Paenibacillus sp. 0602 with rational design and structure-based engineering.

RESULTS

From 26 mutants, two mutants of G241A and G241V showed a higher thermostability compared with the wild-type PL. The mutant K93I showed increasing specific activity at 45 °C. Subsequently, we obtained combinational mutations (K93I/G241A) and found that their thermostability and specific activity improved simultaneously. The K93I/G241A mutant showed a half-life time of 15.9 min longer at 60 °C and a melting temperature of 1.6 °C higher than those of the wild PL. The optimum temperature decreased remarkably from 67.5 °C to 60 °C, accompanied by a 57% decrease in Km compared with the Km value of the wild-type strain. Finally, we found that the intramolecular interaction in PelN was the source in the improvements of molecular properties by comparing the model structures. Rational design of PelN was performed by stabilizing the α-helices with high conservation and increasing the stability of the overall structure of the protein. Two engineering strategies were applied by decreasing the mutation energy calculated by Discovery Studio and predicting the free energy in the process of protein folding by the PoPMuSiC algorithm.

CONCLUSIONS

The results demonstrated that the K93I/G241A mutant was more suitable for industrial production than the wild-type enzyme. Furthermore, the two forementioned strategies could be extended to reveal engineering of other kinds of industrial enzymes.