Laser Ablation Assists Cyclization Reactions of Hydantoic Acid: A Proof for the Near-Attack Conformation Theory?

Applications of the Near Attack Conformation (NAC) approach in the search for Acetylcholinesterase reactivators

The Near Attack Conformation (NAC) approach states that the efficiency of an enzyme-catalyzed reaction depends on the prior attainment of optimal conditions for substrate atom organization and positioning for bond formation. These conditions are prerequisites for the transition state (TS) in which the involved atoms are within the van der Waals range of contact and positioned at an angle similar to that achieved after bond formation. The successful application of this approach to investigate the reactivation mechanism of acetylcholinesterase inhibited by nerve agents has contributed to a better understanding of this mechanism and demonstrated consistent corroboration with experimental data. In this article, we summarize the accomplishments achieved thus far and outline future perspectives.

New Insights into the Cooperativity and Dynamics of Dimeric Enzymes

A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.

Role of distal sites in enzyme engineering

The limitations associated with natural enzyme catalysis have triggered the rise of the field of protein engineering. Traditional rational design was based on the analysis of protein structural information and catalytic mechanisms to identify key active sites or ligand binding sites to reshape the substrate pocket. The role and significance of functional sites in the active center have been studied extensively. With a deeper understanding of the structure-catalysis relationship map, the entire protein molecule can be filled with residues that play a substantial role in its structure and function. However, the catalytic mechanism underlying distal mutations remains unclear. The aim of this review was to highlight the criticality of the distal site in enzyme engineering based on the following three aspects: What can distal mutations exert on function from mutability landscape? How do distal sites influence enzyme function? How to predict and design distal mutations? This review provides insights into the catalytic mechanism of enzymes from the global interaction network, knowledge from sequence-structure-dynamics-function relationships, and strategies for distal mutation-based protein engineering.

Unveiling the Methyl Transfer Mechanisms in the Epigenetic Machinery DNMT3A-3L: A Comprehensive Study Integrating Assembly Dynamics with Catalytic Reactions

In epigenetic mechanisms, DNA methyltransferase 3 alpha (DNMT3A) acts as an initiator for DNA methylation and prevents the downstream genes from expressing. Perturbations of DNMT3A functions may cause uncontrolled gene expression, resulting in pathogenic consequences such as cancers. It is, therefore, vitally important to understand the catalytic process of DNMT3A in its biological macromolecule assembly, viz., heterotetramer: (DNMT3A-3 L)^dimer. In this study, we utilized molecular dynamics (MD) simulations, Markov State Models (MSM), and quantum mechanics/molecular mechanics simulations (QM/MM) to investigate the de novo methyl transfer process. We identified the dynamics of the key residues relevant to the insertion of the target cytosine (dC) into the catalytic domain of DNMT3A, and the detailed potential energy surface of the seven-step reaction referring to methyl transfer. Our calculated potential energy barrier (22.51 kcal/mol) approximates the former experimental data (23.12 kcal/mol). The conformational change of the 5-methyl-cytosine (5mC) intermediate was found necessary in forming a four-water chain for the elimination step, which is unique to the other DNMTs. The biological assembly facilitates the creation of such a water chain, and the elimination occurs in an asynchronized mechanism in the two catalytic pockets. We anticipate the findings can enable a better understanding of the general mechanisms of the de novo methyl transfer for fulfilling the key enzymatic functions in epigenetics. And the unique elimination of DNMT3A might ignite novel methods for designing anti-cancer and tumor inhibitors of DNMTs.

Understanding the abundance of the rare sugar β-D-allose

The conformational landscape of β-D-allose, a rare sugar, has been investigated using laser ablation in combination with high-resolution rotational spectroscopy. Altogether, three species are identified, exhibiting a counter-clockwise intramolecular hydrogen...

TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids

In this work, we introduce TorsiFlex, a user-friendly software written in Python 3 and designed to find all the torsional conformers of flexible acyclic molecules in an automatic fashion. For the mapping of the torsional potential energy surface, the algorithm implemented in TorsiFlex combines two searching strategies: preconditioned and stochastic. The former is a type of systematic search based on chemical knowledge and should be carried out before the stochastic (random) search. The algorithm applies several validation tests to accelerate the exploration of the torsional space. For instance, the optimized structures are stored and this information is used to prevent revisiting these points and their surroundings in future iterations. TorsiFlex operates with a dual-level strategy by which the initial search is carried out at an inexpensive electronic structure level of theory and the located conformers are reoptimized at a higher level. Additionally, the program takes advantage of conformational enantiomerism, when possible. As a case study, and in order to exemplify the effectiveness and capabilities of this program, we have employed TorsiFlex to locate the conformers of the twenty proteinogenic amino acids in their neutral canonical form. TorsiFlex has produced a number of conformers that roughly doubles the amount of the most complete work to date.

An Innovative Approach for the Generation of Species of the Interstellar Medium

The large amount of unstable species in the realm of interstellar chemistry drives an urgent need to develop efficient methods for the in situ generations of molecules that enable their spectroscopic characterizations. Such laboratory experiments are fundamental to decode the molecular universe by matching the interstellar and terrestrial spectra. We propose an approach based on laser ablation of nonvolatile solid organic precursors. The generated chemical species are cooled in a supersonic expansion and probed by high‐resolution microwave spectroscopy. We present a proof of concept through a simultaneous formation of interstellar compounds and the first generation of aminocyanoacetylene using diaminomaleonitrile as a prototypical precursor. With this micro‐laboratory, we open the door to generation of unsuspected species using precursors not typically accessible to traditional techniques such as electric discharge and pyrolysis.

Laboratory Detection of Cyanoacetic Acid: A Jet-Cooled Rotational Study

Herein we present a laboratory rotational study of cyanoacetic acid (CH2(CN)C(O)OH), an organic acid as well as a -CN bearing molecule, that is a candidate molecular system to be detected in the interstellar medium (ISM). Our investigation aims to provide direct experimental frequencies of cyanoacetic acid to guide its eventual astronomical search in low-frequency surveys. Using different jet-cooled rotational spectroscopic techniques in the time domain, we have determined a precise set of the relevant rotational spectroscopic constants, including the 14N nuclear quadrupole coupling constants for the two distinct structures, cis- and gauche- cyanoacetic acid. We believe this work will potentially allow the detection of cyanoacetic acid in the interstellar medium, whose rotational features have remained unknown until now.