An official website of the United States government
Abstract The recent advances in accelerated polymerization ofN-carboxyanhydrides (NCAs) enriched the toolbox to prepare well-defined polypeptide materials. Herein we report the use of crown ether (CE) to catalyze the polymerization of NCA initiated by conventional primary amine initiators in solvents with low polarity and low hydrogen-bonding ability. The cyclic structure of the CE played a crucial role in the catalysis, with 18-crown-6 enabling the fastest polymerization kinetics. The fast polymerization kinetics outpaced common side reactions, enabling the preparation of well-defined polypeptides using an α-helical macroinitiator. Experimental results as well as the simulation methods suggested that CE changed the binding geometry between NCA and propagating amino chain-end, which promoted the molecular interactions and lowered the activation energy for ring-opening reactions of NCAs. This work not only provides an efficient strategy to prepare well-defined polypeptides with functionalized C-termini, but also guides the design of catalysts for NCA polymerization.
more »
« less
Enzyme-mimetic self-catalyzed polymerization of polypeptide helices
Abstract Enzymes provide optimal three-dimensional structures for substrate binding and the subsequent accelerated reaction. Such folding-dependent catalytic behaviors, however, are seldom mechanistically explored with reduced structural complexity. Here, we demonstrate that the α-helix, a much simpler structural motif of enzyme, can facilitate its own growth through the self-catalyzed polymerization ofN-carboxyanhydride (NCA) in dichloromethane. The reversible binding between the N terminus of α-helical polypeptides and NCAs promotes rate acceleration of the subsequent ring-opening reaction. A two-stage, Michaelis–Menten-type kinetic model is proposed by considering the binding and reaction between the propagating helical chains and the monomers, and is successfully utilized to predict the molecular weights and molecular-weight distributions of the resulting polymers. This work elucidates the mechanism of helix-induced, enzyme-mimetic catalysis, emphasizes the importance of solvent choice in the discovery of new reaction type, and provides a route for rapid production of well-defined synthetic polypeptides by taking advantage of self-accelerated ring-opening polymerizations.
more »
« less
- PAR ID:
- 10153787
- Publisher / Repository:
- Nature Publishing Group
- Date Published:
- Journal Name:
- Nature Communications
- Volume:
- 10
- Issue:
- 1
- ISSN:
- 2041-1723
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Polypeptides, as the synthetic analogues of natural proteins, are an important class of biopolymers that are widely studied and used in various biomedical applications. However, the preparation of polypeptide materials from the polymerization of N-carboxyanhydride (NCA) is limited by various side reactions and stringent polymerization conditions. Recently, we report the cooperative covalent polymerization (CCP) of NCA in solvents with low polarity and weak hydrogen-bonding ability (e.g., dichloromethane or chloroform). The polymerization exhibits characteristic two-stage kinetics, which is significantly accelerated compared with conventional polymerization under identical conditions. In this Account, we review our recent studies on the CCP, with the focus on the acceleration mechanism, the kinetic modeling, and the use of fast kinetics for the efficient preparation of polypeptide materials. By studying CCP with several initiating systems, we found that the polymerization rate was dependent on the secondary structure as well as the macromolecular architecture of the propagating polypeptides. The molecular interactions between the α-helical, propagating polypeptide and the monomer played an important role in the acceleration, which catalyzed the ring-opening reaction of NCA in an enzyme-mimetic, Michaelis–Menten manner. Additionally, the proximity between initiating sites further accelerated the polymerization, presumably due to the cooperative interactions of macrodipoles between neighboring helices and/or enhanced binding of monomers. A two-stage kinetic model with a reversible monomer adsorption process in the second stage was developed to describe the CCP kinetics, which highlighted the importance of cooperativity, critical chain length, binding constant, [M]0, and [M]0/[I]0. The kinetic model successfully predicted the polymerization behavior of the CCP and the molecular-weight distribution of resulting polypeptides. The remarkable rate acceleration of the CCP offers a promising strategy for the efficient synthesis of polypeptide materials, since the fast kinetics outpaces various side reactions during the polymerization process. Chain termination and chain transfer were thus minimized, which facilitated the synthesis of high-molecular-weight polypeptide materials and multiblock copolypeptides. In addition, the accelerated polymerization enabled the synthesis of polypeptides in the presence of an aqueous phase, which was otherwise challenging due to the water-induced degradation of monomers. Taking advantage of the incorporation of the aqueous phase, we reported the preparation of well-defined polypeptides from nonpurified NCAs. We believe the studies of CCP not only improve our understanding of biological catalysis, but also benefit the downstream studies in the polypeptide field by providing versatile polypeptide materials.more » « less
-
ABSTRACT CRISPR-Cas12a is widely used for genome editing and biomarker detection since it can create targeted double-stranded DNA breaks and promote non-specific DNA cleavage after identifying specific DNA. To mitigate the off-target DNA cleavage of Cas12a, we previously developed aFrancisella novicidaCas12a variant (FnoCas12aKD2P) by introducing double proline substitutions (K969P/D970P) in a conserved helix called the bridge helix (BH). In this work, we used cryogenic electron microscopy (cryoEM) to understand the molecular mechanisms of BH-mediated activation of Cas12a. We captured five structures of FnoCas12aKD2Pat different states of conformational activation. Comparison with wild-type (FnoCas12aWT) structures unravels a mechanism where BH acts as a trigger that allosterically activates REC lobe movements by tracking the number of base pairs in the growing RNA-DNA hybrid to undergo a loop-to-helical transition and bending to latch onto the hybrid. The transition of the BH is coupled to the previously reported loop-to-helix transition of the “lid”, essential for opening RuvC endonuclease, through direct interactions of residues of the BH and the lid. We also observe structural details of cooperativity of BH and “helix-1” of RuvC for activation, a previously proposed interaction. Overall, our study enables development of high-fidelity Cas12a and Cas9 variants by BH-modifications.more » « less
-
Abstract Carbon‐centered radicals stabilized by adjacent boron atoms are underexplored reaction intermediates in organic synthesis. This study reports the development of vinyl cyclopropyl diborons (VCPDBs) as a versatile source of previously unknown homoallylic α,α‐diboryl radicals via thiyl radical catalyzed diboron‐directed ring opening. These diboryl stabilized radicals underwent smooth [3+2] cycloaddition with a variety of olefins to provide diboryl cyclopentanes in good to excellent diastereoselectivity. In contrast to thetrans‐diastereoselectivity observed with most of the dicarbonyl activated VCPs, the cycloaddition of VCPDBs showed a remarkable preference for formation ofcis‐cyclopentane diastereomer which was confirmed by quantitative NOE and 2D NOESY studies. Thecis‐stereochemistry of cyclopentane products enabled a concise intramolecular Heck reaction approach to rare tricyclic cyclopentanoid framework containing the diboron group. The mild reaction conditions also allowed a one‐pot VCP ring‐opening, cycloaddition‐oxidation sequence to afford disubstituted cyclopentanones. Control experiments and DFT analysis of reaction mechanism support a radical mediated pathway and provide a rationale for the observed diastereoselectivity. To the authors’ knowledge, these are the first examples of the use of geminal diboryl group as an activator of VCP ring opening and cycloaddition reaction of α‐boryl radicals.more » « less
-
Abstract Nat/Ivy is a diverse and ubiquitous CoA‐binding evolutionary lineage that catalyzes acyltransferase reactions, primarily converting thioesters into amides. At the heart of the Nat/Ivy fold is a phosphate‐binding loop that bears a striking resemblance to that of P‐loop NTPases—both are extended, glycine‐rich loops situated between a β‐strand and an α‐helix. Nat/Ivy, therefore, represents an intriguing intersection between thioester chemistry, a putative primitive energy currency, and an ancient mode of phospho‐ligand binding. Current evidence suggests that Nat/Ivy emerged independently of other cofactor‐utilizing enzymes, and that the observed structural similarity—particularly of the cofactor binding site—is the product of shared constraints instead of shared ancestry. The reliance of Nat/Ivy on a β‐α‐β motif for CoA‐binding highlights the extent to which this simple structural motif may have been a fundamental evolutionary “nucleus” around which modern cofactor‐binding domains condensed, as has been suggested for HUP domains, Rossmanns, and P‐loop NTPases. Finally, by dissecting the patterns of conserved interactions between Nat/Ivy families and CoA, the coevolution of the enzyme and the cofactor was analyzed. As with the Rossmann, it appears that the pyrophosphate moiety at the center of the cofactor predates the enzyme, suggesting that Nat/Ivy emerged sometime after the metabolite dephospho‐CoA.more » « less
