Analysis of the electron transfer pathway in small laccase by EPR and UV-vis spectroscopy coupled with redox titration

Bacterial small laccases(SLAC) are promising industrial biocatalysts due to their ability to oxidize a broad range of substrates with exceptional thermostability and tolerance for alkaline p H. Electron transfer between substrate, copper centers, and O2is one of the key steps in the catalytic turnover of SLAC. However, limited research has been conducted on the electron transfer pathway of SLAC and SLAC-catalyzed reactions, hindering further engineering of SLAC to produce tunable biocatalysts for novel applications. Herein, the combinational use of electron paramagnetic resonance(EPR) and ultraviolet-visible(UV-vis) spectroscopic methods coupled with redox titration were employed to monitor the electron transfer processes and obtain further insights into the electron transfer pathway in SLAC. The reduction potentials for type 1 copper(T1Cu), type 2 copper(T2Cu) and type 3copper(T3Cu) were determined to be 367 ± 2 mV, 378 ± 5 m V and 403 ± 2 mV,respectively. Moreover, the reduction potential of a selected substrate of SLAC, hydroquinone(HQ), was determined to be 288 mV using cyclic voltammetry(CV). In this way, an electron transfer pathway was identified based on the reduction potentials. Specifically,electrons are transferred from HQ to T1Cu, then to T2Cu and T3Cu, and finally to O2.Furthermore, superhyperfine splitting observed via EPR during redox titration indicated a modification in the covalency of T2Cu upon electron uptake, suggesting a conformational alteration in the protein environment surrounding the copper sites, which could potentially influence the reduction potential of the copper sites during catalytic processes. The results presented here not only provide a comprehensive method for analyzing the electron transfer pathway in metalloenzymes through reduction potential measurements, but also offer valuable insights for further engineering and directed evolution studies of SLAC in the aim for biotechnological and industrial applications.

Overview and progress of X-nuclei magnetic resonance imaging in biomedical studies

Proton nuclear(^(1)H)is the observed nucleus on which most magnetic resonance imaging(MRI)applications depend.Most traditional^(1)H MRI can provide structural and functional information about organisms,while various non-proton nuclei(X-nuclei)MRI can provide more metabolic information.However,due to the relatively poor signal-to-noise ratio(SNR)of X-nuclei MRI,their applications are quite rare compared to^(1)H.Benefit from the rapid developments of MRI hardware and software technologies,X-nuclei MRI has recently attracted increasing interests in biomedical research.This review firstly introduces some current methods to improve the SNR of X-nuclei MRI.Secondly,this review describes biomedical applications of X-nuclei MRI,especially focusing on the current use of X-nuclei(^(13)C,^(17)O,^(19)F,^(23)Na and^(31)P)MRI to study related diseases in different organs,including the brain,liver,kidney,heart and bone.Finally,perspectives studies on X-nuclei imaging and its potential applications are described in biomedical research.

A cytochrome c551 mediates the cyclic electron transport chain of the anoxygenic phototrophic bacterium Roseiflexus castenholzii

Roseiflexus castenholzii is a gram-negativefilamentous phototrophic bacterium that carries out anoxygenic photosynthesis through a cyclic electron transport chain(ETC).The ETC is composed of a reaction center(RC)–light-harvesting(LH)complex(rcRC–LH);an alternative complex III(rcACIII),which functionally re-places the cytochrome bc1/b6f complex;and the periplasmic electron acceptor auracyanin(rcAc).Although compositionally and structurally different from the bc1/b6f complex,rcACIII plays similar essential roles in oxidizing menaquinol and transferring electrons to the rcAc.However,rcACIII-mediated electron transfer(which includes both an intraprotein route and a downstream route)has not been clearly elucidated,nor have the details of cyclic ETC.Here,we identify a previously unknown monoheme cytochrome c(cyt c551)as a novel periplasmic electron acceptor of rcACIII.It reduces the light-excited rcRC–LH to complete a cyclic ETC.We also reveal the molecular mechanisms involved in the ETC using electron paramagnetic resonance(EPR),spectroelectrochemistry,and enzymatic and structural analyses.Wefind that electrons released from rcACIII-oxidized menaquinol are transferred to two alternative periplasmic electron acceptors(rcAc and cyt c551),which eventually reduce the rcRC to form the complete cyclic ETC.This work serves as a foundation for further studies of ACIII-mediated electron transfer in anoxygenic photosynthesis and broadens our under-standing of the diversity and molecular evolution of prokaryotic ETCs.

Recent advances in chemical protein synthesis:method developments and biological applications

The central dogma of modern biology underscores the pivotal roles proteins play in diverse biological processes,the study of which necessitates advanced methods to produce proteins with precision and versatility.Chemical protein synthesis,a powerful approach utilizing chemical reactions for the de novo construction of structurally accurate proteins,has emerged as a transformative tool for studying proteins and generating protein derivatives/mimics inaccessible by natural biological machinery,including post-translationally modified proteins,proteins comprised of unnatural amino acids,as well as mirror-image proteins.This review summarizes recent strides in synthetic method developments for chemical protein synthesis,including innovative techniques in solid-phase peptide synthesis,the challenges presented by difficult sequences in either synthesis or folding and the exploration of novel ligation reactions using both chemical and enzymatic methods.Furthermore,the review also delves into newly developed protocols for site-selective protein modifications and the generation of stapled or macrocyclized peptides/miniproteins,highlighting the power of chemical methods to make structurally diverse proteins.Recent applications of synthetic proteins in investigating post-translational modifications(phosphorylation,lipidation,glycosylation,ubiquitination,etc.),mirror-image biological processes and drug development are further discussed.Together,these topics provide a comprehensive overview of the current landscape of chemical protein synthesis.

Scalable synthesis of lipid nanoparticles for nucleic acid drug delivery using an isometric channel-size enlarging strategy

Lipid nanoparticles(LNPs)have emerged as highly effective delivery systems for nucleic acid-based therapeutics.However,the broad clinical translation of LNP-based drugs is hampered by the lack of robust and scalable synthesis techniques that can consistently produce formulations from early development to clinical application.In this work,we proposed a method to achieve scalable synthesis of LNPs by scaling inertial microfluidic mixers isometrically in three dimensions.Moreover,a theoretical predictive method,which controls the mixing time to be equal across different chips,is developed to ensure consistent particle size and size distribution of the synthesized LNPs.LNPs loaded with small interfering RNA(siRNA)were synthesized at different flow rates,exhibiting consistent physical properties,including particle size,size distribution and encapsulation efficiency.This work provides a practical approach for scalable synthesis of LNPs consistently,offering the potential to accelerate the transition of nucleic acid drug development into clinical application.

Metabolic state oscillations in cerebral nuclei detected using two-photon fluorescence lifetime imaging microscopy

The fluorescence lifetime of nicotinamide adenine dinucleotide(NADH),a key endogenous coenzyme and metabolic biomarker,can reflect the metabolic state of cells.To implement metabolic imaging of brain tissue at high resolution,we assembled a two-photon fluorescence lifetime imaging microscopy(FLIM)platform and verified the feasibility and stability of NADH-based two-photon FLIM in paraformaldehydefixed mouse cerebral slices.Furthermore,NADH based metabolic state oscillation was observed in cerebral nuclei suprachiasmatic nucleus(SCN).The free NADH fraction displayed a relatively lower level in the daytime than at the onset of night,and an ultradian oscillation at night was observed.Through the combination of high-resolution imaging and immunostaining data,the metabolic tendency of different cell types was detected after the first two hours of the day and at night.Thus,two-photon FLIM analysis of NADH in paraformaldehyde-fixed cerebral slices provides a high-resolution and label-free method to explore the metabolic state of deep brain regions.

Chemical protein synthesis-assisted high-throughput screening strategies for D-peptides in drug discovery

D-peptides are recognized as a new class of synthetic chemical drugs and they possess many interesting advantages such as high enzymatic stability,improved oral bioavailability,as well as high binding affinity and specificity.Recently,D-peptide drugs have been attracting increasing attention in both academic and industrial researches over recent years.One D-peptide etelcalcetide has even entered the market that targets the calcium(Ca2+)-sensing receptor(CaSR) to fight secondary hyperparathyroidism.Effective discovery and optimization of D-peptide ligands that can bind to various disease-related targets with high specificity and potency is of great importance for the development of D-peptide drugs.This review surveys the recent method development in this area especially the chemical protein synthesis-assisted high-throughput screening strategies for D-peptide ligands and their application in drug discovery.

Biochemical properties of K_(11,48)-branched ubiquitin chains

As one of the most widely existing post-translational modification models, ubiquitination regulates diverse cellular activities. In eukaryotes, K-branched ubiquitin chains play key roles in cell cycle and protein quality control. However, the structural and biochemical properties of K-branched ubiquitin chains have not been well examined. Here we employed the synthetic linkage-and length-defined K-branched ubiquitin chains to examine their binding and hydrolysis properties in vitro. Quantitatively affinity determination of ubiquitin chains to the proteasome ubiquitin receptor S5 a indicated that the S5 a exhibited preference binding to K-branched chains over K-linked chains, but not K-conjugated chains. In addition, deubiquitination experiments were carried out and the results showed that K-branched chains were preferably hydrolyzed by proteasome-associated deubiquitinase Rpnll than homotypic Kor K-linked chains.

Total synthesis of snake toxin α-bungarotoxin and its analogues by hydrazide-based native chemical ligation

Nicotinic acetylcholine receptors(nAChRs) play important roles in intercellular communications of nerve cells. α-Bungarotoxins(αBtx) is a moderator for the nAChRs. Chemical synthesis provides a promising way to access aBtx and their analogues. Here, we reported a new method for a-bungarotoxin by combining Fmoc-SPPS and peptide hydrazide based ligation strategy. The two-segment ligation method may enable efficient synthesis of aBtx analogues. These synthetic toxin peptides are useful tools for development of imaging or therapeutic reagents.

Conformational change of E.coli sulfurtransferase YgaP upon SCN- in intact native membrane revealed by fluorescence lifetime and anisotropy

Fluorescence lifetime and anisotropy has become a prevalent tool to detect the structure change and motility property of proteins. YgaP is the only membrane-integrated rhodanese in E. coli. The sulfur transfer process has been characterized by various studies. However, the mechanism of the outward transportation of SCN-remains unclear. In this work, we examined the fluorescence lifetime and anisotropy of site-specific incorporated unnatural amino acid 7-HC to study the conformational change of YgaP upon SCN-binding. We also compared the fluorescence changes between detergent-wrapped environment in DPC and intact native membrane environment in SMA. Our results suggested the presence of at least two different conformations in YgaP protein. Both the residues in the middle of TMH2 and the residues near extracellular side play important roles in the binding and/or output of SCN-. SMA is a good material to reflect the in situ conformation changes of protein than micelles.

In cell measurement of fluorescence lifetime imaging microscopy revealed C-terminal conformation changes of Ferroportin upon addition of Mn^2＋

Fluorescence microscopy, as a sensitive method to detect microenvironment of molecules, is widely used in protein conformation and dynamic studies in live cells. Fluorescence lifetime imaging microscopy（FLIM）, which is independent of fluorophore concentrations, scattering and bleaching, is a suitable tool to analyze membrane proteins in a single cell. Ferroportin（FPN）, a multi-ion exporter in vertebrates, was modulated by metal ions with unknown mechanism. Herein, we fused green fluorescence protein on Cterminal of FPN（FPN-eGFP） and applied fluorescence lifetime to monitor conformation changes of FPN in a live cell. The fluorescence lifetime distribution showed a shift to shorter lifetime upon Mn^（2＋） treatment,suggesting a preference conformation of FPN in Mn^（2＋） exposure. It is also observed that the lifetime（rather than intensity） measurement was not strongly influenced by laser power. The observed fluorescence lifetime changes of FPN-eGFP upon Mn^（2＋） treatments indicated that extracellular metal ions can modulate FPN through conformation exchanges between several different states.

NiH-Catalyzed Reductive Hydrocarbonation of Enol Esters and Ethers

Chiral dialkyl carbinols and their derivatives are significant synthetic building blocks in organic chemistry and related fields.The development of convenient and efficient methods to access these compounds has long been an important endeavor.Herein,we report a NiH-catalyzed reductive hydroalkylation and hydroarylation of enol esters and ethers.α-Oxoalkyl organonickel species were generated in situ in a catalytic mode and then participated in cross-coupling with alkyl or aryl halides.This approach enabled C(sp^(3))–C(sp^(3))and C(sp^(3))–C(sp^(2))bond formation under mild reductive conditions with simple operations,thereby boosting a broad substrate scope and good functional compatibility.Esters of enantioenriched dialkyl carbinols were accessed in a catalytic asymmetric version.Mechanistic studies demonstrated that this reaction proceeded through a syn-addition of Ni–H intermediate to an enol ester with high regio-and enantioselectivity.

Protein-protein interaction analysis in crude bacterial lysates using combinational method of ^19F site-specific incorporation and ^19F NMR

Protein-protein interactions （PPI） are essential for a variety of cellular functions. Many PPI analyses were conducted in vitro, using purified proteins. In this report, the unnatural amino acid tfmF was site-specifically incorporated into several different sites of two Phox-Beml （PB1） domains from two mitogen activated protein kinases （MEKK3 and/ or MEK5） in the E. coil cells.

Fluorescence lifetime based distance measurement illustrates conformation changes of PYL10-CL2 upon ABA binding in solution state

Forster resonance energy transfer(FRET)is a widely used distance measurement method to illustrate protein conformational dynamics.The FRET method relies on the distance between donor and acceptor,as well as the labelling efficiency,the size and the properties of the fluorophores.Here,we labelled a pair of small fluorophores and calculated the energy transferred efficiency through fluorescence lifetime analysis,which can provide more reliable distance measurement than intensity attenuation.The donor fluorophore,7-hydroxycoumarin-4-yl-ethylglycine(HC),was genetically incorporated into specific sites of PYL10,obtaining complete labelling efficiency.The acceptor fluorophore,Alexa488,was labelled through the disulfide bond,whose labelling efficiency was estimated through both absorption peaks and lifetime populations.Fluorescence lifetime and anisotropy analysis showed ABA-induced local conformation changes and dynamics of several HC incorporation sites of PYL10.The lifetime-based FRET distance measurement illustrated the conformation changes of PYL10 with or without ABA application,which is consistent with the previously reported crystal structures.

The putative propeptide of MycP1 in mycobacterial type VII secretion system does not inhibit protease activity but improves protein stability

Mycosin-1 protease(MycP1)is a serine protease anchored to the inner membrane of Mycobacterium tuberculosis,and is essential in virulence factor secretion through the ESX-1 type VII secretion system(T7SS).Bacterial physiology studies demonstrated that MycP1 plays a dual role in the regulation of ESX-1 secretion and virulence,primarily through cleavage of its secretion substrate EspB.MycP1 contains a putative N-terminal inhibitory propeptide and a catalytic triad of Asp-His-Ser,classic hallmarks of a sub-tilase family serine protease.The MycP1 propeptide was previously reported to be initially inactive and activated after prolonged incubation.In this study,we have deter-mined crystal structures of MycP1 with(MycP124-422)and without(MycP1^(63-422))the propeptide,and conducted EspB cleavage assays using the two proteins.Very high struc-tural similarity was observed in the two crystal structures.Interestingly,protease assays demonstrated positive EspB cleavage for both proteins,indicating that the putative propeptide does not inhibit protease activity.Molecu-lar dynamic simulations showed higher rigidity in regions guarding the entrance to the catalytic site in MycP124-422 than in MycP1^(63-422),suggesting that the putative propeptide might contribute to the conformational stability of the active site cleft and surrounding regions.

Total chemical synthesis of bivalently modified H3 by improved three-segment native chemical ligation

The H3 bivalent modifications of trimethylationat Lys9 and acetylation at Lys18(H3-K9 Me3-K18 Ac) were identified to collectively recruit TRIM33 in the nodal signaling pathway.To understand the underlying mechanism of TRIM33 recruitment,the nucleosome core particles(NCPs) containing full-length H3-K9 Me3-K18 Ac were indispensable samples.Herein we developed a pseudo dipeptide strategy to efficiently prepare peptide segments,facilitating the chemical synthesis of H3-K9 Me3-K18 Ac at a tens of milligram scale.The synthetic H3-K9 Me3-K18 Ac was then examined by CD spectroscopy,which demonstrated a prominent shift compared to recombinant H3.Finally,bivalently modified NCPs were assembled and verified by gel mobility shift assay with good homogeneity.

Equilibria between the K^+ binding and cation vacancy conformations of potassium channels

Dear Editor, Potassium channels are integral membrane proteins that selectively con duct K^+ ions across cell membra ne (Hille, 2001). They play essential roles in maintaining cellular ionic homoeostasis and generating action membrane potentials in excitable cells. The mechanism of K^+ selectivity has been evaluated in many biophysical and physiological studies (Zhou et al., 2001;Liu et al., 2015;Schewe et al., 2016). A highly con served signature seque nee, TVGYG, in the selectivity filter of potassium channels (e.g., KcsA) is known to coordinate K^+ ions (Zhou et al., 2001). Carbonyls of these residues point toward the pore, forming four continuous ion binding sites (S1-S4) and resulting in higher selectivity for K^+ over Na^+(Zhou et al., 2001). The NaK channel from Bacillus cereus is a norvselective cation channel that shares high structural homology with KcsA (Shi et al., 2006). Owing to a distinctive primary sequenee of 63TVGDG67, the selectivity filter of NaK preserves only two ion binding sites, allocated similarly as S3 and S4 in KcsA (Alam and Jiang, 2009a, b). Remarkably, the D66Y and N68D double mutations of NaK channel (Fig. S1) transform it into a K^+ selective channel (termed as NaK2K)(Sauer et al., 2013). Crystal structure of NaK and NaK2K have revealed distinet binding coordination of Na^+ and K^+ ions in their selectivity filter (Figs. S2 and S3)(Alam and Jiang, 2009a, b;Sauer et al., 2013). However, dynamics of the NaK and NaK2K selectivity filter with the bind泊g of Na+ or K^+ are still elusive. Especially, it has been known that the membrane environment is highly diverse from deterge nt micelles, which was con sidered to in flue nee the structure and functi on of membrane protei ns dramatically (Cross et al., 2011). Thus, it is necessary to study the cation and binding properties of NaK NaK2K channels in lipid bilayers.

Allosteric conformational changes of G proteins upon its interaction with membrane and GPCR

Current resolved structures of GPCRs and G protein complexes provided important insights into G protein activation. However, the binding or dissociation of GPCRs with G protein is instantaneous and highly dynamic in the intracellular environment. The conformational dynamic of G protein still needs to be addressed. In this study, we applied ^(19)F solution NMR spectroscopy to monitor the conformational changes of G protein upon interact with detergent mimicking membrane and receptor. Our results show that there are two states equilibria in the G_(α)in apo states. The interaction of G_(α)with detergents will accelerate this conformational transformation and induce a state that tends to bind to GPCRs. Finally, the G_(α)proteins presented a fully activation state when they coupled to GPCRs.

Mutation of the critical pH-gating residues histidine 231 to glutamate increase open probability of outer membrane protein G in planar lipid bilayer

Dear Editor,Outer-membrane protein G(OmpG)is a nonspecificβ-barrel porin in the outer membrane of Escherichia coli(E.coli),allowing the passage of ions and molecules up to 900 Da(Fajardo et al.,1998).It comprises of 280 amino acids that form 14-strandedβ-sheets with seven long loops(L1-L7)on the extra-cellular side and six short turns on the periplasmic side(Subbarao and van den Berg,2006;Yildiz et al.,2006;Liang and Tamm,2007).Despite that the OmpG gene exists in the genome of several E.coli strains(Nikaido,1999),expres-sion of OmpG was only observed in E.coli mutants lacking OmpF and LamB(Fajardo et al.,1998)to enable the diffu-sion of maltodextrins across the bacte-rial outer membrane.Very interestingly,unlike usual trimeric channel-forming porins,OmpG exhibits fascinating characteristics of a functional monomer in physiological and structural studies(Conlan and Bayley,2003;Mari et al.,2010).

Effi cient long-distance NMR-PRE and EPR-DEER restraints for two-domain protein structure determination

Dear Editor,The functional diversity of proteins is related to the cooperation of multiple domains.Independent globular domains are typically joined by a fl exible length of polypeptide chain,which makes the structural analysis of multi-domain proteins diffi cult.Here,we describe the combined use of solution NMR(nuclear magnetic resonance)and EPR(elec-tron paramagnetic resonance)for the structural analysis of a protein with two separate domains.The structure of each domain was determined independently using conventional NMR restraints,and the relative orientation of the two separate domains was confi ned using long-distance restraints obtained by NMR-PRE(paramagnetic relaxation enhancement)and EPR-DEER(double electron-electron resonance,also called PELDOR:pulsed electron double reso-nance.