Nuclear Magnetic Resonance Titration Experiments Research Articles

Probing noncovalent binding, spectroscopic characteristics and antiproliferative behavior of inclusion complex between quinoline and para-sulfonatothiacalix[4]arene

The inclusion complex between bowl-shaped para-sulfonatothiacalix[4]arene (TSCX4) macrocycle and quinoline has been studied with a unison of UV–visible, infra-red, flourescence emission and 1H nuclear magnetic resonance (NMR) and 2D nuclear overhauser effect spectroscopy (NOESY), high resolution mass spectrometry (HRMS) experiments. Both 1H NMR titration and HRMS experiments point to 1:1 stoichiometry for the water soluble Q⊂TSCX4 complex. The electronic structure of the inclusion complex obtained from density functional theory (DFT) showed a partial encapsulation of quinoline guest, which is held within the host cavity by C–H---π, π---π and hydrogen bonding interactions. The fluorescence emission spectra upon complexation display marginal blue shift of the 411 nm band in TSCX4. Moreover, the binding constant (7.1 × 103 M−1) determined from fluoresence emission experiments underline the effective host–guest binding in the complex, which was corroborated through frequency up-shift (‘blue shift’) of characteristic Ar-OH (3433 cm−1) and SO3- vibrations (1141 cm−1 and 1037 cm−1) in the measured infrared spectra of TSCX4. The antiproliferative activitities of the Q⊂TSCX4 complex against HeLA, MDA-MB-231and N2a cells are presented. The Q⊂TSCX4 complex has been shown to be efficient against N2a (neuroblastoma) cell line.

Organic-soluble cytosine derivatives for studying base-pair interactions in nonaqueous solution

The presence of higher order G-quadruplex-DNA (G4) structures in human cells in guanine-rich DNA sequences has been well established. In cases of G4 helicase impairment or G4 stabilization via association with G4 ligands, it has been determined that arrest and/or termination of DNA transcription/replication occurs because these structures act as physical barriers to both helicase and polymerase mobility along the DNA. Truncation of transcription or replication may result in the loss of genetic material expression leading to disorders. To ameliorate G4-induced barriers, agents that destabilize or “unwind” the quadraplex structures are sought. Earlier work has shown that the cytosine analogue phenylpyrrolocytosine has potential G4-destabilizing ability. It was hypothesized that the unwinding activity was related to its ability to base pair with guanosine. To facilitate the design and evaluation of the hydrogen bonding ability of cytosine analogues, solubility in aprotic, and low-polarity solvents, e.g., deutero-chloroform (CDCl3), is needed; then, determination of association constants ( Ka) with guanine via 1H nuclear magnetic resonance (NMR) spectroscopy or isothermal titration calorimetry (ITC) will be possible. Herein, we report on the synthesis of three new chloroform-soluble, cytosine analogues: N1-cyclohexylmethyl-7-phenylimidazolocytosine, N1-cyclohexylmethyl-7-(6-(methoxycarbonyl)pyridin-2-yl)imidazolocytosine, and N1-cyclohexylmethyl-7-(6-carbamoylpyridin-2-yl)imidazolocytosine. We further report the binding interactions of each of these analogues with the guanosine derivative 2′,3′,5′- O-tris( tert-butyldimethylsilyl)guanosine through the use of both ITC and 1H NMR titration experiments in chloroform and compare the binding to persilyated ribo-cytidine.

Cooperative Bifurcated Chalcogen Bonding and Hydrogen Bonding as Stereocontrolling Elements for Selective Strain-Release Septanosylation.

The exploitation of noncovalent interactions (NCIs) is emerging as a vital handle in tackling broad stereoselectivity challenges in synthesis. In particular, there has been significant recent interest in the harnessing of unconventional NCIs to surmount difficult selectivity challenges in glycosylations. Herein, we disclose the exploitation of an unconventional bifurcated chalcogen bonding and hydrogen bonding (HB) network, which paves the way for a robust catalytic strategy into biologically useful seven-membered ring sugars. Through 13C nuclear magnetic resonance (NMR) in situ monitoring, NMR titration experiments, and density functional theory (DFT) modeling, we propose a remarkable contemporaneous activation of multiple functional groups consisting of a bifurcated chalcogen bonding mechanism working hand-in-hand with HB activation. Significantly, the ester moiety installed on the glycosyl donor is critical in the establishment of the postulated ternary complex for stereocontrol. Through the 13C kinetic isotopic effect and kinetic studies, our data corroborated that a dissociative SNi-type mechanism forms the stereocontrolling basis for the excellent α-selectivity.

A general electron donor-acceptor complex for photoactivation of arenes via thianthrenation.

General photoactivation of electron donor–acceptor (EDA) complexes between arylsulfonium salts and 1,4-diazabicyclo[2.2.2]octane with visible light or natural sunlight was discovered. This practical and efficient mode enables the production of aryl radicals under mild conditions, providing an unrealized opportunity for two-step para-selective C–H functionalization of complex arenes. The novel mode for generating aryl radicals via an EDA complex was well supported by UV-vis absorbance measurements, nuclear magnetic resonance titration experiments, and density functional theory (DFT) calculations. The method was applied to the regio- and stereo-selective arylation of various N-heterocycles under mild conditions, yielding an assembly of challengingly linked heteroaryl–(hetero)aryl products. Remarkably, the meaningful couplings of bioactive molecules with structurally complex drugs or agricultural pharmaceuticals were achieved to display favorable in vitro antitumor activities, which will be of great value in academia or industry.

Chloroperoxidase-catalyzed oxidative degradation of sulfur mustard

As a natural heme protein catalyzing the oxidation of sulfides to sulfoxides without sulfone formation, chloroperoxidase (CPO) is well suited for the degradation of sulfur mustard (HD), a persistent chemical warfare agent that has been widely disposed since World War II and continuously leaks into aquatic environments. Herein, we report the first systematic investigation of CPO-catalyzed degradation of HD and the potential application of CPO in destroying chemical weapons under mild conditions. The related Michaelis–Menten parameters (Km=0.17 mM, Vmax=0.06 mM s−1 (R2 =0.935), and kcat= 2717 s−1) indicated nearly a prominent enzymatic efficiency. Under optimal conditions, 80% of HD was transformed to bis(2-chloroethyl) sulfoxide as identified by mass spectroscopy and nuclear magnetic resonance (NMR) spectroscopy. Other metabolites were also generated during the decontamination process. A plausible oxidation mechanism was proposed based on the degradation products, NMR titration experiments, and molecular dynamics simulations. CPO also promoted the degradation of other chemical weapon agents, namely, Lewisite (L) and venomous agent X (VX), thereby exhibiting a broad substrate scope. The high potential of the developed system for the decontamination of aquatic environments was demonstrated by the successful hatching of zebrafish embryos after HD degradation and the survival of zebrafish (Danio rerio, AB strain) larvae after the degradation of Agent Yellow (L+HD).

Complexation in situ of 1-methylpiperidine, 1,2-dimethylpyrrolidin, and 1,2-dimethylpiperidine with rhodium(II) tetracarboxylates: Nuclear magnetic resonance spectroscopy, chiral recognition, and density functional theory studies.

Complexation in situ of 1-methylpiperidine, racemic 1,2-dimethylpyrrolidin, and racemic 1,2-dimethylpiperidine with rhodium(II) tetracarboxylates in chloroform was studied by 1 H and 13 C nuclear magnetic resonance (NMR) spectroscopy and density functional theory (DFT) methods. As substrates, three dirhodium(II) compounds were applied, tetraacetate, tetrakistrifluoroacetate, and a derivative of optically pure Mosher's acid. Due to conformational flexibility, free and complexed ligands can adopt potentially various conformations. The NMR titration experiments revealed the subsequent formation of 1:1 and 1:2 complexes, depending on the molar ratio of substrate to ligand. Conformations of free and complexed ligands were examined by the comparison of experimental and DFT gauge-independent atomic orbital (GIAO) calculated chemical shifts and by the analysis of the internal energy of the compounds. For some ligand and substrate combinations, a mixture of complexes differing in ligand conformations was formed. Complexes of Mosher's acid derivative of rhodium(II) with racemic 1,2-dimethylpyrrolidin and 1,2-dimethylpiperidine exhibited NMR chiral recognition phenomenon, manifested by splitting of signals in 13 C NMR and 1 H,13 C HSQC spectra.

From Mono- to Polynuclear Coordination Complexes with a 2,2′-Bipyrimidine-4,4′-dicarboxylate Ligand

The coordination properties of the ligand 2,2'-bipyrimidine-4,4'-dicarboxylic acid (H2bpd) with lanthanide(III) ions (Ln = Eu, Tb, or Lu) were investigated. The syntheses of the H2bpd ligand and its salts, [K2(bpd)(H2O)2] (1) and [(AlkNH)Lu(bpd)2] (Alk = Et, Hex, or en), are described. In the presence of LnCl3 salts (Ln = Lu, Eu, or Tb), the formation of [Ln(bpd)2]- and [Ln(bpd)(H2O)x]+ species was assessed by 1H nuclear magnetic resonance (NMR), spectrophotometry, and spectrofluorometric titrations in aqueous solution. The solid state structure of 1, [K(H2O)2][Lu(bpd)2] (2), and [(Et3NH)Lu(bpd)2] (3) could be determined by X-ray diffraction, showing the ligand to act as a tetradentate unit with formation of three five-membered chelate rings around the central Ln(III). With the aim of building polynuclear assemblies, the coordination between [Lu(bdp)2]- and [Lu(tta)3(H2O)] units (tta = thenoyltrifluoroacetylacetonate) was also investigated. In methanol, 1H NMR titration experiments revealed the formation of complex mixtures from which two new species could be identified, [Lu2(bpd)(tta)4] (4) and H[Lu(bpd)(tta)2] (5), as confirmed by their solid state structure analysis. Using highly lipophilic cations in chloroform, the octametallic complex [enH]4[Lu8(bpd)4(tta)18] (6) could be isolated and its X-ray structure determined.

Epigallocatechin Gallate with Potent Anti-Helicobacter pylori Activity Binds Efficiently to Its Histone-like DNA Binding Protein.

Helicobacter pylori (H. pylori)—a human gastric pathogen—forms a major risk factor for the development of various gastric pathologies such as chronic inflammatory gastritis, peptic ulcer, lymphomas of mucosa-associated lymphoid tissues, and gastric carcinoma. The complete eradication of infection is the primary objective of treating any H. pylori-associated gastric condition. However, declining eradication efficiencies, off-target effects, and patient noncompliance to prolong and broad-spectrum antibiotic treatments has spurred the clinical interest to search for alternative effective and safer therapeutic options. As natural compounds are safe and privileged with high levels of antibacterial-activity, previous studies have tested and reported a plethora of such compounds with potential in vitro/in vivo anti-H. pylori activity. However, the mode of action of majority of these natural compounds is unclear. The present study has been envisaged to compile the information of various such natural compounds and to evaluate their binding with histone-like DNA-binding proteins of H. pylori (referred here as Hup) using in silico molecular docking-based virtual screening experiments. Hup—being a major nucleoid-associated protein expressed by H. pylori—plays a strategic role in its survival and persistent colonization under hostile stress conditions. The ligand with highest binding energy with Hup—that is, epigallocatechin-(−)gallate (EGCG)—was rationally selected for further computational and experimental testing. The best docking poses of EGCG with Hup were first evaluated for their solution stability using long run molecular dynamics simulations and then using fluorescence and nuclear magnetic resonance titration experiments which demonstrated that the binding of EGCG with Hup is fairly strong (the resultant apparent dissociation constant (kD) values were equal to 2.61 and 3.29 ± 0.42 μM, respectively).

Multi-functional regulator MapZ controls both positioning and timing of FtsZ polymerization.

The tubulin-like GTPase protein FtsZ, which forms a discontinuous cytokinetic ring at mid-cell, is a central player to recruit the division machinery to orchestrate cell division. To guarantee the production of two identical daughter cells, the assembly of FtsZ, namely Z-ring, and its precise positioning should be finely regulated. In Streptococcus pneumoniae, the positioning of Z-ring at the division site is mediated by a bitopic membrane protein MapZ (mid-cell-anchored protein Z) through direct interactions between the intracellular domain (termed MapZ-N (the intracellular domain of MapZ)) and FtsZ. Using nuclear magnetic resonance titration experiments, we clearly assigned the key residues involved in the interactions. In the presence of MapZ-N, FtsZ gains a shortened activation delay, a lower critical concentration for polymerization and a higher cooperativity towards GTP hydrolysis. On the other hand, MapZ-N antagonizes the lateral interactions of single-stranded filaments of FtsZ, thus slows down the formation of highly bundled FtsZ polymers and eventually maintains FtsZ at a dynamic state. Altogether, we conclude that MapZ is not only an accelerator to trigger the polymerization of FtsZ, but also a brake to tune the velocity to form the end-product, FtsZ bundles. These findings suggest that MapZ is a multi-functional regulator towards FtsZ that controls both the precise positioning and proper timing of FtsZ polymerization.

Binary Assembly of PbS and Au Nanocrystals: Patchy PbS Surface Ligand Coverage Stabilizes the CuAu Superlattice.

Self-assembly of two sizes of nearly spherical colloidal nanocrystals (NCs) capped with hydrocarbon surface ligands has been shown to produce more than 20 distinct phases of binary nanocrystal superlattices (BNSLs). Such structural diversity, in striking contrast to binary systems of micron-sized colloidal beads, cannot be rationalized by models assuming entropy-driven crystallization of simple spheres. In this work, we show that the PbS ligandbinding equilibrium controls the relative stability of two closely related BNSL structures featuring alternating layers of PbS and Au NCs. At an intermediate size ratio, as-prepared PbS NCs assemble with Au NCs into CuAu BNSLs featuring orientational coherence of PbS NCs across the lattice. Measurement of interparticle separations within CuAu and modeling of the structure reveal that PbS inorganic cores are nearly in contact through (100) NC surfaces in the square tiling of the CuAu basal plane. On the other hand, AlB2 BNSLs with PbS NCs packed in random orientations were found to be the dominant self-assembly product when the same binary NC solution was evaporated in the presence of added oleic acid (OAH). Solution nuclear magnetic resonance titration experiments confirmed that added OAH binds to PbS NCs, implicating ligand surface coverage as an important factor influencing the relative stability of CuAu and AlB2 BNSLs at the experimental size ratio. From these results, we conclude that as-prepared PbS NCs feature sparsely covered (100) surfaces and thus effectively flat patches along NC x-, y-, and z-directions. Such anisotropic PbS-PbS interactions can be efficiently screened by restoring effectively spherical NC shape via addition of OAH to the binary assembly solution. Our findings underscore the important contribution of NC surfaces to superlattice phase stability and offer a strategy for targeted BNSL assembly.

Nuclear Magnetic Resonance at the Interface: Identifying Preferred Binding Regions in Multimodal Cation Exchange Chromatography using Functionalized Nanoparticles

The Fc domain is an important component of complex molecules such as monoclonal antibodies (mAb) based biologics as well as fusion proteins and is highly conserved across a given class of mAbs. Recent work in our lab has shown the importance of specific domains towards binding for mAbs to multimodal (MM) cation exchange chromatographic systems. In this collaborative work, we employ a combination of Nuclear Magnetic Resonance (NMR) spectroscopy and Umbrella sampling simulations to develop a fundamental understanding of how multimodal ligands and surfaces interact with the Fc domain. We performed NMR titration experiments with isotopically labeled Fc and ∼15 nm diameter gold nanoparticles (Au NPs) functionalized with Self Assembled Monolayers (SAMs) presenting different MM ligands at different ligand densities. The results showed the interface of CH2 and CH3 domains and the hinge region to be preferred binding regions for interaction of Fc to MM ligand surfaces. These flexible regions on the protein surface which are rich in positive and aliphatic residues are important for the binding of Fc to MM ligand surfaces. Further, to shed light on the binding mechanisms, we performed umbrella sampling with the Fc held at key orientations above a SAM surface presenting MM ligands at relevant ligand densities similar to those tested experimentally. These simulations suggested that as the Fc was brought close to the surface, the residues near the hinge region first made contact with the surface followed by a tighter binding facilitated by interaction of His, Val, Leu and Ile residues at the interface of the CH2 and CH3 domains. This combined experimental and simulations approach enabled us to develop a molecular level understanding of the binding for complex biological products in MM CEX systems.

A transient helix in the disordered region of dynein light intermediate chain links the motor to structurally diverse adaptors for cargo transport.

All animal cells use the motor cytoplasmic dynein 1 (dynein) to transport diverse cargo toward microtubule minus ends and to organize and position microtubule arrays such as the mitotic spindle. Cargo-specific adaptors engage with dynein to recruit and activate the motor, but the molecular mechanisms remain incompletely understood. Here, we use structural and dynamic nuclear magnetic resonance (NMR) analysis to demonstrate that the C-terminal region of human dynein light intermediate chain 1 (LIC1) is intrinsically disordered and contains two short conserved segments with helical propensity. NMR titration experiments reveal that the first helical segment (helix 1) constitutes the main interaction site for the adaptors Spindly (SPDL1), bicaudal D homolog 2 (BICD2), and Hook homolog 3 (HOOK3). In vitro binding assays show that helix 1, but not helix 2, is essential in both LIC1 and LIC2 for binding to SPDL1, BICD2, HOOK3, RAB-interacting lysosomal protein (RILP), RAB11 family-interacting protein 3 (RAB11FIP3), ninein (NIN), and trafficking kinesin-binding protein 1 (TRAK1). Helix 1 is sufficient to bind RILP, whereas other adaptors require additional segments preceding helix 1 for efficient binding. Point mutations in the C-terminal helix 1 of Caenorhabditis elegans LIC, introduced by genome editing, severely affect development, locomotion, and life span of the animal and disrupt the distribution and transport kinetics of membrane cargo in axons of mechanosensory neurons, identical to what is observed when the entire LIC C-terminal region is deleted. Deletion of the C-terminal helix 2 delays dynein-dependent spindle positioning in the one-cell embryo but overall does not significantly perturb dynein function. We conclude that helix 1 in the intrinsically disordered region of LIC provides a conserved link between dynein and structurally diverse cargo adaptor families that is critical for dynein function in vivo.

Solution NMR structure of CHU_1110 from Cytophaga hutchinsonii, an AHSA1 protein potentially involved in metal ion stress response.

We report the solution nuclear magnetic resonance (NMR) structure of CHU_1110 from Cytophaga hutchinsonii. CHU_1110 contains three α-helices and one antiparallel β-sheet, forming a large cavity in the center of the protein, which are consistent with the structural characteristics of AHSA1 protein family. This protein shows high structural similarities to the prokaryotic proteins RHE_CH02687 from Rhizobium etli and YndB from Bacillus subtilis, which can bind with flavinoids. Unlike these two homologs, CHU_1110 shows no obvious interaction with flavonoids in NMR titration experiments. In addition, no direct interaction has been observed between CHU_1110 and ATP, although many homologous sequences of CHU_1110 have been annotated as ATPase. Combining the analysis of structural similarity of CHU_1110 and genomic context of its encoding gene, we speculate that CHU_1110 may be involved in the stress response of bacteria to heavy metal ions, even though its specific biological functions that need to be further investigated.

Expression, purification and characterization of the full-length SmpB protein from Mycobacterium tuberculosis

The trans-translation system is recognized as an excellent target for developing new drugs to rapidly sterilize Mycobacterium tuberculosis (TB) infection and significantly shorten TB treatment duration. As a vital component of the trans-translation system for rescuing stalled ribosomes, the SmpB protein from Mycobacterium tuberculosis (MtbSmpB, 1-160 a. a.) mediates tmRNA binding to stalled ribosomes through forming a complex with tmRNA. So far, few works have been conducted to prepare, characterize biophysical properties and determine three-dimensional structure for the full-length MtbSmpB protein. In the present work, we successfully expressed and purified the His-tagged full-length MtbSmpB protein in Escherichia coli with a yield of 26.9 mg from 1 L of Luria Bertani medium. We also obtained MtbSmpB with a yield of 18.5 mg from 1 L of M9 minimal medium. The MtbSmpB protein showed a single band in SDS-PAGE with a molecular weight of ∼20 kDa consistent with the measurement from MALDI-TOF-mass spectrometry. The dynamic light scattering experiment indicated that MtbSmpB existed in a monomeric form. Moreover, both circular dichroism and nuclear magnetic resonance (NMR) experiments exhibited that MtbSmpB was well structured, suggesting that it could be feasible to determine its solution structure by NMR spectroscopy. NMR titration experiments showed that MtbSmpB specifically bound to tmRNA. This work lays the essential basis for further determining the solution structure and dynamics of the full-length MtbSmpB protein.

Development of a Molecular Probe Targeting Mitochondrial Fission Protein Fis1

Excessive mitochondrial fragmentation – caused by decreased mitochondrial fusion or increased fission – leads to mitochondrial dysfunction and has been implicated in ischemia‐reperfusion injury and diabetic cardiomyopathy. Genetic or pharmacological inhibition of fission is protective against hyperglycemic‐induced loss of mitochondrial connectivity and reactive oxygen species production. Dynamin‐related protein 1 (Drp1) is a cytosolic GTPase mechanoenzyme or “cutter” known to cause scission of the mitochondria, but what determines a site of scission is unknown. Drp1 is recruited to mitochondria by one of four mitochondrial anchored recruiters; one of which is the tetratricopeptide repeat protein, fission protein 1 (Fis1). Cell lines lacking individual, all, or a combination of Drp1 recruiter proteins demonstrate each recruiter supports Drp1 recruitment in unique pathways. Of the four Drp1 recruiters, Fis1 is the only recruiter conserved in all species with mitochondria, but the involvement of Fis1 in mammalian mitochondrial fission has been disputed. Recent data suggests mammalian Fis1 is specialized for stress‐induced fission but the molecular basis remains unknown. We aimed to develop a molecular probe targeting Fis1 to be used in testing the hypothesis that Fis1 recruits and subsequently activates Drp1 in stress‐induced mammalian mitochondrial fission. If successful, a molecular probe targeting Fis1 could be used to determine the ability of Fis1 to modulate Drp1 activity under a variety of cellular stresses. We are using two approaches to develop molecular probe(s): 1) fragment‐based screening by nuclear magnetic resonance (NMR) and 2) peptide design using molecular docking, molecular dynamics simulations, and NMR validation experiments. Fis1 was screened against ~ 2000 fragments using 1H‐15N SOFAST‐HMQC and 1H‐15N NUS‐HSQC NMR experiments. Fragments that bound Fis1 (hits) were identified using a novel scoring metric, Difference Intensity Analysis (DIA), which quantitates spectral changes in 2D difference spectra and functions regardless of NMR time scale. To determine binding modalities of Fis1‐peptide interactions, we used molecular docking followed by molecular dynamics simulations to dock and sample the conformational space of previously identified Fis1 interacting peptides. To obtain binding affinities and putative binding sites, NMR titration experiments of 15N‐Fis1 with individual fragment hits and synthesized peptides were performed. Our results to date on developing molecular probe(s) against Fis1 will be presented.Support or Funding InformationThis project was supported by the Clinical & Translational Science Institute (CTSI) through the National Center for Advancing Translational Sciences, National Institutes of Health, through Grant Number UL1TR001436. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH. Project also supported by NIH grants NIH R01‐GM067180, and NIH R01‐HL128240.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

ISCU(M108I) and ISCU(D39V) Differ from Wild-Type ISCU in Their Failure To Form Cysteine Desulfurase Complexes Containing Both Frataxin and Ferredoxin.

Whereas iron–sulfur (Fe–S) cluster assembly on the wild-type scaffold protein ISCU, as catalyzed by the human cysteine desulfurase complex (NIA)2, exhibits a requirement for frataxin (FXN), in yeast, ISCU variant M108I has been shown to bypass the FXN requirement. Wild-type ISCU populates two interconverting conformational states: one structured and one dynamically disordered. We show here that variants ISCU(M108I) and ISCU(D39V) of human ISCU populate only the structured state. We have compared the properties of ISCU, ISCU(M108I), and ISCU(D39V), with and without FXN, in both the cysteine desulfurase step of Fe–S cluster assembly and the overall Fe–S cluster assembly reaction catalyzed by (NIA)2. In the cysteine desulfurase step with dithiothreitol (DTT) as the reductant, FXN was found to stimulate cysteine desulfurase activity with both the wild-type and structured variants, although the effect was less prominent with ISCU(D39V) than with the wild-type or ISCU(M108I). In overall Fe–S cluster assembly, frataxin was found to stimulate cluster assembly with both the wild-type and structured variants when the reductant was DTT; however, with the physiological reductant, reduced ferredoxin 2 (rdFDX2), FXN stimulated the reaction with wild-type ISCU but not with either ISCU(M108I) or ISCU(D39V). Nuclear magnetic resonance titration experiments revealed that wild-type ISCU, FXN, and rdFDX2 all bind to (NIA)2. However, when ISCU was replaced by the fully structured variant ISCU(M108I), the addition of rdFDX2 to the [NIA–ISCU(M108I)–FXN]2 complex led to the release of FXN. Thus, the displacement of FXN by rdFDX2 explains the failure of FXN to stimulate Fe–S cluster assembly on ISCU(M108I).

Mechanism of Competitive Inhibition and Destabilization of Acidothermus cellulolyticus Endoglucanase 1 by Ionic Liquids.

The ability of ionic liquids (ILs) to solubilize cellulose has sparked interest in their use for enzymatic biomass processing. However, this potential is yet to be realized, primarily because ILs inactivate requisite cellulases by mechanisms that are yet to be identified. We used a combination of enzymology, circular dichroism (CD), nuclear magnetic resonance (NMR), and molecular dynamics (MD) methods to investigate the molecular basis for the inactivation of the endocellulase 1 (E1) from Acidothermus cellulolyticus by the imidazolium IL 1-butyl-3-methylimidazolium chloride ([BMIM][Cl]). Enzymatic studies revealed that [BMIM][Cl] inactivates E1 in a biphasic manner that involves rapid, reversible inhibition, followed by slow, irreversible deactivation. Backbone NMR signals of the 40.5 kDa E1 were assigned by triple resonance NMR methods, enabling monitoring of residue-specific perturbations. 1H-15N NMR titration experiments revealed that [BMIM][Cl] binds reversibly to the E1 active site, indicating that reversible deactivation is due to competitive inhibition of substrate binding. Prolonged incubation with [BMIM][Cl] led to substantial global changes in the 1H-15N heteronuclear single quantum coherence NMR and CD spectra of E1 indicative of protein denaturation. Notably, weak interactions between [BMIM][Cl] and residues at the termini of several helices were also observed, which, together with MD simulations, suggest that E1 denaturation is promoted by [BMIM][Cl]-induced destabilization of helix capping structures. In addition to identifying determinants of E1 inactivation, our findings establish a molecular framework for engineering cellulases with improved IL compatibility.

Manipulating Protein–Protein Interactions in Nonribosomal Peptide Synthetase Type II Peptidyl Carrier Proteins

In an effort to elucidate and engineer interactions in type II nonribosomal peptide synthetases, we analyzed biomolecular recognition between the essential peptidyl carrier proteins and adenylation domains using nuclear magnetic resonance (NMR) spectroscopy, molecular dynamics, and mutational studies. Three peptidyl carrier proteins, PigG, PltL, and RedO, in addition to their cognate adenylation domains, PigI, PltF, and RedM, were investigated for their cross-species activity. Of the three peptidyl carrier proteins, only PigG showed substantial cross-pathway activity. Characterization of the novel NMR solution structure of holo-PigG and molecular dynamics simulations of holo-PltL and holo-PigG revealed differences in structures and dynamics of these carrier proteins. NMR titration experiments revealed perturbations of the chemical shifts of the loop 1 residues of these peptidyl carrier proteins upon their interaction with the adenylation domain. These experiments revealed a key region for the protein-protein interaction. Mutational studies supported the role of loop 1 in molecular recognition, as mutations to this region of the peptidyl carrier proteins significantly modulated their activities.

Solution NMR structure of the TRIM21 B-box2 and identification of residues involved in its interaction with the RING domain.

Tripartite motif-containing (TRIM) proteins are defined by the sequential arrangement of RING, B-box and coiled-coil domains (RBCC), where the B-box domain is a unique feature of the TRIM protein family. TRIM21 is an E3 ubiquitin-protein ligase implicated in innate immune signaling by acting as an autoantigen and by modifying interferon regulatory factors. Here we report the three-dimensional solution structure of the TRIM21 B-box2 domain by nuclear magnetic resonance (NMR) spectroscopy. The structure of the B-box2 domain, comprising TRIM21 residues 86–130, consists of a short α-helical segment with an N-terminal short β-strand and two anti-parallel β-strands jointly found the core, and adopts a RING-like fold. This ββαβ core largely defines the overall fold of the TRIM21 B-box2 and the coordination of one Zn2+ ion stabilizes the tertiary structure of the protein. Using NMR titration experiments, we have identified an exposed interaction surface, a novel interaction patch where the B-box2 is likely to bind the N-terminal RING domain. Our structure together with comparisons with other TRIM B-box domains jointly reveal how its different surfaces are employed for various modular interactions, and provides extended understanding of how this domain relates to flanking domains in TRIM proteins.

The Polybasic Region of the Polysialyltransferase ST8Sia-IV Binds Directly to the Neural Cell Adhesion Molecule, NCAM.

Polysialic acid (polySia) is a unique post-translational modification found on a small set of mammalian glycoproteins. Composed of long chains of α2,8-linked sialic acid, this large, negatively charged polymer attenuates protein and cell adhesion and modulates signaling mediated by its carriers and proteins that interact with these carriers. PolySia is crucial for the proper development of the nervous system and is upregulated during tissue regeneration and in highly invasive cancers. Our laboratory has previously shown that the neural cell adhesion molecule, NCAM, has an acidic surface patch in its first fibronectin type III repeat (FN1) that is critical for the polysialylation of N-glycans on the adjacent immunoglobulin domain (Ig5). We have also identified a polysialyltransferase (polyST) polybasic region (PBR) that may mediate substrate recognition. However, a direct interaction between the NCAM FN1 acidic patch and the polyST PBR has yet to be demonstrated. Here, we have probed this interaction using isothermal titration calorimetry and nuclear magnetic resonance (NMR) spectroscopy. We observe direct and specific binding between FN1 and the PBR peptide that is dependent upon acidic residues in FN1 and basic residues of the PBR. NMR titration experiments verified the role of the FN1 acidic patch in the recognition of the PBR and suggest a conformational change of the Ig5-FN1 linker region following binding of the PBR to the acidic patch. Finally, mutation of residues identified by NMR titration experiments impacts NCAM polysialylation, supporting their mechanistic role in protein-specific polysialylation.