Synthesis and Olfactory Characterization of Silicon‐Containing Derivatives of the Acyclic Lily‐of‐the‐Valley Odorant 5,7,7‐Trimethyl‐4‐methylideneoctanal

5‐Methyl‐4‐methylidene‐6‐(trimethylsilyl)hexanal ( 1b ), a sila analog of the acyclic lily‐of‐the‐valley odorant 5,7,7‐trimethyl‐4‐methylideneoctanal ( 1a ), and the Si‐containing derivatives 2 – 6 were prepared in multistep syntheses, starting from Cl₃SiH and Cl₂SiMe₂, respectively. Compounds 1b, 2 – 6 , and their new precursors were characterized by elemental analyses (C, H, N) and NMR spectroscopic studies (¹H, ¹³C, ¹⁵N, and ²⁹Si). To gain more information about the structure? odor correlation in the family of lily‐of‐the‐valley or ‘muguet’ odorants, C/Si analogs 1a / 1b and derivatives 2 – 6 were evaluated for their olfactory properties.     

Realizing Three‐Electron Redox Reactions in NASICON‐Structured Na3MnTi(PO4)3 for Sodium‐Ion Batteries

Developing multielectron reaction electrode materials is essential for achieving high specific capacity and high energy density in secondary batteries; however, it remains a great challenge. Herein, Na₃MnTi(PO₄)₃/C hollow microspheres with an open and stable NASICON framework are synthesized by a spray‐drying‐assisted process. When applied as a cathode material for sodium‐ion batteries, the resultant Na₃MnTi(PO₄)₃/C microspheres demonstrate fully reversible three‐electron redox reactions, corresponding to the Ti^3+/4+ (≈2.1 V), Mn^2+/3+ (≈3.5 V), and Mn^3+/4+ (≈4.0 V vs Na⁺/Na) redox couples. In situ X‐ray diffraction results reveals that both solid‐solution and two‐phase electrochemical reactions are involved in the sodiation/desodiation processes. The high specific capacity (160 mAh g^?1 at 0.2 C), outstanding cyclability (≈92% capacity retention after 500 cycles at 2 C), and the facile synthesis make the Na₃MnTi(PO₄)₃/C a prospective cathode material for sodium‐ion batteries.     

FadD3 is an acyl‐CoA synthetase that initiates catabolism of cholesterol rings C and D in actinobacteria

The cholesterol catabolic pathway occurs in most mycolic acid‐containing actinobacteria, such as Rhodococcus jostii RHA1, and is critical for Mycobacterium tuberculosis (Mtb) during infection. FadD3 is one of four predicted acyl‐CoA synthetases potentially involved in cholesterol catabolism. A ΔfadD3 mutant of RHA1 grew on cholesterol to half the yield of wild‐type and accumulated 3aα‐H‐4α(3′‐propanoate)‐7aβ‐methylhexahydro‐1,5‐indanedione (HIP), consistent with the catabolism of half the steroid molecule. This phenotype was rescued by fadD3 of Mtb. Moreover, RHA1 but not ΔfadD3 grew on HIP. Purified FadD3_Mtb catalysed the ATP‐dependent CoA thioesterification of HIP and its hydroxylated analogues, 5α‐OH HIP and 1β‐OH HIP. The apparent specificity constant (k_cat/K_m) of FadD3_Mtb for HIP was 7.3 ± 0.3 × 10⁵ M^?1 s^?1, 165 times higher than for 5α‐OH HIP, while the apparent K_m for CoASH was 110 ± 10 μM. In contrast to enzymes involved in the catabolism of rings A and B, FadD3_Mtb did not detectably transform a metabolite with a partially degraded C17 side‐chain. Overall, these results indicate that FadD3 is a HIP‐CoA synthetase that initiates catabolism of steroid rings C and D after side‐chain degradation is complete. These findings are consistent with the actinobacterial kstR2 regulon encoding ring C/D degradation enzymes.     

Synthesis and Antiproliferative Activities of Novel Substituted 5‐Anilino‐α‐Glucofuranose Derivatives

In order to find novel antitumor candidate agents with high efficiency and low toxicity, 14 novel substituted 5‐anilino‐α‐glucofuranose derivatives have been designed, synthesized and evaluated for antiproliferative activities in vitro. Their structures were characterized by NMR (¹H and ¹³C) and HR‐MS, and configuration (R/S) at C(5) was identified by two‐dimensional ¹H,¹H‐NOESY‐NMR spectrum. Their antiproliferative activities against human tumor cells were investigated by MTT assay. The results demonstrated that most of the synthesized compounds had antiproliferative effects comparable to the reference drugs gefitinib and lapatinib. In particular, (5R)‐5‐O‐(3‐chloro‐4‐{[5‐(4‐fluorophenyl)thiophen‐2‐yl]methyl}anilino)‐5‐deoxy‐1,2‐O‐(1‐methylethylidene)‐α‐glucofuranose ( 9da ) showed the most potent antiproliferative effects against SW480, A431 and A549 cells, with IC₅₀ values of 8.57, 5.15 and 15.24 μm , respectively. This work suggested 5‐anilino‐α‐glucofuranose as an antitumor core structure that may open a new way to develop more potent anti‐cancer agents.     

Formation of truncated peptide by‐products via sequence‐specific formyl group transfer from Trp(For) residues to Nα in the course of Boc‐SPPS

(N^In)‐Formyl protective group of tryptophan has been introduced as a base/nucleophile‐labile protective group. It has long been known that a free Nα‐amino group of the peptide can serve as a nucleophile: an irreversible formyl N^In → NH₂ transfer is consistently observed when deformylation is performed last on an otherwise deprotected peptide that possesses free Nα‐amino group. Obviously, this particular side reaction should be expected any time free amino group is exposed to Trp(For), but, at the best of our knowledge, has never been reported in the course of Boc‐SPPS. In the present communication, we describe a set of appropriately designed model experiments that permitted to detect the title side reaction both in solution and in solid‐phase reactions. We observed intermolecular formyl group transfer with a model compound, Trp(For)‐NH₂. Importantly, we also observed this migration on solid support with the rate roughly estimated to be up to 1% of residues per minute. We also observed that the formyl‐group transfer reaction occurred in a sequence‐dependent manner and was suppressed to a non‐detectable level using ‘in situ neutralization’ technique. Because this side reaction is sequence dependent, there might be situations when the rate of the formation of N_α‐formyl termination by‐products is significant. In other cases, the N_α‐For truncated by‐products would not contaminate the final peptide significantly but still could be a source of microheterogeneity. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.     

Taraxerol 4‐Methoxybenzoate,an in vitro Inhibitor of Photosynthesis Isolated from Pavonia multiflora A. St‐Hil. (Malvaceae)

A phytochemical study of Pavonia multiflora A. St ‐Hil . (Malvaceae) led to the isolation through chromatographic techniques of 10 secondary metabolites: vanillic acid ( 1 ), ferulic acid ( 2 ), p‐hydroxybenzoic acid ( 3 ), p‐coumaric acid ( 4 ), loliolide ( 5 ), vomifoliol ( 6 ), 4,5‐dihydroblumenol A ( 7 ), 3‐oxo‐α‐ionol ( 9 ), blumenol C ( 10 ), and taraxerol 4‐methoxybenzoate ( 8 ), the latter being a novel metabolite. Their structures were identified by ¹H‐ and ¹³C‐NMR, using one‐ and two‐dimensional techniques, and X‐ray crystallography. In this work, we report the effect of compounds 5 and 8 on several photosynthetic activities in an attempt to search for new compounds as potential herbicide agents that affect photosynthesis. Both compounds inhibited the electron flow from H₂O to methyl viologen; therefore, they act as Hill reaction inhibitors. Using polarographic techniques and studies of the fluorescence of chlorophyll a, the interaction sites of these compounds were located at photosystem II.     

Isolation and characterization of the transient,luciferase-bound flavin-4a-hydroxide in the bacterial luciferase reaction

Procedures and conditions have been established such that the unstable enzyme-bound flavin intermediate produced in the bacterial luciferase reaction can be isolated as approximately 70% of the flavin product, the remaining being the final product, FMN. The structure of the intermediate is proposed to be that of a luciferase-bound 4a,5-dihydroflavin-4a-hydroxide. The intermediate has a half-life of 33 min at 2°C and decays spontaneously to give H₂O and luciferase-bound FMN with an activation enthalpy of about 120 kJ/mol. It has an absorption spectrum (λ_max = 360 nm) that is consistent with the proposed structure, and a fluorescence emission (λ_max = 485 nm) that matches the bioluminescence emission closely.     

Flavin oxidation in flavin‐dependent N‐monooxygenases

Siderophore A (SidA) from Aspergillus fumigatus is a flavin‐containing monooxygenase that hydroxylates ornithine (Orn) at the amino group of the side chain. Lysine (Lys) also binds to the active site of SidA; however, hydroxylation is not efficient and H₂O₂ is the main product. The effect of pH on steady‐state kinetic parameters was measured and the results were consistent with Orn binding with the side chain amino group in the neutral form. From the pH dependence on flavin oxidation in the absence of Orn, a pK_a value >9 was determined and assigned to the FAD‐N5 atom. In the presence of Orn, the pH dependence displayed a pK_a value of 6.7 ±0.1 and of 7.70 ±0.10 in the presence of Lys. Q102 interacts with NADPH and, upon mutation to alanine, leads to destabilization of the C4a‐hydroperoxyflavin (FAD_OOH). Flavin oxidation with Q102A showed a pK_a value of ~8.0. The data are consistent with the pK_a of the FAD N5‐atom being modulated to a value >9 in the absence of Orn, which aids in the stabilization of FAD_OOH. Changes in the FAD‐N5 environment lead to a decrease in the pK_a value, which facilitates elimination of H₂O₂ or H₂O. These findings are supported by solvent kinetic isotope effect experiments, which show that proton transfer from the FAD N5‐atom is rate limiting in the absence of a substrate, however, is significantly less rate limiting in the presence of Orn and or Lys.     

A Tannic Acid–Derived N‐, P‐Codoped Carbon‐Supported Iron‐Based Nanocomposite as an Advanced Trifunctional Electrocatalyst for the Overall Water Splitting Cells and Zinc–Air Batteries

Rational design and construction of a multifunctional electrocatalyst featuring with high efficiency and low cost is fundamentally important to realize new energy technologies. Herein, a trifunctional electrocatalyst composed of FeP_x nanoparticles and Fe–N–C moiety supported on the N‐, P‐codoped carbon (NPC) is masterly synthesized by a facile one‐pot pyrolysis of the mixture of tannic acid, ferrous chloride, and sodium hydrogen phosphate. The synergy of each component in the FeP_x/Fe–N–C/NPC catalyst renders high catalytic activities and excellent durability toward both oxygen reduction reaction (ORR), oxygen evolution reaction (OER), and hydrogen evolution reaction (HER). The electrocatalytic performance and practicability of the robust FeP_x/Fe–N–C/NPC catalyst are further investigated under the practical operation conditions. Particularly, the overall water splitting cell assembled by the FeP_x/Fe–N–C/NPC catalyst only requires a voltage of 1.58 V to output the benchmark current density of 10 mA cm^?2, which is superior to that of IrO₂–Pt/C‐based cell. Moreover, the FeP_x/Fe–N–C/NPC‐based zinc–air batteries deliver high round‐trip efficiency and remarkable cycling stability, much better than that of Pt/C–IrO₂ pair‐based batteries. This work offers a new strategy to design and synthesize highly effective multifunctional electrocatalysts using cheaper tannic acid derived carbon as support applied in electrochemical energy devices.     

Pulsatilla decoction and its active ingredients inhibit secretion of NO,ET‐1, TNF‐α, and IL‐1α in LPS‐induced rat intestinal microvascular endothelial cells

To investigate the pharmacological mechanism of the traditional Chinese medicine, Pulsatilla decoction (PD), the levels of nitric oxide (NO), endothelin‐1 (ET‐1), tumor necrosis factor‐α (TNF‐α), and interleukin‐1α (IL‐1α) secreted by cultured rat intestinal microvascular endothelial cells (RIMECs) were determined after treatment with PD and its seven active ingredients, namely anemoside B₄, anemonin, berberine, jatrorrhizine, palmatine, aesculin, and esculetin. RIMECs were challenged with lipopolysaccharide (LPS) at 1 µg ml^?1 for 3 h and then treated with PD at 1, 5, and 10 mg ml^?1 and its seven ingredients at 1, 5, and 10 µg ml^?1 for 21 h, respectively. The results revealed that PD, anemonin, berberine, and esculetin inhibited the production of NO; PD, anemonin, and esculetin inhibited the secretion of ET‐1; PD, anemoside B₄, berberine, jatrorrhizine, and aesculin downregulated TNF‐α expression; PD, anemoside B₄, berberine, and palmatine decreased the content of IL‐1α. It showed that PD and its active ingredients could significantly inhibit the secretion of NO, ET‐1, TNF‐α, and IL‐1α in LPS‐induced RIMECs and suggested they would reduce inflammatory response via these cytokines. Copyright © 2009 John Wiley & Sons, Ltd.     

Nitrogen‐Doping‐Induced Defects of a Carbon Coating Layer Facilitate Na‐Storage in Electrode Materials

A nitrogen‐doped, carbon‐coated Na₃V₂(PO₄)₃ cathode material is synthesized and the formation of doping type of nitrogen‐doped in carbon coating layer is systemically investigated. Three different carbon‐nitrogen species: pyridinic N, pyrrolic N, and quaternary N are identified. The most important finding is that different carbon‐nitrogen species in the carbon layer have different impacts on the improvement of the electrochemical properties of Na₃V₂(PO₄)₃. Pyridinic N and pyrrolic N significantly increase the electronic conductivity and create numerous extrinsic defects and active sites. Quaternary N only increases the electronic conductivity without creating extrinsic defects. Therefore, it is unexpectedly demonstrated that the Na₃V₂(PO₄)₃/C+N, in which with minimize content of quaternary N or exist most extrinsic defects, exhibits the best electrochemical performance, particularly the rate performance and cycling stability. For example, when the discharging rate increased from 0.2 C to 5 C, its capacity of 101.9 mAh g^?1 decays to 84.3 mAh g^?1 and an amazing capacity retention of 83% is achieved. Moreover, even at higher current density of 5 C, an excellent capacity retention of 93% is maintained even after 100 cycles.     

High‐resolution crystal structures reveal a mixture of conformers of the Gly61‐Asp62 peptide bond in an oxidized flavodoxin from Bacillus cereus

Flavodoxins (Flds) are small proteins that shuttle electrons in a range of reactions in microorganisms. Flds contain a redox‐active cofactor, a flavin mononucleotide (FMN), and it is well established that when Flds are reduced by one electron, a peptide bond close to the FMN isoalloxazine ring flips to form a new hydrogen bond with the FMN N5H, stabilizing the one‐electron reduced state. Here, we present high‐resolution crystal structures of Flavodoxin 1 from Bacillus cereus in both the oxidized (ox) and one‐electron reduced (semiquinone, sq) state. We observe a mixture of conformers in the oxidized state; a 50:50 distribution between the established oxidized conformation where the peptide bond is pointing away from the flavin, and a conformation where the peptide bond is pointing toward the flavin, approximating the conformation in the semiquinone state. We use single‐crystal spectroscopy to demonstrate that the mixture of conformers is not caused by radiation damage to the crystal. This is the first time that such a mixture of conformers is reported in a wild‐type Fld. We therefore carried out a survey of published Fld structures, which show that several proteins have a pronounced conformational flexibility of this peptide bond. The degree of flexibility seems to be modulated by the presence, or absence, of stabilizing interactions between the peptide bond carbonyl and its surrounding amino acids. We hypothesize that the degree of conformational flexibility will affect the Fld ox/sq redox potential.     

Detection and identification of 1-methylethyl and methyl radicals generated by irradiating tea tree (Melaleuca alternifolia) oil with visible light (436 nm) in the presence of flavin mononucleotide and ferrous ion

Abstract

Here, we determined the electron spin resonance (ESR) spectra of standard reaction mixtures (I) containing 25 μM flavin mononucleotide (FMN), 0.018% tea tree (Melaleuca alternifolia) oil, 1.9 M acetonitrile, 20 mM phosphate buffer (pH 7.4), 0.1 M α-(4-pyridyl-1-oxide)-N-tert-butylnitrone (4-POBN), and 1.0 mM FeSO₄(NH₄)₂SO₄ irradiated with 436 nm visible light (7.8 J/cm²). Prominent ESR signals (α^N = 1.58 mT and α^Hβ = 0.26 mT) were detected, suggesting that free radicals form in the standard reaction. In order to know whether singlet oxygen (¹O₂) is involved in the radical formation or not, ESR measurement was performed for the standard D₂O reaction mixture (I) which contained 25 μM FMN, 0.0036% tea tree oil, 1.9 M acetonitrile-d3, 20 mM phosphate buffer (pH 7.4), 0.1 M 4-POBN and 1.0 mM FeSO₄ in D₂O. The ESR peak height of the standard D₂O reaction increased to 169 ± 24% of the control. Thus, ¹O₂ seems to be involved in the formation of the radicals because D₂O increases the lifetime of singlet oxygen. High-performance liquid chromatography-ESR-mass spectrometry analyses detected 1-methylethyl and methyl radicals in the standard reaction. The radicals appear to form through the reaction of ferrous ion with α-terpinene endoperoxide (ascaridole), which generated from the reaction of α-terpinene with ¹O₂. The 1-methylethyl and methyl radicals may exert a pro-oxidant effect under these conditions.     

Cofactor‐induced reversible folding of Flavodoxin‐4 from Lactobacillus acidophilus

Flavodoxins in combination with the flavin mononucleotide (FMN) cofactor play important roles for electron transport in prokaryotes. Here, novel insights into the FMN‐binding mechanism to flavodoxins‐4 were obtained from the NMR structures of the apo‐protein from Lactobacillus acidophilus (YP_193882.1) and comparison of its complex with FMN. Extensive reversible conformational changes were observed upon FMN binding and release. The NMR structure of the FMN complex is in agreement with the crystal structure (PDB ID: 3EDO ) and exhibits the characteristic flavodoxin fold, with a central five‐stranded parallel β–sheet and five α‐helices forming an α/β‐sandwich architecture. The structure differs from other flavoproteins in that helix α2 is oriented perpendicular to the β‐sheet and covers the FMN‐binding site. This helix reversibly unfolds upon removal of the FMN ligand, which represents a unique structural rearrangement among flavodoxins.     

The enthalpy of oxidation of flavin mononucleotide

The oxidation enthalpy of reduced flavin mononucleotide at pH 7.0 in 0.2 m phosphate buffer has been studied by determining the heat associated with the reaction: FMNH₂ + 2 Fe(CN)^?3₆ ? FMN + 2 Fe(CN)^?4₆ + 2 H⁺. (a) (The quinone, semiquinone, and hydroquinone forms of FMN are represented as FMN, FMNH, and FMNH₂, respectively.) Calorimetric experiments were performed in a flow microcalorimeter which was modified to prevent sample contamination by oxygen. The enthalpy observed for reaction (a), after correction for dilution and buffer effects, was ?39.2 ± 0.4 kcal (mole FMNH₂)^?1 at 25 °C. The potential difference, ΔE′, developed by reaction (a) was determined potentiometrically and corresponded to a free energy change, ΔG′, of ?30.3 kcal (mole FMNH₂)^?1. The resulting entropy change, ΔS′, was thus calculated to be ?29.8 e.u. Reaction (a) was also studied at temperatures of 7 °C and 35.5 °C. ΔC_p′ for the reaction was calculated as ?155 ± 18 cal deg^?1 (mole FMNH₂)^?1 at 20 °C. ΔH′ for the reaction (b), FMNH₂ ? FMN + H₂, (b) was calculated as +14.2 ± 0.7 kcal mole^?1 at 25 °C, relative to the enthalpy of the hydrogen electrode being identically equal to zero at all values of pH and temperature. The free energy at pH 7.0 for reaction (b), calculated from the potential was found to be ?9.7 kcal mole^?1, which resulted in an entropy for reaction (b) of 80.2 e.u. A thermal titration of reaction (a) was used to calculate the thermodynamic parameters for the formation of semiquinone dimer according to the reaction FMNH₂ + FMN ? (·FMNH)₂. (c) The free energy, enthalpy, and entropy changes for reaction (c) were estimated to be ?6.1 kcal mole^?1, ?7 kcal mole^?1, and ?3 e.u., respectively.     

Binding Pockets and Pathways for Dioxygen through the KijD3 N‐Oxygenase in Complex with Flavin Mononucleotide Cofactor and a 3‐Aminoglucose Substrate: Predictions from Molecular Dynamics Simulations

In this work, two protein systems, Kij3D? FMN? AKM? O₂ and Kij3D? FMN? O₂, made of KijD3 N‐oxygenase, flavin mononucleotide (FMN) cofactor, dTDP‐3‐amino‐2,3,6‐trideoxy‐4‐keto‐3‐methyl‐D ‐glucose (AKM) substrate, and dioxygen (O₂), have been assembled by adding a molecule of O₂, and removing (or not) AKM, to crystal data for the Kij3D? FMN? AKM complex. Egress of AKM and O₂ from these systems was then investigated by applying a tiny external random force, in turn, to their center of mass in the course of molecular dynamics in explicit H₂O. It turned out that the wide AKM channel, even when emptied, does not constitute the main route for O₂ egress. Other routes appear to be also viable, while various binding pockets (BPs) outside the active center are prone to trap O₂. By reversing the reasoning, these can also be considered as routes for uptake of O₂ by the protein, before or after AKM uptake, while BPs may serve as reservoirs of O₂. This shows that the small molecule O₂ is capable of permeating the protein by exploiting all nearby interstices that are created on thermal fluctuations of the protein, rather than having necessarily to look for farther, permanent channels.     

Ultrafine Co3Se4 Nanoparticles in Nitrogen‐Doped 3D Carbon Matrix for High‐Stable and Long‐Cycle‐Life Lithium Sulfur Batteries

Lithium–sulfur batteries are a promising high energy output solution for substitution of traditional lithium ion batteries. In recent times research in this field has stepped into the exploration of practical applications. However, their applications are impeded by cycling stability and short life‐span mainly due to the notorious polysulfide shuttle effect. In this work, a multifunctional sulfur host fabricated by grafting highly conductive Co₃Se₄ nanoparticles onto the surface of an N‐doped 3D carbon matrix to inhibit the polysulfide shuttle and improve the sulfur utilization is proposed. By regulating the carbon matrix and the Co₃Se₄ distribution, N‐CN‐750@Co₃Se₄‐0.1 m with abundant polar sites is experimentally and theoretically shown to be a good LiPSs absorbent and a sulfur conversion accelerator. The S/N‐CN‐750@Co₃Se₄‐0.1 m cathode shows excellent sulfur utilization, rate performance, and cyclic durability. A prolonged cycling test of the as‐fabricated S/N‐CN‐750@Co₃Se₄‐0.1 m cathode is carried out at 0.2 C for more than 5 months which delivers a high initial capacity of 1150.3 mAh g^?1 and retains 531.0 mAh g^?1 after 800 cycles with an ultralow capacity reduction of 0.067% per cycle, maintaining Coulombic efficiency of more than 99.3%. The reaction details are characterized and analyzed by ex situ measurements. This work highly emphasizes the potential capabilities of transition‐metal selenides in lithium–sulfur batteries.     

Active‐Site Imprinting: Preparation of Fe–N–C Catalysts from Zinc Ion–Templated Ionothermal Nitrogen‐Doped Carbons

Atomically dispersed Fe–N–C catalysts are considered the most promising precious‐metal‐free alternative to state‐of‐the‐art Pt‐based oxygen reduction electrocatalysts for proton‐exchange membrane fuel cells. The exceptional progress in the field of research in the last ≈30 years is currently limited by the moderate active site density that can be obtained. Behind this stands the dilemma of metastability of the desired FeN₄ sites at the high temperatures that are believed to be a requirement for their formation. It is herein shown that Zn²⁺ ions can be utilized in the novel concept of active‐site imprinting based on a pyrolytic template ion reaction throughout the formation of nitrogen‐doped carbons. As obtained atomically dispersed Zn–N–Cs comprising ZnN₄ sites as well as metal‐free N₄ sites can be utilized for the coordination of Fe²⁺ and Fe³⁺ ions to form atomically dispersed Fe–N–C with Fe loadings as high as 3.12 wt%. The Fe–N–Cs are active electocatalysts for the oxygen reduction reaction in acidic media with an onset potential of E₀ = 0.85 V versus RHE in 0.1 m HClO₄. Identical location atomic resolution transmission electron microscopy imaging, as well as in situ electrochemical flow cell coupled to inductively coupled plasma mass spectrometry measurements, is employed to directly prove the concept of the active‐site imprinting approach.     

Insight into the redox partner interaction mechanism in cytochrome P450BM‐3 using molecular dynamics simulations

Flavocytochrome P450BM‐3 is a soluble bacterial reductase composed of two flavin (FAD/FMN) and one HEME domains. In this article, we have performed molecular dynamics simulations on both the isolated FMN and HEME domains and their crystallographic complex, with the aim to study their binding modes and to garner insight into the interdomain electron transfer (ET) mechanism. The results evidenced an interdomain conformational rearrangement that reduces the average distance between the FMN and HEME cofactors from 1.81 nm, in the crystal structure, to an average value of 1.41 ± 0.09 nm along the simulation. This modification is in agreement with previously proposed hypotheses suggesting that the crystallographic FMN/HEME complex is not in the optimal arrangement for favorable ET rate under physiological conditions. The calculation of the transfer rate along the simulation, using the Pathways Path method, demonstrated the occurrence of seven ET pathways between the two redox centers, with three of them providing ET rates (K_ET) comparable with the experimental one. The sampled ET pathways comprise the amino acids N319, L322, F390, K391, P392, F393, A399, C400, and Q403 of the HEME domain and M490 of the FMN domain. The values of K_ET closer to the experiment were found along the pathways FMN(C7) → F390 → K391 → P392 → HEME(Fe) and FMN(C8) → M490 → F393 → HEME(Fe). Finally, the analysis of the collective modes of the protein complex evidences a clear correlation of the first two essential modes with the activation of the most effective ET pathways along the trajectory. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 197–209, 2014.     

Global fold of human cannabinoid type 2 receptor probed by solid‐state 13C‐, 15N‐MAS NMR and molecular dynamics simulations

The global fold of human cannabinoid type 2 (CB₂) receptor in the agonist‐bound active state in lipid bilayers was investigated by solid‐state ¹³C‐ and ¹⁵N magic‐angle spinning (MAS) NMR, in combination with chemical‐shift prediction from a structural model of the receptor obtained by microsecond‐long molecular dynamics (MD) simulations. Uniformly ¹³C‐ and ¹⁵N‐labeled CB₂ receptor was expressed in milligram quantities by bacterial fermentation, purified, and functionally reconstituted into liposomes. ¹³C MAS NMR spectra were recorded without sensitivity enhancement for direct comparison of C_α, C_β, and C?O bands of superimposed resonances with predictions from protein structures generated by MD. The experimental NMR spectra matched the calculated spectra reasonably well indicating agreement of the global fold of the protein between experiment and simulations. In particular, the ¹³C chemical shift distribution of C_α resonances was shown to be very sensitive to both the primary amino acid sequence and the secondary structure of CB₂. Thus the shape of the C_α band can be used as an indicator of CB₂ global fold. The prediction from MD simulations indicated that upon receptor activation a rather limited number of amino acid residues, mainly located in the extracellular Loop 2 and the second half of intracellular Loop 3, change their chemical shifts significantly (≥1.5 ppm for carbons and ≥5.0 ppm for nitrogens). Simulated two‐dimensional ¹³C_α(i)? ¹³C?O(i) and ¹³C?O(i)? ¹⁵NH(i + 1) dipolar‐interaction correlation spectra provide guidance for selective amino acid labeling and signal assignment schemes to study the molecular mechanism of activation of CB₂ by solid‐state MAS NMR. Proteins 2014; 82:452–465. © 2013 Wiley Periodicals, Inc.