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1.
J Biomol NMR ; 74(1): 71-82, 2020 Jan.
Article in English | MEDLINE | ID: mdl-31834579

ABSTRACT

Non-uniform sampling has been successfully used for solution and solid-state NMR of homogeneous samples. In the solid state, protein samples are often dominated by inhomogeneous contributions to the homogeneous line widths. In spite of different technical strategies for peak reconstruction by different methods, we validate that NUS can generally be used also for such situations where spectra are made up of complex peak shapes rather than Lorentian lines. Using the RMSD between subsampled and reconstructed data and those spectra obtained with uniform sampling for a sample comprising a wide conformational distribution, we quantitatively evaluate the identity of inhomogeneous peak patterns. The evaluation comprises Iterative Soft Thresholding (hmsIST implementation) as a method explicitly not assuming Lorentian lineshapes, as well as Sparse Multidimensional Iterative Lineshape Enhanced (SMILE) algorithm and Signal Separation Algorithm (SSA) reconstruction, which do work on the basis of Lorentian lineshape models, with different sampling densities. Even though individual peculiarities are apparent, all methods turn out principally viable to reconstruct the heterogeneously broadened peak shapes.


Subject(s)
Algorithms , Nuclear Magnetic Resonance, Biomolecular , N-Formylmethionine Leucyl-Phenylalanine/chemistry
2.
J Biomol NMR ; 74(4-5): 229-237, 2020 May.
Article in English | MEDLINE | ID: mdl-31894471

ABSTRACT

Obtaining site-specific assignments for the NMR spectra of proteins in the solid state is a significant bottleneck in deciphering their biophysics. This is primarily due to the time-intensive nature of the experiments. Additionally, the low resolution in the [Formula: see text]-dimension requires multiple complementary experiments to be recorded to lift degeneracies in assignments. We present here an approach, gleaned from the techniques used in multiple-acquisition experiments, which allows the recording of forward and backward residue-linking experiments in a single experimental block. Spectra from six additional pathways are also recovered from the same experimental block, without increasing the probe duty cycle. These experiments give intra- and inter residue connectivities for the backbone [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text] resonances and should alone be sufficient to assign these nuclei in proteins at MAS frequencies > 60 kHz. The validity of this approach is tested with experiments on a standard tripeptide N-formyl methionyl-leucine-phenylalanine (f-MLF) at a MAS frequency of 62.5 kHz, which is also used as a test-case for determining the sensitivity of each of the experiments. We expect this approach to have an immediate impact on the way assignments are obtained at MAS frequencies [Formula: see text].


Subject(s)
Nuclear Magnetic Resonance, Biomolecular/methods , Carbon Isotopes , N-Formylmethionine Leucyl-Phenylalanine/chemistry , Nitrogen Isotopes
3.
Bioorg Med Chem Lett ; 28(17): 2949-2952, 2018 09 15.
Article in English | MEDLINE | ID: mdl-30006064

ABSTRACT

The tripeptide formyl-Met-Leu-Phe (fMLF) is a prototype of N-formylated chemotactic peptides for neutrophils owing to its ability to bind and activate the G protein-coupled formyl peptide receptor (FPR). Here, we developed an 18F-labeled fMLF derivative targeting FPR as a positron emission tomography (PET) imaging probe for bacterial infections. The study demonstrates that the fMLF derivative fMLFXYk(FB)k (X = Nle) has a high affinity for FPR (Ki = 0.62 ±â€¯0.13 nM). The radiochemical yield and purity of [18F]fMLFXYk(FB)k were 16% and >96%, respectively. The in vivo biodistribution study showed that [18F]fMLFXYk(FB)k uptake was higher in the bacterial infected region than in the non-infected region. We observed considerably higher infection-to-muscle ratio of 4.6 at 60 min after [18F]fMLFXYk(FB)k injection. Furthermore, small-animal PET imaging studies suggested that [18F]fMLFXYk(FB)k uptake in the bacterial infected region was clearly visualized 60 min after injection.


Subject(s)
Escherichia coli Infections/diagnostic imaging , Molecular Probes/chemistry , N-Formylmethionine Leucyl-Phenylalanine/chemistry , Positron-Emission Tomography , Dose-Response Relationship, Drug , Fluorine Radioisotopes , Molecular Probes/chemical synthesis , Molecular Structure , N-Formylmethionine Leucyl-Phenylalanine/chemical synthesis , Structure-Activity Relationship
4.
Mar Drugs ; 15(9)2017 Sep 01.
Article in English | MEDLINE | ID: mdl-28862648

ABSTRACT

A continuing chemical investigation of the ethyl acetate (EtOAc) extract of a reef soft coral Sinularia brassica, which was cultured in a tank, afforded four new steroids with methyl ester groups, sinubrasones A-D (1-4) for the first time. In particular, 1 possesses a ß-D-xylopyranose. The structures of the new compounds were elucidated on the basis of spectroscopic analyses. The cytotoxicities of compounds 1-4 against the proliferation of a limited panel of cancer cell lines were assayed. The anti-inflammatory activities of these new compounds 1-4 were also evaluated by measuring their ability to suppress superoxide anion generation and elastase release in N-formyl-methionyl-leucyl-phenylalanine/cytochalasin B (fMLP/CB)-induced human neutrophils. Compounds 2 and 3 were shown to exhibit significant cytotoxicity, and compounds 3 and 4 were also found to display attracting anti-inflammatory activities.


Subject(s)
Anthozoa/chemistry , Steroids , Acetates/chemistry , Animals , Anti-Inflammatory Agents, Non-Steroidal/pharmacology , Humans , N-Formylmethionine Leucyl-Phenylalanine/chemistry , Neutrophils/drug effects , Pancreatic Elastase/drug effects , Steroids/chemistry , Steroids/isolation & purification , Steroids/pharmacology , Superoxides/metabolism , Xylose/analogs & derivatives , Xylose/chemistry
5.
Pediatr Res ; 80(2): 293-8, 2016 08.
Article in English | MEDLINE | ID: mdl-27055186

ABSTRACT

BACKGROUND: PepT1 transports dietary and bacterial peptides in the gut. We hypothesized that cysteinyl-glycine would ameliorate the inflammatory effect of a bacterial peptide, formyl-methionyl-leucyl-phenylalanine (fMLP), in both sow-fed and parenterally-fed piglets. METHODS: An intestinal perfusion experiment was performed in piglets (N = 12) that were sow-reared or provided with parenteral nutrition (PN) for 4 d. In each piglet, five segments of isolated intestine were perfused with five treatments including cysteine and glycine, cysteinyl-glycine, fMLP, free cysteine and glycine with fMLP, or cysteinyl-glycine with fMLP. Mucosal cytokine responses and intestinal morphology was assessed in each gut segment. RESULTS: PN piglets had lower mucosal IL-10 by approximately 20% (P < 0.01). Cysteinyl-glycine lowered TNF-α response to fMLP in PN-fed animals and IFN-γ response to fMLP in both groups (P < 0.05). The free cysteine and glycine treatment reduced TNF-α in sow-fed animals (P < 0.05). fMLP affected villus height in parenterally (P < 0.05), but not sow-fed animals. CONCLUSION: Parenteral feeding conferred a susceptibility to mucosal damage by fMLP. The dipeptide was more effective at attenuating the inflammatory response to a bacterial peptide than free amino acids. This may be due to competitive inhibition of fMLP transport or a greater efficiency of transport of dipeptides.


Subject(s)
Cytokines/metabolism , Dipeptides/chemistry , Inflammation/metabolism , Mucous Membrane/metabolism , N-Formylmethionine Leucyl-Phenylalanine/chemistry , Animals , Cysteine/chemistry , Disease Models, Animal , Genetic Predisposition to Disease , Glycine/chemistry , Interleukin-10/metabolism , Intestinal Mucosa/metabolism , Mannitol/chemistry , Parenteral Nutrition , Perfusion , Peroxidase/metabolism , Random Allocation , Swine , Time Factors
6.
Phys Chem Chem Phys ; 18(5): 4035-44, 2016 Feb 07.
Article in English | MEDLINE | ID: mdl-26776070

ABSTRACT

Experimental characterization of one-bond heteronuclear dipolar couplings is essential for structural and dynamics characterization of molecules by solid-state NMR. Accurate measurement of heteronuclear dipolar tensor parameters in magic-angle spinning NMR requires that the recoupling sequences efficiently reintroduce the desired heteronuclear dipolar coupling term, fully suppress other interactions (such as chemical shift anisotropy and homonuclear dipolar couplings), and be insensitive to experimental imperfections, such as radio frequency (rf) field mismatch. In this study, we demonstrate that the introduction of window delays into the basic elements of a phase-alternating R-symmetry (PARS) sequence results in a greatly improved protocol, termed windowed PARS (wPARS), which yields clean dipolar lineshapes that are unaffected by other spin interactions and are largely insensitive to experimental imperfections. Higher dipolar scaling factors can be attained in this technique with respect to PARS, which is particularly useful for the measurement of relatively small dipolar couplings. The advantages of wPARS are verified experimentally on model molecules N-acetyl-valine (NAV) and a tripeptide Met-Leu-Phe (MLF). The incorporation of wPARS into 3D heteronuclear or homonuclear correlation experiments permits accurate site-specific determination of dipolar tensors in proteins, as demonstrated on dynein light chain 8 (LC8). Through 3D wPARS recoupling based spectroscopy we have determined both backbone and side chain dipolar tensors in LC8 in a residue-resolved manner. We discuss these in the context of conformational dynamics of LC8. We have addressed the effect of paramagnetic relaxant Cu(ii)-EDTA doping on the dipolar coupling parameters in LC8 and observed no significant differences with respect to the neat sample permitting fast data collection. Our results indicate that wPARS is advantageous with respect to the windowless version of the sequence and is applicable to a broad range of systems including but not limited to biomolecules.


Subject(s)
Dyneins/chemistry , N-Formylmethionine Leucyl-Phenylalanine/analogs & derivatives , Nuclear Magnetic Resonance, Biomolecular , Valine/analogs & derivatives , Copper/chemistry , Edetic Acid/chemistry , N-Formylmethionine Leucyl-Phenylalanine/chemistry , Valine/chemistry
7.
J Biol Chem ; 289(4): 2295-306, 2014 Jan 24.
Article in English | MEDLINE | ID: mdl-24285541

ABSTRACT

Unlike formyl peptide receptor 1 (FPR1), FPR2/ALX (FPR2) interacts with peptides of diverse sequences but has low affinity for the Escherichia coli-derived chemotactic peptide fMet-Leu-Phe (fMLF). Using computer modeling and site-directed mutagenesis, we investigated the structural requirements for FPR2 to interact with formyl peptides of different length and composition. In calcium flux assay, the N-formyl group of these peptides is necessary for activation of both FPR2 and FPR1, whereas the composition of the C-terminal amino acids appears more important for FPR2 than FPR1. FPR2 interacts better with pentapeptides (fMLFII, fMLFIK) than tetrapeptides (fMLFK, fMLFW) and tripeptide (fMLF) but only weakly with peptides carrying negative charges at the C terminus (e.g. fMLFE). In contrast, FPR1 is less sensitive to negative charges at the C terminus. A CXCR4-based homology model of FPR1 and FPR2 suggested that Asp-281(7.32) is crucial for the interaction of FPR2 with certain formyl peptides as its negative charge may be repulsive with the terminal COO- group of fMLF and negatively charged Glu in fMLFE. Asp-281(7.32) might also form a stable interaction with the positively charged Lys in fMLFK. Site-directed mutagenesis was performed to remove the negative charge at position 281 in FPR2. The D281(7.32)G mutant showed improved affinity for fMLFE and fMLF and reduced affinity for fMLFK compared with wild type FPR2. These results indicate that different structural determinants are used by FPR1 and FPR2 to interact with formyl peptides.


Subject(s)
Molecular Dynamics Simulation , N-Formylmethionine Leucyl-Phenylalanine/analogs & derivatives , Receptors, Formyl Peptide/chemistry , Receptors, Lipoxin/chemistry , Amino Acid Substitution , Humans , Ligands , Mutagenesis, Site-Directed , Mutation, Missense , N-Formylmethionine Leucyl-Phenylalanine/chemistry , N-Formylmethionine Leucyl-Phenylalanine/metabolism , Receptors, CXCR4/chemistry , Receptors, CXCR4/genetics , Receptors, CXCR4/metabolism , Receptors, Formyl Peptide/genetics , Receptors, Formyl Peptide/metabolism , Receptors, Lipoxin/genetics , Receptors, Lipoxin/metabolism , Structural Homology, Protein , Structure-Activity Relationship
8.
J Biomol NMR ; 61(2): 97-107, 2015 Feb.
Article in English | MEDLINE | ID: mdl-25510834

ABSTRACT

The measurement of long-range distances remains a challenge in solid-state NMR structure determination of biological macromolecules. In 2D and 3D correlation spectra of uniformly (13)C-labeled biomolecules, inter-residue, inter-segmental, and intermolecular (13)C-(13)C cross peaks that provide important long-range distance constraints for three-dimensional structures often overlap with short-range cross peaks that only reflect the covalent structure of the molecule. It is therefore desirable to develop new approaches to obtain spectra containing only long-range cross peaks. Here we show that a relaxation-compensated modification of the commonly used 2D (1)H-driven spin diffusion (PDSD) experiment allows the clean detection of such long-range cross peaks. By adding a z-filter to keep the total z-period of the experiment constant, we compensate for (13)C T1 relaxation. As a result, the difference spectrum between a long- and a scaled short-mixing time spectrum show only long-range correlation signals. We show that one- and two-bond cross peaks equalize within a few tens of milliseconds. Within ~200 ms, the intensity equilibrates within an amino acid residue and a monosaccharide to a value that reflects the number of spins in the local network. With T1 relaxation compensation, at longer mixing times, inter-residue and inter-segmental cross peaks increase in intensity whereas intra-segmental cross-peak intensities remain unchanged relative to each other and can all be subtracted out. Without relaxation compensation, the difference 2D spectra exhibit both negative and positive intensities due to heterogeneous T1 relaxation in most biomolecules, which can cause peak cancellation. We demonstrate this relaxation-compensated difference PDSD approach on amino acids, monosaccharides, a crystalline model peptide, a membrane-bound peptide and a plant cell wall sample. The resulting difference spectra yield clean multi-bond, inter-residue and intermolecular correlation peaks, which are often difficult to resolve in the parent 2D spectra.


Subject(s)
Carbon-13 Magnetic Resonance Spectroscopy/methods , Cell Wall/chemistry , Nuclear Magnetic Resonance, Biomolecular/methods , Plant Proteins/chemistry , Polysaccharides/chemistry , Arabidopsis , Carbon Isotopes/chemistry , Glucose/chemistry , Glutamine/chemistry , Histidine/chemistry , N-Formylmethionine Leucyl-Phenylalanine/chemistry , Plant Proteins/analysis , Polysaccharides/analysis
9.
Chembiochem ; 15(16): 2420-6, 2014 Nov 03.
Article in English | MEDLINE | ID: mdl-25224835

ABSTRACT

The tripeptide N-formyl-Met-Leu-Phe (fMLF) is a potent neutrophil chemoattractant and the reference agonist for the G protein-coupled N-formylpeptide receptor (FPR). As it plays a very important role in host defense and inflammation, there has been considerable interest in the development of fMLF analogues in the hope of identifying potential therapeutic agents. Herein we report the design, synthesis, and evaluation of AApeptides that mimic the structure and function of fMLF. The lead AApeptides induced calcium mobilization and mitogen-activated protein kinase (MAPK) signal transduction pathways in FPR-transfected rat basophilic leukemic (RBL) cells. More intriguingly, at high concentrations, certain AApeptides were more effective than fMLF in the induction of calcium mobilization. Their agonistic activity is further supported by their ability to stimulate chemotaxis and the production of superoxide in HL-60 cells. Similarly to fMLF, these AApeptides are much more selective towards FPR1 than FPR2. These results suggest that the fMLF-mimicking AApeptides might emerge as a new class of therapeutic agents that target FPRs.


Subject(s)
N-Formylmethionine Leucyl-Phenylalanine/analogs & derivatives , Peptidomimetics/chemical synthesis , Animals , Calcium/metabolism , Cell Line , Chemotaxis , HL-60 Cells , Humans , Mitogen-Activated Protein Kinase 1/metabolism , Mitogen-Activated Protein Kinase 3/metabolism , N-Formylmethionine Leucyl-Phenylalanine/chemistry , Neutrophils/enzymology , Peptidomimetics/chemistry , Rats , Receptors, Formyl Peptide/chemistry , Receptors, Formyl Peptide/genetics , Receptors, Formyl Peptide/metabolism , Receptors, Lipoxin/chemistry , Receptors, Lipoxin/genetics , Receptors, Lipoxin/metabolism , Superoxides/metabolism , Transfection
10.
Bioconjug Chem ; 25(12): 2116-22, 2014 Dec 17.
Article in English | MEDLINE | ID: mdl-25398017

ABSTRACT

Most immunomodulatory materials (e.g., vaccine adjuvants such as alum) modulate adaptive immunity, and yet little effort has focused on developing materials to regulate innate immunity, which get mentioned only when inflammation affects the biocompatibility of biomaterials. Traditionally considered as short-lived effector cells from innate immunity primarily for the clearance of invading microorganisms without specificity, neutrophils exhibit a key role in launching and shaping the immune response. Here we show that the incorporation of unnatural amino acids into a well-known chemoattractant-N-formyl-l-methionyl-l-leucyl-l-phenylalanine (fMLF)-offers a facile approach to create a de novo, multifunctional chemoattractant that self-assembles to form supramolecular nanofibrils and hydrogels. This de novo chemoattractant not only exhibits preserved cross-species chemoattractant activity to human and murine neutrophils, but also effectively resists proteolysis. Thus, its hydrogel, in vivo, releases the chemoattractant and attracts neutrophils to the desired location in a sustainable manner. As a novel and general approach to generate a new class of biomaterials for modulating innate immunity, this work offers a prolonged acute inflammation model for developing various new applications.


Subject(s)
Chemotactic Factors/chemistry , Hydrogels/chemistry , Immunologic Factors/chemistry , N-Formylmethionine Leucyl-Phenylalanine/chemistry , Neutrophils/immunology , Animals , Biomimetic Materials/chemistry , Biomimetic Materials/pharmacology , Chemotactic Factors/immunology , Cross Reactions , Drug Evaluation, Preclinical/methods , Humans , Immunologic Factors/pharmacology , Immunomodulation , Inflammation/immunology , Macrophages/drug effects , Macrophages/immunology , Macrophages/metabolism , Mice , Neutrophils/drug effects , Neutrophils/metabolism , Reactive Oxygen Species/metabolism , Rheology , Structure-Activity Relationship
11.
Mar Drugs ; 12(8): 4677-92, 2014 Aug 22.
Article in English | MEDLINE | ID: mdl-25153765

ABSTRACT

Ten new briarane diterpenoids, briaviolides A-J (1-10), together with six known briaranes, solenolides A and D, excavatolide A, briaexcavatolide I, 4ß-acetoxy-9-deacetystylatulide lactone and 9-deacetylstylatulide lactone, were isolated from the Taiwanese soft coral, Briareum violacea. Their structures were determined on the basis of spectroscopic data ((1)H- and (13)C-NMR, (1)H-(1)H COSY, HSQC, HMBC and NOESY), HR-MS and chemical methods. The absolute configuration of briaviolide A (1) was determined by X-ray crystallographic analysis. Compounds 5, 9 and derivative 11 showed moderate inhibitory activities on superoxide-anion generation and elastase release by human neutrophils in response to N-formyl-methionyl-leucyl-phenylalanine/ Cytochalasin B (fMLP/CB).


Subject(s)
Anthozoa/chemistry , Diterpenes/chemistry , Animals , Cytochalasin B/metabolism , Diterpenes/metabolism , Diterpenes/pharmacology , Humans , N-Formylmethionine Leucyl-Phenylalanine/chemistry , Neutrophils/drug effects , Neutrophils/metabolism , Pancreatic Elastase/metabolism , Superoxides/metabolism , Taiwan
12.
J Magn Reson ; 364: 107710, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38901172

ABSTRACT

Motionally averaged dipolar couplings are an important tool for understanding the complex dynamics of catalysts, polymers, and biomolecules. While there is a plethora of solid-state NMR pulse sequences available for their measurement, in can be difficult to gauge the methods' strengths and weaknesses. In particular, there has not been a comprehensive comparison of their performance in natural abundance samples, where 1H homonuclear dipolar couplings are important and the use of large MAS rotors may be required for sensitivity reasons. In this work, we directly compared some of the more common methods for measuring C-H dipolar couplings in natural abundance samples using L-alanine (L-Ala) and the N-formyl-L-methionyl-L-leucyl-L-phenylalanine (fMLF) tripeptide as model systems. We evaluated their performance in terms of accuracy, resolution, sensitivity, and ease of implementation. We found that, despite the presence of 1H homonuclear dipolar interactions, all methods, with the exception of REDOR, were able to yield the reasonable dipolar coupling strengths for both mobile and static moieties. Of these methods, PDLF provides the most convenient workflow and precision at the expense of low sensitivity. In low-sensitivity cases, MAS-PISEMA and DIPSHIFT appear to be the better options.


Subject(s)
Alanine , Algorithms , Alanine/chemistry , Magnetic Resonance Spectroscopy/methods , N-Formylmethionine Leucyl-Phenylalanine/chemistry , Motion , Nuclear Magnetic Resonance, Biomolecular/methods
13.
Drug Deliv ; 30(1): 2241664, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37545034

ABSTRACT

Gradual loss of neuronal structure and function due to impaired blood-brain barrier (BBB) and neuroinflammation are important factors in multiple sclerosis (MS) progression. Our previous studies demonstrated that the C16 peptide and angiopoietin 1 (Ang-1) compound (C + A) could modulate inflammation and vascular protection in many models of MS. In this study, nanotechnology and a novel nanovector of the leukocyte chemotactic peptide N-formyl-methionyl-leucyl-phenylalanine (fMLP) were used to examine the effects of C + A on MS. The acute experimental autoimmune encephalomyelitis (EAE) model of MS was established in Lewis rats. The C + A compounds were conjugated to control nano-carriers and fMLP-nano-carriers and administered to animals by intravenous injection. The neuropathological changes in the brain cortex and spinal cord were examined using multiple approaches. The stimulation of vascular injection sites was examined using rabbits. The results showed that all C + A compounds (C + A alone, nano-carrier C + A, and fMLP-nano-carrier C + A) reduced neuronal inflammation, axonal demyelination, gliosis, neuronal apoptosis, vascular leakage, and BBB impairment induced by EAE. In addition, the C + A compounds had minimal side effects on liver and kidney functions. Furthermore, the fMLP-nano-carrier C + A compound had better effects compared to C + A alone and the nano-carrier C + A. This study indicated that the fMLP-nano-carrier C + A could attenuate inflammation-related pathological changes in EAE and may be a potential therapeutic strategy for the treatment of MS and EAE.


Subject(s)
Encephalomyelitis, Autoimmune, Experimental , Multiple Sclerosis , Rats , Animals , Rabbits , N-Formylmethionine Leucyl-Phenylalanine/chemistry , N-Formylmethionine Leucyl-Phenylalanine/pharmacology , Multiple Sclerosis/drug therapy , Liposomes , Angiopoietin-1/therapeutic use , Rats, Inbred Lew , Encephalomyelitis, Autoimmune, Experimental/drug therapy , Encephalomyelitis, Autoimmune, Experimental/pathology , Inflammation/drug therapy
14.
J Pept Sci ; 18(6): 418-26, 2012 Jun.
Article in English | MEDLINE | ID: mdl-22528501

ABSTRACT

In the present study, we report synthesis and biological evaluation of the N-Boc-protected tripeptides 4a-l and N-For protected tripeptides 5a-l as new For-Met-Leu-Phe-OMe (fMLF-OMe) analogues. All the new ligands are characterized by the C-terminal Phe residue variously substituted at position 4 of the aromatic ring. The agonism of 5a-l and the antagonism of 4a-l (chemotaxis, superoxide anion production, lysozyme release as well as receptor binding affinity) have been examined on human neutrophils. No synthesized compounds has higher activity than the standard fMLF-OMe tripeptide to stimulate chemotaxis, although compounds 5a and 5c with -CH(3) and -C(CH(3))(3), respectively, in position 4 on the aromatic ring, are better than the standard tripeptide to stimulate the production of superoxide anion, in higher concentration. Compounds 4f and 4i, containing -F and -I in position 4, respectively, on the aromatic ring of phenylalanine, exhibit significant chemotactic antagonism. The influence of the different substitution at the position 4 on the aromatic ring of phenylalanine is discussed.


Subject(s)
Chemotaxis/drug effects , Muramidase/antagonists & inhibitors , N-Formylmethionine Leucyl-Phenylalanine/analogs & derivatives , Neutrophils/drug effects , Oligopeptides/chemical synthesis , Oligopeptides/pharmacology , Phenylalanine/chemistry , Amino Acid Sequence , Anions/antagonists & inhibitors , Anions/metabolism , Humans , Molecular Conformation , Muramidase/metabolism , N-Formylmethionine Leucyl-Phenylalanine/chemical synthesis , N-Formylmethionine Leucyl-Phenylalanine/chemistry , N-Formylmethionine Leucyl-Phenylalanine/pharmacology , Neutrophils/cytology , Oligopeptides/chemistry , Reference Values , Stereoisomerism , Superoxides/antagonists & inhibitors , Superoxides/metabolism
15.
Solid State Nucl Magn Reson ; 45-46: 51-8, 2012.
Article in English | MEDLINE | ID: mdl-22749432

ABSTRACT

A (1)H-(13)C frequency-selective REDOR (FS-REDOR) experiment is developed for measuring intramolecular (1)H-(13)C distances in uniformly (13)C, (15)N-labeled molecules. Theory and simulations show that the experiment removes the interfering homonuclear (1)H-(1)H, (13)C-(13)C and heteronuclear (1)H-(15)N, (13)C-(15)N dipolar interactions while retaining the desired heteronuclear (1)H-(13)C dipolar interaction. Our results indicate that this technique, combined with the numerical fitting, can be used to measure a (1)H-(13)C distance up to 5Å. We also demonstrate that the measured intramolecular (1)H-(13)C distances are useful to determine dihedral angles in proteins.


Subject(s)
Magnetic Resonance Spectroscopy/methods , Peptides/chemistry , Histidine/chemistry , N-Formylmethionine Leucyl-Phenylalanine/chemistry
16.
Nat Commun ; 13(1): 5232, 2022 09 05.
Article in English | MEDLINE | ID: mdl-36064945

ABSTRACT

The formyl peptide receptor 1 (FPR1) is primarily responsible for detection of short peptides bearing N-formylated methionine (fMet) that are characteristic of protein synthesis in bacteria and mitochondria. As a result, FPR1 is critical to phagocyte migration and activation in bacterial infection, tissue injury and inflammation. How FPR1 distinguishes between formyl peptides and non-formyl peptides remains elusive. Here we report cryo-EM structures of human FPR1-Gi protein complex bound to S. aureus-derived peptide fMet-Ile-Phe-Leu (fMIFL) and E. coli-derived peptide fMet-Leu-Phe (fMLF). Both structures of FPR1 adopt an active conformation and exhibit a binding pocket containing the R2015.38XXXR2055.42 (RGIIR) motif for formyl group interaction and receptor activation. This motif works together with D1063.33 for hydrogen bond formation with the N-formyl group and with fMet, a model supported by MD simulation and functional assays of mutant receptors with key residues for recognition substituted by alanine. The cryo-EM model of agonist-bound FPR1 provides a structural basis for recognition of bacteria-derived chemotactic peptides with potential applications in developing FPR1-targeting agents.


Subject(s)
Pathogen-Associated Molecular Pattern Molecules , Staphylococcus aureus , Chemotactic Factors/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Humans , N-Formylmethionine Leucyl-Phenylalanine/chemistry , Neutrophils/metabolism , Pathogen-Associated Molecular Pattern Molecules/metabolism , Peptides/metabolism , Staphylococcus aureus/metabolism
17.
J Magn Reson ; 322: 106857, 2021 01.
Article in English | MEDLINE | ID: mdl-33227675

ABSTRACT

Ultra-fast magic-angle spinning (UFMAS) at a MAS rate (ωR/2π) of 60 kHz or higher has dramatically improved the resolution and sensitivity of solid-state NMR (SSNMR). However, limited polarization transfer efficiency using cross-polarization (CP) between 1H and rare spins such as 13C still restricts the sensitivity and multi-dimensional applications of SSNMR using UFMAS. We propose a novel approach, which we call decoherence-optimized tilted-angle CP (DOTA CP), to improve CP efficiency with prolonged lifetime of 1H coherence in the spin-locked condition and efficient band-selective polarization transfer by incorporating off-resonance irradiation to 1H spins. 13C CP-MAS at ωR/2π of 70-90 kHz suggested that DOTA CP notably outperformed traditional adiabatic CP, a de-facto-standard CP scheme over the past decade, in sensitivity for the aliphatic-region spectra of 13C-labeled GB1 protein and N-formyl-Met-Leu-Phe samples by up to 1.4- and 1.2-fold, respectively. 1H-detected 2D 1H/13C SSNMR for the GB1 sample indicated the effectiveness of this approach in various multidimensional applications.


Subject(s)
Bacterial Proteins/chemistry , N-Formylmethionine Leucyl-Phenylalanine/analogs & derivatives , Nuclear Magnetic Resonance, Biomolecular/methods , N-Formylmethionine Leucyl-Phenylalanine/chemistry , Sensitivity and Specificity
18.
J Am Chem Soc ; 132(17): 5993-6000, 2010 May 05.
Article in English | MEDLINE | ID: mdl-20387894

ABSTRACT

Since experimental measurements of NMR chemical shifts provide time and ensemble averaged values, we investigated how these effects should be included when chemical shifts are computed using density functional theory (DFT). We measured the chemical shifts of the N-formyl-L-methionyl-L-leucyl-L-phenylalanine-OMe (MLF) peptide in the solid state, and then used the X-ray structure to calculate the (13)C chemical shifts using the gauge including projector augmented wave (GIPAW) method, which accounts for the periodic nature of the crystal structure, obtaining an overall accuracy of 4.2 ppm. In order to understand the origin of the difference between experimental and calculated chemical shifts, we carried out first-principles molecular dynamics simulations to characterize the molecular motion of the MLF peptide on the picosecond time scale. We found that (13)C chemical shifts experience very rapid fluctuations of more than 20 ppm that are averaged out over less than 200 fs. Taking account of these fluctuations in the calculation of the chemical shifts resulted in an accuracy of 3.3 ppm. To investigate the effects of averaging over longer time scales we sampled the rotameric states populated by the MLF peptides in the solid state by performing a total of 5 micros classical molecular dynamics simulations. By averaging the chemical shifts over these rotameric states, we increased the accuracy of the chemical shift calculations to 3.0 ppm, with less than 1 ppm error in 10 out of 22 cases. These results suggests that better DFT-based predictions of chemical shifts of peptides and proteins will be achieved by developing improved computational strategies capable of taking into account the averaging process up to the millisecond time scale on which the chemical shift measurements report.


Subject(s)
N-Formylmethionine Leucyl-Phenylalanine/chemistry , Crystallization , Nuclear Magnetic Resonance, Biomolecular , Protein Conformation , Time Factors
19.
Nat Commun ; 11(1): 1208, 2020 03 05.
Article in English | MEDLINE | ID: mdl-32139677

ABSTRACT

The human formyl peptide receptor 2 (FPR2) plays a crucial role in host defense and inflammation, and has been considered as a drug target for chronic inflammatory diseases. A variety of peptides with different structures and origins have been characterized as FPR2 ligands. However, the ligand-binding modes of FPR2 remain elusive, thereby limiting the development of potential drugs. Here we report the crystal structure of FPR2 bound to the potent peptide agonist WKYMVm at 2.8 Å resolution. The structure adopts an active conformation and exhibits a deep ligand-binding pocket. Combined with mutagenesis, ligand binding and signaling studies, key interactions between the agonist and FPR2 that govern ligand recognition and receptor activation are identified. Furthermore, molecular docking and functional assays reveal key factors that may define binding affinity and agonist potency of formyl peptides. These findings deepen our understanding about ligand recognition and selectivity mechanisms of the formyl peptide receptor family.


Subject(s)
Receptors, Formyl Peptide/chemistry , Receptors, Formyl Peptide/metabolism , Receptors, Lipoxin/chemistry , Receptors, Lipoxin/metabolism , Amino Acid Sequence , Binding Sites , Humans , Ligands , Molecular Docking Simulation , Mutation/genetics , N-Formylmethionine Leucyl-Phenylalanine/chemistry , N-Formylmethionine Leucyl-Phenylalanine/metabolism , Protein Conformation , Signal Transduction , Structure-Activity Relationship
20.
J Phys Chem Lett ; 11(21): 8952-8957, 2020 Nov 05.
Article in English | MEDLINE | ID: mdl-33030905

ABSTRACT

The formyl peptide receptor 2 (ALX/FPR2), a G-protein-coupled receptor (GPCR), plays an important role in host defense and inflammation. This receptor can be driven as pro- or anti-inflammatory depending on its agonist, such as N-formyl-Met-Leu-Phe-Lys (fMLFK) and resolvin D1 (RvD1) or its aspirin-triggered 17 (R)-epimer, AT-RvD1, respectively. However, the activation mechanism of ALX/FPR2 by pro- and anti-inflammatory agonists remains unclear. In this work, on the basis of molecular dynamics simulations, we evaluated a model of the ALX/FPR2 receptor activation process using two agonists, fMLFK and AT-RvD1, with opposite effects. The simulations by both fMLFK and AT-RvD1 induced the ALX/FPR2 activation through a set of receptor-core residues, in particular, R205, Q258, and W254. In addition, the activation was dependent on the disruption of electrostatic interactions in the cytoplasmic region of the receptor. We also found that in the AT-RvD1 simulations, the position of the H8 helix was similar to that of the same helix in other class-A GPCRs coupled to arrestin. Thus our results shed light on the mechanism of activation of the ALX/FPR2 receptor by pro-inflammatory and pro-resolution agonists.


Subject(s)
Anti-Inflammatory Agents/chemistry , Docosahexaenoic Acids/chemistry , N-Formylmethionine Leucyl-Phenylalanine/analogs & derivatives , Receptors, Formyl Peptide/agonists , Receptors, Lipoxin/agonists , Amino Acid Sequence , Anti-Inflammatory Agents/pharmacology , Cytoplasm/metabolism , Cytoplasm/ultrastructure , Docosahexaenoic Acids/pharmacology , Glucocorticoids/chemistry , Humans , Molecular Dynamics Simulation , N-Formylmethionine Leucyl-Phenylalanine/chemistry , N-Formylmethionine Leucyl-Phenylalanine/pharmacology , Protein Conformation , Receptors, Formyl Peptide/metabolism , Receptors, Lipoxin/metabolism , Signal Transduction , Static Electricity
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