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1.
Bioorg Med Chem ; 42: 116253, 2021 07 15.
Article in English | MEDLINE | ID: mdl-34130218

ABSTRACT

African trypanosomiasis is a zoonotic protozoan disease affecting the nervous system. Various natural products reportedly exhibit trypanocidal activity. Naturally occurring 2,5-diphenyloxazoles present in Oxytropis lanata, and their derivatives, were synthesized. The trypanocidal activities of the synthesized compounds were evaluated against Trypanosoma brucei brucei, T. b. gambiense, T. b. rhodesiense, T. congolense, and T. evansi. Natural product 1 exhibited trypanocidal activity against all the species/subspecies of trypanosomes, exhibiting half-maximal inhibitory concentrations (IC50) of 1.1-13.5 µM. Modification of the oxazole core improved the trypanocidal activity. The 1,3,4-oxadiazole (7) and 2,4-diphenyloxazole (9) analogs exhibited potency superior to that of 1. However, these compounds exhibited cytotoxicity in Madin-Darby bovine kidney cells. The O-methylated analog of 1 (12) was non-cytotoxic and exhibited selective trypanocidal activity against T. congolense (IC50 = 0.78 µM). Structure-activity relationship studies of the 2,5-diphenyloxazole analogs revealed aspects of the molecular structure critical for maintaining selective trypanocidal activity against T. congolense.


Subject(s)
Biological Products/pharmacology , Oxazoles/pharmacology , Trypanocidal Agents/pharmacology , Trypanosoma/drug effects , Biological Products/chemical synthesis , Biological Products/chemistry , Dose-Response Relationship, Drug , Molecular Structure , Oxazoles/chemical synthesis , Oxazoles/chemistry , Parasitic Sensitivity Tests , Structure-Activity Relationship , Trypanocidal Agents/chemical synthesis , Trypanocidal Agents/chemistry
2.
J Biol Chem ; 296: 100788, 2021.
Article in English | MEDLINE | ID: mdl-34019875

ABSTRACT

The intrinsically disordered human protein α-synuclein (αSN) can self-associate into oligomers and amyloid fibrils. Several lines of evidence suggest that oligomeric αSN is cytotoxic, making it important to devise strategies to either prevent oligomer formation and/or inhibit the ensuing toxicity. (-)-epigallocatechin gallate (EGCG) has emerged as a molecular modulator of αSN self-assembly, as it reduces the flexibility of the C-terminal region of αSN in the oligomer and inhibits the oligomer's ability to perturb phospholipid membranes and induce cell death. However, a detailed structural and kinetic characterization of this interaction is still lacking. Here, we use liquid-state NMR spectroscopy to investigate how EGCG interacts with monomeric and oligomeric forms of αSN. We find that EGCG can bind to all parts of monomeric αSN but exhibits highest affinity for the N-terminal region. Monomeric αSN binds ∼54 molecules of EGCG in total during oligomerization. Furthermore, kinetic data suggest that EGCG dimerization is coupled with the αSN association reaction. In contrast, preformed oligomers only bind ∼7 EGCG molecules per protomer, in agreement with the more compact nature of the oligomer compared with the natively unfolded monomer. In previously conducted cell assays, as little as 0.36 EGCG per αSN reduce oligomer toxicity by 50%. Our study thus demonstrates that αSN cytotoxicity can be inhibited by small molecules at concentrations at least an order of magnitude below full binding capacity. We speculate this is due to cooperative binding of protein-stabilized EGCG dimers, which in turn implies synergy between protein association and EGCG dimerization.


Subject(s)
Catechin/analogs & derivatives , alpha-Synuclein/metabolism , Catechin/pharmacology , Humans , Protein Aggregates/drug effects , Protein Binding , Protein Conformation/drug effects , Protein Multimerization/drug effects , alpha-Synuclein/chemistry , alpha-Synuclein/ultrastructure
3.
Org Lett ; 23(10): 4062-4066, 2021 05 21.
Article in English | MEDLINE | ID: mdl-33938754

ABSTRACT

To develop a new nucleoside analogue applicable to oligonucleotide therapeutics, we designed a 4'-thio analogue of an LNA/BNA monomer. Synthesis of 4'-hydroxymethyl-4'-thioribonucleoside was achieved by a tandem ring-contraction-aldol reaction of a 5-thiopyranose derivative and the subsequent Pummerer-type thioglycosylation reaction of the corresponding sulfoxide. Treatment of 4'-hydroxymethyl-4'-thiopyrimidine nucleosides with diphenyl carbonate in the presence of catalytic NaHCO3 gave the desired 4'-thioLNA/BNA monomers, which were introduced into oligonucleotides.

4.
Biochim Biophys Acta Proteins Proteom ; 1869(3): 140593, 2021 03.
Article in English | MEDLINE | ID: mdl-33359410

ABSTRACT

The 15N-1H heteronuclear single-quantum correlation (HSQC) technique in protein NMR spectroscopy suffers from line-broadening effects, such as chemical exchange of labile protons with solvent, and exchange broadening for residues undergoing conformational dynamics. The amide resonance of ß2-microglobulin residue S88 is not observed in the HSQC spectrum but can be obtained through 13C-detect experiments that circumvent the problem of amide-solvent exchange broadening. Line broadening of S88 resonance beyond detection in the HSQC spectrum is not attributed to conformational exchange but rather to solvent exchange occurring on the order of ~103 s-1.


Subject(s)
Amides/chemistry , Carbon Isotopes/chemistry , Proton Magnetic Resonance Spectroscopy/methods , Solvents/chemistry , beta 2-Microglobulin/chemistry , Protein Conformation
5.
IEEE Trans Cybern ; 51(12): 6294-6304, 2021 Dec.
Article in English | MEDLINE | ID: mdl-32248141

ABSTRACT

This article investigates the design of self-triggered controllers for networked control systems (NCSs), where the dynamics of the plant are unknown a priori. To deal with the unknown transition dynamics, we employ the Gaussian process (GP) regression in order to learn the dynamics of the plant. To design the self-triggered controller, we formulate an optimal control problem, such that the optimal control and communication policies can be jointly designed based on the GP model of the plant. Moreover, we provide an overall implementation algorithm that jointly learns the dynamics of the plant and the self-triggered controller based on a reinforcement learning framework. Finally, a numerical simulation illustrates the effectiveness of the proposed approach.


Subject(s)
Algorithms , Learning , Computer Simulation , Reinforcement, Psychology
6.
Chem Pharm Bull (Tokyo) ; 69(2): 232-235, 2021 Feb 01.
Article in English | MEDLINE | ID: mdl-33239487

ABSTRACT

The concise syntheses of two alkylated hydroquinone natural products, violaceoids A and C, were accomplished by a protecting-group-free method employing the commercially available 2,5-dihydroxybenzaldehyde as the starting material. The key strategy of the syntheses is the utilization of alkenylboronic acid as both the coupling and temporary protective reagents to efficiently introduce the requisite alkenyl side chain of violaceoid A. Moreover, the synthesis of violaceoid C is reported here for the first time.


Subject(s)
Biological Products/chemical synthesis , Hydroquinones/chemistry , Alkylation , Benzaldehydes/chemistry , Biological Products/chemistry , Hydroquinones/chemical synthesis , Temperature
7.
J Biomol NMR ; 74(12): 695-706, 2020 Dec.
Article in English | MEDLINE | ID: mdl-32804297

ABSTRACT

A procedure is presented for the substantial simplification of 2D constant-time 13C-1H heteronuclear single-quantum correlation (HSQC) spectra of 13C-enriched proteins. In this approach, a single pulse sequence simultaneously records eight sub-spectra wherein the phases of the NMR signals depend on spin topology. Signals from different chemical groups are then stratified into different sub-spectra through linear combination based on Hadamard encoding of 13CHn multiplicity (n = 1, 2, and 3) and the chemical nature of neighboring 13C nuclei (aliphatic, carbonyl/carboxyl, aromatic). This results in five sets of 2D NMR spectra containing mutually exclusive signals from: (i) 13Cß-1Hß correlations of asparagine and aspartic acid, 13Cγ-1Hγ correlations of glutamine and glutamic acid, and 13Cα-1Hα correlations of glycine, (ii) 13Cα-1Hα correlations of all residues but glycine, and (iii) 13Cß-1Hß correlations of phenylalanine, tyrosine, histidine, and tryptophan, and the remaining (iv) aliphatic 13CH2 and (v) aliphatic 13CH/13CH3 resonances. As HSQC is a common element of many NMR experiments, the spectral simplification proposed in this article can be straightforwardly implemented in experiments for resonance assignment and structure determination and should be of widespread utility.


Subject(s)
Carbon-13 Magnetic Resonance Spectroscopy , Proton Magnetic Resonance Spectroscopy , Ubiquitin/chemistry , Humans , Time Factors
8.
Org Lett ; 22(14): 5299-5303, 2020 07 17.
Article in English | MEDLINE | ID: mdl-32589438

ABSTRACT

A palladium-catalyzed regioselective three-component coupling of ynamides was developed. The reaction proceeded smoothly to furnish the desired products when carried out at 70 °C in acetonitrile/water with potassium carbonate in the presence of 2.5 mol % Pd2(dba)3·CHCl3 without a ligand. Various iodides and boronic acids were used in this reaction, and a carbon-carbon bond was formed with satisfactory regioselectivity from the ynamides.

9.
Molecules ; 25(12)2020 Jun 19.
Article in English | MEDLINE | ID: mdl-32575625

ABSTRACT

Deoxynojirimycin (DNJ) is the archetypal iminosugar, in which the configuration of the hydroxyl groups in the piperidine ring truly mimic those of d-glucopyranose; DNJ and derivatives have beneficial effects as therapeutic agents, such as anti-diabetic and antiviral agents, and pharmacological chaperones for genetic disorders, because they have been shown to inhibit α-glucosidases from various sources. However, attempts to design a better molecule based solely on structural similarity cannot produce selectivity between α-glucosidases that are localized in multiple organs and tissues, because the differences of each sugar-recognition site are very subtle. In this study, we provide the first example of a design strategy for selective lysosomal acid α-glucosidase (GAA) inhibitors focusing on the alkyl chain storage site. Our design of α-1-C-heptyl-1,4-dideoxy-1,4-imino-l-arabinitol (LAB) produced a potent inhibitor of the GAA, with an IC50 value of 0.44 µM. It displayed a remarkable selectivity toward GAA (selectivity index value of 168.2). A molecular dynamic simulation study revealed that the ligand-binding conformation stability gradually improved with increasing length of the α-1-C-alkyl chain. It is noteworthy that α-1-C-heptyl-LAB formed clearly different interactions from DNJ and had favored hydrophobic interactions with Trp481, Phe525, and Met519 at the alkyl chain storage pocket of GAA. Moreover, a molecular docking study revealed that endoplasmic reticulum (ER) α-glucosidase II does not have enough space to accommodate these alkyl chains. Therefore, the design strategy focusing on the shape and acceptability of long alkyl chain at each α-glucosidase may lead to the creation of more selective and practically useful inhibitors.


Subject(s)
Antiviral Agents/chemistry , Drug Design , Glycoside Hydrolase Inhibitors/chemistry , Imino Sugars/chemistry , Molecular Docking Simulation , alpha-Glucosidases/chemistry , 1-Deoxynojirimycin/chemistry , Glucosamine/analogs & derivatives , Glucosamine/chemistry , Humans
10.
EMBO J ; 39(12): e101732, 2020 06 17.
Article in English | MEDLINE | ID: mdl-32378734

ABSTRACT

Innate immune signaling via TLR4 plays critical roles in pathogenesis of metabolic disorders, but the contribution of different lipid species to metabolic disorders and inflammatory diseases is less clear. GM3 ganglioside in human serum is composed of a variety of fatty acids, including long-chain (LCFA) and very-long-chain (VLCFA). Analysis of circulating levels of human serum GM3 species from patients at different stages of insulin resistance and chronic inflammation reveals that levels of VLCFA-GM3 increase significantly in metabolic disorders, while LCFA-GM3 serum levels decrease. Specific GM3 species also correlates with disease symptoms. VLCFA-GM3 levels increase in the adipose tissue of obese mice, and this is blocked in TLR4-mutant mice. In cultured monocytes, GM3 by itself has no effect on TLR4 activation; however, VLCFA-GM3 synergistically and selectively enhances TLR4 activation by LPS/HMGB1, while LCFA-GM3 and unsaturated VLCFA-GM3 suppresses TLR4 activation. GM3 interacts with the extracellular region of TLR4/MD2 complex to modulate dimerization/oligomerization. Ligand-molecular docking analysis supports that VLCFA-GM3 and LCFA-GM3 act as agonist and antagonist of TLR4 activity, respectively, by differentially binding to the hydrophobic pocket of MD2. Our findings suggest that VLCFA-GM3 is a risk factor for TLR4-mediated disease progression.


Subject(s)
G(M3) Ganglioside/metabolism , Monocytes/metabolism , Obesity/metabolism , Signal Transduction , Toll-Like Receptor 4/metabolism , Animals , G(M3) Ganglioside/chemistry , G(M3) Ganglioside/genetics , HEK293 Cells , Humans , Mice , Mice, Mutant Strains , Monocytes/chemistry , Obesity/genetics , Protein Multimerization , Toll-Like Receptor 4/chemistry , Toll-Like Receptor 4/genetics
11.
Nucleosides Nucleotides Nucleic Acids ; 39(1-3): 365-383, 2020.
Article in English | MEDLINE | ID: mdl-31361181

ABSTRACT

To develop a novel asymmetric organocatalyst based on a ribonucleoside skeleton, we designed and synthesized 2'-aminouridine derivatives. The synthesized 2'-aminouridines having bulky substituents at both base and sugar moieties could catalyze the Diels-Alder reaction between cinnamaldehyde and cyclopentadiene. However, the optical purities of the resulting products were unexpectedly low.


Subject(s)
Chemistry Techniques, Synthetic , Cycloaddition Reaction , Uridine/analogs & derivatives , Uridine/chemical synthesis , Catalysis , Molecular Structure , Structure-Activity Relationship
12.
Proc Natl Acad Sci U S A ; 116(42): 21031-21036, 2019 10 15.
Article in English | MEDLINE | ID: mdl-31570587

ABSTRACT

Although many proteins possess a distinct folded structure lying at a minimum in a funneled free energy landscape, thermal energy causes any protein to continuously access lowly populated excited states. The existence of excited states is an integral part of biological function. Although transitions into the excited states may lead to protein misfolding and aggregation, little structural information is currently available for them. Here, we show how NMR spectroscopy, coupled with pressure perturbation, brings these elusive species to light. As pressure acts to favor states with lower partial molar volume, NMR follows the ensuing change in the equilibrium spectroscopically, with residue-specific resolution. For T4 lysozyme L99A, relaxation dispersion NMR was used to follow the increase in population of a previously identified "invisible" folded state with pressure, as this is driven by the reduction in cavity volume by the flipping-in of a surface aromatic group. Furthermore, multiple partly disordered excited states were detected at equilibrium using pressure-dependent H/D exchange NMR spectroscopy. Here, unfolding reduced partial molar volume by the removal of empty internal cavities and packing imperfections through subglobal and global unfolding. A close correspondence was found for the distinct pressure sensitivities of various parts of the protein and the amount of internal cavity volume that was lost in each unfolding event. The free energies and populations of excited states allowed us to determine the energetic penalty of empty internal protein cavities to be 36 cal⋅Å-3.


Subject(s)
Proteins/chemistry , Bacteriophage T4/chemistry , Muramidase/chemistry , Nuclear Magnetic Resonance, Biomolecular/methods , Pressure , Protein Conformation , Protein Denaturation , Protein Folding
13.
Beilstein J Org Chem ; 14: 1595-1618, 2018.
Article in English | MEDLINE | ID: mdl-30013687

ABSTRACT

To synthesize nucleoside and oligosaccharide derivatives, we often use a glycosylation reaction to form a glycoside bond. Coupling reactions between a nucleobase and a sugar donor in the former case, and the reaction between an acceptor and a sugar donor of in the latter are carried out in the presence of an appropriate activator. As an activator of the glycosylation, a combination of a Lewis acid catalyst and a hypervalent iodine was developed for synthesizing 4'-thionucleosides, which could be applied for the synthesis of 4'-selenonucleosides as well. The extension of hypervalent iodine-mediated glycosylation allowed us to couple a nucleobase with cyclic allylsilanes and glycal derivatives to yield carbocyclic nucleosides and 2',3'-unsaturated nucleosides, respectively. In addition, the combination of hypervalent iodine and Lewis acid could be used for the glycosylation of glycals and thioglycosides to produce disaccharides. In this paper, we review the use of hypervalent iodine-mediated glycosylation reactions for the synthesis of nucleosides and oligosaccharide derivatives.

14.
Chem Pharm Bull (Tokyo) ; 66(2): 139-146, 2018.
Article in English | MEDLINE | ID: mdl-29386464

ABSTRACT

Many attempts have been made to synthesize structurally novel nucleoside derivatives in order to identify effective compounds for the treatment of tumors and virus-caused disease. At our laboratories, as part of our efforts to synthesize 4'-thionucleosides, we have identified and characterized biologically active nucleosides. During the course of our synthetic study, we developed the Pummerer-type thioglycosylation reaction. As a result, we synthesized a potent antineoplastic nucleoside, 1-(2-deoxy-2-fluoro-ß-D-4-thio-arabino-furanosyl)cytosine (4'-thioFAC), and several novel 4'-thionucleosides that possess antiherpes virus activities.


Subject(s)
Antineoplastic Agents/chemical synthesis , Antineoplastic Agents/pharmacology , Antiviral Agents/chemical synthesis , Antiviral Agents/pharmacology , Thionucleosides/chemical synthesis , Thionucleosides/pharmacology , Drug Design , Humans , Molecular Structure , Structure-Activity Relationship
15.
Curr Protoc Nucleic Acid Chem ; 71: 1.43.1-1.43.12, 2017 12 24.
Article in English | MEDLINE | ID: mdl-29275538

ABSTRACT

The detailed practical synthesis of 4'-thionucleosides starting from L-arabinose is described here. 1,4-Anhydro-2,3-O-isopropylidene-4-thioribitol, which is the key intermediate for the synthesis of 4'-thionucleosides, is obtained from L-arabinose in several steps, including a novel reductive ring-contraction reaction. After oxidation of the key intermediate, the sulfoxide is subjected to Pummerer-type thioglycosylation in the presence of persilylated nucleobases to obtain the 4'-thioribonucleosides in good yield and ß-selectively. © 2017 by John Wiley & Sons, Inc.


Subject(s)
Arabinose/chemistry , Ribonucleosides/chemical synthesis , Thionucleosides/chemical synthesis , Glycosylation , Oxidation-Reduction , Structure-Activity Relationship
16.
Biophys J ; 112(10): 2109-2116, 2017 May 23.
Article in English | MEDLINE | ID: mdl-28538148

ABSTRACT

The ability to avoid blue-light radiation is crucial for bacteria to survive. In Halorhodospira halophila, the putative receptor for this response is known as photoactive yellow protein (PYP). Its response to blue light is mediated by changes in the optical properties of the chromophore para-coumaric acid (pCA) in the protein active site. PYP displays photocycle kinetics with a strong pH dependence for ground-state recovery, which has remained enigmatic. To resolve this problem, a comprehensive pKa determination of the active-site residues of PYP is required. Herein, we show that Glu-46 stays protonated from pH 3.4 to pH 11.4 in the ground (pG) state. This conclusion is supported by the observed hydrogen-bonded protons between Glu-46 and pCA and Tyr-42 and pCA, which are persistent over the entire pH range. Our experimental results show that none of the active-site residues of PYP undergo pH-induced changes in the pG state. Ineluctably, the pH dependence of pG recovery is linked to conformational change that is dependent upon the population of the relevant protonation state of Glu-46 and the pCA chromophore in the excited state, collaterally explaining why pG recovery is slow.


Subject(s)
Bacterial Proteins/metabolism , Photoreceptors, Microbial/metabolism , Aspartic Acid/chemistry , Aspartic Acid/metabolism , Bacterial Proteins/chemistry , Glutamic Acid/chemistry , Glutamic Acid/metabolism , Halorhodospira halophila , Hydrogen Bonding , Hydrogen-Ion Concentration , Kinetics , Nuclear Magnetic Resonance, Biomolecular , Photoreceptors, Microbial/chemistry , Protons
17.
J Biol Chem ; 292(20): 8269-8278, 2017 05 19.
Article in English | MEDLINE | ID: mdl-28336532

ABSTRACT

Aberrant protein aggregation underlies a variety of age-related neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. Little is known, however, about the molecular mechanisms that modulate the aggregation process in the cellular environment. Recently, MOAG-4/SERF has been identified as a class of evolutionarily conserved proteins that positively regulates aggregate formation. Here, by using nuclear magnetic resonance (NMR) spectroscopy, we examine the mechanism of action of MOAG-4 by characterizing its interaction with α-synuclein (α-Syn). NMR chemical shift perturbations demonstrate that a positively charged segment of MOAG-4 forms a transiently populated α-helix that interacts with the negatively charged C terminus of α-Syn. This process interferes with the intramolecular interactions between the N- and C-terminal regions of α-Syn, resulting in the protein populating less compact forms and aggregating more readily. These results provide a compelling example of the complex competition between molecular and cellular factors that protect against protein aggregation and those that promote it.


Subject(s)
Caenorhabditis elegans Proteins/chemistry , Caenorhabditis elegans/chemistry , Nerve Tissue Proteins/chemistry , Protein Aggregates , alpha-Synuclein/chemistry , Alzheimer Disease , Animals , Caenorhabditis elegans/genetics , Caenorhabditis elegans/metabolism , Caenorhabditis elegans Proteins/genetics , Caenorhabditis elegans Proteins/metabolism , Humans , Nerve Tissue Proteins/genetics , Nerve Tissue Proteins/metabolism , Parkinson Disease , Static Electricity , alpha-Synuclein/genetics , alpha-Synuclein/metabolism
18.
Angew Chem Int Ed Engl ; 56(1): 239-242, 2017 01 02.
Article in English | MEDLINE | ID: mdl-27897362

ABSTRACT

Because arginine residues in proteins are expected to be in their protonated form almost without exception, reports demonstrating that a protein arginine residue is charge-neutral are rare and potentially controversial. Herein, we present a 13 C-detected NMR experiment for probing individual arginine residues in proteins notwithstanding the presence of chemical and conformational exchange effects. In the experiment, the 15 Nη and 15 Nϵ chemical shifts of an arginine head group are correlated with that of the directly attached 13 Cζ . In the resulting spectrum, the number of protons in the arginine head group can be obtained directly from the 15 N-1 H scalar coupling splitting pattern. We applied this method to unambiguously determine the ionization state of the R52 side chain in the photoactive yellow protein from Halorhodospira halophila. Although only three Hη atoms were previously identified by neutron crystallography, we show that R52 is predominantly protonated in solution.


Subject(s)
Arginine/chemistry , Bacterial Proteins/chemistry , Nuclear Magnetic Resonance, Biomolecular , Photoreceptors, Microbial/chemistry , Carbon Isotopes , Halorhodospira halophila/chemistry
19.
Biochem Biophys Res Commun ; 478(3): 1185-8, 2016 09 23.
Article in English | MEDLINE | ID: mdl-27544032

ABSTRACT

Hydrogen exchange (HX) NMR spectroscopy is widely used for monitoring structure, stability and dynamics of proteins at the level of individual residues. The stochastic replacement of protons by deuterons typically leads to an exponential decrease of the NMR signals. However, an unusual signal increase was observed in HX of several amides for T4 lysozyme L99A. This effect can be attributed to peak sharpening as a result of reduced dipolar relaxation from proximal amide protons that experience more rapid hydrogen/deuterium (H/D) exchange. The behavior was specifically observed at the termini of secondary structure elements, where large differences in protection against H/D exchange are observed. This effect is expected to be more widespread in NMR HX studies, and is important for the accurate determination of protection factors.


Subject(s)
Deuterium Exchange Measurement , Hydrogen/metabolism , Magnetic Resonance Spectroscopy , Signal Processing, Computer-Assisted , Hydrogen Bonding , Models, Biological
20.
Sci Rep ; 6: 20534, 2016 Feb 02.
Article in English | MEDLINE | ID: mdl-26830762

ABSTRACT

Internal cavities are important elements in protein structure, dynamics, stability and function. Here we use NMR spectroscopy to investigate the binding of molecular oxygen (O2) to cavities in a well-studied model for ligand binding, the L99A mutant of T4 lysozyme. On increasing the O2 concentration to 8.9 mM, changes in (1)H, (15)N, and (13)C chemical shifts and signal broadening were observed specifically for backbone amide and side chain methyl groups located around the two hydrophobic cavities of the protein. O2-induced longitudinal relaxation enhancements for amide and methyl protons could be adequately accounted for by paramagnetic dipolar relaxation. These data provide the first experimental demonstration that O2 binds specifically to the hydrophobic, and not the hydrophilic cavities, in a protein. Molecular dynamics simulations visualized the rotational and translational motions of O2 in the cavities, as well as the binding and egress of O2, suggesting that the channel consisting of helices D, E, G, H, and J could be the potential gateway for ligand binding to the protein. Due to strong paramagnetic relaxation effects, O2 gas-pressure NMR measurements can detect hydrophobic cavities when populated to as little as 1%, and thereby provide a general and highly sensitive method for detecting oxygen binding in proteins.


Subject(s)
Binding Sites , Models, Molecular , Oxygen/chemistry , Proteins/chemistry , Hydrophobic and Hydrophilic Interactions , Magnetic Resonance Spectroscopy , Models, Chemical , Molecular Conformation , Molecular Dynamics Simulation , Muramidase/chemistry , Muramidase/metabolism , Oxygen/metabolism , Protein Binding , Proteins/metabolism
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