Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: UNIPROT:Q9UMR3 (NMR)
 150,598 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The basic pancreatic trypsin inhibitor (BPTI) was investigated by high resolution 1H NMR techniques at 360 MHz. Observation of the amide proton resonances of the polypeptide backbone showed that the globular conformation of BPTI determined by X-ray studies in single crystals is maintained in aqueous solution over the temperature range from 4 degrees to 87 degrees. NMR studies over this temperature range of the aromatic amino acid residues of BPTI. i.e. 4 tyrosines and 4 phenylalanines, led to complete assignments of all the aromatic spin systems in the protein. From this, information was obtained on the rotational motions about the C beta--Cv bond axis of the aromatic rings in the globular form of PBTI. At 25 degrees, two tyrosine rings and one phenylalanine ring are rotating rapidly on the NMR time scale. For the other rings the transitions from slow to rapid rotational motions were investigated at variable temperatures and energy barriers for these intramolecular rate processes determined. The studies of the tyrosine resonances had been described in detail in a previous publication. The present paper describes the identification of the phenylalanine resonances and comments on some technical aspects which might be of quite general interest for the analysis of highly resolved 1H NMR spectra of proteins. Data for the tyrosines and the phenylalanines are compiled in three tables, i.e. the pK alpha-values for the tyrosines, the NMR parameters for all eight aromatics, and the parameters delta G not equal to, and, where available, delta H not equal to and delta S not equal to for the rotational motions of the rings.
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PMID:Dynamics of the aromatic amino acid residues in the globular conformation of the basic pancreatic trypsin inhibitor (BPTI). I. 1H NMR studies. 0 65

220 MHz proton Fourier transform (FT) NMR with quadrature phase detection (QPD) technique is applied to observe largely hyperfine-shifted signals of various hemoproteins and hemoenzymes in ferric high-spin state. The binding of F-, OCN-, SCN-, and CH3OH to the ferric heme iron in high-spin state in various hemoproteins has been studied by the use of FT/QPD technique at 220 MHz. The binding of formate ion to metmyoglobin (metMb) has also been studied. The spectrum of the formate complex was compared with that of hemoglobin M Milwaukee where carboxylate groups are bound to the hemes of the beta subunits. The acid-base transition of ferric myoglobin (Mb) was confirmed by monitoring the pH-dependent shift of the heme side methyl signals with the reflection point at pH 9.1. This finding is analyzed on the basis of rapid exchange between alkaline (low spin) and acidic (high spin) forms accompanied by the dissociation and association of one proton in the ferric Mb. The structure of the heme environment of ferric horseradish peroxidase (HRP) was studied. The pH-dependent features of NMR spectra of the ferric enzyme and its complexes with cyanide and azide were discussed in terms of heme environmental structures, comparing with the case of metMb. The results were interpreted as follows: There exists an ionizable amino group near the heme responsible for the ligand binding reactions of the enzyme, which modulates the entry of external azide to the heme iron through protolytic equilibrium of this group. The pK value of this group was determined to be 5.9 by monitoring the pH-dependent shift of the heme peripheral methyl signals of the native enzyme, indicating that the group is probably a histidyl residue. Acid-alkaline transition of metMb was confirmed to associate with the proton dissociation of an iron-bound water molecule, whereas in HRP, pH-dependent spin state change characterized by pK 11 is attributed not to the simple protolytic reaction of the iron-bound water but to the direct coordination of an amino acid residue of the polypeptide chain to the ferric heme iron. Histidyl imidazole is a possible candidate for the new sixth iron ligand in alkaline peroxidase above pH 11. Interaction of HRP with electron donor(indolepropionic acid, IPA) was also studied. The hyperfine-shifted proton signals of the heme peripheral groups of the enzyme showed a small but significant shift with stepwise additions of IPA, indicating that the donor binds at a specific site of HRP. There results are interpreted in terms of the interaction between the enzyme and the donor at the heme edge site.
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PMID:Nuclear magnetic resonance studies of high-spin ferric hemoproteins. 2 54

Natural-abundance 13C NMR spectra (at 15.04 MHz) of the polypeptide cardiac stimulant Anthopleurin-A are presented. The spectra contain many resolved one- and two-carbon resonances from carbonyl and aromatic carbons and a few resolved resonances from aliphatic carbons. Most of these have been assigned to individual carbons in the protein. The effect of pH on the 13C spectrum has been investigated. In conjunction with the resonance assignments, this yields estimates for the pK alpha values of the COOH-terminal and NH2-terminal residues, the side chain carboxylate of 1 of the 2 aspartic acid residues, and the imidazolium groups of the 2 histidine residues. The effects of the lanthanides La3+ and Gd3+ on the spectrum have also been studied. The results suggest that there are at least two binding sites, and further studies will be required to characterize these before they can be utilized as an aid in structural mapping. Finally, the results are discussed in relation to a postulated model for the mode of action of Anthopleurin-A.
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PMID:Natural abundance carbon-13 nuclear magnetic resonance study of anthopleurin-A, a cardiac stimulant from the sea anemone Anthopleura xanthogrammica. 3 35

High resolution 13C and 1H NMR spectra of myelin basic protein over a range of pH and concentrations indicate that intramolecular folding of the polypeptide chain occurs in aqueous solution in the region of residues 85 to 116. At pH 4 in D2O solution, the 13C resonances due to nonprotonated carbons of phenylalanine and tryptophan are broadened and chemically shifted compared to the same resonances when the protein is dissolved in 6M guanidinium hydrochloride. These residues occur in the region of the polypeptide chain in which the intramolecular folding may occur. As the pH is raised and the positive charge on the protein reduced from 28 to 18, intermolecular aggregation occurs, which appears to involve these same folded regions. Data on T1 (longitudinal relaxation times) of protons indicate also that amino-acid sidechains vary considerably in their motional freedoms. The concentration dependence of the proton NMR spectra provides further information on association of protein monomers. The region of the protein involved in folding, polymerization and substrate specificities is conservative in various species and we can surmise that it may have a specialized role in protein-lipid interactions in the myelin membrane. We suggest that the protein forms dimers across the cytoplasmic apposition during the formation of myelin. Estimates of the repulsive energies of interaction between approaching membranes suggest that some special mechanism of this kind is required to overcome the repulsive forces due to breakdown of water structure and electrostatic interaction.
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PMID:Conformation of myelin basic protein and its role in myelin formation. 8 Sep 38

Antibiotic 26a, a weakly basic (pK1 3.85 and pK2 7.1) polypeptide compound, has been recovered from the fermentation fluids of bacillus subtilis cultures as hydrochloride salt easily soluble in water and dimethylsulphoxide, sparingly soluble in lower alcohols and insoluble in several organic solvents. At low concentrations 26a was effective against gram-positive bacteria, mainly micrococci and corynebacteria, moderately active against mycobacteria, and inactive against gram-negative bacteria, yeasts and moulds even at 300 microgram/ml concentration. From the viewpoint of elemental analysis, electrometric titration, optical rotation, UV, IR and NMR spectra, amino acid composition, molecular weight and biological observations, 26a can be considered as an antibiotic, if not identical, then closely related to bacitracin family polypeptides.
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PMID:Polypeptide antibiotic 26a from Bacillus subtilis. III. Physicochemical and biological in vitro properties. 8 84

We have determined the conformation of the channel-forming polypeptide antibiotic gramicidin A in phosphatidylcholine vesicles by using 13C and 19F NMR spectroscopy. The models previously proposed for the conformation of the dimer channel differ in the surface localization of the NH2 and COOH termini. We have incorporated specific 13C and 19F nuclei at both the NH2, and COOH termini of gramicidin and have used 13C and 19F chemical shifts and spin lattice relaxation time measurements to determine the accessibility of these labels to three paramagnetic NMR probes--two in aqueous solution and one attached to the phosphatidylcholine fatty acid chain9 all of our results indicate that the COOH terminus of gramicidin in the channel is located near the surface of the membrane and the NH2 terminus is buried deep within the lipid bilayer. These findings strongly favor an NH2-terminal to NH2-terminal helical dimer as the major conformation for the gramicidin channel in phosphatidylcholine vesicles.
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PMID:Conformation of gramicidin A channel in phospholipid vesicles: a 13C and 19F nuclear magnetic resonance study. 9 25

Sensitive thin layer peptide mapping is employed to establish the identity and the homogeneity of eight singly substituted 4-carboxy-2,6-dinitrophenyl derivatives of horse cytochrome c. Seven of the components, all of greater than 95% homogeneity, are modified at lysyl residues 13, 72, 87, 8, 27, 39, and 60. The eighth component is a mixture of derivatives at lysines 22 and 99. The positions of the modified residues were confirmed by the amino acid analysis and Edman sequential degradation of the CDNP-peptides. Physiochemical properties characteristic of cytochrome c are unchanged in the chemically modified products examined. These properties, that include the proton NMR spectrum, are sensitive probes of the polypeptide organization surrounding the heme prosthetic group. The lack of any discernable changes indicates that modification of the epsilon-amino groups on the surface of cytochrome c does not perturb the overall structure of the protein. The widespread distribution of the modifications on the surface of the molecule, together with the homogeneity and native conformation of the CDNP-derivatives make them well suited for assessing the effects of changes in the charge topography on the electron transfer activity of cytochrome c.
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PMID:Definition of cytochrome c binding domains by chemical modification. II. Identification and properties of singly substituted carboxydinitrophenyl cytochromes c at lysines 8, 13, 22, 27, 39, 60, 72, 87, and 99. 20 15

Polypeptides and proteins in native conformation exhibit 13C NMR spectra which are highly nondegenerate. Assignment of resonances to carbons in particular residues is hence a prerequisite for a structural analysis of the spectroscopic data. For nonprotonated carbonyl carbons, the assignment can be achieved by selective (1H alpha)13C' 2J decoupling. Using this method, we have assigned the Orn1 and Gly2 carbonyl resonances in alumichrome at 67.9 MHz. We show that a single off-resonance experiment with the decoupling frequency centered in the aliphatic proton spectrum is sufficient to assign unequivocally all the protonated carbon resonances via analysis of the reduced 1J heteronuclear splittings. Alumichrome thus becomes the first complex polypeptide spin system whose 1H, 15N, and now 13C nuclear resonances have been fully identified to date. 13C chemical shifts and 1H--13C spin--spin couplings are discussed in terms of structural strain leading to specific orbital hybridizations and on the basis of polarization effects due to electron density shifts toward hydrogen-bonding and metal-binding sites. A number of 3J(13C--C--C--1H) coupling constants measured on selected multiplets after resolution enhancement were used to derive the x-related Karplus relationship 3J(theta) = (10.2 cos2 theta -- 1.3 cos theta + 0.2) Hz.
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PMID:Complete assignment of carbon signals in a stereospecific peptide via selective and single off-resonance proton decoupling experiments. Analysis of the carbon-13 nuclear magnetic resonance spectrum of alumichrome at 67.88 MHz. 48 99

The metal binding sites of a gamma-carboxyglutamic acid-rich fragment derived from bovine prothrombin were examined using paramagnetic lanthanide ions to evaluate the role of gamma-carboxyglutamic acid resideus in metal binding. A gamma-carboxyglutamic acid-rich peptide, fragment 12-44, was isolated from a tryptic digest of prothrombin. Using 153Gd(III), fragment 12-44 was found to contain one high affinity metal binding site (KD = 0.55 microM) and four to six lower affinity metal binding sites (KD approximately 4 to 8 microM). The S-carboxymethyl derivative of fragment 12-44, in which the disulfide bond in fragment 12-44 was reduced and alkylated, contained no high affinity metal binding site and four or five lower affinity sites (KD = 8 microM). The effects of paramagnetic lanthanide ions on fragment 12-44 and its S-carboxymethyl derivative were studied by natural abundance 13C NMR spectroscopy. The 13C NMR spectrum of fragment 12-44 was recorded at 67.88 MHz and the resonances were assigned by comparison to the chemical shift of carbon resonances of amino acids and peptides previously studied. The proximity between bound metal ions and carbon atoms in fragment 12-44 was estimated using Gd(III), based upon the strategy that the magnitude of the change in the transverse relaxation rate of resonances of carbon nuclei induced by bound metal ions is related in part to the interatomic distances between bound metal and carbon nuclei. Titration of fragment 12-44 with Gd(III) resulted in the selective broadening of the gamma-carboxyl carbon, C gamma, C beta, and C alpha resonances of gamma-carboxyglutamic acid, and the C epsilon of the arginines. S-Carboxymethyl fragment 12-44, which lacked the high affinity metal binding site, showed markedly decreased perturbation of the C epsilon of the arginine residues upon titration with Gd(III). These studies indicate that gamma-carboxyglutamic acid residues in prothrombin fragment 12-44 participate in metal liganding. A high affinity metal binding site in fragment 12-44 is in close proximity of Arg 16 and Arg 25 and is stabilized by the disulfide bond. On the basis of these data, a model of the metal binding sites is proposed in which the high affinity site is composed of two gamma-carboxyglutamic acid residues which participate in intramolecular metal-dependent bridging of two regions of the polypeptide chain. The lower affinity metal binding sites, formed by single or paired adjacent gamma-carboxyglutamic acid residues, then may participate in intermolecular metal-dependent protein . protein or protein . membrane complex formation.
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PMID:Metal binding sites of a gamma-carboxyglutamic acid-rich fragment of bovine prothrombin. 50 Jul 29

Monte Carolo calculations were made on unperturbed trans-polysarcosine chain, non-self-intersecting trans-polysarcosine chain, and also non-self-intersecting trans/cis-polysarcosine chain by using a hard-sphere model. In the last case, an attempt was first made to introduce cis amide bond into the Monte Carlo calculation of polypeptide chain. Dipeptide energy maps for four different trans/cis dyad sequences were calculated. The allowed regions were consistent with the pairs of dihedral angles observed in cyclo-pentasarcosyl and cyclo-octasarcosyl. The mean-square end-to-end distance and higher even moments were obtained. The distribution function of the end-to-end distance was calculated from the even moments by using Nagai's equation and compared with the direct Monte Carlo data. The best agreement was obtained by cutting off the terms containing much higher order even moments than a critical order. The fractions of cis amide bond and of the four different trans/cis dyad sequences in polysarcosine were calculated. The results of calculation were compared with the 220-MHz NMR spectra of polysarcosine in three different solvents. Qualitative agreement was stained for longer chains.
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PMID:Monte Carlo calculation on trans/cis-polysarcosine. 94 Mar 52


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