Side chain orientation from methyl 1H-1H residual dipolar couplings measured in highly deuterated proteins

High-level deuteration is a prerequisite for the study of high molecular weight systems using liquid-state NMR. Here, we present new experiments for the measurement of proton-proton dipolar couplings in CH(2)D methyl groups of (13)C labeled, highly deuterated (70-80%) proteins. (1)H-(1)H residual dipolar couplings (RDCs) have been measured in two alignment media for 57 out of 70 possible methyl containing residues in the 167-residue flavodoxin-like domain of the E. coli sulfite reductase. These data yield information on the orientation of the methyl symmetry axis with respect to the molecular alignment frame. The alignment tensor characteristics were obtained very accurately from a set of backbone RDCs measured on the same protein sample. To demonstrate that accurate structural information is obtained from these data, the measured methyl RDCs for Valine residues are analyzed in terms of chi(1) torsion angles and stereospecific assignment of the prochiral methyl groups. On the basis of the previously determined backbone solution structure of this protein, the methyl RDC data proved sufficient to determine the chi(1) torsion angles in seven out of nine valines, assuming a single-rotamer model. Methyl RDCs are complementary to other NMR data, for example, methyl-methyl NOE, to determine side chain conformation in high molecular weight systems.     

Unique incorporation behavior of amino acid-type surfactant into phospholipid vesicle membrane

The incorporation behavior of some anionic surfactants, including amino acid-type surfactants, on phospholipid vesicles was investigated. This was done by measuring the release of a vesicle-entrapped fluorescence probe and the scattered light intensities of vesicle particles in the surfactant solution as a function of surfactant concentration and time. Sodium dodecyl sulfate, sodium dodecanesulfonate, sodium dodecanoyl sarcosinate, and sodium dodecanoyl glutamate were employed in this study. All surfactants ruptured the phospholipid vesicle at around each critical micelle concentration by mixed micelle formation with phospholipid. While leakage of the fluorescence probe took place at a very low concentration in the sulfate- or sulfonate-type surfactant systems, it occurred at the concentration just below the CMC in the amino acid-type surfactant systems. Kinetic analysis of the release of the probe from the vesicles showed that the former surfactants adsorbed independently and homogeneously onto the phospholipid vesicles, while the latter surfactants were cooperatively incorporated.     

Absolute determination method using chirality for glufosinate and bialaphos by gamma-cyclodextrin modified capillary zone electrophoresis.

A novel absolute determination method using chirality without any calibration curves or comparison standards has been proposed for phosphorus-containing amino acid-type herbicides, glufosinate (D,L-GLUF) and bialaphos (BIAL). This method is based on a change in the enantiomeric ratio after the spiking of a known amount of the enantiomers with different enantiomeric ratios to a sample. D,L-GLUF was determined by adding a known amount of L-GLUF to the sample, derivatizing them with dansyl chloride, and measuring the ratio of the peak area of the D-isomer to that of the L-isomer by means of gamma-cyclodextrin modified capillary zone electrophoresis. The accuracy and precision of the method were evaluated using a synthetic sample. The mean values obtained for D- and L-GLUF agreed with the values taken within 1.6%; also the reproducibility was as good as less than 2.8%. The determination of BIAL was achieved by determining GLUF quantitatively produced by the acid hydrolysis of BIAL. The proposed methods were applied to the analysis of commercial herbicides and the validity and usefulness were evaluated.     

Absolute determination method for trace quantities of enantiomer of glufosinate by gamma-cyclodextrin modified capillary zone electrophoresis combined with solid-phase extraction and on-capillary concentration.

A highly sensitive and accurate determination method for trace quantities of enantiomers of glufosinate (D,L-GLUF), a phosphorus-containing amino acid-type herbicide, has been studied. The present method is based on the change in the mole ratio of the enantiomeric isomers after spiking of a known amount of an isomer (L-GLUF). The chiral separation and detection were made by gamma-cyclodextrin modified capillary zone electrophoresis (gamma-CD-CZE) with fluorescence detection. Solid-phase extraction of D,L-GLUF with titania was investigated as the pre-separation method to eliminate coexisting materials such as inorganic salts and organic compounds in river water. A separated D,L-GLUF was labeled with dansyl chloride and subjected to the on-capillary concentration using large-volume sample stacking (LVSS) before gamma-CD-CZE. The detection limit of the present method was as low as 2.0 x 10(-9) M. The present method was successfully applied to a model sample containing 2.0 x 10(-7) M D,L-GLUF in river water. It was confirmed that trace quantities of D-and L-GLUF in environmental samples can be accurately determined without any calibration curves and comparison standards.     

Rotational dynamics of methyl groups in m-xylene

Methyl group dynamics of m-xylene was investigated by using incoherent inelastic and quasi-elastic neutron scattering. Inelastic measurements were carried out at the high flux backscattering spectrometer HFBS at the National Institute of Standards, quasi-elastic measurements at the time-of-flight spectrometer NEAT at the Hahn-Meitner-Institute. Rotational potentials are derived which describe the tunnel splittings, first librational, and activation energies of the two inequivalent CH(3) groups. Indications for coupling of the methyl rotation to low-energy phonons have been found. The finite width of one tunneling transition at He temperature is described by direct methyl-methyl coupling. The combined results of the experiments and the calculations allow a unique assignment of rotor excitations to crystallographic sites.     

Multicanonical parallel simulations of proteins with continuous potentials

The determination of the three‐dimensional (3D) structure of a protein or peptide is a very important research problem in biological and medical sciences. Anfinsen's experiments (Science 1973, 181, 223) on renaturation of denatured proteins have shown that the native 3D structure of a (small) protein at low (room) temperatures is uniquely determined by its amino acid sequence, which suggests that it might be possible to determine the 3D structure of a protein from its amino acid sequence by pure computations. As a step toward that goal, in this article we present a simple approach for parallelization of multicanonical Monte Carlo simulations of proteins with continuous potentials. Our method is based on the parallel calculation of the protein energy function. The algorithm is tested by simulated annealing and multicanonical simulations of two small peptides, and known results are reproduced accurately. An acceptable degree of parallelization can be achieved in the simulation of Protein L using up to 30 PCs. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1287–1296, 2001     

Preparation and biological activities of a bivalent poly(ethylene glycol) hybrid containing an active site and its synergistic site of fibronectin

A bivalent poly(ethylene glycol) or PEG hybrid of fibronectin-related peptides was prepared. An active site peptide (RGD) and its synergistic site peptide (PHSRN) of fibronectin were conjugated with an amino acid-type PEG (aaPEG) to form PHSRN-aaPEG-RGD. A moderate spatial array between RGD and PHSRN in fibronectin may be required for synergic activity. The bivalent hybrid exhibited potent cell spreading activity and exhibited potent anti-metastatic activity in a model of experimental metastasis with B16-BL6 cells in mice. PEG may serve as a spacer for maintaining the desired spatial array.     

Hydroxy- and aminomethylation reactions in the formation of oligomers from l-tyrosine and formaldehyde in basic medium

The study of the reaction of l-tyrosine or its tetrabutylammonium salt with formaldehyde was performed. The results established that this reaction does not lead to macrocyclic amino acid-type compounds, and in all cases, mixtures of linear oligomers of two or more l-tyrosine units bound by methylene groups were obtained. The formation of ion pair-type linear aggregates in the tetrabutylammonium salt hinders the oligomerization reaction, allowing the isolation of an l-tyrosine dimer, unlike the l-tyrosine reaction, in which a trimer could be isolated.     

Peptide drug carrier: studies on incorporation of vasopressin into nano-associates comprising poly(ethylene glycol)-poly( -aspartic acid) block copolymer

To fabricate peptide delivery systems using polymeric drug carriers, an oligopeptide model drug, [Arg⁸]-vasopressin(AVP), was incorporated into nano-associates comprising poly(ethylene glycol)-( -aspartic acid block copolymer (PEG-P(Asp)). Incorporation of the AVP was accomplished using a dialysis method. Static light scattering measurements revealed that the acid-type and mixture-type PEG-P(Asp)s formed nano-associates independently without AVP, while the salt form PEG-P(Asp) did not. High loading of AVP into acid-type PEG-P(Asp) was observed with loading levels controlled by changing the molar ratio of drug and block copolymer. Mixture-type PEG-P(Asp) did not show high loading and the salt-type PEG-P(Asp) form did not at all. Acid-type P(Asp) homopolymer formed associates including AVP, however, it was insoluble in aqueous medium. Dynamic light scattering measurements showed that the acid-type PEG-P(Asp) associates sizes narrowly clustered around 150 nm. This finding suggests that associates of acid-type PEG-P(Asp) effectively incorporates peptides possibly via a hydrogen bonding interaction between the block copolymer and the peptide.     

Novel stereocontrolled addition of allylmetal reagents to alpha-imino esters: efficient synthesis of chiral tetrahydroquinoline derivatives

To prepare in multigram scale new antagonists of the glycine binding site associated to the NMDA receptor, an efficient distereoselective route was set up. The addition of suitable allyltin reagents to chiral N-aryl alpha-imino esters (R-(+)-tert-butyl lactate used as chiral auxiliary), gave the corresponding alpha amino acid-type derivative in high chemical yield and optical purity. This allylation reaction represents a novel example of efficient long-range stereodifferentiation process. In the last part of the synthesis, a regioselective Heck-type cyclization reaction enabled preparation of the target tetrasubstituted exocycle and trisubtituted endocycle double bond derivatives.     

Adsorption properties of ionic species on cross-linked chitosans modified with catechol and salicylic acid moieties.

Catechol-type chitosan resin and salicylic acid-type chitosan resin were easily synthesized for use in estimating the adsorption behavior of 34 elements at pH 1 - 7 in aquatic media. The catechol-type chitosan resin could adsorb Cu(II) at pH 3 - 7, In(III) at pH 4 - 6, Pb(II) and lanthanoids at pH 5 - 7, and U(VI) at pH 4 - 7 more effectively than the salicylic acid-type chitosan resin and the cross-linked chitosan resin (base material). Adsorption ability was in the order: catechol-type chitosan resin > salicylic acid-type chitosan resin > cross-linked chitosan resin.     

Residue-specific pKa determination of lysine and arginine side chains by indirect 15N and 13C NMR spectroscopy: application to apo calmodulin

Electrostatic interactions in proteins can be probed experimentally through determination of residue-specific acidity constants. We describe here triple-resonance NMR techniques for direct determination of lysine and arginine side-chain protonation states in proteins. The experiments are based on detection of nonexchangeable protons over the full range of pH and temperature and therefore are well suited for pKa determination of individual amino acid side chains. The experiments follow the side-chain 15Nzeta (lysine) and 15Nepsilon or 13Czeta (arginine) chemical shift, which changes due to sizable changes in the heteronuclear electron distribution upon (de)protonation. Since heteronuclear chemical shifts are overwhelmed by the charge state of the amino acid side chain itself, these methods supersede 1H-based NMR in terms of accuracy, sensitivity, and selectivity. Moreover, the 15Nzeta and 15Nepsilon nuclei may be used to probe changes in the local electrostatic environment. Applications to three proteins are described: apo calmodulin, calbindin D9k, and FKBP12. For apo calmodulin, residue-specific pKa values of lysine side chains were determined to fall between 10.7 and 11.2 as a result of the high net negative charge on the protein surface. Ideal two-state titration behavior observed for all lysines indicates the absence of significant direct charge interactions between the basic residues. These results are compared with earlier studies based on chemical modification.     

Indexing and mapping of proteins using a modified nonlinear Sammon projection

A modified Sammon algorithm was developed to display a relationship between proteins based on their amino acid composition. In the first stage of the method, a 19-dimensional compositional space of representative proteins was mapped into a two-dimensional space (2D) using the original Sammon projection creating a contour map. In the second stage, this contour map was used as a reference for new proteins projected into 2D. Data analysis showed that proteins belonging to the same structural classes formed characteristic and distinct clusters, which could be potentially useful in the prediction of protein structural classes. However, we observed significant overlapping of the clusters, which may explain the limited success of previous protein folding prediction based solely on amino acid composition. Regardless, the modified Sammon projections can generate a unique index for each individually projected protein related to its amino acid composition, which may be a useful tool in the exploratory classification of proteins. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1049–1059, 1999     

Solid phase extraction of phosphorus-containing amino acid-type herbicides and their metabolites from human blood with titania for determination by capillary electrophoresis.

Phosphorus-containing amino acid-type herbicides (PAAHs) and their metabolites in human plasma and whole blood were extracted with titania and determined by capillary electrophoresis (CE). The recoveries of glyphosate (GLYP), aminomethylphosphonic acid (AMPA), gluphosinate (GLUF), and 3-methylphosphonico-propionic acid (MPPA) from human plasma were 84.6, 76.8, 90.4, and 89.6%, respectively. The recoveries of GLYP, AMPA, GLUF, and MPPA from whole blood were 79.6, 84.4, 36.9, and 31.8%, respectively. The low recoveries of GLUF and MPPA from whole blood were improved by the dilution of whole blood with water to 4-fold.     

Dynamic Interchanging Native States of Lymphotactin Examined by SNAPP-MS

The human chemokine lymphotactin (Ltn) is a remarkable protein that interconverts between two unrelated native state structures in the condensed phase. It is possible to shift the equilibrium toward either conformation with selected sequence substitutions. Previous results have shown that a disulfide-stabilized variant preferentially adopts the canonical chemokine fold (Ltn10), while a single amino acid change (W55D) favors the novel Ltn40 dimeric structure. Selective noncovalent adduct protein probing (SNAPP) is a recently developed method for examining solution phase protein structure. Herein, it is demonstrated that SNAPP can easily recognize and distinguish between the Ltn10 and Ltn40 states of lymphotactin in aqueous solution. The effects of organic denaturants, acid, and disulfide bond reduction and blocking were also examined using SNAPP for the CC3, W55D, and wild type proteins. Only disulfide reduction was shown to significantly perturb the protein, and resulted in considerably decreased adduct formation consistent with loss of tertiary/secondary structure. Cold denaturation experiments demonstrated that wild-type Ltn is the most temperature sensitive of the three proteins. Examination of the higher charge states in all experiments, which are presumed to represent transition state structures between Ltn-10 and Ltn-40, reveals increased 18C6 attachment relative to the more folded structures. This observation is consistent with increased competitive intramolecular hydrogen bonding, which may guide the transition. Experiments examining the gas phase structures revealed that all three proteins can be structurally distinguished in the gas phase. In addition, the gas phase experiments enabled identification of preferred adduct binding sites.     

Studies on thermal degradation of aliphatic polyamides by pyrolysis-glass capillary chromatography

A series of aliphatic polyamides samples (five kinds of α-aminocarboxyclic acid-type nylons and seven kinds of diamine-dicarboxyclic acid-type nylons) were pyrolysed in a vertical microfurnace-type pyrolyser at 550°C, and their high-resolution pyrograms were obtained by a glass capillary gas chromatograph directly attached to the pyrolyser. The characteristic peaks on the resulting pyrograms were identified using a mass spectrometer, which was also attached to the gas chromatograph. On the basis of the various characteristic degradation products identified, such as hydrocarbons, mononitriles, lactams, cyclopentanone hydrocarbons containing one amide group and mononitriles containing one amide group, general mechanisms for the degradation of the aliphatic polyamides were formulated.     

A novel bisnorditerpenelactone from Mikania hirsutissima

A novel bisnorkaurenic acid-type diterpenelactone, named mikanialactone (1), was isolated along with five known kaurenic acid-type diterpenes (2-6) from the aerial parts of Mikania hirsutissima DC (Compositae). The structure of the new bisnorditerpene was determined by spectroscopic means.     

Dynamic nuclear polarization-enhanced solid-state NMR of a 13C-labeled signal peptide bound to lipid-reconstituted Sec translocon

Dynamic nuclear polarization (DNP) has made it possible to record 2D double-quantum-filtered (DQF) solid-state NMR (ssNMR) spectra of a signal peptide bound to a lipid-reconstituted SecYEG translocon complex. The small quantity of peptide in the sample (~40 nmol) normally prohibits multidimensional ssNMR experiments. Such small amounts are not the exception, because for samples involving membrane proteins, most of the limited sample space is occupied by lipids. As a consequence, a conventional 2D DQF ssNMR spectrum with the sample used here would require many weeks if not months of measurement time. With the help of DNP, however, we were able to acquire such a 2D spectrum within 20 h. This development opens up new possibilities for membrane protein studies, particularly in the exploitation of high-resolution spectroscopy and the assignment of individual amino acid signals, in this case for a signal peptide bound to the translocon complex.     

Novel betaines from a micronesian sponge Dysidea herbacea

Three new betaines, dysibetaine PP (1), dysibetaine CPa (2), and dysibetaine CPb (3), were isolated from an aqueous extract of the marine sponge Dysidea herbacea collected in Yap state, Micronesia. The structure of 1 was determined by spectral methods as well as chemical degradation to be a novel dipeptide betaine, and those for 2 and 3 were determined to be unprecedented cyclopropane betaines. Compounds 2 and 3 showed weak affinity toward the N-methyl-D-aspartic acid-type and the kainic acid-type glutamate receptors, respectively, in a radioligand binding assay.     

The graphical representation of protein sequences based on the physicochemical properties and its applications

Based on the chaos game representation, a 2D graphical representation of protein sequences was introduced in which the 20 amino acids are rearranged in a cyclic order according to their physicochemical properties. The Euclidean distances between the corresponding amino acids from the 2‐D graphical representations are computed to find matching (or conserved) fragments of amino acids between the two proteins. Again, the cumulative distance of the 2D‐graphical representations is defined to compare the similarity of protein. And, the examination of the similarity among sequences of the ND5 proteins of nine species shows the utility of our approach. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010