Beta H2 Research Articles

Ginseng Protein Reverses Amyloid Beta Peptide and H2 O2 Cytotoxicity in Neurons, and Ameliorates Cognitive Impairment in AD Rats Induced by a Combination of D-Galactose and AlCl3.

Ginseng (Panax ginseng C.A. Meyer) is one of the most widely used herbal medicines worldwide. The present study evaluated the neuroprotective effects of ginseng protein (GP) and its possible mechanisms in a cellular and animal model of AD. The results demonstrated that GP (10-100 µg/mL) significantly improved the survival rate of neurons and reduced the cells' apoptosis and the mRNA expression of caspase-3 and Bax/Bcl-2. In addition, GP (0.1 g/kg) significantly shortened the escape latency, prolonged the crossing times and the percentage of residence time; reduced the level of Aβ1-42 and p-tau, the activity of T-NOS and iNOS, and the content of MDA and NO, improved the activity of SOD, the concentration of cAMP and the protein expression of p-PKA/PKA and -CREB/CREB. The results demonstrated that GP significantly inhibited Alzheimer-like pathophysiological changes induced by Aβ25-35 or H2 O2 in cells or those induced by D-gal/ Al in animals. These neuroprotective effects of GP may be associated with the cAMP/PKA/CREB pathway. Also, in combination with our previous studies, these results indicate that the anti-AD mechanism of GP was likely to activate the CREB pathway through multiple channels. Copyright © 2016 John Wiley & Sons, Ltd.

Nitroxide radicals as hydrogen bonding acceptors. An infrared and EPR study.

The equilibrium constants for the formation of hydrogen-bonded complexes with phenol, benzyl alcohol and diphenyl amine of a persistent nitroxide radical (TEMPO) have been measured for the first time by IR spectroscopy in solution. By making use of the data obtained with IR measurements it was possible to quantitatively determine the effect of hydrogen bonding on the nitrogen hyperfine-splitting constant. On this basis it is shown that EPR spectroscopy can be used as an alternative to IR spectroscopy for the determination of the thermodynamic parameters of hydrogen bond formation with nitroxides by following the dependence of the experimental EPR nitrogen hyperfine splitting of these radicals upon changing the nature of the solvent. The experimental data obtained from both IR and EPR spectroscopy indicate that nitroxides are versatile hydrogen bond acceptors giving hydrogen bonds of strength similar to that of ethers or esters. The corresponding Abraham's beta 2H values have been determined as 0.46.

HYPER: a hierarchical algorithm for automatic determination of protein dihedral-angle constraints and stereospecific C beta H2 resonance assignments from NMR data.

A new computer program, HYPER, has been developed for automated analysis of protein dihedral angle values and C beta H2 stereospecific assignments from NMR data. HYPER uses a hierarchical grid-search algorithm to determine allowed values of phi, psi, and chi 1 dihedral angles and C beta H2 stereospecific assignments based on a set of NMR-derived distance and/or scalar-coupling constraints. Dihedral-angle constraints are valuable for restricting conformational space and improving convergence in three-dimensional structure calculations. HYPER computes the set of phi, psi, and chi 1 dihedral angles and C beta H2 stereospecific assignments that are consistent with up to nine intraresidue and sequential distance bounds, two pairs of relative distance bounds, thirteen homo- and heteronuclear scalar coupling bounds, and two pairs of relative scalar coupling constant bounds. The program is designed to be very flexible, and provides for simple user modification of Karplus equations and standard polypeptide geometries, allowing it to accommodate recent and future improved calibrations of Karplus curves. The C code has been optimized to execute rapidly (0.3-1.5 CPU-sec residue-1 using a 5 degrees grid) on Silicon Graphics R8000, R10000 and Intel Pentium CPUs, making it useful for interactive evaluation of inconsistent experimental constraints. The HYPER program has been tested for internal consistency and reliability using both simulated and real protein NMR data sets.

Draize eye scores and eye irritation thresholds in man can be combined into one QSAR.

Draize eye scores (DES) of 37 pure organic liquids have been converted into scores for the corresponding vapors, DES/P0, where P0 is the liquid vapor pressure in atmospheres at 298 K. It is shown that there is a constant difference of 6.7 between values of log(DES/P0) and log (1/EIT), where EIT is the eye irritation threshold in parts per million (ppm, by volume) of eight vapors for human subjects. The 37 log(DES/P0) values can be combined with log(1/EIT) values for 17 vapors into one quantitative structure-activity relationship (QSAR) for sensory potency (SP) using our general solvation equation, [formula: see text] where R2 is an excess molar refraction, pi 2H is the compound polarizability/dipolarity, sigma alpha 2H and sigma beta 2H are the compound hydrogen-bond acidity and basicity, and L16 is the gas-hexadecane partition coefficient at 298 K. n is the number of data points, r the correlation coefficient, SD the standard deviation, and F the F-statistic. LogSP is then either [log(DES/P0) - 0.66] or log (1/EIT), confirming the result for the eight common compounds. It is suggested that the equation can be used to predict eye irritancy of organic vapors and pure liquids. It is further suggested that for the compounds in the data set, the main process in eye irritation is transfer of the compound from the vapor or pure liquid to a biological phase, and a number of chemical properties of the biological phase have been mapped out through the equation. These properties are consistent with corresponding properties for a number of organic liquid phases.

Determination of acid dissociation constants of peptide side-chain functional groups by two-dimensional NMR.

An NMR method is described for determining residue-specific acid dissociation constants for peptides which contain more than one residue of the same acidic or basic amino acid. The method is based on using the differences in C alpha H proton chemical shifts which result from peptide sequence nearest-neighbor and possibly secondary structure effects to resolve resonances for carbon-bonded reporter protons adjacent to each side-chain acidic group in two-dimensional total correlation spectroscopy (TOC-SY) spectra. Acid dissociation constants were determined for each of the four lysine side-chain ammonium groups of the peptide Lys-Asn-Asn-Gln-Lys-Ser-Glu-Pro-Leu-Ile-Gly-Arg-Lys-Lys-Thr-NH2. Resonances for the C epsilon H2 protons adjacent to the four side-chain ammonium groups, which overlap in the one-dimensional spectrum, were resolved using the C alpha H-C epsilon H2 cross peaks in the TOCSY spectrum. Chemical shift-pH titration data were obtained for each lysine side-chain ammonium group from one-dimensional subspectra taken from two-dimensional TOCSY spectra measured as a function of pH. The pKAs of the Lys1, Lys5, Lys13, and Lys14 side-chain ammonium groups were determined to be 11.14 +/- 0.01, 10.95 +/- 0.01, 10.96 +/- 0.02, and 11.09 +/- 0.02, respectively. The chemical shift-pH titration data were also analyzed by a pH-independent procedure to obtain relative acid dissociation constants: KA(Lys1)/KA(Lys5) = 0.663 +/- 0.009, KA(Lys1)/KA(Lys13) = 0.703 +/- 0.014, and KA(Lys1)/KA(Lys14) = 0.910 +/- 0.009, which correspond to relative acidities for the side-chain ammonium groups of Lys1, Lys5, Lys13, and Lys14 of 1:1.508:1.422:1.099. To further demonstrate the utility of this method, acid dissociation constants were determined for the six acidic groups of the peptide Glu-Ala-Cys-Asn-Pro-Ala-Ala-Gly-Arg-His-Tyr-Ser-Cys-NH2. Chemical shift-pH titration curves were obtained for the C beta H2 protons adjacent to the two cysteine thiol groups using one-dimensional subspectra taken from TOCSY spectra measured as a function of pH. The pKAs of the CyS3 and Cys13 thiol groups were determined to be 9.21 +/- 0.07 and 8.60 +/- 0.06, respectively. The relative acid dissociation constants (KA(Cys3)/ (KA(Cys13)) were found to be 0.21 +/- 0.06 by the pH-independent calculation procedure.

Symmetric interspecies hybrids of mouse and human hemoglobin: molecular basis of their abnormal oxygen affinity.

Interspecies hybrids of HbA and Hb from mouse C57BL/10 [alpha 2M beta 2H and alpha 2H beta 2M (H = human, M = mouse)], representing 19 and 27 sequence differences per alpha beta dimers (as compared with human alpha beta dimer) have been generated in vitro. The efficiency of the assembly of the interspecies hybrids by the alloplex intermediate pathway is about twofold higher than the low-pH-mediated subunit approach. The interspecies hybrids exhibit a cooperative O2 binding. The intrinsic O2 affinity of mouse Hb is slightly lower than HbA, while the 2,3-diphosphoglycerate (DPG) effect is comparable. Interestingly, the interspecies hybrid alpha 2M beta 2H has high O2 affinity (compared to either human or mouse Hb), while the interspecies hybrid alpha 2H beta 2M exhibits a very low O2 affinity. These results suggest that the mouse beta chain generates a tetramer with very low oxygen affinity. However, the complementarity of the mouse alpha and beta chains generates a set of unique interactions that compensate for the low-oxygen-affinity propensity of the mouse beta chain. DPG binds the tetramer in the central cavity formed by the two beta subunits, hence the DPG effects on the interspecies hybrids should be as in the parent molecule. However, the results of the present study demonstrate that the DPG binding pocket is influenced by the nature of the alpha chain present in the tetramer. The mouse alpha chain reduces considerably the DPG right shift of the O2 affinity of the human beta-chain containing hybrid.(ABSTRACT TRUNCATED AT 250 WORDS)

Liquid chromatographic study of solute hydrogen bond basicity.

The purpose of the present work was to investigate a liquid chromatographic method for the measurement of relative hydrogen bond basicities of dilute species. This type of determination cannot be done with conventional reversed-phase liquid chromatography due to the silanophilic interactions of basic solutes with the silica packing material. The studies were done on a polymeric stationary phase with pendant phenol groups that act as powerful hydrogen bond donors. Solute retention was evaluated in terms of two hydrogen bond basicity scales, beta 2H and beta 2C, and a steric hindrance parameter, Es. beta 2H and beta 2C are basicity scales based on the free energy of forming 1:1 hydrogen bond complexes and the retention on a strong hydrogen bond donor gas chromatographic phase, respectively. The Es parameter characterizes the steric effect experienced by the solute acceptor site. It is shown that retention correlates very strongly with beta 2H and less strongly with beta 2C. The log k' values need only two descriptive parameters, i.e., beta 2H and Es, to give a good fit. As a whole, retention on the phenolic polymeric phase provides an efficient method for the measurement of relative hydrogen bond basicities.

1H- and 13C-NMR investigations on cis-trans isomerization of proline peptide bonds and conformation of aromatic side chains in H-Trp-(Pro)n-Tyr-OH peptides.

1H and 13C high-resolution nmr spectra of cationic, zwitterionic, and anionic forms of the peptides: H-Trp-(Pro)n-Tyr-OH, n = 0-5, and H-Trp-Pro-OCH3 were obtained in D2O solution. Analysis of H alpha (Pro1), H alpha (Trp), C gamma (Pro), H epsilon (Tyr), and H delta (Trp) resonances provided evidence for the presence of two predominant backbone isomers: the all-trans one and another with the Trp-Pro peptide bond in cis conformation; the latter constituted about 0.8 molar fraction of the total peptide (n > 1) concentration. Relative content of these isomers varied in a characteristic way with the number of Pro residues and the ionization state of the peptides. The highest content of the cis (Trp-Pro) isomer, 0.74, was found in the anionic form of H-Trp-Pro-Tyr-OH; it decreased in the order of: anion >> zwitterion approximately cation, and with the number of Pro residues to reach the value of 0.42 in the cationic form of H-Trp-(Pro)5-Tyr-OH. Isomerization equilibria about Pro-Pro bond(s) were found to be shifted far (> or = 0.9) in favor of the trans conformation. Interpretation of the measured vicinal coupling constants J alpha-beta' and J alpha-beta" for C alpha H-C beta H2 proton systems of Trp and Tyr side chains in terms of relative populations of g+, g-, and t staggered rotamers around the chi 1 dihedral angle indicated that in all the peptides studied (a) rotation of Trp indole ring in cis (Trp-Pro) isomers is strongly restricted, and (b) rotation of Tyr phenol ring is relatively free. The most preferred chi 1 rotamer of Trp (0.8-0.9 molar fraction) was assigned as the t one on the basis of a large value of the vicinal coupling constant between the high-field H beta and carbonyl carbon atoms of Trp, estimated for the cis (Pro1) form of H-Trp-Pro-Tyr-OH from a 1H, 13C correlated spectroscopy 1H-detected multiple quantum experiment. This indicates that cis<-->trans equilibrium in the Trp-Pro fragment is governed by nonbonding interactions between the pyrrolidine (Pro) and indole (Trp) rings. A molecular model of the terminal cis Trp-Pro dipeptide fragment is proposed, based on the presented nmr data and the results of our molecular mechanics modeling of low-energy conformers of the peptides, reported elsewhere.

Serine‐containing 10‐membered cyclodepsipeptides

As a part of a research program aimed at studying synthesis and conformation of small ring peptides, the cyclization of diastereoisomeric N-phenylacetyl-seryl-propyl-proline tripeptides has been examined. Two 10-membered peptide lactones, PhCH2CO-DSer-Pro-Pro- 5a and PhCH2CO-DSer-Pro-DPro- 5b, have been isolated by treating the corresponding linear p-nitrophenyl esters with DBU in dry benzene. In these two compounds the serine lactone fragment (a common structural feature of several bioactive cyclodepsipeptides) is inserted into a highly strained small ring system. The conformation in the crystal of 5a and 5b has been studied by X-ray analysis. Both the 10-membered rings of 5a and 5b adopt an overall cis-cis-trans conformation in which the lactone junction is trans. The deviations from planarity of the peptide units vary from delta omega = 30 degrees for the DSer-Pro bond in 5b to delta omega = 5-6 degrees for the DSer-Pro bond in 5a and Pro-DPro bond in 5b. The skeletal atoms of 5b, containing the Pro-DPro sequence, are related by a pseudo-symmetry mirror plane passing through the Pro carbonyl and the opposite DSer C beta H2 group. In both the molecules the exocyclic amide bond adopts an extended conformation with respect to the DSer-Pro ring junction; this arrangement gives rise to a C5-type ring structure which is well evidenced in the case of 5a.

A two-dimensional NMR study of Co(II)7 rabbit liver metallothionein.

The 600-MHz 1H-NMR NOESY spectra on Co(II)7-reconstituted metallothionein (Co7MT), exhibiting hyperfine signals in the range 350 ppm to -50 ppm, with nuclear relaxation times of the order of a few milliseconds, have been measured and several interproton connectivities have been detected. To our knowledge, this is the largest spectral window ever reported for a two-dimensional 1H-NMR spectrum in the case of a paramagnetic metalloprotein. No scalar connectivities could be detected. The hyperfine-shifted signals belong to the cysteine-ligand protons of the Co4S11 cluster of Co7MT. Together with results from one-dimensional NOE experiments, the two-dimensional experiments allowed us to proceed with the pairwise assignment of the isotropically shifted signals of the C beta H2 groups of the metal-coordinated cysteines. With the aid of computer-graphics inspection of the four-metal-cluster domain, based on the NMR solution structure of Cd7MT, it is possible to purpose sequence-specific assignments of a few hyperfine-shifted 1H-NMR signals. In particular, a tentative assignment is given for the six signals whose shifts exhibit an antiCurie temperature dependence. The assignment relies on the theoretical model that qualitatively rationalizes the isotropic-shift pattern and its temperature dependence. Inferences on the solution structure of the Co4S11 cluster are drawn.

NMR studies of the active site of isopenicillin N synthase, a non-heme iron(II) enzyme.

The active site structure of isopenicillin N synthase (IPNS) has been previously studied by the use of Mössbauer, EPR, electronic absorption, and NMR spectroscopies [Chen, V.J., Frolik, C.A., Orville, A.M., Harpel, M.R., Lipscomb, J.D., Surerus, K.K., & Münck, E. (1989) J. Biol. Chem. 264, 21677-21681; Ming, L.-J., Que, L., Jr., Kriauciunas, A., Frolik, C.A., & Chen, V.J. (1990) Inorg. Chem. 26, 1111-1112]. These studies have revealed three coordinated His residues along with three sites for substrate [delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine, ACV], NO, and water binding on the active Fe(II) of IPNS. We report here NMR studies of Fe(II)IPNS and its Co(II)-substituted derivative [Co(II)IPNS]. By the use of NOE techniques on the Co(II)IPNS-ACV complex, we have recognized a -CH2-CH less than spin system at 14.6, 24.3, and 38.6 ppm that is assigned to the alpha and beta protons of a coordinated Asp residue. Corresponding solvent nonexchangeable features are found near 40 ppm in Fe(II)IPNS and the Fe(II)IPNS-ACV complex, but the peaks are too broad for NOE effects to be observed. The binding of NO to the Fe(II) center results in a significant change in the configuration of the metal site: (a) The C beta H2 resonances due to the coordinated Asp residue disappear. The loss of the signal may indicate a change of the carboxylate configuration from syn-like to anti-like or, less likely, its displacement by NO.(ABSTRACT TRUNCATED AT 250 WORDS)

β-deuterium kinetic isotope effects in the purine nucleoside phosphorylase reaction

1. [2'-2H]Inosine was made from inosine by tetraisopropyldisiloxanyl protection of the 3'- and 5'-positions, oxidation with dimethyl sulphoxide and acetic anhydride, immediate NaB2H4 reduction of the oxo sugar product and inversion at C-2' of the resultant protected [2'-2H]arabino-inosine by trifluoromethanesulphonylation and reaction with caesium propionate, followed by deprotection. 2. The equilibrium-perturbation technique was used to measure beta 2H(V/K) for phosphorolysis of this compound by the purine nucleoside phosphorylase of Escherichia coli as a function of pH. 3. The pH variation indicates an intrinsic effect of 1.068 masked by isotopically silent steps near the pH optimum. 4. The similar pH variation of these beta-deuterium effects and the alpha-deuterium effects measured previously [Stein & Cordes (1981) J. Biol. Chem. 256, 767-772; Lehikoinen, Sinnott & Krenitsky (1989) Biochem. J. 257, 355-359] for this reaction provides the first experimental reassurance for the common assumption that pH changes merely mask and unmask the chemical steps in an enzyme-catalysed reaction, and do not detectably alter transition-state structure. 5. The dihedral angle between the C-H-2' bond and the electron-deficient p-orbital at the transition state is in the range 32-48 degrees, in accord with an essentially planar furanose ring.

Koelliker haemoglobins in developing chick embryo.

1. Three Koelliker haemoglobins, HbKE, HbKA and HbKH, derived from a post-translational loss of alpha-Arg-141, were isolated from red cells of chicken embryos. HbKE is typical of embryos up to 7 days of incubation, HbKA and HbKH are found in mature embryos. 2. All the precursor haemoglobins contain alpha A chains. HbKA derives from adult haemoglobin A whose globin composition is alpha A2 beta 2, HbKH from embryonic haemoglobin H with a globin composition alpha A2 beta H2 and HbKE from embryonic haemoglobin E with globin composition alpha A2 epsilon 2. 3. No Koelliker derivatives of haemoglobins with alpha-like chains other than alpha A were observed.

Arrhythmogenic and electrophysiological effects of alpha adrenoceptor stimulation during myocardial ischaemia and reperfusion

To examine possible arrhythmogenic effects of alpha adrenoceptor stimulation, we studied the effects of methoxamine 10(-6) M on arrhythmias and cellular electrophysiology during global myocardial ischaemia and reperfusion in isolated Langendorff perfused guinea-pig hearts. To avoid interference from release of endogenous catecholamines during ischaemia or reperfusion, experiments were performed using catecholamine depleted hearts (myocardial noradrenaline = 11% of control). Catecholamine depletion markedly reduced the incidence of VT and VF during ischaemia and reperfusion and perfusion with methoxamine significantly reversed this. This arrhythmogenic effect of methoxamine was only observed during ischaemia or reperfusion, was independent of beta adrenoceptor blockade and H2 receptor blockade but was abolished by alpha adrenoceptor blockade with phentolamine. Catecholamine depletion blunted the ischaemia induced fall in action potential amplitude and Vmax and prolonged action potential duration and refractory period. Perfusion with methoxamine either partially or completely reversed these effects. Thus, alpha adrenoceptor stimulation has little effect on normally perfused myocardium, but may induce VT or VF during ischaemia or reperfusion.

The complete nucleotide sequence of a beta-globin-like structure, beta h2, from the [Hbb]d mouse BALB/c.

We have determined the complete nucleotide sequence of beta h2, a pseudogene in the mouse beta-globin gene complex. The structure of beta h2 is analogous to that of a normal beta-globin gene, and its nucleotide sequence shares 72% homology with the coding regions of a reference mouse adult beta-globin gene. A frame shift occurs in the first coding region for which a compensatory splicing scheme can be devised. The reading frame is not otherwise disrupted. All of the recognized transcription, translation, and splicing signals in beta h2 are intact, with the exception of the " CCAAT box," which has been altered to GTAAC . We compared the predicted amino acid sequence of beta h2 with other beta-globin sequences. Evidence for a period of divergence without selection in the history of beta h2 was found in a set of codons that are usually highly conserved in productive beta-globin genes. An evolutionary tree constructed from nucleotide sequence suggests that beta h2 originated from the adult genes at least 60 million years ago. After some period as a productive gene, beta h2 was inactivated and has subsequently diverged without selection. Hybridization experiments demonstrated that beta h2 and the surrounding region occur without major alteration in other rodent species. The sequence ( AGCCA - 4n - GTGT ) occurs 5' of the CCAAT box in beta h2 and in many productive globin genes.

The complete nucleotide sequence of a beta-globin-like structure, beta h2, from the [Hbb] d mouse BALB/c.

The complete nucleotide sequence of a beta-globin-like structure, beta h2, from the [Hbb] d mouse BALB/c.

Assignment of the 1H nuclear magnetic resonance spectrum of the proteinase inhibitor IIA from bull seminal plasma by two-dimensional nuclear magnetic resonance at 500 MHz

The assignment of the 1H nuclear magnetic resonance (n.m.r.) spectrum of the protease inhibitor IIA from bull seminal plasma is described and documented. The assignments are based entirely on the amino acid sequence and on two-dimensional n.m.r. experiments at 500 MHz. Individual assignments were obtained at 18 degrees C and 45 degrees C for the backbone protons of all 57 amino acid residues, with the single exception of the N-terminal pyroglutamate amide proton. The amino acid side-chain resonance assignments are complete, with the exception of 17 long side-chains, i.e. Pro13, Met43 and all the Glu, Gln, Lys and Arg, where only one or two resonances of C beta H2 and in some cases C gamma H2 could be identified. The sequential assignments showed that the order of the two C-terminal residues in the previously established primary structure had to be changed; this was then confirmed by chemical methods. The chemical shifts for the assigned resonances at 18 degrees C and 45 degrees C are listed for an aqueous solution at pH 4.9. A preliminary characterization of the polypeptide secondary structure was obtained from the observed patterns of sequential connectivities.

Treatment of Urticaria

Urticaria represents a wide variety of conditions characterized by urticarial papules, wheals, and angioedema. The number of potential causes of urticaria is legion, but a diligent search by careful history and examination is indicated. Laboratory testing depends upon the specific situation, but routine screening examinations are not cost effective. Histamine from mast cells plays an important role in urticaria. Multiple factors, such as aspirin and other nonsteroidal anti-inflammatory agents, direct histamine-releasing agents (including benzoates), tartrazine and other azo dyes, and perhaps blockers of beta 2-adrenergic activity and H2 receptors, adversely influence histamine release either directly or indirectly. Vasodilation is also detrimental. Treatment of both acute and chronic urticaria necessitates removal of the patient from aggravating factors as well as the cause of the outbreak (if one can be found), along with effective antihistaminic agents and perhaps beta 2-adrenergic agonists. Treatment of specific entities within the urticarial group is briefly outlined in this article.

Proton nuclear magnetic resonance study of an active pentapeptide fragment of ubiquitin.

The aqueous solution conformation of Tyr-Asn-Ile-Gln-Lys (UB5) corresponding to positions 59-63 of the polypeptide, ubiquitin, has been investigated by proton NMR. Like the parent protein, UB5 induces nonspecifically both T and B lymphocyte differentiation. The various NH and CH resonances of this pentapeptide have been assigned, and its solution conformation has been probed through a study of chemical shift variations with pH, temperature dependence of amide hydrogen chemical shifts, vicinal NH--C alpha H and C alpha H--C beta H2 coupling constant data, and amide hydrogen-exchange rates. The latter were measured in H2O by using a combination of transfer of solvent saturation and saturation recovery NMR experiments. The data are compatible with the assumption of a highly motile dynamic equilibrium among different conformations for this peptide. The various secondary amide hydrogens remain essentially exposed to the solvent. The temperature-dependence study of the amide hydrogen chemical shifts also did not reveal any strong internal hydrogen bonds. A rotamer population analysis of tyrosine and asparagine side chains suggests that two of the rotomers are predominantly populated for each of these residues. From these results, a picture emerges of the dynamic conformation of UB5 in aqueous solution.

Multiple solution conformations and internal rotations of the decapeptide gramicidin S.

The conformations of every C alpha H-C beta H2 moiety of the peptide gramicidin S are reported. Internal rotation occurs, but distinct preferences for one side chain rotamer, greater than 80%, are found for the D-phenylalanine and ornithine residues. Leucine and valine exhibit more extensive averaging while proline is shown to be at least 90% in the Ramachandran B conformation. The data are consistent with the coexistence of many tertiary conformations of gramicidin S; the statistical weights of the twelve major tertiary conformations consistent with the rotamer populations are reported. The relative statistical weights of the tertiary conformers depend upon temperature and solvent. A comparison of the conclusions from this publication and conformations derived by energy minimization procedures is made. Partial agreement was found, but the calculations have not yet predicted the wealth of coexisting tertiary conformations nor accounted for the subtle effects of solvent. It is proposed that a more complete picture of the conformational dynamics of gramicidin S and other peptides will result from calculations which use as a basis the extensive data reported here.