A method of quantitative determination of stereoisomers of dipeptides in solution by infrared spectroscopy

An infrared spectroscopic method of quantitative analysis of dipeptides CH₃? CONH? CHR₁? CONH? R₂ in solution is proposed. The application of the method to a series of dipeptides with different side chains shows that the amount of the “bent form” tends to become important when the side chain is large.     

Conformational Analysis of the Thrombin Receptor Agonist Peptides SFLLR and SFLLR-NH2 by NMR: Evidence for a Cyclic Bioactive Conformation

The conformational properties of the pentapeptide Ser-Phe-Leu-Leu-Arg (P5), a human thrombin receptor-derived sequence forming part of a tethered ligand which activates the thrombin receptor, and its more active amide derivative Ser-Phe-Leu-Leu-Arg-NH₂ (P5-NH₂), have been studied by proton NMR spectroscopy in dimethylsulfoxide. Measurements of nuclear Overhauser effects, performed using two-dimensional rotating frame nuclear Overhauser (ROESY) and one-dimensional nuclear Overhauser enhancement (NOE) spectroscopy, revealed that P5 exists mainly in an extended conformation. However, proton–proton 1D-NOEs between Phe C_αH and Ser C_αH, Leu³ C_αH and Leu³ NH, and Leu⁴ C_αH and Leu⁴ NH, as well as between the Ser and Arg sidechains, also implicated a minor conformer for P5 having a curved backbone and a near-cyclic structure. In contrast to P5, measurements of NOEs and ROEs for P5-NH₂ revealed a more stabilized cyclic structure which may account for its higher biological potency. Thus strong interresidue sequential NH (i)–NH (i + 1) interactions, as well as C-terminal carboxamide to N-terminal side-chain interactions, i.e., Arg CONH₂ to Phe ring and Arg CONH₂ to Ser $C_\alpha /C_{\beta \beta '} $ , observed at lower levels of the ROESY spectrum, supported a curved backbone structure for SFLLR-NH₂. Since the higher potaency P5-NH₂ analogue adopts predominantly a cyclic structure, a cyclic bioactive conformation for thrombin receptor agonist peptides is suggested.     

Conformational dependence of the vicinal proton coupling constant for the Cα?Cβ bond in peptides

We use the nmr data concerning the C^αH? C^βH fragment in eight peptides with rigid side chains to parametrize a Karplus correlation between the vicinal proton J_αβ coupling constant and the dihedral angle θ. When considering molecules containing the fragment C^αH^α? C^βH^βH^β′, the three-dimensional structure of the model peptides does not need to be known with accurate precision, since each set of J_αβ and J_αβ′ coupling constants is then related to the coefficients of the Karplus equation. A good correlation is observed with the Karplus equation, which is in substantial agreement with the J_αβ coupling constants reported for rigid as well as rotating C^α? C^β bonds in peptides.     

Syntheses and opioid receptor binding properties of carboxamido-substituted opioids

A series of 15 novel opioid derivatives were made where the prototypic phenolic-OH group of traditional opioids was replaced by a carboxamido (CONH₂) group. For 2,6-methano-3-benzazocines and morphinans similar or, in a few instances, enhanced affinity for μ, δ and κ opioid receptors was observed when the OH → CONH₂ switch was applied. For 4,5α-epoxymorphinans, binding affinities for the corresponding carboxamide derivatives were much lower than the OH partner consistent with our pharmacophore hypothesis concerning carboxamide bioactive conformation. The active metabolite of tramadol and its carboxamide counterpart had comparable affinities for the three receptors.     

Simultaneous CT-13C and VT-15N chemical shift labelling: Application to 3D NOESY-CH3NH and 3D 13C,15N HSQC-NOESY-CH3NH

Based on the HSQC scheme, we have designed a 2D heterocorrelated experiment which combines constant time (CT) ¹³C and variable time (VT) ¹⁵N chemical shift labelling. Although applicable to all carbons, this mode is particularly suitable for simultaneous recording of methyl-carbon and nitrogen chemical shifts at high digital resolution. The methyl carbon magnetisation is in the transverse plane during the whole CT period (1/J_CC=28.6 ms). The magnetisation originating from NH protons is initially stored in the 2H_zN_z state, then prior to the VT chemical shift labelling period is converted into 2H_zN_y coherence. The VT -¹⁵N mode eliminates the effect of ¹ J _N,CO and ^1,2 J _N,CA coupling constants without the need for band-selective carbon pulses. An optional editing procedure is incorporated which eliminates signals from CH₂ groups, thus removing any potential overlap with the CH₃ signals. The CT-¹³CH₃,VT-¹⁵N HSQC building block is used to construct two 3D experiments: 3D NOESY-CH₃NH and 3D ¹³C,¹⁵N HSQC-NOESY-CH₃NH. Combined use of these experiments yields proton and heteronuclear chemical shifts for moieties experiencing NOEs with CH₃ and NH protons. These NOE interactions are resolved as a consequence of the high digital resolution in the carbon and nitrogen chemical shifts of CH₃ and NH groups, respectively. The techniques are illustrated using a double labelled sample of the CH domain from calponin.     

Caractéristiques géométriques de la séquence Hα?Cα?N?H de l'isoquinuclidone-3 examinée dans différents etats physiques influence sur la constante de couplage vicinal J

The X-ray structure analysis of a crystalline sample of 2-azabicyclo-[2,2,2]-octanone-3 or 3-isoquinuclidone shows that the molecules of this compound are associated in centrosymmetrical dimers stabilized by two N? H? O?C hydrogen bonds in which the N,H,O atoms are nearly collinear. As a consequence of this interaction, the H atom is shifted from its usual position and the C^α? N? H angle is increased to 125°. Using infrared spectroscopy (ν_N–H frequency range), it is possible to demonstrate that 3-isoquinuclidone is mainly in a dimeric form when dissolved in an inert solvent such as CCl₄ and to observe the dimer-monomer equilibrium on dilution from saturation to a low concentration (0.005 mole/l.). On the contrary, dimers are broken off when operating in a polar medium (acetonitrile, deuterochloroform). In the same experimental conditions, measurements of the J vicinal coupling constant, by nuclear magnetic resonance spectroscopy, afford a concentration-dependent result in the case of CCl₄ solutions (increasing from 5.4 to 5.7 Hz when diluting from 0.5 to 0.005 mole/l.) and a constant one (5.8 Hz) in the case of CH₃CN or CDCl₃ solutions. Then the 0.4-Hz difference can be attributed to geometrical changes in the H^α? C^α? N? H system when dimers are broken off and the valence angle C^α? N? H consequently decreases from 125° to its standard value (about 115°). This experimental observation is consistent with the result of a theoretical analysis performed by the INDO method. Then it seems that the use of the formulas proposed by Karplus to account for the valence angle distorsions in ethane-like systems, in the case of the H^α? C^α? N? H sequence, could yield overstimated corrections.     

Differential expression and signaling of the human histamine H3 receptor isoforms of 445 and 365 amino acids expressed in human neuroblastoma SH-SY5Y cells

In stably-transfected human neuroblastoma SH-SY5Y cells, we have compared the effect of activating two isoforms of 445 and 365 amino acids of the human histamine H₃ receptor (hH₃R₄₄₅ and hH₃R₃₆₅) on [³⁵S]-GTPγS binding, forskolin-induced cAMP formation, depolarization-induced increase in the intracellular concentration of Ca²⁺ ions ([Ca²⁺]i) and depolarization-evoked [^3?H]-dopamine release. Maximal specific binding (B_max) of [^3?H]-N-methyl-histamine to cell membranes was 953?±?204 and 555?±?140?fmol/mg protein for SH-SY5Y-hH₃R₄₄₅ and SH-SY5Y-hH₃R₃₆₅ cells, respectively, with similar dissociation constants (K_d, 0.86?nM and 0.81?nM). The mRNA of the hH₃R₃₆₅ isoform was 40.9?±?7.9% of the hH₃R₄₄₅ isoform. No differences in receptor affinity were found for the H₃R ligands histamine, immepip, (R)(-)-α-methylhistamine (RAMH), A-331440, clobenpropit and ciproxifan. Both the stimulation of [³⁵S]-GTPγS binding and the inhibition of forskolin-stimulated cAMP accumulation by the agonist RAMH were significantly larger in SH-SY5Y-hH₃R₄₄₅ cells ([³⁵S]-GTPγS binding, 158.1?±?7.5% versus 136.5?±?3.6% for SH-SY5Y-hH₃R₃₆₅ cells; cAMP accumulation, ?74.0?±?4.9% versus ?43.5?±?5.3%), with no significant effect on agonist potency. In contrast, there were no differences in the efficacy and potency of RAMH to inhibit [^3?H]-dopamine release evoked by 100?mM K⁺ (?18.9?±?3.0% and ?20.5?±?3.3%, for SH-SY5Y-hH₃R₄₄₅ and SH-SY5Y-hH₃R₃₆₅ cells), or the inhibition of depolarization-induced increase in [Ca²⁺]i (S2/S1 ratios: parental cells 0.967?±?0.069, SH-SY5Y-hH₃R₄₄₅ cells 0.639?±?0.049, SH-SY5Y-hH₃R₃₆₅ cells 0.737?±?0.045). These results indicate that in SH-SY5Y cells, hH₃R₄₄₅ and hH₃R₃₆₅ isoforms regulate in a differential manner the signaling pathways triggered by receptor activation.     

Co-oligopeptides containing two aromatic residues spaced by glycyl residues. X. Proton magnetic resonance study of co-oligopeptides of tryptophan and glycine

The ¹H-nmr spectra of co-oligopeptides of tryptophan and glycine with structure H-Gly-Trp-(Gly)_n-Trp-Gly-OH (n = 0–2) and those of several di- and tripeptides have been recorded at 360 MHz with CD₃OD solutions containing 0.1N NaOD. The assignment of resonance signals was generally possible by comparing the spectra of structurally related peptides with each other. In order to solve the remaining ambiguities in the assignment, H-(αL,βS)(α,β-d₂)Trp-OH, H-Trp-(αL,βS)(α,β-d₂)Trp-OH, and H-Trp-(δ¹,ε²,ζ²,ζ³,η²-d₅)Trp-OH have been prepared and their spectra compared with those of the undeuterated compounds. The distribution of rotamers around the χ₁ and (in two cases) χ₂ torsion angles of the side chains has been obtained from the vicinal coupling constants ³J and from the long-range coupling constants ⁴J. These data and an analysis of the chemical shifts of the Gly-C^α protons suggest that the orientation of the aromatic side chain is influenced by the following order of decreasing interaction with the functional groups at N- and C-side: -NH₂ > –NHCO– > –CONH–> –COO^?. This rule does not hold for the second Trp residue of di- and tripeptides containing the -Trp-Trp- sequence, which has tentatively been attributed to steric effects.     

Crystal and molecular structure of benzyloxycarbonyl-α-aminoisobutyryl-L-prolyl methylamide: The observation of an X2-Pro3 Type III β-Turn

The crystal and molecular structure of N-benzyloxycarbonyl-α-aminoisobutyryl-L -prolyl methylamide, the amino terminal dipeptide fragment of alamethicin, has been determined using direct methods. The compound crystallizes in the orthorhombic system with the space group P2₁2₁2₁. Cell dimensions are a = 7.705 Å, b = 11.365 Å, and c = 21.904 Å. The structure has been refined using conventional procedures to a final R factor of 0.054. The molecular structure possesses a 4 → 1 intramolecular N-H—O hydrogen bond formed between the CO group of the urethane moiety and the NH group of the methylamide function. The peptide backbone adopts the type III β-turn conformation, with ?₂ = ?51.0°, ψ₂ = ?39.7°, ?₃ = ?65.0°, ψ₃ = ?25.4°. An unusual feature is the occurrence of the proline residue at position 3 of the β-turn. The observed structure supports the view that Aib residues initiate the formation of type III β-turn conformations. The pyrrolidine ring is puckered in C^γ-exo fashion.     

Synthesis and characterization of metallatranes with phenyl substituents in atrane cage

A new series of mono- and diphenylsubstituted silatranes and boratranes N(CH₂CH₂O)₂(CHR³CR¹R²O)MZ (M = Si, Z = CH₂Cl, CCPh, H, OMenth, R¹, R², R³ = H, Ph; M = B, Z = nothing, R¹, R², R³ = H, Ph) have been synthesized. Both transalkoxylation and stepwise modification of a preformed metallatrane skeleton were used. The chloromethyl derivatives N(CH₂CH₂O)₂(CHRCHRO)SiCH₂Cl (R = H, Ph) react with tert-BuOK under intramolecular cycle expansion to give 1-tert-butoxy-2-carba-3-oxahomosilatranes N(CH₂CH₂O)(CH₂CH₂OCH₂)(CHRCHRO)SiO^tBu (R = H, Ph). The treatment of boratranes N(CH₂CH₂O)₂(CH₂CR¹R²O)B (R¹,R² = H, Ph) with triflic acid and trimethylsilyl triflate results in the products of electrophilic attack at the nitrogen atom. The molecular structures of four silatranes and one boratrane bearing phenyl groups in the atrane skeleton were determined by the X-ray structure analysis.     

Changes of aliphatic C–H bonds in cyanobacteria during experimental thermal maturation in the presence or absence of silica as evaluated by FTIR microspectroscopy

Aliphatic C–H bonds are one of the major organic signatures detected in Proterozoic organic microfossils, and their origin is a topic of interest. To investigate the influence of the presence of silica on the thermal alteration of aliphatic C–H bonds in prokaryotic cells during diagenesis, cyanobacteria Synechocystis sp. PCC6803 were heated at temperatures of 250–450°C. Changes in the infrared (IR) signals were monitored by micro‐Fourier transform infrared (FTIR) spectroscopy. Micro‐FTIR shows that absorbances at 2,925 cm^?1 band (aliphatic CH₂) and 2,960 cm^?1 band (aliphatic CH₃) decrease during heating, indicating loss of the C–H bonds, which was delayed by the presence of silica. A theoretical approach using solid‐state kinetics indicates that the most probable process for the aliphatic C–H decrease is three‐dimensional diffusion of alteration products under both non‐embedded and silica‐embedded conditions. The extrapolation of the experimental results obtained at 250–450°C to lower temperatures implies that the rate constant for CH₃ (k_CH3) is similar to or lower than that for CH₂ (k_CH2; i.e., CH₃ decreases at a similar rate or more slowly than CH₂). The peak height ratio of 2,960 cm^?1 band (CH₃)/2,925 cm^?1 band (CH₂; R_3/2 values) either increased or remained constant during the heating. These results reveal that the presence of silica does affect the decreasing rate of the aliphatic C–H bonds in cyanobacteria during thermal maturation, but that it does not significantly decrease the R_3/2 values. Meanwhile, studies of microfossils suggest that the R_3/2 values of Proterozoic prokaryotic fossils from the Bitter Springs Group and Gunflint Formation have decreased during fossilization, which is inconsistent with the prediction from our experimental results that R_3/2 values did not decrease after silicification. Some process other than thermal degradation, possibly preservation of specific classes of biomolecules with low R_3/2 values, might have occurred during fossilization.     

Reactions of N-cyanomethyl groups attached to a tetraaza macrocyclic copper(II) complex leading to the formation of various hetero-functionalized macrocyclic complexes

New hetero-functionalized macrocyclic complexes [CuL²](ClO₄)₂ (I) and [CuL³](ClO₄)₂ (II) bearing one N-CH₂CONH₂ or one N-CH₂C(NH)NH(CH₂)₂CH₃ pendant arm as well as one N-CH₂CN group have been prepared by the selective reaction of water or n-propylamine with one of the two N-CH₂CN groups in [CuL¹](ClO₄)₂ (L¹ = 2,13-bis(cyanomethyl)-5,16-dimethyl-2,6,13,17-tetraazatricyclo[16.4.0.^1.180^7.12]docosane). The complex [CuL⁴](ClO₄)₂ (III) bearing both N-CH₂CONH₂ and N-CH₂C(NH)NH(CH₂)₂CH₃ pendant arms can be prepared by either the reaction of I with n-propylamine or the hydrolysis of II. The N-CH₂CONH₂ and/or N-CH₂C(NH)NH(CH₂)₂CH₃ groups of I, II, and III are coordinated to the metal ion. The crystal structure of II shows that the complex has distorted square-pyramidal coordination polyhedron with a considerably strong apical Cu-N (N-CH₂C(NH)NH(CH₂)₂CH₃) bond (2.101(6) Å). The addition of HClO₄ (?0.01 M) to an acetonitrile (or DMSO) solution of II or III produces [Cu(HL³)](ClO₄)₃ (IIa) or [Cu(HL⁴)](ClO₄)₃ (IIIa), showing that the N-CH₂C(NH)NH(CH₂)₂CH₃ pendant arm of each complex is readily protonated in the non-aqueous solvent; the resulting N-CH₂C()NH(CH₂)₂CH₃ group of IIa or IIIa is not involved in coordination. However, the N-CH₂C(NH)NH(CH₂)₂CH₃ group of II is not protonated even in ?1.0 M HClO₄ aqueous solution. In the case of III, most of the complex exists as the protonated form [Cu(HL⁴)]³⁺ in ?0.1 M HClO₄ aqueous solutions.     

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^α(Pro₁), H^α(Trp), C^γ(Pro), H^ε(Tyr), and H^δ(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 ≈ 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 (?0.9) in favor of the trans conformation. Interpretation of the measured vicinal coupling constants J_α?β′ and J_α?β″ for C^αH-C^βH₂ proton systems of Trp and Tyr side chains in terms of relative populations of g⁺, g^?, and t staggered rotamers around the χ₁ 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 χ₁ 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^β 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. © 1993 John Wiley & Sons, Inc.     

Isostructural unbranched alkyl‐chains as tools for stabilizing β‐turn structure

To investigate the structural role played by isostructural unbranched alkyl‐chains on the conformational ensemble and stability of β‐turn structures, the conformational properties of a designed model peptide: Plm‐Pro‐Gly‐Pda ( 1 , Plm: H₃C—(CH₂)₁₄—CONH—; Pda: —CONH— (CH₂)₁₄—CH₃) have been examined and compared with the parent peptide: Boc‐Pro‐Gly‐NHMe ( 2 , Boc: tert‐butoxycarbonyl; NHMe: N‐methylamide). The characteristic ¹³C NMR chemical‐shifts of the Pro C^β and C^γ resonances ascertained the incidence of an all‐trans peptide‐bond in low polarity deuterochloroform solution. Using FTIR and ¹H NMR spectroscopy, we establish that apolar alkyl‐chains flanking a β‐turn promoting Pro‐Gly sequence impart definite incremental stability to the well‐defined hydrogen‐bonded structure. The assessment of ¹H NMR derived thermodynamic parameters of the hydrogen‐bonded amide‐NHs via variable temperature indicate that much weaker hydrophobic interactions do contribute to the stability of folded reverse turn structures. The far‐UV CD spectral patterns of 1 and 2 in 2,2,2‐trifluoroethanol are consistent with Pro‐Gly specific type II β‐turn structure, concomitantly substantiate that the flanking alkyl‐chains induce substantial bias in enhanced β‐turn populations. In view of structural as well as functional importance of the Pro‐Gly mediated secondary structures, besides biochemical and biological significance of proteins lipidation via myristoylation or palmytoilation, we highlight potential convenience of the unbranched Plm and Pda moieities not only as main‐chain N‐ and C‐terminal protecting groups but also to mimic and stabilize specific isolated secondary and supersecondary structural components frequently observed in proteins and polypeptides. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 419–426, 2013.     

Two-Dimensional 1H, 15N NMR investigation of uniformly 15N-labeled Lac Repressor Headpiece

Abstract

¹⁵N uniformly labeled lac repressor and lac repressor headpiece were prepared. ¹⁵N NMR spectra of lac repressor were shown resolution inadequate for detailed study while the data showed that the ¹⁵N labeled N-terminal part of the protein is quite suitable for this type of study allowing future investigation of the specific interaction of the lac repressor headpiece with the lac operator. We report here the total assignment of proton ¹H and nitrogen ¹⁵NH backbone resonances of this headpiece in the free state. Assignments of the ¹⁵N resonances of the protein were obtained in a sequential manner using heteronuclear multiple quantum coherence (HMQC), relayed HMQC nuclear Overhauser and relayed HMQC-HOHAHA spectroscopy. More than 80 per cent of residues were assigned by their ¹⁵NH(i)-N¹H(i+1) and ¹⁵NH(i)-N¹(i-1) connectivities. Values of the ³J_NHα splitting for 39 of the 51 residues of the headpiece were extracted from HMQC and HMQC-J. The observed ¹⁵NH(i)-C^βH cross peaks and the ³J_NHα coupling constants values are in agreement with the three α-helices previously described [Zuiderweg, E.R.P., Scheek, R.M., Boelens, R., van Gunsteren, W.F. and Kaptein, R., Biochimie 67, 707 (1985)]. The ³J_NHα coupling constants can be now used for a more confident determination of the lac repressor headpiece. From these values it is shown that the geometry of the ends of the second and third α-helices exhibit deviation from the canonical α-helix structure. On the basis of NOEs and ³J_NHα values, the geometry of the turn of the helix-turn-helix motif is discussed.     

Quantitative two-dimensional nmr study of dermenkephalin,a highly potent and selective δ-opioid peptide

Dermenkephalin, H-Tyr-(D ) Met-Phe-His-Leu-Met-Asp-NH₂, a highly potent and selective δ-opioid peptide isolated from frog skin, was studied in DMSO-d₆ solution by two-dimensional nmr spectroscopy, including the determination of NH temperature coefficients, the evaluation of ³J coupling constants from phase-sensitive correlated spectroscopy (COSY) and the volumes of nuclear Overhauser effect (NOE) correlations. The two-dimensional NOE spectroscopy (NOESY) spectrum of dermenkephalin revealed sequential, medium-, and long-range effects. To put this information on a quantitative basis, special attention was devoted to J cross-peak suppression, quantification of the NOE volumes and analysis of the overlaps, normalization of the NOEs against diagonal peaks and H_ββ′ geminal interactions. Although most of the dihedral angles deduced from the ³J_Nα coupling constants together with several N_iα_i and α_iN_{i + 1} NOEs pointed to a partially extended peptide backbone, several N_i N_{i + 1} NOEs and β_i N_{i + 1} interactions argued in favor of a folded structure. Moreover, several long-range correlations of strong intensities were found that supported a close spatial proximity between the side chains of D -Met² and Met⁶, Tyr¹ and His⁴, Tyr¹ and Asp⁷, and His⁴ and the C-terminal amide group. In Phe, the g^? rotamer in the side chain is deduced from the ³J_αβ coupling constants and αβ and Nβ NOE correlations. Whereas the amide proton dependency was not indicative of stable hydrogen bonds, the nonuniform values of the temperature coefficient may reflect an equilibrium mixture of folded and extended conformers. The overall data should provide realistic starting models for energy minimization and modelization studies. © 1993 John Wiley & Sons, Inc.     

Conformational energy calculations with averaged potential functions: Application to the repeat peptides of elastin

We present a method that can reduce conformational energy calculations for an arbitrary peptide consisting of n residues (n-peptide) to the complexity of a computation for (Gly)_n. This reduction, and the concomitant savings in computer time, is accomplished by replacing all side chains, as well as the backbone C^αH^α and C^αH₂^α groups, by “interaction centers.” The backbone CONH group is left intact in order to preserve its directional character. The interaction centers “see” each other, and the atoms of the CONH group via Boltzmann and space-averaged effective center-center and center-atom potentials, respectively. This averaged-interaction method is tested on the repeat tetra-, penta-, and hexapeptides of elastin, Val-Pro-Gly-Gly (VPGG), Val-Pro-Gly-Val-Gly (VPGVP), and Ala-Pro-Gly-Val-Gly-Val (APGVGV), using the stereoalphabet strategy for the energy calculations. The excellent qualitative and quantitative agreement we obtain with both full atom-atom calculations and extensive nmr data, coupled with the order-of-magnitude reduction in computer time, augurs well for the potential usefulness of the method.     

Static and dynamic properties of mid-size liquid n- alkanes,C12∼C400: a molecular dynamics simulation study

ABSTRACT

In this paper, we have extended our previous study of the static and dynamic properties (self-diffusion coefficient D_self and friction coefficient ζ) of liquid n-alkane systems up C₄₀₀ at several temperatures (～2300?K) using molecular dynamics (MD) simulations in the canonical ensembles. For the small n-alkanes with n?≤?120 (n: the chain length), the chains are clearly ?R² _ee?/6?R² _g? ≥ 1 (1.06 ～ 1.44), which leads to the conclusion that the liquid n-alkanes are far away from the ideal chain regime. But for the n-alkanes of n?≥?160, the chains are ?R² _ee?/6?R² _g? ≈ 1, indicating that they are Gaussian. It is found that the long chains of these n-alkanes at high temperatures show abnormalities in density and friction coefficient. We observed a clear transition in the power law dependence of n-alkane self-diffusion coefficient on the molecular weight (M) of n-alkane, D_self ～ M^?γ, occurs in the range C₁₂₀～C₁₆₀ at temperatures of 318, and 618?K, corresponding to a crossover from the ‘oligomer’ to the ‘Rouse’ regime. The entanglement lengths (N_e) are calculated by the Z1 code and discussed shortly.     

Correlation of 2J couplings with protein secondary structure

Geminal two‐bond couplings (²J) in proteins were analyzed in terms of correlation with protein secondary structure. NMR coupling constants measured and evaluated for a total six proteins comprise 3999 values of ²J_CαN′, ²J_C′HN, ²J_HNCα, ²J_C′Cα, ²J_HαC′, ²J_HαCα, ²J_CβC′, ²J_N′Hα, ²J_N′Cβ, and ²J_N′C′, encompassing an aggregate 969 amino‐acid residues. A seamless chain of pattern comparisons across the spectrum datasets recorded allowed the absolute signs of all ²J coupling constants studied to be retrieved. Grouped by their mediating nucleus, C′, N′ or C^α, ²J couplings related to C′ and N′ depend significantly on ?,ψ torsion‐angle combinations. β turn types I, I′, II and II′, especially, can be distinguished on the basis of relative‐value patterns of ²J_CαN′, ²J_HNCα, ²J_C′HN, and ²J_HαC′. These coupling types also depend on planar or tetrahedral bond angles, whereas such dependences seem insignificant for other types. ²J_HαCβ appears to depend on amino‐acid type only, showing negligible correlation with torsion‐angle geometry. Owing to its unusual properties, ²J_CαN′ can be considered a “one‐bond” rather than two‐bond interaction, the allylic analog of ¹J_N′Cα, as it were. Of all protein J coupling types, ²J_CαN′ exhibits the strongest dependence on molecular conformation, and among the ²J types, ²J_HNCα comes second in terms of significance, yet was hitherto barely attended to in protein structure work. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Conformational Analysis of the Thrombin Receptor Agonist Peptides SFLLR and SFLLR-NH2 by NMR: Evidence for a Cyclic Bioactive Conformation

The conformational properties of the pentapeptide Ser-Phe-Leu-Leu-Arg (P5), a human thrombin receptor-derived sequence forming part of a tethered ligand which activates the thrombin receptor, and its more active amide derivative Ser-Phe-Leu-Leu-Arg-NH₂ (P5-NH₂), have been studied by proton NMR spectroscopy in dimethylsulfoxide. Measurements of nuclear Overhauser effects, performed using two-dimensional rotating frame nuclear Overhauser (ROESY) and one-dimensional nuclear Overhauser enhancement (NOE) spectroscopy, revealed that P5 exists mainly in an extended conformation. However, proton–proton 1D-NOEs between Phe CH and Ser CH, Leu³ CH and Leu³ NH, and Leu⁴ CH and Leu⁴ NH, as well as between the Ser and Arg sidechains, also implicated a minor conformer for P5 having a curved backbone and a near-cyclic structure. In contrast to P5, measurements of NOEs and ROEs for P5-NH₂ revealed a more stabilized cyclic structure which may account for its higher biological potency. Thus strong interresidue sequential NH (i)–NH (i + 1) interactions, as well as C-terminal carboxamide to N-terminal side-chain interactions, i.e., Arg CONH₂ to Phe ring and Arg CONH₂ to Ser , observed at lower levels of the ROESY spectrum, supported a curved backbone structure for SFLLR-NH₂. Since the higher potaency P5-NH₂ analogue adopts predominantly a cyclic structure, a cyclic bioactive conformation for thrombin receptor agonist peptides is suggested.