bluuebunny/crossref_metadata_2025 huggingface dataset:
Conformational analysis and molecular dynamics simulations of maltose
Authors: Ha S. N. , Madsen L. J. , Brady J. W.
Published: December 2004

Constrained conformational energy minimizations have been used to calculate an adiabatic (Φ, ψ) potential energy surface for the disaccharide β‐maltose. The inclusion of molecular flexibility in the conformational energy analysis of the disaccharide was found to significantly lower the barriers to conformational transitions, as has been observed previously for other systems. Several low energy wells were identified on the adiabatic surface which differ in energy by small amounts and with low absolute barriers separating them, indicating the possibility of a non‐negligible equilibrium population distribution in each well. If such a distribution of conformations existed in the physical system, the conformation observed by NMR NOE measurements would thus be a “virtual” conformation. Molecular dynamics simulations of the motions of this molecule in vacuum were also conducted and indicate that the rate of relaxation of the molecule to the adiabatic surface may be slower than the typical timescale of conformational fluctuations. This effect is apparently due to an unphysical persistence of hydrogen bond patterns in vacuum which does not occur in aqueous solution. Trajectories undergoing transitions between wells were calculated and the effects of such conformational transitions upon the ensemble mean structure, such as might be observed in an NMR experiment, were demonstrated.
A crystal molecular conformation of leucine‐enkephalin related to the morphine molecule
Authors: Aubry A. , Birlirakis N. , Sakarellos‐Daitsiotis M. , Sakarellos C. , Marraud M.
Published: December 2004

Leucine‐enkephalin (Try1‐Gly2‐Gly3‐Phe4‐Leu5) has been crytallized as a trihydrate from water solution. X‐ray diffraction reveals a tightly folded molecular conformation with two fused βIII‐ (Gly2‐Gly3) and βI‐ (Gly3‐Phe4) turns. The Tyr1 and Phe4 aromatic rings have a close orthogonal arrangement analogous to the tyramine and cyclohexenyl rings in morphine. This suggests that the conformation found in the trihydrate crystal structure could be required for recognition by μ‐receptor sites.
1H‐nmr studies of receptor‐selective substance P analogues reveal distinct predominant conformations in DMSO‐d6
Authors: Levian‐Teitelbaum Dina , Kolodny Nancy , Chorev Michael , Selinger Zvi , Gilon Chaim
Published: December 2004

Proton nmr parameters are reported for DMSO‐d6 solutions of two receptor‐selective substance P analogues: Ac[Arg6, Pro9]SP6‐11, which is selective for the NK‐1 (SP‐P) receptor and [pGlu6, N‐MePhe8]SP6‐11, which selectively activates the NK‐3 (SP‐N) receptor. Full peak assignments of both analogues were obtained by COSY experiments. The chemical shifts, coupling constants, and temperature coefficients of amide proton chemical shifts as well as NOESY effects and calculated side‐chain rotamer populations of Phe side chains are reported for both peptides. Analysis of coupling constants and temperature coefficients together with the nuclear Overhauser enhancement spectroscopy effects suggest that Ac[Arg6, Pro9]SP6‐11 has a trans configuration about the Phe8‐Pro9 amide bond and the preferred conformation of this analogue has a type I β‐turn. The nmr data for [pGlu6, N‐MePhe8]SP6‐11 suggest that this peptide exists as a mixture of cis–trans isomers in which the cis isomer can preferably adopt a type VI β‐turn conformation, and the trans isomer can adopt a γ‐turn conformation. There are indications that the two last turns are stabilized by a hydrogen bond between the syn carboxamide proton and the pGlu ring carbonyl.
Selective agonists for receptors of substance P and related neurokinins
Authors: Regoli D. , Dion S. , Rhaleb N.‐E. , Rouissi N. , Tousignant C. , Jukic D. , D'Orleans‐Juste P. , Drapeau G.
Published: December 2004

Neurokinins and their receptors are a complex system consisting of at least three endogenous agents—substance P (SP), neurokinin A (NKA), and neurokinin B (NKB)—and their corresponding receptor types, respectively, NK‐1, NK‐2, and NK‐3. Investigations on receptors have been made using sensitive and fairly selective pharmacological preparations (the dog carotid artery for the NK‐1, the rabbit pulmonary artery devoid of endothelium for the NK‐2, and the rat portal vein for the NK‐3 receptor), and some natural peptides of mammalian and nonmammalian origin. Because of the nonselectivity of the natural peptides, analogues of the neurokinins have been found that act on one receptor only and show therefore high selectivity. The selective agonists [Sar9, Met(O2)11]SP, [Nle10]NKA (4–10), and [MePhe7]‐NKB have been used successfully for (a) characterizing the three neurokinin receptors, (b) identifying isolated organs whose responses to neurokinins depend on the activation of a single (monoreceptor systems) or of more than one (multireceptor systems) receptor, and (c) elucidating some of the physiological function of the three receptor types. It is suggested that NK‐1 mediate peripheral vasodilatation and exocrine secretions, NK‐2 stimulate bronchial muscles and facilitate the release of catecholamines, and NK‐3 promote the release of acetylcholine in peripheral organs.
Bioactive conformation of linear peptides in solution: An elusive goal?
Authors: Temussi Piero A. , Picone Delia , Castiglione‐Morelli Maria A. , Motta Andrea , Tancredi Teodorico
Published: December 2004

Bioactive peptides of natural origin have, in general, short linear sequences, and are characterized by a large conformational flexibility. It is very difficult to study their conformation in solution since they exist, almost invariably, as a complex mixture of numerous conformers, most of which are extended. The so‐called bioactive conformation may be one of them, although the solvents used in solution studies often have properties drastically different from those of the biological system in which the peptide acts. There is, however, no simple way of identifying the bioactive conformation amid the many existing conformers.

It is possible to approach a solution to this problem using two distinct strategies: (a) Limiting the conformational freedom of the peptide, e.g., by increasing the viscosity of the solution and decreasing the temperature, in the assumption that the bioactive conformation is, even slightly, more stable than the others. (b) Trying to mimic in solution the physicochemical features of the more reliable receptor models.

These two approaches will be illustrated with examples taken mainly from oploid peptides.
Regularly alternating L,D‐peptides. I. The double‐stranded left‐handed antiparallel β‐helix in the structure of Boc‐(L‐Val‐D‐Val)4‐OMe
Authors: Di Blasio Benedetto , Benedetti Ettore , Pavone Vincenzo , Pedone Carlo , Spiniello Ottavia , Lorenzi Gian Paolo
Published: December 2004

The structure of Boc‐(L‐Val‐D‐Val)4‐OMe has been determined by x‐ray single‐crystal diffraction analysis. The octapeptide crystallizes in the trigonal system, space group P3221 with a = b = 12.760 Å, c = 63.190 Å and Z = 6. The independent unit is represented by one octapeptide chain. The structure has been solved by direct methods and it was anisotropically refined by least‐squares procedures to a final R value of 0.08 for the 3018 “observed” reflections. One molecule of water was also located in the unit cell. Two octapeptide chains, related by a crystallographic binary axis, wind up around each other giving rise to a double‐stranded left‐handed antiparallel ↑↓ β5.6‐helix. The dimer, stabilized by 14 interstrand NH ⃛OC hydrogen bonds, can be regarded as a cylinder with an hydrophilic inner core represented by the peptide units and an hydrophobic exterior of isopropyl groups. The inner diameter of the cylinder is 5.1 Å.
Mono and two‐dimensional 500‐MHz characterization of synthetic bombesin and related peptides in DMSO and DMSO–water,
Authors: Di Bello Carlo , Gozzini Luigia , Tonellato Mauro , Corradini Maria Grazia , D'Auria Gabriella , Paolillo Livio , Trivellone Enrico
Published: December 2004

The proton nmr characterization of bombesin (BBS) and of two peptide fragments corresponding to the (1–6) and (6–14) sequences has been carried out at 500 MHz in dimethyl sulfoxide (DMSO‐d6) using two‐dimensional (2D) homo and 1H‐13C heterocorrelated techniques. All resonances in the nmr spectra have been assigned and several coupling constants have been measured. The backbone JαCHNH coupling constants are quite similar and around 7.8–8.2 Hz, pointing to an unfolded structure in DMSO‐d6. The possibility of secondary structures in highly viscous mixtures of DMSO‐d6–water was investigated. The existence of sequential nuclear Overhauser enhancement (NOE) effects in the C‐terminal nonapeptide section may indicate a preferential site for secondary structuring.
Conformational analysis of peptide T and of its C‐pentapeptide fragment
Authors: Motta Andrea , Picone Delia , Temussi Piero A. , Marastoni Mauro , Tomatis Roberto
Published: December 2004

The synthetic peptide of sequence H‐Ala‐Ser‐Thr‐Thr‐Thr‐Asn‐Tyr‐Thr‐OH, termed peptide T, a competitor of the Human Immunodeficiency Virus in the binding to human T cells, and its C‐terminal pentapeptide fragment, were studied by 1H‐nmr in DMSO solution to determine conformational preferences. The observation of nuclear Overhauser enhancements (NOEs) for both peptides, and unusual finding for small linear peptides, allowed complete sequence‐specific resonance assignments. Long‐range NOEs, ring‐current shifts, and the very small temperature coefficient of the Thr8 NH chemical shift suggest, for the zwitterionic form of peptide T, the presence in solution of a β‐turn involving Thr5, Asn6, Tyr7 and Thr8. This conformational feature is consistent with previous structure–activity relationship studies indicating the invariance of the same residues in several potent pentapeptide analogues. The studied pentapeptide fragment, although less structured, shows some tendency to fold even in a polar solvent such as DMSO.

Preliminary chemotaxis data on some pentapeptide analogues are consistent with our structural model.
Computer simulations of a tumor surface octapeptide epitope
Authors: Reid Robert H. , Hooper Charles A. , Brooks Bernard R.
Published: December 2004

Molecular dynamics using CHARMM and GEMM programs with the Star Technologies ST 100 array processor functioning at the speed of super computers was used as a searching algorithm for conformational exploration of the octapeptide Gly‐Asn‐Thr‐Ile‐Val‐Ala‐Glu. This poorly soluble octapeptide is the N‐terminal epitope of an 11 KD glycoprotein antigen residing on human ductal carcinoma (breast) cells. Very long (nanoseconds) simulations were required. Both an α‐helix and the N‐acetyl‐N1‐methylamide derived minimized starting structures gave the same lowest potential energy conformation with simulations at 600 K. The same conformation was found only when using the latter starting conformation with simulations at 300 K. The lowest potential energy conformation was stabilized by 4 hydrophobic contacts and 13 H bonds completing one turn of a left‐handed helix.
Molecular mechanics studies on poly(purine) · poly(pyrimidine) sequences in DNA: Polymorphism and local variability
Authors: Bansal Manju , Pattabiraman N.
Published: December 2004

Energy minimization has been carried out on three poly(purine) · poly(pyrimidine) sequences—d(G)10 · d(C)10, d(A)10, d(T)10 and d(AG)5 · d(CT)5—using the molecular mechanics program AMBER (Assisted Model Building and Energy Refinement). In order to extensively scan the conformational space available, five different helical models were studied, three of them being right‐handed helices while the other two were left helical. For all three sequences the right‐handed A‐ and B‐type helices are energetically slightly preferred over the left helices, but the energy difference between the various right‐handed helices is only marginal. A detailed analysis has been carried out to characterize the local structural variability in the refined structures, both in terms of torsion angles as well as other parameters such as base‐pair tilt, wedge roll, and wedge tilt, etc. All three sequences exhibit similar structural features for a particular form, but both the forms A and B show significant deviations from fiber models. In particular, the A‐form structures have higher unit rise (2.7 Å), and lower unit twist (31°) and base‐pair tilt (12°), compared to the fiber model, which has corresponding values of 2.56 Å, 32.7°, 20°, respectively. All these changes indicate that the refined models are closer to the A‐form structure observed in crystals of oligonucleotides. In the refined B‐for models, the helical parameters are close to the fiber B‐form, although the torsion angles show considerable variations. None of the three sequences examined, including the d(A)n · d(T)n sequence, show any pronounced curvature for the B‐form structure.
A differential scanning calorimetric study of the conformational transitions of schizophyllan in mixtures of water and dimethylsulfoxide
Authors: Kitamura Shinichi , Kuge Takashi
Published: December 2004

The thermal conformational transitions of two sonicated samples of schizophyllan were studied in water‐dimethylsulfoxide (DMSO) mixtures by high‐sensitivity differential scanning calorimetry (DSC). Two transitions were observed over most of the range of solvent compositions. These were assigned to an internal change of the triple helix [T. Itou et al. (1986) Macromolecules 19, 1234–1240] and a triple‐helix–single‐coil transition [T. Sato et al. (1981) Carbohydr. Res. 95, 195–204], respectively. In water, the former transition observed at lower temperature for a low molecular weight sample, U‐1, is centered at 3°C and characterized by the specific enthalpy, Δhcal = 3.29 J g−1. A higher molecular weight sample, M‐2, showed this transition at 7°C with Δhcal = 4.39 J g−1. The transition temperature for both samples increased with increasing DMSO concentration up to about 50°C at 70 weight % DMSO, and then rapidly decreased with increasing DMSO concentration, with about 3°C higher for M‐2 than for U‐1 over the DMSO concentration. The transition was not observed when the concentration of DMSO exceeded 87%. It was found that Δhcal for both samples was a linear function of t1/2, the temperature of half‐completion in °C, Δhcal = 0.177t + 2.96. The triple helix‐coil transition was observed at around 127°C for U‐1 and above 130°C for M‐2 in the range of DMSO composition below about 70%. The transition temperature decreased with increasing DMSO concentration at above 70%, and the transition finally disappeared when the DMSO concentration exceeded 90%. The plot of Δhcal vs. t1/2 for the transition of both samples gave a linear relation, Δhcal = 0.253t – 10.58. The reversibility of the transition at lower temperature was demonstrated by the reversibility of the curves when the first heating was stopped before the second transition. Once the heating was performed over the second transition, the reheating DSC curves showed several endothermic peaks, indicating the irreversibility of the transition and heterogeneity in the conformation of the heated schizophyllan.
Dynamic light scattering measurements of the diffusion of probes in filamentous actin solutions
Authors: Newman Jay , Mroczka Nicholas , Schick Kenneth L.
Published: December 2004

The diffusion coefficients of monodisperse polystyrene latex spheres in solutions of polymerized actin were measured using dynamic light scattering. Four different probes with radii R, ranging from 50 to 500 nm, were separately used in actin solutions with concentrations c, ranging from 1.5 to 21 μM, which had been polymerized with either 1 mM MgCl2, 1mM CaCl2, or 100 mM KCl. Under all conditions, and at four different scattering angles in the range of 30°–90°, the measured average diffusion coefficients D of the probes were systematically smaller for samples of increased actin concentration or of increased probe radius. Control experiments indicated that the probes did not bind to the actin. These data for Mg2+‐ and Ca2+ ‐polymerized actin agree and were found to be quite well summarized by the scaling relation D/D0 = exp[–αRδCν], where D0 is the measured diffusion coefficient of the probes in water (and, as also measured, in the starting actin solutions prior to polymerization with added salt), with values of δ = 0.73 ± 0.05, ν = 1.08 ± 0.09, and α = (1.1 ± 0.6) × 10−3 (with c in μM and R in nm). Data for KCl‐polymerized actin show much more restricted diffusivities of the probes at comparable actin concentrations. Inhomogeneities in the solution are reflected in the “effective polydispersity” of the probe diffusion coefficients, which depend on local microviscosity differences.
Solvated helical backbones: X‐ray diffraction study of Boc‐Ala‐Leu‐Aib‐Ala‐Leu‐Aib‐OMe · H2O
Authors: Karle I. L. , Flippen‐Anderson J. L. , Uma K. , Balaram P.
Published: December 2004

A second example of insertion of a water molecule into the helical backbone of an apolar peptide is presented here and compared to a similar occurrence in a longer peptide with the same type of sequence of residues, i.e., Boc‐Aib‐(Ala‐Leu‐Aib)3‐OMe. The backbone of the title compound assumes an approximate 310‐helical form with three 4 → 1 hydrogen bonds. In the place of a fourth 4 → 1 hydrogen bond, a water molecule is inserted between O(1) and N(4), and acts as a bridge by forming hydrogen bonds N(4) … W(1) (2.95 Å) and W(1) … O(1) (2.81 Å). The water molecule participates in a third hydrogen bond with a neighboring peptide molecule, W(1) … O(4) (2.91 Å). The insertion of the water molecule causes the apolar peptide to mimic an amphiphilic helix. Crystals grown from ethyl acetate/petroleum ether (reported here) or from methanol/water solution are in space group P212121 with a = 12.024(4) Å, b = 15.714(6) Å, c = 21.411(7) Å, Z = 4 and dcalc = 1.124 g/cm3 for C32H58N6O9 · H2O. The overall agreement factor R is 6.3% for 2707 reflections observed with intensities > 3σ(F) and the resolution is 0.90 Å.
Comparison of α‐helix stability in peptides having a negatively or positively charged residue block attached either to the N‐ or C‐terminus of an α‐helix: The electrostatic contribution and anisotropic stability of the α‐helix
Authors: Takahashi Sho , Kim Eui‐Ho , Hibino Takeshi , Ooi Tatsuo
Published: December 2004

An estimation of the thermodynamic effects of a charged random coil, which is attached either to the N‐ or C‐terminus of polyalanine, upon α‐helix stability is attempted. A temperature‐induced helix‐coil transition of Ala20Lys20Phe and Lys20Ala20Phe was studied under various conditions of salt concentration and pH. By combining the results with previous ones for Ala20Glu20Phe and Glu20Ala20Phe, which have opposite electric charges to the present system [S. Ihara et al. (1982) Biopolymers 21, 131–145], the free energy of the coil to helix transition of the polyalanine block could be separated into two terms—one term for the electrostatic interaction of electric charges in the random‐coil block with the α‐helix dipole, and a second term for the intrinsic stability of the helix. The first term indicates the significance of the helix dipole‐charge interactions, which affects the helix stability depending on the attaching side of the charged block and on the sign of the charges. This clearly shows the anisotropic stability of the α‐helix. Furthermore, analysis of the dependence of these thermodynamic quantities on salt concentrations showed, assuming that the effect of the attached electric charges was symmetric (in other words, the absolute values of the electrostatic interaction terms were independent of the sign of electric charges), that the intrinsic stability of the α‐helix was dependent on which side of the helix was attached to the random coil: a random coil attached to the N‐terminus of the α‐helix had little effect while that attached to a C‐terminal significantly destabilized the helix.
Small‐angle x‐ray scattering studies of fibrin film: Comparisons of fine and coarse films prepared with thrombin and ancrod
Authors: Müller Michael F. , Ferry John D. , Lin J. S.
Published: December 2004

Measurements of small‐angle x‐ray scattering have been made on films prepared from fine and coarse (i.e., formed at high and low, respectively, pH and ionic strength) clots of bovine fibrin by osmotic shrinkage or compression in one dimension. Intensity profiles were obtained with pinhole geometry on films stretched up to a stretch ratio of 1.43. In unstretched coarse films, repeat spacings were seen at about 245, 120, and 77–80 Å. These peaks can probably be identified with the first, second, and third orders of the well‐known fibrin repeat of 225 Å. In unstretched fine films, only the 77–80 Å spacing was seen. In this case, the first two orders may be weak because the half‐staggered arrangement of monomer units giving rise to the 225 Å reflection is not reinforced by lateral aggregation of protofibrils; the third order may be strong since the molecular subdomains appear to divide the repeat roughly into thirds. After stretching, the 77–80 Å spacing persisted in the meridional direction but almost disappeared in the equatorial. Experiments on unstretched films prepared with ancrod substituted for thrombin gave similar results.
Temperature and concentration behavior of anomalous microwave resonances in DNA
Authors: Davis M. E. , Van Zandt L. L.
Published: December 2004

We have calculated the expected absorption of microwave radiation in the gigaHertz frequency range by fixed‐length DNA polymer molecules dissolved in saline solution. While the effects of counterions and solvent dynamics have been accounted for in detail, the features of the absorption are completely dominated by the interaction between the charged polymer and the so‐called first hydration layer, that is, the nearest layer of solvent water molecules not actually bonded to the polymer. The relevant parameters of the interaction are the strength of the water‐to‐polymer coupling and the average persistence time of the individual water‐to‐polymer bonds. These are presumably hydrogen bonds to the oxygen atoms of the backbone phosphate structure. Using a given parameterization we can obtain the structured absorption corresponding to compressional wave phonon excitations on the polymer, “organ pipe” modes, such as have been claimed to be seen by Edwards, Davis, Swicord, and Saffer. While further studies have not confirmed these resonances, at some frequency and hydration these modes must become visible because of the high relaxation time measured by Lindsay, the existence of the resonances in relatively dry fibers and films of DNA, and the existence of underdamped modes in the ir spectrum of DNA in solution.

We have examined the effects of varying slat concentration and the system temperature. In both cases the effects are virtually nil, in the former because of the Manning condensation phenomenon that preserves a remarkably constant polymer environment over a wide range of bulk ionic strength, and in the latter case because of a fortuitous competition between effects of bulk viscosity and persistence time changes with temperature. Hence any effects seen in the experimental variation of temperature or salinity could be wholly attributed to their modification of the hydration layer properties.
Properties of amidated pectins. II. Polyelectrolyte behavior and calcium binding of amidated pectins and amidated pectic acids
Authors: Racape E. , Thibault J. F. , Reitsma J. C. E. , Pilnik W.
Published: December 2004

The intrinsic pK values, as well as the free fractions of sodium and calcium counterions, were determined on salt‐free solutions of amidated pectinates and amidated pectates. The apparent pK values were non dependent of the degree of amidation but only to the effective charge density of the pectic polymers and an unique value of 2.9 ± 0.1 was found for the intrinsic pK value. The results obtained by conductimetry and with (sodium and calcium) specific electrodes showed a blockwise distribution of amide and acid groups in amidated pectates and a blockwise distribution of amide groups and a rather statistical distribution of acid groups in amidated pectinates.
Dielectric relaxation in synthetic melanin
Authors: Osak Władysław , Tkacz Katarzyna , Sławiński Janusz , Czternastek Halina
Published: December 2004

The charging and discharging currents were investigated in a synthetic melanin sample. The presence of long‐lasting dielectric relaxation was established. The steady state was reached after a long time, from 103 to 105 s, which depends both on temperature and voltage.

The temperature dependence of polarization was of an activation character (Eα = 0.67 eV). The kind of electrode material did not influence the current curves.
Bisintercalation of ditercalinium into a d(CpGpApTpCpG)2 minihelix: A 1H‐ and 31P‐NMR study
Authors: Delepierre M. , Dinh T. Huynd , Roques B. P.
Published: December 2004

The structure of the complex formed in aqueous solution between ditercalinium, a bisintercalating drug, and the self‐complementary hexanucleotide d(CpGpApTpCpG)2 is investigated by 400‐MHz 1H‐nmr and 162‐MHz 31P‐nmr. Whatever the drug to thlix ratio, ditercaliniun occurred in the bound form, whereas free and complexed hexanucleotide and are in slow exchange. This allows unambiguous resonance assignm, ent through two‐dimensional chemical exvhange experiments. The strong upfield shifts measured on most aromatic protons on both drug and bases as well as on DNA imino protons are consistent with bisintercalation of the dimer. Nuclear Overhauser effects observed between drug and nucleeotide protons give a defined geometry for complexation, and suggest a DNA conformational change upon drug binding.
Conformation‐Activity relationships of cyclic dermorphin analogues
Authors: Wilkes Brian C. , Schiller Peter W.
Published: December 2004

A theoretical conformational analysis (molecular mechanics study) of nine cyclic tetrapeptides, structurally related to the highly μ‐receptor‐selective dermorphin analogue , was performed. These compounds display considerable diversity in their μ‐receptor affinity and selectivity. A systematic search and subsequent energy minimization in absence of the exocyclic Tyr1 residue and Phe3 side chain revealed the constrained nature of the 11–13 membered ring structures contained in these analogues. No more than four low‐energy conformers (within 2 kcal/mol of the lowest energy conformation) were found in each case. After attachment of the Tyr1 moiety and Phe3 side chain to the “bare” low‐energy ring structures, a systematic search and energy minimization of these exocyclic moieties resulted in a limited number of low‐energy conformational families for all compounds. Five analogues with high μ‐receptor affinity—
magnified image,
(A2 bu: alpha;, γ‐diaminobutyric acid) and
magnified image
—all showed a tilted stacking interaction between the Tyr1 and Phe3 aromatic rings in the lowest or second lowest energy conformation found. The same kind of stacking was not possible in low‐energy conformers of the four analogues with poor affinity for the μ‐receptor
magnified image,
: [Nα‐methylphenylalanine], and
magnified image
It is concluded that a tilted stacking arrangement of the two aromatic rings may represent a structural requirement for high μ‐receptor affinity of the examined cyclic dermorphin analogues.
Use of t‐butyldimethylsilyl cyanoacetate for preparation of α‐cyano ketones
Authors: Ghosh Soumitra S.
Published: December 2004

The synthesis of t‐butyldimethylsilyl cyanoacetate and the reactions of its anion with acyl donors are described. The reagent was found to be the method of choice for the syntheses of α‐cyano ketone substrate analogues for carboxypeptidase A. These compounds have been shown to be potent mechanism‐based inactivators for the enzyme.
Enkephalin analogues containing β‐naphthylalanine at the fourth position
Authors: Mierke Dale F. , Said‐Nejad Odile E. , Schiller Peter W. , Goodman Murray
Published: December 2004

To examine the importance of the aromatic side chains of enkephalin on opiate activity, we report the synthesis and conformational analysis of a series of analogues related to enkephalin with β‐naphthylalanine in place of phenylalanine at the fourth position. Three linear analogues (Tyr‐D‐Ala‐Gly‐(L and D)‐β Nal(1)‐Leu‐NH2 and Tyr‐D‐Ala‐Gly‐β Nal(2)‐Leu‐NH2) were initially synthesized to examine the effect of the substitution on biological activity. The increased activity of these peptides at the μ‐opiate receptor, compared to native Leu‐enkephalin, prompted us to examine the more conformational constrained analogues, Tr‐c[D‐A2bu‐Gly‐(L and D)‐β Nal(1)‐Leu], incorporating a α,γ‐diaminobutyric acid at the second position and cyclization to the carboxylic end of the leucine. These two cyclic analogues provide insight into the necessity for the L chirality of the aromatic residue at position 4. The Tyr‐c[D‐A2bu‐Gly‐L‐β Nal(1)‐Leu] analogue is highly potent and displays a slight preference for the μ receptor. The conformational analysis indicates that despite the high flexibility of the tyrosine side chain, the aromatic rings of the tyrosine and naphthylalanine are relatively distant from each other. The presence of two intramolecular hydrogen bonds help maintain the conformation of the 14‐membered backbone ring that keeps the side chains directed away from each other. These findings are in agreement with our model of an extended structure required for μ selectivity and a folded form with close aromatic ring placement for δ selectivity.
SV40 Large T‐antigen nuclear signal analogues: Successful nuclear targeting with bovine serum albumin but not low molecular weight fluorescent conjugates
Authors: Lobl Thomas J. , Mitchell Mark A. , Maggiora Linda L.
Published: December 2004

The signal sequence of a nuclear‐directed protein encodes the necessary information for targeting the attached proteins to the cell nucleus. The sequence/structural requirements for a functional transport signal were explored with a series of peptides derived from the simian virus 40 large T‐antigen nuclear signal 126–134 (CPKKKRKVED‐NH2, wild type) conjugated to bovine serum albumin (BSA) through an N‐terminal Cys (1) with m‐maleimidobenzoyl‐N‐hydroxysuccinimide ester. Nuclear accumulation was virtually complete 15 min after microinjection into green monkey kidney cells (TC‐7). Peptides with Asn, Orn, and Gln substituted for Lys128, the reverse wild‐type peptide (DEVKRKKKPC‐NH2) and the long 34‐residue wild‐type analogue (CYDDEATADSQHSTPPKKKRKVEDPKDFESELLS‐NH2), were synthesized and conjugated similarly to BSA. The Orn peptide and the 34‐residue wild‐type analogue conjugated to BSA also transported to the nucleus but at a slower rate than 1. The reverse wild‐type, Asn‐ and Gln‐BSA conjugates of these signal analogues did not show transport to the nucleus after 6 h of incubation. In an effort to learn if such signal sequences would also target a small molecule such as a fluorescent tag to the nucleus, 1 fluorescently tagged with monobromobimane was prepared and microinjected into TC‐7 cells. The peptide was distributed throughout the cell. These results support the notion that a positively charged residue at position 128 is needed for rapid nuclear transport and that the intracellular transport machinery has spatial recognition. The results with fluorophore‐peptide conjugates suggest nuclear localization of these low molecular weight peptides will be difficult to attain even if attached to a functional nuclear localization sequence.
Applications of simulated annealing to peptides
Authors: Wilson Stephen R. , Cui Weili
Published: December 2004

We report the application of a new conformation searching algorithm called simulated annealing to the location of the global miniumum energy conformation of peptides. Simulated annealing is a Metropolis Monte Carlo approach to conformation of generation in which both the energy and temperature dependence of the Boltzmann distribution guides the search for the global minimum. Both uphill and downhill moves are possible, which allows the molecule to escape from local minima. Applications to the 20 natural amino acid “dipeptide models” as well as to polyalanines up to Ala80 are very successful in finding the lowest energy conformation. A history file of the simulated annealing process allows reconstruction and examination of the random walk around conformation space. A separate program, Conf‐Gen, reads the history file and extracts all low‐energy conformations visited during the run.
Synergism through direct covalent bonding between agents: A strategy for rational design of chemotherapeutic combinations
Authors: Rideout Darryl , Calogeropoulou Theodora , Jaworski James , McCarthy Michael
Published: December 2004

Self‐assembling chemotherapeutic agents are mixtures of relatively nontoxic precursors that can combine chemically under physiological conditions to form products with greater cytotoxic and/or antimicrobial activity than either of the precursors. Combinations that form products more rapidly in or near the target (tumor, pathogen, virally infected cell) than in normal tissues will exhibit target‐selective synergism, thus exhibiting an antitarget selectivity that is greater than the selectivities of the product (e.g., a hydrazone) and of either precursor (e.g., a hydrazine derivative or ketone) used singly.

This paper describes the target‐selective cytotoxic synergism of a cationic aldehyde (A) and a cationic acylhydrazine (B) containing a triarylalkylphophonium moiety against Ehrlich ascites carcinoma cells (ELA) in culture, in addition to reviewing previous work on self‐assembling cytotoxins. The synergism between A and B is carcinoma selective when the ELA cells (the target) are compared to CV‐1, A, B and the hydrazone C resulting from their reaction are lipophilic delocalized cations that selectively inhibit ELA growth relative to CV‐1 growth. The hydrazone C is more growth inhibitory than either A or B for both cell lines. A combination of A with an unreactive analogue of B and a combination of B with an unreactive analogue of A did not synergistically inhibit ELA proliferation. The degree of synergism is greater against the ELA cells than against the CV‐1 cells. These data, together with hydrazone formation kinetics, suggest that A and B are both concentrated together selectively inside the ELA due to the transmembrane potentials, reacting inside the ELA cells at a higher velocity than inside the CV‐1 cells to form the more growth‐inhibitory hydrazone C.
17O‐ and 14N‐nmr studies of Leu‐enkephalin and enkephalin‐related fragments in aqueous solution
Authors: Karayannis Theodoros , Gerothanassis Ioannis P. , Sakarellos‐Daitsiotis Maria , Sakarellos Constantinos , Marraud Michel
Published: December 2004

17O‐ and 14N‐nmr chemical shifts and line widths of the carboxyl and amino terminal groups of Leu‐enkephalin—Tyr‐Gly‐Gly‐Phe‐[17O]Leu‐Oh—and enkephalin‐related fragments—[17O]Leu‐OH, Phe‐[17O]Leu‐OH, Gly‐Phe‐[17O]Leu‐OH, and Gly‐Gly‐Phe‐[17O]Leu‐OH—were measured in aqueous solution over the entire pH range. Enrichment in 17O was achieved by saponification of the corresponding O‐methyl esters. Ionization constants and titration shifts were obtained by nonlinear least‐squares fits to one‐protion titration curves. [17O]Leu‐OH exhibits a profound pH‐dependent solvation change on deprotonation of the carboxyl group, as shown by 17O‐ and 14N‐nmr line widths. In contrast, the peptides studied do not exhibit pH‐dependent conformational (solvation) changes on deprotonation of the carboxyl group, and a head‐to‐tail intramolecular association between the ionic terminal groups should be excluded. It is shown that the peptides do not exhibit isotropic overall molecular motion and that segmental motion rather than fast internal motion influences the effective correlation times at the sites of the carboxyl oxygens and the amino nitrogen.
Assessment of protien reorientational diffusion in solution by 13C off‐resonance rotating frame spin–lattice relaxation: Effect of anisotropic tumbling
Authors: Morgan Courtesy F. , Schlieich Thomas , Caines G. Herbert , Michael David
Published: December 2004

The 13C off‐resonance rotating frame spin‐lattice relaxation technique is applicable to the study of protien rotational diffusion behaviour in a variety of experimental situations. The original formalism of James and co‐workers (1978) (J. Amer. Chem. Soc. 100, 3590–3594) was constrained by the assumption of random isotropic reorientational motion. Here we include in the formalism anisotropic tumbling, and present the results of computer simulations illustrating the differences between anisotropic and isotropic reorientational motion for the off‐resonance rotating frame spin–lattice relaxation experiment. In addition, We have included chemical shift anisotropy of the peptide carbonyl carbon as an additional relaxation mechanism contribution, to permit high field nmr protein rotational diffusion measurements.
Restrained energy refinement with two different algorithms and force fields of the structure of the α‐amylase inhibitor tendamistat determined by nmr in solution
Authors: Billeter M. , Schaumann Th. , Braun W. , Wüthrich K.
Published: December 2004

The solution structure of an α‐amylase inhibitor, tendamistat, calculated from nmr data with the distance geometry program DISMAN is subjected to restrained energy minimization. To study the influence of force field parametrizations and the convergence behavior of refinement algorithms, two different programs were used. AMBER is an established software package including a steepest descent and/or conjugent gradient optimizer in the Euclidian space; the name AMBER also represents a force field. The program FANTOM (fast Newton–Raphson torsion angle energy minimizer) is a new restrained energy refinement implementation of the Newton–Raphson algorithm, which uses second derivatives of the conformational energy in dihedral angle space with the ECEPP/2 force field. For both programs the normal energy force field was supplemented with an additional potential of the form ΣA(di − ui)6 (if di > ui), which enforces upper limits ui to selected distances di as measured by nmr. Improvements of the intramolecular interactions with a decrease of the internal energies of about 1000 kcal/mol could be achieved without increasing the distance constraint violations. The restrained energy refinements caused only small changes of the molecular geometries: The root mean square distance values for the backbone atoms between the initial DISMAN structure and the refined structures are about 0.5 Å for AMBER and about 0.7 Å for FANTOM. Local conformational changes during the restrained energy minimizations are analyzed with respect to hydrogen‐bond formation, and with respect to comparisons of the solution structure and the crystal structure.
Influence of solvent composition on the mechanical properties of arterial elastin
Authors: Winlove C. P. , Parker K. H.
Published: December 2004

We have investigated the effects of changes in solution composition on the mechanical properties of rings of arterial elastin. The time course of force equilibration at constant strain following a change in the composition of the bathing solution was measured. Both the force developed during slow extension and force relaxation following rapid straining were also measured in each of the test solutions. The results are difficult to summarize because all of the primitive quantities measured—sample dimension, slope of the force‐extension curve, force overshoot and time of relaxation—as well as the derived quantities such as elastic modulus changed in different and apparently uncorrelated ways. Changes in pH and ionic composition of the bathing solution had small effects consistent with the low fixed charge density of elastin. Solutions of glucose, sucrose, and ethylene glycol had larger effects consistent with changes in hydrophobic interactions. The viscosity of the solution that penetrated the intrafibrillar space of the elastin appeared to be a major determinant of the dynamic response.
A Monte Carlo simulation study of the aqueous hydration of r(GpC)2: Comparison with crystallographic ordered water sites
Authors: Subramanian P. S. , Pitchumani S. , Beveridge D. L. , Berman Helen M.
Published: December 2004

Monte Carlo computer simulation is described for the dinucleotide duplex rGpC together with 562 water molecules at an environmental density of 1 g/cc in a cubic cell under periodic boundary conditions. Water–water interactions were treated using the TIP4P potential and the solute water interactions by TIP4P spliced with the nonbonded interactions from the AMBER 3.0 force field. The simulation was subjected to proximity analysis to obtain solute coordinate numbers and pair interaction energies for each solute atom. Hydration density distributions partitioned into contributions from the major groove side, the minor groove side and the sugar–phosphate backbone were examined, and the probabilities of occurrence for one‐ and two‐water bridges in the simulation were enumerated. The results were compared with observations of crystallographic ordered water sites from x‐ray diffraction studies on G and C containing small molecules, and in crystal structure determinations of the sodium, calcium, and ammonium salts of rGpC. The calculated results are generally consistent with the observed sites, except for cytosine N4, where a hydration site is predicted yet none observed in rGpC salts, and for guanine N3, which appears in this calculation to compete unfavorably with the adjacent donor site at guanine N2. There is, however, a significant probability of finding a one‐water G‐N3–W–G‐N2 bridge indicated in the simulation. An explanation for the guanine N3 discrepancy in terms of electrostatic potentials is also offered. The calculated one‐and two‐water bridges in the rGpC hydration complex coincide in a number of cases to those observed in the ordered water structure of the sodium rGpC crystal hydrate.
Solvent effect on binding thermodynamics of biopolymers
Authors: Ben‐Naim A. , Ting K. L. , Jernigan R. L.
Published: December 2004

The indirect solvent‐induced effect on the free energy of binding of biopolymers is examined within the framework of classical statistical mechanics. We focus specifically on the role of the solute–solvent hydrogen bonding. In particular, we have estimated the first order solvent effedt on the indirect interaction between two biopolymers. We find that the solvent‐induced interactios between two hydrophilic groups through water‐bridged hydrogen bonds could significantly enhance the binding free energy. Some preliminary estimates indicate that this effect is significant and perhaps could be crucial in molecular recognition processes. Furthermore, we have calculated, from crystal structure data, the distance distribution between all the oxygens and nitrogens on the surface of some proteins that do not belong to the binding domain. In most cases we found an enhanced peak in the range of 4–5 Å, which is where we expect to find strong solvent‐induced interactions.
The relative contribution of electrostatic interactions to stabilization of collagen fibrils
Authors: Wallace Donald G.
Published: December 2004

Electrostatic energies of interaction between type I collagen molecules were calculated, using models developed by Timasheff and Hill. These energies, along with a contribution from hydrophobic forces, were then incorporated into an equation due to Flory that described phase equilibria of rod‐like polymers. The Flory formalism in turn permitted a calculation of the overall free energy of fibril formation (ΔFf), and an assessment of the relative contribution of electrostatic and hydrophobic forces to ΔFf. Lastly, ΔFf Lastly, ΔFf was used in a nucleation‐growth model relating halftimes of fibril formation (t1/2) to ionic strength (I) and temperature. Because the theory provided no basis for setting absolute levels of the energetic contributions, five parameters in the model had to be derived from experimental data. Based on the fit of theory to experimental results both for intact and pepsinized collagen, it was found that very low electrostatic energies (about −1 kcal/mole per collagen molecule) were sufficient to explain experimental t1/2 vs I relationships. This energy is equivalent to 1 close charge‐pair interaction per molecule and appears to be lower than the energy assignable to hydrophobic interactions.
Analysis of the charge distribution in the C‐terminal region of histone H1 as related to its interaction with DNA
Authors: Subirana Juan A.
Published: December 2004

We have studied the net positive charge distribution in the C‐terminal region of histone H1. We find that it is not random, but rather uniform. In most histone H1 sequences, 4 ± 1 positive charges are found in this region of the molecule in over 95% of all possible segments that are 10 amino acids long. Neither alternating sequences (basic–;nonbasic) nor more complex repeating sequences are ever found. Clusters of three or more basic amino acids are seldom observed in somatic H1s, yet their presence increases in sperm histones and even more so in protamines. It is concluded that the C‐terminal region of histone H1 has a remarkably uniform distribution of charge, in spite of its apparent variactions in sequence in different proteins and within individual molecules. The functional significance of these findings is discussed, suggesting a purely electrostatic role for the C‐terminal region of histone H1, which may be evenly wrapped around individual segments of DNA molecules, thus decreasin its net charge. A likely candidate for a long α‐helical region in the C‐terminal region of histone H1 from sea urchin spermatozoa also has been located. This region may contribute to the aggregating properties of this histone in sperm chromatin.
Block‐units method for conformational calculations of large nucleic acid chains. I. Block‐units approximation of atomic structure and conformational energy of polynucleotides
Authors: Vorobjev Yu. N.
Published: December 2004

A new block‐units method for rapid conformational calculation of large nucleic acid fragments has been developed. Atomic structure of polynucleotides has been approximated by the block‐units structure. Each monomer of the polynucleotide consists of three one‐center block units: phosphate, ribose, and nucleic base. Full conformational energy of the polynucleotide is separated into two parts. The first part is the energy of the short‐range interactions between adjacent block units and is calculated on the basis of the potential energy surface model of the dinucleotide fragment pXp (where × = A, G, T, U, C). The second part is the energy of the middle‐ and long‐range interactions between separated block units, and is calculated as a sum of the effective interaction energies between centers of the block units. The present block‐units method is in agreement within the range of ±0.5 kcal/mol with the method of the atom‐atom potentials, but the former is 30–100‐fold faster. The block‐units method is recommended for screening of the probable conformations of the large polynucleotide systems.
Thermodynamics of solvation of proteins in guanidine hydrochloride
Authors: Ahmad Faizan , Bigelow Charles C.
Published: December 2004

The interpretation of the thermodynamic quantities of solvation, that is, Gibbs free energy, enthalpy, and entropy changes for the transfer of proteins from water to 6M guanidine hydrochloride, in terms of the thermodynamic transfer parameters of the groups that make up the protein molecule, is unsatisfactory. We believe this is because the latter are assumed to be identical to the transfer parameters of similar groups attached to smaller model compounds (amino acids and dipeptides). We have empirically determined relationships between transfer quantities for individual protein components and similar groups in model compounds. Comparison of calculated values, based on the modified theory, with the experimental values, reveals very good agreement.