bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of basic oligopeptides on the B‐Z transition of poly(dG‐dC)·poly(dG‐dC) in water–methanol solutions
Authors: Votavová H. , Pírková J. , Gut V. , Šponar J. , Bláha K.
Published: December 2004

The effect of basic oligopeptides (Lys‐Ala‐Ala)n (n = 1–5, 10) and (Lys‐Leu‐Ala)n (n = 1–4) on the B‐Z transition of poly (dG‐dC)·poly (dG‐dC) in water–methanol solutions was investigated using CD and uv spectroscopy: In the absence of peptides, the concentration of methanol at the midpoint of the B‐Z transition is 64% at 25°C. The transition is temperature dependent and the B conformation is preferred at higher temperatures.

All peptides tested shift the midpoint of the B‐Z transition to lower concentrations of methanol. For shorter peptides this effect increases with an increasing number of monomeric units, showing the importance of the number of positive charges in the peptide molecule. At conditions of low methanol content, the trimer and tetramer of the (Lys‐Leu‐Ala)n series have a greater effect on the B‐Z transition than the corresponding oligomers of the (Lys‐Ala‐Ala)n series. This indicates an important influence of the presence of hydrophobic groups in the peptide side chains on the binding.

In the presence of peptides, the B‐Z transition is also temperature dependent and the B conformation is preferred at higher temperatures. The addition of peptides results in an increase of the transition midpoint and of the transition width. These parameters were used for the calculation of the transition enthalpy ΔHB‐Z in 65% methanol, which is −1.15 ± 0.25 kcal/base pair. Since the van't Hoff enthalpy ΔHVH calculated from the temperature dependence of the B‐Z transition in the absence of peptides is −130 kcal/mol, the length of the cooperative unit is about 110 base pairs. The results suggest that the mechanism of Z‐DNA induction is similar but not identical with that involved in the action of metal cations in aqueous solution.
1H‐ and 31P‐nmr studies of ditercalinium binding to a d(GCGC)2 and d(CCTATAGG)2 minihelices: A sequence specificity study
Authors: Delepierre Muriel , Milhe Catherine , Namane Abdelkader , Dinh Tam Huynh , Roques Bernard P.
Published: December 2004

The structures of the complexes formed in aqueous solution between ditercalinium, a bisintercalating drug, and both the self‐complementary tetranucleotide d(GCGC)2 and octanucleotided(CCTATAGG)2, have been investigated by 400‐MHz 1H‐nmr and 162‐MHz 31P‐nmr. All the nonexchangeable protons, as well as the exchangeable imino protons and the phosphorus signals, have been assigned. Both oligonucleotides have been shown to adopt a right‐handed B‐DNA type structure. The addition of ditercalinium to the oligo‐nucleotides lead to the formation of complexes in slow exchange at the nmr time scale with the free helices. At all drug‐to‐helix ratios studied, the ditercalinium was found in the bound form, whereas free and complexed oligonucleotides were in slow exchange, allowing resonance assignments through two‐dimensional chemical exchange experiments.

For d(GCGC)2 the strong upfield shifts induced on all aromatic protons of both the bases and the drug by complexation with ditercalinium suggest an interaction by intercalation of the two rings. However, the loss of twofold symmetry upon binding, as well as the chemical shift variation of the drug proton signals of one of the chromophores with temperature and concentration, favor a model in which the drug–nucleotide complexes have one ring of the drug intercalated and the other stacked on top of the external base pair. The intermolecular contacts between drug protons and nucleotide protons give a defined geometry for complexation that is consistent with the proposed model.

In contrast, with d(CCTATAGG)2 several drug–nucleotide complexes were formed and a large increase in line broadening was observed at high drug‐to‐DNA ratios, precluding a detailed analysis of these complexes. However, the large upfield shift in the imino proton resonances together with the shielding of the ditercalinium ring protons favor a model with bis‐intercalation of ditercalinium. This model is supported by the downfield shift of at least 4 out of 14 phosphorus signals. The results are compared with those obtained on ditercalinium binding to the homologous sequences d(CGCG)2 and d(TTCGCGAA)2, and discussed in terms of sequence specificity.
A sequence preference for nucleation of α‐helix—crystal structure of Gly‐L‐Ala‐L‐Val and Gly‐L‐Ala‐L‐Leu: Some comments on the geometry of leucine zippers
Authors: Chaturvedi Sanjeev , Go Kuantee , Parthasarathy R.
Published: December 2004

The synthetic peptide Gly‐L‐Ala‐L‐Val (C10H19N3O4·3H2O; GAV) crystallizes in the monoclinic space group P21, with a = 8.052(2), b = 6.032(2), c = 15.779(7) Å, β = 98.520(1)°, V = 757.8 Å3, Dx = 1.312 g cm−3, and Z = 2. The peptide Gly‐L‐Ala‐L‐Leu (C11H21N3O4·3H2O; GAL) crystallizes in the orthorhombic space group P212121, with a = 6.024(1), b = 8.171(1), c = 32.791(1) Å, V = 1614 Å3, Dx = 1.289 g cm−3, and Z = 4. Their crystal structures were solved by direct methods using the program SHELXS‐86, and refined to an R index of 0.05 for 1489 reflections for GAV and to an R index of 0.05 for 1563 reflections for GAL. The tripeptides exist as a zwitterion in the crystal and assume a near α‐helical backbone conformation with the following torsion angles: ψ1 = −150.7°; ϕ2, ψ2 = −68.7°, −38.1°; ϕ3, ψ31, ψ32, = −74.8°, −44.9°, 135.9° for GAV; ψ1 = −150.3°; ϕ2, ψ2 = −67.7°, −38.9°; ϕ3, ψ31, ψ32 = −72.2°, −45.3°, 137.5°, for GAL. Both the peptide units in both of the tripeptides show significant deviation from planarity [ω1 = −171.3(6)° and ω2 = −172.0(6)° for GAV; ω1 = −171.9(5)° and ω2 = −173.2(6)° for GAL]. The sidechain conformational angles χ21 and χ22 are −61.7(5)° and 175.7(5)°, respectively, for valine, and the side‐chain conformations χ12 and χ23's are −68.5(5)° and (−78.4(6)°, 159.1(5)°) respectively, for leucine. Each of the tripeptide molecule is held in a near helical conformation by a water molecule that bridges the NH and COO− groups, and acts as the fourth residue needed to complete the turn by forming two hydrogen bonds. Two other water molecules form intermolecular hydrogen bonds in stabilizing the helical structure so that the end result is a column of molecules that looks like an α‐helix.
The structure of [D‐Hyi2, L‐Hyi4]meso‐valinomycin revealed by X‐Ray analysis
Authors: Pletnev V. Z. , Mikhailova I. Yu. , Ivanova V. T. , Langs D. A. , Grochulski P. , Duax W. L.
Published: December 2004

Direct x‐ray analysis has been used to determine the crystal structure of [D‐Hyi2, L‐Hyi4]meso‐valinomycin {cyclo[‐D‐Val‐D‐Hyi‐L‐Val‐L‐Hyi‐(D‐Val‐L‐Hyi‐L‐Val‐D‐Hyi)2‐], C60H102N6O18}, which crystallized from acetone with two solvent molecules. The crystals are trigonal, space group P32, number of molecules per unit cell Z = 3, cell parameters a = b = 15.2085 (8) Å, c = 29.3250 (9) Å, γ = 120°. The standard (R)and weighted (Rw) reliability factors after refinement of the atomic coordinates for C, N, and O atoms in the anisotropic thermal motion approximation, allowing for isotropic H atom contributions, were 0.070 and 0.082, respectively. The molecule adopts a distorted bracelet structure which is stabilized by six NH …︁ OC 4 → 1 type intramolecular hydrogen bonds. The side chains predominantly occupy external pseudoaxial positions relative to the cylindrical axis of the molecule. In contrast to meso‐valinomycin, only four of the six Val carbonyl oxygen atoms are directed inwards to form a coordination centre for the molecule, and the carbonyl oxygen atoms of residues D‐Val1 and L‐Val3 are twisted outward and point away from the centre of the molecule. Although the analogue has a partially formed ion‐binding center, it is inaccessible because the hydrophobic isopropyl groups of the D‐Hyi2 and L‐Hyi4 residues screen the molecular cavity on both sides.
Differential scanning calorimetry studies of NaCl effect on the inverse temperature transition of some elastin‐based polytetra‐, polypenta‐, and polynonapeptides
Authors: Luan Chi‐Hao , Parker Timothy M. , Prasad Kari U. , Urry Dan W.
Published: December 2004

Differential scanning calorimetry studies of the effect of NaCl on protein‐based polymer self‐assembly has been carried out on six elastin‐based synthetic sequential polypeptides‐ i.e., the polypentapeptide (L‐Val1‐L‐Pro2‐Gly3‐L‐Val4‐Gly5)n and its more hydrophobic analogues (L‐Leu1‐L‐Pro2‐Gly3‐L‐Val4‐Gly5)n and (L‐Val1‐L‐Pro2‐L‐Ala3‐L‐Val4‐Gly5)n; the polytetrapeptide (L‐Val1‐L‐Pro2‐Gly3‐Gly4)n and its more hydrophobic analogue (L‐IIe1‐L‐Pro2‐Gly3‐Gly4)n; and the polynonapeptide (a pentatetra hybrid), (L‐Val1‐L‐Pro2‐Gly3‐L‐Val4‐Gly5‐L‐Val6‐L‐Pro7‐Gly8‐Gly9)n.

Previous physical characterizations of the polypentapeptides have demonstrated the occurrence of an inverse temperature transition since increase in order of the polypentapeptide, as the temperature is raised from below to above that of the transition, has been repeatedly observed using different physical characterizations.

In the present experiments, it is observed that the transition temperatures of the polypeptides studied are linearly dependent on NaCl concentration. The molar effectiveness of NaCl in shifting the transition temperature ΔTm/[N], is about 14°C/[N], with the dependence on peptide hydrophobicity being fairly small. Interestingly, however, the δΔQ/ [N] does depend on the hydrophobicity of a polypeptide.
Heat capacities of solid poly(amino acids). I. Polyglycine, poly(L‐alanine), and poly(L‐valine)
Authors: Roles K. A. , Wunderlich Bernhard
Published: December 2004

Heat capacities of polyglycine, poly(L‐alanine), and poly(L‐valine) were analyzed using approximate group vibrations and fitting of the skeletal vibrations to a two‐parameter (Θ1, Θ3) Tarasov function. New experimental data were measured by differential scanning calorimetry in the temperature range of 230–390 K. Good agreement between our experimental data and the calculated data was observed for all three poly(amino acids). Previous investigations showed agreement between calculation and reported experimental data for only limited low temperature ranges. At higher temperatures, discrepancies of up to 55% existed between experiment and calculation. The cause of this discrepancy must be assumed to be experimental error. Recommended experimental data are revised on the basis of this investigation. Computed heat capacities are available for the three biopolymers in the solid state from 0 to 1000 K.
Effects of proline ring conformation on theoretical π‐π* absorption and CD spectra of helical poly(L‐proline) forms I and II
Authors: Thomasson Kathryn A. , Applequist Jon
Published: December 2004

Absorption and CD spectra of the π‐π* transition near 200 nm are calculated for helical (Pro)10 forms I and II with a variable proline ring conformation characterized by torsion angle χ2 in the range −60° to 60°. The spectra for poly (Pro) I are not sufficiently sensitive to χ2 to suggest a preferred ring conformation. The spectra for poly (Pro) II are more sensitive to χ2, and suggest preferred ring conformations near either or both of the χ2regions −50 ± 10° and 50 ± 10°.
Dynamic light scattering from weakly bending rods: Estimation of the dynamic bending rigidity of the M13 virus
Authors: Song Lu , Kim Ug‐Sung , Wilcoxon Jess , Schurr J. Michael
Published: December 2004

A theory is presented for the dynamic structure factor [S(K, t)] of weakly bending rods. This treatment is based on a discrete bead model for the Brownian dynamics in which all bead motions associated with bending are constrained to occur in a plane perpendicular to the end‐to‐end vector, thus prohibiting extension or contraction along that axis. Preset hydrodynamic interactions are incorporated in a numerically exact manner. The predicted normalized dynamic structure factor S(K, t)/S(K, 0) should be valid for short times t such that the rms rotation of the end‐to‐end vector around any transverse axis is much less than 1.0 radian. With geometrical parameters appropriate for the M13 virus, the intensity autocorrelation function G(2)(K, t) = 1 + |S(K, t)/S(K, 0)|2 is calculated over a range of times and scattering vectors K for selected values of the persistence length P. The calculated G(2)(K, t) are fitted to a single exponential with unit baseline over the same range of times as the experimental photon correlation functions, and the apparent diffusion coefficients Dapp(K) are obtained from the best‐fit relaxation times. For the sake of completeness, an exact expression is derived for the apparent diffusion coefficient obtained from the initial slope of the dynamic structure factor. However, this does not reduce to the known correct result in the rigid rod limit. To obtain the correct result, the limit of infinite bending rigidity must be taken before the limit of zero time. For this and other reasons, the initial slope value of Dapp(K) is not useful for weakly bending rods.

Photon correlation functions are measured for the M13 virus, which is virtually identical to the often‐studied fd virus. The experimental photon correlation functions are fitted over 8 relaxation times to a single‐exponential plus baseline, and the Dapp(K) are calculated from the best‐fit relaxation times. Theoretical curves of Dapp(K) vs K2 for selected values of P are compared with the experimental data, which are satisfactorily reproduced when P = 22000 ± 2000 Å. This dynamic value is close to the static value, P = 20000 ± 2000 Å, reported for the very similar fd virus. The most recent theories of Maeda and Fujime and their dynamic light scattering studies of fd virus are compared with the present results in some detail. Their optimum value of P is in surprisingly good agreement with the present value.
1H‐ and natural abundance 15N‐nmr studies of a derivative of a rabies glycoprotein fragment
Authors: Molinari Henriette , Consonni Roberto , Pegna Monica , Zetta Lucia , Neri Paolo , Niccolai Neri , Bonci Alessandra , Lozzi Luisa , Rustici Mauro , Scarselli Maria
Published: December 2004

Using a combination of one‐ and two‐dimensional methods, 1H‐ and 15N‐nmr spectroscopy has been employed to perform the complete assignment and the structural determination of the immunogenic undecapeptide CTTTNSRGTTT in DMSO solution. Nuclear Over‐hauser enhancement spectroscopy experiments indicated the presence of secondary structures, mainly turn‐like structures, which only represent a family, albeit a dominant one, of an ensemble of conformations available to the peptide. Since reverse turns may play an important role as intermediates in protein folding, the experimental observations described here may link the immunological and theoretical approaches to protein folding.
Backbone cyclization: A new method for conferring conformational constraint on peptides
Authors: Gilon Chaim , Halle David , Chorev Michael , Selincer Zvi , Byk Gerardo
Published: December 2004

This article describes a new concept of medium‐ and long‐range cyclization of peptides through “backbone cyclization.” In this approach, conformational constraints are conferred on a peptide by linking ω‐substituted alkylidene chains replacing Nα or Cα hydrogens in a peptidic backbone. Backbone cyclization, which is divided into N‐backbone and C‐backbone cyclizations, allow for new modes of cyclization in addition to the classical ones that are limited to cyclization through the side chains and/or the amino or carboxyl terminal groups. The article also describes the application of the N‐backbone cyclization to the active region of substance P. Conformational constraints of this peptide by the classical cyclization modes led to inactive analogues whereas N‐backbone cyclization provided an active, selective, and metabolically stable analogue.
X‐Ray conformational study of hydrazino peptide analogues
Authors: Aubry André , Bayeul Daniel , Mangeot Jean‐Paul , Vidal Joëlle , Sterin Sébastien , Collet André , Lecoq Alain , Marraud Michel
Published: December 2004

We have solved the crystal structures of nine pseudo‐peptide analogues deriving from the hydrazino analogue of glycine or valine (NβH2‐NαH‐CαHR‐CO2H, R = H or iPr) or proline (NβH2‐Nα‐CαH‐CO2H) and containing the hydrazide (CO‐NβH‐Nα) or Nβ‐Z‐aminoamide peptidomimetic link. This study gives access to the average geometry of these two links, to their inter‐ and intramolecular interaction modes, and to their influence on the conformational properties of the molecules.
Information concerning the mechanism of electrophoretic DNA separation provided by quantitative video‐epifluorescence microscopy
Authors: Rampino Nicholas J.
Published: December 2004

Changes in conformation, length, and mobility of individual DNA molecules during agarose gel electrophbresis were measured using video micrographs obtained by epifluorescence microscopy. Globular, V‐shaped, and linear conformations of DNA are found. The mobility, upon transformation from the globular to the V‐shaped conformation, decreases, suggesting a collision with a gel fiber. The duration of interaction between DNA and gel fiber is proportional to the length of DNA. Hypothetically, this proportionality underlies the size separation of DNA by agarose gel electrophoresis.

DNA release from the gel fiber appears to involve the movement of the arms of the V‐shaped molecule around the gel fiber. Concomitant with this movement is a length reduction the degree of which is constant for DNA of various lengths in a particular buffer milieu. The luminant densitometric profiles of DNA molecules in the V conformation show maxima at the ends and apex of the V. The unequal distribution of nucleotides along the DNA chain appears to provide the driving force for the molecular movement around the gel fiber.
The cystine‐stabilized α‐helix: A common structural motif of ion‐channel blocking neurotoxic peptides
Authors: Kobayashi Yuji , Takashima Hiroyuki , Tamaoki Haruhiko , Kyogoku Yoshimasa , Lambert Paul , Kuroda Hisaya , Chino Naoyoshi , Watanabe Takushi X. , Kimura Terutoshi , Sakakibara Shumpei , Moroder Luis
Published: December 2004

Neurotoxic peptides from venoms of scorpions and honey bees exhibit a consensus pattern in the two disulfide bridgings related to the sequence portions Cys‐X‐Cys and Cys‐X‐X‐X‐Cys. A revised three‐dimensional structure of charybdotoxin, as determined by two‐dimensional nmr spectroscopy, confirms that the consensus cystine dislocation generates in all these toxins a common structural element, i.e., the cystine‐stabilized α‐helical (CSH) motif, which may be correlated with their common ion channel blocking activity.
Heat aggregation studies of phycobilisomes, ferritin, insulin, and immunoglobulin by dynamic light scattering
Authors: Singh Brahm Pal , Bohidar Himadri B. , Chopra S.
Published: December 2004

Dynamic laser light scattering studies on the heat aggregation behavior of phycobilisomes (PBS), ferritin, insulin, and immunoglobulin (IgG) in dilute aqueous solutions has been reported. Except for PBS, results are reported for heat aggregation trends in these proteins for three different pH environments (4.0, 7.5, 9.1). For PBS, studies were performed only in the neutral buffer medium (pH 7.5). The experiments were performed in the very dilute concentration regime (between 0.23 and 1.8 gL−1). For all these samples heat aggregation and dissociation trends were found to be linear with temperature. Upon temperature reversal (self‐cooling), hysteresis‐like behavior observed in insulin was found to be predominantly large at pH 7.5. PBS, ferritin, and IgG showed no such behavior at any of three pH values, and retraced their path of aggregation while dissociating on temperature reversal. Heat aggregation and dissociation processes in ferritin were found to be independent of pH. The IgG samples showed smooth aggregation tendency only up to 35°C in the buffer media pH 4.0 and 9.1, whereas for pH 7.0 the same could be observed until 60°C. Low polydispersity in the correlation spectra was observed in case of all these samples.
Conformational preferences of oligopeptides rich in α‐aminoisobutyric acid. II. A model for the 310/α‐helix transition with composition and sequence sensitivity
Authors: Basu Gautam , Kuki Atsuo
Published: December 2004

The analysis of the factors that control the helical folding of Aib‐rich peptides is extended to include sensitivity to sequence patterns, and in particular the presence of contiguous non‐Aib α‐mono‐alkylated residues. The distinct hydrogen‐bonding network of the 310−helix, as contrasted with that of the competing α‐helical structure, is explicitly incorporated into a theoretical model for the 310−helix/α‐helix equilibrium constant for a given peptide. Finite length effects and the “extra” intrahelical hydrogen bond of the 310 form are expressed naturally as a result of this loop analysis. This semiempirical model captures all the established features of existing empirical rules for helical conformational transitions in Aib‐rich sequences, as well as the recently detected helical transition induced solely by sequence permutation.
Molecular conformation of ascidiacyclamide, a cytotoxic cyclic peptide from Ascidian: X‐ray analyses of its free form and solvate crystals
Authors: Ishida Toshimasa , In Yasuko , Doi Mitsunobu , Inoue Masatoshi , Hamada Yasumasa , Shiori Takayuki
Published: December 2004

In order to investigate the conformational variation of ascidiacyclamide, a cytotoxic cyclic peptide from marine tunicate Ascidian, single crystals were prepared from ethanol and aqueous ethanol solutions as its free form (crystal I) and H2O/0.5 C2H5OH solvate (crystal II), respectively, and were determined by the x‐ray diffraction method. Crystal I showed a pseudo C2‐symmetric saddle‐shaped rectangular conformation. Similar conformations were also observed in crystal II, where there were two crystallographically independent C2‐symmetric molecules (named Mol‐A and ‐B) per asymmetric unit. Mol‐A and ‐B included H2O and H2O/C2H5OH solvents within their ring structures, respectively. These water and ethanol molecules were located on the crystallographic dyad axes, and were stabilized by the van der Waals contacts (including hydrogen bonds) with the polar‐ring N atoms and nonpolar D‐Val side‐chain atoms. The conformational characteristics of ascidiacyclamide and its fluctuation/variation were discussed based on the present and previously reported x‐ray results.
Bound water in the collagen‐like triple‐helical structure
Authors: Lazarev Yuri A. , Grishkovsky Boris A. , Khromova Tatyana B. , Lazareva Alisa A. , Grechishko Vera S.
Published: December 2004

The ir amide bands of the triple‐helical polytripeptides and collagens upon hydration of films are investigated. On the basis of our assignment of the amide I components, the formation of hydrogen bonds between the peptide backbone and structural water is studied. The C1O1—HOH hydrogen bonds are found more ordered than the C3O3—HOH hydrogen bonds. The specific incorporation of water in the triple helix is followed by multistep conformational changes and by increasing of the interpeptide hydrogen‐bond strength. The formation of the polypeptide hydrate structure depending on the amino acid composition and the chain length is examined.
Peptide models for the membrane destabilizing actions of viral fusion proteins
Authors: Epand Richard M. , Cheetham James J. , Epand Raquel F. , Yeagle Philip L. , Richardson Christopher D. , Rockwell Arlene , Degrado William F.
Published: December 2004

The fusion of enveloped viruses to target membranes is promoted by certain viral fusion proteins. However, many other proteins and peptides stabilize bilayer membranes and inhibit membrane fusion. We have evaluated some characteristics of the interaction of peptides that are models of segments of measles and influenza fusion proteins with membranes. Our results indicate that these models of the fusogenic domains of viral fusion proteins promote conversion of model membrane bilayers to nonbilayer phases. This is opposite to the effects of peptides and proteins that inhibit viral fusion. A peptide model for the fusion segment of the HA protein of influenza increased membrane leakage as well as promoted the formation of nonbilayer phases upon acidification from pH 7–5. We analyze the gross conformational features of the peptides, and speculate on how these conformational features relate to the structures of the intact proteins and to their role in promoting membrane fusion.
Conformation of uteroglobin fragments
Authors: Mammi Stefano , Foffani Maria Teresa , Improta Sabina , Tessari Marco , Schievano Elisabetta , Peggion Evaristo
Published: December 2004

The conformation of three fragments of uteroglobin in aqueous solution and in the presence of SDS micelles is described. Two of these fragments correspond to helix II and helix III of uteroglobin, the crystal structure of which is made of four helices. The third peptide comprises helices II and III, with the connecting β‐turn. While helix II does not interact strongly with the micelles, helix III adopts a rather clear α‐helix in this system. The elongation of helix III with the addition of helix II at the N‐terminus somewhat stabilizes the ordered structure. It is possible that the β‐turn found in the crystal is also present in solution.
Conformational analysis of an opioid peptide in solvent media that mimic cytoplasm viscosity
Authors: Temussi Piero Andrea , Picone Delia , Saviano Gabriella , Amodeo Piero , Motta Andrea , Tancredi Teodorico , Salvadori Severo , Tomatis Roberto
Published: December 2004

Many neuropeptides exert their action between the presynaptic vesicles and postsynaptic transmembrane receptors, crossing different layers of specialized cytoplasm. Biomimetic media usually employed to study bioactive peptides do not reproduce the physico chemical environment of cytoplasm—in particular, the high viscosity of this biological fluid. Here we describe a Conformational study of a δ‐selective opioid peptide, deltorphin I, at variable temperatures in several biocompatible media characterized by varying values of viscosity and dielectric constant. It was found that only viscosity, among these parameters, induces ordered conformations; that is, it acts as a Conformational sieve. This finding suggests that the high viscosity of the intersynaptic fluid contributes, in addition to the membrane catalysis proposed by Schwyzer, in overcoming the so‐called entropic barrier to the transition state of peptide–receptor interaction by selecting ordered conformations prior to receptor interaction.

The folded conformer found in the 80 : 20 (v : v) DMSOd6/H2O cryoprotective mixture at 265 K has a shape consistent with those of rigid nonpeptidic opiates.
Hydrophobicity‐induced pK shifts in elastin protein‐based polymers
Authors: Urry Dan W. , Peng Shao Qing , Parker Timothy M.
Published: December 2004

Three polypentapeptides—poly[0.8(GVGVP), 0.2(GEGVP)], poly[0.8(GVGIP), 0.2‐(GEGIP)], and poly[0.75(GFGVP), 0.25(GEGVP)]—all analogues of the polypenta‐peptide of elastin—(Val1‐Pro2‐Gly3‐Val4‐Gly5)n or poly(VPGVG)—have been prepared to determine the effect of changing the hydrophobicity, i.e., Val1 → Ile1 (I) and Val4 → Phe4 (F), on the pKa and the temperature dependence of pKa of the Glu (E) residue. Shifts in pKa as large as 1.7 units are observed and the temperature dependence is much steeper for the structure‐dependent proximity of the more hydrophobic Ile1 residues to the Glu4 residue. Even though this system is dominated by the inverse temperature transition of hydrophobically driven folding on raising the temperature, the effect of adding 0.15 N NaCl is to suppress the hydrophobicity‐induced pKa shift.
NMR studies of structure and dynamics of isotope enriched proteins
Authors: Wagner Gerhard , Thanabal V. , Stockman Brian J. , Peng Jeffrey W. , Nirmala N. R. , Hyberts Sven G. , Goldberg Matthew S. , Detlefsen David J. , Clubb Robert T. , Adler Marc
Published: December 2004

Structural studies of globular proteins by nmr can be enhanced by the use of isotope enrichment. We have been working with proteins enriched with 15N, and with both 15N and 13C. Due to the isotope enrichment we could assign several large proteins with up to 186 residues and could address structural questions. Furthermore, we can accurately measure heteronuclear and homonuclear vicinal coupling constants. This involves in part multidimensional multiple resonance experiments. This is important for characterization of minor conformational changes caused by mutations. We have also made use of isotope enrichment to study the internal mobility of proteins. We also have developed novel methods for measuring accurately 15N relaxation parameters, in particular transverse relaxation rates. This has led us toward a method for directly mapping spectral density functions of the rotational motions of N–H bond vectors in proteins. The protein systems that are discussed include the unlabeled proteins kistrin and cytochrome c551, and the labeled proteins eglin c, a flavodoxin, and human dihydrofolate reductase.
The two‐stranded α‐helical coiled‐coil is an ideal model for studying protein stability and subunit interactions
Authors: Zhou Nian E. , Zhu Bing‐Yan , Kay Cyril M. , Hodges Robert S.
Published: December 2004

We have designed de novo a two‐stranded α‐helical coiled‐coil which consists of two identical 35‐residue polypeptide chains arranged in a parallel and in‐register alignment. Their structure is stabilized by interchain hydrophobic interactions from hydrophobes at positions “a” and “d” of a repeating heptad sequence. The formation and stability of the coiled‐coil is dependent on peptide concentration due to the monomer‐dimer equilibrium. In contrast, the coiled‐coil containing an inter‐helical disulfide bond does not show any concentration dependence in the guanidine hydrochloride denaturation experiments as expected. Replacement of one large hydrophobic Leu residue in each chain with Ala significantly decreases coiled‐coil stability in both the reduced and oxidized coiled‐coils [decreases in transition midpoint of 1.6M (2.3 − 0.7) and 2.4M (5.3 − 2.9), respectively]. A large pH dependence on coiled‐coil stability is observed over the pH range 4 to 7 (transition midpoints at pH 4, 5, 5.5, 6 and 7 were 3.8, 3.2, 2.0, 1.2 and 0.7M, respectively). The increasing stability with decreasing pH correlates with the protonation of the Glu acid side‐chains and reduction of intrachain repulsions between Glu‐Glu side‐chains in positions i, i + 3 or i, i + 4 along each α‐helix of the coiled‐coil. In addition, coiled‐coil stability increases with increasing ionic strength.
Determination of the ϕ angle in a peptide backbone by NMR spectroscopy with a combination of homonuclear and heteronuclear coupling constants
Authors: Schmieder Peter , Kessler Horst
Published: December 2004

The ϕ angle in a cyclic peptide is determined by the combined use of homonuclear and heteronuclear coupling constants. Two of the four coupling constants that define the ϕ angle in a peptide are determined exactly, two qualitatively. Via Karplus‐type equations, they are transformed into dihedral angles and a good agreement is found, allowing for a determination of the ϕ angle with a certain range of degrees.
The structure of a rhombohedral R6 insulin hexamer that binds phenol
Authors: Smith G. D. , Dodson G. G.
Published: December 2004

Different hexameric forms of insulin have been crystallized from a variety of conditions. In the presence of 1% phenol, 1.0 M sodium chloride, and at a pH of 8.5, a rhombohedral form is produced with two monomers in the asymmetric unit, space group R3, a = 79.92 Å and c = 40.39 Å. The structure has been solved and refined, using data between 8.0 and 2.5 Å resolution, to a residual of 0.157. Each of the monomers adopts an R conformation, that is residues B1–B8 are α‐helical. As a result of the T to R transition, an elliptical cavity is created between symmetry–related monomers and is occupied by a phenol molecule. A region of density within bonding distance to one of the zinc ions has been interpreted as an additional phenol molecule.
A new constraint potential for the structure refinement of biomolecules in solution using experimental nuclear overhauser effect intensity
Authors: Stawarz Bernard , Genest Monique , Genest Daniel
Published: December 2004

A new constraint potential is proposed for the refinement of the three‐dimensional structure of biomolecules in solution from nmr data. It is based on the nuclear Overhauser effect (NOE) intensity calculations, taking into account the spin diffusion phenomenon. For restrained energy minimization or molecular dynamics techniques, a constraint potential term expressed as a function of the negative inverse of the sixth power of the NOE intensities (NOE−1/6) is added to the classical potential energy function. The properties of this new NOE constraint potential are discussed and compared to those of a harmonic NOE intensity potential.

The method integrated in the molecular modeling program GROMOS is tested on the regular α‐helical structure of a decaglycylpeptide.
Solution structures of cyclic and dicyclic analogues of growth hormone releasing factor as determined by two‐dimensional NMR and CD spectroscopies and constrained molecular dynamics
Authors: Fry David C. , Madison Vincent S. , Greeley David N. , Felix Arthur M. , Heimer Edgar P. , Frohman Lawrence , Campbell Robert M. , Mowles Thomas F. , Toome Voldemar , Wegrzynski Bogda B.
Published: December 2004

Solution structures were determined for a linear analogue of growth hormone releasing factor (GRF), and cyclic and dicyclic analogues in which the side chains of aspartyl and lysyl residues spaced at positions i‐(i + 4) were joined to form a lactam. The four analogues were [Ala15]‐GRF‐(1–29)‐NH2 and its cyclo8–12, cyclo21–25, and dicyclo8–12;21–25 derivatives. The peptides were studied in two solvent systems: 75% methanol/25% water at pH 6.0; and 100% water at pH 3.0. CD spectroscopy was used to assess the overall α‐helical content. Nuclear magnetic resonance spectroscopy was used to determine the structures in more detail. Nearly complete proton resonance assignments were made for each of the peptides, in both solvents. Nuclear Overhauser effects were converted into distance constraints and applied in the molecular dynamics program CHARMM to evaluate the range of low‐energy structures that satisfied the nmr data. In 75% methanol, all of the peptides are comprised of a single α‐helical segment with fraying of one to three residues at each end. The linear analogue has a tendency to kink. In water, the analogues have two helical segments with flexible regions between them and at the termini of the peptides. The linear analogue is helical at residues 7–14 and 21–28. In the cyclo8–12 analogue, the N‐terminal helical region extends to include residues 7–19, while the other helical region is slightly shortened. In the cyclo21–25 analogue, the C‐terminal helical region is extended to include residues 19–28, while the N‐terminal helical region is destabilized. The dicyclic analogue has the largest N‐terminal helix, spanning residues 7–20, but its helical segment at residues 21–28 is not well ordered. All of the analogues exhibit substantial biological activity. The cyclic and dicyclic analogues show dramatically increased resistance to degradation during incubation with human plasma. The i−(i + 4) lactam, therefore, appears to be a synthetic means of stabilizing a local α‐helical conformation, which may be of general use in the design of active, stable peptides.
Molecular structure of cyclo[‐(D‐Val‐L‐Hyi‐L‐Val‐D‐Hyi)2‐] revealed by X‐ray analysis
Authors: Grochulski P. , Smith G. D. , Langs D. A. , Duax W. L. , Pletnev V. Z. , Ivanov V. T.
Published: December 2004

The crystal structure of a synthetic analogue of valinomycin, cyclo [‐(D‐Val‐L‐Hyi‐L‐Val‐D‐Hyi)2‐] (octa‐meso‐valinomycin) (I) (C40H68N4O12 · 1.5 · C4H8O2, Mr = 937.01 + 88.10), has been determined. Crystals grown from dioxane are monoclinic, space group P21/a, with cell parameters a = 21.487(8), b = 16.836(5), c = 16.089(4) Å, β = 111.70(4), and Z = 4. The atomic coordinates for nonhydrogen atoms were refined in the anisotropic thermal motion approximation. H atom positions were included in the structure factor calculations at their geometrically expected positions. Values of the standard and weighted R factors after refinement are 0.11 and 0.13, respectively. The conformation of the depsipeptide crystallized from dioxane is different from that crystallized from chloroform (II). The molecule adopts a rectangular shape with two type IV β–turns containing a hydrogen bond and possesses pseudorotational symmetry. The side chains are located on the molecular periphery. The orientation of the carbonyl groups of the molecule is not conducive for efficient metal‐ion coordination and in the observed conformation cannot behave as an ionophore.

In the crystal the molecules form infinite chains parallel to the c axis, and are stabilized by two intermolecular hydrogen bonds that are shorter and have better geometry than the intramolecular hydrogen bonds.

A ϕ/Ψ plot for dodecadepsipeptides with a (DLLD)3 sequence has well‐defined areas for Val and Hyi residues only in cases when the crystals have been grown from nonpolar or medium‐polar solvents. The Φ/Ψ plot for octadepsipeptides crystallized from chloroform (II) shows this behavior also. There also is a correlation between the polarity of the solvent from which crystals of octa‐meso‐valinomycin or valinomycin analogues with a (DLLD) sequence of configuration have been grown and the number of the intramolecular hydrogen bonds that are formed. The more polar the solvent the fewer the number of intramolecular hydrogen bonds.

Empirical energy calculations on octa‐meso‐valinomycin indicate that for isolated molecules, the energy of the bracelet form (II) is 4.7 kcal/mole lower than that of the rectangular form (I).
Vibrational CD studies of interchain hydrogen‐bonded tripodal peptides
Authors: Paterlini M. Germana , Freedman Teresa B. , Nafie Laurence A. , Tor Yitzhak , Shanzer Abraham
Published: December 2004

The solution conformations of three trispeptides—L,L,L‐1,3,5‐C6H3[CH2NHCOCH(X)‐NHBoc]3, X = CH3 (Ala) or CH2CH (CH3)2 (Leu), and L,L,L‐N{CH2CH2NHCOCH [CH2‐CH(CH3)2]NHBoc}3—have been determined from their ir and vibrational CD (VCD) spectra in the NH stretching and carbonyl stretching regions in apolar solution. The compounds containing L‐Leu are shown to occur primarily in a propeller conformation with C3 symmetry that is stabilized by interchain hydrogen bonds. Through application of the coupled oscillator model of VCD, a right‐handed sense for the hydrogen‐bonded chains in the propeller is deduced, in agreement with previous empirical force field calculations. The spectra also provide evidence for interchain association between two chains, resulting in a C10‐ring. For chains not involved in interchain association, the spectra reveal the presence of C7‐rings within a chain. The trispeptide containing L‐Ala is found to occur primarily in a random form.
Elongational flow studies on DNA in aqueous solution and stress‐induced scission of the double helix
Authors: Atkins E. D. T. , Taylor M. A.
Published: December 2004

Elongational flow techniques are used to investigate the birefringent response and flow‐induced molecular scission of monodisperse phage‐DNA samples in aqueous solution. A 4‐roll mill apparatus was used to characterize the solutions ac low stain rates, \documentclass{article}\pagestyle{empty}\begin{document}$ \dot \varepsilon $\end{document} ≤ 300 s−1, and the opposed jets apparatus used to study fracture of the DNA molecules at strain rates up to 15 × 103 S−1. The molecular weight values were measured before and after fracture in elongational flow using the high‐resolution technique of pulsed field gel electrophoresis (PFGE). The birefringent response incorporates both rigid and flexible components. The birefringence is nonlocalized and rises gradually to a plateau value, similar to rigid‐rod behavior. In addition a certain minimum value in the strain rate is necessary, an onset value \documentclass{article}\pagestyle{empty}\begin{document}$ \dot \varepsilon $\end{document}0, before the signal appears, indicating a flexible component. This behavior is consistent with a hinged‐rod model and is similar to that observed for the protein collagen molecule at elevated temperature. We propose that this type of behavior is likely for multistrand rope‐like macromolecules where localized separation or partial untwisting of the intertwined chains occurs, creating temporary hinges, in accordance with biochemical evidence for sequence‐specific sites of flexibility. Results are presented on the entanglement effects at high concentrations. We have calculated rotational diffusion rates as a function of concentration and molecular weight. Using PFGE to measure the molecular weight profiles, our fracture studies at high strain rates demonstrate chain halving and quartering in accordance with the predictions of the thermally activated barrier to scission theory for single‐chain polymers.
The contribution of residue ion pairs to the helical stability of a model peptide
Authors: Stellwagen Earle , Park Soon‐Ho , Shalongo William , Jain Ashu
Published: December 2004

Comparative CD measurements were made on the model helical peptides acetyl‐YEAAAKEAXAKEAAAKAamide and acety1YEAAAEKAXAKEAAAKAamide in which X represents a nonaromatic nonionic residue. The former peptide contains three potential i, i + 4 complementary ion pairs at neutral pH, while the latter peptide contains one potential complementary and two potential antagonistic i, i + 4 ion pairs. The effect of pH and ionic strength on the mean residue ellipticity of these peptides was measured at 222 nm and 0°C. These measurements were analyzed assuming a common two‐state helix/ coil transition and only i, i, + 4 ion‐pair interactions. The analyses suggest that the central ion pairs do modulate helical content while the peripheral ion pairs do not, presumably due to the location of the peripheral ion pairs in the frayed ends of the helix. The complementary central ion pair stabilizes the helix by about 0.4 kcal/mole and the antagonistic central ion pair destabilizes the helix by about 0.2 kcal/mole. © 1992 John Wiley & Sons, Inc.
Combined use of homo‐ and heteronuclear coupling constants as restraints in molecular dynamics simulations
Authors: Mierke Dale F. , Kessler Horst
Published: December 2004

A penalty function for scalar coupling constants has been applied in molecular dynamics simulations as an experimental constraint. The function is based on the difference between the coupling constant calculated from the dihedral angle and the experimentally measured coupling constant. The method is illustrated on a model cyclic pentapeptide for which 3JHN‐Hα and 3JHN‐Cβ, both about the ϕ backbone dihedral angle, have been measured. The function is efficient in producing structures consistent with the scalar couplings, but removed from the conformation observed in solution. This arises from the lack of J restraints for the ψ dihedral angle. Simulation with both nuclear Overhauser effect (NOE) and J‐coupling restraints illustrates small but significant differences from simulations using only NOEs. © 1992 John Wiley & Sons, Inc.
Molecular dynamics conformational search of six cyclic peptides used in the template assembled synthetic protein approach for protein de novo design
Authors: Floegel Rainer , Mutter Manfred
Published: December 2004

Six cyclic peptides, designed to act as topological templates in the TASP (template assembled synthetic protein) approach in protein de novo design, were investigated employing a 100‐ps, 900‐K molecular dynamics conformational search. The peptides are composed of two Lys‐X‐Lys (X = Gly, Ala) tripeptides connected at its N‐ and C‐terminal end by a Pro‐Gly motif and a cystine bridge (I), two Pro‐Gly units (II), naphthalene derivatives (III), and tetrahydronaphthalene derivatives of different stereochemistry (IV‐VI). The molecular dynamics conformational search established that template I had β‐sheet like geometry. Templates II‐VI showed different preferential geometries, among them, e.g., distinct preferences for type V turns in Pro‐Gly containing peptides and close spatial arrangement of hydrophobic naphthalene moieties. The orientation of the lysine side chains within preferential geometries of the individual templates is analyzed and a tentative evaluation for their potential to stabilize TASP molecules of 4‐helix bundle topology is given. © 1992 John Wiley & Sons, Inc.
A molecular thermodynamic approach to predict the secondary structure of homopolypeptides in aqueous systems
Authors: Chen Chau‐Chyun , Zhu Yizu , King Jonathan A. , Evans Lawrence B.
Published: December 2004

Under physiological conditions, many polypeptide chains spontaneously fold into discrete and tightly packed three‐dimensional structures. The folded polypeptide chain conformation is believed to represent a minimum Gibbs energy of the system, governed by the weak interactions that operate between the amino acid residues and between the residues and the solvent.

A semiempirical molecular thermodynamic model is proposed to represent the Gibbs energy of folding of aqueous homopolypeptide systems. The model takes into consideration both the entropy contribution and the enthalpy contribution of folding homopolypeptide chains in aqueous solutions. The entropy contribution is derived from the Flory‐Huggins expression for the entropy of mixing. It accounts for the entropy loss in folding a random‐coiled polypeptide chain into a specific polypeptide conformation. The enthalpy contribution is derived from a molecular segment‐based Non‐Random Two Liquid (NRTL) local composition model [H. Renon and J. M. Prausnitz (1968) AIChE J., Vol. 14, pp. 135–142; C.‐C. Chen and L. B. Evans (1986) AIChE J., Vol. 32, pp. 444–454], which takes into consideration of the residue‐residue, residue‐solvent, and solvent‐solvent binary physical interactions along with the local compositions of amino acid residues in aqueous homo‐polypeptides. The UNIFAC group contribution method [A. Fredenslund, R. L. Jones, and J. M. Prausnitz (1975) AIChE J., 21, 1086–1099; A. Fredenslund, J. Gmehling, and P. Rasmussen (1977) Vapor‐Liquid Equilibrium Using UNIFAC, Elsevier Scientific Publishing Company, Amsterdam], developed originally to estimate the excess Gibbs energy of solutions of small molecules, was used to estimate the NRTL binary interaction parameters.

The model yields a hydrophobicity scale for the 20 amino acid side chains, which compares favorably with established scales [Y. Nozaki and C. Tanford (1971) Journal of Biological Chemistry, Vol. 46, pp. 2211–2217; E. B. Leodidis and T. A. Hatton (1990) Journal of Physical Chemistry, Vol. 94, pp. 6411–6420]. In addition, the model generates qualitatively correct thermodynamic constants and it accurately predicts thermodynamically favorable folding of a number of aqueous homopolypeptides from random‐coiled states into α‐helices. The model further facilitates estimation of the Zimm‐Bragg helix growth parameter s and the nucleation parameter s for amino acid residues [B. H. Zimm and J. K. Bragg (1959) Journal of Chemical Physics, Vol. 31, pp. 526–535]. The calculated values of the two parameters fall into the ranges suggested by Zimm and Bragg. © 1992 John Wiley & Sons, Inc.