bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis, crystal structure, and molecular conformation of N‐Ac‐dehydro‐Phe‐L‐Val‐L‐Val‐OCH3
Authors: Narula P. , Khandelwal B. , Singh T. P.
Published: December 2004

The peptide N‐Ac‐dehydro‐Phe‐L‐Val‐L‐Val‐OCH3 (C22H31N3O5) was synthesized by the usual workup procedure and finally by coupling the N‐Ac‐dehydro‐Phe‐L‐Val‐OH to valine methyl ester. It was crystallized from its solution in acetonitrile‐water mixture at 4°C. The crystals belong to the space group P1 with a = 8.900(3) Å, b = 11.135(2) Å, c = 12.918(2) Å, α = 90.36(1)°, β = 110.14(3)°, γ = 90.10(3)°, V = 1207.7(6) Å,3 Z = 2, dm = 1.156(5) Mgm−3, dc = 1.148(5) Mgm−3. The structure was determined by direct methods using SHELXS86. The structure was refined by full‐matrix least‐squares procedure to an R value of 0.077 for 3916 observed reflections. The molecular dimensions and conformations of the two crystallographically independent molecules are in good agreement. In the dehydro residues, the average Cα–Cβ distance is 1.31(2) Å whereas the bond angle Cα–Cβ–Cγ is 132(1)°. The average backbone torsion angles are ω0 = 169(1)°, ϕ1 = −40(1)°, ψ1 = −50(1)°, ω1 = −177(1)°, ϕ2 = 54(1)°, ψ2 = 46(1)°, ω2 = −174(l)°, ϕ3 = 103(1)°, ψ = −139(1)°, and θ = −176(1)°. The acetyl group is in the trans conformation, while the backbone adopts a right‐handed and left‐handed helical conformation alternatingly. The two crystallographically independent molecules are held together by three hydrogen bonds: N21–H21–O′12 = 2.911(12) Å, N22–H22–O′11 = 2.941(12) Å and N23–H23–O11 = 3.005 (9) Å. The crystal structure is stabilized by van der Waals forces and three additional hydrogen bonds: N11–H11–O2, = 2.896(15) Å, N12–H12–O′21 = 2.947(14) Å and N13–H13–O21 = 2.987(15) Å.
Mass‐weighted molecular dynamics simulation of cyclic polypeptides
Authors: Mao Boryeu , Maggiora G. M. , Chou K. C.
Published: December 2004

A modified molecular dynamics (MD) method in which atomic masses are weighted was developed previously for studying the conformational flexibility of neuroregulating tetra‐peptide Phe‐Met‐Arg‐Phe‐amide (FMRF‐amide). The method has now been applied to longer and constrained molecules, namely a disulfide‐linked cyclic hexapeptide, c [CYFQNC], and its linear and [pseudo‐cyclic] analogues. The sampling of dihedral conformational space of the linear hexapeptide in mass‐weighted MD simulations was found to be improved significantly over conventional MD simulations, as in the case of the shorter FMRF‐amide molecule studied previously. In the cyclic hexapeptide, the internal constraint of the molecule due to the intramolecular disulfide bond (hence the absence of free terminals in the molecule) does not adversely affect the significant improvement of conformational sampling in mass‐weighted MD simulations over normal MD simulations. The pseudo‐cyclic polypeptide is identical to the linear CYFQNC molecule in amino acid sequence (i.e., side chains of the cysteine residues are reduced), but the positions of its two terminal heavy atoms were held fixed in space such that the molecule has a nearly cyclic conformation. For this molecule, the mass‐weighted MD simulation generated a wide range of polypeptide backbone conformations covering the internal dihedral degrees of freedom; moreover, the physical space of the pseudo‐cyclic structure was also sampled in a complete revolution of the entire molecular fragment about the two fixed termini during the simulation. These characteristics suggest that mass‐weighted MD can also be an extremely useful method for conformational analyses of constrained molecules and, in particular, for modeling loops on protein surfaces.
Drug–DNA interactions: Spectroscopic and footprinting studies of site and sequence specificity of elliptinium
Authors: Mauffret Oliver , Rene Brigitte , Convert Odile , Monnot Monique , Lescot Elie , Fermandjian Serge
Published: December 2004

The binding of the antitumoral ellipticine derivative 2‐methyl‐9‐hydroxyellipticinium acetate (elliptinium; NMHE) to DNA was analyzed by the combined use of DNase I foot‐printing and spectroscopic methods. Using two fragments of pBR322 DNA, five discrete NMHE binding sites of 5–7 protected base pairs (bp) were detected by footprinting at 4°C on the analyzed regions. These corresponded to alternating pyrimidines and purines. The inactive derivative 2‐methyl ellipticinium acetate L(NME) lacking a hydroxy group failed to demonstrate DNA protection even at low temperature. Ultraviolet‐absorption and 1H‐nmr analysis was performed using two autocomplementary octanucleotides d(TGACGTCA) (I) and d(ACTGCAGT) (II). The uv‐absorption titrations resulted in an intercalative binding mode for NMHE in the oligomers. Analysis of the derived biphasic Scatchard plots yielded two binding sites corresponding to ∼6‐bp and 2‐bp sizes and characterized by apparent association constants K1 ∼ 108M−1 and K2 ∼ 106M−1, respectively. The 1H‐nmr analysis of exchangeable (imino) protons and nonexchangeable protons performed in the one‐ and two‐dimensional modes confirmed the intercalation of NMHE, and further revealed the existence of multiple sites on DNA. Assuming that imino resonance line width concerned the sole kinetic effects, 10‐ms order lifetimes were estimated for the drug–oligonucleotide complexes at 7°C, pH 7, and 0.1 ionic strength. Finally examination of every drug–DNA spectra in the light of the footprinting results indicated that there was a preference for binding of NMHE to the CpG (octamer I) and TpG (octamers I and II) steps.
Anti‐insulin antibody structure and conformation. I. Molecular modeling and mechanics of an insulin antibody
Authors: Nell Laura J. , McCammon J. Andrew , Subramaniam Shankar
Published: December 2004

A knowledge‐based three‐dimensional model of an anti‐insulin antibody, 125, was constructed using the structures of conserved residues found in other known crystallographic immunoglobulins. Molecular modeling and mechanics were done with the 125 amino acid sequences using QUANTA and CHARMm on a Silicon Graphics 4D70GT workstation. A minimal model was made by scaffolding using crystallography coordinates of the antibody HyHEL‐5, because it had the highest amino acid sequence homology with 125 (84% light chain, 65% heavy chain). The three hypervariable loop turns that are longer in 125 than in HyHEL‐5 (L1, L3, and H3) were modeled separately and incorporated into the HyHEL‐5 structure; then other amino acid substitutions were made and torsions optimized. The 125 model maintains all the structural attributes of an antibody and the structures conserved in known antibodies. Although there are many polar amino acids (especially serines) in this site, the overall van der Waals surface shape is determined by positions of aromatic side chains. Based on this model, it is suggested that hydrogen bonding may be key in the interaction between the human insulin A chain loop antigenic epitope and 125.
Conformational analysis of a dinucleotide photodimer with the aid of the genetic algorithm
Authors: Blommers Marcel J. J. , Lucasius Carlos B. , Kateman Gerrit , Kaptein Robert
Published: December 2004

The solution structure of the photodimer cis, syn‐dUp [ ]dT is derived with the aid of the genetic algorithm. The conformational space available for the molecule is sampled efficiently using the computer program DENISE and tested against a set of constraints available from nmr experiments. The dominant conformation in solution found with this approach can be described by the following combinations of sugar‐phosphate backbone torsion angles: ε (t), ζ(t), α(+), β(–ac), and γ(t). The conformation of the sugars and glycosidic torsion angles are S type and syn, respectively. The cyclobutane ring and pyrimidines are puckered. In addition, other conformations that exist in equilibrium with the first are found. It is concluded that the cyclobutane‐pyrimidine system is rigid, whereas the sugar‐phosphate backbone is flexible. The solution structures are compared with the crystal structure of the strongly related cyano‐ethyl ester of cis, syn‐dTp [ ]dT.
Conformation and charge distribution of bicyclic β‐lactams: Structure–activity relationships
Authors: Fernández Berta , Carballiera Luís , Ríos Miguel A.
Published: December 2004

The structures of 7‐oxo‐1‐azabicyclo[3.2.0] heptane and its 4‐oxa, 3‐ethylene‐4‐oxa, and 3‐ethylene‐6‐methyl‐4‐oxa derivatives, and of 8‐oxo‐1‐azabicyclo[4.2.0] octane and its 5‐oxa derivative, were studied by ab initio methods. Conformations were refined without constraints using the 4‐21G and the 4‐21G* basis sets, and energies and charge distributions were improved by single‐point 6‐31G*/4‐21G* calculations. The results are interpreted in terms of structural trends related to β‐lactamase inhibitor capability.
Helix‐forming tendencies of amino acids depend on the restrictions of side‐chain rotamer conformations: Crystal structure of the tripeptide GAI in two crystalline forms
Authors: Go Kuantee , Chaturvedi Sanjeev , Parthasarathy R.
Published: December 2004

In our attempts to design crystalline α‐helical peptides, we synthesized and crystallized GAI (C11H21N3O4) in two crystal forms, GAI1 and GAI2. Form 1 (GAI1) Gly‐L‐Ala‐L‐Ile (C11H21N3O4 · 3H2O) crystals are monoclinic, space group P21 with a = 8.171(2), b = 6.072(4), c = 16.443(4) Å, β = 101.24(2)°, V = 800 Å3, Dc = 1.300 g cm‐3 and Z = 2, R = 0.081 for 482 reflections. Form 2 (GAI2) Gly‐L‐Ala‐L‐Ile (C11H21N3O4 · ½H2O) is triclinic, space group P1 with a = 5.830 (1), b = 8.832 (2), c = 15.008(2) Å, α = 102.88 (1), β = 101.16(2), γ = 70.72(2)°, V = 705 Å3, Z = 2, Dc = 1.264 g cm−3, R = 0.04 for 2582 reflections. GAI1 is isomorphous with GAV and forms a helix, whereas GAI2 does not. In GAI1, the tripeptide molecule is held in a near helical conformation by a water molecule that bridges the NH+3 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 incipient a‐helix. GAI2 imitates a cyclic peptide and traps a water molecule. The conformation angles χ11 and χ12 for the side chain are ( –63.7°, 171.1°) for the helical GAI1, and (–65.1°, 58.6°) and (–65.0°, 58.9°) for the two independent nonhelical molecules in GAI2; in GAI1, both the C, atoms point away from the helix, whereas in GAI2 the Cγ atom with the g+ conformation points inward to the helix and causes sterical interaction with atoms in the adjacent peptide plane. From these results, it is clear that the helix‐forming tendencies of amino acids correlate with the restrictions of side‐chain rotamer conformations. Both the peptide units in GAI1 are trans and show significant deviation from planarity [ω1 = –168(1)°; ω2 = –171(1)°] whereas both the peptide units in both the molecules A and B in GAI2 do not show significant deviation from planarity [ω1 = 179.3(3)°; ω2 = –179.3(3)° for molecule A and ω1 = 179.5(3)°; omega;2 = –179.4 (3) ° for molecule B], indicating that the peptide planes in these incipient α‐helical peptides are considerably bent.
β‐Alanine containing peptides: A novel molecular tool for the design of γ‐turns
Authors: Pavone V. , Lombardi A. , D'auria G. , Saviano M. , Nastri F. , Paolillo L , Di Blasio B. , Redone C.
Published: December 2004

In the present paper we describe the synthesis, purification, single crystal x‐ray analysis, and solution conformational characterization of the cyclic tetrapeptide cyclo‐ (L‐Pro‐γ‐Ala‐L‐Pro‐γ‐Ala). This peptide was synthesized by classical solution methods and the cyclization of the free tetrapeptide was accomplished in good yields in diluted methylene chloride solution using N, N‐dicyclohexyl‐carbodiimide (DCCI). The compound crystallizes in the orthorombic space group P212121 from ethyl acetate. All peptide bonds are trans. The molecular conformation is stabilized by two intramolecular hydrogen bonds between the CO and NH groups of the two β‐alanine residues. These hydrogen bonds take part in a C7 structure in which both proline residues occupy the 2 position of an inverse γ‐turn. The two β‐alanine residues have a typical folded conformation (around the Cα‐Cβ bond) observed in other cyclic peptides containing this residue. A detailed 1H‐nmr analysis in CD3CN solution has been carried out. The molecule assumes a twofold symmetry in solution with a molecular conformation consistent with that observed in the solid state.
The low‐temperature heat capacity of solid proteins
Authors: Edelman Jay
Published: December 2004

Several harmonic models of protein fluctuations are used to calculate the heat capacity. They get the spectral density of conformational modes from inelastic neutron scattering, normal mode calculations, or macroscopic elasticity (Debye model). It is assumed that the low‐frequency spectral density depends only weakly on temperature and protein species. The Debye model predicts temperatures below which modes are primarily in their ground states: 10 and 80 K for the lattice and conformational modes, respectively. The models differ most below 100 K. The mode calculations yield the most accurate predictions, though all three models are within twofold of the data. The heat capacity has the power law form aTb for T < 30 K. The experimental b's of proteins are 1.6–1.8, and the theoretical, 1.1–1.3. One possible explanation for the discrepancy is the occurrence of transitions between discrete conformations. All of the models approach the measured data in the range 100–200 K. They are very similar above 200 K, where the heat capacity includes significant contributions from bond stretching and bending. This masks the possible anharmonic behavior of the conformational modes. Hydration substantially increases the heat capacity above 200 K. This effect seems to be a consequence of conformational transitions that have higher energy than the ones seen with low hydration. The analysis also predicts that denaturation with constant hydration produces a negligible increase of heat capacity. The larger increment in solution arises from the different hydration of the folded and unfolded states, and is responsible for the existence of cold denaturation. This phenomenon is thus predicted not to occur when the hydration is constant.
Variations in the turn‐forming characteristics of N‐Acyl proline units
Authors: Liang Gui‐Bai , Rito Christopher J. , Gellman Samuel H.
Published: December 2004

We have examined intramolecular hydrogen bonding in four homologous compounds, N‐acetyl‐, N‐propionyl‐, N‐i‐butyryl‐, and N‐pivaloyl‐proline‐methylamide, in methylene chloride, by means of 1H‐nmr and ir measurements. At room temperature, the major trans conformer of MeCO‐Pro‐NHMe appears to be approximately 68% intramolecularly hydrogen bonded, the trans conformers of EtCO‐Pro‐NHMe and i‐PrCO‐Pro‐NHMe are approximately 75% intramolecularly hydrogen bonded, and t‐BuCO‐Pro‐NHMe is approximately 50% intramolecularly hydrogen bonded. Thus, the internally hydrogen‐bonded state (C7 or γ‐turn) is significantly less populated for the N‐pivaloyl compound than for the other three molecules in this series. Variable temperature measurements indicate that for each proline derivative there is very little enthalpic difference between the intramolecularly hydrogen‐bonded and nonhydrogen bonded states of the trans rotamer. Changing the N‐terminal acyl group also affects intramolecular hydrogen bonding (including β‐turn formation) in end‐blocked Pro‐Gly dipeptides.
Conformational study of endothelins and sarafotoxins with the cystine‐stabilized helical motif by means of CD spectra
Authors: Tamaoki Haruhiko , Kyogoku Yoshimasa , Nakajima Kiichiro , Sakakibara Shumpei , Hayashi Mitsuo , Kobayashi Yuji
Published: December 2004

A series of CD measurements were carried out on members of peptides in the endothelin and sarafotoxin families. The helical structures taken by these peptides containing the helical motif with the sequences of Cys‐X‐X‐X‐Cys and Cys‐X‐Cys [Y. Kobayashi et al. (1991) Neurochemistry International Vol. 18, pp. 525–534] are classified into three groups: a group of structures of ET‐1, ET‐2 and vasoactive intestinal contractor (VIC), a group of sarafotoxin, and a group of ET‐3.
Minimum energy conformations of proline‐containing helices
Authors: Polinsky Alexander , Goodman Murray , Williams Karen A. , Deber Charles M.
Published: December 2004

Proline occurs frequently in transmembrane α‐helices of transport and receptor proteins even though statistical surveys demonstrate the overwhelming preference of this residue for a non‐α‐helical, hydrophilic environment. As a result, membrane‐buried proline has been proposed to be functionally important, with function arising from structural discontinuity or destabilization of the helix. Destabilization may occur by Promediated conformational transitions between discrete states, and may be manifested in membrane protein systems through reversible processes such as channel opening and closing or signal transduction. In this study, computer modeling of a model transmembrane α‐helix, (Ala)8‐Leu‐Pro‐Phe‐(Ala)8, in a medium of low polarity (dielectric = 2), is used to examine the occurrence and energetic accessibility of Pro‐mediated conformational interconversions. Leu ψ and χ1, Pro ψ and Phe ϕ and χ1 torsion angles were assigned random values so that a data base of 200 conformations for each of the cis and trans states was generated. The conformations were minimized and low‐energy structures organized into families. This analysis demonstrated that the most populated lowest energy family is the Trans‐I conformation, corresponding to proline in a kinked α‐helix. Two additional trans structures, Trans‐II and Trans‐III, as well as a cis conformation, Cis‐I, are also energetically competitive. Interconversions between the trans states could thus be mediated by changes at a single torsion angle, accompanied by minor local hydrogen‐bonding rearrangements. This work substantiates that membrane‐buried proline can provide the basis for conformational transitions between discrete α‐helix‐based structures in a nonpolar environment.
Peptidomimetics as receptors agonists or peptidase inhibitors: A structural approach in the field of enkephalins, ANP and CCK
Authors: Roques Bernard P.
Published: December 2004

Stabilization of biologically active conformations of native peptides by cyclization or in‐troduction of hindering residues led to peptidominetics endowed with high affinity and selectivity for one class of receptors and able to cross the blood brain barrier. This is the case of BUBU, Tyr‐D‐Ser(OtBu)‐Gly‐Phe‐Leu‐Thr(OtBu) and BUBUC, Tyr‐D‐Cys‐(OtBu) ‐Gly‐Phe‐Leu‐Thr (OtBu) for the opioid δ receptors and of BC 254, Boc‐γ‐D Glu‐Tyr (SO3H)‐Nle‐D Lys‐Trp‐Nle‐Asp‐PheNH2 and of BC 264, Boc‐Tyr(SO3H) gNle‐mGly‐Trp‐MeNle‐Asp‐PheNH2 for central CCK‐B receptors. Inhibition of metabolizing peptidases such as aminopeptidase N and endopeptidase 24.11 (NEP) for enkephalins and of NEP and ACE for atrial natriuretic peptide and angiotensin I by mixed inhibitors such as kelatorphan and RB 101 or ES14, rationally designed by taking into account the structural differences in the active site of these zinc‐metallopeptidases, led to potent analgesics devoid of the major morphine side effects or to new antihypertensives.
Critical analysis of objections against the biological molecular energy machines
Authors: Křemen Alexandr
Published: December 2004

In the past, two important objections against McClare's idea of biological molecular energy 4 machines were raised. One of the criticisms was concerned with the origin of energy gained in ATP cleavage and with an interpretation of McClare's “excited vibrational state.” The former argument reveals a failure of the critics to comprehend McClare's approach. As to the excited vibrational state, it can be identified with nonequilibrium conformational states of the unit rather than with a single vibrational mode. The other criticism based on Brillouin's energy cost of measurement argued that reversible operation of biological molecular energy machines would be virtually impossible. Using propagation velocities of deformations of the unit's structure (instead of velocity of light), the objections against reversibility are invalidated even in the framework of the critic's approach. McClare's idea and relevant definitions are thus physically correct.
Plausible view on the biological molecular energy machines
Authors: Křemen Alexandr
Published: December 2004

A qualitative picture of operation modes of biological molecular energy machines is presented. It is suggested that there is mutual control between the flow of molecular energy stored in a biological molecular energy machine and the sequence of nonequilibrium conformational states through which the machine passes in doing work. If the structure of the conformational space is favorable, the set of trajectories in this space decomposes into two families, each of which accomplishes another task. This divergence of trajectories enables to distinguish molecular objects according to differences in interaction between the machine and the object, i.e., to perform a measurement on a molecular object and process the object according to the result of that measurement.
Hydrophobic interaction between globin helices
Authors: Weaver David L.
Published: December 2004

The interhelical interfaces have been examined in seven high‐resolution globin chains. The profiles of hydrophobic contact, as measured by the residue solvent‐accessible area loss upon folding, have been calculated. The seven globins studied differ in their overall loss of solvent‐accessible area upon packing of their helices, the order being 1MBD > 1LH1 > 1ECD > 2MHBB > 2HHBB > 2HHBA > 2MHBA, which gives a measure of the difference in stability due to the hydrophobic interaction. The five helix‐pair packings (AH, BE, BG, FH and GH) examined in detail have qualitative similarities. There are, however, substantial quantitative differences both at the equivalent residue level and at the level of overall helix–helix contact, which has significance in some models of folding. The AH pair has the most uniform area loss over the seven globins and the largest variation in accessible area loss on packing among the five helix pairs is the GH pair. The set of residues required to produce the globin fold has been deduced from the residue area losses.
Crystal and molecular structure of the depsipeptide ionophore Hexadecaisoleucinomycin, cyclo‐[‐(D‐Ile‐L‐Lac‐L‐Ile‐D‐Hyi)4‐] (C80H136N8O24)
Authors: Pletnev V. Z. , Ivanov V. T. , Langs D. A. , Strong P. , Duax W. L
Published: December 2004

The crystal structure of a synthetic depsipeptide ionophore hexadecaisoleucinomycin, cyclo[‐(D‐Ile‐L‐Lac‐L‐Ile‐D‐Hyi)4‐] (C80H136N8O24), has been determined by single crystal x‐ray diffraction techniques. The crystals are orthorhombic, space group P212121, number of molecules per unit cell z = 4, and cell parameters a = 11.195, b = 17.853, c = 54.835 Å. The values of the standard ( R) and weighted ( Rw ) discrepancy factors after refinement are 0.122 and 0.135, respectively. The structure is characterized by an elongated bracelet form with a twofold axis of pseudosymmetry. It is stabilized by eight intramolecular 4 → 1 hydrogen bonds between the amide CO and NH groups. The ester carbonyls are directed toward the inside of the molecule, their oxygen atoms forming an ellipsoidal internal cavity. The side chains are located on the molecular periphery. The conformational states of hexadecaisoleucinomycin in solution are discussed in the light of the data obtained.
Presence of a thermostable domain in the helical part of the type I collagen molecule and its role in the mechanism of triple helix folding
Authors: Burjanadze Tengiz V. , Bezhitadze Manama O.
Published: December 2004

A study has been done of the effect of neutral salts (NaCl and CaCl2) on the mechanism of type I collagen triple helix folding and unfolding in concentrated acetic acid solutions (2–8.8M). It is shown that in these conditions, thermoabsorption and secondary structure change in heated solutions proceed in two consecutive stages. Salts exert a different destabilizing effect on different sites of the macromolecule, promoting the detection of a thermostable domain. The presence of a thermostable domain permits one to carry out reversible denaturation of collagen and to study the mechanism of the triple helix folding. Proceeding from the mechanism of the triple helix folding, an assumption has been made on the localization of the thermostable domain and its biological role.
Aggregates and other particles as the origin of the “extraordinary” diffusional phase in polyelectrolyte solutions
Authors: Ghosh Snehasish , Peitzsch Robert M. , Reed Wayne F.
Published: December 2004

The “extraordinary” diffusional phase (EP) at low ionic strength, and the conditions for 1 its removability by filtration were investigated for dilute solutions of the following linear polyelectrolytes: poly(L‐lysine), heparin, chondroitin‐6‐sulfate, hyaluronate, polystyrene sulfonate, and variably ionized polyacrylamide. The EP was not present for all the different types studied, and for heparin, for example, the phase was present only for samples from certain sources. In all cases the phase was removable by filtration through sufficiently small pore‐size membranes. Once filtered, the EP remained absent for over one week. It is concluded that the extraordinary diffusional phase consists of fairly stable polyelectrolyte aggregates, and sometimes also includes other very small particulate impurities. These aggregates and other small particles are thought to be present, or at least nascent, in the dry polyelectrolyte material, so that their properties may depend critically on the manner in which such dry material is produced. Tests for “reversibility” of the EP by cycling between high and low Cs by dialysis further confirm these conclusions. The evidence is thus against the EP representing any type of temporal aggregates or local ordering, at least for the linear polyelectrolytes studied in this work Rather, due to the extremely feeble scattering of ordinary polyelectrolytes at low ionic strength, the weak scattering from residual aggregates and other particles, not removed by ordinary filtration and centrifugation procedures, give autocorrelable scattering signals with long decay times. The “loss” of the extraordinary phase as ionic strength increases appears to be due simply to the weak EP scattering signal getting buried in the sharply increasing scattering from the ordinary polyelectrolyte phase. Model calculations based on experimental data support this latter conclusion. © 1992 John Wiley & Sons, Inc.
The electrostatic potential for the phosphodiester group determined from X‐ray diffraction
Authors: Klooster W. T. , Craven B. M.
Published: December 2004

The charge density distribution in the crystal structure of ammonium dimethylphosphate at 123 K has been determined from x‐ray diffraction data (MoKα) using 8437 reflections with sin θ/λ < 1.33.Å−1 [NH · (CH3)2PO, Mr = 143.08, monoclinic, P21/c, a = 10.007(1), b = 6.926(1), c = 9.599(2) Å, β = 105.40(1) °, V = 641.4(3) Å3, Z = 4, F000 = 304, Dx = 1.4815 g· cm−3, µ = 3.726 cm−1]. Least‐squares structure refinement assuming Stewart's rigid pseudoatom model (variables including Slater‐type radial exponents and electron populations for multipole terms extending to octapoles for C, N, O, and P, and dipoles for H) gave R(F2) = 0.039 for all reflections. The dimethylphosphate anion is in the gauche‐gauche conformation and has approximate twofold symmetry. One phosphoryl O atom forms three hydrogen bonds and the other forms one. Neither of the ester O atoms is hydrogen bonded. For the dimethylphosphate anion isolated from the crystal structure, a map of the electrostatic potential obtained using the pseudoatom charge parameters shows that the phosphoryl O atoms are considerably more electronegative than the ester O atoms. The electrostatic potential distribution obtained in this way has been fitted by least squares to a system of atom‐centered point charges. The potential calculated from these point charges agrees with the experimental result. It also agrees reasonably well with potentials obtained from three other systems of point charges that are widely used as part of the semiempirical force field for molecular mechanics and molecular dynamics calculations involving nucleic acids. © 1992 John Wiley & Sons, Inc.
α‐Elastin coacervate as a protein liquid membrane: Effect of pH on transmembrane potential responses
Authors: Kaibara K. , Sakai K. , Okamoto K. , Uemura Y. , Miyakawa K. , Kondo M.
Published: December 2004

A protein liquid membrane composed of coacervated α‐elastin, a chemical fragmentation product of the biological elastic fiber protein, functioned as an amphoteric liquid ion‐exchange membrane. Ionic permselectivities of the α‐elastin coacervate membrane to a series of metal chlorides were investigated for the concentration‐cell systems by the ordinary electrochemical measurements. Effects of pH on the transmembrane potential responses for NaCl, CaCl2, and MgCl2 systems were examined. Only in the Ca2+ ‐containing system did potential responses stay at constant levels against the pH changes, whereas in the other systems, increasing pH caused potential changes, indicating a improvement of cationic permselectivity across the α‐elastin coacervate membrane. It was suggested that the characteristic Ca2+ transport mechanisms across the α‐elastin coacervate membrane are related in some way to the polypeptide backbone interactions specific and selective to Ca2+ ions. © 1992 John Wiley & Sons, Inc.
Salt bridge induced changes in the secondary structure of ionic polypeptides
Authors: Ismail Ashraf A. , Mantsch Henry H.
Published: December 2004

The carboxylate‐containing homopolypeptides poly(L‐glutamate) [poly(Glu)] and poly(L‐aspartate) [poly(Asp)] were found to form different types of ordered structures in the presence of poly(L‐lysine) [poly(Lys)]. Mixing poly(Glu) with poly(Lys) in aqueous solution at neutral pH results in the instantaneous formation of a gel‐like precipitate. The secondary structure of the gel precipitate can be best described as intermolecular antiparallel β‐strands, involving the backbone amide groups, as evidenced by the presence of characteristic amide I bands in the ir spectrum at 1684 and 1612 cm−1. Mixing poly (Asp) with poly(Lys) under identical conditions results in the formation of a fine precipitate with a different morphology. Examination of the ir spectrum of the precipitate revealed that unlike poly(Glu), poly (Asp) did not yield any discrete secondary structure upon precipitation with poly(Lys). Addition of solutions containing Ca2+ or Mg2+ to the poly (Glu)/poly (Lys) aggregates resulted in complete dissolution of the gel, with the disappearance of the ir bands characteristic of the intermolecular hydrogen‐bonded network. The results demonstrate the importance of salt bridges in establishing strong hydrogen bonds between the backbone amide groups. Reaggregation occurred upon heating the poly (Glu)/poly (Lys) mixture in the presence of Ca2+, but not in the presence of Mg2+ ions. In the presence of Ca2+ ions, aggregation and formation of an extended hydrogen‐bonded network occurred upon heating. The aggregates formed upon heating poly (Glu)/poly (Lys) in the presence of Ca2+ were attributed solely to complexation of Ca2+ to the carboxylate groups of poly (Glu) with poly (Lys) remaining free in solution. Dissolution of the aggregate could be accomplished through addition of Mg2+ at room temperature. © 1992 John Wiley & Sons, Inc.
Facilitated synthesis of peptaibols: Alamethicin via enzymatic segment condensation
Authors: Slomczynska Urszula , Zabrocki Janusz , Kaczmarek Krzysztof , Leplawy Miroslaw T. , Beusen Demise D. , Marshall Garland R.
Published: December 2004

We have used a combined chemical‐enzymatic approach to facilitate the total synthesis of the 20‐residue peptaibol, alamethicin. The 1–11 segment of alamethicin, having a C‐terminal Gly, and the 12–20 segment, having an N‐terminal Leu, were prepared by well‐established chemical methods, and then coupled using papain to afford a 54% yield of alamethicin in straightforward fashion. In contrast to the reported chemical syntheses of alamethicin requiring side‐chain protection at Glu, 18 the papain‐catalyzed coupling proceeded readily and selectively using a C‐terminal segment having a free γ‐carboxyl group at this position. Several alamethicin partial sequences were obtained via enzymatic formation of the Gly 11−Leu12 bond. The high efficiency of this route is illustrated by the enzymatic assembly of the 1–17 alamethicin fragment on a 400–mg scale in 62% yield. An alternative route to alamethicin through enzymatic formation of the Ala6−Gln7 bond was less successful because of a low yield in the final coupling. © 1992 John Wiley & Sons, Inc.
Conformational properties of oxytocin in dimethyl sulfoxide solution: NMR and restrained molecular dynamics studies
Authors: Bhaskaran R. , Chuang Li‐Chin , Yu Chin
Published: December 2004

The conformation of oxytocin, the neurohypophyseal nonapeptide hormone, in solution in deuterated dimethyl sulfoxide has been determined by 1H‐nmr. The structural determination is based on the experimental data set of nuclear Overhauser effect restraints. Obtained after the restrained molecular dynamics simulation on an initial structure of extended conformation, five resultant structures satisfy the experimental restraints well. These structures resemble that of the crystal structure of deamino‐oxytocin, an analogue of oxytocin, in terms of a close correlation observed both at two β‐turn regions of the 20‐membered tocin ring and at the tripeptide tail end. Based on this comparison and analysis of restrained molecular dynamics trajectories, we found that, although the turns are stabilized by the formation of hydrogen bonds, the oxytocin molecule possesses a slight twist in DMSO solution relative to the orientation of deamino‐oxytocin in the crystalline state. Analyses of oxytocin conformation indicate that the tripeptide tail is more flexible than the tocin ring. © 1992 John Wiley & Sons, Inc.
Volume changes correlate with entropies and enthalpies in the formation of nucleic acid homoduplexes: Differential hydration of A and B conformations
Authors: Rentzeperis Dionisios , Kupke Donald W. , Marky Luis A.
Published: December 2004

We have used a combination of densimetric, calorimetric, and uv absorption techniques to obtain a complete thermodynamic characterization for the formation of nucleic acid homoduplexes of known sequence and conformation. The volume change ΔV accompanying the formation of four duplexes was interpreted to reflect changes in hydration based on the electrostriction phenomenon. In 10 mM sodium phosphate buffer at pH 7, the magnitude of the measured ΔV's ranged from −2.0 to +7.2 ml/mol base pair and followed the order of poly(rA) · poly(dT) ∼ poly(dA) · poly(dT) < poly(rA) · poly(dU) ∼ poly(rA) · poly(rU). Inclusion of 100 mM NaCl in the same buffer gave the range of −17.4 to −2.3 mL/mol base pair and the following order: poly(dA) · poly(dT) < poly(rA) · poly(dT) < poly(rA) · poly(rU) ∼ poly(rA) ∼ polyr(dU). Standard thermodynamic profiles of forming these duplexes from their corresponding complementary single strands indicated similar free energies that resulted from the compensation of favorable enthalpies with unfavorable entropies along with a similar counterion uptake at both ionic strengths. The differences in these compensating effects of entropy and enthalpy correlated very well with the volume change measurements in a manner suggesting that the homoduplexes in the B conformation are more hydrated than are those in the A conformation. Moreover, the increased thermal stability of these homoduplexes resulted from an increase in the salt concentration corresponding to larger hydration levels as reflected by the ΔV results. © 1993 John Wiley & Sons, Inc.
Temperature‐Induced conformational transition in xanthans with partially hydrolyzed side chains
Authors: Christensen Bjørn E. , Knudsen Kenneth D. , Smidsrød Olav , Kitamura Shinichi , Takeo Kenichi
Published: December 2004

The conformational properties of xanthans with partially hydrolyzed side chains were in vestigated by optical rotation, CD, and differential scanning calorimetry (DSC). All variants displayed the well‐known temperature‐driven, cooperative order–disorder transition, and both optical rotation and DSC showed that the transition temperature was essentially independent of the content of terminal β‐mannose. It was found that up to 80% of the changes in the specific optical rotation accompanying the transition reflects conformational changes linked to the terminal β‐mannose in the side chains. Modification of the sidechains also affected the CD when xanthan was in the ordered state, but in this case the data suggest that the glucuronic acid is the major component determining the magnitude of the CD signal. DSC measurements showed that the transition enthalpy (ΔHcal) increased linearly with the fraction of β‐mannose, again indicating that a significant part (up to 80%) of ΔHcal reflects conformational changes in the side chains. The conformational transition of the xanthan variants generally showed a higher degree of cooperativity (sharper transition) than unmodified, pyruvated xanthan. Calculation of the cooperativity parameter σ by means of the Zimm–Bragg theory (OR data) or from the ratio between ΔHcal and the van't Hoff enthalpy (ΔHvH) using DSC data showed a correlation between σ and the content of β‐mannose, but the two methods gave different results when the content of β‐mannose approached 100%. The ionic strength dependence of the transition temperature, expressed as d (log I)/d(T−1m), was nearly identical for intact xanthan and a sample containing only 6% of the terminal β‐mannose. Application of the Manning polyelectrolyte theory does not readily account for the observed ΔHcal values, neither does it provide new information on the nature of the ordered and disordered conformations in xanthan. © 1993 John Wiley & Sons, Inc.
Photodynamic induction of DNA–protein cross‐linking in solution by several sensitizers and visible light
Authors: Villanueva A. , Cañete M. , Trigueros C. , Rodriguez‐Borlado L. , Juarranz A.
Published: December 2004

The combined effect of several sensitizers and light on H 2O or D2O solutions of DNA‐histone complexes, as well as the significance of singlet oxygen (1O2), in this photosensitizing reaction has been studied. On H2O solutions, the production of 1O2, as well as the formation of DNA‐protein cross‐links (DPCs), were found to be dependent on light dose for all the sensitizers. Mesotetra (4N‐methylpyridyl) porphine (T4 MPyP), methylene blue (MB), and toluidine blue (TB) were the best photosensitizers with regard to tryptophan photolysis, followed by hematoporphyrin (HP), thioflavine T (TT), and pyronin G (PG). The formation of DPCs showed high initial rates, reaching a plateau at dose over 90 J/cm 2. Under these irradiation conditions, the percentage of DPCs induced by the sensitizers decreases in the order T4 MPyP > MB > TB ≫ HP ≈ TT ≫ PG (≈0). These DPCs were totally destroyed with proteinase K (15μg/ml). The irradiation of the DNA‐histone‐sensitizer solutions in the presence of L‐carnosine (5 × 10‐4 M) produced approximately a 50% of DPCs inhibition for T4 MPyP, MB, and TB, and a total inhibition for HP, TT, and PG. The substitution of H2O by D2O as solvent significantly increased the photodegradation of tryptophan, as well as the photoinduction of DPCs by the sensitizers. The results obtained indicate that singlet oxygen is the main agent responsible in the DNA–protein cross‐linking formation. © 1993 John Wiley & Sons, Inc.
Conformational preference functions for predicting helices in membrane proteins
Authors: Juretić Davor , Lee Byungkook , Trinajstić Nenad , Williams Robert W.
Published: December 2004

A suite of FORTRAN programs, PREF, is described for calculating preference functions from the data base of known protein structures and for comparing smoothed profiles of sequence‐dependent preferences in proteins of unknown structure. Amino acid preferences for a secondary structure are considered as functions of a sequence environment. Sequence environment of amino acid residue in a protein is defined as an average over some physical, chemical, or statistical property of its primary structure neighbors. The frequency distribution of sequence environments in the data base of soluble protein structures is approximately normal for each amino acid type of known secondary conformation. An analytical expression for the dependence of preferences on sequence environment is obtained after each frequency distribution is replaced by corresponding Gaussian function. The preference for the α‐helical conformation increases for each amino acid type with the increase of sequence environment of buried solvent‐accessible surface areas. We show that a set of preference functions based on buried surface area is useful for predicting folding motifs in α‐class proteins and in integral membrane proteins. The prediction accuracy for helical residues is 79% for 5 integral membrane proteins and 74% for 11 α‐class soluble proteins. Most residues found in transmembrane segments of membrane proteins with known α‐helical structure are predicted to be indeed in the helical conformation because of very high middle helix preferences. Both extramembrane and transmembrane helices in the photosynthetic reaction center M and L subunits are correctly predicted. We point out in the discussion that our method of conformational preference functions can identify what physical properties of the amino acids are important in the formation of particular secondary structure elements. © 1993 John Wiley & Sons, Inc.
Predicting polypeptide and protein structures from amino acid sequence: Antlion method applied to melittin
Authors: Head‐Gordon Teresa , Stillinger Frank H.
Published: December 2004

This report continues to explore the use of a strategy known as the antlion method for predicting polypeptide and protein structure. The method involves deformation of a biopolymer's potential energy hypersurface in order to retain only a single minimum, near to the native structure. The vexing multiple minimum problem thus is relieved, and the deformed hypersurface constitutes a key element in three‐dimensional structure predictions with atomic resolution. In this more demanding pilot study, we provide evidence that the antlion method is capable of dramatically simplifying the surface of polypeptides by successfully predicting the native form of the naturally occurring 26‐residue polypeptide melittin. The systematic hypersurface modifications employed in our previous work have been used again for this case, but have been supplemented by the output of a suitable neural network. This neural network involves a new feature: the use of amino acid biophysical scales for improving the secondary structure prediction accuracy of simple perceptrons. © 1993 John Wiley & Sons, Inc.
Synthetic peptide and template‐assembled synthetic protein models of the hen egg white lysozyme 87–97 helix: Importance of a protein‐like framework for conformational stability in a short peptide sequence
Authors: Vuilleumier Stéphane , Mutter Manfred
Published: December 2004

In the native structure of hen egg white lysozyme (HEL), the amino acid sequence 87–97 (HEL 87–97) forms an amphiphilic helix, with hydrophilic residues in the sequence directed toward the solvent. A synthetic version of the HEL 87–97 sequence (with the cysteine corresponding to position 94 of HEL replaced by alanine) displays conformational features in solution typical of an unordered structure as judged by CD. However, various modifications in the sequence result in increased helix‐forming potential of the HEL 87–97 analogues. Further stabilization of the helical conformation in the most helical analogue of the HEL 87–97 sequence is obtained when 4 copies of this peptide sequence are coupled on a peptide carrier molecule following the template‐assembled synthetic protein (TASP) approach M. Mutter and S. Vuilleumier (1989) Angew. Chem. Int. Ed. Engl., Vol. 28, pp. 535–554 “A Chemical Approach to Protein Design–Template‐Assembled Synthetic Proteins (TASP).” This suggests that long‐range interactions of the peptide with its environment contribute to conformational stability in short peptide sequences. TASP molecules may prove useful for the study of the factors that determine secondary structure formation in short peptides by providing a protein‐like framework. © 1993 John Wiley & Sons, Inc.
Accommodation of a D‐Phe residue into a right‐handed 310‐helix: Structure of Boc‐D‐Phe‐(Aib)4‐Gly‐L‐Leu‐(Aib)2‐Ome, an analogue of the amino terminal segment of antiamoebins and emerimicins
Authors: Karle I. L. , Flippen‐Anderson J. L , Uma K. , Balaram P.
Published: December 2004

The crystal structure of the nonapeptide Boc‐D‐Phe‐Aib‐Aib‐Aib‐Aib‐Gly‐Leu‐Aib‐AibOMe (I), which is an analogue of the N‐terminal sequence of antiamoebins and emerimicins, establishes a completely 310‐helical conformation with seven successive intramolecular 4 → 1 hydrogen bonds. The average, ϕ, ψ values for residues 1–8 are −59° and −32°, respectively. Crystal parameters are C47H77N9O12, space group P1, a = 10.636(4) Å, b = 11.239(4) Å, c = 12.227(6) Å, α = 101.17(4)°, β = 97.22(4)°, γ = 89.80(3)°, Z = 1, R = 5.95% for 3018 data with |F0| > 3α(F), resolution 0.93 Å. The use of the torsion angle κ = C(i − 1)N(i)Cα(i)Cβ(i), where κ = 68° for D‐Phe and κ = 164° for L‐Leu, confirms the opposite configurations of these residues. The ϕ, ψ values of −62° and −32° at D‐Phe are unusual, since this region is characteristic of residues with L configurations. Peptide I possesses only two chiral residues of opposing configuration. The observed right‐handed 310‐helical structure suggests that helix sense has probably been determined by the stereo‐chemical preferences of the Leu residue. © 1993 John Wiley & Sons, Inc.
Synthesis, conformation, and activity of HCO‐Met‐ΔZ Leu‐Phe‐Ome, an active analogue of chemotactic N‐formyltripeptides
Authors: Pagani Zecchini G. , Paradisi M. Paglialunga , Torrini I. , Lucente G. , Gavuzzo E. , Mazza F. , Pochetti G. , Paci M. , Sette M. , Di Nola A. , Veglia G. , Traniello S. , Spisani S.
Published: December 2004

In order to induce a β‐turn conformation into the chemotactic linear tripeptide N‐formyl‐L‐methionyl‐L‐leucyl‐L‐phenylalanine (fMLP), the new analogue N‐formyl‐L‐methionyl‐ΔZleucyl‐L‐phenylalanine methyl ester [ ΔZLeu]2f MLP‐OMe (1) has been synthesized. The conformational and biochemical consequences of this chemical modification have been determined. Analogue 1 has been synthesized by using N‐carboxy‐(Z)‐α,β‐didehydroleucine anhydride as key compound to introduce the unsaturated residue at the central position of the tripeptide 1. The x‐ray analysis shows that 1 adopts in the crystal a type II β‐turn conformation in which the new residue occupies the (i + 2) position, and an intramolecular H bond is formed between the formylic oxygen and the Phe NH. 1H‐nmr analysis based on nuclear Overhauser effect measurements suggests that the same folded conformation is preferred in CDCl3 solution; this finding is also supported by molecular dynamics simulation. The biological activity of 1 has been determined on human neutrophils (polymorphonuclear leukocytes) and compared to that shown by f MLP‐OMe. Chemotactic activity, granule enzyme release, and superoxide anion production have been determined. Analogue 1 is practically inactive as chemoattractant, highly active in the superoxide generation, and similar to the parent in the lysozyme release. The conformational restriction imposed on the backbone by the presence of the unsaturated residue is discussed in relation with the observed bioselectivity. © 1993 John Wiley & Sons, Inc.