bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular orbital calculations on the conformation of polypeptides and proteins. II. Conformational energy maps and stereochemical rotational states of aromatic residues
Authors: Maigret Bernard , Pullman Bernard , Perahia David
Published: December 2004

Our previous quantum‐mechanical calculations, by an all‐valence‐electrons method (PCILO) taking into account simultaneously the σ and π electrons of the system, on the conformation energy maps of the glycyl and alanyl residues are extended to the evaluation of these maps and of the stereochemical rotational states of the aromatic residues, phenylalanyl, tyrosyl, histidyl, and tryptophanyl in dipeptides. Calculations on model compounds are used for the predetermination of the side‐chain rotational angles χ1 and χ2 which are then used as selected parameters for the evaluation of the conformational energy maps as function of the backbone rotational angles Φ and ψ. The theory predicts that the most stable conformation for these aromatic residues should occur in the same region, around Φ = 200, ψ = 140°, in which it was predicted to occur for the glycyl and alanyl residues and which was completely overlooked by most of the previous “empirical” computations. Recent experimental work by a group of Russian authors using NMR and infrared techniques seems to confirm the theoretical result for the alanyl and phenylalanyl residues. The paper indicates also the secondary local minima which appear for the different residues. The theoretically allowed general conformational area for the four aromatic residues, within the reasonable value of 5 kcal/mole above the deepest minimum, is somewhat larger than the similar area allowed by the “hard sphere” empirical calculations. Practically all available representative experimental points from the study of small molecules and of the proteins lysozyme and myoglobin fall within the allowed area, the agreement being better with the results of the quantum mechanical calculations than with those of the “hard sphere” approximation. The values of the side‐chain rotational angles χ1 and χ2 and of their allowed combinations agree less satisfactorily with experiment, the experimentally observed combinations being more varied than the theoretically allowed ones. These last ones having, however, been predetermined on studies with model compounds, this situation is not astonishing. It is proposed to refine these results by a minimization with respect to the four parameters Φ, ψ, χ1, and χ2 involved.
Diffusion of DNA at very low concentrations
Authors: Strassburger J. , Rejnert K. E.
Published: December 2004

The diffusion behavior of DNA samples of molecular weights between 1 × 106 and 25 × 106 Daltons was investigated under standard conditions at mean concentrations c̄ between 0.0009 and 0.017 g/dl. Special techniques described previously were used and supplemented. The sensitivity required was accomplished by multiple passage through the sample cells (effective path length of 10–45 cm) and application of the Gouy interference method. The maximum DNA refraction index difference has been determined more precisely from Gouy interference fringes by applying a systematic variation procedure and a linear‐plot criterion. Convection was prevented by a temperature constancy better than 0.002°C/day, vibrationless operation, and by application of a slight density gradient of heavy water, which also improved the boundary‐forming procedure. The corresponding optical HDO gradient was compensated. The concentration dependence of the DNA diffusion coefficient average DA was found to be positive and very small at extremely low concentrations, that is, below c̄ = 0.008 g/dl, for the sample of highest molecular weight investigated. With beginning penetration of different DNA molecules, DA increases markedly. The diffusion constant averages of our polydisperse samples will be corrected for monodisperse subfractions in a following paper. The resulting molecular weights M from diffusion and sedimentation constants (D0, s0) together with data from literature are the basis of new s0–M, D0 − M, and [η]–M relations for monodisperse DNA samples.
DNA–copper(II) complex and the DNA conformation
Authors: Zimmer Ch. , Luck G. , Fritzsche H. , Triebel H.
Published: December 2004

Spectrophotometric, sedimentation, infrared, optical rotatory dispersion (ORD), and circular dichroism (CD) methods have been used to demonstrate the structural changes in DNA induced by the interaction of copper(II) with bases and to elucidate the complex binding sites. As shown by the electrolyte‐induced reversion (addition of salts) of temperature‐denatured copper DNA the effectiveness of re‐formation of the double‐stranded structure depends on the temperature, copper(II) ion concentration, and on the base composition of the DNA. Exposure of heat‐denatured copper DNA to higher temperatures decreases the reversion effect on addition of electrolyte. The results indicate that a greater fraction with a cooperative transition appears on heating DNA to 80 or 100°C at a Cu2+/DNA‐P ratio of 2 : 1 than at a Cu2+/DNA‐P ratio of 1 : 1. With AT‐rich copper DNA, reversion to the native DNA structure was not observed. Selective methylation of guanine residues in DNA also affects the electrolyte‐induced reversion, indicating the importance of GC pairs for copper(II) binding and the reversion to the native structure. Temperature‐denatured copper DNA shows an increased sedimentation coefficient Which decreases again after electrolyte‐induced reversion. This change in s is reduced by selective methylation of DNA. Complex formation between copper(II) and the bases is accompanied by a conformational change of the DNA double‐helical structure as demonstrated by ORD and CD experiments. The ORD profile of GC‐rich DNA is much more affected by copper(II) than that of AT‐rich ones. Even at very low copper(II) concentrations, e.g., at 0.02 and 0.2 Cu2+/DNA‐P, the ORD and CD measurements exhibit conformational changes of the DNA secondary structure at room temperature. By comparing the infrared spectra of deoxynucleosides with that of DNA of different GC content it has been shown that both guanine and cytosine are involved in the formation of the complex of copper(II) with DNA. N‐7 and O at C‐6 in guanine and N‐3 as well as O of C‐2 in cytosine are discussed as the most probable binding sites in DNA. A binding model for the coordination of the copper(II) ion between guanine and cytosine of the opposite strands is suggested. The results are in good agreement with the assumptions and predictions made by Eichhorn and Clark about the complexing of copper(II) with DNA. The recent proposal made by Schreiber and Daune about an interaction of the type guanine–Cu2+–guanine cannot be excluded as an additional kind of coordination of copper(II) in DNA.
Fractionation of poly (dA‐dT) by gel chromatography
Authors: Jang Choong‐Gook , Bartl Paul
Published: December 2004

A commercial sample of poly (dA‐dT), a copolymer of 2′‐deoxyribosyladenosine (dA) and 2′‐deoxyribosylthymidine (dT) of perfectly alternating sequence, was fractionated by chromatography on Agarose gel. Paucidisperse fractions of different molecular size were obtained. The plot of log s020,w values shows a linear dependence on Ve. The buoyant densities of individual fractions do not differ over the molecular size range studied. On the other hand, the heat‐induced hyperchromic effect was found to depend on molecular size below a certain limit, s020,w = 4.12 S.
Molecular orbital calculations on the conformation of polypeptides and proteins. V. Conformational energy maps and stereochemical rotational states of aliphatic residues
Authors: Maigret Bernard , Perahia David , Pullman Bernard
Published: December 2004

The quantum‐mechanical calculations by the PCILO method on the conformation of amino acid residues of proteins have been extended to the valyl, leucyl, and isoleucyl residues. In distinction to the earlier “empirical” computations, the quantum‐mechanical results indicate very similar energy contours for the stable conformations of the three residues. Their general outline is also similar to that of the alanyl residue, although reduced by about 25%. Contrary to the “empirical” computations, the present results predict that the region corresponding to the α‐helix should be one of great stability for the three residues and in particular for the valyl residue. The quantum‐mechanical results are in excellent agreement with the experimental conformations of the aliphatic residues in lysozyme and myoglobin. Their prediction as to the ready availability of the valyl residue in the α‐helical conformation agrees moreover with Ptitsyn's statistical evaluation of the participation of this residue in the inner turns of the helical regions in six globular proteins. The maximum conformational space allowed for the aliphatic residues is somewhat smaller than that allowed for the aromatic ones, while the minimum conformational space (region of stability common to all the residues) is similar in both groups.
Studies on the conformation of amino acids X. Conformations of norvalyl, leucyl and aromatic side groups in a dipeptide unit
Authors: Sasisekharan V. , Ponnuswamy P. K.
Published: December 2004

Backbone‐side group conformations of amino acid residues including one or two δ‐carbons in the side group have been investigated. Conformational energies of norvalyl, leucyl, phenylalanyl, tyrosyl, tryptophenyl, and histidinyl side groups in a dipeptide unit have been calculated by using classical energy expressions. The side group conformations about the Cα—Cβ and Cβ—Cγ bonds are restricted to specific values of the respective rotational angles. Thus, most favourable positions of γ‐ and δ‐atoms of a linear side‐chain (norvalyl) are restricted to (γI, δII) (γII, δI), (γII, δII), (γIII, δII), and (γIII, δIII), whereas those of the side‐chain branching at a sp3 γ‐atom (leueyl) are further restricted. It is also shown that there is a definite correlation between the orientations of the two peptide planes and that of the planar group of the aromatic side chain of phenylalanyl type residues. The studies bring out an important fact that while the γ‐atoms have definite and characteristic effects on the backbone rotational angles ϕ and ψ, the δ atoms and beyond have no effects on the preferred ϕ and ψ values. Thus, the preferred backbone conformations are independent of the preferred side group conformations beyond the γ‐atom and vice versa. The observed ϕ, ψ, χ1, and χ2 values of amino acids, simple peptides, and of the three protein molecules lysozyme, myoglobin, and chymotrypsin have been compared with the theoretical predictions, and the agreement is found to be excellent.
Induced optical activity of acridine orange bound to poly‐S‐carboxymethyl‐L‐cysteine
Authors: Ikkda Shoiohi , Imae Toyoko
Published: December 2004

The absorption and rotatory properties of acridine orange‐poly‐S‐carboxymethyl‐L‐cysteine system in water and in 0.2 M NaCl have been measured at different pH and polymer‐to‐dye mixing ratios. The absorption spectra indicate that the dyes are bound to the polymer in dimeric or highly aggregated forms. At neutral pH where the polymer is randomly coiled, no optical activity is induced on the absorption bands of bound acridine orange. At acid pH where the polymer has the β‐conformation, a pair of positive and negative circular dichroic bands occur at each of the absorption bands, centered around 458 and 261 mμ. The signs of those bands are opposite to those found for α‐helical poly‐L‐glutamic acid. A model for the binding of dye to the β‐form polymer is presented, in which dimeric dyes are attached to ionized carboxyl groups and slack one another to form linear arrays on both sides of an extended polypeptide chain. The observed circular dichroism spectra can be explained by the Tinoco's exciton mechanism, based on this model. Low molecular weight poly‐S‐carboxymethyl‐L‐cysteine induces quite a different circular dichroism on bound acridine orange.
Thermodynamic analysis of thermal transitions in globular proteins. I. Calorimetric study of ribotrypsinogen, ribonuclease and myoglobin
Authors: Privalov P. L. , Khechinashvili N. N. , Atanasov B. P.
Published: December 2004

Thermal confonnalional transformations of globular proteins, chymotrypsinogen, ribo‐nudcase and myoglobin in solutions at different pH values were studied microcalorimetrically. It was shown that the heat effects observed in the process of heating have a complicated form and their explanation necessitates an assumption on the existence of two stages of the process separated by temperature: (I) a pre‐denaturational stage where the protein partial heat capacity changes are probably connected with a labilization of the globule structure and (II) a denaturational stage representing a single‐step transition of the protein into a state with a higher enthalpy. Transitions without enthalpy change, the existence of which is shown for the first time in globular proteins, necessitates a more cautions approach to the thennudynamical analysis of different physical parameters on the basis of the van't Hoff equation.
Configurational statistics of polysaccharide chains. Part III. Linear β‐(1 → 4′) xylan and mannan
Authors: Yathindra X. , Rao V. S. R.
Published: December 2004

The characteristic ratio CN = 〈r2〉0/Nlv2 of the β‐D(1 → 4′)‐linked polysaccharides xylan and mannan has been computed as a function of the angle τ at the bridge oxygen atom and the degree of polymerization N. The calculated values of the characteristic ratio CN are very high relative to their free rotational dimensions. The characteristic ratio of these polysaecharides converges to the asymptotic value at low degree of polymerization at higher τ values. The low values of the calculated characteristic ratio of xylan compared to cellulose and mannan for the same τ value indicate that the former is more flexible and assumes a compact configuration. A pronounced difference in the values of the characteristic ratio CN of cellulose and mannan has also been observed lower τ angles (<120°). On the other hand, nearly the same values of CN have been obtained at higher τ angles (120°–125°), which suggests that, cellulose and mannan may have similar configuralons in certain solvents.
Sensitized fluorescence in polynucleotide‐dye complexes and the problem of energy transfer in polynucleotides
Authors: Kaufmann M. , Weill G.
Published: December 2004

New results on sensitization of fluorescence of Profiuvine, Acridine Orange and Ethidium Bromide complexes wilh double stranded poly A‐poly U upon ultraviolet irradiation are presented. Together with older results on dye DNA complex, they are interpreted to show that base to base transfer plays essentially no role compared to direct base to dye transfer. A lower limit of base to base transfer time (which is at the same time a higher limit for life time of fluorescence) in DNA (2. 10−11 sec.) and poly A‐poly U (2. 10−13 sec.) is obtained which cast some doubt upon the validity of calculations of optical properties using the exciton (strong coupling) approximation.
Sedimentation velocity properties of catenated DNA molecules from HeLa cell mitochondria
Authors: Brown Irving H. , Vinograd Jerome
Published: December 2004

Catenated molecules of closed circular DNA have been isolated from the mitochondrial DNA of HeLs cells. The sedimentation coefficients of several purified species have been investigated. The catenated dimer, made up of two interlocked duplex circles, sediments at 51 S in its superhelical (closed) form. Treatment with pancreatic DNase to relax the duplex circles converts the 51 S doubly closed dimer to a 42 S singly open species, then to a 36 S doubly open catenated dimer. The triply closed trimer sediments at 63 S and is converted to a 45 S triply open form by DNase. Electron microscopy of the DNA samples before and after DNase treatment shows that under the conditions used DNase does not change the catenated nature of the DNA. The measured sedimentation coefficients, have been compared with those estimated from previously proposed correlations of sedimentation coefficient and molecular weight, and with the sedimentation coefficients for catenated DNA presented by Wang. When all the interlocked circles in a catenane are relaxed, the DNA sediments about 5–10% faster than a relaxed multiple‐length circular molecule of the same molecular weight. The sedimentation coefficient, 36 S, of the fully relaxed catenated dimer is 1.4 times that of the relaxed monomer.
Polarization of fluorescence of an oriented solution of rodlike particles bearing a fluorescent label
Authors: Weill G. , Hornick C.
Published: December 2004

The variation of the polarized components of fluorescence of a rodlike particle bearing a fluorescent label upon partial orientation is calculated for some special geometry of the dye macromolecules complexes. Explicit expressions are given for the case where the energy of the molecule in the field depends only on one angle θ, showing that the result is a function of both 〈sin2θ〉 and 〈sin4θ〉. For the case of orientation in an electric field through an anisotropic induced moment, the expressions allow the calculation of this anisotropy of polarizability. The method is applied to the measurement of the polarizability of rodlike fragments of DNA labeled by intercalated molecules of Acridine Orange.
Concentration dependence in three‐component systems in sedimentation equilibrium in buoyant density gradients
Authors: Poon Pak H. , Schumaker Verne N.
Published: December 2004

The data on the band widths and band shapes of several DNA's at various concentrations in sedimentation equilibrium in a CsCl density gradient have recently become available. In the present report, these literature data are treated in the following manner: (1) based on a theory of isotope‐substitution, calculations are made of the molecular weights at infinite dilution, and (2) to explain the concentration dependence of band widths and band shapes, a theory of charge and hydration is put forth, and it is shown that by retaining the terms involving the charge of the macromolecules, it is possible to account for most of the concentration dependence.
Potentiometric titration of poly‐L‐lysine: the coil‐to‐β transition
Authors: Pederson Dennis , Gabriel Don , Hermans Jan
Published: December 2004

We have performed potentiometric titrations of poly‐L‐lysine. From these data we have calculated the free energy and enthalpy changes for the folding of the random coil to the α‐helix in 10% ethanol (−120 and −120 cal/mole) and from the random coil to the β‐structure in water (−140 and 870 cal/mole) and in 10% ethanol (−180 and 980 cal mole). Comparison of these values with each other and with values for the coil → α‐ helix transition in water (−78 and −880 cal/mole) led to the following conclusions. The stabilization by ethanol of ethanol of the α‐helix with respect to the coil is that predicted from the known free energy of transfer of the peptide group from water to 10% ethanol. Similar data to explain the enthalpy difference are not available. The thermodynamic functions for the transition from α‐helix to β‐structure, obtained by subtracting those for the coil → α‐helix and coil → β‐structure transitions, are explained from a consideration of the structural differences: non bonded interactions of the polypeptide backbone are less favorable in the β‐structure than in the α‐helix, causing an increase in the energy, while hydrophobic contacts between side chains raise the entropy of the β‐structure as compared with the α‐helix, so that the free energy difference between the two structures is small, but enthalpy and entropy differences are large. The observation of only small differences in the free energy and enthalpy changes for the transition from coil β‐structure upon going from water to 10% ethanol is expected by considering both the free energy of transfer of the peptide group (as for the α‐helix) and the free energy and enthalpy of transfer of the apolar part of the side chain involved in hydrophobic bond formation.
β‐Carbonylamides in peptide chemistry. I. Optical rotatory properties of N‐acetoacetyl amino acids
Authors: Toniolo Claudio , Filira Fernando , Di Bello Carlo
Published: December 2004

The Cotton effects of N‐acetoacetyl amino acids and derivatives were examined by a circular dichroism technique. A correlation has been established between the sign of the Cotton effect and the absolute configuration of the asymmetric center. The L derivatives show, in dioxane, negative circular dichroism curves, whereas the D antipodes present positive curves. The effect of solvent and pH and influence of alkylation at the amide nitrogen are also discussed.
Stability characteristics of deuterated myoglobin
Authors: Appel Pearl , Brown W. Duane
Published: December 2004

Purified sperm whale myoglobin was deuterated by being exposed to pD 3.5 in D2O buffer for 1 hr, then raised to pD 10.6 for an additional hour, and finally brought to neutrality in a D2O environment. Control myoglobin was similarly treated in H2O. The specific rotation at 233 mμ and/or the absorbance in the Soret region were used to follow the helix‐coil transition of myoglobin subjected to denaturation by acid, alkali, urea and guanidine. Deuterated and control myoglobin had similar 50% transition points in the four denaturing media studied (acid: pH 4.4, pD 4.9; alkali: pH 9.4, pD 10.0; urea, 7.2M; guanidine, 2.5M). The shift toward the alkaline side of 0.5 or 0.6 units of the transition induced by either acid or alkaline denaturation reflects only the weakened acidity of ionizable groups in deuterium systems. Deuterated myoglobin in 3.25M guanidine had a 20% faster denaturation rate than that of control. Acid, urea, and guanidine denaturation curves showed fairly steep transitions, taken as indicative of a one‐step process involving only two states (native and denatured molecules). Supporting this conclusion was the fact that plots of absorption and polarimetry measurements of the helix‐coil transition induced by either acid or guanidine could be superimposed.
Angular dependence of scattered light, rotary frictional coefficients, and distribution of sizes of associated oligomers in solutions of bovine liver glutamate dehydrogenase
Authors: Eisenberg Henryk , Reisler Emil
Published: December 2004

The angular dependence of scattering in solutions of bovine liver glutamate dehydrogenase was studied in 0.2M Na‐phosphate buffer, pH 7, 10−4M EDTA, and in buffered solutions saturated with either toluene or benzene. Whereas the shape of the scattering curves is in qualitative accord with the previously reported polymerization to rodlike linear structures, quantitative agreement between the calculated and experimental curves is poor when the polydispersity consistent with the association mechanism (derived from molecular weight determinations by light scattering and equilibrium sedimentation) is properly taken into account. The measurement of rotary frictional coefficients of macroscopic models of linearly associated glutamate dehydrogenase oligomers allowed the calculation of intrinsic viscosities of enzyme solutions but did not permit discrimination, by hydrodynamic means, between systems with different distributions of length.
Electro‐optical properties of nucleic acids and nucleoproteins III. Kramers‐Kronig relationships in linear birefringence and dichroism. Application to a DNA–proflavine complex
Authors: Houssier Glaude , Kuball Hans‐G
Published: December 2004

The relation between the birefringence dispersion curve in a dichroic absorption band and the corresponding dichroism spectrum is given, using the Cauchy's theorem. The theory was checked on a DNA–proflavine complex with the aid of electro‐optical measurements. An excellent agreement between the experimental results and the theoretical calculations was found. The birefringence and dichroism of the complex appear to be determined by the orientation of the macromolecule while no evidence for a contribution of the hyperpolarizabilities to the electro‐optical effect is found.

The importance of the dichroism correction in the calculation of the birefringence dispersion curve is emphasized.
Oligonucleotide studies: optical rotatory dispersion of normal and 2′‐O‐methylated diribonucleoside monophosphates
Authors: Singh H. , Hillier B.
Published: December 2004

The optical rotatory dispersion (ORD) of several diribonucleoside monophosphates (NpN) and the corresponding 2′‐O‐methyl substituted dinucleoside monophosphates containing 2′‐O‐methyl ribosyl 3′‐nucleotide and a 5′‐nucleoside (NmpN) were measured at pH 1, 7, and 11.2, at 0.1 ionic strength in order to examine the role of the 2′‐hydroxyl group of the ribose in the conformation of the oligoribonucleotides. The optical measurements are reported from 210 to 340 mμ. The pH effect on the ORD spectra of NpN as well as NmpN are large. No dramatic changes are seen in the shapes of the ORD spectra of the NmpN to the corresponding NpN at pH 7. However, a decrease in the amplitude is seen in most of the NmpN over that of the corresponding NpN ranging from 7 percent in the case of UmpG to 46 percent in AmpA. The differences seen in the NpN and the corresponding NmpN ORD results are best explained as a consequence of a change in the ribosyl conformation on 2′‐O‐methylation, rather than the involvement of the 2′‐hydroxyl group in intramolecular hydrogen bonding in the ribo dimmer. The NmpN behave like NpN and not dNpdN, suggesting that the geometry of the stack in NpmN and NpN depends on the oxygen at the 2′‐carbon and not on what is attached to it.
On the conformations of poly‐N‐methyl‐L‐alanine (PNMA) in solution
Authors: Conti F. , De Santis P.
Published: December 2004

High‐resolution nuclear magnetic resonance spectra at 100 MHz have been obtained on poly‐N‐methyl‐L‐alanine in the chloroform–trifluoroacetic acid system under various conditions of solvent composition. Different spectra are observed for the CH3–Cα, Cα–H, and N–CH3 protons. On the basis of conformational analysis an interpretation of the NMR results was attempted.
An infrared study on the conformation of poly‐L‐proline in concentrated aqueous salt solutions
Authors: Swenson Charles A.
Published: December 2004

The infrared absorption of poly‐L‐proline in concentrated aqueous salt solutions was measured in the fundamental region. Of primary interest were the carbonyl absorption of the peptide linkage and the methylene C–H bending absorption of the pyrrolidine ring. These spectral regions each show an additional component in the concentrated salt solutions. Using the position of the absorptions of poly‐L‐proline I (cis) and II (trans) as models, we conclude that both cis–trans linkages are present in the peptide in salt solutions. Increasing the temperature shifts the equilibrium slightly in favor of cis.
Side‐chain conformation in poly(γ‐phenethyl‐L‐glutamate)
Authors: Lefelar Judith A. , Knox James R. , Samulski Edward T.
Published: December 2004

X‐ray diffraction and energy‐minimization results are reported for poly(γ‐phenethyl‐L‐glutamate). Orthorhombic unit‐cell parameters of drawn fibers are a = 15.4 Å, b = 26.6 Å, c = 54.4 Å. Atomic coordinates are derived for an α‐helix peptide conformation that corresponds to a calculated side‐chain internal energy minimum. The side‐chain conformation correlates well with the electron density projection; the side chains wrap around the α‐helical main chain with the phenethyl ester group directed toward the N‐terminus. The para‐axis of the benzene ring is inclined at an angle nearly nearly normal to the helix axis. The x‐ray structure factors calculated for this model, when compared to the 10 observed structure factors, yield a crystallographic reliability index of R = 0.23.
Conformations of proline residues in membrane environments
Authors: Deber Charles M. , Glibowicka Mira , Woolley G. Andrew
Published: December 2004

Although noted as hydrophilic residues with helix‐breaking potential, proline residues are observed in putatively α‐helical transmembrane (TM) segments of many channel‐forming integral membrane proteins. In addition to the recognized property of X‐Pro peptide bonds (where X = any amino acid) to occur in cis as well as trans isomeric states, the tertiary amide character of the X‐Pro bond confers increased propensity for involvement of its carbonyl group in specific H‐bonded structures (e.g., β‐ and γ‐turns) and/or liganding interactions with positively charged species. To examine this latter situation in further detail, we identified Leu‐Pro‐Phe as a consensus sequence triad based on actual occurrences of intramembranous Pro residues in transport protein TM segments. Accordingly, we have undertaken the synthesis of hydrophobic peptides with potential membrane affinity, of which t‐butyloxycarbonyl‐L‐Ala‐L‐Ala‐L‐Leu‐L‐Pro‐L‐Phe‐OH (t‐Boc‐AAALPF‐OH) is an initial compound. Partitioning of this peptide into model membrane environments composed of lipid micelles induces specific conformations(s) for the membrane‐bound hexapeptide, as monitored by 75‐MHz 13C‐nmr spectral behavior of 13C‐enriched Leu and Pro carbonyl carbons, and by 300‐MHz 1H‐nmr spectra of peptide α, β, and aromatic protons. Data are interpreted in terms of an intramolecularly H‐bonded inverse γ‐turn conformation in the membrane environment involving the Leu‐Pro‐Phe triad. The inherent structureal instability of a Pro‐containing segment in a TM helix due to the multiplicity of possible local conformations is discussed as a functional aspect of membrane‐buried prolines in transport proteins.
Synthesis, crystal structure, and molecular conformation of N‐Boc‐L‐Phe‐dehydro‐Leu‐L‐Val‐OCH3
Authors: Narula P. , Patel H. C. , Singh T. P. , Chauhan V. S.
Published: December 2004

The peptide N‐Boc‐L‐Phe‐dehydro‐Leu‐L‐Val‐OCH3was synthesized by the usual workup procedure and finally by coupling the N‐Boc‐L‐Phe‐dehydro‐Leu‐OH to valine methyl ester. It was crystallized from its solution in methanol–water mixture at 4°C. The crystals belong to the triclinic space group P1 witha= 5.972(5) Å,b= 9.455(6) Å,c= 13.101(6) Å, α = 103.00(4)°, β = 97.14(5)°, γ = 102.86(50)°,V= 690.8(8) Å,Z= 1, dm = 1.179(5) Mg m−3and dc = 1.177(5) Mg m−3. The structure was determined by direct methods using SHELXS86. It was refined by block‐diagonal least‐squares procedure to anRvalue of 0.060 for 1674 observed reflections. The C–Cdistance of 1.323(9) Å in dehydro‐Leu is an appropriate double bond length. The bond angle Cα–Cβ–Cγin the dehydro‐Leu residue is 129.4(8)°. The peptide backbone torsion angles are θ1= −168.6(6)°, ω0= 170.0(6)°, ϕ1= −44.5(9)°, ψ1= 134.5(6)°, ω1= 177.3(6)°, ϕ2= 54.5(9)°, ψ2= 31.1(10)°, ω2= 171.7(6)°, ϕ3= 51.9(8)°, ψ= 139.0(6)°, θT= −175.7(6)°. These values show that the backbone adopts a β‐turn II conformation. As a result of β‐turn, an intramolecular hydrogen bond is formed between the oxygen of theith residue and NH of the (i+ 3)th residue at a distance of 3.134(6) Å. The Boc group has atrans–transconformation. The side‐chain torsion angles of the Phe residue are χ1= 171.6(6)°, χ= −102.1(9)°, and χ= 78.6(10)°. The side‐chain conformational angles of dehydro‐Leu residue are χ2= 2.7(13)°, χ= −107.3(11)°, and χ= 131.3(10)°. The torsion angles χand χthat define the conformation of the valyl side chain are −166.16(6)° and 69.1(9)°, respectively. The crystal structure is stabilized by hydrogen bonds along theaandbaxes, while the van der Waals forces are the stabilizing interactions in thecdirection.
Synthetic and conformational studies on dehydroalanine‐containing model peptides
Authors: Gupta Alka , Chauhan V. S.
Published: December 2004

Three model dipeptides containing a dehydroalanine residue (ΔAla) at the C‐terminal, Boc‐X‐ΔAla‐NHCH3[X = Ala, Val, and Phe,] have been synthesized and their solution conformations investigated by1H‐NMR, IR, and CD spectroscopy. NMR studies on these peptides in CDCl3clearly indicate that the NH group of dehydroalanine is involved in an intramolecular hydrogen bond. This conclusion is supported by IR studies also. Nuclear Overhauser effect (NOE) studies are also accommodative of an inverse γ‐turn‐type of conformation that is characterised by conformational angles of ϕ ∼ −70° and ψ ∼ +70° around the X residue, and a CH‐Ni+2H interproton distance of 2.5 Å. It appears that unlike dehydrophenylalanine or dehydroleucine, which tend to stabilize β‐turn type of structures occupying thei+ 2 position of the turn, dehydroalanine favors the formation of an inverse γ‐turn, centered at the proceeding L‐residue in such solvents as CDCl3and (CD3)2SO. A comparison of solution conformation of Boc Val‐ΔAla‐NHCH3with the corresponding saturated analogue, Boc‐Val‐Ala‐NHCH3, is also presented and shows that dehydroalanine is responsible for inducing the turn structure. It may be possible to design peptides with different preferred conformations using the suitable dehydroamino acid.
CD and Fourier transform ir spectroscopic studies of peptides. II. Detection of β‐turns in linear peptides
Authors: Hollósi M. , Majer Zs. , Rónai A. Z. , Magyar A. , Medzihradszky K. , Holly S. , Perczel A. , Fasman G. D.
Published: December 2004

Comparative CD and Fourier transform ir (FTIR) spectroscopic data on N‐Boc protected linear peptides with or without the (Pro‐Gly) β‐turn motif (e.g., Boc‐Tyr‐Pro‐Gly‐Phe‐Leu‐OH and Boc‐Tyr‐Gly‐Pro‐Phe‐Leu‐OH) are reported herein. The CD spectra, reflecting both backbone and aromatic contributions, were not found to be characteristic of the presence of β‐turns. In the amide I region of the FTIR spectra, analyzed by self‐deconvolution and curve‐fitting methods, the β‐turn band shewed up between 1639 and 1633 cm−1 in trifluoroethanol (TFE) but only for models containing the (Pro‐Gly) core. This band war‐also present in the spectra in chloroform but absent in dimethylsulfoxide. These findings, in agreement with recent ir data on cyclic models and 310‐helical polypeptides and protein in D2O [see S. J. Prestrelski, D. M. Byler, and M. P. Thompson (1991), International Journal of Peptide and Protein Research, Vol. 37, pp. 508–512; H. H. Mantsch, A. Perczel. M. Hollósi, and G. D. Fasman (1992), FASEB Journal, Vol. 6, p. A341; H. H. Mantsch. A. Perczel, M. Hollósi, and G. Fasman (1992), Biopolymers. Vol. 33, pp. 201–207; S. M. Miick, G. V. Martinez, W. R. Fiori, A. P. Tedd, and G. L. Millhauser (1992). Nature, Vol. 359, pp. 653–655], suggest that the amide I band, with a major contribution from the acceptor C  O of the 1 ← 4 intramolecular H bond of β‐turns, appears near or below 1640 cm−1, rather than above 1660 cm−1. In TFE, bands between 1670 and 1660 cm−1 are mainly due to “free” carbonyls, that is, C  O's of amides that are solvated but not involved in the characteristic H bonds of periodic secondary structures or β‐turns. © 1994 John Wiley & Sons, Inc.
Electrophoretic mobility of DNA in gels. I. New biased reptation theory including fluctuations
Authors: Duke Thomas , Viovy Jean‐Louis , Semenov Alexander N.
Published: December 2004

In weak electric fields, the motion of DNA molecules undergoing gel electrophoresis may be described by biased reptation. We argue that the degree of molecular orientation induced by the field is determined by a competition between longitudinal fluctuations and drift of the molecule along the tube. A self‐consistent calculation shows that the end‐to‐end vector of long molecules varies with the square root of the field strength, and not linearly as previously supposed. This leads to a number of new predictions about the field dependence of the molecular mobility and the size limit of resolution. We present the results of computer simulations that support the predictions of the theory of biased reptation including fluctuations. Finally, we discuss the correspondence with experimental data and the implications of our findings for the optimization of DNA electrophoresis. © 1994 John Wiley & Sons, Inc.
Conformational transitions of a dipeptide in water: Effects of imposed pathways using umbrella sampling techniques
Authors: Fraternali Franca , Van Gunsteren Wilfred F.
Published: December 2004

The free energy difference between two states of a molecular system separated by an energy barrier can generally be computed using the technique of umbrella sampling along a chosen reaction coordinate or pathway. The effect of a particular choice of pathway upon the obtained free energy difference is investigated by molecular dynamics simulation of a model system consisting of a glycine dipeptide in aqueous solution. Two different reaction coordinates connecting the so‐called C5and C7conformations, one involving intramolecular hydrogen bonds and the other involving the peptide ϕ, ψ angles, are considered.

The Gibbs free energy differences ΔG(C5– C7) are small in both cases, 1.5 ± 1 kJ mol−1and 2.2 ± 1 kJ mol−1, respectively. The two different reaction coordinates yield free energy differences that are identical to within their statistical error. It is found that the exchange of solute–solute, solute–water, and water–water hydrogen bonds involves free energy changes of less thankBT, which points at the existence of a multitutde of low free energy pathways connecting the C5and C7dipeptide conformations. © 1994 John Wiley & Sons, Inc.
Microwave dielectric study on bound water of globule proteins in aqueous solution
Authors: Miura Nobuhiro , Asaka Nobuyuki , Shinyashiki Naoki , Mashimo Satoru
Published: December 2004

A dielectric relaxation peak due to bound water of globule proteins in aqueous solution was observed at first by the use of a time domain reflectometry. This peak locates around 100 MHz as well as that of the aqueous DNA solution and the moist collagen, and has a relaxation strength in proportion to surface of the globule protein except for trypsin and pepsin of hydrolase. It is suggested that this peak is caused by orientation of bound water molecules on the protein surface. The number of bound water molecules estimated is in good agreement with that obtained by other method such as x‐ray analysis. The solution exhibits another peak below 100 MHz, which is caused by the rotation of globule protein supplemented by migration of the counterion. Its relaxation time is completely proportional to the molecular weight of the protein. © 1994 John Wiley & Sons, Inc.
A laser light scattering study of gellan gels
Authors: Burne P. M. , Sellen D. B.
Published: December 2004

A study of gellan has been made using the technique of photon correlation spectroscopy. It has been confirmed that gellan gels are largely stationary at a molecular level like other polysaccharide gels and quite unlike the gels of flexible polymers such as polyacrylamide. Solution‐gel transitions of deacetylated gellan in 0.025MNaCl have been studied both as a function of concentration and temperature, and the results compared with those of a parallel investigation of agarose. The interstitial spaces within gellan gels have also been studied by measuring the diffusion coefficients of dextran fractions within the gels. Since all gels are nonergodic systems, the theory of dynamic light scattering from such systems is discussed insofar as it affects the present work.

It has been shown that the gellan and agarose aqueous systems are fundamentally different, in that agarose does not from a solution at very low concentrations, but splits up into macroscopic gel particles. At very low concentrations, gellan forms a solution in the presence of both gelleing and nongelling ions, the molecules of which shows little change in hydrodynamic diameter with temperature in the range 20–80°C.

At higher concentrations where gels are formed, both gellan and agarose exhibit hystersis in their tempertature transitions from gel to solution and solution to gel, the solution being of large molecular aggregates. The transitions are sharp, but in both cases ther is a continous rearrangement in the structural morphology over the entire temperature range on heating, rendering the system more homogeneous prior to dissociation. In the case of gellan, however, there are two distincit phases in these structural changes—this is not true of agarose. The mean mass per unit length of the gellan fibre in the presence of 0.025M NaCl is 19 k daltons/nm at 0.7% concentration and varies with concentration to the power 0.15. The mass per unit length of the agarose fibre is much larger (ca. 110 k Daltons/nm), this difference being consistent with the difference in properties at very low concentrations. © 1994 John Wiley & Sons, Inc.
Photophysical behavior of poly(L‐lysine) carrying porphyrin and naphthyl chromophores
Authors: Pispisa B. , Venanzi M. , D'alagni M.
Published: December 2004

The photophysical behavior of protoporphyrin IX (P) and 1‐naphthylacetic acid (N), covalently bound to ε‐amino groups of poly (L‐lysine) (PL), was investigated by steady‐state and time‐resolved fluorescence as a function of pH. Within the whole range of pH explored, i.e., 7–11, exciplex emission is minor and nearly pH independent. Fluorescence quantum yields, decay time measurements, and transient absorption spectra suggest that quenching of the excited naphthyl chromophore chiefly occurs by interconversion to the triplet state when the sample is randomly coiled and by intramolecular electron transfer (ET) from ground‐state porphyrin when the polypeptide is in α‐helical conformation. The kinetic law, based on a two‐state model for the polymeric matrix, is presented. The specific rate constant of photoinduced ET is 3.1 · 107 s−1 (25°C), in excellent agreement with that obtained by taking simply into account the lifetimes of naphthalene fluorescence in α‐helical PNPL and NPL (pH 11). The relaxation time of the helix‐coil transition was found to be definitely shorter than 20 ns. © 1994 John Wiley & Sons, Inc.
Solution conformation of a pectic acid fragment by 1H‐nmr and molecular dynamics
Authors: Di Nola A. , Fabrizi G. , Lamba D. , Segre A. L.
Published: December 2004

1H‐NMR and molecular dynamics simulations in vacuo and in water of (1 → 4)‐α‐D‐galacturono‐disaccharide were performed. The results of the molecular dynamics simulations showed that the molecule fluctuates between two conformations characterized by different values of torsion angles around the glycosidic linkage and two different intramolecular hydrogen bonds. When these conformations are extrapolated to a regular polymeric structure, they generate pectic acid compatible with a 21‐ or a right‐handed 31‐helix. © 1994 John Wiley & Sons, Inc.
Unusually stable β‐sheet formation in an ionic self‐complementary oligopeptide
Authors: Zhang Shuguang , Lockshin Curtis , Cook Richard , Rich Alexander
Published: December 2004

A 16‐residue amphiphilic oligopeptide (EAK16) with every other residue alanine and also containing glutamic acid and lysine (Ac‐NH‐AEAEAKAKAEAEAKAK‐CONH2) is able to form an unusually stable β‐sheet structure. The β‐sheet structure is stable at very low concentrations in water and at high temperatures. Various pH changes at 1.5, 3, 7, and 11 had little effect on the stability of the β‐sheet structure. The β‐sheet structure was not altered significantly even in the presence of 0.1% SDS, 7 molar guanidine hydrochloride, or 8 molar urea. One of the structural characteristics of the EAK16 is its ionic self‐complementarity in that ionic bonds and hydrogen bonds between Glu and Lys can form readily between two oligopeptide β‐sheet structures. This structural feature is probably one of the factors that promotes its extreme stability. This is the first example of such an extended ionic self‐complementarity in a protein structure. EAK16 and its related peptides may have applications as useful biomaterials. It also offers a good model for studying the mechanism of β‐sheet formation. Because the oligopeptide can self‐assemble to form a membranous structure, it may have relevance to origin of life research. © 1994 John Wiley & Sons, Inc.
Nmr investigation of CYCLO7,10[C7,X9,C10,Nle12] analogues of the α‐factor from saccharomyces cerevisiae
Authors: Gounarides J. S. , Xue C.‐B. , Becker J. M. , Naider F.
Published: December 2004

The cyclo7,10[Cys7,Cys10,Nle12], cyclo7,10[Cys7,D‐Ala9,Cys10,Nle12], and cyclo7,10[Cys7,L‐Ala9,Cys10,Nle12] analogues of the α‐factor mating pheromone (WHWLQLKPGQPMY) of the yeast Saccharomyces cerevisiae were studied in DMSO/water (80 : 20) and aqueous solution by nmr spectroscopy. In addition, the cyclo7,10[Cys7,D‐Val9,Cys10,Nle12] α‐factor was examined in DMSO/water. Nuclear Overhauser effect (NOE) and NH dδ/dT data indicate that the cyclo7,10[Cys7,D‐Val9,Cys10,Nle12] α‐factor adopts a type II β‐turn in DMSO/water and that the cyclo7,10[Cys7,D‐Ala9,Cys10,Nle12] ‐ and cyclo7,10‐[Cys7,L‐Ala9,Cys10,Nle12] α‐factor analogues adopt type II and type I/III β‐turns, respectively, in both DMSO/water and aqueous solutions. In aqueous solution, residues 8 and 9 of the cyclo7,10[Cys7,Cys10,Nle12] α‐factor appear to adopt at least two distinct conformations, one of these being identified as a type I/III β‐turn. In contrast, the cyclo7,10[Cys7,Cys10,Nle12] α‐factor appears to adopt predominately a type II β‐turn in DMSO/water. Quantitative NOE measurements of the cyclo7,10[Cys7,Cys10,Nle12]‐, cyclo7,10[Cys7,D‐Val9,Cys10,Nle12]‐, and cyclo7,10[Cys7,L‐Ala9,Cys10,Nle12] α‐factors in DMSO/water were used to derive three‐dimensional structures of the cyclo7,10[Cys7,Pro8,X9Cys10] portion of these analogues. © 1994 John Wiley & Sons, Inc.
A new approach for determining low‐frequency normal modes in macromolecules
Authors: Durand Philippe , Trinquier Georges , Sanejouand Yves‐Henri
Published: December 2004

A new method for calculating a set of low‐frequency normal modes in macromolecules is proposed and applied to the case of proteins. In a first step, the protein chain is partitioned into blocks of one or more residues and the low‐frequency modes are evaluated at a low‐resolution level by combining the local translations and rotations of each block. In a second step, these low‐resolution modes are perturbed by high‐frequency modes explicitly calculated in each block, thus leading to the exact low‐frequency modes. The procedure is tested for three cases–decaalanine, icosaleucin, and crambin–using a perturbation‐iteration scheme in the second step. Convergence properties and numerical accuracy are assessed and tested for various partitions. The low‐resolution modes obtained in the first step are always found to be good starting approximations. Potential advantages of the method include a central processing unit time roughly N2 dependent on the size of the problem (N being the number of degrees of freedom), the possibility of using parallel processing, the nonrequirement for loading the complete mass‐weighted second‐derivative input matrix into central memory, and the possibility of introducing in the procedure further structural hierarchy, such as secondary structures or motifs. In addition, any improvement or refinement of the algorithm benefits from the efficient formalism of the effective Hamiltonian theory. © 1994 John Wiley & Sons, Inc.
A CD study of the α‐helix nucleation hypothesis
Authors: Toumadje Arazdordi , Johnson W. Curtis
Published: December 2004

One of the dilemmas in predicting the secondary structure of proteins from their amino acid propensity for a given conformation is the presence of all amino acids in all types of secondary structure, regardless of their propensity for that specific structure. One explanation is the nucleation hypothesis that only a few residues with a strong propensity for the secondary structure, such as the α‐helix structure, initiates its formation and propagates the structure through indifferent sequences until strong breakers terminate the growth on both ends. Eight 15‐mer peptides were studied to examine the α‐helix nucleation hypothesis. The nucleation sequence of VAEAK, with high helix propensity, was mixed with an indifferent sequence of TSDSR in all possible permutations. From the percent α‐helix structure derived from the CD at 222 nm, it appears that helicity does not propagate through the indifferent sequence. © 1994 John Wiley & Sons, Inc.