bluuebunny/crossref_metadata_2025 huggingface dataset:
A sequence‐dependent 1H‐NMR study on the formation of β‐turns in tetrapeptides containing charged residues
Authors: Liu Xiaohong , Scott Paul G. , Otter Albin , Kotovych George
Published: December 2004

The importance of side‐chain charge interactions in the formation of β‐turns was studied. Sixteen protected NAc‐tetrapeptide amides were studied, namely the variants of DEKS: NEKS, EEKS, DDKS, DQKS, NQKS, DERS, NERS, EERS, DDRS, NDRS, DQRS, and DKES. Three tetrapeptides—NPDM, NSDM, and NDDS—were also studied as they have a high probability of forming β‐turns, based on statistical predictions. The results indicate that a small proportion of type I β‐turn exists in solutions of DEKS and DERS in methanol/ water (60/40), while NEKS has an even smaller population of this turn. The other tetrapeptides are present in solution only in the extended conformation. These results clearly show the importance of the salt bridge between the side chains of K2 and E3 or R2 and E3, as well as the importance of the charge on the side chain of the first residue in stabilizing the β‐turn. The relevance of statistical predictions for β‐turns in short peptides is discussed.
The electrostatic contribution to DNA base‐stacking interactions
Authors: Friedman Richard A. , Honig Barry
Published: December 2004

Base‐stacking and phosphate‐phosphate interactions in B‐DNA are studied using the finite difference Poisson–Boltzmann equation. Interaction energies and dielectric constants are calculated and compared to the predictions of simple dielectric models. No extant simple dielectric model adequately describes phosphate–phosphate interactions. Electrostatic effects contribute negligibly to the sequence and conformational dependence of base‐stacking interactions. Electrostatic base‐stacking interactions can be adequately modeled using the Hingerty screening function. The repulsive and dispersive Lennard–Jones interactions dominate the dependence of the stacking interactions on roll, tilt, twist, and propeller. The Lennard–Jones stacking energy in ideal B‐DNA is found to be essentially independent of sequence.
Characterization at atomic resolution of peptide helical structures
Authors: Benedetti E. , Di Blasio B. , Pavone V. , Pedone C. , Toniolo C. , Crisma M.
Published: December 2004

A survey of literature for the various types of helices experimentally observed in highresolution single crystal x‐ray diffraction analyses of peptides has allowed to determine accurate conformational and helical parameters for the various secondary structures such as the α‐helix, the 310‐helix, the fully extended conformation (25‐helix) and the β‐bend ribbon spiral. For each of these structures the characteristic ϕ, ψ conformational parameters, n, the number of residues per turn, h, the height per residues and p, the pitch of the helix are described.
Three‐dimensional structure and active site of three hydrophobic molecule‐binding proteins with significant amino acid sequence similarity
Authors: Monaco Hugo L. , Zanotti Giuseppe
Published: December 2004

We review our work on bovine and human retinol‐binding protein (RBP), bovine beta lactoglobulin (BLG), and bovine odorant‐binding protein (OBP). These three proteins share a sequence similarity high enough to justify the proposal that their three‐dimensional structure ought to be quite similar, and they also share the function of similar or even identical hydrophobic ligand binding, although with a very different degree of specificity. Thus they constitute an ideal system to exhaustively explore the question of three‐dimensional structure prediction from sequence similarity and the related question of binding site prediction for similar ligands.

We have used x‐ray diffraction techniques on single crystals of human and bovine RBP, bovine milk BLG, and bovine nasal mucosa OBP to investigate this problem. The results of these crystallographic studies indicate that to the level of resolution so far attained, the three‐dimensional structure of these three proteins is reasonably predicted from the sequence similarity. The fold is the same and structural differences are rather subtle.

Finally, we present experimental evidence that the binding sites of RBP, BLG, and OBP are in different regions of the molecules. Thus, it appears that although sequence alignment has correctly predicted the protein fold, it has incorrectly predicted the hydrophobic ligand‐binding sites.
Helix formation in methylated copolymers of lysine and alanine
Authors: Bello Jake
Published: December 2004

Random copolymers of lysine and alanine, 2 : 1 and 1 : 1, were trimethylated on the lysine. amino groups to quaternary ammonium groups. Methylated and unmethylated polymers were prepared with Cl− or ClO as the counterion. CD spectra were measured for increasing concentration of peptide without added salt, and at constant peptide concentration in increasing NaCl or NaClO4. Unmethylated peptides, as the chloride, form α‐helix more readily than do the methylated peptides. The opposite occurs with ClO as counterion. The helix‐promoting effect of methylated lysine residues (ClO counterion) is diminished by the presence of alanine, as compared with effects when lysine is the only type of residue. The effect of methylation of proteins on helix formation may depend on the types of anionic groups with which the protein may be involved.
Early assembly pathways of type I collagen
Authors: Wallace Donald G.
Published: December 2004

A method was developed for computing the free energy (ΔFi) of aggregates of type I collagen. The method was based on a treatment of Matheson and Flory describing phase equilibria of rigid rod polymers. It included a polymer–solvent interaction term that depended on near neighbor transfer energies. Extrahelical portions of the molecule were assigned local interaction energies differing from that assigned to the helix. Free energies of reaction for successive steps along assembly pathways (ΔFi–i+1) were computed. When allowance was made for specific pairing between extrahelical and helical domains, the so‐called D‐staggered (D = 670 Å) alignment of molecules was preferred, as opposed to a nonstaggered, or nematic, alignment. Based on ΔFi–i+1 alone, it appeared that 1D‐staggered oligomers arise first in assembly, followed later by addition of molecules in 4D alignment.

Neither 4D dimers nor 4D‐8D trimers were predicted to be major intermediates in assembly. This result is contrary to previous hypotheses. When energies of activation were included in the analysis, the prediction was less certain, and specific circumstances were identified in which 4D dimers and 4D‐8D trimers were the earliest aggregated species in assembly.
Theoretical determination of conformational paths in citrate synthase
Authors: El‐Kettani M. A. Ech‐Cherif , Durup J.
Published: December 2004

Two methods are developed for the theoretical determination of a conformational path between two well‐documented forms, a closed form and the open form [Remington et al. (1982) J. Mol. Biol. 158, 111–152] of pig heart citrate synthase, a dimeric enzyme of 2 × 437 residues. The first method uses the minimization of the sum of the potential energies at a set of equidistant points, according to Elber and Karplus [(1987) Chem. Phys. Lett. 139, 375–380]. The initialization of the algorithm is modified to account for large‐angle rotations of many groups by performing the interpolations in the space of internal polar coordinates of a set of generalized Jacobi vectors earlier introduced by Durup [(1991) J. Phys. Chem. 95, 1817–1829] and by carefully testing all choices of directions of rotation for determining the initialized midpoint between the known forms. The path includes intermediate points, created by successive splittings of each interval into two equal parts, with a partial energy minimization performed after each splitting. The minimization encounters the well‐known local‐minima problem, which here is handled by low‐temperature molecular dynamics annealing. It is shown that the best ratio of potential energy decrease to rms deviation is achieved by running the dynamics at 50 K, as compared to 100 K and above. The main character of the path obtained is the occurrence of strong to‐and‐fro variations of some dihedral angles at specific stages along the path. The second method, which we name directed dynamics, uses only low‐temperature molecular dynamics simulations by starting trajectories from each of the two known forms with initial velocities directed toward the other one. The procedure is iterated by restarting trajectory pairs after the points of closest approach of the preceding pair. The two half‐paths thus built eventually meet after 70 iterations. This method provides a second path with strong similarities, as well as some differences, with respect to the path obtained by the first method.
Thermodynamic substantiation of water‐bridged collagen structure
Authors: Burjanadze Tengiz V.
Published: December 2004

A solution of the problem of topology of a hydrogen bond net in a triple helix of collagen is suggested on the basis of an analysis of thermodynamic data on denaturation of phylogenetically different collagen [T. V. Burjanadze (1982), Vol. 21, pp. 1489–1501; T. V. Burjanadze, E. I. Tiktopulo, and P. L. Privalov (1987), Dokl. Akad, Nauk. USSR, Vol. 293, pp. 720–724] as well as on the earlier evaluation of the energy of the OH group of the 4−hydroxyproline bond [A. R. Ward and P. Mason (1973), Journal of Molecular Biology, Vol. 29, pp. 431–435]. It is shown that only the water‐bridged collagen structure [G. N. Ramachandran and R. Chandrasekharan (1968), Biopolymers, Vol. 6, pp. 1649–1661: G. N. Ramachandran, M. Bansal, and R. S. Bhatnagar (1973), Biochimica Biophysica Acta, Vol. 322, pp. 166–171: M. Bansal, C. Ramakrishnan, and G. N. Ramachandran (1975), Proceedings of the Indian Academy of Sciences, Vol. 82, pp. 152–164] can explain both the change of thermostability upon proline hydroxylation [J. Rosenbloom, M. Harsch. and S. Jimenez (1973), Archives of Biochemistry and Biophysics, Vol. 158, pp. 478–484] and its phylogenetic change [T. V. Burjanadze (1982)].
The CD of ligand‐DNA systems. 2. Poly(dA‐dT) B‐DNA
Authors: Lyng Reidar , Rodger Alison , Nordén Bengt
Published: December 2004

A systematic theoretical study of the CD of [poly(dA‐dT)]2 and its complexes with achiral small molecules is presented. The CD spectra of [poly(dA‐dT)]2 and of poly(dA):poly(dT) are calculated for various DNA structures using the matrix method. The calculated and experimental spectra agree reasonably well for [poly(dA‐dT)]2 but less well for poly (dA):poly (dT). The calculated CD spectrum of [poly (dA‐dT)]2 fails to reproduce the wavelength region of 205–245 nm of the experimental spectrum. This discrepancy can be explained by a magnetic dipole allowed transition contributing significantly to the CD spectrum in this region. The induced CD of a transition moment of a molecule bound to [poly (dA‐dT)]2 is also calculated. As was the case for [poly(dG‐dC)]2, the induced CD of a groove bound molecule is one order of magnitude stronger than that of an intercalated molecule. The calculations also show considerable differences between pyrimidine‐purine sites and purine‐pyrimidine sites. Both signs and magnitudes of the CD induced into ligands bound in the minor groove agree with experimental observations. © 1992 John Wiley & Sons, Inc.
Flexible‐geometry conformational energy maps for the amino acid residue preceding a proline
Authors: Hurley James H. , Mason David A. , Matthews Brian W.
Published: December 2004

Previously calculated Conformational energy maps suggest that the α‐helical conformation for the residue preceding a proline is disfavored relative to the extended conformation by more than 7 kcal/mol. In known protein structures this conformation is observed, however, to occur for about 9% of all prolines. In addition, introduction or removal of prolines at theoretically unfavorable positions in proteins and peptides can have modest effects on stability and structure. To investigate the discrepancy between calculation and experiment, we have determined how the conformation of the proline affects the calculated energy. We have also explored the effect of bond length and bond angle relaxation on the Conformational energy map. The Conformational energy of the preceding residue is found to be unaffected by the conformation of the proline, but the effect of allowing covalent bond relaxation is dramatic. If bond lengths and angles, and dihedral angles within the pyrrolidine ring, are allowed to relax, a calculated energy difference between the α and β conformations of 1.1 kcal/mol is obtained, in reasonable agreement with experiment. The detailed shape of the calculated energy surface is also in excellent agreement with the observed Conformational distributions in known protein structures. © 1992 John Wiley & Sons, Inc.
Model building of DNA/RNA triple helix containing L‐deoxyadenosine
Authors: Tomioka Nobuo , Itai Akiko
Published: December 2004

A three‐dimensional model of DNA/RNA triple helix that contains a poly(L‐deoxyadenosine) (L‐dA) chain is proposed based on computer‐assisted model building and energy calculations. The model building was performed by a new method that systematically searches possible conformations of nucleotide units in the helical chains. Two possible orientations of sugar‐phosphate chains, in which two homopyrimidine strands are parallel or antiparallel with each other, were considered in the systematic search. Several possible base‐pairing models, in which there are one Watson‐Crick base pair and one other base pair, were also considered. Many possible models selected by the systematic search were further refined through molecular mechanics calculation incorporating a helical boundary condition. The preferred model, which was selected on the basis of potential energy, was the one with Watson‐Crick and Hoogsteen base pairs and with its two polypyrimidine chains in the antiparallel orientation. The model can explain the experimental observation that poly (L‐dA) forms a stable triple helix with poly(uridylic acid) (U) but not with poly(deoxythymidylic acid) (dT). © 1992 John Wiley & Sons, Inc.
Viscoelastic behavior of fractionated ovine submaxillary mucins
Authors: McCullagh C. M. , Soby L. M. , Jamieson A. M. , Blackwell J.
Published: December 2004

Solution properties of fractionated ovine submaxillary mucin (OSM) and asialo OSM (aOSM) in aqueous guanidine hydrochloride have been investigated using light scattering and Theological methods. For the first time we present viscometric evidence in both dilute and concentrated solution that the molecular structure of OSM is that of a wormlike chain. The intrinsic viscosity shows molecular weight dependence consistent with the linear extended chain conformation observed by light scattering measurements. The viscoelastic behavior of the OSM fractions in aqueous guanidine hydrochloride was further examined above the overlap concentration as a function of molecular weight and temperature. Under these solvent conditions in which the role of nonbonding intermolecular interactions is minimized, OSM shows predominantly fluid like behavior. However, high molecular weight OSM shows evidence of the existence of an entanglement network at high concentration. The frequency‐dependent shear storage and loss moduli at all concentrations and molecular weights can be scaled to yield a master curve by incorporating typical viscoelastic shift parameters. The entanglement molecular weight and concentration are consistent with literature data for extended, semiflexible wormlike chains. The behavior of aOSM is similar to that of intact OSM at comparable degrees of coil overlap, indicating that the terminal sialic acid residue on the carbohydrate side chain has no effect on the rheology of concentrated OSM solutions beyond that due to an increase in the hydrodynamic volume. © 1992 John Wiley & Sons, Inc.
Interaction of substance P and its N‐ and C‐terminal fragments with Ca2+: Implications for hormone action
Authors: Ananthanarayanan Vettai S. , Orlicky Stephen
Published: December 2004

In an attempt to understand the role of Ca2+ on the bioactive conformation of peptide hormones, we have examined the interaction between Ca2+ and the neuropeptide substance P. Using CD spectroscopy to monitor conformational changes caused by Ca2+ binding, we found no significant binding of the cation by substance P in water. However, a substantial conformational change occurred in the hormone on Ca2+ addition in trifluoroethanol or an 80:20 (v/v) mixture of acetonitrile and trifluoroethanol. A biphasic binding of Ca2+ was observed in these solvents with saturation at 2 cations per hormone molecule. Mg2+ caused a relatively smaller conformational change in the hormone. A peptide corresponding to residues 1–7 at the N‐terminal fragment of substance P showed a weak nonsaturating binding of Ca2+ in the nonpolar solvents whereas the 7–11 C‐terminal fragment peptide displayed a binding indicative of an 1 : 1 Ca2+ / peptide complex. Ca2+ binding by the hormone and the 7–11 fragment was also monitored by changes in fluorescence of the phenylalanyl residues. The results support the conclusion drawn from the CD data about a distinct Ca2+ binding site in the C‐terminal part of substance P. The Kd values obtained from fluorescence data were 160 µM for Ca2+ and 1 mM for Mg2+ binding by substance P. The hormone and the two peptide fragments were also tested for their effect on the stability of dimyristoyl lecithin vesicles. Substance P and the N‐terminal fragment caused no significant leakage of either fluorescent dyes or K+ trapped in the vesicles. Nor did they cause membrane fusion as monitored by the fluorescence quenching method. In contrast, the C‐terminal 7–11 fragment caused considerable leakage of vesicular contents and promoted membrane fusion. When tested for their ability to translocate Ca2+ across the lipid bilayer in dimyristoyl lecithin vesicles containing the Ca2+ indicator Arsenazo III, both substance P and the 7–11 fragment showed significant Ca2+ transport while the 1–7 fragment showed negligible transport. The apparent transport of the 7–11 fragment is attributable to its effect on the integrity of the bilayer membrane. These data distinguish the N‐ and C‐terminal domains of substance P in terms of their lipid‐dependent interaction with Ca2+. In light of the requirement of extracellular Ca2+ for substance P action, the data are also suggestive of the possibility of the involvement of Ca2+ in the bioactive conformation of this hormone and in its interaction with the receptor. © 1992 John Wiley & Sons, Inc.
Characterization of β‐turns in cyclic hexapeptides in solution by fourier transform IR spectroscopy
Authors: Mantsch H. H. , Perczel A. , Hollósi M. , Fasman G. D.
Published: December 2004

The β‐turn represents a structural element frequently encountered in globular proteins. However, in spite of various theoretical and experimental studies the ir signature bands of pure β‐turns are still not established beyond doubt. Although considerable information exists now on the ir spectra of β‐helical and β‐sheet structures, the lack of knowledge concerning turn structures in general, and that of β‐turns in particular, presents a major uncertainty in the estimation of global protein secondary structures from ir spectroscopic data. To obtain more specific information about the characteristic amide bands in β‐turns, we report herein an ir spectroscopic analysis of a series of five cyclic pseudo‐hexapeptides known to form β‐turns from previous CD and nmr studies [A. Perczel, M. Hollósi, B. M. Foxman, and G. D. Fasman (1991) Journal of the American Chemical Society, Volume 113, pp. 9772‐9784 ]. We show here that in these cyclic peptides the amide groups involved in β‐turns that comprise a ten‐membered hydrogen‐bonded ring (and represent the first H‐bond pair in a β‐sheet), give rise to characteristic amide I bands in the range 1638–1646 cm−1, with the exact position depending on the solvent and the nature of the side‐chain substituents. © 1993 John Wiley & Sons, Inc.
Approximation and characterization of molecular surfaces
Authors: Duncan Bruce S. , Olson Arthur J.
Published: December 2004

The representation and characterization of molecular surfaces are important in many areas of molecular modeling. Parametric representations of protein molecular surfaces are a compact way to describe a surface, and are useful for the evaluation of surface properties such as the normal vector, principal curvatures, and principal curvature directions. Simplified representations of molecular surfaces are useful for efficient rendering and for the display of large‐scale surface features. Several techniques for representing surfaces by expansions of spherical harmonic functions have been reported, but these techniques require that the radius function is single valued, that is, each ray from an origin inside the surface intersects the surface at one and only one point. A new technique is described that removes this limitation and can be used to compute surface shape properties. © 1993 John Wiley & Sons, Inc.
Dynamic light scattering of aqueous solutions of linear aggregates induced by thermal denaturation of ovalbumin
Authors: Nemoto Norio , Koike Akihiro , Osaki Kunihiro , Koseki Taihei , Doi Etsushiro
Published: December 2004

Dynamic light scattering measurements were performed on dilute aqueous solutions of native ovalbumin (OA) and on those of linear OA aggregates induced by thermal denaturation at low ionic strength and neutral pH. The weight‐average molecular weight Mw of four aggregates tested ranged from 1,700,000 to 5,500,000. The translational diffusion coefficient D0 of native OA at infinite dilution was estimated as 8.70 × 10 −7 cm2/s, which gave 56.0 Å as the diameter of the rigid spherical particle. The intensity autocorrelation function of linear OA polymers was analyzed with the cumulant method to obtain the first cumulant Λe. The dependence of Λe on the scattering vector q at very low polymer concentration was found intermediate between those of a flexible chain and a rigid rod. The translational diffusion coefficient Dtr [≡ (Te/q2)q → 0] was in proportion to M, and the magnitude was in good agreement with a value calculated from the wormlike cylinder model with values of three parameters determined in an earlier study, ML = 1600 Å−1, d = 120 Å, and Q = 230 Å, where ML, d, and Q are the molecular weight per unit length, diameter, and persistence length, respectively. Based on these results, a new model, to be called as the dimer model, was proposed to interpret the formation mechanism of linear OA polymers induced by thermal denaturation. © 1993 John Wiley & Sons, Inc.
Design of peptides: Crystal and molecular structure of a 310‐helical peptide N‐Boc‐L‐Phe‐dehydro‐Phe‐L‐Val‐L‐Phe‐dehydro‐Phe‐L‐Val‐Och3
Authors: Padmanabhan B. , Singh T. P.
Published: December 2004

Highly specific peptide structures can be designed by inserting dehydro residues into peptide sequences. The peptide N‐Boc‐L‐Phe‐dehydro‐Phe‐L‐Val‐L‐Phe‐dehydro‐Phe‐L‐Val‐OCH3, synthesized by conventional procedures, crystallizes from methanol‐‐water mixtures at 4°C in the tetragonal space group P43 with cell parameters a = b = 13.829 ± 0.003 Å, c = 27.587 ± 0.008 Å, V = 5275.5 ± 0.2 Å3, Z = 4, dm = 1.152 ± 0.005 g cm−3, dcal = 1.150 ± 0.005 g cm−3. The overall residual factor R = 0.084 for 2342 reflections, with 2θmax = 140° using CuKα radiation. The backbone torsion angles are θ1 = −171(1)°, ω0 = 168 (1)°, ϕ1 = 77 (2)°, ψ1 = 41 (2)°, ωl = 169 (1)°, ϕ2 = −46 (2)°, ψ2 = ‐24 (2)°, ω2 = 179 (1)°, ϕ3 = −63 (2)°, ϕ3 = −19 (2)°, ω3 = 171 (1)°, ϕ4 = −67 (2)°, ψ4 = −8 (1)°, ω4 = 169 (1)°, ψ5 = −61 (1)°, ϕ5 = −26(1)°, ω5 = 177(1)°, ψ6 = −122 (1)°, ϕ = 26 (2)°. The peptide adopts a 310‐helical conformation with three intramolecular hydrogen bonds (i + 3 → i) involving carbonyl oxygen atoms of Phe1, dehydro‐Phe2, Val3, and the NH groups of Phe4, dehydro‐Phe5, and Val6 with distances of 3.01 (1), 2.82 (1), and 3.09 (2) Å, respectively. The structure determination revealed that a hexapeptide with two dehydro‐Phe residues at (i + 2) and (i + 5) positions generates a 310‐helical conformation. The helical peptide molecules are arranged in a major helical arrangement about the 43axis. These helices are packed parallel to the c axis and form several interdigitating hydrogen bonds. The interhelix hydrogen‐bonding regions are separated by van der Waals interactions involving the side chains of Phe, dehydro‐Phe, and Val residues. © 1993 John Wiley & Sons, Inc.
Synthesis, biological activity, and conformational analysis of [pGlu6, N‐MePhe8, Aib9] substance P (6–11): A selective agonist for the NK‐3 receptor
Authors: Tallon M. , Ron D. , Halle D. , Amodeo P. , Saviano G. , Temussi P. A. , Selinger Z. , Naider F. , Chorev M.
Published: December 2004

A highly potent and selective agonist to the tachykinin NK‐3 receptor, [pGlu6, N‐MePhe8, Aib9] substance P (6–11) (I), was synthesized via the solid phase method. The ED50 of I was 4n M in the guinea pig ileum in the absence of atropine (NK‐1 + NK‐3 receptors) and this agonist was 5000‐fold less potent in the presence of atropine (NK‐1 receptor). The analogue was virtually inactive in the rat vas deferens (NK‐2 receptor). A detailed analysis of the solution conformation of this analogue in DMSO‐d6 and in a DMSO‐d6 H2O cryornixture was carried out by a combination of 1H‐nmr 2D techniques (DQF‐COSY, TOCSY, NOESY and ROESY) and model building based on empirical energy calculations. Peptide I exists as a mixture of isomers containing cis and trans Phe‐N‐MePhe peptide bonds. The main isomer, containing a cis Phe‐N‐MePhe peptide bond, shows a preferred folded conformation characterized by a type VI β‐turn with Phe and N‐MePhe in the i + 1 and i + 2 positions. The turn is followed by a helical segment extending to the C‐terminal. This conformation is compared to previously reported conformations of other selective tachykinin agonists and may be a promising lead for the design of novel NK‐3 agonists with additional conformational constraints. © 1993 John Wiley & Sons, Inc.
On the “filterable aggregates and other particles” interpretation of the extraordinary regime of polyelectrolytes
Authors: Schmitz Kenneth S.
Published: December 2004

Quasi‐elastic light scattering studies on some polyelectrolyte systems exhibit a somewhat “bizarre” behavior in the profile of the apparent diffusion coefficient Dapp as a function of the salt concentration Cs. As Cs is decreased, Dapp first increases in accordance with polyelectrolyte theories, and then undergoes a precipitous drop in value by over an order of magnitude at a well‐defined critical value Cs = C. This “transition” from Cs > C (ordinary) to Cs < C (extraordinary) is referred to as the “ordinary‐extraordinary” (o‐e) transition.

Ghosh, Peitzsch, and Reed [(1992) Biopolymers, Vol. 32, pp. 1105–1122] proposed a “filterable aggregate” (FA) and “other particle” interpretation for the o‐e transition and its reversibility in regard to ionic strength changes. The present communication examines in detail the FA model as applied to the o‐e transition. It is shown that the FA model fails to account of the established characteristics of the o‐e transition. © 1993 John Wiley & Sons, Inc.
Noncoded residues as building blocks in the design of specific secondary structures: Symmetrically disubstituted glycines and β‐alanine
Authors: Di Blasio Benedetto , Pavone Vincenzo , Lombardi Angela , Pedone Carlo , Benedetti Ettore
Published: December 2004

Structural changes can be induced in a peptide by selective substitution of coded α‐amino acid residues by noncoded α‐amino acid residues and the consequent production of analogues with modified structure and conformational preferences.

In this review article we summarize the solid state structural results and the conformational preferences of two classes of “building blocks”: (a) the linear and cyclic symmetrically α, α‐disubstituted glycines in which either two identical n‐alkyl groups replace the hydrogen atoms of the glycine residue or a cyclic aliphatic side‐chain system is formed by linking the two α‐carbon side chains, respectively; and (b) the β‐alanine residue. Examples, whenever possible, of the use of these residues for the elucidation of the bioactive conformation in the appropriate biological systems will be given. © 1993 John Wiley & Sons, Inc.
Synthesis and conformational study of peptides possessing helically arranged ΔZPhe side chains
Authors: Inai Yoshihito , Ito Takaaki , Hirabayashi Tadamichi , Yokota Kenji
Published: December 2004

Z‐Dehydrophenylalanine (ΔzPhe) possessing four oligopeptides, Boc‐(L‐Ala‐ΔzPhe‐Aib)n‐OCH3 (n = 1–4: Boc, t‐butoxycarbonyl; Aib, α‐aminoisobutyric acid), were synthesized, and their solution conformations were investigated by 1H‐nmr, ir, uv, and CD spectroscopy and theoretical CD calculation. 1H‐nmr (the solvent accessibility of NH groups) and ir studies indicated that all the NH groups except for those belonging to the N‐terminal L‐Ala‐ΔzPhe moiety participate in intramolecular hydrogen bonding in chloroform. This suggests that the peptides n = 2–4 have a 4 → 1 hydrogen‐bonding pattern characteristic of 310‐helical structures. The uv spectra of all these peptides recorded in chloroform and in trimethyl phosphate showed an intense maximum around 276 nm assigned to the ΔzPhe chromophores. The corresponding CD spectra of the peptides n = 2–4 showed exciton couplets with a negative peak at longer wavelengths, whereas that of the peptide n = 1 showed only weak signals. Theoretical CD spectra were calculated for the peptides n = 2–4 of several helical conformations, on the basis of exciton chirality method. This calculation indicated that the three peptides form a helical conformation deviating from the perfect 310‐helix that contains three residues per turn, and that their side chains of Δz Phe residues are arranged regularly along the helix. The center‐to‐center distance between the nearest phenyl pair(s) was estimated to be ∼ 5.5 Å. The chemical shifts of the ΔzPhe side‐chain protons (Hβ and aromatic H) for the peptides n = 2–4 indicated anisotropic shielding effect of neighboring phenyl group(s); the effect also supports a regular arrangement of the Δz Phe side chains along the helical axis. © 1993 John Wiley & Sons, Inc.
The loop problem in proteins: A monte carlo simulated annealing approach
Authors: Carlacci Louis , Englander S. Walter
Published: December 2004

A Monte Carlo simulated annealing (MCSA) algorithm was used to generate the conformations of local regions in bovine pancreatic trypsin inhibitor (BPTI) starting from random initial conformations. In the approach explored, only the conformation of the segment is computed; the rest of the protein is fixed in the known native conformation. Rather than follow a single simulation exhaustively, computer time is better used by performing multiple independent MCSA simulations in which different starting temperatures are employed and the number of conformations sampled is varied. The best computed conformation is chosen on the basis of lowest total energy and refined further. The total energy used in the annealing is the sum of the intrasegment energy, the interaction energy of the segment with the local surrounding region, and a distance constraint to generate a smooth connection of the initially randomized segment with the rest of the protein.

The rms deviations between the main‐chain conformations of the computed segments in BPTI and those of the native x‐ray structure are 0.94 Å for a 5‐residue α‐helical segment, 1.11 Å for a 5‐residue β‐strand segment, and 1.03, 1.61, and 1.87 Ã for 5‐, 7‐, and 9‐residue loop segments. Side‐chain deviations are comparable to the main‐chain deviations for those side chains that interact strongly with the fixed part of the protein. A detailed view of the deviations at an atom‐resolved level is obtained by comparing the predicted segments with their known conformations in the crystal structure of BPTI. These results emphasize the value of predetermined fixed structure against which the computed segment can nest. © 1993 John Wiley & Sons, Inc.
Electromigration behavior of poly‐(L‐glutamate) conformers in concentrated polyacrylamide gels
Authors: Dolník Vladislav , Novotny Milos , Chmelík Josef
Published: December 2004

During electrophoretic separation of anionic polyamino acids, resolution according to the number of peptide units can be achieved in capillaries filled with hydrophilic gels. While polyaspartate preparations yield single peaks for the individual oligomers at pH above 8.0, polyglutamates exhibit an anomalous behavior of peak splitting, which is attributed here to the separation of the oligopeptide conformers. An Asp‐Glu (1:1) copolymer yields single peaks under similar conditions. At pH near 4.5, where polyglutamate is expected to exist in its α‐helix form, peak splitting disappears. Upon heating to 95°C for at least 120 h (procedure described to transform the α‐helix into a β form), peak splitting disappeared, but could be reestablished after cooling for several days. When a highly charged cation spermine was added to the operational electrolyte, triple peaks appeared in the electropherogram due to the ion‐pair formation. The largest peak in every triplet has been tentatively assigned to the α‐helix form. The electrophoretic results described have been largely supported by CD spectra. © 1993 John Wiley & Sons, Inc.
Hybrid Monte Carlo simulations theory and initial comparison with molecular dynamics
Authors: Brass A. , Pendleton B. J. , Chen Y. , Robson B.
Published: December 2004

A formal partially dynamical approach to ergodic sampling, hybrid Monte Carlo, has been adapted for the first time from its proven application in quantum chromodynamics to realistic molecular systems. A series of simulations of pancreatic trypsin inhibitor were run using temperature‐rescaled molecular dynamics and hybrid Monte Carlo. It was found that simulations run using hybrid Monte Carlo equilibrated an order of magnitude faster than those run using temperature‐rescaled molecular dynamics. Certain aspects of improved performance obtained using hybrid Monte Carlo are probably due to the increased efficiency with which this algorithm explores phase space. To discuss this we introduce the notion of “trajectory stiffness”. © 1993 John Wiley & Sons, Inc.
Conformational analysis of the type II and type III collagen α‐1 chain N‐telopeptides by 1H‐NMR spectroscopy and restrained molecular mechanics calculations
Authors: Otter Albin , Scott Paul G. , Kotovych George
Published: December 2004

The type II and type III collagen α‐1 chain N‐telopeptides are a nonadecamer with the sequence pEMAGGFDEKAGGAQLGVMQ‐NH2 and a tetradecamer with the sequence pEYEAYDVKSGVAGG‐NH2, respectively. Their conformations have been studied in CD3OH/H2O (60/40) solution by means of two‐dimensional proton nmr spectroscopy. Based on double quantum filtered correlation spectroscopy, total correlation spectroscopy, rotating frame nuclear Overhauser enhancement (ROE) spectroscopy, and nuclear Over‐hauser enhancement (NOE) spectroscopy experiments, all resonances were assigned and the conformational properties were analyzed in terms of vicinal NH‐Hα coupling constants, sequential and medium‐range NOEs (ROEs), and amide proton temperature coefficients. The NOE distance constraints as well as dihedral constraints based on the vicinal NH‐Hα coupling constants were used as input parameters for restrained molecular mechanics, consisting of restrained molecular dynamics and restrained energy minimization calculations. The type II N‐telopeptide's conformation is dominated by a fused βγ‐turn between Phe6 and Ala10, stabilized by three hydrogen bonds and a salt bridge between the side‐chain end groups of Glu8 and Lys9. The first 5 amino acids are extended with a much higher degree of conformational freedom. The 2 Gly residues following the turns were found to be highly flexible (hinge‐like), leaving the spatial position of the second half of the molecule relative to the fused βγ‐turn undefined. In the type III telopeptide, a series of sequential NH(i)‐NH(i + 1) ROEs were observed between the amino acids Tyr2 and Ser9, indicating that a fraction of the conformational space is helical. However, the absence of medium‐range ROEs and the lack of regularity of the effects associated with α‐helices suggest the presence of a nascent rather than a complete helix. © 1993 John Wiley & Sons, Inc.
Secondary structure of proteins associated in thin films
Authors: Safar Jiri , Roller Peter P. , Ruben George C. , Gajdusek D. Carleton , Gibbs Clarence J.
Published: December 2004

The solid state secondary structure of myoglobin, RNase A, concanavalin A (Con A), poly(L‐lysine), and two linear heterooligomeric peptides were examined by both far‐uv CD spectroscopy1 and by ir spectroscopy. The proteins associated from water solution on glass and mica surfaces into noncrystalline, amorphous films, as judged by transmission electron microscopy of carbon‐platinum replicas of surface and cross‐fractured layer. The association into the solid state induced insignificant changes in the amide CD spectra of all α‐helical myoglobin, decreased the molar ellipticity of the α/β RNase A, and increased the molar ellipticity of all‐β Con A with no change in the positions of the bands' maxima. High‐temperature exposure of the films induced permanent changes in the conformation of all proteins, resulting in less α‐helix and more β‐sheet structure. The results suggest that the protein α‐helices are less stable in films and that the secondary structure may rearrange into β‐sheets at high temperature. Two heterooligomeric peptides and poly (L‐lysine), all in solution at neutral pH with “random coil” conformation, formed films with variable degrees of their secondary structure in β‐sheets or β‐turns. The result corresponded to the protein‐derived Chou‐Fasman amino acid propensities, and depended on both temperature and solvent used. The ir and CD spectra correlations of the peptides in the solid state indicate that the CD spectrum of a “random” structure in films differs from random coil in solution. Formic acid treatment transformed the secondary structure of the protein and peptide films into a stable α‐helix or β‐sheet conformations. The results indicate that the proteins aggregate into a noncrystalline, glass‐like state with preserved secondary structure. The solid state secondary structure may undergo further irreversible transformations induced by heat or solvent. © 1993 John Wiley & Sons, Inc.
Refined three‐dimensional solution structure of a snake cardiotoxin: Analysis of the side‐chain organization suggests the existence of a possible phospholipid binding site
Authors: Gilquin Bernard , Roumestand Christian , Zinn‐Justin Sophie , Ménez André , Toma Flavio
Published: December 2004

The solution structure of toxin γ (60 residues, 4 disulfides) from Naja nigricollis was determined by proton nmr and molecular modeling with DIANA and X‐PLOR. The structures were calculated using 489 distance and 81 dihedral angle constraints. The average atomic rms deviation between the nine refined structures and the average structure is 0.118 nm for the backbone atoms. Toxin γ has an overall folding consisting of three loops stabilized by the four disulfides and forming a two‐ and a three‐stranded β‐sheet (loop I and loops II, III, respectively). The same type of folding has been observed for two homologous cardiotoxins. The very close similarity of the solution structure of toxin γ and the crystal structure of toxin V includes details of the topological arrangement of numerous side chains. Among these are the conserved residues K12, K18, K35, and Y22, known to be critical for the cytolytic activity of toxin γ. A cluster of hydrophobic side chains organized around Y22 is found on one side of the three‐stranded β‐sheet and is spatially close to a group of three lysines (K12, K18, K35). The side chains of these lysines form a cationic site that can accommodate the binding of a phosphate ion as found in the crystal structure of toxin V. The hydrophobic cluster constitutes a possible binding site for the hydrophobic moiety of phospholipids. Together with the complementary cationic site, this hydrophobic surface can form a conserved site by which cardiotoxins bind to membrane phospholipids. © 1993 John Wiley & Sons, Inc.
Overcrossing spectra of protein backbones: Characterization of three‐dimensional molecular shape and global structural homologies
Authors: Arteca Gustavo A.
Published: December 2004

A procedure is developed and applied to characterize the global shape and folding features of the backbone of a chain molecule. The methodology is based on the following concept: the probability of observing a rigid placement of a backbone in 3‐space as a projected curve with N overcrossings. The numerical computation of these probabilities allows one to construct the overcrossing spectrum of a macromolecule at a given configuration. Although the spectrum is built from the knowledge of the nuclear geometry of the main‐chain atoms, the shape descriptor overlooks local geometrical features (such as distances and contacts) and provides a characterization of essential (topological) features of the overall fold, such as its compactness and degree of entanglement. In contrast with other shape descriptors, the present approach gives an absolute characterization of the configuration considered, and not one that is relative to an arbitrarily chosen reference structure. Moreover, it is possible to discriminate between folding features that otherwise may not be distinguished when using other geometrical or topological global descriptors. The overcrossing spectrum is proposed as a tool that complements current structural analyses of macromolecules, especially when monitoring structural homologies within a group of related or unrelated polymers. In this work, we apply the methodology to the analysis of proteins having the globin fold. The results are compared with those of other proteins exhibiting similar size and number of residues. Some basic properties of the spectra as a function of the chain length are also discussed. © 1993 John Wiley & Sons, Inc.
Self‐consistent reaction field computation of the reactive characteristics of DNA bases in water
Authors: Orozco Modesto , Luque F. J.
Published: December 2004

The effect of the solvent in the molecular properties of DNA bases has been explored by using a self‐consistent reaction field (SCRF) method based on the AM1 (Austin Model 1) Hamiltonian and a modified version of the high level Miertus–Scrocco–Tomasi (MST) algorithm. MST/AM1 estimates of free energies of hydration compare qualitatively well with the available experimental data, as well as with the results obtained from molecular dynamic simulations. Furthermore, the changes in the dipole predicted by the MST/AM1 method are in good agreement with Monte Carlo/quantum mechanical data, as well as with AM1‐SM2 (Soluation Model 2) estimates. AM1/MST calculations of Mulliken, and electrostatic charges, dipoles, molecular electrostatic potentials and molecular interaction potentials in both vacuum and solution allowed us to quantify the effect of the water on the reactive characteristics of the DNA bases. This effect is large and complex, and cannot be neglected in theoretical calculations where an accurate representation of the DNA bases is needed. The possibility of including the polarization effect of the water into force‐field simulations of DNA structures is discussed. © 1993 John Wiley & Sons, Inc.
Conformational studies of heterochiral peptides with diastereoisomeric residues: Crystal and molecular structures of linear dipeptides derived from leucine, isoleucine, and allo‐isoleucine
Authors: Di Blasio Benedetto , Saviano Michele , Del Duca Valerio , De Simone Giuseppina , Rossi Filomena , Pedone Carlo , Benedetti Ettore , Lorenzi Gian Paolo
Published: December 2004

The x‐ray diffraction analyses of three N‐ and C‐terminally blocked L, D dipeptides, namely t‐Boc‐D‐Leu‐L‐Leu‐OMe (1), t‐Boc‐L‐Ile‐D‐alle‐OMe (2), and t‐Boc‐D‐aIle‐L‐Ile‐OMe (3) containing enantiomeric or diastereomeric amino acid residues have been carried out. The structures were determined by direct methods and refined anisotropically to final R factors of 0.077. 0.058. and 0.072 for (1) (2) and (3), respectively.

Peptides 1–3 all assume a similar U‐shaped structure with ϕ and ψ torsion angles cosrresponding to one of the possible calculated minimum energy regions (regions E and G for L residues, and F*. D* and H* for D residues). The peptide backbones of 1‐3 are almost super‐imposable [provided that the appropriate inversion of the chiral centers of (2) is made].

Side‐chain conformations of Leu residues in peptide (1) are g− (tg−) for the L‐Leu residue and the mirrored g+ (tg+) for the D‐Leu residue; however, in peptides (2) and (3) the conformations of the isoconfiguralional side chains of the Ile or allo‐Ile residues are (g−t) t and (tg+) tfor the L‐Ile and the D‐allo‐Ile moieties, respectively. In all cases, these conformations correspond to the more populated conformers of β‐branched residues statistically found in crystal structures of small peptides.

The results seem to indicate that, at least in short peptides with enantiomeric or diastereoisomeric residues, the change in chirality in the main‐chain atoms perturbs the backbone conformation to a lesser extent and the side chain conformation to a greater extent. © 1995 John Wiley & Sons, Inc.
Conformation of cyclobradykinin by nmr and distance geometry calculations
Authors: Pellegrini Maria , Mammi Stefano , Gobbo Marina , Rocchi Raniero , Peggion Evaristo
Published: December 2004

The conformation of the head‐to‐tail cyclic analogue of bradykinin in DMSO was investigated by nmr. Three sets of resonances were detected and fully assigned. These were attributed to the presence of three stable conformers, two of which were exchanging on the nmr time scale. A fourth, incomplete set of resonances was detected but not assigned. The three major conformers differ in the conformation at the three X‐Pro bonds present.

From nuclear Overhauser effect spectroscopy (NOESY) spectra, three sets of interproton distances were derived and used in NOE‐restrained distance geometry calculations. The resulting structures were refined by energy minimization to yield families of structures. Conformer I is characterized by the presence of two type VIb β‐turns between Arg1 and Gly4 and between Phe5 and Phe8. The first β‐turn is present also in conformer II, while an inverse γ‐turn bridging Pro3 is the most pronounced structural feature of conformer III. © 1995 John Wiley & Sons, Inc.
1‐dehydrogenation of steroids by Septomyxa affinis
Authors: Koepsell H. J.
Published: December 2004

1‐Dehydrogenation of steroids by Septomyxa affinis is brought about by an inducible enzyme. Only soluble substrate steroid is attacked. Individual steroids are dehydrogenated at different relative rates. The pH‐activity curve is shallow.
An apparatus for aeration of tissue cells in suspended culture with controlled gas mixtures
Authors: Daniels W. F. , Browning E. W.
Published: December 2004

An apparatus is described for the aeration of a series of tissue cultures at rates which may be varied independently for each vessel. The composition of the aerating gas can be adjusted to any desired percentages of CO2 and O2. While designed particularly for study of the aeration requirements of submerged tissue growth, the equipment is equally adaptable for study of submerged growth of bacterial and other systems. The apparatus has been designed for future scale‐up and is adaptable to both the overlay and bubble‐through types of aeration. Flow rates necessary for producing mixtures of 5.0% CO2 and 95.0% air or 5.6% CO2, 14.0% O2, and 80.4% nitrogen are given. The described system has been operated satisfactorily and has proved to be an inexpensive and useful research tool.