bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure of the ion channel peptide antibiotic gramicidin A
Authors: Langs David A.
Published: December 2004

The crystal structure of the uncomplexed orthorhombic form of gramicidin A has been determined at 0.86 Å resolution. The polypeptide crystallizes from ethanol as a left‐handed, double‐stranded, antiparallel β5.6‐helical dimer that is 31 Å long and an average of 4.8 Å in diameter. The uncomplexed channel does not contain ions or solvent molecules, and its diameter is not uniform but varies from a minimum of 3.85 Å to a maximum of 5.47 Å. There are three empty cavities in the channel that have a diameter exceeding 5.25 Å and appear to be large enough to accommodate water molecules or potassium ions in a chemically reasonable coordination environment. The observed crystal structure does not offer any obvious clues as to why an antiparallel β5.6‐helix cannot function as an ion channel in lipid bilayers.
A theoretical investigation of the intercalative binding of 7‐H pyrido[4.3C]carbazole chromophore into a d(CpG)2 minihelix
Authors: Maroun Rachid , Gresh Nohad
Published: December 2004

Theoretical computations are performed of the intercalative binding to a model d(CpG)2 minihelix of 7‐H pyrido[4.3C]carbazole, the precursor of the antitumor bisintercalating drug ditercalinium. The conformations of the intercalation site are generated by the AGNAS procedure (algorithm to generate nucleic acid structures) of Miller and co‐workers. The ligand‐nucleotide interactions and the nucleotide conformational energies are computed with the SIBFA procedures (sum of interactions between fragments ab intio computed), which use formulas of empirical origin that reproduce ab initio SCF (self‐consistent field) computations. Among the candidate intercalation sites most favored energetically, one has a pattern of conformational angles related to the one determined crystallographically by Sobell et al. in a series of x‐ray structural studies of small intercalator–dinucleotide monophosphate complexes. Optimal values of the unwinding angle, found in the range of −12° to −14°, are consistent with available experimental data on DNA.
Calorimetric study of the effect of intrachain cross‐linking on lysozyme unfolding
Authors: Segawa Shin‐Ichi , Sugihara Mitsuru , Maeda Tomoko , Mitsuhisa Yukio , Kodama Michiko , Seki Syûzô , Sakiyama Minoru
Published: December 2004

Thermodynamics of unfolding of lysozyme cross‐linked between Glu 35 and Trp 108 were studied in solutions of various concentrations of 1‐propanol (1‐PrOH) at pH 3.7 by means of scanning microcalorimetry. The transition temperature for the cross‐linked lysozyme increases by 17–19°C due to cross‐linking at every concentration of 1‐PrOH. This corresponds to the increase in the unfolding Gibbs free energy of about 28 kJ · mol−1, which is independent of the concentration of 1‐PrOH. It was found that the unfolding enthalpy of cross‐linked lysozyme is only slightly larger than that of intact one, and the unfolding entropy of the cross‐linked one is nearly equal to that of the intact one, if both are compared at the same temperature. The stabilization mechanism for the cross‐linked lysozyme is discussed on the basis of these calorimetric data.
Site‐specific laser modification (cleavage) of oligodeoxynucleotides
Authors: Benimetskaya L. Z. , Bulychev N. V. , Kozionov A. L. , Koshkin A. A. , Lebedev A. V. , Novozhilov S. Yu. , Stockman M. I.
Published: December 2004

Sequence‐specific photomodification of oligodeoxynucleotide pAGAGTATTGACTTA (“a target”) has been carried out with the aid of complementary fluorescent probes. Such a probe consisted of oligodeoxynucleotide pAATACTCT and a chromophore group attached to its 5′ end. Three different derivatives of ethidium bromide were used as a chromophore. The photomodification was induced by nitrogen laser radiation (337 nm, 15 MW /cm2). The irradiation induces the following photodamages: target cleavage at the specific binding site with a cutting off of the 8‐mer from its 5′ end (yield up to 12%), formation of specific covalent adduct target‐probe with a yield of 20–70%, and piperidine‐sensitive target modifications with a 7–27% yield (for different chromophores). The total yield of specific photodamages of all kinds is 50–80%. The target cleavage and generation of piperidine‐sensitive modifications are optically nonlinear processes. Piperidine treatment of the irradiated samples led to specific cleavage of the target with the yield up to 40%. All kinds of observed modifications are not influenced by high concentrations of free radical scavengers: 1.3M tBuOH and 10 mM cystamine. The pattern of cleavage indicates that the most probable position of the chromophore is between T8 and G9 of the target, i.e., the chromophore stacks on top of the last A · T base pair of the duplex. The aggregate of evidence is in agreement with the mechanism of nonlinear photomodification (the cleavage and generation of piperidine‐sensitive modifications) based on the transfer of two‐photon excitation energy from the chromophore to the target.
Raman spectroscopy of supercoiled and nicked ColE1 plasmid
Authors: Christens‐Barry William A. , Martin James C. , Lebowitz Jacob
Published: December 2004

Native supercoiled and nicked Co1E1 DNA were examined using laser Raman spectroscopy. Co1E1 contains 6646 base pairs (bp) and, when supercoiled, approximately 47 negative supercoils. An analytical buoyant density gradient centrifugation technique developed by Burke and Bauer was scaled to preparative quantities, and used to isolate the supercoiled plasmid fraction from its nicked counterpart. This procedure allowed enriched fractions of the supercoiled plasmid to be extracted without the use of the optical contaminant ethidium bromide. The intensities of several Raman bands were altered between the spectra of the two topological forms. Notably absent were any changes in bands arising from cytosine and guanine vibrations. The observed changes are interpreted in terms of the polymorphic structures which have been observed in many DNA structural studies. The results of this study suggest that accommodation of supercoiling takes place chiefly in A‐T base pairs and backbone moieties, without substantial modification of G‐C base‐pair structure. Premelting effects may account for the observed changes, including a slight shift to lower frequency of a band known to be responsive to base‐pair disruption. Heteronomous ribose sugar pucker is evident in both supercoiled and nicked plasmid species. No gross conformational transitions were detected for native supercoiled DNA, and consequently, subtle rearrangements appear sufficient to absorb the supercoiling deformations.
Local dynamics in biological macromolecules
Authors: Perico Angelo
Published: December 2004

The diffusive approach in the optimized Rouse–Zimm approximation to segment relaxation in the nanosecond time domain (ORZLD) is extended to consider chains of nonequivalent units as occurring in biological macromolecules. The correlation times for second‐order time correlation functions of each virtual bond on the chain are calculated for some homopolypeptides, and random and regular copolypeptides. The expected correlation times for biological macromolecules organized in multiple domains are discussed via a simple model of the ORZLD hierarchy. Dynamic bond correlation times are compared with static local presistence lengths.
1H‐nmr studies of a monointercalating drug into a d(CpGpApTpCpG)2 minihelix
Authors: Delepierre M. , Dinh T. Huyhn , Roques B. P.
Published: December 2004

The structure of the complex formed between the 7H‐pyridocarbazole monomer [{(2‐piperidyl)‐2,1‐ethane‐y1} {10‐methoxy‐7H‐pyrido[4,3‐c]carbazolium} dimethane sulfonate] and the autocomplementary hexanucleotide d(CpGpApTpCpG)2 in aqueous solution is analyzed by 270‐ and 400‐MHz 1H‐nmr. The large upfield shifts observed for both the drug and the self‐complementary hexanucleotide protons provide evidence for intercalated complexes. The observation of intermolecular nuclear Overhauser effects between drug and the hexanucleotide protons gives a privileged orientation of the durg in the intercalation site with the quaternarizing ethyl piperidine chain protruding in the major groove. Moreover, the data suggest an intercalation based on the neighbor exclusion site principle in the three alternating sequences.
Linear dichroism studies of the complexes between CT–DNA and distamycins
Authors: Forni A. , Moretti I. , Marconi G. , Mongelli N. , Samorí B.
Published: December 2004

The study of the monomeric chromophore of the distamycins reported in Ref. 1 was used here to build up a description of the electronic states of the whole oligopeptide by the exciton theory. Liquid crystal–linear dichroism (LC–LD) spectra of the distamycins were recorded by using as orienting solvents both thermotropic and lyotropic mesomorphic media. The agreement between the LD spectra and the polarization assignments by the exciton treatment is satisfactory. On this basis the flow‐LD spectra of the complex between distamycin V and DNA was interpreted in terms of the preferred relative orientations of the guest and host molecules. A single site location of the distamycin within the minor groove does not perfectly match the experimental order parameters. This orientational distribution function could be too simple to explain the experimental data. It may therefore be assumed that a small fraction of the guest molecules are preferentially aligned more parallel to the host chain axis than the minor groove. Alternatively, and probably more likely, the partial mismatch of the experimental data with the minor groove location may be seen as a manifestation of the well‐known stiffening and bending effects at the binding sites, which have already been observed by other techniques.
Characterization of the reaction products of adult human hemoglobin and disuccinimidyloxalate
Authors: Marini M. A. , Christensen S. , Snell S. , Jessee R. , Medina F. , Zegna A.
Published: December 2004

A number of chemically modified hemoglobin preparations have been proposed for use as an emergency resuscitation fluid. The purpose for forming these hemoglobin derivatives is to decrease the oxygen binding (i.e., to increase the P50) and to increase the intravascular retention time. These goals have been met with various degrees of success by using the reaction with pyridoxyl 5‐phosphate to raise the P50, followed by the addition of glutaraldehyde to increase circulating half‐life by polymerization.1,2 Other derivatives have been formed with polyethylene glycol,3,4 bis‐(3,5‐dibromosalicyl) fumarate,5,6 glycolaldehyde,7 and 2‐nor‐2‐formylpyridoxal 5‐phosphate,8,9 as well as with other compounds. All these derivatives introduce a foreign molecule into the hemoglobin, which may not always be desirable. Recently Tharp and Day10 used cyanogen to form intersubunit amide cross‐links in hemoglobin without the incorporation of cyanogen. This approach is attractive if the appropriate functional properties can be attained. Takeda et al.11 showed that equimolar concentrations of amino acids and disuccinimidyloxalate could form peptide bonds in high yield. We report the characteristics of the hemoglobin molecule modified by internal covalent amide bonds, which may be a suitable candidate for a resuscitation fluid.
Structural and electrostatic effects on binding of trivalent cations to double‐stranded and single‐stranded poly[d (AT)]
Authors: Plum G. Eric , Bloomfield Victor A.
Published: December 2004

We have measured the thermal melting profile for poly[d(AT)] · poly[d(TA)] as a function of concentration of three trivalent cations: spermidine, me8spermidine, and hexammine cobalt(III). Using McGhee's (1976) theory of DNA melting in the presence of ligands, we have estimated association constants Kh, Kc and binding site sizes nh, nc for binding to double‐helical (h) and single‐stranded (c) polynucleotide. The results are as follows:

Cation
Kh (M−1)
nh (bp)
Kc (M−1)
nc (bases)

Spermidine
9 × 105
2.2
1.3 × 104
4.5

Me8spermidine
2 × 105
1.4
7 × 103
3

Hexammine cobalt(III)
1.1 × 105
1.5
6 × 102
6

The binding parameters for spermidine and hexammine cobalt(III) to double helical molecules agree fairly well with direct equilibrium dialysis measurements, and are in reasonable accord with predictions of counterion condensation theory. However, despite their identical charges, the three ligands bind to single‐stranded DNA with quite different affinities. Estimates of the charge spacing of single‐stranded DNA suggest that poly[d(AT)] is less elongated in the presence of spermidine and hexammine cobalt (III) than it is when complexed with me8spermidine.
Structural dependence of oligonucleotide photooxidation
Authors: Rokita Steven E. , Lau Bernard , Romero‐Fredes Lorraine
Published: December 2004

Oxidative photosensitization was used to characterize the conformational‐dependent reactivity of various structures formed by oligonucleotides 14–15 nucleotides in length. The rate and product composition from a single hit process was analyzed using quantitative ion exchange chromatography under native and denaturing conditions. The primary damage incurred under aerobic acetone sensitization was base oxidation that, in turn, would induce strand scission upon a secondary treatment with piperidine. The reactive intermediates of this process were not consistent with diffusible radical species or singlet oxygen, as indicated by isotope and quenching studies. Derivatization was most likely initiated through a type I photoprocess with a direct interaction between DNA bases and excited state acetone preceding an irreversible oxidation step. This dominant reaction demonstrated no obvious sequence or site specificity for initial modification; the relative reactivity among the oligonucleotides did not correspond to any simple trend of base composition or near neighbor analysis. Likewise, the steric requirements of base modification allowed for similar rates of oxidation for single‐strand, helical, and aberrant forms of DNA. Hybridization of the most reactive oligonucleotides, however, did suppress their relative single‐strand vs double‐strand reactivity by as much as fourfold.
Inhibition of protein kinase C and calmodulin by the geometric isomers cis‐ and trans‐tamoxifen
Authors: O'Brian Catherine A. , Ioannides Constantin G. , Ward Nancy E. , Liskamp Rob M.
Published: December 2004

The triphenylethylene antiestrogen trans‐tamoxifen is an effective antitumor agent used in the treatment of human breast cancer. While the antiestrogenic activity of trans‐tamoxifen clearly plays an important role in its tumoricidal action, some of the biological effects of trans‐tamoxifen are independent of estrogen. Therapeutic concentrations of trans‐tamoxifen inhibit protein kinase C (PKC) and calmodulin‐dependent enzymes. PKC and calmodulin play critical roles in growth regulation, and there is evidence that inhibition of PKC and calmodulin by trans‐tamoxifen may contribute to the antiumor activity of the drug in vivo.

The geometric isomers cis‐ and trans‐tamoxifen have a number of opposing biological activities that have been attributed to their interactions with the estrogen receptor, Cis‐tamoxifen is generally estrogenic, whereas trans‐tamoxifen is generally antiestrogenic. In this report, we compared the effects of cis‐ and trans‐tamoxifen on PKC activity and on calmodulin‐dependent cAMP phosphodiesterase activity. Cis‐ and trans‐tamoxifen inhibited the Ca2+‐ and phosphatidylserine‐ (PS‐) dependent activity of purified rat brain PKC with indistinguishable potencies, but cis‐tamoxifen was somewhat more potent than the trans isomer in the inhibition of the Ca2+‐ and PS‐independent activity of PKC. In addition, cis‐tamoxifen was the more potent isomer in the inhibition of T lymphocyte activation, an event that entails a PKC‐requiring signal transduction pathway. A modest preference of the cis isomer was also observed in the inhibition of a calmodulin‐dependent cAMP phosphodiesterase. These results suggest a congruence between triphenylethylene binding sites on PKC and on the activated calmodulin–cAMP phosphodiesterase complex. We conclude that the interactions of cis‐ and trans‐tamoxifen with PKC and the activated calmodulin–cAMP phosphodiesterase complex offer a criterion for distinguishing biological effects of triphenylethylenes that are due to interactions with the estrogen receptor from the biological effects resulting from their inhibitory activities against PKC and calmodulin‐dependent processes.
A comparative analysis of single‐ and multiple‐residue substitutions in the alkaline phosphatase signal peptide
Authors: Kendall Debra A. , Doud Suzanne K. , Kaiser Emil Thomas
Published: December 2004

The alkaline phosphatase signal peptide participates in transport of the enzyme to the periplasmic space of Escherichia coli. The signal sequence, like that of other signal peptides, is composed of a polar amino‐terminal segment, a central region rich in hydrophobic residues and a carboxy‐terminal region recognized by signal peptidase. We have previously shown that an alkaline phosphatase signal peptide mutant containing a polyeucine core region functions efficiently in transport of the enzyme [D. A. Kendall, S. C. Bock, and E. T. Kaiser (1986) Nature 321, 706–708]. In this study, some of the amino acid changes involved in the polyleucine sequence are examined individually. A Phe to Leu substitution as the sole change results in impaired transport properties in contrast to when it is combined with three other amino acid changes in the polyleucine‐containing sequence. A mutant with a Pro to Leu substitution in the hydrophobic core region is comparable to wild type while the same type of substitution (Pro to Leu) in the carboxy‐terminal segment results in substantial accumulation of the mutant precursor. Finally, introduction of a basic residue into the hydrophobic segment (Leu to Arg substitution) results in a complete export block. These results exemplify the spectrum of properties produced by individual residue changes and suggest there is some interplay between hydrophobicity and conformation for signal peptide function.
Fluctuation and linkage relations in macromolecular solution
Authors: Schellman John A.
Published: December 2004

It is shown in the appendix that the derivatives of the excess free energy of a macromolecule in solution, with respect to the activities of other solution components, lead to fluctuation and linkage relations among these other components. Solution fluctuation theory is used, but it is specialized to the fluctuations and correlations associated with the presence of a macromolecule, and is developed with a modified ensemble.

The relations of the appendix are used to analyze the interaction of two solution components, A and B, with the macromolecule and with one another. Three cases are considered: (1) A and B are ligands that bind stoichiometrically to the macromolecule. This case reduces to Wyman's binding polynomial analysis. (2) A and B are tow substances at high concentration that interact selectively with the macromolecule. (3) A is a species that binds stoichiometrically to the macromolecule, while B is a component at high concentration that interacts weakly with the macromolecule.
Resolution power of regularization algorithm for binary systems in dynamic light scattering
Authors: Timchenko A. A. , Griko N. B. , Serdyuk I. N.
Published: December 2004

The resolving ability of the SIPP program operating on the regularzation principle was studied in computer experiments and in real experiments on a mixture of particles was two different dimensions as well as on tobacco mosaic virus. It has been shown that the limit of resolution in real dynamic light scattering experiments is achieved when the ratio of the characteristic times of the components is 1:2, provided that the contribution of the “slow” component to scattering is about twice that of the “fast” component.

Some practical rules that serve to obtain the best resolution of the two compnoents have been formulated.
Structural analysis of purified human tracheobronchial mucins
Authors: Gupta R. , Jentoft N. , Jamieson A. M. , Blackwell J.
Published: December 2004

Light scattering has been used to investigate the structure of human tracheobronchial mucin glycoproteins (HTBM) from the sputum of cystic fibrosis patients. The specimen was extracted using 6M guanidinium hydrochloride solution and fractionated by gel exclusion chromatography on Sephacryl S‐1000. The fractionated HTBM was purified by density gradient ultracentrifugation. Purity of the resulting material was confirmed by SDS polyacrylamide gel electrophoresis and uv spectroscopy. Light scattering measurements on the fractionated mucins yield weight‐average molecular weights Mw, and z‐average radii of gyration Rg, z. The native cystic fibrosis HTBM consisted of a high molecular weight fraction with Mw = 9.3 × 106 daltons and a lower molecular weight fraction contanining partly degraded mucins. After reduction and carboxymethylation of the high molecular weight native fraction, the resulting material was separated into three pools with Mw values of 5.1 × 106, 1.6 × 106, and 400,000. The derived molecular weights for the protein cores Mp,w, and the experimental radii of gyration are found to be consistent with the Mp,w – Rg relation established previously for submaxillary, cervical, and gastric mucins. These results imply that HTBM has the same extended‐coil conformation reported for other mucins and has a molecular structure consisting of subunits, linked into linear chains via covalent (disulfide) bonds.
CD of the synthetic RNA duplexes poly[r(A‐T)] and poly[r(A‐U)] in salt and ethanolic solutions
Authors: Voriíčková Michaela , Kypr Jaroslav , Jovin Thomas M. , Planck Max
Published: December 2004

Synthetic RNA poly[r(A‐T)] has been synthesized and its CD spectral properties compared to those of poly[r(A‐U)], poly[d(A‐T)], and poly[d(A‐U)] in various salt and ethanolic solutions. The CD spectra of poly[r(A‐T)] in an aqueous buffer and of poly[d(A‐T)] in 70.8% v/v ethanol are very similar, suggesting that they both adopt the same A conformation. On the other hand, the CD spectra of poly[r(A‐T)] and of poly[r(A‐U)] differ in aqueous, and even more so in ethanolic, solutions. We have recently observed a two‐state salt‐induced isomerization of poly[r(A‐U)] into chiral condensates, perhaps of Z‐RNA [M. Vorlíčková, J. Kypr, and T. M. Jovin, (1988) Biopolymers 27, 351–354]. It is shown here that poly[r(A‐T)] does not undergo this isomerization. Both the changes in secondary structure and tendency to aggregation are different for poly[r(A‐T)] and poly[r(A‐U)] in aqueous salt solutions. In most cases, the CD spectrum of poly[r(A‐U)] shows little modification of its CD spectrum unless the polymer denatures or aggregates, whereas poly[r(A‐T)] displays noncooperative alterations in its CD spectrum and a reduced tendency to aggregation. At high NaCl concentrations, poly[r(A‐T)] and poly[r(A‐U)] condense into ψ (‐) and ψ (+) structures, respectively, indicating that the type of aggregation is dictated by the polynucleotide chemical structure and the corresponding differences in conformational properties.
Synthesis and conformational studies by 1H‐ and 13C‐nmr spectroscopy of a novel, sterically constrained analogue of thyrotropin‐releasing hormone
Authors: Mapelli Claudio , Halbeek Herman Van , Stammer Charles H.
Published: December 2004

A novel thyrotropin‐releasing hormone (TRH) analogue, [2, 4‐MePro3]‐TRH (2, 4‐MePro: 2‐carboxy‐2, 4‐methanopyrrolidine), has been synthesized using a rapid solid phase peptide synthesis method, and its conformational properties investigated by one‐ and two‐ dimensional (2D) nmr spectroscopy and by proton Overhauser measurements. Following a published approach, calibrated interproton Overhauser effects were used together with distance geometry analysis to deduce that the single conformation of the His‐2, 4‐MePro tertiary amide bond is trans in aqueous solution. This conclusion was corroborated by 2D dipolar‐correlated (NOESY) spectroscopy. A preferentially extended conformation is indicated by the nmr data, similar to that of TRH. The ϕ, ψ conformational space of 2, 4‐MePro is, however, significantly different from that of trans proline and the structural consequences of these differences at the C‐terminus are discussed. The distribution of histidine side‐chain conformation in the TRH analogue was deduced from coupling constants and from the short‐range interaction between the imidazole ring and one of the prochiral faces of the 2, 4‐MePro side chain.
Uv resonance Raman spectroscopy of nucleic acid duplexes containing A‐U and A‐T base pairs
Authors: Grygon Christine A. , Spiro Thomas G.
Published: December 2004

Resonance Raman spectra have been obtained at several uv wavelengths (200–266 nm) for poly(rA)‐poly(rU), poly(dA‐dU), poly(dA)‐poly(dT), and poly(dA‐dT), representing nucleic acid duplexes containing A‐U and A‐T base pairs with different stacking interactions and different backbone conformations. Frequency shifts are seen in the exocyclic modes corresponding to coupled C4O and C5C6 stretching of U and T, although the NH2 scissors frequency of A is unshifted relative to that of the mononucleotide. These frequency patterns are interpreted as the superposition of H bonding and dipole–dipole coupling effects. Strong hypochromism is seen for most of the ring modes, resulting from the absorption hypochromism and from shifts in the electronic transitions due to stacking. The effects are larger for A bands in the homopolymers than in the heteropolymer duplexes, reflecting the larger influence of A/A than A/U(T) stacking. Poly(rA)‐poly(rU) stands out among these polymers in showing 10 cm−1 downshifts in one U and several A modes. These shifts may be related to the A form structural parameters of this duplex, but the physical mechanism is not obvious.
Ir and Raman spectroscopic studies on coulombic interaction between water‐soluble porphyrins and nucleic acids
Authors: Nonaka Y. , Lu D. S. , Dwivedi A. , Strommen D. P. , Nakamoto K.
Published: December 2004

We have shown previously that the N‐methylpridyl group vibrations of water‐soluble porphyrins, M(TMpy‐P4), are shifted to lower frequencies (0.5–2.6 cm−1) as a result of coulombic interaction between the N+‐CH3 group of M(TMpy‐P4) and the PO2 group of a nucleic acid. We have now turned over our attention to the effect of this coulombic interaction on the PO2 group vibrations of nucleic acids. Using Fourier transform ir and Raman spectroscopy, we found that the νa(PO2) at 1221 cm−1 is shifted 12 ∼ 17 cm−1 to higher frequencies, whereas the νs(PO2) at 1087 cm−1 is shifted 18 ∼ 26 cm−1 to lower frequencies, when DNA is mixed with M(TMpy‐P4). These results indicate that the N+‐CH3 group of M(TMpy‐P4) interacts preferentially with one of the two oxygen atoms of the PO2 group of the DNA duplex.
The calculated free energy effects of 5‐methyl cytosine on the B to Z transition in DNA
Authors: Pearlman David A. , Kollman Peter A.
Published: December 2004

We have examined the free energy effects of 5‐methylation of cytosine on the B ⟷ Z conformational equilibrium in DNA. Free energy differences were calculated using the free energy perturbation approach, which uses an easily derived equation from classical statistical mechanics to relate the free energy difference between two states to the ensemble average of the potential energy difference between the states. Calculations were carried both in explicit solvent and (for comparison) in vacuo. The free energy values obtained for the explicit solvent systems are total free energies, with contributions from all parts of the system (solvent + solute), and so are relevant to the B ⟷ Z transitions observed under real(physiological) conditions. We calculate that in solution, methylation makes the B → Z transition more favorable by about −0.4 kcal/mole base pair (bp) in free energy. This value compares well with approximate experimentally derived values of about −0.3 kcal/ mole‐bp. We also discuss a method for determining the free energy difference between conformational states poorly maintained by a potential energy model. Finally, the effects of methylation on the melting temperature of DNA are examined.
Solvent effect on the conformation of the hydroxymethyl group established by molecular dynamics simulations of methyl‐β‐D‐glucoside in water
Authors: Kroon‐Batenburg L. M. J. , Kroon J.
Published: December 2004

Molecular dynamics simulations of methyl‐β‐D‐glucoside in water are performed. Although the tg conformation of the hydroxymethylgroup is found to be the lowest in energy for the isolated molecule, it appears to be unstable in water. The well‐known absence of a significant amount of the tg conformation in polar solvents can therefore be explained as a solvent effect.
Structural principles of B‐DNA grooves hydration in fibers as revealed by Monte Carlo simulations and x‐ray diffraction
Authors: Eisenhaber F. , Mannik J. H. , Tumanyan V. G.
Published: December 2004

Being interested in possible effects of sequence‐dependent hydration of B‐DNA with mixed sequence in fibers, we performed a series of Monte Carlo calculations of hydration of polydeoxyribonucleotides in B form, considering all sequences with dinucleotide repeat. The computational results allow the ten base‐stacking types to be classified in accordance with their primary hydration in the minor groove. As a rule, the minor groove is occupied by two water molecules per base pair in the depth of the groove, which are located nearly midway between the planes of successive base pairs and symmetrically according to the dyad there. The primary hydration of the major groove depends on the type of the given base pair. The coordinates of 3 water molecules per base pair in the depth of the major groove are determined by the type of this pair together with its position and orientation in the helix, and are practically independent on the adjacent base pairs. A/T‐homopolymer tracts do not fit into this hydration pattern; the base pair edges are hydrated autonomously in both grooves.

Analysis of the Li‐B‐DNA x‐ray diffraction intensities reveals those two water positions in the minor groove. In the major groove, no electronic density peaks in suffiecient distance from the base edges were found, thus confirming the absence of any helical invariance of primary hydration in this region.

With the help of the rules proposed in this paper it is possible to position the water molecules of the first hydration shell in the grooves of canonical B‐DNA for any given sequence.
Molecular dynamics simulation provides a possible structure for substance P‐like peptides in aqueous solution
Authors: Teleman Olle , Von Der Lieth Claus‐Wilhelm
Published: December 2004

A hypothetical conformation of the undecapeptide Substance P in aqueous solution is generated by molecular dynamics simulation for 284 ps. The conformation takes explicit solvent interactions into account as well as entropic effects to the extent that phase space is sampled in simulation. The initial conformation is taken from energy minimization studies and modified. In spite of fluctuations through 180° in some backbone dihedral angles, the peptide settles with all backbone dihedrals within ± 60° from the initial values. In 130 ps, the radius of gyration decreases from 6.2 Å to 5.5 Å, whereas only fluctuation (± .2 Å) is observed during the last 150 ps. The root‐mean‐square deviation at optimal superposition for a pair of conformations from the last 150 ps is 0.6 Å, based on backbone atoms. The final structure is close‐knit, nearly globular, and stabilized by several long‐lived hydrogen bonds. The simulation conformation agrees with the scarce experimental data including a large number of structure‐activity relationships. Thus, the simulation conformation is a likely candidate for one of the several conformations, the existence of which has been deduced from nuclear magnetic resonance data. Simulation results and experimental modification studies suggest that Phe 8 and Leu 10 are involved in the primary binding of SP to its receptors.
Helix‐coil stability constants for the naturally occurring amino acids in water. XXIII. Proline parameters from random poly(hydroxybutylglutamine‐CO‐L‐proline)
Authors: Altmann K.‐H. , Wójcik J. , Vásquez M. , Scheraga H. A.
Published: December 2004

Water‐soluble random copolymers containing L‐proline and N5‐(4‐hydroxybutyl)‐L‐glutamine were synthesized by copolymerization of the tripeptides H‐L‐Glu(OBzl)‐L‐Glu(OBzl)‐L‐Glu(OBzl)‐OH and H‐L‐Glu(OBzl)‐L‐Pro‐L‐Glu(OBzl)‐OH, using ben‐zotriazolyl‐N‐oxy‐tris(dimethylamino)‐phosphonium hexafluorophosphate as condensing reagent, and subsequent aminolysis of the Bzl ester groups with 4‐amino‐1‐butanol. These copolymers were found to contain significant amounts of N5‐(4‐hydroxybutyl)‐D‐glutamine, thus requiring the synthesis of a binary copolymer containing only D‐ and L‐N5‐(4‐hydroxybutyl)glutamine residues in order to evaluate the possible effects of the D‐residues on the conformational properties of poly(hydroxybutylglutamine‐co‐L‐proline). The different copolymers were fractionated, and their thermally induced helix‐coil transition curves were obtained in water at neutral pH. When proper corrections were applied for the helix‐destabilizing properties of N5‐(4‐hydroxybutyl)‐D‐glutamine, the Zimm‐Bragg parameters σ and s for L‐proline could be deduced from the melting curves of poly (hydroxybutylglutamine‐co‐L‐proline). The results indicate that L‐proline acts as a very strong helix breaker over the entire temperature range from 0 to 60°C.
On the multiple‐minima problem in the conformational analysis of polypeptides. IV. Application of the electrostatically driven monte carlo method to the 20‐residue membrane‐bound portion of melittin
Authors: Ripoll Daniel R. , Scheraca Harold A.
Published: December 2004

The conformational space of the membrane‐bound portion of melittin has been searched using the electrostatically driven Monte Carlo (EDMC) method with the ECEPP/2 (em‐pirical conformational energy program for peptides) algorithm. The former methodology assumes that a polypeptide or protein molecule is driven toward the native structure by the combined action of electrostatic interactions and stochastic conformational changes associated with thermal movements. The algorithm produces a Monte Carlo search in the conformational hyperspace of the polypeptide using electrostatic predict ions and a random sampling technique, combined with local minimization of the energy function, to locate low‐energy conformations. As a result of 8 test calculations on the 20‐residue membrane‐bound portion of melittin, starting from six arbitrary and two completely random conformations, the method was able to locate a very low‐energy region of the potential with a well‐defined structure for the backbone. In all of the cases under study, the method found a cluster of similar low‐energy conformations that agree well with the structure deduced from x‐ray diffraction experiments and with one computed earlier by the build‐up procedure.
A simple statistical field theory of heteropolymer collapse with application to protein folding
Authors: Bryngelson Joseph D. , Wolynes Peter G.
Published: December 2004

A simple statistical extension of the Flory theory of excluded volume is developed, and applied to random heteropolymer collapse and a simple model of protein folding. Sequence heterogeneity is found to lead to new effects. The nucleation of protein folding is also briefly considered.
Thermal unfolding of helices of a C‐peptide analogue of ribonuclease A in sodium dodecyl sulfate solution
Authors: Wu Chuen‐Shang C. , Yang Jen Tsi
Published: December 2004

The conformation of a 13‐residue C‐peptide analogue of ribonuclease A, \documentclass{article}\pagestyle{empty}\begin{document}$ {\rm suc - A}\mathop {\rm E}\limits^ - {\rm T - AAA}\mathop {\rm K}\limits^{\rm + } {\rm FL}\mathop {\rm R}\limits^{\rm + } {\rm A}\mathop {\rm H}\limits^{\rm + } {\rm A - CONH}_2 $\end{document}, in NaDodSo4 solutions with respect to temperature was studied with CD. The equilibrium constant of unfolding yielded a straight line in a van't Hoff plot. In 10 mM NaDodSo4, ΔGu = 120 cal/mol, ΔHu = 700 cal/mol, and ΔSu = 2.0 entropy units all on per helical residue. These values compared fairly well with the thermodynamic parameters of the uncharged helix‐coil transition of (Glu)n in 0.1 M NaCl based on the theories of Zimm and Bragg and Zimm and Rice. The peptide was not unfolded at 75°C completely. Even in water without surfactant it was not a “random coil.”
Problems of CD spectrometers (V): Can we measure CD and LD simultaneously? Comments on differential polarization microscopy (CD and linear dichroism)
Authors: Shindo Yohji , Nishio Motohide , Maeda Shiro
Published: December 2004

An interesting paper on circular dichroism (CD) and linear dichroism (LD) microscopy by Livolant, Mickols, and Maestre [(1988) Biopolymers 27, 1761–1969] has attracted our attention. They reported that they have succeeded in deconvoluting mathematically true CD and LD from signals obtained for their samples of strong and incompatible anisotropies. If this is true, then their method of mathematical deconvolution will open new possibilities in polarization‐modulation spectroscopy. However, after carefully reading through their paper, we found the following obscure points in their results: (1) the hardware of their spectrometer; (2) the sensitivity matrix; (3) the method for separation of CD and LD by using two standards; (4) average CD curves; and (5) circular intensity differential scattering (CIDS) and linear intensity differential scattering (LIDS) in the wavelength range from 300 to 330 nm. Making use of the Mueller matrix analysis, we present our comments on the above subjects together with our data. In conclusion, we maintain that it is difficult to accept their claim of having a general and useful approach to separating true CD and LD from signals observed in macroscopically anisotropic samples.
Complete assignment of the noncarbonylic carbon‐13 resonances of Tendamistat
Authors: Kessler H. , Schmieder P. , Bermel W.
Published: December 2004

The complete assignment of all noncarbonylic carbon‐13 resonances at natural abundance of the α‐amylase inhibitor Tendamistat is presented. Such an assignment can help solve ambiguities in the proton spectrum and forms the basis for further measurements to obtain more structural or dynamic information. Using a nonenriched sample, the low sensitivity due to the small gyromagnetic ratio of 13C to 1H and the low natural abundance of 13C requires sensitive methods to obtain interpretable spectra. Thus all the NMR techniques used incorporate proton detection. With three different techniques, the HMQC, the HMQC with TOCSY‐transfer, and the HMBC, a complete assignment based on the published proton chemical shifts (A. D. Kline, K. Wüthrich J. Mol. Biol. 192(1986)) was possible with spectra recorded in a reasonable time. Especially the HMBC, which yields correlations via 1H‐13C long‐range couplings, proved to be extremely valuable in the assignment procedure.
An optimal formulation of the matrix method in statistical mechanics of one‐dimensional interacting units: Efficient iterative algorithmic procedures
Authors: Yeramian E. , Schaeffer F. , Caudron B. , Claverie P. , Buc H.
Published: December 2004

Statistical mechanical calculations for one‐dimensional interacting units have undergone great development in many fields of macromolecular science. The partition function is the most rigorous description of an ensemble of molecules in equilibrium. Specific methodological formulations and algorithms were developed to handle numerically the inclusion of long‐range effects (as compared to usual nearest neighbor Ising models) and known sequence‐dependent heterogeneities of biological macromolecules. The most successful approach in formulating these problems in a very general and tractable framework was the so‐called matrix method. Despite several improvements, it was claimed that in practical applications this approach had fundamental limitations inherent to any “matrix” formulation. We show here that a new conceptual formulation allows us to overcome these limitations completely. We propose a general iterative procedure that combines the theoretical advantages of the matrix method with the possibility of highly optimized and efficient numerical algorithms.
Conformational analysis and helical preferences of normal and α,α‐dialkyl amino acids
Authors: Hodgkin Edward E. , Clark John D. , Miller Katherine R. , Marshall Garland R.
Published: December 2004

Energy calculations have been performed on right‐handed helical structures of L‐alanine and α‐methylalanine oligomers. A new ′3.610′‐helix is described for α‐methylalanine peptides. The dependence of the relative stability of the α, 310, and 3.610 structural forms on helix length, dielectric, and force‐field, in the gas phase, has been studied. Potential energy surfaces for the interconversion of helices have been generated. The 310‐helix in α‐methylalanine oligomers exhibits a degree of enthalpic and entropic stabilization not observed for alanine. The relevance of the results to the formation of voltage‐sensitive ion channels is discussed.
Amide III frequencies for Ala‐X peptides depend on the X amino acid size
Authors: Weaver James L , Williams Robert W.
Published: December 2004

Raman spectra of series of aqueous solutions of peptides containing two amino acids, glycine‐X, alanine‐X, and serine‐X, where X is an uncharged amino acid, show that the amide III band shifts systematically to lower frequencies as the side chain of the X amino acid becomes larger. The range of this shift is about 20cm−1, starting at 1275cm−1 for alanine‐glycine and moving to 1251 cm−1 for alanine‐tryptophan, with a correlation coefficient of 0.93 with the mass of the X amino acid side chain for 10 peptides. The amide I frequencies remain constant as the X amino acid is changed. This shift may result from a change in the average conformational preference of the peptide, a change in vibrational coupling of the amide III modes with the X amino acid side chain, a change in molecular force constants, or a combination of these. These results present a test for computational methods.
Synthesis and1H‐nmr studies of α‐deuterated analogues ofdes‐Trp1, Nle12‐human minigastrin
Authors: Amonraksa Kitti , Simonetti Mario , Da Rin‐Fioretto Silvio , Mammi Stefano , Peggion Evaristo
Published: December 2004

Three analogues of the tridecapeptide amide H‐Leu‐(Glu)5‐Ala‐Tyr‐Gly‐Nle‐Asp‐Phe‐NH2were synthetized with α‐deuterated glutamate residues in specific positions in order to assign unambiguously the1H nmr spectrum of the parent peptide in water and in water‐trifluoroethanol mixtures. The synthetic route is described and the assignment illustrated. A previous, tentative assignment based solely on indirect evidence [Mammi, S., Mammi, N. J. & Peggioa, E. (1988)Biochemistry27, 1374–1379] was partially modified.
The effect of the L‐azetidine‐2‐carboxylic acid residue on protein conformation. I. Conformations of the residue and of dipeptides
Authors: Zagari Adriana , Némethy George , Scheraga Harold A.
Published: December 2004

The L‐azetidine‐2‐carboxylic acid (Aze) residue can be incorporated into proteins in the place of L‐proline, of which it is the lower homologue. This substitution alters the properties of proteins, especially of collagen. Conformational constraints in N‐acetyl‐Aze‐N′‐methylamide and in several dipeptides containing Aze have been analyzed by means of energy computations. They have been compared with peptides containing Pro. The overall con‐formational preferences of Aze and Pro are similar, but several significant differences occur between them. In general, peptides containing Aze are somewhat more flexible than corresponding peptides containing Pro, because of a decrease in constraints caused by repulsive nonconvalent interactions of the atoms of the ring with neighboring residues. This results in an entropic effect that lessens the stability of ordered polypeptide conformations with respect to the disordered statistical coil. The collagen‐like near‐extended conformation is energetically less favorable for Aze than for Pro in the single residue and in dipeptides. This effect also contributes to a destabilization of the collagen triple helix. The influence of Aze on the conformation of polypeptides is discussed in the accompanying papers.
Evidential study of correlated events in biochemistry: Physicochemical mechanisms of nucleic acid hydration as revealed by factor analysis
Authors: Starikov E. B. , Semenov M. A. , Ya. Maleev V. , Gasan A. I.
Published: December 2004

Using a factor analysis technique, the experimental physicochemical data on the hydration of mononucleotides, several polynucleotides, their double‐helical complexes and natural DNAs were studied. The information about the factors determining the changes in physicochemical parameters vs the hydration was obtained. This work discusses a possible physical sense of the factors obtained and the expedience of using factor analysis to interpret the molecular‐biophysical experiments.
Toward the elucidation of the mechanism of attachment and entry of malaria sporozoites into cells: Synthetic polypeptides from the circumsporozoite protein of Plasmodium falciparumbind Ca2+ and interact with model phospholipid membranes
Authors: Verdini Antonio S. , Chiappinelli Lorella , Zanobi Antonio
Published: December 2004

Through the joint use of CD, Fourier transform ir (FTIR), and attenuated total reflectance FTIR we have found that synthetic polypeptide models of the Plasmodium falciparum circumsporozoite (CS) protein repeat domain bind calcium ions in helicogenic environments. Ca2+‐(NANP)n complexes (n ⩾ 20) interact vectorially with model phospholipid membranes orienting their polypeptide axes preferentially along those of the lipid acyl chains. It is proposed that the P. falciparum CS protein central region, rather than acting as a molecular lure helping the parasite to evade host immune control, plays, as a specific Ca2+ macroligand, a critical functional role during attachment, invasion, and development of the malaria parasite in the hepatic cell.
Conformational preferences and the role of the statine residue in the crystal state
Authors: Precigoux Gilles
Published: December 2004

The present paper is the result of an analysis of the available crystal structure data related to the statine amino acid so as to obtain information about bond lengths, bond angles, and preferential conformations. The number of configurations actually observed is small; nevertheless, some characteristic conformations should be pointed out for statine‐containing peptides. The presence of two additional carbon atoms in the statine main chain enhances the peptide conformational degree of freedom and the statine‐containing peptides are observed in a variety of different conformations including some usual secondary structure‐types as β‐turns and β‐strands.
Conformation‐based design of two cyclic physalaemin analogues
Authors: Hölzemann Günter , Jonczyk Alfred , Eiermann Volker , Pachler Klaus C. R. , Barnickel Gerhard , Regoli Domenico
Published: December 2004

Two new cyclic analogues of physalaemin were designed on the basis of the conformation found in DMSO solution. Glp‐Ala‐cyclo(‐Asp‐Pro‐Asn‐Lys‐)‐Phe‐Tyr‐Gly‐Leu‐Met‐NH2(1) was synthesized by cyclization of physalaemin. In 2 the Asp residue was replaced by Glu. The linear analogue of 2 was synthesized by the solid phase method and subsequently cyclized. Two‐dimensional nmr methods were employed to assign the proton and carbon resonances. Proton–proton distances were extracted from rotating frame nuclear Overhauser effect spectra and used as restraints in the molecular dynamics calculations. Analogue 1 was found to have a similar conformation as physalaemin, whereas 2 did not form intramolecular hydrogen bonds. The pharmacological evaluation revealed that both peptides have similar potencies as physalaemin in the dog carotid artery (NK‐1 receptor). Therefore, the charged side chains of physalaemin appear not essential for NK‐1 activation. However, the other tachykinin receptors show good sensitivity to the cyclic peptides. It is concluded that the replacement of a salt bridge by an amide bond connecting the side chains of natural residues might provide useful information about the biological significance of some charged side chains of neurokinins.