bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of water molecules in the crystal structure of gly‐L‐ala‐L‐phe: A possible sequence preference for nucleation of α‐helix?
Authors: Ramasubbu N. , Parthasarathy R. 
Published: December 2004

AbstractThe synthetic peptide Gly‐L‐Ala‐L‐Phe (C14H19N3O4 · 2H2O; GAF) crystallizes in the monoclinic space group P21, with a = 5.879(1), b = 7.966(1), c = 17.754(2) Å, β = 95.14(2)°, Dx = 1.321 g cm−3, and Z = 2. The crystal structure was solved by direct methods using the program SHELXS‐86 and refined to an R value of 0.031 for 1425 reflections (> 3σ). The tripeptide exists as a zwitterion in the crystal and assumes a near α‐helical backbone conformation with the following torsion angles: ψ1 = −147.8°; ϕ2, ψ2 = −71.2°, −33.4°; ϕ3 ψ3 = −78.3°, −43.3°. In this structure, one water molecule bridges the COO− and NH3+ terminii to complete a turn of an α‐helix and another water molecule participates in head‐to‐tail intermolecular hydrogen bonding, so that the end result is a column of molecules that looks like an α‐helix. Thus, the two water molecules of crystallization play a major role in stabilizing the near α‐helical conformation of each tripeptide molecule and in elongating the helix throughout the crystal. An analysis of all protein sequences around regions containing a GAF fragment by Chou‐Fasman's secondary structure prediction method showed that those regions are likely to assume an α‐helical conformation with twice the probability they are likely to adopt a β‐sheet conformation. It is conceivable that a GAF fragment may be a good part of the nucleation site for forming α‐helical fragments in a polypeptide, with the aqueous medium playing a crucial role in maintaining such transient species.
Crystal structure and molecular conformation of the peptide N‐Boc‐L‐gly‐dehydro‐Phe‐NHCH3
Authors: Singh T. P. , Narula Punit , Chauhan V. S. , Kaur Paramjeet 
Published: December 2004

AbstractThe peptide N‐Boc‐L‐Gly‐dehydro‐Phe‐NHCH3 was synthesized by the combination of N‐Boc‐L‐Gly‐dehydro‐Phe azlactone and methylamine. The peptide crystallizes in orthorhombic space group P212121 with a = 5.679(2) Å, b = 16.423(9) Å, c = 19.198(10) Å, V = 1791(2) Å3, Z = 4, dm = 1.212(5) Mg m−3, dc = 1.237(1) Mg m−3. The structure was determined by direct methods using SHELXS 86. The structure was refined by full‐matrix least squares procedure to an R value of 0.049 for 1509 observed reflections. The molecular dimensions are, in general, in good agreement with the standard values. The bond angle Cα–Cβ–Cγ in the dehydro‐Phe residue is 133.6(5)°. The peptide backbone torsion angles are θ1 = −171.4(4)°, ω0 = 178.2(4)°, ϕ1 = −57.2(6)°, ψ1 = 141.2(4)°, ω1 = −174.4(4)°, ϕ2 = 71.5(6)°, ψ2 = 7.2(6)°, and ω2 = −179.8(5)°. These values show that the backbone adopts the β‐bend type II conformation. The Boc group has a trans‐trans conformation. The side‐chain torsion angles in dehydro‐Phe are χ2 = 1.6(9)°, χ = 0.5(9)°, and χ = 179.8(6)°. The plane of C–C–C is rotated with respect to the plane of the phenyl ring at 0.5(6)°, which indicates that the atoms of the side chain of the dehydro‐Phe residue are essentially coplanar. As a result of the β‐bend in the structure, an intramolecular hydrogen bond is formed between the oxygen of the ith residue and the NH of the (i + 3)th residue at a distance of 2.940(5) Å. The crystal structure is stabilized by a network of hydrogen bonds and van der Waals interactions.
Solvation thermodynamics of biopolymers. II. Correlations between functional groups
Authors: Ben‐Naim A. , Ting K.‐L. , Jernigan R. L. 
Published: December 2004

AbstractThe extent of correlations between functional groups that can form hydrogen bonds with solvent molecules has been estimated. From the observed distance distribution of functional groups on the surfaces of several proteins, and from the extent of correlation between pairs of such functional grups, we conclude that the assumption of independence of functional groups made in part I is probably a good approximation. The reason is that even when correlations exist there is, on average, cancellation of the positive and negative correlations. The relevance of hydrogen bonding with the solvent to the relative stability of different conformers of biopolymers is also indicated.
Relaxation effects in the gel electrophoresis of DNA in intermittent fields
Authors: Jamil Tahir , Frisch Harry L. , Lerman L. S. 
Published: December 2004

AbstractThe electrophoretic mobility of restriction fragments of lambda DNA in agarose gels declines if the field is intermittent rather than continuous, with a greater effect on the longer fragments. The changes are compatible with the assumption of two exponential relaxation processes for field‐dependent configurational changes, one when the field is turned on and another when it terminates. The length dependence at the extrapolated limit of mobility for short pulses with long intervals corresponds closely to the simple inverse proportionality to length expected from theoretical considerations when the molecular configuration is not affected by the electric field. Simple intermittent fields would allow separation of longer molecules than can ordinarily be resolved. The relaxation times for both the change in conformation imposed by the field and the return to field‐free conformation vary as approximately the second power of the length of the molecule, independent of the salt concentration or field strength and varying only slightly with gel density. These relations are not in good agreement with properties expected from reptation theory, and they suggest that a different mechanism must be invoked for the electrophoretic migration of long DNA molecules at ordinary values of field strength.
Conformational transitions of leucine‐containing isomeric sequential basic polytripeptides
Authors: Štokrová Štěpánka , Bohdanecký Miloslav , Bláha Karel , Šponar Jaroslav 
Published: December 2004

AbstractConformational transitions of basic sequential polytripeptides (Lys‐Ala‐Leu)n, (Arg‐Ala‐Ala)n, (Arg‐Leu‐Ala)n, and (Arg‐Ala‐Leu)n, induced by elevated salt concentrations and/or temperatures in aqueous solutions, were investigated by CD, sedimentation equilibrium, and viscometry. The behavior of (Lys‐Ala‐Leu)n was compared with that of the sequential isomer (Lys‐Leu‐Ala)n, studied previously. It was found that both polypeptides are highly helical with a tendency to aggregate in high salt solutions. Although the hydrophobic interactions between Lys and Leu residues play an important role in both cases, the final effect on helix stabilization and aggregation is different. The Arg‐containing polypeptides were found to assume the α‐helical conformation. Compared to the Lys‐containing polypeptides (Lys‐Ala‐Leu)n and (Lys‐Leu‐Ala)n, a very low tendency to aggregate was observed.
Solution conformation of the actinomycin D related pentapeptide lactone using nmr and molecular modeling
Authors: Mauger Anthony B. , Gallagher Kathleen S. , Silverton James V. , Ferretti James A. 
Published: December 2004

AbstractA detailed description of the two observed solution conformations of the pentapeptide lactone fragment of actinomycin D is presented using the distance constraints obtained from two‐dimensional nuclear Overhauser enchancement spectra in combination with minimum energy calculations. Low energy conformational states that are compatible with the experimental distances are found for each of the two conformers. For one conformer, an all trans peptide bond conformation is found with no intramolecular hydrogen bonds. For the other conformer, the D‐Val–Pro and Pro–Sar peptide bonds were cis; this solution conformation is the same as that found in both the crystal structure of the pentapeptide lactone as well as of the native actinomycin D itself. These results are discussed in terms of the combined influence of conformation and the effects of mutual intramolecular association of the pentapeptide lactone moieties in native actinomycin D on its cytotoxic activity.
The concentration dependence of the diffusion coefficient for bovine pancreatic trypsin inhibitor: A dynamic light scattering study of a small protein
Authors: Gallagher Warren H. , Woodward Clare K. 
Published: December 2004

AbstractThis paper reports the use of dynamic light scattering to investigate the concentration dependence of the diffusion coefficient for bovine pancreatic trypsin inhibitor (BPTI). BPTI is a small molecular weight protein (6511 Da) that has been the subject of numerous experimental studies. In addition to addressing questions that remain in the literature concerning the aggregation behavior of BPTI, we show that dynamic light scattering can be practically applied to proteins as small as BPTI, and that it can provide a useful means of parameterizing the solution behavior for proteins. We obtained values for the apparent diffusion coefficient of BPTI as a function of concentration over a range of pH values from 2.59 to 9.92 at an ionic strength of 0.3M, and over a range of ionic strength values from 0.1 to 0.5M at a pH of 7.0. The concentration dependence is linear for nearly all the conditions examined, even up to concentrations as high as 65 mg/mL. The average diffusion coefficient obtained at infinite dilution is 14.4 ± 0.2 × 10−7 cm2/s. This value agrees with that expected for a BPTI monomer hydrated with less than a monolayer of water. We used the theories of Felderhof, of Batchelor, and of Phillies, along with the DLVO theory to interpret the concentration dependence of the apparent diffusion coefficient. The variations observed with pH and ionic strength can be primarily attributed to screened coulombic interactions. In addition, there is an attractive interaction that is slightly stronger than the repulsive coulombic one, and that is essentially independent of pH and ionic strength. The attractive interactions appear to arise from nonspecific van der Waals interactions and do not lead to the formation of stable aggregates of BPTI.
A rigorous mathematical treatment for the excluded volume effect in monte carlo simulations of polymeric chains
Authors: Yeramian E. , Schaeffer F. , Caudron B. , Claverie P. , Buc H. 
Published: December 2004

AbstractIn Monte Carlo simulations of polymeric chains, the chains, the chains are most often represented as spheres, or cylinders with flat ends. In this methodological paper, we adopt a representation of the chains as spherocylinders (continuous cylinders ending in semispheres). With such a representation the testing for chain overlap, which is the crucial step for the incluson of the excluded volume effect in the simulations, can be defined in a rigorous geometrical framework. The treatment we then derive fulfills the following features:

—it allows a very simple, automatic, and exhaustive calsificatim of all the possible configurations;

—it provides a physical representation for steric hindrance effects more natural than the flat‐ended cylinders. Notably, this representation avoids the introduction of artificial anisotropies in the treatments.

This spherocylindrical representation is also well suited for several types of calculations that can be involved in elaborate Monte Carlo simulations.
Superoxide dismutase: Fluctuations in the structure and solvation of the active site channel studied by molecular dynamics simulation
Authors: Shen Jian , Subramaniam Shankar , Wong Chung F. , Mccammon J. Andrew 
Published: December 2004

AbstractThe molecular dynamics (MD) simulation of superoxide dismutase (SOD) in water is carried out for a total of 23 ps. The simulation system is a 26 Å sphere centered at the active site of SOD, including 1602 atoms from SOD and 1761 water molecules. There is no gross deviation from the x‐ray structure for the average MD structure. The structure and potential fluctuations around the active site are examined. The results provide new insight to the interactions between SOD and its substrate superoxide.
Anisotropy of the fluorescence from the monomer, five oligomers, and a polymer of epicatechin
Authors: Cho Donghwan , Mattice Wayne L. , Porter Lawrence J. 
Published: December 2004

AbstractThe steady‐state fluorescence anisotropy r has been measured at 25°C for dilute solutions of epicatechin units connected by interflavan bonds with 4β → 8 stereochemistry. The molecules studied are monodisperse oligomers from the monomer through the hexamer, and a polydisperse sample with a number‐average degree of polymerization xn of 10. The hexamer and smaller oligomers have been removed from the polydisperse sample. All samples have a very small value of r in 1,4‐dioxane and in methanol. Higher values of r are seen in ethylene glycol and in glycerol. In the latter two solvents, the monomer has significantly higher r than any species with xn > 1. This observation is interpreted as evidence for the presence of excitation migration from one monomer to another in the dimer and species of higher xn.
Syntehsis and structural stability of helichrome as an artificial hemeproteins
Authors: Sasaki Tomikazu , Kaiser Emil Thomas 
Published: December 2004

AbstractA detailed procedure is described for the syntehsis of helichrome, which is the first successful example of polypeptide‐based artificial hemeprotein. The segment synthesis‐condensation approach used for the assembly of small proteins has proven to be extremely useful for protein mimetics as well. The final deprotection was performed using the TNSOTf‐thioanisole method instead of the less‐convenient hydrogen fluoride method. The unfolding transition of the α‐helical conformation of helichrome induced by guanidine hydrochloride was studied to understand the stability and dynamics of the folded structure. The resulting parameters (C0.5 = 5.2M and ΔGH2O = −4.4 kcal mol−1) characterizing helichrome denaturation were comparable to that of native globular proteins.
Z‐RNA: The solution NMR structure of r(CGCGCG)
Authors: Davis Peter W. , Adamiak Ryszard W. , Tinoco Ignacio 
Published: December 2004

AbstractLeft‐handed double‐helical Z‐RNA has been studied using the ribohexanucleotide pentaphosphate r(CpGpCpGpCpG). One‐dimensional proton nmr experiments were used to probe the structural details of the left‐handed helix in concentrated sodium perchlorate solution. In 1M NaClO4 the RNA adopts the normal A‐form double helix, and in 6M NaClO4 it is nearly all in the Z form. In 4M NaClO4 it exists as nearly equal parts of A form and Z form. Resonances corresponding to both A and Z form appear in the nmr spectrum, indicating that the duplex exchanges slowly between forms. Spin–spin coupling constants between protons in the ribose rings were used to determine the sugar‐pucker conformations of the individual nucleotides. Quantitative nuclear Overhauser experiments were used to determine proton–proton distances within the nucleoside, and from these distances values for the glycosidic torsion angle were determined. The results show that the cytidines adopt C2′,‐endo sugar puckers (S type) with pseudo‐rotation phase values (P) of ∼ 165°. The bases are in the anti conformation, with χ values of ∼ − 140°. The internal guanosines adopt C3′,‐endo sugar puckers (N type) with P ∼ 18°, while the 3′‐terminal guanosine ribose exists in an equilibrium between S‐ and N‐type conformations. All three guanosine bases adopt the syn conformation, with χ ∼ 70°. The results indicate that the solution structure of Z‐RNA is very similar to that of Z‐DNA.
Conformational analysis of the immunodominant epitopes of the circumsporozoite protein of Plasmodium falciparum and knowlesi
Authors: Fasman Gerald D. , Park Kyusung , Schlesinger David H. 
Published: December 2004

AbstractAll of the coat proteins of the sporozoite and merozoite stages of Plasmodium, determined to date, contain tandem repeats and most of these contain at least one proline residue. These tandemly repeated segments of the circumsporozite (CS) proteins of P. falciparum and P. knowlesi have been shown to constitute an immunodominant epitope. Antibodies to these peptide segments have been shown to be protective and cause the shedding of the CS protein, known as the CSP reaction. In this study, four synthetic peptides were prepared by solid‐phase peptide synthesis. The first peptide corresponds to the tetrapeptide tandem repeat in the CS protein of P. falciparum, repeated eight times, (NANP)8. The second peptide is an analogue of the first in which glycine is substituted for proline, (NANG)8. The third peptide corresponds to the tandem repeat of P. knowlesi, PK(1–24), which is repeated twice (QAQGDGANAGQP)2. The fourth peptide is a tetrapeptide repeat, corresponding to the C‐terminal tetrapeptide of PK(1–24) and is repeated eight times, (AGQP)8. It is shown by CD measurements that the presence of proline in these repeats induces an increase in β‐sheet (β‐turn) content in the (NANP)8 peptide relative to the repeat of (NANG)8 and PK(1–24) peptide in aqueous media. The (AGQP)8 peptide has the highest β‐sheet (β‐turn) content in the synthetic peptides. It is concluded that this increase in defined structure correlates well with and hence may contribute to the increased antigenicity in these repeats.
The most highly amphiphilic α‐helices include two amino acid segments in human immunodeficiency virus glycoprotein 41
Authors: Eisenberg David , Wesson Morgan 
Published: December 2004

AbstractA search for highly amphiphilic α‐helices has been made in a data base of protein sequences, using the helical hydrophobic moment as a criterion of amphiphilicity. The protein segments of largest hydrophobic moment have been analyzed. For the segments whose structures are known, they are in fact α‐helices. Two of the segments having very large hydrophobic moments are from the smaller C‐terminal portion of the human immunodeficiency virus (HIV) envelope glycoprotein gp41. Also, among segments having large hydrophobic moments, but not among the most extreme, are lytic peptides such as melittin. Melittin seeks surfaces between polar and apolar phases, including the membrane–water interface. It is conceivable that the gp41 segments of extreme hydrophobic moment may participate in one of the membrane‐related functions of the HIV virus.
A · U and G · C base pairs in synthetic RNAS have characteristic vacuum UV CD bands
Authors: Johnson Kenneth H. , Gary Donald M. , Morris Patricia A. , Sutherland John C. 
Published: December 2004

AbstractThe vacuum UV CD spectra of GpC, GpC, GpG, poly[r(A)], poly[r(C)], poly[r(U)], poly[r(A‐U)], poly[r(G) · r(C)], poly[r(A) · r(U)], and poly[r(A‐U) · r(A‐U)] were measured down to at least 174 nm. These spectra, together with the published spectra of poly[r(G‐C) · r(G‐C)], CMP, and GMP, were sufficient to estimate the CD changes upon base pairing for four double‐stranded RNAs.The vacuum UV CD bands of poly[r(A)], poly[r(C)], and the dinucleotides GpC and CpG were temperature dependent, suggesting that they were due to intrastrand base stacking. The dinucleotide sequence isomers GpC and CpG had very different vacuum UV CD bands, indicating that the sequence can play a role in the vacuum UV CD of single‐straded RNA.The vacuum UV CD bands of the double‐stranded (G · C)‐containing RNAs, poly[r(G) · r(C)] and poly[r(G‐C) · r(G‐C)], were larger than the measured or estimated vacuum UV CD bands of their constituent single‐stranded RNAs and were similar in having an exceptionally large positive band at about 185 nm and negative bands near 176 and 209 nm. These similarities were enhanced in difference‐CD spectra, obtained by subtracting the CD spectra of the single strands from the CD spectra of the corresponding double strands. The (A · U)‐containing double‐stranded RNAs poly[r(A) · r(U)] and poly[r(A‐U) · r(A‐U)] were similar only in that their vacuum UV CD spectra had a large positive band at 177 nm. The spectrum of poly[r(A) · r(U)] had a shoulder at 188 nm and a negative band at 206 nm, whereas the specturm of poly[r(A‐U) · r(A‐U)] had a positive band at 201 nm. On the other hand, difference spectra of both of the (A · U)‐containing polymers had positive bands at about 177 and 201 nm. Thus, the difference‐CD spectra revealed CD bands characteristic of A · U and G · C base pairing. A · U base pairs induced two positive bands at about 177 and 201 nm, whereas G · C base pair induced a large positive band at 186 nm and negative bands at about 175 and 202 nm.
Small‐angle neutron scattering study of the structure of protein / detergent complexes
Authors: Guo X. H. , Zhao N. M. , Chen S. H. , Teixeira J. 
Published: December 2004

AbstractSmall‐angle neutron scattering (SANS) was used to study the structure of protein/sodium dodecylsulfate complexes. Two water soluble proteins, bovine serum albumin (BSA) and ovalbumin (OVA), were used. The protein concentration was kept constant at 1 wt %, and protein/detergent wt ratio varied between 1/1, 1/1.5, 1/2 and 1/3. Absolute intensities of SANS distributions were analyzed by a fractal model. Analyses of large Q portions of SANS distributions established that sodium dodecylsulfate (SDS) molecules bound to a protein/SDS complex form micelle‐like clusters. On the other hand, analyses of small Q portions of SANS distributions clearly showed that the arrangement of micelle‐like clusters resembles a fractal packing of spheres. We showed that a protein/SDS complex can be characterized by four parameters extracted from the scattering experiment, namely, the average micelle size and its aggregation number, the fractal dimension characterizing the conformation of the micellar chains, the correlation length giving the extent of the unfolded polypeptide chains, and the numbers of micelle‐like clusters in the complex.
Motions of an α‐helical polypeptide: Comparison of molecular and harmonic dynamics
Authors: Perahia D. , Levy R. M. , Karplus M. 
Published: December 2004

AbstractMolecular and harmonic dynamics simulations have been performed for a decaglycine α‐helix. The extent of anharmonicity for various observables is studied by a direct comparison of the two types of simulations, at temperatures ranging from 5 to 300 K. The fluctuations of the cartesian, internal and normal mode coordinates, and their time dependence, are analyzed. The heat capacity of the α‐helix is evaluated both from the temperature response of the system to an energy perturbation and from the fluctuations in the temperature of the system. It is shown that the anharmonicity depends on the kind of observable. The root mean square atomic fluctuations have significant anharmonic components at temperatures above 100 K. In contrast, the dihedral angle fluctuations are much closer to being harmonic at all the temperatures considered. The analysis of potentials of mean force experienced by individual atoms shows that atomic displacements have approximately Gaussian distributions from 50 to 300 K, with different force constants at each temperature (quasi‐harmonic model). At 300 K, the force constants obtained by molecular dynamics are significantly lower than in the harmonic case. The time dependence of the projection of the molecular dynamics displacements on the normal mode coordinates shows that mode mixing is important above 100 K. The motions of the helix associated with the low‐frequency normal modes are described and illustrated.