摘要:

AbstractThe 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‐chai

ISSN:0006-3525    

DOI:10.1002/bip.360330202

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1993

数据来源: WILEY

摘要:

Abstractα, β‐Dehydroamino acids are expected to provide conformational constraint to the peptide backbone. A pentapeptide containing two dehydrophenylalanines (ΔZPhe) separated by oneL‐amino acid has been synthesized and its solid state conformation determined. The pentapeptide, Boc‐Gly‐ΔZPhe‐Leu‐ΔZPhe‐Ala‐NHCH3, crystallizes from aqueous methanol in the orthorhombic space group P212121. There are four formula units, C35H46N6O7, in a unit cell of dimensionsa= 10.155(3),b= 15.175(1), andc= 23.447(2) Å, at room temperature. The structure was solved by direct methods program, SIR88, and refined to a finalR= 0.038 based on 3049 reflections withI>2σ(I). All the peptide links aretransand the backbone conformation of the pentapeptide can be described as a 310‐helix, with mean ϕ, ψ values of −65.1° and −22.8° (the value is averaged over the first four residues). There are four intramolecular 4 → 1 type hydrogen bonds characteristic of 310‐type helices. In the crystal, the helices are held together by intermolecular NH…︁OC head‐to‐tail and lateral hydrogen bonding between symmetry related molecules. This mode of packing is similar to the packing motifs observed so often in other oligopeptides that adopt a 31

ISSN:0006-3525    

DOI:10.1002/bip.360330203

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1993

数据来源: WILEY

摘要:

AbstractThe 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, I

ISSN:0006-3525    

DOI:10.1002/bip.360330204

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1993

数据来源: WILEY

摘要:

AbstractThe description of molecular shape is important in the analysis of protein–protein and protein–ligand interactions. We describe volumetric and surface‐based techniques for computing shape properties of molecular surfaces. The surface is defined as an isocontour of an approximate electron density function. Each technique can compute several scalar and vector surface properties such as the Gaussian and mean curvature, principal curvatures, and principal curvature directions. Shape properties are derived from the eigenvalues and eigenvectors of a 3 by 3 matrix for each surface point. In the volumetric approach, the matrix is the second derivative of an approximate electron density function. In the surface‐based approach, the matrix is the approximate gradient of the surface normal. Derivatives 4 are computed by convolving the density or the surface normals with the derivatives of a Gaussian function. The variance of the Gaussian determines the effective length scale at which the surface is analyzed. Scalar surface properties are displayed as colored dots or shaded triangles, and vector properties are displayed as line segments from each surface point. This report describes the implementation of these procedures and their use in computing the shape properties of Cu‐Zu superoxide dismutase. © 1993 John Wiley

ISSN:0006-3525    

DOI:10.1002/bip.360330205

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1993

数据来源: WILEY

摘要:

AbstractThe combined effect of several sensitizers and light on H2O or D2O solutions of DNA‐histone complexes, as well as the significance of singlet oxygen (1O2), in this photosensitizing reaction has been studied. On H2O solutions, the production of1O2, as well as the formation of DNA‐protein cross‐links (DPCs), were found to be dependent on light dose for all the sensitizers. Mesotetra (4N‐methylpyridyl) porphine (T4MPyP), methylene blue (MB), and toluidine blue (TB) were the best photosensitizers with regard to tryptophan photolysis, followed by hematoporphyrin (HP), thioflavine T (TT), and pyronin G (PG). The formation of DPCs showed high initial rates, reaching a plateau at dose over 90 J/cm2. Under these irradiation conditions, the percentage of DPCs induced by the sensitizers decreases in the order T4MPyP>MB>TB ≫ HP ≈ TT ≫ PG (≈0). These DPCs were totally destroyed with proteinase K (15μg/ml). The irradiation of the DNA‐histone‐sensitizer solutions in the presence ofL‐carnosine (5 × 10‐4M) produced approximately a 50% of DPCs inhibition for T4MPyP, MB, and TB, and a total inhibition for HP, TT, and PG. The substitution of H2O by D2O as solvent significantly increased the photodegradation of tryptophan, as well as the photoinduction of DPCs by the sensitizers. The results obtained indicate that singlet oxygen is the main agent responsible in the DNA–protein cross‐linking formation

ISSN:0006-3525    

DOI:10.1002/bip.360330206

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1993

数据来源: WILEY

摘要:

AbstractFlow linear dichroism is used to measure specific inclinations for each of the four bases in poly[d(AC)]·;poly[d(GT)]and poly[d(AG)]·poly[d(CT)]in both the B and A forms. For the B form in solution the bases are found to have a sizable inclination. Inclination is increased in the A form, as expected. In all cases the pyrimidines are more inclined than the purines. © 1993 John Wiley&Sons, I

ISSN:0006-3525    

DOI:10.1002/bip.360330207

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1993

数据来源: WILEY

摘要:

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

ISSN:0006-3525    

DOI:10.1002/bip.360330208

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1993

数据来源: WILEY

摘要:

AbstractThe structure of tetra‐O‐methyl‐ (+) ‐catechin has been determined in the crystalline state. Two independent molecules, denoted structure A and structure B, exist in the unit cell. Crystals are triclinic, space group P1,a= 4.8125(2) Å,b= 12.9148(8) Å,c= 13.8862(11) Å, α = 86.962(6) °, β = 89.120(5)°, γ = 88.044(5)°,Z= 2, Dc= 1.336 g cm−3,R= 0.033 for 6830 observations. The heterocyclic rings of the crystal structures are compared to previous results for 8‐bromotetra‐O‐methyl‐(+)‐catechin, penta‐O‐acetyl‐(+)‐catechin, and (−) ‐epicatechin. One of the two molecules has a heterocyclic ring conformation similar to that observed previously for (−)‐epicatechin, and the other has a heterocyclic ring conformation similar to one predicted earlier in a theoretical analysis of dimers of (+)‐catechin and (−) ‐epicatechin. Both structure A and structure B in the crystal have heterocyclic ring conformations that place the dimethoxyphenyl substituent at C(2) in the equatorial position. However, this heterocyclic ring conformation does not explain the proton nmr coupling constant measured in solution. Molecular dynamics simulations show an equatorial ⇌ axial interconversion of the heterocyclic ring, which can

ISSN:0006-3525    

DOI:10.1002/bip.360330209

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1993

数据来源: WILEY

摘要:

AbstractDiffusion of acetonitrile into an aqueous solution ofDL‐histidine and succinic acid in 1:3 molar proportions results in the crystals ofDL‐histidine hemisuccinate dihydrate [triclinic, P1,a= 7.654(1),b= 8.723(1),c= 9.260(1) Å, α = 77.23(1), β = 72.37(1) and γ = 82.32 (1)°]. The replacement ofDL‐histidine byL‐histidine in the crystallization experiment under identical conditions leads to crystals ofL‐histidine semisuccinate trihydrate [orthorhombic, P212121,a= 7.030 (1),b= 8.773 (1), andc= 24.332 (3) Å]. The structures were solved using counter data and refined toRvalues of 0.056 and 0.054 for 2356 and 1778 observed reflections, respectively. Histidine molecules in both the complexes exist in open conformation I. Succinate and semisuccinate ions in them are planar, and exactly or nearly centrosymmetric. In theDL‐histidine complex, the amino acid molecules form double ribbons and the succinate ions occupy voids left behind when the double ribbons aggregate, as in inclusion compounds. In theL‐histidine complex, the amino acid molecules form columns; so do the semisuccinate ions and water molecules. The two columns interdigitate to form the complex crystal. There are similarities between the molecular aggregation in the complexes and that in the crystals ofL‐ andDL‐histidine. However, the presence of succinic acid has the effect of disrupting, partially or totally, head‐to‐tail sequences involving amino acid molecules.

ISSN:0006-3525    

DOI:10.1002/bip.360330210

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1993

数据来源: WILEY

摘要:

AbstractThis report continues to explore the use of a strategy known as the antlion method for predicting polypeptide and protein structure. The method involves deformation of a biopolymer's potential energy hypersurface in order to retain only a single minimum, near to the native structure. The vexing multiple minimum problem thus is relieved, and the deformed hypersurface constitutes a key element in three‐dimensional structure predictions with atomic resolution. In this more demanding pilot study, we provide evidence that the antlion method is capable of dramatically simplifying the surface of polypeptides by successfully predicting the native form of the naturally occurring 26‐residue polypeptide melittin. The systematic hypersurface modifications employed in our previous work have been used again for this case, but have been supplemented by the output of a suitable neural network. This neural network involves a new feature: the use of amino acid biophysical scales for improving the secondary structure prediction accuracy of simple perceptrons. © 1993 John Wiley&Sons,

ISSN:0006-3525    

DOI:10.1002/bip.360330211

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1993

数据来源: WILEY