Energy-conformation studies of frequency of beta-turns in tetrapeptide sequences

The optimized energies of seven beta-bends, repeating C5 and C7, and right- and left-handed alpha-helical conformations for each of eight tetrapeptides have been computed using empirical methods. Eight tetramers were selected: four helix-forming sequences with hydrophobic residues such as Val, Leu, Ile and Trp, and four helix-breaking sequences with hydrophilic residues such as Asp, Asn and Ser, as determined by their frequency of occurrence in beta turns in proteins. Analysis of the optimized conformations with energies less than or equal to 2.1 kcal/mol from the absolute minimum energy conformer for each tetramer reveals a correlation between low-energy conformations and those predicted from observed protein structures. These results show that energy calculations on small peptide fragments may be usefulin predicting protein structure.     

Support vector machines for the classification and prediction of beta-turn types.

The support vector machines (SVMs) method is proposed because it can reflect the sequence-coupling effect for a tetrapeptide in not only a beta-turn or non-beta-turn, but also in different types of beta-turn. The results of the model for 6022 tetrapeptides indicate that the rates of self-consistency for beta-turn types I, I', II, II', VI and VIII and non-beta-turns are 99.92%, 96.8%, 98.02%, 97.75%, 100%, 97.19% and 100%, respectively. Using these training data, the rate of correct prediction by the SVMs for a given protein: rubredoxin (54 residues. 51 tetrapeptides) which includes 12 beta-turn type I tetrapeptides, 1 beta-turn type II tetrapeptide and 38 non-beta-turns reached 82.4%. The high quality of prediction of the SVMs implies that the formation of different beta-turn types or non-beta-turns is considerably correlated with the sequence of a tetrapeptide. The SVMs can save CPU time and avoid the overfitting problem compared with the neural network method.     

Low-energy conformations of two lysine-containing tetrapeptides of collagen: implications for posttranslational lysine hydroxylation

The possible role of conformational constraints in the posttranslational hydroxylation of lysyl residues in collagen has been investigated by means of conformational energy computations for the N-acetyl-N′-methylamides of the four tetrapeptides Ala-Xxx-Gly-Ser and Gly-Xxx-Ala-Gly, where Xxx = Lys or Ala. When hydration is taken into account, all four peptides are shown to exist as a mixture of conformations, but there is a strong preference for type II bends in the conformational ensembles of two Ala-Xxx-Gly-Ser tetrapeptides and for type I bends in the conformational ensembles of the other two. The results agree with experimental evidence suggesting that a type II bend is an important conformation for Ac-Ala-Lys-Gly-Ser-NHCH₃, and they support an earlier suggestion that a β-bend may play a role in the posttranslational hydroxylation of Lys residues in position Y of the Gly-X-Y triplet in collagen.     

Optical spectroscopic elucidation of beta-turns in disulfide bridged cyclic tetrapeptides

Vibrational circular dichroism (VCD) spectroscopic features of type II beta-turns were characterized previously, but, criteria for differentiation between beta-turn types had not been established yet. Model tetrapeptides, cyclized through a disulfide bridge, were designed on the basis of previous experimental results and the observed incidence of amino acid residues in the i + 1 and i + 2 positions in beta-turns, to determine the features of VCD spectra of type I and II beta-turns. The results were correlated with electronic circular dichroism (ECD) spectra and VCD spectra calculated from conformational data obtained by molecular dynamics (MD) simulations. All cyclic tetrapeptides yielded VCD signals with a higher frequency negative and a lower frequency positive couplet with negative lobes overlapping. MD simulations confirmed the conformational homogeneity of these peptides in solution. Comparison with ECD spectroscopy, MD, and quantum chemical calculation results suggested that the low frequency component of VCD spectra originating from the tertiary amide vibrations could be used to distinguish between types of beta-turn structures. On the basis of this observation, VCD spectroscopic features of type II and VIII beta-turns and ECD spectroscopic properties of a type VIII beta-turn were suggested. The need for independent experimental as well as theoretical investigations to obtain decisive conformational information was recognized.     

Intervening sequences in human fetal globin genes adopt left-handed Z helices

The large intervening sequences ( IVS2 ) of three human fetal globin genes contain tracts of alternating purine-pyrimidine sequences approximately 40-60 base pairs in length which adopt left-handed Z DNA helices under the influence of negative supercoiling. The amount of negative supercoiling (approximately 0.045) required for the right- to left-handed transitions is within the physiological range. The structural aberrations between the right- and left-handed helices were mapped by sequencing the S1 nuclease cleavage sites. Two-dimensional gel electrophoretic analyses of the supercoil-induced relaxation served to characterize the type and length of left-handed structure. Furthermore, binding studies with several types of antibodies confirmed the presence of left-handed helices. Since these simple sequences appear to be hotspots for recombination and gene conversion, unusual DNA conformations may participate in genetic expression.     

Prediction of beta-turns with learning machines

The support vector machine approach was introduced to predict the beta-turns in proteins. The overall self-consistency rate by the re-substitution test for the training or learning dataset reached 100%. Both the training dataset and independent testing dataset were taken from Chou [J. Pept. Res. 49 (1997) 120]. The success prediction rates by the jackknife test for the beta-turn subset of 455 tetrapeptides and non-beta-turn subset of 3807 tetrapeptides in the training dataset were 58.1 and 98.4%, respectively. The success rates with the independent dataset test for the beta-turn subset of 110 tetrapeptides and non-beta-turn subset of 30,231 tetrapeptides were 69.1 and 97.3%, respectively. The results obtained from this study support the conclusion that the residue-coupled effect along a tetrapeptide is important for the formation of a beta-turn.     

Right-left symmetry preservation by flowers of malvaceae family

The flowers of malvaceae family preserves the symmetry between right and left in a peculiar manner. Plots belonging to this family bear two kinds of flowers, right-handed flowers with anticlockwise twisted petals and left-handed flowers with clockwise twisted petals. The branches of the plant prefers production of one type of flowers in excess of the other. There are two distinct types of branches, dextral branches and sinistral branches. Dextral (sinistral) branches produce more right-handed (left-handed) flowers than left-handed (right-handed) flowers. The average percentage of right-handed flowers in a dextral branch is same as that of left-handed flowers in a sinistral branch.     

β-Turn preference of tetrapeptide sequences as analyzed by CD spectra of their Dnp-pNA derivatives

The Dnp-pNA derivatives of more than 30 tetrapeptides were synthesized and subjected to CD measurements in MeOH. The CD spectra were analyzed on the basis of exciton chirality theory and were found to be useful for estimating β-turn preference of the parent tetrapeptides based on the following facts: (1) when a compound of the series takes the βturn conformation, a pair of strong CD bands with opposite sign are observed at 305 and 350 nm, and (2) when it is in a random or nonfolded conformation, no significant bands are observed at the wavelengths. The intensity of the 350-nm band reflects especially well the βturn preference. The CD spectra can be classified into two groups according to the sign of the band at 350 nm, and the groups seem to correspond to the type of βturn. By summarizing the results obtained, some generalizations concerning the sequence–conformation relationship are proposed.     

Inhibition of iodine-125-labeled human follitropin binding to testicular receptor by epidermal growth factor and synthetic peptides

Two tetrapeptide sequence homologies between mouse epidermal growth factor precursor (mEGFP) and human follitropin (FSH) were revealed by a computer program that identifies identical residues among polypeptide sequences. The two tetrapeptides, Lys-Thr-Cys-Thr (KTCT) and Thr-Arg-Asp-Leu (TRDL), are present in the hormone-specific beta subunit of FSH from all species studied. These tetrapeptides are not present in the alpha subunit, which is common to all pituitary glycoprotein hormones. Both tetrapeptides are also found in mEGFP, and one tetrapeptide, TRDL, is located within the 53-residue form of mEGF purified from mouse submaxillary glands. Computer-generated hydropathy profiles predicted that both tetrapeptides are located in hydrophilic portions of the FSH beta subunit and that TRDL is in a hydrophilic portion of commercially available mEGF. Therefore, the tetrapeptides might be accessible to receptor binding sites for FSH. We report that mEGF inhibits binding of 125I-labeled human FSH to receptors in testis by 50% (I50) at a concentration of 1.8 X 10(-5) M. No binding inhibition was observed by GnRH or arginine-vasopressin at 10(-4) M, neither of which contain the tetrapeptide sequences. FSH beta subunit, which contains both tetrapeptides, also inhibited binding (I50 = 9 X 10(-8) M) of 125I-labeled human FSH to testis receptor. Thus, it appears that FSH beta subunit and mEGF are capable of inhibiting binding of FSH to testicular FSH receptors, presumably through interactions that include the homologous tetrapeptides. This presumption was supported by the observation that the synthetic tetrapeptides (KTCT or TRDL) were also active in inhibiting binding of 125I-labeled human FSH to testis receptor.     

Secondary structure of polypeptide hormones of the anterior lobe of the pituitary gland

The specific secondary structure of a number of polypeptide hormones of the pituitary gland anterior lobe and their fragments were studied by CD in the peptide bond absorption region and by ir spectroscopy. The state of objects was examined in solvents of different polarity over a wide temperature range as well as in the solid state at different relative humidities. The predominant conformational state of a number of hormones in aqueous solution is shown to represent a left-handed helix of the poly(L -proline) II type. The reversible melting process of the left-handed helical conformation when heated in an aqueous solution appears to be noncooperative. Lowering the temperature stabilizes the left-handed structure. The transition mode of the left-handed form to the α-, and the β-forms on changing the solvent conditions was also studied. Contributions of peptide chromophores and of the aromatic amino acid side-group chromophores with CD bands in the region under study were determined by analysis of CD spectra. The data obtained allow correlating the conformation of separate fragments in the hormone chain with functional activity.     

Synthesis, biological activity and conformation of enkephalin analogs structurally related to kyotorphin

[D-Arg2,Leu5]Enkephalin and two series of its N-terminal short-chain analogues with a free and modified C-terminal carboxylic group, viz. amides and ethyl esters of tri- and tetrapeptides, were synthesized in solution and by solid-phase method. Their analgesic activity, assayed by the "tail pinch" method following intracisternal and intravenous administration to mice, was compared with activity of enkephalins and morphine. To study the space structure of the synthesized compounds, conformational calculations and fluorescence spectroscopy were applied to measure distance between aromatic nuclei of tyrosine and phenylalanine residues in the two tetrapeptides. Ethyl esters of the tri- and tetrapeptides exceed in analgesic activity the corresponding carboxylic acids and amides. In contrast to the pentapeptide, the tetrapeptide analogues were active upon intravenous administration. Conformational aspects of this series of analogues are discussed in detail; the abrupt increase in activity upon transition from tri- to tetrapeptides does not appear to be related to conformational changes.     

A test for the structure of the left helix of poly-L-proline type II in peptides

The spectral criterion of a left-handed helix of the poly-L-proline II type was elaborated during the study of a number of synthesized oligopeptides (in a solid state and solution): (Gly-Pro-Pro)1-8, (Gly-Pro)1, (Gly-Pro-Ala)1-4, (Gly-Pro-Gly)1-4, (Gly-Pro-Pro) X (Gly-Pro-Gly)1-2(Gly-Pro-Pro), (Gly-Pro-Pro)n, (Orn3-Gly)n and also rat skin collagen by X-ray diffraction, circular dichroism and infrared spectroscopy methods; the characteristic shape of the left-handed helix CD spectrum was found. The change of spectral characteristics with the change of left-handed helix distortion was established. The linear noncooperative melting process of the left-handed conformation was demonstrated. The data obtained allow to determine qualitatively the presence of the left-handed helix in different polypeptides and proteins.     

Formation of N-[2(3-Alkylpyrazin-2-on-l-yl)acyl]amino Acids or -peptides on Heating Tri- or Tetrapeptides with Glyoxal

The reaction of tri- and tetrapeptides with glyoxal at 100°C and pH 5.0 was studied. A series of new pyrazinone compounds was isolated from the reaction solutions of tri- and tetrapeptides with glyoxal: N-[2(3-alkylpyrazin-2-on-l-yl)acyl] amino acids (I) and 2-(3-alkyl- pyrazin-2-on-l-yl)aIkyl acids (II) from tripeptides, (I), (II) and N-[2(3~alkylpyrazin-2-on-l-y]) acyl]-dipeptides (III) from tetrapeptides. Their chemical structures were determined by UV, IR, MS and NMR spectroscopy.

Aldehydes and free amino acids were also detected as reaction products. The amino acids were proved to be derived from the C-terminals of the peptides. Reaction mechanisms for the reaction of tri- and tetrapeptides with glyoxal were also proposed.     

Features of the Brain Functional Organization in Right- and Left-Handed 6- to 7-Year-Old Children during Visuospatial Performance of Different Complexity: II. Analysis of EEG Parameters during Complex Visuospatial Performance

The features of brain functional organization during complex visuospatial performance were studied in 6- to 7-year-old right- and left-handed children. Differences in the brain functional organization were revealed between children with different profiles of manual asymmetry. Presentation of complex experimental tasks to right-handed children resulted in the formation of selective functional connections between centers, which is indicative of the use of economical and efficient mechanisms of the organization of activity. Generalized functional integration was observed in left-handed children, which reflected an immature type of regulation of cortical activity.     

Rigorous conformational analysis of right and left DNA helices and junction between them

On the basis of complete scanning through conformational space of dihedral angles, twelve structural genera were obtained. Subsequent energy minimization within these genera yielded a limited set of duplexes with stacking: right-handed B-form (Wilkins type), B2-form (Watson and Crick type) and left-handed Ll-form (Sasisekharan type) and the new L2-form. In the polymeric DNA only right-handed double-helices are possible, the left-handed helices are forbidden due to poor 1–5 interchain contacts. In contrast, for short fragments the left- and right-handed helicek have practically the same energies providing some physical ground for side-by-side form, which biologically is possible as recombination form and may be as replication form.     

The extended left-handed helix: a simple nucleic acid-binding motif

The poly-proline type II extended left-handed helical structure is well represented in proteins. In an effort to determine the helix's role in nucleic acid recognition and binding, a survey of 258 nucleic acid-binding protein structures from the Protein Data Bank was conducted. Results indicate that left-handed helices are commonly found at the nucleic acid interfacial regions. Three examples are used to illustrate the utility of this structural element as a recognition motif. The third K homology domain of NOVA-2, the Epstein-Barr nuclear antigen-1, and the Drosophila paired protein homeodomain all contain left-handed helices involved in nucleic acid interactions. In each structure, these helices were previously unidentified as left-handed helices by secondary structure algorithms but, rather, were identified as either having small amounts of hydrogen bond patterns to the rest of the protein or as being "unstructured." Proposed mechanisms for nucleic acid interactions by the extended left-handed helix include both nonspecific and specific recognition. The observed interactions indicate that this secondary structure utilizes an increase in protein backbone exposure for nucleic acid recognition. Both main-chain and side-chain atoms are involved in specific and nonspecific hydrogen bonding to nucleobases or sugar-phosphates, respectively. Our results emphasize the need to classify the left-handed helix as a viable nucleic acid recognition and binding motif, similar to previously identified motifs such as the helix-turn-helix, zinc fingers, leucine zippers, and others.     

A comparison of the antinociceptive and behavioral effects of D-Arg substituted dipeptides and tetrapeptides in mice

Intracerebroventricular administration of D-Arg substituted dipeptides, H-Tyr-D-Arg-OMe and H-Tyr(Et)-D-Arg-OMe, and D-Arg2 substituted N-terminal tetrapeptides of dermorphin, H-Tyr-D-Arg-Phe-Gly-OEt and H-Tyr(Et)-D-Arg-Phe-Gly-OEt resulted in dose-related and naloxone-reversible antinociceptive effects. Among them, tetrapeptides not only exhibited much more potent and prolonged activities than dipeptides but also were significantly antagonized even by a low dose of naloxone. Spontaneous motor activity was lowered by dipeptides throughout the observation period, which was scarcely antagonized by naloxone. Tetrapeptides elicited locomotor hyperactivity following an initial locomotor suppression. Only the locomotor hyperactivity was significantly antagonized by naloxone. These results suggest that tetrapeptides induce the effects via opioid receptors, whereas the effects of dipeptides are involved in various systems non-specifically.     

Prediction of β-Turns

Kohonen's self-organization model, a neural network model, is applied to predict the β-turns in proteins. There are 455 β-turn tetrapeptides and 3807 non-β-turn tetrapeptides in the training database. The rates of correct prediction for the 110 β-turn tetrapeptides and 30,229 non-β-turn tetrapeptides in the testing database are 81.8% and 90.7%, respectively. The high quality of prediction of neural network model implies that the residue-coupled effect along a polypeptide chain is important for the formation of reversal turns, such as β-turns, during the process of protein folding.     

Transferrin receptor internalization sequence YXRF implicates a tight turn as the structural recognition motif for endocytosis

Using detailed functional studies on 24 human transferrin receptor mutants, we identified YXRF as the internalization sequence. Provided that at least 7 residues separate this tetrapeptide from the transmembrane region, changing the tetrapeptide position within the TR cytoplasmic domain does not reduce internalization activity. Thus, any conformational determinant for internalization must be localized to the YXRF sequence. Twenty-eight tetrapeptide analogs of YXRF, found by an unbiased search of all known three-dimensional protein structures, significantly favored tight turns similar to a type I turn. Of the ten tetrapeptides most closely related to YXRF, eight were surface exposed and had tight-turn conformations, as were four of five tetrapeptides with sequences related to the low density lipoprotein receptor internalization motif, NPXY. The internalization sequences of both receptors contain aromatic residues with intervening hydrogen-bonding residues. Thus, two distinct internalization sequences favor a common structural chemistry and implicate an exposed tight turn as the recognition motif for high efficiency endocytosis.