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.     

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.     

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.     

Prediction of β-turns in proteins by 1-4 and 2-3 correlation model

A 1–4 and 2–3 residue-correlation model is proposed to predict the β-turns in proteins. The average rate of correct prediction for the 455 β-turn tetrapeptides and 4018 non-β-turn tetrapeptides in the training data base is 80.1%, and that for the 223 β-turn tetrapeptides and 12562 non-β-turn tetrapeptides in the testing data base is 80.9%. Compared with the rates of correct prediction based on the residue-independent model reported previously, the quality of prediction is significantly improved by the new model, implying that the correlation effect between the 1st and the 4th residues and that between the 2nd and 3rd residues along a tetrapeptide are important for forming a β-turn in a protein during the process of its folding. © 1997 John Wiley & Sons, Inc. Biopoly 41: 673–702, 1997     

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.     

Short fragments of a protein globule with predominant conformation

It has been found that 1500 tetrapeptides out of 160000 possible combinations occurring in proteins exhibit preference for particular conformational states. Most conformationally stable tetrapeptides obtained in the analysis of a sampling containing 706 proteins are in the alpha-helical form. The features of the amino acid composition of conformationally stable oligopeptides have been studied.     

Structural characterization of BRCT-tetrapeptide binding interactions

BRCT(BRCA1) plays a major role in DNA repair pathway, and does so by recognizing the conserved sequence pSXXF in its target proteins. Remarkably, tetrapeptides containing pSXXF motif bind with high specificity and micromolar affinity. Here, we have characterized the binding interactions of pSXXF tetrapeptides using NMR spectroscopy and calorimetry. We show that BRCT is dynamic and becomes structured on binding, that pSer and Phe residues dictate overall binding, and that the binding affinities of the tetrapeptides are intimately linked to structural and dynamic changes both in the BRCT(BRCA1) and tetrapeptides. These results provide critical insights for designing high-affinity BRCT(BRCA1) inhibitors.     

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.     

Left-handed helix conformation of poly-L-proline II type in globular proteins. Statistics of incidence and a role of sequence]

Regions of left-handed polyproline II type conformation in globular proteins were studied throughout the PDB bank. The length and sequence of corresponding fragments were analyzed. It was found that a lot of tetrapeptides (from combinatorial possible ones) show the tendency to be included in the left-handed helices. Much more tetrapeptides do not occur in this structure type.     

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.     

Bicyclic tetrapeptides as potent HDAC inhibitors: Effect of aliphatic loop position and hydrophobicity on inhibitory activity

Several histone deacetylase (HDAC) inhibiting bicyclic tetrapeptides have been designed and synthesized through intramolecular ring-closing metathesis (RCM) reaction and peptide cyclization. We designed bicyclic tetrapeptides based on CHAP31, trapoxin B and HC-toxin I. The HDAC inhibitory and p21 promoter assay results showed that the aliphatic loop position as well as the hydrophobicity plays an important role toward the activity of the bicyclic tetrapeptide HDAC inhibitors.     

Functional characterization of the modified melanocortin peptides responsible for ligand selectivity at the human melanocortin receptors

The melanocortin system plays an important role in energy homeostasis as well as skin pigmentation, steroidogenesis and exocrine gland function. In this study, we examined eight Ac-His-Phe-Arg-Trp-NH(2) tetrapeptides that were modified at the Phe position and pharmacologically characterized their activities at the human MCR wild-types and their mutants. Our results indicate that at the hMC1R, all D stereochemical modified residues at the Phe position of peptides increase cAMP production in a dose-dependent manner. At the hMC3R, the DPhe peptide dose dependently increases cAMP production but all other three tetrapeptides were not. At the hMC4R, both the DPhe and DNal(1') peptides induce cAMP production. However, both DTyr and DNal(2') were not able to induce cAMP production. Further studies indicated that at the hMC1R M128L mutant receptor, the all D-configured tetrapeptides reduce their potencies as compared to that of hMC1R wild-type. However, at the hMC3R and hMC4R L165M and L133M mutant receptors, the DNal(2') and DTyr tetrapeptides possess agonist activity. These findings indicate that DPhe in tetrapeptide plays an important role in ligand selectivity and specific residue TM3 of the melanocortin receptors is crucial for ligand selectivity.     

The preferential human mononuclear leukocyte chemotactic activity of the substituent tetrapeptides of angiotensin II

The amino- and carboxy-terminal substituent tetrapeptides of angiotensin II, Asp-Arg-Val-Tyr and Ile-His-Pro-Phe, elicit substantial human mononuclear leukocyte chemotactic responses $\text{in}\text{vitro}$ that attain maximal levels at tetrapeptide concentrations of 3 × 10^?8 M and 3 × 10^?7 M, respectively. In contrast, the angiotensin II-derived tetrapeptides evoke only marginal human neutrophil chemotactic responses. Amino acid deletions or substitutions that alter the properties of the tetrapeptides, reduce their chemotactic potency and activity. Limited proteolytic cleavage of angiotensin II thus may convert a pathway with predominantly humoral effects to a source of mediators that regulate cellular immunity and chronic inflammatory responses.     

Intestinal handling of two tetrapeptides by rodent small intestine in vitro.

Uptake of free Leu and Ala and uptake of these amino acids from the tetrapeptides Leu-Gly-Gly-Gly and Ala-Gly-Gly-Gly has been studied in rings of everted rodent jejunum in vitro. When mediated uptake of free Leu was virtually saturated addition of Leu-Gly-Gly-Gly gave no significant increase in uptake of Leu. Uptake of Leu and of Ala from the tetrapeptides was strongly inhibited by Met, as was uptake of these amino acids from free solution. The results did not suggest that either tetrapeptide was taken up intact by the jejunum.     

Intestinal handling of two tetrapeptides by rodent small intestine in vitro

Uptake of free Leu and Ala and uptake of these amino acids from the tetrapeptides Leu-Gly-Gly-Gly and Ala-Gly-Gly-Gly has been studied in rings of everted rodent jejunum in vitro. When mediated uptake of free Leu was virtually saturated addition of Leu-Gly-Gly-Gly gave no significant increase in uptake of Leu. Uptake of Leu and of Ala from the tetrapeptides was strongly inhibited by Met, as was uptake of these amino acids from free solution. The results did not suggest that either tetrapeptide was taken up intact by the jejunum.     

Opioid receptor affinity and selectivity effects of second residue and carboxy terminal residue variation in a cyclic disulfide-containing opioid tetrapeptide.

The previously described cyclic, delta opioid receptor-selective tetrapeptide H-Tyr-D-Cys-Phe-D-Pen-OH, where Pen, penicillamine, is beta-beta-dimethylcysteine, was modified at residues 2 and 4 by varying combinations of D- and L-Cys and D- and L-Pen, and effects on mu and delta opioid receptor binding affinities and on potency in the mouse vas deferens (MVD) smooth muscle assay were evaluated. A comparison was drawn between consequences of alterations in this series of analogs and those of analogous modifications in the related cyclic pentapeptide series which includes the highly delta receptor-selective [D-Pen2,D-Pen5]enkephalin, DPDPE. Unlike effects observed in the cyclic pentapeptide series, the mu receptor binding affinities of the cyclic tetrapeptides are not dramatically influenced by substitution of Pen for Cys at residue 2. Conversely, while binding of the pentapeptides is only slightly affected by alteration of the chirality of the carboxy-terminal residue, modification of stereochemistry at the carboxy terminus in the tetrapeptides critically alters binding behavior at both mu and delta sites. In contrast with the pentapeptide series, the tetrapeptides appear to be highly dependent upon primary sequence for binding and activity, as only the lead compound binds with high affinity to the delta site. Results suggest that the less flexible cyclic tetrapeptides, lacking the Gly3 residue, display more stringent structural requirements for binding and activity than do the corresponding cyclic pentapeptides.     

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.     

Prediction of β-Turns

Kohonen's self-organization model, a neural network model, is applied to predict the -turns in proteins. There are 455 -turn tetrapeptides and 3807 non--turn tetrapeptides in the training database. The rates of correct prediction for the 110 -turn tetrapeptides and 30,229 non--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 -turns, during the process of protein folding.     

Nonfarnesylated tetrapeptide inhibitors of protein farnesyltransferase

The protein farnesyltransferase from rat brain was previously shown to be inhibited competitively by tetrapeptides that conform to the consensus Cys-A1-A2-X, where A1 and A2 are aliphatic amino acids and X is methionine, serine, or phenylalanine. In the current studies we use a thin layer chromatography assay to show that most of these tetrapeptides are themselves farnesylated by the purified enzyme. Two classes of tetrapeptides are not farnesylated and therefore act as true inhibitors: 1) those that contain an aromatic residue at the A2 position and 2) those that contain penicillamine (beta,beta-dimethylcysteine) in place of cysteine. The most potent of these pure inhibitors was Cys-Val-Phe-Met, which inhibited farnesyltransferase activity by 50% at less than 0.1 microM. These data indicate that the inclusion of bulky aromatic or methyl residues in a tetrapeptide can abolish prenyl group transfer without blocking binding to the enzyme. This information should be useful in the design of peptides or peptidomimetics that inhibit farnesylation and thus block the action of p21ras proteins in animal cells.     

Preferred conformations of RGDX tetrapeptides to inhibit the binding of fibrinogen to platelets

The conformational study on Arg-Gly-Asp (RGD)-containing tetrapeptides in the unhydrated and hydrated states has been carried out using the force field ECEPP/3 and the hydration shell model. The tetrapeptides studied here are H-RGDX-OH (X = Trp, Tyr, Phe, Leu, Val, Cys, Gln, and Ser), which show the inhibitory activity for binding of fibrinogen to platelets in the order of RGDW approximately equal to RGDY approximately equal to RGDF approximately equal to RGDL > RGDV > or = RGDC > or = RGDQ > or = RGDS. The backbone conformations with two C(7) backbone-to-backbone hydrogen bonds between Asp and Arg residues and between Xaa and Gly residues are in common most probable for the RGD sequence of RGDX tetrapeptides in the hydrated state. The dominant beta-turns for RGDX are found to be the types V' and IV at Gly-Asp and Asp-Xaa sequences, respectively, which are quite similar to the types II' and I (or II), respectively. However, it cannot be ruled out that the extended conformations are also remarkably feasible for RGDX tetrapeptides in water by peering the distributions of backbone conformations. These calculated results are consistent with the experimental results on RGD-containing proteins and conformationally constrained RGD-containing peptides. The reason why the RGDX becomes more potent as the side chain of the X residue is more hydrophobic may be ascribed to that the more hydrophobic is the residue X, the more populated are beta-turn structures for the Gly-Asp sequence. The hydrophobic side chain of X residue exposed to water is likely to interact with the hydrophobic region of receptor easily.