Structural mechanism governing cis and trans isomeric states and an intramolecular switch for cis/trans isomerization of a non-proline peptide bond observed in crystal structures of scorpion toxins

Non-proline cis peptide bonds have been observed in numerous protein crystal structures even though the energetic barrier to this conformation is significant and no non-prolyl-cis/trans-isomerase has been identified to date. While some external factors, such as metal binding or co-factor interaction, have been identified that appear to induce cis/trans isomerization of non-proline peptide bonds, the intrinsic structural basis for their existence and the mechanism governing cis/trans isomerization in proteins remains poorly understood. Here, we report the crystal structure of a newly isolated neurotoxin, the scorpion alpha-like toxin Buthus martensii Karsch (BmK) M7, at 1.4A resolution. BmK M7 crystallizes as a dimer in which the identical non-proline peptide bond between residues 9 and 10 exists either in the cis conformation or as a mixture of cis and trans conformations in either monomer. We also determined the crystal structures of several mutants of BmK M1, a representative scorpion alpha-like toxin that contains an identical non-proline cis peptide bond as that observed in BmK M7, in which residues within or neighboring the cis peptide bond were altered. Substitution of an aspartic acid residue for lysine at residue 8 in the BmK M1 (K8D) mutant converted the cis form of the non-proline peptide bond 9-10 into the trans form, revealing an intramolecular switch for cis-to-trans isomerization. Cis/trans interconversion of the switch residue at position 8 appears to be sequence-dependent as the peptide bond between residues 9 and 10 retains its wild-type cis conformation in the BmK M1 (K8Q) mutant structure. The structural interconversion of the isomeric states of the BmK M1 non-proline cis peptide bond may relate to the conversion of the scorpion alpha-toxins subgroups.     

抗菌肽的结构特征、生物活性及应用

抗菌肽分子呈双亲性的仅一螺旋结构可使细菌、真菌、寄生虫的质膜形成离子通道,从而导致这些病原体死亡。抗菌肽分子也可通过影响它们的能量转运和代谢,损害它们的呼吸链的功能,抑制它们的蛋白质和DNA的合成,以及干扰病毒的侵染过程和抑制病毒的繁殖等机制,对病原体产生抑制或杀灭作用。此外,抗菌肽还可杀伤肿瘤细胞并提高机体的免疫功能。因此,抗菌肽有望开发为防治人和动物疾病的药物,应用前景广阔。     

Novel peptide surface for reversible immobilization of concanavalin A

Concanavalin A (Con A) was spontaneously adsorbed on polymyxin B surface. This peptide-lectin interaction was strong, K(D)=1.9 x 10(-10), based predominantly on creation of hydrophobic bonds, and was completely reversible. Concanavalin A on polymyxin B (PmB) retained higher binding capacity for yeast mannan, compared with covalently immobilized lectin. Kinetics of mannan-concanavalin A interaction were significantly different in dependence on type of concanavalin A immobilization.     

The minimal structural requirement of concanavalin A that retains its functional aspects

A systematic investigation of the effects of several commonly used detergents on the conformation and function of concanavalin A at pH 7 in solution form was made by using circular dichroism (CD), intrinsic fluorescence, 1-anilino 8-sulphonic acid (ANS) binding, dynamic light scattering (DLS) and sugar inhibition assay. In the presence of 6.0 mM sodium dodecyl sulphate (SDS), an anionic detergent, and 0.8 mM cetyl tri methyl ammonium bromide (CTAB), a cationic detergent, intermediate states of concanavalin A were obtained having a negative CD peaks at 222 and 208 nm respectively, a characteristic of alpha-helix. These states also retained tertiary contacts with altered tryptophan environment and high ANS binding (exposed hydrophobic area) which can be characterized as molten globule states. Concanavalin A in the presence of 5.0 mM 3-[(3-cholamidopropyl) dimethyl-ammonio]-1-propanesulphonate (CHAPS), a zwitterionic detergent, and 0.07 mM brij-35, a non-ionic detergent, also exists in intermediate states. These intermediates (molten globules) had high ANS binding with native-like secondary (inherent beta-sheet) and tertiary structure. The intermediate states were characterized further by means of dynamic light-scattering measurements and kinetic data. To study the possible functional requirement of the minimum structure, the intermediate states characterized in the presence of detergents were shown to retain the activity with polysaccharide (dextran). The pattern of activity observed was brij-35 > CHAPS > CTAB > SDS. The specific binding and activity of concanavalin A with ovalbumin was investigated as a function of time by turbidity measurements. Cationic and anionic detergents showed significant effects on the structure of concanavalin A as compared with zwitterionic and non-ionic detergents.     

The rate-limiting step in the folding of the cis-Pro167Thr mutant of TEM-1 β-lactamase is the trans to cis isomerization of a non-proline peptide bond

The stability and kinetics of unfolding and refolding of the P167T mutant of the TEM-1 β-lactamase have been investigated as a function of guanidine hydrochloride concentration. The activity of the mutant enzyme was not significantly modified, which strongly suggests that the Glu166–Thr167 peptide bond, like the Glu166–Pro167, is cis. The mutation, however, led to a significant decrease in the stability of the native state relative to both the thermodynamically stable intermediate and the fully unfolded state of the protein. In contrast to the two slower phases seen in the refolding of the wild-type enzyme, only one phase was detected in the refolding of the mutant, indicating a determining role of proline 167 in the kinetics of folding of the wild-type enzyme. The former phases are replaced by rapid refolding when the enzyme is unfolded for short periods of time, but the latter is independent of the time of unfolding. The monophasic refolding reaction of the mutant is proposed to reflect mainly the trans→cis isomerization of the Glu166–Thr167 peptide bond. © 1996 John Wiley & Sons, Inc.     

A structural comparison of concanavalin a and tomato bushy stunt virus protein

Summary Significant structural equivalence has been found among the polypeptide folds of the two tomato bushy stunt virus (TBSV) subunit domains and concanavalin A. This suggests gene duplication in the TBSV coat protein and leads to speculation on common functional properties of concanavalin A and viral coat proteins.Non-standard abbreviations TBSV tomato bushy stunt virus - SBMV southern bean mosaic virus     

Antigelling and antisickling bisphenyl oligopeptides and peptide analogues have similar structural features

Single-crystal X-ray diffraction was used to determine the three-dimensional structures of two antigelling oligopeptides, L-lysyl-L-phenylalanyl-L-phenylalanine and L-phenylalanylglycylglycyl-D-phenylalanine, and two antisickling peptide analogues, L-phenylalanine benzyl ester and N-phenylacetyl-L-phenylalanine. Although these bisphenyl compounds are chemically quite different from one another, they demonstrate unusual structural similarities: The molecules have compact conformations in which the two phenyl rings are positioned approximately 5 A apart with interplanar angles approaching 90 degrees, thereby making intramolecular edge-to-face interactions. In addition, the polar atoms, nitrogen and oxygen, are in close proximity without forming intramolecular hydrogen bonds. The relative spatial distribution of polar and nonpolar atoms renders the structures compact and amphipathic. The intramolecular edge-to-face interaction between two aromatic rings, which brings a hydrogen atom with relative positive charge near the pi-electron cloud with relative negative charge, is enthalpically favorable and maintains the molecules in a compact and amphipathic conformation. Nonbonded potential energy calculations were used to characterize the energetics of the aromatic-aromatic interaction, and they showed that the observed geometry is stabilized enthalpically by a favorable interaction on the order of -1 to -2 kcal/mol. Structural differences between the two antisickling and the two antigelling agents suggest that molecular volume limits red cell membrane passage. These data provide a molecular structural framework from which to design and synthesize amphipathic bisphenyl compounds that both bind to deoxy sickle cell hemoglobin and cross the erythrocyte membrane.     

Actin polymerization induced by chemotactic peptide and concanavalin A in rat neutrophils

Changes in the state of actin in rat neutrophils were studied after chemotactic peptide and concanavalin A stimulation by using the DNase I inhibition assay. Actin polymerization occurred within seconds after stimulation with F-Met-Leu-Phe and concanavalin A. Pretreatment of cells with cytochalasin D prevented chemotactic peptide-induced actin polymerization. The addition of F-Met-Leu-Phe to lysed cells did not produce any change in actin state. These data offer strong evidence for receptor-induced actin polymerization and support the models implicating actin microfilament formation as a crucial event in cell activation. The observations on platelets, lymphocytes, neutrophils, and islets of Langerhans from different species suggest that actin polymerization might be a universal intracellular event accompanying cell surface receptor perturbation in eukaryotic cells.     

Solvent-dependent structural features of the membrane active peptide trichotoxin A40 as reflected in its dielectric dispersion

The dielectric dispersion of trichotoxin A40 in solvents of diverse lipophilicity (i.e. n-octanol, dioxane and mixtures of these) has been measured between 100 kHz and 50 MHz. In pure octanol also the weight average molecular weight and the concentration dependence of the circular dichroism spectrum were determined. An analysis of the data leads to the conclusion that in octanol an appreciable amount of the solute exists as single monomeric particles which are about 30 A long and 12.5 A in diameter. There is a dipole moment parallel to the long axis. In addition the evidence points at the presence of small aggregates (mainly dimers and trimers) formed by some kind of head-to-tail association. Evidently dioxane added to octanol favors a different structure of the trichotoxin monomer. It is apparently involved in another aggregation process resulting in aggregates of large size but comparatively low dipole moments.     

The slow step of folding of Staphylococcus aureus PC1 β-lactamase involves the collapse of a surface loop rate limited by the Trans to Cis isomerization of a non-proline peptide bond

We wished to test the hypothesis that the non proline cis to trans isomerization of the peptide bond at position 167 in the S. aureus β-lactamase PC1 exerts a significant controlling effect on the folding pathway of this enzyme. The previous data presented in support of this hypothesis could not rule out the effect of factors unrelated to non-proline cis/trans isomerization. We have used the plasmid pET9d to direct soluble overproduction of the S. aureus β-lactamase PC1 and a site-directed mutant (Ile 167 to Pro) in Escherichia coli. Following purification the proteins were subjected to a comparative analysis of the kinetics of unfolding and refolding using the techniques of near- and far-UV circular dichroism spectroscopy and fluorescence spectroscopy in conjunction with “double-jump” experiments. Results show that the fully-unfolded I167P mutant enzyme retains 20% of molecules in a fast-refolding form and that slower-refolding molecules fold faster than the recombinant wild-type enzyme. The final stage of folding involves folding of the Ω-loop into a conformation essential for enzymatic activity. In support of the original hypothesis, the folding of this Ω-loop is rate limited by the isomerization of the Glu 166-Ile 167 peptide bond. Proteins 33:550–557, 1998. © 1998 Wiley-Liss, Inc.     

Orexin/hypocretin receptor chimaeras reveal structural features important for orexin peptide distinction

We wanted to analyze the basis for the distinction between OX(1) and OX(2) orexin receptors by the known agonists, orexin-A, orexin-B and Ala(11), D-Leu(15)-orexin-B, of which the latter two show some selectivity for OX(2). For this, chimaeric OX(1)/OX(2) and OX(2)/OX(1) orexin receptors were generated. The receptors were transiently expressed in HEK-293 cells, and potencies of the agonists to elicit cytosolic Ca(2+) elevation were measured. The results show that the N-terminal regions of the receptor are most important, and the exchange of the area from the C-terminal part of the transmembrane helix 2 to the transmembrane helix 4 is enough to lead to an almost total change of the receptor's ligand profile.     

The luminescence properties of concanavalin A.

1. The luminescence properties of native concanavalin A, both at room temperature and at 77 degrees K, are similar to those of other proteins containing tyrosine and tryptophan. 2. Binding of methyl alpha-D-glucopyranoside to concanavalin A causes a slight reduction of its fluorescence at room temperature. 3. Removal of Mn2+ and Ca2+ ions from concanavalin A causes a small increase in its fluoresence. The fluorescence: phosphorescence ratio and phosphorescence lifetime of apo-concanavalin A are similar to those of tryptophan. 4. Denaturation of concanavalin A by urea and by guanidine hydrochloride apparently takes place in two stages. Apo-concanavalin A is more easily denatured than the native molecule, but concavalin A combined with methyl alpha-D-glucopyranoside is more resistant to denaturation. 5. The luminescence properties of concanavalin A are pH-dependent. 6. The results have been interpreted in terms of the known structure and properties of concanavalin A.     

Proline peptide isomerization and the reactivation of denatured enzymes

The kinetics of slow phase reactivation of 11 single chain denatured enzymes containing between 6 and 28 proline residues were each found to be first-order having half-times ranging from 0.15 to 12.1 minutes, respectively, at 25 °C. The reactivation kinetics of selected enzymes are independent of solvent viscosity and give an activation energy of 19 kcal/mol. These results are consistent with the proposal that cis/trans proline isomerization in the denatured state is responsible for the slow phase of enzyme refolding/reactivation and with biosynthetic rates for enzyme production.     

Conformational features of bradykinin. A circular dichroism study of some peptide fragments and structural analogues of bradykinin.

The vasoactive hormone bradykinin, its N-and C-terminal fragments and some structural analogues were studied by Circular Dichroism. Conformational features of the peptide can be detected by comparative analysis of the various CD spectra recorded as a function of aqueous pH, solvent and temperature. It is shown that the two biologically essential arginine residues (Arg1 and Arg9) are important for the specific folded bradykinin conformation. Differences between bradykinin, its fragments and analogues become clearly established in conformational terms, and are discussed in relation to the biological activity of these peptides.     

The carbohydrate units of asialo-ovomucoid: structural features

The structural features of a heterogeneous glycopeptide fraction from asialo-ovomucoid have been investigated by methylation analysis of the fraction and of products obtained at each stage of its sequential degradation with exo-glycosidases. All glycopeptides in the fraction had a common core-structure beta-D-GlcpNAc-(1 leads to 4)-[beta-D-GlcpNAc-(1 leads to 2)]-alpha-D-Manp-(1 leads to 3)-[beta-D-GlcpNAc-(1 leads to 4)]-[beta-D-GlcpNAc-(1 leads to 2)-alpha-D-Manp-(1 leads to 6)]-beta-D-Manp-(1 leads to 4)-beta-D-GlcpNAc-(1 leads to 4)-beta-D-GlcpNAc leads to Asn. Heterogeneity in the fraction arose from variation in the amount of terminal galactose attached via a hexosaminyl residue to the alpha-D-Manp-(1 leads to 3) residue, and from limited variation in the number of terminal hexosaminyl groups attached to the alpha-D-Manp-(1 leads to 6) residue. One glycopeptide in the fraction contained the unusual feature of two different, triply-substituted mannosyl residues. Other structural features of the glycopeptide are discussed.