Influence of amino acid and peptide counterions on the conformation of DNA

We describe fibre diffraction studies on the interaction of DNA with different amino acids and peptides. The B form of DNA, with ten base-pairs per turn, is always found at high levels of humidity. We suggest that this pitch is observed because the DNA molecules are maintained in a straight position. In solution, the DNA molecules are bent and may have a larger pitch. The A form of DNA is never found upon dehydration. Instead, the B form may be either stabilized by the counterions or altered so that the number of base-pairs per helical turn decreases upon dehydration. Alteration is favoured either by small counterions that have a single charge or by large basic polypeptides and proteins. Stabilization is favoured by small counterions that have several charged groups. A third type of behaviour is found with some amino acids that contain hydrophobic groups, which destabilize the secondary structure of DNA, probably due to a modification of its intramolecular interactions. We have not detected any specific effect of amino acid side-chains, although the amino acid sequence has a clear influence on the interaction. We think that these observations are of interest in the pursuit of more detailed crystallographic studies on protein-DNA interactions.     

Role of peptide backbone conformation on biological activity of chemotactic peptides

To investigate the role of peptide backbone conformation on the biological activity of chemotactic peptides, we synthesized a unique analog of N-formyl-Met-Leu-Phe-OH incorporating the C alpha,alpha disubstituted residue, dipropylglycine (Dpg) in place of Leu. The conformation of the stereochemically constrained Dpg analog was examined in the crystalline state by x-ray diffraction and in solution using NMR, IR, and CD methods. The secretagogue activity of the peptide on human neutrophils was determined and compared with that of a stereochemically constrained, folded type II beta-turn analog incorporating 1-aminocyclohexanecarboxylic acid (Ac6c) at position 2 (f-Met-Ac6c-Phe-OMe), the parent peptide (f-Met-Leu-Phe-OH) and its methyl ester derivative (f-Met-Leu-Phe-OMe). In the solid state, the Dpg analog adopts an extended beta-sheet-like structure with an intramolecular hydrogen bond between the NH and CO groups of the Dpg residue, thereby forming a fully extended (C5) conformation at position 2. The phi and psi values for Met and Phe residues are significantly lower than the values expected for an ideal antiparallel beta conformation causing a twist in the extended backbone both at the N and C termini. Nuclear magnetic resonance studies suggest the presence of a significant population of the peptide molecules in an extended antiparallel beta conformation and the involvement of Dpg NH in a C5 intramolecular hydrogen bond in solutions of deuterated chloroform and deuterated dimethyl sulfoxide. IR studies provide evidence for the presence of an intramolecular hydrogen bond in the molecule and the antiparallel extended conformation in chloroform solution. CD spectra in methanol, trifluoroethanol, and trimethyl phosphate indicate that the Dpg peptide shows slight conformational flexibility, whereas the folded Ac6c analog is quite rigid. The extended Dpg peptide consistently shows the highest activity in human peripheral blood neutrophils, being approximately 8 and 16 times more active than the parent peptide and the folded Ac6c analog, respectively. However, the finding that all four peptides have ED50 (the molar concentration of peptide to induce half-maximal enzyme release) values in the 10(-8)-10(-9) M range suggests that an induced fit mechanism may indeed be important in this ligand-receptor interaction. Moreover, it is also possible that alterations in the backbone conformation at the tripeptide level may not significantly alter the side chain topography and/or the accessibility of key functional groups important for interaction with the receptor.     

Exploring relationships between mimic configuration, peptide conformation and biological activity in indolizidin-2-one amino acid analogs of gramicidin S.

Indolizidin-2-one amino acids (I2aas, 6S- and 6R-1) possessing 6S- and 6R-ring-fusion stereochemistry were introduced into the antimicrobial peptide gramicidin S (GS) to explore the relationships between configuration, peptide conformation and biological activity. Solution-phase and solid-phase techniques were used to synthesize three analogs with I2aa residues in place of the d-Phe-Pro residues at the turn regions of GS: [(6S)-I2aa4-5,4'-5']GS (2), [Lys2,2',(6S)-I2aa4-5,4'-5']GS (3) and [(6R)-I2aa4-5,4'-5']GS (4). Although conformational analysis of [I2aa4-5,4'-5']GS analogs 2-4 indicated that both ring-fusion stereoisomers of I2aa gave peptides with CD and NMR spectral data characteristic of GS, the (6S)-I2aa analogs 2 and 3 exhibited more intense CD curve shapes, as well as greater numbers of nonsequential NOE between opposing Val and Leu residues, relative to the (6R)-I2aa analog 4, suggesting a greater propensity for the (6S)-diastereomer to adopt the beta-turn/antiparallel beta-pleated sheet conformation. In measurements of antibacterial and antifungal activity, the (6S)-I2aa analog 2 exhibited significantly better potency than the (6R)-I2aa diastereomer 4. Relative to GS, [(6S)-I2aa4-5,4'-5']GS (2) exhibited usually 1/2 to 1/4 antimicrobial activity as well as 1/4 hemolytic activity. In certain cases, antimicrobial and hemolytic activities of GS were shown to be dissociated through modification at the peptide turn regions with the (6S)-I2aa diastereomer. The synthesis and evaluation of GS analogs 2-4 has furnished new insight into the importance of ring-fusion stereochemistry for turn mimicry by indolizidin-2-one amino acids as well as novel antimicrobial peptides.     

Range of the influence of the carbohydrate moiety on the conformation of the poly(amino acid) backbone in glycosylated mucins

The influence of glycosylation on the conformational properties of porcine submaxillary gland mucin has been investigated using rotational isomeric state theory. The specific objective was to determine the conditions under which the polypeptide has the relatively large mean square unperturbed radius of gyration mean value of s2(0), demanded by the measurements of Shogren et al., while retaining the overall architecture of a random coil. The mean square dimensions were monitored as the dimensionless characteristic ratio defined as C = mean value of s2(0)/npl2p, and the overall architecture was monitored by another dimensionless ratio mean value of r2(0)/mean value of s2(0), where mean value of r2(0) denotes the mean square unperturbed end-to-end distance. The computed values of C cannot reproduce the measured values if the conformational influence of glycosylation is restricted to each Ser or Thr, or if this influence extends only as far as their nearest neighbors. Values of C compatible with experiment can be obtained if the influence extends to next nearest neighbors. The behavior of the computed values of mean value of r2(0)/mean value of s2(0) permits an assignment of 7 +/- 1 as the likely upper limit to the number of consecutive amino acid residues that experience alterations in phi and psi if the sequence contains a glycosylated Ser or Thr.     

Geometric diversity through permutation of backbone configuration in cyclic peptide libraries

Cyclic peptides offer the possibility of varying both scaffold geometry and R-group functionality. For example, parameters such as ring size and the placement of D-amino acid and proline residues can have a dramatic effect on the conformations of cyclic peptides, allowing access to structurally diverse species based on simple modifications in their linear sequences. We synthesized a cyclic peptide library in which ring size, alpha-carbon stereochemistry, and proline placement were varied. Analysis of the products showed that heptapeptides in general cyclized more readily than hexapeptides, and within these groups the scaffolds with a greater number of pralines cyclized with markedly lower yields than scaffolds with fewer pralines. Split-pool libraries based on a sample set of these scaffolds showed that, in general, scaffold geometry outweighed side chains variation in determining cyclization efficiency. These concepts were applied to the synthesis of cyclodimeric variants of an inhibitor of actin assembly in Xenopus egg extracts, yielding side chain variants with improved potency over the original scaffold.     

Statistically significant dependence of the Xaa-Pro peptide bond conformation on secondary structure and amino acid sequence

Background  

A reliable prediction of the Xaa-Pro peptide bond conformation would be a useful tool for many protein structure calculation methods. We have analyzed the Protein Data Bank and show that the combined use of sequential and structural information has a predictive value for the assessment of the cis versus trans peptide bond conformation of Xaa-Pro within proteins. For the analysis of the data sets different statistical methods such as the calculation of the Chou-Fasman parameters and occurrence matrices were used. Furthermore we analyzed the relationship between the relative solvent accessibility and the relative occurrence of prolines in the cis and in the trans conformation.     

Solid-state vibrational circular dichroism studies on the conformation of an amino acid molecule in crystalline state

The present article reviews the results of solid-state vibrational circular dichroism (SD-VCD) measurements on the crystals of amino acids. The investigated series were Ala, Ile, Leu, Phe, Ser, Val, and Thr. Spectra were recorded for the samples containing both D- and L-enantiomers. The molecular conformation in a crystalline state was compared among the series. Molecule optimization of their conformation under intermolecular interactions in crystalline states was revealed. One noteworthy aspect was that some VCD peaks were remarkably enhanced in comparison with the solution states. This fact was rationalized in terms of vibrationally coupled delocalization in a closely stacked pair. In addition, for a molecule with two asymmetric carbons, the signs of the VCD peaks were determined by the interplay between the two chiral centers. Lastly, the roles of the theoretical approach based on density functional theory calculations were described.     

The effect of electrostatic interactions on the conformation of the sugar-phosphate backbone in DNA]

The influence of sugar ring flexibility in DNA on the mechanism of the B<-->A conformational transition is studied. The dipole moment of the deoxyribose as a function of its puckered states is calculated by the quantum-mechanical method using the MINDO/3 approximation. The interaction of the sugar dipole with the neighbour molecular groups in polynucleotide chain is estimated. The sugar dipole interaction witch phosphate groups and counterions is shown to be strong and capable to deform the pseudorotation potential of deoxyribose. The effective pseudorotation potential of sugar ring in the B- and A-helices is obtained. The results are used to explain the behaviour of Raman bands in the region of sugar-phosphate vibrations. The mechanism of the effect of electrostatic forces on the sugar-phosphate backbone conformation which is essential for the B<-->A and other structure transitions is offered.     

Influence of electrostatic interactions on the sugar–phosphate backbone conformation in DNA

The influence of sugar ring flexibility in DNA on the mechanism of the B ? A conformational transition is studied. The dipole moment of the deoxyribose as a function of its puckered states is calculated by the quantum-mechanical method using the MINDO/3 approximation. The interaction of the sugar dipole with the neighbor molecular groups in polynucleotide chains is estimated. The sugar dipole interaction with phosphate groups and counterions is shown to be strong and capable to deform the pseudorotation potential of deoxyribose. The effective pseudorotation potential of sugar ring in the B and A helices is obtained. The results are used to explain the behavior of Raman bands in the region of sugar–phosphate vibrations. The mechanism of the effect of electrostatic forces on the sugar–phosphate backbone conformation, which is essential for the B ? A and other structure transitions, is offered. © 1993 John Wiley & Sons, Inc.     

NMR studies of the antibody-bound conformation of a carbohydrate-mimetic peptide

Transferred nuclear Overhauser enhancement (TRNOE) experiments have been performed at 800 MHz to investigate the bound conformation of the hexapeptide DRPVPY, a functional molecular mimic of the group A Streptococcus cell-wall polysaccharide. The hexapeptide binds to the monoclonal antibody SA-3, mimicking the branched trisaccharide repeating unit, L-Rha-alpha-(1 --> 2)-(D-GlcNAc-beta-(1 --> 3))-alpha-L-Rha (Rha, rhamnose; GlcNAc, N-acetylglucosamine). The peptide adopts a tight turn conformation with close contacts between the side chains of valine and tyrosine. Relaxation network editing experiments (QUIET-NOESY) were used to confirm the validity of the observed contacts and to evaluate the presence of spin diffusion pathways. Saturation transfer difference (STD-NMR) experiments with selective saturation of protein resonances revealed enhancements of many of the peptide resonances due to close contacts between the peptide and the protein within the antibody combining site.     

NMR and CD studies on the conformation of a synthetic peptide containing epitopes of the human immunodeficiency virus 1 transmembrane protein gp41

CD and nmr characterizations are reported for the 23-mer peptide CMC3, corresponding to residues 577–599 of gp41, the transmembrane glycoprotein of the human immunodeficiency virus 1. Concentration, temperature, and pH dependencies of CD and nmr spectra are indicative of self-association with a consequent stabilization of secondary structural elements in water. The addition to the water solution of small amounts of trifluoroethanol induces a secondary structure, mostly due to the presence of helical elements. The amphipathic character of the helix and the presence of three hydrophobic 4/3 heptad repeats suggest that the peptide could be structured in a symmetric association of helices, such as in a coiled-coil structure. This behavior is discussed in terms of a possible role of this segment in the gp41 envelope oligomerization. © 1996 John Wiley & Sons, Inc.     

NMR and circular dichroic studies on the solution conformation of a synthetic peptide derived from the calmodulin-binding domain of Bordetella pertussis adenylate cyclase

The solution conformation of a synthetic peptide of 20 amino acids (P235-254) derived from the calmodulin-binding domain of Bordetella pertussis adenylate cyclase was studied by proton two-dimensional NMR spectroscopy and circular dichroism. Based on the standard techniques we have assigned all the resonances in the NMR spectrum to the corresponding protons of the peptide. Analysis of the secondary chemical shift distribution and of the nuclear Overhauser effect connectivities showed no evidence for a highly populated regular conformation but suggested the tendency to form an alpha-helix around the unique Trp residue. The propensity for a helical structure is in agreement with the results of circular dichroic spectroscopy showing a slight negative band at 222 nm which was cancelled by 6 M guanidine hydrochloride. Increasing amounts of 2,2,2-trifluoroethanol (up to 40%) increase considerably the helical population of the peptide as reflected in the circular dichroic spectra. Analysis of the present results shows that the free peptide P235-254 has the tendency to form a basic amphiphilic helix. The presence of two acid residues, Glu236 and Asp239, on the hydrophilic side of the alpha-helix, which is mainly composed by basic residues, may explain the lower affinity of this peptide for calmodulin as compared with other peptides derived from calmodulin-activated enzymes.     

Relation between the spectral NMR parameters and conformation characteristics of the amino acid residue backbone. Analysis of elements of the secondary structure of proteins

Based on the analysis of the proton-proton distance dependences from the conformational characteristics of the L-amino acid residues, the correlation diagram of the NOE cross peak intensity waited values with the regions of the sterically allowed space (phi, psi) was proposed. The method for determining the dihedral angles phi, psi values using the information about NOE cross peak intensities was elaborated. By the model spectral NMR parameters of the bovine pancreatic trypsin inhibitor, it is shown that the accuracy of the angles phi, psi determination exceed the corresponding accuracy provided by other methods of the structural interpretation of the two-dimensional NMR spectroscopy data. The analysis of the waited spectral NMR parameters for the different types of protein regular secondary structures and beta-turns was performed.     

Stress-protective effect of the synthetic ACTH-like peptide leucocorticotropin

We found that the tritium-labeled synthetic ACTH-like octapeptide leucocorticotropin corresponding to the 81–88 sequence of the precursor of human interleukin-1α ([³H]GK VLKKRR) is bound by the ACTH receptor of rat adrenal cortex with a high affinity and specificity (K _d 2.2 ± 0.1 nM). This peptide was shown to exert no effect on the adenylate cyclase activity of the membranes of rat adrenal cortex in the concentration range from 1 to 1000 nM. Leucocorticotropin administration three times at doses of 10–20 μg/animal did not change the level of hydroxycorticosteroids (11-HOCS) in the rat adrenal glands in the absence of temperature action. At the same time, the peptide abolishes (at a dose of 20 μg/animal, three times) or significantly decreases (at a dose of 10 μg/animal, three times) the dramatic increase in the 11-HOCS content in the adrenal glands occurring in the case of cold or heat shock. Thus, leucocorticotropin normalizes the 11-HOCS level in the rat adrenal cortex during stress. The stress-protective effect of the peptide is mediated through the ACTH receptor.     

Properties of synthetic ferrihydrite as an amino acid adsorbent and a promoter of peptide bond formation

Summary. Ferrihydrite, an iron oxide hydroxide, is found in all kinds of environments, from hydrothermal hot springs to extraterrestrial materials. It has been shown that this material is nanoporous, and because of its high surface area, it has outstanding adsorption properties and in some cases catalysis properties. In this work we studied the adsorption properties of ferrihydrite with respect to amino acids. Samples of pure ferrihydrite were synthesised and exposed to solutions of amino acids including both proteinaceous and non-proteinaceous species. These experiments revealed important characteristics of this mineral as both an adsorbent of amino acids and a promoter of peptide bond formation.     

Stress-protective effect of the synthetic ACTH-like peptide leucocorticotropin

We found that the tritium-labeled synthetic ACTH-like octapeptide leucocorticotropin corresponding to the 81-88 sequence of the precursor of human interleukin-1alpha ([3H]GKVLKKRR) is bound by the ACTH receptor of rat adrenal cortex with a high affinity and specificity (Kd 2.2 +/- 0.1 nM). This peptide was shown to exert no effect on the adenylate cyclase activity of the membranes of rat adrenal cortex in the concentration range from 1 to 1000 nM. Leucocorticotropin administration three times at doses of 10-20 microg/animal did not change the level of hydroxycorticosteroids (11-HOCS) in the rat adrenal glands in the absence of temperature action. At the same time, the peptide abolishes (at a dose of 20 microg/animal, three times) or significantly decreases (at a dose of 10 microg/animal, three times) the dramatic increase in the 11-HOCS content in the adrenal glands occurring in the case of cold or heat shock. Thus, leucocorticotropin normalizes the 11-HOCS level in the rat adrenal cortex during stress. The stress-protective effect of the peptide is mediated through the ACTH receptor.     

Investigation of the impact of PTMs on the protein backbone conformation

Amino Acids - Post-translational modifications (PTMs) are known to play a critical role in the regulation of protein functions. Their impact on protein structures and their link to disorder regions...