Temperature dependence of looping rates in a short peptide

Knowledge of the influence of chain length and amino acid sequence on the structural and dynamic properties of small peptides in solution provides essential information on protein folding pathways. The combination of time-resolved optical spectroscopy and molecular dynamics (MD) simulation methods has become a powerful tool to investigate the kinetics of end-to-end collisions (looping rates) in short peptides, which are relevant in early protein folding events. We applied the combination of both techniques to study temperature-dependent (280-340 K) looping rates of the Dbo-AlaGlyGln-Trp-NH2 peptide, where Dbo represents a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine, which served as a fluorescent probe in the time-resolved spectroscopic experiments. The experimental looping rates increased from 4.8 x 10(7) s(-1) at 283 K to 2.0 x 10(8) s(-1) at 338 K in H2O. The corresponding Arrhenius plot provided as activation parameters Ea = 21.5 +/- 1.0 kJ mol(-1) and ln(A/s-1) = 26.8 +/- 0.2 in H2O. The results in D2O were consistent with a slight solvent viscosity effect, i.e., the looping rates were 10-20% slower. MD simulations were performed with the GROMOS96 force field in a water solvent model, which required first a parametrization of the synthetic amino acid Dbo. After corrections for solvent viscosity effects, the calculated looping rates varied from 1.5 x 10(8) s(-1) at 280 K to 8.2 x 10(8) s(-1) at 340 K in H2O, which was about four times larger than the experimental data. The calculated activation parameters were Ea = 24.7 +/- 1.5 kJ mol(-1) and ln(A/s(-1)) = 29.4 +/- 0.1 in H2O.     

Effect of the peptide secondary structure on the peptide amphiphile supramolecular structure and interactions

Bottom-up fabrication of self-assembled nanomaterials requires control over forces and interactions between building blocks. We report here on the formation and architecture of supramolecular structures constructed from two different peptide amphiphiles. Inclusion of four alanines between a 16-mer peptide and a 16 carbon long aliphatic tail resulted in a secondary structure shift of the peptide headgroups from α helices to β sheets. A concomitant shift in self-assembled morphology from nanoribbons to core-shell worm-like micelles was observed by cryogenic transmission electron microscopy (cryo-TEM) and atomic force microscopy (AFM). In the presence of divalent magnesium ions, these a priori formed supramolecular structures interacted in distinct manners, highlighting the importance of peptide amphiphile design in self-assembly.     

Effect of backbone flexibility on charge transfer rates in peptide nucleic acid duplexes

Charge transfer (CT) properties are compared between peptide nucleic acid structures with an aminoethylglycine backbone (aeg-PNA) and those with a γ-methylated backbone (γ-PNA). The common aeg-PNA is an achiral molecule with a flexible structure, whereas γ-PNA is a chiral molecule with a significantly more rigid structure than aeg-PNA. Electrochemical measurements show that the CT rate constant through an aeg-PNA bridging unit is twice the CT rate constant through a γ-PNA bridging unit. Theoretical calculations of PNA electronic properties, which are based on a molecular dynamics structural ensemble, reveal that the difference in the CT rate constant results from the difference in the extent of backbone fluctuations of aeg- and γ-PNA. In particular, fluctuations of the backbone affect the local electric field that broadens the energy levels of the PNA nucleobases. The greater flexibility of the aeg-PNA gives rise to more broadening, and a more frequent appearance of high-CT rate conformations than in γ-PNA.     

Photocontrol of peptide secondary structure through non-azobenzene photoswitches

The rapidly expanding field of photoswitchable biomolecules is a major frontier in scientific research and provides unparalleled opportunities for studying biological pathways and disease progression. In particular, the development of photochromic peptides has delivered both scientific tools and candidates for photopharmaceuticals. The action and function of the peptide can be remotely altered using light, allowing detection of its biological role in complex biological settings, while also enabling folding studies that provide greater understanding of protein structure dynamics. In this review we provide a key, comprehensive overview of the different types of photoswitches that have been used to control peptide structure, excluding the already extensively reviewed azobenzene. This will help address the question as to which synthetic photoswitch to use in a given study.     

Design and synthesis of novel conformationally restricted peptide secondary structure mimetics

[structure: see text] A facile synthesis of the novel conformationally restricted reverse turn mimetic is described. The key features are the preparation of the alpha-keto amide and tandem bicyclic ring formation.     

Differential flexibility of the secondary structures of lysozyme and the structure and ordering of surrounding water molecules

We have performed an atomistic molecular dynamics simulation of an aqueous solution of hen egg-white lysozyme at room temperature with explicit water molecules. Several analyses have been carried out to explore the differential flexibility of the secondary structural segments of the protein and the structure and ordering of water around them. It is found that the overall flexibility of the protein molecule is primarily controlled by few large-amplitude bistable motions exhibited by two coils; one connecting two α-helical segments in domain-1 and the other connecting a 3(10) helix and a β-sheet in domain-2 of the protein. The heterogeneous structuring of water around the segments of the protein has been found to depend on the degree of exposure of the segments to water. The ordering of water molecules around the protein segments and their tagged potential energies have been found to be anticorrelated with each other. Some of these findings can be verified by suitable experimental studies.     

The alpha-helical peptide nucleic acid concept: merger of peptide secondary structure and codified nucleic acid recognition

A novel platform for nucleic acid recognition that integrates the alpha-helix secondary structure of peptides with the codified base-pairing capability of nucleic acids is reported. The resulting alpha-helical peptide nucleic acids (alpha PNAs) are composed of a repeating tetrapeptidyl unit, aa(1)-aa(2)-aa(3)-Ser(B), where aa(1) through aa(3) represent generic ancillary amino acids and B = nucleobases linked to Ser via a methylene bridge. Effective syntheses of constituent Fmoc-protected nucleoamino acids (Fmoc-Ser(B)-OH, where B = thymine, cytosine, and uracil) are described along with a protocol for the solid-phase synthesis of 21mer alpha PNAs containing five such nucleobases. By varying the ancillary amino acids, two distinct classes of alpha PNAs were constructed, having a net charge of -1 or +6, respectively, at physiological pH. The modular nature of the alpha PNA platform was illustrated by the synthesis of symmetrical disulfide-bridged alpha PNA dimers containing 10 nucleobases. Hybridization of these alpha PNAs with ssDNA has been examined by thermal denaturation, gel electrophoresis, and circular dichroism (CD) and the data indicated that alpha PNA binds to ssDNA in a cooperative manner with high affinity and sequence specificity. In general, b2 alpha PNAs bind faster and more strongly with ssDNA than do the corresponding b1 alpha PNAs. Parallel alpha PNA-DNA complexes are more stable than their antiparallel counterparts. CD studies also revealed that the hybridization event involves the folding of both species into their helical conformations. Finally, NMR experiments provided conclusive evidence of Watson-Crick base pairing in alpha PNA-ssDNA hybrids.     

Investigation of the association and flexibility of cationic lipidic peptide dendrons by NMR spectroscopy

The cationic peptide dendrons synthesized and studied are lower generation polylysine-based partial dendrimers with or without lipid chains in the core. The dendrons with lipidic chains can be utilized as protein and liposomal mimics because of their unique structural properties. The full assignments of three different dendrons (L)7(NH2)8, (C14)1(L)7(NH2)8 and (C14)3(L)7(NH2)8 were obtained in D2O and H2O/D2O using a 500 MHz NMR spectrometer. The hydrophobic lipidic core of branched polylysine dendrons was found to induce aggregation upon increasing concentration. Because non-lipidic dendrons do not self-assemble, the behaviour and internal structural features of two different dendrons with one and three C14 hydrocarbon chains were explored. The critical association concentration clearly depends on the number of core hydrophobic residues and the association starts at 0.025 mM for (C14)1(L)7(NH2)8 and 0.05 mM for (C14)3(L(7(NH2)8. Chemical shift analysis also revealed that the hydrophobic chains of the dendrons associate in the core, whereas the polar head groups (NH2) are mainly located at the surfaces of the aggregates. The T1 relaxation time measurements showed that the mobility of the hydrocarbon chain is greater with the monomeric form of dendron (C14)1(L)7(NH2)8) than that of monomer (C14)3(L)7(NH2)8. The inter-chain hydrophobic interactions restrict the flexibility of the dendron with three hydrocarbon chains. As expected, the flexibility of the monomeric form is higher than that of the aggregated state for both of the dendrons.     

The secondary structure of a membrane-modifying peptide in a supramolecular assembly studied by PELDOR and CW-ESR spectroscopies.

The new technique of pulsed electron-electron double resonance in electron spin-echo (PELDOR) in combination with the CW-ESR method has been used to investigate the secondary structure of a double spin-labeled peptide (the [TOAC-1,8]-analogue of the peptaibol antibiotic trichogin GA IV) that is hidden into a tetrameric supramolecular assembly of unlabeled peptide molecules. The magnetic dipole-dipole relaxation of spin labels has been experimentally studied in glassy solutions of the double-labeled peptide frozen to 77 K in a mixture of chloroform-toluene with an excess of unlabeled peptide. The PELDOR signal oscillations have been observed at high degrees of dilution with unlabeled peptide. The intramolecular distance between the spin labels of the peptide molecule in the aggregate has been determined from the oscillation frequency to be 15.7 A which is close to the value of (approximately equal to) 14 A calculated for a 3(10)-helical structure. Estimation of the fraction of this ordered secondary structure shows that about 19% of the peptide molecules in aggregates are folded in the 3(10)-helical conformation. The present experimental results are consistent with our molecular model presented in J. Am. Chem. Soc. 2000, 122, 3843-3848, wherein four amphiphilic 3(10)-helical peptide molecules form a vesicular system with the polar amino acid side chains pointing to the interior, and the apolar side chains, to the exterior of the cluster. The experimental data were compared with the results obtained with other techniques.     

Membrane localization and flexibility of a lipidated ras peptide studied by molecular dynamics simulations

Lipid-modified membrane-binding proteins are essential in signal transduction events of the cell, a typical example being the GTPase ras. Recently, membrane binding of a doubly lipid-modified heptapeptide from the C-terminus of the human N-ras protein was studied by spectroscopic techniques. It was found that membrane binding is mainly due to lipid chain insertion, but it is also favored by interactions between apolar side chains and the hydrophobic region of the membrane. Here, 10 explicit solvent molecular dynamics simulations for a total time of about 150 ns are used to investigate the atomic details of the peptide-membrane association. The 16:0 peptide lipid chains are more mobile than the 14:0 phospholipid chains, which is in agreement with (2)H NMR experiments. Peptide-lipid and peptide-solvent interactions, backbone and side-chain distributions, as well as the effects of lipidated peptide insertion onto the structure, and dynamics of a 1,2-dimyristoylglycero-3-phosphocholine bilayer are described. The simulation results validate the structural model proposed by the analysis of spectroscopic data and highlight the main aspects of the insertion mechanism. The peptide in the membrane is rather rigid over the simulation time scale of about 10 ns, but different partially extended conformations devoid of backbone hydrogen bonds are observed in different trajectories.     

Velocity dependence of friction and Kramers relaxation rates

We study the influence of the velocity dependence of friction on the escape rate of a Brownian particle from the deep potential well (Eb>kBT, Eb is the barrier height, kB is the Boltzmann constant, and T is the bath temperature). The bath-induced relaxation is treated within the Rayleigh model (a heavy particle of mass M in the bath of light particles of mass m相似文献   

Conformational flexibility and structure of creatine kinase.

The structural flexibility of creatine kinase has been investigated with the covalent hydrophobic probe 2-[4'-(2"-iodoacetamido) phenyl] aminonaphthalene-6-sulfonic acid (IAANS) which reacts at vastly different rates with the two subunits to give a protein conjugate with fluorescence characteristic of reaction with a site in a hydrophobic cleft. Binding of purine nucleotides greatly enhances the probe fluorescence while pyrimidine nucleotides quench the fluorescence. Small anions bind to nucleotide-free creatine kinase near the location of the transferable phosphoryl group and quench both the IAANS fluorescence of modified creatine kinase and the tryptophan fluorescence of native creatine kinase. Chloride and nitrate non-competitively inhibit MgADP binding both with and without creatine. Fluorescence energy transfer demonstrates that the active sites of creatine kinase are well separated and become further apart after the nucleotide-induced conformational change.     

Energy transfer in the collision induced decomposition of peptide ions formed by field desorption

In the collision induced decomposition of a number of peptide ions formed by field desorption, it has been found that at the optimum pressure of collision gas the translational energy lost by an incident peptide ion increases as peptide ions of increasing mass are considered. The internal energy taken up by any individual peptide ion appears to be directly proportional to its mass.     

Primary and secondary relaxations in supercooled eugenol and isoeugenol at ambient and elevated pressures: dependence on chemical microstructure

Dielectric loss spectra of two glass-forming isomers, eugenol and isoeugenol, measured at ambient and elevated pressures in the normal liquid, supercooled, and glassy states are presented. The isomeric chemical compounds studied differ only by the location of the double bond in the alkyl chain. Above the glass transition temperature T(g), the dielectric loss spectra of both isomers exhibit an excess wing on the high frequency flank of the loss peak of the alpha relaxation and an additional faster gamma process at the megahertz frequency range. By decreasing temperature below T(g) at ambient pressure or by elevating pressure above P(g), the glass transition pressure, at constant temperature, the excess wing of isoeugenol shifts to lower frequencies and is transformed into a secondary beta-loss peak, while in eugenol it becomes a shoulder. These spectral features enable the beta-relaxation time tau(beta) to be determined in the glassy state. These changes indicate that the excess wings in isoeugenol and eugenol are similar and both are secondary beta relaxations that are not resolved in the liquid state. While in both isoeugenol and eugenol the loss peak of the beta relaxation in the glassy state and the corresponding excess wing in the liquid state shifts to lower frequencies on elevating pressure, the locations of their gamma relaxation show little change with increasing pressure. The different pressure sensitivities of the excess wing and gamma relaxation are further demonstrated by the nearly perfect superposition of the alpha-loss peak together with excess wing from the data taken at ambient pressure and at elevated pressure (and higher temperature so as to have the same alpha-peak frequency), but not the gamma-loss peak in both isoeugenol and eugenol. On physical aging isoeugenol, the beta-loss peak shifts to lower frequencies, but not the gamma relaxation. Basing on these experimental facts, the faster gamma relaxation is a local intramolecular process involving a side group and the slower beta relaxation mimics the structural alpha relaxation in behavior, involves the entire molecule and satisfies the criteria for being the Johari-Goldstein beta relaxation. Analysis and interpretation of the spectra utilizing the coupling model further demonstrate that the excess wings seen in the equilibrium liquid states of these two isomers are their genuine Johari-Goldstein beta relaxation.     

The valence electronic structure and conformational flexibility of epichlorohydrin

The electronic structure of epichlorohydrin is investigated in the whole valence region by a combined experimental and theoretical study. The issue of controversial assignments of the molecular electronic structure is here addressed. Photoelectron spectra (PES) and Threshold Photoelectron spectra (TPES) of room temperature molecules in the gas phase are recorded. Geometries and energies of the stable conformers due to internal rotation of the C-C-C-Cl dihedral angle, gauche-II (g-II), gauche-I (g-I), and cis, are calculated, and the effect of the conformational flexibility on the photoionization energetics is studied by DFT and 2h-1p Configuration Interaction (CI) methods. Strong breakdown of the Koopmans Theorem (KT) is obtained for the four outermost ionizations, which are further investigated by higher level ab initio calculations. The full assignment of the spectrum is put on a firm basis by the combination of experimental and theoretical results. The orbital composition from correlated calculations is found closer to the DFT orbitals, which are then used to analyze the electronic structure of the molecule. The Highest Occupied Molecular Orbital (HOMO) and HOMO--2 are n(O)/n(Cl) mixed orbitals. The nature of each valence MO is generally preserved in all the conformers, although the magnitude of the n(O)/n(Cl) mixing in HOMO and HOMO--2 varies to some extent with the C-C-C-Cl dihedral angle. The low energy part of the HOMO PE band is predicted to be substantially affected by the conformational flexibility, as experimentally observed in the spectra. The rest of the spectrum is described in terms of the dominant conformer g-II, and a good agreement between experiment and theory is found. The inner-valence PE spectrum is characterized by satellite structures, due to electron correlation effects, which are interpreted by means of 2h-1p CI calculations.     

Metal compound-mediated hydrolytic cleavage of oxidized insulin B chain:Regioselectivity and influence of peptide secondary structure

The interaction of oxidized insulin B chain(B)with cis-[Pd-(en)Cl2](en=ethylenediamine),cis-[Pd-(dtco-3-OH)Cl2](dtco-3-OH=dithiacyclooctan-3-ol)and CuCl2 was studied by electrospray inass spectrometry.It is discovered that the binding of Pd(Ⅱ)complexes and the sites of cleavage are highly dependent on the secondary structure and local environment of B.The hydrolytic cleavage of denatured B by Pd(Ⅱ)complexes was monitored by HPLC.The reaction is regioselective and follows first order kinetics with half-life of 4.8 days at 40℃.Two amide bonds,i.e.at Leu6-Cys7 and at Gly8-Ser9,which are close to the two potential Pd(Ⅱ)binding sites His5 and His10,are selectively cleaved.In the case of Cu(Ⅱ)ion as promoter,only one cleavage site was observed which is located at Gly8-Ser9 bond.These results provide improved understanding on the design of artificial metallopeptidase.     

A merger of rational drug design and combinatorial chemistry: development and application of peptide secondary structure mimetics

Recent efforts toward the development of peptide secondary structure mimetics at Molecumetics Ltd. for the discoveries of new drug candidates utilizing combinatorial chemistry with solid phase synthesis are described.     

Evidence of secondary structure by high-resolution magic angle spinning NMR spectroscopy of a bioactive peptide bound to different solid supports.

The structure of the 19-amino acid peptide epitope, corresponding to the 141-159 sequence of capsid viral protein VP1 of foot-and-mouth disease virus (FMDV), bound to three different resins, namely, polystyrene-MBHA, PEGA, and POEPOP, has been determined by high-resolution magic angle spinning (HRMAS) NMR spectroscopy. A combination of homonuclear and heteronuclear bidimensional experiments was used for the complete peptide resonance assignment and the qualitative characterization of the peptide folding. The influence of the chemicophysical nature of the different polymers on the secondary structure of the covalently attached FMDV peptide was studied in detail. In the case of polystyrene-MBHA and polyacrylamide-PEGA resins, the analysis of the 2D spectra was hampered by missing signals and extensive overlaps, and only a propensity toward a peptide secondary structure could be derived from the assigned NOE correlations. When the FMDV peptide was linked to the polyoxyethylene-based POEPOP resin, it was found to adopt in dimethylformamide a helical conformation encompassing the C-terminal domain from residues 152 to 159. This conformation is very close to that of the free peptide previously analyzed in 2,2,2-trifluoroethanol. Our study clearly demonstrates that a regular helical structure can be adopted by a resin-bound bioactive peptide. Moreover, a change in the folding was observed when the same peptide-POEPOP conjugate was swollen in aqueous solution, displaying the same conformational features as the free peptide in water. The possibility of studying solid-supported ordered secondary structures by the HRMAS NMR technique in a wide range of solvents can be extended either to other biologically relevant peptides and proteins or to new synthetic oligomers.     

Mass spectrometry and structure of ions of heterocyclic compounds activated by collision: Naphthiridines and benzazines

The dissociation and the structure at the isomeric [M — HCN]⁺ and [M — 2HCN]⁺ ions, formed during the fragmentation of naphthiridines and benzazines, were investigated by the collisionally activated dissociation (CAD) method. It was established that the stable [M — HCN]⁺ ions of 1,5- and 1,8-naphthiridines, 1,6-naphthiridine, quinoxaline, and quinazoline have different structures. The [M — 2HCN]⁺ ions can exist in two isomeric forms, one of which is characteristic of naphthiridines and the other of benzazines.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vo. 25, No. 5, pp. 626–629, September–October, 1989.