Structural Analysis of a Helical Peptide Unfolding Pathway

The analysis of the folding mechanism in peptides adopting well‐defined secondary structure is fundamental to understand protein folding. Herein, we describe the thermal unfolding of a 15‐mer vascular endothelial growth factor mimicking α‐helical peptide (QK_L10A) through the combination of spectroscopic and computational analyses. In particular, on the basis of the temperature dependencies of QK_L10A H_α chemical shifts we show that the first phase of the thermal helix unfolding, ending at around 320 K, involves mainly the terminal regions. A second phase of the transition, ending at around 333 K, comprises the central helical region of the peptide. The determination of high‐resolution QK_L10A conformational preferences in water at 313 K allowed us to identify, at atomic resolution, one intermediate of the folding–unfolding pathway. Molecular dynamics simulations corroborate experimental observations detecting a stable central helical turn, which represents the most probable site for the helix nucleation in the folding direction. The data presented herein allows us to draw a folding–unfolding picture for the small peptide QK_L10A compatible with the nucleation–propagation model. This study, besides contributing to the basic field of peptide helix folding, is useful to gain an insight into the design of stable helical peptides, which could find applications as molecular scaffolds to target protein–protein interactions.     

Peptide recognition: encapsulation and alpha-helical folding of a nine-residue peptide within a hydrophobic dimeric capsule of a bowl-shaped host

A dimeric capsule of coordination bowl 1 encapsulated a nine-residue peptide (Trp-Ala-Glu-Ala-Ala-Ala-Glu-Ala-Trp; 2) within the large hydrophobic cavity in water, and stabilized the alpha-helical conformation of bound 2. An NMR titration experiment revealed that monomeric bowl 1 recognized two Trp residues at the both terminals of 2 through 1/2 = 1:1 to 2:1 complexation. The 1:1 and 2:1 species exist in equilibrium even in the presence of excess 1. It was found that the formation of the 2:1 complex, in which two bowls of 1 wrapped the whole of 2, became dominant by the addition of NaNO3 due to the fact that the enhanced ion strength increased the hydrophobic interaction between Trp residues and the cavity of 1. The alpha-helical conformation of 2 within the dimeric capsule of 1 was elucidated from detailed NOESY analysis.     

Conformational selection of the AGA*IA(M) heparin pentasaccharide when bound to the fibroblast growth factor receptor

The interaction of the synthetic pentasaccharide AGA*IA(M) (GlcNS,6S-GlcA-GlcNS,3S,6S-IdoA2S-GlcNS,6S-Me) with the extracellular Ig2 domain of the fibroblast growth factor receptor (FGFR2) has been studied by NMR and computational methods. Analysis of the heparin pentasaccharide in the free state and in the complex indicates the existence of a conformational selection process. Although an equilibrium exists between the (1)C(4) and (2)S(0) conformers (ratio 60:40) of the 2-O-sulfo-α-L-iduronate ring (IdoA2S) in the free state, FGFR2 selects only the unique twisted-boat (2)S(0) conformation of this IdoA2S residue. In addition, the protein residues involved in the binding with AGA*IA(M) have also been characterized. The NMR results obtained, from both the ligand and protein perspective, were employed to model the bound conformation of the pentasaccharide by a combined docking and molecular dynamic simulation approach.     

On the influence of charged side chains on the folding-unfolding equilibrium of beta-peptides: a molecular dynamics simulation study

The influence of charged side chains on the folding-unfolding equilibrium of beta-peptides was investigated by means of molecular dynamics simulations. Four different peptides containing only negatively charged side chains, positively charged side chains, both types of charged side chains (with the ability to form stabilizing salt bridges) or no charged side chains were studied under various conditions (different simulation temperatures, starting structures and solvent environment). The NMR solution structure in methanol of one of the peptides (A) has already been published; the synthesis and NMR analysis of another peptide (B) is described here. The other peptides (C and D) studied herein have hitherto not been synthesized. All four peptides A-D are expected to adopt a left-handed 3(14)-helix in solution as well as in the simulations. The resulting ensembles of structures were analyzed in terms of conformational space sampled by the peptides, folding behavior, structural properties such as hydrogen bonding, side chain-side chain and side chain-backbone interactions and in terms of the level of agreement with the NMR data available for two of the peptides. It was found that the presence of charged side chains significantly slows down the folding process in methanol solution due to the stabilization of intermediate conformers with side chain-backbone interactions. In water, where the solvent competes with the solute-solute polar interactions, the folding process to the 3(14)-helix is faster in the simulations.     

Poly(phenylacetylene)s bearing a peptide pendant: helical conformational changes of the polymer backbone stimulated by the pendant conformational change

Optically active, cis-transoid poly(phenylacetylene) derivatives bearing a poly(gamma-benzyl-L-glutamate) [poly(PBGAm)] or poly(L-glutamic acid) [poly(PGAm)] chain as the pendant were prepared by polymerisation of the corresponding macromonomer with a rhodium catalyst followed by hydrolysis of the pendant ester groups. Their conformational changes in solution, induced by a helix-coil transition of the pendant polypeptides, were investigated using circular dichroism (CD) and absorption spectroscopies. A series of macromonomers with a different peptide chain lengths was synthesised by the polymerisation of the N-carboxyanhydride of gamma-benzyl-L-glutamate with a phenylacetylene bearing an alanine residue as the initiator. The obtained macromonomers (PBGAm) were further polymerised with a rhodium catalyst in N,N-dimethylformamide (DMF) to yield novel poly(phenylacetylene)s [poly(PBGAm)] with a poly(gamma-benzyl-L-glutamate) pendant. The poly(PBGAm) exhibited an induced circular dichroism (ICD) in the UV/Vis region of the polymer backbone in dimethyl sulfoxide (DMSO), probably due to the prevailing one-handed helix formation. The Cotton effect signs of a DMSO solution of the poly(PBGAm) were inverted and accompanied by a visible colour change in the presence of an increasing amount of chloroform or DMF containing lithium chloride. The results suggest that poly(PBGAm) may undergo a conformational change such as a helix-helix transition with a different helical pitch responding to a change in the alpha-helix content of the poly(gamma-benzyl-L-glutamate) pendant. Moreover, a water-soluble poly(PGAm) also showed a similar, but dramatic change in its helical conformation with a visible colour change stimulated by a helix-coil transition of the pendant poly(L-glutamic acid) chains by changing the pH in water.     

Structural basis for the interaction of a vascular endothelial growth factor mimic peptide motif and its corresponding receptors

Vascular endothelial growth factor (VEGF) is central to the survival and development of the vascular and nervous systems. We screened phage display libraries and built a peptide-based ligand-receptor map of binding sites within the VEGF family. We then validated a cyclic peptide, CPQPRPLC, as a VEGF-mimic that binds specifically to neuropilin-1 and VEGF receptor-1. Here, we use NMR spectroscopy to understand the structural basis of the interaction between our mimic peptide and the VEGF receptors. We show that: (1) CPQPRPLC has multiple interactive conformations; (2) receptor binding is mediated by the motif Arg-Pro-Leu; and (3) the Pro residue within Arg-Pro-Leu participates in binding to neuropilin-1 but not to VEGF receptor-1, perhaps representing an evolutionary gain-of-function. Therefore, Arg-Pro-Leu is a differential ligand motif to VEGF receptors and a candidate peptidomimetic lead for VEGF pathway modulation.     

First-principles molecular dynamics evaluation of thermal effects on the NMR (1)J(Li,C) spin-spin coupling

Car-Parrinello (CP) molecular dynamics were applied to sample conformations of various models of organolithium aggregates which are chosen to estimate (1)J(Li,C) NMR coupling constants. The results show that the deviations from the values computed using static (optimized) geometries are small provided no large-amplitude motions occur within the timescale of the simulations. In the case of the vinyllithium dimer, for which rotation of the vinyl chain is observed, this approach allows analysis of the various contributions to the experimentally measured constants. For the trisolvated methyllithium monomer, partial decoordination of solvating dimethyl ether is observed and results in a significant shift of (1)J(Li,C). All these results highlight that a varied physicochemical machinery is hidden behind general empirical formulas, such as the Bauer-Winchester-Schleyer rule used experimentally.     

A Remarkable Solvent Effect on the Nuclearity of Neutral Titanium(IV)‐Based Helicate Assemblies

The spontaneous self‐assembly of a neutral circular trinuclear Ti^IV‐based helicate is described through the reaction of titanium(IV) isopropoxide with a rationally designed tetraphenolic ligand. The trimeric ring helicate was obtained after diffusion of n‐pentane into a solution with dichloromethane. The circular helicate has been characterized by using single‐crystal X‐ray diffraction study, ¹³C CP‐MAS NMR and ¹H NMR DOSY solution spectroscopic, and positive electrospray ionization mass‐spectrometric analysis. These analytical data were compared with those obtained from a previously reported double‐stranded helicate that crystallizes in toluene. The trimeric ring was unstable in a pure solution with dichloromethane and transformed into the double‐stranded helicate. Thermodynamic analysis by means of the PACHA software revealed that formation of the double‐stranded helicates was characterized by ΔH(toluene)=?30 kJ mol^?1 and ΔS(toluene)=+357 J K^?1 mol^?1, whereas these values were ΔH(CH₂Cl₂)=?75 kJ mol^?1 and ΔS(CH₂Cl₂)=?37 J K^?1 mol^?1 for the ring helicate. The transformation of the ring helicate into the double‐stranded helicate was a strongly endothermic process characterized by ΔH(CH₂Cl₂)=+127 kJ mol^?1 and ΔH(n‐pentane)=+644 kJ mol^?1 associated with a large positive entropy change ΔS=+1115 J K^?1?mol^?1. Consequently, the instability of the ring helicate in pure dichloromethane was attributed to the rather high dielectric constant and dipole moment of dichloromethane relative to n‐pentane. Suggestions for increasing the stability of the ring helicate are given.     

Stereodynamics and characterization of the hexa(4-n-dodecylbiphenylyl)benzene hexaanion that includes a twisted benzene core

Hexa(4-n-dodecylbiphenylyl)benzene (HDBB) was reduced by a series of alkali metals in THF under high vacuum. Three reduction states were identified by NMR spectroscopy, namely the dianion, tetraanion and hexaanion. The NMR spectra of HDBB(6-) revealed a remarkable distortion of symmetry, which is interpreted by adoption of a twisted conformation of the central benzene ring and a slow rotation of the inner phenylene rings of the biphenyl units. Due to the surprising thermal stability of the hexaanion, a dynamic NMR investigation revealed the pseudorotation of the twisted conformation and the phenylene rotation mentioned above.     

Electrochemical aptasensor for the detection of vascular endothelial growth factor (VEGF) based on DNA-templated Ag/Pt bimetallic nanoclusters

In this paper, the DNA-templated Ag/Pt bimetallic nanoclusters were successfully synthesized using an optimized synthetic scheme. The obtained DNA-Ag/Pt NCs have an ultrasmall particle size and excellent distribution. The DNA-Ag/Pt NCs show intrinsic peroxidase-mimicking activity and can effectively catalyze the H₂O₂-mediated oxidation of a substrate, 3,3',5,5'-tetramethylbenzidine (TMB), to produce a blue colored product. Based on this specific property, we employed the aptamer of VEGF to design a label-free electrochemical biosensor for VEGF detection. Under the optimized experimental conditions, a linear range from 6.0 pmol/L to 20 pmol/L was obtained with a detection limit of 4.6 pmol/L. The proposed biosensor demonstrated its high specificity for VEGF and could directly detect the VEGF concentration in human serum samples of breast cancer patients with satisfactory results. This novel electrochemical aptasensor was simple and convenient to use and was cost-effective and label-free in design, and would hold potential applications in medical diagnosis and treatment.     

Effects of vascular endothelial growth factor (VEGF) and chondroitin sulfate A on human monocytic THP-1 cell migration

Angiogenesis serves as a crucial factor in disease development and progression, such as cancer metastasis, and monocyte migration is one of the key steps for angiogenesis. Therapeutic modulation of angiogenesis is a promising new therapeutic avenue under investigation. In this study, effects of vascular endothelial growth factor (VEGF) and chondroitin sulfate A on monocyte migration were investigated. Human monocytic THP-1 cells were from Riken Cell Bank (Tsukuba, Japan) and vascular endothelial cells (VECs) were obtained from swine thoracic aorta. The migration experimental system was adapted from Falcon™ Cell Culture Inserts with pore sizes of 3 and 8 μm cultured endothelial cells or not on the insert polyethylene terephthalate (PET) membranes. Four VEGF concentrations (0, 10, 50 and 100 ng/ml) and three concentrations of chondroitin sulfate A (0, 1.25 and 5.0 mg/ml) were used to investigate their effects on THP-1 cell migration ability through PET membranes and VECs monolayer. The THP-1 cell migration was evaluated by counting the number of migrated cells related to the total number of cells under a microscope. We counted the migration cells every 1 h on a Tatai-type hemocytometer using an inverted microscope for total 7 h. For inserts with pore sizes of 3 and 8 μm, the THP-1 cell migration increased with VEGF concentrations; however, cell migration decreased with the chondroitin sulfate A concentration. Our results demonstrated that VEGF accelerated monocyte migration through endothelial monolayer and chondroitin sulfate A is an effective inhibitor of monocyte migration for angiogenesis.     

Structural and NMR Studies of the Hexameric Copper(I) Complex with N‐n‐butyl‐N′‐ethoxycarbonyl‐thioureate

The copper sulfide mineral flotation collector, N‐n‐butyl‐N′‐ethoxycarbonyl‐thiourea (H₂bectu), and the 1:1 hexameric copper(I) thioureate complex, [Cu(Hbectu)]₆, have been characterized by single crystal X‐ray diffraction. H₂bectu crystallizes in the triclinic space group with a = 5.2754(4), b = 9.0042(7), c = 12.6030(9) Å, α = 80.528(6), β = 90.173(6), γ = 76.472(7)°. An intramolecular N‐H···O hydrogen bond between the thioamide proton and carbonyl oxygen forms a planar six‐membered ring in the central core of the molecule with C=O, C=S and C‐N bond lengths in accord with those reported for other N‐alkyl/aryl‐N′‐acyl‐thiourea compounds. [Cu(Hbectu)]₆ crystallizes in the monoclinic space group C2/c with a = 23.269(5), b = 13.243(4), c = 23.037(7) Å, β = 91.81(2)° as discrete hexameric clusters disposed about a crystallographic centre of symmetry with a Cu₆S₆ core consisting of two Cu₃S₃ chair‐shaped rings linked by coordination of the deprotonated amide nitrogen atom to a copper atom in the adjacent ring. The six ligands assemble as a paddlewheel structure with the ethoxy and n‐butyl substituents packing in an alternating head to tail arrangement. Temperature dependent solution ¹H NMR spectroscopic studies show that the hexameric structure of the complex is maintained in solution.     

Computing the (1)H NMR spectrum of a bulk ionic liquid from snapshots of car-parrinello molecular dynamics simulations.

We have investigated the performance of several computational protocols in predicting the NMR spectrum of a molecular ion in a complex liquid phase such as an ionic liquid. To do this, we computed the proton NMR chemical shifts of the 1-ethyl-3-methylimidazolium cation [emim](+) in [emim][Cl]. Environmental effects on the imidazolium ring proton chemical shifts are quite significant and must be taken into account explicitly. Calculations performed on the isolated imidazolium cation as well as on the [emim][Cl] ion pair grossly fail to reproduce the correct spacing between proton signals. In contrast, calculations performed on clusters extracted from the trajectory of a Car-Parrinello molecular dynamics simulation yield very good results.     

2-羰基丙酸(4-吡啶甲酰基)腙与碱土金属配合物的晶体结构及热 稳定性

报道了2-羰基丙酸(4-吡啶甲酰基)腙(H~2L)与碱土金属(Ca,Mg,Sr,Ba)四种配合物的合成,结构及热稳定性。同时,用X射线单晶衍射仪测定了Mg和Ba两种配合物的晶体结构,结构分析表明两种配合物均属单斜晶系,空间群均为P2~1/c。此外,还比较讨论了各配合物不同成键方式所对应的IR特征及热稳定性变化规律。