Structural Investigation of Hybrid Peptide Foldamers Composed of α-Dipeptide Equivalent β-Oxy-δ5-amino Acids

Due to their equivalent lengths, δ-amino acids can serve as surrogates of α-dipeptides. However, δ-amino acids with proteinogenic side chains have not been well studied because of synthetic difficulties and because of their insolubility in organic solvents. Recently we reported the spontaneous supramolecular gelation of δ-peptides composed of β(O)-δ⁵-amino acids. Here, we report the incorporation of β(O)-δ⁵-amino acids as guests into the host α-helix, α,γ-hybrid peptide 12-helix and their single-crystal conformations. In addition, we studied the solution conformations of hybrid peptides composed of 1:1 alternating α and β(O)-δ⁵-amino acids. In contrast to the control α-helix structures, the crystal structure of peptides with β(O)-δ⁵-amino acids exhibit α-helical conformations consisting of both 13- and 10-membered H-bonds. The α,δ-hybrid peptide adopted mixed 13/11-helix conformation in solution with alternating H-bond directionality. Crystal-structure analysis revealed that the α,γ⁴-hybrid peptide accommodated the guest β(O)-δ⁵-amino acid without significant deviation to the overall helix folding. The results reported here emphasize that β(O)-δ⁵-amino acids with proteinogenic side chains can be accommodated into regular α-helix or 12-helix as guests without much deviation of the overall helix folding of the peptides.     

Chiral sum frequency generation spectroscopy for characterizing protein secondary structures at interfaces

In situ and real-time characterization of protein secondary structures at interfaces is important in biological and bioengineering sciences, yet remains technically challenging. In this study, we used chiral sum frequency generation (SFG) spectroscopy to establish a set of vibrational optical markers for characterizing protein secondary structures at interfaces. We discovered that the N-H stretches along the peptide backbones of α-helices can be detected in chiral SFG spectra. We further observed that the chiral vibrational signatures of the N-H stretch together with the peptide amide I are unique to α-helix, β-sheet, and random coil at interfaces. Using these chiral vibrational signatures, we studied the aggregation of human islet amyloid polypeptide (hIAPP), which is implicated in type II diabetes. We observed in situ and in real time the misfolding of hIAPP from random coils to α-helices and then β-sheets upon interaction with a lipid-water interface. Our findings show that chiral SFG spectroscopy is a powerful tool to follow changes in protein conformations at interfaces and identify interfacial protein secondary structures that elude conventional techniques.     

1H and 13C NMR study of the enol–enolic tautomerism of some cyclic β-ketoaldehydes

Aldehyde (δCH) and enolic (δOH) proton chemical shifts, the corresponding spin–spin coupling constants (JCH,OH) and the ¹³C chemical shifts (δC) have been measured for three cyclic β-ketoaldehydes as a function of temperature. A tautomeric equilibrium has been shown to exist between the aldo–enol ( A ) and hydroxymethylene ketone ( B ) forms. The chemical shifts δCH δOH and δC for the two pure tautomeric forms A and B have been calculated. The enthalpy changes ΔH in the tautomeric process A ? B and the percentages of the tautomeric forms have been determined.     

Peptide models XVI. The identification of selected HCO—L—SER—NH2 conformers via a systematic grid search using ab initio potential energy surfaces

Multidimensional conformational analysis (MDCA) predicted the existence of nine stable backbone conformations (α_L, α_D, β_L, γ_L, γ_D, δ_L, δ_D, ϵ_L, and ϵ_D) on the 2D-Ramachandran map, E = E(ϕ, ψ), for a single amino acid diamide (HCONH-CHR-CONH₂). The potential energy hypersurfaces (E = E[ϕ, ψ, χ₁, χ₂]) of For-L-Ser-NH₂ associated with the α_L-, bgr;_L-, γ_L-, δ_L-, and ϵ_L-type stable backbone orientations are investigated in this article. An appropriate number of side-chain rotamers is associated with each of the backbone conformers. In the case of serine, where R = −CH₂OH, the two sidechain torsional angles (χ₁, χ₂) should lead to 3 * 3 = 9 different sidechain orientations according to MDCA. For certain backbone structures, some of the sidechain conformations were nonexistent. © 1996 by John Wiley & Sons, Inc.     

The amyloid formation mechanism in human IAPP: dimers have β-strand monomer-monomer interfaces

Early oligomerization of human IAPP (hIAPP) is responsible for β-cell death in the pancreas and is increasingly considered a primary pathological process linked to Type II Diabetes (T2D). Yet, the assembly mechanism remains poorly understood, largely due to the inability of conventional techniques to probe distributions or detailed structures of early oligomeric species. Here, we describe the first experimental data on the isolated and unmodified dimers of human (hIAPP) and nonamyloidogenic rat IAPP (rIAPP). The experiments reveal that the human IAPP dimers are more extended than those formed by rat IAPP and likely descend from extended monomers. Independent all-atom molecular dynamics simulations show that rIAPP forms compact helix and coil rich dimers, whereas hIAPP forms β-strand rich dimers that are generally more extended. Also, the simulations reveal that the monomer-monomer interfaces of the hIAPP dimers are dominated by β-strands and that β-strands can recruit coil or helix structured regions during the dimerization process. Our β-rich interface contrasts with an N-terminal helix-to-helix interface proposed in the literature but is consistent with existing experimental data on the self-interaction pattern of hIAPP, mutation effects, and inhibition effects of the N-methylation in the mutation region.     

MM3 Modeling of Ribose and 2-Deoxyribose Ring Puckering

ABSTRACT

Conformational energy maps for furanosyl and pyranosyl rings of α- and β-ribose and 2-deoxyribose were generated with the molecular mechanics program MM3. For the furanosyl tautomers, low-energy Northern and Southern minima were found. For the pyranosyl rings, lowest-energy minima corresponded to chair forms. Hydrogen-hydrogen coupling constants for the minimal-energy conformers were calculated based on Karplus equations. Computational and experimental results indicate that several tautomeric forms of ribose and 2-deoxyribose exist in multiple conformations in solution. Ring conformations of related crystal structures have energies within ～2 kcal/mol of the calculated global minima.     

New Insight in Copper‐Ion Binding to Human Islet Amyloid: The Contribution of Metal‐Complex Speciation To Reveal the Polypeptide Toxicity

Type‐2 diabetes (T2D) is considered to be a potential threat on a global level. Recently, T2D has been listed as a misfolding disease, such as Alzheimer's and Parkinson's diseases. Human islet amyloid polypeptide (hIAPP) is a molecule cosecreted in pancreatic β cells and represents the main constituent of an aggregated amyloid found in individuals affected by T2D. The trace‐element serum level is significantly influenced during the development of diabetes. In particular, the dys‐homeostasis of Cu²⁺ ions may adversely affect the course of the disease. Conflicting results have been reported on the protective role played by complex species formed by Cu²⁺ ions with hIAPP or its peptide fragments in vitro. The histidine (His) residue at position 18 represents the main binding site for the metal ion, but contrasting results have been reported on other residues involved in metal‐ion coordination, in particular those toward the N or C terminus. Sequences that encompass regions 17–29 and 14–22 were used to discriminate between the two models of the hIAPP coordination mode. Due to poor solubility in water, poly(ethylene glycol) (PEG) derivatives were synthesized. A peptide fragment that encompasses the 17–29 region of rat amylin (rIAPP) in which the arginine residue at position 18 was substituted by a histidine residue was also obtained to assess that the PEG moiety does not alter the peptide secondary structure. The complex species formed by Cu²⁺ ions with Ac‐PEG‐hIAPP(17–29)‐NH₂, Ac‐rIAPP(17–29)R18H‐NH₂, and Ac‐PEG‐hIAPP(14–22)‐NH₂ were studied by using potentiometric titrations coupled with spectroscopic methods (UV/Vis, circular dichroism, and EPR). The combined thermodynamic and spectroscopic approach allowed us to demonstrate that hIAPP is able to bind Cu²⁺ ions starting from the His18 imidazole nitrogen atom toward the N‐terminus domain. The stability constants of copper(II) complexes with Ac‐PEG‐hIAPP(14–22)‐NH₂ were used to simulate the different experimental conditions under which aggregate formation and oxidative stress of hIAPP has been reported. Speciation unveils: 1) the protective role played by increased amounts of Cu²⁺ ions on the hIAPP fibrillary aggregation, 2) the effect of adventitious trace amounts of Cu²⁺ ions present in phosphate‐buffered saline (PBS), and 3) a reducing fluorogenic probe on H₂O₂ production attributed to the polypeptide alone.     

Molecular Mechanisms of Amylin Turnover,Misfolding and Toxicity in the Pancreas

Amyloidosis is a common pathological event in which proteins self-assemble into misfolded soluble and insoluble molecular forms, oligomers and fibrils that are often toxic to cells. Notably, aggregation-prone human islet amyloid polypeptide (hIAPP), or amylin, is a pancreatic hormone linked to islet β-cells demise in diabetics. The unifying mechanism by which amyloid proteins, including hIAPP, aggregate and kill cells is still matter of debate. The pathology of type-2 diabetes mellitus (T2DM) is characterized by extracellular and intracellular accumulation of toxic hIAPP species, soluble oligomers and insoluble fibrils in pancreatic human islets, eventually leading to loss of β-cell mass. This review focuses on molecular, biochemical and cell-biology studies exploring molecular mechanisms of hIAPP synthesis, trafficking and degradation in the pancreas. In addition to hIAPP turnover, the dynamics and the mechanisms of IAPP–membrane interactions; hIAPP aggregation and toxicity in vitro and in situ; and the regulatory role of diabetic factors, such as lipids and cholesterol, in these processes are also discussed.     

最短α-螺旋的理论研究

在B3LYP/6-31+G**水平下的溶剂中优化得到4个残基长和5个残基长的α-螺旋. 计算得到的骨架构象与蛋白质晶体结构的统计结果符合得很好. 类似于一般的较长α-螺旋, 观察到了C-端的散开. 对很短的聚丙氨酸肽链, 从焓上看310-螺旋明显比α-螺旋稳定, 然而熵效应不利于310-螺旋结构. 螺旋N2(N-端第二个残基)位上天冬氨酸侧链的加盖(Capping)效应明显使α-螺旋相对310-螺旋更加稳定. 因而, 在同样长度下α-螺旋比310-螺旋多的统计结果能够被理解. 另外, 最短的α-螺旋的C-端倾向于以β-转角结构结束.     

Rearrangements photochimiques d'α-epoxycetones spiranniques et de composes dicarbonyles; nouvelle etude de la photolyse du benzoyloxy-3-5-cholestene-2; photoepimerisation en 5 de la benzoyl-2-5α-cholestanone-3

The photolysis of epoxides derived from 2 - benzylidène - 5α - cholestan - 3 - one depends considerably on stereochemistry. No photoepimerisation can be detected; expected β diketones are formed. Several tautomeric forms of 2 - benzoyl - 5α - cholestan - 3 - one have been isolated in crystalline form, and some exist in neutral solution. A δ hydrogen abstraction by the benzoyl group is involved in the photolysis of this δ-diketone.     

Séparation des isoméres de l'hexachlorocyclohexane par chromatographie en phase gaz

Hexachlorocyclohexane isomers can be separated by a glass bead technique with polypropylene glycol Niax 1025 as the stationary phase. The principal isomers separated are the γ-hexachloro-cyclohexane (Lindane isomer), the α, β, ε, and δ isomers and γ-heptachlorocyclohexane. The life of the glass bead column is short — about 20 days in constant use. A longer column life can be obtained by pretreatment of the glass beads.     

Helical γ-Peptide Foldamers as Dual Inhibitors of Amyloid-β Peptide and Islet Amyloid Polypeptide Oligomerization and Fibrillization

Type 2 diabetes (T2D) and Alzheimer's disease (AD) belong to the 10 deadliest diseases and are sorely lacking in effective treatments. Both pathologies are part of the degenerative disorders named amyloidoses, which involve the misfolding and the aggregation of amyloid peptides, hIAPP for T2D and Aβ_1-42 for AD. While hIAPP and Aβ_1-42 inhibitors have been essentially designed to target β-sheet-rich structures composing the toxic amyloid oligomers and fibrils of these peptides, the strategy aiming at trapping the non-toxic monomers in their helical native conformation has been rarely explored. We report herein the first example of helical foldamers as dual inhibitors of hIAPP and Aβ_1-42 aggregation and able to preserve the monomeric species of both amyloid peptides. A foldamer composed of 4-amino(methyl)-1,3-thiazole-5-carboxylic acid (ATC) units, adopting a 9-helix structure reminiscent of 3₁₀ helix, was remarkable as demonstrated by biophysical assays combining thioflavin-T fluorescence, transmission electronic microscopy, capillary electrophoresis and mass spectrometry.     

The pressure tolerance of different poly-l-lysine conformers in aqueous solution: Infrared spectroscopy and two-dimensional correlation analysis

Poly-l-lysine can form either of three different conformers as α-helix, anti-parallel β-sheet and random coil stably under appropriate conditions. In buffer solution poly-l-lysine exists in a random coil at about pH 4, an α-helix above pH 12, and transforms from α-helix to β-sheet when the sample is heated to 46 °C for 30 min. The effects of elevated hydrostatic pressure on three different initial conformers of poly-l-lysine are investigated with Fourier transform infrared spectroscopy and two-dimensional correlation analysis. Changes observed in the amide I′ band indicate that the α-helix conformer undergo hydration enhancement at low pressure (<400 MPa), then gradually transition into an α′-helix. Two initial conformers, the β-sheet and random coiled polypeptide, undergo conformational changes to an α-helix at low pressure and to an α′-helix at high pressure. Moreover, the conversion occurred at a lower pressure for the β-sheet (∼250 MPa) than for the α-helix (∼300 MPa) and the random coil (∼850 MPa).     

The study of Turnip Mosaic virus coat protein by surface enhanced Raman spectroscopy

Using Turnip Mosaic virus (TuMV) coat protein as material, the secondary structure has been studied by both normal Raman spectroscopy (NRS) and surface enhanced Raman spectroscopy (SERS). The NRS of TuMV coat protein under certain conditions showed the α-helix, β-sheet and random coil structure. The CSSC comformations are trans—gauche—gauche and gauche—gauche—gauche. The SERS spectrum of TuMV coat protein under certain conditions reveals the α-helix structure. By studying SERS at different adsorbing times, we have observed the amide III vibration of α-helix, β-sheet and random coil structure. The CSSC conformations drawn from the SERS spectra are trans—gauche—gauche and trans—gauche—trans. Besides the amide I, amide III and CSSC bands, the CαCN band, aromatic amino acid bands and some other bands can also be seen in the SERS spectra.     

pH值和钙离子对尖吻蝮蛇抗血小板凝集素二级结构的影响

尖吻蝮蛇毒中抗血小板凝集素是凝血因子IX/凝血因子X结合蛋白，它具有抗凝血和抑制血小板凝集双重活性。用红外光谱、拉曼光谱和CD谱研究了抗血小板凝集素的二级结构以及pH值和钙离子对其二级结构的影响。用CD谱测得，在水溶液中，抗血小板凝集素的主要骨架构象为β-折叠(26.3%)和α-螺旋(19.6%)结构。拉曼光谱显示，在粉末状态，其α-螺旋含量显著降低。CD谱还表明，抗血小板凝集素在pH值3.0～11.0范围内保持稳定的天然结构，钙离子诱导的抗血小板凝集素结构变化是可逆的，钙离子在稳定抗血小板凝集素的天然结构中起重要作用。     

Molecular dynamics simulation study on the inhibitory effects of choline-O-sulfate on hIAPP protofibrilation

Type 2 diabetes mellitus (T2Dm) is a neurodegenerative disease, which occurs due to the self-association of human islet amyloid polypeptide (hIAPP), also known as human amylin. It was reported experimentally that choline-O-sulfate (COS), a small organic molecule having a tertiary amino group and sulfate group, can prevent the aggregation of human amylin without providing the mechanism of the action of COS in the inhibition process. In this work, we investigate the influence of COS on the full-length hIAPP peptide by performing 500 ns classical molecular dynamics simulations. From pure water simulation (without COS), we have identified the residues 11–20 and 23–36 that mainly participate in the fibril formation, but in the presence of 1.07 M COS these residues become totally free of β-sheet conformation. Our results also show that the sulfate oxygen of COS directly interacts with the peptide backbone, which leads to the local disruption of peptide–peptide interaction. Moreover, the presence of favorable peptide-COS vdW interaction energy and high coordination number of COS molecules in the first solvation shell of the peptide indicates the hydrophobic solvation of the peptide residues by COS molecules, which also play a crucial role in the prevention of β-sheet formation. Finally, from the potential of mean force (PMFs) calculations, we observe that the free energy between two peptides is more negative in the absence of COS and with increasing concentration of COS, it becomes unfavorable significantly indicating that the peptide dimer formation is most stable in pure water, which becomes less favorable in the presence of COS. © 2019 Wiley Periodicals, Inc.     

Structural insights into the polymorphism of amyloid-like fibrils formed by region 20-29 of amylin revealed by solid-state NMR and X-ray fiber diffraction

Many unrelated proteins and peptides can assemble into amyloid or amyloid-like nanostructures, all of which share the cross-beta motif of repeat arrays of beta-strands hydrogen-bonded along the fibril axis. Yet, paradoxically, structurally polymorphic fibrils may derive from the same initial polypeptide sequence. Here, solid-state nuclear magnetic resonance (SSNMR) analysis of amyloid-like fibrils of the peptide hIAPP 20-29, corresponding to the region S (20)NNFGAILSS (29) of the human islet amyloid polypeptide amylin, reveals that the peptide assembles into two amyloid-like forms, (1) and (2), which have distinct structures at the molecular level. Rotational resonance SSNMR measurements of (13)C dipolar couplings between backbone F23 and I26 of hIAPP 20-29 fibrils are consistent with form (1) having parallel beta-strands and form (2) having antiparallel strands within the beta-sheet layers of the protofilament units. Seeding hIAPP 20-29 with structurally homogeneous fibrils from a 30-residue amylin fragment (hIAPP 8-37) produces morphologically homogeneous fibrils with similar NMR properties to form (1). A model for the architecture of the seeded fibrils is presented, based on the analysis of X-ray fiber diffraction data, combined with an extensive range of SSNMR constraints including chemical shifts, torsional angles, and interatomic distances. The model features a cross-beta spine comprising two beta-sheets with an interface defined by residues F23, A25, and L27, which form a hydrophobic zipper. We suggest that the energies of formation for fibril form containing antiparallel and parallel beta-strands are similar when both configurations can be stabilized by a core of hydrophobic contacts, which has implications for the relationship between amino acid sequence and amyloid polymorphism in general.     

Molecular dynamics studies of the inhibitory mechanism of copper（Ⅱ） on aggregation of amyloid β-peptide

The inhibitory mechanism of copper（Ⅱ） on the aggegation of amyloid β-peptide （Aβ） was investigated by molecular dynamics simulations. The binding mode ofcopper（Ⅱ） with Aβ is characterized by the imidazole nitrogen atom, Nπ, of the histidine residue H 13, acting as the anchoring site, and the backbone＇s deprotoned amide nitogen atoms as the main binding sites. Drove by the coordination bonds and their induced hydrogen bond net, the conformations of Aβ converted from β-sheet non-β-sheet conformations, which destabilized the aggregation of Aβ into fibrils.     

吸附类蛋白质分子二级结构变化的研究

采用蒙特卡罗方法和基于三维格点的ODI模型,研究了类蛋白质分子二级结构变化与表面吸附能的关系.分别计算了链长为29,39,49时、不同吸附能下类蛋白质分子二级结构的个数.包括α螺旋、β折叠、紧密接触对.吸附能参数aε<2εh时,这三类二级结构个数均没有明显的变化,而在2εh<εa<4εh,二级结构的个数迅速减小,εa>4hε时,二级结构的个数基本维持不变.同时发现吸附能增强对螺旋结构变化的影响最大,对折叠结构的影响其次,对紧密接触对影响最小.这体现在螺旋结构的减小幅度为90%,折叠结构减小的幅度为45%,而紧密接触对减小的幅度为35%.通过统计吸附单体个数,得到当吸附单体占总单体数的40%时,二级结构开始变化,直至吸附单体为总单体数的90%时,二级结构基本不变.另外还计算了二级结构个数的涨落δNh、δNc以及吸附单体个数的涨落δNa.在εa>2εh时,涨落突然增大,在aε=2εh时,δNh和δNb具有涨落极大值,这是二级结构相变的临界点.在εa=3.75εh处,δNc和δNa具有极大值.     

Polymorphism in Polyamide of Dytek®-A and Dodecanedioic Acid

Our X-ray work of Dytek®-A, 2-methyl-pentamethylenediamine, containing polyamides shows polymorphism, whereas the polyamides with linear diamines do not. The polyamide of Dytek®-A and dodecanedioic acid, MPMD-12, is singled out for discussion and compared with the unbranched analogs of polyamides 6,12 and 5,12. Due to the presence of the -CH₃ side group in the 2-position of the diamine, the polyamide MPMD-12 exhibits two stable crystal conformations. The new δ polymorph is not seen in linear polyamides 6,12 and 5,12. Studies by DSC polyamide MPMD-12 clearly illustrates at least two crystal forms, γ and δ, coexisting over a wide temperature range, and the isolation of each phase is possible by controlling temperature and time. The DMA modulus in the temperature region between the glass transition (or alpha relaxation) and melting transition shows strong dependence on the thermal history as demonstrated in a study of crystallization kinetics.