Electronic structure and conformation of N-amino-2,5-dimethylpyrrole derivatives and N-formylaniline

From photoelectronic spectroscopy data N-amino-, N-dimethyl-, N-methylphenyl-, and N-methylformylamino-2,5-dimethylpyrrole molecules were found to have an acoplanar-oriented fragment conformation in the gas phase, while N-formylaniline had a planar structure. In aminopyrroles the n-n repulsion energy of unshared pairs exceeded the n-* conjugation energy.A. E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, Kazan 420083. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 3, pp. 602–606, March, 1992.     

The influence of simulation conditions in molecular dynamics investigations of model β-sheet peptides

The influence of simulation methods, cutoff based and particle mesh Ewald (PME) on the accuracy by which experimentally derived nuclear Overhauser effect (NOE) data are reproduced, has been investigated using 500-ns-long molecular dynamics simulations on a model -sheet peptide in explicit solvent. The structural and conformational features under the different conditions were evaluated in terms of flexibility, secondary structure content, hydrogen-bonding pattern and percent of native contacts as a function of time. It was found that the different simulation methods strongly influence the dynamics of the peptide, confirming previous observations based on ideal peptide models simulated for much shorter times. Moreover, the results of our simulations prove once more that it is necessary to reach extremely long time scales to obtain enough statistics to accurately reproduce experimental NOE restraints even in the case of the PME method, despite its tendency to the stabilization of conformations which are structurally closely related to the ones derived through experiment. Possible implications regarding the stabilization and folding mechanisms, together with their relationship to the experimental study of peptide models, are discussed.     

Structural regulation of a peptide-conjugated graft copolymer: a simple model for amyloid formation

The self-assembly of peptides and proteins into beta-sheet-rich high-order structures has attracted much attention as a result of the characteristic nanostructure of these assemblies and because of their association with neurodegenerative diseases. Here we report the structural and conformational properties of a peptide-conjugated graft copolymer, poly(gamma-methyl-L-glutamate) grafted polyallylamine (1) in a water-2,2,2-trifluoroethanol solution as a simple model for amyloid formation. Atomic force microscopy revealed that the globular peptide 1 self-assembles into nonbranching fibrils that are about 4 nm in height under certain conditions. These fibrils are rich in beta-sheets and, similar to authentic amyloid fibrils, bind the amyloidophilic dye Congo red. The secondary and quaternary structures of the peptide 1 can be controlled by manipulating the pH, solution composition, and salt concentration; this indicates that the three-dimensional packing arrangement of peptide chains is the key factor for such fibril formation. Furthermore, the addition of carboxylic acid-terminated poly(ethylene glycol), which interacts with both of amino groups of 1 and hydrophobic PMLG chains, was found to obviously inhibit the alpha-to-beta structural transition for non-assembled peptide 1 and to partially cause a beta-to-alpha structural transition against the 1-assembly in the beta-sheet form. These findings demonstrate that the amyloid fibril formation is not restricted to specific protein sequences but rather is a generic property of peptides. The ability to control the assembled structure of the peptide should provide useful information not only for understanding the amyloid fibril formation, but also for developing novel peptide-based material with well-defined nanostructures.     

Cross-Talk between Overlap Interactions in Biomolecules: A Case Study of the β-Turn Motif

Noncovalent interactions play a pivotal role in regulating protein conformation, stability and dynamics. Among the quantum mechanical (QM) overlap-based noncovalent interactions, n→π* is the best understood with studies ranging from small molecules to β-turns of model proteins such as GB1. However, these investigations do not explore the interplay between multiple overlap interactions in contributing to local structure and stability. In this work, we identify and characterize all noncovalent overlap interactions in the β-turn, an important secondary structural element that facilitates the folding of a polypeptide chain. Invoking a QM framework of natural bond orbitals, we demonstrate the role of several additional interactions such as n→σ* and π→π* that are energetically comparable to or larger than n→π*. We find that these interactions are sensitive to changes in the side chain of the residues in the β-turn of GB1, suggesting that the n→π* may not be the only component in dictating β-turn conformation and stability. Furthermore, a database search of n→σ* and π→π* in the PDB reveals that they are prevalent in most proteins and have significant interaction energies (∼1 kcal/mol). This indicates that all overlap interactions must be taken into account to obtain a comprehensive picture of their contributions to protein structure and energetics. Lastly, based on the extent of QM overlaps and interaction energies, we propose geometric criteria using which these additional interactions can be efficiently tracked in broad database searches.     

Nucleation of β-hairpin structure in a pyrrole amino acid containing peptide

Synthesis and conformational studies of two short peptides containing pyrrole amino acids (1, Paa), Boc-Paa-Paa-d-Pro-Gly-Xaa-Paa-Paa-OMe (2: Xaa=Ala; 3: Xaa=Val), were carried out in which it was established that replacement of Ala in 2 with a Val residue helps peptide 3 to adopt a well-defined β-hairpin conformation in a nonpolar solvent, like CDCl₃.     

Conformation of poly(L-glutamic acid) in aqueous solutions of linear amphiphiles with a cationic group at both ends

The conformations of poly(l-glutamic acid) [P(Glu)] in solutions of the bipolar amphiphile 1,20-icosanediylbis(alkylammonium chloride) [C20(RA)₂], where RA includes trimethylammonium (TMA), dimethylammonium (DMA), or methylammonium (MA), were investigated with measurements of the circular dichroism spectra at 10–35 °C. All C20(RA)₂ induced an α-helix of P(Glu) in the aqueous solutions. The residue molar ellipticity at 222 nm showed a similar dependence on the amphiphile concentration (C _s) below 0.5 of the ratio of 2C _s to the residue concentration (C _p) of P(Glu), but it separated into three directions at 2C _s/C _p>0.5. C20(MA)₂ induced an α-helix of P(Glu) at 2C _s/C _p<0.5 followed by a helix aggregate at 2C _s/C _p>0.5. C20(DMA)₂ and C20(TMA)₂ also induced an α-helix, but a helix aggregate. C20(TMA)₂ indicated a strong temperature dependence and did not induce a complete α-helix at 35 °C. Received: 20 June 2001 Accepted: 6 September 2001     

Synthesis, Crystal Structure, Physical Properties, and Application of a Series of Functional Dibenzo[d,f][1,3]dioxepine Derivatives

The twisted aromatics, functional dibenzo[d,f][1,3]dioxepine derivatives were synthesized in high yields from reactions of 5,5＇-dibromo-2,2＇-biphenol with corresponding ketal or ketone compounds under acid catalysis. The structures of these compounds were characterized by ^1H NMR, elemental analysis, UV-Vis absorption spectrum and X-ray diffraction analysis. The conformation of O--C--O bridged biphenyl derivatives with varied substitute groups on 6,6＇-position was studied by X-ray crystallography and force-field simulation. The result of calculations by UNIVERSAL 1.02 force field in Cerius2 package（4.6） indicates that dibenzo[d,f][1,3]dioxepine derivatives show twisted conformations and the twisted angle between the phenyl rings is about 40°, which is accordant with the result from crystal structure determination, though the obtained angles in the crystal of dibenzo[d,f][1,3]dioxepine derivatives with the varied substitute groups on 6,6＇-position are shown to be slightly shifted to 40° owing to intermolecular interactions in crystal stacking. DSC studies exhibit that the substitute groups on 6,6＇-position can induce a large variation of endothermic peaks ranging from 80 to 135 ℃. The conjugated polymers based on dibenzo[d,f][1,3]dioxepine derivatives, which have ultraviolet emitting with a quantum efficiency of 10%, were obtained by Yamamoto coupling.     

亲水性两性离子聚合物刷的构象与结构

本文应用分子场理论,研究暴露于水蒸气中的亲水性两性离子聚合物(HP)刷的构象与结构.理论模型考虑HP-水(P-W)氢键和水-水(W-W)氢键效应,以及HP单体之间的偶极-偶极相互作用.研究发现,P-W与W-W氢键决定着HP的水合性,P-W氢键形成,会诱导HP刷溶胀.我们通过考察HP单体间的偶极-偶极相互作用发现,随着偶极-偶极相互作用增强,HP链在垂直培基表面沿着链方向,形成了结节状结构.这是由于HP单体之间的偶极-偶极静电吸引作用导致单体间汇聚结节,这种结节在刷内产生了较强的排斥体积作用,因此,这种HP刷具有抗污性能.在较高的接枝密度环境下,由于HP链间单体之间的偶极-偶极静电吸引作用,会形成链间单体-单体的结节,在刷内形成结节网络状凝胶结构,这种结构的出现,会使得HP刷呈现极强的抗污性.另外,当体系中水蒸气浓度增加、水合相互作用增强时,增加的P-W氢键将平衡HP单体之间的偶极-偶极相互作用,使得结节解开,聚合物链伸展.我们的理论结果符合实验观测,由此表明,P-W氢键效应,以及HP单体之间的偶极-偶极相互作用决定着HP刷的构象转变和结构特性,刷内出现的两性离子聚合物链内单体间的结节和链间单体结节状凝胶结构,是两性离子聚合物刷呈现较强抗污性的本质特性.     

Studies on the Molecular Chain Conformation Stability of Aminated Konjac Glucomannan

Konjac glucomannan （KGM） was aminated by 2-chloroethyl-amine （CEA） as reagent so as to study the influence of concentration of CEA （based on the amount of KGM）, concentration of NaOH, reaction time and temperature on the extent of amination. And the molecular simulation technology was adopted to analyze the conformation stability of aminate （AKGM）. The results indicate that when the amount of CEA is higher, the extent of amination is higher. The optimum concentration of NaOH, reaction time and temperature are 10% NaOH, 70 ℃ and 45 rain, respectively. IR shows KGM is successfully aminated. The conformation of AKGM is in a random clew-like shape.     

Absolute configurations of C34 and C35 of antibiotic niphimycin A

The relative configurations of four stereogenic centers of the C33‐C42 fragment of niphimycin A were assigned as 2S*, 3R*, 4S* and 6S*, based upon ¹H NMR analysis with double‐quantum filtered COSY and nuclear Overhauser spectroscopy experiments. These data were then correlated with absolute configurations at C36 and C38 of niphimycin A, which were declared previously as 36S and 38S [3]. This allowed for the assignment of the absolute configurations at C34 and C35 of niphimycin A as 34S and 35R. Copyright © 2012 John Wiley & Sons, Ltd.