Interaction of 18-residue peptides derived from amphipathic helical segments of globular proteins with model membranes

We investigated the interaction of six 18-residue peptides derived from amphipathic helical segments of globular proteins with model membranes. The net charge of the peptides at neutral pH varies from −1 to +6. Circular dichroism spectra indicate that peptides with a high net positive charge tend to fold into a helical conformation in the presence of negatively charged lipid vesicles. In helical conformation, their average hydrophobic moment and hydrophobicity would render them surface-active. The composition of amino acids on the polar face of the helix in the peptides is considerably different. The peptides show variations in their ability to permeabilise zwitterionic and anionic lipid vesicles. Whereas increased net positive charge favours greater permeabilisation, the distribution of charged residues in the polar face also plays a role in determining membrane activity. The distribution of amino acids in the polar face of the helix in the peptides that were investigated do not fall into the canonical classes described. Amphipathic helices, which are part of proteins, with a pattern of amino acid distribution different from those observed in class L, A and others, could help in providing newer insights into peptide-membrane interactions.     

抗菌肽结构改造与人工智能研发策略

抗菌肽是一类广泛存在于生物体内的小分子肽,参与构成生物体先天免疫,可以有效抵抗病原微生物的入侵。抗菌肽具有广谱抗菌活性,且不易产生耐药性等特点,在治疗感染性疾病方面具有独特的优势,有望成为理想的抗感染药物。然而,由于部分抗菌肽尚存在稳定性差、毒性高等问题,限制了抗菌肽的广泛应用。由于人工智能算法能有效合成具有高稳定性、低毒性的抗菌肽,在探索天然抗菌肽中展现了巨大的潜力,因此本文简述了抗菌肽的抗菌机制、结构改造以及利用机器学习和深度学习等人工智能算法进行新型抗菌肽研发的优化策略,以期为抗菌肽结构优化及研发提供新思路。     

Incorporation of pairwise interactions into the Lifson-Roig model for helix prediction.

The helix/coil equilibrium of a peptide in solution can be modulated by a variety of side-chain interactions that are not incorporated into the standard statistical mechanical models for prediction of peptide helical content. In this report, we describe a recursive formulation of the Lifson-Roig model that facilitates incorporation of specific pairwise side-chain interactions as well as nonspecific individual side-chain capping interactions. Application of this extended model to a series of host/guest peptides indicates that the apparent delta G value for a pairwise apolar interaction is dependent upon the spacing and orientation but not the sequential location of the participating residues. The apparent delta G values for such interactions are about 40% greater than the corresponding apparent delta delta G values obtained from difference measurements.     

Osmolyte effects on helix formation in peptides and the stability of coiled-coils

The ability of several naturally occurring substances known as osmolytes to induce helix formation in an alanine-based peptide have been investigated. As predicted by the osmophobic effect hypothesis, the osmolytes studies here do induce helix formation. Trimethylamine-N-oxide (TMAO) is the best structure-inducing osmolytes investigated here, but it is not as effective in promoting helix formation as the common cosolvent trifluoroethanol (TFE). We also provide a semiquantitative study of the ability of TMAO to induce helix formation and urea, which acts as a helix (and protein) denaturant. We find that on a molar basis, these agents are exactly counteractive as structure inducing and unfolding agents. Finally, we extend the investigations to the effects of urea and TMAO on the stability of a dimeric coiled-coil peptide and find identical results. Together these results support the tenets of the osmophobic hypothesis and highlight the importance of the polypeptide backbone in protein folding and stability.     

抗菌肽的结构分析、抗菌机制及改造应用的研究进展

细菌感染已成为威胁人类健康的重要公共卫生问题之一,而抗生素的滥用又加快了细菌耐药性的进程。抗菌肽因其广谱抗菌活性、快速杀菌作用、低毒性和不易产生耐药性等特点受到了广泛关注。然而,抗菌肽的天然结构也预示了其应用存在一些限制,如易降解、不稳定、低渗透和高成本等。如何改良抗菌肽仍是需要解决的难题。本文从抗菌肽的来源和结构特征出发,分析了与抗菌相关的空间结构及其所对应的抗菌机制,总结了现有抗菌肽的改良策略,为寻求新型改良方案奠定基础。希望为今后抗菌肽的改造与临床应用提供新的思路和方向。     

Cyanobacterial peptides as a prototype for the design of cathepsin D inhibitors

Cathepsin D (Cath D) is overexpressed and secreted in a number of solid tumors and involved in the progress of tumor invasion, proliferation, metastasis, and apoptosis. Inhibition of Cath D is regarded as an attractive pathway for the development of novel anticancer drugs. Our previous studies revealed that tasiamide B, a cyanobacterial peptide that contained a statine‐like unit, exhibited good inhibition against Cath D and other aspartic proteases. Using this natural product as prototype, we designed and synthesized three new analogs, which bear isophthalic acid fragment at the N‐terminus and isobutyl amine ( 1 ), cyclopropyl amine ( 2 ), or 3‐methoxybenzyl amine ( 3 ) moiety at the C‐terminus. Enzymatic assays revealed that all these three compounds showed moderate‐to‐good inhibition against Cath D, with IC₅₀s of 15, 884, and 353 nM, respectively. Notably, compound 1 showed extreme selectivity for Cath D with 576‐fold over Cath E and 554‐fold over BACE1, which could be a valuable template for the design of highly potent and selective Cath D inhibitors. Additionally, compound 1 showed moderated activity against HeLa cell lines with IC₅₀ of 41.8 μM. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.     

Construction of an intermediate-resolution lattice model and re-examination of the helix-coil transition: a dynamic Monte Carlo simulation

In protein modeling, spatial resolution and computational efficiency are always incompatible. As a compromise, an intermediate-resolution lattice model has been constructed in the present work. Each residue is decomposed into four basic units, i.e. the α-carbon group, the carboxyl group, the imino group, and the side-chain group, and each basic coarse-grained unit is represented by a minimum cubic box with eight lattice sites. The spacing of the lattice is about 0.56?Å, holding the highest spatial resolution for the present lattice protein models. As the first report of this new model, the helix-coil transition of a polyalanine chain was examined via dynamic Monte Carlo simulation. The period of formed α-helix was about 3.68 residues, close to that of a natural α-helix. The resultant backbone motion was found to be in the realistic regions of the conformational space in the Ramachandran plot. Helix propagation constant and nucleation constant were further determined through the dynamic hydrogen bonding process and torsional angle variation, and the results were used to make comparison between classical Zimm-Bragg theory and Lifson-Roig theory based on the Qian-Schellman relationship. The simulation results confirmed that our lattice model can reproduce the helix-coil transition of polypeptide and construct a moderately fine α-helix conformation without significantly weakening the priority in efficiency for a lattice model.     

N‐terminal diproline and charge group effects on the stabilization of helical conformation in alanine‐based short peptides: CD studies with water and methanol as solvent

Protein folding problem remains a formidable challenge as main chain, side chain and solvent interactions remain entangled and have been difficult to resolve. Alanine‐based short peptides are promising models to dissect protein folding initiation and propagation structurally as well as energetically. The effect of N‐terminal diproline and charged side chains is assessed on the stabilization of helical conformation in alanine‐based short peptides using circular dichroism (CD) with water and methanol as solvent. A1 (Ac–Pro–Pro–Ala–Lys–Ala–Lys–Ala–Lys–Ala–NH₂) is designed to assess the effect of N‐terminal homochiral diproline and lysine side chains to induce helical conformation. A2 (Ac–Pro–Pro–Glu–Glu–Ala–Ala–Lys–Lys–Ala–NH₂) and A3 (Ac–d Pro–Pro–Glu–Glu–Ala–Ala–Lys–Lys–Ala–NH₂) with N‐terminal homochiral and heterochiral diproline, respectively, are designed to assess the effect of Glu...Lys (i , i  + 4) salt bridge interactions on the stabilization of helical conformation. The CD spectra of A1 , A2 and A3 in water manifest different amplitudes of the observed polyproline II (PPII) signals, which indicate different conformational distributions of the polypeptide structure. The strong effect of solvent substitution from water to methanol is observed for the peptides, and CD spectra in methanol evidence A2 and A3 as helical folds. Temperature‐dependent CD spectra of A1 and A2 in water depict an isodichroic point reflecting coexistence of two conformations, PPII and β‐strand conformation, which is consistent with the previous studies. The results illuminate the effect of N‐terminal diproline and charged side chains in dictating the preferences for extended‐β, semi‐extended PPII and helical conformation in alanine‐based short peptides. The results of the present study will enhance our understanding on stabilization of helical conformation in short peptides and hence aid in the design of novel peptides with helical structures. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.     

Differential effect of amino acid residues on the stability of double helices formed from polyribonucleotides and its possible relation to the evolution of the genetic code

Summary The interaction of amino acid residues with polyribonucleotides was characterized by measurements of melting temperatures (t_m) for poly(A) poly(U) and poly(I)poly(C) as functions of the concentrations of various amino acid amides. The amides of hydrophilic amino acids lead to a continuous increase of tm with increasing concentration, whereas amides of hydrophobic amino acids induce a decrease of t_m at low concentrations (1 mM) followed by an increase at higher concentrations. Analysis of the data by a simple site model provides the affinity of each ligand for the double helix relative to that for the single strands. This parameter decreases in the order Ala>Gly>Ser>Asn>Pro>Met, Val>Ile, Leu for poly(A) poly(U) and Ala, Gly, Ser>Asn>Pro>Val>Ile, Met, Leu for poly(I)poly(C). The special effects of hydrophobic amino acids may be related to the similarity of the codons for these amino acids. A simple model for assignment of codons to amino acids is proposed.     

Effects of L-alanine and L-alanine peptides on the chemotaxis of tetrahymena: Evolutionary conclusions

L-alanine and its peptides (L-Ala-2–6) do not attract or repulse Tetrahymena in a 10^–8M concentration. In 10^–10M concentration there is a consistent repellent effect. Twenty four hours after L-alanine or L-alanine-peptides' pretreatment (imprinting) the progeny generation of the cells react differently to the same materials. L-Alanine, L-alanine penta- and hexapeptide in both concentrations are chemoattractant, while L-alanine tetrapeptide is repellent. L-Alanine dipeptide is inert in 10^–10M and repellent at 10^–8M concentrations, while L-alanine tripeptide is strongly repellent at 10^–10M and attractant at 10^–8M concentrations. This means, that the first encounter (imprinting) with an exogeneous amino acid or peptide is decisive to the later reaction of the protozoan cell. The chain length is important in the imprinting, however the reaction is not consistent. The experiments call the attention to the significance of imprinting in the receptor and hormone evolution.     

Terminal effect of chiral residue on helical screw sense in achiral peptides

To understand the terminal effect of chiral residue for determining a helical screw sense, we adopted five kinds of peptides I – V containing N‐ and/or C‐terminal chiral Leu residue(s): Boc–L ‐Leu–(Aib–ΔPhe)₂–Aib–OMe ( I ), Boc–(Aib–ΔPhe)₂–L ‐Leu–OMe ( II ), Boc–L ‐Leu–(Aib–ΔPhe)₂–L ‐Leu–OMe ( III ), Boc–D ‐Leu–(Aib–ΔPhe)₂–L ‐Leu–OMe ( IV ), and Boc–D ‐Leu–(Aib–ΔPhe)₂–Aib–OMe ( V ). The segment –(Aib–ΔPhe)₂– was used for a backbone composed of two “enantiomeric” (left‐/right‐handed) helices. Actually, this could be confirmed by ¹H‐nmr [nuclear Overhauser effect (NOE) and solvent accessibility of NH resonances] and CD spectroscopy on Boc–(Aib–ΔPhe)₂–Aib–OMe, which took a left‐/right‐handed 3₁₀‐helix. Peptides I – V were also found to take 3₁₀‐type helical conformations in CDCl₃, from difference NOE measurement and solvent accessibility of NH resonances. Chloroform, acetonitrile, methanol, and tetrahydrofuran were used for CD measurement. The CD spectra of peptides I – III in all solvents showed marked exciton couplets with a positive peak at longer wavelengths, indicating that their main chains prefer a left‐handed screw sense over a right‐handed one. Peptide V in all solvents showed exciton couplets with a negative peak at longer wavelengths, indicating it prefers a right‐handed screw sense. Peptide IV in chloroform showed a nonsplit type CD pattern having only a small negative signal around 280 nm, meaning that left‐ and right‐handed helices should exist with almost the same content. In the other solvents, peptide IV showed exciton couplets with a negative peak at longer wavelengths, corresponding to a right‐handed screw sense. From conformational energy calculation and the above ¹H‐nmr studies, an N‐ or C‐terminal L ‐Leu residue in the lowest energy left‐handed 3₁₀‐helical conformation was found to take an irregular conformation that deviates from a left‐handed helix. The positional effect of the L ‐residue on helical screw sense was discussed based on CD data of peptides I – V and of Boc–(L ‐Leu–ΔPhe)_n–L ‐Leu–OMe (n = 2 and 3). © 1999 John Wiley & Sons, Inc. Biopoly 49: 551–564, 1999     

Influence of lysine residue in amphipathic helical peptides on targeted delivery of RNA into cancer cells

The cRGD-conjugated Aib-containing amphipathic helical peptide, MAP(Aib) derivative (PI), has been reported to be a useful carrier for siRNA delivery into cells. We have conducted a series of structure-activity relationship studies of the influence of the balance between hydrophobicity and basicity on the amphipathicity of PI, and synthesized peptides having a larger number of Lys residues than PI. Increasing the number of basic residues in the amphipathic helix suppressed the ability to deliver siRNA into cells. It was concluded that the balance between hydrophobicity and basicity in the PI helix was important for siRNA delivery into cells. Furthermore, the siRNA delivering ability of PI was specific to cancer cells, such as A549, U-87 MG, and WiDr cells, and was low in normal cells, namely, NIH3T3 cells. Next, we examined the potential of PI as a carrier for the delivery of microRNA-133b (miR-133b), which is known to be an anti-oncomiR. PI enhanced the delivery of miR-133b into WiDr cells, which resulted in the suppression of endogenous protein expression.     

肺内调节肽对兔支气管上皮细胞与嗜酸性粒细胞粘附功能的影响及机制探讨

为了探讨肺内调节肽在各类过敏性炎症发生,发展中的作用,我们观察了血管活性肠肽（vasoactive intestinal peptide,VIP)、表皮生长因子（epidermal growth factor,EGF)、内皮素-1（endothelin-1,ET-1)、降钙素基因相关肽（calcitonin gene-related peptide,CGRP)在未受应激与臭氧应激两种条件下对支气管上皮细胞（bronchial epithelial cell,BEC)与嗜酸性粒细胞（eosinophil,EOS)粘附的影响,结果发现,VIP、EGF可使O3应激的BEC与EOS的粘附率下降,下调气道上皮炎症反应：ET-1、CGRP可使未受应激的BEC与EOS的粘附率增加,诱发炎症损伤反应;CGRP还能加重臭氧的应激反应;ET-1、CGRP的效应可被W7、H7阻断,抗细胞间粘附分子-1（intercel-lular adhesion molecule,ICAM-1)抗体能阻断BEC与EOS的粘附,提示介导BEC与EOS粘附的粘附分子可能是ICAM-1。     

基于植被羰基硫通量估算陆地生态系统总初级生产力研究进展

羰基硫(COS)是大气中的长周期痕量气体,其分子结构、对流层大气混合比的昼夜和季节动态类似于二氧化碳(CO₂)。植物光合作用及其水解过程中,受扩散通路导度和酶活性影响,气孔的COS与CO₂吸收紧密相关,同时,植物自养呼吸并不释放COS。最新研究中,采用植被COS通量直接指示生态系统总初级生产力(GPP)。综述了植被COS通量与光合作用中碳固定过程的关联机制,以及采用涡度相关观测、整合大气COS监测和生态系统过程模型等方法开展植被COS通量与GPP研究的最新进展,探讨了关键生态过程和参数,发现方法存在以下瓶颈：(1)生理过程、尺度效应和解析效应影响了COS与CO₂的叶片相对吸收率,(2)观测与模拟手段有待进一步耦合,(3)全球COS观测密度限制了方法验证,(4)硫循环过程影响了多区域模拟精度。方法发展的前沿领域包括：(1)开展重点地区植被COS通量观测,(2)提高COS卫星柱浓度的覆盖范围,(3)完善生态系统过程模型的COS吸收机理。展望未来研究关注的科学问题是：对于亚热带等尚待开展COS连续观测的区域,采用植被COS通量...     

Facile transition between 3(10)- and alpha-helix: structures of 8-, 9-, and 10-residue peptides containing the -(Leu-Aib-Ala)2-Phe-Aib- fragment.

A structural transition from a 3(10)-helix to an alpha-helix has been characterized at high resolution for an octapeptide segment located in 3 different sequences. Three synthetic peptides, decapeptide (A) Boc-Aib-Trp-(Leu-Aib-Ala)2-Phe-Aib-OMe, nonapeptide (B) Boc-Trp-(Leu-Aib-Ala)2-Phe-Aib-OMe, and octapeptide (C) Boc-(Leu-Aib-Ala)2-Phe-Aib-OMe, are completely helical in their respective crystals. At 0.9 A resolution, R factors for A, B, and C are 8.3%, 5.4%, and 7.3%, respectively. The octapeptide and nonapeptide form ideal 3(10)-helices with average torsional angles phi(N-C alpha) and psi(C alpha-C') of -57 degrees, -26 degrees C and -60 degrees, -27 degrees for B. The 10-residue peptide (A) begins as a 3(10)-helix and abruptly changes to an alpha-helix at carbonyl O(3), which is the acceptor for both a 4-->1 hydrogen bond with N(6)H and a 5-->1 hydrogen with N(7)H, even though the last 8 residues have the same sequence in all 3 peptides. The average phi, psi angles in the decapeptide are -58 degrees, -28 degrees for residues 1-3 and -63 degrees, -41 degrees for residues 4-10. The packing of helices in the crystals does not provide any obvious reason for the transition in helix type. Fourier transform infrared studies in the solid state also provide evidence for a 3(10)- to alpha-helix transition with the amide I band appearing at 1,656-1,657 cm-1 in the 9- and 10-residue peptides, whereas in shorter sequences the band is observed at 1,667 cm-1.     

太阳辐射减弱对冬小麦旗叶光合速率的影响

以冬小麦扬麦13号为供试材料,设计了15%(T₁₅)、20%(T₂₀)、40%(T₄₀)、60%(T₆₀)和100%（CK）自然光5个处理,在大田条件下研究了模拟太阳辐射减弱对
冬小麦旗叶光合速率日变化及其影响因素的影响.结果表明：太阳辐射减弱显著提高了冬小麦叶绿素和叶黄素含量,降低了光合速率（P_n）.不同辐射减弱条件下冬小麦P_n日变化差异较大,日最高值表现为CK＞60%自然光＞40%自然光＞20%自然光＞15%自然光,其中CK呈双峰曲线变化,有明显的“午休”现象,其他各处理均呈单峰型曲线变化,“午休”现象不明显,但峰值出现时间滞后.相关分析表明,太阳辐射减弱是影响P_n日变化的主导因子,但其他因子也显著影响P_n.与CK相比,60%和40%自然光处理中光合有效辐射（PAR）、叶温（T_l）、气孔导度（G_s）和蒸腾速率（T_r）与P_n均呈显著正相关,表明上述因子对P_n有正效应;冬小麦叶片胞间二氧化碳浓度（C_i）和气孔导度限制值（L_s）在60%和40%自然光处理中与P_n呈显著负相关,但在20%和15%自然光处理中与P_n呈显著正相关,说明太阳辐射强度高于40%自然光时C_i和L_s对P_n有负效应,太阳辐射强度低于40%自然光时则为正效应.     

The increasing effect of some synthetic peptides on luminol-dependent chemiluminescence of mouse blood

Some synthetic peptides increased the luminol-dependent chemiluminescence of mouse blood during phagocytosis. It is suggested that the levels of antimicrobial activity of the neutrophil peroxidase system can be raised very quickly (within some dozen of seconds) by these peptides. This raises the possibility of finding a new approach to the therapy for infectious diseases.     

Effects of phthalic anhydride modification on horseradish peroxidase stability and activity

Phthalic anhydride (PA) modification stabilizes horseradish peroxidase (HRP) by reversal of the positive charge on two of HRP's six lysine residues. Native and PA-HRP had half-inactivation temperatures of 51 and 65 degrees C and half-lives at 65 degrees C of 4 and 17 min, respectively. PA-HRP was more resistant to dimethylformamide at room temperature and tetrahydrofuran at 60 degrees C and to unfolding by heat, guanidine chloride, EDTA, and the reducing agent tris(2-carboxyethyl)phosphine hydrochloride. Binding of the hydrophobic probe Nile Red to the native enzyme and to PA-HRP was similar. The kinetics of both HRPs with the substrates ABTS, ferrocyanide, ferulic acid, and indole-3-propionic acid were measured, as was binding of the inhibitor benzhydroxamic acid. Small improvements in the catalytic properties were detected.     

Effects of myoinhibitory peptides on food intake in the German cockroach

Abstract.  Insect myoinhibitory peptides were discovered through their inhibitory activity on visceral muscle contraction. The present study tests the antimyotropic gut properties of three galanin-related myoinhibitory peptides (Mas-MIP II: GWQDLNSAW-NH2; Grb-AST-B1: GWQDLNGGW-NH₂; and Grb-AST-B3: AWRDLSGGW-NH2) in adult females of the cockroach Blattella germanica (L.) (Dictyoptera, Blattellidae). The three peptides elicit a strong inhibitory effect on both foregut and hindgut contractions, with ID₅₀ values in all the cases within the nanomolar range. In addition, the modulatory effects of these three peptides on food intake are studied on previously starved female cockroaches. The results show that Grb-AST-B3 is the most active peptide, inhibiting food intake by 60–80% at doses between 15 and 50 µg, followed by Grb-AST-B1 (45% inhibition of food intake at the 50 µg dose), whereas Mas-MIP II is inactive even at the 50 µg dose. The differences between the three peptides may be due to a differential effect of their structure on activity or to a differential degradation. These results show that myomodulatory gut activity in vitro and antifeeding effects do not always correlate.