计算肽学

肽作为重要的生理活性物质一直受到相关领域的广泛关注。近年来,由于肽在细胞信号转导中所扮演的中心角色以及作为生物药物靶向蛋白质相互作用网络等特殊性质的发现,再次唤起了人们对肽的浓厚兴趣。与之相伴的是,肽的理论和计算研究工作快速增长,并取得了长足进展。本文以“计算肽学”为主题系统概括了该领域的研究范畴和研究特点,并分别从肽的数据库构建、功能活性预测、分子对接、动力学模拟、结构数据分析、分子设计修饰以及系统生物学行为等几方面分类介绍了计算肽学的主要研究方向和当前发展状况。重点在于探讨采用计算化学和生物信息学方法剖析肽与蛋白质识别和相互作用的分子机制和理化基础,进而为肽类药物设计提供理论指导。此外,本文还提出了计算肽学在肽类纳米材料及生物表面活性剂等领域的潜在应用前景。     

小分子玉米肽Leu-Asp-Tyr-Glu保护线粒体抗氧化损伤的研究

线粒体是细胞内氧代谢的主要场所,其膜上富含不饱和脂肪酸,使得线粒体成为自由基进攻的主要靶部位^[1].自由基作用于线粒体膜发生脂质过氧化损伤反应,引起膜的结构与功能改变,使得膜上一系列重要的酶空间排列紊乱,活性降低,膜的通透性改变,诱发多种疾病^[2].目前,抗氧化肽类作为一种非酶类自由基清除剂的研究正在兴起^[3].来源于玉米醇溶蛋白酶降解物中的低分子量肽具有许多重要的生理功能,如促进乙醇代谢、抗疲劳作用以及降血脂等功效^[4].而这些功能的实现主要依赖于其抗氧化活性^[5].最近,我们从玉米蛋白酶解物中获得了一种新的小分子抗氧化肽Leu-Asp-Tyr-Glu(LD YE,LD YE经文献检索为一种新的寡肽)^[6].     

壳聚糖膜固定生物活性短肽RGDS的研究

为改善壳聚糖对细胞的特异性吸附,采用水溶性碳二亚胺将生物活性短肽精氨酸-甘氨酸-天冬氨酸-丝氨酸(RGDS)固定到壳聚糖膜的表面,采用X射线光电子能谱检测固定多肽前后的壳聚糖膜表面,发现反应后壳聚糖膜表面氮元素含量增大,Nls和Cls曲线拟合谱中酰胺键增多,表明RGDS短肽已固定到壳聚糖膜的表面;人角膜缘上皮细胞体外培养实验表明,固定RGDS后壳聚糖膜的细胞黏附率有了明显提高,固定RGDS后的壳聚糖膜在角膜组织工程支架等方面有更好的应用潜力。     

谷胱甘肽和凋亡酶-3响应的环肽分子荧光探针

设计、合成了一类新型谷胱甘肽(glutathione,GSH)和凋亡酶-3(Caspase-3)响应的环肽分子荧光探针.该类探针主要由能量共振转移(FRET)分子荧光对、Caspase-3特异性识别多肽序列和GSH响应双硫键组成,分为不含穿膜肽序列(CP)和包含穿膜肽序列(cp CP)的两种不同环肽分子荧光探针.2种环肽分子荧光探针均能实现在GSH和Caspase-3同时存在情况下的精确成像,同时具有良好的响应性、特异性和高信噪比.该类环肽分子荧光探针在细胞培养环境中具有良好的稳定性和生物相容性.利用该探针,可以实现对星形孢菌素(STS)诱发的细胞凋亡进行实时、原位的成像监测,并对抗肿瘤药物阿霉素(DOX)和顺铂(cisplatin)诱导的细胞凋亡进行成像.这种具有多重响应并能用于精确成像的分子荧光探针将极大地促进疾病的精确诊断.     

具有抗炎、抗过敏活性磷脂酶抑制剂的研究进展

磷脂酶参与细胞跨膜信息传递, 磷脂酶A2 还是机体炎症、过敏介质产生的关键酶。因此, 磷脂酶抑制剂的合成研究对研究细胞表达某种功能的信息传递机制及与磷脂酶A2 激活相关的疾病治疗机制和药物研究具有重要意义。本文主要综述了近期有关磷脂酶A2 抑制剂的合成、结构、抑效性能、构效关系及应用前景等, 对磷脂酶C和磷脂酶D的抑制剂作了简要介绍。     

非水相酶促肽合成的研究进展

生物活性肽 ,特别是寡肽 ,在免疫调节、激素调节、酶抑制、抗菌、抗病毒等方面有很大的应用潜力[1] .另外 ,调味肽也越来越显示出其在应用上的重要性 .肽作为一种终产品或者前体物质 ,在食品和药物生产上的商业潜力非常巨大 ,从而促进了肽合成的研究和发展 .目前肽合成主要有 3种方法 :化学法、重组DNA技术、酶法 .每种方法都有其优点和缺点 .总体上来说 ,在工业上化学法仍然使用得最多 ,其热力学动力学模型已经很好地建立起来 ;重组 DNA技术 ,由于需要一个长期、昂贵的研究和发展阶段 ,而且在发酵阶段存在表达效率低和产品提取回收困难…     

不同的引导肽对丝状噬菌体基因8蛋白展示外源多肽的影响

为了研究不同的引导肽对在基因8蛋白上展示外源多肽的影响,利用基因工程方法将一短肽插入基因8蛋白的N端,并将引导多肽去除或用基因3蛋白的引导肽序列替代基因8的引导肽序列.采用放射性脉冲追踪技术检测不同的引导肽对在基因8蛋白上展示外源多肽的作用.结果表明,无引导肽序列的引导,蛋白前体无法向成熟蛋白转化.基因3蛋白的引导肽可以引导展示有外源多肽的基因8蛋白,完成从前体向成熟蛋白的转化,但转化率明显下降.研究结果对阐明噬菌体外壳蛋白在大肠杆菌中的跨膜机制具有重要的意义.     

硅基底金纳米粒子微阵列电极的制备及其电化学性质的研究— 多孔硅电致发光 生物传感器研究的前期探索

用Frens法制备了不同粒径的金纳米粒子,并用透射电镜、紫外可见分光光度法进行了表征。用自组装技术得到了金膜电极表面的金纳米粒子二维阵列电极,用扫描电镜、电化学等方法对该微阵列电极进行了表征。结果表明,当金电极表面被自组装膜完全覆盖后,电化学反应不再发生,而将金纳米粒子组装到膜上以膈,才得到电化学信号。我们认为,金纳米粒子在这里对电荷的跨膜转移有很强的促进作用。对于该过程的研究,用助于理解电荷的转移机制,对进一步理解电荷隧穿过程有一定的指导意义。     

化妆品中的肽化学*

随着科技进步和产业提升,人们不断从本源上追求美、从长效上保持美、从机制上激发美。众多肽类化合物,已被证实在人体内具有独特的生物学促进或抑制作用,也因此被广泛应用于美妆产品。以化妆品中生物活性肽的不同功效为主线,对其化学结构进行分析并阐述其中的生理作用机制。     

人神经母细胞瘤的磷酸化膜蛋白质组分析

针对人神经母细胞瘤SH-SY5Y细胞系的磷酸化膜蛋白质组,发展了基于多酶酶解法结合杂化硅胶基质固定化钛离子亲和色谱(Ti4+-IMAC)整体柱富集的分析策略。该方法通过对细胞裂解液进行超速离心,以及1 mol/L NaCl和0.1 mol/L Na2CO3顺序清洗,获得膜蛋白质组分。所提取的蛋白质分别经胰蛋白酶、胰凝乳蛋白酶和胃蛋白酶平行酶解,产生的肽段经Ti4+-IMAC整体柱选择性富集磷酸肽后,采用纳升级反相液相色谱分离和质谱鉴定,成功鉴定到43个磷酸化蛋白质,其中有14个定位于膜上。研究结果表明,采用该策略开展SH-SY5Y细胞系磷酸化膜蛋白质组学分析有望加速对该肿瘤的研究和相关潜在标记物的筛选。     

An efficient method for the solid-phase synthesis of fluorescently labelled peptides

Fluorescent labelling of peptides is necessary in a wide range of cell biological applications. In the last decade, the application of cell-penetrating molecules has been advanced by the use of peptides, which have proven efficient in aiding nonpermeant molecules to cross the cell membrane. Currently, the development of new cell-penetrating peptides based on the design and synthesis of labelled peptide libraries is becoming critically important. Here we report an improved method for the solid-phase labelling of peptides, mediated by the activation of 5(6)-carboxyfluorescein with PyAOP/ HOAt.     

Inverted micelle formation of cell-penetrating peptide studied by coarse-grained simulation: importance of attractive force between cell-penetrating peptides and lipid head group

Arginine-rich peptide and Antennapedia are cell-penetrating peptides (CPPs) which have the ability to permeate plasma membrane. Deformation of the plasma membrane with CPPs is the key to understand permeation mechanism. We investigate the dynamics of CPP and the lipid bilayer membrane by coarse-grained simulation. We found that the peptide makes inverted micelle in the lipid bilayer membrane, when the attractive potential between the peptide and lipid heads is strong. The inverted micelle is formed to minimize potential energy of the peptide. For vesicle membrane, the peptide moves from the outer vesicle to the inner vesicle through the membrane. The translocation of the peptide suggests inverted micelle model as a possible mechanism of CPPs.     

A dimerization "switch" in the internalization mechanism of a cell-penetrating peptide

The internalization mechanism of a cell-penetrating peptide has been explored through combinatorial selection of a phage-displayed peptide dimer library, chemical synthesis, and biophysical characterization. Both energy-dependent and energy-independent modes for peptide uptake by the target mammalian cells were observed, suggesting a role for higher-order structure in modulating the action of this novel cell-penetrating peptide.     

Photoinduced Endosomal Escape Mechanism: A View from Photochemical Internalization Mediated by CPP-Photosensitizer Conjugates

Endosomal escape in cell-penetrating peptide (CPP)-based drug/macromolecule delivery systems is frequently insufficient. The CPP-fused molecules tend to remain trapped inside endosomes and end up being degraded rather than delivered into the cytosol. One of the methods for endosomal escape of CPP-fused molecules is photochemical internalization (PCI), which is based on the use of light and a photosensitizer and relies on photoinduced endosomal membrane destabilization to release the cargo molecule. Currently, it remains unclear how this delivery strategy behaves after photostimulation. Recent findings, including our studies using CPP-cargo-photosensitizer conjugates, have shed light on the photoinduced endosomal escape mechanism. In this review, we discuss the structural design of CPP-photosensitizer and CPP-cargo-photosensitizer conjugates, and the PCI mechanism underlying their application.     

TAT peptide internalization: seeking the mechanism of entry

During the last decade several peptides have been extensively studied for their ability to translocate across the plasma membrane. These peptides have been called "cell penetrating peptides" (CPP) or "protein transduction domains" (PTD). These peptides also promote the cellular uptake of various cargo molecules. Their mechanism of cellular entry appeared very intriguing since most publications in the field highlighted an energy-independent process. Indeed, cellular uptake of these peptides was still observed by fluorescence microscopy at low temperature or in the presence of several drugs known to inhibit active transport. In addition, internalization was reported to be much faster than known endocytic processes. However the involvement of a specific cellular component responsible for this uptake process appeared unlikely following intensive structure activity relationship studies using a wide panel of Tat analogues. Several reports about a possible artefactual redistribution of CPPs, and their associated cargos, during the cell fixation step commonly used for fluorescence microscopy have recently emerged in the literature. Moreover strong ionic interactions of CPPs with the cell surface also led to an overestimation of the recorded cell-associated fluorescent signal. It now seems well established that arginine-rich peptides are internalized by an energy dependent process involving endocytosis. Whatever the case, however, an increasing number of data indicate that the conjugation of non-permeant molecules to these CPPs allows their cellular uptake and leads to the expected biological responses, thus pointing to the interest of this delivery strategy. However, initial structure activity relationship studies of these CPPs will have to be reconsidered and the relative potency of each peptide (and their analogues) to vectorize the cargos to their most appropriate subcellular compartment will require careful re-evaluation.     

Cell–Membrane Penetration of Tat‐Conjugated Polymeric Micelles: Effect of Tat Coating Density

Considerable efforts have been devoted to enhancing the cell penetration of nanoparticles by coating cell‐penetrating peptides (CPPs) on the surface. However, the internalization mechanism for a CPP at different concentrations varies a lot. It is acknowledged that the mechanism is restricted to endocytic pathway at relatively low concentrations; however, direct translocation becomes dominant at high concentrations. This raises an interesting question on how the surface Tat coating density of the nanoparticles would influence their cell–membrane interaction and the consequent internalization behavior. This study systematically investigates the effect of Tat peptides on the internalization behavior of polymeric micelles by tuning surface Tat coating density, incubation concentrations, incubation time, and other factors using poly(ethylene glycol)–poly(ε‐caprolactone) copolymer (PEG‐PCL) micelles. It is found that both energy‐dependent and energy‐independent pathways are involved in the cellular uptake process, and the Tat‐conjugated polymeric micelles strongly accumulated on the cell surface at initial stage. The membrane‐anchoring and internalization rate increase with the increasing Tat coating density. Furthermore, the increasing of Tat coating density accelerates the energy‐independent pathway. It is envisioned that this finding will further shed light on the surface modification of nanoparticles for enhanced cell penetration and direct translocation into cell cytoplasm.     

Cell-Penetrating Peptides: Correlation between Peptide-Lipid Interaction and Penetration Efficiency

Cell-penetrating peptides are used in the delivery of peptides and biologics, with some cell-penetrating peptides found to be more efficient than others. The exact mechanism of how they interact with the cell membrane and penetrate it, however, remains unclear. This study attempts to investigate the difference in free energy profiles of three cell-penetrating peptides (TAT, CPP1 and CPP9) with a model lipid bilayer (DOPC) using molecular dynamics pulling simulations with umbrella sampling. Potential mean force (PMF) and free energy barrier between the peptides and DOPC are determined using WHAM analysis and MM-PBSA analysis, respectively. CPP9 is found to have the smallest PMF value, followed by CPP1 and TAT, consistent with the experimental data. YDEGE peptide, however, does not give the highest PMF value, although it is a non-cell-permeable peptide. YDEGE is also found to form water pores, alongside with TAT and CPP9, suggesting that it is difficult to distinguish true water pore formation from artefacts arising from pulling simulations. On the contrary, free energy analysis of the peptide-DOPC complex at the lipid-water interface with MM-PBSA provides results consistent with experimental data with CPP9 having the least interaction with DOPC and lowest free energy barrier, followed by CPP1, TAT and YDEGE. These findings suggest that peptide-lipid interaction at the lipid-water interface has a direct correlation with the penetration efficiency of peptides across the lipid bilayer.     

Energy-independent intracellular gene delivery mediated by polymeric biomimetics of cell-penetrating peptides

Efficient gene transfer into mammalian cells mediated by small molecular amphiphile-polymer conjugates, bile acid-polyethylenimine (BA-PEI), is demonstrated, opening an efficient transport route for genetic materials across the cell membrane. This process occurs without the aid of endocytosis or other energy-consuming processes, thus mimicking macromolecular transduction by cell-penetrating peptides. The exposure of a hydrophilic face of the amphiphilic BA moiety on the surface of BA-PEI/DNA complex that mediates direct contact of the BA molecules to the cell surface seems to play an important role in the endocytosis- and energy-independent internalization process. The new modality of the polymeric biomimetics can be applied to enhanced delivery of macromolecular therapeutics.     

The Combined Use of Gold Nanoparticles and Infrared Radiation Enables Cytosolic Protein Delivery

Cytosolic protein delivery remains elusive. The inability of most proteins to cross the cellular membrane is a huge hurdle. Here we explore the unique photothermal properties of gold nanorods (AuNRs) to trigger cytosolic delivery of proteins. Both partners, protein and AuNRs, are modified with a protease-resistant cell-penetrating peptide with nuclear targeting properties to induce internalization. Once internalized, spatiotemporal control of protein release is achieved by near-infrared laser irradiation in the safe second biological window. Importantly, catalytic amounts of AuNRs are sufficient to trigger cytosolic protein delivery. To the best of our knowledge, this is the first time that AuNRs with their maximum of absorption in the second biological window are used to deliver proteins into the intracellular space. This strategy represents a powerful tool for the cytosolic delivery of virtually any class of protein.     

Macrocyclic peptides as regulators of protein-protein interactions

Protein-protein interactions are attractive but challenging targets for drug discovery. Recent technological progress and examples using macrocyclic peptides as protein interaction modulators are reviewed.