分析蛋白质-蛋白质相互作用界面的新方法

疏水性和氢键是蛋白质-蛋白质相互作用中的主要因素.提出一种新的计算方法，从蛋白受体的结合部位推导出蛋白配体相应部位应该具有的疏水性质和氢键性质.应用这种方法可以很容易地找出影响相互作用的关键残基，并且将界面的这两种特征用图形软件显示出来.在应用到实际蛋白-蛋白相互作用中时，发现它的用途并不限于此.它可以作为研究蛋白相互作用的一个基本工具.     

蛋白质相互作用: 界面分析, 结合自由能计算与相互作用设计

蛋白质相互作用在生命活动中起着重要作用. 研究蛋白质间相互作用的本质有助于了解生命活动中这些基本单元的作用. 本文主要综述了近期蛋白质相互作用研究的进展, 包括蛋白质相互作用界面的基本性质, 蛋白质结合自由能的计算方法, 不同相互作用在蛋白质结合/解离中的角色和差异, 以及上述知识在蛋白质相互作用设计中的应用. 蛋白质相互作用界面的特性, 例如界面大小、保守性以及结构的动态性质, 使得具有生物功能的蛋白质相互作用界面区别于非特异性的晶体堆积界面. 生物功能界面的一个重要结构特征是界面上存在着关键残基以及相对独立的相互作用模块. 利用多种方法, 如MM-PBSA、统计平均势以及不同的相互作用自由能模型, 可以在不同的精度上计算蛋白质相互作用自由能. 利用蛋白质相互作用界面的特点, 从不同的角度进行蛋白质相互作用对的设计与改造, 近年来已经有了不少成功的例子, 但还存在着很大的挑战. 我们认为在今后的蛋白质相互作用设计中, 考虑各种因素对蛋白质结合与解离的动力学过程的影响将有助于提高人类控制蛋白质相互作用的能力.     

海藻糖和氨基酸之间相互作用的分子动力学模拟

虽然海藻糖已经广泛用于蛋白质稳定性研究,但海藻糖稳定蛋白质的作用机理尚不清晰. 本文利用全原子分子动力学模拟研究了20种常见氨基酸和海藻糖之间的分子机理. 结果表明,所有氨基酸,尤其是极性和带电氨基酸,均优先与水分子结合. 相反,仅有疏水性氨基酸与海藻糖发生相互作用,尤其是芳香族和疏水性氨基酸的侧链更易于和海藻糖接触. 所有氨基酸的主链与水分子接触的趋势一致. 虽然氨基酸和海藻糖与水之间均形成氢键,但氨基酸和海藻糖之间的氢键相互作用要弱于氨基酸和水之间的氢键相互作用. 上述分子模拟的结果对于海藻糖稳定蛋白质作用机理的解析及高效蛋白质稳定剂的理性设计具有非常重要的理论指导意义.     

海藻糖和氨基酸之间相互作用的分子动力学模拟

虽然海藻糖已经广泛用于蛋白质稳定性研究,但海藻糖稳定蛋白质的作用机理尚不清晰.本文利用全原子分子动力学模拟研究了20种常见氨基酸和海藻糖之间的分子机理.结果表明,所有氨基酸,尤其是极性和带电氨基酸,均优先与水分子结合.相反,仅有疏水性氨基酸与海藻糖发生相互作用,尤其是芳香族和疏水性氨基酸的侧链更易于和海藻糖接触.所有氨基酸的主链与水分子接触的趋势一致.虽然氨基酸和海藻糖与水之间均形成氢键,但氨基酸和海藻糖之间的氢键相互作用要弱于氨基酸和水之间的氢键相互作用.上述分子模拟的结果对于海藻糖稳定蛋白质作用机理的解析及高效蛋白质稳定剂的理性设计具有非常重要的理论指导意义.     

蛋白质-蛋白质分子对接中打分函数研究进展

分子对接是研究分子间相互作用与识别的有效方法.其中,用于近天然构象挑选的打分函数的合理设计对于对接中复合物结构的成功预测至关重要.本文回顾了蛋白质-蛋白质分子对接组合打分函数中一些主要打分项,包括几何互补项、界面接触面积、范德华相互作用能、静电相互作用能以及统计成对偏好势等打分项的计算方法.结合本研究小组的工作,介绍了目前普遍使用的打分方案以及利用与结合位点有关的信息进行结构筛选的几种策略,比较并总结了常用打分函数的特点.最后,分析并指出了当前蛋白质-蛋白质对接打分函数所存在的主要问题,并对未来的工作进行了展望.     

蛋白质中氨基酸残基和肽片段间的特异识别研究

本文从蛋白质晶体数据库中选取了125种非同源蛋白质,对其平行和反平行相互作用肽片段中残基间的亲和性进行了统计分析,得到了氨基酸残基和肽片段间的配对规律.本文所报道的残基间配对亲和性可用于蛋白质的折叠计算、结构预测和蛋白质工程实验设计中.     

载体材料与蛋白质的相互作用及对其构象的影响

蛋白质与载体材料间存在着疏水性、静电等相互作用力。这些作用力不仅决定了蛋白质分子在载体表面吸附的数量,也导致吸附蛋白质分子构象发生变化,引起蛋白质活性的改变。蛋白质的特性(分子量和浓度等)、载体材料的表面结构(表面化学组成和物理结构等)及溶液性质(pH和离子强度等)对蛋白质与载体材料间的相互作用产生影响。利用各种先进的分析技术对载体材料表面的蛋白质分子构象进行表征是这一研究领域的热点。本文对这一方面的最新研究进展进行综述。     

豆浆凝固过程中大豆蛋白质二级结构的研究

用变温ATR-FT-IR测定了豆浆加热、豆浆凝固过程中蛋白质二级结构的变化,结果显示:随着温度的升高,熟豆浆中蛋白质分子间强相互作用氢键(1β)和总相互作用氢键(1β 2β)明显下降,豆浆从20℃升温到80℃时,1β由29.2%下降到16.1%,表明蛋白质分子间的相互作用减弱;豆腐的核心结构(β α)约38.0%变化不大。随豆腐凝胶强度增加,1β由17.4%上升到43.3%,而维持蛋白质紧密结构的氢键(β α)由38.8%下降到17.4%。豆浆凝固过程中1β的变化与其凝胶特性G*变化完全一致,说明蛋白质分子间强相互作用氢键与豆腐的硬度有关。     

纳米材料-蛋白质界面相互作用的分子机制

纳米材料由于其优异的性能在化工、电子、机械、环境、能源、航天等各个领域已经得到了广泛的应用,并且在生物医学方面的应用越来越受到重视。纳米材料-蛋白质界面相互作用是纳米生物医学领域重要的科学问题,对于纳米材料的生物医学应用以及生物安全性评价至关重要。蛋白质分子与纳米材料在界面的相互作用,一方面可以诱导蛋白质的构象、组装结构甚至功能的改变,另一方面可以引起纳米材料的表面亲疏水性、电荷性质等表面物理化学性质的改变。基于蛋白质与纳米材料相互作用检测技术及结果,本文从分子水平阐述了纳米材料与蛋白质分子在界面之间的相互作用机理及相应的结构与性质的变化,从而可以深化对两者之间复杂的相互作用机制的理解,对于推进纳米材料在生物医学的应用及健康、安全、持续发展具有重要意义。     

金纳米粒子与蛋白质的相互作用及其应用

金纳米粒子与蛋白质间存在多种作用方式,包括物理吸附、化学共价结合以及非共价特异性吸附等.金纳米粒子表面等离子体共振效应引起可见光区的特征吸收及表面增强拉曼散射,常用来研究金纳米粒子与蛋白质间的相互作用.金纳米粒子与蛋白质间的作用与纳米粒子的尺寸、表面化学及蛋白质的大小、电荷、氨基酸残基有关.利用金纳米粒子与蛋白质的相互作用及纳米金的谱学性质,可以对疾病或环境污染进行简单、高效、低成本检测,也可用于疾病治疗.     

Characterizing hydrophobicity at the nanoscale: a molecular dynamics simulation study

We use molecular dynamics (MD) simulations of water near nanoscopic surfaces to characterize hydrophobic solute-water interfaces. By using nanoscopic paraffin like plates as model solutes, MD simulations in isothermal-isobaric ensemble have been employed to identify characteristic features of such an interface. Enhanced water correlation, density fluctuations, and position dependent compressibility apart from surface specific hydrogen bond distribution and molecular orientations have been identified as characteristic features of such interfaces. Tetrahedral order parameter that quantifies the degree of tetrahedrality in the water structure and an orientational order parameter, which quantifies the orientational preferences of the second solvation shell water around a central water molecule, have also been calculated as a function of distance from the plate surface. In the vicinity of the surface these two order parameters too show considerable sensitivity to the surface hydrophobicity. The potential of mean force (PMF) between water and the surface as a function of the distance from the surface has also been analyzed in terms of direct interaction and induced contribution, which shows unusual effect of plate hydrophobicity on the solvent induced PMF. In order to investigate hydrophobic nature of these plates, we have also investigated interplate dewetting when two such plates are immersed in water.     

WATGEN: an algorithm for modeling water networks at protein-protein interfaces

Water molecules at protein-protein interfaces contribute to the close packing of atoms and ensure complementarity between the protein surfaces, as well as mediating polar interactions. Therefore, modeling of interface water is of importance in understanding the structural basis of biomolecular association. We present an algorithm, WATGEN, which predicts locations for water molecules at a protein-protein or protein-peptide interface, given the atomic coordinates of the protein and peptide. A key element of the WATGEN algorithm is the prediction of water sites that can form multiple hydrogen bonds that bridge the binding interface. Trial calculations were performed on water networks predicted by WATGEN at 126 protein-peptide interfaces (X-ray resolutions 相似文献   

Dynamics of water confined in the interdomain region of a multidomain protein

Molecular dynamics simulations are performed to study the dynamics of interfacial water confined in the interdomain region of a two-domain protein, BphC enzyme. The results show that near the protein surface the water diffusion constant is much smaller and the water-water hydrogen bond lifetime is much longer than that in bulk. The diffusion constant and hydrogen bond lifetime can vary by a factor of as much as 2 in going from the region near the hydrophobic domain surface to the bulk. Water molecules in the first solvation shell persist for a much longer time near local concave sites than near convex sites. Also, the water layer survival correlation time shows that on average water molecules near the extended hydrophilic surfaces have longer residence times than those near hydrophobic surfaces. These results indicate that local surface curvature and hydrophobicity have a significant influence on water dynamics.     

Protein folding at emulsion oil/water interfaces

It has long been known that proteins change their conformation upon adsorption to emulsion oil/water interfaces. However, it is only recently that details of the specifics of these structural changes have emerged. The development of synchrotron radiation circular dichroism (SRCD), combined with advances in FTIR spectroscopy, has allowed the secondary and tertiary structure of proteins adsorbed at emulsion oil/water interfaces to be studied. SRCD in particular has provided quantitative information and has enabled new insights into the mechanisms and forces driving protein structure re-arrangement to be achieved.The extent of conformational re-arrangement of proteins at emulsion interfaces is influenced by several factors including; the inherit flexibility of the protein, the distribution of hydrophobic/hydrophilic domains within the protein sequence and the hydrophobicity of the oil phase. In general, proteins lose much of their tertiary structure upon adsorption to the oil/water interface and have considerable amounts of non-native secondary structure. Two key conformations have been identified in the structure of proteins at interfaces, intermolecular β-sheet and α-helix. The preferred conformation appears to be the α-helix which is the most compact amphipathic conformation at the oil/water interface. The polarity of the oil phase can have a considerable influence on the degree of protein conformational re-arrangement because it acts as a solvent for hydrophobic amino acids. The new conformation of proteins at interfaces also means that proteins undergo less heat induced re-arrangement at interfaces than in solution. Different conformations of proteins at interfaces impact on emulsification capability, emulsion stability and protein/emulsion digestion. Hence advances in the understanding of protein conformation at interfaces can help to identify suitable proteins and conditions for the preparation of emulsion based food products.     

PET suppression of acridinedione dyes by urea derivatives in water and methanol

Spectroscopic investigations involving the interaction of acridinedione dyes with urea and its derivatives in water and methanol were carried out by absorption, steady-state fluorescence, and time-resolved fluorescence measurements. The hydrogen-bonding properties of urea and derivatives in aqueous solutions are found to be distinctly different from those observed in methanol. Urea, which can serve both as a hydrogen bond donor as well as an acceptor and has a unique hydrogen-bonding feature, helps in studying urea interaction with fluorophores in aqueous solutions, micelles, and alcohol. In our studies, we have used acridinedione dyes as the probe. We report that the hydrophobic interaction of urea with dye predominates by weakening of the hydrogen-bonding interaction of the solvent and urea derivatives with increase in the hydrophobicity of urea derivatives. In methanol, the hydrogen bonding between solvent and urea derivatives predominating over the hydrophobicity of the urea derivatives is observed. The presence of alkyl group substitution in the N-H moiety with a function of increasing concentration resulting in the creation of a more favorable hydrophobic environment to the dye molecule to reside in the hydrophobic shell phase rather than in the bulk aqueous phase is illustrated. The hydrophobic interaction of dye with urea in aqueous solution predominates because of the weakening of the hydrogen bonding of the solvent and urea derivatives, and the photoinduced electron transfer (PET) process is used as a marker to identify the hydrophobic interaction illustrated in our studies.     

A strategy based on protein-protein interface motifs may help in identifying drug off-targets

Networks are increasingly used to study the impact of drugs at the systems level. From the algorithmic standpoint, a drug can "attack" nodes or edges of a protein-protein interaction network. In this work, we propose a new network strategy, "The Interface Attack", based on protein-protein interfaces. Similar interface architectures can occur between unrelated proteins. Consequently, in principle, a drug that binds to one has a certain probability of binding to others. The interface attack strategy simultaneously removes from the network all interactions that consist of similar interface motifs. This strategy is inspired by network pharmacology and allows inferring potential off-targets. We introduce a network model that we call "Protein Interface and Interaction Network (P2IN)", which is the integration of protein-protein interface structures and protein interaction networks. This interface-based network organization clarifies which protein pairs have structurally similar interfaces and which proteins may compete to bind the same surface region. We built the P2IN with the p53 signaling network and performed network robustness analysis. We show that (1) "hitting" frequent interfaces (a set of edges distributed around the network) might be as destructive as eleminating high degree proteins (hub nodes), (2) frequent interfaces are not always topologically critical elements in the network, and (3) interface attack may reveal functional changes in the system better than the attack of single proteins. In the off-target detection case study, we found that drugs blocking the interface between CDK6 and CDKN2D may also affect the interaction between CDK4 and CDKN2D.     

Distribution, structure, and dynamics of cesium and iodide ions at the H2O-CCl4 and H2O-vapor interfaces

Molecular dynamics simulations utilizing many-body potentials of H2O-CCl4 and H2O-vapor interfaces were carried out at different cesium and iodide ion concentrations to compare ion distribution, interfacial orientational and structural properties, and dynamics. It was found that cesium was repelled by both interfaces, and iodide was active at both interfaces, but to a much greater degree at the H2O-vapor interface. At the interface, the iodide dipole was strongly induced, orienting perpendicular to the interface for both systems, leading to stronger hydrogen bonds with water. For the H2O-CCl4 interface, though, there was a compensation between these strong hydrogen bonds and short to moderate ranged repulsion between iodide and CCl4. Hydrogen bond distance and angular distributions showed weaker water-water hydrogen bonds at both interfaces, but generally stronger water-iodide hydrogen bonds. Both translational and rotational dynamics of water were faster at the interface, while for CCl4, its translational dynamics was slower, but rotational dynamics faster at the interface. For many of the studied systems and species, translational diffusion was found to be anisotropic at both interfacial and bulk regions.     

Hot spots and transient pockets: predicting the determinants of small-molecule binding to a protein-protein interface

Protein-protein interfaces are considered difficult targets for small-molecule protein-protein interaction modulators (PPIMs ). Here, we present for the first time a computational strategy that simultaneously considers aspects of energetics and plasticity in the context of PPIM binding to a protein interface. The strategy aims at identifying the determinants of small-molecule binding, hot spots, and transient pockets, in a protein-protein interface in order to make use of this knowledge for predicting binding modes of and ranking PPIMs with respect to their affinity. When applied to interleukin-2 (IL-2), the computationally inexpensive constrained geometric simulation method FRODA outperforms molecular dynamics simulations in sampling hydrophobic transient pockets. We introduce the PPIAnalyzer approach for identifying transient pockets on the basis of geometrical criteria only. A sequence of docking to identified transient pockets, starting structure selection based on hot spot information, RMSD clustering and intermolecular docking energies, and MM-PBSA calculations allows one to enrich IL-2 PPIMs from a set of decoys and to discriminate between subgroups of IL-2 PPIMs with low and high affinity. Our strategy will be applicable in a prospective manner where nothing else than a protein-protein complex structure is known; hence, it can well be the first step in a structure-based endeavor to identify PPIMs.     

Hydration free energies and entropies for water in protein interiors

Free energy calculations for the transfer of a water molecule from the pure liquid to an interior cavity site in a protein are presented. Two different protein cavities, in bovine pancreatic trypsin inhibitor (BPTI) and in the I76A mutant of barnase, represent very different environments for the water molecule: one which is polar, forming four water-protein hydrogen bonds, and one which is more hydrophobic, forming only one water-protein hydrogen bond. The calculations give very different free energies for the different cavities, with only the polar BPTI cavity predicted to be hydrated. The corresponding entropies for the transfer to the interior cavities are calculated as well and show that the transfer to the polar cavity is significantly entropically unfavorable while the transfer to the nonpolar cavity is entropically favorable. For both proteins an analysis of the fluctuations in the positions of the protein atoms shows that the addition of a water molecule makes the protein more flexible. This increased flexibility appears to be due to an increased length and weakened strength of protein-protein hydrogen bonds near the cavity.