Characterization of fiber-forming peptides and proteins by means of atomic force microscopy

The atomic force microscope (AFM) is widely used in biological sciences due to its ability to perform imaging experiments at high resolution in a physiological environment, without special sample preparation such as fixation or staining. AFM is unique, in that it allows single molecule information of mechanical properties and molecular recognition to be gathered. This review sets out to identify methodological applications of AFM for characterization of fiber-forming proteins and peptides. The basics of AFM operation are detailed, with in-depth information for any life scientist to get a grasp on AFM capabilities. It also briefly describes antibody recognition imaging and mapping of nanomechanical properties on biological samples. Subsequently, examples of AFM application to fiber-forming natural proteins, and fiber-forming synthetic peptides are given. Here, AFM is used primarily for structural characterization of fibers in combination with other techniques, such as circular dichroism and fluorescence spectroscopy. More recent developments in antibody recognition imaging to identify constituents of protein fibers formed in human disease are explored. This review, as a whole, seeks to encourage the life scientists dealing with protein aggregation phenomena to consider AFM as a part of their research toolkit, by highlighting the manifold capabilities of this technique.     

Combined AFM and two-focus SFCS study of raft-exhibiting model membranes.

Dioleoylphosphatidylcholine/sphingomyelin/cholesterol (DOPC/SM/cholesterol) model membranes exhibit liquid-liquid phase separation and therefore provide a physical model for the putative liquid-ordered domains present in cells. Here we present a combination of atomic force microscopy (AFM) imaging, force measurements, confocal fluorescence imaging and two-focus scanning fluorescence correlation spectroscopy (two-focus SFCS) to obtain structural and dynamical information about this model membrane system. Partition coefficients and diffusion coefficients in the different phases were measured with two-focus SFCS for numerous fluorescent lipid analogues and proteins, while being directly related to the lateral organization of the membrane and its mechanical properties probed by AFM. Moreover we show how the combination of these different approaches is effective in reducing artifacts resulting from the use of a single technique.     

Strategies for in vivo imaging of enzyme activity: an overview and recent advances

Imaging of enzyme activity in living subjects promises many applications in both basic and translational researches from helping elucidate the enzyme function and mechanism in biology to better disease detection and monitoring, but the complexity and dynamics of enzymatic reactions in living systems present unique challenges for probe design. This critical review examines the approaches in recent literature to in vivo imaging of the activity of a variety of enzyme targets with an emphasis on the chemical perspective of probe design, structure and function. Strategies for designing enzyme-activated probes based on a variety of molecular scaffolds including small molecules, organic and inorganic nanoparticles, and genetically encoded proteins for commonly used molecular imaging modalities--whole body optical (fluorescence, bioluminescence) imaging, magnetic resonance imaging, and radionuclide-based tomographic imaging, are critically evaluated. Recent advances in combining multiple modalities to imaging enzyme activity in living subjects are also highlighted (255 references).     

AFM for nanoscale microbe analysis

The nanoscale surface analysis of microbial cells represents a significant challenge of current microbiology and is critical for developing new biotechnological and biomedical applications. Using atomic force microscopy (AFM) topographic imaging, researchers can visualize the ultrastructure of live cells under physiological conditions and their subtle modifications upon cell growth or treatment with drugs. Chemical force microscopy, in which AFM tips are modified with specific functional groups, allows investigators to measure molecular forces and chemical properties of cell surfaces on a scale of only 25 functional groups. Molecular recognition imaging using AFM offers a means to localize specific receptors on cells, such as cell adhesion proteins or antibiotic binding sites. With this Highlight on AFM, it is hoped that more and more microbiologists and biophysicists will take advantage of this powerful, multifunctional nanotechnique.     

Immobilization of histidine-tagged proteins on nickel by electrochemical dip pen nanolithography

Dip-pen nanolithography (DPN) is becoming a popular technique to "write" molecules on a surface by using the tip of an atomic force microscope (AFM) coated with the desired molecular "ink". In this work, we demonstrate that poly-histidine-tagged peptides and proteins, and free-base porphyrins coated on AFM probes, can be chelated to ionized regions on a metallic nickel surface by applying an electric potential to the AFM tip in the DPN process. DPN has been accomplished in the Tapping Mode of AFM, which creates many possible applications of positioning and subsequently imaging biomolecules, especially on soft surfaces.     

Probing supported model and native membranes using AFM

Atomic Force Microscopy (AFM) has gained lots of interest since its ability to get high resolution imaging in liquid environment. In the last years, this technique was particularly successful in probing the surface of membrane model systems of biological interest and spectacular results have been obtained with native specialized membranes. In this review, we aim at highlighting the recent developments that illustrate the unique powerfulness of AFM in determining the nanoscale organization of membranes and their local physical properties. An important part will focus on AFM high resolution imaging of transmembrane proteins in model and native membranes and on the study of few applications such as biosensors. An overview of main recent developments of AFM as well as new possibilities gained by combination with other techniques will also be addressed.     

原子力显微镜在蛋白单分子结构与功能研究中的应用

原子力显微镜(AFM)以其超常的信噪比、空间分辨率和灵活的探测环境使得单个蛋白分子能在生理条件下成像,在蛋白单分子结构与功能研究中得到广泛地应用。论文介绍了AFM在分子马达、光合蛋白、分子伴侣等蛋白表面结构表征中的应用;AFM在蛋白单分子表面的粘弹性、电荷分布、分子间相互作用等物理属性研究中的进展;总结了AFM在蛋白分子功能研究和单分子操纵中的应用。     

细胞膜上信号转导蛋白的单分子成像与分析

结合本课题组的研究工作, 介绍了单分子荧光成像原理、 荧光标记方法及数据分析方法, 并进一步综述了单分子荧光成像在几种重要的膜蛋白信号转导分子机制和相关药物研究中的进展.     

Strategies to prepare and characterize native membrane proteins and protein membranes by AFM

Progress in characterizing native membrane proteins and protein membranes by atomic force microscopy (AFM) opens exciting possibilities. While the structure, oligomeric state and supramolecular assembly of membrane proteins are assessed directly by AFM, single-molecule force spectroscopy (SMFS) identifies interactions that stabilize the fold, and characterize the switching between functional states of membrane proteins. But what is next? How can we approach cell biological, pharmaceutical and medical questions associated with native cellular membranes? How can we probe the functional state of cell membranes and study the dynamic formation of compartments? Such questions have been addressed by immobilizing membranes on solid supports, which ensures the integrity of the native state of membrane proteins but does not necessarily provide a native-like environment. Direct attachment of membranes to solid supports involves non-specific interactions that may change the physical state of supported lipids and proteins possibly hindering the assembly of membrane proteins into native functional compartments. Thus, to observe the dynamic assembly and working of proteins in native membranes by AFM, supports are required that mimic the native environment of the cell membrane as closely as possible. This review reports on recent progress in characterizing native membrane proteins by AFM, and surveys conventional and new approaches of supporting surfaces, which will allow the function, dynamics, and assembly of membrane proteins to be studied by AFM in native cell membranes.     

Atomic force microscopy of microbial cells: application to nanomechanical properties, surface forces and molecular recognition forces

In recent years, the physical properties and interaction forces of microbial cell surfaces have been extensively studied using atomic force microscopy (AFM). A variety of AFM force spectroscopy approaches have been developed for investigating native cell surfaces with piconewton (nanonewton) sensitivity and nanometer lateral resolution, providing novel information on the nanomechanical properties of cell walls, on surface forces such as van der Waals and electrostatic forces, solvation and steric/bridging forces, and on the forces and localization of molecular recognition events. The intention of this article is to survey these different applications and to discuss related methodologies (how to prepare tips and samples, how to record and interpret force curves).     

Atomic force microscopy of the three-dimensional crystal of membrane protein, OmpC porin

Three-dimensional microcrystals of OmpC osmoporin were air-dried slowly and imaged in air with an atomic force microscope (AFM). The overall structural features in AFM images are in good agreement with the X-ray diffraction data of these OmpC osmoporin crystals: monoclinic P2₁ with the unit cell constants a=117.6 Å, b=110 Å, c=298.4 Å, β=97°. Such a good correspondence between X-ray diffraction and AFM data suggests that the slow and mild air-drying of these crystals did not induce any significant alterations in the crystal lattices as expected upon crystal dehydration. At the (100) crystal face, individual trimeric protein–detergent complexes were resolved. These results show the potential for studying the molecular structure of microcrystals of integral membrane proteins. This study also suggests that the crystal grew in a fashion of rapid two-dimensional expansion along the bc plane followed by a slow deposition along the a axis, perhaps as a rate-limiting nucleation process. Thus, AFM imaging of air-dried crystals would also be of considerable use in the early stages of a project to grow large three-dimensional crystals of membrane proteins suitable for high-resolution X-ray diffraction studies.     

Molecular views and measurements of hemostatic processes using atomic force microscopy

Hemostasis and thrombosis are highly complex and coordinated interfacial responses to vascular injury. In recent years, atomic force microscopy (AFM) has proven to be a very useful approach for studying hemostatic processes under near physiologic conditions. In this report, we review recent progress in the use of AFM for studying hemostatic processes, including molecular level visualization of plasma proteins, protein aggregation and multimer assembly, and structural and morphological details of vascular cells under aqueous conditions. AFM offers opportunities for visualizing surface-dependent molecular and cellular interactions in three dimensions on a nanoscale and for sensitive, picoNewton level, measurements of intermolecular forces. AFM has been used to obtain molecular and sub-molecular, resolution of many biological molecules and assemblies, including coagulation proteins and cell surfaces. Surface-dependent molecular processes including protein adsorption, conformational changes, and subsequent interactions with cellular components have been described. This review outlines the basic principles and utility of AFM for imaging and force measurements, and offers objective perspectives on both the advantages and disadvantages. We focus primarily on molecular level events related to hemostasis and thrombosis, particularly coagulation proteins, and blood platelets, but also explore the use of AFM in force measurements and surface property mapping.     

Energy Landscape of Aptamer/Protein Complexes Studied by Single‐Molecule Force Spectroscopy

Aptamers are single‐stranded nucleic acid molecules selected in vitro to bind to a variety of target molecules. Aptamers bound to proteins are emerging as a new class of molecules that rival commonly used antibodies in both therapeutic and diagnostic applications. With the increasing application of aptamers as molecular probes for protein recognition, it is important to understand the molecular mechanism of aptamer–protein interaction. Recently, we developed a method of using atomic force microscopy (AFM) to study the single‐molecule rupture force of aptamer/protein complexes. In this work, we investigate further the unbinding dynamics of aptamer/protein complexes and their dissociation‐energy landscape by AFM. The dependence of single‐molecule force on the AFM loading rate was plotted for three aptamer/protein complexes and their dissociation rate constants, and other parameters characterizing their dissociation pathways were obtained. Furthermore, the single‐molecule force spectra of three aptamer/protein complexes were compared to those of the corresponding antibody/protein complexes in the same loading‐rate range. The results revealed two activation barriers and one intermediate state in the unbinding process of aptamer/protein complexes, which is different from the energy landscape of antibody/protein complexes. The results provide new information for the study of aptamer–protein interaction at the molecular level.     

Synthesis of magnetite nanoparticles for bio- and nanotechnology: genetic engineering and biomimetics of bacterial magnetosomes

Magnetotactic bacteria (MTB) have the ability to navigate along the Earth's magnetic field. This so-called magnetotaxis is a result of the presence of magnetosomes, organelles which comprise nanometer-sized intracellular crystals of magnetite (Fe(3)O(4)) enveloped by a membrane. Because of their unique characteristics, magnetosomes have a high potential for nano- and biotechnological applications, which require a specifically designed particle surface. The functionalization of magnetosomes is possible either by chemical modification of purified particles or by genetic engineering of magnetosome membrane proteins. The second approach is potentially superior to chemical approaches as a large variety of biological functions such as protein tags, fluorophores, and enzymes may be directly incorporated in a site-specific manner during magnetosome biomineralization. An alternative to the bacterial production of magnetosomes are biomimetic approaches, which aim to mimic the bacterial biomineralization pathway in vitro. In MTB a number of magnetosome proteins with putative functions in the biomineralization of the nanoparticles have been identified by genetic and biochemical approaches. The initial results obtained by several groups indicate that some of these proteins have an impact on nanomagnetite properties in vitro. In this article the key features of magnetosomes are discussed, an overview of their potential applications are given, and different strategies are proposed for the functionalization of magnetosome particles and for the biomimetism of their biomineralization pathway.     

Solubilization of supported lipid membranes by octyl glucoside observed by time-lapse atomic force microscopy

Detergents are very useful for the purification of membrane proteins. A good detergent for protein extraction has to prevent denaturation by unfolding, and to avoid aggregation. Therefore, gaining access to the mechanism of biomembranes’ solubilization by detergents is crucial in biochemical research. Among the wide range of detergents used to purify membrane proteins, n-octyl β-d-glucopyranoside (OG) is one of the most important as it can be easily removed from final protein extracts.

Here, we used real-time atomic force microscopy (AFM) imaging to visualize the behavior of a model supported lipid bilayer in the presence of OG. Two kinds of supported model membranes were prepared by fusion of unilamellar vesicles: with an equimolar mixing of dioleoylphosphatidylcholine/dipalmitoylphosphatidylcholine (DOPC/DPPC) or with DPPC alone. Time-lapse AFM experiments evidenced that below its critical micelle concentration (CMC), OG was not able to solubilize the bilayer but the gel DPPC domains were instantly dissolved into the DOPC matrix. This result was interpreted as a disorganization of the DPPC molecular packing induced by OG. When membranes were incubated with OG at concentrations higher than CMC, the detergent immediately provoked the complete and immediate desorption of the whole bilayer for both compositions: DPPC and DOPC/DPPC. After a while, some patches appeared onto the bare mica surface. This redeposition activity, together with fusion events, progressively led to the recovery of a continuous bilayer. These results provide a new insight on the unique properties of OG employed in membrane reconstitution protocols.     

Mechanosensing using drag force for imaging soft biological membranes

We investigate physical processes taking place during nanoscale mechanosensing of soft biological membranes in liquid environments. Examples include tapping mode imaging by atomic force microscope (AFM) and microscopy based on the Brownian motion of a nanoparticle in an optical-tweezers-controlled trap. The softness and fluidity of the cellular membrane make it difficult to accurately detect (i.e., image) the shape of the cell using traditional mechanosensing methods. The aim of the reported work is to theoretically evaluate whether the drag force acting on the nanoscale mechanical probe due to a combined effect of intra- and extracellular environments can be exploited to develop a new imaging mode suitable for soft cellular interfaces. We approach this problem by rigorous modeling of the fluid mechanics of a complex viscoelastic biosystem in which the probe sensing process is intimately coupled to the membrane biomechanics. The effects of the probe dimensions and elastic properties of the membrane as well as intra- and extracellular viscosities are investigated in detail to establish the structure and evolution of the fluid field as well as the dynamics of membrane deformation. The results of numerical simulations, supported by predictions of the scaling analysis of forces acting on the probe, suggest that viscous drag is the dominant force dictating the probe dynamics as it approaches a biological interface. The increase in the drag force is shown to be measurable, to scale linearly with an increase in the viscosity ratio of the fluids on either side of the membrane, and to be inversely proportional to the probe-to-membrane distance. This leads to the postulation of a new strategy for lipid membrane imaging by AFM or other mechanosensing methods using a variation in the maximum drag force as an indicator of the membrane position.     

利用原子力显微镜研究在单分子水平上DNA与组蛋白的相互作用

核小体是DNA被压缩成染色质的第一级压缩结构. 为了更深刻描述DNA与组蛋白的相互作用,利用透析方法将DNA和组蛋白构建成核小体,并且应用原子力显微镜进行单分子水平上的观察. 实验结果表明利用透析方法得到了核小体的“串珠型排列”,并且对在两种不同的结合条件下DNA与组蛋白的相互作用进行了观察和比较.     

Correlating polymer structure,dynamics, and function with atomic force microscopy

Since its development, atomic force microscopy (AFM) has become an indispensable tool for investigating fundamental and technological applications of polymer materials. The versatility of AFM imaging modes and operating conditions allows for nanoscale characterization of a range of dynamic processes, such as crystallization, phase separation, self assembly, and electronic transport. Advances in AFM technology, particularly high-speed and high-resolution imaging, enable investigation of polymer structure, function, and dynamics in real world conditions and across a range of relevant spatial and temporal scales. In this perspective, we highlight a collection of recent polymer studies that utilize AFM to correlate the function and structure of polymer films, with focus on its multiparametric imaging capabilities. As the complexity of polymer materials and morphologies continues to increase, AFM is well poised to meet the accompanying demand for nanoscale imaging and characterization.     

Molecular motions in drug design: the coming age of the metadynamics method

Metadynamics is emerging as a useful free energy method in physics, chemistry and biology. Recently, it has been applied also to investigate ligand binding to biomolecules of pharmacological interest. Here, after introducing the basic idea of the method, we review applications to challenging targets for pharmaceutical intervention. We show that this methodology, especially when combined with a variety of other computational approaches such as molecular docking and/or molecular dynamics simulation, may be useful to predict structure and energetics of ligand/target complexes even when the targets lack a deep binding cavity, such as DNA and proteins undergoing fibrillation in neurodegenerative diseases. Furthermore, the method allows investigating the routes of molecular recognition and the associated binding energy profiles, providing a molecular interpretation to experimental data.     

Force measurements for membrane protein manipulation

The force curve measurement mode of the atomic force microscope (AFM) enables us to measure hitherto unobservable mechanical properties of nanometer sized biological specimens. By applying this mode, we attempted to conduct such mechanical manipulations of membrane proteins as: (1) measurement of the separation force between a membrane bound receptor and a covalently cross-linked ligand molecule on the AFM tip; and (2) extraction of membrane proteins after harnessing them on a modified tip with covalent cross-linkers. Since the limiting tensile force of the covalent system used in our experiment was a crucial factor for successful manipulations, we first estimated the force to terminate the covalent cross-linking system at the single molecular level to be 1.6–1.7 nN, based on our previous data. The method was then applied to measure the force required to separate α₂-macroglobulin (α₂-M) from its receptor on the cell membrane using an AFM tip coated with the receptor binding form of the protein. From a bimodal distribution of rupture force, we obtained an average value of 120 pN as the force to separate a non-covalent association of α₂-M with its receptor. When modified tips with covalent cross-linkers aimed at amino groups on the cell surface were used, distribution of the rupture force shifted toward higher values, with a peak in the histogram ≈400–500 pN. Since the force to sever covalent cross-linking system was 1.6–1.7 nN, the observed force was ascribed to the force required to extract membrane proteins from the cell membrane after covalent bond formation.