Atomic force microscopy and other scanning probe microscopies

Basement membrane macromolecules: insights from atomic force microscopy

The major macromolecules of basement membranes-collagen IV, laminin-1, and heparan sulfate proteoglycan (HSPG)-have been analyzed by atomic force microscopy (AFM), both individually and in combination with each other. The positions of laminin binding to collagen IV were mapped and compared with the positions of imperfections in the amino acid sequence of collagen IV; the apparent molecular volumes of the HSPG proteoglycans were measured and used to estimate the corresponding molecular weights. Even the thin, thread-like strands of the polyanion heparan sulfate can be visualized with AFM without staining, coating, or fixation. These strands are single polysaccharide chains and are thus thinner than single-stranded DNA. The heparan sulfate strands in HSPG are necessary for protein filtration in kidney basement membranes. We propose that these thin strands filter proteins by functioning as an entropic brush-i.e., that they filter proteins by their constant thermally driven motion in the basement membrane. These AFM analyses in air are a step toward AFM analyses under fluid of basement membrane macromolecules interacting with each other.

Pushing, pulling, dragging, and vibrating renal epithelia by using atomic force microscopy

Renal physiologists focus on events that take place on and around the surfaces of cells. Various techniques have been developed that follow transport functions at the molecular level, but until recently none of these techniques has been capable of making the behavior of molecular structures visible under physiological conditions. This apparent gap may be filled in the future by the application of atomic force microscopy. This technique produces an image not by optical means, but by "feeling" its way across a surface. Atomic force microscopy can, however, be modified in a number of ways, which means that besides producing a high-resolution image, it is possible to obtain several types of data on the interactions between the ultrastructural components of cell membranes (such as proteins) and other biologically active molecules (such as ATP). In this review we describe the recent use of the atomic force microscope in renal physiology, ranging from experiments in intact cells to those in isolated renal transport protein molecules, include examples of these extended applications of the technique, and point to uses that the microscope has recently found in other areas of biology that should prove fruitful in renal physiology in the near future.

The micro-mechanics of single molecules studied with atomic force microscopy

The atomic force microscope (AFM) in its force-measuring mode is capable of effecting displacements on an angstrom scale (10 A = 1 nm) and measuring forces of a few piconewtons. Recent experiments have applied AFM techniques to study the mechanical properties of single biological polymers. These properties contribute to the function of many proteins exposed to mechanical strain, including components of the extracellular matrix (ECM). The force-bearing proteins of the ECM typically contain multiple tandem repeats of independently folded domains, a common feature of proteins with structural and mechanical roles. Polysaccharide moieties of adhesion glycoproteins such as the selectins are also subject to strain. Force-induced extension of both types of molecules with the AFM results in conformational changes that could contribute to their mechanical function. The force-extension curve for amylose exhibits a transition in elasticity caused by the conversion of its glucopyranose rings from the chair to the boat conformation. Extension of multi-domain proteins causes sequential unraveling of domains, resulting in a force-extension curve displaying a saw tooth pattern of peaks. The engineering of multimeric proteins consisting of repeats of identical domains has allowed detailed analysis of the mechanical properties of single protein domains. Repetitive extension and relaxation has enabled direct measurement of rates of domain unfolding and refolding. The combination of site-directed mutagenesis with AFM can be used to elucidate the amino acid sequences that determine mechanical stability. The AFM thus offers a novel way to explore the mechanical functions of proteins and will be a useful tool for studying the micro-mechanics of exocytosis.

Probing the Saccharomyces cerevisiae centromeric DNA (CEN DNA)-binding factor 3 (CBF3) kinetochore complex by using atomic force microscopy

Yeast centromeric DNA (CEN DNA) binding factor 3 (CBF3) is a multisubunit protein complex that binds to the essential CDEIII element in CEN DNA. The four CBF3 proteins are required for accurate chromosome segregation and are considered to be core components of the yeast kinetochore. We have examined the structure of the CBF3-CEN DNA complex by atomic force microscopy. Assembly of CBF3-CEN DNA complexes was performed by combining purified CBF3 proteins with a DNA fragment that includes the CEN region from yeast chromosome III. Atomic force microscopy images showed DNA molecules with attached globular bodies. The contour length of the DNA containing the complex is approximately 9% shorter than the DNA alone, suggesting some winding of DNA within the complex. The measured location of the single binding site indicates that the complex is located asymmetrically to the right of CDEIII extending away from CDEI and CDEII, which is consistent with previous data. The CEN DNA is bent approximately 55 degrees at the site of complex formation. A significant fraction of the complexes are linked in pairs, showing three to four DNA arms, with molecular volumes approximately three times the mean volumes of two-armed complexes. These multi-armed complexes indicate that CBF3 can bind two DNA molecules together in vitro and, thus, may be involved in holding together chromatid pairs during mitosis.