Measuring the forces that control protein interactions

Molecular interactions mediating T cell antigen recognition

Over the past decade, key protein interactions contributing to T cell antigen recognition have been characterized in molecular detail. These have included interactions involving the T cell antigen receptor (TCR) itself, its coreceptors CD4 and CD8, the accessory molecule CD2, and the costimulatory receptors CD28 and CTLA-4. A clear view is emerging of how these molecules interact with their ligands at the cell-cell interface. Structural and binding studies have confirmed that the proteins span small but comparable distances and that, overall, they interact very weakly. However, there have been important surprises as well: that TCR interactions with peptide-MHC are topologically constrained and characterized by considerable conformational flexibility at the binding interface; that coreceptors engage peptide-MHC with extraordinarily fast kinetics and at angles apparently precluding direct interactions with the TCR bound to the same peptide-MHC; that the structural mechanisms allowing recognition by costimulatory and accessory molecules to be weak and yet specific are very heterogeneous; and that because of differences in both binding affinity and stoichiometry, there is enormous variation in the stability of the various costimulatory receptor/ligand complexes. These studies provide the necessary framework for exploring how these molecular interactions initiate T cell activation.

Chromatin fibers, one-at-a-time

Eukaryotic DNA is presented to the enzymatic machineries that use DNA as a template in the form of chromatin fibers. At the first level of organization, DNA is wrapped around histone octamers to form nucleosomal particles that are connected with stretches of linker DNA; this beads-on-a-string structure folds further to reach a very compact state in the nucleus. Chromatin structure is in constant flux, changing dynamically to accommodate the needs of the cell to replicate, transcribe, and repair the DNA, and to regulate all these processes in time and space. The more conventional biochemical and biophysical techniques used to study chromatin structure and dynamics have been recently complemented by an array of single-molecule approaches, in which chromatin fibers are investigated one-at-a-time. Here we describe single-molecule efforts to see nucleosomes, touch them, put them together, and then take them apart, one-at-a-time. The beginning is exciting and promising, but much more effort will be needed to take advantage of the huge potential that the new physics-based techniques offer.

The nature of molecular recognition by T cells

Considerable progress has been made in characterizing four key sets of interactions controlling antigen responsiveness in T cells, involving the following: the T cell antigen receptor, its coreceptors CD4 and CD8, the costimulatory receptors CD28 and CTLA-4, and the accessory molecule CD2. Complementary work has defined the general biophysical properties of interactions between cell surface molecules. Among the major conclusions are that these interactions are structurally heterogeneous, often reflecting clear-cut functional constraints, and that, although they all interact relatively weakly, hierarchical differences in the stabilities of the signaling complexes formed by these molecules may influence the sequence of steps leading to T cell activation. Here we review these developments and highlight the major challenges remaining as the field moves toward formulating quantitative models of T cell recognition.

Thermal folding and mechanical unfolding pathways of protein secondary structures

Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force versus displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession of stretching events, as measured by the order in which contacts are ruptured, is compared to the sequencing of events during thermal folding and unfolding. Opposite cross-correlations are found for an alpha-helix and a beta-hairpin structure. In a tandem of two alpha-helices, the two constituent helices unravel nearly simultaneously. A simple condition for simultaneous versus sequential unraveling of repeat units is presented.

Measuring forces with the AFM: polymeric surfaces in liquids

This review links together for the first time both the practicalities of force measurement and the work carried out to date on force detection between polymeric surfaces in liquids using the atomic force microscope (AFM). Also included is some of the recent work that has been carried out between surfactant surfaces and biologically coated surfaces with the AFM. The emphasis in this review is on the practical issues involved with force measurement between these types of surfaces, and the similarities and irregularities between the observed types of forces measured. Comparison is made between AFM and surface force apparatus (SFA) measurements, as there is a much longer history of work with the latter. Results indicate that forces between the surfaces reviewed here are a complicated mixture of steric-type repulsion, conformational behaviour on separation and long-range attraction, which is often ascribed to 'hydrophobic' forces. The origin of this latter force remains uncertain, despite its almost ubiquitous appearance in force measurements with these types of surfaces.

Measurement of membrane binding between recoverin, a calcium-myristoyl switch protein, and lipid bilayers by AFM-based force spectroscopy

Myristoyl switch is a feature of several peripheral membrane proteins involved in signal transduction pathways. This unique molecular property is best illustrated by the "Ca(2+)-myristoyl switch" of recoverin, which is a Ca(2+)-binding protein present in retinal rod cells of vertebrates. In this transduction pathway, the Ca(2+)-myristoyl switch acts as a calcium sensor involved in cell recovery from photoactivation. Ca(2+) binding by recoverin induces the extrusion of its myristoyl group to the solvent, which leads to its translocation from cytosol to rod disk membranes. Force spectroscopy, based on atomic force microscope (AFM) technology, was used to determine the extent of membrane binding of recoverin in the absence and presence of calcium, and to quantify this force of binding. An adhesion force of 48 +/- 5 pN was measured between recoverin and supported phospholipid bilayers in the presence of Ca(2+). However, no binding was observed in the absence of Ca(2+). Experiments with nonmyristoylated recoverin confirmed these observations. Our results are consistent with previously measured extraction forces of lipids from membranes.

Structural transitions in neutral and charged proteins in vacuo

In vacuo proteins provide a simple laboratory to explore the roles of sequence, temperature, charge state, and initial configuration in protein folding. Moreover, by the very absence of solvent, the study of anhydrous proteins in vacuo will also help us to understand specific environmental effects. From the experimental viewpoint, these systems are now beginning to be characterized at low resolution. Molecular dynamics (MD) simulations, in combination with tools for protein shape analysis, can complement experiments and provide further insights on the folding-unfolding transitions of these proteins. We review some aspects of this issue by using the results from a detailed MD study of hen egg-white lysozyme. For lysozyme ions, unfolding can be triggered by Coulombic repulsion. In neutral lysozyme, unfolding can be induced by centrifugal forces and also by weakening the monomer-monomer interaction. In both cases, the resulting unfolded transients can be used as initial configurations for relaxation dynamics. All trajectories are analyzed in terms of global molecular shape features of the backbone, including its anisometry and chain entanglement complexity. This strategy allows us to quantify separately the degree of polymer collapse and the evolution of large-scale folding features. Using these last two notions, we discuss some basic questions regarding the nature of the accessible paths associated with unfolding from, and refolding into, compact conformers.

Global configuration of single titin molecules observed through chain-associated rhodamine dimers

The global configuration of individual, surface-adsorbed molecules of the giant muscle protein titin, labeled with rhodamine conjugates, was followed with confocal microscopy. Fluorescence-emission intensity was reduced because of self-quenching caused by the close spacing between rhodamine dye molecules that formed dimers. In the presence of chemical denaturants, fluorescence intensity increased, reversibly, up to 5-fold in a fast reaction; the kinetics were followed at the single-molecule level. We show that dimers formed in a concentrated rhodamine solution dissociate when exposed to chemical denaturants. Furthermore, titin denaturation, followed by means of tryptophan fluorescence, is dominated by a slow reaction. Therefore, the rapid fluorescence change of the single molecules reflects the direct action of the denaturants on rhodamine dimers rather than the unfolding/refolding of the protein. Upon acidic denaturation, which we have shown not to dissociate rhodamine dimers, fluorescence intensity change was minimal, suggesting that dimers persist because the unfolded molecule has contracted into a small volume. The highly contractile nature of the acid-unfolded protein molecule derives from a significant increase in chain flexibility. We discuss the potential implications this finding could have for the passive mechanical behavior of striated muscle.

Single molecule measurements of titin elasticity

Titin, with a massive single chain of 3--4MDa and multiple modular motifs, spans the half-sarcomere of skeletal and cardiac muscles and serves important, multifaceted functions. In recent years, titin has become a favored subject of single molecule observations by atomic force microscopy (AFM) and laser optical trap (LOT). Here we review these single titin molecule extension studies with an emphasis on understanding their relevance to titin elasticity in muscle function. Some fundamental aspects of the methods for single titin molecule investigations, including the application of dynamic force, the elasticity models for filamentous titin motifs, the technical foundations and calibrations of AFM and LOT, and titin sample preparations are provided. A chronological review of major publications on recent single titin extension observations is presented. This is followed by summary evaluations of titin domain folding/unfolding results and of elastic properties of filamentous titin motifs. Implications of these single titin measurements for muscle physiology/pathology are discussed and forthcoming advances in single titin studies are anticipated.

Atomic force microscopy of macromolecular interactions

The introduction of functional imaging tools and techniques that operate at molecular-length scales has provided investigators with unique approaches to characterizing biomolecular structure and function relationships. Recent advances in the field of scanning probe techniques and, in particular, atomic force microscopy have yielded tantalizing insights into the dynamics of protein self-assembly and the mechanics of protein unfolding.

Pectins: structure, biosynthesis, and oligogalacturonide-related signaling

Pectin is a family of complex polysaccharides present in all plant primary cell walls. The complicated structure of the pectic polysaccharides, and the retention by plants of the large number of genes required to synthesize pectin, suggests that pectins have multiple functions in plant growth and development. In this review we summarize the current level of understanding of pectin primary and tertiary structure, and describe new methods that may be useful to study localized pectin structure in the plant cell wall. We also discuss progress in our understanding of how pectin is biosynthesized and review the biological activities and possible modes of action of pectic oligosaccharides referred to as oligogalacturonides. We present our view of critical questions regarding pectin structure, biosynthesis, and function that need to be addressed in the coming decade. As the plant community works towards understanding the functions of the tens of thousands of genes expressed by plants, a large number of those genes are likely to be involved in the synthesis, turnover, biological activity, and restructuring of pectin. A combination of genetic, molecular, biochemical and chemical approaches will be necessary to fully understand the function and biosynthesis of pectin.