We directly measured at the single-molecule level the forces and lifetimes of DNA base-pair stacking interactions for all stack sequence combinations. Our experimental approach combined dual-beam optical tweezers with DNA origami components to allow positioning of blunt-end DNA helices so that the weak stacking force could be isolated. Base-pair stack arrays that lacked a covalent backbone connection spontaneously dissociated at average rates ranging from 0.02 to 500 per second, depending on the sequence combination and stack array size. Forces in the range from 2 to 8 piconewtons that act along the helical direction only mildly accelerated the stochastic unstacking process. The free-energy increments per stack that we estimate from the measured forward and backward kinetic rates ranged from -0.8 to -3.4 kilocalories per mole, depending on the sequence combination. Our data contributes to understanding the mechanics of DNA processing in biology, and it is helpful for designing the kinetics of DNA-based nanoscale devices according to user specifications.

Actin-binding proteins (ABPs) regulate the assembly of actin filaments (F-actin) into networks and bundles that provide the structural integrity of the cell. Two of these ABPs, filamin and ␣-actinin, have been extensively used to model the mechanical properties of actin networks grown in vitro; however, there is a lack in the understanding of how the molecular interactions between ABPs and F-actin regulate the dynamic properties of the cytoskeleton. Here, we present a native-like assay geometry to test the rupture force of a complex formed by an ABP linking two quasiparallel actin filaments. We readily demonstrate the adaptability of this assay by testing it with two different ABPs: filamin and ␣-actinin. For filamin/actin and ␣-actinin/actin, we measured similar rupture forces of 40 -80 pN for loading rates between 4 and 50 pN/s. Both ABP unfolding and conformational transition events were observed, demonstrating that both are important and may be a significant mechanism for the temporal regulation of the mechanical properties of the actin cytoskeleton. With this modular, singlemolecule assay, a wide range of ABP/actin interactions can be studied to better understand cytoskeletal and cell dynamics.␣-actinin ͉ filamin ͉ optical tweezers ͉ single-molecule force spectroscopy

Mechanical forces are important signals for cell response and development, but detailed molecular mechanisms of force sensing are largely unexplored. The cytoskeletal protein filamin is a key connecting element between the cytoskeleton and transmembrane complexes such as integrins or the von Willebrand receptor glycoprotein Ib. Here, we show using single-molecule mechanical measurements that the recently reported Ig domain pair 20-21 of human filamin A acts as an autoinhibited force-activatable mechanosensor. We developed a mechanical single-molecule competition assay that allows online observation of binding events of target peptides in solution to the strained domain pair. We find that filamin force sensing is a highly dynamic process occurring in rapid equilibrium that increases the affinity to the target peptides by up to a factor of 17 between 2 and 5 pN. The equilibrium mechanism we find here can offer a general scheme for cellular force sensing.optical tweezers | mechanosensing

Bridging the gap: Rigid DNA linkers (blue, see picture) between microspheres (green) for high‐resolution single‐molecule mechanical experiments were constructed using DNA origami. The resulting DNA helical bundles greatly reduce the noise generated in studies of conformation changes using optical tweezers and were applied to study small DNA secondary structures.

The heat shock protein 90 (Hsp90) is a dimeric molecular chaperone essential in numerous cellular processes. Its three domains (N, M, and C) are connected via linkers that allow the rearrangement of domains during Hsp90's chaperone cycle. A unique linker, called charged linker (CL), connects the N-and M-domain of Hsp90. We used an integrated approach, combining single-molecule techniques and biochemical and in vivo methods, to study the unresolved structure and function of this region. Here we show that the CL facilitates intramolecular rearrangements on the milliseconds timescale between a state in which the N-domain is docked to the M-domain and a state in which the N-domain is more flexible. The docked conformation is stabilized by 1.1 k B T (2.7 kJ/mol) through binding of the CL to the Ndomain of Hsp90. Docking and undocking of the CL affects the much slower intermolecular domain movement and Hsp90's chaperone cycle governing client activation, cell viability, and stress tolerance. T he molecular chaperone Hsp90 (heat shock protein 90) is essential for the folding, maturation, and activation of approximately 10% of the yeast proteome. The set of substrate proteins is structurally and functionally diverse and ranges from telomerase to kinases and transcription factors (1-3). Processing of these substrates requires ATP turnover and large conformational rearrangements within Hsp90 (4-6). Interestingly, these conformational states of yeast Hsp90 are not strictly coupled to the binding of nucleotides (7) but are recognized and regulated by the interaction with cochaperones (8) and substrate proteins (9).Hsp90 is a dimer with each monomer consisting of three domains (N, M, and C). The N-terminal domain comprises the nucleotide binding site, whereas the M-domain is important for the binding of many substrates. The C-terminal domain is mainly responsible for the dimerization of the protein. A long charged linker (CL) region, amino acids 211-272 in yeast, connects the N-and M-domain in eukaryotes (Fig. 1A). The crystal structure of yeast Hsp90 was obtained by partly deleting the CL region and shows a closed, compact conformation in the presence of AMP-PNP [Adenosine 5′-(β,γ-imido)triphosphate] and Sba1/p23 (10). The fact that the CL region is difficult to map structurally led to the assumption that this region is disordered and flexible, thereby enabling the conformational rearrangements of Hsp90 (11,12). Besides the structural indetermination of the CL, its ultimate function remains elusive as well (13). Early studies show that parts of the CL region (amino acids 211-259) are dispensable in yeast (14), whereas more extended deletions affect cell viability, substrate maturation, and regulation by cochaperones (11). These deficiencies can be partially rescued by a short linker consisting of an artificial sequence (11), but its specific amino acid sequence is associated with a gain of function, probably an additional Hsp90 regulatory mechanism (15).Single-molecule experiments have recently provided detailed insight int...

Spontaneous folding of a polypeptide chain into a knotted structure remains one of the most puzzling and fascinating features of protein folding. The folding of knotted proteins is on the timescale of minutes and thus hard to reproduce with atomistic simulations that have been able to reproduce features of ultrafast folding in great detail. Furthermore, it is generally not possible to control the topology of the unfolded state. Single-molecule force spectroscopy is an ideal tool for overcoming this problem: by variation of pulling directions, we controlled the knotting topology of the unfolded state of the 5 2 -knotted protein ubiquitin C-terminal hydrolase isoenzyme L1 (UCH-L1) and have therefore been able to quantify the influence of knotting on its folding rate. Here, we provide direct evidence that a threading event associated with formation of either a 3 1 or 5 2 knot, or a step closely associated with it, significantly slows down the folding of UCH-L1. The results of the optical tweezers experiments highlight the complex nature of the folding pathway, many additional intermediate structures being detected that cannot be resolved by intrinsic fluorescence. Mechanical stretching of knotted proteins is also of importance for understanding the possible implications of knots in proteins for cellular degradation. Compared with a simple 3 1 knot, we measure a significantly larger size for the 5 2 knot in the unfolded state that can be further tightened with higher forces. Our results highlight the potential difficulties in degrading a 5 2 knot compared with a 3 1 knot.knotted proteins | protein folding | single molecule | optical tweezers | ubiquitin C-terminal hydrolase

Enzymes are molecular machines that bind substrates specifically, provide an adequate chemical environment for catalysis and exchange products rapidly, to ensure fast turnover rates. Direct information about the energetics that drive conformational changes is difficult to obtain. We used subnanometre single-molecule force spectroscopy to study the energetic drive of substrate-dependent lid closing in the enzyme adenylate kinase. Here we show that in the presence of the bisubstrate inhibitor diadenosine pentaphosphate (AP5A), closing and opening of both lids is cooperative and tightly coupled to inhibitor binding. Surprisingly, binding of the substrates ADP and ATP exhibits a much smaller energetic drive towards the fully closed state. Instead, we observe a new dominant energetic minimum with both lids half closed. Our results, combining experiment and molecular dynamics simulations, give detailed mechanical insights into how an enzyme can cope with the seemingly contradictory requirements of rapid substrate exchange and tight closing, to ensure efficient catalysis.

The regulation of protein function through ligand-induced conformational changes is crucial for many signal transduction processes. The binding of a ligand alters the delicate energy balance within the protein structure, eventually leading to such conformational changes. In this study, we elucidate the energetic and mechanical changes within the subdomains of the nucleotide binding domain (NBD) of the heat shock protein of 70 kDa (Hsp70) chaperone DnaK upon nucleotide binding. In an integrated approach using single molecule optical tweezer experiments, loop insertions, and steered coarse-grained molecular simulations, we find that the C-terminal helix of the NBD is the major determinant of mechanical stability, acting as a glue between the two lobes. After helix unraveling, the relative stability of the two separated lobes is regulated by ATP/ADP binding. We find that the nucleotide stays strongly bound to lobe II, thus reversing the mechanical hierarchy between the two lobes. Our results offer general insights into the nucleotide-induced signal transduction within members of the actin/sugar kinase superfamily.ATPase | laser trapping | elasticity | force | protein extension