Ultrafast folding kinetics and cooperativity of villin headpiece in single-molecule force spectroscopy

Gabriel Žoldáka, Johannes Stigler, Benjamin Pelz, Hongbin Li, and Matthias Rief

In this study we expand the accessible dynamic range of single-molecule force spectroscopy by optical tweezers to the microsecond range by fast sampling. We are able to investigate a single molecule for up to 15 min and with 300-kHz bandwidth as the protein undergoes tens of millions of folding/unfolding transitions. Using equilibrium analysis and autocorrelation analysis of the time traces, the full energetics as well as real-time kinetics of the ultrafast folding of villin headpiece 35 and a stable asparagine 68 alanine/lysine 70 methionine variant can be measured directly. We also performed Brownian dynamics simulations of the response of the bead-DNA system to protein-folding fluctuations. All key features of the force-dependent deflection fluctuations could be reproduced: SD, skewness, and autocorrelation function. Our measurements reveal a difference in folding pathway and cooperativity between wild-type and stable variant of headpiece 35. Autocorrelation force spectroscopy pushes the time resolution of single-molecule force spectroscopy to ∼10 µs thus approaching the timescales accessible for all atom molecular dynamics simulations.

DOI

Journal: Proceedings of the National Academy of Sciences

Synthetic polyubiquitinated α-Synuclein reveals important insights into the roles of the ubiquitin chain in regulating its pathophysiology

Mahmood Haj-Yahya, Bruno Fauvet, Yifat Herman-Bachinsky, Mirva Hejjaoui, Sudhir N. Bavikara, Subramanian Vedhanarayanan Karthikeyan, Aaron Ciechanover, Hilal A. Lashuel, and Ashraf Brik

Ubiquitination regulates, via different modes of modifications, a variety of biological processes, and aberrations in the process have been implicated in the pathogenesis of several neurodegenerative diseases. However, our ability to dissect the pathophysiological relevance of the ubiquitination code has been hampered due to the lack of methods that allow site-specific introduction of ubiquitin (Ub) chains to a specific substrate. Here, we describe chemical and semisynthetic strategies for site-specific incorporation of K48-linked di- or tetra-Ub chains onto the side chain of Lys12 of α-Synuclein (α-Syn). These advances provided unique opportunities to elucidate the role of ubiquitination and Ub chain length in regulating α-Syn stability, aggregation, phosphorylation, and clearance. In addition, we investigated the cross-talk between phosphorylation and ubiquitination, the two most common α-Syn pathological modifications identified within Lewy bodies and Parkinson disease. Our results suggest that α-Syn functions under complex regulatory mechanisms involving cross-talk among different posttranslational modifications.

DOI

Journal: Proceedings of the National Academy of Sciences

Single-molecule fluorescence probes dynamics of barrier crossing

Hoi Sung Chung, and William A. Eaton

Kramers developed the theory on how chemical reaction rates are influenced by the viscosity of the medium1. At the viscosity of water, the kinetics of unimolecular reactions are described by diffusion of a Brownian particle over a free-energy barrier separating reactants and products. For reactions in solution this famous theory extended Eyring’s transition state theory, and is widely applied in physics, chemistry and biology, including to reactions as complex as protein folding. Because the diffusion coefficient of Kramers’ theory is determined by the dynamics in the sparsely populated region of the barrier top, its properties have not been directly measured for any molecular system. Here we show that the Kramers diffusion coefficient and free-energy barrier can be characterized by measuring the temperature- and viscosity-dependence of the transition path time for protein folding. The transition path is the small fraction of an equilibrium trajectory for a single molecule when the free-energy barrier separating two states is actually crossed. Its duration, the transition path time, can now be determined from photon trajectories for single protein molecules undergoing folding/unfolding transitions5. Our finding of a long transition path time with an unusually small solvent viscosity dependence suggests that internal friction as well as solvent friction determine the Kramers diffusion coefficient for α-helical proteins, as opposed to a breakdown of his theory, which occurs for many small-molecule reactions2. It is noteworthy that the new and fundamental information concerning Kramers’ theory and the dynamics of barrier crossings obtained here come from experiments on a protein rather than a much simpler chemical or physical system.

DOI

Journal: Nature

Nanomechanics of HaloTag Tethers

Ionel Popa , Ronen Berkovich, Jorge Alegre-Cebollada, Carmen L. Badilla, Jaime Andrés Rivas-Pardo, Yukinori Taniguchi , Masaru Kawakami , and Julio M. Fernandez 

The active site of the Haloalkane Dehydrogenase (HaloTag) enzyme can be covalently attached to a chloroalkane ligand providing a mechanically strong tether, resistant to large pulling forces. Here we demonstrate the covalent tethering of protein L and I27 polyproteins between an atomic force microscopy (AFM) cantilever and a glass surface using HaloTag anchoring at one end and thiol chemistry at the other end. Covalent tethering is unambiguously confirmed by the observation of full length polyprotein unfolding, combined with high detachment forces that range up to 2000 pN. We use these covalently anchored polyproteins to study the remarkable mechanical properties of HaloTag proteins. We show that the force that triggers unfolding of the HaloTag protein exhibits a 4-fold increase, from 131 to 491 pN, when the direction of the applied force is changed from the C-terminus to the N-terminus. Force-clamp experiments reveal that unfolding of the HaloTag protein is twice as sensitive to pulling force compared to protein L and refolds at a slower rate. We show how these properties allow for the long-term observation of protein folding–unfolding cycles at high forces, without interference from the HaloTag tether.

DOI

Journal: Journal of the American Chemical Society

Reshaping of the conformational search of a protein by the chaperone trigger factor

Alireza Mashaghi, Günter Kramer, Philipp Bechtluft, Beate Zachmann-Brand, Arnold J. M. Driessen, Bernd Bukau, and Sander J. Tans

Protein folding is often described as a search process, in which polypeptides explore different conformations to find their native structure. Molecular chaperones are known to improve folding yields by suppressing aggregation between polypeptides before this conformational search starts as well as by rescuing misfolds after it ends. Although chaperones have long been speculated to also affect the conformational search itself—by reshaping the underlying folding landscape along the folding trajectory—direct experimental evidence has been scarce so far. In Escherichia coli, the general chaperone trigger factor (TF) could play such a role. TF has been shown to interact with nascent chains at the ribosome, with polypeptides released from the ribosome into the cytosol, and with fully folded proteins before their assembly into larger complexes. To investigate the effect of TF from E. coli on the conformational search of polypeptides to their native state, we investigated individual maltose binding protein (MBP) molecules using optical tweezers. Here we show that TF binds folded structures smaller than one domain, which are then stable for seconds and ultimately convert to the native state. Moreover, TF stimulates native folding in constructs of repeated MBP domains. The results indicate that TF promotes correct folding by protecting partially folded states from distant interactions that produce stable misfolded states. As TF interacts with most newly synthesized proteins in E. coli, we expect these findings to be of general importance in understanding protein folding pathways.

DOI

Journal: Nature

Nuclear Lamin-A Scales with Tissue Stiffness and Enhances Matrix-Directed Differentiation

Joe Swift, Irena L. Ivanovska, Amnon Buxboim, Takamasa Harada, P. C. Dave P. Dingal, Joel Pinter, J. David Pajerowski, Kyle R. Spinler, Jae-Won Shin, Manorama Tewari, Florian Rehfeldt, David W. Speicher, Dennis E. Discher

Tissues can be soft like fat, which bears little stress, or stiff like bone, which sustains high stress, but whether there is a systematic relationship between tissue mechanics and differentiation is unknown. Here, proteomics analyses revealed that levels of the nucleoskeletal protein lamin-A scaled with tissue elasticity, E, as did levels of collagens in the extracellular matrix that determine E. Stem cell differentiation into fat on soft matrix was enhanced by low lamin-A levels, whereas differentiation into bone on stiff matrix was enhanced by high lamin-A levels. Matrix stiffness directly influenced lamin-A protein levels, and, although lamin-A transcription was regulated by the vitamin A/retinoic acid (RA) pathway with broad roles in development, nuclear entry of RA receptors was modulated by lamin-A protein. Tissue stiffness and stress thus increase lamin-A levels, which stabilize the nucleus while also contributing to lineage determination.

DOI

Journal: Science

Switching of a coupled spin pair in a single-molecule junction

Stefan Wagner, Ferdinand Kisslinger, Stefan Ballmann, Frank Schramm, Rajadurai Chandrasekar, Tilmann Bodenstein, Olaf Fuhr, Daniel Secker, Karin Fink, Mario Ruben, and Heiko B. Weber

Single-molecule spintronics investigates electron transport through magnetic molecules that have an internal spin degree of freedom. To understand and control these individual molecules it is important to read their spin state. For unpaired spins, the Kondo effect has been observedas a low-temperature anomaly at small voltages. Here, we show that a coupled spin pair in a single magnetic molecule can be detected and that a bias voltage can be used to switch between two states of the molecule. In particular, we use the mechanically controlled break-junction technique to measure electronic transport through a single-molecule junction containing two coupled spin centres that are confined on two Co2+ ions. Spin–orbit configuration interaction methods are used to calculate the combined spin system, where the ground state is found to be a pseudo-singlet and the first excitations behave as a pseudo-triplet. Experimentally, these states can be assigned to the absence and occurrence of a Kondo-like zero-bias anomaly in the low-temperature conductance data, respectively. By applying finite bias, we can repeatedly switch between the pseudo-singlet state and the pseudo-triplet state.

DOI

Journal: Nature Nanotechnology