Self-Assembled Enzymatic Monolayer Directly Bound to a Gold Surface: Activity and Molecular Recognition Force Spectroscopy Studies

Lindsay R. Ditzler, Arundhuti Sen, Michael J. Gannon, Amnon Kohen, and Alexei V. Tivanski


Escherichia coli dihydrofolate reductase (ecDHFR) has one surface cysteine, C152, located opposite and distal to the active site. Here, we show that the enzyme spontaneously assembles on an ultraflat gold surface as a homogeneous, covalently bound monolayer. Surprisingly, the activity of the gold-immobilized ecDHFR as measured by radiographic analysis was found to be similar to that of the free enzyme in solution. Molecular recognition force spectroscopy was used to study the dissociation forces involved in the rupture of AFM probe-tethered methotrexate (MTX, a tight-binding inhibitor of DHFR) from the gold-immobilized enzyme. Treatment of the ecDHFR monolayer with free MTX diminished the interaction of the functionalized tip with the surface, suggesting that the interaction was indeed active-site specific. These findings demonstrate the viability of a simple and direct enzymatic surface-functionalization without the use of spacers, thus, opening the door to further applications in the area of biomacromolecular force spectroscopy.
DOI
Journal: Journal of the American Chemical Society

A single synthetic small molecule that generates force against a load

• Perrine Lussis,
• Tiziana Svaldo-Lanero,
• Andrea Bertocco,
• Charles-André Fustin,
• David A. Leigh, and 
• Anne-Sophie Duwez

• Some biomolecules are able to generate directional forces by rectifying random thermal motions. This allows these molecular machines to perform mechanical tasks such as intracellular cargo transport or muscle contraction in plants and animals. Although some artificial molecular machines have been synthesized and used collectively to perform mechanical tasks, so far there have been no direct measurements of mechanical processes at the single-molecule level. Here we report measurements of the mechanical work performed by a synthetic molecule less than 5 nm long. We show that biased Brownian motion of the sub-molecular components in a hydrogen-bonded [2]rotaxane—a molecular ring threaded onto a molecular axle—can be harnessed to generate significant directional forces. We used the cantilever of an atomic force microscope to apply a mechanical load to the ring during single-molecule pulling–relaxing cycles. The ring was pulled along the axle, away from the thermodynamically favoured binding site, and was then found to travel back to this site against an external load of 30 pN. Using fluctuation theorems, we were able to relate measurements of the work done at the level of individual rotaxane molecules to the free-energy change as previously determined from ensemble measurements. The results show that individual rotaxanes can generate directional forces of similar magnitude to those generated by natural molecular machines.

• DOI

• Journal: Nature Nanotechnology

Visualization of the nanospring dynamics of the IκBα ankyrin repeat domain in real time

Jorge A. Lamboy, Hajin Kimb, Kyung Suk Lee, Taekjip Ha, and Elizabeth A. Komives


IκBα is a crucial regulator of NFκB transcription. NFκB-mediated gene activation is robust because levels of free IκBα are kept extremely low by rapid, ubiquitin-independent degradation of newly synthesized IκBα. IκBα has a weakly folded ankyrin repeat 5–6 (AR5–6) region that is critical in establishing its short intracellular half-life. The AR5–6 region of IκBα folds upon binding to NFκB. The NFκB-bound IκBα has a long half-life and requires ubiquitin-targeted degradation. We present single molecule FRET evidence that the native state of IκBα transiently populates an intrinsically disordered state characterized by a more extended structure and fluctuations on the millisecond time scale. Binding to NFκB or introduction of stabilizing mutations in AR 6 suppressed the fluctuations, whereas higher temperature or small amounts of urea increased them. The results reveal that intrinsically disordered protein regions transition between collapsed and extended conformations under native conditions.


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Journal: Proceedings of the National Academy of Sciences

Simulation studies of protein folding/unfolding equilibrium under polar and non-polar confinement

Jianhui Tian and Angel E Garcia


We study the equilibrium folding/unfolding thermodynamics of a small globular mini-protein, the Trp-cage, that is confined to the interior of a 2 nm radius fullerene ball. The interactions of the fullerene surface are changed from non-polar to polar to mimic the interior of the GroEL/ES chaperonin that assists proteins to fold in vivo. We find that non-polar confinement stabilizes the folded state of the protein due to the effects of volume reduction that destabilize the unfolded state, and also due to interactions with the fullerene surface. For the Trp-cage, polar confinement has a net destabilizing effect that results from the stabilizing confinement and the competitive exclusion effect that keeps the protein away from the surface hydration shell, and stronger interactions between charged side chains in the protein with the polar surface that competes against the formation of an ion pair that stabilizes the protein folded state. We show that confinement effects due to volume reduction can be overcome by sequence specific interactions of the protein side chains with the encapsulating surface. This study shows that there is a complex balance among many competing effects that determine the mechanism of GroEL chaperonin in enhancing folding rate of polypeptide inside its cavity.


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Journal: Journal of the American Chemical Society

Cytoskeletal Control of CD36 Diffusion Promotes Its Receptor and Signaling Function

Khuloud Jaqaman, Hirotaka Kuwata, Nicolas Touret, Richard Collins, William S. Trimble, Gaudenz Danuser, and Sergio Grinstein


The mechanisms that govern receptor coalescence into functional clusters—often a critical step in their stimulation by ligand—are poorly understood. We used single-molecule tracking to investigate the dynamics of CD36, a clustering-responsive receptor that mediates oxidized LDL uptake by macrophages. We found that CD36 motion in the membrane was spatially structured by the cortical cytoskeleton. A subpopulation of receptors diffused within linear confinement regions whose unique geometry simultaneously facilitated freedom of movement along one axis while increasing the effective receptor density. Co-confinement within troughs enhanced the probability of collisions between unligated receptors and promoted their clustering. Cytoskeleton perturbations that inhibited diffusion in linear confinement regions reduced receptor clustering in the absence of ligand and, following ligand addition, suppressed CD36-mediated signaling and internalization. These observations demonstrate a role for the cytoskeleton in controlling signal transduction by structuring receptor diffusion within membrane regions that increase their collision frequency.


DOI


Journal: Cell

Electrostatic Interactions Involving the Extreme C Terminus of Nuclear Export Factor CRM1 Modulate Its Affinity for Cargo

Abigail M. Fox, Danguole Ciziene, Stephen H. McLaughlin, and Murray Stewart



The toroid-shaped nuclear protein export factor CRM1 is constructed from 21 tandem HEAT repeats, each of which contains an inner (B) and outer (A) α-helix joined by loops. Proteins targeted for export have a nuclear export signal (NES) that binds between the A-helices of HEAT repeats 11 and 12 on the outer surface of CRM1. RanGTP binding increases the affinity of CRM1 for NESs. In the absence of RanGTP, the CRM1 C-terminal helix, together with the HEAT repeat 9 loop, modulates its affinity for NESs. Here we show that there is an electrostatic interaction between acidic residues at the extreme distal tip of the C-terminal helix and basic residues on the HEAT repeat 12 B-helix that lies on the inner surface of CRM1 beneath the NES binding site. Small angle x-ray scattering indicates that the increased affinity for NESs generated by mutations in the C-terminal helix is not associated with large scale changes in CRM1 conformation, consistent with the modulation of NES affinity being mediated by a local change in CRM1 near the NES binding site. These data also suggest that in the absence of RanGTP, the C-terminal helix lies across the CRM1 toroid in a position similar to that seen in the CRM1-Snurportin crystal structure. By creating local changes that stabilize the NES binding site in its closed conformation and thereby reducing the affinity of CRM1 for NESs, the C-terminal helix and HEAT 9 loop facilitate release of NES-containing cargo in the cytoplasm and also inhibit their return to the nucleus.


DOI


Journal: The Journal of Biological Chemistry

Mechanosensitive shivering of model tissues under controlled aspiration

Karine Guevorkian, David Gonzalez-Rodriguez, Camille Carlier,Sylvie Dufour, and Françoise Brochard-Wyart
During embryonic development and wound healing, the mechanical signals transmitted from cells to their neighbors induce tissue rearrangement and directional movements. It has been observed that forces exerted between cells in a developing tissue under stress are not always monotonically varying, but they can be pulsatile. Here we investigate the response of model tissues to controlled external stresses. Spherical cellular aggregates are subjected to one-dimensional stretching forces using micropipette aspiration. At large enough pressures, the aggregate flows smoothly inside the pipette. However, in a narrow range of moderate aspiration pressures, the aggregate responds by pulsed contractions or “shivering.” We explain the emergence of this shivering behavior by means of a simple analytical model where the uniaxially stretched cells are represented by a string of Kelvin–Voigt elements. Beyond a deformation threshold, cells contract and pull on neighboring cells after a time delay for cell response. Such an active behavior has previously been found to cause tissue pulsation during dorsal closure of Drosophila embryo.
DOI
Journal: Proceedings of the National Academy of Sciences

Quantitative fluorescence imaging of protein diffusion and interaction in living cells

Jérémie Capoulade, Malte Wachsmuth, Lars Hufnagel, and Michael Knop


Diffusion processes and local dynamic equilibria inside cells lead to nonuniform spatial distributions of molecules, which are essential for processes such as nuclear organization and signaling in cell division, differentiation and migration. To understand these mechanisms, spatially resolved quantitative measurements of protein abundance, mobilities and interactions are needed, but current methods have limited capabilities to study dynamic parameters. Here we describe a microscope based on light-sheet illumination that allows massively parallel fluorescence correlation spectroscopy (FCS) measurements and use it to visualize the diffusion and interactions of proteins in mammalian cells and in isolated fly tissue. Imaging the mobility of heterochromatin protein HP1α in cell nuclei we could provide high-resolution diffusion maps that reveal euchromatin areas with heterochromatin-like HP1α-chromatin interactions. We expect that FCS imaging will become a useful method for the precise characterization of cellular reaction-diffusion processes.


DOI


Journal: Nature Biotechnology

Growth cones as soft and weak force generators

Timo Betz, Daniel Koch, Yun-Bi Lu, Kristian Franze, and Josef A. Käs

Many biochemical processes in the growth cone finally target its biomechanical properties, such as stiffness and force generation, and thus permit and control growth cone movement. Despite the immense progress in our understanding of biochemical processes regulating neuronal growth, growth cone biomechanics remains poorly understood. Here, we combine different experimental approaches to measure the structural and mechanical properties of a growth cone and to simultaneously determine its actin dynamics and traction force generation. Using fundamental physical relations, we exploited these measurements to determine the internal forces generated by the actin cytoskeleton in the lamellipodium. We found that, at timescales longer than the viscoelastic relaxation time ofτ = 8.5 ± 0.5 sec, growth cones show liquid-like characteristics, whereas at shorter time scales they behaved elastically with a surprisingly low elastic modulus of E = 106 ± 21 Pa. Considering the growth cone’s mechanical properties and retrograde actin flow, we determined the internal stress to be on the order of 30 pN per μm². Traction force measurements confirmed these values. Hence, our results indicate that growth cones are particularly soft and weak structures that may be very sensitive to the mechanical properties of their environment.

DOI

Journal: Proceedings of the National Academy of Sciences

Fast-folding α-helices as reversible strain absorbers in the muscle protein myomesin

Felix Berkemeier, Morten Bertz, Senbo Xiao , Nikos Pinotsis , Matthias Wilmanns, Frauke Gräter, and Matthias Rief




The highly oriented filamentous protein network of muscle constantly experiences significant mechanical load during muscle operation. The dimeric protein myomesin has been identified as an important M-band component supporting the mechanical integrity of the entire sarcomere. Recent structural studies have revealed a long α-helical linker between the C-terminal immunoglobulin (Ig) domains My12 and My13 of myomesin. In this paper, we have used single-molecule force spectroscopy in combination with molecular dynamics simulations to characterize the mechanics of the myomesin dimer comprising immunoglobulin domains My12–My13. We find that at forces of approximately 30 pN the α-helical linker reversibly elongates allowing the molecule to extend by more than the folded extension of a full domain. High-resolution measurements directly reveal the equilibrium folding/unfolding kinetics of the individual helix. We show that α-helix unfolding mechanically protects the molecule homodimerization from dissociation at physiologically relevant forces. As fast and reversible molecular springs the myomesin α-helical linkers are an essential component for the structural integrity of the M band.


DOI


Journal: Proceedings of the National Academy of Sciences

Highly Anisotropic Stability and Folding Kinetics of a Single Coiled Coil Protein under Mechanical Tension

Ying Gao, George Sirinakis, and Yongli Zhang



Coiled coils are one of the most abundant protein structural motifs and widely mediate protein interactions and force transduction or sensation. They are thus model systems for protein engineering and folding studies, particularly the GCN4 coiled coil. Major single-molecule methods have also been applied to this protein and revealed its folding kinetics at various spatiotemporal scales. Nevertheless, the folding energy and the kinetics of a single GCN4 coiled coil domain have not been well determined at a single-molecule level. Here we used high-resolution optical tweezers to characterize the folding and unfolding reactions of a single GCN4 coiled coil domain and their dependence on the pulling direction. In one axial and two transverse pulling directions, we observed reversible, two-state transitions of the coiled coil in real time. The transitions equilibrate at pulling forces ranging from 6 to 12 pN, showing different stabilities of the coiled coil in regard to pulling direction. Furthermore, the transition rates vary with both the magnitude and the direction of the pulling force by greater than 1000 folds, indicating a highly anisotropic and topology-dependent energy landscape for protein transitions under mechanical tension. We developed a new analytical theory to extract energy and kinetics of the protein transition at zero force. The derived folding energy does not depend on the pulling direction and is consistent with the measurement in bulk, which further confirms the applicability of the single-molecule manipulation approach for energy measurement. The highly anisotropic thermodynamics of proteins under tension should play important roles in their biological functions.

DOI

Journal: Journal of the American Chemical Society

Molecular Recognition of Insulin by a Synthetic Receptor

Jordan M. Chinai, Alexander B. Taylor, Lisa M. Ryno, Nicholas D. Hargreaves, Christopher A. Morris, P. John Hart, and Adam R. Urbach



The discovery of molecules that bind tightly and selectively to desired proteins continues to drive innovation at the interface of chemistry and biology. This paper describes the binding of human insulin by the synthetic receptor cucurbit[7]uril (Q7) in vitro. Isothermal titration calorimetry and fluorescence spectroscopy experiments show that Q7 binds to insulin with an equilibrium association constant of 1.5 × 10E6 M−1 and with 50−100-fold selectivity versus proteins that are much larger but lack an N-terminal aromatic residue, and with >1000-fold selectivity versus an insulin variant lacking the N-terminal phenylalanine (Phe) residue. The crystal structure of the Q7·insulin complex shows that binding occurs at the N-terminal Phe residue and that the N-terminus unfolds to enable binding. These findings suggest that site-selective recognition is based on the properties inherent to a protein terminus, including the unique chemical epitope presented by the terminal residue and the greater freedom of the terminus to unfold, like the end of a ball of string, to accommodate binding. Insulin recognition was predicted accurately from studies on short peptides and exemplifies an approach to protein recognition by targeting the terminus.

DOI

Journal: Journal of the American Chemical Society

Histone fold modifications control nucleosome unwrapping and disassembly

Marek Simon, Justin A. North, John C. Shimko, Robert A. Forties, Michelle B. Ferdinand, Mridula Manohar, Meng Zhang, Richard Fishel, Jennifer J. Ottesen, and Michael G. Poirier



Nucleosomes are stable DNA–histone protein complexes that must be unwrapped and disassembled for genome expression, replication, and repair. Histone posttranslational modifications (PTMs) are major regulatory factors of these nucleosome structural changes, but the molecular mechanisms associated with PTM function remains poorly understood. Here we demonstrate that histone PTMs within distinct structured regions of the nucleosome directly regulate the inherent dynamic properties of the nucleosome. Precise PTMs were introduced into nucleosomes by chemical ligation. Single molecule magnetic tweezers measurements determined that only PTMs near the nucleosome dyad increase the rate of histone release in unwrapped nucleosomes. In contrast, FRET and restriction enzyme analysis reveal that only PTMs throughout the DNA entry–exit region increase unwrapping and enhance transcription factor binding to nucleosomal DNA. These results demonstrate that PTMs in separate structural regions of the nucleosome control distinct dynamic events, where the dyad regulates disassembly while the DNA entry–exit region regulates unwrapping. These studies are consistent with the conclusion that histone PTMs may independently influence nucleosome dynamics and associated chromatin functions.

DOI


Journal:  Proceedings of the National Academy of Sciences

High-Speed Atomic Force Microscopy Reveals Rotary Catalysis of Rotorless F1-ATPase

Takayuki Uchihashi, Ryota Iino, Toshio Ando,and Hiroyuki Noji



F1 is an adenosine triphosphate (ATP)–driven motor in which three torque-generating β subunits in the α3β3 stator ring sequentially undergo conformational changes upon ATP hydrolysis to rotate the central shaft γ unidirectionally. Although extensive experimental and theoretical work has been done, the structural basis of cooperative torque generation to realize the unidirectional rotation remains elusive. We used high-speed atomic force microscopy to show that the rotorless F1 still “rotates”; in the isolated α3β3 stator ring, the three β subunits cyclically propagate conformational states in the counterclockwise direction, similar to the rotary shaft rotation in F1. The structural basis of unidirectionality is programmed in the stator ring. These findings have implications for cooperative interplay between subunits in other hexameric ATPases.



DOI


Journal: Science

Pulsed Pressure Perturbations, an Extra Dimension in NMR Spectroscopy of Proteins

Werner Kremer , Martin Arnold , Claudia Elisabeth Munte , Rainer Hartl , Markus Beck Erlach , Joerg Koehler , Alexander Meier , and Hans Robert Kalbitzer


The introduction of the multidimensional NMR spectroscopy was a breakthrough in biological NMR me-thodology since it allowed the unequivocal correlation of different spin states of the system. The introduction of large pressure perturbations in the corresponding radio frequency (RF) pulse sequences adds an extra structural dimension into these experiments. We have developed a microprocessor controlled pressure jump unit that is able to introduce fast, strong pressure changes at any point in the pulse sequences. Repetitive pressure changes of 80 MPa in the sample tube are thus feasible in less than 30 ms. Two general forms of these experiments are proposed here, the pressure perturbation transient state spectroscopy (PPTSS) and the pressure perturbation state correlation spectroscopy (PPSCS). PPTSS can be used to measure the rate constants and the activation energies and activation volumes for the transition between different conformational states including the folded and unfolded state of proteins, for polymerisation-depolymerisation processes and for ligand binding at atomic resolution. PPSCS spectroscopy correlates the NMR parameters of different pressure induced states of the system thus allowing the measurement of properties of a given pressure induced state such as a folding intermediate in a different state e. g. the folded state. Selected examples for PPTSS and PPSCS spectroscopy are presented in this paper.


DOI


Journal: Journal of the American Chemical Society

Protein Unfolding under Force: Crack Propagation in a Network

Adam M.R. de Graff, Gareth Shannon, Daniel W. Farrell, Philip M. Williams, and M.F. Thorpe

The mechanical unfolding of a set of 12 proteins with diverse topologies is investigated using an all-atom constraint-based model. Proteins are represented as polypeptides cross-linked by hydrogen bonds, salt bridges, and hydrophobic contacts, each modeled as a harmonic inequality constraint capable of supporting a finite load before breaking. Stereochemically acceptable unfolding pathways are generated by minimally overloading the network in an iterative fashion, analogous to crack propagation in solids. By comparing the pathways to those from molecular dynamics simulations and intermediates identified from experiment, it is demonstrated that the dominant unfolding pathways for 9 of the 12 proteins studied are well described by crack propagation in a network.


DOI


Journal: Biophysical Journal

Single Molecule Detection of One, Two and Multiplex Proteins Involved in DNA/RNA Transaction

Yupeng Qiu and Sua Myong


Cellular processes involve complex arrangement of proteins engaged in a multitude of reactions, yet in a highly coordinated manner. The level of complexity, however, makes it difficult to investigate the role played by the individual protein constituent. Data taken from the conventional bulk solution methods suffer from ensemble averaging effect in which information from individual molecules is masked. The single molecule detection method overcomes this limitation by offering unique tools for monitoring the activity of individual molecules in isolation and in real-time dynamics. Included in this review are recent articles of single molecule studies representing a diverse array of experimental platforms which demonstrate the power and spectrum of single molecule detection.


DOI


Journal: Cellular and Molecular Bioengineering