Hysteresis-based mechanism for the directed motility of the Ncd motor

Ncd is a Kinesin-14 family protein that walks to the microtubule's minus end. Although available structures show its α-helical neck in either pre- or post-stroke orientations, little is known about the transition between these two states. Using a combination of molecular dynamics simulations and structural analyses, we find that the neck sequentially makes intermediate contacts with the motor head along its mostly longitudinal path, and it develops a 24° twist in the post-stroke orientation. The forward (pre-stroke to post-stroke) motion has an ∼4.5 k_BT (where k_B is the Boltzmann constant, and T = 300 K) free-energy barrier and is a diffusion guided by the intermediate contacts. The post-stroke free-energy minimum is higher and is formed ∼10° before reaching the orientation in the post-stroke crystal structure, consistent with previous structural data. The importance of intermediate contacts correlates with the existing motility data, including those for mutant Ncds. Unlike the forward motion, the recovery stroke goes nearly downhill in free energy, powered in part by torsional relaxation of the neck. The hysteresis in the energetics of the neck motion arises from the mechanical compliance of the protein, and together with guided diffusion, it may be key to the directed motility of Ncd.     

Experimental evidence for membrane-mediated protein-protein interaction

Membrane proteins diffuse within the membrane, form oligomers and supramolecular assemblies. Using high-speed atomic force microscopy, we present direct experimental measure of an in-membrane-plane interaction potential between membrane proteins. In purple membranes, ATP-synthase c-rings formed dimers that temporarily dissociated. C-ring dimers revealed subdiffusive motion, while dissociated monomers diffused freely. C-rings center-to-center distance probability distribution allowed the calculation and modeling of an in-membrane-plane energy landscape that presented repulsion at 80 Å, most stable dimer association at 103 Å (−3.5 k_BT strength), and dissociation at 125 Å (−1 k_BT strength). This first experimental data of nonlabeled membrane protein diffusion and the corresponding in-membrane-plane interaction energy landscape characterized membrane protein interaction with an attractive range of several k_BT that reaches to a radius of ∼50 Å within the membrane plane.     

Structural Effects and Translocation of Doxorubicin in a DPPC/Chol Bilayer: The Role of Cholesterol

We use molecular dynamics simulations to characterize the influence of cholesterol (Chol) on the interaction between the anticancer drug doxorubicin (DOX) and a dipalmitoyl phosphatidylcholine/Chol lipid bilayer. We calculate the potential of mean force, which gives us an estimate of the free energy barrier for DOX translocation across the membrane. We find free energy barriers of 23.1 ± 3.1 k_BT, 36.8 ± 5.1 k_BT, and 54.5 ± 4.7 k_BT for systems composed of 0%, 15%, and 30% Chol, respectively. Our predictions agree with Arrhenius activation energies from experiments using phospholipid membranes, including 20 k_BT for 0% Chol and 37.2 k_BT for 20% Chol. The location of the free energy barrier for translocation across the bilayer is dependent on composition. As Chol concentration increases, this barrier changes from the release of DOX into the water to flip-flop over the membrane center. The drug greatly affects local membrane structure by attracting dipalmitoyl phosphatidylcholine headgroups, curving the membrane, and allowing water penetration. Despite its hydrophobicity, DOX facilitates water transport via its polar groups.     

(Un)Folding Mechanisms of the FBP28 WW Domain in Explicit Solvent Revealed by Multiple Rare Event Simulation Methods

We report a numerical study of the (un)folding routes of the truncated FBP28 WW domain at ambient conditions using a combination of four advanced rare event molecular simulation techniques. We explore the free energy landscape of the native state, the unfolded state, and possible intermediates, with replica exchange molecular dynamics. Subsequent application of bias-exchange metadynamics yields three tentative unfolding pathways at room temperature. Using these paths to initiate a transition path sampling simulation reveals the existence of two major folding routes, differing in the formation order of the two main hairpins, and in hydrophobic side-chain interactions. Having established that the hairpin strand separation distances can act as reasonable reaction coordinates, we employ metadynamics to compute the unfolding barriers and find that the barrier with the lowest free energy corresponds with the most likely pathway found by transition path sampling. The unfolding barrier at 300 K is ∼17 k_BT ≈ 42 kJ/mol, in agreement with the experimental unfolding rate constant. This work shows that combining several powerful simulation techniques provides a more complete understanding of the kinetic mechanism of protein folding.     

Temperature Dependences of Torque Generation and Membrane Voltage in the Bacterial Flagellar Motor

In their natural habitats bacteria are frequently exposed to sudden changes in temperature that have been shown to affect their swimming. With our believed to be new methods of rapid temperature control for single-molecule microscopy, we measured here the thermal response of the Na⁺-driven chimeric motor expressed in Escherichia coli cells. Motor torque at low load (0.35 μm bead) increased linearly with temperature, twofold between 15°C and 40°C, and torque at high load (1.0 μm bead) was independent of temperature, as reported for the H⁺-driven motor. Single cell membrane voltages were measured by fluorescence imaging and these were almost constant (∼120 mV) over the same temperature range. When the motor was heated above 40°C for 1–2 min the torque at high load dropped reversibly, recovering upon cooling below 40°C. This response was repeatable over as many as 10 heating cycles. Both increases and decreases in torque showed stepwise torque changes with unitary size ∼150 pN nm, close to the torque of a single stator at room temperature (∼180 pN nm), indicating that dynamic stator dissociation occurs at high temperature, with rebinding upon cooling. Our results suggest that the temperature-dependent assembly of stators is a general feature of flagellar motors.     

PicoNewton-millisecond force steps reveal the transition kinetics and mechanism of the double-stranded DNA elongation

We study the kinetics of the overstretching transition in λ-phage double-stranded (ds) DNA from the basic conformation (B state) to the 1.7-times longer and partially unwound conformation (S state), using the dual-laser optical tweezers under force-clamp conditions at 25°C. The unprecedented resolution of our piezo servo-system, which can impose millisecond force steps of 0.5–2 pN, reveals the exponential character of the elongation kinetics and allows us to test the two-state nature of the B-S transition mechanism. By analyzing the load-dependence of the rate constant of the elongation, we find that the elementary elongation step is 5.85 nm, indicating a cooperativity of ∼25 basepairs. This mechanism increases the free energy for the elementary reaction to ∼94 k_BT, accounting for the stability of the basic conformation of DNA, and explains why ds-DNA can remain in equilibrium as it overstretches.     

Reaction of the Co(II)-substrate radical pair catalytic intermediate in coenzyme B12-dependent ethanolamine ammonia-lyase in frozen aqueous solution from 190 to 217 K

The decay kinetics of the aminoethanol-generated Co^II-substrate radical pair catalytic intermediate in ethanolamine ammonia-lyase from Salmonella typhimurium have been measured on timescales of <10⁵ s in frozen aqueous solution from 190 to 217 K. X-band continuous-wave electron paramagnetic resonance (EPR) spectroscopy of the disordered samples has been used to continuously monitor the full radical pair EPR spectrum during progress of the decay after temperature step reaction initiation. The decay to a diamagnetic state is complete and no paramagnetic intermediate states are detected. The decay exhibits three kinetic regimes in the measured temperature range, as follows. i), Low temperature range, 190 ≤ T ≤ 207 K: the decay is biexponential with constant fast (0.57 ± 0.04) and slow (0.43 ± 0.04) phase amplitudes. ii), Transition temperature range, 207 < T < 214 K: the amplitude of the slow phase decreases to zero with a compensatory rise in the fast phase amplitude, with increasing temperature. iii), High temperature range, T ≥ 214 K: the decay is monoexponential. The observed first-order rate constants for the monoexponential (k_obs,m) and the fast phase of the biexponential decay (k_obs,f) adhere to the same linear relation on an lnk versus T⁻¹ (Arrhenius) plot. Thus, k_obs,m and k_obs,f correspond to the same apparent Arrhenius prefactor and activation energy (logA_app,f (s⁻¹) = 13.0, E_a,app,f = 15.0 kcal/mol), and therefore, a common decay mechanism. We propose that k_obs,m and k_obs,f represent the native, forward reaction of the substrate through the radical rearrangement step. The slow phase rate constant (k_obs,s) for 190 ≤ T ≤ 207 K obeys a different linear Arrhenius relation (logA_app,s (s⁻¹) = 13.9, E_a,app,s = 16.6 kcal/mol). In the transition temperature range, k_obs,s displays a super-Arrhenius increase with increasing temperature. The change in E_a,app,s with temperature and the narrow range over which it occurs suggest an origin in a liquid/glass or dynamical transition. A discontinuity in the activation barrier for the chemical reaction is not expected in the transition temperature range. Therefore, the transition arises from a change in the properties of the protein. We propose that a protein dynamical contribution to the reaction, which is present above the transition temperature, is lost below the transition temperature, owing to an increase in the activation energy barrier for protein motions that are coupled to the reaction. For both the fast and slow phases of the low temperature decay, the dynamical transition in protein motions that are obligatorily coupled to the reaction of the Co^II-substrate radical pair lies below 190 K.     

Single-molecule measurements of dissociation rates and energy landscapes of binary trans snare complexes in parallel versus antiparallel orientation

Interactions between synaptobrevin 2 (Sb2) and syntaxin 1A (Sx1A) can be readily isolated and studied with the use of force spectroscopy single-molecule measurements. We studied interactions between Sx1A and Sb2 in two different orientations (parallel and antiparallel) using four different terminus configurations of these proteins. Force-loading experiments indicated that protein pairs in any configuration/orientation are zippered. We measured the extension and force for disassembly of these interactions, calculated the spontaneous dissociation lifetimes, and determined their free energies, enthalpies, and entropies. Although the free energies were very similar for all four configurations (∼28 k_BT (Eyring model) and ∼20 k_BT (Kramers model)), the enthalpy changes of binary Sx1A-Sb2 interactions varied between 24.7 k_BT and 33.1 k_BT. This variation is consistent with the conformation changes that occur during disassembly of the various protein terminus configurations, as verified by alterations in the extension. The parallel interactions appear to be energetically somewhat advantageous over antiparallel configurations/orientation, especially when the N-termini of Sx1A-Sb2 are left to interact freely.     

The use of small subcutaneous transponders for quantifying thermal biology and torpor in small mammals

Remote measurements of body temperature (T_b) in animals require implantation of relatively large temperature-sensitive radio-transmitters or data loggers, whereas rectal temperature (T_rec) measurements require handling and therefore may bias the results. We investigated whether ∼0.1 g temperature-sensitive subcutaneously implanted transponders can be reliably used to quantify thermal biology and torpor use in small mammals. We examined (i) the precision of transponder readings as a function of temperature and (ii) whether subcutaneous transponders can be used to remotely record subcutaneous temperature (T_sub). Five adult male dunnarts (Sminthopsis macroura, body mass 24 g) were implanted with subcutaneous transponders to determine T_sub as a function of time and ambient temperature (T_a), and in comparison to thermocouple readings of T_rec. Transponder temperature was highly correlated with water bath temperature (r²=0.96–0.99) over a range of approximately 10.0–40.0 °C. Transponders provided reliable data (±0.6 °C) over the T_sub of 21.4–36.9 °C and could be read from a distance of up to 5 cm. Below 21.4 °C, accuracy was reduced to ±2.8 °C, but individual transponder accuracy varied. Consequently, small subcutaneous transponders are useful to remotely quantify thermal physiology and torpor patterns without having to disturb the animal and disrupt torpor. Even at T_sub<21.4 °C where the accuracy of the temperature readings was reduced, transponders do provide reliable data on whether and when torpor is used.     

Thermoregulation of water foraging honeybees—Balancing of endothermic activity with radiative heat gain and functional requirements

Foraging honeybees are subjected to considerable variations of microclimatic conditions challenging their thermoregulatory ability. Solar heat is a gain in the cold but may be a burden in the heat. We investigated the balancing of endothermic activity with radiative heat gain and physiological functions of water foraging Apis mellifera carnica honeybees in the whole range of ambient temperatures (T_a) and solar radiation they are likely to be exposed in their natural environment in Middle Europe.The mean thorax temperature (T_th) during foraging stays was regulated at a constantly high level (37.0-38.5 °C) in a broad range of T_a (3-30 °C). At warmer conditions (T_a = 30-39 °C) T_th increased to a maximal level of 45.3 °C. The endothermic temperature excess (difference of T_body − T_a of living and dead bees) was used to assess the endogenously generated temperature elevation as a correlate of energy turnover. Up to a T_a of ∼30 °C bees used solar heat gain for a double purpose: to reduce energetic expenditure and to increase T_th by about 1-3 °C to improve force production of flight muscles. At higher T_a they exhibited cooling efforts to get rid of excess heat. A high T_th also allowed regulation of the head temperature high enough to guarantee proper function of the bees’ suction pump even at low T_a. This shortened the foraging stays and this way reduced energetic costs. With decreasing T_a bees also reduced arrival body weight and crop loading to do both minimize costs and optimize flight performance.     

Electron heat transport through the plasma-electrode boundary in weakly ionized plasma

The average electron thermal energies in the emission flux from the electrode into the plasma, ? ₁, and from the plasma toward the electrode, ? ₂, are determined for the cases of large and small values of the coefficient of kinetic reflection. It is shown that these energies vary within the ranges 0.5k _B T _c < ? ₁ < 2k _B T _c and 0.5k _B T _e < ? ₂ < 2k _B T _e , where T _c and T _e are the temperatures of the cathode and plasma electrons, respectively. The obtained values can be used to formulate the boundary conditions for the hydrodynamic equations at the electrode or a dielectric wall.     

The Effect of Myofilament Compliance on Kinetics of Force Generation by Myosin Motors in Muscle

We use the inhibitor of isometric force of skeletal muscle N-benzyl-p-toluene sulfonamide (BTS) to decrease, in a dose dependent way, the number of myosin motors attached to actin during the steady isometric contraction of single fibers from frog skeletal muscle (4°C, 2.1 μm sarcomere length). In this way we can reduce the strain in the myofilament compliance during the isometric tetanus (T₀) from 3.54 nm in the control solution (T_0,NR) to ∼0.5 nm in 1 μM BTS, where T₀ is reduced to ∼0.15 T_0,NR. The quick force recovery after a step release (1-3 nm per half-sarcomere) becomes faster with the increase of BTS concentration and the decrease of T₀. The simulation of quick force recovery with a multistate model of force generation, that adapts Huxley and Simmons model to account for both the high stiffness of the myosin motor (∼3 pN/nm) and the myofilament compliance, shows that the increase in the rate of quick force recovery by BTS is explained by the reduced strain in the myofilaments, consequent to the decrease in half-sarcomere force. The model estimates that i), for the same half-sarcomere release the state transition kinetics in the myosin motor are five times faster in the absence of filament compliance than in the control; and ii), the rate of force recovery from zero to T₀ is ∼6000/s in the absence of filament compliance.     

Combined ventilatory responses to aerial hypoxia and temperature in the South American lungfish Lepidosiren paradoxa

The control of pulmonary ventilation in South American lungfish Lepidosiren paradoxa is poorly understood. Interactions between temperature and hypoxia are particularly relevant due to large seasonal variations of its habitat. Therefore, we tested the hypothesis that the ventilatory responses to aerial hypoxia of Lepidosiren are highly dependent on ambient temperature. We used a pneumotachograph to measure pulmonary ventilation (V_E), tidal volume (V_T) and respiratory frequency (f_R) during normoxic (21% O₂) and hypoxic (12%, 10% and 7% O₂) conditions at two temperatures (25 and 35 °C). Blood gases, arterial PO₂ (PaO₂), arterial PCO₂ (PaCO₂) and arterial pH (pH_a) were also evaluated. At 25 °C, V_E increased significantly at 10% and 7% hypoxic levels when compared to the control value (21% O₂). At 35 °C, all hypoxic levels elicited a significant increase of V_E relative to control values. V_E is augmented mostly by increases of respiratory frequency (f_R), and there were significant interactions (p<0.001) between aerial hypoxia and temperature. PaCO₂ increased from ∼22 mmHg (normoxic value at 25 °C) to ∼32 mmHg (normoxic value at 35 °C). Concomitantly, the pH_a decreased from 7.51 (25 °C) to 7.38 (35 °C). Hypoxia-induced hyperventilation caused a reduction in PaCO₂ and an increase in pH_a, which were more pronounced at 35 °C than at 25 °C, reflecting an increased hyperventilation under the high temperature. In conclusion, the magnitude of ventilatory response is highly temperature-dependent in L. paradoxa, which is important for an animal experiencing large seasonal variations.     

Temperature dependence of structure, bending rigidity, and bilayer interactions of dioleoylphosphatidylcholine bilayers

X-ray diffuse scattering was measured from oriented stacks and unilamellar vesicles of dioleoylphosphatidylcholine lipid bilayers to obtain the temperature dependence of the structure and of the material properties. The area/molecule, A, was 75.5 Å² at 45°C, 72.4 Å² at 30°C, and 69.1 Å² at 15°C, which gives the area expansivity α_A = 0.0029/deg at 30°C, and we show that this value is in excellent agreement with the polymer brush theory. The bilayer becomes thinner with increasing temperature; the contractivity of the hydrocarbon portion was α_Dc = 0.0019/deg; the difference between α_A and α_Dc is consistent with the previously measured volume expansivity α_Vc = 0.0010/deg. The bending modulus K_C decreased as exp(455/T) with increasing T (K). Our area compressibility modulus K_A decreased with increasing temperature by 5%, the same as the surface tension of dodecane/water, in agreement again with the polymer brush theory. Regarding interactions between bilayers, the compression modulus B as a function of interbilayer water spacing D′_W was found to be nearly independent of temperature. The repulsive fluctuation pressure calculated from B and K_C increased with temperature, and the Hamaker parameter for the van der Waals interaction was nearly independent of temperature; this explains why the fully hydrated water spacing, D′_W, that we obtain from our structural results increases with temperature.     

A Link between Hinge-Bending Domain Motions and the Temperature Dependence of Catalysis in 3-Isopropylmalate Dehydrogenase

Enzyme function depends on specific conformational motions. We show that the temperature dependence of enzyme kinetic parameters can provide insight into these functionally relevant motions. While investigating the catalytic properties of IPMDH from Escherichia coli, we found that its catalytic efficiency (k_cat/K_M,IPM) for the substrate IPM has an unusual temperature dependence, showing a local minimum at ∼35°C. In search of an explanation, we measured the individual constants k_cat and K_M,IPM as a function of temperature, and found that the van 't Hoff plot of K_M,IPM shows sigmoid-like transition in the 20-40°C temperature range. By means of various measurements including hydrogen-deuterium exchange and fluorescence resonance energy transfer, we showed that the conformational fluctuations, including hinge-bending domain motions increase more steeply with temperatures >30°C. The thermodynamic parameters of ligand binding determined by isothermal titration calorimetry as a function of temperature were found to be strongly correlated to the conformational fluctuations of the enzyme. Because the binding of IPM is associated with a hinge-bending domain closure, the more intense hinge-bending fluctuations at higher temperatures increasingly interfere with IPM binding, thereby abruptly increasing its dissociation constant and leading to the observed unusual temperature dependence of the catalytic efficiency.     

Daily cycles of hibernation in the kangaroo rat, Dipodomys merriami

Thirty-six kangaroo rats were captured in the Mojave Desert near Las Vegas. Eight rats, group A, were kept at room temperature, 25 ± 2 °C. Ten, Group B, were kept at 13–15 °C and fed ad libitum. Eighteen, group C, were kept at 13–15 °C and fed only 2 g of dry oats daily. Rate of O₂ consumption, VO₂, food intake, rectal temperature, T_re., body weight and composition were measured in all groups. Group B showed a significant increase in VO₂, and food intake and no change in T_re body weight as compared to group A. After 2 days on the limited food intake group C began to lose weight, and T_re then began to fluctuate ranging between 14 and 36 °C; the animals exhibited hibernation when the T_re was low. Eight of the 18 rats of group C reached T_re values of 14 °C or below; only one of these survived. The lowest T_re in the other 10 was 15 °C; all survived. Chemical analysis of the homogenized rats showed a significant decrease in body fat in group C to average 1.0% contrasted with 7.8% in group B and 3.7% in group A. The VO₂ ranged from 1.9 ml/g hr at a T_re of 36.5 to 0.2 ml/g hr at a T_re of 15 °C. In conclusion D. merriami utilizes hibernation as an effective adaptive mechanism to carry out their essential body functions when on a limited food intake. It seems that maintaining a level of more than 1.5% of body fat is essential for successful arousal from hibernation.     

Comparative thermodynamics of opioid receptor ligand interaction in the bovine adrenal medulla membranes—Evidence of opioid site heterogeneity

1. A marked dependence on temperature of agonist binding δ, μ and κ₁₋₃, opioid sites in the bovine adrenal medulla was observed, at the range of 0 to 37°C. These changes concern kinetic (k₁) and equilibrium constants (K_d), but not binding capacities (B_max).2. These dependences are different for each ligand and each opioid receptor, suggesting their molecular heterogeneity.3. The comparative thermodynamics indicates that the interaction of opioid agonists with their receptor is exergonic (ΔG° < 0) and entropy driven (ΔS° > 0).4. The comparison of Van't Hoff and Arrhenius plots indicates a discrete mechanism in the binding of each opioid receptor.     

Temperature and competitive anion-binding studies of carbonic anhydrase

The ³⁵Cl-nmr line width for solutions of human carbonic anhydrase B in 0.5 m NaCl at pH 6.46 and 8.59 has been examined as a function of temperature. An Arrhenius plot of the line width decreases linearly with decreasing temperature over the temperature range 0–38.5 °C. This behavior indicates that the lifetime of the enzyme-zinc-chloride complex is the dominating relaxation time of the system. The value of k_off at pH 6.46 and 8.59 at 25 °C is 1 × 10⁶ sec⁻¹ and 7.3 × 10⁵ sec⁻¹, respectively. Using a value of K_i of 0.2 m values for k_on are 5 × 10⁶m⁻¹ sec⁻¹ and 3.7 × 10⁶m⁻¹ sec⁻¹. These values are somewhat lower than that for aqueous zinc ion and may be related to the hindered nature of the zinc site in the enzyme. The energy of activation obtained for the chloride exchange process is 3.6 kcal/mole. Anion competitive binding studies for bovine carbonic anhydrase have also been made for a number of monovalent anions. K_I values obtained by analysis of chloride line broadening are in agreement with those determined kinetically. Although chloride and iodide competitive binding studies can be interpreted in terms of zinc-iodide binding, the results do not distinguish between the possible E-Zn-OH₂-I and E-Zn-I forms of the complex.     

Evaluation of the relevance of the glassy state as stability criterion for freeze-dried bacteria by application of the Arrhenius and WLF model

The aim of this work was to describe the temperature dependence of microbial inactivation for several storage conditions and protective systems (lactose, trehalose and dextran) in relation to the physical state of the sample, i.e. the glassy or non-glassy state. The resulting inactivation rates k were described by applying two models, Arrhenius and Williams–Landel–Ferry (WLF), in order to evaluate the relevance of diffusional limitation as a protective mechanism. The application of the Arrhenius model revealed a significant decrease in activation energy E_a for storage conditions close to T_g. This finding is an indication that the protective effect of a surrounding glassy matrix can, at least, partly be ascribed to its inherent restricted diffusion and mobility. The application of the WLF model revealed that the temperature dependence of microbial inactivation above T_g is significantly weaker than predicted by the universal coefficients. Thus, it can be concluded that microbial inactivation is not directly linked with the mechanical relaxation behavior of the surrounding matrix as it was reported for viscosity and crystallization phenomena in case of disaccharide systems.     

Evaluation of the relevance of the glassy state as stability criterion for freeze-dried bacteria by application of the Arrhenius and WLF model

The aim of this work was to describe the temperature dependence of microbial inactivation for several storage conditions and protective systems (lactose, trehalose and dextran) in relation to the physical state of the sample, i.e. the glassy or non-glassy state. The resulting inactivation rates k were described by applying two models, Arrhenius and Williams–Landel–Ferry (WLF), in order to evaluate the relevance of diffusional limitation as a protective mechanism. The application of the Arrhenius model revealed a significant decrease in activation energy E_a for storage conditions close to T_g. This finding is an indication that the protective effect of a surrounding glassy matrix can, at least, partly be ascribed to its inherent restricted diffusion and mobility. The application of the WLF model revealed that the temperature dependence of microbial inactivation above T_g is significantly weaker than predicted by the universal coefficients. Thus, it can be concluded that microbial inactivation is not directly linked with the mechanical relaxation behavior of the surrounding matrix as it was reported for viscosity and crystallization phenomena in case of disaccharide systems.