Identical sequences, different behaviors: Protein diversity captured at the single-molecule level

The classical "one sequence, one structure, one function" paradigm has shaped much of our intuition of how proteins work inside the cell. Partially due to the insight provided by bulk biochemical assays, individual biomolecules are often assumed to behave as identical entities, and their characterization relies on ensemble averages that flatten any conformational diversity into a unique phenotype. While the emergence of single-molecule techniques opened the gates to interrogating individual molecules, technical shortcomings typically limit the duration of these measurements, which precludes a complete characterization of an individual protein and, hence, capturing the heterogeneity among molecular populations. Here, we introduce an ultrastable magnetic tweezers design, which enables us to measure the folding dynamics of a single protein during several uninterrupted days with high temporal and spatial resolution. Thanks to this instrumental development, we fully characterize the nanomechanics of two proteins with a very distinct force response, the talin R3IVVI domain and protein L. Days-long recordings on the same protein individual accumulate thousands of folding transitions with submicrosecond resolution, allowing us to reconstruct their free energy landscapes and describe how they evolve with force. By mapping the nanomechanical identity of many different protein individuals, we directly capture their molecular diversity as a quantifiable dispersion on their force response and folding kinetics. By significantly expanding the measurable timescales, our instrumental development offers a tool for profiling individual molecules, opening the gates to directly characterizing biomolecular heterogeneity.

Embryonic cerebrospinal fluid influence in the subependymal neurogenic niche in adult mouse hippocampus

The adult mouse hippocampal neurogenic niche is a complex structure which is not completely understood. It has mainly been related to the Subgranular layer of the dentate gyrus; however, as a result of differential neural stem cell populations reported in the subventricular zone of the lateral ventricle and associated with the hippocampus, the possibility remains of a multifocal niche reproducing developmental stages. Here, using a set of molecular markers for neural precursors, we describe in the adult mouse brain hippocampus the existence of a disperse population of neural precursors in the Subependymal Zone, the Dentate Migratory Stream and the hilus; these display dynamic behaviour compatible with neurogenesis. This supports the idea that the adult hippocampal niche cannot be restricted to the dentate gyrus subgranular layer. In other neurogenic niches such as the Subventricular Zone, a functional periventricular dependence has been shown due to the ability to respond to embryonic cerebro-spinal fluid. In this study, we demonstrate that neural precursors from the three areas studied (Sub-ependymal Zone, Dentate Migratory Stream and hilus) are able to modify their behaviour by increasing neurogenesis in a locally differential manner. Our results are compatible with the persistence in the adult mouse hippocampus of a neurogenic niche with the same spatial structure as that seen during development and early postnatal stages.

Protein folding modulates the chemical reactivity of a Gram-positive adhesin

Gram-positive bacteria colonize mucosal tissues, withstanding large mechanical perturbations such as coughing, which generate shear forces that exceed the ability of non-covalent bonds to remain attached. To overcome these challenges, the pathogen Streptococcus pyogenes utilizes the protein Cpa, a pilus tip-end adhesin equipped with a Cys-Gln thioester bond. The reactivity of this bond towards host surface ligands enables covalent anchoring; however, colonization also requires cell migration and spreading over surfaces. The molecular mechanisms underlying these seemingly incompatible requirements remain unknown. Here we demonstrate a magnetic tweezers force spectroscopy assay that resolves the dynamics of the Cpa thioester bond under force. When folded at forces <6 pN, the Cpa thioester bond reacts reversibly with amine ligands, which are common in inflammation sites; however, mechanical unfolding and exposure to forces >6 pN block thioester reformation. We hypothesize that this folding-coupled reactivity switch (termed a smart covalent bond) could allow the adhesin to undergo binding and unbinding to surface ligands under low force and remain covalently attached under mechanical stress.

Direct observation of a coil-to-helix contraction triggered by vinculin binding to talin

Vinculin binds unfolded talin domains in focal adhesions, which recruits actin filaments to reinforce the mechanical coupling of this organelle. However, it remains unknown how this interaction is regulated and its impact on the force transmission properties of this mechanotransduction pathway. Here, we use magnetic tweezers to measure the interaction between vinculin head and the talin R3 domain under physiological forces. For the first time, we resolve individual binding events as a short contraction of the unfolded talin polypeptide caused by the reformation of the vinculin-binding site helices, which dictates a biphasic mechanism that regulates this interaction. Force favors vinculin binding by unfolding talin and exposing the vinculin-binding sites; however, the coil-to-helix contraction introduces an energy penalty that increases with force, defining an optimal binding regime. This mechanism implies that the talin-vinculin-actin association could operate as a negative feedback mechanism to stabilize force on focal adhesions.

[Intermittent theta-burst transcranial magnetic stimulation for the treatment of spasticity in patients with recurring multiple sclerosis: the results of a double-blind randomised clinical trial]

AIM

It has been suggested that the repetitive transcranial magnetic stimulation could be useful as a non-pharmacological treatment for spasticity. The aim of this study was to evaluate the clinical and neurophysiological effects of high-frequency intermittent theta burst stimulation (iTBS) on lower limb spasticity in patients with relapsing multiple sclerosis in a randomized, double-blind placebo controlled trial.

PATIENTS AND METHODS

Seventeen patients in the remitting phase of the disease were randomly allocated to sham or magnetic therapy group and underwent iTBS over contralateral motor cortex of the most affected leg once a day for two weeks. Each session consisted of 10 bursts containing three pulses at 50 Hz repeated at 200 ms intervals (5 Hz) every 10 s for a total of 600 stimuli. The iTBS effect was assessed by using clinical (such as the Modified Ashworth Scale) and neuro-physiological (H/M amplitude ratio and cortical silent period duration) parameters.

RESULTS

Two-week iTBS over motor cortex of the most affected leg did not produce any significant clinical effect on spasticity. However, it decreases the H/M amplitude ratio and increases duration of cortical silent period but not significantly, in patients with relapsing multiple sclerosis.

CONCLUSION

The stimulation protocol used in this study does not have significant therapeutic effect. Therefore, we do recommend further studies as neurophysiological changes were evident.

Staff lens doses in interventional urology. A comparison with interventional radiology, cardiology and vascular surgery values

The purpose of this work is to evaluate radiation doses to the lens of urologists during interventional procedures and to compare them with values measured during interventional radiology, cardiology and vascular surgery. The measurements were carried out in a surgical theatre using a mobile C-arm system and electronic occupational dosimeters (worn over the lead apron). Patient and staff dose measurements were collected in a sample of 34 urology interventions (nephrolithotomies). The same dosimetry system was used in other medical specialties for comparison purposes. Median and 3rd quartile values for urology procedures were: patient doses 30 and 40 Gy cm(2); personal dose equivalent Hp(10) over the apron (μSv/procedure): 393 and 848 (for urologists); 21 and 39 (for nurses). Median values of over apron dose per procedure for urologists resulted 18.7 times higher than those measured for radiologists and cardiologists working with proper protection (using ceiling suspended screens) in catheterisation laboratories, and 4.2 times higher than the values measured for vascular surgeons at the same hospital. Comparison with passive dosimeters worn near the eyes suggests that dosimeters worn over the apron could be a reasonable conservative estimate for ocular doses for interventional urology. Authors recommend that at least the main surgeon uses protective eyewear during interventional urology procedures.

A set of patient and staff dose data for validation of Monte Carlo calculations in interventional cardiology

The purpose of this paper is to report a set of experimental values of patient and staff doses in a cardiac catheterisation laboratory using the range of radiographic and geometric parameters from routine clinical practice. The data obtained will be available for validation of Monte Carlo calculations and for training purposes. They will also help optimise radiation protection for patients and staff. Experimental measurements were made with an anthropomorphic phantom, and a monoplane flat detector-based X-ray system was used for interventional cardiology procedures. Standard operational protocols used in clinical practice were applied. Around 1000 patient dose and 5000 staff dose values were measured for different operational conditions (angulations, distances, collimation and wedge filter, magnification, phantom thicknesses, using Copper absorber, etc.). Uncertainties were also estimated. Increase factors of 3-10 for patients and staff doses were measured for the different C-arm angulations.

Estimation of staff lens doses during interventional procedures. Comparing cardiology, neuroradiology and interventional radiology

The purpose of this article is to estimate lens doses using over apron active personal dosemeters in interventional catheterisation laboratories (cardiology IC, neuroradiology IN and radiology IR) and to investigate correlations between occupational lens doses and patient doses. Active electronic personal dosemeters placed over the lead apron were used on a sample of 204 IC procedures, 274 IN and 220 IR (all performed at the same university hospital). Patient dose values (kerma area product) were also recorded to evaluate correlations with occupational doses. Operators used the ceiling-suspended screen in most cases. The median and third quartile values of equivalent dose Hp(10) per procedure measured over the apron for IC, IN and IR resulted, respectively, in 21/67, 19/44 and 24/54 µSv. Patient dose values (median/third quartile) were 75/128, 83/176 and 61/159 Gy cm(2), respectively. The median ratios for dosemeters worn over the apron by operators (protected by the ceiling-suspended screen) and patient doses were 0.36; 0.21 and 0.46 µSv Gy(-1) cm(-2), respectively. With the conservative approach used (lens doses estimated from the over apron chest dosemeter) we came to the conclusion that more than 800 procedures y(-1) and per operator were necessary to reach the new lens dose limit for the three interventional specialties.

Identifying sequential substrate binding at the single-molecule level by enzyme mechanical stabilization

Enzyme-substrate binding is a dynamic process intimately coupled to protein structural changes, which in turn changes the unfolding energy landscape. By the use of single-molecule force spectroscopy (SMFS), we characterize the open-to-closed conformational transition experienced by the hyperthermophilic adenine diphosphate (ADP)-dependent glucokinase from Thermococcus litoralis triggered by the sequential binding of substrates. In the absence of substrates, the mechanical unfolding of TlGK shows an intermediate 1, which is stabilized in the presence of Mg·ADP(-), the first substrate to bind to the enzyme. However, in the presence of this substrate, an additional unfolding event is observed, intermediate 1*. Finally, in the presence of both substrates, the unfolding force of intermediates 1 and 1* increases as a consequence of the domain closure. These results show that SMFS can be used as a powerful experimental tool to investigate binding mechanisms of different enzymes with more than one ligand, expanding the repertoire of protocols traditionally used in enzymology.

The elastic free energy of a tandem modular protein under force

Recent studies have provided a theoretical framework for including entropic elasticity in the free energy landscape of proteins under mechanical force. Accounting for entropic elasticity using polymer physics models has helped explain the hopping behavior seen in single molecule experiments in the low force regime. Here, we expand on the construction of the free energy of a single protein domain under force proposed by Berkovich et al. to provide a free energy landscape for N tandem domains along a continuous polypeptide. Calculation of the free energy of individual domains followed by their concatenation provides a continuous free energy landscape whose curvature is dominated by the worm-like chain at forces below 20 pN. We have validated our free energy model using Brownian dynamics and reproduce key features of protein folding. This free energy model can predict the effects of changes in the elastic properties of a multidomain protein as a consequence of biological modifications such as phosphorylation or the formation of disulfide bonds. This work lays the foundations for the modeling of tissue elasticity, which is largely determined by the properties of tandem polyproteins.

Dynamics of equilibrium folding and unfolding transitions of titin immunoglobulin domain under constant forces

The mechanical stability of force-bearing proteins is crucial for their functions. However, slow transition rates of complex protein domains have made it challenging to investigate their equilibrium force-dependent structural transitions. Using ultra stable magnetic tweezers, we report the first equilibrium single-molecule force manipulation study of the classic titin I27 immunoglobulin domain. We found that individual I27 in a tandem repeat unfold/fold independently. We obtained the force-dependent free energy difference between unfolded and folded I27 and determined the critical force (∼5.4 pN) at which unfolding and folding have equal probability. We also determined the force-dependent free energy landscape of unfolding/folding transitions based on measurement of the free energy cost of unfolding. In addition to providing insights into the force-dependent structural transitions of titin I27, our results suggest that the conformations of titin immunoglobulin domains can be significantly altered during low force, long duration muscle stretching.

Measurements of eye lens doses in interventional cardiology using OSL and electronic dosemeters†

The purpose of this paper is to test the appropriateness of OSL and electronic dosemeters to estimate eye lens doses at interventional cardiology environment. Using TLD as reference detectors, personal dose equivalent was measured in phantoms and during clinical procedures. For phantom measurements, OSL dose values resulted in an average difference of -15 % vs. TLD. Tests carried out with other electronic dosemeters revealed differences up to ±20 % versus TLD. With dosemeters positioned outside the goggles and when TLD doses were >20 μSv, the average difference OSL vs. TLD was -9 %. Eye lens doses of almost 700 μSv per procedure were measured in two cases out of a sample of 33 measurements in individual clinical procedures, thus showing the risk of high exposure to the lenses of the eye when protection rules are not followed. The differences found between OSL and TLD are acceptable for the purpose and range of doses measured in the survey.

Probing the effect of force on HIV-1 receptor CD4

Cell-surface proteins are central for the interaction of cells with their surroundings and are also associated with numerous diseases. These molecules are exposed to mechanical forces, but the exact relation between force and the functions and pathologies associated with cell-surface proteins is unclear. An important cell-surface protein is CD4, the primary receptor of HIV-1. Here we show that mechanical force activates conformational and chemical changes on CD4 that may be important during viral attachment. We have used single-molecule force spectroscopy and analysis on HIV-1 infectivity to demonstrate that the mechanical extension of CD4 occurs in a time-dependent manner and correlates with HIV-1 infectivity. We show that Ibalizumab, a monoclonal antibody that blocks HIV-1, prevents the mechanical extension of CD4 domains 1 and 2. Furthermore, we demonstrate that thiol/disulfide exchange in CD4 requires force for exposure of cryptic disulfide bonds. This mechanical perspective provides unprecedented information that can change our understanding on how viruses interact with their hosts.

Altered thiol chemistry in human amyotrophic lateral sclerosis-linked mutants of superoxide dismutase 1

Neurodegenerative diseases share a common characteristic, the presence of intracellular or extracellular deposits of protein aggregates in nervous tissues. Amyotrophic Lateral Sclerosis (ALS) is a severe and fatal neurodegenerative disorder, which affects preferentially motoneurons. Changes in the redox state of superoxide dismutase 1 (SOD1) are associated with the onset and development of familial forms of ALS. In human SOD1 (hSOD1), a conserved disulfide bond and two free cysteine residues can engage in anomalous thiol/disulfide exchange resulting in non-native disulfides, a hallmark of ALS that is related to protein misfolding and aggregation. Because of the many competing reaction pathways, traditional bulk techniques fall short at quantifying individual thiol/disulfide exchange reactions. Here, we adapt recently developed single-bond chemistry techniques to study individual disulfide isomerization reactions in hSOD1. Mechanical unfolding of hSOD1 leads to the formation of a polypeptide loop held by the disulfide. This loop behaves as a molecular jump rope that brings reactive Cys-111 close to the disulfide. Using force-clamp spectroscopy, we monitor nucleophilic attack of Cys-111 at either sulfur of the disulfide and determine the selectivity of the reaction. Disease-causing mutations G93A and A4V show greatly altered reactivity patterns, which may contribute to the progression of familial ALS.

Influence of the true number of Bacillus Calmette-Guérin instillations on the prognosis of non-muscle invasive bladder tumors

OBJECTIVES

To analyze if the true number of BCG instillations applied in non-muscle invasive bladder tumors has any influence on their prognosis as well as other tumor and clinical characteristics: age, sex, different protocols, BCG dose, whether primary or recurrent, solitary or multiple, tumor size G3 or Cis.

PATIENTS AND METHODS

A total of 324 high grade NMIBC (15 TaG3, 184 T1G3, 125 Cis) out of 1491 cases included in the CUETO database were analyzed. Following 6 post transurethral resection (RTU) BCG instillations, the patients were scheduled to receive one instillation every two weeks (3-6 times), for a total of 9-12 instillations. One third of the dose (27 mg) (112 cases) or total dose of 81 mg (212 cases). Mean follow-up was 59.6 months. Statistical Analysis: Kaplan-Meier, Cox-regression (uni-multivariate).

RESULTS

A higher level of recurrence (p = 0.032) and progression (P = .013) risk as well as worse Ca-specific survival (P = .005) were obtained if there were fewer than 12 instillations with the Kaplan-Meier and Cox-regression multivariate analysis. A 27 mg (P = .008) dosage and being a female (P < .001) were independent factors for a higher recurrence risk, but not for progression or Ca-specific survival. The remaining characteristics studied were not statistically significant.

CONCLUSIONS

In accordance with the results obtained, we can conclude that the number of BCG instillations applied has some influence on the outcome of high grade NMIBC. The optimum number of instillations as well as their time of application must still be determined. A dose of 27 mg and being a female are predictive factors of recurrence.

Conservation of protein structure over four billion years

Little is known about the evolution of protein structures and the degree of protein structure conservation over planetary time scales. Here, we report the X-ray crystal structures of seven laboratory resurrections of Precambrian thioredoxins dating up to approximately four billion years ago. Despite considerable sequence differences compared with extant enzymes, the ancestral proteins display the canonical thioredoxin fold, whereas only small structural changes have occurred over four billion years. This remarkable degree of structure conservation since a time near the last common ancestor of life supports a punctuated-equilibrium model of structure evolution in which the generation of new folds occurs over comparatively short periods and is followed by long periods of structural stasis.

Nanomechanics of HaloTag tethers

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.

Force dependency of biochemical reactions measured by single-molecule force-clamp spectroscopy

Here we describe a protocol for using force-clamp spectroscopy to precisely quantify the effect of force on biochemical reactions. A calibrated force is used to control the exposure of reactive sites in a single polyprotein substrate composed of repeated domains. The use of polyproteins allows the identification of successful single-molecule recordings from unambiguous mechanical unfolding fingerprints. Biochemical reactions are then measured directly by detecting the length changes of the substrate held at a constant force. We present the layout of a force-clamp spectrometer along with protocols to design and conduct experiments. These experiments measure reaction kinetics as a function of applied force. We show sample data of the force dependency of two different reactions, protein unfolding and disulfide reduction. These data, which can be acquired in just a few days, reveal mechanistic details of the reactions that currently cannot be resolved by any other technique.

Patient radiation dose management in the follow-up of potential skin injuries in neuroradiology

BACKGROUND AND PURPOSE

Radiation exposure from neurointerventional procedures can be substantial, with risk of radiation injuries. We present the results of a follow-up program applied to potential skin injuries in interventional neuroradiology based on North American and European guidelines.

MATERIALS AND METHODS

The following guidelines approved in 2009 by SIR and CIRSE have been used over the last 2 years to identify patients with potential skin injuries requiring clinical follow-up: peak skin dose >3 Gy, air kerma at the patient entrance reference point >5 Gy, kerma area product >500 Gy · cm(2), or fluoroscopy time >60 minutes.

RESULTS

A total of 708 procedures (325 in 2009 and 383 in 2010) were included in the study. After analyzing each dose report, 19 patients (5.9%) were included in a follow-up program for potential skin injuries in 2009, while in 2010, after introducing several optimizing actions and refining the selection criteria, only 4 patients (1.0%) needed follow-up. Over the last 2 years, only 3 patients required referral to a dermatology service.

CONCLUSIONS

The application of the guidelines to patient radiation dose management helped standardize the selection criteria for including patients in the clinical follow-up program of potential skin radiation injuries. The peak skin dose resulted in the most relevant parameter. The refinement of selection criteria and the introduction of a low-dose protocol in the x-ray system, combined with a training program focused on radiation protection, reduced the number of patients requiring clinical follow-up.

Protein Folding Under Mechanical Forces: A Physiological View

Mechanical forces regulate the function of numerous proteins relevant to physiology. The functions and folding of proteins have been under scrutiny for decades, but it was not until recently that mechanical forces have been considered. Here, we review different techniques for studying protein folding, highlighting their physiological significance.

Automatic management system for dose parameters in interventional radiology and cardiology

The purpose of this work was to develop an automatic management system to archive and analyse the major study parameters and patient doses for fluoroscopy guided procedures performed in cardiology and interventional radiology systems. The X-ray systems used for this trial have the capability to export at the end of the procedure and via e-mail the technical parameters of the study and the patient dose values. An application was developed to query and retrieve from a mail server, all study reports sent by the imaging modality and store them on a Microsoft SQL Server data base. The results from 3538 interventional study reports generated by 7 interventional systems were processed. In the case of some technical parameters and patient doses, alarms were added to receive malfunction alerts so as to immediately take appropriate corrective actions.

Single-molecule paleoenzymology probes the chemistry of resurrected enzymes

A journey back in time is possible at the molecular level by reconstructing proteins from extinct organisms. Here we report the reconstruction, based on sequence predicted by phylogenetic analysis, of seven Precambrian thioredoxin enzymes (Trx), dating back between ~1.4 and ~4 billion years (Gyr). The reconstructed enzymes are up to 32° C more stable than modern enzymes and the oldest show significantly higher activity than extant ones at pH 5. We probed their mechanisms of reduction using single-molecule force spectroscopy. From the force-dependency of the rate of reduction of an engineered substrate, we conclude that ancient Trxs utilize chemical mechanisms of reduction similar to those of modern enzymes. While Trx enzymes have maintained their reductase chemistry unchanged, they have adapted over a 4 Gyr time span to the changes in temperature and ocean acidity that characterize the evolution of the global environment from ancient to modern Earth.

Circulation and suspended sediment transport in a coral reef lagoon: the south-west lagoon of New Caledonia

The south-west lagoon of New Caledonia is a wide semi-open coral reef lagoon bounded by an intertidal barrier reef and bisected by numerous deep inlets. This paper synthesizes findings from the 2000-2008 French National Program EC2CO-PNEC relative to the circulation and the transport of suspended particles in this lagoon. Numerical model development (hydrodynamic, fine suspended sediment transport, wind-wave, small-scale atmospheric circulation) allowed the determination of circulation patterns in the lagoon and the charting of residence time, the later of which has been recently used in a series of ecological studies. Topical studies based on field measurements permitted the parameterisation of wave set-up induced by the swell breaking on the reef barrier and the validation of a wind-wave model in a fetch-limited environment. The analysis of spatial and temporal variability of suspended matter concentration over short and long time-scales, the measurement of grain size distribution and the density of suspended matter (1.27 kg l(-1)), and the estimation of erodibility of heterogeneous (sand/mud, terrigenous/biogenic) soft bottoms was also conducted. Aggregates were shown to be more abundant near or around reefs and a possible biological influence on this aggregation is discussed. Optical measurements enabled the quantification of suspended matter either in situ (monochromatic measurements) or remotely (surface spectral measurements and satellite observations) and provided indirect calibration and validation of a suspended sediment transport model. The processes that warrant further investigation in order to improve our knowledge of circulation and suspended sediment transport in the New Caledonia lagoon as well as in other coral reef areas are discussed, as are the relevance and reliability of the numerical models for this endeavour.

Single-molecule force spectroscopy approach to enzyme catalysis

Enzyme catalysis has been traditionally studied using a diverse set of techniques such as bulk biochemistry, x-ray crystallography, and NMR. Recently, single-molecule force spectroscopy by atomic force microscopy has been used as a new tool to study the catalytic properties of an enzyme. In this approach, a mechanical force ranging up to hundreds of piconewtons is applied to the substrate of an enzymatic reaction, altering the conformational energy of the substrate-enzyme interactions during catalysis. From these measurements, the force dependence of an enzymatic reaction can be determined. The force dependence provides valuable new information about the dynamics of enzyme catalysis with sub-angstrom resolution, a feat unmatched by any other current technique. To date, single-molecule force spectroscopy has been applied to gain insight into the reduction of disulfide bonds by different enzymes of the thioredoxin family. This minireview aims to present a perspective on this new approach to study enzyme catalysis and to summarize the results that have already been obtained from it. Finally, the specific requirements that must be fulfilled to apply this new methodology to any other enzyme will be discussed.

Spatial patterns and recruitment processes of coral assemblages among contrasting environmental conditions in the southwestern lagoon of New Caledonia

We investigated the spatial distribution of adult and juvenile coral assemblages in the southwestern lagoon of New Caledonia, from disturbed fringing reefs within bays, to oceanic barrier reefs. Generic richness, abundance, and percent cover were highly variable at this scale, but no clear cross-shelf gradient was found. Rather, community composition was more related to reef biotopes. Correlations and canonical correspondence analyses revealed that composition and abundance of coral assemblages were related to substrate types (cover of turf algae and cover of encrusting coralline algae), but not to water quality or metal concentrations in sediments. We found a strong relationship between juvenile and adult distribution for all dominant genera, which suggests that recruitment processes are also a major factor structuring these populations. The densities of juveniles and their proportion in the coral assemblages were relatively low, which implies that replenishment capacities and potential for recovery are probably limited for these reefs.

Extended Kalman filter estimates the contour length of a protein in single molecule atomic force microscopy experiments

Atomic force microscopy force spectroscopy has become a powerful biophysical technique for probing the dynamics of proteins at the single molecule level. Extending a polyprotein at constant velocity produces the now familiar sawtooth pattern force-length relationship. Customarily, manual fits of the wormlike chain (WLC) model of polymer elasticity to sawtooth pattern data have been used to measure the contour length L(c) of the protein as it unfolds one module at a time. The change in the value of L(c) measures the number of amino acids released by an unfolding protein and can be used as a precise locator of the unfolding transition state. However, manual WLC fits are slow and introduce inevitable operator-driven errors which reduce the accuracy of the L(c) estimates. Here we demonstrate an extended Kalman filter that provides operator-free real time estimates of L(c) from sawtooth pattern data. The filter design is based on a cantilever-protein arrangement modeled by a simple linear time-invariant cantilever model and by a nonlinear force-length relationship function for the protein. The resulting Kalman filter applied to sawtooth pattern data demonstrates its real time, operator-free ability to accurately measure L(c). These results are a marked improvement over the earlier techniques and the procedure is easily extended or modified to accommodate further quantities of interest in force spectroscopy.

Modulation of titin-based stiffness by disulfide bonding in the cardiac titin N2-B unique sequence

The giant protein titin is responsible for the elasticity of nonactivated muscle sarcomeres. Titin-based passive stiffness in myocardium is modulated by titin-isoform switching and protein-kinase (PK)A- or PKG-dependent titin phosphorylation. Additional modulatory effects on titin stiffness may arise from disulfide bonding under oxidant stress, as many immunoglobulin-like (Ig-)domains in titin's spring region have a potential for S-S formation. Using single-molecule atomic force microscopy (AFM) force-extension measurements on recombinant Ig-domain polyprotein constructs, we show that titin Ig-modules contain no stabilizing disulfide bridge, contrary to previous belief. However, we demonstrate that the human N2-B-unique sequence (N2-B(us)), a cardiac-specific, physiologically extensible titin segment comprising 572 amino-acid residues, contains up to three disulfide bridges under oxidizing conditions. AFM force spectroscopy on recombinant N2-B(us) molecules demonstrated a much shorter contour length in the absence of a reducing agent than in its presence, consistent with intramolecular S-S bonding. In stretch experiments on isolated human heart myofibrils, the reducing agent thioredoxin lowered titin-based stiffness to a degree that could be explained (using entropic elasticity theory) by altered extensibility solely of the N2-B(us). We conclude that increased oxidant stress can elevate titin-based stiffness of cardiomyocytes, which may contribute to the global myocardial stiffening frequently seen in the aging or failing heart.

Diversity of chemical mechanisms in thioredoxin catalysis revealed by single-molecule force spectroscopy

Thioredoxins (Trxs) are oxidoreductase enzymes, present in all organisms, that catalyze the reduction of disulfide bonds in proteins. By applying a calibrated force to a substrate disulfide, the chemical mechanisms of Trx catalysis can be examined in detail at the single-molecule level. Here we use single-molecule force-clamp spectroscopy to explore the chemical evolution of Trx catalysis by probing the chemistry of eight different Trx enzymes. All Trxs show a characteristic Michaelis-Menten mechanism that is detected when the disulfide bond is stretched at low forces, but at high forces, two different chemical behaviors distinguish bacterial-origin from eukaryotic-origin Trxs. Eukaryotic-origin Trxs reduce disulfide bonds through a single-electron transfer reaction (SET), whereas bacterial-origin Trxs show both nucleophilic substitution (S(N)2) and SET reactions. A computational analysis of Trx structures identifies the evolution of the binding groove as an important factor controlling the chemistry of Trx catalysis.

Stretching single talin rod molecules activates vinculin binding

The molecular mechanism by which a mechanical stimulus is translated into a chemical response in biological systems is still unclear. We show that mechanical stretching of single cytoplasmic proteins can activate binding of other molecules. We used magnetic tweezers, total internal reflection fluorescence, and atomic force microscopy to investigate the effect of force on the interaction between talin, a protein that links liganded membrane integrins to the cytoskeleton, and vinculin, a focal adhesion protein that is activated by talin binding, leading to reorganization of the cytoskeleton. Application of physiologically relevant forces caused stretching of single talin rods that exposed cryptic binding sites for vinculin. Thus in the talin-vinculin system, molecular mechanotransduction can occur by protein binding after exposure of buried binding sites in the talin-vinculin system. Such protein stretching may be a more general mechanism for force transduction.