Solvation effects on like-charge attraction.

PubMed

Ghanbarian, Shahzad; Rottler, Jörg

2013-02-28

We present results of molecular dynamics simulations of the electrostatic interaction between two parallel charged rods in the presence of divalent counterions. Such polyelectrolytes have been considered as a simple model for understanding electrostatic interactions in highly charged biomolecules such as DNA. Since there are correlations between the free charge carriers, the phenomenon of like charge attraction appears for specific parameters. We explore the role of solvation effects and the resulting deviations from Coulomb's law on the nanoscale on this peculiar phenomenon. The behavior of the force between the charged rods in a simulation with atomistic representation of water molecules is completely different from a model in which water is modeled as a continuum dielectric. By calculating counterion-rodion pair correlation functions, we find that the presence of water molecules changes the structure of the counterion cloud and results in both qualitative and quantitative changes of the force between highly charged polyelectrolytes.

Protein denaturants at aqueous-hydrophobic interfaces: self-consistent correlation between induced interfacial fluctuations and denaturant stability at the interface.

PubMed

Cui, Di; Ou, Shu-Ching; Patel, Sandeep

2015-01-08

The notion of direct interaction between denaturing cosolvent and protein residues has been proposed in dialogue relevant to molecular mechanisms of protein denaturation. Here we consider the correlation between free energetic stability and induced fluctuations of an aqueous-hydrophobic interface between a model hydrophobically associating protein, HFBII, and two common protein denaturants, guanidinium cation (Gdm(+)) and urea. We compute potentials of mean force along an order parameter that brings the solute molecule close to the known hydrophobic region of the protein. We assess potentials of mean force for different relative orientations between the protein and denaturant molecule. We find that in both cases of guanidinium cation and urea relative orientations of the denaturant molecule that are parallel to the local protein-water interface exhibit greater stability compared to edge-on or perpendicular orientations. This behavior has been observed for guanidinium/methylguanidinium cations at the liquid-vapor interface of water, and thus the present results further corroborate earlier findings. Further analysis of the induced fluctuations of the aqueous-hydrophobic interface upon approach of the denaturant molecule indicates that the parallel orientation, displaying a greater stability at the interface, also induces larger fluctuations of the interface compared to the perpendicular orientations. The correlation of interfacial stability and induced interface fluctuation is a recurring theme for interface-stable solutes at hydrophobic interfaces. Moreover, observed correlations between interface stability and induced fluctuations recapitulate connections to local hydration structure and patterns around solutes as evidenced by experiment (Cooper et al., J. Phys. Chem. A 2014, 118, 5657.) and high-level ab initio/DFT calculations (Baer et al., Faraday Discuss 2013, 160, 89).

Protein Denaturants at Aqueous–Hydrophobic Interfaces: Self-Consistent Correlation between Induced Interfacial Fluctuations and Denaturant Stability at the Interface

PubMed Central

2015-01-01

The notion of direct interaction between denaturing cosolvent and protein residues has been proposed in dialogue relevant to molecular mechanisms of protein denaturation. Here we consider the correlation between free energetic stability and induced fluctuations of an aqueous–hydrophobic interface between a model hydrophobically associating protein, HFBII, and two common protein denaturants, guanidinium cation (Gdm+) and urea. We compute potentials of mean force along an order parameter that brings the solute molecule close to the known hydrophobic region of the protein. We assess potentials of mean force for different relative orientations between the protein and denaturant molecule. We find that in both cases of guanidinium cation and urea relative orientations of the denaturant molecule that are parallel to the local protein–water interface exhibit greater stability compared to edge-on or perpendicular orientations. This behavior has been observed for guanidinium/methylguanidinium cations at the liquid–vapor interface of water, and thus the present results further corroborate earlier findings. Further analysis of the induced fluctuations of the aqueous–hydrophobic interface upon approach of the denaturant molecule indicates that the parallel orientation, displaying a greater stability at the interface, also induces larger fluctuations of the interface compared to the perpendicular orientations. The correlation of interfacial stability and induced interface fluctuation is a recurring theme for interface-stable solutes at hydrophobic interfaces. Moreover, observed correlations between interface stability and induced fluctuations recapitulate connections to local hydration structure and patterns around solutes as evidenced by experiment (Cooper et al., J. Phys. Chem. A2014, 118, 5657.) and high-level ab initio/DFT calculations (Baer et al., Faraday Discuss2013, 160, 89). PMID:25536388

Forces on nuclei moving on autoionizing molecular potential energy surfaces.

PubMed

Moiseyev, Nimrod

2017-01-14

Autoionization of molecular systems occurs in diatomic molecules and in small biochemical systems. Quantum chemistry packages enable calculation of complex potential energy surfaces (CPESs). The imaginary part of the CPES is associated with the autoionization decay rate, which is a function of the molecular structure. Molecular dynamics simulations, within the framework of the Born-Oppenheimer approximation, require the definition of a force field. The ability to calculate the forces on the nuclei in bio-systems when autoionization takes place seems to rely on an understanding of radiative damages in RNA and DNA arising from the release of slow moving electrons which have long de Broglie wavelengths. This work addresses calculation of the real forces on the nuclei moving on the CPES. By using the transformation of the time-dependent Schrödinger equation, previously used by Madelung, we proved that the classical forces on nuclei moving on the CPES correlated with the gradient of the real part of the CPES. It was proved that the force on the nuclei of the metastable molecules is time independent although the probability to detect metastable molecules exponentially decays. The classical force is obtained from the transformed Schrödinger equation when ℏ=0 and the Schrödinger equation is reduced to the classical (Newtonian) equations of motion. The forces on the nuclei regardless on what potential energy surface they move (parent CPES or product real PESs) vary in time due to the autoionization process.

Force determination in lateral magnetic tweezers combined with TIRF microscopy.

PubMed

Madariaga-Marcos, J; Hormeño, S; Pastrana, C L; Fisher, G L M; Dillingham, M S; Moreno-Herrero, F

2018-03-01

Combining single-molecule techniques with fluorescence microscopy has attracted much interest because it allows the correlation of mechanical measurements with directly visualized DNA : protein interactions. In particular, its combination with total internal reflection fluorescence microscopy (TIRF) is advantageous because of the high signal-to-noise ratio this technique achieves. This, however, requires stretching long DNA molecules across the surface of a flow cell to maximize polymer exposure to the excitation light. In this work, we develop a module to laterally stretch DNA molecules at a constant force, which can be easily implemented in regular or combined magnetic tweezers (MT)-TIRF setups. The pulling module is further characterized in standard flow cells of different thicknesses and glass capillaries, using two types of micrometer size superparamagnetic beads, long DNA molecules, and a home-built device to rotate capillaries with mrad precision. The force range achieved by the magnetic pulling module was between 0.1 and 30 pN. A formalism for estimating forces in flow-stretched tethered beads is also proposed, and the results compared with those of lateral MT, demonstrating that lateral MT achieve higher forces with lower dispersion. Finally, we show the compatibility with TIRF microscopy and the parallelization of measurements by characterizing DNA binding by the centromere-binding protein ParB from Bacillus subtilis. Simultaneous MT pulling and fluorescence imaging demonstrate the non-specific binding of BsParB on DNA under conditions restrictive to condensation.

DNA unzipping phase diagram calculated via replica theory.

PubMed

Roland, C Brian; Hatch, Kristi Adamson; Prentiss, Mara; Shakhnovich, Eugene I

2009-05-01

We show how single-molecule unzipping experiments can provide strong evidence that the zero-force melting transition of long molecules of natural dsDNA should be classified as a phase transition of the higher-order type (continuous). Toward this end, we study a statistical-mechanics model for the fluctuating structure of a long molecule of dsDNA, and compute the equilibrium phase diagram for the experiment in which the molecule is unzipped under applied force. We consider a perfect-matching dsDNA model, in which the loops are volume-excluding chains with arbitrary loop exponent c . We include stacking interactions, hydrogen bonds, and main-chain entropy. We include sequence heterogeneity at the level of random sequences; in particular, there is no correlation in the base-pairing (bp) energy from one sequence position to the next. We present heuristic arguments to demonstrate that the low-temperature macrostate does not exhibit degenerate ergodicity breaking. We use this claim to understand the results of our replica-theoretic calculation of the equilibrium properties of the system. As a function of temperature, we obtain the minimal force at which the molecule separates completely. This critical-force curve is a line in the temperature-force phase diagram that marks the regions where the molecule exists primarily as a double helix versus the region where the molecule exists as two separate strands. We compare our random-sequence model to magnetic tweezer experiments performed on the 48 502 bp genome of bacteriophage lambda . We find good agreement with the experimental data, which is restricted to temperatures between 24 and 50 degrees C . At higher temperatures, the critical-force curve of our random-sequence model is very different for that of the homogeneous-sequence version of our model. For both sequence models, the critical force falls to zero at the melting temperature T_{c} like |T-T_{c}|;{alpha} . For the homogeneous-sequence model, alpha=1/2 almost exactly, while for the random-sequence model, alpha approximately 0.9 . Importantly, the shape of the critical-force curve is connected, via our theory, to the manner in which the helix fraction falls to zero at T_{c} . The helix fraction is the property that is used to classify the melting transition as a type of phase transition. In our calculation, the shape of the critical-force curve holds strong evidence that the zero-force melting transition of long natural dsDNA should be classified as a higher-order (continuous) phase transition. Specifically, the order is 3rd or greater.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sahu, Pooja; Ali, Sk. M., E-mail: musharaf@barc.gov.in

Water in nanotube exhibits remarkably different properties from the bulk phase, which can be exploited in various nanoconfinement based technologies. The properties of water within nanotube can be further tuned by varying the nanotube electrostatics and functionalization of nanotube ends. Here, therefore, we investigate the effect of quantum partial charges and carbon nanotube (CNT) termination in terms of associated entropic forces. An attempt has been made to correlate the entropic forces with various dynamical and structural properties. The simulated structural features are consistent with general theoretical aspects, in which the interfacial water molecules at H terminated CNT are found tomore » be distributed in a different way as compared to other CNTs. The rotational entropy components for different cases of CNTs are well corroborated by the decay time of hydrogen bond (HB) correlation functions. A part of this event has been explained in terms of orientation of water molecules in the chain, i.e., the change in direction of dipole moment of water molecules in the chain and it has been revealed that the HBs of CNT confined water molecules show long preserving correlation if their rotations inside CNT are restricted. Furthermore, the translational entropy components are rationally integrated with the differing degree of translational constraints, added by the CNTs. To the best of our information, perhaps this is the first study where the thermodynamic effects introduced by H-termination and induced dipole of CNT have been investigated. Additionally, we present a bridge relation between “translational diffusivity and configurational entropy” for water transport from bulk phase to inside CNTs.« less

Surface correlation behaviors of metal-organic Langmuir-Blodgett films on differently passivated Si(001) surfaces

NASA Astrophysics Data System (ADS)

Bal, J. K.; Kundu, Sarathi

2013-03-01

Langmuir-Blodgett films of standard amphiphilic molecules like nickel arachidate and cadmium arachidate are grown on wet chemically passivated hydrophilic (OH-Si), hydrophobic (H-Si), and hydrophilic plus hydrophobic (Br-Si) Si(001) surfaces. Top surface morphologies and height-difference correlation functions g(r) with in-plane separation (r) are obtained from the atomic force microscopy studies. Our studies show that deposited bilayer and trilayer films have self-affine correlation behavior irrespective of different passivations and different types of amphiphilic molecules, however, liquid like correlation coexists only for a small part of r, which is located near the cutoff length (1/κ) or little below the correlation length ξ obtained from the liquid like and self-affine fitting, respectively. Thus, length scale dependent surface correlation behavior is observed for both types of Langmuir-Blodgett films. Metal ion specific interactions (ionic, covalent, etc.,) in the headgroup and the nature of the terminated bond (polar, nonpolar, etc.,) of Si surface are mainly responsible for having different correlation parameters.

Covalent bond force profile and cleavage in a single polymer chain

NASA Astrophysics Data System (ADS)

Garnier, Lionel; Gauthier-Manuel, Bernard; van der Vegte, Eric W.; Snijders, Jaap; Hadziioannou, Georges

2000-08-01

We present here the measurement of the single-polymer entropic elasticity and the single covalent bond force profile, probed with two types of atomic force microscopes (AFM) on a synthetic polymer molecule: polymethacrylic acid in water. The conventional AFM allowed us to distinguish two types of interactions present in this system when doing force spectroscopic measurements: the first interaction is associated with adsorption sites of the polymer chains onto a bare gold surface, the second interaction is directly correlated to the rupture process of a single covalent bond. All these bridging interactions allowed us to stretch the single polymer chain and to determine the various factors playing a role in the elasticity of these molecules. To obtain a closer insight into the bond rupture process, we moved to a force sensor stable in position when measuring attractive forces. By optimizing the polymer length so as to fulfill the elastic stability conditions, we were able for the first time to map out the entire force profile associated with the cleavage of a single covalent bond. Experimental data coupled with molecular quantum mechanical calculations strongly suggest that the breaking bond is located at one end of the polymer chain.

Scanning superlens microscopy for non-invasive large field-of-view visible light nanoscale imaging

NASA Astrophysics Data System (ADS)

Wang, Feifei; Liu, Lianqing; Yu, Haibo; Wen, Yangdong; Yu, Peng; Liu, Zhu; Wang, Yuechao; Li, Wen Jung

2016-12-01

Nanoscale correlation of structural information acquisition with specific-molecule identification provides new insight for studying rare subcellular events. To achieve this correlation, scanning electron microscopy has been combined with super-resolution fluorescent microscopy, despite its destructivity when acquiring biological structure information. Here we propose time-efficient non-invasive microsphere-based scanning superlens microscopy that enables the large-area observation of live-cell morphology or sub-membrane structures with sub-diffraction-limited resolution and is demonstrated by observing biological and non-biological objects. This microscopy operates in both non-invasive and contact modes with ~200 times the acquisition efficiency of atomic force microscopy, which is achieved by replacing the point of an atomic force microscope tip with an imaging area of microspheres and stitching the areas recorded during scanning, enabling sub-diffraction-limited resolution. Our method marks a possible path to non-invasive cell imaging and simultaneous tracking of specific molecules with nanoscale resolution, facilitating the study of subcellular events over a total cell period.

Correlating single-molecule and ensemble-average measurements of peptide adsorption onto different inorganic materials.

PubMed

Kim, Seong-Oh; Jackman, Joshua A; Mochizuki, Masahito; Yoon, Bo Kyeong; Hayashi, Tomohiro; Cho, Nam-Joon

2016-06-07

The coating of solid-binding peptides (SBPs) on inorganic material surfaces holds significant potential for improved surface functionalization at nano-bio interfaces. In most related studies, the goal has been to engineer peptides with selective and high binding affinity for a target material. The role of the material substrate itself in modulating the adsorption behavior of a peptide molecule remains less explored and there are few studies that compare the interaction of one peptide with different inorganic substrates. Herein, using a combination of two experimental techniques, we investigated the adsorption of a 16 amino acid-long random coil peptide to various inorganic substrates - gold, silicon oxide, titanium oxide and aluminum oxide. Quartz crystal microbalance-dissipation (QCM-D) experiments were performed in order to measure the peptide binding affinity for inorganic solid supports at the ensemble average level, and atomic force microscopy (AFM) experiments were conducted in order to determine the adhesion force of a single peptide molecule. A positive trend was observed between the total mass uptake of attached peptide and the single-molecule adhesion force on each substrate. Peptide affinity for gold was appreciably greater than for the oxide substrates. Collectively, the results obtained in this study offer insight into the ways in which inorganic materials can differentially influence and modulate the adhesion of SBPs.

Anharmonic Potential Constants and Their Dependence Upon Bond Length

DOE R&D Accomplishments Database

Herschbach, D. R.; Laurie, V. W.

1961-01-01

Empirical study of cubic and quartic vibrational force constants for diatomic molecules shows them to be approximately exponential functions of internuclear distance. A family of curves is obtained, determined by the location of the bonded atoms in rows of the periodic table. Displacements between successive curves correspond closely to those in Badger's rule for quadratic force constants (for which the parameters are redetermined to accord with all data now available). Constants for excited electronic and ionic states appear on practically the same curves as those for the ground states. Predictions based on the diatomic correlations agree with the available cubic constants for bond stretching in polyatomic molecules, regardless of the type of bonding involved. Implications of these regularities are discussed. (auth)

Atomic force microscopy and tribology study of the adsorption of alcohols on diamond-like carbon coatings and steel

NASA Astrophysics Data System (ADS)

Kalin, M.; Simič, R.

2013-04-01

Polar molecules are known to affect the friction and wear of steel contacts via adsorption onto the surface, which represents one of the fundamental boundary-lubrication mechanisms. Since the basic chemical and physical effects of polar molecules on diamond-like carbon (DLC) coatings have been investigated only very rarely, it is important to find out whether such molecules have a similar effect on DLC coatings as they do on steel. In our study the adsorption of hexadecanol in various concentrations (2-20 mmol/l) on DLC was studied under static conditions using an atomic force microscope (AFM). The amount of surface coverage, the size and the density of the adsorbed islands of alcohol molecules were analyzed. Tribological tests were also performed to correlate the wear and friction behaviours with the adsorption of molecules on the surface. In this case, steel surfaces served as a reference. The AFM was successfully used to analyze the adsorption ability of polar molecules onto the DLC surfaces and a good correlation between the AFM results and the tribological behaviour of the DLC and the steel was found. We confirmed that alcohols can adsorb physically and chemically onto the DLC surfaces and are, therefore, potential boundary-lubrication agents for the DLC coatings. The adsorption of alcohol onto the DLC surfaces reduces the wear of the coatings, but it is less effective in reducing the friction because of the already inherently low-friction properties of DLC. Tentative adsorption mechanisms that include the environmental species effect, the temperature effect and the tribological rubbing effect are proposed for DLC and steel surfaces.

Substitution Structures of Large Molecules and Medium Range Correlations in Quantum Chemistry Calculations

NASA Astrophysics Data System (ADS)

Evangelisti, Luca; Pate, Brooks

2017-06-01

A study of the minimally exciting topic of agreement between experimental and measured rotational constants of molecules was performed on a set of large molecules with 16-18 heavy atoms (carbon and oxygen). The molecules are: nootkatone (C_{15}H_{22}O), cedrol (C_{15}H_{26}O), ambroxide (C_{16}H_{28}O), sclareolide (C_{16}H_{22}O_{2}), and dihydroartemisinic acid (C_{15}H_{24}O_{2}). For this set of molecules we obtained 13C-subsitution structures for six molecules (this includes two conformers of nootkatone). A comparison of theoretical structures and experimental substitution structures was performed in the spirit of the recent work of Grimme and Steinmetz.[1] Our analysis focused the center-of-mass distance of the carbon atoms in the molecules. Four different computational methods were studied: standard DFT (B3LYP), dispersion corrected DFT (B3LYP-D3BJ), hybrid DFT with dispersion correction (B2PLYP-D3), and MP2. A significant difference in these theories is how they handle medium range correlation of electrons that produce dispersion forces. For larger molecules, these dispersion forces produce an overall contraction of the molecule around the center-of-mass. DFT poorly treats this effect and produces structures that are too expanded. MP2 calculations overestimate the correction and produce structures that are too compact. Both dispersion corrected DFT methods produce structures in excellent agreement with experiment. The analysis shows that the difference in computational methods can be described by a linear error in the center-of-mass distance. This makes it possible to correct poorer performing calculations with a single scale factor. We also reexamine the issue of the "Costain error" in substitution structures and show that it is significantly larger in these systems than in the smaller molecules used by Costain to establish the error limits. [1] Stefan Grimme and Marc Steinmetz, "Effects of London dispersion correction in density functional theory on structures of organic molecules in the gas phase", Phys. Chem. Chem. Phys. 15, 16031-16042 (2013).

An Accurate ab initio Quartic Force Field and Vibrational Frequencies for CH4 and Isotopomers

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Martin, Jan M. L.; Taylor, Peter R.

1995-01-01

A very accurate ab initio quartic force field for CH4 and its isotopomers is presented. The quartic force field was determined with the singles and doubles coupled-cluster procedure that includes a quasiperturbative estimate of the effects of connected triple excitations, CCSD(T), using the correlation consistent polarized valence triple zeta, cc-pVTZ, basis set. Improved quadratic force constants were evaluated with the correlation consistent polarized valence quadruple zeta, cc-pVQZ, basis set. Fundamental vibrational frequencies are determined using second-order perturbation theory anharmonic analyses. All fundamentals of CH4 and isotopomers for which accurate experimental values exist and for which there is not a large Fermi resonance, are predicted to within +/- 6 cm(exp -1). It is thus concluded that our predictions for the harmonic frequencies and the anharmonic constants are the most accurate estimates available. It is also shown that using cubic and quartic force constants determined with the correlation consistent polarized double zeta, cc-pVDZ, basis set in conjunction with the cc-pVQZ quadratic force constants and equilibrium geometry leads to accurate predictions for the fundamental vibrational frequencies of methane, suggesting that this approach may be a viable alternative for larger molecules. Using CCSD(T), core correlation is found to reduce the CH4 r(e), by 0.0015 A. Our best estimate for r, is 1.0862 +/- 0.0005 A.

Minimizing pulling geometry errors in atomic force microscope single molecule force spectroscopy.

PubMed

Rivera, Monica; Lee, Whasil; Ke, Changhong; Marszalek, Piotr E; Cole, Daniel G; Clark, Robert L

2008-10-01

In atomic force microscopy-based single molecule force spectroscopy (AFM-SMFS), it is assumed that the pulling angle is negligible and that the force applied to the molecule is equivalent to the force measured by the instrument. Recent studies, however, have indicated that the pulling geometry errors can drastically alter the measured force-extension relationship of molecules. Here we describe a software-based alignment method that repositions the cantilever such that it is located directly above the molecule's substrate attachment site. By aligning the applied force with the measurement axis, the molecule is no longer undergoing combined loading, and the full force can be measured by the cantilever. Simulations and experimental results verify the ability of the alignment program to minimize pulling geometry errors in AFM-SMFS studies.

Energy Minimization of Molecular Features Observed on the (110) Face of Lysozyme Crystals

NASA Technical Reports Server (NTRS)

Perozzo, Mary A.; Konnert, John H.; Li, Huayu; Nadarajah, Arunan; Pusey, Marc

1999-01-01

Molecular dynamics and energy minimization have been carried out using the program XPLOR to check the plausibility of a model lysozyme crystal surface. The molecular features of the (110) face of lysozyme were observed using atomic force microscopy (AFM). A model of the crystal surface was constructed using the PDB file 193L, and was used to simulate an AFM image. Molecule translations, van der Waals radii, and assumed AFM tip shape were adjusted to maximize the correlation coefficient between the experimental and simulated images. The highest degree of 0 correlation (0.92) was obtained with the molecules displaced over 6 A from their positions within the bulk of the crystal. The quality of this starting model, the extent of energy minimization, and the correlation coefficient between the final model and the experimental data will be discussed.

Single-molecule techniques in biophysics: a review of the progress in methods and applications.

PubMed

Miller, Helen; Zhou, Zhaokun; Shepherd, Jack; Wollman, Adam J M; Leake, Mark C

2018-02-01

Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k B T, where k B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in 'force spectroscopy' techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including correlative atomic force microscopy and fluorescence imaging, to probe questions closer to native physiological behaviour. We identify the trade-offs, limitations and applications of these techniques, and discuss exciting new directions.

Single-molecule techniques in biophysics: a review of the progress in methods and applications

NASA Astrophysics Data System (ADS)

Miller, Helen; Zhou, Zhaokun; Shepherd, Jack; Wollman, Adam J. M.; Leake, Mark C.

2018-02-01

Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k B T, where k B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in ‘force spectroscopy’ techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including correlative atomic force microscopy and fluorescence imaging, to probe questions closer to native physiological behaviour. We identify the trade-offs, limitations and applications of these techniques, and discuss exciting new directions.

Length-scale crossover of the hydrophobic interaction in a coarse-grained water model

NASA Astrophysics Data System (ADS)

Chaimovich, Aviel; Shell, M. Scott

2013-11-01

It has been difficult to establish a clear connection between the hydrophobic interaction among small molecules typically studied in molecular simulations (a weak, oscillatory force) and that found between large, macroscopic surfaces in experiments (a strong, monotonic force). Here, we show that both types of interaction can emerge with a simple, core-softened water model that captures water's unique pairwise structure. As in hydrophobic hydration, we find that the hydrophobic interaction manifests a length-scale dependence, exhibiting distinct driving forces in the molecular and macroscopic regimes. Moreover, the ability of this simple model to capture both regimes suggests that several features of the hydrophobic force can be understood merely through water's pair correlations.

Length-scale crossover of the hydrophobic interaction in a coarse-grained water model.

PubMed

Chaimovich, Aviel; Shell, M Scott

2013-11-01

It has been difficult to establish a clear connection between the hydrophobic interaction among small molecules typically studied in molecular simulations (a weak, oscillatory force) and that found between large, macroscopic surfaces in experiments (a strong, monotonic force). Here, we show that both types of interaction can emerge with a simple, core-softened water model that captures water's unique pairwise structure. As in hydrophobic hydration, we find that the hydrophobic interaction manifests a length-scale dependence, exhibiting distinct driving forces in the molecular and macroscopic regimes. Moreover, the ability of this simple model to capture both regimes suggests that several features of the hydrophobic force can be understood merely through water's pair correlations.

An integrated platform for surface forces measurements and fluorescence correlation spectroscopy

NASA Astrophysics Data System (ADS)

Mukhopadhyay, Ashis; Zhao, Jiang; Bae, Sung Chul; Granick, Steve

2003-06-01

We describe an apparatus to measure the diffusion of dilute fluorophores in molecularly thin liquid films within a surface forces apparatus (SFA). The design is a significant modification of the traditional SFA in that it allows one to combine nanorheology with the single-molecule sensitive technique of fluorescence correlation spectroscopy. The primary enabling idea was to place a miniaturized SFA onto the stage of an optical microscope equipped with a long working distance objective and illuminated by a femtosecond laser. A secondary enabling idea was that the silver coating on the backside of mica, normally used in the traditional SFA design for interferometric measurements of the film thickness, was replaced by multilayer dielectric coatings that allowed simultaneous interferometry and fluorescence measurements in different regions of the optical spectrum. To illustrate the utility of this instrument, we contrast the translational diffusion of rhodamine dye molecules (in the solvent, 1,2-propane diol), in the unconfined bulk state and confined between mica sheets to the thickness 2.5 nm. The diffusion coefficient is found to decrease by 2 orders of magnitude under confinement.

Early Detection of Junctional Adhesion Molecule-1 (JAM-1) in the Circulation after Experimental and Clinical Polytrauma

PubMed Central

Denk, Stephanie; Wiegner, Rebecca; Hönes, Felix M.; Messerer, David A. C.; Radermacher, Peter; Kalbitz, Miriam; Braumüller, Sonja; McCook, Oscar; Gebhard, Florian; Weckbach, Sebastian; Huber-Lang, Markus

2015-01-01

Severe tissue trauma-induced systemic inflammation is often accompanied by evident or occult blood-organ barrier dysfunctions, frequently leading to multiple organ dysfunction. However, it is unknown whether specific barrier molecules are shed into the circulation early after trauma as potential indicators of an initial barrier dysfunction. The release of the barrier molecule junctional adhesion molecule-1 (JAM-1) was investigated in plasma of C57BL/6 mice 2 h after experimental mono- and polytrauma as well as in polytrauma patients (ISS ≥ 18) during a 10-day period. Correlation analyses were performed to indicate a linkage between JAM-1 plasma concentrations and organ failure. JAM-1 was systemically detected after experimental trauma in mice with blunt chest trauma as a driving force. Accordingly, JAM-1 was reduced in lung tissue after pulmonary contusion and JAM-1 plasma levels significantly correlated with increased protein levels in the bronchoalveolar lavage as a sign for alveolocapillary barrier dysfunction. Furthermore, JAM-1 was markedly released into the plasma of polytrauma patients as early as 4 h after the trauma insult and significantly correlated with severity of disease and organ dysfunction (APACHE II and SOFA score). The data support an early injury- and time-dependent appearance of the barrier molecule JAM-1 in the circulation indicative of a commencing trauma-induced barrier dysfunction. PMID:26556956

The Acinar Cage: Basement Membranes Determine Molecule Exchange and Mechanical Stability of Human Breast Cell Acini.

PubMed

Gaiko-Shcherbak, Aljona; Fabris, Gloria; Dreissen, Georg; Merkel, Rudolf; Hoffmann, Bernd; Noetzel, Erik

2015-01-01

The biophysical properties of the basement membrane that surrounds human breast glands are poorly understood, but are thought to be decisive for normal organ function and malignancy. Here, we characterize the breast gland basement membrane with a focus on molecule permeation and mechanical stability, both crucial for organ function. We used well-established and nature-mimicking MCF10A acini as 3D cell model for human breast glands, with ether low- or highly-developed basement membrane scaffolds. Semi-quantitative dextran tracer (3 to 40 kDa) experiments allowed us to investigate the basement membrane scaffold as a molecule diffusion barrier in human breast acini in vitro. We demonstrated that molecule permeation correlated positively with macromolecule size and intriguingly also with basement membrane development state, revealing a pore size of at least 9 nm. Notably, an intact collagen IV mesh proved to be essential for this permeation function. Furthermore, we performed ultra-sensitive atomic force microscopy to quantify the response of native breast acini and of decellularized basement membrane shells against mechanical indentation. We found a clear correlation between increasing acinar force resistance and basement membrane formation stage. Most important native acini with highly-developed basement membranes as well as cell-free basement membrane shells could both withstand physiologically relevant loads (≤ 20 nN) without loss of structural integrity. In contrast, low-developed basement membranes were significantly softer and more fragile. In conclusion, our study emphasizes the key role of the basement membrane as conductor of acinar molecule influx and mechanical stability of human breast glands, which are fundamental for normal organ function.

Multi-Step Fibrinogen Binding to the Integrin αIIbβ3 Detected Using Force Spectroscopy

PubMed Central

Litvinov, Rustem I.; Bennett, Joel S.; Weisel, John W.; Shuman, Henry

2005-01-01

The regulated ability of integrin αIIbβ3 to bind fibrinogen plays a crucial role in platelet aggregation and hemostasis. We have developed a model system based on laser tweezers, enabling us to measure specific rupture forces needed to separate single receptor-ligand complexes. First of all, we performed a thorough and statistically representative analysis of nonspecific protein-protein binding versus specific αIIbβ3-fibrinogen interactions in combination with experimental evidence for single-molecule measurements. The rupture force distribution of purified αIIbβ3 and fibrinogen, covalently attached to underlying surfaces, ranged from ∼20 to 150 pN. This distribution could be fit with a sum of an exponential curve for weak to moderate (20–60 pN) forces, and a Gaussian curve for strong (>60 pN) rupture forces that peaked at 80–90 pN. The interactions corresponding to these rupture force regimes differed in their susceptibility to αIIbβ3 antagonists or Mn2+, an αIIbβ3 activator. Varying the surface density of fibrinogen changed the total binding probability linearly >3.5-fold but did not affect the shape of the rupture force distribution, indicating that the measurements represent single-molecule binding. The yield strength of αIIbβ3-fibrinogen interactions was independent of the loading rate (160–16,000 pN/s), whereas their binding probability markedly correlated with the duration of contact. The aggregate of data provides evidence for complex multi-step binding/unbinding pathways of αIIbβ3 and fibrinogen revealed at the single-molecule level. PMID:16040750

Adsorption of DNA to mica mediated by divalent counterions: a theoretical and experimental study.

PubMed

Pastré, David; Piétrement, Olivier; Fusil, Stéphane; Landousy, Fabrice; Jeusset, Josette; David, Marie-Odile; Hamon, Loïc; Le Cam, Eric; Zozime, Alain

2003-10-01

The adsorption of DNA molecules onto a flat mica surface is a necessary step to perform atomic force microscopy studies of DNA conformation and observe DNA-protein interactions in physiological environment. However, the phenomenon that pulls DNA molecules onto the surface is still not understood. This is a crucial issue because the DNA/surface interactions could affect the DNA biological functions. In this paper we develop a model that can explain the mechanism of the DNA adsorption onto mica. This model suggests that DNA attraction is due to the sharing of the DNA and mica counterions. The correlations between divalent counterions on both the negatively charged DNA and the mica surface can generate a net attraction force whereas the correlations between monovalent counterions are ineffective in the DNA attraction. DNA binding is then dependent on the fractional surface densities of the divalent and monovalent cations, which can compete for the mica surface and DNA neutralizations. In addition, the attraction can be enhanced when the mica has been pretreated by transition metal cations (Ni(2+), Zn(2+)). Mica pretreatment simultaneously enhances the DNA attraction and reduces the repulsive contribution due to the electrical double-layer force. We also perform end-to-end distance measurement of DNA chains to study the binding strength. The DNA binding strength appears to be constant for a fixed fractional surface density of the divalent cations at low ionic strength (I < 0.1 M) as predicted by the model. However, at higher ionic strength, the binding is weakened by the screening effect of the ions. Then, some equations were derived to describe the binding of a polyelectrolyte onto a charged surface. The electrostatic attraction due to the sharing of counterions is particularly effective if the polyelectrolyte and the surface have nearly the same surface charge density. This characteristic of the attraction force can explain the success of mica for performing single DNA molecule observation by AFM. In addition, we explain how a reversible binding of the DNA molecules can be obtained with a pretreated mica surface.

Ultrafast dynamics of low-energy electron attachment via a non-valence correlation-bound state

NASA Astrophysics Data System (ADS)

Rogers, Joshua P.; Anstöter, Cate S.; Verlet, Jan R. R.

2018-03-01

The primary electron-attachment process in electron-driven chemistry represents one of the most fundamental chemical transformations with wide-ranging importance in science and technology. However, the mechanistic detail of the seemingly simple reaction of an electron and a neutral molecule to form an anion remains poorly understood, particularly at very low electron energies. Here, time-resolved photoelectron imaging was used to probe the electron-attachment process to a non-polar molecule using time-resolved methods. An initially populated diffuse non-valence state of the anion that is bound by correlation forces evolves coherently in ∼30 fs into a valence state of the anion. The extreme efficiency with which the correlation-bound state serves as a doorway state for low-energy electron attachment explains a number of electron-driven processes, such as anion formation in the interstellar medium and electron attachment to fullerenes.

Thermal noise in confined fluids.

PubMed

Sanghi, T; Aluru, N R

2014-11-07

In this work, we discuss a combined memory function equation (MFE) and generalized Langevin equation (GLE) approach (referred to as MFE/GLE formulation) to characterize thermal noise in confined fluids. Our study reveals that for fluids confined inside nanoscale geometries, the correlation time and the time decay of the autocorrelation function of the thermal noise are not significantly different across the confinement. We show that it is the strong cross-correlation of the mean force with the molecular velocity that gives rise to the spatial anisotropy in the velocity-autocorrelation function of the confined fluids. Further, we use the MFE/GLE formulation to extract the thermal force a fluid molecule experiences in a MD simulation. Noise extraction from MD simulation suggests that the frequency distribution of the thermal force is non-Gaussian. Also, the frequency distribution of the thermal force near the confining surface is found to be different in the direction parallel and perpendicular to the confinement. We also use the formulation to compute the noise correlation time of water confined inside a (6,6) carbon-nanotube (CNT). It is observed that inside the (6,6) CNT, in which water arranges itself in a highly concerted single-file arrangement, the correlation time of thermal noise is about an order of magnitude higher than that of bulk water.

Thermal noise in confined fluids

NASA Astrophysics Data System (ADS)

Sanghi, T.; Aluru, N. R.

2014-11-01

In this work, we discuss a combined memory function equation (MFE) and generalized Langevin equation (GLE) approach (referred to as MFE/GLE formulation) to characterize thermal noise in confined fluids. Our study reveals that for fluids confined inside nanoscale geometries, the correlation time and the time decay of the autocorrelation function of the thermal noise are not significantly different across the confinement. We show that it is the strong cross-correlation of the mean force with the molecular velocity that gives rise to the spatial anisotropy in the velocity-autocorrelation function of the confined fluids. Further, we use the MFE/GLE formulation to extract the thermal force a fluid molecule experiences in a MD simulation. Noise extraction from MD simulation suggests that the frequency distribution of the thermal force is non-Gaussian. Also, the frequency distribution of the thermal force near the confining surface is found to be different in the direction parallel and perpendicular to the confinement. We also use the formulation to compute the noise correlation time of water confined inside a (6,6) carbon-nanotube (CNT). It is observed that inside the (6,6) CNT, in which water arranges itself in a highly concerted single-file arrangement, the correlation time of thermal noise is about an order of magnitude higher than that of bulk water.

Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy

PubMed Central

Neuman, Keir C.; Nagy, Attila

2012-01-01

Single-molecule force spectroscopy has emerged as a powerful tool to investigate the forces and motions associated with biological molecules and enzymatic activity. The most common force spectroscopy techniques are optical tweezers, magnetic tweezers and atomic force microscopy. These techniques are described and illustrated with examples highlighting current capabilities and limitations. PMID:18511917

The correlations of the electronic structure and film growth of 2,7-diocty[1]benzothieno[3,2-b]benzothiophene (C8-BTBT) on SiO2.

PubMed

Lyu, Lu; Niu, Dongmei; Xie, Haipeng; Zhao, Yuan; Cao, Ningtong; Zhang, Hong; Zhang, Yuhe; Liu, Peng; Gao, Yongli

2017-01-04

Combining ultraviolet photoemission spectroscopy (UPS), X-ray photoemission spectroscopy (XPS), atomic force microscopy (AFM) and small angle X-ray diffraction (SAXD) measurements, we perform a systematic investigation on the correlations of the electronic structure, film growth and molecular orientation of 2,7-diocty[1]benzothieno[3,2-b]benzothiophene (C8-BTBT) on silicon oxide (SiO 2 ). AFM analysis reveals a phase transition of disorderedly oriented molecules in clusters in thinner films to highly ordered standing-up molecules in islands in thicker films. SAXD peaks consistently support the standing-up configuration in islands. The increasing ordering of the molecular orientation with film thickness contributes to the changing of the shape and lowering of the leading edge of the highest occupied molecular orbital (HOMO). The end methyl of the highly ordered standing molecules forms an outward pointing dipole layer which makes the work function (WF) decrease with increasing thickness. The downward shift of the HOMO and a decrease of WF result in unconventional downward band bending and decreased ionization potential (IP). The correlations of the orientation ordering of molecules, film growth and interface electronic structures provide a useful design strategy to improve the performance of C8-BTBT thin film based field effect transistors.

Probing Protein-Protein Interactions by Dynamic Force Correlation Spectroscopy

NASA Astrophysics Data System (ADS)

Barsegov, V.; Thirumalai, D.

2005-10-01

We develop a formalism for single molecule dynamic force spectroscopy to map the energy landscape of protein-protein complex (P1P2). The joint distribution P(τ1,τ2) of unbinding lifetimes τ1 and τ2, measurable in a compression-tension cycle, which accounts for the internal relaxation dynamics of the proteins under tension, shows that the histogram of τ1 is not Poissonian. The theory is applied to the forced unbinding of protein P1, modeled as a wormlike chain, from P1P2. We propose a new class of experiments which can resolve the effect of internal protein dynamics on the unbinding lifetimes.

Force-Manipulation Single-Molecule Spectroscopy Studies of Enzymatic Dynamics

NASA Astrophysics Data System (ADS)

Lu, H. Peter; He, Yufan; Lu, Maolin; Cao, Jin; Guo, Qing

2014-03-01

Subtle conformational changes play a crucial role in protein functions, especially in enzymatic reactions involving complex substrate-enzyme interactions and chemical reactions. We applied AFM-enhanced and magnetic tweezers-correlated single-molecule spectroscopy to study the mechanisms and dynamics of enzymatic reactions involved with kinase and lysozyme proteins. Enzymatic reaction turnovers and the associated structure changes of individual protein molecules were observed simultaneously in real-time by single-molecule FRET detections. Our single-molecule spectroscopy measurements of enzymatic conformational dynamics have revealed time bunching effect and intermittent coherence in conformational state change dynamics involving in enzymatic reaction cycles. The coherent conformational state dynamics suggests that the enzymatic catalysis involves a multi-step conformational motion along the coordinates of substrate-enzyme complex formation and product releasing. Our results support a multiple-conformational state model, being consistent with a complementary conformation selection and induced-fit enzymatic loop-gated conformational change mechanism in substrate-enzyme active complex formation.

Myocardial short-range force responses increase with age in F344 rats

PubMed Central

Mitov, Mihail I.; Holbrook, Anastasia M.; Campbell, Kenneth S.

2009-01-01

The mechanical properties of triton-permeabilized ventricular preparations isolated from 4, 18 and 24-month-old F344 rats were analyzed to provide information about the molecular mechanisms that lead to age-related increases in diastolic myocardial stiffness in these animals. Passive stiffness (measured in solutions with minimal free Ca2+) did not change with age. This implies that the aging-associated dysfunction is not due to changes in titin or collagen molecules. Ca2+-activated preparations exhibited a characteristic short-range force response: force rose rapidly until the muscle reached its elastic limit and less rapidly thereafter. The elastic limit increased from 0.43 ± 0.01 % l0 (where l0 is the initial muscle length) in preparations from 4-month-old animals to 0.49 ± 0.01 % l0 in preparations from 24-month-old rats (p<0.001, ANOVA). Relative short-range force was defined as the maximum force produced during the short-range response normalized to the prevailing tension. This parameter increased from 0.110 ± 0.002 to 0.142 ± 0.002 over the same age-span (p<0.001, ANOVA). Analytical gel electrophoresis showed that the maximum stiffness of the preparations during the short-range response and the relative short-range force increased (p=0.031 and p=0.005 respectively) with the relative content of slow β myosin heavy chain molecules. Elastic limit values did not correlate with myosin isoform content. Simulations based on these results suggest that attached β myosin heavy chain cross-bridges are stiffer than links formed by α myosin heads. In conclusion, elevated content of stiffer β myosin heavy chain molecules may contribute to aging-associated increases in myocardial stiffness. PMID:19007786

Characterization of the viscoelastic behavior of a simplified collagen micro-fibril based on molecular dynamics simulations.

PubMed

Ghodsi, Hossein; Darvish, Kurosh

2016-10-01

Collagen fibril is a major component of connective tissues such as bone, tendon, blood vessels, and skin. The mechanical properties of this highly hierarchical structure are greatly influenced by the presence of covalent cross-links between individual collagen molecules. This study investigates the viscoelastic behavior of a collagen lysine-lysine cross-link based on creep simulations with applied forces in the range or 10 to 2000pN using steered molecular dynamics (SMD). The viscoelastic model of the cross-link was combined with a system composed by two segments of adjacent collagen molecules hence representing a reduced viscoelastic model for a simplified micro-fibril. It was found that the collagen micro-fibril assembly had a steady-state Young׳s modulus ranging from 2.24 to 3.27GPa, which is in agreement with reported experimental measurements. The propagation of longitudinal force wave along the molecule was implemented by adding a delay element to the model. The force wave speed was found to be correlated with the speed of one-dimensional elastic waves in rods. The presented reduced model with three degrees of freedom can serve as a building block for developing models of the next level of hierarchy, i.e., a collagen fibril. Copyright © 2016 Elsevier Ltd. All rights reserved.

Identification of stepped changes of binding affinity during interactions between the disintegrin rhodostomin and integrin αIIbβ3 in living cells using optical tweezers

NASA Astrophysics Data System (ADS)

Hsieh, Chia-Fen; Chang, Bo-Jui; Pai, Chyi-Huey; Chen, Hsuan-Yi; Chi, Sien; Hsu, Long; Tsai, Jin-Wu; Lin, Chi-Hung

2004-10-01

Integrin receptors serve as both mechanical links and signal transduction mediators between the cell and its environment. Experimental evidence demonstrates that conformational changes and lateral clustering of the integrin proteins may affect their binding to ligands and regulate downstream cellular responses; however, experimental links between the structural and functional correlations of the ligand-receptor interactions are not yet elucidated. In the present report, we utilized optical tweezers to measure the dynamic binding between the snake venom rhodostomin, coated on a microparticle and functioned as a ligand, and the membrane receptor integrin alpha(IIb)beta(3) expressed on a Chinese Hamster Ovary (CHO) cell. A progressive increase of total binding affinity was found between the bead and CHO cell in the first 300 sec following optical tweezers-guided contact. Further analysis of the cumulative data revealed the presence of "unit binding force" presumably exerted by a single rhodostomin-integrin pair. Interestingly, two such units were found. Among the measurements of less total binding forces, presumably taken at the early stage of ligand-receptor interactions, a unit of 4.15 pN per molecule pair was derived. This unit force dropped to 2.54 pN per molecule pair toward the later stage of interactions when the total binding forces were relatively large. This stepped change of single molecule pair binding affinity was not found when mutant rhodostomin proteins were used as ligands (a single unit of 1.81 pN per pair was found). These results were interpreted along with the current knowledge about the conformational changes of integrins during the "molecule activation" process.

Direct Observation of Azimuthal Correlations between DNA in Hydrated Aggregates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kornyshev, Alexei A.; Lee, Dominic J.; Wynveen, Aaron

2005-09-30

This study revisits the classical x-ray diffraction patterns from hydrated, noncrystalline fibers originally used to establish the helical structure of DNA. We argue that changes in these diffraction patterns with DNA packing density reveal strong azimuthally dependent interactions between adjacent molecules up to {approx}40 A interaxial or {approx}20 A surface-to-surface separations. These interactions appear to force significant torsional 'straightening' of DNA and strong azimuthal alignment of nearest neighbor molecules. The results are in good agreement with the predictions of recent theoretical models relating DNA-DNA interactions to the helical symmetry of their surface charge patterns.

Force-detected nanoscale absorption spectroscopy in water at room temperature using an optical trap

NASA Astrophysics Data System (ADS)

Parobek, Alexander; Black, Jacob W.; Kamenetska, Maria; Ganim, Ziad

2018-04-01

Measuring absorption spectra of single molecules presents a fundamental challenge for standard transmission-based instruments because of the inherently low signal relative to the large background of the excitation source. Here we demonstrate a new approach for performing absorption spectroscopy in solution using a force measurement to read out optical excitation at the nanoscale. The photoinduced force between model chromophores and an optically trapped gold nanoshell has been measured in water at room temperature. This photoinduced force is characterized as a function of wavelength to yield the force spectrum, which is shown to be correlated to the absorption spectrum for four model systems. The instrument constructed for these measurements combines an optical tweezer with frequency domain absorption spectroscopy over the 400-800 nm range. These measurements provide proof-of-principle experiments for force-detected nanoscale spectroscopies that operate under ambient chemical conditions.

Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for -1 ribosomal frameshifting stimulation

NASA Astrophysics Data System (ADS)

Zhong, Zhensheng; Yang, Lixia; Zhang, Haiping; Shi, Jiahao; Vandana, J. Jeya; Lam, Do Thuy Uyen Ha; Olsthoorn, René C. L.; Lu, Lanyuan; Chen, Gang

2016-12-01

Minus-one ribosomal frameshifting is a translational recoding mechanism widely utilized by many RNA viruses to generate accurate ratios of structural and catalytic proteins. An RNA pseudoknot structure located in the overlapping region of the gag and pro genes of Simian Retrovirus type 1 (SRV-1) stimulates frameshifting. However, the experimental characterization of SRV-1 pseudoknot (un)folding dynamics and the effect of the base triple formation is lacking. Here, we report the results of our single-molecule nanomanipulation using optical tweezers and theoretical simulation by steered molecular dynamics. Our results directly reveal that the energetic coupling between loop 2 and stem 1 via minor-groove base triple formation enhances the mechanical stability. The terminal base pair in stem 1 (directly in contact with a translating ribosome at the slippery site) also affects the mechanical stability of the pseudoknot. The -1 frameshifting efficiency is positively correlated with the cooperative one-step unfolding force and inversely correlated with the one-step mechanical unfolding rate at zero force. A significantly improved correlation was observed between -1 frameshifting efficiency and unfolding rate at forces of 15-35 pN, consistent with the fact that the ribosome is a force-generating molecular motor with helicase activity. No correlation was observed between thermal stability and -1 frameshifting efficiency.

Combining single-molecule manipulation and single-molecule detection.

PubMed

Cordova, Juan Carlos; Das, Dibyendu Kumar; Manning, Harris W; Lang, Matthew J

2014-10-01

Single molecule force manipulation combined with fluorescence techniques offers much promise in revealing mechanistic details of biomolecular machinery. Here, we review force-fluorescence microscopy, which combines the best features of manipulation and detection techniques. Three of the mainstay manipulation methods (optical traps, magnetic traps and atomic force microscopy) are discussed with respect to milestones in combination developments, in addition to highlight recent contributions to the field. An overview of additional strategies is discussed, including fluorescence based force sensors for force measurement in vivo. Armed with recent exciting demonstrations of this technology, the field of combined single-molecule manipulation and single-molecule detection is poised to provide unprecedented views of molecular machinery. Copyright © 2014 Elsevier Ltd. All rights reserved.

Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions

PubMed Central

2015-01-01

We parametrize a linear-scaling quantum mechanical force field called mDC for the accurate reproduction of nonbonded interactions. We provide a new benchmark database of accurate ab initio interactions between sulfur-containing molecules. A variety of nonbond databases are used to compare the new mDC method with other semiempirical, molecular mechanical, ab initio, and combined semiempirical quantum mechanical/molecular mechanical methods. It is shown that the molecular mechanical force field significantly and consistently reproduces the benchmark results with greater accuracy than the semiempirical models and our mDC model produces errors twice as small as the molecular mechanical force field. The comparisons between the methods are extended to the docking of drug candidates to the Cyclin-Dependent Kinase 2 protein receptor. We correlate the protein–ligand binding energies to their experimental inhibition constants and find that the mDC produces the best correlation. Condensed phase simulation of mDC water is performed and shown to produce O–O radial distribution functions similar to TIP4P-EW. PMID:24803856

The correlated molecular electrostatic potential and electric field of 2 (1H)-pyrimidone and 2-hydroxypyrimidine

NASA Astrophysics Data System (ADS)

Leś, Andrzej; Adamowicz, Ludwik

1991-06-01

The molecular electrostatic potential and molecular electric field have been estimated by means of the expectation values of the respective one-electron operators. We used the molecular density matrix that includes the electron correlation effects up to the second-order of the many body perturbation theory. The results show that around the 2(1H)-pyrimidone molecule one may distinguish the electrophilic and nucleophilic regions, the latter characterized by two potential minima of -2.9 V. In the tautomeric form, 2-hydroxypyrimidine, a third potential minimum of -2.1 V appears close to the N1 nitrogen atom. For both molecules strong orientational forces acting on polar solvents are predicted in the vicinity of oxygen (O7) and nitrogen (N3) atoms. The electron correlation effects do not significantly alter the SCF values of the electrostatic potential and electric field at the distances within the van der Waals envelope of the pyrimidine bases. At larger distances, however, the correlation correction is significant, particularly in the direction facing the proton transfer path.

Understanding the Origins of Dipolar Couplings and Correlated Motion in the Vibrational Spectrum of Water.

PubMed

Heyden, Matthias; Sun, Jian; Forbert, Harald; Mathias, Gerald; Havenith, Martina; Marx, Dominik

2012-08-16

The combination of vibrational spectroscopy and molecular dynamics simulations provides a powerful tool to obtain insights into the molecular details of water structure and dynamics in the bulk and in aqueous solutions. Applying newly developed approaches to analyze correlations of charge currents, molecular dipole fluctuations, and vibrational motion in real and k-space, we compare results from nonpolarizable water models, widely used in biomolecular modeling, to ab initio molecular dynamics. For the first time, we unfold the infrared response of bulk water into contributions from correlated fluctuations in the three-dimensional, anisotropic environment of an average water molecule, from the OH-stretching region down to the THz regime. Our findings show that the absence of electronic polarizability in the force field model not only results in differences in dipolar couplings and infrared absorption but also induces artifacts into the correlated vibrational motion between hydrogen-bonded water molecules, specifically at the intramolecular bending frequency. Consequently, vibrational motion is partially ill-described with implications for the accuracy of non-self-consistent, a posteriori methods to add polarizability.

Stiffness, working stroke, and force of single-myosin molecules in skeletal muscle: elucidation of these mechanical properties via nonlinear elasticity evaluation.

PubMed

Kaya, Motoshi; Higuchi, Hideo

2013-11-01

In muscles, the arrays of skeletal myosin molecules interact with actin filaments and continuously generate force at various contraction speeds. Therefore, it is crucial for myosin molecules to generate force collectively and minimize the interference between individual myosin molecules. Knowledge of the elasticity of myosin molecules is crucial for understanding the molecular mechanisms of muscle contractions because elasticity directly affects the working and drag (resistance) force generation when myosin molecules are positively or negatively strained. The working stroke distance is also an important mechanical property necessary for elucidation of the thermodynamic efficiency of muscle contractions at the molecular level. In this review, we focus on these mechanical properties obtained from single-fiber and single-molecule studies and discuss recent findings associated with these mechanical properties. We also discuss the potential molecular mechanisms associated with reduction of the drag effect caused by negatively strained myosin molecules.

Investigating single molecule adhesion by atomic force spectroscopy.

PubMed

Stetter, Frank W S; Kienle, Sandra; Krysiak, Stefanie; Hugel, Thorsten

2015-02-27

Atomic force spectroscopy is an ideal tool to study molecules at surfaces and interfaces. An experimental protocol to couple a large variety of single molecules covalently onto an AFM tip is presented. At the same time the AFM tip is passivated to prevent unspecific interactions between the tip and the substrate, which is a prerequisite to study single molecules attached to the AFM tip. Analyses to determine the adhesion force, the adhesion length, and the free energy of these molecules on solid surfaces and bio-interfaces are shortly presented and external references for further reading are provided. Example molecules are the poly(amino acid) polytyrosine, the graft polymer PI-g-PS and the phospholipid POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine). These molecules are desorbed from different surfaces like CH3-SAMs, hydrogen terminated diamond and supported lipid bilayers under various solvent conditions. Finally, the advantages of force spectroscopic single molecule experiments are discussed including means to decide if truly a single molecule has been studied in the experiment.

Investigating Single Molecule Adhesion by Atomic Force Spectroscopy

PubMed Central

Stetter, Frank W. S.; Kienle, Sandra; Krysiak, Stefanie; Hugel, Thorsten

2015-01-01

Atomic force spectroscopy is an ideal tool to study molecules at surfaces and interfaces. An experimental protocol to couple a large variety of single molecules covalently onto an AFM tip is presented. At the same time the AFM tip is passivated to prevent unspecific interactions between the tip and the substrate, which is a prerequisite to study single molecules attached to the AFM tip. Analyses to determine the adhesion force, the adhesion length, and the free energy of these molecules on solid surfaces and bio-interfaces are shortly presented and external references for further reading are provided. Example molecules are the poly(amino acid) polytyrosine, the graft polymer PI-g-PS and the phospholipid POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine). These molecules are desorbed from different surfaces like CH3-SAMs, hydrogen terminated diamond and supported lipid bilayers under various solvent conditions. Finally, the advantages of force spectroscopic single molecule experiments are discussed including means to decide if truly a single molecule has been studied in the experiment. PMID:25867282

Statistical-Mechanical Studies of the Collective Binding of Proteins to DNA

NASA Astrophysics Data System (ADS)

Zhang, Houyin

My dissertation work focuses on the microscopic statistical-mechanical studies of DNA-protein interactions and mainly comprises of three projects. In living cells, binding of proteins to DNA controls gene expression and packaging of the genome. Single-DNA stretching and twisting experiments provide a powerful tool to detect binding of proteins, via detection of their modification of DNA mechanical properties. However, it is often difficult or impossible to determine the numbers of proteins bound in such experiments, especially when the proteins interact nonspecifically with DNA. In the first project, we developed single-molecule versions of classical thermodynamic Maxwell relations and proposed that these relations could be used to measure DNA-bound protein numbers, changes in DNA double-helix torque with force, and many other quantities which are hard to directly measure. This approach does not need any theoretical assumptions beyond the existence of thermodynamic equilibrium and has been used in single-DNA experiments. Many single-molecule experiments associated with DNA-bending proteins suggest the existence of cooperative interactions between adjacent DNA-bound proteins. In the second project, we studied a statistical-mechanical worm-like chain model including binding cooperativity effects and found that the intrinsic cooperativity of binding sharpens force-extension curves and causes enhancement of fluctuation of extension and protein occupation. This model also allows us to estimate the intrinsic cooperativity in experiments. We also analyzed force-generated cooperativity and found that the related interaction between proteins is always attractive. This suggests that tension in DNA in vivo could alter the distribution of proteins bound along DNA, causing chromosome refolding, or changes in gene expression. In the third project, we investigated the correlations along DNA-protein complexes. We found there are two different correlation lengths corrected to the geometry of DNA bending - the shorter “longitudinal” correlation length ξ∥(f, μ) and the longer “transverse” correlation length ξ⊥( f, μ). In the high-force limit, ξ∥(f, μ) = ξ⊥(f, μ)/2 = A/4bf . Surprisingly, the range of the interaction between DNA-bending proteins is controlled by the second-longest correlation length. The effect arises from the protein-bend contribution to the Hamiltonian having an axial rotational symmetry which eliminates its coupling to the transverse bending fluctuations.

Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

DOE PAGES

Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; ...

2015-06-04

Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstratemore » prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.« less

Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space

PubMed Central

2015-01-01

Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies. PMID:26113956

HDL particles incorporate into lipid bilayers - a combined AFM and single molecule fluorescence microscopy study.

PubMed

Plochberger, Birgit; Röhrl, Clemens; Preiner, Johannes; Rankl, Christian; Brameshuber, Mario; Madl, Josef; Bittman, Robert; Ros, Robert; Sezgin, Erdinc; Eggeling, Christian; Hinterdorfer, Peter; Stangl, Herbert; Schütz, Gerhard J

2017-11-21

The process, how lipids are removed from the circulation and transferred from high density lipoprotein (HDL) - a main carrier of cholesterol in the blood stream - to cells, is highly complex. HDL particles are captured from the blood stream by the scavenger receptor, class B, type I (SR-BI), the so-called HDL receptor. The details in subsequent lipid-transfer process, however, have not yet been completely understood. The transfer has been proposed to occur directly at the cell surface across an unstirred water layer, via a hydrophobic channel in the receptor, or after HDL endocytosis. The role of the target lipid membrane for the transfer process, however, has largely been overlooked. Here, we studied at the single molecule level how HDL particles interact with synthetic lipid membranes. Using (high-speed) atomic force microscopy and fluorescence correlation spectroscopy (FCS) we found out that, upon contact with the membrane, HDL becomes integrated into the lipid bilayer. Combined force and single molecule fluorescence microscopy allowed us to directly monitor the transfer process of fluorescently labelled amphiphilic lipid probe from HDL particles to the lipid bilayer upon contact.

Non-additivity of molecule-surface van der Waals potentials from force measurements.

PubMed

Wagner, Christian; Fournier, Norman; Ruiz, Victor G; Li, Chen; Müllen, Klaus; Rohlfing, Michael; Tkatchenko, Alexandre; Temirov, Ruslan; Tautz, F Stefan

2014-11-26

Van der Waals (vdW) forces act ubiquitously in condensed matter. Despite being weak on an atomic level, they substantially influence molecular and biological systems due to their long range and system-size scaling. The difficulty to isolate and measure vdW forces on a single-molecule level causes our present understanding to be strongly theory based. Here we show measurements of the attractive potential between differently sized organic molecules and a metal surface using an atomic force microscope. Our choice of molecules and the large molecule-surface separation cause this attraction to be purely of vdW type. The experiment allows testing the asymptotic vdW force law and its validity range. We find a superlinear growth of the vdW attraction with molecular size, originating from the increased deconfinement of electrons in the molecules. Because such non-additive vdW contributions are not accounted for in most first-principles or empirical calculations, we suggest further development in that direction.

Preparation of translationally cold neutral molecules.

PubMed

Di Domenicantonio, Giulia; Bertsche, Benjamin; Osterwalder, Andreas

2011-01-01

Efforts at EPFL to obtain translationally cold neutral molecules are described. Active deceleration of polar molecules is performed by confining the molecules in moving three-dimensional electrostatic traps, and by appropriately choosing the velocity of those traps. Alternatively, cold molecules can be obtained by velocity filtering. Here, the velocity of the molecules is not changed, but instead the cold molecules are extracted from a thermal sample by using the competition between the electrostatic force and the centrifugal force inside a bent electrostatic guide for polar molecules.

Direct observation of the actin filament by tip-scan atomic force microscopy

PubMed Central

Narita, Akihiro; Usukura, Eiji; Yagi, Akira; Tateyama, Kiyohiko; Akizuki, Shogo; Kikumoto, Mahito; Matsumoto, Tomoharu; Maéda, Yuichiro; Ito, Shuichi; Usukura, Jiro

2016-01-01

Actin filaments, the actin–myosin complex and the actin–tropomyosin complex were observed by a tip-scan atomic force microscope (AFM), which was recently developed by Olympus as the AFM part of a correlative microscope. This newly developed AFM uses cantilevers of similar size as stage-scan AFMs to improve substantially the spatial and temporal resolution. Such an approach has previously never been possible by a tip-scan system, in which a cantilever moves in the x, y and z directions. We evaluated the performance of this developed tip-scan AFM by observing the molecular structure of actin filaments and the actin–tropomyosin complex. In the image of the actin filament, the molecular interval of the actin subunits (∼5.5 nm) was clearly observed as stripes. From the shape of the stripes, the polarity of the actin filament was directly determined and the results were consistent with the polarity determined by myosin binding. In the image of the actin–tropomyosin complex, each tropomyosin molecule (∼2 nm in diameter) on the actin filament was directly observed without averaging images of different molecules. Each tropomyosin molecule on the actin filament has never been directly observed by AFM or electron microscopy. Thus, our developed tip-scan AFM offers significant potential in observing purified proteins and cellular structures at nanometer resolution. Current results represent an important step in the development of a new correlative microscope to observe nm-order structures at an acceptable frame rate (∼10 s/frame) by AFM at the position indicated by the fluorescent dye observed under a light microscope. PMID:27242058

The Chemical Structure and Acid Deterioration of Paper.

ERIC Educational Resources Information Center

Hollinger, William K., Jr.

1984-01-01

Describes the chemical structure of paper, including subatomic particles, atoms and molecules, and the forces that bond atoms into molecules, molecules into chains, chains into sheets, and sheets into layers. Acid is defined, and the deleterious role of acid in breaking the forces that bond atoms into molecules is detailed. (EJS)

Coherent Bichromatic Force Deflection of Molecules

NASA Astrophysics Data System (ADS)

Kozyryev, Ivan; Baum, Louis; Aldridge, Leland; Yu, Phelan; Eyler, Edward E.; Doyle, John M.

2018-02-01

We demonstrate the effect of the coherent optical bichromatic force on a molecule, the polar free radical strontium monohydroxide (SrOH). A dual-frequency retroreflected laser beam addressing the X˜2Σ+↔A˜2Π1 /2 electronic transition coherently imparts momentum onto a cryogenic beam of SrOH. This directional photon exchange creates a bichromatic force that transversely deflects the molecules. By adjusting the relative phase between the forward and counterpropagating laser beams we reverse the direction of the applied force. A momentum transfer of 70 ℏk is achieved with minimal loss of molecules to dark states. Modeling of the bichromatic force is performed via direct numerical solution of the time-dependent density matrix and is compared with experimental observations. Our results open the door to further coherent manipulation of molecular motion, including the efficient optical deceleration of diatomic and polyatomic molecules with complex level structures.

Compressive Force Spectroscopy: From Living Cells to Single Proteins.

PubMed

Wang, Jiabin; Liu, Meijun; Shen, Yi; Sun, Jielin; Shao, Zhifeng; Czajkowsky, Daniel Mark

2018-03-23

One of the most successful applications of atomic force microscopy (AFM) in biology involves monitoring the effect of force on single biological molecules, often referred to as force spectroscopy. Such studies generally entail the application of pulling forces of different magnitudes and velocities upon individual molecules to resolve individualistic unfolding/separation pathways and the quantification of the force-dependent rate constants. However, a less recognized variation of this method, the application of compressive force, actually pre-dates many of these "tensile" force spectroscopic studies. Further, beyond being limited to the study of single molecules, these compressive force spectroscopic investigations have spanned samples as large as living cells to smaller, multi-molecular complexes such as viruses down to single protein molecules. Correspondingly, these studies have enabled the detailed characterization of individual cell states, subtle differences between seemingly identical viral structures, as well as the quantification of rate constants of functionally important, structural transitions in single proteins. Here, we briefly review some of the recent achievements that have been obtained with compressive force spectroscopy using AFM and highlight exciting areas of its future development.

Simple horizontal magnetic tweezers for micromanipulation of single DNA molecules and DNA–protein complexes

PubMed Central

McAndrew, Christopher P.; Tyson, Christopher; Zischkau, Joseph; Mehl, Patrick; Tuma, Pamela L.; Pegg, Ian L.; Sarkar, Abhijit

2016-01-01

We report the development of a simple-to-implement magnetic force transducer that can apply a wide range of piconewton (pN) scale forces on single DNA molecules and DNA–protein complexes in the horizontal plane. The resulting low-noise force-extension data enable very high-resolution detection of changes in the DNA tether’s extension: ~0.05 pN in force and <10 nm change in extension. We have also verified that we can manipulate DNA in near equilibrium conditions through the wide range of forces by ramping the force from low to high and back again, and observing minimal hysteresis in the molecule’s force response. Using a calibration technique based on Stokes’ drag law, we have confirmed our force measurements from DNA force-extension experiments obtained using the fluctuation-dissipation theorem applied to transverse fluctuations of the magnetic microsphere. We present data on the force-distance characteristics of a DNA molecule complexed with histones. The results illustrate how the tweezers can be used to study DNA binding proteins at the single molecule level. PMID:26757808

Micro-hole array fluorescent sensor based on AC-Dielectrophoresis (DEP) for simultaneous analysis of nano-molecules

NASA Astrophysics Data System (ADS)

Kim, Hye Jin; Kang, Dong-Hoon; Lee, Eunji; Hwang, Kyo Seon; Shin, Hyun-Joon; Kim, Jinsik

2018-02-01

We propose a simple fluorescent bio-chip based on two types of alternative current-dielectrophoretic (AC-DEP) force, attractive (positive DEP) and repulsive (negative DEP) force, for simultaneous nano-molecules analysis. Various radius of micro-holes on the bio-chip are designed to apply the different AC-DEP forces, and the nano-molecules are concentrated inside the micro-hole arrays according to the intensity of the DEP force. The bio-chip was fabricated by Micro Electro Mechanical system (MEMS) technique, and was composed of two layers; a SiO2 layer and Ta/Pt layer were accomplished for an insulation layer and a top electrode with micro-hole arrays to apply electric fields for DEP force, respectively. Each SiO2 and Ta/Pt layers were deposited by thermal oxidation and sputtering, and micro-hole arrays were fabricated with Inductively Coupled Plasma (ICP) etching process. For generation of each positive and negative DEP at micro-holes, we applied two types of sine-wave AC voltage with different frequency range alternately. The intensity of the DEP force was controlled by the radius of the micro-hole and size of nano-molecule, and calculated with COMSOL multi-physics. Three types of nano-molecules labelled with different fluorescent dye were used and the intensity of nano-molecules was examined by the fluorescent optical analysis after applying the DEP force. By analyzing the fluorescent intensities of the nano-molecules, we verify the various nano-molecules in analyte are located successfully inside corresponding micro-holes with different radius according to their size.

Repurposing a Benchtop Centrifuge for High-Throughput Single-Molecule Force Spectroscopy.

PubMed

Yang, Darren; Wong, Wesley P

2018-01-01

We present high-throughput single-molecule manipulation using a benchtop centrifuge, overcoming limitations common in other single-molecule approaches such as high cost, low throughput, technical difficulty, and strict infrastructure requirements. An inexpensive and compact Centrifuge Force Microscope (CFM) adapted to a commercial centrifuge enables use by nonspecialists, and integration with DNA nanoswitches facilitates both reliable measurements and repeated molecular interrogation. Here, we provide detailed protocols for constructing the CFM, creating DNA nanoswitch samples, and carrying out single-molecule force measurements.

Protein Conformational Dynamics Probed by Single-Molecule Electron Transfer

NASA Astrophysics Data System (ADS)

Yang, Haw; Luo, Guobin; Karnchanaphanurach, Pallop; Louie, Tai-Man; Rech, Ivan; Cova, Sergio; Xun, Luying; Xie, X. Sunney

2003-10-01

Electron transfer is used as a probe for angstrom-scale structural changes in single protein molecules. In a flavin reductase, the fluorescence of flavin is quenched by a nearby tyrosine residue by means of photo-induced electron transfer. By probing the fluorescence lifetime of the single flavin on a photon-by-photon basis, we were able to observe the variation of flavin-tyrosine distance over time. We could then determine the potential of mean force between the flavin and the tyrosine, and a correlation analysis revealed conformational fluctuation at multiple time scales spanning from hundreds of microseconds to seconds. This phenomenon suggests the existence of multiple interconverting conformers related to the fluctuating catalytic reactivity.

Advances in Quantum Mechanochemistry: Electronic Structure Methods and Force Analysis.

PubMed

Stauch, Tim; Dreuw, Andreas

2016-11-23

In quantum mechanochemistry, quantum chemical methods are used to describe molecules under the influence of an external force. The calculation of geometries, energies, transition states, reaction rates, and spectroscopic properties of molecules on the force-modified potential energy surfaces is the key to gain an in-depth understanding of mechanochemical processes at the molecular level. In this review, we present recent advances in the field of quantum mechanochemistry and introduce the quantum chemical methods used to calculate the properties of molecules under an external force. We place special emphasis on quantum chemical force analysis tools, which can be used to identify the mechanochemically relevant degrees of freedom in a deformed molecule, and spotlight selected applications of quantum mechanochemical methods to point out their synergistic relationship with experiments.

Like-charge attraction and opposite-charge decomplexation between polymers and DNA molecules

NASA Astrophysics Data System (ADS)

Buyukdagli, Sahin

2017-02-01

We scrutinize the effect of polyvalent ions on polymer-DNA interactions. We extend a recently developed test-charge theory [S. Buyukdagli et al., Phys. Rev. E 94, 042502 (2016), 10.1103/PhysRevE.94.042502] to the case of a stiff polymer interacting with a DNA molecule in an electrolyte mixture. The theory accounts for one-loop level electrostatic correlation effects such as the ionic cloud deformation around the strongly charged DNA molecule as well as image-charge forces induced by the low DNA permittivity. Our model can reproduce and explain various characteristics of the experimental phase diagrams for polymer solutions. First, the addition of polyvalent cations to the electrolyte solution results in the attraction of the negatively charged polymer by the DNA molecule. The glue of the like-charge attraction is the enhanced shielding of the polymer charges by the dense counterion layer at the DNA surface. Second, through the shielding of the DNA-induced electrostatic potential, mono- and polyvalent cations of large concentration both suppress the like-charge attraction. Within the same formalism, we also predict a new opposite-charge repulsion effect between the DNA molecule and a positively charged polymer. In the presence of polyvalent anions such as sulfate or phosphate, their repulsion by the DNA charges leads to the charge screening deficiency of the region around the DNA molecule. This translates into a repulsive force that results in the decomplexation of the polymer from DNA. This opposite-charge repulsion phenomenon can be verified by current experiments and the underlying mechanism can be beneficial to gene therapeutic applications where the control over polymer-DNA interactions is the key factor.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Maoyuan; Besford, Quinn Alexander; Mulvaney, Thomas

The entropy of hydrophobic solvation has been explained as the result of ordered solvation structures, of hydrogen bonds, of the small size of the water molecule, of dispersion forces, and of solvent density fluctuations. We report a new approach to the calculation of the entropy of hydrophobic solvation, along with tests of and comparisons to several other methods. The methods are assessed in the light of the available thermodynamic and spectroscopic information on the effects of temperature on hydrophobic solvation. Five model hydrophobes in SPC/E water give benchmark solvation entropies via Widom’s test-particle insertion method, and other methods and modelsmore » are tested against these particle-insertion results. Entropies associated with distributions of tetrahedral order, of electric field, and of solvent dipole orientations are examined. We find these contributions are small compared to the benchmark particle-insertion entropy. Competitive with or better than other theories in accuracy, but with no free parameters, is the new estimate of the entropy contributed by correlations between dipole moments. Dipole correlations account for most of the hydrophobic solvation entropy for all models studied and capture the distinctive temperature dependence seen in thermodynamic and spectroscopic experiments. Entropies based on pair and many-body correlations in number density approach the correct magnitudes but fail to describe temperature and size dependences, respectively. Hydrogen-bond definitions and free energies that best reproduce entropies from simulations are reported, but it is difficult to choose one hydrogen bond model that fits a variety of experiments. The use of information theory, scaled-particle theory, and related methods is discussed briefly. Our results provide a test of the Frank-Evans hypothesis that the negative solvation entropy is due to structured water near the solute, complement the spectroscopic detection of that solvation structure by identifying the structural feature responsible for the entropy change, and point to a possible explanation for the observed dependence on length scale. Our key results are that the hydrophobic effect, i.e. the signature, temperature-dependent, solvation entropy of nonpolar molecules in water, is largely due to a dispersion force arising from correlations between rotating permanent dipole moments, that the strength of this force depends on the Kirkwood g-factor, and that the strength of this force may be obtained exactly without simulation.« less

A wireless centrifuge force microscope (CFM) enables multiplexed single-molecule experiments in a commercial centrifuge.

PubMed

Hoang, Tony; Patel, Dhruv S; Halvorsen, Ken

2016-08-01

The centrifuge force microscope (CFM) was recently introduced as a platform for massively parallel single-molecule manipulation and analysis. Here we developed a low-cost and self-contained CFM module that works directly within a commercial centrifuge, greatly improving accessibility and ease of use. Our instrument incorporates research grade video microscopy, a power source, a computer, and wireless transmission capability to simultaneously monitor many individually tethered microspheres. We validated the instrument by performing single-molecule force shearing of short DNA duplexes. For a 7 bp duplex, we observed over 1000 dissociation events due to force dependent shearing from 2 pN to 12 pN with dissociation times in the range of 10-100 s. We extended the measurement to a 10 bp duplex, applying a 12 pN force clamp and directly observing single-molecule dissociation over an 85 min experiment. Our new CFM module facilitates simple and inexpensive experiments that dramatically improve access to single-molecule analysis.

Reverse engineering of an affinity-switchable molecular interaction characterized by atomic force microscopy single-molecule force spectroscopy.

PubMed

Anselmetti, Dario; Bartels, Frank Wilco; Becker, Anke; Decker, Björn; Eckel, Rainer; McIntosh, Matthew; Mattay, Jochen; Plattner, Patrik; Ros, Robert; Schäfer, Christian; Sewald, Norbert

2008-02-19

Tunable and switchable interaction between molecules is a key for regulation and control of cellular processes. The translation of the underlying physicochemical principles to synthetic and switchable functional entities and molecules that can mimic the corresponding molecular functions is called reverse molecular engineering. We quantitatively investigated autoinducer-regulated DNA-protein interaction in bacterial gene regulation processes with single atomic force microscopy (AFM) molecule force spectroscopy in vitro, and developed an artificial bistable molecular host-guest system that can be controlled and regulated by external signals (UV light exposure and thermal energy). The intermolecular binding functionality (affinity) and its reproducible and reversible switching has been proven by AFM force spectroscopy at the single-molecule level. This affinity-tunable optomechanical switch will allow novel applications with respect to molecular manipulation, nanoscale rewritable molecular memories, and/or artificial ion channels, which will serve for the controlled transport and release of ions and neutral compounds in the future.

Force and Conductance Spectroscopy of Single Molecule Junctions

NASA Astrophysics Data System (ADS)

Frei, Michael

Investigation of mechanical properties of single molecule junctions is crucial to develop an understanding and enable control of single molecular junctions. This work presents an experimental and analytical approach that enables the statistical evaluation of force and simultaneous conductance data of metallic atomic point contacts and molecular junctions. A conductive atomic force microscope based break junction technique is developed to form single molecular junctions and collect conductance and force data simultaneously. Improvements of the optical components have been achieved through the use of a super-luminescent diode, enabling tremendous increases in force resolution. An experimental procedure to collect data for various molecular junctions has been developed and includes deposition, calibration, and analysis methods. For the statistical analysis of force, novel approaches based on two dimensional histograms and a direct force identification method are presented. The two dimensional method allows for an unbiased evaluation of force events that are identified using corresponding conductance signatures. This is not always possible however, and in these situations, the force based identification of junction rearrangement events is an attractive alternative method. This combined experimental and analytical approach is then applied to three studies: First, the impact of molecular backbones to the mechanical behavior of single molecule junctions is investigated and it is found that junctions formed with identical linkers but different backbone structure result in junctions with varying breaking forces. All molecules used show a clear molecular signature and force data can be evaluated using the 2D method. Second, the effects of the linker group used to attach molecules to gold electrodes are investigated. A study of four alkane molecules with different linkers finds a drastic difference in the evolution of donor-acceptor and covalently bonded molecules respectively. In fact, the covalent bond is found to significantly distort the metal electrode rearrangement such that junction rearrangement events can no longer be identified with a clean and well defined conductance signature. For this case, the force based identification process is used. Third, results for break junction measurements with different metals are presented. It is found that silver and palladium junctions rupture with forces different from those of gold contacts. In the case of silver experiments in ambient conditions, we can also identify oxygen impurities in the silver contact formation process, leading to force and conductance measurements of silver-oxygen structures. For the future, this work provides an experimental and analytical foundation that will enable insights into single molecule systems not previously accessible.

Molecular interactions in ethyl acetate-chlorobenzene binary solution: Dielectric, spectroscopic studies and quantum chemical calculations.

PubMed

Karthick, N K; Kumbharkhane, A C; Joshi, Y S; Mahendraprabu, A; Shanmugam, R; Elangovan, A; Arivazhagan, G

2017-05-05

Dielectric studies using Time Domain Reflectometry method has been carried out on the binary solution of Ethyl acetate (EA) with Chlorobenzene (CBZ) over the entire composition range. Spectroscopic (FTIR and 13 C NMR) signatures of neat EA, CBZ and their equimolar binary solution have also been recorded. The results of the spectroscopic studies favour the presence of (CBZ) CH⋯OC (EA), (EA) methylene CH⋯π electrons (CBZ) and (EA) methyl CH⋯Cl (CBZ) contacts which have been validated using quantum chemical calculations. Dimerization of CBZ has been identified. Presence of β-clusters has been identified in all the solutions. Although EA and CBZ molecules have nearly equal molar volumes, CBZ molecules experience larger hindrance for the rotation than EA molecules. Very small excess dielectric constant (ε E ) values may be correlated with weak heteromolecular forces and/or closed heteromolecular association. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular interactions in ethyl acetate-chlorobenzene binary solution: Dielectric, spectroscopic studies and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Karthick, N. K.; Kumbharkhane, A. C.; Joshi, Y. S.; Mahendraprabu, A.; Shanmugam, R.; Elangovan, A.; Arivazhagan, G.

2017-05-01

Dielectric studies using Time Domain Reflectometry method has been carried out on the binary solution of Ethyl acetate (EA) with Chlorobenzene (CBZ) over the entire composition range. Spectroscopic (FTIR and 13C NMR) signatures of neat EA, CBZ and their equimolar binary solution have also been recorded. The results of the spectroscopic studies favour the presence of (CBZ) Csbnd H ⋯ Odbnd C (EA), (EA) methylene Csbnd H ⋯ π electrons (CBZ) and (EA) methyl Csbnd H ⋯ Cl (CBZ) contacts which have been validated using quantum chemical calculations. Dimerization of CBZ has been identified. Presence of β-clusters has been identified in all the solutions. Although EA and CBZ molecules have nearly equal molar volumes, CBZ molecules experience larger hindrance for the rotation than EA molecules. Very small excess dielectric constant (εE) values may be correlated with weak heteromolecular forces and/or closed heteromolecular association.

Two-particle microrheology of quasi-2D viscous systems.

PubMed

Prasad, V; Koehler, S A; Weeks, Eric R

2006-10-27

We study the spatially correlated motions of colloidal particles in a quasi-2D system (human serum albumin protein molecules at an air-water interface) for different surface viscosities eta s. We observe a transition in the behavior of the correlated motion, from 2D interface dominated at high eta s to bulk fluid dependent at low eta s. The correlated motions can be scaled onto a master curve which captures the features of this transition. This master curve also characterizes the spatial dependence of the flow field of a viscous interface in response to a force. The scale factors used for the master curve allow for the calculation of the surface viscosity eta s that can be compared to one-particle measurements.

Adsorption mechanisms for fatty acids on DLC and steel studied by AFM and tribological experiments

NASA Astrophysics Data System (ADS)

Simič, R.; Kalin, M.

2013-10-01

Fatty acids are known to affect the friction and wear of steel contacts via adsorption onto the surface, which is one of the fundamental boundary-lubrication mechanisms. The understanding of the lubrication mechanisms of polar molecules on diamond-like carbon (DLC) is, however, still insufficient. In this work we aimed to find out whether such molecules have a similar effect on DLC coatings as they do on steel. The adsorption of hexadecanoic acid in various concentrations (2-20 mmol/l) on DLC was studied under static conditions using an atomic force microscope (AFM). The amount of surface coverage of the adsorbed fatty-acid molecules was analysed. In addition, tribological tests were performed to correlate the wear and friction behaviours in tribological contacts with the adsorption of molecules on the surface under static conditions. A good correlation between the AFM results and the tribological behaviour was observed. We confirmed that fatty acids can adsorb onto the DLC surfaces and are, therefore, potential boundary-lubrication agents for DLC coatings. The adsorption of the fatty acid onto the DLC surfaces reduces the wear of the coatings, but it is less effective in reducing the friction. Tentative adsorption mechanisms that include an environmental species effect, a temperature effect and a tribochemical effect are proposed for DLC and steel surfaces based on our results and few potential mechanisms found in literature.

Particle-based simulations of self-motile suspensions

NASA Astrophysics Data System (ADS)

Hinz, Denis F.; Panchenko, Alexander; Kim, Tae-Yeon; Fried, Eliot

2015-11-01

A simple model for simulating flows of active suspensions is investigated. The approach is based on dissipative particle dynamics. While the model is potentially applicable to a wide range of self-propelled particle systems, the specific class of self-motile bacterial suspensions is considered as a modeling scenario. To mimic the rod-like geometry of a bacterium, two dissipative particle dynamics particles are connected by a stiff harmonic spring to form an aggregate dissipative particle dynamics molecule. Bacterial motility is modeled through a constant self-propulsion force applied along the axis of each such aggregate molecule. The model accounts for hydrodynamic interactions between self-propelled agents through the pairwise dissipative interactions conventional to dissipative particle dynamics. Numerical simulations are performed using a customized version of the open-source software package LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) software package. Detailed studies of the influence of agent concentration, pairwise dissipative interactions, and Stokes friction on the statistics of the system are provided. The simulations are used to explore the influence of hydrodynamic interactions in active suspensions. For high agent concentrations in combination with dominating pairwise dissipative forces, strongly correlated motion patterns and a fluid-like spectral distributions of kinetic energy are found. In contrast, systems dominated by Stokes friction exhibit weaker spatial correlations of the velocity field. These results indicate that hydrodynamic interactions may play an important role in the formation of spatially extended structures in active suspensions.

Water-mediated influence of a crowded environment on internal vibrations of a protein molecule.

PubMed

Kuffel, Anna; Zielkiewicz, Jan

2016-02-14

The influence of crowding on the protein inner dynamics is examined by putting a single protein molecule close to one or two neighboring protein molecules. The presence of additional molecules influences the amplitudes of protein fluctuations. Also, a weak dynamical coupling of collective velocities of surface atoms of proteins separated by a layer of water is detected. The possible mechanisms of these phenomena are described. The cross-correlation function of the collective velocities of surface atoms of two proteins was decomposed into the Fourier series. The amplitude spectrum displays a peak at low frequencies. Also, the results of principal component analysis suggest that the close presence of an additional protein molecule influences the high-amplitude, low-frequency modes in the most prominent way. This part of the spectrum covers biologically important protein motions. The neighbor-induced changes in the inner dynamics of the protein may be connected with the changes in the velocity power spectrum of interfacial water. The additional protein molecule changes the properties of solvation water and in this way it can influence the dynamics of the second protein. It is suggested that this phenomenon may be described, at first approximation, by a damped oscillator driven by an external random force. This model was successfully applied to conformationally rigid Choristoneura fumiferana antifreeze protein molecules.

Intermolecular Casimir-Polder forces in water and near surfaces

NASA Astrophysics Data System (ADS)

Thiyam, Priyadarshini; Persson, Clas; Sernelius, Bo E.; Parsons, Drew F.; Malthe-Sørenssen, Anders; Boström, Mathias

2014-09-01

The Casimir-Polder force is an important long-range interaction involved in adsorption and desorption of molecules in fluids. We explore Casimir-Polder interactions between methane molecules in water, and between a molecule in water near SiO2 and hexane surfaces. Inclusion of the finite molecular size in the expression for the Casimir-Polder energy leads to estimates of the dispersion contribution to the binding energies between molecules and between one molecule and a planar surface.

Electromagnetic tweezers with independent force and torque control

NASA Astrophysics Data System (ADS)

Jiang, Chang; Lionberger, Troy A.; Wiener, Diane M.; Meyhofer, Edgar

2016-08-01

Magnetic tweezers are powerful tools to manipulate and study the mechanical properties of biological molecules and living cells. In this paper we present a novel, bona fide electromagnetic tweezer (EMT) setup that allows independent control of the force and torque applied via micrometer-sized magnetic beads to a molecule under study. We implemented this EMT by combining a single solenoid that generates force (f-EMT) with a set of four solenoids arranged into a symmetric quadrupole to generate torque (τ-EMT). To demonstrate the capability of the tweezers, we attached optically asymmetric Janus beads to single, tethered DNA molecules. We show that tension in the piconewton force range can be applied to single DNA molecules and the molecule can simultaneously be twisted with torques in the piconewton-nanometer range. Furthermore, the EMT allows the two components to be independently controlled. At various force levels applied to the Janus bead, the trap torsional stiffness can be continuously changed simply by varying the current magnitude applied to the τ-EMT. The flexible and independent control of force and torque by the EMT makes it an ideal tool for a range of measurements where tensional and torsional properties need to be studied simultaneously on a molecular or cellular level.

Influence of the adsorption geometry of PTCDA on Ag(111) on the tip-molecule forces in non-contact atomic force microscopy.

PubMed

Langewisch, Gernot; Falter, Jens; Schirmeisen, André; Fuchs, Harald

2014-01-01

Perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA) adsorbed on a metal surface is a prototypical organic-anorganic interface. In the past, scanning tunneling microscopy and scanning tunneling spectroscopy studies of PTCDA adsorbed on Ag(111) have revealed differences in the electronic structure of the molecules depending on their adsorption geometry. In the work presented here, high-resolution 3D force spectroscopy measurements at cryogenic temperatures were performed on a surface area that contained a complete PTCDA unit cell with the two possible geometries. At small tip-molecule separations, deviations in the tip-sample forces were found between the two molecule orientations. These deviations can be explained by a different electron density in both cases. This result demonstrates the capability of 3D force spectroscopy to detect even small effects in the electronic properties of organic adsorbates.

Linker Dependent Bond Rupture Force Measurements in Single-Molecule Junctions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Frei M.; Hybertsen M.; Aradhya S.V.

We use a modified conducting atomic force microscope to simultaneously probe the conductance of a single-molecule junction and the force required to rupture the junction formed by alkanes terminated with four different chemical link groups which vary in binding strength and mechanism to the gold electrodes. Molecular junctions with amine, methylsulfide, and diphenylphosphine terminated molecules show clear conductance signatures and rupture at a force that is significantly smaller than the measured 1.4 nN force required to rupture the single-atomic gold contact. In contrast, measurements with a thiol terminated alkane which can bind covalently to the gold electrode show conductance andmore » force features unlike those of the other molecules studied. Specifically, the strong Au-S bond can cause structural rearrangements in the electrodes, which are accompanied by substantial conductance changes. Despite the strong Au-S bond and the evidence for disruption of the Au structure, the experiments show that on average these junctions also rupture at a smaller force than that measured for pristine single-atom gold contacts.« less

Observation of DNA Molecules Using Fluorescence Microscopy and Atomic Force Microscopy

ERIC Educational Resources Information Center

Ito, Takashi

2008-01-01

This article describes experiments for an undergraduate instrumental analysis laboratory that aim to observe individual double-stranded DNA (dsDNA) molecules using fluorescence microscopy and atomic force microscopy (AFM). dsDNA molecules are observed under several different conditions to discuss their chemical and physical properties. In…

Principal Component Analysis of Lipid Molecule Conformational Changes in Molecular Dynamics Simulations.

PubMed

Buslaev, Pavel; Gordeliy, Valentin; Grudinin, Sergei; Gushchin, Ivan

2016-03-08

Molecular dynamics simulations of lipid bilayers are ubiquitous nowadays. Usually, either global properties of the bilayer or some particular characteristics of each lipid molecule are evaluated in such simulations, but the structural properties of the molecules as a whole are rarely studied. Here, we show how a comprehensive quantitative description of conformational space and dynamics of a single lipid molecule can be achieved via the principal component analysis (PCA). We illustrate the approach by analyzing and comparing simulations of DOPC bilayers obtained using eight different force fields: all-atom generalized AMBER, CHARMM27, CHARMM36, Lipid14, and Slipids and united-atom Berger, GROMOS43A1-S3, and GROMOS54A7. Similarly to proteins, most of the structural variance of a lipid molecule can be described by only a few principal components. These major components are similar in different simulations, although there are notable distinctions between the older and newer force fields and between the all-atom and united-atom force fields. The DOPC molecules in the simulations generally equilibrate on the time scales of tens to hundreds of nanoseconds. The equilibration is the slowest in the GAFF simulation and the fastest in the Slipids simulation. Somewhat unexpectedly, the equilibration in the united-atom force fields is generally slower than in the all-atom force fields. Overall, there is a clear separation between the more variable previous generation force fields and significantly more similar new generation force fields (CHARMM36, Lipid14, Slipids). We expect that the presented approaches will be useful for quantitative analysis of conformations and dynamics of individual lipid molecules in other simulations of lipid bilayers.

Monodisperse measurement of the biotin-streptavidin interaction strength in a well-defined pulling geometry

PubMed Central

Sedlak, Steffen M.; Bauer, Magnus S.; Kluger, Carleen; Schendel, Leonard C.; Milles, Lukas F.; Pippig, Diana A.

2017-01-01

The widely used interaction of the homotetramer streptavidin with the small molecule biotin has been intensively studied by force spectroscopy and has become a model system for receptor ligand interaction. However, streptavidin’s tetravalency results in diverse force propagation pathways through the different binding interfaces. This multiplicity gives rise to polydisperse force spectroscopy data. Here, we present an engineered monovalent streptavidin tetramer with a single cysteine in its functional subunit that allows for site-specific immobilization of the molecule, orthogonal to biotin binding. Functionality of streptavidin and its binding properties for biotin remain unaffected. We thus created a stable and reliable molecular anchor with a unique high-affinity binding site for biotinylated molecules or nanoparticles, which we expect to be useful for many single-molecule applications. To characterize the mechanical properties of the bond between biotin and our monovalent streptavidin, we performed force spectroscopy experiments using an atomic force microscope. We were able to conduct measurements at the single-molecule level with 1:1-stoichiometry and a well-defined geometry, in which force exclusively propagates through a single subunit of the streptavidin tetramer. For different force loading rates, we obtained narrow force distributions of the bond rupture forces ranging from 200 pN at 1,500 pN/s to 230 pN at 110,000 pN/s. The data are in very good agreement with the standard Bell-Evans model with a single potential barrier at Δx0 = 0.38 nm and a zero-force off-rate koff,0 in the 10−6 s-1 range. PMID:29206886

Monodisperse measurement of the biotin-streptavidin interaction strength in a well-defined pulling geometry.

PubMed

Sedlak, Steffen M; Bauer, Magnus S; Kluger, Carleen; Schendel, Leonard C; Milles, Lukas F; Pippig, Diana A; Gaub, Hermann E

2017-01-01

The widely used interaction of the homotetramer streptavidin with the small molecule biotin has been intensively studied by force spectroscopy and has become a model system for receptor ligand interaction. However, streptavidin's tetravalency results in diverse force propagation pathways through the different binding interfaces. This multiplicity gives rise to polydisperse force spectroscopy data. Here, we present an engineered monovalent streptavidin tetramer with a single cysteine in its functional subunit that allows for site-specific immobilization of the molecule, orthogonal to biotin binding. Functionality of streptavidin and its binding properties for biotin remain unaffected. We thus created a stable and reliable molecular anchor with a unique high-affinity binding site for biotinylated molecules or nanoparticles, which we expect to be useful for many single-molecule applications. To characterize the mechanical properties of the bond between biotin and our monovalent streptavidin, we performed force spectroscopy experiments using an atomic force microscope. We were able to conduct measurements at the single-molecule level with 1:1-stoichiometry and a well-defined geometry, in which force exclusively propagates through a single subunit of the streptavidin tetramer. For different force loading rates, we obtained narrow force distributions of the bond rupture forces ranging from 200 pN at 1,500 pN/s to 230 pN at 110,000 pN/s. The data are in very good agreement with the standard Bell-Evans model with a single potential barrier at Δx0 = 0.38 nm and a zero-force off-rate koff,0 in the 10-6 s-1 range.

Multiplexed single-molecule force spectroscopy using a centrifuge.

PubMed

Yang, Darren; Ward, Andrew; Halvorsen, Ken; Wong, Wesley P

2016-03-17

We present a miniature centrifuge force microscope (CFM) that repurposes a benchtop centrifuge for high-throughput single-molecule experiments with high-resolution particle tracking, a large force range, temperature control and simple push-button operation. Incorporating DNA nanoswitches to enable repeated interrogation by force of single molecular pairs, we demonstrate increased throughput, reliability and the ability to characterize population heterogeneity. We perform spatiotemporally multiplexed experiments to collect 1,863 bond rupture statistics from 538 traceable molecular pairs in a single experiment, and show that 2 populations of DNA zippers can be distinguished using per-molecule statistics to reduce noise.

Multiplexed single-molecule force spectroscopy using a centrifuge

PubMed Central

Yang, Darren; Ward, Andrew; Halvorsen, Ken; Wong, Wesley P.

2016-01-01

We present a miniature centrifuge force microscope (CFM) that repurposes a benchtop centrifuge for high-throughput single-molecule experiments with high-resolution particle tracking, a large force range, temperature control and simple push-button operation. Incorporating DNA nanoswitches to enable repeated interrogation by force of single molecular pairs, we demonstrate increased throughput, reliability and the ability to characterize population heterogeneity. We perform spatiotemporally multiplexed experiments to collect 1,863 bond rupture statistics from 538 traceable molecular pairs in a single experiment, and show that 2 populations of DNA zippers can be distinguished using per-molecule statistics to reduce noise. PMID:26984516

A single-molecule force spectroscopy study of the interactions between lectins and carbohydrates on cancer and normal cells

NASA Astrophysics Data System (ADS)

Zhao, Weidong; Cai, Mingjun; Xu, Haijiao; Jiang, Junguang; Wang, Hongda

2013-03-01

The interaction forces between carbohydrates and lectins were investigated by single-molecule force spectroscopy on both cancer and normal cells. The binding kinetics was also studied, which shows that the carbohydrate-lectin complex on cancer cells is less stable than that on normal cells.The interaction forces between carbohydrates and lectins were investigated by single-molecule force spectroscopy on both cancer and normal cells. The binding kinetics was also studied, which shows that the carbohydrate-lectin complex on cancer cells is less stable than that on normal cells. Electronic supplementary information (ESI) available: Experimental details. See DOI: 10.1039/c3nr00553d

Detachment of agglutinin-bonded red blood cells. I. Forces to rupture molecular-point attachments.

PubMed Central

Evans, E; Berk, D; Leung, A

1991-01-01

A simple micromechanical method has been developed to measure the rupture strength of a molecular-point attachment (focal bond) between two macroscopically smooth membrane capsules. In the procedure, one capsule is prepared with a low density coverage of adhesion molecules, formed as a stiff sphere, and held at fixed position by a micropipette. The second capsule without adhesion molecules is pressurized into a spherical shape with low suction by another pipette. This capsule is maneuvered to initiate point contact at the pole opposite the stiff capsule which leads to formation of a few (or even one) molecular attachments. Then, the deformable capsule is slowly withdrawn by displacement of the pipette. Analysis shows that the end-to-end extension of the capsule provides a direct measure of the force at the point contact and, therefore, the rupture strength when detachment occurs. The range for point forces accessible to this technique depends on the elastic moduli of the membrane, membrane tension, and the size of the capsule. For biological and synthetic vesicle membranes, the range of force lies between 10(-7)-10(-5) dyn (10(-12)-10(-10) N) which is 100-fold less than presently measurable by Atomic Force Microscopy! Here, the approach was used to study the forces required to rupture microscopic attachments between red blood cells formed by a monoclonal antibody to red cell membrane glycophorin, anti-A serum, and a lectin from the snail-helix pomatia. Failure of the attachments appeared to be a stochastic function of the magnitude and duration of the detachment force. We have correlated the statistical behavior observed for rupture with a random process model for failure of small numbers of molecular attachments. The surprising outcome of the measurements and analysis was that the forces deduced for short-time failure of 1-2 molecular attachments were nearly the same for all of the agglutinin, i.e., 1-2 x 10(-6) dyn. Hence, microfluorometric tests were carried out to determine if labeled agglutinins and/or labeled surface molecules were transferred between surfaces after separation of large areas of adhesive contact. The results showed that the attachments failed because receptors were extracted from the membrane. Images FIGURE 1 FIGURE 4 PMID:2065188

Final Scientific/Technical Report (DE-FG02-05ER46201)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Car, Roberto

The research supported by this grant focused on the quantum mechanical theory of the electrons in materials and molecules. Progress was made in dealing with electronic correlation effects in the ground state energy of molecular systems, and with topological concepts to classify the electronic state of molecules and materials, including excitation and transport properties. The physical and chemical properties of molecules and materials derive from their electronic structure, but the latter cannot be calculated exactly even with the most powerful computers because the computational cost of solving the exact equations of quantum mechanics increases exponentially with the number of electrons.more » The exponential cost originates from the correlations among the electrons that repel each other via Coulombic forces. In this project we have developed a new functional approximation for the ground state electronic energy that includes explicitly, and in a controllable way, the effects of the interelectronic correlations. In addition we have further developed topological concepts for classifying the electronic states of periodic ring molecules and solids. Topological concepts are very powerful because they allow us to predict subtle properties of materials and molecules using very general geometrical properties of the electron wavefunctions that do not depend on the quantitative details of the electronic interactions, which are very difficult to calculate with high accuracy. The development of a new class of controlled functional approximations for the ground state energy of molecules and materials was the main goal of the project. It has been fulfilled with the formulation of the occupation-probabilities natural orbital functional theory (OP-NOFT). This approach introduces new theoretical concepts but practical application has proved to be harder than anticipated. So far it has been utilized only at its lowest level of approximation in the context of relatively small molecules (with up to 16 atoms). The study of topological properties of the electron wavefunctions in materials was not proposed in the original proposal but was prompted during the funding period by our interaction with leading experimental groups in materials chemistry and physics at Princeton University.« less

Roles of urea and TMAO on the interaction between extended non-polar peptides

NASA Astrophysics Data System (ADS)

Su, Zhaoqian; Dias, Cristiano

Urea and trimethylamine n-oxide (TMAO) are small molecules known to destabilize and stabilize, respectively, the structure of proteins when added to aqueous solution. To unravel the molecular mechanisms of these cosolvents on protein structure we perform explicit all-atom molecular dynamics simulations of extended poly-alanine and polyleucine dimers. We use an umbrella sampling protocol to compute the potential of mean force (PMF) of dimers at different concentrations of urea and TMAO. We find that the large non-polar side chain of leucine is affected by urea whereas backbone atoms and alanine's side chain are not. Urea is found to occupy positions between leucine's side chains that are not accessible to water. This accounts for extra Lennard-Jones bonds between urea and side chains that favors the unfolded state. These bonds compete with urea-solvent interactions that favor the folded state. The sum of these two energetic terms provide the enthalpic driving force for unfolding. We show here that this enthalpy correlate with the potential of mean force of poly-leucine dimers. Moreover, the framework developed here is general and may be used to provide insights into effects of other small molecules on protein interactions. The effect of the TMAO will be in the presentation. Department of Physics, University Heights, Newark, New Jersey, 07102-1982.

Substrate Deformation Predicts Neuronal Growth Cone Advance

PubMed Central

Athamneh, Ahmad I.M.; Cartagena-Rivera, Alexander X.; Raman, Arvind; Suter, Daniel M.

2015-01-01

Although pulling forces have been observed in axonal growth for several decades, their underlying mechanisms, absolute magnitudes, and exact roles are not well understood. In this study, using two different experimental approaches, we quantified retrograde traction force in Aplysia californica neuronal growth cones as they develop over time in response to a new adhesion substrate. In the first approach, we developed a novel method, to our knowledge, for measuring traction forces using an atomic force microscope (AFM) with a cantilever that was modified with an Aplysia cell adhesion molecule (apCAM)-coated microbead. In the second approach, we used force-calibrated glass microneedles coated with apCAM ligands to guide growth cone advance. The traction force exerted by the growth cone was measured by monitoring the microneedle deflection using an optical microscope. Both approaches showed that Aplysia growth cones can develop traction forces in the 100–102 nN range during adhesion-mediated advance. Moreover, our results suggest that the level of traction force is directly correlated to the stiffness of the microneedle, which is consistent with a reinforcement mechanism previously observed in other cell types. Interestingly, the absolute level of traction force did not correlate with growth cone advance toward the adhesion site, but the amount of microneedle deflection did. In cases of adhesion-mediated growth cone advance, the mean needle deflection was 1.05 ± 0.07 μm. By contrast, the mean deflection was significantly lower (0.48 ± 0.06 μm) when the growth cones did not advance. Our data support a hypothesis that adhesion complexes, which can undergo micron-scale elastic deformation, regulate the coupling between the retrogradely flowing actin cytoskeleton and apCAM substrates, stimulating growth cone advance if sufficiently abundant. PMID:26445437

Substrate preparation for reliable imaging of DNA molecules with the scanning force microscope.

PubMed

Vesenka, J; Guthold, M; Tang, C L; Keller, D; Delaine, E; Bustamante, C

1992-07-01

A simple method of substrate preparation for imaging circular DNA molecules with the scanning force microscope (SFM) is presented. These biomolecules are adsorbed onto mica that has been soaked in magnesium acetate, sonicated and glow-discharged. The stylus-sample forces that may be endured before sample damage occurs depends on the ambient relative humidity. Images of circular DNA molecules have been obtained routinely using tips specially modified by an electron beam with a radius of curvature, Rc, of about 10 nm [D. Keller and C. Chih-Chung, Surf. Sci. 268 (1992) 333]. The resolution of these adsorbed biomolecules is determined by the Rc. At higher forces individual circular DNA molecules can be manipulated with the SFM stylus. Strategies to develop still sharper probes will be discussed.

Resonances arising from hydrodynamic memory in Brownian motion.

PubMed

Franosch, Thomas; Grimm, Matthias; Belushkin, Maxim; Mor, Flavio M; Foffi, Giuseppe; Forró, László; Jeney, Sylvia

2011-10-05

Observation of the Brownian motion of a small probe interacting with its environment provides one of the main strategies for characterizing soft matter. Essentially, two counteracting forces govern the motion of the Brownian particle. First, the particle is driven by rapid collisions with the surrounding solvent molecules, referred to as thermal noise. Second, the friction between the particle and the viscous solvent damps its motion. Conventionally, the thermal force is assumed to be random and characterized by a Gaussian white noise spectrum. The friction is assumed to be given by the Stokes drag, suggesting that motion is overdamped at long times in particle tracking experiments, when inertia becomes negligible. However, as the particle receives momentum from the fluctuating fluid molecules, it also displaces the fluid in its immediate vicinity. The entrained fluid acts back on the particle and gives rise to long-range correlations. This hydrodynamic 'memory' translates to thermal forces, which have a coloured, that is, non-white, noise spectrum. One hundred years after Perrin's pioneering experiments on Brownian motion, direct experimental observation of this colour is still elusive. Here we measure the spectrum of thermal noise by confining the Brownian fluctuations of a microsphere in a strong optical trap. We show that hydrodynamic correlations result in a resonant peak in the power spectral density of the sphere's positional fluctuations, in strong contrast to overdamped systems. Furthermore, we demonstrate different strategies to achieve peak amplification. By analogy with microcantilever-based sensors, our results reveal that the particle-fluid-trap system can be considered a nanomechanical resonator in which the intrinsic hydrodynamic backflow enhances resonance. Therefore, instead of being treated as a disturbance, details in thermal noise could be exploited for the development of new types of sensor and particle-based assay in lab-on-a-chip applications.

Probing of miniPEGγ-PNA-DNA Hybrid Duplex Stability with AFM Force Spectroscopy.

PubMed

Dutta, Samrat; Armitage, Bruce A; Lyubchenko, Yuri L

2016-03-15

Peptide nucleic acids (PNA) are synthetic polymers, the neutral peptide backbone of which provides elevated stability to PNA-PNA and PNA-DNA hybrid duplexes. It was demonstrated that incorporation of diethylene glycol (miniPEG) at the γ position of the peptide backbone increased the thermal stability of the hybrid duplexes (Sahu, B. et al. J. Org. Chem. 2011, 76, 5614-5627). Here, we applied atomic force microscopy (AFM) based single molecule force spectroscopy and dynamic force spectroscopy (DFS) to test the strength and stability of the hybrid 10 bp duplex. This hybrid duplex consisted of miniPEGγ-PNA and DNA of the same length (γ(MP)PNA-DNA), which we compared to a DNA duplex with a homologous sequence. AFM force spectroscopy data obtained at the same conditions showed that the γ(MP)PNA-DNA hybrid is more stable than the DNA counterpart, 65 ± 15 pN vs 47 ± 15 pN, respectively. The DFS measurements performed in a range of pulling speeds analyzed in the framework of the Bell-Evans approach yielded a dissociation constant, koff ≈ 0.030 ± 0.01 s⁻¹ for γ(MP)PNA-DNA hybrid duplex vs 0.375 ± 0.18 s⁻¹ for the DNA-DNA duplex suggesting that the hybrid duplex is much more stable. Correlating the high affinity of γ(MP)PNA-DNA to slow dissociation kinetics is consistent with prior bulk characterization by surface plasmon resonance. Given the growing interest in γ(MP)PNA as well as other synthetic DNA analogues, the use of single molecule experiments along with computational analysis of force spectroscopy data will provide direct characterization of various modifications as well as higher order structures such as triplexes and quadruplexes.

Cholesterol orientation and tilt modulus in DMPC bilayers

PubMed Central

Khelashvili, George; Pabst, Georg; Harries, Daniel

2010-01-01

We performed molecular dynamics (MD) simulations of hydrated bilayers containing mixtures of dimyristoylphosphatidylcholine (DMPC) and Cholesterol at various ratios, to study the effect of cholesterol concentration on its orientation, and to characterize the link between cholesterol tilt and overall phospholipid membrane organization. The simulations show a substantial probability for cholesterol molecules to transiently orient perpendicular to the bilayer normal, and suggest that cholesterol tilt may be an important factor for inducing membrane ordering. In particular, we find that as cholesterol concentration increases (1%–40% cholesterol) the average cholesterol orientation changes in a manner strongly (anti)correlated with the variation in membrane thickness. Furthermore, cholesterol orientation is found to be determined by the aligning force exerted by other cholesterol molecules. To quantify this aligning field, we analyzed cholesterol orientation using, to our knowledge, the first estimates of the cholesterol tilt modulus χ from MD simulations. Our calculations suggest that the aligning field that determines χ is indeed strongly linked to sterol composition. This empirical parameter (χ) should therefore become a useful quantitative measure to describe cholesterol interaction with other lipids in bilayers, particularly in various coarse-grained force fields. PMID:20518573

Atomic Forces for Geometry-Dependent Point Multipole and Gaussian Multipole Models

PubMed Central

Elking, Dennis M.; Perera, Lalith; Duke, Robert; Darden, Thomas; Pedersen, Lee G.

2010-01-01

In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise due to 1) the transfer of torque between neighboring atoms, and 2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry-dependent multipole models. In the current study, atomic force expressions for geometry-dependent multipoles are presented for use in simulations of flexible molecules. The atomic forces are derived by first proposing a new general expression for Wigner function derivatives ∂Dlm′m/∂Ω. The force equations can be applied to electrostatic models based on atomic point multipoles or Gaussian multipole charge density. Hydrogen bonded dimers are used to test the inter-molecular electrostatic energies and atomic forces calculated by geometry-dependent multipoles fit to the ab initio electrostatic potential (ESP). The electrostatic energies and forces are compared to their reference ab initio values. It is shown that both static and geometry-dependent multipole models are able to reproduce total molecular forces and torques with respect to ab initio, while geometry-dependent multipoles are needed to reproduce ab initio atomic forces. The expressions for atomic force can be used in simulations of flexible molecules with atomic multipoles. In addition, the results presented in this work should lead to further development of next generation force fields composed of geometry-dependent multipole models. PMID:20839297

MATCH: An Atom- Typing Toolset for Molecular Mechanics Force Fields

PubMed Central

Yesselman, Joseph D.; Price, Daniel J.; Knight, Jennifer L.; Brooks, Charles L.

2011-01-01

We introduce a toolset of program libraries collectively titled MATCH (Multipurpose Atom-Typer for CHARMM) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion from multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges and force field parameters is achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In the present work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM CGENFF force field (Vanommeslaeghe, et al., JCC., 2010, 31, 671–690), one million molecules from the PubChem database of small molecules are typed, parameterized and minimized. PMID:22042689

Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields.

PubMed

Paranahewage, S Shanaka; Gierhart, Cassidy S; Fennell, Christopher J

2016-11-01

Alchemical transformation of solutes using classical fixed-charge force fields is a popular strategy for assessing the free energy of transfer in different environments. Accurate estimations of transfer between phases with significantly different polarities can be difficult because of the static nature of the force fields. Here, we report on an application of such calculations in the SAMPL5 experiment that also involves an effort in balancing solute and solvent interactions via their expected static dielectric constants. This strategy performs well with respect to predictive accuracy and correlation with unknown experimental values. We follow this by performing a series of retrospective investigations which highlight the potential importance of proper balancing in these systems, and we use a null hypothesis analysis to explore potential biases in the comparisons with experiment. The collective findings indicate that considerations of force field compatibility through dielectric behavior is a potential strategy for future improvements in transfer processes between disparate environments.

FRET measurements of cell-traction forces and nano-scale clustering of adhesion ligands varied by substrate stiffness.

PubMed

Kong, Hyun Joon; Polte, Thomas R; Alsberg, Eben; Mooney, David J

2005-03-22

The mechanical properties of cell adhesion substrates regulate cell phenotype, but the mechanism of this relation is currently unclear. It may involve the magnitude of traction force applied by the cell, and/or the ability of the cells to rearrange the cell adhesion molecules presented from the material. In this study, we describe a FRET technique that can be used to evaluate the mechanics of cell-material interactions at the molecular level and simultaneously quantify the cell-based nanoscale rearrangement of the material itself. We found that these events depended on the mechanical rigidity of the adhesion substrate. Furthermore, both the proliferation and differentiation of preosteoblasts (MC3T3-E1) correlated to the magnitude of force that cells generate to cluster the cell adhesion ligands, but not the extent of ligand clustering. Together, these data demonstrate the utility of FRET in analyzing cell-material interactions, and suggest that regulation of phenotype with substrate stiffness is related to alterations in cellular traction forces.

Phoretic forces on convex particles from kinetic theory and nonequilibrium thermodynamics

NASA Astrophysics Data System (ADS)

Hütter, Markus; Kröger, Martin

2006-01-01

In this article we derive the phoretic forces acting on a tracer particle, which is assumed to be small compared to the mean free path of the surrounding nonequilibrium gas, but large compared to the size of the surrounding gas molecules. First, we review and extend the calculations of Waldmann [Z. Naturforsch. A 14A, 589 (1959)] using half-sphere integrations and an accommodation coefficient characterizing the collision process. The presented methodology is applied to a gas subject to temperature, pressure, and velocity gradients. Corresponding thermophoretic, barophoretic, and rheophoretic forces are derived, and explicit expressions for spherical particles are compared to known results. Second, nonequilibrium thermodynamics is used to join the diffusion equation for the tracer particle with the continuum equations of nonisothermal hydrodynamics of the solvent. So doing, the distinct origin of the thermophoretic and barophoretic forces is demonstrated. While the latter enters similarly to an interaction potential, the former is given by flux-flux correlations in terms of a Green-Kubo relation, as shown in detail.

Evaluation of synthetic linear motor-molecule actuation energetics

PubMed Central

Brough, Branden; Northrop, Brian H.; Schmidt, Jacob J.; Tseng, Hsian-Rong; Houk, Kendall N.; Stoddart, J. Fraser; Ho, Chih-Ming

2006-01-01

By applying atomic force microscope (AFM)-based force spectroscopy together with computational modeling in the form of molecular force-field simulations, we have determined quantitatively the actuation energetics of a synthetic motor-molecule. This multidisciplinary approach was performed on specifically designed, bistable, redox-controllable [2]rotaxanes to probe the steric and electrostatic interactions that dictate their mechanical switching at the single-molecule level. The fusion of experimental force spectroscopy and theoretical computational modeling has revealed that the repulsive electrostatic interaction, which is responsible for the molecular actuation, is as high as 65 kcal·mol−1, a result that is supported by ab initio calculations. PMID:16735470

PLASS: Protein-ligand affinity statistical score a knowledge-based force-field model of interaction derived from the PDB

NASA Astrophysics Data System (ADS)

Ozrin, V. D.; Subbotin, M. V.; Nikitin, S. M.

2004-04-01

We have developed PLASS (Protein-Ligand Affinity Statistical Score), a pair-wise potential of mean-force for rapid estimation of the binding affinity of a ligand molecule to a protein active site. This scoring function is derived from the frequency of occurrence of atom-type pairs in crystallographic complexes taken from the Protein Data Bank (PDB). Statistical distributions are converted into distance-dependent contributions to the Gibbs free interaction energy for 10 atomic types using the Boltzmann hypothesis, with only one adjustable parameter. For a representative set of 72 protein-ligand structures, PLASS scores correlate well with the experimentally measured dissociation constants: a correlation coefficient R of 0.82 and RMS error of 2.0 kcal/mol. Such high accuracy results from our novel treatment of the volume correction term, which takes into account the inhomogeneous properties of the protein-ligand complexes. PLASS is able to rank reliably the affinity of complexes which have as much diversity as in the PDB.

Imaging and Force Recognition of Single Molecular Behaviors Using Atomic Force Microscopy

PubMed Central

Li, Mi; Dang, Dan; Liu, Lianqing; Xi, Ning; Wang, Yuechao

2017-01-01

The advent of atomic force microscopy (AFM) has provided a powerful tool for investigating the behaviors of single native biological molecules under physiological conditions. AFM can not only image the conformational changes of single biological molecules at work with sub-nanometer resolution, but also sense the specific interactions of individual molecular pair with piconewton force sensitivity. In the past decade, the performance of AFM has been greatly improved, which makes it widely used in biology to address diverse biomedical issues. Characterizing the behaviors of single molecules by AFM provides considerable novel insights into the underlying mechanisms guiding life activities, contributing much to cell and molecular biology. In this article, we review the recent developments of AFM studies in single-molecule assay. The related techniques involved in AFM single-molecule assay were firstly presented, and then the progress in several aspects (including molecular imaging, molecular mechanics, molecular recognition, and molecular activities on cell surface) was summarized. The challenges and future directions were also discussed. PMID:28117741

Hydration and distance dependence of intermolecular shearing between collagen molecules in a model microfibril.

PubMed

Gautieri, Alfonso; Pate, Monica I; Vesentini, Simone; Redaelli, Alberto; Buehler, Markus J

2012-08-09

In vertebrates, collagen tissues are the main component responsible for force transmission. In spite of the physiological importance of these phenomena, force transmission mechanisms are still not fully understood, especially at smaller scales, including in particular collagen molecules and fibrils. Here we investigate the mechanism of molecular sliding between collagen molecules within a fibril, by shearing a central molecule in a hexagonally packed bundle mimicking the collagen microfibril environment, using varied lateral distance between the molecules in both dry and solvated conditions. In vacuum, the central molecule slides under a stick-slip mechanism that is due to the characteristic surface profile of collagen molecules, enhanced by the breaking and reformation of H-bonds between neighboring collagen molecules. This mechanism is consistently observed for varied lateral separations between molecules. The high shearing force (>7 nN) found for the experimentally observed intermolecular distance (≈1.1 nm) suggests that in dry samples the fibril elongation mechanism relies almost exclusively on molecular stretching, which may explain the higher stiffnesses found in dry fibrils. When hydrated, the slip-stick behavior is observed only below 1.3 nm of lateral distance, whereas above 1.3 nm the molecule shears smoothly, showing that the water layer has a strong lubricating effect. Moreover, the average force required to shear is approximately the same in solvated as in dry conditions (≈2.5 nN), which suggests that the role of water at the intermolecular level includes the transfer of load between molecules. Copyright © 2012 Elsevier Ltd. All rights reserved.

Single-Molecule Unbinding Forces between the Polysaccharide Hyaluronan and Its Binding Proteins.

PubMed

Bano, Fouzia; Tammi, Markku I; Kang, David W; Harris, Edward N; Richter, Ralf P

2018-06-19

The extracellular polysaccharide hyaluronan (HA) is ubiquitous in all vertebrate tissues, where its various functions are encoded in the supramolecular complexes and matrices that it forms with HA-binding proteins (hyaladherins). In tissues, these supramolecular architectures are frequently subjected to mechanical stress, yet how this affects the intermolecular bonding is largely unknown. Here, we used a recently developed single-molecule force spectroscopy platform to analyze and compare the mechanical strength of bonds between HA and a panel of hyaladherins from the Link module superfamily, namely the complex of the proteoglycan aggrecan and cartilage link protein, the proteoglycan versican, the inflammation-associated protein TSG-6, the HA receptor for endocytosis (stabilin-2/HARE), and the HA receptor CD44. We find that the resistance to tensile stress for these hyaladherins correlates with the size of the HA-binding domain. The lowest mean rupture forces are observed for members of the type A subgroup (i.e., with the shortest HA-binding domains; TSG-6 and HARE). In contrast, the mechanical stability of the bond formed by aggrecan in complex with cartilage link protein (two members of the type C subgroup, i.e., with the longest HA-binding domains) and HA is equal or even superior to the high affinity streptavidin⋅biotin bond. Implications for the molecular mechanism of unbinding of HA⋅hyaladherin bonds under force are discussed, which underpin the mechanical properties of HA⋅hyaladherin complexes and HA-rich extracellular matrices. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Nanotechnology Provides a New Perspective on Chemical Thermodynamics

ERIC Educational Resources Information Center

Haverkamp, Richard G.

2009-01-01

A small mechanical device, the atomic force microscope, measuring a force and the distance over which this force is applied, can be used on a single polysaccharide molecule to obtain the Gibbs energy of a conformational change within the polysaccharide. This well-defined conformational change within certain types of polysaccharide molecules is…

Analysis and modification of defective surface aggregates on PCDTBT:PCBM solar cell blends using combined Kelvin probe, conductive and bimodal atomic force microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noh, Hanaul; Diaz, Alfredo J.; Solares, Santiago D.

Organic photovoltaic systems comprising donor polymers and acceptor fullerene derivatives are attractive for inexpensive energy harvesting. Extensive research on polymer solar cells has provided insight into the factors governing device-level efficiency and stability. However, the detailed investigation of nanoscale structures is still challenging. Here we demonstrate the analysis and modification of unidentified surface aggregates. The aggregates are characterized electrically by Kelvin probe force microscopy and conductive atomic force microscopy (C-AFM), whereby the correlation between local electrical potential and current confirms a defective charge transport. Bimodal AFM modification confirms that the aggregates exist on top of the solar cell structure, andmore » is used to remove them and to reveal the underlying active layer. The systematic analysis of the surface aggregates suggests that the structure consists of PCBM molecules.« less

Analysis and modification of defective surface aggregates on PCDTBT:PCBM solar cell blends using combined Kelvin probe, conductive and bimodal atomic force microscopy

DOE PAGES

Noh, Hanaul; Diaz, Alfredo J.; Solares, Santiago D.

2017-03-08

Organic photovoltaic systems comprising donor polymers and acceptor fullerene derivatives are attractive for inexpensive energy harvesting. Extensive research on polymer solar cells has provided insight into the factors governing device-level efficiency and stability. However, the detailed investigation of nanoscale structures is still challenging. Here we demonstrate the analysis and modification of unidentified surface aggregates. The aggregates are characterized electrically by Kelvin probe force microscopy and conductive atomic force microscopy (C-AFM), whereby the correlation between local electrical potential and current confirms a defective charge transport. Bimodal AFM modification confirms that the aggregates exist on top of the solar cell structure, andmore » is used to remove them and to reveal the underlying active layer. The systematic analysis of the surface aggregates suggests that the structure consists of PCBM molecules.« less

Analysis and modification of defective surface aggregates on PCDTBT:PCBM solar cell blends using combined Kelvin probe, conductive and bimodal atomic force microscopy

PubMed Central

Noh, Hanaul; Diaz, Alfredo J

2017-01-01

Organic photovoltaic systems comprising donor polymers and acceptor fullerene derivatives are attractive for inexpensive energy harvesting. Extensive research on polymer solar cells has provided insight into the factors governing device-level efficiency and stability. However, the detailed investigation of nanoscale structures is still challenging. Here we demonstrate the analysis and modification of unidentified surface aggregates. The aggregates are characterized electrically by Kelvin probe force microscopy and conductive atomic force microscopy (C-AFM), whereby the correlation between local electrical potential and current confirms a defective charge transport. Bimodal AFM modification confirms that the aggregates exist on top of the solar cell structure, and is used to remove them and to reveal the underlying active layer. The systematic analysis of the surface aggregates suggests that the structure consists of PCBM molecules. PMID:28382247

Research Update: Nanoscale surface potential analysis of MoS2 field-effect transistors for biomolecular detection using Kelvin probe force microscopy

NASA Astrophysics Data System (ADS)

Kim, Min Hyung; Park, Heekyeong; Lee, Hyungbeen; Nam, Kihwan; Jeong, Seokhwan; Omkaram, Inturu; Yoon, Dae Sung; Lee, Sei Young; Kim, Sunkook; Lee, Sang Woo

2016-10-01

We used high-resolution Kelvin probe force microscopy (KPFM) to investigate the immobilization of a prostate specific antigen (PSA) antibody by measuring the surface potential (SP) on a MoS2 surface over an extensive concentration range (1 pg/ml-100 μg/ml). After PSA antibody immobilization, we demonstrated that the SP on the MoS2 surface characterized by KPFM strongly correlated to the electrical signal of a MoS2 bioFET. This demonstration can not only be used to optimize the immobilization conditions for captured molecules, but can also be applied as a diagnostic tool to complement the electrical detection of a MoS2 FET biosensor.

Phoretic Force Measurement for Microparticles Under Microgravity Conditions

NASA Technical Reports Server (NTRS)

Davis, E. J.; Zheng, R.

1999-01-01

This theoretical and experimental investigation of the collisional interactions between gas molecules and solid and liquid surfaces of microparticles involves fundamental studies of the transfer of energy, mass and momentum between gas molecules and surfaces. The numerous applications include particle deposition on semiconductor surfaces and on surfaces in combustion processes, containerless processing, the production of nanophase materials, pigments and ceramic precursors, and pollution abatement technologies such as desulfurization of gaseous effluents from combustion processes. Of particular emphasis are the forces exerted on microparticles present in a nonuniform gas, that is, in gaseous surroundings involving temperature and concentration gradients. These so-called phoretic forces become the dominant forces when the gravitational force is diminished, and they are strongly dependent on the momentum transfer between gas molecules and the surface. The momentum transfer, in turn, depends on the gas and particle properties and the mean free path and kinetic energy of the gas molecules. The experimental program involves the particle levitation system shown. A micrometer size particle is held between two heat exchangers enclosed in a vacuum chamber by means of ac and dc electric fields. The ac field keeps the particle centered on the vertical axis of the chamber, and the dc field balances the gravitational force and the thermophoretic force. Some measurements of the thermophoretic force are presented in this paper.

The solvation of ions in acetonitrile and acetone. II. Monte Carlo simulations using polarizable solvent models

NASA Astrophysics Data System (ADS)

Fischer, R.; Richardi, J.; Fries, P. H.; Krienke, H.

2002-11-01

Structural properties and energies of solvation are simulated for alkali and halide ions. The solvation structure is discussed in terms of various site-site distribution functions, of solvation numbers, and of orientational correlation functions of the solvent molecules around the ions. The solvent polarizability has notable effects which cannot be intuitively predicted. In particular, it is necessary to reproduce the experimental solvation numbers of small ions. The changes of solvation properties are investigated along the alkali and halide series. By comparing the solvation of ions in acetone to that in acetonitrile, it is shown that the spatial correlations among the solvent molecules around an ion result in a strong screening of the ion-solvent direct intermolecular potential and are essential to understand the changes in the solvation structures and energies between different solvents. The solvation properties derived from the simulations are compared to earlier predictions of the hypernetted chain (HNC) approximation of the molecular Ornstein-Zernike (MOZ) theory [J. Richardi, P. H. Fries, and H. Krienke, J. Chem. Phys. 108, 4079 (1998)]. The MOZ(HNC) formalism gives an overall qualitatively correct picture of the solvation and its various unexpected findings are corroborated. For the larger ions, its predictions become quantitative. The MOZ approach allows to calculate solvent-solvent and ion-solvent potentials of mean force, which shed light on the 3D labile molecular and ionic architectures in the solution. These potentials of mean force convey a unique information which is necessary to fully interpret the angle-averaged structural functions computed from the simulations. Finally, simulations of solutions at finite concentrations show that the solvent-solvent and ion-solvent spatial correlations at infinite dilution are marginally altered by the introduction of fair amounts of ions.

DNA under Force: Mechanics, Electrostatics, and Hydration.

PubMed

Li, Jingqiang; Wijeratne, Sithara S; Qiu, Xiangyun; Kiang, Ching-Hwa

2015-02-25

Quantifying the basic intra- and inter-molecular forces of DNA has helped us to better understand and further predict the behavior of DNA. Single molecule technique elucidates the mechanics of DNA under applied external forces, sometimes under extreme forces. On the other hand, ensemble studies of DNA molecular force allow us to extend our understanding of DNA molecules under other forces such as electrostatic and hydration forces. Using a variety of techniques, we can have a comprehensive understanding of DNA molecular forces, which is crucial in unraveling the complex DNA functions in living cells as well as in designing a system that utilizes the unique properties of DNA in nanotechnology.

Going Vertical To Improve the Accuracy of Atomic Force Microscopy Based Single-Molecule Force Spectroscopy.

PubMed

Walder, Robert; Van Patten, William J; Adhikari, Ayush; Perkins, Thomas T

2018-01-23

Single-molecule force spectroscopy (SMFS) is a powerful technique to characterize the energy landscape of individual proteins, the mechanical properties of nucleic acids, and the strength of receptor-ligand interactions. Atomic force microscopy (AFM)-based SMFS benefits from ongoing progress in improving the precision and stability of cantilevers and the AFM itself. Underappreciated is that the accuracy of such AFM studies remains hindered by inadvertently stretching molecules at an angle while measuring only the vertical component of the force and extension, degrading both measurements. This inaccuracy is particularly problematic in AFM studies using double-stranded DNA and RNA due to their large persistence length (p ≈ 50 nm), often limiting such studies to other SMFS platforms (e.g., custom-built optical and magnetic tweezers). Here, we developed an automated algorithm that aligns the AFM tip above the DNA's attachment point to a coverslip. Importantly, this algorithm was performed at low force (10-20 pN) and relatively fast (15-25 s), preserving the connection between the tip and the target molecule. Our data revealed large uncorrected lateral offsets for 100 and 650 nm DNA molecules [24 ± 18 nm (mean ± standard deviation) and 180 ± 110 nm, respectively]. Correcting this offset yielded a 3-fold improvement in accuracy and precision when characterizing DNA's overstretching transition. We also demonstrated high throughput by acquiring 88 geometrically corrected force-extension curves of a single individual 100 nm DNA molecule in ∼40 min and versatility by aligning polyprotein- and PEG-based protein-ligand assays. Importantly, our software-based algorithm was implemented on a commercial AFM, so it can be broadly adopted. More generally, this work illustrates how to enhance AFM-based SMFS by developing more sophisticated data-acquisition protocols.

Crystallographic order and decomposition of [MnIII 6CrIII]3+ single-molecule magnets deposited in submonolayers and monolayers on HOPG studied by means of molecular resolved atomic force microscopy (AFM) and Kelvin probe force microscopy in UHV

NASA Astrophysics Data System (ADS)

Gryzia, Aaron; Volkmann, Timm; Brechling, Armin; Hoeke, Veronika; Schneider, Lilli; Kuepper, Karsten; Glaser, Thorsten; Heinzmann, Ulrich

2014-02-01

Monolayers and submonolayers of [Mn III 6 Cr III ] 3+ single-molecule magnets (SMMs) adsorbed on highly oriented pyrolytic graphite (HOPG) using the droplet technique characterized by non-contact atomic force microscopy (nc-AFM) as well as by Kelvin probe force microscopy (KPFM) show island-like structures with heights resembling the height of the molecule. Furthermore, islands were found which revealed ordered 1D as well as 2D structures with periods close to the width of the SMMs. Along this, islands which show half the heights of intact SMMs were observed which are evidences for a decomposing process of the molecules during the preparation. Finally, models for the structure of the ordered SMM adsorbates are proposed to explain the observations.

Polycyclic aromatic hydrocarbon optical properties and contribution to the acceleration of stellar outflows

NASA Technical Reports Server (NTRS)

Cherchneff, Isabelle; Barker, John R.; Tielens, Alexander G. G. M.

1991-01-01

The optical constants of four polycyclic aromatic hydrocarbon (PAH) molecules (benzene, pyrene, pentacene, and coronene) are determined from their measured laboratory absorption spectra. The Planck mean of the radiation pressure cross section is computed for each molecule and for amorphous carbon (AC) grains, and semiempirically estimated for large PAH molecules up to 400 carbon atoms. Assuming that PAHs are present in carbon-rich stellar outflows, the radiation pressure forces acting on them are calculated and compared with the radiation forces on AC particles. The results show that PAHs possess very different optical properties from AC grains. Small PAHs may experience an 'inverse greenhouse' effect in the inner part of the envelope, as they decouple from the gas close to the photosphere. The radiation pressure force on PAHs is always much less than the force at work on AC grains, and PAH molecules do not affect significantly the dynamics of the outflow.

Potentials of mean force for biomolecular simulations: Theory and test on alanine dipeptide

NASA Astrophysics Data System (ADS)

Pellegrini, Matteo; Grønbech-Jensen, Niels; Doniach, Sebastian

1996-06-01

We describe a technique for generating potentials of mean force (PMF) between solutes in an aqueous solution. We first generate solute-solvent correlation functions (CF) using Monte Carlo (MC) simulations in which we place a single atom solute in a periodic boundary box containing a few hundred water molecules. We then make use of the Kirkwood superposition approximation, where the 3-body correlation function is approximated as the product of 2-body CFs, to describe the mean water density around two solutes. Computing the force generated on the solutes by this average water density allows us to compute potentials of mean force between the two solutes. For charged solutes an additional approximation involving dielectric screening is made, by setting the dielectric constant of water to ɛ=80. These potentials account, in an approximate manner, for the average effect of water on the atoms. Following the work of Pettitt and Karplus [Chem. Phys. Lett. 121, 194 (1985)], we approximate the n-body potential of mean force as a sum of the pairwise potentials of mean force. This allows us to run simulations of biomolecules without introducing explicit water, hence gaining several orders of magnitude in efficiency with respect to standard molecular dynamics techniques. We demonstrate the validity of this technique by first comparing the PMFs for methane-methane and sodium-chloride generated with this procedure, with those calculated with a standard Monte Carlo simulation with explicit water. We then compare the results of the free energy profiles between the equilibria of alanine dipeptide generated by the two methods.

Evidence of G-protein-coupled receptor and substrate transporter heteromerization at a single molecule level.

PubMed

Fischer, Jana; Kleinau, Gunnar; Rutz, Claudia; Zwanziger, Denise; Khajavi, Noushafarin; Müller, Anne; Rehders, Maren; Brix, Klaudia; Worth, Catherine L; Führer, Dagmar; Krude, Heiko; Wiesner, Burkhard; Schülein, Ralf; Biebermann, Heike

2018-06-01

G-protein-coupled receptors (GPCRs) can constitute complexes with non-GPCR integral membrane proteins, while such interaction has not been demonstrated at a single molecule level so far. We here investigated the potential interaction between the thyrotropin receptor (TSHR) and the monocarboxylate transporter 8 (MCT8), a member of the major facilitator superfamily (MFS), using fluorescence cross-correlation spectroscopy (FCCS). Both the proteins are expressed endogenously on the basolateral plasma membrane of the thyrocytes and are involved in stimulation of thyroid hormone production and release. Indeed, we demonstrate strong interaction between both the proteins which causes a suppressed activation of G q/11 by TSH-stimulated TSHR. Thus, we provide not only evidence for a novel interaction between the TSHR and MCT8, but could also prove this interaction on a single molecule level. Moreover, this interaction forces biased signaling at the TSHR. These results are of general interest for both the GPCR and the MFS research fields.

Greenhouse effect in planetary atmospheres caused by molecular symmetry breaking in intermolecular interactions

NASA Astrophysics Data System (ADS)

Vigasin, A. A.; Mokhov, I. I.

2017-03-01

It is believed that the greenhouse effect is related to the parameters of absorption spectra of polyatomic molecules, usually trace gases, in planetary atmospheres. The main components of all known atmospheres of celestial bodies are symmetrical molecules that do not possess the dipole-allowed purely rotational (and in the case of diatomic molecules, vibrational-rotational) absorption spectrum. Upon increased pressure, a weak absorption appears, induced by intermolecular interaction, which can lead to a greenhouse effect. The contribution of the induced absorption in radiative forcing of a dense atmosphere may amount to a few or even tens of W/m2. In conditions typical for the atmospheres of terrestrial planets (including paleoatmospheres), the collision-induced absorption and associated greenhouse effect may lead to an increase in surface temperature above the freezing point of water. There is a correlation between the temperature of an atmosphere and the intermolecular bonding energy of gases that dominate in planetary atmospheres of the Solar System.

Structure-based prediction of free energy changes of binding of PTP1B inhibitors

NASA Astrophysics Data System (ADS)

Wang, Jing; Ling Chan, Shek; Ramnarayan, Kal

2003-08-01

The goals were (1) to understand the driving forces in the binding of small molecule inhibitors to the active site of PTP1B and (2) to develop a molecular mechanics-based empirical free energy function for compound potency prediction. A set of compounds with known activities was docked onto the active site. The related energy components and molecular surface areas were calculated. The bridging water molecules were identified and their contributions were considered. Linear relationships were explored between the above terms and the binding free energies of compounds derived based on experimental inhibition constants. We found that minimally three terms are required to give rise to a good correlation (0.86) with predictive power in five-group cross-validation test (q2 = 0.70). The dominant terms are the electrostatic energy and non-electrostatic energy stemming from the intra- and intermolecular interactions of solutes and from those of bridging water molecules in complexes.

Mechanical regulation of T-cell functions

PubMed Central

Chen, Wei; Zhu, Cheng

2013-01-01

Summary T cells are key players of the mammalian adaptive immune system. They experience different mechanical microenvironments during their life cycles, from the thymus, secondary lymph organs, and peripheral tissues that are free of externally applied force but display variable substrate rigidities, to the blood and lymphatic circulation systems where complicated hydrodynamic forces are present. Regardless of whether T cells are subject to external forces or generate their own internal forces, they response and adapt to different biomechanical cues to modulate their adhesion, migration, trafficking, and triggering of immune functions through mechanical regulation of various molecules that bear force. These include adhesive receptors, immunoreceptors, motor proteins, cytoskeletal proteins, and their associated molecules. Here we discuss the forces acting on various surface and cytoplasmic proteins of a T cell in different mechanical milieus. We review existing data on how force regulates protein conformational changes and interactions with counter molecules, including integrins, actin, and the T-cell receptor, and how each relates to T-cell functions. PMID:24117820

Optimized Free Energies from Bidirectional Single-Molecule Force Spectroscopy

NASA Astrophysics Data System (ADS)

Minh, David D. L.; Adib, Artur B.

2008-05-01

An optimized method for estimating path-ensemble averages using data from processes driven in opposite directions is presented. Based on this estimator, bidirectional expressions for reconstructing free energies and potentials of mean force from single-molecule force spectroscopy—valid for biasing potentials of arbitrary stiffness—are developed. Numerical simulations on a model potential indicate that these methods perform better than unidirectional strategies.

Harmonic force spectroscopy measures load-dependent kinetics of individual human β-cardiac myosin molecules.

PubMed

Sung, Jongmin; Nag, Suman; Mortensen, Kim I; Vestergaard, Christian L; Sutton, Shirley; Ruppel, Kathleen; Flyvbjerg, Henrik; Spudich, James A

2015-08-04

Molecular motors are responsible for numerous cellular processes from cargo transport to heart contraction. Their interactions with other cellular components are often transient and exhibit kinetics that depend on load. Here, we measure such interactions using 'harmonic force spectroscopy'. In this method, harmonic oscillation of the sample stage of a laser trap immediately, automatically and randomly applies sinusoidally varying loads to a single motor molecule interacting with a single track along which it moves. The experimental protocol and the data analysis are simple, fast and efficient. The protocol accumulates statistics fast enough to deliver single-molecule results from single-molecule experiments. We demonstrate the method's performance by measuring the force-dependent kinetics of individual human β-cardiac myosin molecules interacting with an actin filament at physiological ATP concentration. We show that a molecule's ADP release rate depends exponentially on the applied load, in qualitative agreement with cardiac muscle, which contracts with a velocity inversely proportional to external load.

Harmonic force spectroscopy measures load-dependent kinetics of individual human β-cardiac myosin molecules

PubMed Central

Sung, Jongmin; Nag, Suman; Mortensen, Kim I.; Vestergaard, Christian L.; Sutton, Shirley; Ruppel, Kathleen; Flyvbjerg, Henrik; Spudich, James A.

2015-01-01

Molecular motors are responsible for numerous cellular processes from cargo transport to heart contraction. Their interactions with other cellular components are often transient and exhibit kinetics that depend on load. Here, we measure such interactions using ‘harmonic force spectroscopy'. In this method, harmonic oscillation of the sample stage of a laser trap immediately, automatically and randomly applies sinusoidally varying loads to a single motor molecule interacting with a single track along which it moves. The experimental protocol and the data analysis are simple, fast and efficient. The protocol accumulates statistics fast enough to deliver single-molecule results from single-molecule experiments. We demonstrate the method's performance by measuring the force-dependent kinetics of individual human β-cardiac myosin molecules interacting with an actin filament at physiological ATP concentration. We show that a molecule's ADP release rate depends exponentially on the applied load, in qualitative agreement with cardiac muscle, which contracts with a velocity inversely proportional to external load. PMID:26239258

Single ricin detection by atomic force microscopy chemomechanical mapping

NASA Astrophysics Data System (ADS)

Chen, Guojun; Zhou, Jianfeng; Park, Bosoon; Xu, Bingqian

2009-07-01

The authors report on a study of detecting ricin molecules immobilized on chemically modified Au (111) surface by chemomechanically mapping the molecular interactions with a chemically modified atomic force microscopy (AFM) tip. AFM images resolved the different fold-up conformations of single ricin molecule as well as their intramolecule structure of A- and B-chains. AFM force spectroscopy study of the interaction indicates that the unbinding force has a linear relation with the logarithmic force loading rate, which agrees well with calculations using one-barrier bond dissociation model.

Atomic force microscopy and force spectroscopy on the assessment of protein folding and functionality.

PubMed

Carvalho, Filomena A; Martins, Ivo C; Santos, Nuno C

2013-03-01

Atomic force microscopy (AFM) applied to biological systems can, besides generating high-quality and well-resolved images, be employed to study protein folding via AFM-based force spectroscopy. This approach allowed remarkable advances in the measurement of inter- and intramolecular interaction forces with piconewton resolution. The detection of specific interaction forces between molecules based on the AFM sensitivity and the manipulation of individual molecules greatly advanced the understanding of intra-protein and protein-ligand interactions. Apart from the academic interest in the resolution of basic scientific questions, this technique has also key importance on the clarification of several biological questions of immediate biomedical relevance. Force spectroscopy is an especially appropriate technique for "mechanical proteins" that can provide crucial information on single protein molecules and/or domains. Importantly, it also has the potential of combining in a single experiment spatial and kinetic measurements. Here, the main principles of this methodology are described, after which the ability to measure interactions at the single-molecule level is discussed, in the context of relevant protein-folding examples. We intend to demonstrate the potential of AFM-based force spectroscopy in the study of protein folding, especially since this technique is able to circumvent some of the difficulties typically encountered in classical thermal/chemical denaturation studies. Copyright © 2012 Elsevier Inc. All rights reserved.

Direct, concurrent measurements of the forces and currents affecting DNA in a nanopore with comparable topography.

PubMed

Nelson, Edward M; Li, Hui; Timp, Gregory

2014-06-24

We report direct, concurrent measurements of the forces and currents associated with the translocation of a single-stranded DNA molecule tethered to the tip of an atomic force microscope (AFM) cantilever through synthetic pores with topagraphies comparable to the DNA. These measurements were performed to gauge the signal available for sequencing and the electric force required to impel a single molecule through synthetic nanopores ranging from 1.0 to 3.5 nm in diameter in silicon nitride membranes 6-10 nm thick. The measurements revealed that a molecule can slide relatively frictionlessly through a pore, but regular fluctuations are observed intermittently in the force (and the current) every 0.35-0.72 nm, which are attributed to individual nucleotides translating through the nanopore in a turnstile-like motion.

Quantitative single molecule measurements on the interaction forces of poly(L-glutamic acid) with calcite crystals.

PubMed

Sonnenberg, Lars; Luo, Yufei; Schlaad, Helmut; Seitz, Markus; Cölfen, Helmut; Gaub, Hermann E

2007-12-12

The interaction between poly(L-glutamic acid) (PLE) and calcite crystals was studied with AFM-based single molecule force spectroscopy. Block copolymers of poly(ethylene oxide) (PEO) and PLE were synthesized and covalently attached to the tip of an AFM cantilever. In desorption measurements the molecules were allowed to adsorb on the calcite crystal faces and afterward successively desorbed. The corresponding desorption forces were detected with high precision, showing for example a force transition between the two blocks. Because of its importance in the crystallization process in biominerals, the PLE-calcite interaction was investigated as a function of the pH as well as the calcium concentration of the aqueous solution. The sensitivity of the technique was underlined by resolving different interaction forces for calcite (104) and calcite (100).

Order from Force; A natural history of the vacuum

NASA Astrophysics Data System (ADS)

Williams, Jeffrey H.

2015-11-01

The laws of physics govern our lives, and the fundamental constants of Nature (for example, the mass and charge of the electron) define our very morphology. If a human body were totally dehydrated there would only remain about thirty kilograms of crystals and powder, after having removed about fifty litres of water. Yet the amazing machine that is our body functions because of the forces of interaction (attraction and repulsion) that exist between the molecules in that powder when fully hydrated. These forces of interaction are mediated and directed by the vast amount of water that is present. It is the precise orientation of one hydrated molecule with respect to another hydrated molecule, at a well-defined separation, in our central nervous systems that allows a nerve impulse to tunnel quantum-mechanically through the intermediate space between two nerve cells at a synapse. Thereby allowing us to observe our environment, and contemplate our existence. It is the arrangement of the water molecules along molecules of muscle proteins that allows one protein molecule to slide over neighbouring protein molecules, thereby allowing us to do exercise and work, or to hunt and to gather. The precise distances and orientations between the molecules of which our bodies are composed are determined by subtle intermolecular electrostatic forces, whose magnitude is determined by the various constants of Nature, and whose operation is dictated by the laws of physics. We are merely living representations of these immutable physical laws.

Thermal Quantum Correlations in Photosynthetic Light-Harvesting Complexes

NASA Astrophysics Data System (ADS)

Mahdian, M.; Kouhestani, H.

2015-08-01

Photosynthesis is one of the ancient biological processes, playing crucial role converting solar energy to cellular usable currency. Environmental factors and external perturbations has forced nature to choose systems with the highest efficiency and performance. Recent theoretical and experimental studies have proved the presence of quantum properties in biological systems. Energy transfer systems like Fenna-Matthews-Olson (FMO) complex shows quantum entanglement between sites of Bacteriophylla molecules in protein environment and presence of decoherence. Complex biological systems implement more truthful mechanisms beside chemical-quantum correlations to assure system's efficiency. In this study we investigate thermal quantum correlations in FMO protein of the photosynthetic apparatus of green sulfur bacteria by quantum discord measure. The results confirmed existence of remarkable quantum correlations of of BChla pigments in room temperature. This results approve involvement of quantum correlation mechanisms for information storage and retention in living organisms that could be useful for further evolutionary studies. Inspired idea of this study is potentially interesting to practice by the same procedure in genetic data transfer mechanisms.

Quantitative modeling of forces in electromagnetic tweezers

NASA Astrophysics Data System (ADS)

Bijamov, Alex; Shubitidze, Fridon; Oliver, Piercen M.; Vezenov, Dmitri V.

2010-11-01

This paper discusses numerical simulations of the magnetic field produced by an electromagnet for generation of forces on superparamagnetic microspheres used in manipulation of single molecules or cells. Single molecule force spectroscopy based on magnetic tweezers can be used in applications that require parallel readout of biopolymer stretching or biomolecular binding. The magnetic tweezers exert forces on the surface-immobilized macromolecule by pulling a magnetic bead attached to the free end of the molecule in the direction of the field gradient. In a typical force spectroscopy experiment, the pulling forces can range between subpiconewton to tens of piconewtons. In order to effectively provide such forces, an understanding of the source of the magnetic field is required as the first step in the design of force spectroscopy systems. In this study, we use a numerical technique, the method of auxiliary sources, to investigate the influence of electromagnet geometry and material parameters of the magnetic core on the magnetic forces pulling the target beads in the area of interest. The close proximity of the area of interest to the magnet body results in deviations from intuitive relations between magnet size and pulling force, as well as in the force decay with distance. We discuss the benefits and drawbacks of various geometric modifications affecting the magnitude and spatial distribution of forces achievable with an electromagnet.

Modified atomic force microscope applied to the measurement of elastic modulus for a single peptide molecule

NASA Astrophysics Data System (ADS)

Ptak, Arkadiusz; Takeda, Seiji; Nakamura, Chikashi; Miyake, Jun; Kageshima, Masami; Jarvis, Suzanne P.; Tokumoto, Hiroshi

2001-09-01

A modified atomic force microscopy (AFM) system, based on a force modulation technique, has been used to find an approximate value for the elastic modulus of a single peptide molecule directly from a mechanical test. For this purpose a self-assembled monolayer built from two kinds of peptides, reactive (able to anchor to the AFM tip) and nonreactive, was synthesized. In a typical experiment a single C3K30C (C=cysteine, K=lysine) peptide molecule was stretched between a Au(111) substrate and the gold-coated tip of an AFM cantilever to which it was attached via gold-sulfur bonds. The amplitude of the cantilever oscillations, due to an external force applied via a magnetic particle to the cantilever, was recorded by a lock-in amplifier and recalculated into stiffness of the stretched molecule. A longitudinal Young's modulus for the α-helix of a single peptide molecule and for the elongated state of this molecule has been estimated. The obtained values; 1.2±0.3 and 50±15 GPa, for the peptide α-helix and elongated peptide backbone, respectively, seem to be reasonable comparing them to the Young's modulus of protein crystals and linear organic polymers. We believe this research opens up a means by which scientists can perform quantitative studies of the elastic properties of single molecule, especially of biologically important polymers like peptides or DNA.

Scanning probe microscopy for the analysis of composite Ti/hydrocarbon plasma polymer thin films

NASA Astrophysics Data System (ADS)

Choukourov, A.; Grinevich, A.; Slavinska, D.; Biederman, H.; Saito, N.; Takai, O.

2008-03-01

Composite Ti/hydrocarbon plasma polymer films with different Ti concentration were deposited on silicon by dc magnetron sputtering of titanium in an atmosphere of argon and hexane. As measured by Kelvin force microscopy and visco-elastic atomic force microscopy, respectively, surface potential and hardness increase with increasing Ti content. Adhesion force to silicon and to fibrinogen molecules was stronger for the Ti-rich films as evaluated from the AFM force-distance curves. Fibrinogen forms a very soft layer on these composites with part of the protein molecules embedded in the outermost region of the plasma polymer. An increase of the surface charge due to fibrinogen adsorption has been observed and attributed to positively charged αC domains of fibrinogen molecule.

The Ehrenfest force field: Topology and consequences for the definition of an atom in a molecule.

PubMed

Martín Pendás, A; Hernández-Trujillo, J

2012-10-07

The Ehrenfest force is the force acting on the electrons in a molecule due to the presence of the other electrons and the nuclei. There is an associated force field in three-dimensional space that is obtained by the integration of the corresponding Hermitian quantum force operator over the spin coordinates of all of the electrons and the space coordinates of all of the electrons but one. This paper analyzes the topology induced by this vector field and its consequences for the definition of molecular structure and of an atom in a molecule. Its phase portrait reveals: that the nuclei are attractors of the Ehrenfest force, the existence of separatrices yielding a dense partitioning of three-dimensional space into disjoint regions, and field lines connecting the attractors through these separatrices. From the numerical point of view, when the Ehrenfest force field is obtained as minus the divergence of the kinetic stress tensor, the induced topology was found to be highly sensitive to choice of gaussian basis sets at long range. Even the use of large split valence and highly uncontracted basis sets can yield spurious critical points that may alter the number of attraction basins. Nevertheless, at short distances from the nuclei, in general, the partitioning of three-dimensional space with the Ehrenfest force field coincides with that induced by the gradient field of the electron density. However, exceptions are found in molecules where the electron density yields results in conflict with chemical intuition. In these cases, the molecular graphs of the Ehrenfest force field reveal the expected atomic connectivities. This discrepancy between the definition of an atom in a molecule between the two vector fields casts some doubts on the physical meaning of the integration of Ehrenfest forces over the basins of the electron density.

The structure of [MnIII6 CrIII]3+ single-molecule magnets deposited in submono-layers and monolayers on surfaces studied by means of molecular resolved atomic force microscopy (AFM) and Kelvin Probe Force Microscopy in UHV

NASA Astrophysics Data System (ADS)

Heinzmann, U.; Gryzia, A.; Volkmann, T.; Brechling, A.; Hoeke, V.; Glaser, T.

2014-04-01

Single molecule magnets (SMM) deposited in submonolayers and monolayers have been analyzed with respect to their structures by means of non-contact AFM (topographic as well as damping mode) and Kelvin Probe Force Microscopy with molecular resolution.

Dynamics of the sol—gel transition in organic—inorganic nanocomposites

NASA Astrophysics Data System (ADS)

Judeinstein, P.; Oliveira, P. W.; Krug, H.; Schmidt, H.

1994-03-01

Two different techniques have been used to follow the gelation of photochromic organic—inorganic nanocomposites. The variations of molecular and macromolecular motions in these complex systems have been analyzed. Photo-correlation spectroscopy probes the formation of the gel network. Forced Rayleigh scattering experiences the microstructure of the mixtures via the measurement of the translational diffusion coefficient of entrapped photoreactive targets. In the different mixtures, a drop of the network mobility could be observed around the sol to gel conversion, while the entrapped molecules do not experience the macroscopic transition.

Mechanical Properties of β-Catenin Revealed by Single-Molecule Experiments

PubMed Central

Valbuena, Alejandro; Vera, Andrés Manuel; Oroz, Javier; Menéndez, Margarita; Carrión-Vázquez, Mariano

2012-01-01

β-catenin is a central component of the adaptor complex that links cadherins to the actin cytoskeleton in adherens junctions and thus, it is a good candidate to sense and transmit mechanical forces to trigger specific changes inside the cell. To fully understand its molecular physiology, we must first investigate its mechanical role in mechanotransduction within the cadherin system. We have studied the mechanical response of β-catenin to stretching using single-molecule force spectroscopy and molecular dynamics. Unlike most proteins analyzed to date, which have a fixed mechanical unfolding pathway, the β-catenin armadillo repeat region (ARM) displays low mechanostability and multiple alternative unfolding pathways that seem to be modulated by its unstructured termini. These results are supported by steered molecular dynamics simulations, which also predict its mechanical stabilization and unfolding pathway restrictions when the contiguous α-helix of the C-terminal unstructured region is included. Furthermore, simulations of the ARM/E-cadherin cytosolic tail complex emulating the most probable stress geometry occurring in vivo show a mechanical stabilization of the interaction whose magnitude correlates with the length of the stretch of the cadherin cytosolic tail that is in contact with the ARM region. PMID:23083718

Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel

NASA Astrophysics Data System (ADS)

Zhang, Ce; Zhang, Fang; van Kan, Jeroen A.; van der Maarel, Johan R. C.

2008-06-01

Single T4-DNA molecules were confined in rectangular-shaped channels with a depth of 300 nm and a width in the range of 150-300 nm casted in a poly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA molecules were measured with fluorescence microscopy as a function of the ionic strength and composition of the buffer as well as the DNA intercalation level by the YOYO-1 dye. The data were interpreted with the scaling theory for a wormlike polymer in good solvent, including the effects of confinement, charge, and self-avoidance. It was found that the elongation of the DNA molecules with decreasing ionic strength can be interpreted in terms of an increase of the persistence length. Self-avoidance effects on the extension are moderate, due to the small correlation length imposed by the channel cross-sectional diameter. Intercalation of the dye results in an increase of the DNA contour length and a partial neutralization of the DNA charge, but besides effects of electrostatic origin it has no significant effect on the bare bending rigidity. In the presence of divalent cations, the DNA molecules were observed to contract, but they do not collapse into a condensed structure. It is proposed that this contraction results from a divalent counterion mediated attractive force between the segments of the DNA molecule.

Orientation-dependent energy level alignment and film growth of 2,7-diocty[1]benzothieno[3,2-b]benzothiophene (C8-BTBT) on HOPG

NASA Astrophysics Data System (ADS)

Lyu, Lu; Niu, Dongmei; Xie, Haipeng; Cao, Ningtong; Zhang, Hong; Zhang, Yuhe; Liu, Peng; Gao, Yongli

2016-01-01

Combining ultraviolet photoemission spectroscopy, X-ray photoemission spectroscopy, atomic force microscopy, and X-ray diffraction measurements, we performed a systematic investigation on the correlation of energy level alignment, film growth, and molecular orientation of 2,7-diocty[1]benzothieno[3,2-b]benzothiophene (C8-BTBT) on highly oriented pyrolytic graphite. The molecules lie down in the first layer and then stand up from the second layer. The ionization potential shows a sharp decrease from the lying down region to the standing up region. When C8-BTBT molecules start standing up, unconventional energy level band-bending-like shifts are observed as the film thickness increases. These shifts are ascribed to gradual decreasing of the molecular tilt angle about the substrate normal with the increasing film thickness.

Orientation-dependent energy level alignment and film growth of 2,7-diocty[1]benzothieno[3,2-b]benzothiophene (C8-BTBT) on HOPG.

PubMed

Lyu, Lu; Niu, Dongmei; Xie, Haipeng; Cao, Ningtong; Zhang, Hong; Zhang, Yuhe; Liu, Peng; Gao, Yongli

2016-01-21

Combining ultraviolet photoemission spectroscopy, X-ray photoemission spectroscopy, atomic force microscopy, and X-ray diffraction measurements, we performed a systematic investigation on the correlation of energy level alignment, film growth, and molecular orientation of 2,7-diocty[1]benzothieno[3,2-b]benzothiophene (C8-BTBT) on highly oriented pyrolytic graphite. The molecules lie down in the first layer and then stand up from the second layer. The ionization potential shows a sharp decrease from the lying down region to the standing up region. When C8-BTBT molecules start standing up, unconventional energy level band-bending-like shifts are observed as the film thickness increases. These shifts are ascribed to gradual decreasing of the molecular tilt angle about the substrate normal with the increasing film thickness.

Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant.

PubMed

Caleman, Carl; van Maaren, Paul J; Hong, Minyan; Hub, Jochen S; Costa, Luciano T; van der Spoel, David

2012-01-10

The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys.2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed exposé of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem.2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields.

Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant

PubMed Central

2011-01-01

The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys.2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed exposé of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem.2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields. PMID:22241968

A programmable DNA origami nanospring that reveals force-induced adjacent binding of myosin VI heads

PubMed Central

Iwaki, M.; Wickham, S. F.; Ikezaki, K.; Yanagida, T.; Shih, W. M.

2016-01-01

Mechanosensitive biological nanomachines such as motor proteins and ion channels regulate diverse cellular behaviour. Combined optical trapping with single-molecule fluorescence imaging provides a powerful methodology to clearly characterize the mechanoresponse, structural dynamics and stability of such nanomachines. However, this system requires complicated experimental geometry, preparation and optics, and is limited by low data-acquisition efficiency. Here we develop a programmable DNA origami nanospring that overcomes these issues. We apply our nanospring to human myosin VI, a mechanosensory motor protein, and demonstrate nanometre-precision single-molecule fluorescence imaging of the individual motor domains (heads) under force. We observe force-induced transitions of myosin VI heads from non-adjacent to adjacent binding, which correspond to adapted roles for low-load and high-load transport, respectively. Our technique extends single-molecule studies under force and clarifies the effect of force on biological processes. PMID:27941751

A programmable DNA origami nanospring that reveals force-induced adjacent binding of myosin VI heads.

PubMed

Iwaki, M; Wickham, S F; Ikezaki, K; Yanagida, T; Shih, W M

2016-12-12

Mechanosensitive biological nanomachines such as motor proteins and ion channels regulate diverse cellular behaviour. Combined optical trapping with single-molecule fluorescence imaging provides a powerful methodology to clearly characterize the mechanoresponse, structural dynamics and stability of such nanomachines. However, this system requires complicated experimental geometry, preparation and optics, and is limited by low data-acquisition efficiency. Here we develop a programmable DNA origami nanospring that overcomes these issues. We apply our nanospring to human myosin VI, a mechanosensory motor protein, and demonstrate nanometre-precision single-molecule fluorescence imaging of the individual motor domains (heads) under force. We observe force-induced transitions of myosin VI heads from non-adjacent to adjacent binding, which correspond to adapted roles for low-load and high-load transport, respectively. Our technique extends single-molecule studies under force and clarifies the effect of force on biological processes.

Exploring the folding pattern of a polymer chain in a single crystal by combining single-molecule force spectroscopy and steered molecular dynamics simulations.

PubMed

Song, Yu; Feng, Wei; Liu, Kai; Yang, Peng; Zhang, Wenke; Zhang, Xi

2013-03-26

Understanding the folding pattern of a single polymer chain within its single crystal will shed light on the mechanism of crystallization. Here, we use the combined techniques of atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) and steered molecular dynamics (SMD) simulations to study the folding pattern of a polyethylene oxide (PEO) chain in its single crystal. Our results show that the folding pattern of a PEO chain in the crystal formed in dilute solution follows the adjacent re-entry folding model. While in the crystal obtained from the melt, the nonadjacent folding with large and irregular loops contributes to big force fluctuations in the force-extension curves. The method established here can offer a novel strategy to directly unravel the chain-folding pattern of polymer single crystals at single-molecule level.

Thermophoretic force and velocity of nanoparticles in the free molecule regime.

PubMed

Li, Zhigang; Wang, Hai

2004-08-01

We extend our previous gas-kinetic theory analysis of drag force in a uniform temperature field [Li and Wang, Phys. Rev. E. 68, 061206 (2003); 68, 061207 (2003)] to particle transport in fluids with nonuniform temperature. Formulations for drag and thermophoretic forces are proposed for nanoparticle transport in low-density gases. We specifically consider the influence of nonrigid body collision due to van der Waals or other forces between the particle and gas molecules and find that these forces play a notable role for particles a few nanometers in size. It is shown that the present formulations can be easily reduced to the classical result of Waldmann [Z. Naturforsch. A 14a, 589 (1959)] by assuming rigid body collision. From the force formulations we also obtain the equation governing the thermophoretic velocity. This velocity is found to be highly sensitive to the potential energy of interactions between gas molecules and particle, and as such Waldmann's thermophoretic velocity is not expected to be accurate for nanosized particles.

Stimulated Raman spectroscopy and nanoscopy of molecules using near field photon induced forces without resonant electronic enhancement gain

NASA Astrophysics Data System (ADS)

Tamma, Venkata Ananth; Huang, Fei; Nowak, Derek; Kumar Wickramasinghe, H.

2016-06-01

We report on stimulated Raman spectroscopy and nanoscopy of molecules, excited without resonant electronic enhancement gain, and recorded using near field photon induced forces. Photon-induced interaction forces between the sharp metal coated silicon tip of an Atomic Force Microscope (AFM) and a sample resulting from stimulated Raman excitation were detected. We controlled the tip to sample spacing using the higher order flexural eigenmodes of the AFM cantilever, enabling the tip to come very close to the sample. As a result, the detection sensitivity was increased compared with previous work on Raman force microscopy. Raman vibrational spectra of azobenzene thiol and l-phenylalanine were measured and found to agree well with published results. Near-field force detection eliminates the need for far-field optical spectrometer detection. Recorded images show spatial resolution far below the optical diffraction limit. Further optimization and use of ultrafast pulsed lasers could push the detection sensitivity towards the single molecule limit.

Stimulated Raman spectroscopy and nanoscopy of molecules using near field photon induced forces without resonant electronic enhancement gain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tamma, Venkata Ananth; Huang, Fei; Kumar Wickramasinghe, H., E-mail: hkwick@uci.edu

We report on stimulated Raman spectroscopy and nanoscopy of molecules, excited without resonant electronic enhancement gain, and recorded using near field photon induced forces. Photon-induced interaction forces between the sharp metal coated silicon tip of an Atomic Force Microscope (AFM) and a sample resulting from stimulated Raman excitation were detected. We controlled the tip to sample spacing using the higher order flexural eigenmodes of the AFM cantilever, enabling the tip to come very close to the sample. As a result, the detection sensitivity was increased compared with previous work on Raman force microscopy. Raman vibrational spectra of azobenzene thiol andmore » l-phenylalanine were measured and found to agree well with published results. Near-field force detection eliminates the need for far-field optical spectrometer detection. Recorded images show spatial resolution far below the optical diffraction limit. Further optimization and use of ultrafast pulsed lasers could push the detection sensitivity towards the single molecule limit.« less

On the abnormal "forced hydration" behavior of P(MEA-co-OEGA) aqueous solutions during phase transition from infrared spectroscopic insights.

PubMed

Hou, Lei; Wu, Peiyi

2016-06-21

Turbidity, DLS and FTIR measurements in combination with the perturbation correlation moving window (PCMW) technique and 2D correlation spectroscopy (2Dcos) analysis have been utilized to investigate the LCST-type transition of a oligo ethylene glycol acrylate-based copolymer (POEGA) in aqueous solutions in this work. As demonstrated in turbidity and DLS curves, the macroscopic phase separation was sharp and slightly concentration dependent. Moreover, individual chemical groups along polymer chains also display abrupt changes in temperature-variable IR spectra. However, according to conventional IR analysis, the C-H groups present obvious dehydration, whereas C[double bond, length as m-dash]O and C-O-C groups exhibit anomalous "forced hydration" during the steep phase transition. From these analyses together with the PCMW and 2Dcos results, it has been confirmed that the hydrophobic interaction among polymer chains drove the chain collapse and dominated the phase transition. In addition, the unexpected enhanced hydration behavior of C[double bond, length as m-dash]O and C-O-C groups was induced by forced hydrogen bonding between polar groups along polymer chains and entrapped water molecules in the aggregates, which originated from the special chemical structure of POEGA.

Conformational variety for the ansa chain of rifamycins: Comparison of observed crystal structures and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Bacchi, Alessia; Pelizzi, Giancarlo

1999-07-01

The antibiotic activity (via inhibition of DNA-dependent RNA polymerase, DDRP) of rifamycins has been correlated to the conformation of the ansa chain, which can be described by means of 17 torsion angles defined along the ansa backbone. It has been shown that favourable or unfavourable conformations of the ansa chain in rifamycin crystals are generally diagnostic of activity or inactivity against isolated DDRP. The principles of structure correlation suggest that the torsional variety observed in rifamycin crystals should mimic the dynamic flexibility of the ansa chain in solution. Twenty-six crystal structures of rifamycins are grouped into two classes (active and non-active). For each class the variance of the 17 ansa backbone torsion angles is analysed. Active compounds show a well-defined common pattern, while non-active molecules are more scattered, mainly due to steric constraints forcing the molecules into unfavourable conformations. The experimental distributions of torsion angles are compared to the torsional freedom of the ansa chain simulated by molecular dynamics calculations performed at different temperatures and conditions on rifamycin S and rifamycin O, which represent a typical active and a typical sterically constrained molecule, respectively. It is shown that the torsional variety found in the crystalline state samples the dynamic behaviour of the ansa chain for active compounds. The methods of circular statistics are illustrated to describe torsion angle distributions.

Single-molecule Force Spectroscopy Approach to Enzyme Catalysis*

PubMed Central

Alegre-Cebollada, Jorge; Perez-Jimenez, Raul; Kosuri, Pallav; Fernandez, Julio M.

2010-01-01

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. PMID:20382731

Single-molecule force spectroscopy approach to enzyme catalysis.

PubMed

Alegre-Cebollada, Jorge; Perez-Jimenez, Raul; Kosuri, Pallav; Fernandez, Julio M

2010-06-18

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.

Measurement of Intramolecular Energy Dissipation and Stiffness of a Single Peptide Molecule by Magnetically Modulated Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Kageshima, Masami; Takeda, Seiji; Ptak, Arkadiusz; Nakamura, Chikashi; Jarvis, Suzanne P.; Tokumoto, Hiroshi; Miyake, Jun

2004-12-01

A method for measuring intramolecular energy dissipation as well as stiffness variation in a single biomolecule in situ by atomic force microscopy (AFM) is presented. An AFM cantilever is magnetically modulated at an off-resonance frequency while it elongates a single peptide molecule in buffer solution. The molecular stiffness and the energy dissipation are measured via the amplitude and phase lag in the response signal. Data showing a peculiar feature in both profiles of stiffness and dissipation is presented. This suggests that the present method is more sensitive to the state of the molecule than the conventional force-elongation measurement is.

Modulating Beta-Cardiac Myosin Function at the Molecular and Tissue Levels

PubMed Central

Tang, Wanjian; Blair, Cheavar A.; Walton, Shane D.; Málnási-Csizmadia, András; Campbell, Kenneth S.; Yengo, Christopher M.

2017-01-01

Inherited cardiomyopathies are a common form of heart disease that are caused by mutations in sarcomeric proteins with beta cardiac myosin (MYH7) being one of the most frequently affected genes. Since the discovery of the first cardiomyopathy associated mutation in beta-cardiac myosin, a major goal has been to correlate the in vitro myosin motor properties with the contractile performance of cardiac muscle. There has been substantial progress in developing assays to measure the force and velocity properties of purified cardiac muscle myosin but it is still challenging to correlate results from molecular and tissue-level experiments. Mutations that cause hypertrophic cardiomyopathy are more common than mutations that lead to dilated cardiomyopathy and are also often associated with increased isometric force and hyper-contractility. Therefore, the development of drugs designed to decrease isometric force by reducing the duty ratio (the proportion of time myosin spends bound to actin during its ATPase cycle) has been proposed for the treatment of hypertrophic cardiomyopathy. Para-Nitroblebbistatin is a small molecule drug proposed to decrease the duty ratio of class II myosins. We examined the impact of this drug on human beta cardiac myosin using purified myosin motor assays and studies of permeabilized muscle fiber mechanics. We find that with purified human beta-cardiac myosin para-Nitroblebbistatin slows actin-activated ATPase and in vitro motility without altering the ADP release rate constant. In permeabilized human myocardium, para-Nitroblebbistatin reduces isometric force, power, and calcium sensitivity while not changing shortening velocity or the rate of force development (ktr). Therefore, designing a drug that reduces the myosin duty ratio by inhibiting strong attachment to actin while not changing detachment can cause a reduction in force without changing shortening velocity or relaxation. PMID:28119616

DNA combing on low-pressure oxygen plasma modified polysilsesquioxane substrates for single-molecule studies

PubMed Central

Sriram, K. K.; Chang, Chun-Ling; Rajesh Kumar, U.; Chou, Chia-Fu

2014-01-01

Molecular combing and flow-induced stretching are the most commonly used methods to immobilize and stretch DNA molecules. While both approaches require functionalization steps for the substrate surface and the molecules, conventionally the former does not take advantage of, as the latter, the versatility of microfluidics regarding robustness, buffer exchange capability, and molecule manipulation using external forces for single molecule studies. Here, we demonstrate a simple one-step combing process involving only low-pressure oxygen (O2) plasma modified polysilsesquioxane (PSQ) polymer layer to facilitate both room temperature microfluidic device bonding and immobilization of stretched single DNA molecules without molecular functionalization step. Atomic force microscopy and Kelvin probe force microscopy experiments revealed a significant increase in surface roughness and surface potential on low-pressure O2 plasma treated PSQ, in contrast to that with high-pressure O2 plasma treatment, which are proposed to be responsible for enabling effective DNA immobilization. We further demonstrate the use of our platform to observe DNA-RNA polymerase complexes and cancer drug cisplatin induced DNA condensation using wide-field fluorescence imaging. PMID:25332730

Time dependent wettability of graphite upon ambient exposure: The role of water adsorption

NASA Astrophysics Data System (ADS)

Amadei, Carlo A.; Lai, Chia-Yun; Heskes, Daan; Chiesa, Matteo

2014-08-01

We report the temporal evolution of the wettability of highly ordered pyrolytic graphite (HOPG) exposed to environmental conditions. Macroscopic wettability is investigated by static and dynamic contact angles (SCA and DCA) obtaining values comparable to the ones presented in the literature. SCA increases from ˜68° to ˜90° during the first hour of exposure after cleaving, whereas DCA is characterized by longer-scale (24 h) time evolution. We interpret these results in light of Fourier transform infrared spectroscopy, which indicates that the evolution of the HOPG wettability is due to adsorption of molecules from the surrounding atmosphere. This hypothesis is further confirmed by nanoscopic observations obtained by atomic force microscope (AFM)-based force spectroscopy, which monitor the evolution of surface properties with a spatial resolution superior to macroscopic experiments. Moreover, we observe that the results of macro- and nanoscale measurements evolve in similar fashion with time and we propose a quantitative correlation between SCA and AFM measurements. Our results suggest that the cause of the transition in the wettability of HOPG is due to the adsorption of hydrocarbon contaminations and water molecules from the environment. This is corroborated by annealing the HOPG is vacuum conditions at 150°, allowing the desorption of molecules on the surface, and thus re-establishing the initial macro and nano surface properties. Our findings can be used in the interpretation of the wettability of more complicated systems derived from HOPG (i.e., graphene).

Time dependent wettability of graphite upon ambient exposure: The role of water adsorption

DOE Office of Scientific and Technical Information (OSTI.GOV)

Amadei, Carlo A.; Lai, Chia-Yun; Heskes, Daan

We report the temporal evolution of the wettability of highly ordered pyrolytic graphite (HOPG) exposed to environmental conditions. Macroscopic wettability is investigated by static and dynamic contact angles (SCA and DCA) obtaining values comparable to the ones presented in the literature. SCA increases from ∼68° to ∼90° during the first hour of exposure after cleaving, whereas DCA is characterized by longer-scale (24 h) time evolution. We interpret these results in light of Fourier transform infrared spectroscopy, which indicates that the evolution of the HOPG wettability is due to adsorption of molecules from the surrounding atmosphere. This hypothesis is further confirmedmore » by nanoscopic observations obtained by atomic force microscope (AFM)-based force spectroscopy, which monitor the evolution of surface properties with a spatial resolution superior to macroscopic experiments. Moreover, we observe that the results of macro- and nanoscale measurements evolve in similar fashion with time and we propose a quantitative correlation between SCA and AFM measurements. Our results suggest that the cause of the transition in the wettability of HOPG is due to the adsorption of hydrocarbon contaminations and water molecules from the environment. This is corroborated by annealing the HOPG is vacuum conditions at 150°, allowing the desorption of molecules on the surface, and thus re-establishing the initial macro and nano surface properties. Our findings can be used in the interpretation of the wettability of more complicated systems derived from HOPG (i.e., graphene)« less

Adsorption Mechanism of Inhibitor and Guest Molecules on the Surface of Gas Hydrates.

PubMed

Yagasaki, Takuma; Matsumoto, Masakazu; Tanaka, Hideki

2015-09-23

The adsorption of guest and kinetic inhibitor molecules on the surface of methane hydrate is investigated by using molecular dynamics simulations. We calculate the free energy profile for transferring a solute molecule from bulk water to the hydrate surface for various molecules. Spherical solutes with a diameter of ∼0.5 nm are significantly stabilized at the hydrate surface, whereas smaller and larger solutes exhibit lower adsorption affinity than the solutes of intermediate size. The range of the attractive force is subnanoscale, implying that this force has no effect on the macroscopic mass transfer of guest molecules in crystal growth processes of gas hydrates. We also examine the adsorption mechanism of a kinetic hydrate inhibitor. It is found that a monomer of the kinetic hydrate inhibitor is strongly adsorbed on the hydrate surface. However, the hydrogen bonding between the amide group of the inhibitor and water molecules on the hydrate surface, which was believed to be the driving force for the adsorption, makes no contribution to the adsorption affinity. The preferential adsorption of both the kinetic inhibitor and the spherical molecules to the surface is mainly due to the entropic stabilization arising from the presence of cavities at the hydrate surface. The dependence of surface affinity on the size of adsorbed molecules is also explained by this mechanism.

Simple method of DNA stretching on glass substrate for fluorescence image and spectroscopy

NASA Astrophysics Data System (ADS)

Neupane, Guru P.; Dhakal, Krishna P.; Lee, Hyunsoo; Guthold, Martin; Joseph, Vincent S.; Hong, Jong-Dal; Kim, Jeongyong

2013-05-01

Study of biological molecule DNA has contributed to developing many breaking thoughts and wide applications in multidisciplinary fields, such as genomic, medical, sensing and forensic fields. Stretching of DNA molecules is an important supportive tool for AFM or spectroscopic studies of DNA in a single molecular level. In this article, we established a simple method of DNA stretching (to its full length) that occurred on a rotating negatively-charged surface of glass substrate. The isolation of a single DNA molecule was attained by the two competitive forces on DNA molecules, that is, the electrostatic attraction developed between the positively charged YOYO-1 stained DNA and the negatively charged substrate, and the centrifugal force of the rotating substrate, which separates the DNA aggregates into the single molecule. Density of stretched DNA molecules was controlled by selecting the specific parameters such as spinning time and rates, loading volume of DNA-dye complex solution etc. The atomic force microscopy image exhibited a single DNA molecule on the negatively-charged substrate in an isolated state. Further, the photoluminescence spectra of a single DNA molecule stained with YOYO-1 were achieved using the method developed in the present study, which is strongly believed to effectively support the spectroscopic analysis of DNA in a single molecular level.

ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs

NASA Astrophysics Data System (ADS)

Cleves, Ann E.; Jain, Ajay N.

2017-05-01

We introduce the ForceGen method for 3D structure generation and conformer elaboration of drug-like small molecules. ForceGen is novel, avoiding use of distance geometry, molecular templates, or simulation-oriented stochastic sampling. The method is primarily driven by the molecular force field, implemented using an extension of MMFF94s and a partial charge estimator based on electronegativity-equalization. The force field is coupled to algorithms for direct sampling of realistic physical movements made by small molecules. Results are presented on a standard benchmark from the Cambridge Crystallographic Database of 480 drug-like small molecules, including full structure generation from SMILES strings. Reproduction of protein-bound crystallographic ligand poses is demonstrated on four carefully curated data sets: the ConfGen Set (667 ligands), the PINC cross-docking benchmark (1062 ligands), a large set of macrocyclic ligands (182 total with typical ring sizes of 12-23 atoms), and a commonly used benchmark for evaluating macrocycle conformer generation (30 ligands total). Results compare favorably to alternative methods, and performance on macrocyclic compounds approaches that observed on non-macrocycles while yielding a roughly 100-fold speed improvement over alternative MD-based methods with comparable performance.

Functionalization of Probe Tips and Supports for Single-Molecule Recognition Force Microscopy

NASA Astrophysics Data System (ADS)

Ebner, Andreas; Wildling, Linda; Zhu, Rong; Rankl, Christian; Haselgrübler, Thomas; Hinterdorfer, Peter; Gruber, Hermann J.

The measuring tip of a force microscope can be converted into a monomolecular sensor if one or few "ligand" molecules are attached to the apex of the tip while maintaining ligand function. Functionalized tips are used to study fine details of receptor-ligand interaction by force spectroscopy or to map cognate "receptor" molecules on the sample surface. The receptor (or target) molecules can be present on the surface of a biological specimen; alternatively, soluble target molecules must be immobilized on ultraflat supports. This review describes the methods of tip functionalization, as well as target molecule immobilization. Silicon nitride tips, silicon chips, and mica have usually been functionalized in three steps: (1) aminofunctionalization, (2) crosslinker attachment, and (3) ligand/receptor coupling, whereby numerous crosslinkers are available to couple widely different ligand molecules. Gold-covered tips and/or supports have usually been coated with a self-assembled monolayer, on top of which the ligand/receptor molecule has been coupled either directly or via a crosslinker molecule. Apart from these general strategies, many simplified methods have been used for tip and/or support functionalization, even single-step methods such as adsorption or chemisorption being very efficient under suitable circumstances. All methods are described with the same explicitness and critical parameters are discussed. In conclusion, this review should help to find suitable methods for specific problems of tip and support functionalization.

P-cadherin promotes collective cell migration via a Cdc42-mediated increase in mechanical forces

PubMed Central

Plutoni, Cédric; Bazellieres, Elsa; Le Borgne-Rochet, Maïlys; Comunale, Franck; Brugues, Agusti; Séveno, Martial; Planchon, Damien; Thuault, Sylvie; Morin, Nathalie; Bodin, Stéphane; Trepat, Xavier

2016-01-01

Collective cell migration (CCM) is essential for organism development, wound healing, and metastatic transition, the primary cause of cancer-related death, and it involves cell–cell adhesion molecules of the cadherin family. Increased P-cadherin expression levels are correlated with tumor aggressiveness in carcinoma and aggressive sarcoma; however, how P-cadherin promotes tumor malignancy remains unknown. Here, using integrated cell biology and biophysical approaches, we determined that P-cadherin specifically induces polarization and CCM through an increase in the strength and anisotropy of mechanical forces. We show that this mechanical regulation is mediated by the P-cadherin/β-PIX/Cdc42 axis; P-cadherin specifically activates Cdc42 through β-PIX, which is specifically recruited at cell–cell contacts upon CCM. This mechanism of cell polarization and migration is absent in cells expressing E- or R-cadherin. Thus, we identify a specific role of P-cadherin through β-PIX–mediated Cdc42 activation in the regulation of cell polarity and force anisotropy that drives CCM. PMID:26783302

Single molecule views of Nature's nano-machines

NASA Astrophysics Data System (ADS)

Ha, Taekjip

2006-03-01

We are interested in the perturbational analysis of biological molecules to better understand their mechanisms. Our readout is the fluorescence signal from individual biomolecules, mainly in the form of single molecule fluorescence resonance energy transfer (FRET). We are pioneering approaches to perturb and control biomolecular conformations using external force (combination of single molecule FRET and optical trap) or other biological motifs (DNA hybridization, G-quadruplex, aptamers,.). In this talk, I will present our latest results on mapping the conformational energy landscape of the Holliday junction through simultaneous fluorescence and force measurements. In addition, a new nanomechanical device called single molecule nano-metronome will be discussed with an outlook toward controlling protein conformations using nucleic acids motifs.

Single-molecule imaging of DNA polymerase I (Klenow fragment) activity by atomic force microscopy

NASA Astrophysics Data System (ADS)

Chao, J.; Zhang, P.; Wang, Q.; Wu, N.; Zhang, F.; Hu, J.; Fan, C. H.; Li, B.

2016-03-01

We report a DNA origami-facilitated single-molecule platform that exploits atomic force microscopy to study DNA replication. We imaged several functional activities of the Klenow fragment of E. coli DNA polymerase I (KF) including binding, moving, and dissociation from the template DNA. Upon completion of these actions, a double-stranded DNA molecule was formed. Furthermore, the direction of KF activities was captured and then confirmed by shifting the KF binding sites on the template DNA.We report a DNA origami-facilitated single-molecule platform that exploits atomic force microscopy to study DNA replication. We imaged several functional activities of the Klenow fragment of E. coli DNA polymerase I (KF) including binding, moving, and dissociation from the template DNA. Upon completion of these actions, a double-stranded DNA molecule was formed. Furthermore, the direction of KF activities was captured and then confirmed by shifting the KF binding sites on the template DNA. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr06544e

Synthetic oligorotaxanes exert high forces when folding under mechanical load

NASA Astrophysics Data System (ADS)

Sluysmans, Damien; Hubert, Sandrine; Bruns, Carson J.; Zhu, Zhixue; Stoddart, J. Fraser; Duwez, Anne-Sophie

2018-01-01

Folding is a ubiquitous process that nature uses to control the conformations of its molecular machines, allowing them to perform chemical and mechanical tasks. Over the years, chemists have synthesized foldamers that adopt well-defined and stable folded architectures, mimicking the control expressed by natural systems1,2. Mechanically interlocked molecules, such as rotaxanes and catenanes, are prototypical molecular machines that enable the controlled movement and positioning of their component parts3-5. Recently, combining the exquisite complexity of these two classes of molecules, donor-acceptor oligorotaxane foldamers have been synthesized, in which interactions between the mechanically interlocked component parts dictate the single-molecule assembly into a folded secondary structure6-8. Here we report on the mechanochemical properties of these molecules. We use atomic force microscopy-based single-molecule force spectroscopy to mechanically unfold oligorotaxanes, made of oligomeric dumbbells incorporating 1,5-dioxynaphthalene units encircled by cyclobis(paraquat-p-phenylene) rings. Real-time capture of fluctuations between unfolded and folded states reveals that the molecules exert forces of up to 50 pN against a mechanical load of up to 150 pN, and displays transition times of less than 10 μs. While the folding is at least as fast as that observed in proteins, it is remarkably more robust, thanks to the mechanically interlocked structure. Our results show that synthetic oligorotaxanes have the potential to exceed the performance of natural folding proteins.

Fundamental High-Speed Limits in Single-Molecule, Single-Cell, and Nanoscale Force Spectroscopies

PubMed Central

2016-01-01

Force spectroscopy is enhancing our understanding of single-biomolecule, single-cell, and nanoscale mechanics. Force spectroscopy postulates the proportionality between the interaction force and the instantaneous probe deflection. By studying the probe dynamics, we demonstrate that the total force acting on the probe has three different components: the interaction, the hydrodynamic, and the inertial. The amplitudes of those components depend on the ratio between the resonant frequency and the frequency at which the data are measured. A force–distance curve provides a faithful measurement of the interaction force between two molecules when the inertial and hydrodynamic components are negligible. Otherwise, force spectroscopy measurements will underestimate the value of unbinding forces. Neglecting the above force components requires the use of frequency ratios in the 50–500 range. These ratios will limit the use of high-speed methods in force spectroscopy. The theory is supported by numerical simulations. PMID:27359243

The structure and function of cell membranes examined by atomic force microscopy and single-molecule force spectroscopy.

PubMed

Shan, Yuping; Wang, Hongda

2015-06-07

The cell membrane is one of the most complicated biological complexes, and long-term fierce debates regarding the cell membrane persist because of technical hurdles. With the rapid development of nanotechnology and single-molecule techniques, our understanding of cell membranes has substantially increased. Atomic force microscopy (AFM) has provided several unprecedented advances (e.g., high resolution, three-dimensional and in situ measurements) in the study of cell membranes and has been used to systematically dissect the membrane structure in situ from both sides of membranes; as a result, novel models of cell membranes have recently been proposed. This review summarizes the new progress regarding membrane structure using in situ AFM and single-molecule force spectroscopy (SMFS), which may shed light on the study of the structure and functions of cell membranes.

Molecular mechanisms of mechanotransduction in integrin-mediated cell-matrix adhesion

PubMed Central

Li, Zhenhai; Lee, Hyunjung; Zhu, Cheng

2016-01-01

Cell-matrix adhesion complexes are multi-protein structures linking the extracellular matrix (ECM) to the cytoskeleton. They are essential to both cell motility and function by bidirectionally sensing and transmitting mechanical and biochemical stimulations. Several types of cell-matrix adhesions have been identified and they share many key molecular components, such as integrins and actin-integrin linkers. Mechanochemical coupling between ECM molecules and the actin cytoskeleton has been observed from the single cell to the single molecule level and from immune cells to neuronal cells. However, the mechanisms underlying force regulation of integrin-mediated mechanotransduction still need to be elucidated. In this review article, we focus on integrin-mediated adhesions and discuss force regulation of cell-matrix adhesions and key adaptor molecules, three different force-dependent behaviors, and molecular mechanisms for mechanochemical coupling in force regulation. PMID:27720950

Signatures of van der Waals binding: A coupling-constant scaling analysis

NASA Astrophysics Data System (ADS)

Jiao, Yang; Schröder, Elsebeth; Hyldgaard, Per

2018-02-01

The van der Waals (vdW) density functional (vdW-DF) method [Rep. Prog. Phys. 78, 066501 (2015), 10.1088/0034-4885/78/6/066501] describes dispersion or vdW binding by tracking the effects of an electrodynamic coupling among pairs of electrons and their associated exchange-correlation holes. This is done in a nonlocal-correlation energy term Ecnl, which permits density functional theory calculation in the Kohn-Sham scheme. However, to map the nature of vdW forces in a fully interacting materials system, it is necessary to also account for associated kinetic-correlation energy effects. Here, we present a coupling-constant scaling analysis, which permits us to compute the kinetic-correlation energy Tcnl that is specific to the vdW-DF account of nonlocal correlations. We thus provide a more complete spatially resolved analysis of the electrodynamical-coupling nature of nonlocal-correlation binding, including vdW attraction, in both covalently and noncovalently bonded systems. We find that kinetic-correlation energy effects play a significant role in the account of vdW or dispersion interactions among molecules. Furthermore, our mapping shows that the total nonlocal-correlation binding is concentrated to pockets in the sparse electron distribution located between the material fragments.

Correlative Super-Resolution Microscopy: New Dimensions and New Opportunities.

PubMed

Hauser, Meghan; Wojcik, Michal; Kim, Doory; Mahmoudi, Morteza; Li, Wan; Xu, Ke

2017-06-14

Correlative microscopy, the integration of two or more microscopy techniques performed on the same sample, produces results that emphasize the strengths of each technique while offsetting their individual weaknesses. Light microscopy has historically been a central method in correlative microscopy due to its widespread availability, compatibility with hydrated and live biological samples, and excellent molecular specificity through fluorescence labeling. However, conventional light microscopy can only achieve a resolution of ∼300 nm, undercutting its advantages in correlations with higher-resolution methods. The rise of super-resolution microscopy (SRM) over the past decade has drastically improved the resolution of light microscopy to ∼10 nm, thus creating exciting new opportunities and challenges for correlative microscopy. Here we review how these challenges are addressed to effectively correlate SRM with other microscopy techniques, including light microscopy, electron microscopy, cryomicroscopy, atomic force microscopy, and various forms of spectroscopy. Though we emphasize biological studies, we also discuss the application of correlative SRM to materials characterization and single-molecule reactions. Finally, we point out current limitations and discuss possible future improvements and advances. We thus demonstrate how a correlative approach adds new dimensions of information and provides new opportunities in the fast-growing field of SRM.

A novel coarsening mechanism of droplets in immiscible fluid mixtures

NASA Astrophysics Data System (ADS)

Shimizu, Ryotaro; Tanaka, Hajime

2015-06-01

In our daily lives, after shaking a salad dressing, we see the coarsening of oil droplets suspended in vinegar. Such a demixing process is observed everywhere in nature and also of technological importance. For a case of high droplet density, domain coarsening proceeds with inter-droplet collisions and the resulting coalescence. This phenomenon has been explained primarily by the so-called Brownian-coagulation mechanism: stochastic thermal forces exerted by molecules induce random motion of individual droplets, causing accidental collisions and subsequent interface-tension-driven coalescence. Contrary to this, here we demonstrate that the droplet motion is not random, but hydrodynamically driven by the composition Marangoni force due to an interfacial tension gradient produced in each droplet as a consequence of composition correlation among droplets. This alters our physical understanding of droplet coarsening in immiscible liquid mixtures on a fundamental level.

On contribution of known atomic partial charges of protein backbone in electrostatic potential density maps.

PubMed

Wang, Jimin

2017-06-01

Partial charges of atoms in a molecule and electrostatic potential (ESP) density for that molecule are known to bear a strong correlation. In order to generate a set of point-field force field parameters for molecular dynamics, Kollman and coworkers have extracted atomic partial charges for each of all 20 amino acids using restrained partial charge-fitting procedures from theoretical ESP density obtained from condensed-state quantum mechanics. The magnitude of atomic partial charges for neutral peptide backbone they have obtained is similar to that of partial atomic charges for ionized carboxylate side chain atoms. In this study, the effect of these known atomic partial charges on ESP is examined using computer simulations and compared with the experimental ESP density recently obtained for proteins using electron microscopy. It is found that the observed ESP density maps are most consistent with the simulations that include atomic partial charges of protein backbone. Therefore, atomic partial charges are integral part of atomic properties in protein molecules and should be included in model refinement. © 2017 The Protein Society.

On contribution of known atomic partial charges of protein backbone in electrostatic potential density maps

PubMed Central

2017-01-01

Abstract Partial charges of atoms in a molecule and electrostatic potential (ESP) density for that molecule are known to bear a strong correlation. In order to generate a set of point‐field force field parameters for molecular dynamics, Kollman and coworkers have extracted atomic partial charges for each of all 20 amino acids using restrained partial charge‐fitting procedures from theoretical ESP density obtained from condensed‐state quantum mechanics. The magnitude of atomic partial charges for neutral peptide backbone they have obtained is similar to that of partial atomic charges for ionized carboxylate side chain atoms. In this study, the effect of these known atomic partial charges on ESP is examined using computer simulations and compared with the experimental ESP density recently obtained for proteins using electron microscopy. It is found that the observed ESP density maps are most consistent with the simulations that include atomic partial charges of protein backbone. Therefore, atomic partial charges are integral part of atomic properties in protein molecules and should be included in model refinement. PMID:28370507

Insights into the Interactions of Amino Acids and Peptides with Inorganic Materials Using Single-Molecule Force Spectroscopy.

PubMed

Das, Priyadip; Duanias-Assaf, Tal; Reches, Meital

2017-03-06

The interactions between proteins or peptides and inorganic materials lead to several interesting processes. For example, combining proteins with minerals leads to the formation of composite materials with unique properties. In addition, the undesirable process of biofouling is initiated by the adsorption of biomolecules, mainly proteins, on surfaces. This organic layer is an adhesion layer for bacteria and allows them to interact with the surface. Understanding the fundamental forces that govern the interactions at the organic-inorganic interface is therefore important for many areas of research and could lead to the design of new materials for optical, mechanical and biomedical applications. This paper demonstrates a single-molecule force spectroscopy technique that utilizes an AFM to measure the adhesion force between either peptides or amino acids and well-defined inorganic surfaces. This technique involves a protocol for attaching the biomolecule to the AFM tip through a covalent flexible linker and single-molecule force spectroscopy measurements by atomic force microscope. In addition, an analysis of these measurements is included.

Kinetics of molecular transitions with dynamic disorder in single-molecule pulling experiments

NASA Astrophysics Data System (ADS)

Zheng, Yue; Li, Ping; Zhao, Nanrong; Hou, Zhonghuai

2013-05-01

Macromolecular transitions are subject to large fluctuations of rate constant, termed as dynamic disorder. The individual or intrinsic transition rates and activation free energies can be extracted from single-molecule pulling experiments. Here we present a theoretical framework based on a generalized Langevin equation with fractional Gaussian noise and power-law memory kernel to study the kinetics of macromolecular transitions to address the effects of dynamic disorder on barrier-crossing kinetics under external pulling force. By using the Kramers' rate theory, we have calculated the fluctuating rate constant of molecular transition, as well as the experimentally accessible quantities such as the force-dependent mean lifetime, the rupture force distribution, and the speed-dependent mean rupture force. Particular attention is paid to the discrepancies between the kinetics with and without dynamic disorder. We demonstrate that these discrepancies show strong and nontrivial dependence on the external force or the pulling speed, as well as the barrier height of the potential of mean force. Our results suggest that dynamic disorder is an important factor that should be taken into account properly in accurate interpretations of single-molecule pulling experiments.

Synthesis, spectroscopic characterization and a comparative study of the corrosion inhibitive efficiency of an α-aminophosphonate and Schiff base derivatives: Experimental and theoretical investigations

NASA Astrophysics Data System (ADS)

Benbouguerra, Khalissa; Chafaa, Salah; Chafai, Nadjib; Mehri, Mouna; Moumeni, Ouahiba; Hellal, Abdelkader

2018-04-01

New α-aminophosphonate (α-APD) and Schiff base (E-NDPIMA) derivatives have been prepared and their structures ware proved by IR, UV-Vis, 1H, 13C and 31P NMR spectroscopy. Their inhibitive capacities on the XC48 carbon steel corrosion in 0.5 mol L-1 H2SO4 solution were explored by weight loss, Tafel polarization, electrochemical impedance spectroscopy (EIS) and atomic force microscope (AFM). Experimental results illustrate that the synthesized compounds are an effectives inhibitors and the adsorption of inhibitors molecules on the carbon steel surface obeys Langmuir adsorption isotherm. In addition, quantum chemical calculations performed with density function theory (DFT) method have been used to correlate the inhibition efficiency established experimentally. Also, the molecular dynamics simulations have been utilized to simulate the interactions between the inhibitors molecules and Fe (100) surface in aqueous solution.

Orientation-dependent energy level alignment and film growth of 2,7-diocty[1]benzothieno[3,2-b]benzothiophene (C8-BTBT) on HOPG

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lyu, Lu; Niu, Dongmei, E-mail: mayee@csu.edu.cnmailto; Xie, Haipeng

Combining ultraviolet photoemission spectroscopy, X-ray photoemission spectroscopy, atomic force microscopy, and X-ray diffraction measurements, we performed a systematic investigation on the correlation of energy level alignment, film growth, and molecular orientation of 2,7-diocty[1]benzothieno[3,2-b]benzothiophene (C8-BTBT) on highly oriented pyrolytic graphite. The molecules lie down in the first layer and then stand up from the second layer. The ionization potential shows a sharp decrease from the lying down region to the standing up region. When C8-BTBT molecules start standing up, unconventional energy level band-bending-like shifts are observed as the film thickness increases. These shifts are ascribed to gradual decreasing of the molecularmore » tilt angle about the substrate normal with the increasing film thickness.« less

Hydrophobic Hydration of Stimulus-Responsive Polyproteins Measured by Single Molecule Force Spectroscopy

NASA Astrophysics Data System (ADS)

Zauscher, Stefan

2007-03-01

We present a new procedure to reduce and analyze force-extension data obtained by single molecule force spectroscopy (SMFS). This approach allows, for the first time, to infer effects of solvent quality and minor changes in molecular architecture on molecular-elasticity of individual (bio)macromolecules. Specifically, we show how changes in the effective Kuhn segment length can be used to interpret the hydrophobic hydration behavior of elastin-like polypeptides (ELPs).Our results are intriguing as they suggest that SMFS in combination with our analysis procedure can be used to study the subtleties of polypeptide-water interactions on the single molecule level. We also report on the force-induced cis-trans isomerization of prolines, which are repeated every fifth residue in the main chain of ELPs. We present evidence for this mechanism by Monte Carlo simulations of the force-extension curves using an elastically coupled two-state system. Our results suggest that SMFS could be used to assay proline cis-trans isomerization in proteins and may thus have significant potential diagnostic utility.

Machine learning of accurate energy-conserving molecular force fields.

PubMed

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E; Poltavsky, Igor; Schütt, Kristof T; Müller, Klaus-Robert

2017-05-01

Using conservation of energy-a fundamental property of closed classical and quantum mechanical systems-we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol -1 for energies and 1 kcal mol -1 Å̊ -1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods.

Machine learning of accurate energy-conserving molecular force fields

PubMed Central

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E.; Poltavsky, Igor; Schütt, Kristof T.; Müller, Klaus-Robert

2017-01-01

Using conservation of energy—a fundamental property of closed classical and quantum mechanical systems—we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol−1 for energies and 1 kcal mol−1 Å̊−1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods. PMID:28508076

Towards force spectroscopy of single tip-link bonds

NASA Astrophysics Data System (ADS)

Koussa, Mounir A.; Sotomayor, Marcos; Wong, Wesley P.; Corey, David P.

2015-12-01

Inner-ear mechanotransduction relies on tip links, fine protein filaments made of cadherin-23 and protocadherin-15 that convey tension to mechanosensitive channels at the tips of hair-cell stereocilia. The tip-link cadherins are thought to form a heterotetrameric complex, with two cadherin-23 molecules forming the upper part of the filament and two protocadherin-15 molecules forming the lower end. The interaction between cadherin-23 and protocadherin-15 is mediated by their N-terminal tips. Missense mutations that modify the interaction interface impair binding and lead to deafness. Molecular dynamics simulations predict that the tip-link bond is mechanically strong enough to withstand forces in hair cells, but its experimentally determined strength is unknown. We have developed molecular tools to facilitate single-molecule force spectroscopy on the tip link bond. Self-assembling DNA nanoswitches are functionalized with the interacting tips of cadherin-23 and protocadherin-15 using the enzyme sortase under conditions that preserve protein function. These tip link nanoswitches are designed to provide a signature force-extension profile. This molecular signature should allow us to identify single-molecule rupture events in pulling experiments.

Exchange and correlation in positronium-molecule scattering

NASA Astrophysics Data System (ADS)

Fabrikant, I. I.; Wilde, R. S.

2018-05-01

Exchange and correlations play a particularly important role in positronium (Ps) collisions with atoms and molecules, since the static potential for Ps interaction with a neutral system is zero. Theoretical description of both effects is a very challenging task. In the present work we use the free-electron-gas model to describe exchange and correlations in Ps collisions with molecules similar to the approach widely used in the theory of electron-molecule collisions. The results for exchange and correlation energies are presented as functions of the Fermi momentum of the electron gas and the Ps incident energy. Using the Thomas-Fermi model, these functions can be converted into exchange and correlation potentials for Ps interaction with molecules as functions of the distance between the projectile and the target.

THE ROLE OF COMPETITION EFFECT IN THE SELF-ASSEMBLY STRUCTURE OF 3,5-DIPHENYLBENZOIC ACID AND 2,2‧:6‧,2″-TERPYRIDINE-4‧-CARBOXYLIC ACID ON Ag(110)

NASA Astrophysics Data System (ADS)

Hu, Yufen; Li, Wei; Lu, Yan; Wang, Zhongping; Leng, Xinli; Liao, Qinghua; Liu, Xiaoqing; Wang, Li

The self-assembly structures of 2,2‧:6‧,2‧‧-terpyridine-4‧-carboxylic acid (C16H11N3O2; YN) molecules and 3,5-diphenylbenzoic acid (C19H14O2; YC) molecules on Ag(110) surface have been investigated by scanning tunneling microscopy (STM) and Density Functional Theory (DFT) calculation. The YC molecules form two different well-organized structures due to the π-π stacking and dipole-dipole interactions. When three C atoms of YC molecules are replaced by three N atoms to form YN molecules, the main driving force to form ordered assembly structures of YN molecule is changed to metal-organic coordination bond and hydrogen bond. The dramatic changes of main driving force between YC/Ag(110) and YN/Ag(110) system demonstrate that the N atoms are apt to form metal-organic coordination bond and hydrogen bond but dipole-dipole interactions and π-π stacking are relative to C atoms. These findings further reveal that the optimization design of organic molecules could vary the main driving force and then lead to the change of the molecular self-assembly structures.

Opalescence in monoclonal antibody solutions and its correlation with intermolecular interactions in dilute and concentrated solutions.

PubMed

Raut, Ashlesha S; Kalonia, Devendra S

2015-04-01

Opalescence indicates physical instability of a formulation because of the presence of aggregates or liquid-liquid phase separation in solution and has been reported for monoclonal antibody (mAb) formulations. Increased solution opalescence can be attributed to attractive protein-protein interactions (PPIs). Techniques including light scattering, AUC, or membrane osmometry are routinely employed to measure PPIs in dilute solutions, whereas opalescence is seen at relatively higher concentrations, where both long- and short-range forces contribute to overall PPIs. The mAb molecule studied here shows a unique property of high opalescence because of liquid-liquid phase separation. In this study, opalescence measurements are correlated to PPIs measured in diluted and concentrated solutions using light scattering (kD ) and high-frequency rheology (G'), respectively. Charges on the molecules were calculated using zeta potential measurements. Results indicate that high opalescence and phase separation are a result of the attractive interactions in solution; however, the presence of attractive interactions do not always imply phase separation. Temperature dependence of opalescence suggests that thermodynamic contribution to opalescence is significant and Tcloud can be utilized as a potential tool to assess attractive interactions in solution. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Constrained-pairing mean-field theory. IV. Inclusion of corresponding pair constraints and connection to unrestricted Hartree-Fock theory.

PubMed

Tsuchimochi, Takashi; Henderson, Thomas M; Scuseria, Gustavo E; Savin, Andreas

2010-10-07

Our previously developed constrained-pairing mean-field theory (CPMFT) is shown to map onto an unrestricted Hartree-Fock (UHF) type method if one imposes a corresponding pair constraint to the correlation problem that forces occupation numbers to occur in pairs adding to one. In this new version, CPMFT has all the advantages of standard independent particle models (orbitals and orbital energies, to mention a few), yet unlike UHF, it can dissociate polyatomic molecules to the correct ground-state restricted open-shell Hartree-Fock atoms or fragments.

The lanthanide contraction beyond coordination chemistry

DOE PAGES

Ferru, Geoffroy; Reinhart, Benjamin; Bera, Mrinal K.; ...

2016-04-06

Lanthanide chemistry is dominated by the ‘lanthanide contraction’, which is conceptualized traditionally through coordination chemistry. Here we break this mold, presenting evidence that the lanthanide contraction manifests outside of the coordination sphere, influencing weak interactions between groups of molecules that drive mesoscale-assembly and emergent behavior in an amphiphile solution. Furthermore, changes in these weak interactions correlate with differences in lanthanide ion transport properties, suggesting new forces to leverage rare earth separation and refining. Our results show that the lanthanide contraction paradigm extends beyond the coordination sphere, influencing structure and properties usually associated with soft matter science.

The lanthanide contraction beyond coordination chemistry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ferru, Geoffroy; Reinhart, Benjamin; Bera, Mrinal K.

Lanthanide chemistry is dominated by the ‘lanthanide contraction’, which is conceptualized traditionally through coordination chemistry. Here we break this mold, presenting evidence that the lanthanide contraction manifests outside of the coordination sphere, influencing weak interactions between groups of molecules that drive mesoscale-assembly and emergent behavior in an amphiphile solution. Furthermore, changes in these weak interactions correlate with differences in lanthanide ion transport properties, suggesting new forces to leverage rare earth separation and refining. Our results show that the lanthanide contraction paradigm extends beyond the coordination sphere, influencing structure and properties usually associated with soft matter science.

[Interactions of DNA bases with individual water molecules. Molecular mechanics and quantum mechanics computation results vs. experimental data].

PubMed

Gonzalez, E; Lino, J; Deriabina, A; Herrera, J N F; Poltev, V I

2013-01-01

To elucidate details of the DNA-water interactions we performed the calculations and systemaitic search for minima of interaction energy of the systems consisting of one of DNA bases and one or two water molecules. The results of calculations using two force fields of molecular mechanics (MM) and correlated ab initio method MP2/6-31G(d, p) of quantum mechanics (QM) have been compared with one another and with experimental data. The calculations demonstrated a qualitative agreement between geometry characteristics of the most of local energy minima obtained via different methods. The deepest minima revealed by MM and QM methods correspond to water molecule position between two neighbor hydrophilic centers of the base and to the formation by water molecule of hydrogen bonds with them. Nevertheless, the relative depth of some minima and peculiarities of mutual water-base positions in' these minima depend on the method used. The analysis revealed insignificance of some differences in the results of calculations performed via different methods and the importance of other ones for the description of DNA hydration. The calculations via MM methods enable us to reproduce quantitatively all the experimental data on the enthalpies of complex formation of single water molecule with the set of mono-, di-, and trimethylated bases, as well as on water molecule locations near base hydrophilic atoms in the crystals of DNA duplex fragments, while some of these data cannot be rationalized by QM calculations.

Surface Biology of DNA by Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Hansma, Helen G.

2001-10-01

The atomic force microscope operates on surfaces. Since surfaces occupy much of the space in living organisms, surface biology is a valid and valuable form of biology that has been difficult to investigate in the past owing to a lack of good technology. Atomic force microscopy (AFM) of DNA has been used to investigate DNA condensation for gene therapy, DNA mapping and sizing, and a few applications to cancer research and to nanotechnology. Some of the most exciting new applications for atomic force microscopy of DNA involve pulling on single DNA molecules to obtain measurements of single-molecule mechanics and thermodynamics.

Motor-motor interactions in ensembles of muscle myosin: using theory to connect single molecule to ensemble measurements

NASA Astrophysics Data System (ADS)

Walcott, Sam

2013-03-01

Interactions between the proteins actin and myosin drive muscle contraction. Properties of a single myosin interacting with an actin filament are largely known, but a trillion myosins work together in muscle. We are interested in how single-molecule properties relate to ensemble function. Myosin's reaction rates depend on force, so ensemble models keep track of both molecular state and force on each molecule. These models make subtle predictions, e.g. that myosin, when part of an ensemble, moves actin faster than when isolated. This acceleration arises because forces between molecules speed reaction kinetics. Experiments support this prediction and allow parameter estimates. A model based on this analysis describes experiments from single molecule to ensemble. In vivo, actin is regulated by proteins that, when present, cause the binding of one myosin to speed the binding of its neighbors; binding becomes cooperative. Although such interactions preclude the mean field approximation, a set of linear ODEs describes these ensembles under simplified experimental conditions. In these experiments cooperativity is strong, with the binding of one molecule affecting ten neighbors on either side. We progress toward a description of myosin ensembles under physiological conditions.

Molecular hydrogen solvated in water – A computational study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Śmiechowski, Maciej, E-mail: Maciej.Smiechowski@pg.gda.pl

2015-12-28

The aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H{sub 2} molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the H{sub 2} molecule without major structural distortions and two-dimensional, radial-angular distribution functions indicate that as opposed to strictly tangential, the orientation of these water molecules is such that the solute is solvated with one of the free electronmore » pairs of H{sub 2}O. The calculated self-diffusion coefficient of H{sub 2}(aq) agrees very well with experimental results and the time dependence of mean square displacement suggests the presence of caging on a time scale corresponding to hydrogen bond network vibrations in liquid water. Orientational correlation function of H{sub 2} experiences an extremely short-scale decay, making the H{sub 2}–H{sub 2}O interaction potential essentially isotropic by virtue of rotational averaging. The inclusion of explicit polarizability in the model allows for the calculation of Raman spectra that agree very well with available experimental data on H{sub 2}(aq) under differing pressure conditions, including accurate reproduction of the experimentally noted trends with solute pressure or concentration.« less

Reconstructing Folding Energy Landscapes by Single-Molecule Force Spectroscopy

PubMed Central

Woodside, Michael T.; Block, Steven M.

2015-01-01

Folding may be described conceptually in terms of trajectories over a landscape of free energies corresponding to different molecular configurations. In practice, energy landscapes can be difficult to measure. Single-molecule force spectroscopy (SMFS), whereby structural changes are monitored in molecules subjected to controlled forces, has emerged as a powerful tool for probing energy landscapes. We summarize methods for reconstructing landscapes from force spectroscopy measurements under both equilibrium and nonequilibrium conditions. Other complementary, but technically less demanding, methods provide a model-dependent characterization of key features of the landscape. Once reconstructed, energy landscapes can be used to study critical folding parameters, such as the characteristic transition times required for structural changes and the effective diffusion coefficient setting the timescale for motions over the landscape. We also discuss issues that complicate measurement and interpretation, including the possibility of multiple states or pathways and the effects of projecting multiple dimensions onto a single coordinate. PMID:24895850

Chemical bond imaging using higher eigenmodes of tuning fork sensors in atomic force microscopy

NASA Astrophysics Data System (ADS)

Ebeling, Daniel; Zhong, Qigang; Ahles, Sebastian; Chi, Lifeng; Wegner, Hermann A.; Schirmeisen, André

2017-05-01

We demonstrate the ability of resolving the chemical structure of single organic molecules using non-contact atomic force microscopy with higher normal eigenmodes of quartz tuning fork sensors. In order to achieve submolecular resolution, CO-functionalized tips at low temperatures are used. The tuning fork sensors are operated in ultrahigh vacuum in the frequency modulation mode by exciting either their first or second eigenmode. Despite the high effective spring constant of the second eigenmode (on the order of several tens of kN/m), the force sensitivity is sufficiently high to achieve atomic resolution above the organic molecules. This is observed for two different tuning fork sensors with different tip geometries (small tip vs. large tip). These results represent an important step towards resolving the chemical structure of single molecules with multifrequency atomic force microscopy techniques where two or more eigenmodes are driven simultaneously.

'Single molecule': theory and experiments, an introduction

PubMed Central

2013-01-01

At scales below micrometers, Brownian motion dictates most of the behaviors. The simple observation of a colloid is striking: a permanent and random motion is seen, whereas inertial forces play a negligible role. This Physics, where velocity is proportional to force, has opened new horizons in biology. The random feature is challenged in living systems where some proteins - molecular motors - have a directed motion whereas their passive behaviors of colloid should lead to a Brownian motion. Individual proteins, polymers of living matter such as DNA, RNA, actin or microtubules, molecular motors, all these objects can be viewed as chains of colloids. They are submitted to shocks from molecules of the solvent. Shapes taken by these biopolymers or dynamics imposed by motors can be measured and modeled from single molecules to their collective effects. Thanks to the development of experimental methods such as optical tweezers, Atomic Force Microscope (AFM), micropipettes, and quantitative fluorescence (such as Förster Resonance Energy Transfer, FRET), it is possible to manipulate these individual biomolecules in an unprecedented manner: experiments allow to probe the validity of models; and a new Physics has thereby emerged with original biological insights. Theories based on statistical mechanics are needed to explain behaviors of these systems. When force-extension curves of these molecules are extracted, the curves need to be fitted with models that predict the deformation of free objects or submitted to a force. When velocity of motors is altered, a quantitative analysis is required to explain the motions of individual molecules under external forces. This lecture will give some elements of introduction to the lectures of the session 'Nanophysics for Molecular Biology'. PMID:24565227

Force Induced Globule-to-Coil Transition of Single Polymer Chains.

NASA Astrophysics Data System (ADS)

Gunari, Nikhil; Walker, Gilbert

2008-03-01

Force induced structural transitions of individual homopolymer chains have been studied in different solvent conditions using single molecule force spectroscopy. Single molecule mechanics in the ``fly-fishing'' mode showed a first-order like transition for polystyrene (PS) in water exhibiting a characteristic three regime force extension curve. In contrast, poly methylmethacrylate (PMMA) showed a characteristic saw-tooth pattern reminiscent of multidomain disassembly behavior similar to that seen in modular protein mechanics. The plateau force for PS and the saw-tooth pattern for PMMA disappear when measured in aqueous guanidine hydrochloride solution and in other non-solvents showing that the characteristic deformational behavior observed for the two polymers in water may be due to hydrophobic interactions .

Determination of thermodynamics and kinetics of RNA reactions by force

PubMed Central

Tinoco, Ignacio; Li, Pan T. X.; Bustamante, Carlos

2008-01-01

Single-molecule methods have made it possible to apply force to an individual RNA molecule. Two beads are attached to the RNA; one is on a micropipette, the other is in a laser trap. The force on the RNA and the distance between the beads are measured. Force can change the equilibrium and the rate of any reaction in which the product has a different extension from the reactant. This review describes use of laser tweezers to measure thermodynamics and kinetics of unfolding/refolding RNA. For a reversible reaction the work directly provides the free energy; for irreversible reactions the free energy is obtained from the distribution of work values. The rate constants for the folding and unfolding reactions can be measured by several methods. The effect of pulling rate on the distribution of force-unfolding values leads to rate constants for unfolding. Hopping of the RNA between folded and unfolded states at constant force provides both unfolding and folding rates. Force-jumps and force-drops, similar to the temperature jump method, provide direct measurement of reaction rates over a wide range of forces. The advantages of applying force and using single-molecule methods are discussed. These methods, for example, allow reactions to be studied in non-denaturing solvents at physiological temperatures; they also simplify analysis of kinetic mechanisms because only one intermediate at a time is present. Unfolding of RNA in biological cells by helicases, or ribosomes, has similarities to unfolding by force. PMID:17040613

Water's role in the force-induced unfolding of ubiquitin.

PubMed

Li, Jingyuan; Fernandez, Julio M; Berne, B J

2010-11-09

In atomic force spectroscopic studies of the elastomeric protein ubiquitin, the β-strands 1-5 serve as the force clamp. Simulations show how the rupture force in the force-induced unfolding depends on the kinetics of water molecule insertion into positions where they can eventually form hydrogen bonding bridges with the backbone hydrogen bonds in the force-clamp region. The intrusion of water into this region is slowed down by the hydrophobic shielding effect of carbonaceous groups on the surface residues of β-strands 1-5, which thereby regulates water insertion prior to hydrogen bond breakage. The experiments show that the unfolding of the mechanically stressed protein is nonexponential due to static disorder. Our simulations show that different numbers and/or locations of bridging water molecules give rise to a long-lived distribution of transition states and static disorder. We find that slowing down the translational (not rotational) motions of the water molecules by increasing the mass of their oxygen atoms, which leaves the force field and thereby the equilibrium structure of the solvent unchanged, increases the average rupture force; however, the early stages of the force versus time behavior are very similar for our "normal" and fictitious "heavy" water models. Finally, we construct six mutant systems to regulate the hydrophobic shielding effect of the surface residues in the force-clamp region. The mutations in the two termini of β-sheets 1-5 are found to determine a preference for different unfolding pathways and change mutant's average rupture force.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maaloum, M.; Muller, P.; Beker, A-F.

Almost two decades ago, measurements of force versus extension on isolated double-stranded DNA molecules revealed a force plateau. This unusual stretching phenomenon in DNA suggests that the long molecules may be extended from the usual B form into a new conformation. Different models have been proposed to describe the nature of DNA in its stretched form, S-DNA. Using atomic force microscopy combined with a molecular combing method, we identified the structure of {lambda}-phage DNA for different stretching values. We provide strong evidence for the existence of a first-order transition between B form and S form. Beyond a certain extension ofmore » the natural length, DNA molecules adopt a new double-helix conformation characterized by a diameter of 1.2 nm and a helical pitch of18 nm.« less

Intermolecular artifacts in probe microscope images of C60 assemblies

NASA Astrophysics Data System (ADS)

Jarvis, Samuel Paul; Rashid, Mohammad Abdur; Sweetman, Adam; Leaf, Jeremy; Taylor, Simon; Moriarty, Philip; Dunn, Janette

2015-12-01

Claims that dynamic force microscopy has the capability to resolve intermolecular bonds in real space continue to be vigorously debated. To date, studies have been restricted to planar molecular assemblies with small separations between neighboring molecules. Here we report the observation of intermolecular artifacts over much larger distances in 2D assemblies of C60 molecules, with compelling evidence that in our case the tip apex is terminated by a C60 molecule (rather than the CO termination typically exploited in ultrahigh resolution force microscopy). The complete absence of directional interactions such as hydrogen or halogen bonding, the nonplanar structure of C60, and the fullerene termination of the tip apex in our case highlight that intermolecular artifacts are ubiquitous in dynamic force microscopy.

Electromagnetic torque tweezers: a versatile approach for measurement of single-molecule twist and torque.

PubMed

Janssen, Xander J A; Lipfert, Jan; Jager, Tessa; Daudey, Renier; Beekman, Jaap; Dekker, Nynke H

2012-07-11

The well-established single-molecule force-spectroscopy techniques have recently been complemented by methods that can measure torque and twist directly, notably magnetic torque tweezers and the optical torque wrench. A limitation of the current torque measurement schemes is the intrinsic coupling between the force and torque degrees of freedom. Here we present electromagnetic torque tweezers (eMTT) that combine permanent and electromagnets to enable independent control of the force and torsional trap stiffness for sensitive measurements of single molecule torque and twist. Using the eMTT, we demonstrate sensitive torque measurements on tethered DNA molecules from simple tracking of the beads' (x,y)-position, obviating the need for any angular tracking algorithms or markers. Employing the eMTT for high-resolution torque measurements, we experimentally confirm the theoretically predicted torque overshoot at the DNA buckling transition in high salt conditions. We envision that the flexibility and control afforded by the eMTT will enable a range of new torque and twist measurement schemes from single-molecules to living cells.

Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing

PubMed Central

Vanommeslaeghe, K.; MacKerell, A. D.

2012-01-01

Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug-like molecules alone or interacting with biological systems. In simulations involving biological macromolecules, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matching general (organic) force field. In order to apply these general force fields to an arbitrary drug-like molecule, functionality for assignment of atom types, parameters and charges is required. In the present article, which is part I of a series of two, we present the algorithms for bond perception and atom typing for the CHARMM General Force Field (CGenFF). The CGenFF atom typer first associates attributes to the atoms and bonds in a molecule, such as valence, bond order, and ring membership among others. Of note are a number of features that are specifically required for CGenFF. This information is then used by the atom typing routine to assign CGenFF atom types based on a programmable decision tree. This allows for straightforward implementation of CGenFF’s complicated atom typing rules and for equally straightforward updating of the atom typing scheme as the force field grows. The presented atom typer was validated by assigning correct atom types on 477 model compounds including in the training set as well as 126 test-set molecules that were constructed to specifically verify its different components. The program may be utilized via an online implementation at https://www.paramchem.org/. PMID:23146088

Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing.

PubMed

Vanommeslaeghe, K; MacKerell, A D

2012-12-21

Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug-like molecules alone or interacting with biological systems. In simulations involving biological macromolecules, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matching general (organic) force field. In order to apply these general force fields to an arbitrary drug-like molecule, functionality for assignment of atom types, parameters, and charges is required. In the present article, which is part I of a series of two, we present the algorithms for bond perception and atom typing for the CHARMM General Force Field (CGenFF). The CGenFF atom typer first associates attributes to the atoms and bonds in a molecule, such as valence, bond order, and ring membership among others. Of note are a number of features that are specifically required for CGenFF. This information is then used by the atom typing routine to assign CGenFF atom types based on a programmable decision tree. This allows for straightforward implementation of CGenFF's complicated atom typing rules and for equally straightforward updating of the atom typing scheme as the force field grows. The presented atom typer was validated by assigning correct atom types on 477 model compounds including in the training set as well as 126 test-set molecules that were constructed to specifically verify its different components. The program may be utilized via an online implementation at https://www.paramchem.org/ .

β-connectin studies by small-angle x-ray scattering and single-molecule force spectroscopy by atomic force microscopy

NASA Astrophysics Data System (ADS)

Marchetti, S.; Sbrana, F.; Toscano, A.; Fratini, E.; Carlà, M.; Vassalli, M.; Tiribilli, B.; Pacini, A.; Gambi, C. M. C.

2011-05-01

The three-dimensional structure and the mechanical properties of a β-connectin fragment from human cardiac muscle, belonging to the I band, from I27 to I34, were investigated by small-angle x-ray scattering (SAXS) and single-molecule force spectroscopy (SMFS). This molecule presents an entropic elasticity behavior, associated to globular domain unfolding, that has been widely studied in the last 10 years. In addition, atomic force microscopy based SMFS experiments suggest that this molecule has an additional elastic regime, for low forces, probably associated to tertiary structure remodeling. From a structural point of view, this behavior is a mark of the fact that the eight domains in the I27-I34 fragment are not independent and they organize in solution, assuming a well-defined three-dimensional structure. This hypothesis has been confirmed by SAXS scattering, both on a diluted and a concentrated sample. Two different models were used to fit the SAXS curves: one assuming a globular shape and one corresponding to an elongated conformation, both coupled with a Coulomb repulsion potential to take into account the protein-protein interaction. Due to the predominance of the structure factor, the effective shape of the protein in solution could not be clearly disclosed. By performing SMFS by atomic force microscopy, mechanical unfolding properties were investigated. Typical sawtooth profiles were obtained and the rupture force of each unfolding domain was estimated. By fitting a wormlike chain model to each peak of the sawtooth profile, the entropic elasticity of octamer was described.

Bronchial biopsy evidence for leukocyte infiltration and upregulation of leukocyte-endothelial cell adhesion molecules 6 hours after local allergen challenge of sensitized asthmatic airways.

PubMed Central

Montefort, S; Gratziou, C; Goulding, D; Polosa, R; Haskard, D O; Howarth, P H; Holgate, S T; Carroll, M P

1994-01-01

We have examined the mucosal changes occurring in bronchial biopsies from six atopic asthmatics 5-6 h after local endobronchial allergen challenge and compared them with biopsies from saline-challenged segments from the same subjects at the same time point. All the subjects developed localized bronchoconstriction in the allergen-challenged segment and had a decrease in forced expiratory volume in 1 s (FEV1) (P < 0.01) and a decrease in their methacholine provocative concentration of agonist required to reduce FEV1 from baseline by 20% (P < 0.05) 24 h postchallenge. At 6 h we observed an increase in neutrophils (P = 0.03), eosinophils (P = 0.025), mast cells (P = 0.03), and CD3+ lymphocytes (P = 0.025), but not in CD4+ or CD8+ lymphocyte counts. We also detected an increase in endothelial intercellular adhesion molecule type 1 (P < 0.05) and E-selectin (P < 0.005), but not vascular cell adhesion molecule type 1 expression with a correlative increase in submucosal and epithelial LFA+ leucocytes (P < 0.01). Thus, in sensitized asthmatics, local endobronchial allergen instillation leads to an increased inflammatory cell infiltrate of the airway mucosa that involves upregulation of specific adhesion molecules expressed on the microvasculature. Images PMID:7512980

Modeling single molecule junction mechanics as a probe of interface bonding

NASA Astrophysics Data System (ADS)

Hybertsen, Mark S.

2017-03-01

Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of an ensemble of nanoscale junction structures. This paper focuses on the relationship between the measured force extension characteristics including bond rupture and the properties of the interface bonds in the junction. A set of exemplary model junction structures has been analyzed using density functional theory based calculations to simulate the adiabatic potential surface that governs the junction elongation. The junction structures include representative molecules that bond to the electrodes through amine, methylsulfide, and pyridine links. The force extension characteristics are shown to be most effectively analyzed in a scaled form with maximum sustainable force and the distance between the force zero and force maximum as scale factors. Widely used, two parameter models for chemical bond potential energy versus bond length are found to be nearly identical in scaled form. Furthermore, they fit well to the present calculations of N-Au and S-Au donor-acceptor bonds, provided no other degrees of freedom are allowed to relax. Examination of the reduced problem of a single interface, but including relaxation of atoms proximal to the interface bond, shows that a single-bond potential form renormalized by an effective harmonic potential in series fits well to the calculated results. This allows relatively accurate extraction of the interface bond energy. Analysis of full junction models shows cooperative effects that go beyond the mechanical series inclusion of the second bond in the junction, the spectator bond that does not rupture. Calculations for a series of diaminoalkanes as a function of molecule length indicate that the most important cooperative effect is due to the interactions between the dipoles induced by the donor-acceptor bond formation at the junction interfaces. The force extension characteristic of longer molecules such as diaminooctane, where the dipole interaction effects drop to a negligible level, accurately fit to the renormalized single-bond potential form. The results suggest that measured force extension characteristics for single molecule junctions could be analyzed with a modified potential form that accounts for the energy stored in deformable mechanical components in series.

Modeling single molecule junction mechanics as a probe of interface bonding

DOE PAGES

Hybertsen, Mark S.

2017-03-07

Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of an ensemble of nanoscale junction structures. This paper focuses on the relationship between the measured force extension characteristics including bond rupture and the properties of the interface bonds in the junction. We analyzed a set of exemplary model junction structures using density functional theory based calculations to simulate the adiabatic potential surface that governs the junction elongation. The junction structures include representative molecules that bond tomore » the electrodes through amine, methylsulfide, and pyridine links. The force extension characteristics are shown to be most effectively analyzed in a scaled form with maximum sustainable force and the distance between the force zero and force maximum as scale factors. Widely used, two parameter models for chemical bond potential energy versus bond length are found to be nearly identical in scaled form. Furthermore, they fit well to the present calculations of N–Au and S–Au donor-acceptor bonds, provided no other degrees of freedom are allowed to relax. Examination of the reduced problem of a single interface, but including relaxation of atoms proximal to the interface bond, shows that a single-bond potential form renormalized by an effective harmonic potential in series fits well to the calculated results. This, then, allows relatively accurate extraction of the interface bond energy. Analysis of full junction models shows cooperative effects that go beyond the mechanical series inclusion of the second bond in the junction, the spectator bond that does not rupture. Calculations for a series of diaminoalkanes as a function of molecule length indicate that the most important cooperative effect is due to the interactions between the dipoles induced by the donor-acceptor bond formation at the junction interfaces. The force extension characteristic of longer molecules such as diaminooctane, where the dipole interaction effects drop to a negligible level, accurately fit to the renormalized single-bond potential form. Our results suggest that measured force extension characteristics for single molecule junctions could be analyzed with a modified potential form that accounts for the energy stored in deformable mechanical components in series.« less

Modeling single molecule junction mechanics as a probe of interface bonding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hybertsen, Mark S.

Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of an ensemble of nanoscale junction structures. This paper focuses on the relationship between the measured force extension characteristics including bond rupture and the properties of the interface bonds in the junction. We analyzed a set of exemplary model junction structures using density functional theory based calculations to simulate the adiabatic potential surface that governs the junction elongation. The junction structures include representative molecules that bond tomore » the electrodes through amine, methylsulfide, and pyridine links. The force extension characteristics are shown to be most effectively analyzed in a scaled form with maximum sustainable force and the distance between the force zero and force maximum as scale factors. Widely used, two parameter models for chemical bond potential energy versus bond length are found to be nearly identical in scaled form. Furthermore, they fit well to the present calculations of N–Au and S–Au donor-acceptor bonds, provided no other degrees of freedom are allowed to relax. Examination of the reduced problem of a single interface, but including relaxation of atoms proximal to the interface bond, shows that a single-bond potential form renormalized by an effective harmonic potential in series fits well to the calculated results. This, then, allows relatively accurate extraction of the interface bond energy. Analysis of full junction models shows cooperative effects that go beyond the mechanical series inclusion of the second bond in the junction, the spectator bond that does not rupture. Calculations for a series of diaminoalkanes as a function of molecule length indicate that the most important cooperative effect is due to the interactions between the dipoles induced by the donor-acceptor bond formation at the junction interfaces. The force extension characteristic of longer molecules such as diaminooctane, where the dipole interaction effects drop to a negligible level, accurately fit to the renormalized single-bond potential form. Our results suggest that measured force extension characteristics for single molecule junctions could be analyzed with a modified potential form that accounts for the energy stored in deformable mechanical components in series.« less

Atomic force microscope characterization of self-assembly behaviors of cyclo[8] pyrrole on solid substrates

NASA Astrophysics Data System (ADS)

Xu, Hai; Zhao, Siqi; Xiong, Xiang; Jiang, Jinzhi; Xu, Wei; Zhu, Daoben; Zhang, Yi; Liang, Wenjie; Cai, Jianfeng

2017-04-01

Cyclo [8] pyrrole (CP) is a porphyrin analogue containing eight α-conjugated pyrrole units which are arranged in a nearly coplanar conformation. The π-π interactions between CP molecules lead to regular aggregations through a solution casting process. Using tapping mode atomic force microscope (AFM), we investigated the morphology of self-assembled aggregates formed by deposition of different CP solutions on different substrates. We found that in the n-butanol solution, nanofibrous structures could be formed on the silicon or mica surface. Interestingly, on the highly oriented pyrolytic graphite (HOPG) surface, or silicon and mica surface with a toluene solution, only irregular spherical structures were identified. The difference in the nanomorphology may be attributed to distinct interactions between molecule-molecule, molecule-solvent and molecule-substrate.

Mechanism underlying bioinertness of self-assembled monolayers of oligo(ethyleneglycol)-terminated alkanethiols on gold: protein adsorption, platelet adhesion, and surface forces.

PubMed

Hayashi, Tomohiro; Tanaka, Yusaku; Koide, Yuki; Tanaka, Masaru; Hara, Masahiko

2012-08-07

The mechanism underlying the bioinertness of the self-assembled monolayers of oligo(ethylene glycol)-terminated alkanethiol (OEG-SAM) was investigated with protein adsorption experiments, platelet adhesion tests, and surface force measurements with an atomic force microscope (AFM). In this work, we performed systematic analysis with SAMs having various terminal groups (-OEG, -OH, -COOH, -NH(2), and -CH(3)). The results of the protein adsorption experiment by the quartz crystal microbalance (QCM) method suggested that having one EG unit and the neutrality of total charges of the terminal groups are essential for protein-resistance. In particular, QCM with energy dissipation analyses indicated that proteins absorb onto the OEG-SAM via a very weak interaction compared with other SAMs. Contrary to the protein resistance, at least three EG units as well as the charge neutrality of the SAM are found to be required for anti-platelet adhesion. When the identical SAMs were formed on both AFM probe and substrate, our force measurements revealed that only the OEG-SAMs possessing more than two EG units showed strong repulsion in the range of 4 to 6 nm. In addition, we found that the SAMs with other terminal groups did not exhibit such repulsion. The repulsion between OEG-SAMs was always observed independent of solution conditions [NaCl concentration (between 0 and 1 M) and pH (between 3 and 11)] and was not observed in solution mixed with ethanol, which disrupts the three-dimensional network of the water molecules. We therefore concluded that the repulsion originated from structured interfacial water molecules. Considering the correlation between the above results, we propose that the layer of the structured interfacial water with a thickness of 2 to 3 nm (half of the range of the repulsion observed in the surface force measurements) plays an important role in deterring proteins and platelets from adsorption or adhesion.

Blind Predictions of DNA and RNA Tweezers Experiments with Force and Torque

PubMed Central

Chou, Fang-Chieh; Lipfert, Jan; Das, Rhiju

2014-01-01

Single-molecule tweezers measurements of double-stranded nucleic acids (dsDNA and dsRNA) provide unprecedented opportunities to dissect how these fundamental molecules respond to forces and torques analogous to those applied by topoisomerases, viral capsids, and other biological partners. However, tweezers data are still most commonly interpreted post facto in the framework of simple analytical models. Testing falsifiable predictions of state-of-the-art nucleic acid models would be more illuminating but has not been performed. Here we describe a blind challenge in which numerical predictions of nucleic acid mechanical properties were compared to experimental data obtained recently for dsRNA under applied force and torque. The predictions were enabled by the HelixMC package, first presented in this paper. HelixMC advances crystallography-derived base-pair level models (BPLMs) to simulate kilobase-length dsDNAs and dsRNAs under external forces and torques, including their global linking numbers. These calculations recovered the experimental bending persistence length of dsRNA within the error of the simulations and accurately predicted that dsRNA's “spring-like” conformation would give a two-fold decrease of stretch modulus relative to dsDNA. Further blind predictions of helix torsional properties, however, exposed inaccuracies in current BPLM theory, including three-fold discrepancies in torsional persistence length at the high force limit and the incorrect sign of dsRNA link-extension (twist-stretch) coupling. Beyond these experiments, HelixMC predicted that ‘nucleosome-excluding’ poly(A)/poly(T) is at least two-fold stiffer than random-sequence dsDNA in bending, stretching, and torsional behaviors; Z-DNA to be at least three-fold stiffer than random-sequence dsDNA, with a near-zero link-extension coupling; and non-negligible effects from base pair step correlations. We propose that experimentally testing these predictions should be powerful next steps for understanding the flexibility of dsDNA and dsRNA in sequence contexts and under mechanical stresses relevant to their biology. PMID:25102226

Atomic force microscopy investigation of growth process of organic TCNQ aggregates on SiO2 and mica substrates

NASA Astrophysics Data System (ADS)

Huan, Qing; Hu, Hao; Pan, Li-Da; Xiao, Jiang; Du, Shi-Xuan; Gao, Hong-Jun

2010-08-01

Deposition patterns of tetracyanoquinodimethane (TCNQ) molecules on different surfaces are investigated by atomic force microscopy. A homemade physical vapour deposition system allows the better control of molecule deposition. Taking advantage of this system, we investigate TCNQ thin film growth on both SiO2 and mica surfaces. It is found that dense island patterns form at a high deposition rate, and a unique seahorse-like pattern forms at a low deposition rate. Growth patterns on different substrates suggest that the fractal pattern formation is dominated by molecule-molecule interaction. Finally, a phenomenal “two-branch" model is proposed to simulate the growth process of the seahorse pattern.

Gas density effect on dropsize of simulated fuel sprays

NASA Technical Reports Server (NTRS)

Ingebo, Robert D.

1989-01-01

Two-phase flow in pneumatic two-fluid fuel nozzles was investigated experimentally to determine the effect of atomizing-gas density and gas mass-flux on liquid-jet breakup in sonic-velocity gas-flow. Dropsize data were obtained for the following atomizing-gases: nitrogen; argon; carbon dioxide; and helium. They were selected to cover a gas molecular-weight range of 4 to 44. Atomizing-gas mass-flux ranged from 6 to 50 g/sq cm-sec and four differently sized two-fluid fuel nozzles were used having orifice diameters that varied from 0.32 to 0.56 cm. The ratio of liquid-jet diameter to SMD, D sub o/D sub 32, was correlated with aerodynamic and liquid-surface forces based on the product of the Weber and Reynolds number, We*Re, and gas-to-liquid density ratio, rho sub g/rho sub l. To correlate spray dropsize with breakup forces produced by using different atomizing-gases, a new molecular-scale dimensionless group was derived. The derived dimensionless group was used to obtain an expression for the ratio of liquid-jet diameter to SMD, D sub o/D sub 32. The mathematical expression of this phenomenon incorporates the product of the Weber and Reynolds number, liquid viscosity, surface tension, acoustic gas velocity, the RMS velocity of gas molecules, the acceleration of gas molecules due to gravity, and gas viscosity. The mathematical expression encompassing these parameters agrees well with the atomization theory for liquid-jet breakup in high velocity gas flow. Also, it was found that at the same gas mass-flux, helium was considerably more effective than nitrogen in producing small droplet sprays with SMD's in the order of 5 micrometers.

A Simple Bioconjugate Attachment Protocol for Use in Single Molecule Force Spectroscopy Experiments Based on Mixed Self-Assembled Monolayers

PubMed Central

Attwood, Simon J.; Simpson, Anna M. C.; Stone, Rachael; Hamaia, SamirW.; Roy, Debdulal; Farndale, RichardW.; Ouberai, Myriam; Welland, Mark E.

2012-01-01

Single molecule force spectroscopy is a technique that can be used to probe the interaction force between individual biomolecular species. We focus our attention on the tip and sample coupling chemistry, which is crucial to these experiments. We utilised a novel approach of mixed self-assembled monolayers of alkanethiols in conjunction with a heterobifunctional crosslinker. The effectiveness of the protocol is demonstrated by probing the biotin-avidin interaction. We measured unbinding forces comparable to previously reported values measured at similar loading rates. Specificity tests also demonstrated a significant decrease in recognition after blocking with free avidin. PMID:23202965

Integrated magnetic tweezers and single-molecule FRET for investigating the mechanical properties of nucleic acid.

PubMed

Long, Xi; Parks, Joseph W; Stone, Michael D

2016-08-01

Many enzymes promote structural changes in their nucleic acid substrates via application of piconewton forces over nanometer length scales. Magnetic tweezers (MT) is a single molecule force spectroscopy method widely used for studying the energetics of such mechanical processes. MT permits stable application of a wide range of forces and torques over long time scales with nanometer spatial resolution. However, in any force spectroscopy experiment, the ability to monitor structural changes in nucleic acids with nanometer sensitivity requires the system of interest to be held under high degrees of tension to improve signal to noise. This limitation prohibits measurement of structural changes within nucleic acids under physiologically relevant conditions of low stretching forces. To overcome this challenge, researchers have integrated a spatially sensitive fluorescence spectroscopy method, single molecule-FRET, with MT to allow simultaneous observation and manipulation of nanoscale structural transitions over a wide range of forces. Here, we describe a method for using this hybrid instrument to analyze the mechanical properties of nucleic acids. We expect that this method for analysis of nucleic acid structure will be easily adapted for experiments aiming to interrogate the mechanical responses of other biological macromolecules. Copyright © 2016 Elsevier Inc. All rights reserved.

Direct Force Measurements of Receptor-Ligand Interactions on Living Cells

NASA Astrophysics Data System (ADS)

Eibl, Robert H.

The characterization of cell adhesion between two living cells at the level of single receptor-ligand bonds is an experimental challenge. This chapter describes how the extremely sensitive method of atomic force microscopy (AFM) based force spectroscopy can be applied to living cells in order to probe for cell-to-cell or cell-to-substrate interactions mediated by single pairs of adhesion receptors. In addition, it is outlined how single-molecule AFM force spectroscopy can be used to detect physiologic changes of an adhesion receptor in a living cell. This force spectroscopy allows us to detect in living cells rapidly changing, chemokine SDF-1 triggered activation states of single VLA-4 receptors. This recently developed AFM application will allow for the detailed investigation of the integrin-chemokine crosstalk of integrin activation mechanisms and on how other adhesion receptors are modulated in health and disease. As adhesion molecules, living cells and even bacteria can be studied by single-molecule AFM force spectroscopy, this method is set to become a powerful tool that can not only be used in biophysics, but in cell biology as well as in immunology and cancer research.

Integrated magnetic tweezers and single-molecule FRET for investigating the mechanical properties of nucleic acid

PubMed Central

Long, Xi; Parks, Joseph W.; Stone, Michael D.

2017-01-01

Many enzymes promote structural changes in their nucleic acid substrates via application of piconewton forces over nanometer length scales. Magnetic tweezers (MT) is a single molecule force spectroscopy method widely used for studying the energetics of such mechanical processes. MT permits stable application of a wide range of forces and torques over long time scales with nanometer spatial resolution. However, in any force spectroscopy experiment, the ability to monitor structural changes in nucleic acids with nanometer sensitivity requires the system of interest to be held under high degrees of tension to improve signal to noise. This limitation prohibits measurement of structural changes within nucleic acids under physiologically relevant conditions of low stretching forces. To overcome this challenge, researchers have integrated a spatially sensitive fluorescence spectroscopy method, single molecule-FRET, with MT to allow simultaneous observation and manipulation of nanoscale structural transitions over a wide range of forces. Here, we describe a method for using this hybrid instrument to analyze the mechanical properties of nucleic acids. We expect that this method for analysis of nucleic acid structure will be easily adapted for experiments aiming to interrogate the mechanical responses of other biological macromolecules. PMID:27320203

Transition paths in single-molecule force spectroscopy

NASA Astrophysics Data System (ADS)

Cossio, Pilar; Hummer, Gerhard; Szabo, Attila

2018-03-01

In a typical single-molecule force spectroscopy experiment, the ends of the molecule of interest are connected by long polymer linkers to a pair of mesoscopic beads trapped in the focus of two laser beams. At constant force load, the total extension, i.e., the end-to-end distance of the molecule plus linkers, is measured as a function of time. In the simplest systems, the measured extension fluctuates about two values characteristic of folded and unfolded states, with occasional transitions between them. We have recently shown that molecular (un)folding rates can be recovered from such trajectories, with a small linker correction, as long as the characteristic time of the bead fluctuations is shorter than the residence time in the unfolded (folded) state. Here, we show that accurate measurements of the molecular transition path times require an even faster apparatus response. Transition paths, the trajectory segments in which the molecule (un)folds, are properly resolved only if the beads fluctuate more rapidly than the end-to-end distance of the molecule. Therefore, over a wide regime, the measured rates may be meaningful but not the transition path times. Analytic expressions for the measured mean transition path times are obtained for systems diffusing anisotropically on a two-dimensional free energy surface. The transition path times depend on the properties both of the molecule and of the pulling device.

Self-assembled molecular magnets on patterned silicon substrates: bridging bio-molecules with nanoelectronics.

PubMed

Chang, Chia-Ching; Sun, Kien Wen; Lee, Shang-Fan; Kan, Lou-Sing

2007-04-01

The paper reports the methods of preparing molecular magnets and patterning of the molecules on a semiconductor surface. A highly magnetically aligned metallothionein containing Mn and Cd (Mn,Cd-MT-2) is first synthesized, and the molecules are then placed into nanopores prepared on silicon (001) surfaces using electron beam lithography and reactive ion-etching techniques. We have observed the self-assemble growth of the MT molecules on the patterned Si surface such that the MT molecules have grown into rod or ring type three-dimensional nanostructures, depending on the patterned nanostructures on the surface. We also provide scanning electron microscopy, atomic force microscopy, and magnetic force microscope studies of the molecular nanostructures. This engineered molecule shows molecular magnetization and is biocompatible with conventional semiconductors. These features make Mn,Cd-MT-2 a good candidate for biological applications and sensing sources of new nanodevices. Using molecular self-assembly and topographical patterning of the semiconductor substrate, we can close the gap between bio-molecules and nanoelectronics built into the semiconductor chip.

Resolving dual binding conformations of cellulosome cohesin-dockerin complexes using single-molecule force spectroscopy.

PubMed

Jobst, Markus A; Milles, Lukas F; Schoeler, Constantin; Ott, Wolfgang; Fried, Daniel B; Bayer, Edward A; Gaub, Hermann E; Nash, Michael A

2015-10-31

Receptor-ligand pairs are ordinarily thought to interact through a lock and key mechanism, where a unique molecular conformation is formed upon binding. Contrary to this paradigm, cellulosomal cohesin-dockerin (Coh-Doc) pairs are believed to interact through redundant dual binding modes consisting of two distinct conformations. Here, we combined site-directed mutagenesis and single-molecule force spectroscopy (SMFS) to study the unbinding of Coh:Doc complexes under force. We designed Doc mutations to knock out each binding mode, and compared their single-molecule unfolding patterns as they were dissociated from Coh using an atomic force microscope (AFM) cantilever. Although average bulk measurements were unable to resolve the differences in Doc binding modes due to the similarity of the interactions, with a single-molecule method we were able to discriminate the two modes based on distinct differences in their mechanical properties. We conclude that under native conditions wild-type Doc from Clostridium thermocellum exocellulase Cel48S populates both binding modes with similar probabilities. Given the vast number of Doc domains with predicted dual binding modes across multiple bacterial species, our approach opens up new possibilities for understanding assembly and catalytic properties of a broad range of multi-enzyme complexes.

Decoding the mechanical fingerprints of biomolecules.

PubMed

Dudko, Olga K

2016-01-01

The capacity of biological macromolecules to act as exceedingly sophisticated and highly efficient cellular machines - switches, assembly factors, pumps, or motors - is realized through their conformational transitions, that is, their folding into distinct shapes and selective binding to other molecules. Conformational transitions can be induced, monitored, and manipulated by pulling individual macromolecules apart with an applied force. Pulling experiments reveal, for a given biomolecule, the relationship between applied force and molecular extension. Distinct signatures in the force-extension relationship identify a given biomolecule and thus serve as the molecule's 'mechanical fingerprints'. But, how can these fingerprints be decoded to uncover the energy barriers crossed by the molecule in the course of its conformational transition, as well as the associated timescales? This review summarizes a powerful class of approaches to interpreting single-molecule force spectroscopy measurements - namely, analytically tractable approaches. On the fundamental side, analytical theories have the power to reveal the unifying principles underneath the bewildering diversity of biomolecules and their behaviors. On the practical side, analytical expressions that result from these theories are particularly well suited for a direct fit to experimental data, yielding the important parameters that govern biological processes at the molecular level.

Actomyosin tension as a determinant of metastatic cancer mechanical tropism

NASA Astrophysics Data System (ADS)

McGrail, Daniel J.; Kieu, Quang Minh N.; Iandoli, Jason A.; Dawson, Michelle R.

2015-04-01

Despite major advances in the characterization of molecular regulators of cancer growth and metastasis, patient survival rates have largely stagnated. Recent studies have shown that mechanical cues from the extracellular matrix can drive the transition to a malignant phenotype. Moreover, it is also known that the metastatic process, which results in over 90% of cancer-related deaths, is governed by intracellular mechanical forces. To better understand these processes, we identified metastatic tumor cells originating from different locations which undergo inverse responses to altered matrix elasticity: MDA-MB-231 breast cancer cells that prefer rigid matrices and SKOV-3 ovarian cancer cells that prefer compliant matrices as characterized by parameters such as tumor cell proliferation, chemoresistance, and migration. Transcriptomic analysis revealed higher expression of genes associated with cytoskeletal tension and contractility in cells that prefer stiff environments, both when comparing MDA-MB-231 to SKOV-3 cells as well as when comparing bone-metastatic to lung-metastatic MDA-MB-231 subclones. Using small molecule inhibitors, we found that blocking the activity of these pathways mitigated rigidity-dependent behavior in both cell lines. Probing the physical forces exerted by cells on the underlying substrates revealed that though force magnitude may not directly correlate with functional outcomes, other parameters such as force polarization do correlate directly with cell motility. Finally, this biophysical analysis demonstrates that intrinsic levels of cell contractility determine the matrix rigidity for maximal cell function, possibly influencing tissue sites for metastatic cancer cell engraftment during dissemination. By increasing our understanding of the physical interactions of cancer cells with their microenvironment, these studies may help develop novel therapeutic strategies.

Dynamic effects in friction and adhesion through cooperative rupture and formation of supramolecular bonds.

PubMed

Blass, Johanna; Albrecht, Marcel; Bozna, Bianca L; Wenz, Gerhard; Bennewitz, Roland

2015-05-07

We introduce a molecular toolkit for studying the dynamics in friction and adhesion from the single molecule level to effects of multivalency. As experimental model system we use supramolecular bonds established by the inclusion of ditopic adamantane connector molecules into two surface-bound cyclodextrin molecules, attached to a tip of an atomic force microscope (AFM) and to a flat silicon surface. The rupture force of a single bond does not depend on the pulling rate, indicating that the fast complexation kinetics of adamantane and cyclodextrin are probed in thermal equilibrium. In contrast, the pull-off force for a group of supramolecular bonds depends on the unloading rate revealing a non-equilibrium situation, an effect discussed as the combined action of multivalency and cantilever inertia effects. Friction forces exhibit a stick-slip characteristic which is explained by the cooperative rupture of groups of host-guest bonds and their rebinding. No dependence of friction on the sliding velocity has been observed in the accessible range of velocities due to fast rebinding and the negligible delay of cantilever response in AFM lateral force measurements.

Machine Learning of Accurate Energy-Conserving Molecular Force Fields

NASA Astrophysics Data System (ADS)

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel; Poltavsky, Igor; Schütt, Kristof; Müller, Klaus-Robert; GDML Collaboration

Efficient and accurate access to the Born-Oppenheimer potential energy surface (PES) is essential for long time scale molecular dynamics (MD) simulations. Using conservation of energy - a fundamental property of closed classical and quantum mechanical systems - we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio MD trajectories (AIMD). The GDML implementation is able to reproduce global potential-energy surfaces of intermediate-size molecules with an accuracy of 0.3 kcal/mol for energies and 1 kcal/mol/Å for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, malonaldehyde, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative MD simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods.

Rapid assessment of oxidation via middle-down LCMS correlates with methionine side-chain solvent-accessible surface area for 121 clinical stage monoclonal antibodies.

PubMed

Yang, Rong; Jain, Tushar; Lynaugh, Heather; Nobrega, R Paul; Lu, Xiaojun; Boland, Todd; Burnina, Irina; Sun, Tingwan; Caffry, Isabelle; Brown, Michael; Zhi, Xiaoyong; Lilov, Asparouh; Xu, Yingda

Susceptibility of methionine to oxidation is an important concern for chemical stability during the development of a monoclonal antibody (mAb) therapeutic. To minimize downstream risks, leading candidates are usually screened under forced oxidation conditions to identify oxidation-labile molecules. Here we report results of forced oxidation on a large set of in-house expressed and purified mAbs with variable region sequences corresponding to 121 clinical stage mAbs. These mAb samples were treated with 0.1% H 2 O 2 for 24 hours before enzymatic cleavage below the hinge, followed by reduction of inter-chain disulfide bonds for the detection of the light chain, Fab portion of heavy chain (Fd) and Fc by liquid chromatography-mass spectrometry. This high-throughput, middle-down approach allows detection of oxidation site(s) at the resolution of 3 distinct segments. The experimental oxidation data correlates well with theoretical predictions based on the solvent-accessible surface area of the methionine side-chains within these segments. These results validate the use of upstream computational modeling to predict mAb oxidation susceptibility at the sequence level.

Toward ab initio molecular dynamics modeling for sum-frequency generation spectra; an efficient algorithm based on surface-specific velocity-velocity correlation function.

PubMed

Ohto, Tatsuhiko; Usui, Kota; Hasegawa, Taisuke; Bonn, Mischa; Nagata, Yuki

2015-09-28

Interfacial water structures have been studied intensively by probing the O-H stretch mode of water molecules using sum-frequency generation (SFG) spectroscopy. This surface-specific technique is finding increasingly widespread use, and accordingly, computational approaches to calculate SFG spectra using molecular dynamics (MD) trajectories of interfacial water molecules have been developed and employed to correlate specific spectral signatures with distinct interfacial water structures. Such simulations typically require relatively long (several nanoseconds) MD trajectories to allow reliable calculation of the SFG response functions through the dipole moment-polarizability time correlation function. These long trajectories limit the use of computationally expensive MD techniques such as ab initio MD and centroid MD simulations. Here, we present an efficient algorithm determining the SFG response from the surface-specific velocity-velocity correlation function (ssVVCF). This ssVVCF formalism allows us to calculate SFG spectra using a MD trajectory of only ∼100 ps, resulting in the substantial reduction of the computational costs, by almost an order of magnitude. We demonstrate that the O-H stretch SFG spectra at the water-air interface calculated by using the ssVVCF formalism well reproduce those calculated by using the dipole moment-polarizability time correlation function. Furthermore, we applied this ssVVCF technique for computing the SFG spectra from the ab initio MD trajectories with various density functionals. We report that the SFG responses computed from both ab initio MD simulations and MD simulations with an ab initio based force field model do not show a positive feature in its imaginary component at 3100 cm(-1).

Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning.

PubMed

Cole, Daniel J; Vilseck, Jonah Z; Tirado-Rives, Julian; Payne, Mike C; Jorgensen, William L

2016-05-10

Molecular mechanics force fields, which are commonly used in biomolecular modeling and computer-aided drug design, typically treat nonbonded interactions using a limited library of empirical parameters that are developed for small molecules. This approach does not account for polarization in larger molecules or proteins, and the parametrization process is labor-intensive. Using linear-scaling density functional theory and atoms-in-molecule electron density partitioning, environment-specific charges and Lennard-Jones parameters are derived directly from quantum mechanical calculations for use in biomolecular modeling of organic and biomolecular systems. The proposed methods significantly reduce the number of empirical parameters needed to construct molecular mechanics force fields, naturally include polarization effects in charge and Lennard-Jones parameters, and scale well to systems comprised of thousands of atoms, including proteins. The feasibility and benefits of this approach are demonstrated by computing free energies of hydration, properties of pure liquids, and the relative binding free energies of indole and benzofuran to the L99A mutant of T4 lysozyme.

Correlating the vibrational spectra of structurally related molecules: A spectroscopic measure of similarity.

PubMed

Tao, Yunwen; Zou, Wenli; Cremer, Dieter; Kraka, Elfi

2018-03-05

Using catastrophe theory and the concept of a mutation path, an algorithm is developed that leads to the direct correlation of the normal vibrational modes of two structurally related molecules. The mutation path is defined by weighted incremental changes in mass and geometry of the molecules in question, which are successively applied to mutate a molecule into a structurally related molecule and thus continuously converting their normal vibrational spectra from one into the other. Correlation diagrams are generated that accurately relate the normal vibrational modes to each other by utilizing mode-mode overlap criteria and resolving allowed and avoided crossings of vibrational eigenstates. The limitations of normal mode correlation, however, foster the correlation of local vibrational modes, which offer a novel vibrational measure of similarity. It will be shown how this will open new avenues for chemical studies. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Analysis of DNA interactions using single-molecule force spectroscopy.

PubMed

Ritzefeld, Markus; Walhorn, Volker; Anselmetti, Dario; Sewald, Norbert

2013-06-01

Protein-DNA interactions are involved in many biochemical pathways and determine the fate of the corresponding cell. Qualitative and quantitative investigations on these recognition and binding processes are of key importance for an improved understanding of biochemical processes and also for systems biology. This review article focusses on atomic force microscopy (AFM)-based single-molecule force spectroscopy and its application to the quantification of forces and binding mechanisms that lead to the formation of protein-DNA complexes. AFM and dynamic force spectroscopy are exciting tools that allow for quantitative analysis of biomolecular interactions. Besides an overview on the method and the most important immobilization approaches, the physical basics of the data evaluation is described. Recent applications of AFM-based force spectroscopy to investigate DNA intercalation, complexes involving DNA aptamers and peptide- and protein-DNA interactions are given.

The role of correlation and solvation in ion interactions with B-DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sushko, Maria L.; Thomas, Dennis G.; Pabit, Suzette

Ionic atmosphere around nucleic acids plays important roles in biological function. Large-scale explicit solvent simulations coupled to experimental assays such as anomalous small-angle X-ray scattering (ASAXS) can provide important insights into the structure and energetics of the ionic atmosphere but are time- and resource-intensive. In this paper, we demonstrate the use of classical density functional theory to model DNA-ion interactions and explore the balance between ion-DNA, ion-water, and ion-ion interactions. In particular, we compute the distribution of RbCl, SrCl2, and CoHexCl3 (cobalt hexammine chlo- ride) around a B-form DNA molecule. The accuracy of the DFT calculations was assessed by comparisonmore » between simulated and experimental ASAXS curves. As expected, these calculations revealed significant differences between the monovalent, divalent, and trivalent cations. About half of the DNA-bound Rb+ ions penetrate into the minor groove of the DNA and half adsorb on the DNA strands. The fraction of cations in the minor groove decreases for the larger Sr2+ ions and becomes zero for CoHex3+ ions, which all adsorb on the DNA strands. The distribution of CoHex3+ ions is mainly determined by Coulomb interactions, while ion-correlation forces play a central role in the monovalent Rb+ distribution and a combination of ion-correlation and hydration forces affect the Sr2+ distribution around DNA.« less

Structural and mechanical heterogeneity of the erythrocyte membrane reveals hallmarks of membrane stability.

PubMed

Picas, Laura; Rico, Félix; Deforet, Maxime; Scheuring, Simon

2013-02-26

The erythrocyte membrane, a metabolically regulated active structure that comprises lipid molecules, junctional complexes, and the spectrin network, enables the cell to undergo large passive deformations when passing through the microvascular system. Here we use atomic force microscopy (AFM) imaging and quantitative mechanical mapping at nanometer resolution to correlate structure and mechanics of key components of the erythrocyte membrane, crucial for cell integrity and function. Our data reveal structural and mechanical heterogeneity modulated by the metabolic state at unprecedented nanometer resolution. ATP-depletion, reducing skeletal junction phosphorylation in RBC cells, leads to membrane stiffening. Analysis of ghosts and shear-force opened erythrocytes show that, in the absence of cytosolic kinases, spectrin phosphorylation results in membrane stiffening at the extracellular face and a reduced junction remodeling in response to loading forces. Topography and mechanical mapping of single components at the cytoplasmic face reveal that, surprisingly, spectrin phosphorylation by ATP softens individual filaments. Our findings suggest that, besides the mechanical signature of each component, the RBC membrane mechanics is regulated by the metabolic state and the assembly of its structural elements.

Phenazine redox cycling enhances anaerobic survival in Pseudomonas aeruginosa by facilitating generation of ATP and a proton-motive force

PubMed Central

Glasser, Nathaniel R.; Kern, Suzanne E.

2014-01-01

Summary While many studies have explored the growth of Pseudomonas aeruginosa, comparatively few have focused on its survival. Previously, we reported that endogenous phenazines support the anaerobic survival of P. aeruginosa, yet the physiological mechanism underpinning survival was unknown. Here, we demonstrate that phenazine redox cycling enables P. aeruginosa to oxidize glucose and pyruvate into acetate, which promotes survival by coupling acetate and ATP synthesis through the activity of acetate kinase. By measuring intracellular NAD(H) and ATP concentrations, we show that survival is correlated with ATP synthesis, which is tightly coupled to redox homeostasis during pyruvate fermentation but not during arginine fermentation. We also show that ATP hydrolysis is required to generate a proton-motive force using the ATP synthase complex during fermentation. Together, our results suggest that phenazines enable maintenance of the proton-motive force by promoting redox homeostasis and ATP synthesis. This work demonstrates the more general principle that extracellular redox-active molecules, such as phenazines, can broaden the metabolic versatility of microorganisms by facilitating energy generation. PMID:24612454

Polarizable atomic multipole-based force field for DOPC and POPE membrane lipids

NASA Astrophysics Data System (ADS)

Chu, Huiying; Peng, Xiangda; Li, Yan; Zhang, Yuebin; Min, Hanyi; Li, Guohui

2018-04-01

A polarizable atomic multipole-based force field for the membrane bilayer models 1,2-dioleoyl-phosphocholine (DOPC) and 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE) has been developed. The force field adopts the same framework as the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) model, in which the charge distribution of each atom is represented by the permanent atomic monopole, dipole and quadrupole moments. Many-body polarization including the inter- and intra-molecular polarization is modelled in a consistent manner with distributed atomic polarizabilities. The van der Waals parameters were first transferred from existing AMOEBA parameters for small organic molecules and then optimised by fitting to ab initio intermolecular interaction energies between models and a water molecule. Molecular dynamics simulations of the two aqueous DOPC and POPE membrane bilayer systems, consisting of 72 model molecules, were then carried out to validate the force field parameters. Membrane width, area per lipid, volume per lipid, deuterium order parameters, electron density profile, etc. were consistent with experimental values.

In silico screening of drug-membrane thermodynamics reveals linear relations between bulk partitioning and the potential of mean force

NASA Astrophysics Data System (ADS)

Menichetti, Roberto; Kanekal, Kiran H.; Kremer, Kurt; Bereau, Tristan

2017-09-01

The partitioning of small molecules in cell membranes—a key parameter for pharmaceutical applications—typically relies on experimentally available bulk partitioning coefficients. Computer simulations provide a structural resolution of the insertion thermodynamics via the potential of mean force but require significant sampling at the atomistic level. Here, we introduce high-throughput coarse-grained molecular dynamics simulations to screen thermodynamic properties. This application of physics-based models in a large-scale study of small molecules establishes linear relationships between partitioning coefficients and key features of the potential of mean force. This allows us to predict the structure of the insertion from bulk experimental measurements for more than 400 000 compounds. The potential of mean force hereby becomes an easily accessible quantity—already recognized for its high predictability of certain properties, e.g., passive permeation. Further, we demonstrate how coarse graining helps reduce the size of chemical space, enabling a hierarchical approach to screening small molecules.

Measurement and control of detailed electronic properties in a single molecule break junction.

PubMed

Wang, Kun; Hamill, Joseph; Zhou, Jianfeng; Guo, Cunlan; Xu, Bingqian

2014-01-01

The lack of detailed experimental controls has been one of the major obstacles hindering progress in molecular electronics. While large fluctuations have been occurring in the experimental data, specific details, related mechanisms, and data analysis techniques are in high demand to promote our physical understanding at the single-molecule level. A series of modulations we recently developed, based on traditional scanning probe microscopy break junctions (SPMBJs), have helped to discover significant properties in detail which are hidden in the contact interfaces of a single-molecule break junction (SMBJ). For example, in the past we have shown that the correlated force and conductance changes under the saw tooth modulation and stretch-hold mode of PZT movement revealed inherent differences in the contact geometries of a molecular junction. In this paper, using a bias-modulated SPMBJ and utilizing emerging data analysis techniques, we report on the measurement of the altered alignment of the HOMO of benzene molecules with changing the anchoring group which coupled the molecule to metal electrodes. Further calculations based on Landauer fitting and transition voltage spectroscopy (TVS) demonstrated the effects of modulated bias on the location of the frontier molecular orbitals. Understanding the alignment of the molecular orbitals with the Fermi level of the electrodes is essential for understanding the behaviour of SMBJs and for the future design of more complex devices. With these modulations and analysis techniques, fruitful information has been found about the nature of the metal-molecule junction, providing us insightful clues towards the next step for in-depth study.

Molecule nanoweaver

DOEpatents

Gerald, II; Rex, E [Brookfield, IL; Klingler, Robert J [Glenview, IL; Rathke, Jerome W [Homer Glen, IL; Diaz, Rocio [Chicago, IL; Vukovic, Lela [Westchester, IL

2009-03-10

A method, apparatus, and system for constructing uniform macroscopic films with tailored geometric assemblies of molecules on the nanometer scale. The method, apparatus, and system include providing starting molecules of selected character, applying one or more force fields to the molecules to cause them to order and condense with NMR spectra and images being used to monitor progress in creating the desired geometrical assembly and functionality of molecules that comprise the films.

Correlations and adsorption mechanisms of aromatic compounds on biochars produced from various biomass at 700 °C.

PubMed

Yang, Kun; Jiang, Yuan; Yang, Jingjing; Lin, Daohui

2018-02-01

Knowledge of adsorption behavior of organic contaminants on high heat temperature treated biochars is essential for application of biochars as adsorbents in wastewater treatment and soil remediation. In this study, isotherms of 25 aromatic compounds adsorption on biochars pyrolyzed at 700 °C from biomass including wood chips, rice straw, bamboo chips, cellulose, lignin and chitin were investigated to establish correlations between adsorption behavior and physicochemical properties of biochars. Isotherms were well fitted by Polanyi theory-based Dubinin-Ashtakhov (DA) model with three parameters, i.e., adsorption capacity (Q 0 ) and adsorption affinity (E and b). Besides the negative correlation of Q 0 with molecular maximum cross-sectional areas (σ) of organic compounds, positive correlations of Q 0 with total pore volume (V total ) and average diameter of micropore (D) of biochars were observed, indicating that adsorption by biochars is captured by the pore-filling mechanism with molecular sieving effect in biochar pores. Linear solvation energy relationships (LSERs) of adsorption affinity (E) with solvatochromic parameters of organic compounds (i. e., α m and π ∗ ) were established, suggesting that hydrophobic effect, π-π interaction and hydrogen-bonding interaction are the main forces responsible for adsorption. The regression coefficient (π 1 ) and intercept (C) of obtained LSERs are correlated with biochar H/C and R micro , respectively, implying that biochars with higher aromaticity and more micropores have stronger π-π bonding potential and hydrophobic effect potential with aromatic molecule, respectively. However, hydrogen-bonding potential of biochars for organic molecules is not changed significantly with properties of biochars. A negative correlation of b with biochar H/C is also obtained. These correlations could be used to predict the adsorption behavior of organic compounds on high heat temperature treated biochars from various biomass for the application of biochars as sorbents and for the estimating of environmental risks of organic compounds in the present of biochars. Copyright © 2017 Elsevier Ltd. All rights reserved.

Interaction of methotrexate with trypsin analyzed by spectroscopic and molecular modeling methods

NASA Astrophysics Data System (ADS)

Wang, Yanqing; Zhang, Hongmei; Cao, Jian; Zhou, Qiuhua

2013-11-01

Trypsin is one of important digestive enzymes that have intimate correlation with human health and illness. In this work, the interaction of trypsin with methotrexate was investigated by spectroscopic and molecular modeling methods. The results revealed that methotrexate could interact with trypsin with about one binding site. Methotrexate molecule could enter into the primary substrate-binding pocket, resulting in inhibition of trypsin activity. Furthermore, the thermodynamic analysis implied that electrostatic force, hydrogen bonding, van der Waals and hydrophobic interactions were the main interactions for stabilizing the trypsin-methotrexate system, which agreed well with the results from the molecular modeling study.

Molecular Structure and Equilibrium Forces of Bovine Submaxillary Mucin Adsorbed at a Solid-Liquid Interface.

PubMed

Zappone, Bruno; Patil, Navinkumar J; Madsen, Jan B; Pakkanen, Kirsi I; Lee, Seunghwan

2015-04-21

By combining dynamic light scattering, circular dichroism spectroscopy, atomic force microscopy, and surface force apparatus, the conformation of bovine submaxillary mucin in dilute solution and nanomechanical properties of mucin layers adsorbed on mica have been investigated. The samples were prepared by additional chromatographic purification of commercially available products. The mucin molecule was found to have a z-average hydrodynamic diameter of ca. 35 nm in phosphate buffered solution, without any particular secondary or tertiary structure. The contour length of the mucin is larger than, yet of the same order of magnitude as the diameter, indicating that the molecule can be modeled as a relatively rigid polymeric chain due to the large persistence length of the central glycosylated domain. Mucin molecules adsorbed abundantly onto mica from saline buffer, generating polymer-like, long-ranged, repulsive, and nonhysteretic forces upon compression of the adsorbed layers. Detailed analysis of such forces suggests that adsorbed mucins had an elongated conformation favored by the stiffness of the central domain. Acidification of aqueous media was chosen as means to reduce mucin-mucin and mucin-substrate electrostatic interactions. The hydrodynamic diameter in solution did not significantly change when the pH was lowered, showing that the large persistence length of the mucin molecule is due to steric hindrance between sugar chains, rather than electrostatic interactions. Remarkably, the force generated by an adsorbed layer with a fixed surface coverage also remained unaltered upon acidification. This observation can be linked to the surface-protective, pH-resistant role of bovine submaxillary mucin in the variable environmental conditions of the oral cavity.

Loosely-Bound Diatomic Molecules.

ERIC Educational Resources Information Center

Balfour, W. J.

1979-01-01

Discusses concept of covalent bonding as related to homonuclear diatomic molecules. Article draws attention to the existence of bound rare gas and alkaline earth diatomic molecules. Summarizes their molecular parameters and offers spectroscopic data. Strength and variation with distance of interatomic attractive forces is given. (Author/SA)

Controlling direct contact force for wet adhesion with different wedged film stabilities

NASA Astrophysics Data System (ADS)

Li, Meng; Xie, Jun; Shi, Liping; Huang, Wei; Wang, Xiaolei

2018-04-01

In solid–liquid–solid adhesive systems, wedged films often feature instability at microscopic thicknesses, which can easily disrupt the adhesive strength of their remarkable direct contact force. Here, sodium dodecyl sulfate (SDS) was employed to tune the instability of adhesion in wedged glass–water–rubber films, achieving controllable direct contact. Experimental results showed that the supplement of SDS molecules significantly weakened the direct contact force for wet adhesion and eliminated it at high concentrations. The underlying reason was suggested to be the repulsive double-layer force caused by SDS molecules, which lowers the instability of the wedged film and balances the preload, disrupting the direct contact in wet adhesion.

Efficient geometry optimization by Hellmann-Feynman forces with the anti-Hermitian contracted Schrödinger equation

NASA Astrophysics Data System (ADS)

Foley, Jonathan J.; Mazziotti, David A.

2010-10-01

An efficient method for geometry optimization based on solving the anti-Hermitian contracted Schrödinger equation (ACSE) is presented. We formulate a reduced version of the Hellmann-Feynman theorem (HFT) in terms of the two-electron reduced Hamiltonian operator and the two-electron reduced density matrix (2-RDM). The HFT offers a considerable reduction in computational cost over methods which rely on numerical derivatives. While previous geometry optimizations with numerical gradients required 2M evaluations of the ACSE where M is the number of nuclear degrees of freedom, the HFT requires only a single ACSE calculation of the 2-RDM per gradient. Synthesizing geometry optimization techniques with recent extensions of the ACSE theory to arbitrary electronic and spin states provides an important suite of tools for accurately determining equilibrium and transition-state structures of ground- and excited-state molecules in closed- and open-shell configurations. The ability of the ACSE to balance single- and multi-reference correlation is particularly advantageous in the determination of excited-state geometries where the electronic configurations differ greatly from the ground-state reference. Applications are made to closed-shell molecules N2, CO, H2O, the open-shell molecules B2 and CH, and the excited state molecules N2, B2, and BH. We also study the HCN ↔ HNC isomerization and the geometry optimization of hydroxyurea, a molecule which has a significant role in the treatment of sickle-cell anaemia.

Hierarchical atom type definitions and extensible all-atom force fields.

PubMed

Jin, Zhao; Yang, Chunwei; Cao, Fenglei; Li, Feng; Jing, Zhifeng; Chen, Long; Shen, Zhe; Xin, Liang; Tong, Sijia; Sun, Huai

2016-03-15

The extensibility of force field is a key to solve the missing parameter problem commonly found in force field applications. The extensibility of conventional force fields is traditionally managed in the parameterization procedure, which becomes impractical as the coverage of the force field increases above a threshold. A hierarchical atom-type definition (HAD) scheme is proposed to make extensible atom type definitions, which ensures that the force field developed based on the definitions are extensible. To demonstrate how HAD works and to prepare a foundation for future developments, two general force fields based on AMBER and DFF functional forms are parameterized for common organic molecules. The force field parameters are derived from the same set of quantum mechanical data and experimental liquid data using an automated parameterization tool, and validated by calculating molecular and liquid properties. The hydration free energies are calculated successfully by introducing a polarization scaling factor to the dispersion term between the solvent and solute molecules. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Comparison of force fields on the basis of various model approaches--how to design the best model for the [CnMIM][NTf2] family of ionic liquids.

PubMed

Köddermann, Thorsten; Reith, Dirk; Ludwig, Ralf

2013-10-07

In this contribution, we present two new united-atom force fields (UA-FFs) for 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide [C(n)MIM][NTf(2)] (n=1, 2, 4, 6, 8) ionic liquids (ILs). One is parametrized manually, and the other is developed with the gradient-based optimization workflow (GROW). By doing so, we wanted to perform a hard test to determine how researchers could benefit from semiautomated optimization procedures. As with our already published all-atom force field (AA-FF) for [C(n)MIM][NTf(2)] (T. Köddermann, D. Paschek, R. Ludwig, ChemPhysChem- 2007, 8, 2464), the new force fields were derived to fit experimental densities, self-diffusion coefficients, and NMR rotational correlation times for the IL cation and for water molecules dissolved in [C(2)MIM][NTf(2)]. In the manual force field, the alkyl chains of the cation and the CF3 groups of the anion were treated as united atoms. In the GROW force field, only the alkyl chains of the cation were united. All other parts of the structures of the ions remained unchanged to prevent any loss of physical information. Structural, dynamic, and thermodynamic properties such as viscosity, cation rotational correlation times, and heats of vaporization calculated with the new force fields were compared with values simulated with the previous AA-FF and the experimental data. All simulated properties were in excellent agreement with the experimental values. Altogether, the UA-FFs are slightly superior for speed-up reasons. The UA-FF speeds up the simulation by about 100 % and reduces the demanded disk space by about 78 %. More importantly, real time and efforts to generate force fields could be significantly reduced by utilizing GROW. The real time for the GROW parametrization in this work was 2 months. Manual parametrization, in contrast, may take up to 12 months, and this is, therefore, a significant increase in speed, though it is difficult to estimate the duration of manual parametrization. Copyright © 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim.

Solvent effects on the Raman spectra of the isolated carbon-hydrogen stretches of cyclohexane-d11: A molecular dynamics simulation study of liquid and supercritical solvation

NASA Astrophysics Data System (ADS)

Frankland, Sarah-Jane Victoria

Molecular dynamics simulations of solvent effects on the Raman spectra of isotopically isolated C-H stretches of cyclohexane-d11 were performed in liquids and supercritical CO2. The red spectral shifts from the gas phase origin were derived three different ways: (1) from the Lennard-Jones force on the normal coordinate of the vibration; (2) from this force with an additional term to account for the polarizabilily change on excitation, and (3) as an empirical difference potential between the v = 0 and v = 1 state of the hydrogen atom involved in the vibration. Model 3 was successfully parametrized to reproduce the experimental spectral shifts and linewidths. The simulated lineshapes from these models were homogeneously broadened from gas to liquid densities primarily by collisions of nearby solvent molecules with the solute. Both the simulations and isolated binary collision theory showed the density dependence of the linewidth to be related to that of the collision rate. Two additional projects were done which use Monte-Carlo algorithms involving two molecules. In the first project 1:1 complexes of solute and solvent were formed at the potential surface minima such that the geometries of conformers, energies of formation, and electronic spectral shifts could be studied. Complexes between 7- azaindole, indole, carbazole, and 1-azacarbazole and hydrogen-bonding solvents were most stable when the solvent was hydrogen-bonded at the solute N-H site. The energies of formation compared well with values obtained from ab initio calculations. Complexes of coumarins 102 and 153 and fluorinated alcohols showed the more stable conformers to have the alcohols bound at the coumarin carbonyl group. In the second project, one solvent molecule was randomly placed around the solute molecule in order to simplify bulk liquid simulation to only two molecules. This approximation was rised to show that the dynamic Stokes shift of coumarin 153 in over 30 solvents correlates with the permanent charge distribution of the solvent.

Watching How Molecules Orient in a Surface Forces Apparatus, Using Confocal Raman Spectroscopy

NASA Astrophysics Data System (ADS)

Jiang, Shan; Kim, Minsu; Bae, Sung Chul; Granick, Steve

2006-03-01

Much is known about surface forces, less about where they come from. This laboratory is engaged in direct vibrational spectroscopic measurements of how molecules orient in confined geometries. Regarding force measurements, PDMS (polydimethylsiloxane) was a model system for many years. In this study, we describe direct experiments using a novel version of confocal Raman spectroscopy. This experiment allows direct measurement of how the PDMS molecules orient under confinment as well as under subsequent shear. When the thickness of the fluid film is less than the unperturbed radius of gyration of the polymer, we obtain two novel findings: (a) linewidth analysis of peaks reveals that vibrational relaxation times are perturbed in this confined geometry; (b) orientation of the chain backbone is not everywhere the same within the molecularly-thin film; domains of various orientation are observed instead.

Study of hydrogen-molecule guests in type II clathrate hydrates using a force-matched potential model parameterised from ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Burnham, Christian J.; Futera, Zdenek; English, Niall J.

2018-03-01

The force-matching method has been applied to parameterise an empirical potential model for water-water and water-hydrogen intermolecular interactions for use in clathrate-hydrate simulations containing hydrogen guest molecules. The underlying reference simulations constituted ab initio molecular dynamics (AIMD) of clathrate hydrates with various occupations of hydrogen-molecule guests. It is shown that the resultant model is able to reproduce AIMD-derived free-energy curves for the movement of a tagged hydrogen molecule between the water cages that make up the clathrate, thus giving us confidence in the model. Furthermore, with the aid of an umbrella-sampling algorithm, we calculate barrier heights for the force-matched model, yielding the free-energy barrier for a tagged molecule to move between cages. The barrier heights are reasonably large, being on the order of 30 kJ/mol, and are consistent with our previous studies with empirical models [C. J. Burnham and N. J. English, J. Phys. Chem. C 120, 16561 (2016) and C. J. Burnham et al., Phys. Chem. Chem. Phys. 19, 717 (2017)]. Our results are in opposition to the literature, which claims that this system may have very low barrier heights. We also compare results to that using the more ad hoc empirical model of Alavi et al. [J. Chem. Phys. 123, 024507 (2005)] and find that this model does very well when judged against the force-matched and ab initio simulation data.

Reducing uncertainties in energy dissipation measurements in atomic force spectroscopy of molecular networks and cell-adhesion studies.

PubMed

Biswas, Soma; Leitao, Samuel; Theillaud, Quentin; Erickson, Blake W; Fantner, Georg E

2018-06-20

Atomic force microscope (AFM) based single molecule force spectroscopy (SMFS) is a valuable tool in biophysics to investigate the ligand-receptor interactions, cell adhesion and cell mechanics. However, the force spectroscopy data analysis needs to be done carefully to extract the required quantitative parameters correctly. Especially the large number of molecules, commonly involved in complex networks formation; leads to very complicated force spectroscopy curves. One therefore, generally characterizes the total dissipated energy over a whole pulling cycle, as it is difficult to decompose the complex force curves into individual single molecule events. However, calculating the energy dissipation directly from the transformed force spectroscopy curves can lead to a significant over-estimation of the dissipated energy during a pulling experiment. The over-estimation of dissipated energy arises from the finite stiffness of the cantilever used for AFM based SMFS. Although this error can be significant, it is generally not compensated for. This can lead to significant misinterpretation of the energy dissipation (up to the order of 30%). In this paper, we show how in complex SMFS the excess dissipated energy caused by the stiffness of the cantilever can be identified and corrected using a high throughput algorithm. This algorithm is then applied to experimental results from molecular networks and cell-adhesion measurements to quantify the improvement in the estimation of the total energy dissipation.

The Use of Ultrashort Picosecond Laser Pulses to Generate Quantum Optical Properties of Single Molecules in Biophysics

NASA Astrophysics Data System (ADS)

Ly, Sonny

Generation of quantum optical states from ultrashort laser-molecule interactions have led to fascinating discoveries in physics and chemistry. In recent years, these interactions have been extended to probe phenomena in single molecule biophysics. Photons emitted from a single fluorescent molecule contains important properties about how the molecule behave and function in that particular environment. Analysis of the second order coherence function through fluorescence correlation spectroscopy plays a pivotal role in quantum optics. At very short nanosecond timescales, the coherence function predicts photon antibunching, a purely quantum optical phenomena which states that a single molecule can only emit one photon at a time. Photon antibunching is the only direct proof of single molecule emission. From the nanosecond to microsecond timescale, the coherence function gives information about rotational diffusion coefficients, and at longer millisecond timescales, gives information regarding the translational diffusion coefficients. In addition, energy transfer between molecules from dipole-dipole interaction results in FRET, a highly sensitive method to probe conformational dynamics at nanometer distances. Here I apply the quantum optical techniques of photon antibunching, fluorescence correlation spectroscopy and FRET to probe how lipid nanodiscs form and function at the single molecule level. Lipid nanodiscs are particles that contain two apolipoprotein (apo) A-I circumventing a lipid bilayer in a belt conformation. From a technological point of view, nanodiscs mimics a patch of cell membrane that have recently been used to reconstitute a variety of membrane proteins including cytochrome P450 and bacteriorhodopsin. They are also potential drug transport vehicles due to its small and stable 10nm diameter size. Biologically, nanodiscs resemble to high degree, high density lipoproteins (HDL) in our body and provides a model platform to study lipid-protein interactions and their dynamic formation to lipoprotein particles without having to extract from human blood plasma. Although HDL has been studied extensively within the last thirty years, many questions still remain regarding the structure of apoA-I, the protein associated exclusively with it. Despite our ability to detect and image these nanodiscs by blotting, atomic force microscopy (AFM), or electron microscopy (EM), many basic properties such as their specific hydrated shape in solution, or the precise conformation of the apolipoproteins surrounding the particles are still unknown. The dynamic interactions of apoA-I with lipids are also rather poorly understood on a fundamental level, and are only characterized in bulk (biochemical blotting) or stationary methods (AFM, EM), making it impossible to study individual steps with high spatial or temporal resolution.

Evaluation of Hydration Free Energy by Level-Set Variational Implicit-Solvent Model with Coulomb-Field Approximation.

PubMed

Guo, Zuojun; Li, Bo; Dzubiella, Joachim; Cheng, Li-Tien; McCammon, J Andrew; Che, Jianwei

2013-03-12

In this article, we systematically apply a novel implicit-solvent model, the variational implicit-solvent model (VISM) together with the Coulomb-Field Approximation (CFA), to calculate the hydration free energy of a large set of small organic molecules. Because these molecules have been studied in detail by molecular dynamics simulations and other implicit-solvent models, they provide a good benchmark for evaluating the performance of VISM-CFA. With all-atom Amber force field parameters, VISM-CFA is able to reproduce well not only the experimental and MD simulated total hydration free energy but also the polar and nonpolar contributions individually. The correlation between VISM-CFA and experiments is R 2 = 0.763 for the total hydration free energy, with a root-mean-square deviation (RMSD) of 1.83 kcal/mol, and the correlation to results from TIP3P explicit water MD simulations is R 2 = 0.839 with a RMSD = 1.36 kcal/mol. In addition, we demonstrate that VISM captures dewetting phenomena in the p53/MDM2 complex and hydrophobic characteristics in the system. This work demonstrates that the level-set VISM-CFA can be used to study the energetic behavior of realistic molecular systems with complicated geometries in solvation, protein-ligand binding, protein-protein association, and protein folding processes.

Computing many-body wave functions with guaranteed precision: the first-order Møller-Plesset wave function for the ground state of helium atom.

PubMed

Bischoff, Florian A; Harrison, Robert J; Valeev, Edward F

2012-09-14

We present an approach to compute accurate correlation energies for atoms and molecules using an adaptive discontinuous spectral-element multiresolution representation for the two-electron wave function. Because of the exponential storage complexity of the spectral-element representation with the number of dimensions, a brute-force computation of two-electron (six-dimensional) wave functions with high precision was not practical. To overcome the key storage bottlenecks we utilized (1) a low-rank tensor approximation (specifically, the singular value decomposition) to compress the wave function, and (2) explicitly correlated R12-type terms in the wave function to regularize the Coulomb electron-electron singularities of the Hamiltonian. All operations necessary to solve the Schrödinger equation were expressed so that the reconstruction of the full-rank form of the wave function is never necessary. Numerical performance of the method was highlighted by computing the first-order Møller-Plesset wave function of a helium atom. The computed second-order Møller-Plesset energy is precise to ~2 microhartrees, which is at the precision limit of the existing general atomic-orbital-based approaches. Our approach does not assume special geometric symmetries, hence application to molecules is straightforward.

Prediction of potency of protease inhibitors using free energy simulations with polarizable quantum mechanics-based ligand charges and a hybrid water model.

PubMed

Das, Debananda; Koh, Yasuhiro; Tojo, Yasushi; Ghosh, Arun K; Mitsuya, Hiroaki

2009-12-01

Reliable and robust prediction of the binding affinity for drug molecules continues to be a daunting challenge. We simulated the binding interactions and free energy of binding of nine protease inhibitors (PIs) with wild-type and various mutant proteases by performing GBSA simulations in which each PI's partial charge was determined by quantum mechanics (QM) and the partial charge accounts for the polarization induced by the protease environment. We employed a hybrid solvation model that retains selected explicit water molecules in the protein with surface-generalized Born (SGB) implicit solvent. We examined the correlation of the free energy with the antiviral potency of PIs with regard to amino acid substitutions in protease. The GBSA free energy thus simulated showed strong correlations (r > 0.75) with antiviral IC(50) values of PIs when amino acid substitutions were present in the protease active site. We also simulated the binding free energy of PIs with P2-bis-tetrahydrofuranylurethane (bis-THF) or related cores, utilizing a bis-THF-containing protease crystal structure as a template. The free energy showed a strong correlation (r = 0.93) with experimentally determined anti-HIV-1 potency. The present data suggest that the presence of selected explicit water in protein and protein polarization-induced quantum charges for the inhibitor, compared to lack of explicit water and a static force-field-based charge model, can serve as an improved lead optimization tool and warrants further exploration.

Statistical mechanical theory of liquid entropy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wallace, D.C.

The multiparticle correlation expansion for the entropy of a classical monatomic liquid is presented. This entropy expresses the physical picture in which there is no free particle motion, but rather, each atom moves within a cage formed by its neighbors. The liquid expansion, including only pair correlations, gives an excellent account of the experimental entropy of most liquid metals, of liquid argon, and the hard sphere liquid. The pair correlation entropy is well approximated by a universal function of temperature. Higher order correlation entropy, due to n-particle irreducible correlations for n{ge}3, is significant in only a few liquid metals, andmore » its occurrence suggests the presence of n-body forces. When the liquid theory is applied to the study of melting, the author discovers the important classification of normal and anomalous melting, according to whether there is not or is a significant change in the electronic structure upon melting, and he discovers the universal disordering entropy for melting of a monatomic crystal. Interesting directions for future research are: extension to include orientational correlations of molecules, theoretical calculation of the entropy of water, application to the entropy of the amorphous state, and correlational entropy of compressed argon. The author clarifies the relation among different entropy expansions in the recent literature.« less

Effect of genomic long-range correlations on DNA persistence length: from theory to single molecule experiments.

PubMed

Moukhtar, Julien; Faivre-Moskalenko, Cendrine; Milani, Pascale; Audit, Benjamin; Vaillant, Cedric; Fontaine, Emeline; Mongelard, Fabien; Lavorel, Guillaume; St-Jean, Philippe; Bouvet, Philippe; Argoul, Françoise; Arneodo, Alain

2010-04-22

Sequence dependency of DNA intrinsic bending properties has been emphasized as a possible key ingredient to in vivo chromatin organization. We use atomic force microscopy (AFM) in air and liquid to image intrinsically straight (synthetic), uncorrelated (hepatitis C RNA virus) and persistent long-range correlated (human) DNA fragments in various ionic conditions such that the molecules freely equilibrate on the mica surface before being captured in a particular conformation. 2D thermodynamic equilibrium is experimentally verified by a detailed statistical analysis of the Gaussian nature of the DNA bend angle fluctuations. We show that the worm-like chain (WLC) model, commonly used to describe the average conformation of long semiflexible polymers, reproduces remarkably well the persistence length estimates for the first two molecules as consistently obtained from (i) mean square end-to-end distance measurement and (ii) mean projection of the end-to-end vector on the initial orientation. Whatever the operating conditions (air or liquid, concentration of metal cations Mg(2+) and/or Ni(2+)), the persistence length found for the uncorrelated viral DNA underestimates the value obtained for the straight DNA. We show that this systematic difference is the signature of the presence of an uncorrelated structural intrinsic disorder in the hepatitis C virus (HCV) DNA fragment that superimposes on local curvatures induced by thermal fluctuations and that only the entropic disorder depends upon experimental conditions. In contrast, the WLC model fails to describe the human DNA conformations. We use a mean-field extension of the WLC model to account for the presence of long-range correlations (LRC) in the intrinsic curvature disorder of human genomic DNA: the stronger the LRC, the smaller the persistence length. The comparison of AFM imaging of human DNA with LRC DNA simulations confirms that the rather small mean square end-to-end distance observed, particularly for G+C-rich human DNA molecules, more likely results from a large-scale intrinsic curvature due to a persistent distribution of DNA curvature sites than from some increased flexibility.

A measurement of the hysteresis loop in force-spectroscopy curves using a tuning-fork atomic force microscope

PubMed Central

van Vörden, Dennis; Möller, Rolf

2012-01-01

Summary Measurements of the frequency shift versus distance in noncontact atomic force microscopy (NC-AFM) allow measurements of the force gradient between the oscillating tip and a surface (force-spectroscopy measurements). When nonconservative forces act between the tip apex and the surface the oscillation amplitude is damped. The dissipation is caused by bistabilities in the potential energy surface of the tip–sample system, and the process can be understood as a hysteresis of forces between approach and retraction of the tip. In this paper, we present the direct measurement of the whole hysteresis loop in force-spectroscopy curves at 77 K on the PTCDA/Ag/Si(111) √3 × √3 surface by means of a tuning-fork-based NC-AFM with an oscillation amplitude smaller than the distance range of the hysteresis loop. The hysteresis effect is caused by the making and breaking of a bond between PTCDA molecules on the surface and a PTCDA molecule at the tip. The corresponding energy loss was determined to be 0.57 eV by evaluation of the force–distance curves upon approach and retraction. Furthermore, a second dissipation process was identified through the damping of the oscillation while the molecule on the tip is in contact with the surface. This dissipation process occurs mainly during the retraction of the tip. It reaches a maximum value of about 0.22 eV/cycle. PMID:22496993

Continuous all-optical deceleration of molecular beams

NASA Astrophysics Data System (ADS)

Jayich, Andrew; Chen, Gary; Long, Xueping; Wang, Anna; Campbell, Wesley

2014-05-01

A significant impediment to generating ultracold molecules is slowing a molecular beam to velocities where the molecules can be cooled and trapped. We report on progress toward addressing this issue with a general optical deceleration technique for molecular and atomic beams. We propose addressing the molecular beam with a pump and dump pulse sequence from a mode-locked laser. The pump pulse counter-propagates with respect to the beam and drives the molecules to the excited state. The dump pulse co-propagates and stimulates emission, driving the molecules back to the ground state. This cycle transfers 2 ℏk of momentum and can generate very large optical forces, not limited by the spontaneous emission lifetime of the molecule or atom. Importantly, avoiding spontaneous emission limits the branching to dark states. This technique can later be augmented with cooling and trapping. We are working towards demonstrating this optical force by accelerating a cold atomic sample.

Resolving dual binding conformations of cellulosome cohesin-dockerin complexes using single-molecule force spectroscopy

PubMed Central

Jobst, Markus A; Milles, Lukas F; Schoeler, Constantin; Ott, Wolfgang; Fried, Daniel B; Bayer, Edward A; Gaub, Hermann E; Nash, Michael A

2015-01-01

Receptor-ligand pairs are ordinarily thought to interact through a lock and key mechanism, where a unique molecular conformation is formed upon binding. Contrary to this paradigm, cellulosomal cohesin-dockerin (Coh-Doc) pairs are believed to interact through redundant dual binding modes consisting of two distinct conformations. Here, we combined site-directed mutagenesis and single-molecule force spectroscopy (SMFS) to study the unbinding of Coh:Doc complexes under force. We designed Doc mutations to knock out each binding mode, and compared their single-molecule unfolding patterns as they were dissociated from Coh using an atomic force microscope (AFM) cantilever. Although average bulk measurements were unable to resolve the differences in Doc binding modes due to the similarity of the interactions, with a single-molecule method we were able to discriminate the two modes based on distinct differences in their mechanical properties. We conclude that under native conditions wild-type Doc from Clostridium thermocellum exocellulase Cel48S populates both binding modes with similar probabilities. Given the vast number of Doc domains with predicteddual binding modes across multiple bacterial species, our approach opens up newpossibilities for understanding assembly and catalytic properties of a broadrange of multi-enzyme complexes. DOI: http://dx.doi.org/10.7554/eLife.10319.001 PMID:26519733

Exploring the dynamic behaviors and transport properties of gas molecules in a transmembrane cyclic peptide nanotube.

PubMed

Li, Rui; Fan, Jianfen; Li, Hui; Yan, Xiliang; Yu, Yi

2013-12-05

The dynamic behaviors and transport properties of O2, CO2, and NH3 molecules through a transmembrane cyclic peptide nanotube (CPNT) of 8×cyclo-(WL)4/POPE have been investigated by steered molecular dynamics (SMD) simulations and adaptive biasing force (ABF) samplings. Different external forces are needed for three gas molecules to enter the channel. The periodic change of the pulling force curve for a gas traveling through the channel mainly arises from the regular and periodic arrangement of the composed CP subunits of the CPNT. Radial distribution functions (RDFs) between gas and water disclose the density decrease of channel water, which strongly aggravates the discontinuity of H-bond formation between a gas molecule and the neighboring water. Compared to hardly any H-bond formation between CO2 (or O2) and the framework of the CPNT, NH3 can form abundant H-bonds with the carbonyl/amide groups of the CPNT, leading to a fierce competition to NH3-water H-bonded interactions. In addition to direct H-bonded interactions, all three gases can form water bridges with the tube. The potential profile of mean force coincides with the occurring probability of a gas molecule along the tube axis. The energy barriers at two mouths of the CPNT elucidate the phenomenon that CO2 and O2 are thoroughly confined in the narrow lumen while NH3 can easily go outside the tube. Intermolecular interactions of each gas with channel water and the CPNT framework and the formation of H-bonds and water bridges illuminate the different gas translocation behaviors. The results uncover interesting and comprehensive mechanisms underlying the permeation characteristics of three gas molecules traveling through a transmembrane CPNT.

Techniques for estimating Space Station aerodynamic characteristics

NASA Technical Reports Server (NTRS)

Thomas, Richard E.

1993-01-01

A method was devised and calculations were performed to determine the effects of reflected molecules on the aerodynamic force and moment coefficients for a body in free molecule flow. A procedure was developed for determining the velocity and temperature distributions of molecules reflected from a surface of arbitrary momentum and energy accommodation. A system of equations, based on momentum and energy balances for the surface, incident, and reflected molecules, was solved by a numerical optimization technique. The minimization of a 'cost' function, developed from the set of equations, resulted in the determination of the defining properties of the flow reflected from the arbitrary surface. The properties used to define both the incident and reflected flows were: average temperature of the molecules in the flow, angle of the flow with respect to a vector normal to the surface, and the molecular speed ratio. The properties of the reflected flow were used to calculate the contribution of multiply reflected molecules to the force and moments on a test body in the flow. The test configuration consisted of two flat plates joined along one edge at a right angle to each other. When force and moment coefficients of this 90 deg concave wedge were compared to results that did not include multiple reflections, it was found that multiple reflections could nearly double lift and drag coefficients, with nearly a 50 percent increase in pitching moment for cases with specular or nearly specular accommodation. The cases of diffuse or nearly diffuse accommodation often had minor reductions in axial and normal forces when multiple reflections were included. There were several cases of intermediate accommodation where the addition of multiple reflection effects more than tripled the lift coefficient over the convex technique.

The correcting method for the estimation of correlation energies of MF2 (M = Be, Mg, Ca) set molecules

NASA Astrophysics Data System (ADS)

Zhuo, Shuping; Wei, Jichong; Ju, Guanzhi

The intrapair and interpair correlation energies of MF2 (M = Be, Mg, Ca) set molecules are calculated and analysed, and the transferability of inner core correlation effects of Mδ+ are investigated. A detailed analysis of the comparison of correlation energies of neutral atoms with their corresponding ions of Mδ+ and Fδ-/2 is given in terms of the correlation contribution of this component. The study reveals that the total correlation energy of MF2 molecules can be obtained by summing the correlation contributions of Mδ+ and two Fδ-/2 components. This simple estimation method does shed light on the importance of searching useful means for the calculation of electron correlation energy for large biological systems.

QuickFF: A program for a quick and easy derivation of force fields for metal-organic frameworks from ab initio input.

PubMed

Vanduyfhuys, Louis; Vandenbrande, Steven; Verstraelen, Toon; Schmid, Rochus; Waroquier, Michel; Van Speybroeck, Veronique

2015-05-15

QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal-organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from ab initio data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterward, a force field is generated for the system using a three-step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step, the parameters are refined by imposing the force field parameters to reproduce the ab initio Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to metal-organic frameworks (MOFs), QuickFF is used to determine force fields for MIL-53(Al) and MOF-5. For both materials, accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing ab initio calculations. As a result, accurate force fields are generated with minimal effort. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Measuring the Adhesion Forces for the Multivalent Binding of Vancomycin-Conjugated Dendrimer to Bacterial Cell-Wall Peptide.

PubMed

Peterson, Elizabeth; Joseph, Christine; Peterson, Hannah; Bouwman, Rachael; Tang, Shengzhuang; Cannon, Jayme; Sinniah, Kumar; Choi, Seok Ki

2018-06-19

Multivalent ligand-receptor interaction provides the fundamental basis for the hypothetical notion that high binding avidity relates to the strong force of adhesion. Despite its increasing importance in the design of targeted nanoconjugates, an understanding of the physical forces underlying the multivalent interaction remains a subject of urgent investigation. In this study, we designed three vancomycin (Van)-conjugated dendrimers G5(Van) n ( n = mean valency = 0, 1, 4) for bacterial targeting with generation 5 (G5) poly(amidoamine) dendrimer as a multivalent scaffold and evaluated both their binding avidity and physical force of adhesion to a bacterial model surface by employing surface plasmon resonance (SPR) spectroscopy and atomic force microscopy. The SPR experiment for these conjugates was performed in a biosensor chip surface immobilized with a bacterial cell-wall peptide Lys-d-Ala-d-Ala. Of these, G5(Van) 4 bound most tightly with a K D of 0.34 nM, which represents an increase in avidity by 2 or 3 orders of magnitude relative to a monovalent conjugate G5(Van) 1 or free vancomycin, respectively. By single-molecule force spectroscopy, we measured the adhesion force between G5(Van) n and the same cell-wall peptide immobilized on the surface. The distribution of adhesion forces increased in proportion to vancomycin valency with the mean force of 134 pN at n = 4 greater than 96 pN at n = 1 at a loading rate of 5200 pN/s. In summary, our results are strongly supportive of the positive correlation between the avidity and adhesion force in the multivalent interaction of vancomycin nanoconjugates.

Simultaneous Single-Molecule Force and Fluorescence Sampling of DNA Nanostructure Conformations Using Magnetic Tweezers.

PubMed

Kemmerich, Felix E; Swoboda, Marko; Kauert, Dominik J; Grieb, M Svea; Hahn, Steffen; Schwarz, Friedrich W; Seidel, Ralf; Schlierf, Michael

2016-01-13

We present a hybrid single-molecule technique combining magnetic tweezers and Förster resonance energy transfer (FRET) measurements. Through applying external forces to a paramagnetic sphere, we induce conformational changes in DNA nanostructures, which are detected in two output channels simultaneously. First, by tracking a magnetic bead with high spatial and temporal resolution, we observe overall DNA length changes along the force axis. Second, the measured FRET efficiency between two fluorescent probes monitors local conformational changes. The synchronized orthogonal readout in different observation channels will facilitate deciphering the complex mechanisms of biomolecular machines.

Communication: atomic force detection of single-molecule nonlinear optical vibrational spectroscopy.

PubMed

Saurabh, Prasoon; Mukamel, Shaul

2014-04-28

Atomic Force Microscopy (AFM) allows for a highly sensitive detection of spectroscopic signals. This has been first demonstrated for NMR of a single molecule and recently extended to stimulated Raman in the optical regime. We theoretically investigate the use of optical forces to detect time and frequency domain nonlinear optical signals. We show that, with proper phase matching, the AFM-detected signals closely resemble coherent heterodyne-detected signals. Applications are made to AFM-detected and heterodyne-detected vibrational resonances in Coherent Anti-Stokes Raman Spectroscopy (χ((3))) and sum or difference frequency generation (χ((2))).

Computational Study of the Bulk Properties of a Novel Molecule: alpha-Tocopherol-Ascorbic Acid Surfactant

NASA Astrophysics Data System (ADS)

Stirling, Shannon; Kim, Hye-Young

Alpha-tocopherol-ascorbic acid surfactant (EC) is a novel amphiphilic molecule of antioxidant properties, which has a hydrophobic vitamin E and a hydrophilic vitamin C chemically linked. We have developed atomistic force fields (g54a7) for a protonated (neutral) EC molecule. Our goal is to carry out molecular dynamics (MD) simulations of protonated EC molecules using the newly developed force fields and study the molecular properties. First we ran energy minimization (EM) with one molecule in a vacuum to obtain the low energy molecular configuration with emtol =10. We then used Packmol to insert 125 EC molecules in a 3nm cube. We then performed MD simulations of the bulk system composed of 125 EC molecules, from which we measured the bulk density and the evaporation energy of the molecular system. Gromacs2016 is used for the EM and MD simulation studies. We will present the results of the ongoing research. National Institute Of General Medical Sciences of the National Institutes of Health under Award Number P20GM103424 (Kim). Computational resources were provided by the Louisiana Optical Network Initiative.

Prediction of molecular crystal structures by a crystallographic QM/MM model with full space-group symmetry.

PubMed

Mörschel, Philipp; Schmidt, Martin U

2015-01-01

A crystallographic quantum-mechanical/molecular-mechanical model (c-QM/MM model) with full space-group symmetry has been developed for molecular crystals. The lattice energy was calculated by quantum-mechanical methods for short-range interactions and force-field methods for long-range interactions. The quantum-mechanical calculations covered the interactions within the molecule and the interactions of a reference molecule with each of the surrounding 12-15 molecules. The interactions with all other molecules were treated by force-field methods. In each optimization step the energies in the QM and MM shells were calculated separately as single-point energies; after adding both energy contributions, the crystal structure (including the lattice parameters) was optimized accordingly. The space-group symmetry was maintained throughout. Crystal structures with more than one molecule per asymmetric unit, e.g. structures with Z' = 2, hydrates and solvates, have been optimized as well. Test calculations with different quantum-mechanical methods on nine small organic molecules revealed that the density functional theory methods with dispersion correction using the B97-D functional with 6-31G* basis set in combination with the DREIDING force field reproduced the experimental crystal structures with good accuracy. Subsequently the c-QM/MM method was applied to nine compounds from the CCDC blind tests resulting in good energy rankings and excellent geometric accuracies.

Probing static disorder in Arrhenius kinetics by single-molecule force spectroscopy.

PubMed

Kuo, Tzu-Ling; Garcia-Manyes, Sergi; Li, Jingyuan; Barel, Itay; Lu, Hui; Berne, Bruce J; Urbakh, Michael; Klafter, Joseph; Fernández, Julio M

2010-06-22

The widely used Arrhenius equation describes the kinetics of simple two-state reactions, with the implicit assumption of a single transition state with a well-defined activation energy barrier DeltaE, as the rate-limiting step. However, it has become increasingly clear that the saddle point of the free-energy surface in most reactions is populated by ensembles of conformations, leading to nonexponential kinetics. Here we present a theory that generalizes the Arrhenius equation to include static disorder of conformational degrees of freedom as a function of an external perturbation to fully account for a diverse set of transition states. The effect of a perturbation on static disorder is best examined at the single-molecule level. Here we use force-clamp spectroscopy to study the nonexponential kinetics of single ubiquitin proteins unfolding under force. We find that the measured variance in DeltaE shows both force-dependent and independent components, where the force-dependent component scales with F(2), in excellent agreement with our theory. Our study illustrates a novel adaptation of the classical Arrhenius equation that accounts for the microscopic origins of nonexponential kinetics, which are essential in understanding the rapidly growing body of single-molecule data.

First-principles study of pollutant molecules absorbed on polymeric adsorbents using the vdW-DF2 functional

NASA Astrophysics Data System (ADS)

Zhu, Jinguo; Wang, Yapeng; Tian, Ting; Zhang, Qianfan

2018-03-01

Polymeric adsorbents have been attracting increasing attention because of their favorable structrual properties and effectiveness of solving small molecules contaminants. However, due to the absence of deep insight into the adsorption mechanism of polymeric adsorbents, researches on new polymeric adsorbents can only be carried out by repeated experiments and tests, which is extremely inefficient. Therefore, investigating the adsorption process of polymeric adsorbents, especially the mechanism of adsorbing various air pollutant molecules by materials modelling and simulation, is of great significance. Here in this work, we systematically studied the adsorption mechanism by first-principles computation with van der Waals interaction. It demonstrates that the adsorption between them was pure physisorption originating from the hydrogen bond and intermolecular forces consisting of Keesom force, Debye force and London dispersion force. The proportions of these forces varied according to different adsorption systems. The adsorption effects were determined by the polymers’ dipole moment and polarizability. The adsorption performance of some polymers with special structures was also investigated to explore their possibility as potential adsorbents. The results of our simulation can provide some guidance for developing new polymeric adsorbents with better performance.

Ab Initio Classical Dynamics Simulations of CO_2 Line-Mixing Effects in Infrared Bands

NASA Astrophysics Data System (ADS)

Lamouroux, Julien; Hartmann, Jean-Michel; Tran, Ha; Snels, Marcel; Stefani, Stefania; Piccioni, Giuseppe

2013-06-01

Ab initio calculations of line-mixing effects in CO_2 infrared bands are presented and compared with experiments. The predictions were carried using requantized Classical Dynamics Molecular Simulations (rCDMS) based on an approach previously developed and successfully tested for CO_2 isolated line shapes. Using classical dynamics equations, the force and torque applied to each molecule by the surrounding molecules (described by an ab initio intermolecular potential) are computed at each time step. This enables, using a requantization procedure, to predict dipole and isotropic polarizability auto-correlation functions whose Fourier-Laplace transforms yield the spectra. The quality of the rCDMS calculations is demonstrated by comparisons with measured spectra in the spectral regions of the 3ν_3 and 2ν_1+2ν_2+ν_3 Infrared bands. J.-M. Hartmann, H. Tran, N. H. Ngo, et al., Phys. Rev. Lett. A {87} (2013), 013403. H. Tran, C. Boulet, M. Snels, S. Stefani, J. Quant. Spectrosc. Radiat. Transfer {112} (2011), 925-936.

Communication: Understanding molecular representations in machine learning: The role of uniqueness and target similarity

NASA Astrophysics Data System (ADS)

Huang, Bing; von Lilienfeld, O. Anatole

2016-10-01

The predictive accuracy of Machine Learning (ML) models of molecular properties depends on the choice of the molecular representation. Inspired by the postulates of quantum mechanics, we introduce a hierarchy of representations which meet uniqueness and target similarity criteria. To systematically control target similarity, we simply rely on interatomic many body expansions, as implemented in universal force-fields, including Bonding, Angular (BA), and higher order terms. Addition of higher order contributions systematically increases similarity to the true potential energy and predictive accuracy of the resulting ML models. We report numerical evidence for the performance of BAML models trained on molecular properties pre-calculated at electron-correlated and density functional theory level of theory for thousands of small organic molecules. Properties studied include enthalpies and free energies of atomization, heat capacity, zero-point vibrational energies, dipole-moment, polarizability, HOMO/LUMO energies and gap, ionization potential, electron affinity, and electronic excitations. After training, BAML predicts energies or electronic properties of out-of-sample molecules with unprecedented accuracy and speed.

Lorentz-like force emerging from kinematic interactions between electrons and nuclei in molecules: A quantum mechanical origin of symmetry breaking that can trigger molecular chirality.

PubMed

Takatsuka, Kazuo

2017-02-28

The Longuet-Higgins (Berry) phase arising from nonadiabatic dynamics and the Aharonov-Bohm phase associated with the dynamics of a charged particle in the electromagnetic vector potential are well known to be individually a manifestation of a class of the so-called geometrical phase. We herein discuss another similarity between the force working on a charged particle moving in a magnetic field, the Lorentz force, and a force working on nuclei while passing across a region where they have a strong quantum mechanical kinematic (nonadiabatic) coupling with electrons in a molecule. This kinematic force is indeed akin to the Lorentz force in that its magnitude is proportional to the velocity of the relevant nuclei and works in the direction perpendicular to its translational motion. Therefore this Lorentz-like nonadiabatic force is realized only in space of more or equal to three dimensions, thereby highlighting a truly multi-dimensional effect of nonadiabatic interaction. We investigate its physical significance qualitatively in the context of breaking of molecular spatial symmetry, which is not seen otherwise without this force. This particular symmetry breaking is demonstrated in application to a coplanar collision between a planar molecule and an atom sharing the same plane. We show that the atom is guided by this force to the direction out from the plane, resulting in a configuration that distinguishes one side of the mirror plane from the other. This can serve as a trigger for the dynamics towards molecular chirality.

Displacement of disordered water molecules from hydrophobic pocket creates enthalpic signature: binding of phosphonamidate to the S₁'-pocket of thermolysin.

PubMed

Englert, L; Biela, A; Zayed, M; Heine, A; Hangauer, D; Klebe, G

2010-11-01

Prerequisite for the design of tight binding protein inhibitors and prediction of their properties is an in-depth understanding of the structural and thermodynamic details of the binding process. A series of closely related phosphonamidates was studied to elucidate the forces underlying their binding affinity to thermolysin. The investigated inhibitors are identical except for the parts penetrating into the hydrophobic S₁'-pocket. A correlation of structural, kinetic and thermodynamic data was carried out by X-ray crystallography, kinetic inhibition assay and isothermal titration calorimetry. Binding affinity increases with larger ligand hydrophobic P₁'-moieties accommodating the S₁'-pocket. Surprisingly, larger P₁'-side chain modifications are accompanied by an increase in the enthalpic contribution to binding. In agreement with other studies, it is suggested that the release of largely disordered waters from an imperfectly hydrated pocket results in an enthalpically favourable integration of these water molecules into bulk water upon inhibitor binding. This enthalpically favourable process contributes more strongly to the binding energetics than the entropy increase resulting from the release of water molecules from the S₁'-pocket or the formation of apolar interactions between protein and inhibitor. Displacement of highly disordered water molecules from a rather imperfectly hydrated and hydrophobic specificity pocket can reveal an enthalpic signature of inhibitor binding. Copyright © 2010 Elsevier B.V. All rights reserved.

Hands-on Force Spectroscopy: Weird Springs and Protein Folding

ERIC Educational Resources Information Center

Euler, Manfred

2008-01-01

A force spectroscopy model experiment is presented using a low-cost tensile apparatus described earlier. Force-extension measurements of twisted rubber bands are obtained. They exhibit a complex nonlinear elastic behaviour that resembles atomic force spectroscopy investigations of molecules of titin, a muscle protein. The model experiments open up…

Anomalous Protein-Protein Interactions in Multivalent Salt Solution.

PubMed

Pasquier, Coralie; Vazdar, Mario; Forsman, Jan; Jungwirth, Pavel; Lund, Mikael

2017-04-13

The stability of aqueous protein solutions is strongly affected by multivalent ions, which induce ion-ion correlations beyond the scope of classical mean-field theory. Using all-atom molecular dynamics (MD) and coarse grained Monte Carlo (MC) simulations, we investigate the interaction between a pair of protein molecules in 3:1 electrolyte solution. In agreement with available experimental findings of "reentrant protein condensation", we observe an anomalous trend in the protein-protein potential of mean force with increasing electrolyte concentration in the order: (i) double-layer repulsion, (ii) ion-ion correlation attraction, (iii) overcharge repulsion, and in excess of 1:1 salt, (iv) non Coulombic attraction. To efficiently sample configurational space we explore hybrid continuum solvent models, applicable to many-protein systems, where weakly coupled ions are treated implicitly, while strongly coupled ones are treated explicitly. Good agreement is found with the primitive model of electrolytes, as well as with atomic models of protein and solvent.

Analytic calculations of hyper-Raman spectra from density functional theory hyperpolarizability gradients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ringholm, Magnus; Ruud, Kenneth; Bast, Radovan

We present the first analytic calculations of the geometrical gradients of the first hyperpolarizability tensors at the density-functional theory (DFT) level. We use the analytically calculated hyperpolarizability gradients to explore the importance of electron correlation effects, as described by DFT, on hyper-Raman spectra. In particular, we calculate the hyper-Raman spectra of the all-trans and 11-cis isomers of retinal at the Hartree-Fock (HF) and density-functional levels of theory, also allowing us to explore the sensitivity of the hyper-Raman spectra on the geometrical characteristics of these structurally related molecules. We show that the HF results, using B3LYP-calculated vibrational frequencies and force fields,more » reproduce the experimental data for all-trans-retinal well, and that electron correlation effects are of minor importance for the hyper-Raman intensities.« less

Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge

PubMed Central

Tofoleanu, Florentina; Pickard, Frank C.; König, Gerhard; Huang, Jing; Damjanović, Ana; Baek, Minkyung; Seok, Chaok; Brooks, Bernard R.

2016-01-01

Herein, we report the absolute binding free energy calculations of CBClip complexes in the SAMPL5 blind challenge. Initial conformations of CBClip complexes were obtained using docking and molecular dynamics simulations. Free energy calculations were performed using thermodynamic integration (TI) with soft-core potentials and Bennett’s acceptance ratio (BAR) method based on a serial insertion scheme. We compared the results obtained with TI simulations with soft-core potentials and Hamiltonian replica exchange simulations with the serial insertion method combined with the BAR method. The results show that the difference between the two methods can be mainly attributed to the van der Waals free energies, suggesting that either the simulations used for TI or the simulations used for BAR, or both are not fully converged and the two sets of simulations may have sampled difference phase space regions. The penalty scores of force field parameters of the 10 guest molecules provided by CHARMM Generalized Force Field can be an indicator of the accuracy of binding free energy calculations. Among our submissions, the combination of docking and TI performed best, which yielded the root mean square deviation of 2.94 kcal/mol and an average unsigned error of 3.41 kcal/mol for the ten guest molecules. These values were best overall among all participants. However, our submissions had little correlation with experiments. PMID:27677749

Capping of Aβ42 Oligomers by Small Molecule Inhibitors

PubMed Central

2015-01-01

Aβ42 peptides associate into soluble oligomers and protofibrils in the process of forming the amyloid fibrils associated with Alzheimer’s disease. The oligomers have been reported to be more toxic to neurons than fibrils, and have been targeted by a wide range of small molecule and peptide inhibitors. With single touch atomic force microscopy (AFM), we show that monomeric Aβ42 forms two distinct types of oligomers, low molecular weight (MW) oligomers with heights of 1–2 nm and high MW oligomers with heights of 3–5 nm. In both cases, the oligomers are disc-shaped with diameters of ∼10–15 nm. The similar diameters suggest that the low MW species stack to form the high MW oligomers. The ability of Aβ42 inhibitors to interact with these oligomers is probed using atomic force microscopy and NMR spectroscopy. We show that curcumin and resveratrol bind to the N-terminus (residues 5–20) of Aβ42 monomers and cap the height of the oligomers that are formed at 1–2 nm. A second class of inhibitors, which includes sulindac sulfide and indomethacin, exhibit very weak interactions across the Aβ42 sequence and do not block the formation of the high MW oligomers. The correlation between N-terminal interactions and capping of the height of the Aβ oligomers provides insights into the mechanism of inhibition and the pathway of Aβ aggregation. PMID:25422864

Crystal Engineering; How molecules build solids

NASA Astrophysics Data System (ADS)

Williams, Jeffrey H.

2017-09-01

There are more than 20 million chemicals in the literature, with new materials being synthesized each week. Most of these molecules are stable, and the 3-dimensional arrangement of the atoms in the molecules, in the various solids may be determined by routine x-ray crystallography. When this is done, it is found that this vast range of molecules, with varying sizes and shapes can be accommodated by only a handful of solid structures. This limited number of architectures for the packing of molecules of all shapes and sizes, to maximize attractive intermolecular forces and minimizing repulsive intermolecular forces, allows us to develop simple models of what holds the molecules together in the solid. In this volume we look at the origin of the molecular architecture of crystals; a topic that is becoming increasingly important and is often termed, crystal engineering. Such studies are a means of predicting crystal structures, and of designing crystals with particular properties by manipulating the structure and interaction of large molecules. That is, creating new crystal architectures with desired physical characteristics in which the molecules pack together in particular architectures; a subject of particular interest to the pharmaceutical industry.

High-speed atomic force microscopy for observing protein molecules in dynamic action

NASA Astrophysics Data System (ADS)

Ando, T.

2017-02-01

Directly observing protein molecules in dynamic action at high spatiotemporal resolution has long been a holy grail for biological science. To materialize this long quested dream, I have been developing high-speed atomic force microscopy (HS-AFM) since 1993. Tremendous strides were recently accomplished in its high-speed and low-invasive performances. Consequently, various dynamic molecular actions, including bipedal walking of myosin V and rotary propagation of structural changes in F1-ATPase, were successfully captured on video. The visualized dynamic images not only provided irrefutable evidence for speculated actions of the protein molecules but also brought new discoveries inaccessible with other approaches, thus giving great mechanistic insights into how the molecules function. HS-AFM is now transforming "static" structural biology into dynamic structural bioscience.

Resolving DNA-ligand intercalation in the entropic stretching regime

NASA Astrophysics Data System (ADS)

Almaqwashi, Ali A.

Single molecule studies of DNA intercalation are typically conducted by applying stretching forces to obtain force-dependent DNA elongation measurements. The zero-force properties of DNA intercalation are determined by equilibrium and kinetic force-analysis. However, the applied stretching forces that are above the entropic regime (>5 pN) prevent DNA-DNA contact which may eliminate competitive DNA-ligand interactions. In particular, it is noted that cationic mono-intercalators investigated by single molecule force spectroscopy are mostly found to intercalate DNA with single rate, while bulk studies reported additional slower rates. Here, a proposed framework quantifies DNA intercalation by cationic ligands in competition with relatively rapid kinetic DNA-ligand aggregation. At a constant applied force in the entropic stretching regime, the analysis illustrates that DNA intercalation would be measurably optimized only within a narrow range of low ligand concentrations. As DNA intercalators are considered for potential DNA-targeted therapeutics, this analysis provides insights in tuning ligand concertation to maximize therapeutics efficiency.

Nanoscale Trapping and Squeeze-Out of Confined Alkane Monolayers.

PubMed

Gosvami, N N; O'Shea, S J

2015-12-01

We present combined force curve and conduction atomic force microscopy (AFM) data for the linear alkanes CnH2n+2 (n = 10, 12, 14, 16) confined between a gold-coated AFM tip and a graphite surface. Solvation layering is observed in the force curves for all liquids, and conduction AFM is used to study in detail the removal of the confined (mono)layer closest to the graphite surface. The squeeze-out behavior of the monolayer can be very different depending upon the temperature. Below the monolayer melting transition temperatures the molecules are in an ordered state on the graphite surface, and fast and complete removal of the confined molecules is observed. However, above the melting transition temperature the molecules are in a disordered state, and even at large applied pressure a few liquid molecules are trapped within the tip-sample contact zone. These findings are similar to a previous study for branched alkanes [ Gosvami Phys. Rev. Lett. 2008, 100, 076101 ], but the observation for the linear alkane homologue series demonstrates clearly the dependence of the squeeze-out and trapping on the state of the confined material.

Releasing the brakes while hanging on: Cortactin effects on actin-driven motility.

PubMed

Gov, Nir S; Bernheim-Groswasser, Anne

2012-01-01

Actin polymerization plays a major role in many cellular processes, including cell motility, vesicle trafficking, and pathogen propulsion. The transformation of the (protrusive) polymerization forces into directed motion requires that the growing filaments are positioned next to the surface. This is achieved by localization of surface actin nucleators (WASP), which then activate Arp2/3 complex to form new actin branches. Yet, the same surface-bound WASP molecule which initiates the nucleation of new actin branches, also inherently prevents the translation of the polymerization forces into motion, essentially because the WASP molecule has to be in contact with the network during the formation of the new branch. In our recent paper we show that cortactin relaxes this internal inhibition by enhancing the release of WASP-VCA molecule from the new branching site after nucleation is initiated. We show that this enhanced release has two major effects; it increases the turnover rate of branching per WASP molecule, and it decreases the friction-like force caused by the binding of the moving surface with respect to the growing actin network.

Effect of genome sequence on the force-induced unzipping of a DNA molecule.

PubMed

Singh, N; Singh, Y

2006-02-01

We considered a dsDNA polymer in which distribution of bases are random at the base pair level but ordered at a length of 18 base pairs and calculated its force elongation behaviour in the constant extension ensemble. The unzipping force F(y) vs. extension y is found to have a series of maxima and minima. By changing base pairs at selected places in the molecule we calculated the change in F(y) curve and found that the change in the value of force is of the order of few pN and the range of the effect depending on the temperature, can spread over several base pairs. We have also discussed briefly how to calculate in the constant force ensemble a pause or a jump in the extension-time curve from the knowledge of F(y).

A force-based protein biochip

NASA Astrophysics Data System (ADS)

Blank, K.; Mai, T.; Gilbert, I.; Schiffmann, S.; Rankl, J.; Zivin, R.; Tackney, C.; Nicolaus, T.; Spinnler, K.; Oesterhelt, F.; Benoit, M.; Clausen-Schaumann, H.; Gaub, H. E.

2003-09-01

A parallel assay for the quantification of single-molecule binding forces was developed based on differential unbinding force measurements where ligand-receptor interactions are compared with the unzipping forces of DNA hybrids. Using the DNA zippers as molecular force sensors, the efficient discrimination between specific and nonspecific interactions was demonstrated for small molecules binding to specific receptors, as well as for protein-protein interactions on protein arrays. Finally, an antibody sandwich assay with different capture antibodies on one chip surface and with the detection antibodies linked to a congruent surface via the DNA zippers was used to capture and quantify a recombinant hepatitis C antigen from solution. In this case, the DNA zippers enable not only discrimination between specific and nonspecific binding, but also allow for the local application of detection antibodies, thereby eliminating false-positive results caused by cross-reactive antibodies and nonspecific binding.

Digital force-feedback for protein unfolding experiments using atomic force microscopy

NASA Astrophysics Data System (ADS)

Bippes, Christian A.; Janovjak, Harald; Kedrov, Alexej; Muller, Daniel J.

2007-01-01

Since its invention in the 1990s single-molecule force spectroscopy has been increasingly applied to study protein (un-)folding, cell adhesion, and ligand-receptor interactions. In most force spectroscopy studies, the cantilever of an atomic force microscope (AFM) is separated from a surface at a constant velocity, thus applying an increasing force to folded bio-molecules or bio-molecular bonds. Recently, Fernandez and co-workers introduced the so-called force-clamp technique. Single proteins were subjected to a defined constant force allowing their life times and life time distributions to be directly measured. Up to now, the force-clamping was performed by analogue PID controllers, which require complex additional hardware and might make it difficult to combine the force-feedback with other modes such as constant velocity. These points may be limiting the applicability and versatility of this technique. Here we present a simple, fast, and all-digital (software-based) PID controller that yields response times of a few milliseconds in combination with a commercial AFM. We demonstrate the performance of our feedback loop by force-clamp unfolding of single Ig27 domains of titin and the membrane proteins bacteriorhodopsin (BR) and the sodium/proton antiporter NhaA.

Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

NASA Technical Reports Server (NTRS)

Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

Thermophoretic force on nonspherical particles in the free-molecule regime

NASA Astrophysics Data System (ADS)

Yu, Song; Wang, Jun; Xia, Guodong; Zong, Luxiang

2018-05-01

The present paper is devoted to studying the thermophoresis of a nonspherical convex particle suspended in a gas with nonuniform temperature distribution in the free-molecule regime. Based on the gas kinetic theory and the assumption of a rigid-body collision for the gas-particle interaction, analytical expressions for the thermophoretic forces are obtained for several typical nonspherical bodies, including cylinders, spheroids, needles, disks, and cuboids. The orientation dependences of the thermophoretic forces and thermophoretic velocities are evaluated based on these expressions. It is found that the influence of the pitching effect of the nonspheres can be significant. The expressions for the orientation-averaged thermophoretic forces are also obtained under the assumption of a uniform particle orientation distribution.

CO tip functionalization in subatomic resolution atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Minjung; Chelikowsky, James R.

2015-10-01

Noncontact atomic force microscopy (nc-AFM) employing a CO-functionalized tip displays dramatically enhanced resolution wherein covalent bonds of polycyclic aromatic hydrocarbon can be imaged. Employing real-space pseudopotential first-principles calculations, we examine the role of CO in functionalizing the nc-AFM tip. Our calculations allow us to simulate full AFM images and ascertain the enhancement mechanism of the CO molecule. We consider two approaches: one with an explicit inclusion of the CO molecule and one without. By comparing our simulations to existing experimental images, we ascribe the enhanced resolution of the CO functionalized tip to the special orbital characteristics of the CO molecule.

CO tip functionalization in subatomic resolution atomic force microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Minjung; Chelikowsky, James R.

2015-10-19

Noncontact atomic force microscopy (nc-AFM) employing a CO-functionalized tip displays dramatically enhanced resolution wherein covalent bonds of polycyclic aromatic hydrocarbon can be imaged. Employing real-space pseudopotential first-principles calculations, we examine the role of CO in functionalizing the nc-AFM tip. Our calculations allow us to simulate full AFM images and ascertain the enhancement mechanism of the CO molecule. We consider two approaches: one with an explicit inclusion of the CO molecule and one without. By comparing our simulations to existing experimental images, we ascribe the enhanced resolution of the CO functionalized tip to the special orbital characteristics of the CO molecule.

Single-molecule force spectroscopy study of interactions between angiotensin II type 1 receptor and different biased ligands in living cells.

PubMed

Li, Wenhui; Xu, Jiachao; Kou, Xiaolong; Zhao, Rong; Zhou, Wei; Fang, Xiaohong

2018-05-01

Angiotensin II type 1 receptor (AT1R), a typical G protein-coupled receptor, plays a key role in regulating many cardiovascular functions. Different ligands can bind with AT1R to selectively activate either G protein (Gq) or β-arrestin (β-arr) pathway, or both pathways, but the molecular mechanism is not clear yet. In this work, we used, for the first time, atomic force microscopy-based single molecule force spectroscopy (SMFS) to study the interactions of AT1R with three types of ligands, balanced ligand, Gq-biased ligand, and β-arr-biased ligand, in living cells. The results revealed their difference in binding force and binding stability. The complex of the Gq-biased ligand-AT1R overcame two energy barriers with an intermediate state during dissociation, whereas that of β-arr-biased ligand-AT1R complex overcame one energy barrier. This indicated that AT1R had different ligand-binding conformational substates and underwent different structural changes to activate downstream signaling pathways with variable agonist efficacies. Quantitative analysis of AT1R-ligand binding in living cells at the single-molecule level offers a new tool to study the molecular mechanism of AT1R biased activation. Graphical Abstract Single-molecule force measurement on the living cell expressing AT1R-eGFP with a ligand modified AFM tip (left), the dynamic force spectra of β-arrestin biased ligands-AT1R (middle), and Gq-biased ligands-AT1R (right). The complexes of β-arr-biased ligand-AT1R overcame one energy barrier, with one linear region in the spectra, whereas the Gq-biased ligand-AT1R complexes overcame two energy barriers with two linear regions.

Radical Chemistry and Charge Manipulation with an Atomic Force Microscope

NASA Astrophysics Data System (ADS)

Gross, Leo

The fuctionalization of tips by atomic manipulation dramatically increased the resolution of atomic force microscopy (AFM). The combination of high-resolution AFM with atomic manipulation now offers the unprecedented possibility to custom-design individual molecules by making and breaking bonds with the tip of the microscope and directly characterizing the products on the atomic scale. We recently applied this technique to generate and study reaction intermediates and to investigate chemical reactions trigged by atomic manipulation. We formed diradicals by dissociating halogen atoms and then reversibly triggered ring-opening and -closing reactions via atomic manipulation, allowing us to switch and control the molecule's reactivity, magnetic and optical properties. Additional information about charge states and charge distributions can be obtained by Kelvin probe force spectroscopy. On multilayer insulating films we investigated single-electron attachment, detachment and transfer between individual molecules. EU ERC AMSEL (682144), EU project PAMS (610446).

Measuring the mechanical properties of molecular conformers

NASA Astrophysics Data System (ADS)

Jarvis, S. P.; Taylor, S.; Baran, J. D.; Champness, N. R.; Larsson, J. A.; Moriarty, P.

2015-09-01

Scanning probe-actuated single molecule manipulation has proven to be an exceptionally powerful tool for the systematic atomic-scale interrogation of molecular adsorbates. To date, however, the extent to which molecular conformation affects the force required to push or pull a single molecule has not been explored. Here we probe the mechanochemical response of two tetra(4-bromophenyl)porphyrin conformers using non-contact atomic force microscopy where we find a large difference between the lateral forces required for manipulation. Remarkably, despite sharing very similar adsorption characteristics, variations in the potential energy surface are capable of prohibiting probe-induced positioning of one conformer, while simultaneously permitting manipulation of the alternative conformational form. Our results are interpreted in the context of dispersion-corrected density functional theory calculations which reveal significant differences in the diffusion barriers for each conformer. These results demonstrate that conformational variation significantly modifies the mechanical response of even simple porpyhrins, potentially affecting many other flexible molecules.

Ab initio simulations of subatomic resolution images in noncontact atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Minjung; Chelikowsky, James R.

2015-03-01

Direct imaging of polycyclic aromatic molecules with a subatomic resolution has recently been achieved with noncontact atomic force microscopy (nc-AFM). Specifically, nc-AFM employing a CO functionalized tip has provided details of the chemical bond in aromatic molecules, including the discrimination of bond order. However, the underlying physics of such high resolution imaging remains problematic. By employing new, efficient algorithms based on real space pseudopotentials, we calculate the forces between the nc-AFM tip and specimen. We simulate images of planar organic molecules with two different approaches: 1) with a chemically inert tip and 2) with a CO functionalized tip. We find dramatic differences in the resulting images, which are consistent with recent experimental work. Our work is supported by the DOE under DOE/DE-FG02-06ER46286 and by the Welch Foundation under Grant F-1837. Computational resources were provided by NERSC and XSEDE.

Chiral Asymmetric Structures in Aspartic Acid and Valine Crystals Assessed by Atomic Force Microscopy.

PubMed

Teschke, Omar; Soares, David Mendez

2016-03-29

Structures of crystallized deposits formed by the molecular self-assembly of aspartic acid and valine on silicon substrates were imaged by atomic force microscopy. Images of d- and l-aspartic acid crystal surfaces showing extended molecularly flat sheets or regions separated by single molecule thick steps are presented. Distinct orientation surfaces were imaged, which, combined with the single molecule step size, defines the geometry of the crystal. However, single molecule step growth also reveals the crystal chirality, i.e., growth orientations. The imaged ordered lattice of aspartic acid (asp) and valine (val) mostly revealed periodicities corresponding to bulk terminations, but a previously unreported molecular hexagonal lattice configuration was observed for both l-asp and l-val but not for d-asp or d-val. Atomic force microscopy can then be used to identify the different chiral forms of aspartic acid and valine crystals.

Fast kinetics of chromatin assembly revealed by single-molecule videomicroscopy and scanning force microscopy

PubMed Central

Ladoux, Benoit; Quivy, Jean-Pierre; Doyle, Patrick; Roure, Olivia du; Almouzni, Geneviève; Viovy, Jean-Louis

2000-01-01

Fluorescence videomicroscopy and scanning force microscopy were used to follow, in real time, chromatin assembly on individual DNA molecules immersed in cell-free systems competent for physiological chromatin assembly. Within a few seconds, molecules are already compacted into a form exhibiting strong similarities to native chromatin fibers. In these extracts, the compaction rate is more than 100 times faster than expected from standard biochemical assays. Our data provide definite information on the forces involved (a few piconewtons) and on the reaction path. DNA compaction as a function of time revealed unique features of the assembly reaction in these extracts. They imply a sequential process with at least three steps, involving DNA wrapping as the final event. An absolute and quantitative measure of the kinetic parameters of the early steps in chromatin assembly under physiological conditions could thus be obtained. PMID:11114182

Entangling and disentangling many-electron quantum systems with an electric field

NASA Astrophysics Data System (ADS)

Sajjan, Manas; Head-Marsden, Kade; Mazziotti, David A.

2018-06-01

We show that the electron correlation of a molecular system can be enhanced or diminished through the application of a homogeneous electric field antiparallel or parallel to the system's intrinsic dipole moment. More generally, we prove that any external stimulus that significantly changes the expectation value of a one-electron operator with nondegenerate minimum and maximum eigenvalues can be used to control the degree of a molecule's electron correlation. Computationally, the effect is demonstrated in HeH+, MgH+, BH, HCN, H2O , HF, formaldehyde, and a fluorescent dye. Furthermore, we show in calculations with an array of formaldehyde (CH2O ) molecules that the field can control not only the electron correlation of a single formaldehyde molecule but also the entanglement among formaldehyde molecules. The quantum control of correlation and entanglement has potential applications in the design of molecules with tunable properties and the stabilization of qubits in quantum computations.

Harmonic force spectroscopy reveals a force-velocity curve from a single human beta cardiac myosin motor

NASA Astrophysics Data System (ADS)

Sung, Jongmin; Nag, Suman; Vestergaard, Christian; Mortensen, Kim; Flyvbjerg, Henrik; Spudich, James

2014-03-01

A muscle contracts rapidly under low load, but slowly under high load. Its molecular mechanisms remain to be elucidated, however. During contraction, myosins in thick filaments interact with actin in thin filaments in the sarcomere, cycling between a strongly bound (force producing) state and a weakly bound (relaxed) state. Huxley et al. have previously proposed that the transition from the strong to the weak interaction can be modulated by a load. We use a new method we call ``harmonic force spectroscopy'' to extract a load-velocity curve from a single human beta cardiac myosin II motor. With a dual-beam optical trap, we hold an actin dumbbell over a myosin molecule anchored to the microscope stage that oscillates sinusoidally. Upon binding, the motor experiences an oscillatory load with a mean that is directed forward or backward, depending on binding location We find that the bound time at saturating [ATP] is exponentially correlated with the mean load, which is explained by Arrhenius transition theory. With a stroke size measurement, we obtained a load-velocity curve from a single myosin. We compare the curves for wild-type motors with mutants that cause hypertrophic cardiomyopathies, to understand the effects on the contractile cycle

Monovalent Strep-Tactin for strong and site-specific tethering in nanospectroscopy.

PubMed

Baumann, Fabian; Bauer, Magnus S; Milles, Lukas F; Alexandrovich, Alexander; Gaub, Hermann E; Pippig, Diana A

2016-01-01

Strep-Tactin, an engineered form of streptavidin, binds avidly to the genetically encoded peptide Strep-tag II in a manner comparable to streptavidin binding to biotin. These interactions have been used in protein purification and detection applications. However, in single-molecule studies, for example using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS), the tetravalency of these systems impedes the measurement of monodispersed data. Here, we introduce a monovalent form of Strep-Tactin that harbours a unique binding site for Strep-tag II and a single cysteine that allows Strep-Tactin to specifically attach to the atomic force microscope cantilever and form a consistent pulling geometry to obtain homogeneous rupture data. Using AFM-SMFS, the mechanical properties of the interaction between Strep-tag II and monovalent Strep-Tactin were characterized. Rupture forces comparable to biotin:streptavidin unbinding were observed. Using titin kinase and green fluorescent protein, we show that monovalent Strep-Tactin is generally applicable to protein unfolding experiments. We expect monovalent Strep-Tactin to be a reliable anchoring tool for a range of single-molecule studies.

Monovalent Strep-Tactin for strong and site-specific tethering in nanospectroscopy

NASA Astrophysics Data System (ADS)

Baumann, Fabian; Bauer, Magnus S.; Milles, Lukas F.; Alexandrovich, Alexander; Gaub, Hermann E.; Pippig, Diana A.

2016-01-01

Strep-Tactin, an engineered form of streptavidin, binds avidly to the genetically encoded peptide Strep-tag II in a manner comparable to streptavidin binding to biotin. These interactions have been used in protein purification and detection applications. However, in single-molecule studies, for example using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS), the tetravalency of these systems impedes the measurement of monodispersed data. Here, we introduce a monovalent form of Strep-Tactin that harbours a unique binding site for Strep-tag II and a single cysteine that allows Strep-Tactin to specifically attach to the atomic force microscope cantilever and form a consistent pulling geometry to obtain homogeneous rupture data. Using AFM-SMFS, the mechanical properties of the interaction between Strep-tag II and monovalent Strep-Tactin were characterized. Rupture forces comparable to biotin:streptavidin unbinding were observed. Using titin kinase and green fluorescent protein, we show that monovalent Strep-Tactin is generally applicable to protein unfolding experiments. We expect monovalent Strep-Tactin to be a reliable anchoring tool for a range of single-molecule studies.

Single Molecule Junctions: A Laboratory for Chemistry, Mechanics and Bond Rupture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hybertsen M. S.

Simultaneous measurement [1] of junction conductance and sustained force in single molecule junctions bridging metal electrodes provides a powerful tool in the quantitative study of the character of molecule-metal bonds. In this talk I will discuss three topics. First, I will describe chemical trends in link bond strength based on experiments and Density Functional Theory based calculations. Second, I will focus on the specific case of pyridine-linked junctions. Bond rupture from the high conductance junction structure shows a requires a force that exceeds the rupture force of gold point contacts and clearly indicates the role of additional forces, beyond themore » specific N-Au donor acceptor bond. DFT-D2 calculations with empirical addition of dispersion interactions illustrates the interplay between the donor-acceptor bonding and the non-specific van der Waals interactions between the pyridine rings and Au asperities. Third, I will describe recent efforts to characterize the diversity of junction structures realized in break-junction experiments with suitable models for the potential surfaces that are observed. [1] Venkataraman Group, Columbia University.« less

Microgravity

NASA Image and Video Library

2000-11-15

Watching molecules of the iron-storing protein apoferritin come together to form a nucleus reveals some interesting behavior. In this series of images, researchers observed clusters of four molecules at the corners of a diamond shape (top). As more molecules attach to the cluster, they arrange themselves into rods (second from top), and a raft-like configuration of molecules forms the critical nucleus (third from top), suggesting that crystal growth is much slower than it could be were the molecules arranged in a more compact formation. In the final image, a crystallite consisting of three layers containing approximately 60 to 70 molecules each is formed. Atomic force microscopy made visualizing the process of nucleation possible for the first time. The principal investigator is Peter Vekilov, of the University of Alabama in Huntsville. Vekilov's team at UAH studies protein solutions as they change phases from liquids to crystalline solids. They want to know if the molecules in the solution interact with one another, and if so, how, from the perspectives of thermodynamics and kinetics. They want to understand which forces -- electrical, electrostatic, hydrodynamic, or other kinds of forces -- are responsible for the interactions. They also study nucleation, the begirning stage of crystallization. This process is important to understand because it sets the stage for crystal growth in all kinds of solutions and liquid melts that are important in such diverse fields as agriculture, medicine, and the fabrication of metal components. Nucleation can determine the rate of crystal growth, the number of crystals that will be formed, and the quality and size of the crystals.

Cost-Effective Method for Free-Energy Minimization in Complex Systems with Elaborated Ab Initio Potentials.

PubMed

Bistafa, Carlos; Kitamura, Yukichi; Martins-Costa, Marilia T C; Nagaoka, Masataka; Ruiz-López, Manuel F

2018-06-12

We describe a method to locate stationary points in the free-energy hypersurface of complex molecular systems using high-level correlated ab initio potentials. In this work, we assume a combined QM/MM description of the system although generalization to full ab initio potentials or other theoretical schemes is straightforward. The free-energy gradient (FEG) is obtained as the mean force acting on relevant nuclei using a dual level strategy. First, a statistical simulation is carried out using an appropriate, low-level quantum mechanical force-field. Free-energy perturbation (FEP) theory is then used to obtain the free-energy derivatives for the target, high-level quantum mechanical force-field. We show that this composite FEG-FEP approach is able to reproduce the results of a standard free-energy minimization procedure with high accuracy, while simultaneously allowing for a drastic reduction of both computational and wall-clock time. The method has been applied to study the structure of the water molecule in liquid water at the QCISD/aug-cc-pVTZ level of theory, using the sampling from QM/MM molecular dynamics simulations at the B3LYP/6-311+G(d,p) level. The obtained values for the geometrical parameters and for the dipole moment of the water molecule are within the experimental error, and they also display an excellent agreement when compared to other theoretical estimations. The developed methodology represents therefore an important step toward the accurate determination of the mechanism, kinetics, and thermodynamic properties of processes in solution, in enzymes, and in other disordered chemical systems using state-of-the-art ab initio potentials.

Understanding gas-surface interactions from direct force measurements using a specialized torsion balance

NASA Technical Reports Server (NTRS)

Cook, S. R.; Hoffbauer, M. A.

1996-01-01

The first comprehensive measurements of the magnitude and direction of the forces exerted on surfaces by molecular beams are discussed and used to obtain information about the microscopic properties of the gas-surface interactions. This unique approach is not based on microscopic measurements of the scattered molecules. The reduced force coefficients are introduced as a new set of parameters that completely describe the macroscopic average momentum transfer to a surface by an incident molecular beam. By using a specialized torsion balance and molecular beams of N2, CO, CO2, and H2, the reduced force coefficients are determined from direct measurements of the force components exerted on surface of a solar panel array material, Kapton, SiO2-coated Kapton, and Z-93 as a function of the angle of incidence ranging from 0 degrees to 85 degrees. The absolute flux densities of the molecular beams were measured using a different torsion balance with a beam-stop that nullified the force of the scattered molecules. Standard time-of-flight techniques were used to determine the flux-weighted average velocities of the various molecular beams ranging from 1600 m/s to 4600 m/s. The reduced force coefficients can be used to directly obtain macroscopic average properties of the scattered molecules, such as the flux-weighted average velocity and translational energy, that can then be used to determine microscopic details concerning gas-surface interactions without the complications associated with averaging microscopic measurements.

Constitutive Models for the Force-Extension Behavior of Biological Filaments

NASA Astrophysics Data System (ADS)

Palmer, J. S.; Castro, C. E.; Arslan, M.; Boyce, M. C.

Biopolymer filaments form the molecular backbone of biological structures throughout the body. The biomechanical response of single filaments yields insight into their individual behavior at the molecular level as well as their concerted networked behavior at the cellular and tissue scales. This paper focuses on modeling approaches for axial force vs. extension behavior of single biopolymer filaments within three stiffness regimes: flexible, semiflexible, and stiff. The end-to-end force-extension behaviors of flexible and semiflexible filaments arise as a result of a reduction in configurational space as the filament is straightened and are captured with entropic models including the freely jointed chain model and the worm-like chain model. As the filament is straightened and the end-to-end distance approaches the filament contour length, the contour length is directly axially extended and an internal energy contribution governs the force-extension behavior in this limiting extension regime. On the other hand, for stiff filaments in originally crimped or kinked configurations, the end-to-end force vs. extension behavior results from the unbending (straightening) of the crimped configuration as governed by an internal energy based elastica approximation which is also complemented by an axial stretching contribution once the end-to-end distance approaches the contour length of the filament. Simplified, analytical force-extension relationships are developed for the worm-like chain model for semiflexible filaments, and for the Euler elastica model for stiffer, wavy fibers. For the case of flexible molecules containing modular folded domains, the influence of force-induced unfolding on the force-extension behavior of single molecules and assemblies of multiple molecules is also presented.

Molecular simulation study on Hofmeister cations and the aqueous solubility of benzene.

PubMed

Ganguly, Pritam; Hajari, Timir; van der Vegt, Nico F A

2014-05-22

We study the ion-specific salting-out process of benzene in aqueous alkali chloride solutions using Kirkwood-Buff (KB) theory of solutions and molecular dynamics simulations with different empirical force field models for the ions and benzene. Despite inaccuracies in the force fields, the simulations indicate that the decrease of the Setchenow salting-out coefficient for the series NaCl > KCl > RbCl > CsCl is determined by direct benzene-cation correlations, with the larger cations showing weak interactions with benzene. Although ion-specific aqueous solubilities of benzene may be affected by indirect ion-ion, ion-water, and water-water correlations, too, these correlations are found to be unimportant, with little to no effect on the Setchenow salting-out coefficients of the various salts. We further considered LiCl, which is experimentally known to be a weaker salting-out agent than NaCl and KCl and, therefore, ranks at an unusual position within the Hofmeister cation series. The simulations indicate that hydrated Li(+) ions can take part of the benzene hydration shell while the other cations are repelled by it. This causes weaker Li(+) exclusion around the solute and a resulting, weaker salting-out propensity of LiCl compared to that of the other salts. Removing benzene-water and benzene-salt electrostatic interactions in the simulations does not affect this mechanism, which may therefore also explain the smaller effect of LiCl, as compared to that of NaCl or KCl, on aqueous solvation and hydrophobic interaction of nonpolar molecules.

Thermophoresis of dissolved molecules and polymers: Consideration of the temperature-induced macroscopic pressure gradient

NASA Astrophysics Data System (ADS)

Semenov, Semen; Schimpf, Martin

2004-01-01

The movement of molecules and homopolymer chains dissolved in a nonelectrolyte solvent in response to a temperature gradient is considered a consequence of temperature-induced pressure gradients in the solvent layer surrounding the solute molecules. Local pressure gradients are produced by nonuniform London van der Waals interactions, established by gradients in the concentration (density) of solvent molecules. The density gradient is produced by variations in solvent thermal expansion within the nonuniform temperature field. The resulting expression for the velocity of the solute contains the Hamaker constants for solute-solvent and solute-solute interactions, the radius of the solute molecule, and the viscosity and cubic coefficient of thermal expansion of the solvent. In this paper we consider an additional force that arises from directional asymmetry in the interaction between solvent molecules. In a closed cell, the resulting macroscopic pressure gradient gives rise to a volume force that affects the motion of dissolved solutes. An expression for this macroscopic pressure gradient is derived and the resulting force is incorporated into the expression for the solute velocity. The expression is used to calculate thermodiffusion coefficients for polystyrene in several organic solvents. When these values are compared to those measured in the laboratory, the consistency is better than that found in previous reports, which did not consider the macroscopic pressure gradient that arises in a closed thermodiffusion cell. The model also allows for the movement of solute in either direction, depending on the relative values of the solvent and solute Hamaker constants.

Molecular mechanism of extreme mechanostability in a pathogen adhesin.

PubMed

Milles, Lukas F; Schulten, Klaus; Gaub, Hermann E; Bernardi, Rafael C

2018-03-30

High resilience to mechanical stress is key when pathogens adhere to their target and initiate infection. Using atomic force microscopy-based single-molecule force spectroscopy, we explored the mechanical stability of the prototypical staphylococcal adhesin SdrG, which targets a short peptide from human fibrinogen β. Steered molecular dynamics simulations revealed, and single-molecule force spectroscopy experiments confirmed, the mechanism by which this complex withstands forces of over 2 nanonewtons, a regime previously associated with the strength of a covalent bond. The target peptide, confined in a screwlike manner in the binding pocket of SdrG, distributes forces mainly toward the peptide backbone through an intricate hydrogen bond network. Thus, these adhesins can attach to their target with exceptionally resilient mechanostability, virtually independent of peptide side chains. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Rapid internal contraction boosts DNA friction.

PubMed

Otto, Oliver; Sturm, Sebastian; Laohakunakorn, Nadanai; Keyser, Ulrich F; Kroy, Klaus

2013-01-01

Macroscopic objects are usually manipulated by force and observed with light. On the nanoscale, however, this is often done oppositely: individual macromolecules are manipulated by light and monitored with force. This procedure, which is the basis of single-molecule force spectroscopy, has led to much of our quantitative understanding of how DNA works, and is now routinely applied to explore molecular structure and interactions, DNA-protein reactions and protein folding. Here we develop the technique further by introducing a dynamic force spectroscopy set-up for a non-invasive inspection of the tension dynamics in a taut strand of DNA. The internal contraction after a sudden release of the molecule is shown to give rise to a drastically enhanced viscous friction, as revealed by the slow relaxation of an attached colloidal tracer. Our systematic theory explains the data quantitatively and provides a powerful tool for the rational design of new dynamic force spectroscopy assays.

Elastin-like Polypeptide Linkers for Single-Molecule Force Spectroscopy.

PubMed

Ott, Wolfgang; Jobst, Markus A; Bauer, Magnus S; Durner, Ellis; Milles, Lukas F; Nash, Michael A; Gaub, Hermann E

2017-06-27

Single-molecule force spectroscopy (SMFS) is by now well established as a standard technique in biophysics and mechanobiology. In recent years, the technique has benefitted greatly from new approaches to bioconjugation of proteins to surfaces. Indeed, optimized immobilization strategies for biomolecules and refined purification schemes are being steadily adapted and improved, which in turn has enhanced data quality. In many previously reported SMFS studies, poly(ethylene glycol) (PEG) was used to anchor molecules of interest to surfaces and/or cantilever tips. The limitation, however, is that PEG exhibits a well-known trans-trans-gauche to all-trans transition, which results in marked deviation from standard polymer elasticity models such as the worm-like chain, particularly at elevated forces. As a result, the assignment of unfolding events to protein domains based on their corresponding amino acid chain lengths is significantly obscured. Here, we provide a solution to this problem by implementing unstructured elastin-like polypeptides as linkers to replace PEG. We investigate the suitability of tailored elastin-like polypeptides linkers and perform direct comparisons to PEG, focusing on attributes that are critical for single-molecule force experiments such as linker length, monodispersity, and bioorthogonal conjugation tags. Our results demonstrate that by avoiding the ambiguous elastic response of mixed PEG/peptide systems and instead building the molecular mechanical systems with only a single bond type with uniform elastic properties, we improve data quality and facilitate data analysis and interpretation in force spectroscopy experiments. The use of all-peptide linkers allows alternative approaches for precisely defining elastic properties of proteins linked to surfaces.

Reactions and Transport: Diffusion, Inertia, and Subdiffusion

NASA Astrophysics Data System (ADS)

Méndez, Vicenç; Fedotov, Sergei; Horsthemke, Werner

Particles, such as molecules, atoms, or ions, and individuals, such as cells or animals, move in space driven by various forces or cues. In particular, particles or individuals can move randomly, undergo velocity jump processes or spatial jump processes [333]. The steps of the random walk can be independent or correlated, unbiased or biased. The probability density function (PDF) for the jump length can decay rapidly or exhibit a heavy tail. Similarly, the PDF for the waiting time between successive jumps can decay rapidly or exhibit a heavy tail. We will discuss these various possibilities in detail in Chap. 3. Below we provide an introduction to three transport processes: standard diffusion, transport with inertia, and anomalous diffusion.

Conformational Equilibria in Monomeric α-Synuclein at the Single-Molecule Level

PubMed Central

Tessari, Isabella; Mammi, Stefano; Bergantino, Elisabetta; Musiani, Francesco; Brucale, Marco; Bubacco, Luigi; Samorì, Bruno

2008-01-01

Human α-Synuclein (αSyn) is a natively unfolded protein whose aggregation into amyloid fibrils is involved in the pathology of Parkinson disease. A full comprehension of the structure and dynamics of early intermediates leading to the aggregated states is an unsolved problem of essential importance to researchers attempting to decipher the molecular mechanisms of αSyn aggregation and formation of fibrils. Traditional bulk techniques used so far to solve this problem point to a direct correlation between αSyn's unique conformational properties and its propensity to aggregate, but these techniques can only provide ensemble-averaged information for monomers and oligomers alike. They therefore cannot characterize the full complexity of the conformational equilibria that trigger the aggregation process. We applied atomic force microscopy–based single-molecule mechanical unfolding methodology to study the conformational equilibrium of human wild-type and mutant αSyn. The conformational heterogeneity of monomeric αSyn was characterized at the single-molecule level. Three main classes of conformations, including disordered and “β-like” structures, were directly observed and quantified without any interference from oligomeric soluble forms. The relative abundance of the “β-like” structures significantly increased in different conditions promoting the aggregation of αSyn: the presence of Cu2+, the pathogenic A30P mutation, and high ionic strength. This methodology can explore the full conformational space of a protein at the single-molecule level, detecting even poorly populated conformers and measuring their distribution in a variety of biologically important conditions. To the best of our knowledge, we present for the first time evidence of a conformational equilibrium that controls the population of a specific class of monomeric αSyn conformers, positively correlated with conditions known to promote the formation of aggregates. A new tool is thus made available to test directly the influence of mutations and pharmacological strategies on the conformational equilibrium of monomeric αSyn. PMID:18198943

Extracting physics of life at the molecular level: A review of single-molecule data analyses.

PubMed

Colomb, Warren; Sarkar, Susanta K

2015-06-01

Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques. Copyright © 2015 Elsevier B.V. All rights reserved.

Improving single molecule force spectroscopy through automated real-time data collection and quantification of experimental conditions

PubMed Central

Scholl, Zackary N.; Marszalek, Piotr E.

2013-01-01

The benefits of single molecule force spectroscopy (SMFS) clearly outweigh the challenges which include small sample sizes, tedious data collection and introduction of human bias during the subjective data selection. These difficulties can be partially eliminated through automation of the experimental data collection process for atomic force microscopy (AFM). Automation can be accomplished using an algorithm that triages usable force-extension recordings quickly with positive and negative selection. We implemented an algorithm based on the windowed fast Fourier transform of force-extension traces that identifies peaks using force-extension regimes to correctly identify usable recordings from proteins composed of repeated domains. This algorithm excels as a real-time diagnostic because it involves <30 ms computational time, has high sensitivity and specificity, and efficiently detects weak unfolding events. We used the statistics provided by the automated procedure to clearly demonstrate the properties of molecular adhesion and how these properties change with differences in the cantilever tip and protein functional groups and protein age. PMID:24001740

Forces and Dynamics of Glucose and Inhibitor Binding to Sodium Glucose Co-transporter SGLT1 Studied by Single Molecule Force Spectroscopy*

PubMed Central

Neundlinger, Isabel; Puntheeranurak, Theeraporn; Wildling, Linda; Rankl, Christian; Wang, Lai-Xi; Gruber, Hermann J.; Kinne, Rolf K. H.; Hinterdorfer, Peter

2014-01-01

Single molecule force spectroscopy was employed to investigate the dynamics of the sodium glucose co-transporter (SGLT1) upon substrate and inhibitor binding on the single molecule level. CHO cells stably expressing rbSGLT1 were probed by using atomic force microscopy tips carrying either thioglucose, 2′-aminoethyl β-d-glucopyranoside, or aminophlorizin. Poly(ethylene glycol) (PEG) chains of different length and varying end groups were used as tether. Experiments were performed at 10, 25 and 37 °C to address different conformational states of SGLT1. Unbinding forces between ligands and SGLT1 were recorded at different loading rates by changing the retraction velocity, yielding binding probability, width of energy barrier of the binding pocket, and the kinetic off rate constant of the binding reaction. With increasing temperature, width of energy barrier and average life time increased for the interaction of SGLT1 with thioglucose (coupled via acrylamide to a long PEG) but decreased for aminophlorizin binding. The former indicates that in the membrane-bound SGLT1 the pathway to sugar translocation involves several steps with different temperature sensitivity. The latter suggests that also the aglucon binding sites for transport inhibitors have specific, temperature-sensitive conformations. PMID:24962566

Titin domains progressively unfolded by force are homogenously distributed along the molecule.

PubMed

Bianco, Pasquale; Mártonfalvi, Zsolt; Naftz, Katalin; Kőszegi, Dorina; Kellermayer, Miklós

2015-07-21

Titin is a giant filamentous protein of the muscle sarcomere in which stretch induces the unfolding of its globular domains. However, the mechanisms of how domains are progressively selected for unfolding and which domains eventually unfold have for long been elusive. Based on force-clamp optical tweezers experiments we report here that, in a paradoxical violation of mechanically driven activation kinetics, neither the global domain unfolding rate, nor the folded-state lifetime distributions of full-length titin are sensitive to force. This paradox is reconciled by a gradient of mechanical stability so that domains are gradually selected for unfolding as the magnitude of the force field increases. Atomic force microscopic screening of extended titin molecules revealed that the unfolded domains are distributed homogenously along the entire length of titin, and this homogeneity is maintained with increasing overstretch. Although the unfolding of domains with progressively increasing mechanical stability makes titin a variable viscosity damper, the spatially randomized variation of domain stability ensures that the induced structural changes are not localized but are distributed along the molecule's length. Titin may thereby provide complex safety mechanims for protecting the sarcomere against structural disintegration under excessive mechanical conditions. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

A single molecule assay to probe monovalent and multivalent bonds between hyaluronan and its key leukocyte receptor CD44 under force

NASA Astrophysics Data System (ADS)

Bano, Fouzia; Banerji, Suneale; Howarth, Mark; Jackson, David G.; Richter, Ralf P.

2016-09-01

Glycosaminoglycans (GAGs), a category of linear, anionic polysaccharides, are ubiquitous in the extracellular space, and important extrinsic regulators of cell function. Despite the recognized significance of mechanical stimuli in cellular communication, however, only few single molecule methods are currently available to study how monovalent and multivalent GAG·protein bonds respond to directed mechanical forces. Here, we have devised such a method, by combining purpose-designed surfaces that afford immobilization of GAGs and receptors at controlled nanoscale organizations with single molecule force spectroscopy (SMFS). We apply the method to study the interaction of the GAG polymer hyaluronan (HA) with CD44, its receptor in vascular endothelium. Individual bonds between HA and CD44 are remarkably resistant to rupture under force in comparison to their low binding affinity. Multiple bonds along a single HA chain rupture sequentially and independently under load. We also demonstrate how strong non-covalent bonds, which are versatile for controlled protein and GAG immobilization, can be effectively used as molecular anchors in SMFS. We thus establish a versatile method for analyzing the nanomechanics of GAG·protein interactions at the level of single GAG chains, which provides new molecular-level insight into the role of mechanical forces in the assembly and function of GAG-rich extracellular matrices.

Rapid parameterization of small molecules using the Force Field Toolkit.

PubMed

Mayne, Christopher G; Saam, Jan; Schulten, Klaus; Tajkhorshid, Emad; Gumbart, James C

2013-12-15

The inability to rapidly generate accurate and robust parameters for novel chemical matter continues to severely limit the application of molecular dynamics simulations to many biological systems of interest, especially in fields such as drug discovery. Although the release of generalized versions of common classical force fields, for example, General Amber Force Field and CHARMM General Force Field, have posited guidelines for parameterization of small molecules, many technical challenges remain that have hampered their wide-scale extension. The Force Field Toolkit (ffTK), described herein, minimizes common barriers to ligand parameterization through algorithm and method development, automation of tedious and error-prone tasks, and graphical user interface design. Distributed as a VMD plugin, ffTK facilitates the traversal of a clear and organized workflow resulting in a complete set of CHARMM-compatible parameters. A variety of tools are provided to generate quantum mechanical target data, setup multidimensional optimization routines, and analyze parameter performance. Parameters developed for a small test set of molecules using ffTK were comparable to existing CGenFF parameters in their ability to reproduce experimentally measured values for pure-solvent properties (<15% error from experiment) and free energy of solvation (±0.5 kcal/mol from experiment). Copyright © 2013 Wiley Periodicals, Inc.

The Building Blocks of Materials: Gathering Knowledge at the Molecular Level

NASA Technical Reports Server (NTRS)

2003-01-01

Two start-up positions were created within SD46 to pursue developments in the rapidly expanding areas of biomineralization and nano-technology. As envisioned by Dr. Sandor Lehoczy, the new laboratories to be developed must have the capacity to investigate not only processes associated with the self-assembly of molecules but also the examination of self-assembled structures. For these purposes, laboratories capable of performing the intended function, particularly light scattering spectroscopy and atomic force microscopy were created. What follows then are recent advances arising from the development of these new laboratories. With the implementation of the Atomic Force Microscopy Facility, examples of investigations that determine a correlation between the molecular structure of materials and their macroscopic physical properties are provided. In addition, examples of investigations with particular emphasis on the physical properties of protein crystals, at the molecular level, and subsequent macroscopic characteristics are as provided. Finally, progress in fabrication of technology at the nano-scale levels at the developmental stage is also presented.

Direct quantitative measurement of the C═O⋅⋅⋅H–C bond by atomic force microscopy

PubMed Central

Kawai, Shigeki; Nishiuchi, Tomohiko; Kodama, Takuya; Spijker, Peter; Pawlak, Rémy; Meier, Tobias; Tracey, John; Kubo, Takashi; Meyer, Ernst; Foster, Adam S.

2017-01-01

The hydrogen atom—the smallest and most abundant atom—is of utmost importance in physics and chemistry. Although many analysis methods have been applied to its study, direct observation of hydrogen atoms in a single molecule remains largely unexplored. We use atomic force microscopy (AFM) to resolve the outermost hydrogen atoms of propellane molecules via very weak C═O⋅⋅⋅H–C hydrogen bonding just before the onset of Pauli repulsion. The direct measurement of the interaction with a hydrogen atom paves the way for the identification of three-dimensional molecules such as DNAs and polymers, building the capabilities of AFM toward quantitative probing of local chemical reactivity. PMID:28508080

1,3,5-trinitro-1,3,5-triazine decomposition and chemisorption on Al(111) surface: first-principles molecular dynamics study.

PubMed

Umezawa, Naoto; Kalia, Rajiv K; Nakano, Aiichiro; Vashista, Priya; Shimojo, Fuyuki

2007-06-21

We have investigated the decomposition and chemisorption of a 1,3,5-trinitro-1,3,5-triazine (RDX) molecule on Al(111) surface using molecular dynamics simulations, in which interatomic forces are computed quantum mechanically in the framework of the density functional theory (DFT). The real-space DFT calculations are based on higher-order finite difference and norm-conserving pseudopotential methods. Strong attractive forces between oxygen and aluminum atoms break N-O and N-N bonds in the RDX and, subsequently, the dissociated oxygen atoms and NO molecules oxidize the Al surface. In addition to these Al surface-assisted decompositions, ring cleavage of the RDX molecule is also observed. These reactions occur spontaneously without potential barriers and result in the attachment of the rest of the RDX molecule to the surface. This opens up the possibility of coating Al nanoparticles with RDX molecules to avoid the detrimental effect of oxidation in high energy density material applications.

Influence of external extrusion on stability of hydrogen molecule and its chaotic behavior

NASA Astrophysics Data System (ADS)

Jarosik, M. W.; SzczÈ©śniak, R.; Durajski, A. P.; Kalaga, J. K.; Leoński, W.

2018-01-01

We have determined the stability conditions of the hydrogen molecule under the influence of an external force of harmonic-type explicitly dependent on the amplitude (A) and frequency (Ω). The ground state of the molecule has been determined in the framework of the Born-Oppenheimer approximation, whereas the energy of the electronic subsystem has been calculated using the Hubbard model including all two-site electron interactions. The diagram of RT0(A ,Ω) , where RT0 denotes the distance between protons after the fixed initial time T0, allowed us to visualize the area of the instability with the complicated structure. We have shown that the vibrations of the hydrogen molecule have a chaotic nature for some points of the instability region. In addition to the amplitude and frequency of the extrusion, the control parameter of the stability of the molecule is the external force associated with pressure. The increase in its value causes the disappearance of the area of the instability and chaotic vibrations.

The structure and intermolecular forces of DNA condensates.

PubMed

Yoo, Jejoong; Aksimentiev, Aleksei

2016-03-18

Spontaneous assembly of DNA molecules into compact structures is ubiquitous in biological systems. Experiment has shown that polycations can turn electrostatic self-repulsion of DNA into attraction, yet the physical mechanism of DNA condensation has remained elusive. Here, we report the results of atomistic molecular dynamics simulations that elucidated the microscopic structure of dense DNA assemblies and the physics of interactions that makes such assemblies possible. Reproducing the setup of the DNA condensation experiments, we measured the internal pressure of DNA arrays as a function of the DNA-DNA distance, showing a quantitative agreement between the results of our simulations and the experimental data. Analysis of the MD trajectories determined the DNA-DNA force in a DNA condensate to be pairwise, the DNA condensation to be driven by electrostatics of polycations and not hydration, and the concentration of bridging cations, not adsorbed cations, to determine the magnitude and the sign of the DNA-DNA force. Finally, our simulations quantitatively characterized the orientational correlations of DNA in DNA arrays as well as diffusive motion of DNA and cations. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Surface force and vibrational spectroscopic analyses of interfacial water molecules in the vicinity of methoxy-tri(ethylene glycol)-terminated monolayers: mechanisms underlying the effect of lateral packing density on bioinertness.

PubMed

Sekine, Taito; Asatyas, Syifa; Sato, Chikako; Morita, Shigeaki; Tanaka, Masaru; Hayashi, Tomohiro

Unequivocal dependence of bioinertness of self-assembled monolayers of methoxy-tri(ethylene glycol)-terminated alkanethiol (EG3-OMe SAMs) on their packing density has been a mystery for more than two decades. We tackled this long-standing question by performing surface force and surface-enhanced infrared absorption (SEIRA) spectroscopic measurements. Our surface force measurements revealed a physical barrier of interfacial water in the vicinity of the Au-supported EG3-OMe SAM (low packing density), whereas the Ag-supported one (high packing density) did not possess such interfacial water. In addition, the results of SEIRA measurements clearly exhibited that hydrogen bonding states of the interfacial water differ depending on the substrates. We also characterized the bioinertness of these SAMs by protein adsorption tests and adhesion assays of platelet and human umbilical vein endothelial cells. The hydrogen bonding states of the interfacial water and water-induced interaction clearly correlated with the bioinertness of the SAMs, suggesting that the interfacial water plays an important role determining the interaction of the SAMs with biomolecules and cells.

Opening of DNA chain due to force applied on different locations.

PubMed

Singh, Amar; Modi, Tushar; Singh, Navin

2016-09-01

We consider a homogeneous DNA molecule and investigate the effect of random force applied on the unzipping profile of the molecule. How the critical force varies as a function of the chain length or number of base pairs is the objective of this study. In general, the ratio of the critical forces that is applied on the middle of the chain to that which is applied on one of the ends is two. Our study shows that this ratio depends on the length of the chain. This means that the force which is applied to a point can be experienced by a section of the chain. Beyond a length, the base pairs have no information about the applied force. In the case when the chain length is shorter than this length, this ratio may vary. Only in the case when the chain length exceeds a critical length, this ratio is found to be two. Based on the de Gennes formulation, we developed a method to calculate these forces at zero temperature. The exact results at zero temperature match numerical calculations.

Analysis of acid-base interactions at Al2O3 (11-20) interfaces by means of single molecule force spectroscopy

NASA Astrophysics Data System (ADS)

Mosebach, Bastian; Ozkaya, Berkem; Giner, Ignacio; Keller, Adrian; Grundmeier, Guido

2017-10-01

Single molecule force spectroscopy (SMFS) was employed to investigate the interaction forces between aliphatic amino, hydroxyl and ether groups and aluminum oxide single crystal surfaces in an aqueous electrolyte at pH = 6. The force studies were based on the variation of the terminal group of polyethylene glycol which was bound via a Ssbnd Au bond to the gold coated AFM tip. X-ray Photoelectron Spectroscopy (XPS) was performed to characterize the surface chemistry of the substrate. Force distance curves were measured between the PEG-NH2, sbnd OH and sbnd OCH3 functionalized atomic force microscope (AFM) tip and the non-polar single crystalline Al2O3(11-20) surface. The experimental results exhibit non-equilibrium desorption events which hint at acid-base interactions of the electron donating hydroxyl and amino groups with Al-ions in the surface of the oxide. The observed desorption forces for the sbnd NH2, sbnd OH/Al2O3(11-20) were in the range of 100-200 pN.

Following aptamer-ricin specific binding by single molecule recognition and force spectroscopy measurements

USDA-ARS?s Scientific Manuscript database

The atomic force microscope (AFM) recognition and dynamic force spectroscopy (DFS) experiments provide both morphology and interaction information of the aptamer and protein, which can be used for the future study on the thermodynamics and kinetics properties of ricin-aptamer/antibody interactions. ...

Nano-funnels as electro-osmotic ``tweezers and pistons''

NASA Astrophysics Data System (ADS)

Wang, Yanqian; Panyukov, Sergey; Zhou, Jinsheng; Menard, Laurent D.; Ramsey, J. Michael; Rubinstien, Michael

2014-03-01

An electric field is used to force a DNA molecule into a nano-channel by compensating the free energy penalty that results from the reduced conformational entropy of the confined macromolecule. Narrow nano-channels require high critical electric fields to achieve DNA translocation, leading to short dwell times of DNA in these channels. We demonstrate that nano-funnels integrated with nano-channels reduce the free energy barrier and lower the critical electric field required for DNA translocation. A focused electric field within the funnel increases the electric force on the DNA, compresses the molecule, and increases the osmotic pressure at the nano-channel entrance. This ``electro-osmotic piston'' forces the molecule into the nano-channel at lower electric fields than those observed without the funnel. Appropirately designed nano-funnels can also function as tweezers that allow manipulation of the position of the DNA molecule. The predictions of our theory describing double-stranded DNA behavior in nano-funnel - nano-channel devices are consistent with experimental results. Thanks for the financial support from NSF (DMR-1309892, DMR-1121107, DMR-1122483), NIH (1-P50-HL107168, 1-P01-HL108808-01A1, R01HG02647), NHGRI and CF Foundation.

Elongated unique DNA strand deposition on microstructured substrate by receding meniscus assembly and capillary force

PubMed Central

Charlot, B.; Bardin, F.; Sanchez, N.; Roux, P.; Teixeira, S.; Schwob, E.

2014-01-01

Ordered deposition of elongated DNA molecules was achieved by the forced dewetting of a DNA solution droplet over a microstructured substrate. This technique allows trapping, uncoiling, and deposition of DNA fragments without the need of a physicochemical anchoring of the molecule and results in the combing of double stranded DNA from the edge of microwells on a polydimethylsiloxane (PDMS) substrate. The technique involves scanning a droplet of DNA solution caught between a movable blade and a PDMS substrate containing an array of microwells. The deposition and elongation appears when the receding meniscus dewets microwells, the latter acting here as a perturbation in the dewetting line forcing the water film to break locally. Thus, DNA molecules can be deposited in an ordered manner and elongated conformation based solely on a physical phenomenon, allowing uncoiled DNA molecules to be observed in all their length. However, the exact mechanism that governs the deposition of DNA strands is not well understood. This paper is an analysis of the physical phenomenon occurring in the deposition process and is based on observations made with the use of high frame/second rate video microscopy. PMID:24753724

Discriminating Intercalative Effects of Threading Intercalator Nogalamycin, from Classical Intercalator Daunomycin, Using Single Molecule Atomic Force Spectroscopy.

PubMed

Banerjee, T; Banerjee, S; Sett, S; Ghosh, S; Rakshit, T; Mukhopadhyay, R

2016-01-01

DNA threading intercalators are a unique class of intercalating agents, albeit little biophysical information is available on their intercalative actions. Herein, the intercalative effects of nogalamycin, which is a naturally-occurring DNA threading intercalator, have been investigated by high-resolution atomic force microscopy (AFM) and spectroscopy (AFS). The results have been compared with those of the well-known chemotherapeutic drug daunomycin, which is a non-threading classical intercalator bearing structural similarity to nogalamycin. A comparative AFM assessment revealed a greater increase in DNA contour length over the entire incubation period of 48 h for nogalamycin treatment, whereas the contour length increase manifested faster in case of daunomycin. The elastic response of single DNA molecules to an externally applied force was investigated by the single molecule AFS approach. Characteristic mechanical fingerprints in the overstretching behaviour clearly distinguished the nogalamycin/daunomycin-treated dsDNA from untreated dsDNA-the former appearing less elastic than the latter, and the nogalamycin-treated DNA distinguished from the daunomycin-treated DNA-the classically intercalated dsDNA appearing the least elastic. A single molecule AFS-based discrimination of threading intercalation from the classical type is being reported for the first time.

Discriminating Intercalative Effects of Threading Intercalator Nogalamycin, from Classical Intercalator Daunomycin, Using Single Molecule Atomic Force Spectroscopy

PubMed Central

Sett, S.; Ghosh, S.; Rakshit, T.; Mukhopadhyay, R.

2016-01-01

DNA threading intercalators are a unique class of intercalating agents, albeit little biophysical information is available on their intercalative actions. Herein, the intercalative effects of nogalamycin, which is a naturally-occurring DNA threading intercalator, have been investigated by high-resolution atomic force microscopy (AFM) and spectroscopy (AFS). The results have been compared with those of the well-known chemotherapeutic drug daunomycin, which is a non-threading classical intercalator bearing structural similarity to nogalamycin. A comparative AFM assessment revealed a greater increase in DNA contour length over the entire incubation period of 48 h for nogalamycin treatment, whereas the contour length increase manifested faster in case of daunomycin. The elastic response of single DNA molecules to an externally applied force was investigated by the single molecule AFS approach. Characteristic mechanical fingerprints in the overstretching behaviour clearly distinguished the nogalamycin/daunomycin-treated dsDNA from untreated dsDNA—the former appearing less elastic than the latter, and the nogalamycin-treated DNA distinguished from the daunomycin-treated DNA—the classically intercalated dsDNA appearing the least elastic. A single molecule AFS-based discrimination of threading intercalation from the classical type is being reported for the first time. PMID:27183010

The formation of quasi-alicyclic rings in alkyl-aromatic compounds

NASA Astrophysics Data System (ADS)

Straka, Pavel; Buryan, Petr; Bičáková, Olga

2018-02-01

The alkyl side chains of n-alkyl phenols, n-alkyl benzenes and n-alkyl naphthalenes are cyclised, as demonstrated by GC measurements, FTIR spectroscopy and molecular mechanics calculations. Cyclisation occurs due to the intramolecular interaction between an aromatic ring (-δ) and a hydrogen of the terminal methyl group (+δ) of an alkyl chain. In fact, conventional molecules are not aliphatic-aromatic, but quasi-alicyclic-aromatic. With the aromatic molecules formed with a quasi-alicyclic ring, the effect of van der Waals attractive forces increases not only intramolecularly but also intermolecularly. This effect is strong in molecules with propyl and higher alkyl substituents. The increase of intermolecular van der Waals attractive forces results in bi-linearity in the GC retention time of the compounds in question, observed in the dependence of the logarithm of the relative retention time on the number of carbons in a molecule in both polar and nonpolar stationary phases with both capillary and packed columns. The role of van der Waals forces has been demonstrated using the potential energies of covalent and noncovalent interactions for 2-n-alkyl phenols, n-alkyl benzenes and 1-n-alkyl- and 2-n-alkyl naphthalenes.

Force-field parametrization and molecular dynamics simulations of Congo red

NASA Astrophysics Data System (ADS)

Król, Marcin; Borowski, Tomasz; Roterman, Irena; Piekarska, Barbara; Stopa, Barbara; Rybarska, Joanna; Konieczny, Leszek

2004-01-01

Congo red, a diazo dye widely used in medical diagnosis, is known to form supramolecular systems in solution. Such a supramolecular system may interact with various proteins. In order to examine the nature of such complexes empirical force field parameters for the Congo red molecule were developed. The parametrization of bonding terms closely followed the methodology used in the development of the charmm22 force field, except for the calculation of charges. Point charges were calculated from a fit to a quantum mechanically derived electrostatic potential using the CHELP-BOW method. Obtained parameters were tested in a series of molecular dynamics simulations of both a single molecule and a micelle composed of Congo red molecules. It is shown that newly developed parameters define a stable minimum on the hypersurface of the potential energy and crystal and ab initio geometries and rotational barriers are well reproduced. Furthermore, rotations around C-N bonds are similar to torsional vibrations observed in crystals of diphenyl-diazene, which confirms that the flexibility of the molecule is correct. Comparison of results obtained from micelles molecular dynamics simulations with experimental data shows that the thermal dependence of micelle creation is well reproduced.

Observation of correlated excitations in bimolecular collisions

NASA Astrophysics Data System (ADS)

Gao, Zhi; Karman, Tijs; Vogels, Sjoerd N.; Besemer, Matthieu; van der Avoird, Ad; Groenenboom, Gerrit C.; van de Meerakker, Sebastiaan Y. T.

2018-02-01

Although collisions between atoms and molecules are largely understood, collisions between two molecules have proven much harder to study. In both experiment and theory, our ability to determine quantum-state-resolved bimolecular cross-sections lags behind their atom-molecule counterparts by decades. For many bimolecular systems, even rules of thumb—much less intuitive understanding—of scattering cross sections are lacking. Here, we report the measurement of state-to-state differential cross sections on the collision of state-selected and velocity-controlled nitric oxide (NO) radicals and oxygen (O2) molecules. Using velocity map imaging of the scattered NO radicals, the full product-pair correlations of rotational excitation that occurs in both collision partners from individual encounters are revealed. The correlated cross sections show surprisingly good agreement with quantum scattering calculations using ab initio NO-O2 potential energy surfaces. The observations show that the well-known energy-gap law that governs atom-molecule collisions does not generally apply to bimolecular excitation processes, and reveal a propensity rule for the vector correlation of product angular momenta.

Hydration and vibrational dynamics of betaine (N,N,N-trimethylglycine)

NASA Astrophysics Data System (ADS)

Li, Tanping; Cui, Yaowen; Mathaga, John; Kumar, Revati; Kuroda, Daniel G.

2015-06-01

Zwitterions are naturally occurring molecules that have a positive and a negative charge group in its structure and are of great importance in many areas of science. Here, the vibrational and hydration dynamics of the zwitterionic system betaine (N,N,N-trimethylglycine) is reported. The linear infrared spectrum of aqueous betaine exhibits an asymmetric band in the 1550-1700 cm-1 region of the spectrum. This band is attributed to the carboxylate asymmetric stretch of betaine. The potential of mean force computed from ab initio molecular dynamic simulations confirms that the two observed transitions of the linear spectrum are related to two different betaine conformers present in solution. A model of the experimental data using non-linear response theory agrees very well with a vibrational model comprising of two vibrational transitions. In addition, our modeling shows that spectral parameters such as the slope of the zeroth contour plot and central line slope are both sensitive to the presence of overlapping transitions. The vibrational dynamics of the system reveals an ultrafast decay of the vibrational population relaxation as well as the correlation of frequency-frequency correlation function (FFCF). A decay of ˜0.5 ps is observed for the FFCF correlation time and is attributed to the frequency fluctuations caused by the motions of water molecules in the solvation shell. The comparison of the experimental observations with simulations of the FFCF from ab initio molecular dynamics and a density functional theory frequency map shows a very good agreement corroborating the correct characterization and assignment of the derived parameters.

Hydration and vibrational dynamics of betaine (N,N,N-trimethylglycine)

PubMed Central

Li, Tanping; Cui, Yaowen; Mathaga, John; Kumar, Revati; Kuroda, Daniel G.

2015-01-01

Zwitterions are naturally occurring molecules that have a positive and a negative charge group in its structure and are of great importance in many areas of science. Here, the vibrational and hydration dynamics of the zwitterionic system betaine (N,N,N-trimethylglycine) is reported. The linear infrared spectrum of aqueous betaine exhibits an asymmetric band in the 1550-1700 cm−1 region of the spectrum. This band is attributed to the carboxylate asymmetric stretch of betaine. The potential of mean force computed from ab initio molecular dynamic simulations confirms that the two observed transitions of the linear spectrum are related to two different betaine conformers present in solution. A model of the experimental data using non-linear response theory agrees very well with a vibrational model comprising of two vibrational transitions. In addition, our modeling shows that spectral parameters such as the slope of the zeroth contour plot and central line slope are both sensitive to the presence of overlapping transitions. The vibrational dynamics of the system reveals an ultrafast decay of the vibrational population relaxation as well as the correlation of frequency-frequency correlation function (FFCF). A decay of ∼0.5 ps is observed for the FFCF correlation time and is attributed to the frequency fluctuations caused by the motions of water molecules in the solvation shell. The comparison of the experimental observations with simulations of the FFCF from ab initio molecular dynamics and a density functional theory frequency map shows a very good agreement corroborating the correct characterization and assignment of the derived parameters. PMID:26049458

Self-assembly of heterogeneous supramolecular structures with uniaxial anisotropy.

PubMed

Ruiz-Osés, M; Gonzalez-Lakunza, N; Silanes, I; Gourdon, A; Arnau, A; Ortega, J E

2006-12-28

Uniaxial anisotropy in two-dimensional self-assembled supramolecular structures is achieved by the coadsorption of two different linear molecules with complementary amine and imide functionalization. The two-dimensional monolayer is defined by a one-dimensional stack of binary chains, which can be forced to line up along steps in vicinal surfaces. The competing driving forces in the self-organization process are discussed in light of the structures observed during single molecule adsorption and coadsorption on flat and vicinal surfaces and the corresponding theoretical calculations.

Regulation of adhesion behavior of murine macrophage using supported lipid membranes displaying tunable mannose domains

NASA Astrophysics Data System (ADS)

Kaindl, T.; Oelke, J.; Pasc, A.; Kaufmann, S.; Konovalov, O. V.; Funari, S. S.; Engel, U.; Wixforth, A.; Tanaka, M.

2010-07-01

Highly uniform, strongly correlated domains of synthetically designed lipids can be incorporated into supported lipid membranes. The systematic characterization of membranes displaying a variety of domains revealed that the equilibrium size of domains significantly depends on the length of fluorocarbon chains, which can be quantitatively interpreted within the framework of an equivalent dipole model. A mono-dispersive, narrow size distribution of the domains enables us to treat the inter-domain correlations as two-dimensional colloidal crystallization and calculate the potentials of mean force. The obtained results demonstrated that both size and inter-domain correlation can precisely be controlled by the molecular structures. By coupling α-D-mannose to lipid head groups, we studied the adhesion behavior of the murine macrophage (J774A.1) on supported membranes. Specific adhesion and spreading of macrophages showed a clear dependence on the density of functional lipids. The obtained results suggest that such synthetic lipid domains can be used as a defined platform to study how cells sense the size and distribution of functional molecules during adhesion and spreading.

Correlative nanoscale imaging of actin filaments and their complexes

NASA Astrophysics Data System (ADS)

Sharma, Shivani; Zhu, Huanqi; Grintsevich, Elena E.; Reisler, Emil; Gimzewski, James K.

2013-06-01

Actin remodeling is an area of interest in biology in which correlative microscopy can bring a new way to analyze protein complexes at the nanoscale. Advances in EM, X-ray diffraction, fluorescence, and single molecule techniques have provided a wealth of information about the modulation of the F-actin structure and its regulation by actin binding proteins (ABPs). Yet, there are technological limitations of these approaches to achieving quantitative molecular level information on the structural and biophysical changes resulting from ABPs interaction with F-actin. Fundamental questions about the actin structure and dynamics and how these determine the function of ABPs remain unanswered. Specifically, how local and long-range structural and conformational changes result in ABPs induced remodeling of F-actin needs to be addressed at the single filament level. Advanced, sensitive and accurate experimental tools for detailed understanding of ABP-actin interactions are much needed. This article discusses the current understanding of nanoscale structural and mechanical modulation of F-actin by ABPs at the single filament level using several correlative microscopic techniques, focusing mainly on results obtained by Atomic Force Microscopy (AFM) analysis of ABP-actin complexes.

Unfolding single RNA molecules: bridging the gap between equilibrium and non-equilibrium statistical thermodynamics.

PubMed

Bustamante, Carlos

2005-11-01

During the last 15 years, scientists have developed methods that permit the direct mechanical manipulation of individual molecules. Using this approach, they have begun to investigate the effect of force and torque in chemical and biochemical reactions. These studies span from the study of the mechanical properties of macromolecules, to the characterization of molecular motors, to the mechanical unfolding of individual proteins and RNA. Here I present a review of some of our most recent results using mechanical force to unfold individual molecules of RNA. These studies make it possible to follow in real time the trajectory of each molecule as it unfolds and characterize the various intermediates of the reaction. Moreover, if the process takes place reversibly it is possible to extract both kinetic and thermodynamic information from these experiments at the same time that we characterize the forces that maintain the three-dimensional structure of the molecule in solution. These studies bring us closer to the biological unfolding processes in the cell as they simulate in vitro, the mechanical unfolding of RNAs carried out in the cell by helicases. If the unfolding process occurs irreversibly, I show here that single-molecule experiments can still provide equilibrium, thermodynamic information from non-equilibrium data by using recently discovered fluctuation theorems. Such theorems represent a bridge between equilibrium and non-equilibrium statistical mechanics. In fact, first derived in 1997, the first experimental demonstration of the validity of fluctuation theorems was obtained by unfolding mechanically a single molecule of RNA. It is perhaps a sign of the times that important physical results are these days used to extract information about biological systems and that biological systems are being used to test and confirm fundamental new laws in physics.

Slow approach to steady motion of a concave body in a free-molecular gas

NASA Astrophysics Data System (ADS)

Tsuji, Tetsuro; Arai, Junichi; Kawano, Satoyuki

2015-07-01

A body in a free-molecular gas accelerated by a constant external force is considered on the basis of kinetic theory. The body is an infinitely long rectangular hollow column with one face removed, and thus it has a squarish U -shaped cross section. The concave part of the body points toward the direction of motion, and thus the gas molecules may be trapped in the concavity. Gas molecules undergo diffuse reflection on a base part, whereas specular reflection on two lateral parts. It is numerically shown that the velocity of the body approaches a terminal velocity, for which a drag force exerted by the gas counterbalances the external force, in such a way that their difference decreases in proportion to the inverse square of time for a large time. This rate of approach is slower than the known rate proportional to the inverse cube of time in the case of a body without concavity [Aoki et al., Phys. Rev. E 80, 016309 (2009), 10.1103/PhysRevE.80.016309]. Based on the detailed investigation on the velocity distribution function of gas molecules impinging on the body, it is clarified that the concavity prevents some molecules from escaping to infinity. This trapping enhances the effect of recollision between the body and the gas molecules, which is the cause of the inverse power laws, and thus leads to the slower approach.

Normal coordinate analysis of the vibrational spectrum of benzil molecule

NASA Astrophysics Data System (ADS)

Volovšek, V.; Colombo, L.

1993-03-01

Normal coordinate analysis is performed for the benzil molecule. Force constants of phenyl rings are transferred from earlier studies on binuclear aromatic molecules. The existance of some low-frequency internal modes have been proved, thus eliminating the earlier explanations of the excess of the bands observed in the low-frequency Raman and FIR spectra of benzil crystal.

Force feedback effects on single molecule hopping and pulling experiments

NASA Astrophysics Data System (ADS)

Rico-Pasto, M.; Pastor, I.; Ritort, F.

2018-03-01

Single-molecule experiments with optical tweezers have become an important tool to study the properties and mechanisms of biological systems, such as cells and nucleic acids. In particular, force unzipping experiments have been used to extract the thermodynamics and kinetics of folding and unfolding reactions. In hopping experiments, a molecule executes transitions between the unfolded and folded states at a preset value of the force [constant force mode (CFM) under force feedback] or trap position [passive mode (PM) without feedback] and the force-dependent kinetic rates extracted from the lifetime of each state (CFM) and the rupture force distributions (PM) using the Bell-Evans model. However, hopping experiments in the CFM are known to overestimate molecular distances and folding free energies for fast transitions compared to the response time of the feedback. In contrast, kinetic rate measurements from pulling experiments have been mostly done in the PM while the CFM is seldom implemented in pulling protocols. Here, we carry out hopping and pulling experiments in a short DNA hairpin in the PM and CFM at three different temperatures (6 °C, 25 °C, and 45 °C) exhibiting largely varying kinetic rates. As expected, we find that equilibrium hopping experiments in the CFM and PM perform well at 6 °C (where kinetics are slow), whereas the CFM overestimates molecular parameters at 45 °C (where kinetics are fast). In contrast, nonequilibrium pulling experiments perform well in both modes at all temperatures. This demonstrates that the same kind of feedback algorithm in the CFM leads to more reliable determination of the folding reaction parameters in irreversible pulling experiments.

Influence of impurities and contact scale on the lubricating properties of bovine submaxillary mucin (BSM) films on a hydrophobic surface.

PubMed

Nikogeorgos, Nikolaos; Madsen, Jan Busk; Lee, Seunghwan

2014-10-01

Lubricating properties of bovine submaxillary mucin (BSM) on a compliant, hydrophobic surface were studied as influenced by impurities, in particular bovine serum albumin (BSA), at macro and nanoscale contacts by means of pin-on-disk tribometry and friction force microscopy (FFM), respectively. At both contact scales, the purity of BSM and the presence of BSA were quantitatively discriminated. The presence of BSA was responsible for higher frictional forces observed from BSM samples containing relatively larger amount of BSA. But, the mechanisms contributing to higher friction forces by BSA were different at different contact scales. At the macroscale contact, higher friction forces were caused by faster and dominant adsorption of BSA into the contacting area under a continuous cycle of desorption and re-adsorption of the macromolecules from tribostress. Nevertheless, all BSMs lowered the interfacial friction forces due to large contact area and a large number of BSM molecules in the contact area. At the nanoscale contact, however, no significant desorption of the macromolecules is expected in tribological contacts because of too small contact area and extremely small number of BSM molecules involved in the contact area. Instead, increasingly higher friction forces with increasing amount of BSA in BSM layer are attributed to higher viscosity caused by BSA in the layer. Comparable size of AFM probes with BSM molecules allowed them to penetrate through the BSM layers and to scratch on the underlying substrates, and thus induced higher friction forces compared to the sliding contact on bare substrates. Copyright © 2014 Elsevier B.V. All rights reserved.

Force feedback effects on single molecule hopping and pulling experiments.

PubMed

Rico-Pasto, M; Pastor, I; Ritort, F

2018-03-28

Single-molecule experiments with optical tweezers have become an important tool to study the properties and mechanisms of biological systems, such as cells and nucleic acids. In particular, force unzipping experiments have been used to extract the thermodynamics and kinetics of folding and unfolding reactions. In hopping experiments, a molecule executes transitions between the unfolded and folded states at a preset value of the force [constant force mode (CFM) under force feedback] or trap position [passive mode (PM) without feedback] and the force-dependent kinetic rates extracted from the lifetime of each state (CFM) and the rupture force distributions (PM) using the Bell-Evans model. However, hopping experiments in the CFM are known to overestimate molecular distances and folding free energies for fast transitions compared to the response time of the feedback. In contrast, kinetic rate measurements from pulling experiments have been mostly done in the PM while the CFM is seldom implemented in pulling protocols. Here, we carry out hopping and pulling experiments in a short DNA hairpin in the PM and CFM at three different temperatures (6 °C, 25 °C, and 45 °C) exhibiting largely varying kinetic rates. As expected, we find that equilibrium hopping experiments in the CFM and PM perform well at 6 °C (where kinetics are slow), whereas the CFM overestimates molecular parameters at 45 °C (where kinetics are fast). In contrast, nonequilibrium pulling experiments perform well in both modes at all temperatures. This demonstrates that the same kind of feedback algorithm in the CFM leads to more reliable determination of the folding reaction parameters in irreversible pulling experiments.

Molecular docking and 3D-QSAR studies on triazolinone and pyridazinone, non-nucleoside inhibitor of HIV-1 reverse transcriptase.

PubMed

Sivan, Sree Kanth; Manga, Vijjulatha

2010-06-01

Nonnucleoside reverse transcriptase inhibitors (NNRTIs) are allosteric inhibitors of the HIV-1 reverse transcriptase. Recently a series of Triazolinone and Pyridazinone were reported as potent inhibitors of HIV-1 wild type reverse transcriptase. In the present study, docking and 3D quantitative structure activity relationship (3D QSAR) studies involving comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on 31 molecules. Ligands were built and minimized using Tripos force field and applying Gasteiger-Hückel charges. These ligands were docked into protein active site using GLIDE 4.0. The docked poses were analyzed; the best docked poses were selected and aligned. CoMFA and CoMSIA fields were calculated using SYBYL6.9. The molecules were divided into training set and test set, a PLS analysis was performed and QSAR models were generated. The model showed good statistical reliability which is evident from the r2 nv, q2 loo and r2 pred values. The CoMFA model provides the most significant correlation of steric and electrostatic fields with biological activities. The CoMSIA model provides a correlation of steric, electrostatic, acceptor and hydrophobic fields with biological activities. The information rendered by 3D QSAR model initiated us to optimize the lead and design new potential inhibitors.

A nu-space for image correlation spectroscopy: characterization and application to measure protein transport in live cells

NASA Astrophysics Data System (ADS)

Potvin-Trottier, Laurent; Chen, Lingfeng; Horwitz, Alan Rick; Wiseman, Paul W.

2013-08-01

We introduce a new generalized theoretical framework for image correlation spectroscopy (ICS). Using this framework, we extend the ICS method in time-frequency (ν, nu) space to map molecular flow of fluorescently tagged proteins in individual living cells. Even in the presence of a dominant immobile population of fluorescent molecules, nu-space ICS (nICS) provides an unbiased velocity measurement, as well as the diffusion coefficient of the flow, without requiring filtering. We also develop and characterize a tunable frequency-filter for spatio-temporal ICS (STICS) that allows quantification of the density, the diffusion coefficient and the velocity of biased diffusion. We show that the techniques are accurate over a wide range of parameter space in computer simulation. We then characterize the retrograde flow of adhesion proteins (α6- and αLβ2-GFP integrins and mCherry-paxillin) in CHO.B2 cells plated on laminin and intercellular adhesion molecule 1 (ICAM-1) ligands respectively. STICS with a tunable frequency filter, in conjunction with nICS, measures two new transport parameters, the density and transport bias coefficient (a measure of the diffusive character of a flow/biased diffusion), showing that molecular flow in this cell system has a significant diffusive component. Our results suggest that the integrin-ligand interaction, along with the internal myosin-motor generated force, varies for different integrin-ligand pairs, consistent with previous results.

Visualizing the orientational dependence of an intermolecular potential

NASA Astrophysics Data System (ADS)

Sweetman, Adam; Rashid, Mohammad A.; Jarvis, Samuel P.; Dunn, Janette L.; Rahe, Philipp; Moriarty, Philip

2016-02-01

Scanning probe microscopy can now be used to map the properties of single molecules with intramolecular precision by functionalization of the apex of the scanning probe tip with a single atom or molecule. Here we report on the mapping of the three-dimensional potential between fullerene (C60) molecules in different relative orientations, with sub-Angstrom resolution, using dynamic force microscopy (DFM). We introduce a visualization method which is capable of directly imaging the variation in equilibrium binding energy of different molecular orientations. We model the interaction using both a simple approach based around analytical Lennard-Jones potentials, and with dispersion-force-corrected density functional theory (DFT), and show that the positional variation in the binding energy between the molecules is dominated by the onset of repulsive interactions. Our modelling suggests that variations in the dispersion interaction are masked by repulsive interactions even at displacements significantly larger than the equilibrium intermolecular separation.

Torque measurement at the single-molecule level.

PubMed

Forth, Scott; Sheinin, Maxim Y; Inman, James; Wang, Michelle D

2013-01-01

Methods for exerting and measuring forces on single molecules have revolutionized the study of the physics of biology. However, it is often the case that biological processes involve rotation or torque generation, and these parameters have been more difficult to access experimentally. Recent advances in the single-molecule field have led to the development of techniques that add the capability of torque measurement. By combining force, displacement, torque, and rotational data, a more comprehensive description of the mechanics of a biomolecule can be achieved. In this review, we highlight a number of biological processes for which torque plays a key mechanical role. We describe the various techniques that have been developed to directly probe the torque experienced by a single molecule, and detail a variety of measurements made to date using these new technologies. We conclude by discussing a number of open questions and propose systems of study that would be well suited for analysis with torsional measurement techniques.

Feedback traps for virtual potentials

NASA Astrophysics Data System (ADS)

Gavrilov, Momčilo; Bechhoefer, John

2017-03-01

Feedback traps are tools for trapping and manipulating single charged objects, such as molecules in solution. An alternative to optical tweezers and other single-molecule techniques, they use feedback to counteract the Brownian motion of a molecule of interest. The trap first acquires information about a molecule's position and then applies an electric feedback force to move the molecule. Since electric forces are stronger than optical forces at small scales, feedback traps are the best way to trap single molecules without `touching' them (e.g. by putting them in a small box or attaching them to a tether). Feedback traps can do more than trap molecules: they can also subject a target object to forces that are calculated to be the gradient of a desired potential function U(x). If the feedback loop is fast enough, it creates a virtual potential whose dynamics will be very close to those of a particle in an actual potential U(x). But because the dynamics are entirely a result of the feedback loop-absent the feedback, there is only an object diffusing in a fluid-we are free to specify and then manipulate in time an arbitrary potential U(x,t). Here, we review recent applications of feedback traps to studies on the fundamental connections between information and thermodynamics, a topic where feedback plays an even more fundamental role. We discuss how recursive maximum-likelihood techniques allow continuous calibration, to compensate for drifts in experiments that last for days. We consider ways to estimate work and heat, using them to measure fluctuating energies to a precision of ±0.03 kT over these long experiments. Finally, we compare work and heat measurements of the costs of information erasure, the Landauer limit of kT ln 2 per bit of information erased. We argue that, when you want to know the average heat transferred to a bath in a long protocol, you should measure instead the average work and then infer the heat using the first law of thermodynamics. This article is part of the themed issue 'Horizons of cybernetical physics'.

Microgravity

NASA Image and Video Library

2001-06-06

Atomic force microscopy uses laser technology to reveal a defect, a double-screw dislocation, on the surface of this crystal of canavalin, a major source of dietary protein for humans and domestic animals. When a crystal grows, attachment kinetics and transport kinetics are competing for control of the molecules. As a molecule gets close to the crystal surface, it has to attach properly for the crystal to be usable. NASA has funded investigators to look at those attachment kinetics from a theoretical standpoint and an experimental standpoint. Dr. Alex McPherson of the University of California, Irvine, is one of those investigators. He uses X-ray diffraction and atomic force microscopy in his laboratory to answer some of the many questions about how protein crystals grow. Atomic force microscopy provides a means of looking at how individual molecules are added to the surface of growing protein crystals. This helps McPherson understand the kinetics of protein crystal growth. McPherson asks, How fast do crystals grow? What are the forces involved? Investigators funded by NASA have clearly shown that such factors as the level of supersaturation and the rate of growth all affect the habit [characteristic arrangement of facets] of the crystal and the defects that occur in the crystal.

Protein crystal growth

NASA Technical Reports Server (NTRS)

2001-01-01

Atomic force microscopy uses laser technology to reveal a defect, a double-screw dislocation, on the surface of this crystal of canavalin, a major source of dietary protein for humans and domestic animals. When a crystal grows, attachment kinetics and transport kinetics are competing for control of the molecules. As a molecule gets close to the crystal surface, it has to attach properly for the crystal to be usable. NASA has funded investigators to look at those attachment kinetics from a theoretical standpoint and an experimental standpoint. Dr. Alex McPherson of the University of California, Irvine, is one of those investigators. He uses X-ray diffraction and atomic force microscopy in his laboratory to answer some of the many questions about how protein crystals grow. Atomic force microscopy provides a means of looking at how individual molecules are added to the surface of growing protein crystals. This helps McPherson understand the kinetics of protein crystal growth. McPherson asks, How fast do crystals grow? What are the forces involved? Investigators funded by NASA have clearly shown that such factors as the level of supersaturation and the rate of growth all affect the habit [characteristic arrangement of facets] of the crystal and the defects that occur in the crystal.

Mechanosensing drives acuity of αβ T-cell recognition

PubMed Central

Feng, Yinnian; Brazin, Kristine N.; Kobayashi, Eiji; Mallis, Robert J.; Reinherz, Ellis L.; Lang, Matthew J.

2017-01-01

T lymphocytes use surface αβ T-cell receptors (TCRs) to recognize peptides bound to MHC molecules (pMHCs) on antigen-presenting cells (APCs). How the exquisite specificity of high-avidity T cells is achieved is unknown but essential, given the paucity of foreign pMHC ligands relative to the ubiquitous self-pMHC array on an APC. Using optical traps, we determine physicochemical triggering thresholds based on load and force direction. Strikingly, chemical thresholds in the absence of external load require orders of magnitude higher pMHC numbers than observed physiologically. In contrast, force applied in the shear direction (∼10 pN per TCR molecule) triggers T-cell Ca2+ flux with as few as two pMHC molecules at the interacting surface interface with rapid positional relaxation associated with similarly directed motor-dependent transport via ∼8-nm steps, behaviors inconsistent with serial engagement during initial TCR triggering. These synergistic directional forces generated during cell motility are essential for adaptive T-cell immunity against infectious pathogens and cancers. PMID:28811364

Monte Carlo study of disorder in HMTA

NASA Astrophysics Data System (ADS)

Goossens, D. J.; Welberry, T. R.

2001-12-01

We investigate disordered solids by automated fitting of a Monte Carlo simulation of a crystal to observed single-crystal diffuse X-ray scattering. This method has been extended to the study of crystals of relatively large organic molecules by using a z-matrix to describe the molecules. This allows exploration of motions within molecules. We refer to the correlated thermal motion observed in benzil, and to the occupational and thermal disorder in the 1:1 adduct of hexamethylenetetramine and azelaic acid, HMTA. The technique is capable of giving insight into modes of vibration within molecules and correlated motions between molecules.

Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field.

PubMed

Abella, Jayvee R; Cheng, Sara Y; Wang, Qiantao; Yang, Wei; Ren, Pengyu

2014-07-08

The orthogonal space random walk (OSRW) method has shown enhanced sampling efficiency in free energy calculations from previous studies. In this study, the implementation of OSRW in accordance with the polarizable AMOEBA force field in TINKER molecular modeling software package is discussed and subsequently applied to the hydration free energy calculation of 20 small organic molecules, among which 15 are positively charged and five are neutral. The calculated hydration free energies of these molecules are compared with the results obtained from the Bennett acceptance ratio method using the same force field, and overall an excellent agreement is obtained. The convergence and the efficiency of the OSRW are also discussed and compared with BAR. Combining enhanced sampling techniques such as OSRW with polarizable force fields is very promising for achieving both accuracy and efficiency in general free energy calculations.

Surface force analysis of glycine adsorption on different crystal surfaces of titanium dioxide (TiO2).

PubMed

Ganbaatar, Narangerel; Imai, Kanae; Yano, Taka-Aki; Hara, Masahiko

2017-01-01

Surface force analysis with atomic force microscope (AFM) in which a single amino acid residue was mounted on the tip apex of AFM probe was carried out for the first time at the molecular level on titanium dioxide (TiO 2 ) as a representative mineral surface for prebiotic chemical evolution reactions. The force analyses on surfaces with three different crystal orientations revealed that the TiO 2 (110) surface has unique characteristics for adsorbing glycine molecules showing different features compared to those on TiO 2 (001) and (100). To examine this difference, we investigated thermal desorption spectroscopy (TDS) and the interaction between the PEG cross-linker and the three TiO 2 surfaces. Our data suggest that the different single crystal surfaces would provide different chemical evolution field for amino acid molecules.

Single molecule force measurements delineate salt, pH and surface effects on biopolymer adhesion

NASA Astrophysics Data System (ADS)

Pirzer, T.; Geisler, M.; Scheibel, T.; Hugel, T.

2009-06-01

In this paper we probe the influence of surface properties, pH and salt on the adhesion of recombinant spider silk proteins onto solid substrates with single molecule force spectroscopy. A single engineered spider silk protein (monomeric C16 or dimeric (QAQ)8NR3) is covalently bound with one end to an AFM tip, which assures long-time measurements for hours with one and the same protein. The tip with the protein is brought into contact with various substrates at various buffer conditions and then retracted to desorb the protein. We observe a linear dependence of the adhesion force on the concentration of three selected salts (NaCl, NaH2PO4 and NaI) and a Hofmeister series both for anions and cations. As expected, the more hydrophobic C16 shows a higher adhesion force than (QAQ)8NR3, and the adhesion force rises with the hydrophobicity of the substrate. Unexpected is the magnitude of the dependences—we never observe a change of more than 30%, suggesting a surprisingly well-regulated balance between dispersive forces, water-structure-induced forces as well as co-solute-induced forces in biopolymer adhesion.

Improved free-energy landscape reconstruction of bacteriorhodopsin highlights local variations in unfolding energy.

PubMed

Heenan, Patrick R; Yu, Hao; Siewny, Matthew G W; Perkins, Thomas T

2018-03-28

Precisely quantifying the energetics that drive the folding of membrane proteins into a lipid bilayer remains challenging. More than 15 years ago, atomic force microscopy (AFM) emerged as a powerful tool to mechanically extract individual membrane proteins from a lipid bilayer. Concurrently, fluctuation theorems, such as the Jarzynski equality, were applied to deduce equilibrium free energies (ΔG 0 ) from non-equilibrium single-molecule force spectroscopy records. The combination of these two advances in single-molecule studies deduced the free-energy of the model membrane protein bacteriorhodopsin in its native lipid bilayer. To elucidate this free-energy landscape at a higher resolution, we applied two recent developments. First, as an input to the reconstruction, we used force-extension curves acquired with a 100-fold higher time resolution and 10-fold higher force precision than traditional AFM studies of membrane proteins. Next, by using an inverse Weierstrass transform and the Jarzynski equality, we removed the free energy associated with the force probe and determined the molecular free-energy landscape of the molecule under study, bacteriorhodopsin. The resulting landscape yielded an average unfolding free energy per amino acid (aa) of 1.0 ± 0.1 kcal/mol, in agreement with past single-molecule studies. Moreover, on a smaller spatial scale, this high-resolution landscape also agreed with an equilibrium measurement of a particular three-aa transition in bacteriorhodopsin that yielded 2.7 kcal/mol/aa, an unexpectedly high value. Hence, while average unfolding ΔG 0 per aa is a useful metric, the derived high-resolution landscape details significant local variation from the mean. More generally, we demonstrated that, as anticipated, the inverse Weierstrass transform is an efficient means to reconstruct free-energy landscapes from AFM data.

Improved free-energy landscape reconstruction of bacteriorhodopsin highlights local variations in unfolding energy

NASA Astrophysics Data System (ADS)

Heenan, Patrick R.; Yu, Hao; Siewny, Matthew G. W.; Perkins, Thomas T.

2018-03-01

Precisely quantifying the energetics that drive the folding of membrane proteins into a lipid bilayer remains challenging. More than 15 years ago, atomic force microscopy (AFM) emerged as a powerful tool to mechanically extract individual membrane proteins from a lipid bilayer. Concurrently, fluctuation theorems, such as the Jarzynski equality, were applied to deduce equilibrium free energies (ΔG0) from non-equilibrium single-molecule force spectroscopy records. The combination of these two advances in single-molecule studies deduced the free-energy of the model membrane protein bacteriorhodopsin in its native lipid bilayer. To elucidate this free-energy landscape at a higher resolution, we applied two recent developments. First, as an input to the reconstruction, we used force-extension curves acquired with a 100-fold higher time resolution and 10-fold higher force precision than traditional AFM studies of membrane proteins. Next, by using an inverse Weierstrass transform and the Jarzynski equality, we removed the free energy associated with the force probe and determined the molecular free-energy landscape of the molecule under study, bacteriorhodopsin. The resulting landscape yielded an average unfolding free energy per amino acid (aa) of 1.0 ± 0.1 kcal/mol, in agreement with past single-molecule studies. Moreover, on a smaller spatial scale, this high-resolution landscape also agreed with an equilibrium measurement of a particular three-aa transition in bacteriorhodopsin that yielded 2.7 kcal/mol/aa, an unexpectedly high value. Hence, while average unfolding ΔG0 per aa is a useful metric, the derived high-resolution landscape details significant local variation from the mean. More generally, we demonstrated that, as anticipated, the inverse Weierstrass transform is an efficient means to reconstruct free-energy landscapes from AFM data.

Force, Torque and Stiffness: Interactions in Perceptual Discrimination

PubMed Central

Wu, Bing; Klatzky, Roberta L.; Hollis, Ralph L.

2011-01-01

Three experiments investigated whether force and torque cues interact in haptic discrimination of force, torque and stiffness, and if so, how. The statistical relation between force and torque was manipulated across four experimental conditions: Either one type of cue varied while the other was constant, or both varied so as to be positively correlated, negatively correlated, or uncorrelated. Experiment 1 showed that the subjects’ ability to discriminate force was improved by positively correlated torque but impaired with uncorrelated torque, as compared to the constant torque condition. Corresponding effects were found in Experiment 2 for the influence of force on torque discrimination. These findings indicate that force and torque are integrated in perception, rather than being processed as separate dimensions. A further experiment demonstrated facilitation of stiffness discrimination by correlated force and torque, whether the correlation was positive or negative. The findings suggest new means of augmenting haptic feedback to facilitate perception of the properties of soft objects. PMID:21359137

Label-Free Detection of Bacillus anthracis Spore Uptake in Macrophage Cells Using Analytical Optical Force Measurements.

PubMed

Hebert, Colin G; Hart, Sean; Leski, Tomasz A; Terray, Alex; Lu, Qin

2017-10-03

Understanding the interaction between macrophage cells and Bacillus anthracis spores is of significant importance with respect to both anthrax disease progression, spore detection for biodefense, as well as understanding cell clearance in general. While most detection systems rely on specific molecules, such as nucleic acids or proteins and fluorescent labels to identify the target(s) of interest, label-free methods probe changes in intrinsic properties, such as size, refractive index, and morphology, for correlation with a particular biological event. Optical chromatography is a label free technique that uses the balance between optical and fluidic drag forces within a microfluidic channel to determine the optical force on cells or particles. Here we show an increase in the optical force experienced by RAW264.7 macrophage cells upon the uptake of both microparticles and B. anthracis Sterne 34F2 spores. In the case of spores, the exposure was detected in as little as 1 h without the use of antibodies or fluorescent labels of any kind. An increase in the optical force was also seen in macrophage cells treated with cytochalasin D, both with and without a subsequent exposure to spores, indicating that a portion of the increase in the optical force arises independent of phagocytosis. These results demonstrate the capability of optical chromatography to detect subtle biological differences in a rapid and sensitive manner and suggest future potential in a range of applications, including the detection of biological threat agents for biodefense and pathogens for the prevention of sepsis and other diseases.

Single-cell force spectroscopy as a technique to quantify human red blood cell adhesion to subendothelial laminin.

PubMed

Maciaszek, Jamie L; Partola, Kostyantyn; Zhang, Jing; Andemariam, Biree; Lykotrafitis, George

2014-12-18

Single-cell force spectroscopy (SCFS), an atomic force microscopy (AFM)-based assay, enables quantitative study of cell adhesion while maintaining the native state of surface receptors in physiological conditions. Human healthy and pathological red blood cells (RBCs) express a large number of surface proteins which mediate cell-cell interactions, or cell adhesion to the extracellular matrix. In particular, RBCs adhere with high affinity to subendothelial matrix laminin via the basal cell adhesion molecule and Lutheran protein (BCAM/Lu). Here, we established SCFS as an in vitro technique to study human RBC adhesion at baseline and following biochemical treatment. Using blood obtained from healthy human subjects, we recorded adhesion forces from single RBCs attached to AFM cantilevers as the cell was pulled-off of substrates coated with laminin protein. We found that an increase in the overall cell adhesion measured via SCFS is correlated with an increase in the resultant total force measured on 1 µm(2) areas of the RBC membrane. Further, we showed that SCFS can detect significant changes in the adhesive response of RBCs to modulation of the cyclic adenosine monophosphate (cAMP) and protein kinase A (PKA) pathway. Lastly, we identified variability in the RBC adhesion force to laminin amongst the human subjects, suggesting that RBCs maintain diverse levels of active BCAM/Lu adhesion receptors. By using single-cell measurements, we established a powerful new method for the quantitative measurement of single RBC adhesion with specific receptor-mediated binding. Copyright © 2014 Elsevier Ltd. All rights reserved.

Scaling from single molecule to macroscopic adhesion at polymer/metal interfaces.

PubMed

Utzig, Thomas; Raman, Sangeetha; Valtiner, Markus

2015-03-10

Understanding the evolution of macroscopic adhesion based on fundamental molecular interactions is crucial to designing strong and smart polymer/metal interfaces that play an important role in many industrial and biomedical applications. Here we show how macroscopic adhesion can be predicted on the basis of single molecular interactions. In particular, we carry out dynamic single molecule-force spectroscopy (SM-AFM) in the framework of Bell-Evans' theory to gain information about the energy barrier between the bound and unbound states of an amine/gold junction. Furthermore, we use Jarzynski's equality to obtain the equilibrium ground-state energy difference of the amine/gold bond from these nonequilibrium force measurements. In addition, we perform surface forces apparatus (SFA) experiments to measure macroscopic adhesion forces at contacts where approximately 10(7) amine/gold bonds are formed simultaneously. The SFA approach provides an amine/gold interaction energy (normalized by the number of interacting molecules) of (36 ± 1)k(B)T, which is in excellent agreement with the interaction free energy of (35 ± 3)k(B)T calculated using Jarzynski's equality and single-molecule AFM experiments. Our results validate Jarzynski's equality for the field of polymer/metal interactions by measuring both sides of the equation. Furthermore, the comparison of SFA and AFM shows how macroscopic interaction energies can be predicted on the basis of single molecular interactions, providing a new strategy to potentially predict adhesive properties of novel glues or coatings as well as bio- and wet adhesion.

Interaction of finger enslaving and error compensation in multiple finger force production.

PubMed

Martin, Joel R; Latash, Mark L; Zatsiorsky, Vladimir M

2009-01-01

Previous studies have documented two patterns of finger interaction during multi-finger pressing tasks, enslaving and error compensation, which do not agree with each other. Enslaving is characterized by positive correlation between instructed (master) and non-instructed (slave) finger(s) while error compensation can be described as a pattern of negative correlation between master and slave fingers. We hypothesize that pattern of finger interaction, enslaving or compensation depends on the initial force level and the magnitude of the targeted force change. Subjects were instructed to press with four fingers (I index, M middle, R ring, and L little) from a specified initial force to target forces following a ramp target line. Force-force relations between master and each of three slave fingers were analyzed during the ramp phase of trials by calculating correlation coefficients within each master-slave pair and then two-factor ANOVA was performed to determine effect of initial force and force increase on the correlation coefficients. It was found that, as initial force increased, the value of the correlation coefficient decreased and in some cases became negative, i.e. the enslaving transformed into error compensation. Force increase magnitude had a smaller effect on the correlation coefficients. The observations support the hypothesis that the pattern of inter-finger interaction--enslaving or compensation--depends on the initial force level and, to a smaller degree, on the targeted magnitude of the force increase. They suggest that the controller views tasks with higher steady-state forces and smaller force changes as implying a requirement to avoid large changes in the total force.

Atoms and Molecules. Physical Science in Action[TM]. Schlessinger Science Library. [Videotape].

ERIC Educational Resources Information Center

2000

There are more than 20 million known substances in the universe, and they are all made of the same basic ingredients--atoms and molecules. In this fun and engaging program, kids will learn about the three main subatomic particles--protons, neutrons and electrons--as well as the forces that keep atoms and molecules together. They'll discover how…

Potential interstellar noble gas molecules: ArOH+ and NeOH+ rovibrational analysis from quantum chemical quartic force fields

NASA Astrophysics Data System (ADS)

Theis, Riley A.; Fortenberry, Ryan C.

2016-03-01

The discovery of ArH+ in the interstellar medium has shown that noble gas chemistry may be of more chemical significance than previously believed. The present work extends the known chemistry of small noble gas molecules to NeOH+ and ArOH+. Besides their respective neonium and argonium diatomic cation cousins, these hydroxyl cation molecules are the most stable small noble gas molecules analyzed of late. ArOH+ is once again more stable than the neon cation, but both are well-behaved enough for a complete quartic force field analysis of their rovibrational properties. The Ar-O bond in ArOH+ , for instance, is roughly three-quarters of the strength of the Ar-H bond in ArH+ highlighting the rigidity of this system. The rotational constants, geometries, and vibrational frequencies for both molecules and their various isotopologues are computed from ab initio quantum chemical theory at high-level, and it is shown that these cations may form in regions where peroxy or weakly-bound alcohols may be present. The resulting data should be of significant assistance for the laboratory or observational analysis of these potential interstellar molecules.

Scaled Hartree-Fock force field calculations for organothallium compounds: Normal-mode analysis for TlCH sub 3 Tl(CH sub 3 ) sub 2 sup + , Tl(CH sub 3 ) sub 3 , Tl(CH sub 3 ) sub 2 Br, and Tl(CH sub 3 ) sub 4 sup minus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schwerdtfeger, P.; Bowmaker, G.A.; Boyd, P.D.W.

1990-02-01

In a recent paper we presented Hartree-Fock (HF) calculations for aliphatic organothallium compounds. The diagonal HF force constants obtained from a Fletcher-Powell geometry optimization are now used for a normal-mode analysis of TlCH{sub 3}, Tl(CH{sub 3}){sub 2}{sup +}, Tl(CH{sub 3}){sub 3}, Tl(CH{sub 3}){sub 2}Br, and Tl(CH{sub 3}){sub 4}{sup {minus}}. In order to calculate frequencies comparable to experimental values, the HF force field has been scaled by using scaling factors obtained from experimental infrared and Raman measurements on Tl(CH{sub 3}){sub 2}{sup +} and TlBr. The vibrational spectra of Tl(CH{sub 3}){sub 2}{sup +} were remeasured (infrared and Raman) in order to obtainmore » an accurate force field. Predictions are made for the vibrational spectrum of the as yet undetected TlCH{sub 3} molecule. Experimental infrared and Raman results for Tl(CH{sub 3}){sub 3} compare reasonably well with our calculated frequencies. Relativistic and correlation effects are analyzed for the vibrational frequencies of Tl(CH{sub 3}){sub 2}{sup +}.« less

Order statistics inference for describing topological coupling and mechanical symmetry breaking in multidomain proteins

NASA Astrophysics Data System (ADS)

Kononova, Olga; Jones, Lee; Barsegov, V.

2013-09-01

Cooperativity is a hallmark of proteins, many of which show a modular architecture comprising discrete structural domains. Detecting and describing dynamic couplings between structural regions is difficult in view of the many-body nature of protein-protein interactions. By utilizing the GPU-based computational acceleration, we carried out simulations of the protein forced unfolding for the dimer WW - WW of the all-β-sheet WW domains used as a model multidomain protein. We found that while the physically non-interacting identical protein domains (WW) show nearly symmetric mechanical properties at low tension, reflected, e.g., in the similarity of their distributions of unfolding times, these properties become distinctly different when tension is increased. Moreover, the uncorrelated unfolding transitions at a low pulling force become increasingly more correlated (dependent) at higher forces. Hence, the applied force not only breaks "the mechanical symmetry" but also couples the physically non-interacting protein domains forming a multi-domain protein. We call this effect "the topological coupling." We developed a new theory, inspired by order statistics, to characterize protein-protein interactions in multi-domain proteins. The method utilizes the squared-Gaussian model, but it can also be used in conjunction with other parametric models for the distribution of unfolding times. The formalism can be taken to the single-molecule experimental lab to probe mechanical cooperativity and domain communication in multi-domain proteins.

Mapping the force field of a hydrogen-bonded assembly

NASA Astrophysics Data System (ADS)

Sweetman, A. M.; Jarvis, S. P.; Sang, Hongqian; Lekkas, I.; Rahe, P.; Wang, Yu; Wang, Jianbo; Champness, N. R.; Kantorovich, L.; Moriarty, P.

2014-05-01

Hydrogen bonding underpins the properties of a vast array of systems spanning a wide variety of scientific fields. From the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the hydrogen bond continue to be vigorously debated. Here we use dynamic force microscopy (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide molecules hydrogen-bonded in two-dimensional assemblies. A comparison of experimental images and force spectra with their simulated counterparts shows that intermolecular contrast arises from repulsive tip-sample interactions whose interpretation can be aided via an examination of charge density depletion across the molecular system. Interpreting DFM images of hydrogen-bonded systems therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism.

Quantitative analysis of single-molecule force spectroscopy on folded chromatin fibers

PubMed Central

Meng, He; Andresen, Kurt; van Noort, John

2015-01-01

Single-molecule techniques allow for picoNewton manipulation and nanometer accuracy measurements of single chromatin fibers. However, the complexity of the data, the heterogeneity of the composition of individual fibers and the relatively large fluctuations in extension of the fibers complicate a structural interpretation of such force-extension curves. Here we introduce a statistical mechanics model that quantitatively describes the extension of individual fibers in response to force on a per nucleosome basis. Four nucleosome conformations can be distinguished when pulling a chromatin fiber apart. A novel, transient conformation is introduced that coexists with single wrapped nucleosomes between 3 and 7 pN. Comparison of force-extension curves between single nucleosomes and chromatin fibers shows that embedding nucleosomes in a fiber stabilizes the nucleosome by 10 kBT. Chromatin fibers with 20- and 50-bp linker DNA follow a different unfolding pathway. These results have implications for accessibility of DNA in fully folded and partially unwrapped chromatin fibers and are vital for understanding force unfolding experiments on nucleosome arrays. PMID:25779043

Entropic-elasticity-controlled dissociation and energetic-elasticity-controlled rupture induce catch-to-slip bonds in cell-adhesion molecules.

PubMed

Wei, YuJie

2008-03-01

We develop a physical model to describe the kinetic behavior in cell-adhesion molecules. Unbinding of noncovalent biological bonds is assumed to occur by both bond dissociation and bond rupture. Such a decomposition of debonding processes is a space decomposition of the debonding events. Dissociation under thermal fluctuation is nondirectional in a three-dimensional space, and its energy barrier to escape is not influenced by a tensile force, but the microstates that could lead to dissociation are changed by the tensile force; rupture happens along the tensile force direction. An applied force effectively lowers the energy barrier to escape along the loading direction. The lifetime of the biological bond, due to the two concurrent off rates, may grow with increasing tensile force to a moderate amount and then decrease with further increasing load. We hypothesize that a catch-to-slip bond transition is a generic feature in biological bonds. The model also predicts that catch bonds in a more flexible molecular structure have longer lifetimes and need less force to be fully activated.

Ultrafast single molecule technique for the study of force dependent kinetics and conformational changes of actin-protein interaction involved in mechanotransduction

NASA Astrophysics Data System (ADS)

Sergides, M.; Arbore, C.; Pavone, F. S.; Capitanio, M.

2018-02-01

Mechanical signals occurring at the interface between cell membrane and extracellular matrix and at intercellular junctions trigger biochemical signals that are fundamental for cell growth, development and regulation. Adaptor proteins, which link the cell membrane to the actin cytoskeleton, seem to partake in this process of mechanotransduction. In particular, catenins play a key role in intercellular junctions, where they act as a bridge between the cell membrane and actin. Studies suggest that α-catenin contains a domain that normally masks vinculin binding sites, which can become accessible after a conformational change induced by an external force. Here we demonstrate a single-molecule technique for investigating actin-protein interactions at different forces (up to 17 pN) with adequate temporal resolution (sub-ms). This system is based on the ultrafast force-clamp spectroscopy technique that has been recently developed by our group and is adapted to study and measure force-dependent kinetics of the catenin-actin interaction, as well as the amplitude of the expected conformational changes such as force-induced protein unfolding.

Force Generation by Membrane-Associated Myosin-I

PubMed Central

Pyrpassopoulos, Serapion; Arpağ, Göker; Feeser, Elizabeth A.; Shuman, Henry; Tüzel, Erkan; Ostap, E. Michael

2016-01-01

Vertebrate myosin-IC (Myo1c) is a type-1 myosin that links cell membranes to the cytoskeleton via its actin-binding motor domain and its phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2)-binding tail domain. While it is known that Myo1c bound to PtdIns(4,5)P2 in fluid-lipid bilayers can propel actin filaments in an unloaded motility assay, its ability to develop forces against external load on actin while bound to fluid bilayers has not been explored. Using optical tweezers, we measured the diffusion coefficient of single membrane-bound Myo1c molecules by force-relaxation experiments, and the ability of ensembles of membrane-bound Myo1c molecules to develop and sustain forces. To interpret our results, we developed a computational model that recapitulates the basic features of our experimental ensemble data and suggests that Myo1c ensembles can generate forces parallel to lipid bilayers, with larger forces achieved when the myosin works away from the plane of the membrane or when anchored to slowly diffusing regions. PMID:27156719

Proposed alteration of images of molecular orbitals obtained using a scanning tunneling microscope as a probe of electron correlation.

PubMed

Toroz, Dimitrios; Rontani, Massimo; Corni, Stefano

2013-01-04

Scanning tunneling spectroscopy (STS) allows us to image single molecules decoupled from the supporting substrate. The obtained images are routinely interpreted as the square moduli of molecular orbitals, dressed by the mean-field electron-electron interaction. Here we demonstrate that the effect of electron correlation beyond the mean field qualitatively alters the uncorrelated STS images. Our evidence is based on the ab initio many-body calculation of STS images of planar molecules with metal centers. We find that many-body correlations alter significantly the image spectral weight close to the metal center of the molecules. This change is large enough to be accessed experimentally, surviving to molecule-substrate interactions.

Submolecular resolution in scanning probe images of Sn-phthalocyanines on Cu(1 0 0) using metal tips

NASA Astrophysics Data System (ADS)

Buchmann, Kristof; Hauptmann, Nadine; Foster, Adam S.; Berndt, Richard

2017-10-01

Single Sn-phthalocyanine (SnPc) molecules adsorb on Cu(1 0 0) with the Sn ion above (Sn-up) or below (Sn-down) the molecular plane. Here we use a combination of atomic force microscopy (AFM), scanning tunnelling microscopy (STM) and first principles calculations to understand the adsorption configuration and origin of observed contrast of molecules in the Sn-down state. AFM with metallic tips images the pyrrole nitrogen atoms in these molecules as attractive features while STM reveals a chirality of the electronic structure of the molecules close to the Fermi level E_F, which is not observed in AFM. Using density functional theory calculations, the origin of the submolecular contrast is analysed and, while the electrostatic forces turn out to be negligible, the van der Waals interaction between the phenyl rings of SnPc and the substrate deform the molecule, push the pyrrole nitrogen atoms away from the substrate and thus induce the observed submolecular contrast. Simulated STM images reproduce the chirality of the electronic structure near E_F.

Recognition Imaging with a DNA Aptamer

PubMed Central

Lin, Liyun; Wang, Hongda; Liu, Yan; Yan, Hao; Lindsay, Stuart

2006-01-01

We have used a DNA-aptamer tethered to an atomic force microscope probe to carry out recognition imaging of IgE molecules attached to a mica substrate. The recognition was efficient (∼90%) and specific, being blocked by injection of IgE molecules in solution, and not being interfered with by high concentrations of a second protein. The signal/noise ratio of the recognition signal was better than that obtained with antibodies, despite the fact that the average force required to break the aptamer-protein bonds was somewhat smaller. PMID:16513776

High-speed atomic force microscopy coming of age

NASA Astrophysics Data System (ADS)

Ando, Toshio

2012-02-01

High-speed atomic force microscopy (HS-AFM) is now materialized. It allows direct visualization of dynamic structural changes and dynamic processes of functioning biological molecules in physiological solutions, at high spatiotemporal resolution. Dynamic molecular events unselectively appear in detail in an AFM movie, facilitating our understanding of how biological molecules operate to function. This review describes a historical overview of technical development towards HS-AFM, summarizes elementary devices and techniques used in the current HS-AFM, and then highlights recent imaging studies. Finally, future challenges of HS-AFM studies are briefly discussed.

PACSAB: Coarse-Grained Force Field for the Study of Protein-Protein Interactions and Conformational Sampling in Multiprotein Systems.

PubMed

Emperador, Agustí; Sfriso, Pedro; Villarreal, Marcos Ariel; Gelpí, Josep Lluis; Orozco, Modesto

2015-12-08

Molecular dynamics simulations of proteins are usually performed on a single molecule, and coarse-grained protein models are calibrated using single-molecule simulations, therefore ignoring intermolecular interactions. We present here a new coarse-grained force field for the study of many protein systems. The force field, which is implemented in the context of the discrete molecular dynamics algorithm, is able to reproduce the properties of folded and unfolded proteins, in both isolation, complexed forming well-defined quaternary structures, or aggregated, thanks to its proper evaluation of protein-protein interactions. The accuracy and computational efficiency of the method makes it a universal tool for the study of the structure, dynamics, and association/dissociation of proteins.

Anharmonic force field and vibrational dynamics of CH2F2 up to 5000 cm(-1) studied by Fourier transform infrared spectroscopy and state-of-the-art ab initio calculations.

PubMed

Tasinato, Nicola; Regini, Giorgia; Stoppa, Paolo; Pietropolli Charmet, Andrea; Gambi, Alberto

2012-06-07

Difluoromethane (CH(2)F(2), HFC-32) is a molecule used in refrigerant mixtures as a replacement of the more environmentally hazardous, ozone depleting, chlorofluorocarbons. On the other hand, presenting strong vibration-rotation bands in the 9 μm atmospheric window, it is a greenhouse gas which contributes to global warming. In the present work, the vibrational and ro-vibrational properties of CH(2)F(2), providing basic data for its atmospheric modeling, are studied in detail by coupling medium resolution Fourier transform infrared spectroscopy to high-level electronic structure ab initio calculations. Experimentally a full quantum assignment and accurate integrated absorption cross sections are obtained up to 5000 cm(-1). Ab initio calculations are carried out by using CCSD(T) theory and large basis sets of either the correlation consistent or atomic natural orbital hierarchies. By using vibrational perturbation theory to second order a complete set of vibrational and ro-vibrational parameters is derived from the ab initio quartic anharmonic force fields, which well compares with the spectroscopic constants retrieved experimentally. An excellent agreement between theory and experiment is achieved for vibrational energy levels and integrated absorption cross sections: transition frequencies up to four quanta of vibrational excitation are reproduced with a root mean square deviation (RMSD) of 7 cm(-1) while intensities are predicted within few km mol(-1) from the experiment. Basis set performances and core correlation effects are discussed throughout the paper. Particular attention is focused in the understanding of the anharmonic couplings which rule the vibrational dynamics of the |ν(1)>, |2ν(8)>, |2ν(2)> three levels interacting system. The reliability of the potential energy and dipole moment surfaces in reproducing the vibrational eigenvalues and intensities as well as in modeling the vibrational and ro-vibrational mixings over the whole 400-5000 cm(-1) region is also demonstrated by spectacular spectral simulations carried out by using the ro-vibrational Hamiltonian constants, and the relevant coupling terms, obtained from the perturbation treatment of the ab initio anharmonic force field. The present results suggest CH(2)F(2) as a prototype molecule to test ab initio calculations and theoretical models.

Anharmonic force field and vibrational dynamics of CH2F2 up to 5000 cm-1 studied by Fourier transform infrared spectroscopy and state-of-the-art ab initio calculations

NASA Astrophysics Data System (ADS)

Tasinato, Nicola; Regini, Giorgia; Stoppa, Paolo; Charmet, Andrea Pietropolli; Gambi, Alberto

2012-06-01

Difluoromethane (CH2F2, HFC-32) is a molecule used in refrigerant mixtures as a replacement of the more environmentally hazardous, ozone depleting, chlorofluorocarbons. On the other hand, presenting strong vibration-rotation bands in the 9 μm atmospheric window, it is a greenhouse gas which contributes to global warming. In the present work, the vibrational and ro-vibrational properties of CH2F2, providing basic data for its atmospheric modeling, are studied in detail by coupling medium resolution Fourier transform infrared spectroscopy to high-level electronic structure ab initio calculations. Experimentally a full quantum assignment and accurate integrated absorption cross sections are obtained up to 5000 cm-1. Ab initio calculations are carried out by using CCSD(T) theory and large basis sets of either the correlation consistent or atomic natural orbital hierarchies. By using vibrational perturbation theory to second order a complete set of vibrational and ro-vibrational parameters is derived from the ab initio quartic anharmonic force fields, which well compares with the spectroscopic constants retrieved experimentally. An excellent agreement between theory and experiment is achieved for vibrational energy levels and integrated absorption cross sections: transition frequencies up to four quanta of vibrational excitation are reproduced with a root mean square deviation (RMSD) of 7 cm-1 while intensities are predicted within few km mol-1 from the experiment. Basis set performances and core correlation effects are discussed throughout the paper. Particular attention is focused in the understanding of the anharmonic couplings which rule the vibrational dynamics of the |ν1⟩, |2ν8⟩, |2ν2⟩ three levels interacting system. The reliability of the potential energy and dipole moment surfaces in reproducing the vibrational eigenvalues and intensities as well as in modeling the vibrational and ro-vibrational mixings over the whole 400-5000 cm-1 region is also demonstrated by spectacular spectral simulations carried out by using the ro-vibrational Hamiltonian constants, and the relevant coupling terms, obtained from the perturbation treatment of the ab initio anharmonic force field. The present results suggest CH2F2 as a prototype molecule to test ab initio calculations and theoretical models.

Synthesis And Single Molecule Force Spectroscopy Of Poly(hydroxyethyl methacrylate-g-ethylene glycol)

NASA Astrophysics Data System (ADS)

Zhang, Dong; Ortiz, Christine

2003-03-01

With the advent of nanotechnology, miniaturized devices will soon need nanoscale springs with well-controlled nanomechanical properties such as shock absorbers, or to control the adhesive interactions between two components. In order to understand, manipulate, and control single macromolecule nanomechanical properties, mono(thiol)-terminated poly(hydroxyethyl methacrylate-g-ethylene glycol) has been synthesized via atom transfer radical polymerization. End-functionalization, chemical structure, molecular weight, side-chain graft density, radius of gyration, and polydispersity were characterized by 1H nuclear magnetic resonance, static light scattering, and gel permeation chromatography. The polymer chains were attached to Au-coated Si wafers via chemisorption to prepare well-separated "mushrooms", as verified by atomic force microscopy. Single molecule force spectroscopy was then used to measure the extensional elastic properties, i.e. force (nN) versus end-to-end separation distance (nm), of the individual chains by tethering to a Si3N4 probe tip via nonspecific, physisorption interactions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang Huayan; Yu Junping; Fu Guo

The interaction between integrin macrophage differentiation antigen associated with complement three receptor function (Mac-1) and intercellular adhesion molecule-1 (ICAM-1), which is controlled tightly by the ligand-binding activity of Mac-1, is central to the regulation of neutrophil adhesion in host defense. Several 'inside-out' signals and extracellular metal ions or antibodies have been found to activate Mac-1, resulting in an increased adhesiveness of Mac-1 to its ligands. However, the molecular basis for Mac-1 activation is not well understood yet. In this work, we have carried out a single-molecule study of Mac-1/ICAM-1 interaction force in living cells by atomic force microscopy (AFM). Ourmore » results showed that the binding probability and adhesion force of Mac-1 with ICAM-1 increased upon Mac-1 activation. Moreover, by comparing the dynamic force spectra of different Mac-1 mutants, we expected that Mac-1 activation is governed by the downward movement of its {alpha}7 helix.« less

Communication: Calculation of interatomic forces and optimization of molecular geometry with auxiliary-field quantum Monte Carlo

NASA Astrophysics Data System (ADS)

Motta, Mario; Zhang, Shiwei

2018-05-01

We propose an algorithm for accurate, systematic, and scalable computation of interatomic forces within the auxiliary-field quantum Monte Carlo (AFQMC) method. The algorithm relies on the Hellmann-Feynman theorem and incorporates Pulay corrections in the presence of atomic orbital basis sets. We benchmark the method for small molecules by comparing the computed forces with the derivatives of the AFQMC potential energy surface and by direct comparison with other quantum chemistry methods. We then perform geometry optimizations using the steepest descent algorithm in larger molecules. With realistic basis sets, we obtain equilibrium geometries in agreement, within statistical error bars, with experimental values. The increase in computational cost for computing forces in this approach is only a small prefactor over that of calculating the total energy. This paves the way for a general and efficient approach for geometry optimization and molecular dynamics within AFQMC.

Molecular simulation of caloric properties of fluids modelled by force fields with intramolecular contributions: Application to heat capacities

NASA Astrophysics Data System (ADS)

Smith, William R.; Jirsák, Jan; Nezbeda, Ivo; Qi, Weikai

2017-07-01

The calculation of caloric properties such as heat capacity, Joule-Thomson coefficients, and the speed of sound by classical force-field-based molecular simulation methodology has received scant attention in the literature, particularly for systems composed of complex molecules whose force fields (FFs) are characterized by a combination of intramolecular and intermolecular terms. The calculation of a thermodynamic property for a system whose molecules are described by such a FF involves the calculation of the residual property prior to its addition to the corresponding ideal-gas property, the latter of which is separately calculated, either using thermochemical compilations or nowadays accurate quantum mechanical calculations. Although the simulation of a volumetric residual property proceeds by simply replacing the intermolecular FF in the rigid molecule case by the total (intramolecular plus intermolecular) FF, this is not the case for a caloric property. We describe the correct methodology required to perform such calculations and illustrate it in this paper for the case of the internal energy and the enthalpy and their corresponding molar heat capacities. We provide numerical results for cP, one of the most important caloric properties. We also consider approximations to the correct calculation procedure previously used in the literature and illustrate their consequences for the examples of the relatively simple molecule 2-propanol, CH3CH(OH)CH3, and for the more complex molecule monoethanolamine, HO(CH2)2NH2, an important fluid used in carbon capture.

Magnetic tweezers for the measurement of twist and torque.

PubMed

Lipfert, Jan; Lee, Mina; Ordu, Orkide; Kerssemakers, Jacob W J; Dekker, Nynke H

2014-05-19

Single-molecule techniques make it possible to investigate the behavior of individual biological molecules in solution in real time. These techniques include so-called force spectroscopy approaches such as atomic force microscopy, optical tweezers, flow stretching, and magnetic tweezers. Amongst these approaches, magnetic tweezers have distinguished themselves by their ability to apply torque while maintaining a constant stretching force. Here, it is illustrated how such a "conventional" magnetic tweezers experimental configuration can, through a straightforward modification of its field configuration to minimize the magnitude of the transverse field, be adapted to measure the degree of twist in a biological molecule. The resulting configuration is termed the freely-orbiting magnetic tweezers. Additionally, it is shown how further modification of the field configuration can yield a transverse field with a magnitude intermediate between that of the "conventional" magnetic tweezers and the freely-orbiting magnetic tweezers, which makes it possible to directly measure the torque stored in a biological molecule. This configuration is termed the magnetic torque tweezers. The accompanying video explains in detail how the conversion of conventional magnetic tweezers into freely-orbiting magnetic tweezers and magnetic torque tweezers can be accomplished, and demonstrates the use of these techniques. These adaptations maintain all the strengths of conventional magnetic tweezers while greatly expanding the versatility of this powerful instrument.

Azobenzenes as light-controlled molecular electronic switches in nanoscale metal-molecule-metal junctions.

PubMed

Mativetsky, Jeffrey M; Pace, Giuseppina; Elbing, Mark; Rampi, Maria A; Mayor, Marcel; Samorì, Paolo

2008-07-23

Conductance switching associated with the photoisomerization of azobenzene-based (Azo) molecules was observed in nanoscopic metal-molecule-metal junctions. The junctions were formed by using a conducting atomic force microscope (C-AFM) approach, where a metallic AFM tip was used to electrically contact a gold-supported Azo self-assembled monolayer. The measured 30-fold increase in conductance is consistent with the expected decrease in tunneling barrier length resulting from the conformational change of the Azo molecule.

Nervous System Complexity Baffles Scientists.

ERIC Educational Resources Information Center

Fox, Jeffrey L.

1982-01-01

New research findings about how nerve cells transmit signals are forcing researchers to overhaul their simplistic ideas about the nervous system. Topics highlighted include the multiple role of peptides in the nervous system, receptor molecules, and molecules that form ion channels within membranes. (Author/JN)

Can correlations among receptors affect the information about the stimulus?

NASA Astrophysics Data System (ADS)

Singh, Vijay; Tchernookov, Martin; Nemenman, Ilya

2014-03-01

In the context of neural information processing, it has been observed that, compared to the case of independent receptors, correlated receptors can often carry more information about the stimulus. We explore similar ideas in the context of molecular information processing, analyzing a cell with receptors whose activity is intrinsically negatively correlated because they compete for the same ligand molecules. We show analytically that, in case the involved biochemical interactions are linear, the information between the number of molecules captured by the receptors and the ligand concentration does not depend on correlations among the receptors. For a nonlinear kinetic network, correlations similarly do not change the amount of information for observation times much shorter or much longer than the characteristic time scale of ligand molecule binding and unbinding. However, at intermediate times, correlations can increase the amount of available information. This work has been supported by the James S McDonnell foundation.

Lack of correlation between reaction speed and analytical sensitivity in isothermal amplification reveals the value of digital methods for optimization: validation using digital real-time RT-LAMP

PubMed Central

Khorosheva, Eugenia M.; Karymov, Mikhail A.; Selck, David A.; Ismagilov, Rustem F.

2016-01-01

In this paper, we asked if it is possible to identify the best primers and reaction conditions based on improvements in reaction speed when optimizing isothermal reactions. We used digital single-molecule, real-time analyses of both speed and efficiency of isothermal amplification reactions, which revealed that improvements in the speed of isothermal amplification reactions did not always correlate with improvements in digital efficiency (the fraction of molecules that amplify) or with analytical sensitivity. However, we observed that the speeds of amplification for single-molecule (in a digital device) and multi-molecule (e.g. in a PCR well plate) formats always correlated for the same conditions. Also, digital efficiency correlated with the analytical sensitivity of the same reaction performed in a multi-molecule format. Our finding was supported experimentally with examples of primer design, the use or exclusion of loop primers in different combinations, and the use of different enzyme mixtures in one-step reverse-transcription loop-mediated amplification (RT-LAMP). Our results show that measuring the digital efficiency of amplification of single-template molecules allows quick, reliable comparisons of the analytical sensitivity of reactions under any two tested conditions, independent of the speeds of the isothermal amplification reactions. PMID:26358811

Biophysical Aspects of T Lymphocyte Activation at the Immune Synapse

PubMed Central

Hivroz, Claire; Saitakis, Michael

2016-01-01

T lymphocyte activation is a pivotal step of the adaptive immune response. It requires the recognition by T-cell receptors (TCR) of peptides presented in the context of major histocompatibility complex molecules (pMHC) present at the surface of antigen-presenting cells (APCs). T lymphocyte activation also involves engagement of costimulatory receptors and adhesion molecules recognizing ligands on the APC. Integration of these different signals requires the formation of a specialized dynamic structure: the immune synapse. While the biochemical and molecular aspects of this cell–cell communication have been extensively studied, its mechanical features have only recently been addressed. Yet, the immune synapse is also the place of exchange of mechanical signals. Receptors engaged on the T lymphocyte surface are submitted to many tensile and traction forces. These forces are generated by various phenomena: membrane undulation/protrusion/retraction, cell mobility or spreading, and dynamic remodeling of the actomyosin cytoskeleton inside the T lymphocyte. Moreover, the TCR can both induce force development, following triggering, and sense and convert forces into biochemical signals, as a bona fide mechanotransducer. Other costimulatory molecules, such as LFA-1, engaged during immune synapse formation, also display these features. Moreover, T lymphocytes themselves are mechanosensitive, since substrate stiffness can modulate their response. In this review, we will summarize recent studies from a biophysical perspective to explain how mechanical cues can affect T lymphocyte activation. We will particularly discuss how forces are generated during immune synapse formation; how these forces affect various aspects of T lymphocyte biology; and what are the key features of T lymphocyte response to stiffness. PMID:26913033

Pseudomonas aeruginosa quorum sensing molecules correlate with clinical status in cystic fibrosis.

PubMed

Barr, Helen L; Halliday, Nigel; Cámara, Miguel; Barrett, David A; Williams, Paul; Forrester, Douglas L; Simms, Rebecca; Smyth, Alan R; Honeybourne, David; Whitehouse, Joanna L; Nash, Edward F; Dewar, Jane; Clayton, Andrew; Knox, Alan J; Fogarty, Andrew W

2015-10-01

Pseudomonas aeruginosa produces quorum sensing signal molecules that are potential biomarkers for infection.A prospective study of 60 cystic fibrosis patients with chronic P. aeruginosa, who required intravenous antibiotics for pulmonary exacerbations, was undertaken. Clinical measurements and biological samples were obtained at the start and end of the treatment period. Additional data were available for 29 of these patients when they were clinically stable.Cross-sectionally, quorum sensing signal molecules were detectable in the sputum, plasma and urine of 86%, 75% and 83% patients, respectively. They were positively correlated between the three biofluids. Positive correlations were observed for most quorum sensing signal molecules in sputum, plasma and urine, with quantitative measures of pulmonary P. aeruginosa load at the start of a pulmonary exacerbation. Plasma concentrations of 2-nonyl-4-hydroxy-quinoline (NHQ) were significantly higher at the start of a pulmonary exacerbation compared to clinical stability (p<0.01). Following the administration of systemic antibiotics, plasma 2-heptyl-4-hydroxyquinoline (p=0.02) and NHQ concentrations (p<0.01) decreased significantly.In conclusion, quorum sensing signal molecules are detectable in cystic fibrosis patients with pulmonary P. aeruginosa infection and are positively correlated with quantitative measures of P. aeruginosa. NHQ correlates with clinical status and has potential as a novel biomarker for P. aeruginosa infection. Copyright ©ERS 2015.

Pseudomonas aeruginosa quorum sensing molecules correlate with clinical status in cystic fibrosis

PubMed Central

Halliday, Nigel; Cámara, Miguel; Barrett, David A.; Williams, Paul; Forrester, Douglas L.; Simms, Rebecca; Smyth, Alan R.; Honeybourne, David; Whitehouse, Joanna L.; Nash, Edward F.; Dewar, Jane; Clayton, Andrew; Knox, Alan J.; Fogarty, Andrew W.

2015-01-01

Pseudomonas aeruginosa produces quorum sensing signal molecules that are potential biomarkers for infection. A prospective study of 60 cystic fibrosis patients with chronic P. aeruginosa, who required intravenous antibiotics for pulmonary exacerbations, was undertaken. Clinical measurements and biological samples were obtained at the start and end of the treatment period. Additional data were available for 29 of these patients when they were clinically stable. Cross-sectionally, quorum sensing signal molecules were detectable in the sputum, plasma and urine of 86%, 75% and 83% patients, respectively. They were positively correlated between the three biofluids. Positive correlations were observed for most quorum sensing signal molecules in sputum, plasma and urine, with quantitative measures of pulmonary P. aeruginosa load at the start of a pulmonary exacerbation. Plasma concentrations of 2-nonyl-4-hydroxy-quinoline (NHQ) were significantly higher at the start of a pulmonary exacerbation compared to clinical stability (p<0.01). Following the administration of systemic antibiotics, plasma 2-heptyl-4-hydroxyquinoline (p=0.02) and NHQ concentrations (p<0.01) decreased significantly. In conclusion, quorum sensing signal molecules are detectable in cystic fibrosis patients with pulmonary P. aeruginosa infection and are positively correlated with quantitative measures of P. aeruginosa. NHQ correlates with clinical status and has potential as a novel biomarker for P. aeruginosa infection. PMID:26022946

Atomic force microscope observation of branching in single transcript molecules derived from human cardiac muscle

NASA Astrophysics Data System (ADS)

Reed, Jason; Hsueh, Carlin; Mishra, Bud; Gimzewski, James K.

2008-09-01

We have used an atomic force microscope to examine a clinically derived sample of single-molecule gene transcripts, in the form of double-stranded cDNA, (c: complementary) obtained from human cardiac muscle without the use of polymerase chain reaction (PCR) amplification. We observed a log-normal distribution of transcript sizes, with most molecules being in the range of 0.4-7.0 kilobase pairs (kb) or 130-2300 nm in contour length, in accordance with the expected distribution of mRNA (m: messenger) sizes in mammalian cells. We observed novel branching structures not previously known to exist in cDNA, and which could have profound negative effects on traditional analysis of cDNA samples through cloning, PCR and DNA sequencing.

High-Speed Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Ando, Toshio; Uchihashi, Takayuki; Kodera, Noriyuki

2012-08-01

The technology of high-speed atomic force microscopy (HS-AFM) has reached maturity. HS-AFM enables us to directly visualize the structure and dynamics of biological molecules in physiological solutions at subsecond to sub-100 ms temporal resolution. By this microscopy, dynamically acting molecules such as myosin V walking on an actin filament and bacteriorhodopsin in response to light are successfully visualized. High-resolution molecular movies reveal the dynamic behavior of molecules in action in great detail. Inferences no longer have to be made from static snapshots of molecular structures and from the dynamic behavior of optical markers attached to biomolecules. In this review, we first describe theoretical considerations for the highest possible imaging rate, then summarize techniques involved in HS-AFM and highlight recent imaging studies. Finally, we briefly discuss future challenges to explore.

The Cytoskeleton and Force Response Mechanisms

NASA Technical Reports Server (NTRS)

Allen, Philip Goodwin

2003-01-01

The long term aim of this project was to define the mechanisms by which cells sense and respond to the physical forces experienced at 1g and missing in microgravity. Identification and characterization of the elements of the cells force response mechanism could provide pathways and molecules to serve as targets for pharmacological intervention to mitigate the pathologic effects of microgravity. Mechanical forces experienced by the organism can be transmitted to cells through molecules that allow cells to bind to the extracellular matrix and through other types of molecules which bind cells to each other. These molecules are coupled in large complexes of proteins to structural elements such as the actin cytoskeleton that give the cell the ability to sense, resist and respond to force. Application of small forces to tissue culture cells causes local elevation of intracellular calcium through stretch activated ion channels, increased tyrosine phosphorylation and a restructuring of the actin cytoskeleton. Using collagen coated iron oxide beads and strong magnets, we can apply different levels of force to cells in culture. We have found that force application causes the cells to polymerize actin at the site of mechanical deformation and unexpectedly, to depolymerize actin across the rest of the cell. Observations of GFP- actin expressing cells demonstrate that actin accumulates at the site of deformation within the first five minutes of force application and is maintained for many tens of minutes after force is removed. Consistent with the reinforcement of the cytoskeletal structures underlying the integrin-bead interaction, force also alters the motion of bound magnetic beads. This effect is seen following the removal of the magnetic field, and is only partially ablated by actin disruption with cytochalsin B. While actin is polymerizing locally at the site of force application, force also stimulates a global reduction in actin filament content within the cells. We have examined the roles of several actin filament disassembly factors in the global reduction of cellular actin filaments. The calcium regulated actin filament severing protein gelsolin is not necessary for the increased actin turnover, as cells derived from gelsolin null and wildtype mice still show a reduction in total actin filament content. Instead, our work suggests that the actin binding protein cofilin may be important for these changes in actin dynamics. Cofilin binds to and enhances the disassembly of actin filaments. Using immunological methods, we observe transient changes in the phosphorylation state of cofilin upon force application that suggests that cofilin may mediate actin filament turnover. Early after force application, cofilin is transiently dephosphorylated, activating its actin disassembly activity. Subsequently, we find a hyper-phosphorylation of cofilin, rendering it inactive. This reduction in cofilin activity may explain the stability of the force induced actin structuttes. In testing this hypothesis, we aimed to generate cells that express the constituitively active kinase (LIM-kinase) that phosphorylates cofilin. lnidial attempts in the cell lines used for the our previous studies proved unsuccessful. While we prepare this work for pubication, we are continuing to study other cell lines and tissue sources to determine whether they show a reduction in F-actin content after force application.

Micropipette force probe to quantify single-cell force generation: application to T-cell activation

PubMed Central

Sawicka, Anna; Babataheri, Avin; Dogniaux, Stéphanie; Barakat, Abdul I.; Gonzalez-Rodriguez, David; Hivroz, Claire; Husson, Julien

2017-01-01

In response to engagement of surface molecules, cells generate active forces that regulate many cellular processes. Developing tools that permit gathering mechanical and morphological information on these forces is of the utmost importance. Here we describe a new technique, the micropipette force probe, that uses a micropipette as a flexible cantilever that can aspirate at its tip a bead that is coated with molecules of interest and is brought in contact with the cell. This technique simultaneously allows tracking the resulting changes in cell morphology and mechanics as well as measuring the forces generated by the cell. To illustrate the power of this technique, we applied it to the study of human primary T lymphocytes (T-cells). It allowed the fine monitoring of pushing and pulling forces generated by T-cells in response to various activating antibodies and bending stiffness of the micropipette. We further dissected the sequence of mechanical and morphological events occurring during T-cell activation to model force generation and to reveal heterogeneity in the cell population studied. We also report the first measurement of the changes in Young’s modulus of T-cells during their activation, showing that T-cells stiffen within the first minutes of the activation process. PMID:28931600

Investigation of the heparin-thrombin interaction by dynamic force spectroscopy.

PubMed

Wang, Congzhou; Jin, Yingzi; Desai, Umesh R; Yadavalli, Vamsi K

2015-06-01

The interaction between heparin and thrombin is a vital step in the blood (anti)coagulation process. Unraveling the molecular basis of the interactions is therefore extremely important in understanding the mechanisms of this complex biological process. In this study, we use a combination of an efficient thiolation chemistry of heparin, a self-assembled monolayer-based single molecule platform, and a dynamic force spectroscopy to provide new insights into the heparin-thrombin interaction from an energy viewpoint at the molecular scale. Well-separated single molecules of heparin covalently attached to mixed self-assembled monolayers are demonstrated, whereby interaction forces with thrombin can be measured via atomic force microscopy-based spectroscopy. Further these interactions are studied at different loading rates and salt concentrations to directly obtain kinetic parameters. An increase in the loading rate shows a higher interaction force between the heparin and thrombin, which can be directly linked to the kinetic dissociation rate constant (koff). The stability of the heparin/thrombin complex decreased with increasing NaCl concentration such that the off-rate was found to be driven primarily by non-ionic forces. These results contribute to understanding the role of specific and nonspecific forces that drive heparin-thrombin interactions under applied force or flow conditions. Copyright © 2015 Elsevier B.V. All rights reserved.

Hydrogen/deuterium (H/D) exchange of gelatinized starch studied by two-dimensional (2D) near-infrared (NIR) correlation spectroscopy

NASA Astrophysics Data System (ADS)

Shinzawa, Hideyuki; Mizukado, Junji

2018-05-01

Hydrogen/deuterium (H/D) exchange of gelatinized starch was probed by in-situ near-infrared (NIR) monitoring coupled with two-dimensional (2D) correlation spectroscopy. Gelatinized starch undergoes spontaneous H/D exchange in D2O. During the substitution, the exchange rate essentially becomes different depending on solvent accessibility of various parts of the molecule. Thus, by analyzing the change in the NIR feature observed during the substitution, it becomes possible to sort out local structure and dynamics of the system. 2D correlation analysis of the time-dependent NIR spectra reveals the presence of different local structure of the starch, each having different solvent accessibility. For example, during the H/D exchange, the D2O is first absorbed by starch molecules especially around the surface area between the starch and water, where the water molecules are weakly interacted with the starch molecules. This absorption is quickly followed by the development of HDO species. Further absorption of the D2O results in the penetration of the molecules inside the starch and eventually develops the relatively strong interaction between the HDO and starch molecules because of the presence of dominant starch molecules.

Applications of Traction Force Microscopy in Measuring Adhesion Molecule Dependent Cell Contractility

ERIC Educational Resources Information Center

Mann, Cynthia Marie

2009-01-01

This work describes the use of polyacrylamide hydrogels as controlled elastic modulus substrates for single cell traction force microscopy studies. The first section describes the use of EDC/NHS chemistry to convalently link microbeads to the hydrogel matrix for the purpose of performing long-term traction force studies (7 days). The final study…

Shear-driven motion of supported lipid bilayers in microfluidic channels.

PubMed

Jönsson, Peter; Beech, Jason P; Tegenfeldt, Jonas O; Höök, Fredrik

2009-04-15

In this work, we demonstrate how a lateral motion of a supported lipid bilayer (SLB) and its constituents can be created without relying on self-spreading forces. The force driving the SLB is instead a viscous shear force arising from a pressure-driven bulk flow acting on the SLB that is formed on a glass wall inside a microfluidic channel. In contrast to self-spreading bilayers, this method allows for accurate control of the bilayer motion by altering the bulk flow in the channel. Experiments showed that an egg yolk phosphatidylcholine SLB formed on a glass support moved in a rolling motion under these shear forces, with the lipids in the upper leaflet of the bilayer moving at twice the velocity of the bilayer front. The drift velocity of different lipid probes in the SLB was observed to be sensitive to the interactions between the lipid probe and the surrounding molecules, resulting in drift velocities that varied by up to 1 order of magnitude for the different lipid probes in our experiments. Since the method provides a so far unattainable control of the motion of all molecules in an SLB, we foresee great potential for this technique, alone or in combination with other methods, for studies of lipid bilayers and different membrane-associated molecules.

Nanomechanics of multidomain neuronal cell adhesion protein contactin revealed by single molecule AFM and SMD.

PubMed

Mikulska-Ruminska, Karolina; Kulik, Andrej J; Benadiba, Carine; Bahar, Ivet; Dietler, Giovanni; Nowak, Wieslaw

2017-08-18

Contactin-4 (CNTN4) is a complex cell adhesion molecule (CAM) localized at neuronal membranes, playing a key role in maintaining the mechanical integrity and signaling properties of the synapse. CNTN4 consists of six immunoglobulin C2 type (IgC2) domains and four fibronectin type III (FnIII) domains that are shared with many other CAMs. Mutations in CNTN4 gene have been linked to various psychiatric disorders. Toward elucidating the response of this modular protein to mechanical stress, we studied its force-induced unfolding using single molecule atomic force microscopy (smAFM) and steered molecular dynamics (SMD) simulations. Extensive smAFM and SMD data both indicate the distinctive mechanical behavior of the two types of modules distinguished by unique force-extension signatures. The data also reveal the heterogeneity of the response of the individual FNIII and IgC2 modules, which presumably plays a role in the adaptability of CNTN4 to maintaining cell-cell communication and adhesion properties under different conditions. Results show that extensive sampling of force spectra, facilitated by robot-enhanced AFM, can help reveal the existence of weak stabilizing interactions between the domains of multidomain proteins, and provide insights into the nanomechanics of such multidomain or heteromeric proteins.

Organic ion association in aqueous phase and ab initio-based force fields: The case of carboxylate/ammonium salts

NASA Astrophysics Data System (ADS)

Houriez, Céline; Vallet, Valérie; Réal, Florent; Meot-Ner Mautner, Michael; Masella, Michel

2017-10-01

We performed molecular dynamics simulations of carboxylate/methylated ammonium ion pairs solvated in bulk water and of carboxylate/methylated ammonium salt solutions at ambient conditions using an ab initio-based polarizable force field whose parameters are assigned to reproduce only high end quantum computations, at the Møller-Plesset second-order perturbation theory/complete basis set limit level, regarding single ions and ion pairs as isolated and micro-hydrated in gas phase. Our results agree with the available experimental results regarding carboxylate/ammonium salt solutions. For instance, our force field approach predicts the percentage of acetate associated with ammonium ions in CH3 COO-/CH3 NH3+ solutions at the 0.2-0.8M concentration scale to range from 14% to 35%, in line with the estimates computed from the experimental ion association constant in liquid water. Moreover our simulations predict the number of water molecules released from the ion first hydration shell to the bulk upon ion association to be about 2.0 ± 0.6 molecules for acetate/protonated amine ion pairs, 3.1 ± 1.5 molecules for the HCOO-/NH4+ pair and 3.3 ± 1.2 molecules for the CH3COO-/(CH3)4N+ pair. For protonated amine-based ion pairs, these values are in line with experiment for alkali/halide pairs solvated in bulk water. All these results demonstrate the promising feature of ab initio-based force fields, i.e., their capacity in accurately modeling chemical systems that cannot be readily investigated using available experimental techniques.

Molecular Simulations of The Formation of Gold-Molecule-Gold Junctions

NASA Astrophysics Data System (ADS)

Wang, Huachuan

2013-03-01

We perform classical molecular simulations by combining grand canonical Monte Carlo (GCMC) sampling with molecular dynamics (MD) simulation to explore the dynamic gold nanojunctions in a Alkenedithiol (ADT) solvent. With the aid of a simple driving-spring model, which can reasonably represent the long-range elasticity of the gold electrode, the spring forces are obtained during the dynamic stretching procedure. A specific multi-time-scale double reversible reference system propagator (double-RESPA) algorithm has been designed for the metal-organic complex in MD simulations to identify the detailed metal-molecule bonding geometry at metal-molecule-metal interface. We investigate the variations of bonding sites of ADT molecules on gold nanojunctions at Au (111) surface at a constant chemical potential. Simulation results show that an Au-ADT-Au interface is formed on Au nanojunctions, bond-breaking intersection is at 1-1 bond of the monatomic chain of the cross-section, instead of at the Au-S bond. Breaking force is around 1.5 nN. These are consistent with the experimental measurements.

Influence of atomic tip structure on the intensity of inelastic tunneling spectroscopy data analyzed by combined scanning tunneling spectroscopy, force microscopy, and density functional theory

NASA Astrophysics Data System (ADS)

Okabayashi, Norio; Gustafsson, Alexander; Peronio, Angelo; Paulsson, Magnus; Arai, Toyoko; Giessibl, Franz J.

2016-04-01

Achieving a high intensity in inelastic scanning tunneling spectroscopy (IETS) is important for precise measurements. The intensity of the IETS signal can vary by up to a factor of 3 for various tips without an apparent reason accessible by scanning tunneling microscopy (STM) alone. Here, we show that combining STM and IETS with atomic force microscopy enables carbon monoxide front-atom identification, revealing that high IETS intensities for CO/Cu(111) are obtained for single-atom tips, while the intensity drops sharply for multiatom tips. Adsorption of the CO molecule on a Cu adatom [CO/Cu/Cu(111)] such that the molecule is elevated over the substrate strongly diminishes the tip dependence of IETS intensity, showing that an elevated position channels most of the tunneling current through the CO molecule even for multiatom tips, while a large fraction of the tunneling current bypasses the CO molecule in the case of CO/Cu(111).

SPM for functional identification of individual biomolecules

NASA Astrophysics Data System (ADS)

Ros, Robert; Schwesinger, Falk; Padeste, Celestino; Plueckthun, Andreas; Anselmetti, Dario; Guentherodt, Hans-Joachim; Tiefenauer, Louis

1999-06-01

The identification of specific binding molecules is of increasing interest in the context of drug development based on combinatorial libraries. Scanning Probe Microscopy (SPM) is the method of choice to image and probe individual biomolecules on a surface. Functional identification of biomolecules is a first step towards screening on a single molecule level. As a model system we use recombinant single- chain Fv fragment (scFv) antibody molecules directed against the antigen fluorescein. The scFv's are covalently immobilized on a flat gold surface via the C-terminal cysteine, resulting in a high accessibility of the binding site. The antigen is immobilized covalently via a long hydrophilic spacer to the silicon nitride SPM-tip. This arrangement allows a direct measurement of binding forces. Thus, closely related antibody molecules differing in only one amino acid at their binding site could be distinguished. A novel SPM-software has been developed which combines imaging, force spectroscopic modes, and online analysis. This is a major prerequisite for future screening methods.

Torque Measurement at the Single Molecule Level

PubMed Central

Forth, Scott; Sheinin, Maxim Y.; Inman, James; Wang, Michelle D.

2017-01-01

Methods for exerting and measuring forces on single molecules have revolutionized the study of the physics of biology. However, it is often the case that biological processes involve rotation or torque generation, and these parameters have been more difficult to access experimentally. Recent advances in the single molecule field have led to the development of techniques which add the capability of torque measurement. By combining force, displacement, torque, and rotational data, a more comprehensive description of the mechanics of a biomolecule can be achieved. In this review, we highlight a number of biological processes for which torque plays a key mechanical role. We describe the various techniques that have been developed to directly probe the torque experienced by a single molecule, and detail a variety of measurements made to date using these new technologies. We conclude by discussing a number of open questions and propose systems of study which would be well suited for analysis with torsional measurement techniques. PMID:23541162

Stop-Frame Filming and Discovery of Reactions at the Single-Molecule Level by Transmission Electron Microscopy

PubMed Central

2017-01-01

We report an approach, named chemTEM, to follow chemical transformations at the single-molecule level with the electron beam of a transmission electron microscope (TEM) applied as both a tunable source of energy and a sub-angstrom imaging probe. Deposited on graphene, disk-shaped perchlorocoronene molecules are precluded from intermolecular interactions. This allows monomolecular transformations to be studied at the single-molecule level in real time and reveals chlorine elimination and reactive aryne formation as a key initial stage of multistep reactions initiated by the 80 keV e-beam. Under the same conditions, perchlorocoronene confined within a nanotube cavity, where the molecules are situated in very close proximity to each other, enables imaging of intermolecular reactions, starting with the Diels–Alder cycloaddition of a generated aryne, followed by rearrangement of the angular adduct to a planar polyaromatic structure and the formation of a perchlorinated zigzag nanoribbon of graphene as the final product. ChemTEM enables the entire process of polycondensation, including the formation of metastable intermediates, to be captured in a one-shot “movie”. A molecule with a similar size and shape but with a different chemical composition, octathio[8]circulene, under the same conditions undergoes another type of polycondensation via thiyl biradical generation and subsequent reaction leading to polythiophene nanoribbons with irregular edges incorporating bridging sulfur atoms. Graphene or carbon nanotubes supporting the individual molecules during chemTEM studies ensure that the elastic interactions of the molecules with the e-beam are the dominant forces that initiate and drive the reactions we image. Our ab initio DFT calculations explicitly incorporating the e-beam in the theoretical model correlate with the chemTEM observations and give a mechanism for direct control not only of the type of the reaction but also of the reaction rate. Selection of the appropriate e-beam energy and control of the dose rate in chemTEM enabled imaging of reactions on a time frame commensurate with TEM image capture rates, revealing atomistic mechanisms of previously unknown processes. PMID:28191929

Behavior of P85 and P188 Poloxamer Molecules: Computer Simulations Using United Atom Force Field.

DOE PAGES

Goliaei, Ardeshir; Lau, Edmond Y.; Adhikari, Upendra; ...

2016-05-27

To study the interaction between poloxamer molecules and lipid bilayers using molecular dynamics simulation technique with the united atom resolution, we augmented the GROMOS force field to include poloxamers. We validated the force field by calculating the radii of gyration of two poloxamers, P85 and P188, solvated in water and by considering the poloxamer density distributions at the air/water interface. The emphasis of our simulations was on the study of the interaction between poloxamers and lipid bilayer. At the water/lipid bilayer interface, we observed that both poloxamers studied, P85 and P188, behaved like surfactants: the hydrophilic blocks of poloxamers becamemore » adsorbed at the polar interface, while their hydrophobic block penetrated the interface into the aliphatic tail region of the lipid bilayer. We also observed that when P85 and P188 poloxamers interacted with damaged membranes that contained pores, the hydrophobic blocks of copolymers penetrated into the membrane in the vicinity of the pore and compressed the membrane. Lastly, due to this compression, water molecules were evacuated from the pore.« less

Entropy, energy, and entanglement of localized states in bent triatomic molecules

NASA Astrophysics Data System (ADS)

Yuan, Qiang; Hou, Xi-Wen

2017-05-01

The dynamics of quantum entropy, energy, and entanglement is studied for various initial states in an important spectroscopic Hamiltonian of bent triatomic molecules H2O, D2O, and H2S. The total quantum correlation is quantified in terms of the mutual information and the entanglement by the concurrence borrowed from the theory of quantum information. The Pauli entropy and the intramolecular energy usually used in the theory of molecules are calculated to establish a possible relationship between both theories. Sections of two quantities among these four quantities are introduced to visualize such relationship. Analytic and numerical simulations demonstrate that if an initial state is taken to be the stretch- or the bend-vibrationally localized state, the mutual information, the Pauli entropy, and the concurrence are dominant-positively correlated while they are dominantly anti-correlated with the interacting energy among three anharmonic vibrational modes. In particular, such correlation is more distinct for the localized state with high excitations in the bending mode. The nice quasi-periodicity of those quantities in D2O molecule reveals that this molecule prepared in the localized state in the stretching or the bending mode can be more appreciated for molecular quantum computation. However, the dynamical correlations of those quantities behave irregularly for the dislocalized states. Moreover, the hierarchy of the mutual information and the Pauli entropy is explicitly proved. Quantum entropy and energy in every vibrational mode are investigated. Thereby, the relation between bipartite and tripartite entanglements is discussed as well. Those are useful for the understanding of quantum correlations in high-dimensional states in polyatomic molecules from quantum information and intramolecular dynamics.

Linearisation of λDNA molecules by instantaneous variation of the trapping electrode voltage inside a micro-channel

NASA Astrophysics Data System (ADS)

Hanasaki, Itsuo; Yukimoto, Naoya; Uehara, Satoshi; Shintaku, Hirofumi; Kawano, Satoyuki

2015-04-01

Because long DNA molecules usually exist in random coil states due to the entropic effect, linearisation is required for devices equipped with nanopores where electrical sequencing is necessary during single-file translocation. We present a novel technique for linearising DNA molecules in a micro-channel. In our device, electrodes are embedded in the bottom surface of the channel. The application of a voltage induces the trapping of λDNA molecules on the positive electrode. An instantaneous voltage drop is used to put the λDNA molecules in a partly released state and the hydrodynamic force of the solution induces linearisation. Phenomena were directly observed using an optical microscopy system equipped with a high-speed camera and the linearisation principle was explored in detail. Furthermore, we estimate the tensile characteristics produced by the flow of the solution through a numerical model of a tethered polymer subject to a Poiseuille flow. The mean tensile force is in the range of 0.1-1 pN. This is sufficiently smaller than the structural transition point of λDNA but counterbalances the entropic elasticity that causes the random coil shape of λDNA molecules in solution. We show the important role of thermal fluctuation in the manipulation of molecules in solution and clarify the tensile conditions required for DNA linearisation using a combination of solution flow and voltage variation in a microchannel.

Mechanically adjustable single-molecule transistors and stencil mask nanofabrication of high-resolution scanning probes

NASA Astrophysics Data System (ADS)

Champagne, Alexandre

This dissertation presents the development of two original experimental techniques to probe nanoscale objects. The first one studies electronic transport in single organic molecule transistors in which the source-drain electrode spacing is mechanically adjustable. The second involves the fabrication of high-resolution scanning probe microscopy sensors using a stencil mask lithography technique. We describe the fabrication of transistors in which a single organic molecule can be incorporated. The source and drain leads of these transistors are freely suspended above a flexible substrate, and their spacing can be adjusted by bending the substrate. We detail the technology developed to carry out measurements on these samples. We study electronic transport in single C60 molecules at low temperature. We observe Coulomb blockaded transport and can resolve the discrete energy spectrum of the molecule. We are able to mechanically tune the spacing between the electrodes (over a range of 5 A) to modulate the lead-molecule coupling, and can electrostatically tune the energy levels on the molecule by up to 160 meV using a gate electrode. Initial progress in studying different transport regimes in other molecules is also discussed. We present a lithographic process that allows the deposition of metal nanostructures with a resolution down to 10 nm directly onto atomic force microscope (AFM) tips. We show that multiple layers of lithography can be deposited and aligned. We fabricate high-resolution magnetic force microscopy (MFM) probes using this method and discuss progress to fabricate other scanning probe microscopy (SPM) sensors.

Interactions and aggregation of apoferritin molecules in solution: effects of added electrolytes.

PubMed Central

Petsev, D N; Thomas, B R; Yau, S; Vekilov, P G

2000-01-01

We have studied the structure of the protein species and the protein-protein interactions in solutions containing two apoferritin molecular forms, monomers and dimers, in the presence of Na(+) and Cd(2+) ions. We used chromatographic, and static and dynamic light scattering techniques, and atomic force microscopy (AFM). Size-exclusion chromatography was used to isolate these two protein fractions. The sizes and shapes of the monomers and dimers were determined by dynamic light scattering and AFM. Although the monomer is an apparent sphere with a diameter corresponding to previous x-ray crystallography determinations, the dimer shape corresponds to two, bound monomer spheres. Static light scattering was applied to characterize the interactions between solute molecules of monomers and dimers in terms of the second osmotic virial coefficients. The results for the monomers indicate that Na(+) ions cause strong intermolecular repulsion even at concentrations higher than 0.15 M, contrary to the predictions of the commonly applied Derjaguin-Landau-Verwey-Overbeek theory. We argue that the reason for such behavior is hydration force due to the formation of a water shell around the protein molecules with the help of the sodium ions. The addition of even small amounts of Cd(2+) changes the repulsive interactions to attractive but does not lead to oligomer formation, at least at the protein concentrations used. Thus, the two ions provide examples of strong specificity of their interactions with the protein molecules. In solutions of the apoferritin dimer, the molecules attract even in the presence of Na(+) only, indicating a change in the surface of the apoferritin molecule. In view of the strong repulsion between the monomers, this indicates that the dimers and higher oligomers form only after partial denaturation of some of the apoferritin monomers. These observations suggest that aggregation and self-assembly of protein molecules or molecular subunits may be driven by forces other than those responsible for crystallization and other phase transitions in the protein solution. PMID:10733984

Surface conformations of an anti-ricin aptamer and its affinity for ricin determined by atomic force microscopy and surface plasmon resonance.

PubMed

Wang, B; Lou, Z; Park, B; Kwon, Y; Zhang, H; Xu, B

2015-01-07

We used atomic force microscopy (AFM) and surface plasmon resonance (SPR) to study the surface conformations of an anti-ricin aptamer and its specific binding affinity for ricin molecules. The effect of surface modification of the Au(111) substrate on the aptamer affinity was also estimated. The AFM topography images had a resolution high enough to distinguish different aptamer conformations. The specific binding site on the aptamer molecule was clearly located by the AFM recognition images. The aptamer on a Au(111) surface modified with carboxymethylated-dextran (CD) showed both similarities to and differences from the one without CD modification. The influence of CD modification was evaluated using AFM images of various aptamer conformations on the Au(111) surface. The affinity between ricin and the anti-ricin aptamer was estimated using the off-rate values measured using AFM and SPR. The SPR measurements of the ricin sample were conducted in the range from 83.3 pM to 8.33 nM, and the limit of detection was estimated as 25 pM (1.5 ng mL(-1)). The off-rate values of the ricin-aptamer interactions were estimated using both single-molecule dynamic force spectroscopy (DFS) and SPR as (7.3 ± 0.4) × 10(-4) s(-1) and (1.82 ± 0.067) × 10(-2) s(-1), respectively. The results show that single-molecule measurements can obtain different reaction parameters from bulk solution measurements. In AFM single-molecule measurements, the various conformations of the aptamer immobilized on the gold surface determined the availability of each specific binding site to the ricin molecules. The SPR bulk solution measurements averaged the signals from specific and non-specific interactions. AFM images and DFS measurements provide more specific information on the interactions of individual aptamer and ricin molecules.

Simulations of the OKE Response in Simple Liquids Using a Polarizable and a Nonpolarizable Force Field.

PubMed

Polok, Kamil

2018-02-08

Recently polarizable force fields are becoming increasingly popular for molecular dynamics simulations. As the signal obtained in the optical Kerr effect (OKE) experiment is due to the polarizability dynamics of the investigated system, a study is conducted in order to compare the experimental results with those obtained with the polarizable AMOEBA force field. The comparison is made in the frequency domain; however, time domain data are also included. The selected molecular systems are the isotropic carbon tetrachloride molecule, the anisotropic chloroform, carbon disulfide and acetone molecules, and the hydrogen-bonded water and methanol molecules. Different dipole-induced-dipole (DID) method variants are used for calculation of the OKE response, showing the importance of use of the all-atom approach with preoptimized atomic polarizabilities. In order to obtain a good intermolecular to intramolecular components amplitude ratio, the isotropic polarizability in the Thole correction needs to be updated between iterations. The convergence of the spectra calculated with different DID variants is also considered, and the approach that appears to be the best gives a very good approximation after three iterations. The comparison of the experimental and simulated spectra shows a rather good agreement for the non-hydrogen-bonded molecules, although the contribution of the reorientation of anisotropic molecules is overestimated. In the case of the hydrogen-bonded molecules, the theoretical spectra are far from the experimental ones. The highly overestimated librational bands indicate excessive polarizability anisotropy introduced by the potential model. Finally, in order to verify the significance of different components of the AMOEBA model, it is gradually simplified and compared with a simple reference potential model. Removal of polarizability shows a tremendous change in the case of hydrogen-bonded liquids, whereas for the other molecules it is of minor importance. The non-hydrogen-bonded liquids are, however, more sensitive to the presence of atomic multipoles in the model.

The Amateur Scientist.

ERIC Educational Resources Information Center

Walker, Jearl

1985-01-01

Discusses forces that shape the behavior of water as a drop meanders down a windowpane. A homemade apparatus for studying meanders is described along with several experiments. Contact angles, molecule attraction, surface area, air tension, and gravity drag forces are some of the topics addressed. (DH)

Quantitative evaluation of cross correlation between two finite-length time series with applications to single-molecule FRET.

PubMed

Hanson, Jeffery A; Yang, Haw

2008-11-06

The statistical properties of the cross correlation between two time series has been studied. An analytical expression for the cross correlation function's variance has been derived. On the basis of these results, a statistically robust method has been proposed to detect the existence and determine the direction of cross correlation between two time series. The proposed method has been characterized by computer simulations. Applications to single-molecule fluorescence spectroscopy are discussed. The results may also find immediate applications in fluorescence correlation spectroscopy (FCS) and its variants.

Progressive Stereo Locking (PSL): A Residual Dipolar Coupling Based Force Field Method for Determining the Relative Configuration of Natural Products and Other Small Molecules.

PubMed

Cornilescu, Gabriel; Ramos Alvarenga, René F; Wyche, Thomas P; Bugni, Tim S; Gil, Roberto R; Cornilescu, Claudia C; Westler, William M; Markley, John L; Schwieters, Charles D

2017-08-18

Establishing the relative configuration of a bioactive natural product represents the most challenging part in determining its structure. Residual dipolar couplings (RDCs) are sensitive probes of the relative spatial orientation of internuclear vectors. We adapted a force field structure calculation methodology to allow free sampling of both R and S configurations of the stereocenters of interest. The algorithm uses a floating alignment tensor in a simulated annealing protocol to identify the conformations and configurations that best fit experimental RDC and distance restraints (from NOE and J-coupling data). A unique configuration (for rigid molecules) or a very small number of configurations (for less rigid molecules) of the structural models having the lowest chiral angle energies and reasonable magnitudes of the alignment tensor are provided as the best predictions of the unknown configuration. For highly flexible molecules, the progressive locking of their stereocenters into their statistically dominant R or S state dramatically reduces the number of possible relative configurations. The result is verified by checking that the same configuration is obtained by initiating the locking from different regions of the molecule. For all molecules tested having known configurations (with conformations ranging from mostly rigid to highly flexible), the method accurately determined the correct configuration.

Chemical activation of molecules by metals: Experimental studies of electron distributions and bonding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lichtenberger, D.L.

1991-10-01

The formal relationship between measured molecular ionization energies and thermodynamic bond dissociation energies has been developed into a single equation which unifies the treatment of covalent bonds, ionic bonds, and partially ionic bonds. This relationship has been used to clarify the fundamental thermodynamic information relating to metal-hydrogen, metal-alkyl, and metal-metal bond energies. We have been able to obtain a direct observation and measurement of the stabilization energy provided by the agostic interaction of the C-H bond with the metal. The ionization energies have also been used to correlate the rates of carbonyl substitution reactions of ({eta}{sup 5}-C{sub 5}H{sub 4}X)Rh(CO){sub 2}more » complexes, and to reveal the electronic factors that control the stability of the transition state. The extent that the electronic features of these bonding interactions transfer to other chemical systems is being investigated in terms of the principle of additivity of ligand electronic effects. Specific examples under study include metal- phosphines, metal-halides, and metallocenes. Especially interesting has been the recent application of these techniques to the characterization of the soccer-ball shaped C{sub 60} molecule, buckminsterfullerene, and its interaction with a metal surface. The high-resolution valence ionizations in the gas phase reveal the high symmetry of the molecule, and studies of thin films of C{sub 60} reveal weak intermolecular interactions. Scanning tunneling and atomic force microscopy reveal the arrangement of spherical molecules on gold substrates, with significant delocalization of charge from the metal surface. 21 refs.« less

Toward Accurate Adsorption Energetics on Clay Surfaces

PubMed Central

2016-01-01

Clay minerals are ubiquitous in nature, and the manner in which they interact with their surroundings has important industrial and environmental implications. Consequently, a molecular-level understanding of the adsorption of molecules on clay surfaces is crucial. In this regard computer simulations play an important role, yet the accuracy of widely used empirical force fields (FF) and density functional theory (DFT) exchange-correlation functionals is often unclear in adsorption systems dominated by weak interactions. Herein we present results from quantum Monte Carlo (QMC) for water and methanol adsorption on the prototypical clay kaolinite. To the best of our knowledge, this is the first time QMC has been used to investigate adsorption at a complex, natural surface such as a clay. As well as being valuable in their own right, the QMC benchmarks obtained provide reference data against which the performance of cheaper DFT methods can be tested. Indeed using various DFT exchange-correlation functionals yields a very broad range of adsorption energies, and it is unclear a priori which evaluation is better. QMC reveals that in the systems considered here it is essential to account for van der Waals (vdW) dispersion forces since this alters both the absolute and relative adsorption energies of water and methanol. We show, via FF simulations, that incorrect relative energies can lead to significant changes in the interfacial densities of water and methanol solutions at the kaolinite interface. Despite the clear improvements offered by the vdW-corrected and the vdW-inclusive functionals, absolute adsorption energies are often overestimated, suggesting that the treatment of vdW forces in DFT is not yet a solved problem. PMID:27917256

Determining the elastic properties of aptamer-ricin single molecule multiple pathways

USDA-ARS?s Scientific Manuscript database

Ricin and an anti-ricin aptamer showed three stable binding conformations with their special chemomechanical properties. The elastic properties of the ricin-aptamer single-molecule interactions were investigated by the dynamic force spectroscopy (DFS). The worm-like-chain model and Hook’s law were ...

Large-eddy simulations of a forced homogeneous isotropic turbulence with polymer additives

NASA Astrophysics Data System (ADS)

Wang, Lu; Cai, Wei-Hua; Li, Feng-Chen

2014-03-01

Large-eddy simulations (LES) based on the temporal approximate deconvolution model were performed for a forced homogeneous isotropic turbulence (FHIT) with polymer additives at moderate Taylor Reynolds number. Finitely extensible nonlinear elastic in the Peterlin approximation model was adopted as the constitutive equation for the filtered conformation tensor of the polymer molecules. The LES results were verified through comparisons with the direct numerical simulation results. Using the LES database of the FHIT in the Newtonian fluid and the polymer solution flows, the polymer effects on some important parameters such as strain, vorticity, drag reduction, and so forth were studied. By extracting the vortex structures and exploring the flatness factor through a high-order correlation function of velocity derivative and wavelet analysis, it can be found that the small-scale vortex structures and small-scale intermittency in the FHIT are all inhibited due to the existence of the polymers. The extended self-similarity scaling law in the polymer solution flow shows no apparent difference from that in the Newtonian fluid flow at the currently simulated ranges of Reynolds and Weissenberg numbers.

Graphene Visualizes the Ion Distribution on Air-Cleaved Mica.

PubMed

Bampoulis, Pantelis; Sotthewes, Kai; Siekman, Martin H; Zandvliet, Harold J W; Poelsema, Bene

2017-03-06

The distribution of potassium (K + ) ions on air-cleaved mica is important in many interfacial phenomena such as crystal growth, self-assembly and charge transfer on mica. However, due to experimental limitations to nondestructively probe single ions and ionic domains, their exact lateral organization is yet unknown. We show, by the use of graphene as an ultra-thin protective coating and scanning probe microscopies, that single potassium ions form ordered structures that are covered by an ice layer. The K + ions prefer to minimize the number of nearest neighbour K + ions by forming row-like structures as well as small domains. This trend is a result of repulsive ionic forces between adjacent ions, weakened due to screening by the surrounding water molecules. Using high resolution conductive atomic force microscopy maps, the local conductance of the graphene is measured, revealing a direct correlation between the K + distribution and the structure of the ice layer. Our results shed light on the local distribution of ions on the air-cleaved mica, solving a long-standing enigma. They also provide a detailed understanding of charge transfer from the ionic domains towards graphene.

Poorly Understood Aspects of Striated Muscle Contraction

PubMed Central

Månsson, Alf

2015-01-01

Muscle contraction results from cyclic interactions between the contractile proteins myosin and actin, driven by the turnover of adenosine triphosphate (ATP). Despite intense studies, several molecular events in the contraction process are poorly understood, including the relationship between force-generation and phosphate-release in the ATP-turnover. Different aspects of the force-generating transition are reflected in the changes in tension development by muscle cells, myofibrils and single molecules upon changes in temperature, altered phosphate concentration, or length perturbations. It has been notoriously difficult to explain all these events within a given theoretical framework and to unequivocally correlate observed events with the atomic structures of the myosin motor. Other incompletely understood issues include the role of the two heads of myosin II and structural changes in the actin filaments as well as the importance of the three-dimensional order. We here review these issues in relation to controversies regarding basic physiological properties of striated muscle. We also briefly consider actomyosin mutation effects in cardiac and skeletal muscle function and the possibility to treat these defects by drugs. PMID:25961006

Poorly understood aspects of striated muscle contraction.

PubMed

Månsson, Alf; Rassier, Dilson; Tsiavaliaris, Georgios

2015-01-01

Muscle contraction results from cyclic interactions between the contractile proteins myosin and actin, driven by the turnover of adenosine triphosphate (ATP). Despite intense studies, several molecular events in the contraction process are poorly understood, including the relationship between force-generation and phosphate-release in the ATP-turnover. Different aspects of the force-generating transition are reflected in the changes in tension development by muscle cells, myofibrils and single molecules upon changes in temperature, altered phosphate concentration, or length perturbations. It has been notoriously difficult to explain all these events within a given theoretical framework and to unequivocally correlate observed events with the atomic structures of the myosin motor. Other incompletely understood issues include the role of the two heads of myosin II and structural changes in the actin filaments as well as the importance of the three-dimensional order. We here review these issues in relation to controversies regarding basic physiological properties of striated muscle. We also briefly consider actomyosin mutation effects in cardiac and skeletal muscle function and the possibility to treat these defects by drugs.

Adsorption of Xyloglucan onto Cellulose Surfaces of Different Morphologies: An Entropy-Driven Process.

PubMed

Benselfelt, Tobias; Cranston, Emily D; Ondaral, Sedat; Johansson, Erik; Brumer, Harry; Rutland, Mark W; Wågberg, Lars

2016-09-12

The temperature-dependence of xyloglucan (XG) adsorption onto smooth cellulose model films regenerated from N-methylmorpholine N-oxide (NMMO) was investigated using surface plasmon resonance spectroscopy, and it was found that the adsorbed amount increased with increasing temperature. This implies that the adsorption of XG to NMMO-regenerated cellulose is endothermic and supports the hypothesis that the adsorption of XG onto cellulose is an entropy-driven process. We suggest that XG adsorption is mainly driven by the release of water molecules from the highly hydrated cellulose surfaces and from the XG molecules, rather than through hydrogen bonding and van der Waals forces as previously suggested. To test this hypothesis, the adsorption of XG onto cellulose was studied using cellulose films with different morphologies prepared from cellulose nanocrystals (CNC), semicrystalline NMMO-regenerated cellulose, and amorphous cellulose regenerated from lithium chloride/dimethylacetamide. The total amount of high molecular weight xyloglucan (XGHMW) adsorbed was studied by quartz crystal microbalance and reflectometry measurements, and it was found that the adsorption was greatest on the amorphous cellulose followed by the CNC and NMMO-regenerated cellulose films. There was a significant correlation between the cellulose dry film thickness and the adsorbed XG amount, indicating that XG penetrated into the films. There was also a correlation between the swelling of the films and the adsorbed amounts and conformation of XG, which further strengthened the conclusion that the water content and the subsequent release of the water upon adsorption are important components of the adsorption process.

Dynamics of single-stranded DNA tethered to a solid

NASA Astrophysics Data System (ADS)

Radiom, Milad; Paul, Mark R.; Ducker, William A.

2016-06-01

Tethering is used to deliver specific biological and industrial functions. For example, single-stranded DNA (ssDNA) is tethered to polymerases and long sequences of double-stranded DNA (dsDNA) during replication, and to solids in DNA microarrays. However, tethering ssDNA to a large object limits not only the available ssDNA conformations, but also the range of time-scales over which the mechanical responses of ssDNA are important. In this work we examine the effect of tethering by measurement of the mechanical response of ssDNA that is tethered at each end to two separate atomic force microscope cantilevers in aqueous solution. Thermal motion of the cantilevers drives the ends of the ssDNA chain at frequencies near 2 kHz. The presence of a tethered molecule makes a large difference to the asymmetric cross-correlation of two cantilevers, which enables resolution of the mechanical properties in our experiments. By analysis of the correlated motion of the cantilevers we extract the friction and stiffness of the ssDNA. We find that the measured friction is much larger than the friction that is usually associated with the unencumbered motion of ssDNA. We also find that the measured relaxation time, ∼30 μs, is much greater than prior measurements of the free-molecule relaxation time. We attribute the difference to the loss of conformational possibilities as a result of constraining the ends of the ssDNA.

Trapping of a microsphere pendulum resonator in an optical potential

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ward, J. M.; Photonics Centre, Tyndall National Institute, Prospect Row, Cork; Wu, Y.

We propose a method to spatially confine or corral the movements of a micropendulum via the optical forces produced by two simultaneously excited optical modes of a photonic molecule comprising two microspherical cavities. We discuss how the cavity-enhanced optical force generated in the photonic molecule can create an optomechanical potential of about 10 eV deep and 30 pm wide, which can be used to trap the pendulum at any given equilibrium position by a simple choice of laser frequencies. This result presents opportunities for very precise all-optical self-alignment of microsystems.

Expression levels of MHC class I molecules are inversely correlated with promiscuity of peptide binding

PubMed Central

Chappell, Paul E; Meziane, El Kahina; Harrison, Michael; Magiera, Łukasz; Hermann, Clemens; Mears, Laura; Wrobel, Antoni G; Durant, Charlotte; Nielsen, Lise Lotte; Buus, Søren; Ternette, Nicola; Mwangi, William; Butter, Colin; Nair, Venugopal; Ahyee, Trudy; Duggleby, Richard; Madrigal, Alejandro; Roversi, Pietro; Lea, Susan M; Kaufman, Jim

2015-01-01

Highly polymorphic major histocompatibility complex (MHC) molecules are at the heart of adaptive immune responses, playing crucial roles in many kinds of disease and in vaccination. We report that breadth of peptide presentation and level of cell surface expression of class I molecules are inversely correlated in both chickens and humans. This relationship correlates with protective responses against infectious pathogens including Marek's disease virus leading to lethal tumours in chickens and human immunodeficiency virus infection progressing to AIDS in humans. We propose that differences in peptide binding repertoire define two groups of MHC class I molecules strategically evolved as generalists and specialists for different modes of pathogen resistance. We suggest that differences in cell surface expression level ensure the development of optimal peripheral T cell responses. The inverse relationship of peptide repertoire and expression is evidently a fundamental property of MHC molecules, with ramifications extending beyond immunology and medicine to evolutionary biology and conservation. DOI: http://dx.doi.org/10.7554/eLife.05345.001 PMID:25860507

Comparison of one-particle basis set extrapolation to explicitly correlated methods for the calculation of accurate quartic force fields, vibrational frequencies, and spectroscopic constants: Application to H2O, N2H+, NO2+, and C2H2

NASA Astrophysics Data System (ADS)

Huang, Xinchuan; Valeev, Edward F.; Lee, Timothy J.

2010-12-01

One-particle basis set extrapolation is compared with one of the new R12 methods for computing highly accurate quartic force fields (QFFs) and spectroscopic data, including molecular structures, rotational constants, and vibrational frequencies for the H2O, N2H+, NO2+, and C2H2 molecules. In general, agreement between the spectroscopic data computed from the best R12 and basis set extrapolation methods is very good with the exception of a few parameters for N2H+ where it is concluded that basis set extrapolation is still preferred. The differences for H2O and NO2+ are small and it is concluded that the QFFs from both approaches are more or less equivalent in accuracy. For C2H2, however, a known one-particle basis set deficiency for C-C multiple bonds significantly degrades the quality of results obtained from basis set extrapolation and in this case the R12 approach is clearly preferred over one-particle basis set extrapolation. The R12 approach used in the present study was modified in order to obtain high precision electronic energies, which are needed when computing a QFF. We also investigated including core-correlation explicitly in the R12 calculations, but conclude that current approaches are lacking. Hence core-correlation is computed as a correction using conventional methods. Considering the results for all four molecules, it is concluded that R12 methods will soon replace basis set extrapolation approaches for high accuracy electronic structure applications such as computing QFFs and spectroscopic data for comparison to high-resolution laboratory or astronomical observations, provided one uses a robust R12 method as we have done here. The specific R12 method used in the present study, CCSD(T)R12, incorporated a reformulation of one intermediate matrix in order to attain machine precision in the electronic energies. Final QFFs for N2H+ and NO2+ were computed, including basis set extrapolation, core-correlation, scalar relativity, and higher-order correlation and then used to compute highly accurate spectroscopic data for all isotopologues. Agreement with high-resolution experiment for 14N2H+ and 14N2D+ was excellent, but for 14N16O2+ agreement for the two stretching fundamentals is outside the expected residual uncertainty in the theoretical values, and it is concluded that there is an error in the experimental quantities. It is hoped that the highly accurate spectroscopic data presented for the minor isotopologues of N2H+ and NO2+ will be useful in the interpretation of future laboratory or astronomical observations.

Direct observation of λ-DNA molecule reversal movement within microfluidic channels under electric field with single molecule imaging technique

NASA Astrophysics Data System (ADS)

Fengyun, Yang; Kaige, Wang; Dan, Sun; Wei, Zhao; Hai-qing, Wang; Xin, He; Gui-ren, Wang; Jin-tao, Bai

2016-07-01

The electrodynamic characteristics of single DNA molecules moving within micro-/nano-fluidic channels are important in the design of biomedical chips and bimolecular sensors. In this study, the dynamic properties of λ-DNA molecules transferring along the microchannels driven by the external electrickinetic force were systemically investigated with the single molecule fluorescence imaging technique. The experimental results indicated that the velocity of DNA molecules was strictly dependent on the value of the applied electric field and the diameter of the channel. The larger the external electric field, the larger the velocity, and the more significant deformation of DNA molecules. More meaningfully, it was found that the moving directions of DNA molecules had two completely different directions: (i) along the direction of the external electric field, when the electric field intensity was smaller than a certain threshold value; (ii) opposite to the direction of the external electric field, when the electric field intensity was greater than the threshold electric field intensity. The reversal movement of DNA molecules was mainly determined by the competition between the electrophoresis force and the influence of electro-osmosis flow. These new findings will theoretically guide the practical application of fluidic channel sensors and lab-on-chips for precisely manipulating single DNA molecules. Project supported by the National Natural Science Foundation of China (Grant No. 61378083), the International Cooperation Foundation of the National Science and Technology Major Project of the Ministry of Science and Technology of China (Grant No. 2011DFA12220), the Major Research Plan of National Natural Science Foundation of China (Grant No. 91123030), and the Natural Science Foundation of Shaanxi Province of China (Grant Nos. 2010JS110 and 2013SZS03-Z01).

Thermodynamics of fluid conduction through hydrophobic channel of carbon nanotubes: The exciting force for filling of nanotubes with polar and nonpolar fluids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sahu, Pooja; Ali, Sk. M., E-mail: musharaf@barc.gov.in; Shenoy, K. T.

2015-02-21

Thermodynamic properties of the fluid in the hydrophobic pores of nanotubes are known to be different not only from the bulk phase but also from other conventional confinements. Here, we use a recently developed theoretical scheme of “two phase thermodynamic (2PT)” model to understand the driving forces inclined to spontaneous filling of carbon nanotubes (CNTs) with polar (water) and nonpolar (methane) fluids. The CNT confinement is found to be energetically favorable for both water and methane, leading to their spontaneous filling inside CNT(6,6). For both the systems, the free energy of transfer from bulk to CNT confinement is favored bymore » the increased entropy (TΔS), i.e., increased translational entropy and increased rotational entropy, which were found to be sufficiently high to conquer the unfavorable increase in enthalpy (ΔE) when they are transferred inside CNT. To the best of our knowledge, this is the first time when it has been established that the increase in translational entropy during confinement in CNT(6,6) is not unique to water-like H bonding fluid but is also observed in case of nonpolar fluids such as methane. The thermodynamic results are explained in terms of density, structural rigidity, and transport of fluid molecules inside CNT. The faster diffusion of methane over water in bulk phase is found to be reversed during the confinement in CNT(6,6). Studies reveal that though hydrogen bonding plays an important role in transport of water through CNT, but it is not the solitary driving factor, as the nonpolar fluids, which do not have any hydrogen bond formation capacity can go inside CNT and also can flow through it. The associated driving force for filling and transport of water and methane is enhanced translational and rotational entropies, which are attributed mainly by the strong correlation between confined fluid molecules and availability of more free space for rotation of molecule, i.e., lower density of fluid inside CNT due to their single file-like arrangement. To the best of our information, this is perhaps the first study of nonpolar fluid within CNT using 2PT method. Furthermore, the fast flow of polar fluid (water) over nonpolar fluid (methane) has been captured for the first time using molecular dynamic simulations.« less

Study of correlations from Ab-Initio Simulations of Liquid Water

NASA Astrophysics Data System (ADS)

Soto, Adrian; Fernandez-Serra, Marivi; Lu, Deyu; Yoo, Shinjae

An accurate understanding of the dynamics and the structure of H2O molecules in the liquid phase is of extreme importance both from a fundamental and from a practical standpoint. Despite the successes of Molecular Dynamics (MD) with Density Functional Theory (DFT), liquid water remains an extremely difficult material to simulate accurately and efficiently because of fine balance between the covalent O-H bond, the hydrogen bond and the attractive the van der Waals forces. Small errors in those produce dramatic changes in the macroscopic properties of the liquid or in its structural properties. Different density functionals produce answers that differ by as much as 35% in ambient conditions, with none producing quantitative results in agreement with experiment at different mass densities. In order to understand these differences we perform an exhaustive scanning of the geometrical coordinates of MD simulations and study their statistical correlations with the simulation output quantities using advanced correlation analyses and machine learning techniques. This work was partially supported by DOE Award No. DE-FG02-09ER16052, by DOE Early Career Award No. DE-SC0003871, by BNL LDRD 16-039 project and BNL Contract No. DE-SC0012704.

Study of correlations from Ab-Initio Simulations of Liquid Water

NASA Astrophysics Data System (ADS)

Soto, Adrian; Fernandez-Serra, Marivi; Lu, Deyu; Yoo, Shinjae

An accurate understanding of the dynamics and the structure of H2O molecules in the liquid phase is of extreme importance both from a fundamental and from a practical standpoint. Despite the successes of Molecular Dynamics (MD) with Density Functional Theory (DFT), liquid water remains an extremely difficult material to simulate accurately and efficiently because of fine balance between the covalent O-H bond, the hydrogen bond and the attractive the van der Waals forces. Small errors in those produce dramatic changes in the macroscopic properties of the liquid or in its structural properties. Different density functionals produce answers that differ by as much as 35% in ambient conditions, with none producing quantitative results in agreement with experiment at different mass densities [J. Chem Phys. 139, 194502(2013)]. In order to understand these differences we perform an exhaustive scanning of the geometrical coordinates of MD simulations and study their statistical correlations with the simulation output quantities using advanced correlation analyses and machine learning techniques. This work was partially supported by DOE Award No. DE-FG02-09ER16052, by DOE Early Career Award No. DE-SC0003871, by BNL LDRD 16-039 project and BNL Contract No. DE-SC0012704.

Adiabatic Field-Free Alignment of Asymmetric Top Molecules with an Optical Centrifuge.

PubMed

Korobenko, A; Milner, V

2016-05-06

We use an optical centrifuge to align asymmetric top SO_{2} molecules by adiabatically spinning their most polarizable O-O axis. The effective centrifugal potential in the rotating frame confines the sulfur atoms to the plane of the laser-induced rotation, leading to the planar molecular alignment that persists after the molecules are released from the centrifuge. The periodic appearance of the full three-dimensional alignment, typically observed only with linear and symmetric top molecules, is also detected. Together with strong in-plane centrifugal forces, which bend the molecules by up to 10 deg, permanent field-free alignment offers new ways of controlling molecules with laser light.

Single-molecule experiments in biological physics: methods and applications.

PubMed

Ritort, F

2006-08-16

I review single-molecule experiments (SMEs) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SMEs it is possible to manipulate molecules one at a time and measure distributions describing molecular properties, characterize the kinetics of biomolecular reactions and detect molecular intermediates. SMEs provide additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SMEs it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level, emphasizing the importance of SMEs to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SMEs from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOTs), magnetic tweezers (MTs), biomembrane force probes (BFPs) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation) and proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SMEs to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.

TOPICAL REVIEW: Single-molecule experiments in biological physics: methods and applications

NASA Astrophysics Data System (ADS)

Ritort, F.

2006-08-01

I review single-molecule experiments (SMEs) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SMEs it is possible to manipulate molecules one at a time and measure distributions describing molecular properties, characterize the kinetics of biomolecular reactions and detect molecular intermediates. SMEs provide additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SMEs it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level, emphasizing the importance of SMEs to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SMEs from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOTs), magnetic tweezers (MTs), biomembrane force probes (BFPs) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation) and proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SMEs to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.

Enhanced Chiral Discriminatory van der Waals Interactions Mediated by Chiral Surfaces

NASA Astrophysics Data System (ADS)

Barcellona, Pablo; Safari, Hassan; Salam, A.; Buhmann, Stefan Yoshi

2017-05-01

We predict a discriminatory interaction between a chiral molecule and an achiral molecule which is mediated by a chiral body. To achieve this, we generalize the van der Waals interaction potential between two ground-state molecules with electric, magnetic, and chiral response to nontrivial environments. The force is evaluated using second-order perturbation theory with an effective Hamiltonian. Chiral media enhance or reduce the free interaction via many-body interactions, making it possible to measure the chiral contributions to the van der Waals force with current technology. The van der Waals interaction is discriminatory with respect to enantiomers of different handedness and could be used to separate enantiomers. We also suggest a specific geometric configuration where the electric contribution to the van der Waals interaction is zero, making the chiral component the dominant effect.

Computational study of small molecule binding for both tethered and free conditions

PubMed Central

2010-01-01

Using a calix[4]arene-benzene complex as a test system we compare the potential of mean force for when the calix[4]arene is tethered versus free. When the complex is in vacuum our results show that the difference between tethered and free is primarily due to the entropic contribution to the potential of mean force resulting in a significant binding free energy difference of 6.6 kJ/mol. By contrast, when the complex is in water our results suggest that there is no appreciable difference between tethered and free. This study elucidates the roles of entropy and enthalpy for this small molecule system and emphasizes the point that tethering the receptor has the potential to dramatically impact the binding properties. These findings should be taken into consideration when using calixarene molecules in nanosensor design. PMID:20369865

Assembly, Thermodynamics, and Structure of a Two-Wheeled Composite of a Dumbbell-Shaped Molecule and Cylindrical Molecules with Different Edges.

PubMed

Matsuno, Taisuke; Kamata, Sho; Sato, Sota; Yokoyama, Atsutoshi; Sarkar, Parantap; Isobe, Hiroyuki

2017-11-20

A carbonaceous dumbbell was able to spontaneously glue two tubular receptors to form a unique two-wheeled composite through van der Waals interactions, thus forcing the wheel components into contact with each other at the edges. In the present study, two tubular receptors with enantiomeric carbon networks were assembled on the dumbbell joint, and the handedness of the receptors was discriminated, thus leading to the self-sorting of homomeric receptors from a mixture of enantiomeric tubes. The crystal structures of the composites revealed the structural origins of the molecular recognition driven by van der Waals forces as well as the presence of a columnar array of C 120 molecules in a 1:1 composite. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The nature of the force-induced conformation transition of dsDNA studied by using single molecule force spectroscopy.

PubMed

Liu, Ningning; Bu, Tianjia; Song, Yu; Zhang, Wei; Li, Jinjing; Zhang, Wenke; Shen, Jiacong; Li, Hongbin

2010-06-15

Single-stranded DNA binding proteins (SSB) interact with single-stranded DNA (ssDNA) specifically. Taking advantage of this character, we have employed Bacillus subtilis SSB protein to investigate the nature of force-induced conformation transition of double-stranded DNA (dsDNA) by using AFM-based single molecule force spectroscopy (SMFS) technique. Our results show that, when a dsDNA is stretched beyond its contour length, the dsDNA is partially melted, producing some ssDNA segments which can be captured by SSB proteins. We have also systematically investigated the effects of stretching length, waiting time, and salt concentration on the conformation transition of dsDNA and SSB-ssDNA interactions, respectively. Furthermore, the effect of proflavine, a DNA intercalator, on the SSB-DNA interactions has been investigated, and the results indicate that the proflavine-saturated dsDNA can be stabilized to the extent that the dsDNA will no longer melt into ssDNA under the mechanical force even up to 150 pN, and no SSB-DNA interactions are detectable.

Lack of correlation between reaction speed and analytical sensitivity in isothermal amplification reveals the value of digital methods for optimization: validation using digital real-time RT-LAMP.

PubMed

Khorosheva, Eugenia M; Karymov, Mikhail A; Selck, David A; Ismagilov, Rustem F

2016-01-29

In this paper, we asked if it is possible to identify the best primers and reaction conditions based on improvements in reaction speed when optimizing isothermal reactions. We used digital single-molecule, real-time analyses of both speed and efficiency of isothermal amplification reactions, which revealed that improvements in the speed of isothermal amplification reactions did not always correlate with improvements in digital efficiency (the fraction of molecules that amplify) or with analytical sensitivity. However, we observed that the speeds of amplification for single-molecule (in a digital device) and multi-molecule (e.g. in a PCR well plate) formats always correlated for the same conditions. Also, digital efficiency correlated with the analytical sensitivity of the same reaction performed in a multi-molecule format. Our finding was supported experimentally with examples of primer design, the use or exclusion of loop primers in different combinations, and the use of different enzyme mixtures in one-step reverse-transcription loop-mediated amplification (RT-LAMP). Our results show that measuring the digital efficiency of amplification of single-template molecules allows quick, reliable comparisons of the analytical sensitivity of reactions under any two tested conditions, independent of the speeds of the isothermal amplification reactions. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Thermal characterization of static and dynamical properties of the confined molecular systems interacting through dispersion force.

PubMed

Ramos, Sergio Luis L M; Ogino, Michihiko; Oguni, Masaharu

2015-01-28

We investigated the thermal properties of liquid methylcyclohexane and racemic sec-butylcyclohexane, as representatives of a molecular system with only dispersion-force intermolecular interactions, confined in the pores (thickness/diameter d = 12, 6, 1.1 nm) of silica gels by adiabatic calorimetry. The results imply a heterogeneous picture for molecular aggregate under confinement consisting of an interfacial region and an inner pore one. In the vicinity of a glass-transition temperature T(g,bulk) of bulk liquid, two distinguishable relaxation phenomena were observed for the confined systems and their origins were attributed to the devitrification, namely glass transition, processes of (1) a layer of interfacial molecules adjacent to the pore walls and (2) the molecules located in the middle of the pore. A third glass-transition phenomenon was observed at lower temperatures and ascribed to a secondary relaxation process. The glass transition of the interfacial-layer molecules was found to proceed at temperatures rather above T(g,bulk), whereas that of the molecules located in the inner pore region occurred at temperatures below T(g,bulk). We discuss the reason why the molecules located in different places in the pores reveal the respectively different dynamical properties.

Influence of Polarization on Carbohydrate Hydration: A Comparative Study Using Additive and Polarizable Force Fields.

PubMed

Pandey, Poonam; Mallajosyula, Sairam S

2016-07-14

Carbohydrates are known to closely modulate their surrounding solvent structures and influence solvation dynamics. Spectroscopic investigations studying far-IR regions (below 1000 cm(-1)) have observed spectral shifts in the libration band (around 600 cm(-1)) of water in the presence of monosaccharides and polysaccharides. In this paper, we use molecular dynamics simulations to gain atomistic insight into carbohydrate-water interactions and to specifically highlight the differences between additive (nonpolarizable) and polarizable simulations. A total of six monosaccharide systems, α and β anomers of glucose, galactose, and mannose, were studied using additive and polarizable Chemistry at HARvard Macromolecular Mechanics (CHARMM) carbohydrate force fields. Solvents were modeled using three additive water models TIP3P, TIP4P, and TIP5P in additive simulations and polarizable water model SWM4 in polarizable simulations. The presence of carbohydrate has a significant effect on the microscopic water structure, with the effects being pronounced for proximal water molecules. Notably, disruption of the tetrahedral arrangement of proximal water molecules was observed due to the formation of strong carbohydrate-water hydrogen bonds in both additive and polarizable simulations. However, the inclusion of polarization resulted in significant water-bridge occupancies, improved ordered water structures (tetrahedral order parameter), and longer carbohydrate-water H-bond correlations as compared to those for additive simulations. Additionally, polarizable simulations also allowed the calculation of power spectra from the dipole-dipole autocorrelation function, which corresponds to the IR spectra. From the power spectra, we could identify spectral signatures differentiating the proximal and bulk water structures, which could not be captured from additive simulations.

Charge transfer in the weak driving force limit in blends of MDMO-PPV and dithienylthiazolo[5,4-d]thiazoles towards organic photovoltaics with high V(OC).

PubMed

Nevil, Nissy; Ling, Yun; Van Mierloo, Sarah; Kesters, Jurgen; Piersimoni, Fortunato; Adriaensens, Peter; Lutsen, Laurence; Vanderzande, Dirk; Manca, Jean; Maes, Wouter; Van Doorslaer, Sabine; Goovaerts, Etienne

2012-12-05

A series of three 5'-aryl-2,5-dithienylthiazolo[5,4-d]thiazole (DTTzTz) semiconducting molecules with different aryl substituents has been investigated as alternative acceptor materials in combination with the donor polymer poly[2-methoxy-5-(3',7'-dimethyloctyloxy)-1,4-phenylene vinylene] (MDMO-PPV) in order to evaluate the photoinduced charge transfer (CT) efficiency in the resulting blends, designed towards possible application in organic photovoltaics. Photoluminescence quenching together with polaron detection by electron paramagnetic resonance and photoinduced absorption (PIA) demonstrate an increasing charge transfer efficiency when the DTTzTz substituents are varied from thien-2-yl to 4-trifluoromethylphenyl and 4-cyanophenyl groups, correlating well with the increasing acceptor strength in this series of molecules. In line with this observation, there is a decrease in the effective optical bandgap relative to pure MDMO-PPV that becomes more pronounced along this series of acceptor compounds, reaching 0.12 eV in the blend with 4-CN-Ph-DTTzTz. Intermolecular interactions between the blend components lead to lower energy transitions which are found to contribute significantly to the device external quantum efficiency. The high V(OC) reached in devices based on MDMO-PPV:4-CN-Ph-DTTzTz blends meets the expectations for such a donor:acceptor combination. However, thermal activation of charge carrier recombination occurs because of the weak driving force for charge transfer, as shown by time-dependent PIA measurements, and this is suggested as a cause for the observed low photovoltaic performance.

Structural, dynamical, and transport properties of the hydrated halides: How do At{sup −} bulk properties compare with those of the other halides, from F{sup −} to I{sup −}?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Réal, Florent, E-mail: florent.real@univ-lille1.fr; Severo Pereira Gomes, André; Guerrero Martínez, Yansel Omar

2016-03-28

The properties of halides from the lightest, fluoride (F{sup −}), to the heaviest, astatide (At{sup −}), have been studied in water using a polarizable force-field approach based on molecular dynamics (MD) simulations at the 10 ns scale. The selected force-field explicitly treats the cooperativity within the halide-water hydrogen bond networks. The force-field parameters have been adjusted to ab initio data on anion/water clusters computed at the relativistic Möller-Plesset second-order perturbation theory level of theory. The anion static polarizabilities of the two heaviest halides, I{sup −} and At{sup −}, were computed in the gas phase using large and diffuse atomic basis sets,more » and taking into account both electron correlation and spin-orbit coupling within a four-component framework. Our MD simulation results show the solvation properties of I{sup −} and At{sup −} in aqueous phase to be very close. For instance, their first hydration shells are structured and encompass 9.2 and 9.1 water molecules at about 3.70 ± 0.05 Å, respectively. These values have to be compared to the F{sup −}, Cl{sup −}, and Br{sup −} ones, i.e., 6.3, 8.4, and 9.0 water molecules at 2.74, 3.38, and 3.55 Å, respectively. Moreover our computations predict the solvation free energy of At{sup −} in liquid water at ambient conditions to be 68 kcal mol{sup −1}, a value also close the I{sup −} one, about 70 kcal mol{sup −1}. In all, our simulation results for I{sup −} are in excellent agreement with the latest neutron- and X-ray diffraction studies. Those for the At{sup −} ion are predictive, as no theoretical or experimental data are available to date.« less

Tunneling mechanism and contact mechanics of colloidal nanoparticle assemblies.

PubMed

Biaye, Moussa; Zbydniewska, Ewa; Mélin, Thierry; Deresmes, Dominique; Copie, Guillaume; Cleri, Fabrizio; Sangeetha, Neralagatta; Decorde, Nicolas; Viallet, Benoit; Grisolia, Jérémie; Ressier, Laurence; Diesinger, Heinrich

2016-11-25

Nanoparticle assemblies with thiol-terminated alkyl chains are studied by conducting atomic force microscopy (c-AFM) regarding their use as strain gauges for touch-sensitive panels. Current-force spectroscopy is used as a characterization tool complementary to the macroscopic setup since it allows a bias to be applied to a limited number of junctions, overcoming the Coulomb blockade energy and focusing on the contact electromechanics and the transport mechanism across the ligand. First, transition voltage spectroscopy is applied with varying force to target the underlying tunneling mechanism by observing whether the transition between the ohmic and exponential current-voltage behavior is force-dependent. Secondly, current-force spectroscopy in the ohmic range below the transition voltage is performed. The current-force behavior of the AFM probe in contact with a nanoparticle multilayer is associated with the spread of force and current within the nanoparticle lattice and at the level of adjacent particles by detailed contact mechanics treatment. The result is twofold: concerning the architecture of sensors, this work is a sample case of contact electromechanics at scales ranging from the device scale down to the individual ligand molecule. Regarding transport across the molecule, the vacuum tunneling mechanism is favored over the conduction by coherent molecular states, which is a decision-making aid for the choice of ligand in applications.

Atomic force microscopy imaging and single molecule recognition force spectroscopy of coat proteins on the surface of Bacillus subtilis spore.

PubMed

Tang, Jilin; Krajcikova, Daniela; Zhu, Rong; Ebner, Andreas; Cutting, Simon; Gruber, Hermann J; Barak, Imrich; Hinterdorfer, Peter

2007-01-01

Coat assembly in Bacillus subtilis serves as a tractable model for the study of the self-assembly process of biological structures and has a significant potential for use in nano-biotechnological applications. In the present study, the morphology of B. subtilis spores was investigated by magnetically driven dynamic force microscopy (MAC mode atomic force microscopy) under physiological conditions. B. subtilis spores appeared as prolate structures, with a length of 0.6-3 microm and a width of about 0.5-2 microm. The spore surface was mainly covered with bump-like structures with diameters ranging from 8 to 70 nm. Besides topographical explorations, single molecule recognition force spectroscopy (SMRFS) was used to characterize the spore coat protein CotA. This protein was specifically recognized by a polyclonal antibody directed against CotA (anti-CotA), the antibody being covalently tethered to the AFM tip via a polyethylene glycol linker. The unbinding force between CotA and anti-CotA was determined as 55 +/- 2 pN. From the high-binding probability of more than 20% in force-distance cycles it is concluded that CotA locates in the outer surface of B. subtilis spores. Copyright (c) 2007 John Wiley & Sons, Ltd.

Force Generation in Single Conventional Actomyosin Complexes under High Dynamic Load

PubMed Central

Takagi, Yasuharu; Homsher, Earl E.; Goldman, Yale E.; Shuman, Henry

2006-01-01

The mechanical load borne by a molecular motor affects its force, sliding distance, and its rate of energy transduction. The control of ATPase activity by the mechanical load on a muscle tunes its efficiency to the immediate task, increasing ATP hydrolysis as the power output increases at forces less than isometric (the Fenn effect) and suppressing ATP hydrolysis when the force is greater than isometric. In this work, we used a novel ‘isometric’ optical clamp to study the mechanics of myosin II molecules to detect the reaction steps that depend on the dynamic properties of the load. An actin filament suspended between two beads and held in separate optical traps is brought close to a surface that is sparsely coated with motor proteins on pedestals of silica beads. A feedback system increases the effective stiffness of the actin by clamping the force on one of the beads and moving the other bead electrooptically. Forces measured during actomyosin interactions are increased at higher effective stiffness. The results indicate that single myosin molecules transduce energy nearly as efficiently as whole muscle and that the mechanical control of the ATP hydrolysis rate is in part exerted by reversal of the force-generating actomyosin transition under high load without net utilization of ATP. PMID:16326899

On the Boiling Points of the Alkyl Halides.

ERIC Educational Resources Information Center

Correia, John

1988-01-01

Discusses the variety of explanations in organic chemistry textbooks of a physical property of organic compounds. Focuses on those concepts explaining attractive forces between molecules. Concludes that induction interactions play a major role in alkyl halides and other polar organic molecules and should be given wider exposure in chemistry texts.…

The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building.

PubMed

Dupradeau, François-Yves; Pigache, Adrien; Zaffran, Thomas; Savineau, Corentin; Lelong, Rodolphe; Grivel, Nicolas; Lelong, Dimitri; Rosanski, Wilfried; Cieplak, Piotr

2010-07-28

Deriving atomic charges and building a force field library for a new molecule are key steps when developing a force field required for conducting structural and energy-based analysis using molecular mechanics. Derivation of popular RESP charges for a set of residues is a complex and error prone procedure because it depends on numerous input parameters. To overcome these problems, the R.E.D. Tools (RESP and ESP charge Derive, ) have been developed to perform charge derivation in an automatic and straightforward way. The R.E.D. program handles chemical elements up to bromine in the periodic table. It interfaces different quantum mechanical programs employed for geometry optimization and computing molecular electrostatic potential(s), and performs charge fitting using the RESP program. By defining tight optimization criteria and by controlling the molecular orientation of each optimized geometry, charge values are reproduced at any computer platform with an accuracy of 0.0001 e. The charges can be fitted using multiple conformations, making them suitable for molecular dynamics simulations. R.E.D. allows also for defining charge constraints during multiple molecule charge fitting, which are used to derive charges for molecular fragments. Finally, R.E.D. incorporates charges into a force field library, readily usable in molecular dynamics computer packages. For complex cases, such as a set of homologous molecules belonging to a common family, an entire force field topology database is generated. Currently, the atomic charges and force field libraries have been developed for more than fifty model systems and stored in the RESP ESP charge DDataBase. Selected results related to non-polarizable charge models are presented and discussed.

Importance of Preserving Cross-correlation in developing Statistically Downscaled Climate Forcings and in estimating Land-surface Fluxes and States

NASA Astrophysics Data System (ADS)

Das Bhowmik, R.; Arumugam, S.

2015-12-01

Multivariate downscaling techniques exhibited superiority over univariate regression schemes in terms of preserving cross-correlations between multiple variables- precipitation and temperature - from GCMs. This study focuses on two aspects: (a) develop an analytical solutions on estimating biases in cross-correlations from univariate downscaling approaches and (b) quantify the uncertainty in land-surface states and fluxes due to biases in cross-correlations in downscaled climate forcings. Both these aspects are evaluated using climate forcings available from both historical climate simulations and CMIP5 hindcasts over the entire US. The analytical solution basically relates the univariate regression parameters, co-efficient of determination of regression and the co-variance ratio between GCM and downscaled values. The analytical solutions are compared with the downscaled univariate forcings by choosing the desired p-value (Type-1 error) in preserving the observed cross-correlation. . For quantifying the impacts of biases on cross-correlation on estimating streamflow and groundwater, we corrupt the downscaled climate forcings with different cross-correlation structure.

Correlation-driven charge migration following double ionization and attosecond transient absorption spectroscopy

NASA Astrophysics Data System (ADS)

Hollstein, Maximilian; Santra, Robin; Pfannkuche, Daniela

2017-05-01

We theoretically investigate charge migration following prompt double ionization. Thereby, we extend the concept of correlation-driven charge migration, which was introduced by Cederbaum and coworkers for single ionization [Chem. Phys. Lett. 307, 205 (1999), 10.1016/S0009-2614(99)00508-4], to doubly ionized molecules. This allows us to demonstrate that compared to singly ionized molecules, in multiply ionized molecules, electron dynamics originating from electronic relaxation and correlation are particularly prominent. In addition, we also discuss how these correlation-driven electron dynamics might be evidenced and traced experimentally using attosecond transient absorption spectroscopy. For this purpose, we determine the time-resolved absorption cross section and find that the correlated electron dynamics discussed are reflected in it with exceptionally great detail. Strikingly, we find that features in the cross section can be traced back to electron hole populations and time-dependent partial charges and hence, can be interpreted with surprising ease. By taking advantage of element-specific core-to-valence transitions even atomic spatial resolution can be achieved. Thus, with the theoretical considerations presented, not only do we predict particularly diverse and correlated electron dynamics in molecules to follow prompt multiple ionization but we also identify a promising route towards their experimental investigation.

Imaging the square of the correlated two-electron wave function of a hydrogen molecule

DOE PAGES

Waitz, M.; Bello, R. Y.; Metz, D.; ...

2017-12-22

The toolbox for imaging molecules is well-equipped today. Some techniques visualize the geometrical structure, others the electron density or electron orbitals. Molecules are many-body systems for which the correlation between the constituents is decisive and the spatial and the momentum distribution of one electron depends on those of the other electrons and the nuclei. Such correlations have escaped direct observation by imaging techniques so far. Here, we implement an imaging scheme which visualizes correlations between electrons by coincident detection of the reaction fragments after high energy photofragmentation. With this technique, we examine the H 2 two-electron wave function in whichmore » electron-electron correlation beyond the mean-field level is prominent. We visualize the dependence of the wave function on the internuclear distance. High energy photoelectrons are shown to be a powerful tool for molecular imaging. Finally, our study paves the way for future time resolved correlation imaging at FELs and laser based X-ray sources.« less

Imaging the square of the correlated two-electron wave function of a hydrogen molecule.

PubMed

Waitz, M; Bello, R Y; Metz, D; Lower, J; Trinter, F; Schober, C; Keiling, M; Lenz, U; Pitzer, M; Mertens, K; Martins, M; Viefhaus, J; Klumpp, S; Weber, T; Schmidt, L Ph H; Williams, J B; Schöffler, M S; Serov, V V; Kheifets, A S; Argenti, L; Palacios, A; Martín, F; Jahnke, T; Dörner, R

2017-12-22

The toolbox for imaging molecules is well-equipped today. Some techniques visualize the geometrical structure, others the electron density or electron orbitals. Molecules are many-body systems for which the correlation between the constituents is decisive and the spatial and the momentum distribution of one electron depends on those of the other electrons and the nuclei. Such correlations have escaped direct observation by imaging techniques so far. Here, we implement an imaging scheme which visualizes correlations between electrons by coincident detection of the reaction fragments after high energy photofragmentation. With this technique, we examine the H 2 two-electron wave function in which electron-electron correlation beyond the mean-field level is prominent. We visualize the dependence of the wave function on the internuclear distance. High energy photoelectrons are shown to be a powerful tool for molecular imaging. Our study paves the way for future time resolved correlation imaging at FELs and laser based X-ray sources.

Imaging the square of the correlated two-electron wave function of a hydrogen molecule

DOE Office of Scientific and Technical Information (OSTI.GOV)

Waitz, M.; Bello, R. Y.; Metz, D.

The toolbox for imaging molecules is well-equipped today. Some techniques visualize the geometrical structure, others the electron density or electron orbitals. Molecules are many-body systems for which the correlation between the constituents is decisive and the spatial and the momentum distribution of one electron depends on those of the other electrons and the nuclei. Such correlations have escaped direct observation by imaging techniques so far. Here, we implement an imaging scheme which visualizes correlations between electrons by coincident detection of the reaction fragments after high energy photofragmentation. With this technique, we examine the H 2 two-electron wave function in whichmore » electron-electron correlation beyond the mean-field level is prominent. We visualize the dependence of the wave function on the internuclear distance. High energy photoelectrons are shown to be a powerful tool for molecular imaging. Finally, our study paves the way for future time resolved correlation imaging at FELs and laser based X-ray sources.« less

Electrical Conductivity of Ferritin Proteins by Conductive AFM

NASA Technical Reports Server (NTRS)

Xu, Degao; Watt, Gerald D.; Harb, John N.; Davis, Robert C.

2005-01-01

Electrical conductivity measurements were performed on single apoferritin and holoferritin molecules by conductive atomic force microscopy. Conductivity of self-assembled monolayer films of ferritin molecules on gold surfaces was also measured. Holoferritin was 5-25 times more conductive than apoferritin, indicating that for holoferritin most electron-transfer goes through the ferrihydrite core. With 1 V applied, the average electrical currents through single holoferritin and apoferritin molecules were 2.6 PA and 0.19 PA, respectively.

Studying Chemical Reactions, One Bond at a Time, with Single Molecule AFM Techniques

NASA Astrophysics Data System (ADS)

Fernandez, Julio M.

2008-03-01

The mechanisms by which mechanical forces regulate the kinetics of a chemical reaction are unknown. In my lecture I will demonstrate how we use single molecule force-clamp spectroscopy and protein engineering to study the effect of force on the kinetics of thiol/disulfide exchange. Reduction of disulfide bond via the thiol/disulfide exchange chemical reaction is crucial in regulating protein function and is of common occurrence in mechanically stressed proteins. While reduction is thought to proceed through a substitution nucleophilic bimolecular (SN2) reaction, the role of a mechanical force in modulating this chemical reaction is unknown. We apply a constant stretching force to single engineered disulfide bonds and measure their rate of reduction by dithiothreitol (DTT). We find that while the reduction rate is linearly dependent on the concentration of DTT, it is exponentially dependent on the applied force, increasing 10-fold over a 300 pN range. This result predicts that the disulfide bond lengthens by 0.34 å at the transition state of the thiol/disulfide exchange reaction. In addition to DTT, we also study the reduction of the engineered disulfide bond by the E. coli enzyme thioredoxin (Trx). Thioredoxins are enzymes that catalyze disulfide bond reduction in all organisms. As before, we apply a mechanical force in the range of 25-450 pN to the engineered disulfide bond substrate and monitor the reduction of these bonds by individual enzymes. In sharp contrast with the data obtained with DTT, we now observe two alternative forms of the catalytic reaction, the first requiring a reorientation of the substrate disulfide bond, causing a shortening of the substrate polypeptide by 0.76±0.07 å, and the second elongating the substrate disulfide bond by 0.21±0.01 å. These results support the view that the Trx active site regulates the geometry of the participating sulfur atoms, with sub-ångström precision, in order to achieve efficient catalysis. Single molecule atomic force microscopy (AFM) techniques, as shown here, can probe dynamic rearrangements within an enzyme's active site which cannot be resolved with any other current structural biological technique. Furthermore, our work at the single bond level directly demonstrates that thiol/disulfide exchange in proteins is a force-dependent chemical reaction. Our findings suggest that mechanical force plays a role in disulfide reduction in vivo, a property which has never been explored by traditional biochemistry. 1.-Wiita, A.P., Ainavarapu, S.R.K., Huang, H.H. and Julio M. Fernandez (2006) Force-dependent chemical kinetics of disulfide bond reduction observed with single molecule techniques. Proc Natl Acad Sci U S A. 103(19):7222-7 2.-Wiita, A.P., Perez-Jimenez, R., Walther, K.A., Gräter, F. Berne, B.J., Holmgren, A., Sanchez-Ruiz, J.M., and Fernandez, J.M. (2007) Probing the chemistry of thioredoxin catalysis with force. Nature, 450:124-7.

DNA-psoralen interaction: a single molecule experiment.

PubMed

Rocha, M S; Viana, N B; Mesquita, O N

2004-11-15

By attaching one end of a single lambda-DNA molecule to a microscope coverslip and the other end to a polystyrene microsphere trapped by an optical tweezers, we can study the entropic elasticity of the lambda-DNA by measuring force versus extension as we stretch the molecule. This powerful method permits single molecule studies. We are particularly interested in the effects of the photosensitive drug psoralen on the elasticity of the DNA molecule. We have illuminated the sample with different light sources, studying how the different wavelengths affect the psoralen-DNA linkage. To do this, we measure the persistence length of individual DNA-psoralen complexes.

Beyond experimental noise: Analyzing single-molecule data of heterogeneous systems. Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb and S.K. Sarkar

NASA Astrophysics Data System (ADS)

Meroz, Yasmine

2015-06-01

In the 1980s the world witnessed the advent of single-molecule experiments. The first atomic resolution characterization of a surface was reported by scanning tunneling microscope (STM) in 1982 [1], followed by atomic force microscope (AFM) in 1986 [2]. The first optical detection and spectroscopy of a single molecule in a solid took place in 1989 [3,4], in a time where essentially all chemical experiments were made on bulk, i.e. averaging over millions of copies of the same molecule.

Revealing time bunching effect in single-molecule enzyme conformational dynamics.

PubMed

Lu, H Peter

2011-04-21

In this perspective, we focus our discussion on how the single-molecule spectroscopy and statistical analysis are able to reveal enzyme hidden properties, taking the study of T4 lysozyme as an example. Protein conformational fluctuations and dynamics play a crucial role in biomolecular functions, such as in enzymatic reactions. Single-molecule spectroscopy is a powerful approach to analyze protein conformational dynamics under physiological conditions, providing dynamic perspectives on a molecular-level understanding of protein structure-function mechanisms. Using single-molecule fluorescence spectroscopy, we have probed T4 lysozyme conformational motions under the hydrolysis reaction of a polysaccharide of E. coli B cell walls by monitoring the fluorescence resonant energy transfer (FRET) between a donor-acceptor probe pair tethered to T4 lysozyme domains involving open-close hinge-bending motions. Based on the single-molecule spectroscopic results, molecular dynamics simulation, a random walk model analysis, and a novel 2D statistical correlation analysis, we have revealed a time bunching effect in protein conformational motion dynamics that is critical to enzymatic functions. Bunching effect implies that conformational motion times tend to bunch in a finite and narrow time window. We show that convoluted multiple Poisson rate processes give rise to the bunching effect in the enzymatic reaction dynamics. Evidently, the bunching effect is likely common in protein conformational dynamics involving in conformation-gated protein functions. In this perspective, we will also discuss a new approach of 2D regional correlation analysis capable of analyzing fluctuation dynamics of complex multiple correlated and anti-correlated fluctuations under a non-correlated noise background. Using this new method, we are able to map out any defined segments along the fluctuation trajectories and determine whether they are correlated, anti-correlated, or non-correlated; after which, a cross correlation analysis can be applied for each specific segment to obtain a detailed fluctuation dynamics analysis.

Force Spectroscopy with 9-μs Resolution and Sub-pN Stability by Tailoring AFM Cantilever Geometry.

PubMed

Edwards, Devin T; Faulk, Jaevyn K; LeBlanc, Marc-André; Perkins, Thomas T

2017-12-19

Atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) is a powerful yet accessible means to characterize the unfolding/refolding dynamics of individual molecules and resolve closely spaced, transiently occupied folding intermediates. On a modern commercial AFM, these applications and others are now limited by the mechanical properties of the cantilever. Specifically, AFM-based SMFS data quality is degraded by a commercial cantilever's limited combination of temporal resolution, force precision, and force stability. Recently, we modified commercial cantilevers with a focused ion beam to optimize their properties for SMFS. Here, we extend this capability by modifying a 40 × 18 μm 2 cantilever into one terminated with a gold-coated, 4 × 4 μm 2 reflective region connected to an uncoated 2-μm-wide central shaft. This "Warhammer" geometry achieved 8.5-μs resolution coupled with improved force precision and sub-pN stability over 100 s when measured on a commercial AFM. We highlighted this cantilever's biological utility by first resolving a calmodulin unfolding intermediate previously undetected by AFM and then measuring the stabilization of calmodulin by myosin light chain kinase at dramatically higher unfolding velocities than in previous AFM studies. More generally, enhancing data quality via an improved combination of time resolution, force precision, and force stability will broadly benefit biological applications of AFM. Published by Elsevier Inc.

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.

PubMed

Vanquelef, Enguerran; Simon, Sabrina; Marquant, Gaelle; Garcia, Elodie; Klimerak, Geoffroy; Delepine, Jean Charles; Cieplak, Piotr; Dupradeau, François-Yves

2011-07-01

R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and molecular dynamics simulations. R.E.D. Server interfaces quantum mechanics programs, the RESP program and the latest version of the R.E.D. tools. A two step approach has been developed. The first one consists of preparing P2N file(s) to rigorously define key elements such as atom names, topology and chemical equivalencing needed when building a force field library. Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format. In complex cases an entire set of force field libraries or force field topology database is generated. Other features developed in R.E.D. Server include help services, a demonstration, tutorials, frequently asked questions, Jmol-based tools useful to construct PDB input files and parse R.E.D. Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs.

New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy

DOE PAGES

Van Vleet, Mary J.; Misquitta, Alston J.; Schmidt, J. R.

2017-12-21

Nearly all standard force fields employ the “sum-of-spheres” approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly nonspherical shapes, leading to interatomic interaction energies with strong orientation dependencies. Neglecting this “atomic-level anisotropy” can lead to significant errors in predicting interaction energies. Herein, we propose a simple, transferable, and computationally efficient model (MASTIFF) whereby atomic-level orientation dependence can be incorporated into ab initio intermolecular force fields. MASTIFF includes anisotropic exchange-repulsion, charge penetration, and dispersion effects, in conjunction with a standard treatment of anisotropic long-range (multipolar) electrostatics. To validate our approach, we benchmarkmore » MASTIFF against various sum-of-spheres models over a large library of intermolecular interactions between small organic molecules. MASTIFF achieves quantitative accuracy, with respect to both high-level electronic structure theory and experiment, thus showing promise as a basis for “next-generation” force field development.« less

A Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces

PubMed Central

Zhou, Y. C.; Holst, Michael; McCammon, J. Andrew

2008-01-01

In this paper we propose a nonlinear elasticity model of macromolecular conformational change (deformation) induced by electrostatic forces generated by an implicit solvation model. The Poisson-Boltzmann equation for the electrostatic potential is analyzed in a domain varying with the elastic deformation of molecules, and a new continuous model of the electrostatic forces is developed to ensure solvability of the nonlinear elasticity equations. We derive the estimates of electrostatic forces corresponding to four types of perturbations to an electrostatic potential field, and establish the existance of an equilibrium configuration using a fixed-point argument, under the assumption that the change in the ionic strength and charges due to the additional molecules causing the deformation are sufficiently small. The results are valid for elastic models with arbitrarily complex dielectric interfaces and cavities, and can be generalized to large elastic deformation caused by high ionic strength, large charges, and strong external fields by using continuation methods. PMID:19461946

R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries

PubMed Central

Dupradeau, François-Yves; Cézard, Christine; Lelong, Rodolphe; Stanislawiak, Élodie; Pêcher, Julien; Delepine, Jean Charles; Cieplak, Piotr

2008-01-01

The web-based RESP ESP charge DataBase (R.E.DD.B., http://q4md-forcefieldtools.org/REDDB) is a free and new source of RESP and ESP atomic charge values and force field libraries for model systems and/or small molecules. R.E.DD.B. stores highly effective and reproducible charge values and molecular structures in the Tripos mol2 file format, information about the charge derivation procedure, scripts to integrate the charges and molecular topology in the most common molecular dynamics packages. Moreover, R.E.DD.B. allows users to freely store and distribute RESP or ESP charges and force field libraries to the scientific community, via a web interface. The first version of R.E.DD.B., released in January 2006, contains force field libraries for molecules as well as molecular fragments for standard residues and their analogs (amino acids, monosaccharides, nucleotides and ligands), hence covering a vast area of relevant biological applications. PMID:17962302

New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Vleet, Mary J.; Misquitta, Alston J.; Schmidt, J. R.

Nearly all standard force fields employ the “sum-of-spheres” approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly nonspherical shapes, leading to interatomic interaction energies with strong orientation dependencies. Neglecting this “atomic-level anisotropy” can lead to significant errors in predicting interaction energies. Herein, we propose a simple, transferable, and computationally efficient model (MASTIFF) whereby atomic-level orientation dependence can be incorporated into ab initio intermolecular force fields. MASTIFF includes anisotropic exchange-repulsion, charge penetration, and dispersion effects, in conjunction with a standard treatment of anisotropic long-range (multipolar) electrostatics. To validate our approach, we benchmarkmore » MASTIFF against various sum-of-spheres models over a large library of intermolecular interactions between small organic molecules. MASTIFF achieves quantitative accuracy, with respect to both high-level electronic structure theory and experiment, thus showing promise as a basis for “next-generation” force field development.« less

Deciphering molecular interactions of native membrane proteins by single-molecule force spectroscopy.

PubMed

Kedrov, Alexej; Janovjak, Harald; Sapra, K Tanuj; Müller, Daniel J

2007-01-01

Molecular interactions are the basic language of biological processes. They establish the forces interacting between the building blocks of proteins and other macromolecules, thus determining their functional roles. Because molecular interactions trigger virtually every biological process, approaches to decipher their language are needed. Single-molecule force spectroscopy (SMFS) has been used to detect and characterize different types of molecular interactions that occur between and within native membrane proteins. The first experiments detected and localized molecular interactions that stabilized membrane proteins, including how these interactions were established during folding of alpha-helical secondary structure elements into the native protein and how they changed with oligomerization, temperature, and mutations. SMFS also enables investigators to detect and locate molecular interactions established during ligand and inhibitor binding. These exciting applications provide opportunities for studying the molecular forces of life. Further developments will elucidate the origins of molecular interactions encoded in their lifetimes, interaction ranges, interplay, and dynamics characteristic of biological systems.

Action and Traction: Cytoskeletal Control of Receptor Triggering at the Immunological Synapse

PubMed Central

Comrie, William A.; Burkhardt, Janis K.

2016-01-01

It is well known that F-actin dynamics drive the micron-scale cell shape changes required for migration and immunological synapse (IS) formation. In addition, recent evidence points to a more intimate role for the actin cytoskeleton in promoting T cell activation. Mechanotransduction, the conversion of mechanical input into intracellular biochemical changes, is thought to play a critical role in several aspects of immunoreceptor triggering and downstream signal transduction. Multiple molecules associated with signaling events at the IS have been shown to respond to physical force, including the TCR, costimulatory molecules, adhesion molecules, and several downstream adapters. In at least some cases, it is clear that the relevant forces are exerted by dynamics of the T cell actomyosin cytoskeleton. Interestingly, there is evidence that the cytoskeleton of the antigen-presenting cell also plays an active role in T cell activation, by countering the molecular forces exerted by the T cell at the IS. Since actin polymerization is itself driven by TCR and costimulatory signaling pathways, a complex relationship exists between actin dynamics and receptor activation. This review will focus on recent advances in our understanding of the mechanosensitive aspects of T cell activation, paying specific attention to how F-actin-directed forces applied from both sides of the IS fit into current models of receptor triggering and activation. PMID:27014258

Effect of polarization forces on carbon deposition on a non-spherical nanoparticle. Monte Carlo simulations [Effect of polarization forces on atom deposition on a non-spherical nanoparticle. Monte Carlo simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nemchinsky, V.; Khrabry, A.

Trajectories of a polarizable species (atoms or molecules) in the vicinity of a negatively charged nanoparticle (at a floating potential) are considered. The atoms are pulled into regions of strong electric field by polarization forces. The polarization increases the deposition rate of the atoms and molecules at the nanoparticle. The effect of the non-spherical shape of the nanoparticle is investigated by the Monte Carlo method. The shape of the non-spherical nanoparticle is approximated by an ellipsoid. The total deposition rate and its flux density distribution along the nanoparticle surface are calculated. As a result, it is shown that the fluxmore » density is not uniform along the surface. It is maximal at the nanoparticle tips.« less

Simple Model for the Benzene Hexafluorobenzene Interaction

DOE PAGES

Tillack, Andreas F.; Robinson, Bruce H.

2017-06-05

While the experimental intermolecular distance distribution functions of pure benzene and pure hexafluorobenzene are well described by transferable all-atom force fields, the interaction between the two molecules (in a 1:1 mixture) is not well simulated. We demonstrate that the parameters of the transferable force fields are adequate to describe the intermolecular distance distribution if the charges are replaced by a set of charges that are not located at the atoms. Here, the simplest model that well describes the experimental distance distribution, between benzene and hexafluorobenzene, is that of a single ellipsoid for each molecule, representing the van der Waals interactions,more » and a set of three point charges (on the axis perpendicular to the arene plane) which give the same quadrupole moment as do the all atom charges from the transferable force fields.« less

Effect of polarization forces on carbon deposition on a non-spherical nanoparticle. Monte Carlo simulations [Effect of polarization forces on atom deposition on a non-spherical nanoparticle. Monte Carlo simulations

DOE PAGES

Nemchinsky, V.; Khrabry, A.

2018-02-01

Trajectories of a polarizable species (atoms or molecules) in the vicinity of a negatively charged nanoparticle (at a floating potential) are considered. The atoms are pulled into regions of strong electric field by polarization forces. The polarization increases the deposition rate of the atoms and molecules at the nanoparticle. The effect of the non-spherical shape of the nanoparticle is investigated by the Monte Carlo method. The shape of the non-spherical nanoparticle is approximated by an ellipsoid. The total deposition rate and its flux density distribution along the nanoparticle surface are calculated. As a result, it is shown that the fluxmore » density is not uniform along the surface. It is maximal at the nanoparticle tips.« less

Simple Model for the Benzene Hexafluorobenzene Interaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tillack, Andreas F.; Robinson, Bruce H.

While the experimental intermolecular distance distribution functions of pure benzene and pure hexafluorobenzene are well described by transferable all-atom force fields, the interaction between the two molecules (in a 1:1 mixture) is not well simulated. We demonstrate that the parameters of the transferable force fields are adequate to describe the intermolecular distance distribution if the charges are replaced by a set of charges that are not located at the atoms. Here, the simplest model that well describes the experimental distance distribution, between benzene and hexafluorobenzene, is that of a single ellipsoid for each molecule, representing the van der Waals interactions,more » and a set of three point charges (on the axis perpendicular to the arene plane) which give the same quadrupole moment as do the all atom charges from the transferable force fields.« less

The relationship between oral tori and bite force.

PubMed

Jeong, Chan-Woo; Kim, Kyung-Ho; Jang, Hyo-Won; Kim, Hye-Sun; Huh, Jong-Ki

2018-01-12

Objective The relationship between bite force and torus palatinus or mandibularis remains to be explained. The major aim of this study was to determine the correlation between bite force and oral tori. Methods The bite force of 345 patients was measured with a bite force recorder; impressions of the shape and size of the oral tori were taken on plaster models prior to orthodontic treatments. Subsequently, the relationship between oral tori and bite force was analyzed. Results The size, shape, and incidence of torus palatinus was not significantly correlated with bite force. However, the size of torus mandibularis increased significantly in proportion to the bite force (p = 0.020). The occurrence of different types of oral tori was not correlated with the bite force. Discussion The size of torus mandibularis provides information about bite force and can thus be used to clinically assess occlusal stress.

Molecules, muscles, and machines: Universal performance characteristics of motors

PubMed Central

Marden, James H.; Allen, Lee R.

2002-01-01

Animal- and human-made motors vary widely in size and shape, are constructed of vastly different materials, use different mechanisms, and produce an enormous range of mass-specific power. Despite these differences, there is remarkable consistency in the maximum net force produced by broad classes of animal- and human-made motors. Motors that use force production to accomplish steady translational motion of a load (myosin, kinesin, dynein, and RNA polymerase molecules, muscle cells, whole muscles, winches, linear actuators, and rockets) have maximal force outputs that scale as the two-thirds power of mass, i.e., with cross-sectional area. Motors that use cyclical motion to generate force and are more subject to multiaxial stress and vibration have maximal force outputs that scale as a single isometric function of motor mass with mass-specific net force output averaging 57 N⋅kg−1 (SD = 14). Examples of this class of motors includes flying birds, bats, and insects, swimming fish, various taxa of running animals, piston engines, electric motors, and all types of jets. Dependence of force production and stress resistance on cross-sectional area is well known, but the isometric scaling and common upper limit of mass-specific force production by cyclical motion motors has not been recognized previously and is not explained by an existing body of theory. Remarkably, this finding indicates that most of the motors used by humans and animals for transportation have a common upper limit of mass-specific net force output that is independent of materials and mechanisms. PMID:11917097

Molecules, muscles, and machines: universal performance characteristics of motors.

PubMed

Marden, James H; Allen, Lee R

2002-04-02

Animal- and human-made motors vary widely in size and shape, are constructed of vastly different materials, use different mechanisms, and produce an enormous range of mass-specific power. Despite these differences, there is remarkable consistency in the maximum net force produced by broad classes of animal- and human-made motors. Motors that use force production to accomplish steady translational motion of a load (myosin, kinesin, dynein, and RNA polymerase molecules, muscle cells, whole muscles, winches, linear actuators, and rockets) have maximal force outputs that scale as the two-thirds power of mass, i.e., with cross-sectional area. Motors that use cyclical motion to generate force and are more subject to multiaxial stress and vibration have maximal force outputs that scale as a single isometric function of motor mass with mass-specific net force output averaging 57 N x kg(-1) (SD = 14). Examples of this class of motors includes flying birds, bats, and insects, swimming fish, various taxa of running animals, piston engines, electric motors, and all types of jets. Dependence of force production and stress resistance on cross-sectional area is well known, but the isometric scaling and common upper limit of mass-specific force production by cyclical motion motors has not been recognized previously and is not explained by an existing body of theory. Remarkably, this finding indicates that most of the motors used by humans and animals for transportation have a common upper limit of mass-specific net force output that is independent of materials and mechanisms.

AFM force measurements of the gp120-sCD4 and gp120 or CD4 antigen-antibody interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Yong, E-mail: dr_yongchen@hotmail.com; Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612; Zeng, Gucheng

2011-04-08

Highlights: {yields} The unbinding force of sCD4-gp120 interaction was 25.45 {+-} 20.46 pN. {yields} The unbinding force of CD4 antigen-antibody interaction was 51.22 {+-} 34.64 pN. {yields} The unbinding force of gp120 antigen-antibody interaction was 89.87 {+-} 44.63 pN. {yields} The interaction forces between various HIV inhibitors and the target molecules are significantly different. {yields} Functionalizing on AFM tip or substrate of an interaction pair caused different results. -- Abstract: Soluble CD4 (sCD4), anti-CD4 antibody, and anti-gp120 antibody have long been regarded as entry inhibitors in human immunodeficiency virus (HIV) therapy. However, the interactions between these HIV entry inhibitors andmore » corresponding target molecules are still poorly understood. In this study, atomic force microscopy (AFM) was utilized to investigate the interaction forces among them. We found that the unbinding forces of sCD4-gp120 interaction, CD4 antigen-antibody interaction, and gp120 antigen-antibody interaction were 25.45 {+-} 20.46, 51.22 {+-} 34.64, and 89.87 {+-} 44.63 pN, respectively, which may provide important mechanical information for understanding the effects of viral entry inhibitors on HIV infection. Moreover, we found that the functionalization of an interaction pair on AFM tip or substrate significantly influenced the results, implying that we must perform AFM force measurement and analyze the data with more caution.« less

A Correlational Analysis of Tethered Swimming, Swim Sprint Performance and Dry-land Power Assessments.

PubMed

Loturco, I; Barbosa, A C; Nocentini, R K; Pereira, L A; Kobal, R; Kitamura, K; Abad, C C C; Figueiredo, P; Nakamura, F Y

2016-03-01

Swimmers are often tested on both dry-land and in swimming exercises. The aim of this study was to test the relationships between dry-land, tethered force-time curve parameters and swimming performances in distances up to 200 m. 10 young male high-level swimmers were assessed using the maximal isometric bench-press and quarter-squat, mean propulsive power in jump-squat, squat and countermovement jumps (dry-land assessments), peak force, average force, rate of force development (RFD) and impulse (tethered swimming) and swimming times. Pearson product-moment correlations were calculated among the variables. Peak force and average force were very largely correlated with the 50- and 100-m swimming performances (r=- 0.82 and -0.74, respectively). Average force was very-largely/largely correlated with the 50- and 100-m performances (r=- 0.85 and -0.67, respectively). RFD and impulse were very-largely correlated with the 50-m time (r=- 0.72 and -0.76, respectively). Tethered swimming parameters were largely correlated (r=0.65 to 0.72) with mean propulsive power in jump-squat, squat-jump and countermovement jumps. Finally, mean propulsive power in jump-squat was largely correlated (r=- 0.70) with 50-m performance. Due to the significant correlations between dry-land assessments and tethered/actual swimming, coaches are encouraged to implement strategies able to increase leg power in sprint swimmers. © Georg Thieme Verlag KG Stuttgart · New York.

Direct Observation of Markovian Behavior of the Mechanical Unfolding of Individual Proteins

PubMed Central

Cao, Yi; Kuske, Rachel; Li, Hongbin

2008-01-01

Single-molecule force-clamp spectroscopy is a valuable tool to analyze unfolding kinetics of proteins. Previous force-clamp spectroscopy experiments have demonstrated that the mechanical unfolding of ubiquitin deviates from the generally assumed Markovian behavior and involves the features of glassy dynamics. Here we use single molecule force-clamp spectroscopy to study the unfolding kinetics of a computationally designed fast-folding mutant of the small protein GB1, which shares a similar β-grasp fold as ubiquitin. By treating the mechanical unfolding of polyproteins as the superposition of multiple identical Poisson processes, we developed a simple stochastic analysis approach to analyze the dwell time distribution of individual unfolding events in polyprotein unfolding trajectories. Our results unambiguously demonstrate that the mechanical unfolding of NuG2 fulfills all criteria of a memoryless Markovian process. This result, in contrast with the complex mechanical unfolding behaviors observed for ubiquitin, serves as a direct experimental demonstration of the Markovian behavior for the mechanical unfolding of a protein and reveals the complexity of the unfolding dynamics among structurally similar proteins. Furthermore, we extended our method into a robust and efficient pseudo-dwell-time analysis method, which allows one to make full use of all the unfolding events obtained in force-clamp experiments without categorizing the unfolding events. This method enabled us to measure the key parameters characterizing the mechanical unfolding energy landscape of NuG2 with improved precision. We anticipate that the methods demonstrated here will find broad applications in single-molecule force-clamp spectroscopy studies for a wide range of proteins. PMID:18375518

Development and Demonstration of a Multiplexed Magnetic Tweezers Assay

NASA Astrophysics Data System (ADS)

Johnson, Keith Charles

This dissertation is concerned with the methods and applications of single molecule force spectroscopy. In the introduction, the traditional single molecule force spectroscopy instruments are introduced and the advantages and drawbacks of each are discussed. The first chapter is a review of methods to ensure that biomolecular bond lifetime parameter estimations are not contaminated by multiple bond data. This review culminates in an examination of the literature on the strength of the bond between biotin and streptavidin and finds that by filtering the numerous publications for those that clearly demonstrate specific single bond behavior, there is a consensus of the bond strength and kinetic parameters. The second chapter of the dissertation discusses the capabilities of a magnetic tweezer assay, which combines massive multiplexing, precision bead tracking, and bi-directional force control into a flexible and stabile platform for examining single molecule behavior. Using a novel method for increasing the precision of force estimations on heterogeneous paramagnetic beads, I demonstrate the instrument by examining the force dependence of uncoiling and recoiling velocity of type 1 fimbriae from Eschericia coli (E. coli) bacteria, and see similar results to previous studies. Chapter 3 is a study of the lifetime of the activated FimH-mannose bond under various force conditions using the previously described magnetic tweezer. The bond is found to be extremely long-lived at forces less than 30 pN, with an average lifetime > 1000 times longer than the biotin-streptavidin bond, making it one of the strongest non-covalent interactions known in nature. Furthermore, the average lifetime of the bond is similar between 9 and 30 pN of force, suggesting a force range at which the lifetime is force-independent, demonstrating ideal bond behavior for the first time in a natural system. It is hypothesized that the long lifetime and ideal behavior is due to a gateway that locks mannose into the binding pocket and opens at a rate independent of force. This study elucidates a mechanism for very strong biological binding, and provides insight into approaches for developing novel antiadhesive therapies. This dissertation is concluded with a review of the body of work in chapters 1-3 and a discussion of the future directions for this research.

Electrons, Photons, and Force: Quantitative Single-Molecule Measurements from Physics to Biology

PubMed Central

2011-01-01

Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution. PMID:21338175

Tip-Enhanced Nano-Spectroscopy, Imaging, and Control: From Single Molecules to van der Waals Materials

NASA Astrophysics Data System (ADS)

Park, Kyoung-Duck

Photon-induced phenomena in molecules and other materials play a significant role in device applications as well as understanding their physical properties. While a range of device applications using organic and inorganic molecules and soft and hard materials have led striking developments in modern technologies, using bulk systems has reached the limit in their functions, performance, and regarding application range. Recently, low-dimensional systems have emerged as appealing resources for the advanced technologies based on their significantly improved functions and properties. Hence, understanding light-matter interactions at their natural length scale is of fundamental significance, in addition to the next generation device applications. This thesis demonstrates a range of new functions and behaviors of low-dimensional materials revealed and controlled by the advanced tip-enhanced near-field spectroscopy and imaging techniques exceeding the current instrumental limits. To understand the behaviors of zero-dimensional (0D) molecular systems in interacting environments, we explore new regimes in tip-enhanced Raman spectroscopy (TERS) and scanning near-field optical microscopy (SNOM), revealing the fundamental nature of single-molecule dynamics and nanoscale spatial heterogeneity of biomolecules on the cell membranes. To gain insight into intramolecular properties and dynamic processes of single molecules, we use TERS at cryogenic temperatures. From temperature-dependent line narrowing and splitting, we investigate and quantify ultrafast vibrational dephasing, intramolecular coupling, and conformational heterogeneity. Through correlation analysis of fluctuations of individual modes, we observe rotational motion and spectral fluctuations of single-molecule. We extend single-molecule spectroscopy study into in situ nano-biomolecular imaging of cancer cells by developing in-liquid SNOM. We use a new mechanical resonance control, achieving a high-Q force sensing of the near-field probe. We reveal nanoscale correlations between surface biomolecules and intracellular organelle structures through near-field imaging of the spatial distribution of EGFRs on the membrane of A431 cancer cells. In addition, to understand modified spontaneous emission properties of single quantum dots coupled strongly with localized plasmon, we perform tip-enhanced photoluminescence (TEPL) spectroscopy of the single CdSe/ZnS quantum dots on gold film. We probe and control nanoscale processes in van der Waals two-dimensional (2D) materials. To understand lattice and electronic structure as well as elastic and phonon scattering properties of grain boundaries (GBs) in large-area graphene, we perform TERS imaging. Through correlated analysis of multispectral TERS images with corresponding topography and near-field scattering image, we reveal bilayer structure of GBs in the form of twisted stacking. In addition, we determine the misorientation angles of the bilayer GBs from a detailed quantitative investigation of the Raman modes. In addition, we present a new hybrid nano-optomechanical tip-enhanced spectroscopy and imaging approach combining TERS, TEPL, and atomic force local strain manipulation to probe the heterogeneous PL responses at nanoscale defects and control the local bandgap in transition metal dichalcogenide (TMD) monolayer. We further extend this approach to probe and control the radiative emission of dark excitons and localized excitons. Based on nano-tip enhanced spectroscopy with 600,000-fold PL enhancement induced by the plasmonic Purcell effect and few-fs radiative dynamics of the optical antenna tip, we can directly probe and actively modulate the dark exciton and localized exciton emissions in time ( ms) and space (<15 nm) at room temperature. Lastly, to extend the range of tip-enhanced microscopy applications to nano-crystallography and nonlinear optics, we present a generalizable approach controlling the excitation polarizability for both in-plane and out-of-plane vector fields by breaking the axial symmetry of a conventional Au tip. This vector field control with the tip enables probing of nonlinear optical second harmonic generation (SHG) responses from a range of ferroic materials as well as van der Waals 2D materials. Specifically, we demonstrate SHG nano-crystallography results for MoS2 monolayer film, ferroelectric YMnO3, BaTiO3-BiFeO3 multiferroics, and PbTiO3/SrTiO 3 superlattices.

The Relationship Between the Push Off Ground Reaction Force and Ball Speed in High School Baseball Pitchers.

PubMed

Oyama, Sakiko; Myers, Joseph B

2018-05-01

Oyama, S and Myers, JB. The relationship between the push off ground reaction force and ball speed in high school baseball pitchers. J Strength Cond Res 32(5): 1324-1328, 2018-Baseball pitching is a sequential movement that requires transfer of momentum from the lower extremity to the throwing arm. Therefore, the ground reaction force (GRF) during push off is suggested to play a role in production of ball speed. The purpose of this study was to investigate the correlation between GRF characteristics during push off and ball speed in high school baseball pitchers. A total of 52 pitchers performed fast pitches from an indoor pitching mound. A force plate embedded in an indoor mound was used to capture the push off GRF. The GRF characteristics (peak anterior, vertical, and resultant forces, vertical and resultant forces at the time of peak anterior GRF, and impulse produced by the anterior GRF) from the 3 fastest strike pitches from each pitcher were used for analyses. Spearman's rank correlation coefficients were used to describe the relationships between ball speed and the GRF characteristics. Ball speed was only weakly correlated with peak resultant force (ρ = 0.32, p = 0.02) and vertical (ρ = 0.45, p < 0.001) and resultant (ρ = 0.42, p = 0.002) forces at the time of peak anterior force. The ball speed was not correlated with other variables. The correlation between ball speed and push off force in high school pitchers was weak, especially when compared with what was reported for adult pitchers in other studies. Unlike for adult pitchers, higher push off force is only weakly correlated with ball velocity in high school pitchers, which suggests that training to better use body momentum may help high school pitchers improve ball speed.

From genes to protein mechanics on a chip.

PubMed

Otten, Marcus; Ott, Wolfgang; Jobst, Markus A; Milles, Lukas F; Verdorfer, Tobias; Pippig, Diana A; Nash, Michael A; Gaub, Hermann E

2014-11-01

Single-molecule force spectroscopy enables mechanical testing of individual proteins, but low experimental throughput limits the ability to screen constructs in parallel. We describe a microfluidic platform for on-chip expression, covalent surface attachment and measurement of single-molecule protein mechanical properties. A dockerin tag on each protein molecule allowed us to perform thousands of pulling cycles using a single cohesin-modified cantilever. The ability to synthesize and mechanically probe protein libraries enables high-throughput mechanical phenotyping.

Computational Study of Nonadiabatic Effects in Atom-Molecule Reactive Scattering.

DTIC Science & Technology

1982-11-15

a similar interpretation to those in Fig. 4-a, with the rotational effects most evident in the reactant tube (due to the mixing of the two open rotor ...AD-A125 135 COMPUTATIONAL STUDY OF NONRDIABATIC EFFECTS IN 1/2 ATOM-MOLECULE REACTIVE SCATTERING(U) CHEMICAL DYNAMICS CORP COLUMBUS OH B C GARRETT...COMPUTATIONAL STUDY OF NONADIABATIC EFFECTS [ Z IN ATOM-MOLECULE REACTIVE SCATTERING C:) TO AIR FORCE OFFICE OF SCIENTIFIC RESEARCHk CONTRACT NO. F49620-81

DNA and RNA sequencing by nanoscale reading through programmable electrophoresis and nanoelectrode-gated tunneling and dielectric detection

DOEpatents

Lee, James W.; Thundat, Thomas G.

2005-06-14

An apparatus and method for performing nucleic acid (DNA and/or RNA) sequencing on a single molecule. The genetic sequence information is obtained by probing through a DNA or RNA molecule base by base at nanometer scale as though looking through a strip of movie film. This DNA sequencing nanotechnology has the theoretical capability of performing DNA sequencing at a maximal rate of about 1,000,000 bases per second. This enhanced performance is made possible by a series of innovations including: novel applications of a fine-tuned nanometer gap for passage of a single DNA or RNA molecule; thin layer microfluidics for sample loading and delivery; and programmable electric fields for precise control of DNA or RNA movement. Detection methods include nanoelectrode-gated tunneling current measurements, dielectric molecular characterization, and atomic force microscopy/electrostatic force microscopy (AFM/EFM) probing for nanoscale reading of the nucleic acid sequences.

Analyte detection using an active assay

DOEpatents

Morozov, Victor; Bailey, Charles L.; Evanskey, Melissa R.

2010-11-02

Analytes using an active assay may be detected by introducing an analyte solution containing a plurality of analytes to a lacquered membrane. The lacquered membrane may be a membrane having at least one surface treated with a layer of polymers. The lacquered membrane may be semi-permeable to nonanalytes. The layer of polymers may include cross-linked polymers. A plurality of probe molecules may be arrayed and immobilized on the lacquered membrane. An external force may be applied to the analyte solution to move the analytes towards the lacquered membrane. Movement may cause some or all of the analytes to bind to the lacquered membrane. In cases where probe molecules are presented, some or all of the analytes may bind to probe molecules. The direction of the external force may be reversed to remove unbound or weakly bound analytes. Bound analytes may be detected using known detection types.