Microsecond folding experiments and simulations: a match is made
Microsecond protein folding experiments and computation combine to provide validated atomistic pictures of folding for small proteins.
The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies
Current state-of-the-art in X-ray crystallography, quantum chemistry and molecular simulation studies of the nucleic acids backbone is reviewed.
The ‘sticky business’ of cleaning gas-phase membrane
proteins: a detergent oriented perspective
Structure and organisation of detergent clusters using ion mobility mass spectrometry. Mechanism of gas-phase detergent release from membrane protein complexes.
Solution, surface, and single molecule platforms for the study of DNA-mediated charge transport
The parameters governing the rate, yield, and mechanism of DNA-mediated charge transport are explored in a variety of experimental systems.
Mapping viscosity in cells using molecular rotors
Small synthetic fluorophores termed ‘molecular rotors’ were used for quantitative measurements and imaging of microviscosity in live biological cells.
Rate constants and mechanisms of intrinsically disordered
proteins binding to structured targets
Dock-and-coalesce is the unifying mechanism for the binding of intrinsically disordered proteins, and allows for calculation of binding rate constants.
Lipidology and lipidomics––quo vadis? A new era for the physical chemistry of lipids
The physical chemistry of lipids in lipid membranes is entering a new era.
Diffusion models of
Descriptions of protein folding as diffusion along low-dimensional reaction coordinates capture the observed simulation dynamics and help interpret single-molecule experiments.
The shape-shifting quasispecies of RNA: one sequence, many functional folds
Rugged RNA folding landscapes give rise to multiple native states that may impart adaptive advantages on an evolving RNA quasispecies.
Electrostatic interactions in biological DNA-related systems
Recent developments in the theory of charge effects in biological DNA-related systems are discussed.
Functional liposomes and supported
lipid bilayers: towards the complexity of biological archetypes
Oligonucleotide building blocks with tailored properties for controlled self-assembly complex structural motifs.
optical trapping, fluorescence microscopy and micro-fluidics for single molecule studies of DNA– protein interactions
Using a combination of optical trapping, fluorescence microscopy and microfluidics allows studying individual proteins binding to DNA with a localization accuracy of better than 10 nm.
Revealing time bunching effect in single-molecule
enzyme conformational dynamics
Time bunching effect, implying that conformational motion times tend to bunch in a finite time window, is identified to be associated with substrate-enzyme complex formation in T4 lysozyme conformational dynamics under enzymatic reactions.
protein– DNA interactions: mechanisms of facilitated target search
A critical review of theoretical approaches to explain protein search for targets on DNA is presented.
Optical imaging of excited-state tautomerization in single molecules
Optical imaging of single molecules using azimuthally and radially polarized laser modes gives a new insight into excited-state tautomerization.
Seeing the forest for the trees: fluorescence studies of single enzymes in the context of ensemble experiments
Single-molecule enzyme studies are discussed in the context of complementary ensemble averaged experimental techniques.
Design and development of
quantum dots and other nanoparticles based cellular imaging probe
This article discusses the non-specific binding problem in developing cellular imaging nanoprobes and the role of coating chemistry to solve it.
cells: expanding fuel diversity to amino acids
Mitochondria, considered the “powerhouse” of the living cell, can do bioelectrocatalysis of pyruvate, fatty acids, and amino acids at electrode surfaces for biofuel cell applications.
lipid interfaces for protein adsorption studies
Supported lipid bilayers at different surface charge and composition as nanoplatforms for the electrostatically-driven immobilization of ferritin.
chemical imaging of segregated lipid domains using tip-enhanced Raman spectroscopy
The lipid distribution in a mixed supported lipid monolayer was directly measured with high lateral resolution in the first full-spectral image on phase separated lipid domains.
On the role of mercury in the non-covalent stabilisation of consecutive U–HgII–U metal-mediated nucleic acid base pairs: metallophilic attraction enters the world of nucleic acids
Heavy metal glue: metallophilic attraction and the metal⋯base interactions reinforce stability of HgII–nucleic acid.
A novel method for automatic single molecule tracking of blinking molecules at low intensities
We present a novel method for single molecule tracking which results in reliable trajectories even for blinking molecules of low intensity.
Electric-field induced mutation of DNA: a theoretical investigation of the GC base pair
We performed theoretical calculations to investigate the stability of the guanine–cytosine base pair under the influence of electric fields. Our results demonstrate that the base pair geometry might be tuned by modulating the intensity of the field, which in turn governs the promotion of selective mutations of DNA.
Effect of heavy water on phospholipid membranes: experimental confirmation of molecular dynamics simulations
Time-resolved physicochemical properties of phospholipid bilayers are influenced by the presence of D2O: molecular dynamics simulations are verified by fluorescence measurements.
The road not taken: a theoretical view of an unexpected cryptochrome charge transfer path
Atomistic simulations and new theoretical concepts help to rationalize the surprising charge transfer pathway in a blue light receptor protein.
Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the Aβ16–22 dimer and trimer
A systematic comparison of the AMBER, GROMOS and OPLS force fields on small Aβ16–22 oligomers.
Photoinduced pH drops in
A 2-hydroxyazobenzene platform is used to reversibly photo-generate up to one unit pH drops in pure water under UV illumination.
Mechanisms and advancement of antifading agents for
fluorescence microscopy and single-molecule spectroscopy
Confocal microscopy and single-molecule spectroscopy reveal the working action and principles of antifading agents (ROXS and commercially available compounds such as Vectashield and Ibidi-MM) used for fluorescence-based biological imaging and general fluorescence applications.
Solvent-assisted conformational isomerization and the conformationally-pure REMPI spectrum of 3-aminophenol
Conformational isomerization occurs during supersonic expansion with solvents.
Unfolding dynamics of
cytochrome c revealed by single-molecule and ensemble-averaged spectroscopy
The combination of the single-molecule and the ensemble-averaged spectroscopy is necessary to provide convincing and comprehensive assignments of protein kinetics.
Free energy evaluation of the p53-Mdm2 complex from unbinding work measured by
dynamic force spectroscopy
The energy landscape of the p53-Mdm2 complex is derived from the Jarzynski identity by analyzing the unbinding and stretching data.
photon echo of azido-probes for biomolecular dynamics
Two-dimensional infrared spectra of N3 vibrations of 2′-azido-2′-deoxyuridine establish its vibrational frequency–frequency correlation function in water and THF, and its improved sensitivity compared with nitriles.
transport of amino acids into the gas phase: driving forces for amino acid solubilization in gas-phase reverse micelles
Selective encapsulation and transport of amino acid from solution to the gas phase.
Extracting the underlying effective free energy landscape from single-molecule time series—local equilibrium states and their network
A new self-consistent procedure to construct temperature-dependent multidimensional conformation space networks from single molecule time series.
On the different roles of anions and cations in the solvation of enzymes in ionic liquids
The main contributions to interactions of enzymes with typical ionic liquids are electrostatic interactions with anions and van der Waals interactions with cations.
Single particle tracking in systems showing anomalous diffusion: the role of weak ergodicity breaking
Tracking individual molecules in cells reveals subdiffusion with apparently random amplitudes—we here analyse time averages and discuss data analysis methods.
Photoblinking and photobleaching of rylene diimide dyes
Power law blinking of single TDI molecules can be suppressed by red excitation, increasing the photostability by two orders of magnitude.
gold nanoparticles fluorescent for simultaneous absorption and fluorescence detection on the single particle level
The fluorescence of single 20 nm diameter gold nanoparticles is increased several orders of magnitude upon a controlled moderate local heating by a laser beam.
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