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Themed collection Biophysics and biophysical chemistry in PCCP

38 items
Perspective

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.

Graphical abstract: Microsecond folding experiments and simulations: a match is made
From the themed collection: Biophysics and biophysical chemistry in PCCP
Perspective

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.

Graphical abstract: The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies
From the themed collection: Biophysics and biophysical chemistry in PCCP
Perspective

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.

Graphical abstract: The ‘sticky business’ of cleaning gas-phase membrane proteins: a detergent oriented perspective
From the themed collection: Biophysics and biophysical chemistry in PCCP
Perspective

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.

Graphical abstract: Solution, surface, and single molecule platforms for the study of DNA-mediated charge transport
From the themed collection: Electron Transfer Theory
Perspective

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.

Graphical abstract: Mapping viscosity in cells using molecular rotors
From the themed collection: Biophysics and biophysical chemistry in PCCP
Perspective

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.

Graphical abstract: Rate constants and mechanisms of intrinsically disordered proteins binding to structured targets
From the themed collection: Biophysics and biophysical chemistry in PCCP
Perspective

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.

Graphical abstract: Lipidology and lipidomics––quo vadis? A new era for the physical chemistry of lipids
From the themed collection: Biophysics and biophysical chemistry in PCCP
Perspective

Diffusion models of protein folding

Descriptions of protein folding as diffusion along low-dimensional reaction coordinates capture the observed simulation dynamics and help interpret single-molecule experiments.

Graphical abstract: Diffusion models of protein folding
From the themed collection: Biophysics and biophysical chemistry in PCCP
Perspective

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.

Graphical abstract: The shape-shifting quasispecies of RNA: one sequence, many functional folds
From the themed collection: Biophysics and biophysical chemistry in PCCP
Perspective

Electrostatic interactions in biological DNA-related systems

Recent developments in the theory of charge effects in biological DNA-related systems are discussed.

Graphical abstract: Electrostatic interactions in biological DNA-related systems
Perspective

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.

Graphical abstract: Functional liposomes and supported lipid bilayers: towards the complexity of biological archetypes
From the themed collection: Biophysics and biophysical chemistry in PCCP
Perspective

Combining 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.

Graphical abstract: Combining optical trapping, fluorescence microscopy and micro-fluidics for single molecule studies of DNA–protein interactions
From the themed collection: Biophysics and biophysical chemistry in PCCP
Perspective

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.

Graphical abstract: Revealing time bunching effect in single-molecule enzyme conformational dynamics
From the themed collection: Biophysics and biophysical chemistry in PCCP
Perspective

Physics of proteinDNA interactions: mechanisms of facilitated target search

A critical review of theoretical approaches to explain protein search for targets on DNA is presented.

Graphical abstract: Physics of protein–DNA interactions: mechanisms of facilitated target search
From the themed collection: Biophysics and biophysical chemistry in PCCP
Perspective

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.

Graphical abstract: Optical imaging of excited-state tautomerization in single molecules
Perspective

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.

Graphical abstract: Seeing the forest for the trees: fluorescence studies of single enzymes in the context of ensemble experiments
Perspective

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.

Graphical abstract: Design and development of quantum dots and other nanoparticles based cellular imaging probe
From the themed collection: Biophysics and biophysical chemistry in PCCP
Perspective

Mitochondrial biofuel 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.

Graphical abstract: Mitochondrial biofuel cells: expanding fuel diversity to amino acids
From the themed collection: Biophysics and biophysical chemistry in PCCP
Communication

Well-defined lipid interfaces for protein adsorption studies

Supported lipid bilayers at different surface charge and composition as nanoplatforms for the electrostatically-driven immobilization of ferritin.

Graphical abstract: Well-defined lipid interfaces for protein adsorption studies
From the themed collection: Biophysics and biophysical chemistry in PCCP
Communication

Nanoscale 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.

Graphical abstract: Nanoscale chemical imaging of segregated lipid domains using tip-enhanced Raman spectroscopy
Communication

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.

Graphical abstract: 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
From the themed collection: Biophysics and biophysical chemistry in PCCP
Paper

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.

Graphical abstract: A novel method for automatic single molecule tracking of blinking molecules at low intensities
From the themed collection: Biophysics and biophysical chemistry in PCCP
Paper

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.

Graphical abstract: Electric-field induced mutation of DNA: a theoretical investigation of the GC base pair
From the themed collection: Biophysics and biophysical chemistry in PCCP
Paper

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.

Graphical abstract: Effect of heavy water on phospholipid membranes: experimental confirmation of molecular dynamics simulations
From the themed collection: Biophysics and biophysical chemistry in PCCP
Paper

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.

Graphical abstract: The road not taken: a theoretical view of an unexpected cryptochrome charge transfer path
From the themed collection: Biophysics and biophysical chemistry in PCCP
Paper

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.

Graphical abstract: Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the Aβ16–22 dimer and trimer
From the themed collection: Biophysics and biophysical chemistry in PCCP
Paper

Photoinduced pH drops in water

A 2-hydroxyazobenzene platform is used to reversibly photo-generate up to one unit pH drops in pure water under UV illumination.

Graphical abstract: Photoinduced pH drops in water
From the themed collection: Biophysics and biophysical chemistry in PCCP
Paper

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.

Graphical abstract: Mechanisms and advancement of antifading agents for fluorescence microscopy and single-molecule spectroscopy
From the themed collection: Biophysics and biophysical chemistry in PCCP
Paper

Solvent-assisted conformational isomerization and the conformationally-pure REMPI spectrum of 3-aminophenol

Conformational isomerization occurs during supersonic expansion with solvents.

Graphical abstract: Solvent-assisted conformational isomerization and the conformationally-pure REMPI spectrum of 3-aminophenol
From the themed collection: Biophysics and biophysical chemistry in PCCP
Paper

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.

Graphical abstract: Unfolding dynamics of cytochrome c revealed by single-molecule and ensemble-averaged spectroscopy
From the themed collection: Biophysics and biophysical chemistry in PCCP
Paper

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.

Graphical abstract: Free energy evaluation of the p53-Mdm2 complex from unbinding work measured by dynamic force spectroscopy
From the themed collection: Biophysics and biophysical chemistry in PCCP
Paper

2D IR 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.

Graphical abstract: 2D IR photon echo of azido-probes for biomolecular dynamics
From the themed collection: Biophysics and biophysical chemistry in PCCP
Paper

Selective 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.

Graphical abstract: Selective transport of amino acids into the gas phase: driving forces for amino acid solubilization in gas-phase reverse micelles
From the themed collection: Biophysics and biophysical chemistry in PCCP
Paper

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.

Graphical abstract: Extracting the underlying effective free energy landscape from single-molecule time series—local equilibrium states and their network
From the themed collection: Biophysics and biophysical chemistry in PCCP
Paper

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.

Graphical abstract: On the different roles of anions and cations in the solvation of enzymes in ionic liquids
From the themed collection: Biophysics and biophysical chemistry in PCCP
Paper

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.

Graphical abstract: Single particle tracking in systems showing anomalous diffusion: the role of weak ergodicity breaking
Paper

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.

Graphical abstract: Photoblinking and photobleaching of rylene diimide dyes
Paper

Making 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.

Graphical abstract: Making gold nanoparticles fluorescent for simultaneous absorption and fluorescence detection on the single particle level
From the themed collection: Biophysics and biophysical chemistry in PCCP
38 items

About this collection

We would like to share with you some great articles recently published in the fields of biophysics and biophysical chemistry in Physical Chemistry Chemical Physics (PCCP).

 Publishing work of the highest quality in the broad fields of physical chemistry, chemical physics and biophysical chemistry, PCCP is the ideal place to publish your research.

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