Themed collection Biophysics and biophysical chemistry in PCCP
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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.
Phys. Chem. Chem. Phys., 2013,15, 3372-3388
https://doi.org/10.1039/C3CP43992E
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.
Phys. Chem. Chem. Phys., 2012,14, 15257-15277
https://doi.org/10.1039/C2CP41987D
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.
Phys. Chem. Chem. Phys., 2012,14, 14439-14449
https://doi.org/10.1039/C2CP41687E
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.
Phys. Chem. Chem. Phys., 2012,14, 13754-13771
https://doi.org/10.1039/C2CP41602F
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.
Phys. Chem. Chem. Phys., 2012,14, 12671-12686
https://doi.org/10.1039/C2CP41674C
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.
Phys. Chem. Chem. Phys., 2012,14, 10466-10476
https://doi.org/10.1039/C2CP41196B
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.
Phys. Chem. Chem. Phys., 2011,13, 19195-19205
https://doi.org/10.1039/C1CP22484K
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.
Phys. Chem. Chem. Phys., 2011,13, 16902-16911
https://doi.org/10.1039/C1CP21541H
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.
Phys. Chem. Chem. Phys., 2011,13, 11524-11537
https://doi.org/10.1039/C1CP20576E
Electrostatic interactions in biological DNA-related systems
Recent developments in the theory of charge effects in biological DNA-related systems are discussed.
Phys. Chem. Chem. Phys., 2011,13, 9942-9968
https://doi.org/10.1039/C0CP02796K
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.
Phys. Chem. Chem. Phys., 2011,13, 8769-8782
https://doi.org/10.1039/C0CP02400G
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.
Phys. Chem. Chem. Phys., 2011,13, 7263-7272
https://doi.org/10.1039/C0CP02844D
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.
Phys. Chem. Chem. Phys., 2011,13, 6734-6749
https://doi.org/10.1039/C0CP02860F
Physics of protein –DNA interactions: mechanisms of facilitated target search
A critical review of theoretical approaches to explain protein search for targets on DNA is presented.
Phys. Chem. Chem. Phys., 2011,13, 2088-2095
https://doi.org/10.1039/C0CP01966F
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.
Phys. Chem. Chem. Phys., 2011,13, 1722-1733
https://doi.org/10.1039/C0CP02228D
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.
Phys. Chem. Chem. Phys., 2011,13, 1709-1721
https://doi.org/10.1039/C0CP02412K
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.
Phys. Chem. Chem. Phys., 2011,13, 385-396
https://doi.org/10.1039/C0CP00726A
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.
Phys. Chem. Chem. Phys., 2011,13, 86-92
https://doi.org/10.1039/C0CP01362E
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.
Phys. Chem. Chem. Phys., 2012,14, 16695-16698
https://doi.org/10.1039/C2CP43254D
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.
Phys. Chem. Chem. Phys., 2011,13, 9978-9981
https://doi.org/10.1039/C0CP02832K
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.
Phys. Chem. Chem. Phys., 2011,13, 100-103
https://doi.org/10.1039/C0CP01534B
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.
Phys. Chem. Chem. Phys., 2013,15, 6196-6205
https://doi.org/10.1039/C3CP44693J
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.
Phys. Chem. Chem. Phys., 2013,15, 4548-4553
https://doi.org/10.1039/C2CP44066K
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.
Phys. Chem. Chem. Phys., 2012,14, 14516-14522
https://doi.org/10.1039/C2CP41275F
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.
Phys. Chem. Chem. Phys., 2012,14, 11518-11524
https://doi.org/10.1039/C2CP40793K
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.
Phys. Chem. Chem. Phys., 2011,13, 9778-9788
https://doi.org/10.1039/C1CP20323A
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.
Phys. Chem. Chem. Phys., 2011,13, 6493-6499
https://doi.org/10.1039/C0CP02464C
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.
Phys. Chem. Chem. Phys., 2011,13, 6699-6709
https://doi.org/10.1039/C0CP01919D
Solvent -assisted conformational isomerization and the conformationally-pure REMPI spectrum of 3-aminophenol
Conformational isomerization occurs during supersonic expansion with solvents.
Phys. Chem. Chem. Phys., 2011,13, 7037-7042
https://doi.org/10.1039/C0CP02592E
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.
Phys. Chem. Chem. Phys., 2011,13, 5651-5658
https://doi.org/10.1039/C0CP02689A
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.
Phys. Chem. Chem. Phys., 2011,13, 2738-2743
https://doi.org/10.1039/C0CP01474E
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.
Phys. Chem. Chem. Phys., 2011,13, 2237-2241
https://doi.org/10.1039/C0CP01625J
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.
Phys. Chem. Chem. Phys., 2011,13, 1466-1478
https://doi.org/10.1039/C0CP00823K
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.
Phys. Chem. Chem. Phys., 2011,13, 1395-1406
https://doi.org/10.1039/C0CP00694G
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.
Phys. Chem. Chem. Phys., 2011,13, 1649-1662
https://doi.org/10.1039/C0CP01509A
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.
Phys. Chem. Chem. Phys., 2011,13, 1800-1812
https://doi.org/10.1039/C0CP01879A
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.
Phys. Chem. Chem. Phys., 2011,13, 1776-1785
https://doi.org/10.1039/C0CP01814G
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.
Phys. Chem. Chem. Phys., 2011,13, 149-153
https://doi.org/10.1039/C0CP01389G
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).
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