Volume 1
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Research article
Jin Wang, Li Xu, Erkang Wang PMC Biophysics 2008, 1:7 (30 December 2008)
We have uncovered the underlying potential energy landscape of a simple cyanobacteria biochemical network, and the corresponding flux which is the driving force for the oscillation of the circadian clock. Our approach is quite general and can be applied to other oscillatory cellular networks. -
Research article
Jorge J Wenz, Francisco J Barrantes PMC Biophysics 2008, 1:6 (18 December 2008)
Resolution of complex fluorescence spectra of lipids and nicotinic acetylcholine receptor by multivariate analysis reveals protein-mediated effects on the receptor's immediate microenvironment, rigidifying the surrounding lipid and preferring dioleoylphosphatidic acid over dioleoylphosphatidylcholine. -
Research article
Stochastic reconstruction of protein structures from effective connectivity profiles
Katrin Wolff, Michele Vendruscolo, Markus Porto PMC Biophysics 2008, 1:5 (26 November 2008)
A stochastic approach for reconstructing the native structures of proteins is discussed, which uses knowledge of the "effective connectivity" - a one-dimensional structural profile constructed as a linear combination of the eigenvectors of the contact map of the target structure. It is suggested that the protocol presented here could be combined effectively with current methods for predicting native structures. -
Research article
Label-free electrical quantification of the dielectrophoretic response of DNA
Anja Henning, Jörg Henkel, Frank F Bier, Ralph Hölzel PMC Biophysics 2008, 1:4 (5 November 2008)
A purely electrical sensing scheme is presented that determines the concentration of macromolecules in solution, in good agreement with dielectrophotoretic studies. The method has been applied to the characterisation of the dielectrophoretic response of DNA without the need for any chemical modifications. Extension of the method down to the single molecule level appears feasible. -
Research article
Muhammad S Ahmad, Bushra Mirza, Mukhtiar Hussain, Muhammad Hanif, Saqib Ali, Michael J Walsh, Francis L Martin PMC Biophysics 2008, 1:3 (5 November 2008)
The environmental impact of metal complexes such as organotin(IV) compounds is of increasing concern. This work shows that IR spectra, derived following ATR-FTIR spectroscopy, from organotin-treated MCF-7 cells exhibit molecular alterations following low-dose exposures. This approach highlights the potential applicability of mid-IR spectroscopy to signature toxic effects at sub-lethal concentrations following typical environmental exposures to environmental contaminants. -
Research article
On the electrostatic component of protein-protein binding free energy
Kemper Talley, Carmen Ng, Michael Shoppell, Petras Kundrotas, Emil Alexov PMC Biophysics 2008, 1:2 (5 November 2008)
This paper presents a comprehensive statistical analysis of the sensitivity of the electrostatic component of binding free energy (DDGel) with respect with different force fields (Charmm, Amber, and OPLS), different values of the internal dielectric constant, and different presentations of molecular surface (different values of the probe radius). -
Editorial
Huan-Xiang Zhou PMC Biophysics 2008, 1:1 (5 November 2008)
