Molecular simulation of protein-surface interactions: Benefits, problems, solutions, and future directions (Review)
Robert A. Latour
While the importance of protein adsorption to materials surfaces is widely recognized, little is understood at this time regarding how to design surfaces to control protein adsorption behavior. All-atom empirical force field molecular simulation methods have enormous potential to address this proble ... [Biointerphases 3, FC2 (2008)] published Thu Sep 4, 2008.
Electrochemical switching of the flavoprotein dodecin at gold surfaces modified by flavin-DNA hybrid linkers
Martin Grininger, Gilbert Noll, Sibylle Trawoger, Eva-Kathrin Sinner, and Dieter Oesterhelt
Dodecin from Halobacterium salinarum is a dodecameric, hollow-spherical protein, which unspecifically adopts flavin molecules. Reduction of flavin dodecin holocomplexes induces dissociation into apododecin and free flavin. Unspecific binding and dissociation upon reduction were used as key propertie ... [Biointerphases 3, 51 (2008)] published Thu Sep 4, 2008.
Amide-I relaxation-induced hydrogen bond distortion: An intermediate in electron capture dissociation mass spectrometry of alpha-helical peptides?
Vincent Pouthier and Yury O. Tsybin
Electron capture dissociation (ECD) of peptides and proteins in the gas phase is a powerful tool in tandem mass spectrometry whose current description is not sufficient to explain many experimental observations. Here, we attempt to bridge the current understanding of the vibrational dynamics in alph ... [J. Chem. Phys. 129, 095106 (2008)] published Thu Sep 4, 2008.
Amide-I relaxation-induced hydrogen bond distortion: An intermediate in electron capture dissociation mass spectrometry of alpha-helical peptides?
Vincent Pouthier and Yury O. Tsybin
Electron capture dissociation (ECD) of peptides and proteins in the gas phase is a powerful tool in tandem mass spectrometry whose current description is not sufficient to explain many experimental observations. Here, we attempt to bridge the current understanding of the vibrational dynamics in alph ... [J. Chem. Phys. 129, 095106 (2008)] published Thu Sep 4, 2008.
Influence of correlations on molecular recognition
Hans Behringer and Friederike Schmid
The influence of the patchiness and correlations in the distribution of hydrophobic and polar residues at the interface between two rigid biomolecules on their recognition ability is investigated in idealized coarse-grained lattice models. A general two-stage approach is utilized where an ensemble o ... [Phys. Rev. E 78, 031903 (2008)] published Wed Sep 3, 2008.
Ab initio determination of the electron affinities of DNA and RNA nucleobases
Daniel Roca-Sanjuan, Manuela Merchan, Luis Serrano-Andres, and Mercedes Rubio
High-level quantum-chemical ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute the vertical and adiabatic electron affinities of the five canonical DNA and RNA nucleobases: uracil, thymine, cytosine, adenine, and guanine. The present results aim for the ... [J. Chem. Phys. 129, 095104 (2008)] published Wed Sep 3, 2008.
Ab initio determination of the electron affinities of DNA and RNA nucleobases
Daniel Roca-Sanjuan, Manuela Merchan, Luis Serrano-Andres, and Mercedes Rubio
High-level quantum-chemical ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute the vertical and adiabatic electron affinities of the five canonical DNA and RNA nucleobases: uracil, thymine, cytosine, adenine, and guanine. The present results aim for the ... [J. Chem. Phys. 129, 095104 (2008)] published Wed Sep 3, 2008.
Three-dimensional orientation determination of the emission dipoles of single molecules: The shot-noise limit
Johannes Hohlbein and Christian G. Hubner
The power of three-dimensional orientation detection of single emitting dipoles using a sophisticated scheme with three detectors in a confocal microscope is quantitatively explored by means of Monte Carlo simulations. We show that several hundreds of photons are sufficient for a reliable orientatio ... [J. Chem. Phys. 129, 094703 (2008)] published Tue Sep 2, 2008.
Generating properly weighted ensemble of conformations of proteins from sparse or indirect distance constraints
Ming Lin, Hsiao-Mei Lu, Rong Chen, and Jie Liang
Inferring three-dimensional structural information of biomacromolecules such as proteins from limited experimental data is an important and challenging task. Nuclear Overhauser effect measurements based on nucleic magnetic resonance, disulfide linking, and electron paramagnetic resonance labeling st ... [J. Chem. Phys. 129, 094101 (2008)] published Tue Sep 2, 2008.
Quantum Monte Carlo study of porphyrin transition metal complexes
Jun Koseki, Ryo Maezono, Masanori Tachikawa, M. D. Towler, and R. J. Needs
Diffusion quantum Monte Carlo (DMC) calculations for transition metal (M) porphyrin complexes (MPo, M=Ni,Cu,Zn) are reported. We calculate the binding energies of the transition metal atoms to the porphin molecule. Our DMC results are in reasonable agreement with those obtained from density function ... [J. Chem. Phys. 129, 085103 (2008)] published Fri Aug 29, 2008.
Quantum Monte Carlo study of porphyrin transition metal complexes
Jun Koseki, Ryo Maezono, Masanori Tachikawa, M. D. Towler, and R. J. Needs
Diffusion quantum Monte Carlo (DMC) calculations for transition metal (M) porphyrin complexes (MPo, M=Ni,Cu,Zn) are reported. We calculate the binding energies of the transition metal atoms to the porphin molecule. Our DMC results are in reasonable agreement with those obtained from density function ... [J. Chem. Phys. 129, 085103 (2008)] published Fri Aug 29, 2008.