Hydrodynamic modeling of diffusion tensor properties of flexible molecules

Barone, Vincenzo; Zerbetto, Mirco; Polimeno, Antonino

doi:10.1002/jcc.21007

Cited by 38 publications

(86 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It has shown to yield structures and interaction energies which deviate only insignificantly from coupled-cluster results. 25,26 However, since it still suffers from the GGA self-interaction error, reaction barriers are systematically underestimated. For graphite a slight overbinding has been confirmed.…”

Section: Methods Of Calculationmentioning

confidence: 99%

Electronic structure of superlattices of graphene and hexagonal boron nitride

2012

View full text Add to dashboard Cite

CitationKaloni TP, Cheng YC, Schwingenschlögl U (2011) We study the electronic structure of superlattices consisting of graphene and hexagonal boron nitride slabs, using ab initio density functional theory. We find that the system favors a short C-B bond length at the interface between the two component materials. A sizeable band gap at the Dirac point is opened for superlattices with single graphene layers but not for superlattices with graphene bilayers. The system is promising for applications in electronic devices such as field effect transistors and metal-oxide semiconductors.

show abstract

Section: Methods Of Calculationmentioning

confidence: 99%

Electronic structure of superlattices of graphene and hexagonal boron nitride

2012

View full text Add to dashboard Cite

show abstract

“…The overall rotational correlation time of the HydF dimer was estimated using the program by Zerbetto et al . 53 . Details are reported in Supplementary information.…”

Section: Methodsmentioning

confidence: 99%

Identifying conformational changes with site-directed spin labeling reveals that the GTPase domain of HydF is a molecular switch

Galazzo

Maso

Rosa

et al. 2017

Sci Rep

View full text Add to dashboard Cite

[FeFe]-hydrogenases catalyse the reduction of protons to hydrogen at a complex 2Fe[4Fe4S] center called H-cluster. The assembly of this active site is a multistep process involving three proteins, HydE, HydF and HydG. According to the current models, HydF has the key double role of scaffold, upon which the final H-cluster precursor is assembled, and carrier to transfer it to the target hydrogenase. The X-ray structure of HydF indicates that the protein is a homodimer with both monomers carrying two functional domains: a C-terminal FeS cluster-binding domain, where the precursor is assembled, and a N-terminal GTPase domain, whose exact contribution to cluster biogenesis and hydrogenase activation is still elusive. We previously obtained several hints suggesting that the binding of GTP to HydF could be involved in the interactions of this scaffold protein with the other maturases and with the hydrogenase itself. In this work, by means of site directed spin labeling coupled to EPR/PELDOR spectroscopy, we explored the conformational changes induced in a recombinant HydF protein by GTP binding, and provide the first clue that the HydF GTPase domain could be involved in the H-cluster assembly working as a molecular switch similarly to other known small GTPases.Biohydrogen production, one of the most promising frontiers in the field of renewable energies, is achieved in nature by several prokaryotic and eukaryotic microorganisms through a general class of evolutionarily unrelated metalloenzymes called hydrogenases. Among them, [FeFe]-and [NiFe]-hydrogenases are the most widespread 1 . These proteins have different distribution, catalytic properties and molecular architectures, but they are both able to reversibly reduce protons to H 2 by means of metal clusters with some key similarities, including the coordination to the polypeptide chain through four conserved cysteine residues and the presence of iron-bound CO and CN − ligands 2 . In the case of [FeFe]-hydrogenases, the active site (referred to as the H-cluster) is particularly complex since it is composed of a [4Fe4S] cubane linked via a cysteine bridge to a 2Fe subcluster comprising the CO and CN -molecules and an additional dithiomethylamine ligand 3-5 . This 2Fe subcluster needs a specific set of maturation proteins to be first assembled in the active form and then inserted into the target functional [FeFe]-hydrogenase. Three conserved proteins are involved in its biosynthesis and delivery, i.e. HydE, HydF and HydG, discovered in the unicellular green alga Chlamydomonas reinhardtii and then found in all microorganisms containing a [FeFe]-hydrogenase 6 . Both HydE and HydG are radical S-adenosylmethionine (SAM) proteins whereas HydF is a GTPase carrying a [4Fe4S] cluster binding motif 6 . The 3D crystal structures of all these maturases have been solved [7][8][9][10] , and several in vitro and cell-free experiments using purified recombinant proteins have been performed to understand their functions, allowing to propose a two-steps model that describes a H-cluste...

show abstract

“…The tensor contains all the translational, rotational and internal parts and coupling terms. This methodology showed to have good predictivity for the evaluation of the diffusion tensor of molecules of any size [43].…”

Section: Diffusive Propertiesmentioning

confidence: 98%

“…E-SpiReS includes all the necessary steps to directly evaluate friction/diffusion tensorial properties of molecules of a given geometry, and previously implemented in the stand alone code DiTe (Diffusion Tensor) [43], which is aimed at the calculation of diffusion tensor of rigid and flexible molecules of general topology.…”

Section: Diffusive Propertiesmentioning

confidence: 99%