Search results for "molecular dynamics"
showing 10 items of 1075 documents
Construction of Chimeric Dual-Chain Avidin by Tandem Fusion of the Related Avidins
2011
BackgroundAvidin is a chicken egg-white protein with high affinity to vitamin H, also known as D-biotin. Many applications in life science research are based on this strong interaction. Avidin is a homotetrameric protein, which promotes its modification to symmetrical entities. Dual-chain avidin, a genetically engineered avidin form, has two circularly permuted chicken avidin monomers that are tandem-fused into one polypeptide chain. This form of avidin enables independent modification of the two domains, including the two biotin-binding pockets; however, decreased yields in protein production, compared to wt avidin, and complicated genetic manipulation of two highly similar DNA sequences i…
Molecular dynamics near the glass transition
1993
Solid state 13C NMR spectroscopy has been applied to investigate the time scale and the geometry of rotational motions near the glass transition of the low-molar-mass van der Waals glass former 1,3,5-tri-α-naphthylbenzene (T g = 342 K). Two-dimensional 13C exchange spectra were taken between 347 and 372 K. With the principal values of the 13C chemical shift tensors determined from 13C CP/MAS spectra and static one-dimensional 13C spectra, the two-dimensional spectra are interpreted according to the isotropic rotational diffusional model to yield mean correlation times τ0 in the range 10 ms ˇ- τ0 ˇ- 50 s, and a log-Gaussian distribution of correlation times with a width of 1·5 decades. The m…
Solid-state NMR and computational studies of tetratolyl urea calix[4]arene inclusion compounds.
2009
Solid-state guest dynamics of tetratolyl tetraurea calix[4]arene tetrapentylether dimeric capsules filled with different types of aromatic guests such as benzene-d6, fluorobenzene-d5 and 1,4-difluorobenzene were studied. Upon inclusion, all guest moieties revealed complexation-induced shifts varying from 2.8 ppm to 5.1 ppm. All guest molecules were shown to undergo distinct motions, ranging from mere C6-rotations of benzene-d6 to (ill-defined) 180 degrees phenyl flips of fluorobenzene-d5. In all cases, dynamic heterogeneities were identified based on 2H lineshape deconvolution. In addition, by combination of both a computed nucleus independent chemical shift (NICS) map and explicit 19F and …
Conformation and dynamics of the ligand shell of a water-soluble Au102 nanoparticle
2016
Inorganic nanoparticles, stabilized by a passivating layer of organic molecules, form a versatile class of nanostructured materials with potential applications in material chemistry, nanoscale physics, nanomedicine and structural biology. While the structure of the nanoparticle core is often known to atomic precision, gaining precise structural and dynamical information on the organic layer poses a major challenge. Here we report a full assignment of 1H and 13C NMR shifts to all ligands of a water-soluble, atomically precise, 102-atom gold nanoparticle stabilized by 44 para-mercaptobenzoic acid ligands in solution, by using a combination of multidimensional NMR methods, density functional t…
Rotational Correlation Functions of Single Molecules
2004
Single molecule rotational correlation functions are analyzed for several reorientation geometries. Even for the simplest model of isotropic rotational diffusion our findings predict non-exponential correlation functions to be observed by polarization sensitive single molecule fluorescence microscopy. This may have a deep impact on interpreting the results of molecular reorientation measurements in heterogeneous environments.
De Novo Mutations in SLC25A24 Cause a Disorder Characterized by Early Aging, Bone Dysplasia, Characteristic Face, and Early Demise
2017
International audience; A series of simplex cases have been reported under various diagnoses sharing early aging, especially evident in congenitally decreased subcutaneous fat tissue and sparse hair, bone dysplasia of the skull and fingers, a distinctive facial gestalt, and prenatal and postnatal growth retardation. For historical reasons, we suggest naming the entity Fontaine syndrome. Exome sequencing of four unrelated affected individuals showed that all carried the de novo missense variant c.649C>T (p.Arg217Cys) or c.650G>A (p.Arg217His) in SLC25A24, a solute carrier 25 family member coding for calcium-binding mitochondrial carrier protein (SCaMC-1, also known as SLC25A24). SLC25A24 all…
Circular Dichroism of DNA G-Quadruplexes: Combining Modeling and Spectroscopy To Unravel Complex Structures
2016
We report on the comparison between the computational and experimental determination of electronic circular dichroism spectra of different guanine quadruplexes obtained from human telomeric sequences. In particular the difference between parallel, antiparallel, and hybrid structures is evidenced, as well as the induction of transitions between the polymorphs depending on the solution environment. Extensive molecular dynamics simulations (MD) are used to probe the conformational space of the different quadruplexes, and subsequently state-of-the-art hybrid quantum mechanics/molecular mechanics (QM/MM) techniques coupled with excitonic semiempirical Hamiltonian are used to simulate the macromo…
A step forward in disclosing the secret of stradivari's varnish by NMR spectroscopy
2017
It is commonly thought that the varnishes used by the great violin-maker Antonio Stradivari may have a role in determining not only the esthetical features but also the acoustic properties of his instruments, and the idea of a “lost secret” is still widespread among musicians and violin-makers. Previous scientific researches on varnish samples of Stradivari's instruments revealed that they were generally made by a mix of linseed oil with and colophony or metal rosinates in different ratios ranging between 75/25 (oil/resin) and 60/40 (oil/rosinate). However, it is still not clear whether the mixture composition can be related to any structural and/or functional feature of the resulting varni…
Mechanical and Structural Tuning of Reversible Hydrogen Bonding in Interlocked Calixarene Nanocapsules
2019
We present force probe molecular dynamics simulations of dimers of interlocked calixarene nanocapsules and study the impact of structural details and solvent properties on the mechanical unfolding pathways. The system consists of two calixarene "cups" that form a catenane structure via interlocked aliphatic loops of tunable length. The dimer shows reversible rebinding, and the kinetics of the system can be understood in terms of a two-state model for shorter loops (≤14 CH2 units) and a three-state model for longer loops (≥15 CH2 units). The various conformational states of the dimer are stabilized by networks of hydrogen bonds, the mechanical susceptibility of which can be altered by changi…
Microscopic properties of liquid water from combined ab initio molecular dynamics and energy decomposition studies
2013
The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water cluste…