Search results for "hydrogen bonding"
showing 10 items of 290 documents
Atomically Precise Nanocluster Assemblies Encapsulating Plasmonic Gold Nanorods.
2018
The self-assembled structures of atomically precise, ligand-protected noble metal nanoclusters leading to encapsulation of plasmonic gold nanorods (GNRs) is presented. Unlike highly sophisticated DNA nanotechnology, this strategically simple hydrogen bonding-directed self-assembly of nanoclusters leads to octahedral nanocrystals encapsulating GNRs. Specifically, the p-mercaptobenzoic acid (pMBA)-protected atomically precise silver nanocluster, Na4 [Ag44 (pMBA)30 ], and pMBA-functionalized GNRs were used. High-resolution transmission and scanning transmission electron tomographic reconstructions suggest that the geometry of the GNR surface is responsible for directing the assembly of silver …
Programmable assembly of peptide amphiphile via noncovalent-to-covalent bond conversion
2017
Controlling the number of monomers in a supramolecular polymer has been a great challenge in programmable self-assembly of organic molecules. One approach has been to make use of frustrated growth of the supramolecular assembly by tuning the balance of attractive and repulsive intermolecular forces. We report here on the use of covalent bond formation among monomers, compensating for intermolecular electrostatic repulsion, as a mechanism to control the length of a supramolecular nanofiber formed by self-assembly of peptide amphiphiles. Circular dichroism spectroscopy in combination with dynamic light scattering, size-exclusion chromatography, and transmittance electron microscope analyses r…
Lipid carbonyl groups terminate the hydrogen bond network of membrane-bound water.
2015
We present a combined experimental sum-frequency generation (SFG) spectroscopy and ab initio molecular dynamics simulations study to clarify the structure and orientation of water at zwitterionic phosphatidylcholine (PC) lipid and amine N-oxide (AO) surfactant monolayers. Simulated O-H stretch SFG spectra of water show good agreement with the experimental data. The SFG response at the PC interface exhibits positive peaks, whereas both negative and positive bands are present for the similar zwitterionic AO interface. The positive peaks at the water/PC interface are attributed to water interacting with the lipid carbonyl groups, which act as efficient hydrogen bond acceptors. This allows the …
Unzipping Nucleoside Channels by Means of Alcohol Disassembly
2013
Gold nanoparticles capped with simple adenosine derivatives can form colloidal aggregates in nonpolar solvents. Theoretical calculations indicate the formation of organic channels by the supramolecular assembly of the nanoparticles by means of hydrogen bonds between the adenine moieties. The aggregates were only negligibly sensitive to nPrOH, iPrOH, and tBuOH, whereas some showed a similar response to MeOH and EtOH, and others showed high selectivity toward MeOH. DNA nucleoside derivatives (1-(2-deoxy-β-D-ribofuranosyl)-5-methyluracil and 2′,3′-O-isopropylideneadenosine) as well as thymine and other aromatic compounds such as pyrene derivatives (pyrene, 1-chloropyrene, 1-hydroxypyrene, (1-p…
[2,6-Bis(di-tert-butylphosphinomethyl)phenyl-κ3P,C1,P′](trifluoroacetato)palladium(II)
2010
The Pd(II) atom in the title compound, [Pd(C(2)F(3)O(2))(C(24)H(43)P(2))], adopts a distorted square-planar geometry with the P atoms in a trans arrangement, forming two five-membered chelate rings. Four intra-molecular C-H⋯O hydrogen bonds occur. The crystal packing reveals one weak inter-molecular C-H⋯O hydrogen bond, which self-assembles the mol-ecules into infinite chains parallel to the b axis.
Proenzyme Structure and Activation of Astacin Metallopeptidase
2010
Proteolysis is regulated by inactive (latent) zymogens, with a prosegment preventing access of substrates to the active-site cleft of the enzyme. How latency is maintained often depends on the catalytic mechanism of the protease. For example, in several families of the metzincin metallopeptidases, a >cysteine switch> mechanism involves a conserved prosegment motif with a cysteine residue that coordinates the catalytic zinc ion. Another family of metzincins, the astacins, do not possess a cysteine switch, so latency is maintained by other means. We have solved the high resolution crystal structure of proastacin from the European crayfish, Astacus astacus. Its prosegment is the shortest struc…
Pharmacophore Models Derived from Molecular Dynamics Simulations of Protein-Ligand Complexes: A Case Study
2018
A single, merged pharmacophore hypothesis is derived combining 2000 pharmacophore models obtained during a 20 ns molecular dynamics simulation of a protein-ligand complex with one pharmacophore model derived from the initial PDB structure. This merged pharmacophore model contains all features that are present during the simulation and statistical information about the dynamics of the pharmacophore features. Based on the dynamics of the pharmacophore features we derive two distinctive feature patterns resulting in two different pharmacophore models for the analyzed system – the first model consists of features that are obtained from the PDB structure and the second uses two features that ca…
Porphyrin-templated synthetic G-quartet (PorphySQ): a second prototype of G-quartet-based G-quadruplex ligand.
2012
Template-assembled synthetic G-quartet (TASQ) has been reported recently as a G-quadruplex ligand interacting with DNA according to an unprecedented, nature-inspired ‘like likes like’ approach, based on the association between two G-quartets, one being native (quadruplex) and the other one artificial (ligand). Herein, a novel TASQ-based ligand is designed, synthesized and its quadruplex-recognition properties are evaluated in vitro: PorphySQ (for porphyrin-templated synthetic G-quartet) displays enhanced quadruplex recognition properties as compared to the very first reported prototype (DOTASQ, for DOTA-templated synthetic G-quartet), since the porphyrin template insures a more stable intra…
Changes in the hydrogen-bonding strength of internal water molecules and cysteine residues in the conductive state of channelrhodopsin-1
2014
Water plays an essential role in the structure and function of proteins, particularly in the less understood class of membrane proteins. As the first of its kind, channelrhodopsin is a light-gated cation channel and paved the way for the new and vibrant field of optogenetics, where nerve cells are activated by light. Still, the molecular mechanism of channelrhodopsin is not understood. Here, we applied time-resolved FT-IR difference spectroscopy to channelrhodopsin-1 from Chlamydomonas augustae. It is shown that the (conductive) P2(380) intermediate decays with τ ≈ 40 ms and 200 ms after pulsed excitation. The vibrational changes between the closed and the conductive states were analyzed in…
Internal dynamics and protein-matrix coupling in trehalose-coated proteins.
2005
Abstract We review recent studies on the role played by non-liquid, water-containing matrices on the dynamics and structure of embedded proteins. Two proteins were studied, in water–trehalose matrices: a water-soluble protein (carboxy derivative of horse heart myoglobin) and a membrane protein (reaction centre from Rhodobacter sphaeroides ). Several experimental techniques were used: Mossbauer spectroscopy, elastic neutron scattering, FTIR spectroscopy, CO recombination after flash photolysis in carboxy-myoglobin, kinetic optical absorption spectroscopy following pulsed and continuous photoexcitation in Q B containing or Q B deprived reaction centre from R. sphaeroides . Experimental result…