Structuring of bridged silsesquioxanes via cooperative weak interactions: H-bonding of urea groups and hydrophobic interactions of long alkylene chains

2005 ◽  
Vol 15 (35-36) ◽  
pp. 3929 ◽  
Author(s):  
Joël J. E. Moreau ◽  
Benoît P. Pichon ◽  
Catherine Bied ◽  
Michel Wong Chi Man
Keyword(s):  
Hydrophobic Interactions ◽  
Weak Interactions ◽  
Bridged Silsesquioxanes

Towards a semi-quantitative description of a bimolecular association involving weak interactions in aqueous solution

1993 ◽  
Vol 345 (1674) ◽  
pp. 11-21 ◽  
Keyword(s):  
Aqueous Solution ◽  
Free Energy ◽  
Hydrophobic Interactions ◽  
Weak Interactions ◽  
Quantitative Description ◽  
Using Data ◽  
Binding Enthalpy ◽  
Vancomycin Group ◽  
The Cost ◽  
Free Energy Of Binding

We present a description of a bimolecular association in aqueous solution by dividing the free energy of binding into a number of terms representing ‘costs’ and ‘benefits'. Using data on the binding of cell-wall peptide analogues to vancomycin-group antibiotics, we have established an experimental basis for the adverse free energy of restricting internal rotations, the benefit in free energy from hydrophobic interactions and polar functional group interactions (amide-amide hydrogen bonds). Collating data from the literature on weak associations in non-polar solvents, a relation between the electrostatics of binding (enthalpy) and the dynamics (entropy) is presented. This provides an approximate, but useful, relation between the magnitude of the enthalpic barrier to dissociation for complexes in aqueous solution, and the cost in translational and rotational free energy of the reverse bimolecular association.

Lamellar Bridged Silsesquioxanes: Self-Assembly through a Combination of Hydrogen Bonding and Hydrophobic Interactions

2005 ◽  
Vol 11 (5) ◽  
pp. 1527-1537 ◽  
Author(s):  
Joël J. E. Moreau ◽  
Luc Vellutini ◽  
Michel Wong Chi Man ◽  
Catherine Bied ◽  
Philippe Dieudonné ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Self Assembly ◽  
Hydrophobic Interactions ◽  
Bridged Silsesquioxanes

scholarly journals The denaturation and degradation of stable enzymes at high temperatures

1996 ◽  
Vol 317 (1) ◽  
pp. 1-11 ◽  
Author(s):  
Roy M. DANIEL ◽  
Mark DINES ◽  
Helen H. PETACH
Keyword(s):  
Hydrophobic Interactions ◽  
Weak Interactions ◽  
Conformational Stability ◽  
Peptide Bond ◽  
Amino Acid Residues ◽  
Temperature Dependent ◽  
Upper Limit ◽  
Conformational Freedom ◽  
The Difference ◽  
Enhanced Stability

Now that enzymes are available that are stable above 100 °C it is possible to investigate conformational stability at this temperature, and also the effect of high-temperature degradative reactions in functioning enzymes and the inter-relationship between degradation and denaturation. The conformational stability of proteins depends upon stabilizing forces arising from a large number of weak interactions, which are opposed by an almost equally large destabilizing force due mostly to conformational entropy. The difference between these, the net free energy of stabilization, is relatively small, equivalent to a few interactions. The enhanced stability of very stable proteins can be achieved by an additional stabilizing force which is again equivalent to only a few stabilizing interactions. There is currently no strong evidence that any particular interaction (e.g. hydrogen bonds, hydrophobic interactions) plays a more important role in proteins that are stable at 100 °C than in those stable at 50 °C, or that the structures of very stable proteins are systematically different from those of less stable proteins. The major degradative mechanisms are deamidation of asparagine and glutamine, and succinamide formation at aspartate and glutamate leading to peptide bond hydrolysis. In addition to being temperature-dependent, these reactions are strongly dependent upon the conformational freedom of the susceptible amino acid residues. Evidence is accumulating which suggests that even at 100 °C deamidation and succinamide formation proceed slowly or not at all in conformationally intact (native) enzymes. Whether this is the case at higher temperatures is not yet clear, so it is not known whether denaturation or degradation will set the upper limit of stability for enzymes.

Two [Ln4] molecular rings folded as compact tetrahedra

2020 ◽  
Vol 49 (21) ◽  
pp. 7182-7188
Author(s):  
Jorge Salinas-Uber ◽  
Leoní A. Barrios ◽  
Olivier Roubeau ◽  
Guillem Aromí
Keyword(s):  
Weak Interactions ◽  
Molecular Rings

A new highly photo-switchable ligand furnishes supramolecular tetrahedral nanomagnets with Ln(iii) ions (Ln = Dy, Tb). Intramolecular weak interactions define the conformation of the ligand, quenching the photochromic activity.

BETA DECAY OPENS THE WAY TO WEAK INTERACTIONS

1982 ◽  
Vol 43 (C8) ◽  
pp. C8-261-C8-300
Author(s):  
E. Amaldi
Keyword(s):  
Beta Decay ◽  
Weak Interactions ◽  
The Way

Molecular Basis of Iterative C–H Oxidation by TamI, a Multifunctional P450 Monooxygenase from the Tirandamycin Biosynthetic Pathway

2020 ◽  
Author(s):  
Sean A. Newmister ◽  
Kinshuk Raj Srivastava ◽  
Rosa V. Espinoza ◽  
Kersti Caddell Haatveit ◽  
Yogan Khatri ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Basis ◽  
Hydrophobic Interactions ◽  
Cytochromes P450 ◽  
Targeted Mutagenesis ◽  
P450 Monooxygenase ◽  
Bond Functionalization ◽  
Dynamics Simulations

Biocatalysis offers an expanding and powerful strategy to construct and diversify complex molecules by C-H bond functionalization. Due to their high selectivity, enzymes have become an essential tool for C-H bond functionalization and offer complementary reactivity to small-molecule catalysts. Hemoproteins, particularly cytochromes P450, have proven effective for selective oxidation of unactivated C-H bonds. Previously, we reported the in vitro characterization of an oxidative tailoring cascade in which TamI, a multifunctional P450 functions co-dependently with the TamL flavoprotein to catalyze regio- and stereoselective hydroxylations and epoxidation to yield tirandamycin A and tirandamycin B. TamI follows a defined order including 1) C10 hydroxylation, 2) C11/C12 epoxidation, and 3) C18 hydroxylation. Here we present a structural, biochemical, and computational investigation of TamI to understand the molecular basis of its substrate binding, diverse reactivity, and specific reaction sequence. The crystal structure of TamI in complex with tirandamycin C together with molecular dynamics simulations and targeted mutagenesis suggest that hydrophobic interactions with the polyene chain of its natural substrate are critical for molecular recognition. QM/MM calculations and molecular dynamics simulations of TamI with variant substrates provided detailed information on the molecular basis of sequential reactivity, and pattern of regio- and stereo-selectivity in catalyzing the three-step oxidative cascade.<br>

Coaction of Electrostatic and Hydrophobic Interactions: Dynamic Constraints on Disordered TrkA Juxtamembrane Domain

2019 ◽  
Author(s):  
Zichen Wang ◽  
Huaxun Fan ◽  
Xiao Hu ◽  
John Khamo ◽  
Jiajie Diao ◽  
...  
Keyword(s):  
Single Molecule ◽  
Protein Function ◽  
Hydrophobic Interactions ◽  
Transmembrane Helix ◽  
Point Mutations ◽  
Salt Bridge ◽  
Receptor Activation ◽  
Membrane Dynamics ◽  
Juxtamembrane Domain ◽  
Joint Work

<p>The receptor tyrosine kinase family transmits signals into cell via a single transmembrane helix and a flexible juxtamembrane domain (JMD). Membrane dynamics makes it challenging to study the structural mechanism of receptor activation experimentally. In this study, we employ all-atom molecular dynamics with Highly Mobile Membrane-Mimetic to capture membrane interactions with the JMD of tropomyosin receptor kinase A (TrkA). We find that PIP<sub>2 </sub>lipids engage in lasting binding to multiple basic residues and compete with salt bridge within the peptide. We discover three residues insertion into the membrane, and perturb it through computationally designed point mutations. Single-molecule experiments indicate the contribution from hydrophobic insertion is comparable to electrostatic binding, and in-cell experiments show that enhanced TrkA-JMD insertion promotes receptor ubiquitination. Our joint work points to a scenario where basic and hydrophobic residues on disordered domains interact with lipid headgroups and tails, respectively, to restrain flexibility and potentially modulate protein function.</p>

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