Conformational changes of DNA induced by a trans-azobenzene derivative via non-covalent interactions

2018 ◽  
Vol 20 (35) ◽  
pp. 22645-22651 ◽  
Author(s):  
Hong Zhang ◽  
Haohao Fu ◽  
Xueguang Shao ◽  
Christophe Chipot ◽  
Antonio Monari ◽  
...  
Keyword(s):  
Conformational Change ◽  
Conformational Changes ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
Trans Azobenzene

The presence of only one interacting azobenzene is not sufficient to lead to a global conformational change from B- to A-DNA.

scholarly journals The relation between intrinsic protein conformational changes and ligand binding

2020 ◽  
Author(s):  
Marijn de Boer
Keyword(s):  
Conformational Changes ◽  
Structural Changes ◽  
Conformational Equilibrium ◽  
Biological Function ◽  
Free Protein ◽  
Classical Statistical Mechanics ◽  
Protein Conformational Changes ◽  
Ligand Free ◽  
Non Covalent Interactions ◽  
Covalent Interactions

1ABSTRACTStructural changes in proteins allow them to exist in several conformations. Non-covalent interactions with ligands drive the structural changes, thereby allowing the protein to perform its biological function. Recent findings suggest that many proteins are always in an equilibrium of different conformations and that each of these conformations can be formed by both the ligand-free and ligand-bound protein. By using classical statistical mechanics, we derived the equilibrium probabilities of forming a conformation with and without ligand. We found, under certain conditions, that increasing the probability of forming a conformation by the ligand-free protein also increases the probability of forming the same conformation when the protein has a ligand bound. Further, we found that changes in the conformational equilibrium of the ligand-free protein can increase or decrease the affinity for the ligand.

scholarly journals In silico decryption of serotonin–receptor binding: local non-covalent interactions and long-range conformational changes

RSC Advances ◽  
2020 ◽  
Vol 10 (62) ◽  
pp. 37995-38003
Author(s):  
Padmabati Mondal
Keyword(s):  
Long Range ◽  
Receptor Binding ◽  
Conformational Changes ◽  
In Silico ◽  
Serotonin Receptor ◽  
Receptor Complexes ◽  
Serotonin Receptor Binding ◽  
Non Covalent Interactions ◽  
The Stability ◽  
Covalent Interactions

This study is focused on identifying the main non-covalent interactions controlling the stability of serotonin–receptor complexes as well as the main conformational changes in the receptor due to serotonin–receptor binding.

scholarly journals Correction: In silico decryption of serotonin–receptor binding: local non-covalent interactions and long-range conformational changes

RSC Advances ◽  
2021 ◽  
Vol 11 (17) ◽  
pp. 9837-9839
Author(s):  
Padmabati Mondal
Keyword(s):  
Long Range ◽  
Receptor Binding ◽  
Conformational Changes ◽  
In Silico ◽  
Serotonin Receptor ◽  
Serotonin Receptor Binding ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Correction for ‘In silico decryption of serotonin–receptor binding: local non-covalent interactions and long-range conformational changes’ by Padmabati Mondal et al., RSC Adv., 2020, 10, 37995–38003, DOI: 10.1039/D0RA05559J.

scholarly journals NEDD8 Deamidation Inhibits Cullin RING Ligase Dynamics

2021 ◽  
Vol 12 ◽  
Author(s):  
Priyesh Mohanty ◽  
Kiran Sankar Chatterjee ◽  
Ranabir Das
Keyword(s):  
Conformational Changes ◽  
Salt Bridge ◽  
Md Simulations ◽  
Enteric Bacteria ◽  
Covalent Attachment ◽  
E3 Ligases ◽  
Ring E3 Ligase ◽  
Non Covalent Interactions ◽  
Ring E3 ◽  
Covalent Interactions

Cullin-RING ligases (CRLs) are a significant subset of Ubiquitin E3 ligases that regulate multiple cellular substrates involved in innate immunity, cytoskeleton modeling, and cell cycle. The glutamine deamidase Cycle inhibitory factor (Cif) from enteric bacteria inactivates CRLs to modulate these processes in the host cell. The covalent attachment of a Ubiquitin-like protein NEDD8 catalytically activates CRLs by driving conformational changes in the Cullin C-terminal domain (CTD). NEDDylation results in a shift from a compact to an open CTD conformation through non-covalent interactions between NEDD8 and the WHB subdomain of CTD, eliminating the latter’s inhibitory interactions with the RING E3 ligase-Rbx1/2. It is unknown whether the non-covalent interactions are sufficient to stabilize Cullin CTD’s catalytic conformation. We studied the dynamics of Cullin-CTD in the presence and absence of NEDD8 using atomistic molecular dynamics (MD) simulations. We uncovered that NEDD8 engages in non-covalent interactions with 4HB/αβ subdomains in Cullin-CTD to promote open conformations. Cif deamidates glutamine 40 in NEDD8 to inhibit the conformational change in CRLs by an unknown mechanism. We investigated the effect of glutamine deamidation on NEDD8 and its interaction with the WHB subdomain post-NEDDylation using MD simulations and NMR spectroscopy. Our results suggest that deamidation creates a new intramolecular salt bridge in NEDD8 to destabilize the NEDD8/WHB complex and reduce CRL activity.

Functional and conformational changes to soy proteins accompanying anthocyanins: Focus on covalent and non-covalent interactions

2018 ◽  
Vol 245 ◽  
pp. 871-878 ◽  
Author(s):  
Xiaonan Sui ◽  
Hongbo Sun ◽  
Baokun Qi ◽  
Min Zhang ◽  
Yang Li ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Soy Proteins ◽  
Non Covalent Interactions ◽  
Covalent Interactions

NON COVALENT INTERACTIONS IN LARGE DIAMONDOID DIMERS IN THE GAS PHASE - A MICROWAVE STUDY

2017 ◽  
Author(s):  
Cristobal Perez ◽  
Melanie Schnell ◽  
Peter Schreiner ◽  
Norbert Mitzel ◽  
Yury Vishnevskiy ◽  
...  
Keyword(s):  
Gas Phase ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Vapour Pressure Isotope Effect on Evaporation from Pure Organic Phases - a PIMD Approach

2020 ◽  
Author(s):  
Luis Vasquez ◽  
Agnieszka Dybala-Defratyka
Keyword(s):  
Path Integral ◽  
Vapour Pressure ◽  
Density Functional ◽  
Isotope Effects ◽  
Tight Binding ◽  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Special Importance ◽  
Non Covalent Interactions ◽  
Covalent Interactions

<p></p><p>Very often in order to understand physical and chemical processes taking place among several phases fractionation of naturally abundant isotopes is monitored. Its measurement can be accompanied by theoretical determination to provide a more insightful interpretation of observed phenomena. Predictions are challenging due to the complexity of the effects involved in fractionation such as solvent effects and non-covalent interactions governing the behavior of the system which results in the necessity of using large models of those systems. This is sometimes a bottleneck and limits the theoretical description to only a few methods.<br> In this work vapour pressure isotope effects on evaporation from various organic solvents (ethanol, bromobenzene, dibromomethane, and trichloromethane) in the pure phase are estimated by combining force field or self-consistent charge density-functional tight-binding (SCC-DFTB) atomistic simulations with path integral principle. Furthermore, the recently developed Suzuki-Chin path integral is tested. In general, isotope effects are predicted qualitatively for most of the cases, however, the distinction between position-specific isotope effects observed for ethanol was only reproduced by SCC-DFTB, which indicates the importance of using non-harmonic bond approximations.<br> Energy decomposition analysis performed using the symmetry-adapted perturbation theory (SAPT) revealed sometimes quite substantial differences in interaction energy depending on whether the studied system was treated classically or quantum mechanically. Those observed differences might be the source of different magnitudes of isotope effects predicted using these two different levels of theory which is of special importance for the systems governed by non-covalent interactions.</p><br><p></p>

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