Relation between the Catalytic Efficiency of the Synthetic Analogues of Catechol Oxidase with Their Electrochemical Property in the Free State and Substrate-Bound State

2014 ◽  
Vol 53 (16) ◽  
pp. 8257-8269 ◽  
Author(s):  
Prateeti Chakraborty ◽  
Jaydeep Adhikary ◽  
Bipinbihari Ghosh ◽  
Ria Sanyal ◽  
Shyamal Kumar Chattopadhyay ◽  
...  
Keyword(s):  
Electrochemical Property ◽  
Catalytic Efficiency ◽  
Bound State ◽  
Free State ◽  
Catechol Oxidase ◽  
Synthetic Analogues

Roles of basicity and steric crowding of anionic coligands in catechol oxidase-like activity of Cu(ii)–Mn(ii) complexes

2020 ◽  
Vol 49 (32) ◽  
pp. 11268-11281 ◽  
Author(s):  
Sabarni Dutta ◽  
Pradip Bhunia ◽  
Júlia Mayans ◽  
Michael G. B. Drew ◽  
Ashutosh Ghosh
Keyword(s):  
Catalytic Efficiency ◽  
Catechol Oxidase ◽  
Steric Crowding

Catalytic efficiency of heterometallic Cu(ii)–Mn(ii) complexes towards oxidation of 3,5-DTBC to 3,5-DTBQ is dependent on the basicity and steric requirement of anionic co-ligands.

scholarly journals Continuous absorption

1930 ◽  
Vol 229 (670-680) ◽  
pp. 163-204 ◽  
Keyword(s):  
Absorption Coefficient ◽  
Bound State ◽  
Free State ◽  
X Rays ◽  
Classical Electromagnetism ◽  
Considerable Difficulty ◽  
Positive Nucleus ◽  
Continuous Absorption ◽  
The Matrix ◽  
Good Agreement

For some years astrophysicists have been looking for an adequate theory of continuous—as opposed to line—absorption. The natural and generally accepted mechanism is the transition of an electron from a bound state to a free state, or from one free state in the neighbourhood of an ion to another free state of greater energy. The theory hitherto used is KRAMERS’ theory of the converse process of emission by a free electron passing a positive nucleus. Since emission and absorption are intimately connected by thermodynamics, the absorption coefficient can be calculated from KRAMERS’ formulae. Unfortunately, although KRAMERS’ work is in good agreement with laboratory observations of X-rays, it gives an absorption coefficient many times smaller than that found from astronomical observations. KRAMERS used classical electromagnetism, and got over the difficulty of the quantisation of negative energies by distributing the classical emission that involved captures somewhat arbitrarily among the various stationary states. It was evidently desirable to do the same work by means of quantum theory, both for the sake of greater rigour, and in the hope of finding a larger absorption. The foundations of such a theory were laid by OPPENHEIMER,|| upon the bed-rock of SCHRODINGER’s equation, in a paper to which this one is much indebted. The matrix-elements involving positive energies present considerable difficulty, and the approximations used by OPPENHEIMER in his paper of 1927 are unsuitable for stellar applications.

scholarly journals Application of the Movable Type Free Energy Method to the Caspase-Inhibitor BindingAffinity Study

2019 ◽  
Vol 20 (19) ◽  
pp. 4850
Author(s):  
Xue ◽  
Liu ◽  
Zheng
Keyword(s):  
Free Energy ◽  
Energy Method ◽  
Structural Changes ◽  
Binding Free Energy ◽  
Bound State ◽  
Free State ◽  
Caspase Inhibitor ◽  
Caspase Inhibition ◽  
Test Sets ◽  
Inhibitor Interaction

Many studies have provided evidence suggesting that caspases not only contribute to the neurodegeneration associated with Alzheimer’s disease (AD) but also play essential roles in promoting the underlying pathology of this disease. Studies regarding the caspase inhibition draw researchers’ attention through time due to its therapeutic value in the treatment of AD. In this work, we apply the “Movable Type” (MT) free energy method, a Monte Carlo sampling method extrapolating the binding free energy by simulating the partition functions for both free-state and bound-state protein and ligand configurations, to the caspase-inhibitor binding affinity study. Two test benchmarks are introduced to examine the robustness and sensitivity of the MT method concerning the caspase inhibition complexing. The first benchmark employs a large-scale test set including more than a hundred active inhibitors binding to caspase-3. The second benchmark includes several smaller test sets studying the relative binding free energy differences for minor structural changes at the caspase-inhibitor interaction interfaces. Calculation results show that the RMS errors for all test sets are below 1.5 kcal/mol compared to the experimental binding affinity values, demonstrating good performance in simulating the caspase-inhibitor complexing. For better understanding the protein-ligand interaction mechanism, we then take a closer look at the global minimum binding modes and free-state ligand conformations to study two pairs of caspase-inhibitor complexes with (1) different caspase targets binding to the same inhibitor, and (2) different polypeptide inhibitors targeting the same caspase target. By comparing the contact maps at the binding site of different complexes, we revealed how small structural changes affect the caspase-inhibitor interaction energies. Overall, this work provides a new free energy approach for studying the caspase inhibition, with structural insight revealed for both free-state and bound-state molecular configurations.

Molecular Crowding Stabilizes Both the Intrinsically Disordered Calcium-Free State and the Folded Calcium-Bound State of a Repeat in Toxin (RTX) Protein

2013 ◽  
Vol 135 (32) ◽  
pp. 11929-11934 ◽  
Author(s):  
Ana-Cristina Sotomayor-Pérez ◽  
Orso Subrini ◽  
Audrey Hessel ◽  
Daniel Ladant ◽  
Alexandre Chenal
Keyword(s):  
Bound State ◽  
Free State ◽  
Molecular Crowding ◽  
Intrinsically Disordered

scholarly journals Crystal structure of the spliceosomal DEAH-box ATPase Prp2

2018 ◽  
Vol 74 (7) ◽  
pp. 643-654 ◽  
Author(s):  
Andreas Schmitt ◽  
Florian Hamann ◽  
Piotr Neumann ◽  
Ralf Ficner
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Bound State ◽  
Free State ◽  
Dead Box ◽  
Catalytically Active ◽  
Terminal Domains

The DEAH-box ATPase Prp2 plays a key role in the activation of the spliceosome as it promotes the transition from the Bactto the catalytically active B* spliceosome. Here, four crystal structures of Prp2 are reported: one of the nucleotide-free state and three different structures of the ADP-bound state. The overall conformation of the helicase core, formed by two RecA-like domains, does not differ significantly between the ADP-bound and the nucleotide-free states. However, intrinsic flexibility of Prp2 is observed, varying the position of the C-terminal domains with respect to the RecA domains. Additionally, in one of the structures a unique ADP conformation is found which has not been observed in any other DEAH-box, DEAD-box or NS3/NPH-II helicase.

scholarly journals Structural states of a RNA aptamer, molecular dynamics simulation study

2016 ◽  
Author(s):  
Ida Autiero ◽  
Luigi Vitagliano ◽  
Roberto Improta ◽  
Menotti - Ruvo
Keyword(s):  
Rna Folding ◽  
Physiological Role ◽  
Bound State ◽  
Dynamics Simulation ◽  
Free State ◽  
Rna Aptamer ◽  
Dynamic Features ◽  
Structural Arrangement ◽  
Wide Range

Motivation RNA, which adopts a wide range of secondary structures is involved in several kind of chemical interactions and shows a notable structural plasticity. Due to remarkable chemical properties and an important physiological role of RNAs, there is a growing interest in development of RNA-based drugs and ligands of clinical relevance. However, RNAs structural and dynamic features as well as the main RNA-protein recognition effects remain largely unaddressed. We have studied the conformational behaviour and the dynamic of two different structural arrangements of an aptamer binding the bacillus anthracis ribosomal protein S8. This RNA aptamer has experimentally shown two different topologies in free state and in protein-bound state, although sequences differ for just few residues beyond the common internal loop. The role of the interacting protein on the RNA folding, stabilizing or inducing a particular conformation will be discussed. Methods Three molecular dynamic simulations of 300 ns each have been performed starting from three distinct aptamer structures: i) the aptamer free-state, using a representative model of a NMR ensemble of structures (pdb 2lun); ii) a similar aptamer bound to its target protein (4pdb) iii); an aptamer model built using the sequence of the RNA in the free state but with the structural arrangement of the bound-state to investigate a possible influence of the sequence on the RNA folding. All the systems under investigations were solvated in a truncated octahedral water box using explicit water models, with a least a 1.1 Å distance to the border, using Na+ counter-ions to neutralize. 6 steps of heating simulation from 50 K to 300K were carried out before to perform the final MD run of 300 ns in NPT conditions without restrains. The trajectories were analysed using the GROMACS utilities and X3DNA program. Results Our data show that both bound-state RNA arrangements are structurally stable, holding all the main interactions since the beginning of the simulations. The free-state RNA is the system with the largest flexibility, reaching an equilibrium after 40 ns of simulation. Although the NMR structure appears less rigid, during the total run it never matches the arrangement of the bound state. Definitely, within our time scale, a convergence of the free state with the bound-state trajectories has never been observed and the two different arrangements show differences in flexibility. Preliminary data suggest a significantly different behaviour of the free- and bound-state structures supporting a preminent role of the interacting partner protein on the RNA overall folding to induce a particular stable structural arrangement.

scholarly journals Structural states of a RNA aptamer, molecular dynamics simulation study

2016 ◽  
Author(s):  
Ida Autiero ◽  
Luigi Vitagliano ◽  
Roberto Improta ◽  
Menotti - Ruvo
Keyword(s):  
Rna Folding ◽  
Physiological Role ◽  
Bound State ◽  
Dynamics Simulation ◽  
Free State ◽  
Rna Aptamer ◽  
Dynamic Features ◽  
Structural Arrangement ◽  
Wide Range

Motivation RNA, which adopts a wide range of secondary structures is involved in several kind of chemical interactions and shows a notable structural plasticity. Due to remarkable chemical properties and an important physiological role of RNAs, there is a growing interest in development of RNA-based drugs and ligands of clinical relevance. However, RNAs structural and dynamic features as well as the main RNA-protein recognition effects remain largely unaddressed. We have studied the conformational behaviour and the dynamic of two different structural arrangements of an aptamer binding the bacillus anthracis ribosomal protein S8. This RNA aptamer has experimentally shown two different topologies in free state and in protein-bound state, although sequences differ for just few residues beyond the common internal loop. The role of the interacting protein on the RNA folding, stabilizing or inducing a particular conformation will be discussed. Methods Three molecular dynamic simulations of 300 ns each have been performed starting from three distinct aptamer structures: i) the aptamer free-state, using a representative model of a NMR ensemble of structures (pdb 2lun); ii) a similar aptamer bound to its target protein (4pdb) iii); an aptamer model built using the sequence of the RNA in the free state but with the structural arrangement of the bound-state to investigate a possible influence of the sequence on the RNA folding. All the systems under investigations were solvated in a truncated octahedral water box using explicit water models, with a least a 1.1 Å distance to the border, using Na+ counter-ions to neutralize. 6 steps of heating simulation from 50 K to 300K were carried out before to perform the final MD run of 300 ns in NPT conditions without restrains. The trajectories were analysed using the GROMACS utilities and X3DNA program. Results Our data show that both bound-state RNA arrangements are structurally stable, holding all the main interactions since the beginning of the simulations. The free-state RNA is the system with the largest flexibility, reaching an equilibrium after 40 ns of simulation. Although the NMR structure appears less rigid, during the total run it never matches the arrangement of the bound state. Definitely, within our time scale, a convergence of the free state with the bound-state trajectories has never been observed and the two different arrangements show differences in flexibility. Preliminary data suggest a significantly different behaviour of the free- and bound-state structures supporting a preminent role of the interacting partner protein on the RNA overall folding to induce a particular stable structural arrangement.

scholarly journals Molecular Crowding Stabilizes Both the Intrinsically Disordered Calcium-Free State and the Folded Calcium-Bound State of an RTX Protein: Implication for Toxin Secretion

2014 ◽  
Vol 106 (2) ◽  
pp. 271a
Author(s):  
Ana Cristina Sotomayor Pérez ◽  
Orso Subrini ◽  
Audrey Hessel ◽  
Daniel Ladant ◽  
Alexandre Chenal
Keyword(s):  
Bound State ◽  
Free State ◽  
Molecular Crowding ◽  
Intrinsically Disordered ◽  
Toxin Secretion
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