Applying comparative molecular modelling techniques on diverse hydroxamate-based HDAC2 inhibitors: an attempt to identify promising structural features for potent HDAC2 inhibition

2022 ◽  
pp. 1-22
Author(s):  
V. Yadav ◽  
S. Banerjee ◽  
S.K. Baidya ◽  
N. Adhikari ◽  
T. Jha
Keyword(s):  
Molecular Modelling ◽  
Structural Features ◽  
Modelling Techniques

2D X-ray diffraction and molecular modelling of the crystalline structure of polyesters under uniaxial stress

2021 ◽  
pp. 096739112199822
Author(s):  
Ahmed I Abou-Kandil ◽  
Gerhard Goldbeck
Keyword(s):  
Crystalline Structure ◽  
Molecular Modelling ◽  
Three Dimensional ◽  
Uniaxial Stress ◽  
X Ray Diffraction ◽  
X Ray ◽  
Wide Range ◽  
Modelling Techniques ◽  
Diffraction Patterns

Studying the crystalline structure of uniaxially and biaxially drawn polyesters is of great importance due to their wide range of applications. In this study, we shed some light on the behaviour of PET and PEN under uniaxial stress using experimental and molecular modelling techniques. Comparing experiment with modelling provides insights into polymer crystallisation with extended chains. Experimental x-ray diffraction patterns are reproduced by means of models of chains sliding along the c-axis leading to some loss of three-dimensional order, i.e. moving away from the condition of perfect register of the fully extended chains in triclinic crystals of both PET and PEN. This will help us understand the mechanism of polymer crystallisation under uniaxial stress and the appearance of mesophases in some cases as discussed herein.

scholarly journals Proteomic analysis and molecular modelling characterize the iron-regulatory protein haemojuvelin/repulsive guidance molecule c

2013 ◽  
Vol 452 (1) ◽  
pp. 87-95 ◽  
Author(s):  
Mahta Nili ◽  
Larry David ◽  
Johannes Elferich ◽  
Ujwal Shinde ◽  
Peter Rotwein
Keyword(s):  
Ab Initio ◽  
Molecular Modelling ◽  
Electron Transfer Dissociation ◽  
Structural Information ◽  
Regulatory Protein ◽  
Structural Features ◽  
Single Chain ◽  
Disulfide Linkages ◽  
Repulsive Guidance Molecule ◽  
Guidance Molecule

HJV (haemojuvelin) plays a key role in iron metabolism in mammals by regulating expression of the liver-derived hormone hepcidin, which controls systemic iron uptake and release. Mutations in HJV cause juvenile haemochromatosis, a rapidly progressing iron overload disorder in humans. HJV, also known as RGMc (repulsive guidance molecule c), is a member of the three-protein RGM family. RGMs are GPI (glycosylphosphatidylinositol)-linked glycoproteins that share ~50% amino acid identity and several structural motifs, including the presence of 14 cysteine residues in analogous locations. Unlike RGMa and RGMb, HJV/RGMc is composed of both single-chain and two-chain isoforms. To date there is no structural information for any member of the RGM family. In the present study we have mapped the disulfide bonds in mouse HJV/RGMc using a proteomics strategy combining sequential MS steps composed of ETD (electron transfer dissociation) and CID (collision-induced dissociation), in which ETD induces cleavage of disulfide linkages, and CID establishes disulfide bond assignments between liberated peptides. The results of the present study identified an HJV/RGMc molecular species containing four disulfide linkages. We predict using ab initio modelling that this molecule is a single-chain HJV/RGMc isoform. Our observations outline a general approach using tandem MS and ab initio molecular modelling to define unknown structural features in proteins.

Application of Molecular Modelling Techniques to Pheromones of the Marine Brown Algae Cutleria multifida and Ectocarpus siliculosus (Phaeophyceae). Metalloproteins as Chemoreceptors?

1989 ◽  
Vol 44 (9-10) ◽  
pp. 829-837 ◽  
Author(s):  
Wilhelm Boland ◽  
Franz-Peter Hoever ◽  
Bernd-Wieland Krüger
Keyword(s):  
Data Base ◽  
Molecular Mechanics ◽  
Molecular Modelling ◽  
Metal Cation ◽  
Brown Algae ◽  
Software Package ◽  
Structural Data ◽  
Molecular Mechanics Calculations ◽  
Ectocarpus Siliculosus ◽  
Modelling Techniques

The conformation of the two algal pheromones ectocarpene (1) and multifidene (2) was studied by the active analogue approach using molecular mechanics calculations within the software package SYBYL. A common conformation for both pheromones and all active analogues was filtered out by superposition- and energy minimizing procedures starting from crystallographic data of the Cambridge Structural Data Base (CSD). The interaction of the algal receptor systems with their olefinic pheromones and heteroanalogues is in excellent agreement with the assumption of a receptor-bound metal cation acting as the binding side.

scholarly journals N.m.r. and molecular-modelling studies of the solution conformation of heparin

1993 ◽  
Vol 293 (3) ◽  
pp. 849-858 ◽  
Author(s):  
B Mulloy ◽  
M J Forster ◽  
C Jones ◽  
D B Davies
Keyword(s):  
Molecular Modelling ◽  
Relaxation Times ◽  
Lattice Relaxation ◽  
Spin Lattice Relaxation ◽  
Spin Lattice ◽  
Conformational Energy Calculations ◽  
Molecular Modelling Studies ◽  
Modelling Studies ◽  
Modelling Techniques ◽  
Nuclear Overhauser

The solution conformations of heparin and de-N-sulphated, re-N-acetylated heparin have been determined by a combination of n.m.r. spectroscopic and molecular-modelling techniques. The 1H- and 13C-n.m.r. spectra of these polysaccharides have been assigned. Observed 1H-1H nuclear Overhauser enhancements (n.O.e.s) have been simulated using the program NOEMOL [Forster, Jones and Mulloy (1989) J. Mol. Graph. 7, 196-201] for molecular models derived from conformational-energy calculations; correlation times for the simulations were chosen to fit experimentally determined 13C spin-lattice relaxation times. In order to achieve good agreement between calculated and observed 1H-1H n.O.e.s it was necessary to assume that the reorientational motion of the polysaccharide molecules was not isotropic, but was that of a symmetric top. The resulting model of heparin in solution is similar to that determined in the fibrous state by X-ray-diffraction techniques [Nieduszynski, Gardner and Atkins (1977) Am. Chem. Soc. Symp. Ser. 48, 73-80].

scholarly journals Elucidating molecular connetion between IAHSP onset and Alsin protein by means of Homology Modelling and Molecular Dynamics

2021 ◽  
Vol 4 (s1) ◽  
Author(s):  
Marcello Miceli ◽  
Cecile Exertier ◽  
Beatrice Vallone ◽  
Marco Cavaglià ◽  
Marco A. Deriu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Modelling ◽  
Atomic Structure ◽  
Homology Modelling ◽  
Complete Understanding ◽  
Spastic Paralysis ◽  
Aberrant Behaviour ◽  
Lack Of Information ◽  
Folding Dynamics ◽  
Modelling Techniques

The Infantile-onset Ascending Hereditary Spastic Paralysis (IAHSP) is an incurable rare neurodegerative disease related to a mutation-driven aberrant behaviour of the Alsin protein. The lack of information on Alsin atomic structure limits a complete understanding on pathology mechanisms. In this work, molecular modelling techniques have been applied to shed lights on Alsin folding dynamics and misfunction induced by aberrant mutations.

scholarly journals Computational molecular modelling as a platform for a deeper understanding of protein dynamics and rational drug design

2020 ◽  
Author(s):  
Gianvito Grasso ◽  
Lorenzo Pallante ◽  
Jack A. Tuszynski ◽  
Umberto Morbiducci ◽  
Marco A. Deriu
Keyword(s):  
Molecular Modelling ◽  
Molecular Level ◽  
Structural Features ◽  
Rational Drug Design ◽  
Therapeutic Approaches ◽  
Amyloidogenic Proteins ◽  
Rational Drug ◽  
Aggregation Inhibitors ◽  
The Stability ◽  
Toxicity Pathways

Elucidating structural features of protein aggregation at molecular level may provide novel opportunities for overarching therapeutic approaches such as blocking common aggregation-induced cellular toxicity pathways. In this context molecular modelling stimulates further research on amyloid aggregation modulators and modelling platforms can be used to test the efficiency of potential aggregation inhibitors aimed at destabilizing/reducing the stability of the amyloidogenic proteins

Properties of a new fluorescent coumarin derivatization reagent employing molecular modelling techniques

2005 ◽  
Vol 724 (1-3) ◽  
pp. 135-142 ◽  
Author(s):  
Evagelos Gikas ◽  
Maria Parissi-Poulou ◽  
Michael Kazanis ◽  
Andreas Vavagiannis
Keyword(s):  
Molecular Modelling ◽  
Modelling Techniques

Molecular modelling of self-assembled alkynyl monolayer structures — Unnatural symmetry units, surface bonding, and topochemical polymerization1

2003 ◽  
Vol 81 (11) ◽  
pp. 1228-1240 ◽  
Author(s):  
Adam J Dickie ◽  
Ashok K Kakkar ◽  
Michael A Whitehead
Keyword(s):  
Molecular Modelling ◽  
Self Assembled Monolayers ◽  
Head Group ◽  
Topochemical Polymerization ◽  
Assembled Monolayers ◽  
Molecular Modelling Studies ◽  
Modelling Studies ◽  
Modelling Techniques ◽  
Self Assembled ◽  
Group Structures

Geometric modelling techniques are used to map the potential energies of packing for self-assembled alkyl- and phenyl-backboned monolayers across a range of intermolecular separations. Natural packing distances of 4.2–4.4 Å produce less stable, more isotropic monolayers because of repulsive interchain contacts. Optimizations at unnatural surface densities found thin films of lower energy and higher symmetry existed at increased chain–chain separations. Head-group bonding is therefore identified as a force for controlling monolayer order. Analysis of the natural monolayer structures on a silicon dioxide surface determined the favourable head-group structures, and allowed the topochemical polymerization of p-bis(butadiynyl)benzene monolayers to be rationalized.Key words: self-assembled monolayers, molecular modelling studies, repeating symmetry units, thin-film order, topochemical polymerization.

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