scholarly journals NMR and molecular modeling reveal key structural features of synthetic nodulation factors

Glycobiology ◽  
2011 ◽  
Vol 21 (6) ◽  
pp. 824-833 ◽  
Author(s):  
Maria A Morando ◽  
Alessandra Nurisso ◽  
Nathalie Grenouillat ◽  
Boris Vauzeilles ◽  
Jean-Marie Beau ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Structural Features ◽  
Nodulation Factors

scholarly journals Three-Dimensional Structures of Carbohydrates and Where to Find Them

2020 ◽  
Vol 21 (20) ◽  
pp. 7702 ◽  
Author(s):  
Sofya I. Scherbinina ◽  
Philip V. Toukach
Keyword(s):  
Experimental Data ◽  
Molecular Modeling ◽  
Computational Methods ◽  
Three Dimensional ◽  
Structural Diversity ◽  
Structural Data ◽  
Structural Features ◽  
Data Validation ◽  
Data Generation ◽  
Efficient Treatment

Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.

scholarly journals The Nature of Interactions and UV-Induced Response within α-Zirconium Phosphate Intercalation Compounds with Azobenzenes

Materials ◽  
2019 ◽  
Vol 12 (9) ◽  
pp. 1436 ◽  
Author(s):  
Anna Koteja ◽  
Jakub Matusik ◽  
Katarzyna Luberda-Durnaś ◽  
Marek Szczerba
Keyword(s):  
Molecular Modeling ◽  
Zirconium Phosphate ◽  
Interlayer Space ◽  
Hydrophobic Interactions ◽  
Functional Materials ◽  
Structural Features ◽  
Solid Support ◽  
Induced Response ◽  
Low Density ◽  
Experimental Approaches

Azobenzenes immobilization on a solid support enables the usage of their trans-cis isomerization ability for preparation of functional materials. The behavior of azobenzenes in the interlayer space of α-zirconium phosphate (ZrP) upon the UV–Vis irradiation was investigated. Two experimental approaches were performed: (1) co-intercalation of benzylalkylammonium surfactants and azobenzene in the interlayers of ZrP (ZBCnA), and (2) intercalation of p-aminoazobenzene (ZpA). The materials were characterized with XRD, FTIR, UV–Vis, CHN analysis, and the molecular modeling. The molecules in ZBCnA samples were sparsely packed and held by weak hydrophobic interactions. Conversely, the molecules in ZpA sample were strongly H-bonded to the ZrP, well-ordered, and densely packed. These structural features determined the samples’ photoresponsive behavior. Low density of molecules in the ZBCnA samples, allowed the effective, fast, and reversible isomerization of azobenzene. Whereas the ZpA sample did not react to the UV irradiation because of the steric hindrance of tightly packed molecules.

scholarly journals Brown Seaweed Defensive Chemicals: A Structure-activity Relationship Approach for the Marine Environment

2009 ◽  
Vol 4 (2) ◽  
pp. 1934578X0900400 ◽  
Author(s):  
Éverson Miguel Bianco ◽  
Valéria Laneuville Teixeira ◽  
Renato Crespo Pereira ◽  
Alessandra Mendonça Teles de Souza ◽  
Pedro Nucci ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Pathogenic Bacteria ◽  
Brown Seaweed ◽  
Structure Activity Relationship ◽  
Structural Features ◽  
Activity Relationship ◽  
Chemical Structures ◽  
Structure Activity ◽  
Minimum Requirements ◽  
New Perspective

The literature describes several diterpenes from brown seaweeds that act as defensive chemicals against natural enemies, such as competitors, epiphytes, pathogenic bacteria and herbivores. A structure-activity relationship is here presented using a new molecular modeling approach to identify structural and chemical features important to the defensive profile of four structurally related diterpenes (three dolastanes and one seco-dolastane) from Canistrocarpus cervicornis against the feeding process of the omnivorous sea urchin Lytechinus variegatus. Our experimental data revealed the herbivory inhibitory profile (HIE) for three of these evaluated compounds with (4R, 7R, 14S)-4α, 7α-diacetoxy-14-hydroxydolast-1(15),8-diene presenting the highest effect (HIE = 70%). Interestingly, the molecular modeling results infer that this biological activity seems to be related to several different structural features, including HOMO distribution, the molecular structure conformation, and the fulfillment of minimum requirements regarding molecular weight. These results reinforce the hypothesis about the intricate biological mechanism of these molecules due to the complexity of their chemical structures. Our work may help in the understanding of these defensive mechanisms and point to a new perspective of ecological and/or evolutionary evaluation in this area.

Identifying the structural features and diversifying the chemical domain of peripherally acting CB1 receptor antagonists using molecular modeling techniques

RSC Advances ◽  
2016 ◽  
Vol 6 (2) ◽  
pp. 1466-1483 ◽  
Author(s):  
Mayank Kumar Sharma ◽  
Prashant R. Murumkar ◽  
Guanglin Kuang ◽  
Yun Tang ◽  
Mange Ram Yadav
Keyword(s):  
Molecular Modeling ◽  
Virtual Screening ◽  
3D Qsar ◽  
Structural Features ◽  
Cb1 Receptor ◽  
Receptor Antagonists ◽  
Modeling Techniques ◽  
Qsar Models ◽  
Cb1 Receptor Antagonists

A four featured pharmacophore and predictive 3D-QSAR models were developed which were used for virtual screening of the Asinex database to get chemically diverse hits of peripherally active CB1 receptor antagonists.

scholarly journals Molecular modeling and chemometric study of anticancer derivatives of artemisinin

2011 ◽  
Vol 76 (9) ◽  
pp. 1263-1282 ◽  
Author(s):  
Jardel Barbosa ◽  
João Ferreira ◽  
Antonio Figueiredo ◽  
Ruth Almeida ◽  
Osmarina Silva ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Molecular Docking ◽  
Molecular Modeling ◽  
Anticancer Activity ◽  
Structural Features ◽  
Active Compounds ◽  
Gap Energy ◽  
Multivariate Study ◽  
Derivatives Of

In this work, a molecular modeling and multivariate study involving artemisinin and 28 derivatives with activity against human hepatocellular carcinoma HepG2 is reported. The studied calculations of the compounds were performed at the B3LYP/6-31G level. MEP maps were used in an attempt to identify key structural features of artemisinin and its derivatives that are necessary for their activities, and to investigate their interaction with the transferrin. The chemometrics methods PCA, HCA, KNN, SIMCA and SDA were employed in order to reduce dimensionality and to investigate which subset of variables could be more effective for classification of the compounds according to their degree of anticancer activity. Chemometric studies revealed that the ALOGPS_logs, Mor29m, IC5 and the Gap energy descriptors are responsible for the separation into more active and less active compounds. In addition, molecular docking was used to investigate the interaction between ligands and receptor. The results showed that the ligands approached the receptor through the endoperoxide bond.

Structural Features of the Glutamate Binding Site in Recombinant NR1/NR2A N-Methyl-d-aspartate Receptors Determined by Site-Directed Mutagenesis and Molecular Modeling

2005 ◽  
Vol 67 (5) ◽  
pp. 1470-1484 ◽  
Author(s):  
Philip E. Chen ◽  
Matthew T. Geballe ◽  
Phillip J. Stansfeld ◽  
Alexander R. Johnston ◽  
Hongjie Yuan ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Binding Site ◽  
Structural Features ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Glutamate Binding

Structure-Electronic Properties Relationships in Conducting Polymers: CP-MAS NMR and MM Analysis

1995 ◽  
Vol 413 ◽  
Author(s):  
S. Bradamante ◽  
A. Berlin ◽  
A. Canavesi ◽  
G. Zotti
Keyword(s):  
Molecular Modeling ◽  
Solid State ◽  
High Resolution ◽  
Conducting Polymers ◽  
Electronic Properties ◽  
Oxidative Polymerization ◽  
Structural Features ◽  
High Resolution Nmr ◽  
Torsional Angles ◽  
Cp Mas Nmr

ABSTRACTThe anodic oxidative polymerization of alkyl functionalized 4H-cyclopenta[2, 1-b:3,4-b']- dithiophene (CPDT) followed by undoping provides soluble and processable materials. We used CP MAS and high resolution NMR to analyze the monomers and polymers with the aim of correlating their structural features and conductivity. T1 relaxation values in solution and solid state were compared. Information about the preferred conformations of the polymers (backbone, distances, torsional angles) was deduced using the Molecular Modeling approach. The conclusions were derived by combining the indications obtained from both the spectroscopic and computational methods.

scholarly journals Structure, Dynamics, and Interactions of GPI-Anchored Human Glypican-1 with Heparan Sulfates in a Membrane

Glycobiology ◽  
2020 ◽  
Author(s):  
Chuqiao Dong ◽  
Yeol Kyo Choi ◽  
Jumin Lee ◽  
X Frank Zhang ◽  
Aurelia Honerkamp-Smith ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Modeling And Simulation ◽  
Degrees Of Freedom ◽  
Membrane Surface ◽  
Structural Features ◽  
Growth Factor Signaling ◽  
Gpi Anchor ◽  
Structure Dynamics ◽  
Heparan Sulfates ◽  
High Flexibility

Abstract Glypican-1 and its heparan sulfate (HS) chains play important roles in modulating many biological processes including growth factor signaling. Glypican-1 is bound to a membrane surface via a glycosylphosphatidylinositol (GPI)-anchor. In this study, we used all-atom molecular modeling and simulation to explore the structure, dynamics, and interactions of GPI-anchored glypican-1, three HS chains, membranes, and ions. The folded glypican-1 core structure is stable, but has substantial degrees of freedom in terms of movement and orientation with respect to the membrane due to the long unstructured C-terminal region linking the core to the GPI-anchor. With unique structural features depending on the extent of sulfation, high flexibility of HS chains can promote multi-site interactions with surrounding molecules near and above the membrane. This study is a first step toward all-atom molecular modeling and simulation of the glycocalyx, as well as its modulation of interactions between growth factors and their receptors.

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