scholarly journals Structural and Thermodynamic Characteristics of the Exosite Binding Pocket on the Human BACE1: A Molecular Modeling Approach

2010 ◽  
Vol 114 (37) ◽  
pp. 10261-10269 ◽  
Author(s):  
Lucas J. Gutierrez ◽  
Ricardo D. Enriz ◽  
Héctor A. Baldoni
Keyword(s):  
Molecular Modeling ◽  
Thermodynamic Characteristics ◽  
Binding Pocket ◽  
Modeling Approach

Toward Reducing hERG Affinities for DAT Inhibitors with a Combined Machine Learning and Molecular Modeling Approach

2021 ◽  
Vol 61 (9) ◽  
pp. 4266-4279 ◽  
Author(s):  
Kuo Hao Lee ◽  
Andrew D. Fant ◽  
Jiqing Guo ◽  
Andy Guan ◽  
Joslyn Jung ◽  
...  
Keyword(s):  
Machine Learning ◽  
Molecular Modeling ◽  
Modeling Approach

Study of surface heterogeneity and nitrogen functionalizing of biochars: Molecular modeling approach

Carbon ◽  
2021 ◽  
Vol 171 ◽  
pp. 161-170
Author(s):  
Hanieh Bamdad ◽  
Sadegh Papari ◽  
Stephanie MacQuarrie ◽  
Kelly Hawboldt
Keyword(s):  
Molecular Modeling ◽  
Surface Heterogeneity ◽  
Modeling Approach

scholarly journals Dynamic and thermodynamic characteristics associated with the glass transition of amorphous trehalose–water mixtures

2014 ◽  
Vol 16 (23) ◽  
pp. 11555-11565 ◽  
Author(s):  
Lindong Weng ◽  
Gloria D. Elliott
Keyword(s):  
Glass Transition ◽  
Molecular Modeling ◽  
Thermodynamic Characteristics

Tg behavior of trehalose–water mixtures is reproduced by molecular modeling with insights into the dynamic/thermodynamic characteristics associated with vitrification.

scholarly journals COVID-19: Vaccine Delivery System, Drug Repurposing and Application of Molecular Modeling Approach

2021 ◽  
Vol Volume 15 ◽  
pp. 3313-3330
Author(s):  
Soha R Abd El Hadi ◽  
Esmat E Zien El-Deen ◽  
Mostafa M Bahaa ◽  
Abdelfattah A Sadakah ◽  
Heba A Yassin
Keyword(s):  
Molecular Modeling ◽  
Delivery System ◽  
Vaccine Delivery ◽  
Drug Repurposing ◽  
Vaccine Delivery System ◽  
Modeling Approach

scholarly journals Identifying ligand-binding specificity of the oligopeptide receptor OppA from Bifidobacterium longum KACC91563 by Structure-based molecular modeling

2020 ◽  
Author(s):  
Han-Ha Chai ◽  
Young Ran Kim ◽  
Jun-Sang Ham ◽  
Tae-Hun Kim ◽  
Dajeong Lim
Keyword(s):  
Molecular Modeling ◽  
Structure Function ◽  
Binding Site ◽  
Bifidobacterium Longum ◽  
Peptide Binding ◽  
Binding Pocket ◽  
Host Organism ◽  
Specialized Structure ◽  
Function Relationship ◽  
The Relationship

Abstract Background: The OppA receptor as a ATP-binding cassette (ABC) transporter plays key roles in protecting host organism and transport nutrients across the intestine by the oligopeptide transporter from symbiotic bacteria directs maturation of the host immune system. Among lactic acid bacteria, Bifidobacterium longum KACC91563, isolated from fecal samples of healthy Korean neonates, has the capability to alleviate food allergy effects. The extracellular OppA receptor from gram-positive Bifidobacterium longum KACC91563 translocate nutrients-peptides from the outside environment of intestinal tract to the inside of the symbiotic cell, as a peptide importer. Hence, it was attempting to explicate the relationship between the substrate’s specificity from the OppA importer and the probiotic effects of B. logum KACC91563 in the host intestine. The probiotic effects of B. logum KACC91563 were attributed to the enhancement of the epithelial barrier by several different strain sepcific ways to prevent the strong adhesion of pathogens. The specialized structure-function relationship from the OppA importer could provide the abstract of substrate specificity into unique immunological properties of that the host organism.Results: In the study, we characterized the extracellular OppA importer from B. longum KACC91563 of intestinal microbiome by various protein structure-based modelings in silico. Structural characterization by conserved 5 patches and 4 functional motifs from specific trace residues of the OppA importer. The hydrate surface of the binding site had been decipted by specific trace residues of the OppA that trace residues of Thr58, Lys185, Trp443, and Tyr447, which were characterized in highly exposed hydrophobic binding pocket by its aggregation prones. Therefore, the spatial aggregation propensity in the binding site of the extracellular OppA importer plays a vital role in the specific interaction determinant for peptide binding. In addition, alanine mutation energy values allowed for the virtual determination of the relationships between the energy effects of the peptide binding site mutation on the transporter structural stability, the peptide binding affinity, and the transporter-related peptide substrate selectivity from OppA importer. In particular, distinctive seven pharmacophoric features comprised of two H-bonding donor(P1), three H-bonding acceptor(P8), and two hydrophobic points (P5 and P8) matched the the OppA receptor-peptide ligand interactions within their binding pocket structure. There are distinct interactions to fix the positions of the N(P1) and C(P8) termini of the complex of OppA-peptide from B. longum KACC91563 such as side chain-specific interactions with the OppA, compared to that of the Lactococcus latis (L. lactics) OppA.Conclusions: The specialized structure-function relationship from the OppA import could provide the abstract of substrate specificity into unique immunological properties of the host organism by stucutre-based molecular modeling. In the current study, we attempted explication of the relationship between the substrate’s specificity from the OppA importer and the probiotic effects of B. longum KACC91563 in the host intestine based on the structure-function perspectives of the OppA importer. Moreover, functional characterization of solute-binding proteins (such as 15 cell wall proteins and 20 extracellular proteins) on the B. longum KACC91563 genome will lead to insight of key switch for substate’s metabolism into reprogramming immune responses in the host intestine.

On the GABAA receptor: A molecular modeling approach

1989 ◽  
Vol 23 (2) ◽  
pp. 129-135 ◽  
Author(s):  
M. H. Aprison ◽  
K. B. Lipkowitz
Keyword(s):  
Molecular Modeling ◽  
Gabaa Receptor ◽  
Modeling Approach

scholarly journals A critical study on the interactions of hesperitin with human hemoglobin: Fluorescence spectroscopic and molecular modeling approach

2012 ◽  
Vol 132 (6) ◽  
pp. 1522-1528 ◽  
Author(s):  
Sandipan Chakraborty ◽  
Sudip Chaudhuri ◽  
Biswapathik Pahari ◽  
Jasmine Taylor ◽  
Pradeep K. Sengupta ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Critical Study ◽  
Human Hemoglobin ◽  
Modeling Approach
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