The Insight into Protein-Ligand Interactions, a Novel Way of Buffering Protein Noise in Gene Expression

2019 ◽  
Vol 26 (1) ◽  
pp. 86-95
Author(s):  
Shih-Chiang Lo ◽  
Feng-You Liu ◽  
Wun-Sin Jhang ◽  
Che-Chi Shu
Keyword(s):  
Gene Expression ◽  
Protein Ligand Interactions ◽  
Ligand Interactions ◽  
Noise In Gene Expression ◽  
Insight Into

scholarly journals Molecular determinants and bottlenecks in the unbinding dynamics of biotin-streptavidin

2017 ◽  
Author(s):  
Pratyush Tiwary
Keyword(s):  
Atomistic Simulations ◽  
Enhanced Sampling ◽  
Protein Ligand Interactions ◽  
Direct Benefits ◽  
Molecular Determinants ◽  
Bond Stretching ◽  
Ligand Interactions ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
Insight Into

Biotin-streptavidin is a very popular system used to gain insight into protein-ligand interactions. In its tetrameric form, it is well-known for its extremely long residence times, being one of the strongest known non-covalent interactions in nature, and is heavily used across the biotechnological industry. In this work we gain understanding into the molecular determinants and bottlenecks in the unbinding of the dimeric biotinstreptavidin system in its wild type and with N23A mutation. Using new enhanced sampling methods with full atomistic resolution, we reproduce the variation caused by N23A mutation in experimentally reported residence time. We also answer a longstanding question regarding cause/effect in the coupled events of bond stretching and bond hydration during unbinding and establish that in this system, it is the bond stretching and not hydration which forms the bottleneck in the early parts of the unbinding. We believe these calculations represent a step forward in the use of atomistic simulations to study pharmacodynamics. An improved understanding of biotin-streptavidin unbinding dynamics should also have direct benefits in biotechnological and nanobiotechnological applications.

New Insight into Protein−Ligand Interactions. The Case of thed-Galactose/d-Glucose-Binding Protein fromEscherichia coli

2011 ◽  
Vol 115 (12) ◽  
pp. 2765-2773 ◽  
Author(s):  
Olga V. Stepanenko ◽  
Olesya V. Stepanenko ◽  
Olga I. Povarova ◽  
Alexander V. Fonin ◽  
Irina M. Kuznetsova ◽  
...  
Keyword(s):  
Binding Protein ◽  
Fromescherichia Coli ◽  
Protein Ligand Interactions ◽  
Glucose Binding ◽  
Ligand Interactions ◽  
Glucose Binding Protein ◽  
Insight Into

Mechanistic insight into gramicidin-based detection of protein–ligand interactions via sensitized photoinactivation

2010 ◽  
Vol 22 (45) ◽  
pp. 454118 ◽  
Author(s):  
Tatyana I Rokitskaya ◽  
Michael X Macrae ◽  
Steven Blake ◽  
Natalya S Egorova ◽  
Elena A Kotova ◽  
...  
Keyword(s):  
Protein Ligand Interactions ◽  
Mechanistic Insight ◽  
Ligand Interactions ◽  
Insight Into

Calorimetry as a tool for understanding biomolecular interactions and an aid to drug design

2010 ◽  
Vol 38 (4) ◽  
pp. 888-893 ◽  
Author(s):  
John E. Ladbury
Keyword(s):  
Drug Development ◽  
Biomolecular Interactions ◽  
Titration Calorimetry ◽  
Decision Making Process ◽  
Biomolecular Interaction ◽  
Covalent Bonds ◽  
Protein Ligand Interactions ◽  
Ligand Interactions ◽  
Insight Into

The binding of two biomolecules viewed from the atomic level is highly complex. It involves the formation or removal of many individual non-covalent bonds both between the interacting molecules as well as with solvent. Currently, our understanding of the thermodynamic quantification of biomolecular interactions is somewhat naïve. ITC (isothermal titration calorimetry) provides a rapid route to a full thermodynamic characterization of a biomolecular interaction. Armed with these data, what are we really able to understand about complex formation and can any of this information provide a useful tool to aid drug development? Correlations between thermodynamic data and structural detail have been investigated, allowing insight into ways in which these can be used to understand protein–ligand interactions and provide input into the decision-making process in drug development.

Nanoparticle-plasma Membrane Interactions: Thermodynamics, Toxicity and Cellular Response

2020 ◽  
Vol 27 (20) ◽  
pp. 3330-3345
Author(s):  
Ana G. Rodríguez-Hernández ◽  
Rafael Vazquez-Duhalt ◽  
Alejandro Huerta-Saquero
Keyword(s):  
Gene Expression ◽  
Immune Responses ◽  
Cellular Response ◽  
Cellular Level ◽  
Membrane Interactions ◽  
Daily Lives ◽  
Cellular Physiology ◽  
Associated Proteins ◽  
First Contact ◽  
Insight Into

Nanomaterials have become part of our daily lives, particularly nanoparticles contained in food, water, cosmetics, additives and textiles. Nanoparticles interact with organisms at the cellular level. The cell membrane is the first protective barrier against the potential toxic effect of nanoparticles. This first contact, including the interaction between the cell membranes -and associated proteins- and the nanoparticles is critically reviewed here. Nanoparticles, depending on their toxicity, can cause cellular physiology alterations, such as a disruption in cell signaling or changes in gene expression and they can trigger immune responses and even apoptosis. Additionally, the fundamental thermodynamics behind the nanoparticle-membrane and nanoparticle-proteins-membrane interactions are discussed. The analysis is intended to increase our insight into the mechanisms involved in these interactions. Finally, consequences are reviewed and discussed.

19F-NMR in Target-based Drug Discovery

2019 ◽  
Vol 26 (26) ◽  
pp. 4964-4983 ◽  
Author(s):  
CongBao Kang
Keyword(s):  
Drug Discovery ◽  
Conformational Changes ◽  
Protein Structures ◽  
19F Nmr ◽  
Binding Affinities ◽  
Protein Ligand Interactions ◽  
Compound Libraries ◽  
Ligand Interactions ◽  
Reference Ligand ◽  
Hit Identification

Solution NMR spectroscopy plays important roles in understanding protein structures, dynamics and protein-protein/ligand interactions. In a target-based drug discovery project, NMR can serve an important function in hit identification and lead optimization. Fluorine is a valuable probe for evaluating protein conformational changes and protein-ligand interactions. Accumulated studies demonstrate that 19F-NMR can play important roles in fragment- based drug discovery (FBDD) and probing protein-ligand interactions. This review summarizes the application of 19F-NMR in understanding protein-ligand interactions and drug discovery. Several examples are included to show the roles of 19F-NMR in confirming identified hits/leads in the drug discovery process. In addition to identifying hits from fluorinecontaining compound libraries, 19F-NMR will play an important role in drug discovery by providing a fast and robust way in novel hit identification. This technique can be used for ranking compounds with different binding affinities and is particularly useful for screening competitive compounds when a reference ligand is available.

Combiphore (Structure and Ligand Based Pharmacophore) - Approach for the Design of GPR40 Modulators in the Management of Diabetes

2020 ◽  
Vol 17 (2) ◽  
pp. 233-247
Author(s):  
Krishna A. Gajjar ◽  
Anuradha K. Gajjar
Keyword(s):  
Molecular Docking ◽  
Structural Information ◽  
Docking Studies ◽  
Structural Motif ◽  
Roc Curve Analysis ◽  
Ligand Complex ◽  
Discovery Studio ◽  
Protein Ligand Interactions ◽  
Ligand Interactions ◽  
Pharmacophore Models

Background: Pharmacophore mapping and molecular docking can be synergistically integrated to improve the drug design and discovery process. A rational strategy, combiphore approach, derived from the combined study of Structure and Ligand based pharmacophore has been described to identify novel GPR40 modulators. Methods: DISCOtech module from Discovery studio was used for the generation of the Structure and Ligand based pharmacophore models which gave hydrophobic aromatic, ring aromatic and negative ionizable as essential pharmacophoric features. The generated models were validated by screening active and inactive datasets, GH scoring and ROC curve analysis. The best model was exposed as a 3D query to screen the hits from databases like GLASS (GPCR-Ligand Association), GPCR SARfari and Mini-Maybridge. Various filters were applied to retrieve the hit molecules having good drug-like properties. A known protein structure of hGPR40 (pdb: 4PHU) having TAK-875 as ligand complex was used to perform the molecular docking studies; using SYBYL-X 1.2 software. Results and Conclusion: Clustering both the models gave RMSD of 0.89. Therefore, the present approach explored the maximum features by combining both ligand and structure based pharmacophore models. A common structural motif as identified in combiphore for GPR40 modulation consists of the para-substituted phenyl propionic acid scaffold. Therefore, the combiphore approach, whereby maximum structural information (from both ligand and biological protein) is explored, gives maximum insights into the plausible protein-ligand interactions and provides potential lead candidates as exemplified in this study.

Xanthine Oxidase and Transforming Growth Factor Beta-activated Kinase 1: potential Targets for Gout Intervention

2020 ◽  
Vol 16 ◽  
Author(s):  
Rajesh Basnet ◽  
Sandhya Khadka ◽  
Buddha Bahadur Basnet ◽  
Til Bahadur Basnet ◽  
Buddhi Bal Chidi ◽  
...  
Keyword(s):  
Growth Factor ◽  
Xanthine Oxidase ◽  
Transforming Growth Factor Beta ◽  
Transforming Growth Factor ◽  
Developed Countries ◽  
Structure Based Drug Design ◽  
Protein Ligand Interactions ◽  
Ligand Interactions ◽  
Moderate Condition ◽  
Growth Factor Beta

Background: Gout, an inflammatory arthritis, caused by the deposition of monosodium urate crystals into affected joints and other tissues has become one of the major health problems of today's world. The main risk factor for gout is hyperuricemia, which may be caused by excessive or insufficient excretion of uric acid. The incidence is usually in the age group of 30- 50 years, commonly in males. In developed countries, the incidence of gout ranges from 1 to 4%. Despite effective treatments, there has been an increase in the number of cases over the past few decades. Objective: In recent years, the development of targeted drugs in gout has made significant achievements. The global impact of gout continues to increase, and as a result, the focus of disease-modifying therapies remains elusive. In addition, the characterization of available instrumental compounds is urgently needed to explore the use of novel selective and key protein-ligand interactions for the effective treatment of gout. Xanthine oxidase (XO) is a key target in gout to consider the use of XO inhibitors in patients with mild to moderate condition, however, the costs are high and no other direct progress has been made. Despite many XO inhibitors, a selective potent inhibitor for XO is limited. Likewise, in recent years, attention has been focused on different strategies for the discovery and development of new selectivity ligands against transforming growth factor beta-activated kinase 1 (TAK1), a potential therapeutic target for gout. Therefore the insight on human XO structure and TAK1 provides a clue into protein-ligand interactions and provides the basis for molecular modeling and structure-based drug design. Conclusion: In this review, we briefly introduce the clinical characteristics, the development of crystal, inhibitors, and crystal structure of XO and TAK1 protein.

scholarly journals Gene Expression and Carcass Traits Are Different between Different Quality Grade Groups in Red-Faced Hereford Steers

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1910
Author(s):  
Bailey Engle ◽  
Molly Masters ◽  
Jane Ann Boles ◽  
Jennifer Thomson
Keyword(s):  
Gene Expression ◽  
Transcriptome Profiling ◽  
Fat Deposition ◽  
Lower Shear ◽  
The Us ◽  
Quality Grade ◽  
Longissimus Lumborum ◽  
Muscle Biochemistry ◽  
Marbling Deposition ◽  
Insight Into

Fat deposition is important to carcass value and some palatability characteristics. Carcasses with higher USDA quality grades produce more value for producers and processors in the US system and are more likely to have greater eating satisfaction. Using genomics to identify genes impacting marbling deposition provides insight into muscle biochemistry that may lead to ways to better predict fat deposition, especially marbling and thus quality grade. Hereford steers (16) were managed the same from birth through harvest after 270 days on feed. Samples were obtained for tenderness and transcriptome profiling. As expected, steaks from Choice carcasses had a lower shear force value than steaks from Select carcasses; however, steaks from Standard carcasses were not different from steaks from Choice carcasses. A significant number of differentially expressed (DE) genes was observed in the longissimus lumborum between Choice and Standard carcass RNA pools (1257 genes, p < 0.05), but not many DE genes were observed between Choice and Select RNA pools. Exploratory analysis of global muscle tissue transcriptome from Standard and Choice carcasses provided insight into muscle biochemistry, specifically the upregulation of extracellular matrix development and focal adhesion pathways and the downregulation of RNA processing and metabolism in Choice versus Standard. Additional research is needed to explore the function and timing of gene expression changes.

Sign in / Sign up

Export Citation Format

Share Document