scholarly journals In Silico Design of a Peptide Receptor for Dopamine Recognition

Molecules ◽  
2020 ◽  
Vol 25 (23) ◽  
pp. 5509
Author(s):  
Luna Rodriguez-Salazar ◽  
James Guevara-Pulido ◽  
Andrés Cifuentes
Keyword(s):  
Hot Spots ◽  
In Silico ◽  
Active Sites ◽  
Direct Relationship ◽  
Binding Free Energy ◽  
Autodock Vina ◽  
Peptide Receptor ◽  
The Past ◽  
Regulatory Functions

Dopamine (DA) is an important neurotransmitter with a fundamental role in regulatory functions related to the central, peripheral, renal, and hormonal nervous systems. Dopaminergic neurotransmission dysfunctions are commonly associated with several diseases; thus, in situ quantification of DA is a major challenge. To achieve this goal, enzyme-based biosensors have been employed for substrate recognition in the past. However, due to their sensitivity to changes in temperature and pH levels, new peptide bioreceptors have been developed. Therefore, in this study, four bioreceptors were designed in silico to exhibit a higher affinity for DA than the DA transporters (DATs). The design was based on the hot spots of the active sites of crystallized enzyme structures that are physiologically related to DA. The affinities between the chosen targets and designed bioreceptors were calculated using AutoDock Vina. Additionally, the binding free energy, ∆G, of the dopamine-4xp1 complex was calculated by molecular dynamics (MD). This value presented a direct relationship with the E_refine value obtained from molecular docking based on the ∆G functions obtained from MOE of the promising bioreceptors. The control variables in the design were amino acids, bond type, steric volume, stereochemistry, affinity, and interaction distances. As part of the results, three out of the four bioreceptor candidates presented promising values in terms of DA affinity and distance.

scholarly journals In Silico Design of a Peptide Receptor for Dopamine Recognition

2020 ◽  
Author(s):  
Luna Rodriguez-Salazar ◽  
James Guevara Pulido
Keyword(s):  
Amino Acids ◽  
Interaction Energy ◽  
In Silico ◽  
Active Sites ◽  
Substrate Recognition ◽  
Autodock Vina ◽  
Peptide Receptor ◽  
The Past ◽  
Regulatory Functions

Abstract Background: Dopamine (DA) is an important neurotransmitter with a fundamental role in regulatory functions related to the central, peripheral, renal, and hormonal nervous systems. Dopaminergic neurotransmission dysfunctions are commonly associated with several diseases; thus, in situ quantification of DA is a major challenge. To achieve this goal, enzyme-based biosensors have been employed for substrate recognition in the past. However, owing to their sensitivity to changes in temperature and pH levels. Results: New peptide bioreceptors have been developed. Based on this, 45 in silico bioreceptors were designed to exhibit a higher affinity than that of the DA transporters (DATs). The design was based on the active sites of crystallized enzyme structures that are physiologically related to DA. These affinities were calculated using AutoDock Vina and by assessing the interaction energy between DA and the active DAT site. The controlled variables in the design were amino acids, bond type, steric volume, stereochemistry, affinity, and interaction distances. Conclusions: Three bioreceptor candidates presenting promising values ​​in terms of DA affinity and distance were obtained.

scholarly journals In Silico Design of a Peptide Receptor for Dopamine Recognition

2019 ◽  
Author(s):  
Luna Rodriguez-Salazar ◽  
James Guevara Pulido
Keyword(s):  
Amino Acids ◽  
Interaction Energy ◽  
In Silico ◽  
Active Sites ◽  
Substrate Recognition ◽  
Autodock Vina ◽  
Peptide Receptor ◽  
The Past ◽  
Regulatory Functions

Abstract Background: Dopamine (DA) is an important neurotransmitter with a fundamental role in regulatory functions related to the central, peripheral, renal, and hormonal nervous systems. Dopaminergic neurotransmission dysfunctions are commonly associated with several diseases; thus, in situ quantification of DA is a major challenge. To achieve this goal, enzyme-based biosensors have been employed for substrate recognition in the past. However, owing to their sensitivity to changes in temperature and pH levels. Results: New peptide bioreceptors have been developed. Based on this, 45 in silico bioreceptors were designed to exhibit a higher affinity than that of the DA transporters (DATs). The design was based on the active sites of crystallized enzyme structures that are physiologically related to DA. These affinities were calculated using AutoDock Vina and by assessing the interaction energy between DA and the active DAT site. The controlled variables in the design were amino acids, bond type, steric volume, stereochemistry, affinity, and interaction distances. Conclusions: Three bioreceptor candidates presenting promising values ​​in terms of DA affinity and distance were obtained.

The Use of Advanced Analytical Techniques for Characterization of the Chemical, Physical, and Crystallographic Nature of a Surface

1973 ◽  
Vol 31 ◽  
pp. 132-133 ◽  
Author(s):  
R. E. Herfert
Keyword(s):  
Surface Characterization ◽  
Analytical Techniques ◽  
X Ray Diffraction ◽  
Depth Of Penetration ◽  
X Ray ◽  
The Past ◽  
Transmission Electron ◽  
Scanning Electron

Studies of the nature of a surface, either metallic or nonmetallic, in the past, have been limited to the instrumentation available for these measurements. In the past, optical microscopy, replica transmission electron microscopy, electron or X-ray diffraction and optical or X-ray spectroscopy have provided the means of surface characterization. Actually, some of these techniques are not purely surface; the depth of penetration may be a few thousands of an inch. Within the last five years, instrumentation has been made available which now makes it practical for use to study the outer few 100A of layers and characterize it completely from a chemical, physical, and crystallographic standpoint. The scanning electron microscope (SEM) provides a means of viewing the surface of a material in situ to magnifications as high as 250,000X.

In situ microprobe quantitation of inorganic particle burden in paraffin sections of lung tissue

1988 ◽  
Vol 46 ◽  
pp. 990-991
Author(s):  
Jerrold L. Abraham
Keyword(s):  
Lung Tissue ◽  
Quantitative Information ◽  
Particulate Material ◽  
Paraffin Sections ◽  
Tissue Samples ◽  
Qualitative And Quantitative ◽  
The Past ◽  
Quantitative Analyses ◽  
Data Result

Inorganic particulate material of diverse types is present in the ambient and occupational environment, and exposure to such materials is a well recognized cause of some lung disease. To investigate the interaction of inhaled inorganic particulates with the lung it is necessary to obtain quantitative information on the particulate burden of lung tissue in a wide variety of situations. The vast majority of diagnostic and experimental tissue samples (biopsies and autopsies) are fixed with formaldehyde solutions, dehydrated with organic solvents and embedded in paraffin wax. Over the past 16 years, I have attempted to obtain maximal analytical use of such tissue with minimal preparative steps. Unique diagnostic and research data result from both qualitative and quantitative analyses of sections. Most of the data has been related to inhaled inorganic particulates in lungs, but the basic methods are applicable to any tissues. The preparations are primarily designed for SEM use, but they are stable for storage and transport to other laboratories and several other instruments (e.g., for SIMS techniques).

An atomic-resolution microscope study of Al contracts on GaAs

1986 ◽  
Vol 44 ◽  
pp. 726-727
Author(s):  
Z. Liliental-Weber ◽  
C. Nelson ◽  
R. Ludeke ◽  
R. Gronsky ◽  
J. Washburn
Keyword(s):  
High Speed ◽  
Schottky Contacts ◽  
Detailed Knowledge ◽  
The Past ◽  
Semiconductor Interfaces ◽  
Deposited Metal ◽  
Microwave Applications ◽  
Free Interfaces ◽  
Potential Use

The properties of metal/semiconductor interfaces have received considerable attention over the past few years, and the Al/GaAs system is of special interest because of its potential use in high-speed logic integrated optics, and microwave applications. For such materials a detailed knowledge of the geometric and electronic structure of the interface is fundamental to an understanding of the electrical properties of the contact. It is well known that the properties of Schottky contacts are established within a few atomic layers of the deposited metal. Therefore surface contamination can play a significant role. A method for fabricating contamination-free interfaces is absolutely necessary for reproducible properties, and molecularbeam epitaxy (MBE) offers such advantages for in-situ metal deposition under UHV conditions

scholarly journals 3D-Bioprinting Strategies Based on In Situ Bone-Healing Mechanism for Vascularized Bone Tissue Engineering

Micromachines ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 287
Author(s):  
Ye Lin Park ◽  
Kiwon Park ◽  
Jae Min Cha
Keyword(s):  
Tissue Engineering ◽  
Bone Tissue Engineering ◽  
Bone Tissue ◽  
Bone Healing ◽  
Critical Size ◽  
Current Knowledge ◽  
3D Bioprinting ◽  
The Past ◽  
Regeneration Processes

Over the past decades, a number of bone tissue engineering (BTE) approaches have been developed to address substantial challenges in the management of critical size bone defects. Although the majority of BTE strategies developed in the laboratory have been limited due to lack of clinical relevance in translation, primary prerequisites for the construction of vascularized functional bone grafts have gained confidence owing to the accumulated knowledge of the osteogenic, osteoinductive, and osteoconductive properties of mesenchymal stem cells and bone-relevant biomaterials that reflect bone-healing mechanisms. In this review, we summarize the current knowledge of bone-healing mechanisms focusing on the details that should be embodied in the development of vascularized BTE, and discuss promising strategies based on 3D-bioprinting technologies that efficiently coalesce the abovementioned main features in bone-healing systems, which comprehensively interact during the bone regeneration processes.

scholarly journals Electrokinetic and in situ spectroscopic investigations of CO electrochemical reduction on copper

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jing Li ◽  
Xiaoxia Chang ◽  
Haochen Zhang ◽  
Arnav S. Malkani ◽  
Mu-jeng Cheng ◽  
...  
Keyword(s):  
Mass Transport ◽  
Active Sites ◽  
Gas Diffusion ◽  
Reduction Reaction ◽  
Adsorbed Hydrogen ◽  
Diffusion Type ◽  
Proton Coupled Electron Transfer ◽  
Alkaline Electrolytes ◽  
Reaction Orders

AbstractRigorous electrokinetic results are key to understanding the reaction mechanisms in the electrochemical CO reduction reaction (CORR), however, most reported results are compromised by the CO mass transport limitation. In this work, we determined mass transport-free CORR kinetics by employing a gas-diffusion type electrode and identified dependence of catalyst surface speciation on the electrolyte pH using in-situ surface enhanced vibrational spectroscopies. Based on the measured Tafel slopes and reaction orders, we demonstrate that the formation rates of C2+ products are most likely limited by the dimerization of CO adsorbate. CH4 production is limited by the CO hydrogenation step via a proton coupled electron transfer and a chemical hydrogenation step of CO by adsorbed hydrogen atom in weakly (7 < pH < 11) and strongly (pH > 11) alkaline electrolytes, respectively. Further, CH4 and C2+ products are likely formed on distinct types of active sites.

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