scholarly journals Interactive Auditory Navigation in the Molecular Structures of Amino Acids: A Case Study Using Multiple Concurrent Sound Sources Representing Nearby Atoms

2019 ◽  
Author(s):  
Danyi Liu ◽  
Edwin van der Heide
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Research And Development ◽  
Three Dimensional ◽  
Molecular Structures ◽  
Acid Molecule ◽  
Auditory Masking ◽  
Amino Acid Molecule ◽  
Sound Sources

We are interested in sonifying the molecular structures of amino acids. This paper describes the context and the first design choices for our approach. So far, we believe an amino acid molecule is too complex to be perceived at once. Therefore, we have designed an interactive form of sonification in which the listener navigates through the molecule over the network of carbon atoms. We describe our different approaches and discuss the topic of immediacy: the time it takes to recognize the structure surrounding the listener’s position while navigating. Furthermore, we touch upon the question how many atoms we can sonify simultaneously and the role auditory masking plays in this context. To overcome auditory masking, we propose to use irregular but easy to recognize sounds. We conclude with an interest in a three-dimensional navigation environment using general molecular structures for further research and development.

Amino Acids in Insects

1953 ◽  
Vol 85 (2) ◽  
pp. 63-68 ◽  
Author(s):  
Jacques L. Auclair
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Organic Compound ◽  
Organic Compounds ◽  
Research Work ◽  
Carboxyl Group ◽  
Acid Molecule ◽  
Amino Acid Molecule

The object of this paper is to summarize some of the latest research work that has been done concerning the amino acids in insects and especially the research work in which I have collaborated.The Amino Acid MoleculeAn amino acid is an organic compound which contains a grouping with gcidic properties. Such a grouping in organic compounds is the carboxyl group.

PREDICTION OF THE THREE-DIMENSIONAL STRUCTURE OF THE ENZYMATIC PART OF T-PA

1987 ◽  
Author(s):  
A Heckel ◽  
K M Hasselbach
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Active Site ◽  
Serine Proteases ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
Salt Bridges ◽  
Three Dimensional Structure ◽  
Insertions And Deletions

Up to now the three-dimensional structure of t-PA or parts of this enzyme is unknown. Using computer graphical methods the spatial structure of the enzymatic part of t-PA is predicted on the hypothesis, the three-dimensional backbone structure of t-PA being similar to that of other serine proteases. The t-PA model was built up in three steps:1) Alignment of the t-PA sequence with other serine proteases. Comparison of enzyme structures available from Brookhaven Protein Data Bank proved elastase as a basis for modeling.2) Exchange of amino acids of elastase differing from the t-PA sequence. The replacement of amino acids was performed such that backbone atoms overlapp completely and side chains superpose as far as possible.3) Modeling of insertions and deletions. To determine the spatial arrangement of insertions and deletions parts of related enzymes such as chymotrypsin or trypsin were used whenever possible. Otherwise additional amino acid sequences were folded to a B-turn at the surface of the proteine, where all insertions or deletions are located. Finally the side chain torsion angles of amino acids were optimised to prevent close contacts of neigh bouring atoms and to improve hydrogen bonds and salt bridges.The resulting model was used to explain binding of arginine 560 of plasminogen to the active site of t-PA. Arginine 560 interacts with Asp 189, Gly 19 3, Ser 19 5 and Ser 214 of t-PA (chymotrypsin numbering). Furthermore interaction of chromo-genic substrate S 2288 with the active site of t-PA was studied. The need for D-configuration of the hydrophobic amino acid at the N-terminus of this tripeptide derivative could be easily explained.

scholarly journals Amino Acids Sequence Based in Silico Analysis of RuBisCO (Ribulose-1,5 Bisphosphate Carboxylase Oxygenase) Proteins in Some Carthamus L. ssp.

2017 ◽  
Vol 9 (2) ◽  
pp. 204-208 ◽  
Author(s):  
Emre SEVİNDİK
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Average Length ◽  
3D Structure ◽  
Three Dimensional ◽  
In Silico Analysis ◽  
Bisphosphate Carboxylase ◽  
Molecular Weights ◽  
Acid Ratio ◽  
Important Enzyme

RuBisCO is an important enzyme for plants to photosynthesize and balance carbon dioxide in the atmosphere. This study aimed to perform sequence, physicochemical, phylogenetic and 3D (three-dimensional) comparative analyses of RuBisCO proteins in the Carthamus ssp. using various bioinformatics tools. The sequence lengths of the RuBisCO proteins were between 166 and 477 amino acids, with an average length of 411.8 amino acids. Their molecular weights (Mw) ranged from 18711.47 to 52843.09 Da; the most acidic and basic protein sequences were detected in C. tinctorius (pI = 5.99) and in C. tenuis (pI = 6.92), respectively. The extinction coefficients of RuBisCO proteins at 280 nm ranged from 17,670 to 69,830 M-1 cm-1, the instability index (II) values for RuBisCO proteins ranged from 33.31 to 39.39, while the GRAVY values of RuBisCO proteins ranged from -0.313 to -0.250. The most abundant amino acid in the RuBisCO protein was Gly (9.7%), while the least amino acid ratio was Trp (1.6 %). The putative phosphorylation sites of RuBisCO proteins were determined by NetPhos 2.0. Phylogenetic analysis revealed that RuBisCO proteins formed two main clades. A RAMPAGE analysis revealed that 96.3%-97.6% of residues were located in the favoured region of RuBisCO proteins. To predict the three dimensional (3D) structure of the RuBisCO proteins PyMOL was used. The results of the current study provide insights into fundamental characteristic of RuBisCO proteins in Carthamus ssp.

scholarly journals Molecular design and virtual docking of oligopeptides for binding and elimination interleukin-6 from blood plasma

2019 ◽  
Vol 64 (3) ◽  
pp. 350-358
Author(s):  
T. V. Ryabzeva ◽  
D. A. Makarevich ◽  
E. M. Ermola ◽  
V. P. Golubovich ◽  
V. V. Kirkovskiy
Keyword(s):  
Amino Acids ◽  
Blood Plasma ◽  
Interleukin 6 ◽  
Molecular Design ◽  
Three Dimensional ◽  
Aromatic Amino Acids ◽  
Allergic Diseases ◽  
Molecular Structures ◽  
Autoimmune Pathology

Binding of interleukin-6 (IL-6) is the perspective target for the anti-inflammatory therapy in many pathological conditions (sepsis, autoimmune pathology, allergic diseases). The aim of this work was to develop and study the binding IL-6 oligopeptides. To achieve the goal, were set and successfully solved the following tasks: studying three-dimensional models of molecular structures of IL-6 incombination with the R-IL-6 and gp130, prediction and virtual synthesis low molecular weight oligopeptides; evaluating the free energy of IL-6 binding for identity the most effective oligopeptide; studying the changing the concentration of IL-6 inthe model solution after contact with experimental oligopeptides. In the article presents the binding IL-6 energy of 62 peptides, designed using the PyMol. Energy was calculated in the Chimera program using the AutodockVina application. There are also presented results of in vitro experiments interacting 7 sextapeptides, 2 tetrapeptides, and 3 tripeptides with recombinant IL-6. The effectiveness of the peptides was calculated by reducing the concentration of cytokine in solution as a percentage of the initial concentration.The free binding energy has shown that the efficiency of binding increases with an increase in the total number of amino acids and, in particular, of aromatic amino acids in the oligopeptide. Correlation analysis showed that the molecular modeling method is not absolutely effective for predicting the structure of an oligopeptide, however, it can be used as one of the preliminary steps for analyzing the interaction between molecules and studying the optimal interaction points. Two oligopeptides were identified as the most promising for further synthesis as the ligands for binding and evaluating IL-6 inhuman blood plasma.

scholarly journals Directly Detection of a Single Amino Acid Molecule with an Aerolysin Nanopore

2020 ◽  
Vol 118 (3) ◽  
pp. 356a
Author(s):  
Bo Yuan ◽  
Xueyuan Wu ◽  
Shuang Li ◽  
Yilun Ying ◽  
Yi-Tao Long
Keyword(s):  
Amino Acid ◽  
Single Amino Acid ◽  
Acid Molecule ◽  
Amino Acid Molecule

On the influence of low-energy ionizing radiation on the amino acid molecule: proline

2016 ◽  
Vol 70 (6) ◽  
Author(s):  
Jelena Tamuliene ◽  
Liudmila Romanova ◽  
Vasyl Vukstich ◽  
Alexander Papp ◽  
Serhiy Shkurin ◽  
...  
Keyword(s):  
Amino Acid ◽  
Ionizing Radiation ◽  
Low Energy ◽  
Acid Molecule ◽  
Amino Acid Molecule
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