scholarly journals Mathematical Characterization of Protein Transmembrane Regions

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Amrita Roy Choudhury ◽  
Nikolay Zhukov ◽  
Marjana Novič
Keyword(s):  
Amino Acid ◽  
Adjacency Matrix ◽  
Protein Sequences ◽  
Evolutionary Information ◽  
Sequence Information ◽  
Physiochemical Properties ◽  
Novel Method ◽  
Encoding Protein

Graphical bioinformatics has paved a unique way of mathematical characterization of proteins and proteomic maps. The graphics representations and the corresponding mathematical descriptors have proved to be useful and have provided unique solutions to problems related to identification, comparisons, and analyses of protein sequences and proteomics maps. Based on sequence information alone, these descriptors are independent from physiochemical properties of amino acids and evolutionary information. In this work, we have presented invariants from amino acid adjacency matrix and decagonal isometries matrix as potential descriptors of protein sequences. Encoding protein sequences into amino acid adjacency matrix is already well established. We have shown its application in classification of transmembrane and nontransmembrane regions of membrane protein sequences. We have introduced the dodecagonal isometries matrix, which is a novel method of encoding protein sequences based on decagonal isometries group.

Computational Analysis of Therapeutic Enzyme Uricase from Different Source Organisms

2020 ◽  
Vol 17 (1) ◽  
pp. 59-77
Author(s):  
Anand Kumar Nelapati ◽  
JagadeeshBabu PonnanEttiyappan
Keyword(s):  
Uric Acid ◽  
Amino Acid ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Protein Sequences ◽  
Amino Acid Sequences ◽  
Amino Acid Residues ◽  
Multiple Sequence ◽  
Physiochemical Properties ◽  
Pharmaceutical Industries

Background:Hyperuricemia and gout are the conditions, which is a response of accumulation of uric acid in the blood and urine. Uric acid is the product of purine metabolic pathway in humans. Uricase is a therapeutic enzyme that can enzymatically reduces the concentration of uric acid in serum and urine into more a soluble allantoin. Uricases are widely available in several sources like bacteria, fungi, yeast, plants and animals.Objective:The present study is aimed at elucidating the structure and physiochemical properties of uricase by insilico analysis.Methods:A total number of sixty amino acid sequences of uricase belongs to different sources were obtained from NCBI and different analysis like Multiple Sequence Alignment (MSA), homology search, phylogenetic relation, motif search, domain architecture and physiochemical properties including pI, EC, Ai, Ii, and were performed.Results:Multiple sequence alignment of all the selected protein sequences has exhibited distinct difference between bacterial, fungal, plant and animal sources based on the position-specific existence of conserved amino acid residues. The maximum homology of all the selected protein sequences is between 51-388. In singular category, homology is between 16-337 for bacterial uricase, 14-339 for fungal uricase, 12-317 for plants uricase, and 37-361 for animals uricase. The phylogenetic tree constructed based on the amino acid sequences disclosed clusters indicating that uricase is from different source. The physiochemical features revealed that the uricase amino acid residues are in between 300- 338 with a molecular weight as 33-39kDa and theoretical pI ranging from 4.95-8.88. The amino acid composition results showed that valine amino acid has a high average frequency of 8.79 percentage compared to different amino acids in all analyzed species.Conclusion:In the area of bioinformatics field, this work might be informative and a stepping-stone to other researchers to get an idea about the physicochemical features, evolutionary history and structural motifs of uricase that can be widely used in biotechnological and pharmaceutical industries. Therefore, the proposed in silico analysis can be considered for protein engineering work, as well as for gout therapy.

scholarly journals A novel method for achieving an optimal classification of the proteinogenic amino acids

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Andre Then ◽  
Karel Mácha ◽  
Bashar Ibrahim ◽  
Stefan Schuster
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Interaction Potential ◽  
Binary Separation ◽  
Multiple Alignments ◽  
Novel Method ◽  
Optimal Classification ◽  
Helix Propensity ◽  
Α Helix

Abstract The classification of proteinogenic amino acids is crucial for understanding their commonalities as well as their differences to provide a hint for why life settled on the usage of precisely those amino acids. It is also crucial for predicting electrostatic, hydrophobic, stacking and other interactions, for assessing conservation in multiple alignments and many other applications. While several methods have been proposed to find “the” optimal classification, they have several shortcomings, such as the lack of efficiency and interpretability or an unnecessarily high number of discriminating features. In this study, we propose a novel method involving a repeated binary separation via a minimum amount of five features (such as hydrophobicity or volume) expressed by numerical values for amino acid characteristics. The features are extracted from the AAindex database. By simple separation at the medians, we successfully derive the five properties volume, electron–ion-interaction potential, hydrophobicity, α-helix propensity, and π-helix propensity. We extend our analysis to separations other than by the median. We further score our combinations based on how natural the separations are.

scholarly journals Genomic Characterization of Severe Acute Respiratory Syndrome-Related Coronavirus in European Bats and Classification of Coronaviruses Based on Partial RNA-Dependent RNA Polymerase Gene Sequences

2010 ◽  
Vol 84 (21) ◽  
pp. 11336-11349 ◽  
Author(s):  
Jan Felix Drexler ◽  
Florian Gloza-Rausch ◽  
Jörg Glende ◽  
Victor Max Corman ◽  
Doreen Muth ◽  
...  
Keyword(s):  
Amino Acid ◽  
Severe Acute Respiratory Syndrome ◽  
Surface Expression ◽  
Emerging Viruses ◽  
Reading Frame ◽  
High Frequencies ◽  
Nyctalus Leisleri ◽  
Genomic Characterization

ABSTRACT Bats may host emerging viruses, including coronaviruses (CoV). We conducted an evaluation of CoV in rhinolophid and vespertilionid bat species common in Europe. Rhinolophids carried severe acute respiratory syndrome (SARS)-related CoV at high frequencies and concentrations (26% of animals are positive; up to 2.4 × 108 copies per gram of feces), as well as two Alphacoronavirus clades, one novel and one related to the HKU2 clade. All three clades present in Miniopterus bats in China (HKU7, HKU8, and 1A related) were also present in European Miniopterus bats. An additional novel Alphacoronavirus clade (bat CoV [BtCoV]/BNM98-30) was detected in Nyctalus leisleri. A CoV grouping criterion was developed by comparing amino acid identities across an 816-bp fragment of the RNA-dependent RNA polymerases (RdRp) of all accepted mammalian CoV species (RdRp-based grouping units [RGU]). Criteria for defining separate RGU in mammalian CoV were a >4.8% amino acid distance for alphacoronaviruses and a >6.3% distance for betacoronaviruses. All the above-mentioned novel clades represented independent RGU. Strict associations between CoV RGU and host bat genera were confirmed for six independent RGU represented simultaneously in China and Europe. A SARS-related virus (BtCoV/BM48-31/Bulgaria/2008) from a Rhinolophus blasii (Rhi bla) bat was fully sequenced. It is predicted that proteins 3b and 6 were highly divergent from those proteins in all known SARS-related CoV. Open reading frame 8 (ORF8) was surprisingly absent. Surface expression of spike and staining with sera of SARS survivors suggested low antigenic overlap with SARS CoV. However, the receptor binding domain of SARS CoV showed higher similarity with that of BtCoV/BM48-31/Bulgaria/2008 than with that of any Chinese bat-borne CoV. Critical spike domains 472 and 487 were identical and similar, respectively. This study underlines the importance of assessments of the zoonotic potential of widely distributed bat-borne CoV.

Old versus new characters for systematics: Cautionary tales from virology

1990 ◽  
Vol 3 (1) ◽  
pp. 159
Author(s):  
A Gibbs ◽  
A Ding ◽  
J Howe ◽  
P Keese ◽  
A MacKenzie ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genetic Recombination ◽  
Large Subunit ◽  
Molecular Taxonomy ◽  
Amino Acid Sequences ◽  
Sequence Information ◽  
Molecular Sequence ◽  
Taxonomic Methods ◽  
Cautionary Tales

Molecular sequence information about viruses has mostly confirmed the groupings devised by traditional taxonomic methods, but shown in addition that the genes of related species may differ in number, arrangement, orientation and in sequence homology. It has also revealed that true genetic recombination between viruses has been common, even among those with RNA genomes, indeed most virus groups seem to have arisen y recombination. Thus, there is an unexpected wealth of genetic chaos hidden behind the fatade of the phenotype, and it is possible that the difficulties that plant taxonomists have had in identifying the relationships of the major groupings of plants could have similar causes. Nonetheless, molecular taxonomy does give sensible results and this is illustrated by a classification of the large subunit Rubisco proteins of 21 plant species based on their amino acid sequences.

scholarly journals Drug-Target Interaction Prediction Based on Drug Fingerprint Information and Protein Sequence

Molecules ◽  
2019 ◽  
Vol 24 (16) ◽  
pp. 2999 ◽  
Author(s):  
Yang Li ◽  
Yu-An Huang ◽  
Zhu-Hong You ◽  
Li-Ping Li ◽  
Zheng Wang
Keyword(s):  
Drug Target ◽  
Large Scale ◽  
Protein Sequences ◽  
Performance Comparison ◽  
Target Pair ◽  
Evolutionary Information ◽  
Support Vector ◽  
Sequence Information ◽  
Rotation Forest ◽  
Comparison Results

The identification of drug-target interactions (DTIs) is a critical step in drug development. Experimental methods that are based on clinical trials to discover DTIs are time-consuming, expensive, and challenging. Therefore, as complementary to it, developing new computational methods for predicting novel DTI is of great significance with regards to saving cost and shortening the development period. In this paper, we present a novel computational model for predicting DTIs, which uses the sequence information of proteins and a rotation forest classifier. Specifically, all of the target protein sequences are first converted to a position-specific scoring matrix (PSSM) to retain evolutionary information. We then use local phase quantization (LPQ) descriptors to extract evolutionary information in the PSSM. On the other hand, substructure fingerprint information is utilized to extract the features of the drug. We finally combine the features of drugs and protein together to represent features of each drug-target pair and use a rotation forest classifier to calculate the scores of interaction possibility, for a global DTI prediction. The experimental results indicate that the proposed model is effective, achieving average accuracies of 89.15%, 86.01%, 82.20%, and 71.67% on four datasets (i.e., enzyme, ion channel, G protein-coupled receptors (GPCR), and nuclear receptor), respectively. In addition, we compared the prediction performance of the rotation forest classifier with another popular classifier, support vector machine, on the same dataset. Several types of methods previously proposed are also implemented on the same datasets for performance comparison. The comparison results demonstrate the superiority of the proposed method to the others. We anticipate that the proposed method can be used as an effective tool for predicting drug-target interactions on a large scale, given the information of protein sequences and drug fingerprints.

scholarly journals Novel Numerical Characterization of Protein Sequences Based on Individual Amino Acid and Its Application

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Yan-ping Zhang ◽  
Ya-jun Sheng ◽  
Wei Zheng ◽  
Ping-an He ◽  
Ji-shuo Ruan
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Catalytic Mechanism ◽  
Graphical Representation ◽  
Sequence Similarity ◽  
Protein Sequences ◽  
Numerical Characteristic ◽  
Individual Amino Acid ◽  
Numerical Characterization

The hydrophobicity and hydrophilicity of amino acids play a very important role in protein folding and its interaction with the environment and other molecules, as well as its catalytic mechanism. Based on the two physicochemical indexes, a 2D graphical representation of protein sequences is introduced; meanwhile, a new numerical characteristic has been proposed to compute the distance of different sequences for analysis of sequence similarity/dissimilarity on the basis of this graphical representation. Furthermore, we apply the new distance in the similarities/dissimilarities of ND5 proteins of nine species and predict the four major classes based on the dataset containing 639 domains. The results show that the method is simple and effective.

scholarly journals Cloning and characterization of cobA, one of vitamin B12 biosynthesis pathway genes from Selenomonas ruminantium

2021 ◽  
Vol 10 (2) ◽  
pp. 131-135
Author(s):  
Lívia Fecskeová ◽  
Peter Pristaš ◽  
Peter Javorský
Keyword(s):  
Amino Acid ◽  
Vitamin B12 ◽  
Biosynthetic Pathway ◽  
Anaerobic Bacteria ◽  
Protein Sequences ◽  
Synthesis Process ◽  
Biosynthesis Pathway ◽  
Selenomonas Ruminantium ◽  
Main Producer

Bacterial biosynthesis of vitamin B12 can occur via either aerobic or anaerobic route. While the aerobic pathway has been fully elucidated and understood, less is known about the anaerobic pathway. Selenomonas ruminantium is thought to be the main producer of this vitamin in rumen environment and must use the anaerobic pathway. In our work we found one of the genes of vitamin B12 biosynthetic pathway of S. ruminantium, encoding for the cobalamin adenosyltransferase, enzyme taking part at the last steps of the synthesis process. Deduced amino acid sequence showed the highest similarity to cobalamin adenosyltransferases of other ruminal anaerobic bacteria and that of species Selenomonas. Phylogenetic comparisons of CobA protein sequences of several anaerobic bacteria of Clostridiale order indicate possible horizontal transfer of this gene.

scholarly journals Bacterial lipolytic enzymes: classification and properties

1999 ◽  
Vol 343 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Jean Louis ARPIGNY ◽  
Karl-Erich JAEGER
Keyword(s):  
Amino Acid ◽  
Structural Features ◽  
Biological Properties ◽  
Amino Acid Sequences ◽  
Important Class ◽  
Lipolytic Enzymes ◽  
Disulphide Bonds ◽  
Enzyme Families

Knowledge of bacterial lipolytic enzymes is increasing at a rapid and exciting rate. To obtain an overview of this industrially very important class of enzymes and their characteristics, we have collected and classified the information available from protein and nucleotide databases. Here we propose an updated and extensive classification of bacterial esterases and lipases based mainly on a comparison of their amino acid sequences and some fundamental biological properties. These new insights result in the identification of eight different families with the largest being further divided into six subfamilies. Moreover, the classification enables us to predict (1) important structural features such as residues forming the catalytic site or the presence of disulphide bonds, (2) types of secretion mechanism and requirement for lipase-specific foldases, and (3) the potential relationship to other enzyme families. This work will therefore contribute to a faster identification and to an easier characterization of novel bacterial lipolytic enzymes.

scholarly journals A Classification of Ramanujan Unitary Cayley Graphs

10.37236/478 ◽  
2010 ◽  
Vol 17 (1) ◽  
Author(s):  
Andrew Droll
Keyword(s):  
Cayley Graph ◽  
Regular Graph ◽  
Adjacency Matrix ◽  
Complete Characterization ◽  
Absolute Value ◽  
Ramanujan Graph ◽  
Vertex Set ◽  
Unitary Cayley Graph

The unitary Cayley graph on $n$ vertices, $X_n$, has vertex set ${\Bbb Z}/{n\Bbb Z}$, and two vertices $a$ and $b$ are connected by an edge if and only if they differ by a multiplicative unit modulo $n$, i.e. ${\rm gcd}(a-b,n) = 1$. A $k$-regular graph $X$ is Ramanujan if and only if $\lambda(X) \leq 2\sqrt{k-1}$ where $\lambda(X)$ is the second largest absolute value of the eigenvalues of the adjacency matrix of $X$. We obtain a complete characterization of the cases in which the unitary Cayley graph $X_n$ is a Ramanujan graph.

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